[ { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ch9jq-hc145", "eprint_status": "archive", "datestamp": "2024-01-10 20:00:52", "lastmod": "2024-01-10 20:00:52", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhou-Tingtao", "name": { "family": "Zhou", "given": "Tingtao" }, "orcid": "0000-0002-1766-719X" }, { "id": "Wan-Xuan", "name": { "family": "Wan", "given": "Xuan" }, "orcid": "0000-0002-6165-6340" }, { "id": "Huang-Daniel-Zhengyu", "name": { "family": "Huang", "given": "Daniel Zhengyu" } }, { "id": "Li-Zongyi", "name": { "family": "Li", "given": "Zongyi" }, "orcid": "0000-0003-2081-9665" }, { "id": "Peng-Zhiwei", "name": { "family": "Peng", "given": "Zhiwei" }, "orcid": "0000-0002-9486-2837" }, { "id": "Anandkumar-A", "name": { "family": "Anandkumar", "given": "Anima" }, "orcid": "0000-0002-6974-6797" }, { "id": "Brady-J-F", "name": { "family": "Brady", "given": "John F." }, "orcid": "0000-0001-5817-9128" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Daraio-C", "name": { "family": "Daraio", "given": "Chiara" }, "orcid": "0000-0001-5296-4440" } ] }, "title": "AI-aided geometric design of anti-infection catheters", "ispublished": "pub", "full_text_status": "public", "keywords": "Multidisciplinary", "note": "
© 2024 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY).
\n\nThis work was supported by the following: the Donna and Benjamin M. Rosen Bioengineering Center Pilot Research Grant (J.F.B. and C.D.), the Heritage Medical Institute at Caltech (C.D.), and the National Science Foundation, Center to Stream Healthcare in Place (C2SHIP), award no. 2052827 (C.D.). D.Z.H. is supported by the generosity of Eric and Wendy Schmidt by recommendation of the Schmidt Futures program. Z.L. is supported in part by the PIMCO Fellowship and Amazon AI4Science Fellowship. A.A. and P.W.S. are supported by Bren Professorships.
\n\nX.W., T.Z., P.W.S., and C.D. designed experiments. X.W. and T.Z. performed experiments and analyzed data. T.Z. and Z.P. performed simulations. D.Z.H. and Z.L. designed the AI model and performed optimization. A.A. conceptualized and planned the AI framework. T.Z., J.F.B., and C.D. conceived the project. P.W.S. and C.D. supervised the project. All authors discussed the results and contributed to the manuscript writing.
\n\nAll data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Supplementary data for the optimization process are included in the following link: https://data.caltech.edu/records/mdj7m-ajv14.
\n\nCalifornia Institute of Technology (Caltech) has a patent pending related to the discoveries in this manuscript. Patent status: Pending. Name of organization issuing patent: The United States Patent and Trademark Office (USPTO). All authors are inventors. Filing date: 13 March 2023. Serial number: 63/451,788. The authors declare that they have no other competing interests.
", "abstract": "Bacteria can swim upstream in a narrow tube and pose a clinical threat of urinary tract infection to patients implanted with catheters. Coatings and structured surfaces have been proposed to repel bacteria, but no such approach thoroughly addresses the contamination problem in catheters. Here, on the basis of the physical mechanism of upstream swimming, we propose a novel geometric design, optimized by an artificial intelligence model. Using\n Escherichia coli\n , we demonstrate the anti-infection mechanism in microfluidic experiments and evaluate the effectiveness of the design in three-dimensionally printed prototype catheters under clinical flow rates. Our catheter design shows that one to two orders of magnitude improved suppression of bacterial contamination at the upstream end, potentially prolonging the in-dwelling time for catheter use and reducing the overall risk of catheter-associated urinary tract infection.", "date": "2024-01-05", "date_type": "published", "publication": "Science Advances", "volume": "10", "number": "1", "publisher": "American Association for the Advancement of Science", "pagerange": "eadj1741", "issn": "2375-2548", "official_url": "https://authors.library.caltech.edu/records/ch9jq-hc145", "funders": { "items": [ { "grant_number": "Donna and Benjamin M. Rosen Bioengineering Center" }, { "grant_number": "Heritage Medical Research Institute" }, { "grant_number": "CNS-2052827" }, {}, { "grant_number": "Amazon AI4Science Fellowship" }, { "grant_number": "Bren Professor of Computing and Mathematical Sciences" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" }, { "id": "Rosen-Bioengineering-Center" }, { "id": "Heritage-Medical-Research-Institute" } ] }, "doi": "10.1126/sciadv.adj1741", "pmcid": "PMC10776022", "primary_object": { "basename": "sciadv.adj1741.pdf", "url": "https://authors.library.caltech.edu/records/ch9jq-hc145/files/sciadv.adj1741.pdf" }, "related_objects": [ { "basename": "sciadv.adj1741_movies_s1_to_s3.zip", "url": "https://authors.library.caltech.edu/records/ch9jq-hc145/files/sciadv.adj1741_movies_s1_to_s3.zip" }, { "basename": "sciadv.adj1741_sm.pdf", "url": "https://authors.library.caltech.edu/records/ch9jq-hc145/files/sciadv.adj1741_sm.pdf" } ], "resource_type": "article", "pub_year": "2024", "author_list": "Zhou, Tingtao; Wan, Xuan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/r1jxp-49247", "eprint_status": "archive", "datestamp": "2023-12-15 19:36:30", "lastmod": "2024-01-09 22:19:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nava-Stephanie", "name": { "family": "Nava", "given": "Stephanie" }, "orcid": "0000-0002-5643-6693" }, { "id": "Palma-Wilber", "name": { "family": "Palma", "given": "Wilber" }, "orcid": "0000-0001-9382-9640" }, { "id": "Wan-Xuan", "name": { "family": "Wan", "given": "Xuan" }, "orcid": "0000-0002-6165-6340" }, { "id": "Oh-Jun-Young", "name": { "family": "Oh", "given": "Jun Young" }, "orcid": "0000-0002-5158-9017" }, { "id": "Gharib-Shahla", "name": { "family": "Gharib", "given": "Shahla" } }, { "id": "Wang-Han", "name": { "family": "Wang", "given": "Han" }, "orcid": "0000-0002-1933-5762" }, { "id": "Revanna-Jasmin-S", "name": { "family": "Revanna", "given": "Jasmin S." }, "orcid": "0000-0003-3637-9705" }, { "id": "Tan-Minyi", "name": { "family": "Tan", "given": "Minyi" } }, { "id": "Zhang-Mark", "name": { "family": "Zhang", "given": "Mark" }, "orcid": "0000-0002-0802-300X" }, { "id": "Liu-Jonathan", "name": { "family": "Liu", "given": "Jonathan" }, "orcid": "0000-0002-5761-8704" }, { "id": "Chen-Chun-Hao", "name": { "family": "Chen", "given": "Chun-Hao" }, "orcid": "0000-0003-3603-5304" }, { "id": "Lee-James-S", "name": { "family": "Lee", "given": "James S." }, "orcid": "0000-0002-4959-7237" }, { "name": { "family": "Perry", "given": "Barbara" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "A cGAL-UAS bipartite expression toolkit for Caenorhabditis elegans sensory neurons", "ispublished": "pub", "full_text_status": "public", "keywords": "Multidisciplinary", "note": "\u00a9 2023 the Author(s). Published by PNAS. This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).
\n\nWe thank members of our laboratory for insightful discussions through the course of this work and Cynthia Chai for constructs. We thank Sharan Prakash and other members of the Sternberg Lab for their comments on the manuscript. We thank our colleagues who contributed effector genes fragments: Bill Schafer (MRC); Cori Bargmann (Rockefeller); Dengke Ma (UCSF); Douglas Portman (Rochester); Kevin Collins (University of Miami); Steve Flavell (MIT); and Yishi Jin (USCD). Promoter details for sra-6 and gpa-13 were kindly provided by Bill Schafer. Some strains were provided by the Caenorhabditis Genetics Center, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). WormBase provided information about genome sequence and annotations. This study was supported by R21MH115454, UF1NS111697, and R01NS113119 (P.W.S.). M.Z. was supported by F31 NS120501. H.W. was supported by K99GM126137.
\n\nX.W., H.W., J.L., and P.W.S. designed research; S.N., W.P., X.W., J.Y.O., S.G., J.S.R., M.T., M.Z., C.-H.C., J.S.L., and B.P. performed research; and S.N., W.P., X.W., C.-H.C., and P.W.S. wrote the paper.
\n\nAll study data are included in the article and/or supporting information.
\n\nThe authors declare no competing interest.
", "abstract": "Animals integrate sensory information from the environment and display various behaviors in response to external stimuli. In Caenorhabditis elegans hermaphrodites, 33 types of sensory neurons are responsible for chemosensation, olfaction, and mechanosensation. However, the functional roles of all sensory neurons have not been systematically studied due to the lack of facile genetic accessibility. A bipartite cGAL-UAS system has been previously developed to study tissue- or cell-specific functions in C. elegans. Here, we report a toolkit of new cGAL drivers that can facilitate the analysis of a vast majority of the 60 sensory neurons in C. elegans hermaphrodites. We generated 37 sensory neuronal cGAL drivers that drive cGAL expression by cell-specific regulatory sequences or intersection of two distinct regulatory regions with overlapping expression (split cGAL). Most cGAL-drivers exhibit expression in single types of cells. We also constructed 28 UAS effectors that allow expression of proteins to perturb or interrogate sensory neurons of choice. This cGAL-UAS sensory neuron toolkit provides a genetic platform to systematically study the functions of C. elegans sensory neurons.
", "date": "2023-12-19", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences", "volume": "120", "number": "51", "publisher": "National Academy of Sciences", "pagerange": "e2221680120", "issn": "0027-8424", "official_url": "https://authors.library.caltech.edu/records/r1jxp-49247", "funders": { "items": [ { "grant_number": "P40 OD010440" }, { "grant_number": "R21 MH115454" }, { "grant_number": "UF1NS111697" }, { "grant_number": "R01NS113119" }, { "grant_number": "F31 NS120501" }, { "grant_number": "K99GM126137" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1073/pnas.2221680120", "primary_object": { "basename": "nava-et-al-2023-a-cgal-uas-bipartite-expression-toolkit-for-caenorhabditis-elegans-sensory-neurons.pdf", "url": "https://authors.library.caltech.edu/records/r1jxp-49247/files/nava-et-al-2023-a-cgal-uas-bipartite-expression-toolkit-for-caenorhabditis-elegans-sensory-neurons.pdf" }, "related_objects": [ { "basename": "pnas.2221680120.sapp.pdf", "url": "https://authors.library.caltech.edu/records/r1jxp-49247/files/pnas.2221680120.sapp.pdf" }, { "basename": "pnas.2221680120.sd01.xlsx", "url": "https://authors.library.caltech.edu/records/r1jxp-49247/files/pnas.2221680120.sd01.xlsx" }, { "basename": "pnas.2221680120.sd02.xlsx", "url": "https://authors.library.caltech.edu/records/r1jxp-49247/files/pnas.2221680120.sd02.xlsx" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Nava, Stephanie; Palma, Wilber; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/n6k3c-dpn19", "eprint_status": "archive", "datestamp": "2023-12-21 20:31:35", "lastmod": "2024-01-09 22:24:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schwartz-Hillel-T", "name": { "family": "Schwartz", "given": "Hillel T." }, "orcid": "0000-0002-3448-8652" }, { "id": "Tan-Chieh-Hsiang", "name": { "family": "Tan", "given": "Chieh-Hsiang" }, "orcid": "0000-0002-5432-0160" }, { "id": "Peraza-Jackeline", "name": { "family": "Peraza", "given": "Jackeline" }, "orcid": "0009-0007-2594-2378" }, { "id": "Raymundo-Krystal-Louise-T", "name": { "family": "Raymundo", "given": "Krystal Louise T." }, "orcid": "0000-0001-9114-9043" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W,." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Molecular identification of a peroxidase gene controlling body size in the entomopathogenic nematode Steinernema hermaphroditum", "ispublished": "pub", "full_text_status": "public", "keywords": "Genetics", "note": "\u00a9 The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/pages/standard-publication-reuse-rights)
\n\nWe thank Erich Schwarz for generously providing early access to unpublished versions of the S. hermaphroditum genome and its annotation; Jennifer Heppert and Heidi Goodrich-Blair for unpublished HGB2511 sequence; Heenam Park and Tsui-Fen Chou for CRISPR reagents and advice; Mengyi Cao for information about Steinernema CRISPR; Barbara Perry, Wilber Palma, and Stephanie Nava for technical assistance; WormBase and WormBase ParaSite for C. elegans and Steinernema genome information; Mona Shagholi of the Caltech Mass Spectrometry service center; and Daniel Semlow and Anton Gartner for advice about the effects of EMS mutagenesis. Some strains were provided by the CGC, funded by P40 OD010440.
\n\nThis work was supported by NSF-EDGE grant 2128267 (to PWS) and Caltech's Center for Evolutionary Science (CES) and Center for Environmental Microbial Interactions (CEMI). This research benefited from the use of instrumentation made available by the Caltech CCE Multiuser Mass Spectrometry Laboratory, enabled by funds from DOW Next Generation Instrumentation.
", "abstract": "The entomopathogenic nematode Steinernema hermaphroditum was recently rediscovered and is being developed as a genetically tractable experimental system for the study of previously unexplored biology, including parasitism of its insect hosts and mutualism with its bacterial endosymbiont Xenorhabdus griffiniae. Through whole-genome re-sequencing and genetic mapping we have for the first time molecularly identified the gene responsible for a mutationally defined phenotypic locus in an entomopathogenic nematode. In the process we observed an unexpected mutational spectrum following EMS mutagenesis in this species. We find that the ortholog of the essential C. elegans peroxidase gene skpo-2 controls body size and shape in S. hermaphroditum. We confirmed this identification by generating additional loss-of-function mutations in the gene using CRISPR-Cas9. We propose that the identification of skpo-2 will accelerate gene targeting in other Steinernema entomopathogenic nematodes used commercially in pest control, as skpo-2 is X-linked and males hemizygous for loss of its function can mate, making skpo-2 an easily recognized and maintained marker for use in co-CRISPR.
", "date": "2023-12-11", "date_type": "published", "publication": "Genetics", "publisher": "Oxford University Press", "issn": "1943-2631", "official_url": "https://authors.library.caltech.edu/records/n6k3c-dpn19", "funders": { "items": [ { "grant_number": "P40 OD010440" }, { "grant_number": "IOS-2128267" }, { "grant_number": "Dow Next Generation Educator Fund" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" }, { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Caltech-Center-for-Environmental-Microbial-Interactions-(CEMI)" }, { "id": "Caltech-Center-for-Evolutionary-Science" } ] }, "doi": "10.1093/genetics/iyad209", "primary_object": { "basename": "iyad209.pdf", "url": "https://authors.library.caltech.edu/records/n6k3c-dpn19/files/iyad209.pdf" }, "related_objects": [ { "basename": "iyad209_supplementary_data.zip", "url": "https://authors.library.caltech.edu/records/n6k3c-dpn19/files/iyad209_supplementary_data.zip" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Schwartz, Hillel T.; Tan, Chieh-Hsiang; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/233af-kt179", "eprint_status": "archive", "datestamp": "2023-11-21 21:52:52", "lastmod": "2024-01-09 22:20:41", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bult-Carol-J", "name": { "family": "Bult", "given": "Carol J." }, "orcid": "0000-0001-9433-210X" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The alliance of genome resources: transforming comparative genomics", "ispublished": "pub", "full_text_status": "public", "keywords": "Genetics", "note": "\u00a9 The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
\n\nThe authors acknowledge and thank all of the software developers and biocuration scientists who make the Alliance of Genome Resources possible. We also thank the Alliance Central Scientific Advisory Board members (Gary Bader, Alex Bateman, Helen Berman, Titus Brown, Shawn Burgess, Andrew Chisholm, Phil Hieter, Calum MacRae, Brian Oliver, Abraham Palmer, and Michelle Southard-Smith) for their guidance and advice. Members of the Alliance of Genome Resources Executive Committee provide input and oversight for organizational and operational aspects of the Alliance (Brian Calvi, J. Michael Cherry, Anne Kwitek, Chris Mungall, Paul Thomas, Aaron Zorn, Monte Westerfield).
\n\nCJB wrote the main manuscript and prepared the figures. PWS reviewed and edited the manuscript.
\n\nAlliance Central is funded by the National Human Genome Research Institute (NHGRI) HG0101859.
\n\nThe annotations available from the Alliance of Genome Resources web portal (https://alliancegenome.org) are distributed under a CC BY 4.0 license.
\n\nThe authors declare no competing interests.
\n\nPart of a collection: Special Issue: Mammalian Genetic Resources 2023
", "abstract": "Comparing genomic and biological characteristics across multiple species is essential to using model systems to investigate the molecular and cellular mechanisms underlying human biology and disease and to translate mechanistic insights from studies in model organisms for clinical applications. Building a scalable knowledge commons platform that supports cross-species comparison of rich, expertly curated knowledge regarding gene function, phenotype, and disease associations available for model organisms and humans is the primary mission of the Alliance of Genome Resources (the Alliance). The Alliance is a consortium of seven model organism knowledgebases (mouse, rat, yeast, nematode, zebrafish, frog, fruit fly) and the Gene Ontology resource. The Alliance uses a common set of gene ortholog assertions as the basis for comparing biological annotations across the organisms represented in the Alliance. The major types of knowledge associated with genes that are represented in the Alliance database currently include gene function, phenotypic alleles and variants, human disease associations, pathways, gene expression, and both protein\u2013protein and genetic interactions. The Alliance has enhanced the ability of researchers to easily compare biological annotations for common data types across model organisms and human through the implementation of shared programmatic access mechanisms, data-specific web pages with a unified \"look and feel\", and interactive user interfaces specifically designed to support comparative biology. The modular infrastructure developed by the Alliance allows the resource to serve as an extensible \"knowledge commons\" capable of expanding to accommodate additional model organisms.
", "date": "2023-12", "date_type": "published", "publication": "Mammalian Genome", "volume": "34", "number": "4", "publisher": "Springer Science and Business Media LLC", "pagerange": "531-544", "issn": "0938-8990", "official_url": "https://authors.library.caltech.edu/records/233af-kt179", "funders": { "items": [ { "grant_number": "HG0101859" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1007/s00335-023-10015-2", "pmcid": "PMC10628019", "primary_object": { "basename": "335_2023_Article_10015.pdf", "url": "https://authors.library.caltech.edu/records/233af-kt179/files/335_2023_Article_10015.pdf" }, "resource_type": "article", "pub_year": "2023", "author_list": "Bult, Carol J. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/rgtvr-37181", "eprint_status": "archive", "datestamp": "2023-12-21 20:42:07", "lastmod": "2024-01-09 22:23:26", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Banerjee-Navonil", "name": { "family": "Banerjee", "given": "Navonil" }, "orcid": "0000-0001-9613-5652" }, { "id": "Rojas-Palato-Elisa-J", "name": { "family": "Rojas Palato", "given": "Elisa J." } }, { "id": "Shih-Pei-Yin", "name": { "family": "Shih", "given": "Pei-Yin" }, "orcid": "0000-0003-3082-9242" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Hallem-Elissa-A", "name": { "family": "Hallem", "given": "Elissa A." }, "orcid": "0000-0003-0260-3174" } ] }, "title": "Distinct neurogenetic mechanisms establish the same chemosensory valence state at different life stages in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "Genetics (clinical); Genetics; Molecular Biology", "note": "\u00a9 The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
\n\nWe thank Shai Shaham, Oliver Hobert, Cori Bargmann, Ikue Mori, and Gary Ruvkun for providing strains. Some strains were provided by the Caenorhabditis Genetics Center (CGC), which is funded by the National Institutes of Health Office of Research Infrastructure Programs (P40 OD010440).
\n\nThis work was funded by National Institutes of Health F32 AI147617 (N.B.), National Institutes of Health MARC T34 GM008563 (E.J.R.P.), National Institutes of Health UF1 NS111697 (P.W.S.), and National Institutes of Health R01 DC017959 and a Howard Hughes Medical Institute Faculty Scholar Award (E.A.H.).
\n\nN.B., P.-Y.S., P.W.S., and E.A.H. conceived the study. N.B. and E.J.R.P. performed experiments. N.B. and E.J.R.P. analyzed the data. N.B. and E.A.H. wrote the manuscript. All authors read and approved the final manuscript.
\n\ntrains and plasmids are available upon request. All raw data and statistical analysis from this study are included in Supplementary File S1.
Supplemental material available at G3 online.
\n\nThe authors declare no conflict of interest.
", "abstract": "An animal's preference for many chemosensory cues remains constant despite dramatic changes in the animal's internal state. The mechanisms that maintain chemosensory preference across different physiological contexts remain poorly understood. We previously showed that distinct patterns of neural activity and motor output are evoked by carbon dioxide (CO\u2082) in starved adults vs dauers of Caenorhabditis elegans, despite the two life stages displaying the same preference (attraction) for CO\u2082. However, how the distinct CO\u2082-evoked neural dynamics and motor patterns contribute to CO\u2082 attraction at the two life stages remained unclear. Here, using a CO\u2082 chemotaxis assay, we show that different interneurons are employed to drive CO\u2082 attraction at the two life stages. We also investigate the molecular mechanisms that mediate CO\u2082 attraction in dauers vs adults. We show that insulin signaling promotes CO\u2082 attraction in dauers but not starved adults and that different combinations of neurotransmitters and neuropeptides are used for CO\u2082 attraction at the two life stages. Our findings provide new insight into the distinct molecular and cellular mechanisms used by C. elegans at two different life stages to generate attractive behavioral responses to CO\u2082.
", "date": "2023-11-23", "date_type": "published", "publication": "G3: Genes, Genomes, Genetics", "publisher": "Oxford University Press", "issn": "2160-1836", "official_url": "https://authors.library.caltech.edu/records/rgtvr-37181", "funders": { "items": [ { "grant_number": "P40 OD010440" }, { "grant_number": "F32 AI147617" }, { "grant_number": "T34 GM008563" }, { "grant_number": "UF1 NS111697" }, { "grant_number": "R01 DC017959" }, {} ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" }, { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" } ] }, "doi": "10.1093/g3journal/jkad271", "primary_object": { "basename": "jkad271.pdf", "url": "https://authors.library.caltech.edu/records/rgtvr-37181/files/jkad271.pdf" }, "related_objects": [ { "basename": "jkad271_supplementary_data.zip", "url": "https://authors.library.caltech.edu/records/rgtvr-37181/files/jkad271_supplementary_data.zip" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Banerjee, Navonil; Rojas Palato, Elisa J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/v70c6-19f12", "eprint_status": "archive", "datestamp": "2023-11-16 23:44:33", "lastmod": "2024-01-09 22:23:04", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Prakash-Sharan-J", "name": { "family": "Prakash", "given": "Sharan J." }, "orcid": "0000-0003-1777-0987" }, { "id": "Van-Auken-Kimberly-M", "name": { "family": "Van Auken", "given": "Kimberly M." }, "orcid": "0000-0002-1706-4196" }, { "id": "Hill-David-P", "name": { "family": "Hill", "given": "David P." }, "orcid": "0000-0001-7476-6306" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Semantic representation of neural circuit knowledge in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "Cognitive Neuroscience; Computer Science Applications; Neurology", "note": "\u00a9 The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
\n\nWe thank all members of the Sternberg lab at Caltech for their feedback during the course of the project. We also thank Raymond Lee (WormBase) and members of the Gene Ontology Consortium, as well as Susan Bello (Mouse Genome Informatics) and members of the Unified Phenotype Ontology working group for helpful discussions.
\n\nKV.A. and D.P.H. are funded by the National Human Genome Research Institute (U24HG012212). S.J.P. and P.W.S. are funded by NIH U24HG010859-03S2.
\n\nPWS and SJP conceived and designed the study, SJP, KVA and DPH conducted the study. SJP, KVA, DPH and PWS wrote and revised the manuscript. SJP prepared all the figures. All authors approved the manuscript.
\n\nAll data generated or analysed during this study are included in this published article (and its Additional file information files).
\n\nThe authors declare that they have no competing interests.
", "abstract": "AbstractIn modern biology, new knowledge is generated quickly, making it challenging for researchers to efficiently acquire and synthesise new information from the large volume of primary publications. To address this problem, computational approaches that generate machine-readable representations of scientific findings in the form of knowledge graphs have been developed. These representations can integrate different types of experimental data from multiple papers and biological knowledge bases in a unifying data model, providing a complementary method to manual review for interacting with published knowledge. The Gene Ontology Consortium (GOC) has created a semantic modelling framework that extends individual functional gene annotations to structured descriptions of causal networks representing biological processes (Gene Ontology\u2013Causal Activity Modelling, or GO\u2013CAM). In this study, we explored whether the GO\u2013CAM framework could represent knowledge of the causal relationships between environmental inputs, neural circuits and behavior in the model nematode C. elegans [C. elegans Neural\u2013Circuit Causal Activity Modelling (CeN\u2013CAM)]. We found that, given extensions to several relevant ontologies, a wide variety of author statements from the literature about the neural circuit basis of egg-laying and carbon dioxide (CO\u2082) avoidance behaviors could be faithfully represented with CeN\u2013CAM. Through this process, we were able to generate generic data models for several categories of experimental results. We also discuss how semantic modelling may be used to functionally annotate the C. elegans connectome. Thus, Gene Ontology-based semantic modelling has the potential to support various machine-readable representations of neurobiological knowledge.
", "date": "2023-11-10", "date_type": "published", "publication": "Brain Informatics", "volume": "10", "publisher": "Springer Science and Business Media LLC", "pagerange": "30", "issn": "2198-4018", "official_url": "https://authors.library.caltech.edu/records/v70c6-19f12", "funders": { "items": [ { "grant_number": "U24HG012212" }, { "grant_number": "U24HG010859-03S2" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1186/s40708-023-00208-5", "pmcid": "PMC10638142", "primary_object": { "basename": "40708_2023_208_MOESM2_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/v70c6-19f12/files/40708_2023_208_MOESM2_ESM.xlsx" }, "related_objects": [ { "basename": "40708_2023_208_MOESM3_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/v70c6-19f12/files/40708_2023_208_MOESM3_ESM.xlsx" }, { "basename": "40708_2023_Article_208.pdf", "url": "https://authors.library.caltech.edu/records/v70c6-19f12/files/40708_2023_Article_208.pdf" }, { "basename": "40708_2023_208_MOESM1_ESM.pptx", "url": "https://authors.library.caltech.edu/records/v70c6-19f12/files/40708_2023_208_MOESM1_ESM.pptx" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Prakash, Sharan J.; Van Auken, Kimberly M.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/dqnnv-knv04", "eprint_id": 122026, "eprint_status": "archive", "datestamp": "2023-08-20 16:49:52", "lastmod": "2023-12-22 23:39:45", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Prakash-Sharan-J", "name": { "family": "Prakash", "given": "Sharan J." }, "orcid": "0000-0003-1777-0987" }, { "id": "Van-Auken-Kimberly-M", "name": { "family": "Van Auken", "given": "Kimberly M." }, "orcid": "0000-0002-1706-4196" }, { "id": "Hill-D-P", "name": { "family": "Hill", "given": "David P." }, "orcid": "0000-0001-7476-6306" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Semantic Representation of Neural Circuit Knowledge in Caenorhabditis elegans", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. \n\nWe thank all members of the Sternberg lab at Caltech for their feedback during the course of the project. We also thank Raymond Lee (WormBase) and members of the Gene Ontology Consortium, as well as Susan Bello (Mouse Genome Informatics) and members of the Unified Phenotype Ontology working group for helpful discussions. \n\nK.V.A. & D.P.H. are funded by the National Human Genome Research Institute (U24HG012212). S.J.P. is funded by NIH U24HG010859-03S2. \n\nData & Materials Availability. All data generated or analysed during this study are included in this published article (and its supplementary information files). \n\nThe authors declare that they have no competing interests.\n\nSubmitted - nihpp-2023.04.28.538760v1.pdf
Supplemental Material - media-1.docx
Supplemental Material - media-2.xlsx
Supplemental Material - media-3.xlsx
Supplemental Material - media-4.docx
", "abstract": "In modern biology, new knowledge is generated quickly, making it challenging for researchers to efficiently acquire and synthesise new information from the large volume of primary publications. To address this problem, computational approaches that generate machine-readable representations of scientific findings in the form of knowledge graphs have been developed. These representations can integrate different types of experimental data from multiple papers and biological knowledge bases in a unifying data model, providing a complementary method to manual review for interacting with published knowledge. The Gene Ontology Consortium (GOC) has created a semantic modelling framework that extends individual functional gene annotations to structured descriptions of causal networks representing biological processes (Gene Ontology Causal Activity Modelling, or GO-CAM). In this study, we explored whether the GO-CAM framework could represent knowledge of the causal relationships between environmental inputs, neural circuits and behavior in the model nematode C. elegans (C. elegans Neural Circuit Causal Activity Modelling (CeN-CAM)). We found that, given extensions to several relevant ontologies, a wide variety of author statements from the literature about the neural circuit basis of egg-laying and carbon dioxide (CO2) avoidance behaviors could be faithfully represented with CeN-CAM. Through this process, we were able to generate generic data models for several categories of experimental results. We also generated representations of multisensory integration and sensory adaptation, and we discuss how semantic modelling may be used to functionally annotate the C. elegans connectome. Thus, Gene Ontology-based semantic modelling has the potential to support various machine-readable representations of neurobiological knowledge.", "date": "2023-06-29", "date_type": "published", "id_number": "CaltechAUTHORS:20230628-257134000.27", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230628-257134000.27", "funders": { "items": [ { "agency": "NIH", "grant_number": "U24HG012212" }, { "agency": "NIH", "grant_number": "U24HG010859-03S2" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2023.04.28.538760", "pmcid": "PMC10168330", "primary_object": { "basename": "nihpp-2023.04.28.538760v1.pdf", "url": "https://authors.library.caltech.edu/records/dqnnv-knv04/files/nihpp-2023.04.28.538760v1.pdf" }, "related_objects": [ { "basename": "media-1.docx", "url": "https://authors.library.caltech.edu/records/dqnnv-knv04/files/media-1.docx" }, { "basename": "media-2.xlsx", "url": "https://authors.library.caltech.edu/records/dqnnv-knv04/files/media-2.xlsx" }, { "basename": "media-3.xlsx", "url": "https://authors.library.caltech.edu/records/dqnnv-knv04/files/media-3.xlsx" }, { "basename": "media-4.docx", "url": "https://authors.library.caltech.edu/records/dqnnv-knv04/files/media-4.docx" } ], "resource_type": "monograph", "pub_year": "2023", "author_list": "Prakash, Sharan J.; Van Auken, Kimberly M.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/jcnhz-jm818", "eprint_status": "archive", "datestamp": "2023-10-26 20:59:10", "lastmod": "2024-01-09 22:19:23", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Truong-Lisa", "name": { "family": "Truong", "given": "Lisa" } }, { "id": "Chen-Yen-Wei", "name": { "family": "Chen", "given": "Yen-Wei" } }, { "id": "Barrere-Cain-Rio", "name": { "family": "Barrere-Cain", "given": "Rio" }, "orcid": "0000-0002-0522-253X" }, { "id": "Levenson-Max-T", "name": { "family": "Levenson", "given": "Max T." }, "orcid": "0000-0002-1470-3968" }, { "id": "Shuck-Karissa", "name": { "family": "Shuck", "given": "Karissa" } }, { "id": "Xiao-Wen", "name": { "family": "Xiao", "given": "Wen" }, "orcid": "0000-0001-6559-3036" }, { "id": "da-Veiga-Beltrame-Eduardo", "name": { "family": "da Veiga Beltrame", "given": "Eduardo" }, "orcid": "0000-0002-1529-9207" }, { "id": "Panter-Blake", "name": { "family": "Panter", "given": "Blake" } }, { "id": "Reich-Ella", "name": { "family": "Reich", "given": "Ella" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Yang-Xia", "name": { "family": "Yang", "given": "Xia" } }, { "id": "Allard-Patrick", "name": { "family": "Allard", "given": "Patrick" }, "orcid": "0000-0001-7765-1547" } ] }, "title": "Single-nucleus resolution mapping of the adult C.\u00a0elegans and its application to elucidate inter- and trans-generational response to alcohol", "ispublished": "pub", "full_text_status": "public", "keywords": "General Biochemistry, Genetics and Molecular Biology", "note": "\u00a9 2023 The Author(s). Under a Creative Commons license CC BY-NC-ND 4.0
\n\nThe authors would like to thank Doug Arneson for input on single-nucleus sequencing parameters; Ingrid Cely, In Sook Ahn, and Graciel Diamante for discussions and troubleshooting advice; Eyal Ben David for advice on single-cell/-nuclei dissociation methods; Jessica Scholes, Jeffrey Calim, Felicia Codrea, and Salem Haile for guidance with single-nucleus cytometry; Michael Mashock and Marco De Simone for their library preparation and sequencing expertise; the CNSI ALMS (RRID: SCR_022789) for their guidance with advanced microscopy; and Matteo Pellegrini for advice and input on data analysis. We thank Judith Kimble, Tina Lynch, and Sarah Crittenden for advice on smFISH and providing the sygl-1 probe. The Caenorhabditis Genetics Center (CGC) (RRID:SCR_007341) provided the strains used in this study. We thank Yuji Kohara for permission to use NEXTDB (RRID:SCR_004480) in situ data. Figure 1A and the graphical abstract were created with BioRender.com. L.T. is supported by the NIH Training Grant in Genomic Analysis and Interpretation T32 HG002536; Y.-W.C. is supported by the UCLA Eureka fellowship and Burroughs Wellcome Fund Inter-school Training Program in Chronic Diseases; P.A. is supported by NIEHS R01 ES027487, NIAAA R21 AA024889, the John Templeton Foundation, and the Burroughs Wellcome Innovation in Regulatory Science Award. E.d.V.B. and P.W.S. are supported by U24HG002223.
\n\nL.T., R.B.-C., K.S., W.X., M.T.L., B.P., and E.R. performed biological experiments and corresponding analyses; Y.-W.C. performed bioinformatic analyses; P.A. and X.Y. supervised experiments; P.A. and X.Y. supervised analyses; E.d.V.B. devised a visualization approach that assisted cell-type assignment and cluster identification, which P.S. supervised; and L.T., R.B.-C., M.T.L., Y.-W.C., X.Y., and P.A. wrote the manuscript.
\n\nThe data can be accessed and browsed through the Broad Single Cell Portal: https://singlecell.broadinstitute.org/single_cell/study/SCP922/single-nucleus-resolution-mapping-of-the-adult-c-elegans-and-its-application-to-elucidate-inter-and-trans-generational-response-to-alcohol.
\n\nThe authors declare no competing interests.
", "abstract": "Single-cell transcriptomic platforms provide an opportunity to map an organism's response to environmental cues with high resolution. Here, we applied single-nucleus RNA sequencing (snRNA-seq) to establish the tissue and cell type-resolved transcriptome of the adult C. elegans and characterize the inter- and trans-generational transcriptional impact of ethanol. We profiled the transcriptome of 41,749 nuclei resolving into 31 clusters, representing a diverse array of adult cell types including syncytial tissues. Following exposure to human-relevant doses of alcohol, several germline, striated muscle, and neuronal clusters were identified as being the most transcriptionally impacted at the F1 and F3 generations. The effect on germline clusters was confirmed by phenotypic enrichment analysis as well as by functional validation, which revealed a remarkable inter- and trans-generational increase in germline apoptosis, aneuploidy, and embryonic lethality. Together, snRNA-seq represents a valuable approach for the detailed examination of an adult organism's response to environmental exposures.
", "date": "2023-06-27", "date_type": "published", "publication": "Cell Reports", "volume": "42", "number": "6", "publisher": "Cell Press", "pagerange": "112535", "issn": "2211-1247", "official_url": "https://authors.library.caltech.edu/records/jcnhz-jm818", "funders": { "items": [ { "grant_number": "T32 HG002536" }, {}, {}, { "grant_number": "R01 ES027487" }, { "grant_number": "R21 AA024889" }, {}, { "grant_number": "U24HG002223" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.celrep.2023.112535", "pmcid": "PMC10592506", "primary_object": { "basename": "1-s2.0-S2211124723005466-main.pdf", "url": "https://authors.library.caltech.edu/records/jcnhz-jm818/files/1-s2.0-S2211124723005466-main.pdf" }, "related_objects": [ { "basename": "ScienceDirect_files_26Oct2023_20-33-19.871.zip", "url": "https://authors.library.caltech.edu/records/jcnhz-jm818/files/ScienceDirect_files_26Oct2023_20-33-19.871.zip" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Truong, Lisa; Chen, Yen-Wei; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/bbgkh-xrc87", "eprint_id": 121453, "eprint_status": "archive", "datestamp": "2023-08-22 20:51:21", "lastmod": "2023-12-22 23:21:21", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Banerjee-Navonil", "name": { "family": "Banerjee", "given": "Navonil" }, "orcid": "0000-0001-9613-5652" }, { "id": "Shih-Pei-Yin", "name": { "family": "Shih", "given": "Pei-Yin" }, "orcid": "0000-0003-3082-9242" }, { "id": "Rojas-Palato-Elisa-J", "name": { "family": "Rojas Palato", "given": "Elisa J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Hallem-Elissa-A", "name": { "family": "Hallem", "given": "Elissa A." }, "orcid": "0000-0003-0260-3174" } ] }, "title": "Differential processing of a chemosensory cue across life stages sharing the same valence state in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "Multidisciplinary", "note": "\u00a9 2023 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY). \n\nWe thank Cynthia Chai for the AIB::NaChBac strain. We thank Astra Bryant, Michelle Castelletto, and Ricardo Frausto for insightful comments on the manuscript. This work was funded by NIH F32 AI147617 (N.B.), NIH MARC T34 GM008563 (E.J.R.P.), NIH UF1 NS111697 (P.W.S.), and NIH R01 DC017959 and an HHMI Faculty Scholar Award (E.A.H.). \n\nAuthor contributions: N.B., P.-Y.S., P.W.S., and E.A.H. designed research; N.B., P.-Y.S., and E.J.R.P. performed research; N.B. and E.A.H. analyzed data; and N.B., P.-Y.S., P.W.S., and E.A.H. wrote the paper. \n\nThe authors declare no competing interest.\n\nPublished - pnas.2218023120.pdf
Supplemental Material - pnas.2218023120.sapp.pdf
Supplemental Material - pnas.2218023120.sd01.xlsx
", "abstract": "Many chemosensory cues evoke responses of the same valence under widely varying physiological conditions. It remains unclear whether similar or distinct neural mechanisms are involved in the detection and processing of such chemosensory cues across contexts. We show that in Caenorhabditis elegans, a chemosensory cue is processed by distinct neural mechanisms at two different life stages that share the same valence state. Both starved adults and dauer larvae are attracted to carbon dioxide (CO\u2082), but CO\u2082 evokes different patterns of neural activity and different motor outputs at the two life stages. Moreover, the same interneuron within the CO\u2082 microcircuit plays a different role in driving CO\u2082-evoked motor output at the two life stages. The dauer-specific patterns of CO\u2082-evoked activity in this interneuron require a dauer-specific gap junction complex and insulin signaling. Our results demonstrate that functionally distinct microcircuits are engaged in response to a chemosensory cue that triggers the same valence state at different life stages, revealing an unexpected complexity to chemosensory processing.", "date": "2023-05-01", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "120", "number": "19", "publisher": "National Academy of Sciences", "pagerange": "Art. No. e2218023120", "id_number": "CaltechAUTHORS:20230519-1616000.12", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230519-1616000.12", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Postdoctoral Fellowship", "grant_number": "F32 AI147617" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T34 GM008563" }, { "agency": "NIH", "grant_number": "UF1 NS111697" }, { "agency": "NIH", "grant_number": "R01 DC017959" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1073/pnas.2218023120", "pmcid": "PMC10175840", "primary_object": { "basename": "pnas.2218023120.pdf", "url": "https://authors.library.caltech.edu/records/bbgkh-xrc87/files/pnas.2218023120.pdf" }, "related_objects": [ { "basename": "pnas.2218023120.sapp.pdf", "url": "https://authors.library.caltech.edu/records/bbgkh-xrc87/files/pnas.2218023120.sapp.pdf" }, { "basename": "pnas.2218023120.sd01.xlsx", "url": "https://authors.library.caltech.edu/records/bbgkh-xrc87/files/pnas.2218023120.sd01.xlsx" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Banerjee, Navonil; Shih, Pei-Yin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/gy7y5-cmc27", "eprint_id": 120292, "eprint_status": "archive", "datestamp": "2023-08-22 20:30:25", "lastmod": "2023-12-22 23:21:55", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Reilly-Douglas-K", "name": { "family": "Reilly", "given": "Douglas K." }, "orcid": "0000-0001-8260-8690" }, { "id": "Schwarz-Erich-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Muirhead-Caroline-S", "name": { "family": "Muirhead", "given": "Caroline S." } }, { "id": "Robidoux-Annalise-N", "name": { "family": "Robidoux", "given": "Annalise N." } }, { "id": "Narayan-Anusha", "name": { "family": "Narayan", "given": "Anusha" } }, { "id": "Doma-Meenakshi-K", "name": { "family": "Doma", "given": "Meenakshi K." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Srinivasan-Jagan", "name": { "family": "Srinivasan", "given": "Jagan" }, "orcid": "0000-0001-5449-7938" } ] }, "title": "Transcriptomic profiling of sex-specific olfactory neurons reveals subset-specific receptor expression in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "Genetics", "note": "\u00a9 The Author(s) 2023. Published by Oxford University Press on behalf of the Genetics Society of America. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/pages/standard-publication-reuse-rights).\n\nWe thank the Caenorhabditis Genetics Center, which is funded by the NIH Office of Research Infrastructure Programs (P40 OD01044), as well as the National BioResource Project, Ding Xue (University of Colorado, Boulder), L. Rene Garcia (Texas A&M University), and Douglas Portman (University of Rochester Medical Center) for providing strains. We also thank Igor Antoshechkin, Caltech Genomics facility for sequencing, and InVivo Biosystems for generating transgenic and CRISPR knockout animals. The synthetic ascr#8 utilized in this study was provided by Frank Schroeder (Cornell University). \n\nThe research reported in this publication was supported by National Institutes of Health R01 DC016058 (J.S.), R01 GM084389 (P.W.S.), the Howard Hughes Medical Institute (P.W.S.), Moore Foundation Grant No. 4551 (E.M.S.), and Cornell startup funding (E.M.S.). We thank Titus Brown and the Michigan State University High-Performance Computing Center (supported by U.S. Department of Agriculture grant 2010-65205-20361 and NIFA\u2013National Science Foundation (NSF) grant IOS-0923812) for computational support; additional computing was enabled by start-up and research allocations from NSF XSEDE (TG-MCB180039 and TG-MCB190010). \n\nData availability. RNA-seq reads have been deposited in the NCBI Sequence Read Archive (SRA) under the BioProject accession number PRJNA781271. Supplementary Table 5 is available at figshare: https://doi.org/10.25386/genetics.22057019.\n\nThe authors declare no conflict of interest.\n\nSupplemental Material - iyad026_supplementary_data.pdf
", "abstract": "The nematode Caenorhabditis elegans utilizes chemosensation to navigate an ever-changing environment for its survival. A class of secreted small-molecule pheromones, termed ascarosides, play an important role in olfactory perception by affecting biological functions ranging from development to behavior. The ascaroside #8 (ascr#8) mediates sex-specific behaviors, driving avoidance in hermaphrodites and attraction in males. Males sense ascr#8 via the ciliated male-specific cephalic sensory (CEM) neurons, which exhibit radial symmetry along dorsal\u2013ventral and left\u2013right axes. Calcium imaging studies suggest a complex neural coding mechanism that translates stochastic physiological responses in these neurons to reliable behavioral outputs. To test the hypothesis that neurophysiological complexity arises from differential expression of genes, we performed cell-specific transcriptomic profiling; this revealed between 18 and 62 genes with at least twofold higher expression in a specific CEM neuron subtype vs both other CEM neurons and adult males. These included two G protein\u2013coupled receptor (GPCR) genes, srw-97 and dmsr-12, that were specifically expressed in nonoverlapping subsets of CEM neurons and whose expression was confirmed by GFP reporter analysis. Single CRISPR-Cas9 knockouts of either srw-97 or dmsr-12 resulted in partial defects, while a double knockout of both srw-97 and dmsr-12 completely abolished the attractive response to ascr#8. Together, our results suggest that the evolutionarily distinct GPCRs SRW-97 and DMSR-12 act nonredundantly in discrete olfactory neurons to facilitate male-specific sensation of ascr#8.", "date": "2023-04", "date_type": "published", "publication": "Genetics", "volume": "223", "number": "4", "publisher": "Oxford University Press", "pagerange": "Art. No. iyad026", "id_number": "CaltechAUTHORS:20230321-822411600.85", "issn": "1943-2631", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230321-822411600.85", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P40 OD010440" }, { "agency": "NIH", "grant_number": "R01 DC016058" }, { "agency": "NIH", "grant_number": "R01 GM084389" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "4551" }, { "agency": "Cornell University" }, { "agency": "Department of Agriculture", "grant_number": "2010-65205-20361" }, { "agency": "NSF", "grant_number": "IOS-0923812" }, { "agency": "NSF", "grant_number": "TG-MCB190010" }, { "agency": "NSF", "grant_number": "TG-MCB180039" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/genetics/iyad026", "primary_object": { "basename": "iyad026_supplementary_data.pdf", "url": "https://authors.library.caltech.edu/records/gy7y5-cmc27/files/iyad026_supplementary_data.pdf" }, "resource_type": "article", "pub_year": "2023", "author_list": "Reilly, Douglas K.; Schwarz, Erich M.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/gmkyw-h0h31", "eprint_id": 120360, "eprint_status": "archive", "datestamp": "2023-08-20 08:30:34", "lastmod": "2023-12-13 17:16:04", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Brugman-Katherine-I", "name": { "family": "Brugman", "given": "Katherine I." }, "orcid": "0000-0003-2625-2903" }, { "id": "Susoy-Vladislav", "name": { "family": "Susoy", "given": "Vladislav" }, "orcid": "0000-0002-0669-0087" }, { "id": "Whittaker-Allyson-J", "name": { "family": "Whittaker", "given": "Allyson J." } }, { "id": "Palma-Wilber", "name": { "family": "Palma", "given": "Wilber" }, "orcid": "0000-0001-9382-9640" }, { "id": "Nava-Stephanie", "name": { "family": "Nava", "given": "Stephanie" }, "orcid": "0000-0002-5643-6693" }, { "id": "Samuel-Aravinthan-D-T", "name": { "family": "Samuel", "given": "Aravinthan D. T." }, "orcid": "0000-0002-1672-8720" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "PEZO-1 and TRP-4 mechanosensors are involved in mating behavior in Caenorhabditis elegans", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license. \n\nWe thank WormBase for genome information, CGC for providing strains, Ian Kimbell for help with data collecting, Xiaofei Bai for providing AG570 pezo-1(av240), Shawn Xu for sharing a plasmid containing trp-4, and Tsui-Fen Chou for providing Cas9 protein. This work was supported by NIH R01-NS113119 (PWS and ADTS). KB was supported by NIH-Training Grant T32GM007616. \n\nThe authors have declared no competing interest.\n\nSubmitted - 2022.08.31.506045v1.full.pdf
", "abstract": "Male mating in Caenorhabditis elegans is a complex behavior with a strong mechanosensory component. C. elegans has several characterized mechanotransducer proteins, but few have been shown to contribute to mating. Here, we investigated the roles of PEZO-1, a piezo channel, and TRP-4, a mechanotransducing TRPN channel, in male mating behavior. We show that pezo-1 is expressed in several male-specific neurons with known roles in mating. We show that, among other neurons, trp-4 is expressed in the PCA sensory neuron, which monitors relative sliding between the male and the hermaphrodite and inhibits neurons involved in vulva detection. Mutations in both genes compromise many steps of mating, including initial response to the hermaphrodite, scanning, turning, and vulva detection. We performed pan-neuronal imaging during mating between freely-moving mutant males and hermaphrodites. Both pezo-1 and trp-4 mutants showed spurious activation of the sensory neurons involved in vulva detection. In trp-4 mutants, this spurious activation might be caused by PCA failure to inhibit vulva-detecting neurons during scanning. Indeed, we show that without functional TRP-4, PCA fails to detect the relative sliding between the male and hermaphrodite. Cell-specific TRP-4 expression restores PCA's mechanosensory function. Our results demonstrate new roles for both PEZO-1 and TRP-4 mechanotransducers in C. elegans mating behavior.", "date": "2023-03-26", "date_type": "published", "id_number": "CaltechAUTHORS:20230323-69637000.1", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230323-69637000.1", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 NS113119" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM007616" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2022.08.31.506045", "primary_object": { "basename": "2022.08.31.506045v1.full.pdf", "url": "https://authors.library.caltech.edu/records/gmkyw-h0h31/files/2022.08.31.506045v1.full.pdf" }, "resource_type": "monograph", "pub_year": "2023", "author_list": "Brugman, Katherine I.; Susoy, Vladislav; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/t3k1f-dtw80", "eprint_id": 120139, "eprint_status": "archive", "datestamp": "2023-08-20 09:07:12", "lastmod": "2023-12-13 17:18:00", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tan-Chieh-Hsiang", "name": { "family": "Tan", "given": "Chieh-Hsiang" }, "orcid": "0000-0002-5432-0160" }, { "id": "Cheng-Kai-Wen", "name": { "family": "Cheng", "given": "Kai-Wen" }, "orcid": "0000-0001-9888-9773" }, { "id": "Park-Heenam", "name": { "family": "Park", "given": "Heenam" }, "orcid": "0000-0001-7911-5828" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "LINKIN-associated proteins necessary for tissue integrity during collective cell migration", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. \n\nWe thank Barbara Perry, Wilber Palma and Stephanie Nava for laboratory assistance. We thank members of our laboratory for discussions. Mutant alleles- mvk-1(tm6628), trd-1(tm2764), vha-19(tm2225), prx-3(tm6469), and rod-1(tm6186) were provided by the MITANI Lab through the National Bio-Resource Project of the MEXT, Japan. Some strains were obtained from the Caenorhabditis Genetics Center (CGC), which is funded by the NIH Office of Research Infrastructure Programs (P40 OD010440). This work was also facilitated by WormBase, a knowledgebase for nematode research; and by the Alliance of Genome Resources, a research platform that facilitates cross species research, This research was supported by NIH R01HD086596 (PWS and TFC), R01HD091327 (PWS), and R24 0D023041 (PWS). \n\nThe authors have declared no competing interest.\n\nSubmitted - 2023.02.08.527750v1.full.pdf
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Supplemental Material - media-4.xlsx
Supplemental Material - media-5.docx
Supplemental Material - media-6.docx
", "abstract": "Cell adhesion plays essential roles in almost every aspect of metazoan biology. Previously, using the developmental migration of the nematode male gonad as a platform, LINKIN (Human: ITFG1,C. elegans: lnkn-1), a relatively understudied transmembrane protein conserved across the metazoa, was found to be necessary for tissue integrity during migration. InC. elegans, loss of lnkn-1 results in the detachment of the lead migratory cell from the rest of the developing male gonad. Three interactors of ITFG1/lnkn-1-RUVBL1/ruvb-1, RUVBL2/ruvb-2, and alpha-tubulin were identified by proteomic analysis using the human HEK293T cells and validated in the nematode male gonad. The ITFG1-RUVBL1 interaction has since been independently validated in a breast cancer cell line model that also implicates the involvement of the pair in metastasis. In this study, we showed that epitope-tagged ITFG1 localized to the cell surface of MDA-MB-231 breast cancer cells. Using unbiased mass spectrometry-based proteomics, we identified a new list of potential interactors of ITFG1. Loss-of-function analysis of their C. elegans orthologs found that three of the interactors - ATP9A/tat-5, NME1/ndk-1, and ANAPC2/apc-2 displayed migratory detachment phenotypes similar to that of lnkn-1. Taken together with the other genes whose reduction of function phenotype is the same as LINKIN (notably cohesion and condensin) suggests the involvement of membrane remodeling and chromosome biology in the tight adhesion dependent on LINKIN, and support the hypothesis for a structure role of chromosomes in post-mitotic cells.", "date": "2023-03-21", "date_type": "published", "id_number": "CaltechAUTHORS:20230316-182235000.22", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230316-182235000.22", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Ministry of Education, Culture, Sports, Science and Technology (MEXT)" }, { "agency": "NIH", "grant_number": "P40 OD010440" }, { "agency": "NIH", "grant_number": "R01HD086596" }, { "agency": "NIH", "grant_number": "R01HD091327" }, { "agency": "NIH", "grant_number": "R24 0D023041" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2023.02.08.527750", "primary_object": { "basename": "media-3.xlsx", "url": "https://authors.library.caltech.edu/records/t3k1f-dtw80/files/media-3.xlsx" }, "related_objects": [ { "basename": "media-4.xlsx", "url": "https://authors.library.caltech.edu/records/t3k1f-dtw80/files/media-4.xlsx" }, { "basename": "media-5.docx", "url": "https://authors.library.caltech.edu/records/t3k1f-dtw80/files/media-5.docx" }, { "basename": "media-6.docx", "url": "https://authors.library.caltech.edu/records/t3k1f-dtw80/files/media-6.docx" }, { "basename": "2023.02.08.527750v1.full.pdf", "url": "https://authors.library.caltech.edu/records/t3k1f-dtw80/files/2023.02.08.527750v1.full.pdf" }, { "basename": "media-1.xlsx", "url": "https://authors.library.caltech.edu/records/t3k1f-dtw80/files/media-1.xlsx" }, { "basename": "media-2.xlsx", "url": "https://authors.library.caltech.edu/records/t3k1f-dtw80/files/media-2.xlsx" } ], "resource_type": "monograph", "pub_year": "2023", "author_list": "Tan, Chieh-Hsiang; Cheng, Kai-Wen; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/f6ew7-v9x64", "eprint_id": 121309, "eprint_status": "archive", "datestamp": "2023-08-22 20:16:56", "lastmod": "2023-12-22 23:22:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Holman-Elizabeth-A", "name": { "family": "Holman", "given": "Elizabeth A." }, "orcid": "0000-0002-5158-4689" }, { "id": "Krishnan-Harinarayan", "name": { "family": "Krishnan", "given": "Harinarayan" }, "orcid": "0000-0001-8018-0547" }, { "id": "Holman-Derek-N", "name": { "family": "Holman", "given": "Derek R." }, "orcid": "0000-0002-3482-832X" }, { "id": "Holman-Hoi-Ying-N", "name": { "family": "Holman", "given": "Hoi-Ying N." }, "orcid": "0000-0002-7534-2625" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Toward implementing autonomous adaptive data acquisition for scanning hyperspectral imaging of biological systems", "ispublished": "pub", "full_text_status": "public", "keywords": "General Physics and Astronomy", "note": "\u00a9 2023 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). \n\nE.A.H. was supported by Howard Hughes Medical Institute (HHMI) under Grant No. 047-101, with which P.W.S. was an investigator. H.-Y.N.H. was supported by the Berkeley Synchrotron Infrared Structural Biology (BSISB) Imaging program sponsored by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Contract No. DE-AC02-05CH11231. \n\nAuthor Contributions. E.A.H. prepared, wrote, and edited the manuscript. H.K. contributed computer science domain expertise and edited the manuscript. D.R.H. reviewed, discussed, and edited the manuscript. H.-Y.N.H. contributed infrared spectroscopy of biological systems domain expertise and edited the manuscript. P.W.S. contributed biology domain expertise and edited the manuscript. \n\nElizabeth Anne Holman: Conceptualization (lead); Methodology (lead); Writing \u2013 original draft (lead); Writing \u2013 review & editing (equal). Harinarayan Krishnan: Methodology (supporting); Writing \u2013 review & editing (supporting). Derek Rudolf Holman: Writing \u2013 review & editing (equal). Hoi-Ying N. Holman: Funding acquisition (equal); Writing \u2013 review & editing (equal). Paul W. Sternberg: Funding acquisition (equal); Writing \u2013 review & editing (supporting). \n\nDATA AVAILABILITY. Data sharing is not applicable to this article as no new data were created or analyzed in this study. \n\nThe authors have no conflicts to disclose.\n\nPublished - 011319_1_online.pdf
", "abstract": "Autonomous experimentation is an emerging area of research, primarily related to autonomous vehicles, scientific combinatorial discovery approaches in materials science and drug discovery, and iterative research loops of planning, experimentation, and analysis. However, autonomous approaches developed in these contexts are difficult to apply to high-dimensional mapping technologies, such as scanning hyperspectral imaging of biological systems, due to sample complexity and heterogeneity. We briefly cover the history of adaptive sampling algorithms and surrogate modeling in order to define autonomous adaptive data acquisition as an objective-based, flexible building block for future biological imaging experimentation driven by intelligent infrastructure. We subsequently summarize the recent implementations of autonomous adaptive data acquisition (AADA) for scanning hyperspectral imaging, assess how these address the difficulties of autonomous approaches in hyperspectral imaging, and highlight the AADA design variation from a goal-oriented perspective. Finally, we present a modular AADA architecture that embeds AADA-driven flexible building blocks to address the challenge of time resolution for high-dimensional scanning hyperspectral imaging of nonequilibrium dynamical systems. In our example research-driven experimental design case, we propose an AADA infrastructure for time-resolved, noninvasive, and label-free scanning hyperspectral imaging of living biological systems. This AADA infrastructure can accurately target the correct state of the system for experimental workflows that utilize subsequent expensive, high-information-content analytical techniques.", "date": "2023-03", "date_type": "published", "publication": "Applied Physics Reviews", "volume": "10", "number": "1", "publisher": "American Institute of Physics", "pagerange": "Art. No. 011319", "id_number": "CaltechAUTHORS:20230502-387779700.4", "issn": "1931-9401", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230502-387779700.4", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)", "grant_number": "047-101" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-AC02-05CH11231" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1063/5.0123278", "primary_object": { "basename": "011319_1_online.pdf", "url": "https://authors.library.caltech.edu/records/f6ew7-v9x64/files/011319_1_online.pdf" }, "resource_type": "article", "pub_year": "2023", "author_list": "Holman, Elizabeth A.; Krishnan, Harinarayan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/epdn6-7ga71", "eprint_id": 120349, "eprint_status": "archive", "datestamp": "2023-08-20 08:43:47", "lastmod": "2023-12-22 23:12:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Brugman-Katherine-I", "name": { "family": "Brugman", "given": "Katherine I." }, "orcid": "0000-0003-2625-2903" }, { "id": "Susoy-Vladislav", "name": { "family": "Susoy", "given": "Vladislav" }, "orcid": "0000-0002-0669-0087" }, { "id": "Whittaker-Allyson-J", "name": { "family": "Whittaker", "given": "Allyson J." } }, { "id": "Palma-Wilber", "name": { "family": "Palma", "given": "Wilber" }, "orcid": "0000-0001-9382-9640" }, { "id": "Nava-Stephanie", "name": { "family": "Nava", "given": "Stephanie" }, "orcid": "0000-0002-5643-6693" }, { "id": "Samuel-Aravinthan-D-T", "name": { "family": "Samuel", "given": "Aravinthan D. T." }, "orcid": "0000-0002-1672-8720" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "PEZO-1 and TRP-4 mechanosensors are involved in mating behavior in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2022. Published by Oxford University Press on behalf of the National Academy of Sciences. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nWe thank WormBase: Davis P, Zarowiecki M, Arnaboldi V, Becerra A, Cain S, Chan J, Chen WJ, Cho J, da Veiga Beltrame E, Diamantakis S, Gao S, Grigoriadis D, Grove CA, Harris TW, Kishore R, Le T, Lee RYN, Luypaert M, M\u00fcller HM, Nakamura C, Nuin P, Paulini M, Quinton-Tulloch M, Raciti D, Rodgers FH, Russell M, Schindelman G, Singh A, Stickland T, Van Auken K, Wang Q, Williams G, Wright AJ, Yook K, Berriman M, Howe KL, Schedl T, Stein L, Sternberg PW. WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans. Genetics. 2022 Apr 4;220(4):iyac003. doi: 10.1093/genetics/iyac003. PMID: 35134929; for genome information, CGC for providing strains, Ian Kimbell for help with data collecting, Xiaofei Bai for providing AG570 pezo-1(av240), Shawn Xu for sharing a plasmid containing trp-4, and Tsui-Fen Chou for providing Cas9 protein. \n\nThis work was supported by NIH R01-NS113119 (P.W.S. and A.D.T.S.). K.B. was supported by NIH-Training Grant T32GM007616. \n\nAuthors' Contributions. K.B., V.S., and P.W. designed the project. K.B., V.S., and A.W. performed the experiments. K.B., W.P. and S.N. created essential reagents. K.B. and V.S. collected and analyzed the data. K.B., V.S., A.S., and P.W wrote the manuscript. \n\nK.I.B and V.S contributed equally to this work. \n\nData Availability. All data are included in the manuscript and/or Supplementary Material. \n\nThe authors declare no conflict of interest.\n\nPublished - pgac213.pdf
Supplemental Material - pgac213_supplemental_files.zip
", "abstract": "Male mating in Caenorhabditis elegans is a complex behavior with a strong mechanosensory component. C. elegans has several characterized mechanotransducer proteins, but few have been shown to contribute to mating. Here, we investigated the roles of PEZO-1, a piezo channel, and TRP-4, a mechanotransducing TRPN channel, in male mating behavior. We show that pezo-1 is expressed in several male-specific neurons with known roles in mating. We show that, among other neurons, trp-4 is expressed in the Post-Cloacal sensilla neuron type A (PCA) sensory neuron, which monitors relative sliding between the male and the hermaphrodite and inhibits neurons involved in vulva detection. Mutations in both genes compromise many steps of mating, including initial response to the hermaphrodite, scanning, turning, and vulva detection. We performed pan-neuronal imaging during mating between freely moving mutant males and hermaphrodites. Both pezo-1 and trp-4 mutants showed spurious activation of the sensory neurons involved in vulva detection. In trp-4 mutants, this spurious activation might be caused by PCA failure to inhibit vulva-detecting neurons during scanning. Indeed, we show that without functional TRP-4, PCA fails to detect the relative sliding between the male and hermaphrodite. Cell-specific TRP-4 expression restores PCA's mechanosensory function. Our results demonstrate new roles for both PEZO-1 and TRP-4 mechanotransducers in C. elegans mating behavior.", "date": "2022-11", "date_type": "published", "publication": "PNAS Nexus", "volume": "1", "number": "5", "publisher": "Oxford University Press", "pagerange": "Art. No. pgac213", "id_number": "CaltechAUTHORS:20230322-368341000.35", "issn": "2752-6542", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230322-368341000.35", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01-NS113119" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM007616" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/pnasnexus/pgac213", "pmcid": "PMC9802279", "primary_object": { "basename": "pgac213.pdf", "url": "https://authors.library.caltech.edu/records/epdn6-7ga71/files/pgac213.pdf" }, "related_objects": [ { "basename": "pgac213_supplemental_files.zip", "url": "https://authors.library.caltech.edu/records/epdn6-7ga71/files/pgac213_supplemental_files.zip" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Brugman, Katherine I.; Susoy, Vladislav; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/1fa07-8m912", "eprint_id": 115161, "eprint_status": "archive", "datestamp": "2023-10-30 16:54:15", "lastmod": "2024-01-09 22:20:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chai-Cynthia-M", "name": { "family": "Chai", "given": "Cynthia M." }, "orcid": "0000-0001-6118-2926" }, { "id": "Park-Heenam", "name": { "family": "Park", "given": "Heenam" }, "orcid": "0000-0001-7911-5828" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Brain-wide bidirectional neuropeptide modulation of individual neuron classes regulates a developmental decision", "ispublished": "pub", "full_text_status": "public", "keywords": "neuropeptide; G protein-coupled receptor; systems physiology; developmental plasticity; diapause; decision-making; General Agricultural and Biological Sciences; General Biochemistry, Genetics and Molecular Biology", "note": "\u00a9 2022 Elsevier. \n\nReceived 12 January 2022, Revised 6 May 2022, Accepted 17 May 2022, Available online 8 June 2022. \n\nWe thank Wilber Palma for sharing the flp-8 and pks-1 promoter fragments. We also thank Barbara J. Perry for assistance with strain freezing and Dr. Tsui-Fen Chou for providing Cas9 protein. Figures 1A, 4A, and 4C were created with BioRender.com. Some strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). Some strains were provided by the lab of Dr. Shohei Mitani as part of the National Bioresource Project. P.W.S., C.M.C., and H.P. were funded by NIH grants R24OD023041 and UF1NS111697. \n\nAuthor contributions. Conceptualization and methodology, C.M.C.; crude pheromone extraction, dauer formation assays, molecular cloning, transgenesis, microscopy, data analysis, and visualization, C.M.C.; CRISPR mutagenesis, H.P.; funding acquisition, P.W.S.; paper writing, C.M.C. \n\nData and code availability. All data reported in this paper will be shared by the lead contact upon request. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request. This study did not generate any unique code. \n\nThe authors declare no competing interests.\n\nSupplemental Material - 1-s2.0-S096098222200851X-mmc1.pdf
Supplemental Material - 1-s2.0-S096098222200851X-mmc2.xlsx
Supplemental Material - 1-s2.0-S096098222200851X-mmc3.xlsx
Supplemental Material - 1-s2.0-S096098222200851X-mmc4.xlsx
Supplemental Material - 1-s2.0-S096098222200851X-mmc5.xlsx
Supplemental Material - 1-s2.0-S096098222200851X-mmc6.xlsx
", "abstract": "Secreted neuromodulators, like biogenic amines and neuropeptides, can reconfigure circuit functions both locally and at a distance and establish global brain states that alter circuit outputs over prolonged timescales. Despite their diversity and ubiquitous presence, many studies on neuromodulation tend to focus on dissecting the function and site of action of individual neuropeptides. Here, we take a different approach by conducting a systems-level investigation of neuropeptide receptor signaling function and cell-type-specific distribution in the context of the Caenorhabditis elegans diapause entry developmental decision. C. elegans diapause entry is controlled by sensory perception of external factors and is regulated by neuropeptide signaling. We performed a comprehensive functional screen of neuropeptide receptor mutants for pheromone-induced diapause entry phenotypes and integrated these results with published C. elegans single-cell RNA-seq data to reveal that almost all neuron classes expressed at least one receptor with a role in diapause entry. Our receptor expression analysis also identified four highly modulated neural hubs with no previously reported roles in diapause entry that are distributed throughout the animal's body, possibly as a means of synchronizing the whole-organism transition into the appropriate larval morph. Furthermore, most neuron classes expressed unique neuropeptide receptor repertoires that have opposing effects on the diapause entry decision. We propose that brain-wide antagonistic neuropeptide modulation of individual neuron classes by distinct neuropeptide receptor subsets could serve as a strategy against overmodulation and that this motif might generalize to other decision-making paradigms in other organisms.", "date": "2022-08-08", "date_type": "published", "publication": "Current Biology", "volume": "32", "number": "15", "publisher": "Cell Press", "pagerange": "3365-3373", "id_number": "CaltechAUTHORS:20220614-940225000", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220614-940225000", "funders": { "items": [ { "agency": "NIH", "grant_number": "P40 OD010440" }, { "agency": "NIH", "grant_number": "R24OD023041" }, { "agency": "NIH", "grant_number": "UF1NS111697" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.cub.2022.05.048", "pmcid": "PMC10588560", "primary_object": { "basename": "nihms-1811048.pdf", "url": "https://authors.library.caltech.edu/records/1fa07-8m912/files/nihms-1811048.pdf" }, "related_objects": [ { "basename": "1-s2.0-S096098222200851X-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/1fa07-8m912/files/1-s2.0-S096098222200851X-mmc1.pdf" }, { "basename": "1-s2.0-S096098222200851X-mmc2.xlsx", "url": "https://authors.library.caltech.edu/records/1fa07-8m912/files/1-s2.0-S096098222200851X-mmc2.xlsx" }, { "basename": "1-s2.0-S096098222200851X-mmc3.xlsx", "url": "https://authors.library.caltech.edu/records/1fa07-8m912/files/1-s2.0-S096098222200851X-mmc3.xlsx" }, { "basename": "1-s2.0-S096098222200851X-mmc4.xlsx", "url": "https://authors.library.caltech.edu/records/1fa07-8m912/files/1-s2.0-S096098222200851X-mmc4.xlsx" }, { "basename": "1-s2.0-S096098222200851X-mmc5.xlsx", "url": "https://authors.library.caltech.edu/records/1fa07-8m912/files/1-s2.0-S096098222200851X-mmc5.xlsx" }, { "basename": "1-s2.0-S096098222200851X-mmc6.xlsx", "url": "https://authors.library.caltech.edu/records/1fa07-8m912/files/1-s2.0-S096098222200851X-mmc6.xlsx" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Chai, Cynthia M.; Park, Heenam; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/d3h3d-ctj75", "eprint_id": 115810, "eprint_status": "archive", "datestamp": "2023-08-20 08:15:24", "lastmod": "2023-12-13 17:17:38", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Truong-Lisa", "name": { "family": "Truong", "given": "Lisa" } }, { "id": "Chen-Yen-Wei", "name": { "family": "Chen", "given": "Yen-Wei" } }, { "id": "Barrere-Cain-Rio", "name": { "family": "Barrere-Cain", "given": "Rio" }, "orcid": "0000-0002-0522-253X" }, { "id": "Shuck-Karissa", "name": { "family": "Shuck", "given": "Karissa" } }, { "id": "Xiao-Wen", "name": { "family": "Xiao", "given": "Wen" }, "orcid": "0000-0001-6559-3036" }, { "id": "Levenson-Max-T", "name": { "family": "Levenson", "given": "Max T." }, "orcid": "0000-0002-1470-3968" }, { "id": "da-Veiga-Beltrame-Eduardo", "name": { "family": "da Veiga Beltrame", "given": "Eduardo" }, "orcid": "0000-0002-1529-9207" }, { "id": "Panter-Blake", "name": { "family": "Panter", "given": "Blake" } }, { "id": "Reich-Ella", "name": { "family": "Reich", "given": "Ella" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Yang-Xia", "name": { "family": "Yang", "given": "Xia" } }, { "id": "Allard-Patrick", "name": { "family": "Allard", "given": "Patrick" }, "orcid": "0000-0001-7765-1547" } ] }, "title": "Single-nucleus resolution mapping of the adult C. elegans and its application to elucidate inter- and trans-generational response to alcohol", "ispublished": "unpub", "full_text_status": "public", "keywords": "C. elegans, snRNA-seq, ethanol, alcohol", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. \n\nThe authors would like to thank Doug Arneson for input on single-nucleus sequencing parameters; Ingrid Cely, In Sook Ahn, and Graciel Diamante for discussions and trouble-shooting advice; Eyal Ben David for advice on single-cell/nuclei dissociation methods; Jessica Scholes, Jeffrey Calim, Felicia Codrea, and Salem Haile for guidance with single-nucleus cytometry; Michael Mashock and Marco De Simone for their library preparation and sequencing expertise. Matteo Pellegrini for advice and input on data analysis. We thank Judith Kimble, Tina Lynch, and Sarah Crittenden for advice on smFISH and providing the sygl-1 probe. The Caenorhabditis Genetics Center (CGC) provided the strains used in this study. We thank Yuji Kohara for permission to use NEXTDB in situ data. \n\nLT is supported by the NIH Training Grant in Genomic Analysis and Interpretation T32 HG002536; YWC is supported by the UCLA Eureka fellowship and Burroughs Wellcome Fund Inter-school Training Program in Chronic Diseases; PA is supported by NIEHS R01 ES027487, NIAAA R21 AA024889, the John Templeton Foundation, and the Burroughs Wellcome Innovation in Regulatory Science Award. EDVB and PWS are supported by U24HG002223. \n\nAuthor Contributions. LT, RBC, KS, WX, MTL, BP, and EL performed biological experiments and corresponding analyses, YWC performed bioinformatic analyses, PA and XY supervised experiments, PA and XY supervised analyses, EB devised a visualization approach that assisted cell type assignment and cluster identification which PS supervised, LT, RBC, YWC, XY, and PA wrote the manuscript. \n\nDATA AVAILABILITY. All raw data is accessible on NCBI's Gene Expression Omnibus (GEO), at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208229\n\nThe data is also available through the Broad Single Cell Portal: \n\nhttps://singlecell.broadinstitute.org/single_cell/study/SCP922/single-nucleus-resolution-mapping-of-the-adult-c-elegans-and-its-application-to-elucidate-inter-and-transgenerational-response-to-alcohol\n\nThe authors have declared no competing interest.\n\nSubmitted - 2022.07.21.500524v1.full.pdf
Supplemental Material - media-1.docx
Supplemental Material - media-2.pdf
Supplemental Material - media-3.xlsx
Supplemental Material - media-4.xlsx
Supplemental Material - media-5.xlsx
Supplemental Material - media-6.csv
Supplemental Material - media-7.xlsx
Supplemental Material - media-8.xlsx
", "abstract": "Single-cell RNA transcriptomic platforms have significantly contributed to our understanding of tissue heterogeneity as well as of developmental and cellular differentiation trajectories. They also provide an opportunity to map an organism's response to environmental cues with high resolution and unbiasedly identify the cell types that are the most transcriptionally sensitive to exposures. Here, we applied single nucleus RNA-seq experimental and computational approaches to C. elegans to establish the transcriptome of the adult nematode and comprehensively characterize the transcriptional impact of ethanol as a model environmental exposure on the entire organism at cell type-resolution over several generations. Clustering, tissue and phenotype enrichment, and gene ontology analyses identified 31 clusters representing a diverse number of adult cell types, including those from syncytial and multi-nucleated tissues which are difficult to assess by single cell RNA-seq, such as the mitotic and meiotic germline, hypodermal cells, and the intestine. We applied this method to identify the impact of inter- and trans-generational exposure to two human-relevant doses of alcohol. Cell type proportions were not significantly altered by ethanol. However, Euclidean distance analysis identified several germline, striated muscle, and neuronal clusters as being major transcriptional targets of ethanol at both the F1 and F3 generations although the relative order of clusters changed between generations. The impact on germline clusters was further confirmed by phenotypic enrichment analysis as well as functional validation, namely a remarkable inter- and trans-generational increase in germline apoptosis, aneuploidy, and embryonic lethality. Together, snRNA-seq of the adult C. elegans represents a powerful approach for the detailed examination of an adult organism's response to environmental cues.", "date": "2022-07-27", "date_type": "published", "id_number": "CaltechAUTHORS:20220725-414617000", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220725-414617000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 HG002536" }, { "agency": "UCLA" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "NIH", "grant_number": "R01 ES027487" }, { "agency": "NIH", "grant_number": "R21 AA024889" }, { "agency": "John Templeton Foundation" }, { "agency": "NIH", "grant_number": "U24HG002223" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2022.07.21.500524", "primary_object": { "basename": "2022.07.21.500524v1.full.pdf", "url": "https://authors.library.caltech.edu/records/d3h3d-ctj75/files/2022.07.21.500524v1.full.pdf" }, "related_objects": [ { "basename": "media-6.csv", "url": "https://authors.library.caltech.edu/records/d3h3d-ctj75/files/media-6.csv" }, { "basename": "media-8.xlsx", "url": "https://authors.library.caltech.edu/records/d3h3d-ctj75/files/media-8.xlsx" }, { "basename": "media-4.xlsx", "url": "https://authors.library.caltech.edu/records/d3h3d-ctj75/files/media-4.xlsx" }, { "basename": "media-5.xlsx", "url": "https://authors.library.caltech.edu/records/d3h3d-ctj75/files/media-5.xlsx" }, { "basename": "media-7.xlsx", "url": "https://authors.library.caltech.edu/records/d3h3d-ctj75/files/media-7.xlsx" }, { "basename": "media-1.docx", "url": "https://authors.library.caltech.edu/records/d3h3d-ctj75/files/media-1.docx" }, { "basename": "media-2.pdf", "url": "https://authors.library.caltech.edu/records/d3h3d-ctj75/files/media-2.pdf" }, { "basename": "media-3.xlsx", "url": "https://authors.library.caltech.edu/records/d3h3d-ctj75/files/media-3.xlsx" } ], "resource_type": "monograph", "pub_year": "2022", "author_list": "Truong, Lisa; Chen, Yen-Wei; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/e58z0-f5m77", "eprint_id": 111088, "eprint_status": "archive", "datestamp": "2023-08-20 08:06:58", "lastmod": "2023-12-22 23:39:40", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jhaveri-Nikita", "name": { "family": "Jhaveri", "given": "Nikita" } }, { "id": "van-den-Berg-Wouter", "name": { "family": "van den Berg", "given": "Wouter" }, "orcid": "0000-0001-6824-5993" }, { "id": "Hwang-Byung-Joon", "name": { "family": "Hwang", "given": "Byung Joon" }, "orcid": "0000-0003-2449-0684" }, { "id": "M\u00fcller-Hans-Michael", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Gupta-Bhagwati-P", "name": { "family": "Gupta", "given": "Bhagwati P." }, "orcid": "0000-0001-8572-7054" } ] }, "title": "Genome annotation of Caenorhabditis briggsae by TEC-RED identifies new exons, paralogs, and conserved and novel operons", "ispublished": "pub", "full_text_status": "public", "keywords": "Nematode, C. briggsae, Trans-splicing, Spliced leader, Operons, Paralog, Genome annotation", "note": "\u00a9 The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived: 30 January 2022; Accepted: 14 April 2022; Published: 29 April 2022. \n\nWe thank WormBase for assistance with some aspects of data analysis, Mary Ann Allen and Tom Blumenthal for discussions on C. elegans operons, and members of the Gupta lab for feedback on the manuscript. We are especially grateful to Paulo Nuin and Scott Cain (WormBase) for allowing us to use the demo version of Jbrowse 2 (https://jbrowse.org/jb2/) for some of the figures. \n\nThis work was supported by grants to BPG (Natural Sciences and Engineering Research Council of Canada, Discovery grant) and PWS (U24-HG002223). PWS was an Investigator with the Howard Hughes Medical Institute, which partially supported this work. \n\nThe authors declare that there are no conflicts of interests.\n\nPublished - jkac101.pdf
Submitted - 2021.09.24.461604v2.full.pdf
Supplemental Material - jkac101_supplementary_data.zip
", "abstract": "The nematode Caenorhabditis briggsae is routinely used in comparative and evolutionary studies involving its well-known cousin C. elegans. The C. briggsae genome sequence has accelerated research by facilitating the generation of new resources, tools, and functional studies of genes. While substantial progress has been made in predicting genes and start sites, experimental evidence is still lacking in many cases. Here, we report an improved annotation of the C. briggsae genome using the Trans-spliced Exon Coupled RNA End Determination (TEC-RED) technique. In addition to identifying the 5' ends of expressed genes, we have discovered operons and paralogs. In summary, our analysis yielded 10,243 unique 5' end sequence tags with matches in the C. briggsae genome. Of these, 6,395 were found to represent 4,252 unique genes along with 362 paralogs and 52 previously unknown exons. These genes included 14 that are exclusively trans-spliced in C. briggsae when compared with C. elegans orthologs. A major contribution of this study is the identification of 493 operons, of which two-thirds are fully supported by tags. In addition, two SL1-type operons were discovered. Interestingly, comparisons with C. elegans showed that only 40% of operons are conserved. Of the remaining operons, 73 are novel, including 12 that entirely lack orthologs in C. elegans. Further analysis revealed that four of the 12 novel operons are conserved in C. nigoni. Altogether, the work described here has significantly advanced our understanding of the C. briggsae system and serves as a rich resource to aid biological studies involving this species.", "date": "2022-07", "date_type": "published", "publication": "G3: Genes, Genomes, Genetics", "volume": "12", "number": "7", "publisher": "Oxford University Press", "pagerange": "Art. No. jkac101", "id_number": "CaltechAUTHORS:20210929-161511442", "issn": "2160-1836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210929-161511442", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)" }, { "agency": "NIH", "grant_number": "U24-HG002223" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/g3journal/jkac101", "pmcid": "PMC9258526", "primary_object": { "basename": "jkac101.pdf", "url": "https://authors.library.caltech.edu/records/e58z0-f5m77/files/jkac101.pdf" }, "related_objects": [ { "basename": "jkac101_supplementary_data.zip", "url": "https://authors.library.caltech.edu/records/e58z0-f5m77/files/jkac101_supplementary_data.zip" }, { "basename": "2021.09.24.461604v2.full.pdf", "url": "https://authors.library.caltech.edu/records/e58z0-f5m77/files/2021.09.24.461604v2.full.pdf" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Jhaveri, Nikita; van den Berg, Wouter; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/xycb9-tdq94", "eprint_id": 115051, "eprint_status": "archive", "datestamp": "2023-08-20 07:52:25", "lastmod": "2023-12-22 23:22:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tan-Chieh-Hsiang", "name": { "family": "Tan", "given": "Chieh-Hsiang" }, "orcid": "0000-0002-5432-0160" }, { "id": "Park-Heenam", "name": { "family": "Park", "given": "Heenam" }, "orcid": "0000-0001-7911-5828" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Loss of famh-136/ FAM136A results in minor locomotion and behavioral changes in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2022 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: 3/26/2022. Revision Received: 4/23/2022. Accepted: 5/30/2022. Published: 6/2/2022. \n\nWe thank Tsui-Fen Chou for providing Cas9 protein and Wan-Rong Wong for experimental and technical advice. We would also like to thank all members of the Sternberg lab for experimental support and discussions. This work was supported by NIH grants R24OD023041 and R01 HD086596 (PWS).\n\nFunding: NIH grants R24OD023041 and R01 HD086596 (PWS).\n\nAuthor Contributions. \n\nChieh-Hsiang Tan: Conceptualization, Formal analysis, Investigation, Methodology, Visualization, Writing - original draft, Writing - review & editing \n\nHeenam Park: Investigation, Resources, Writing - review & editing \n\nPaul W. Sternberg: Conceptualization, Funding acquisition, Supervision, Writing - review & editing\n\nPublished - 25789430-2022-micropub.biology.000578.pdf
", "abstract": "The human gene FAM136A (family with sequence similarity 136 member A) has been associated with familial Meniere's disease (MD) (Requena et al., 2015), a chronic disorder of the inner ear (Nakashima et al., 2016). There is also a suggestion that the expression of the gene could be associated with lung cancer prognosis (Zhao et al., 2020). FAM136A is evolutionary conserved, with orthologs identified in various metazoan species (Alliance of Genome Resources, 2022). However, with the exception of some expression data and omics level analysis (Alliance of Genome Resources, 2022; Stuckenholz et al., 2009), very little is known about FAM136A.", "date": "2022-06-02", "date_type": "published", "publication": "microPublication Biology", "volume": "2022", "publisher": "Caltech Library", "pagerange": "Art. No. 000553", "id_number": "CaltechAUTHORS:20220607-425206000", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220607-425206000", "funders": { "items": [ { "agency": "NIH", "grant_number": "R24OD023041" }, { "agency": "NIH", "grant_number": "R01 HD086596" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.17912/micropub.biology.000553", "pmcid": "PMC9163966", "primary_object": { "basename": "25789430-2022-micropub.biology.000578.pdf", "url": "https://authors.library.caltech.edu/records/xycb9-tdq94/files/25789430-2022-micropub.biology.000578.pdf" }, "resource_type": "article", "pub_year": "2022", "author_list": "Tan, Chieh-Hsiang; Park, Heenam; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/td0k5-xtd27", "eprint_id": 111872, "eprint_status": "archive", "datestamp": "2023-08-22 15:42:01", "lastmod": "2023-12-22 23:21:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chai-Cynthia-M", "name": { "family": "Chai", "given": "Cynthia M." }, "orcid": "0000-0001-6118-2926" }, { "id": "Torkashvand-Mahdi", "name": { "family": "Torkashvand", "given": "Mahdi" }, "orcid": "0000-0002-4381-0367" }, { "id": "Seyedolmohadesin-Maedeh", "name": { "family": "Seyedolmohadesin", "given": "Maedeh" }, "orcid": "0000-0003-3742-394X" }, { "id": "Park-Heenam", "name": { "family": "Park", "given": "Heenam" }, "orcid": "0000-0001-7911-5828" }, { "id": "Venkatachalam-Vivek", "name": { "family": "Venkatachalam", "given": "Vivek" }, "orcid": "0000-0002-2414-7416" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Interneuron control of C. elegans developmental decision-making", "ispublished": "pub", "full_text_status": "public", "keywords": "developmental plasticity; interneuron; neuropeptide; G-protein coupled receptor; pheromone; circuits; metabotropic glutamate receptor; physiology; metabolism", "note": "\u00a9 2022 Elsevier Inc. \n\nReceived 10 November 2021, Revised 13 March 2022, Accepted 30 March 2022, Available online 20 April 2022. \n\nSome strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). Some strains were provided by the lab of Dr. Shohei Mitani as part of the National Bioresource Project. Figure 1A was generated with https://biorender.com. P.W.S., C.M.C., and H.P. were supported by NIH grants R24OD023041, UF1NS111697, and R21MH115454. V.V., M.T., and M.S. were supported by a Burroughs Wellcome Fund Career Award at the Scientific Interface and the American Federation for Aging Research. \n\nAuthor contributions: Conceptualization, C.M.C. and P.W.S.; methodology, C.M.C., V.V., and M.T.; crude pheromone extraction, dauer formation assays, coelomocyte uptake assays, molecular cloning, transgenesis, and microscopy, C.M.C.; calcium imaging experiments, M.T. and M.S.; CRISPR mutagenesis, H.P.; data analysis and visualization, C.M.C., M.T., and M.S.; funding acquisition, P.W.S. and V.V.; writing the paper with input from coauthors, C.M.C. \n\nThe authors declare no competing interests. \n\nData and code availability: All data reported in this paper will be shared by the lead contact upon request. All original code used for calcium imaging experiments has been deposited at https://github.com/venkatachalamlab/Chai-2022-GCaMP and is publicly available as of the date of publication. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.\n\nAccepted Version - nihms-1801159.pdf
Submitted - 2021.11.07.467589v2.full.pdf
Supplemental Material - 1-s2.0-S0960982222005644-mmc1.pdf
", "abstract": "Natural environments are highly dynamic, and this complexity challenges animals to accurately integrate external cues to shape their responses. Adaptive developmental plasticity enables organisms to remodel their physiology, morphology, and behavior to better suit the predicted future environment and ultimately enhance their ecological success. Understanding how an animal generates a neural representation of current and forecasted environmental conditions and converts these circuit computations into a predictive adaptive physiological response may provide fundamental insights into the molecular and cellular basis of decision-making over developmentally relevant timescales. Although it is known that sensory cues usually trigger the developmental switch and that downstream inter-tissue signaling pathways enact the alternative developmental phenotype, the integrative neural mechanisms that transduce external inputs into effector pathways are less clear. In adverse environments, Caenorhabditis elegans larvae can enter a stress-resistant diapause state with arrested metabolism and reproductive physiology. Amphid sensory neurons feed into both rapid chemotactic and short-term foraging mode decisions, mediated by amphid and pre-motor interneurons, as well as the long-term diapause entry decision. Here, we identify amphid interneurons that integrate pheromone cues and propagate this information via a neuropeptidergic pathway to influence larval developmental fate, bypassing the pre-motor system. AIA interneuron-derived FLP-2 neuropeptide signaling promotes reproductive growth, and AIA activity is suppressed by pheromones. FLP-2 signaling is inhibited by upstream glutamatergic transmission via the metabotropic receptor MGL-1 and mediated by the broadly expressed neuropeptide G-protein-coupled receptor NPR-30. Thus, metabotropic signaling allows the reuse of parts of a sensory system for a decision with a distinct timescale.", "date": "2022-05-23", "date_type": "published", "publication": "Current Biology", "volume": "32", "number": "10", "publisher": "Cell Press", "pagerange": "2316-2324", "id_number": "CaltechAUTHORS:20211115-191646400", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211115-191646400", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P40 OD010440" }, { "agency": "NIH", "grant_number": "R24OD023041" }, { "agency": "NIH", "grant_number": "UF1NS111697" }, { "agency": "NIH", "grant_number": "R21MH115454" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "American Federation for Aging Research" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.cub.2022.03.077", "pmcid": "PMC9270850", "primary_object": { "basename": "nihms-1801159.pdf", "url": "https://authors.library.caltech.edu/records/td0k5-xtd27/files/nihms-1801159.pdf" }, "related_objects": [ { "basename": "1-s2.0-S0960982222005644-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/td0k5-xtd27/files/1-s2.0-S0960982222005644-mmc1.pdf" }, { "basename": "2021.11.07.467589v2.full.pdf", "url": "https://authors.library.caltech.edu/records/td0k5-xtd27/files/2021.11.07.467589v2.full.pdf" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Chai, Cynthia M.; Torkashvand, Mahdi; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ydakf-kwr20", "eprint_id": 114690, "eprint_status": "archive", "datestamp": "2023-08-22 15:35:17", "lastmod": "2023-12-22 23:21:44", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shinya-Ryoji", "name": { "family": "Shinya", "given": "Ryoji" }, "orcid": "0000-0002-2450-3054" }, { "id": "Sun-Simo", "name": { "family": "Sun", "given": "Simo" } }, { "id": "Dayi-Mehmet", "name": { "family": "Dayi", "given": "Mehmet" }, "orcid": "0000-0002-5367-918X" }, { "id": "Tsai-Isheng-Jason", "name": { "family": "Tsai", "given": "Isheng Jason" }, "orcid": "0000-0002-2123-5058" }, { "id": "Miyama-Atsushi", "name": { "family": "Miyama", "given": "Atsushi" } }, { "id": "Chen-Anthony-Fu", "name": { "family": "Chen", "given": "Anthony Fu" } }, { "id": "Hasegawa-Koichi", "name": { "family": "Hasegawa", "given": "Koichi" }, "orcid": "0000-0002-9968-8129" }, { "id": "Antoshechkin-Igor", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Kikuchi-Taisei", "name": { "family": "Kikuchi", "given": "Taisei" }, "orcid": "0000-0003-2759-9167" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Possible stochastic sex determination in Bursaphelenchus nematodes", "ispublished": "pub", "full_text_status": "public", "keywords": "Comparative genomics; Development; Evolutionary genetics; General Physics and Astronomy; General Biochemistry, Genetics and Molecular Biology; General Chemistry", "note": "\u00a9 The Author(s) 2022. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 24 August 2021; Accepted 19 April 2022; Published 11 May 2022. \n\nWe sincerely thank Ms. Miwako Kobayashi, Meiji University, Dr. Sota Ozawa, FFPRI, and Akemi Yoshida, the University of Miyazaki for their technical assistance in maintaining mutant nematodes and sequencing. This study was funded by JSPS Grant-in-Aid for Early-Career Scientists JP19K15853 (to R.S.), JSPS Grants-in-Aid for Scientific Research (B) 19H03212 (to T.K.), JST PRESTO Grant Number JPMJPR17Q5 (to R.S.) and JST CREST Grant Number JPMJCR18S7 (to T.K.). P.W.S. was an Investigator with the Howard Hughes Medical Institute, which supported this work. \n\nData availability: All sequence data generated during and/or analyzed during the current study have been deposited at DDBJ/ENA/GenBank under BioProject accession PRJEB40022, PRJEB40023, and PRJDB10466 The reference genomes, v5.1 for B. xylophilus and v2.0 for B. okinawaensis are available from GenBank assembly accessions GCA_904066235.2 and GCA_904066225.2, respectively. All other relevant data are available from the authors. Supplementary Data 1\u20136 detail the genes differentially expressed between males and hermaphrodites, between wild-type and tra mutant males, between wild-type and tra mutant hermaphrodites, and the Gene Ontology analysis for each. Supplementary Data 7\u20138 list the genes in two clusters that are commonly upregulated or commonly downregulated in tra mutants of both B. okinawaensis and C. elegans based on their orthology relationships. Source data are provided in this paper. \n\nContributions: R.S., K.H., T.K., and P.W.S. designed the research; R.S., S.S., M.D., I.J.T., A.M., A.F.C., I.A., and T.K. performed the research; R.S., S.S., M.D., I.J.T., and T.K. analyzed the data; and R.S., K.H., T.K., and P.W.S. wrote the paper. \n\nThe authors declare no competing interests. \n\nPeer review information: Nature Communications thanks Andre Pires da Silva and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.\n\nPublished - s41467-022-30173-2.pdf
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", "abstract": "Sex determination mechanisms evolve surprisingly rapidly, yet little is known in the large nematode phylum other than for Caenorhabditis elegans, which relies on chromosomal XX-XO sex determination and a dosage compensation mechanism. Here we analyze by sex-specific genome sequencing and genetic analysis sex determination in two fungal feeding/plant-parasitic Bursaphelenchus nematodes and find that their sex differentiation is more likely triggered by random, epigenetic regulation than by more well-known mechanisms of chromosomal or environmental sex determination. There is no detectable difference in male and female chromosomes, nor any linkage to sexual phenotype. Moreover, the protein sets of these nematodes lack genes involved in X chromosome dosage counting or compensation. By contrast, our genetic screen for sex differentiation mutants identifies a Bursaphelenchus ortholog of tra-1, the major output of the C. elegans sex determination cascade. Nematode sex determination pathways might have evolved by \"bottom-up\" accretion from the most downstream regulator, tra-1.", "date": "2022-05-11", "date_type": "published", "publication": "Nature Communications", "volume": "13", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 2574", "id_number": "CaltechAUTHORS:20220511-863713500", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220511-863713500", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Japan Society for the Promotion of Science (JSPS)", "grant_number": "JP19K15853" }, { "agency": "Japan Society for the Promotion of Science (JSPS)", "grant_number": "19H03212" }, { "agency": "Japan Society for the Promotion of Science (JSPS)", "grant_number": "JPMJPR17Q5" }, { "agency": "Japan Science and Technology Agency", "grant_number": "JPMJCR18S7" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41467-022-30173-2", "primary_object": { "basename": "41467_2022_30173_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/ydakf-kwr20/files/41467_2022_30173_MOESM1_ESM.pdf" }, "related_objects": [ { "basename": "41467_2022_30173_MOESM3_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/ydakf-kwr20/files/41467_2022_30173_MOESM3_ESM.xlsx" }, { "basename": "41467_2022_30173_MOESM4_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/ydakf-kwr20/files/41467_2022_30173_MOESM4_ESM.xlsx" }, { "basename": "41467_2022_30173_MOESM6_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/ydakf-kwr20/files/41467_2022_30173_MOESM6_ESM.xlsx" }, { "basename": "41467_2022_30173_MOESM9_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/ydakf-kwr20/files/41467_2022_30173_MOESM9_ESM.xlsx" }, { "basename": "41467_2022_30173_MOESM12_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/ydakf-kwr20/files/41467_2022_30173_MOESM12_ESM.xlsx" }, { "basename": "41467_2022_30173_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/ydakf-kwr20/files/41467_2022_30173_MOESM2_ESM.pdf" }, { "basename": "41467_2022_30173_MOESM5_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/ydakf-kwr20/files/41467_2022_30173_MOESM5_ESM.xlsx" }, { "basename": "41467_2022_30173_MOESM7_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/ydakf-kwr20/files/41467_2022_30173_MOESM7_ESM.xlsx" }, { "basename": "41467_2022_30173_MOESM11_ESM.pdf", "url": "https://authors.library.caltech.edu/records/ydakf-kwr20/files/41467_2022_30173_MOESM11_ESM.pdf" }, { "basename": "s41467-022-30173-2.pdf", "url": "https://authors.library.caltech.edu/records/ydakf-kwr20/files/s41467-022-30173-2.pdf" }, { "basename": "41467_2022_30173_MOESM10_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/ydakf-kwr20/files/41467_2022_30173_MOESM10_ESM.xlsx" }, { "basename": "41467_2022_30173_MOESM8_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/ydakf-kwr20/files/41467_2022_30173_MOESM8_ESM.xlsx" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Shinya, Ryoji; Sun, Simo; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/h23k7-krr08", "eprint_id": 110804, "eprint_status": "archive", "datestamp": "2023-08-20 07:35:05", "lastmod": "2023-12-22 23:22:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhang-Mark-G", "name": { "family": "Zhang", "given": "Mark G." }, "orcid": "0000-0002-0802-300X" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Both entry to and exit from diapause arrest in Caenorhabditis elegans are regulated by a steroid hormone pathway", "ispublished": "pub", "full_text_status": "public", "keywords": "Dauer, Diapause, Hormone, Decision, daf-9, daf-12", "note": "\u00a9 2022. Published by The Company of Biologists Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed. \n\nReceived:06 Sep 2021; Accepted: 24 Mar 2022. \n\n\u03947-DA was a gift from the lab of Frank Schroeder (Cornell University). We thank Mengyi Cao and Stephanie Nava for the XXX cGAL driver. Some strains were provided by the Caenorhabditis Genetics Center, which is funded by National Institutes of Health Office of Research Infrastructure Programs (P40 OD010440). We are grateful to members of the Sternberg lab for their feedback on the manuscript, particularly Hillel Schwartz. \n\nM.G.Z. was funded by National Institutes of Health Grant F31 NS120501-01. A National Institutes of Health Grant UF1-NS111697 (P.W.S.) supported the research material and research assistance. Open access funding provided by California Institute of Technology. Deposited in PMC for immediate release. \n\nAuthor contributions: Conceptualization: M.G.Z., P.W.S.; Methodology: M.G.Z.; Formal analysis: M.G.Z.; Investigation: M.G.Z., P.W.S.; Data curation: M.G.Z.; Writing - original draft: M.G.Z.; Writing - review & editing: M.G.Z., P.W.S.; Supervision: P.W.S.; Project administration: M.G.Z.; Funding acquisition: M.G.Z., P.W.S. \n\nThe authors declare no competing or financial interests.\n\nPublished - dev200173.pdf
Submitted - 2021.09.04.458989v1.full.pdf
Supplemental Material - dev200173supp.pdf
", "abstract": "Diapause arrest in animals such as Caenorhabditis elegans is tightly regulated so that animals make appropriate developmental decisions amidst environmental challenges. Fully understanding diapause requires mechanistic insight of both entry and exit from the arrested state. Although a steroid hormone pathway regulates the entry decision into C. elegans dauer diapause, its role in the exit decision is less clear. A complication to understanding steroid hormonal regulation of dauer has been the peculiar fact that steroid hormone mutants such as daf-9 form partial dauers under normal growth conditions. Here, we corroborate previous findings that daf-9 mutants remain capable of forming full dauers under unfavorable growth conditions and establish that the daf-9 partial dauer state is likely a partially exited dauer that has initiated but cannot complete the dauer exit process. We show that the steroid hormone pathway is both necessary for and promotes complete dauer exit, and that the spatiotemporal dynamics of steroid hormone regulation during dauer exit resembles that of dauer entry. Overall, dauer entry and dauer exit are distinct developmental decisions that are both controlled by steroid hormone signaling.", "date": "2022-05", "date_type": "published", "publication": "Development", "volume": "149", "number": "9", "publisher": "Company of Biologists", "pagerange": "Art. No. dev200173", "id_number": "CaltechAUTHORS:20210910-174112976", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210910-174112976", "funders": { "items": [ { "agency": "NIH Postdoctoral Fellowship", "grant_number": "F31 NS120501-01" }, { "agency": "NIH", "grant_number": "UF1-NS111697" }, { "agency": "NIH", "grant_number": "P40 OD010440" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1242/dev.200173", "pmcid": "PMC9148571", "primary_object": { "basename": "dev200173.pdf", "url": "https://authors.library.caltech.edu/records/h23k7-krr08/files/dev200173.pdf" }, "related_objects": [ { "basename": "dev200173supp.pdf", "url": "https://authors.library.caltech.edu/records/h23k7-krr08/files/dev200173supp.pdf" }, { "basename": "2021.09.04.458989v1.full.pdf", "url": "https://authors.library.caltech.edu/records/h23k7-krr08/files/2021.09.04.458989v1.full.pdf" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Zhang, Mark G. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/r7yym-m0j48", "eprint_id": 114173, "eprint_status": "archive", "datestamp": "2023-08-22 14:52:03", "lastmod": "2023-12-22 23:22:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Agapite-Julie", "name": { "family": "Agapite", "given": "Julie" } }, { "name": { "family": "Albou", "given": "Laurent-Philippe" }, "orcid": "0000-0001-5801-1974" }, { "name": { "family": "Aleksander", "given": "Suzanne A." } }, { "name": { "family": "Alexander", "given": "Micheal" } }, { "name": { "family": "Anagnostopoulos", "given": "Anna V." } }, { "name": { "family": "Antonazzo", "given": "Giulia" } }, { "name": { "family": "Argasinska", "given": "Joanna" } }, { "id": "Arnaboldi-Valerio", "name": { "family": "Arnaboldi", "given": "Valerio" }, "orcid": "0000-0002-2563-5374" }, { "name": { "family": "Attrill", "given": "Helen" }, "orcid": "0000-0003-3212-6364" }, { "name": { "family": "Becerra", "given": "Andr\u00e9s" } }, { "name": { "family": "Bello", "given": "Susan M." } }, { "name": { "family": "Blake", "given": "Judith A." }, "orcid": "0000-0001-8522-334X" }, { "name": { "family": "Blodgett", "given": "Olin" } }, { "name": { "family": "Bradford", "given": "Yvonne M." } }, { "name": { "family": "Bult", "given": "Carol J." } }, { "name": { "family": "Cain", "given": "Scott" } }, { "name": { "family": "Calvi", "given": "Brian R." } }, { "name": { "family": "Carbon", "given": "Seth" }, "orcid": "0000-0001-8244-1536" }, { "id": "Chan-Juancarlos-N", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "Chen-Wen-J", "name": { "family": "Chen", "given": "Wen J." } }, { "name": { "family": "Cherry", "given": "J. Michael" }, "orcid": "0000-0001-9163-5180" }, { "id": "Cho-Jaehyoung", "name": { "family": "Cho", "given": "Jaehyoung" } }, { "name": { "family": "Christie", "given": "Karen R." } }, { "name": { "family": "Crosby", "given": "Madeline A." } }, { "name": { "family": "Davis", "given": "Paul" }, "orcid": "0000-0001-5545-0824" }, { "id": "da-Veiga-Beltrame-Eduardo", "name": { "family": "da Veiga Beltrame", "given": "Eduardo" }, "orcid": "0000-0002-1529-9207" }, { "name": { "family": "De Pons", "given": "Jeffrey L." } }, { "name": { "family": "D'Eustachio", "given": "Peter" }, "orcid": "0000-0002-5494-626X" }, { "name": { "family": "Diamantakis", "given": "Stavros" } }, { "name": { "family": "Dolan", "given": "Mary E." }, "orcid": "0000-0001-7732-3295" }, { "name": { "family": "dos Santos", "given": "Gilberto" } }, { "name": { "family": "Douglass", "given": "Eric" } }, { "name": { "family": "Dunn", "given": "Barbara" } }, { "name": { "family": "Eagle", "given": "Anne" } }, { "name": { "family": "Ebert", "given": "Dustin" } }, { "name": { "family": "Engel", "given": "Stacia R." }, "orcid": "0000-0001-5472-917X" }, { "name": { "family": "Fashena", "given": "David" } }, { "name": { "family": "Foley", "given": "Saoirse" }, "orcid": "0000-0002-1791-2837" }, { "name": { "family": "Frazer", "given": "Ken" } }, { "name": { "family": "Gao", "given": "Sibyl" } }, { "name": { "family": "Gibson", "given": "Adam C." } }, { "name": { "family": "Gondwe", "given": "Felix" } }, { "name": { "family": "Goodman", "given": "Josh" } }, { "name": { "family": "Gramates", "given": "L. Sian" } }, { "id": "Grove-Christian-A", "name": { "family": "Grove", "given": "Christian A." }, "orcid": "0000-0001-9076-6015" }, { "name": { "family": "Hale", "given": "Paul" } }, { "name": { "family": "Harris", "given": "Todd" }, "orcid": "0000-0003-3406-163X" }, { "name": { "family": "Thomas Hayman", "given": "G." } }, { "name": { "family": "Hill", "given": "David P." }, "orcid": "0000-0001-7476-6306" }, { "name": { "family": "Howe", "given": "Douglas G." } }, { "name": { "family": "Howe", "given": "Kevin L." }, "orcid": "0000-0002-1751-9226" }, { "name": { "family": "Hu", "given": "Yanhui" } }, { "name": { "family": "Jha", "given": "Sagar" } }, { "name": { "family": "Kadin", "given": "James A." } }, { "name": { "family": "Kaufman", "given": "Thomas C." } }, { "name": { "family": "Kalita", "given": "Patrick" } }, { "name": { "family": "Karra", "given": "Kalpana" } }, { "id": "Kishore-Ranjana", "name": { "family": "Kishore", "given": "Ranjana" }, "orcid": "0000-0002-1478-7671" }, { "name": { "family": "Kwitek", "given": "Anne E." } }, { "name": { "family": "Laulederkind", "given": "Stanley J. F." } }, { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "Raymond" }, "orcid": "0000-0002-8151-7479" }, { "name": { "family": "Longden", "given": "Ian" } }, { "name": { "family": "Luypaert", "given": "Manuel" }, "orcid": "0000-0003-3966-849X" }, { "name": { "family": "MacPherson", "given": "Kevin A." } }, { "name": { "family": "Martin", "given": "Ryan" } }, { "name": { "family": "Marygold", "given": "Steven J." } }, { "name": { "family": "Matthews", "given": "Beverley" } }, { "name": { "family": "McAndrews", "given": "Monica S." } }, { "name": { "family": "Millburn", "given": "Gillian" } }, { "name": { "family": "Miyasato", "given": "Stuart" } }, { "name": { "family": "Motenko", "given": "Howie" } }, { "name": { "family": "Moxon", "given": "Sierra" } }, { "id": "M\u00fcller-Hans-Michael", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } }, { "name": { "family": "Mungall", "given": "Christopher J." }, "orcid": "0000-0002-6601-2165" }, { "name": { "family": "Muruganujan", "given": "Anushya" } }, { "name": { "family": "Mushayahama", "given": "Tremayne" } }, { "name": { "family": "Nalabolu", "given": "Harika S." } }, { "name": { "family": "Nash", "given": "Robert S." } }, { "name": { "family": "Ng", "given": "Patrick" } }, { "name": { "family": "Nuin", "given": "Paulo" }, "orcid": "0000-0003-4915-664X" }, { "name": { "family": "Paddock", "given": "Holly" } }, { "name": { "family": "Paulini", "given": "Michael" }, "orcid": "0000-0002-6968-2340" }, { "name": { "family": "Perrimon", "given": "Norbert" } }, { "name": { "family": "Pich", "given": "Christian" } }, { "name": { "family": "Quinton-Tulloch", "given": "Mark" }, "orcid": "0000-0001-5713-0736" }, { "id": "Raciti-Daniela", "name": { "family": "Raciti", "given": "Daniela" } }, { "name": { "family": "Ramachandran", "given": "Sridhar" } }, { "name": { "family": "Richardson", "given": "Joel E." } }, { "name": { "family": "Russo Gelbart", "given": "Susan" } }, { "name": { "family": "Ruzicka", "given": "Leyla" } }, { "name": { "family": "Schaper", "given": "Kevin" } }, { "id": "Schindelman-Gary", "name": { "family": "Schindelman", "given": "Gary" } }, { "name": { "family": "Shimoyama", "given": "Mary" } }, { "name": { "family": "Simison", "given": "Matt" } }, { "name": { "family": "Shaw", "given": "David R." } }, { "name": { "family": "Shrivatsav", "given": "Ajay" } }, { "name": { "family": "Singer", "given": "Amy" } }, { "name": { "family": "Skrzypek", "given": "Marek" } }, { "name": { "family": "Smith", "given": "Constance M." } }, { "name": { "family": "Smith", "given": "Cynthia L." } }, { "name": { "family": "Smith", "given": "Jennifer R." } }, { "name": { "family": "Stein", "given": "Lincoln" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "name": { "family": "Tabone", "given": "Christopher J." } }, { "name": { "family": "Thomas", "given": "Paul D." }, "orcid": "0000-0002-9074-3507" }, { "name": { "family": "Thorat", "given": "Ketaki" } }, { "name": { "family": "Thota", "given": "Jyothi" } }, { "name": { "family": "Toro", "given": "Sabrina" } }, { "name": { "family": "Tomczuk", "given": "Monika" } }, { "name": { "family": "Trovisco", "given": "Vitor" } }, { "name": { "family": "Tutaj", "given": "Marek A." } }, { "name": { "family": "Tutaj", "given": "Monika" } }, { "name": { "family": "Urbano", "given": "Jose-Maria" } }, { "id": "Van-Auken-Kimberly-M", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "name": { "family": "Van Slyke", "given": "Ceri E." }, "orcid": "0000-0002-2244-7917" }, { "id": "Wang-Qinghua", "name": { "family": "Wang", "given": "Qinghua" } }, { "name": { "family": "Wang", "given": "Shur-Jen" } }, { "name": { "family": "Weng", "given": "Shuai" } }, { "name": { "family": "Westerfield", "given": "Monte" } }, { "name": { "family": "Williams", "given": "Gary" } }, { "name": { "family": "Wilming", "given": "Laurens G." } }, { "name": { "family": "Wong", "given": "Edith D." } }, { "name": { "family": "Wright", "given": "Adam" }, "orcid": "0000-0002-5719-4024" }, { "id": "Yook-Karen-J", "name": { "family": "Yook", "given": "Karen" }, "orcid": "0000-0002-4457-6787" }, { "name": { "family": "Zarowiecki", "given": "Magdalena" }, "orcid": "0000-0001-6102-7731" }, { "name": { "family": "Zhou", "given": "Pinglei" } }, { "name": { "family": "Zytkovicz", "given": "Mark" } } ] }, "title": "Harmonizing model organism data in the Alliance of Genome Resources", "ispublished": "pub", "full_text_status": "restricted", "keywords": "genome, knowledgebase, phenotype, data mining, biocuration, gene function, gene expression, gene interaction, variants; Genetics", "note": "\u00a9 The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived: 12 December 2021. Accepted: 26 January 2022. Published: 25 February 2022. \n\nThe authors thank our user communities for their patience as we transition our heavily used resources to shared infrastructure, as well as for contributing data and suggestions. They also thank the members of our Scientific Advisory Board (Gary Bader, Alex Bateman, Helen Berman, Shawn Burgess, Andrew Chisholm, Phil Hieter, Brian Oliver, Calum Macrae, Titus Brown, Abraham Palmer and Michelle Southard-Smith) for cogent advice, and NGHRI Program Staff (Valentina di Francesco, Ajay Pillai, Sean Garin, and Helen Thompson) for advice. \n\nThe core funding for the Alliance is from the National Human Genome Research Institute and the National Heart, Lung and Blood Institute (U24HG010859). The curation of data and its harmonization is supported by National Human Genome Research Institute grants U24HG002659 (ZFIN), U24HG002223 (WormBase), U41HG000739 (FlyBase), U24HG001315 (SGD), U24HG000330 (MGD), and U41HG002273 (GO Consortium), as well as grant R01HL064541 from the National Heart, Lung and Blood Institute (RGD), P41HD062499 from the Eunice Kennedy Shriver National Institute of Child Health and Human Development (GXD), and the Medical Research Council-UK grant MR/L001020/1 (WormBase). Additional effort was supported by DOE DE-AC02-05CH11231. \n\nData availability. Data are available by browsing, displays analytical tools, downloads, and APIs via the Portal at alliancegenome.org. \n\nConflicts of interest: None declared.", "abstract": "The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein\u2013protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.", "date": "2022-04", "date_type": "published", "publication": "Genetics", "volume": "220", "number": "4", "publisher": "Oxford University Press", "pagerange": "Art. No. iyac022", "id_number": "CaltechAUTHORS:20220406-521823507", "issn": "1943-2631", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220406-521823507", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U24HG010859" }, { "agency": "NIH", "grant_number": "U24HG002659" }, { "agency": "NIH", "grant_number": "U24HG002223" }, { "agency": "NIH", "grant_number": "U41HG000739" }, { "agency": "NIH", "grant_number": "U24HG001315" }, { "agency": "NIH", "grant_number": "U24HG000330" }, { "agency": "NIH", "grant_number": "U41HG002273" }, { "agency": "NIH", "grant_number": "R01HL064541" }, { "agency": "NIH", "grant_number": "P41HD062499" }, { "agency": "Medical Research Council (UK)", "grant_number": "MR/L001020/1" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-AC02-05CH11231" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "corp_creators": { "items": [ "Alliance of Genome Resources Consortium" ] }, "doi": "10.1093/genetics/iyac022", "pmcid": "PMC8982023", "resource_type": "article", "pub_year": "2022", "author_list": "Agapite, Julie; Albou, Laurent-Philippe; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ax9qa-w5481", "eprint_id": 113875, "eprint_status": "archive", "datestamp": "2023-08-22 14:50:32", "lastmod": "2023-12-22 23:30:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Davis-Paul", "name": { "family": "Davis", "given": "Paul" }, "orcid": "0000-0001-5545-0824" }, { "name": { "family": "Zarowiecki", "given": "Magdalena" }, "orcid": "0000-0001-6102-7731" }, { "id": "Arnaboldi-Valerio", "name": { "family": "Arnaboldi", "given": "Valerio" }, "orcid": "0000-0002-2563-5374" }, { "name": { "family": "Becerra", "given": "Andr\u00e9s" } }, { "name": { "family": "Cain", "given": "Scott" } }, { "id": "Chan-Juancarlos-N", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "Chen-Wen-J", "name": { "family": "Chen", "given": "Wen J." } }, { "id": "Cho-Jaehyoung", "name": { "family": "Cho", "given": "Jaehyoung" } }, { "id": "da-Veiga-Beltrame-Eduardo", "name": { "family": "da Veiga Beltrame", "given": "Eduardo" }, "orcid": "0000-0002-1529-9207" }, { "name": { "family": "Diamantakis", "given": "Stavros" } }, { "name": { "family": "Gao", "given": "Sibyl" } }, { "name": { "family": "Grigoriadis", "given": "Dionysis" } }, { "id": "Grove-Christian-A", "name": { "family": "Grove", "given": "Christian A." }, "orcid": "0000-0001-9076-6015" }, { "name": { "family": "Harris", "given": "Todd W." }, "orcid": "0000-0003-3406-163X" }, { "id": "Kishore-Ranjana", "name": { "family": "Kishore", "given": "Ranjana" }, "orcid": "0000-0002-1478-7671" }, { "name": { "family": "Le", "given": "Tuan" } }, { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "Raymond Y. N." }, "orcid": "0000-0002-8151-7479" }, { "name": { "family": "Luypaert", "given": "Manuel" }, "orcid": "0000-0003-3966-849X" }, { "id": "M\u00fcller-Hans-Michael", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } }, { "id": "Nakamura-Cecilia", "name": { "family": "Nakamura", "given": "Cecilia" }, "orcid": "0000-0002-4689-7314" }, { "name": { "family": "Nuin", "given": "Paulo" }, "orcid": "0000-0003-4915-664X" }, { "name": { "family": "Paulini", "given": "Michael" }, "orcid": "0000-0002-6968-2340" }, { "name": { "family": "Quinton-Tulloch", "given": "Mark" }, "orcid": "0000-0001-5713-0736" }, { "id": "Raciti-Daniela", "name": { "family": "Raciti", "given": "Daniela" } }, { "name": { "family": "Rodgers", "given": "Faye H." }, "orcid": "0000-0003-2391-9573" }, { "name": { "family": "Russell", "given": "Matthew" }, "orcid": "0000-0001-6140-6723" }, { "id": "Schindelman-Gary", "name": { "family": "Schindelman", "given": "Gary" } }, { "name": { "family": "Singh", "given": "Archana" }, "orcid": "0000-0002-5027-4582" }, { "name": { "family": "Stickland", "given": "Tim" }, "orcid": "0000-0003-3185-1433" }, { "id": "Van-Auken-Kimberly", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Wang-Qinghua", "name": { "family": "Wang", "given": "Qinghua" } }, { "name": { "family": "Williams", "given": "Gary" } }, { "name": { "family": "Wright", "given": "Adam J." }, "orcid": "0000-0002-5719-4024" }, { "id": "Yook-Karen-J", "name": { "family": "Yook", "given": "Karen" }, "orcid": "0000-0002-4457-6787" }, { "name": { "family": "Berriman", "given": "Matt" }, "orcid": "0000-0002-9581-0377" }, { "name": { "family": "Howe", "given": "Kevin L." }, "orcid": "0000-0002-1751-9226" }, { "name": { "family": "Schedl", "given": "Tim" }, "orcid": "0000-0003-2148-2996" }, { "name": { "family": "Stein", "given": "Lincoln" }, "orcid": "0000-0002-1983-4588" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "WormBase in 2022\u2014data, processes, and tools for analyzing Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "Caenorhabditis elegans, caenorhabditis, nematode, resource, model, database, data, community, software, gene, curation, annotation, research, literature, mining, tools, health, human, platform; Genetics", "note": "\u00a9 The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nThe authors wish to thank the US National Human Genome Research Institute; UK Medical Research Council funding agencies for their ongoing support of WormBase and members of the C. elegans research community whose insights and explorations form the purpose of WormBase, all those contributing data through AFP or data submission forms, and all the WormBase users, for all your feedback, input and requests which inspire and guide us. \n\nFunding for WormBase is from US National Human Genome Research Institute [U24 HG002223]; UK Medical Research Council [MR/S000453/1]. Funding for open access charge: US National Human Genome Research Institute [U24 HG002223]. \n\nConflicts of interest: None declared.\n\nPublished - iyac003.pdf
", "abstract": "WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by the published nematode genetics literature. Here, we provide a broad overview of the current state of WormBase in terms of data type, curation workflows, analysis, and tools, including exciting new advances for analysis of single-cell data, text mining and visualization, and the new community collaboration forum. Concurrently, we continue the integration and harmonization of infrastructure, processes, and tools with the Alliance of Genome Resources, of which WormBase is a founding member.", "date": "2022-04", "date_type": "published", "publication": "Genetics", "volume": "220", "number": "4", "publisher": "Oxford University Press", "pagerange": "Art. No. iyac003", "id_number": "CaltechAUTHORS:20220310-752284000", "issn": "1943-2631", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220310-752284000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U24 HG002223" }, { "agency": "Medical Research Council (UK)", "grant_number": "MR/S000453/1" } ] }, "local_group": { "items": [ { "id": "WormBase" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/genetics/iyac003", "pmcid": "PMC8982018", "primary_object": { "basename": "iyac003.pdf", "url": "https://authors.library.caltech.edu/records/ax9qa-w5481/files/iyac003.pdf" }, "resource_type": "article", "pub_year": "2022", "author_list": "Davis, Paul; Zarowiecki, Magdalena; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/4a7mt-ccj86", "eprint_id": 115453, "eprint_status": "archive", "datestamp": "2023-08-22 14:42:27", "lastmod": "2023-12-22 23:39:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "da-Veiga-Beltrame-Eduardo", "name": { "family": "da Veiga Beltrame", "given": "Eduardo" }, "orcid": "0000-0002-1529-9207" }, { "id": "Arnaboldi-Valerio", "name": { "family": "Arnaboldi", "given": "Valerio" }, "orcid": "0000-0002-2563-5374" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "WormBase single-cell tools", "ispublished": "pub", "full_text_status": "public", "keywords": "General Medicine", "note": "\u00a9 The Author(s) 2022. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived: 07 September 2021. Revision received: 28 February 2022. Editorial decision: 19 March 2022. Accepted: 26 March 2022. Published: 28 March 2022. Corrected and typeset: 06 July 2022. \n\nThe authors would like to thank Paulo Nuin and David Brown for reviewing the code, Tom Morrell for assistance with CaltechData and Valentine Svensson for suggestions on the manuscript. \n\nAuthor contributions. E.B. conceived the tools design and curated the data. E.B. implemented scefg with input from V.A. V.A. implemented wormcells-viz with input from E.B. E.B., V.A. and P.W.S. wrote and reviewed the manuscript. \n\nThis work was supported by grant numbers NIH U24HG010859 and NIH U24HG002223. \n\nConflict of Interest: none declared.\n\nPublished - vbac018.pdf
Supplemental Material - vbac018_supplementary_data.pdf
", "abstract": "We present two web apps for interactively performing common tasks with single-cell RNA sequencing data: scdefg for differential expression and wormcells-viz for visualization of gene expression. We deployed these tools with public Caenorhabditis elegans datasets curated by WormBase at https://single-cell.wormbase.org. Source code for deploying these tools with other datasets is available at https://github.com/WormBase/scdefg and https://github.com/WormBase/wormcells-viz.", "date": "2022-03-28", "date_type": "published", "publication": "Bioinformatics Advances", "volume": "2", "number": "1", "publisher": "Oxford University Press", "pagerange": "vbac018", "id_number": "CaltechAUTHORS:20220711-347663000", "issn": "2635-0041", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220711-347663000", "funders": { "items": [ { "agency": "NIH", "grant_number": "U24HG010859" }, { "agency": "NIH", "grant_number": "U24HG002223" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/bioadv/vbac018", "pmcid": "PMC9258504", "primary_object": { "basename": "vbac018.pdf", "url": "https://authors.library.caltech.edu/records/4a7mt-ccj86/files/vbac018.pdf" }, "related_objects": [ { "basename": "vbac018_supplementary_data.pdf", "url": "https://authors.library.caltech.edu/records/4a7mt-ccj86/files/vbac018_supplementary_data.pdf" } ], "resource_type": "article", "pub_year": "2022", "author_list": "da Veiga Beltrame, Eduardo; Arnaboldi, Valerio; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/r6tc4-wdj46", "eprint_id": 113623, "eprint_status": "archive", "datestamp": "2023-08-22 14:27:28", "lastmod": "2023-12-22 23:22:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shinoda-Kenta", "name": { "family": "Shinoda", "given": "Kenta" } }, { "id": "Choe-Andrea", "name": { "family": "Choe", "given": "Andrea" } }, { "id": "Hirahara-Kiyoshi", "name": { "family": "Hirahara", "given": "Kiyoshi" } }, { "id": "Kiuchi-Masahiro", "name": { "family": "Kiuchi", "given": "Masahiro" } }, { "id": "Kobuko-Kota", "name": { "family": "Kokubo", "given": "Kota" }, "orcid": "0000-0001-6896-1981" }, { "id": "Ichikawa-Tomomi", "name": { "family": "Ichikawa", "given": "Tomomi" } }, { "id": "Hoki-Jason-S", "name": { "family": "Hoki", "given": "Jason S." } }, { "id": "Suzuki-Akane-S", "name": { "family": "Suzuki", "given": "Akane S." } }, { "id": "Bose-Neelanjan", "name": { "family": "Bose", "given": "Neelanjan" } }, { "id": "Appleton-Judith-A", "name": { "family": "Appleton", "given": "Judith A." } }, { "id": "Aroian-Raffi-V", "name": { "family": "Aroian", "given": "Raffi V." } }, { "id": "Schroeder-Frank-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Nakayama-Toshinori", "name": { "family": "Nakayama", "given": "Toshinori" }, "orcid": "0000-0002-1434-2007" } ] }, "title": "Nematode ascarosides attenuate mammalian type 2 inflammatory responses", "ispublished": "pub", "full_text_status": "public", "keywords": "asthma; mouse model; nematode; small molecules; ascarosides; Multidisciplinary", "note": "\u00a9 2022 the Author(s). Published by PNAS. This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND). \n\nContributed by Paul W. Sternberg; received May 13, 2021; accepted December 28, 2021; reviewed by Rick Maizels and Steven Ziegler. \n\nWe thank Ellen Rothenberg, Mary Yui, and Sylvia Vetrone for their invaluable discussions and advice. We thank Ed Platzer for his assistance with the smES preparation and Stephan H. von Reuss and Sydney Campbell for analyzing nematode extracts. We also thank Kaoru Sugaya and Toshihiro Ito for their excellent technical assistance. This work was supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT Japan) Grants-in-Aid for Scientific Research (S) JP19H05650, (B) 20H03685, (C) 17K08876, 18K07164, and 19K16683, Transformative Research Areas (B) JP21H05120, and JP21H05121; JST FOREST Program (JPMJFR200R); Practical Research Project for Allergic Diseases and Immunology (Research on Allergic Diseases and Immunology) from the Japan Agency for Medical Research and Development (AMED) (Nos. JP21ek0410082, JP21ek0410060, and JP19ek0410045); Japan Agency for Medical Research and Development (AMED)-PRIME, AMED (No. JP20gm6110005); Japan Agency for Medical Research and Development (AMED)-CREST, AMED (No. JP20gm1210003); Mochida Memorial Foundation for Medical and Pharmaceutical Research, MSD Life Science Foundation, the Naito Foundation, and the Takeda Science Foundation. P.W.S. was an investigator of the Howard Hughes Medical Institute, which supported this work. We further acknowledge support from the Atkinson Center for a Sustainable Future (to F.C.S. and J.A.A.), the Triad Foundation (to F.C.S.), and NIH CBI training grant T32GM008500 (to J.S.H.). \n\nK.S., A.C., and K.H. contributed equally to this work. \n\nAuthor contributions: K.S., A.C., K.H., F.C.S., P.W.S., and T.N. designed research; K.S., A.C., M.K., K.K., T.I., J.S.H., A.S.S., N.B., J.A.A., and R.V.A. performed research; J.S.H., J.A.A., R.V.A., and F.C.S. contributed new reagents/analytic tools; K.S., K.H., M.K., T.I., A.S.S., N.B., F.C.S., and T.N. analyzed data; and K.S., A.C., K.H., F.C.S., and T.N. wrote the paper. \n\nReviewers: R.M., University of Glasgow; and S.Z., Benaroya Research Institute at Virginia Mason. \n\nCompeting interest statement: The patent rights related to the results reported here have been licensed to Holoclara, Inc., a privately held company that has been pursuing ascr#7-related compounds as potential therapeutics since its founding in 2017. A.C., P.W.S., and F.C.S. are cofounders and stockholders of Holoclara, Inc., and A.C. is the company's chief executive officer. The patent rights have also been licensed to Ascribe Bioscience, Inc., a privately held company where F.C.S. is a cofounder and a stockholder. While most of the studies reported here predate the founding of the company, Holoclara, Inc. funded part of the work. Holoclara, Inc. is not publicly traded and there are no plans for an initial public offering.\n\nPublished - e2108686119.full.pdf
Supplemental Material - 23/2108686119.DCSupplemental/pnas.2108686119.sapp.pdf
", "abstract": "Mounting evidence suggests that nematode infection can protect against disorders of immune dysregulation. Administration of live parasites or their excretory/secretory (ES) products has shown therapeutic effects across a wide range of animal models for immune disorders, including asthma. Human clinical trials of live parasite ingestion for the treatment of immune disorders have produced promising results, yet concerns persist regarding the ingestion of pathogenic organisms and the immunogenicity of protein components. Despite extensive efforts to define the active components of ES products, no small molecules with immune regulatory activity have been identified from nematodes. Here we show that an evolutionarily conserved family of nematode pheromones called ascarosides strongly modulates the pulmonary immune response and reduces asthma severity in mice. Screening the inhibitory effects of ascarosides produced by animal-parasitic nematodes on the development of asthma in an ovalbumin (OVA) murine model, we found that administration of nanogram quantities of ascr#7 prevented the development of lung eosinophilia, goblet cell metaplasia, and airway hyperreactivity. Ascr#7 suppressed the production of IL-33 from lung epithelial cells and reduced the number of memory-type pathogenic Th2 cells and ILC2s in the lung, both key drivers of the pathology of asthma. Our findings suggest that the mammalian immune system recognizes ascarosides as an evolutionarily conserved molecular signature of parasitic nematodes. The identification of a nematode-produced small molecule underlying the well-documented immunomodulatory effects of ES products may enable the development of treatment strategies for allergic diseases.", "date": "2022-03-01", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "119", "number": "9", "publisher": "National Academy of Sciences", "pagerange": "Art. No. e2108686119", "id_number": "CaltechAUTHORS:20220228-619279000", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220228-619279000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)", "grant_number": "047-101" }, { "agency": "Ministry of Education, Culture, Sports, Science and Technology (MEXT)", "grant_number": "JP19H05650" }, { "agency": "Ministry of Education, Culture, Sports, Science and Technology (MEXT)", "grant_number": "20H03685" }, { "agency": "Ministry of Education, Culture, Sports, Science and Technology (MEXT)", "grant_number": "17K08876" }, { "agency": "Ministry of Education, Culture, Sports, Science and Technology (MEXT)", "grant_number": "18K07164" }, { "agency": "Ministry of Education, Culture, Sports, Science and Technology (MEXT)", "grant_number": "19K16683" }, { "agency": "Ministry of Education, Culture, Sports, Science and Technology (MEXT)", "grant_number": "JP21H05120" }, { "agency": "Ministry of Education, Culture, Sports, Science and Technology (MEXT)", "grant_number": "JP21H05121" }, { "agency": "Japan Science and Technology Agency", "grant_number": "JPMJFR200R" }, { "agency": "Japan Agency for Medical Research and Development", "grant_number": "JP20ek0410082" }, { "agency": "Japan Agency for Medical Research and Development", "grant_number": "JP20ek0410060" }, { "agency": "Japan Agency for Medical Research and Development", "grant_number": "JP19ek0410045" }, { "agency": "Japan Agency for Medical Research and Development", "grant_number": "P20gm6110005" }, { "agency": "Japan Agency for Medical Research and Development", "grant_number": "JP20gm1210003" }, { "agency": "Mochida Memorial Foundation for Medical and Pharmaceutical Research" }, { "agency": "MSD Life Science Foundation" }, { "agency": "Naito Foundation" }, { "agency": "Takeda Science Foundation" }, { "agency": "Atkinson Center for a Sustainable Future" }, { "agency": "Triad Foundation" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM008500" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1073/pnas.2108686119", "pmcid": "PMC8892368", "primary_object": { "basename": "e2108686119.full.pdf", "url": "https://authors.library.caltech.edu/records/r6tc4-wdj46/files/e2108686119.full.pdf" }, "resource_type": "article", "pub_year": "2022", "author_list": "Shinoda, Kenta; Choe, Andrea; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/tyteb-89e65", "eprint_id": 113790, "eprint_status": "archive", "datestamp": "2023-08-22 14:19:59", "lastmod": "2023-12-22 23:22:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cohen-Sarah-M", "name": { "family": "Cohen", "given": "Sarah M." }, "orcid": "0000-0002-5233-2280" }, { "id": "Wrobel-Chester-J-J", "name": { "family": "Wrobel", "given": "Chester J. J." }, "orcid": "0000-0001-6047-4644" }, { "id": "Prakash-Sharan-J", "name": { "family": "Prakash", "given": "Sharan J." } }, { "id": "Schroeder-Frank-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Formation and function of dauer ascarosides in the nematodes Caenorhabditis briggsae and Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "C. elegans, C. briggsae, ascarosides, dauer, daf-22, glo-1; Genetics (clinical); Genetics; Molecular Biology", "note": "\u00a9 The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived: July 19, 2021. Accepted: December 22, 2021. \n\nThe authors thank all members of the Sternberg and Schroeder labs especially Mengyi Cao, Hillel Schwartz, Heenam Park, Jessica Sun, and Katherine Norton for their input, assistance, and helpful comments throughout the project. They thank the Caenorhabditis Genetics Center, which is funded by the NIH Office of Research Infrastructure Programs (P40 OD010440) for some C. elegans strains used in these experiments, WormBase for sequences, and Tsui-Fen Chou for Cas9 protein. \n\nThis work was supported by the National Science Foundation Graduate Research Fellowship under Grant DGE 1745301 to SMC, the National Institutes of Health through Grants UF1NS111697 and R24OD023041 to PWS, and the National Institutes of Health through Grant R01GM113692 to FCS. FCS is also a Faculty Scholar of the Howard Hughes Medical Institute. \n\nData availability. Strains are available upon request. The authors affirm that all data necessary for confirming the conclusions of the article are present within the article, figures, and tables. \n\nSupplemental material is available at G3 online. \n\nConflicts of interest. None declared.\n\nPublished - jkac014.pdf
Supplemental Material - jkac014_supplementary_data.pdf
", "abstract": "The biosynthetic pathways and functions of ascaroside signaling molecules in the nematode Caenorhabditis elegans have been studied to better understand complex, integrative developmental decision-making. Although it is known that ascarosides play multiple roles in the development and behavior of nematode species other than C. elegans, these parallel pheromone systems have not been well-studied. Here, we show that ascarosides in the nematode Caenorhabditis briggsae are biosynthesized in the same manner as C. elegans and act to induce the alternative developmental pathway that generates the stress-resistant dauer lifestage. We show that ascr#2 is the primary component of crude dauer pheromone in C. briggsae; in contrast, C. elegans dauer pheromone relies on a combination of ascr#2, ascr#3, and several other components. We further demonstrate that Cbr-daf-22, like its C. elegans ortholog Cel-daf-22, is necessary to produce short-chain ascarosides. Moreover, Cbr-daf-22 and Cel-daf-22 mutants produce an ascaroside-independent metabolite that acts antagonistically to crude dauer pheromone and inhibits dauer formation.", "date": "2022-03", "date_type": "published", "publication": "G3", "volume": "12", "number": "3", "publisher": "Genetics Society of America", "pagerange": "Art. No. jkac014", "id_number": "CaltechAUTHORS:20220308-35596000", "issn": "2160-1836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220308-35596000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF Graduate Research Fellowship", "grant_number": "DGE-1745301" }, { "agency": "NIH", "grant_number": "UF1NS111697" }, { "agency": "NIH", "grant_number": "R24OD023041" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/g3journal/jkac014", "pmcid": "PMC8895998", "primary_object": { "basename": "jkac014.pdf", "url": "https://authors.library.caltech.edu/records/tyteb-89e65/files/jkac014.pdf" }, "related_objects": [ { "basename": "jkac014_supplementary_data.pdf", "url": "https://authors.library.caltech.edu/records/tyteb-89e65/files/jkac014_supplementary_data.pdf" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Cohen, Sarah M.; Wrobel, Chester J. J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/snxfg-0s413", "eprint_id": 113620, "eprint_status": "archive", "datestamp": "2023-08-20 07:03:41", "lastmod": "2023-12-22 23:22:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Garg-Pranjal", "name": { "family": "Garg", "given": "Pranjal" } }, { "id": "Tan-Chieh-Hsiang", "name": { "family": "Tan", "given": "Chieh-Hsiang" }, "orcid": "0000-0002-5432-0160" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "DiI staining of sensory neurons in the entomopathogenic nematode Steinernema hermaphroditum", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2022 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nHistory: Received January 12, 2022 Revision received January 26, 2022 Accepted February 10, 2022 Published February 24, 2022. \n\nFunding: NSF EDGE grant 2128267 to PWS. \n\nAuthor Contributions: Pranjal Garg: Formal analysis, Investigation, Methodology, Visualization, Writing - original draft. Chieh-Hsiang Tan: Conceptualization, Methodology, Supervision, Writing - original draft. Paul W. Sternberg: Conceptualization, Funding acquisition, Supervision, Writing - review and editing. \n\nReviewed By: Ray Hong.\n\nPublished - 25789430-2022-micropub.biology.000516.pdf
", "abstract": "Steinernema hermaphroditum entomopathogenic nematodes (EPN) and their Xenorhabdus griffiniae symbiotic bacteria have recently been shown to be a genetically tractable system for the study of both parasitic and mutualistic symbiosis. In their infective juvenile (IJ) stage, EPNs search for insect hosts to invade and quickly kill them with the help of the symbiotic bacteria they contain. The mechanisms behind these behaviors have not been well characterized, including how the nematodes sense their insect hosts. In the well-studied free\u2011living soil nematode Caenorhabditis elegans, ciliated amphid neurons enable the worms to sense their environment, including chemosensation. Some of these neurons have also been shown to control the decision to develop as a stress-resistant dauer larva, analogous to the infective juveniles of EPNs, or to exit from dauer and resume larval development. In C. elegans and other nematodes, dye-filling with DiI is an easy and efficient method to label these neurons. We developed a protocol for DiI staining of S. hermaphroditum sensory neurons. Using this method, we could identify neurons positionally analogous to the C. elegans amphid neurons ASI, ADL, ASK, ASJ, as well as inner labial neurons IL1 and IL2. Similar to findings in other EPNs, we also found that the IJs of S. hermaphroditum are dye-filling resistant.", "date": "2022-02-24", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "id_number": "CaltechAUTHORS:20220228-618839000", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220228-618839000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "IOS-2128267" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.17912/micropub.biology.000516", "pmcid": "PMC8874337", "primary_object": { "basename": "25789430-2022-micropub.biology.000516.pdf", "url": "https://authors.library.caltech.edu/records/snxfg-0s413/files/25789430-2022-micropub.biology.000516.pdf" }, "resource_type": "article", "pub_year": "2022", "author_list": "Garg, Pranjal; Tan, Chieh-Hsiang; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/g7849-qd950", "eprint_id": 112240, "eprint_status": "archive", "datestamp": "2023-08-22 13:02:25", "lastmod": "2023-12-22 23:22:03", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chai-Cynthia-M", "name": { "family": "Chai", "given": "Cynthia M." }, "orcid": "0000-0001-6118-2926" }, { "id": "Chen-Wen", "name": { "family": "Chen", "given": "Wen" } }, { "id": "Wong-Wan-Rong", "name": { "family": "Wong", "given": "Wan-Rong" }, "orcid": "0000-0002-9757-8145" }, { "id": "Park-Heenam", "name": { "family": "Park", "given": "Heenam" }, "orcid": "0000-0001-7911-5828" }, { "id": "Cohen-Sarah-M", "name": { "family": "Cohen", "given": "Sarah M." }, "orcid": "0000-0002-5233-2280" }, { "id": "Wan-Xuan", "name": { "family": "Wan", "given": "Xuan" }, "orcid": "0000-0002-6165-6340" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "A conserved behavioral role for a nematode interneuron neuropeptide receptor", "ispublished": "pub", "full_text_status": "public", "keywords": "neuropeptide, interneurons, locomotion, G-protein coupled receptor, Caenorhabditis briggsae, escape behavior, Brugia malayi, Onchocerca volvulus, neurogenetics; Genetics", "note": "\u00a9 The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model). \n\nReceived: 24 August 2021; Accepted: 28 October 2021; Published: 06 November 2021; Corrected and typeset: 25 November 2021. \n\nSome strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). WormBase provided key molecular and genetic information. Some strains were provided by the lab of Dr Shohei Mitani as part of the National Bioresource Project. We thank Shu Fay Ung for generating the schematic in Figure 1A. \n\nConceptualization\u2014C.M.C. and P.W.S. Experimental design and data analysis\u2014C.M.C., W.C., W.W., and X.W. Molecular cloning and transgenesis\u2014C.M.C. Caenorhabditis elegans CRISPR mutagenesis\u2014H.P. Caenorhabditis briggsae CRISPR mutagenesis\u2014S.M.C. Touch-evoked escape response assays\u2014W.C. Motility assays\u2014W.W. Male mating assays\u2014X.W. Microscopy and neuron identification\u2014C.M.C. C.M.C. wrote the paper with input from all coauthors. Funding acquisition\u2014P.W.S. \n\nThis work was funded by NIH grants R240D023041 and R01NS113119 to P.W.S. \n\nCynthia M. Chai, Wen Chen and Wan-Rong Wong contributed equally to this work. \n\nThe authors declare that there is no conflict of interest.\n\nSupplemental Material - iyab198_supplementary_data.pdf
", "abstract": "Neuropeptides are evolutionarily conserved modulators of many aspects of animal behavior and physiology, and expand the repertoire of processes that can be controlled by a limited number of neurons. Deciphering the neuropeptidergic codes that govern distinct processes requires systematic functional analyses of neuropeptides and their cognate receptors. Even in well-studied model organisms like Caenorhabditis elegans, however, such efforts have been precluded by a lack of mutant reagents. Here, we generated and screened 21 C. elegans neuropeptide G-protein coupled receptor mutants with no pre-existing reagents for the touch-evoked escape response, and implicated six receptors expressed in diverse neuron classes representing multiple circuit levels in this behavior. We further characterized the mutant with the most severe phenotype, frpr-14, which was defective in multiple behavioral paradigms. We leveraged this range of phenotypes to reveal that FRPR-14 modulation of different precommand interneuron classes, AVH and AIB, can drive distinct behavioral subsets, demonstrating cellular context-dependent roles for FRPR-14 signaling. We then show that Caenorhabditis briggsae CBR-FRPR-14 modulates an AVH-like interneuron pair to regulate the same behaviors as C. elegans but to a smaller extent. Our results also suggest that differences in touch-evoked escape circuit architecture between closely related species results from changes in neuropeptide receptor expression pattern, as opposed to ligand\u2013receptor pairing. This study provides insights into the principles utilized by a compact, multiplexed nervous system to generate intraspecific behavioral complexity and interspecific variation.", "date": "2022-01", "date_type": "published", "publication": "Genetics", "volume": "220", "number": "1", "publisher": "Oxford University Press", "pagerange": "Art. No. iyab198", "id_number": "CaltechAUTHORS:20211206-235720208", "issn": "1943-2631", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211206-235720208", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P40 OD010440" }, { "agency": "NIH", "grant_number": "R240D023041" }, { "agency": "NIH", "grant_number": "R01NS113119" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/genetics/iyab198", "pmcid": "PMC8733633", "primary_object": { "basename": "iyab198_supplementary_data.pdf", "url": "https://authors.library.caltech.edu/records/g7849-qd950/files/iyab198_supplementary_data.pdf" }, "resource_type": "article", "pub_year": "2022", "author_list": "Chai, Cynthia M.; Chen, Wen; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/n1101-2dq81", "eprint_id": 110679, "eprint_status": "archive", "datestamp": "2023-08-22 13:00:25", "lastmod": "2023-12-22 23:35:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cao-Mengyi", "name": { "family": "Cao", "given": "Mengyi" }, "orcid": "0000-0002-3117-3401" }, { "id": "Schwartz-Hillel-T", "name": { "family": "Schwartz", "given": "Hillel T." }, "orcid": "0000-0002-3448-8652" }, { "id": "Tan-Chieh-Hsiang", "name": { "family": "Tan", "given": "Chieh-Hsiang" }, "orcid": "0000-0002-5432-0160" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The entomopathogenic nematode Steinernema hermaphroditum is a self-fertilizing hermaphrodite and a genetically tractable system for the study of parasitic and mutualistic symbiosis", "ispublished": "pub", "full_text_status": "public", "keywords": "symbiosis; mutualism; parasitism; entomopathogenic; nematode; hermaphroditism; Steinernema; Xenorhabdus; model\nsystem; genetic screen", "note": "\u00a9 The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model). \n\nReceived: 25 August 2021; Accepted: 29 September 2021; Published: 11 October 2021; Corrected and typeset: 17 November 2021. \n\nWe are overwhelmingly grateful for S. hermaphroditum as a generous gift from nature and a superb organism to explore scientific curiosities. We thank Adler Dillman of University of California Riverside for generously sharing the S. hermaphroditum-India strain CS34 and for comments on this manuscript. We also thank Heidi Goodrich-Blair and Jennifer Heppert of the University of Tennessee Knoxville for helpful discussions and editorial suggestions. We are also grateful for valuable suggestions from Zuzana Kocsisova. We appreciate our correspondence with Christine Griffin on the mode of reproduction of S. hermaphroditum-Indonesia. The monoclonal anti-MSP antibody 4A5 developed by David Greenstein of the University of Minnesota was obtained from the Developmental Studies Hybridoma Bank, created by the NICHD of the NIH and maintained at The University of Iowa Department of Biology. Bacterial strains HB101 and DA1877 were obtained from the Caenorhabditis Genetics Center (CGC), which is funded by the NIH Office of Research Infrastructure Programs (P40 OD010440). This work was also facilitated by WormBase and ParaSite, a knowledgebase for nematode research. Figures 2D and 5A are created with BioRender.com. \n\nThis research was supported by National Institutes of Health (NIH) Ruth L. Kirschstein National Research Service Award (NRSA) Individual Postdoctoral Fellowship F32 5F32GM131570 (M.C.); National Science Foundation (NSF) Enabling Discovery through GEnomics (EDGE) grant 2128267, and the Center for Evolutionary Science at California Institute of Technology. \n\nData availability: Strains described in this work are available upon request. 16S rRNA gene sequences of the X. griffiniae bacterial symbionts of the S. hermaphroditum isolate CS34 are available in the Genbank database. The accession numbers for 16S rRNA sequence (including HGB2511) are MZ913116\u2013MZ913125. Supplemental material is available at figshare: https://doi.org/10.25386/genetics.16689217. \n\nThe authors declare that there is no conflict of interest.\n\nSubmitted - 2021.08.26.457822v1.full.pdf
", "abstract": "Entomopathogenic nematodes (EPNs), including Heterorhabditis and Steinernema, are parasitic to insects and contain mutualistically symbiotic bacteria in their intestines (Photorhabdus and Xenorhabdus, respectively) and therefore offer opportunities to study both mutualistic and parasitic symbiosis. The establishment of genetic tools in EPNs has been impeded by limited genetic tractability, inconsistent growth in vitro, variable cryopreservation, and low mating efficiency. We obtained the recently described Steinernema hermaphroditum strain CS34 and optimized its in vitro growth, with a rapid generation time on a lawn of its native symbiotic bacteria Xenorhabdus griffiniae. We developed a simple and efficient cryopreservation method. Previously, S. hermaphroditum isolated from insect hosts was described as producing hermaphrodites in the first generation. We discovered that CS34, when grown in vitro, produced consecutive generations of autonomously reproducing hermaphrodites accompanied by rare males. We performed mutagenesis screens in S. hermaphroditum that produced mutant lines with visible and heritable phenotypes. Genetic analysis of the mutants demonstrated that this species reproduces by self-fertilization rather than parthenogenesis and that its sex is determined chromosomally. Genetic mapping has thus far identified markers on the X chromosome and three of four autosomes. We report that S. hermaphroditum CS34 is the first consistently hermaphroditic EPN and is suitable for genetic model development to study naturally occurring mutualistic symbiosis and insect parasitism.", "date": "2022-01", "date_type": "published", "publication": "Genetics", "volume": "220", "number": "1", "publisher": "Oxford University Press", "pagerange": "Art. No. iyab170", "id_number": "CaltechAUTHORS:20210831-223307133", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210831-223307133", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Postdoctoral Fellowship", "grant_number": "5F32GM131570" }, { "agency": "NSF", "grant_number": "IOS-2128267" }, { "agency": "Caltech Center for Evolutionary Science" }, { "agency": "NIH", "grant_number": "P40 OD010440" } ] }, "local_group": { "items": [ { "id": "Caltech-Center-for-Evolutionary-Science" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/genetics/iyab170", "pmcid": "PMC8733455", "primary_object": { "basename": "2021.08.26.457822v1.full.pdf", "url": "https://authors.library.caltech.edu/records/n1101-2dq81/files/2021.08.26.457822v1.full.pdf" }, "resource_type": "article", "pub_year": "2022", "author_list": "Cao, Mengyi; Schwartz, Hillel T.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/qhpqv-6t471", "eprint_id": 111706, "eprint_status": "archive", "datestamp": "2023-08-20 05:44:44", "lastmod": "2023-12-13 17:17:19", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Reilly-Douglas-K", "name": { "family": "Reilly", "given": "Douglas K." }, "orcid": "0000-0001-8260-8690" }, { "id": "Schwarz-Erich-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Muirhead-Caroline-S", "name": { "family": "Muirhead", "given": "Caroline S." } }, { "id": "Robidoux-Annalise-N", "name": { "family": "Robidoux", "given": "Annalise N." } }, { "id": "Antoshechkin-Igor-A", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Narayan-Anusha", "name": { "family": "Narayan", "given": "Anusha" } }, { "id": "Doma-Meenakshi-K", "name": { "family": "Doma", "given": "Meenakshi K." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Srinivasan-Jagan", "name": { "family": "Srinivasan", "given": "Jagan" }, "orcid": "0000-0001-5449-7938" } ] }, "title": "Transcriptomic profiling of sex-specific olfactory neurons reveals subset-specific receptor expression in C. elegans", "ispublished": "unpub", "full_text_status": "public", "keywords": "C. elegans, Pheromone, Sex-specific, G Protein-Coupled Receptors, Transcriptomes, Single-Cell", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. \n\nWe thank the Caenorhabditis Genetics Center, which is funded by the NIH Office of Research Infrastructure Programs (P40 OD01044), as well as the National BioResource Project, Ding Xue (University of Colorado, Boulder), L. Rene Garcia (Texas A&M University), and Douglas Portman (University of Rochester Medical Center) for providing strains. We also thank Igor Antoshechkin, Caltech Genomics facility for sequencing and InVivo Biosystems for generating transgenic and CRISPR knockout animals. The synthetic ascr#8 utilized in this study was provided by Frank Schroeder (Cornell University). The research reported in this publication was supported by NIH R01 DC016058 (J.S.), R01 GM084389 (P.W.S.), the Howard Hughes Medical Institute (P.W.S.), Moore Foundation Grant No. 4551 (E.M.S.), and Cornell startup funding (E.M.S.). We thank Titus Brown and the Michigan State University High-Performance Computing Center (supported by U.S. Department of Agriculture grant 2010-65205-20361 and NIFA\u2013National Science Foundation (NSF) grant IOS-0923812) for computational support; additional computing was enabled by start-up and research allocations from NSF XSEDE (TG538 MCB180039 and TG-MCB190010). \n\nData availability: RNA-seq reads have been deposited in the NCBI Sequence Read Archive (SRA) under the BioProject accession number PRJNA781271. \n\nThe authors have declared no competing interest.\n\nSubmitted - 2021.10.26.465928v2.full.pdf
Supplemental Material - media-1.pdf
Supplemental Material - media-2.xlsx
Supplemental Material - media-3.xlsx
Supplemental Material - media-4.xlsx
", "abstract": "The nematode Caenorhabditis elegans utilizes chemosensation to navigate an ever-changing environment for its survival. A class of secreted small-molecule pheromones, termed ascarosides, play an important role in olfactory perception by affecting biological functions ranging from development to behavior. The ascaroside ascr#8 mediates sex-specific behaviors, driving avoidance in hermaphrodites and attraction in males. Males sense ascr#8 via the ciliated male-specific cephalic sensory (CEM) neurons, which exhibit radial symmetry along dorsal-ventral and left-right axes. Calcium imaging studies suggest a complex neural coding mechanism that translates stochastic physiological responses in these neurons to reliable behavioral outputs. To test the hypothesis that neurophysiological complexity arises from differential expression of genes, we performed cell-specific transcriptomic profiling; this revealed between 18 and 62 genes with at least two-fold higher expression in a specific CEM neuron type versus both other CEM neurons and adult males. These included two G protein coupled receptor (GPCR) genes, srw-97 and dmsr-12, that were specifically expressed in non-overlapping subsets of CEM neurons and whose expression was confirmed by GFP reporter analysis. Single CRISPR-Cas9 knockouts of either srw-97 or dmsr-12 resulted in partial defects, while a double knockout of both srw-97 and dmsr-12 completely abolished the attractive response to ascr#8. Together, our results suggest that the evolutionarily distinct GPCRs SRW-97 and DMSR-12 act non-redundantly in discrete olfactory neurons to facilitate male-specific sensation of ascr#8.", "date": "2021-11-02", "date_type": "published", "id_number": "CaltechAUTHORS:20211102-173632613", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211102-173632613", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P40 OD010440" }, { "agency": "NIH", "grant_number": "R01 DC016058" }, { "agency": "NIH", "grant_number": "R01 GM084389" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "4551" }, { "agency": "Cornell University" }, { "agency": "Department of Agriculture", "grant_number": "2010-65205-20361" }, { "agency": "NSF", "grant_number": "IOS-0923812" }, { "agency": "NSF", "grant_number": "TG538 MCB180039" }, { "agency": "NSF", "grant_number": "TG-MCB190010" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2021.10.26.465928", "primary_object": { "basename": "media-2.xlsx", "url": "https://authors.library.caltech.edu/records/qhpqv-6t471/files/media-2.xlsx" }, "related_objects": [ { "basename": "media-3.xlsx", "url": "https://authors.library.caltech.edu/records/qhpqv-6t471/files/media-3.xlsx" }, { "basename": "media-4.xlsx", "url": "https://authors.library.caltech.edu/records/qhpqv-6t471/files/media-4.xlsx" }, { "basename": "2021.10.26.465928v2.full.pdf", "url": "https://authors.library.caltech.edu/records/qhpqv-6t471/files/2021.10.26.465928v2.full.pdf" }, { "basename": "media-1.pdf", "url": "https://authors.library.caltech.edu/records/qhpqv-6t471/files/media-1.pdf" } ], "resource_type": "monograph", "pub_year": "2021", "author_list": "Reilly, Douglas K.; Schwarz, Erich M.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/79nt9-7vb91", "eprint_id": 110642, "eprint_status": "archive", "datestamp": "2023-08-20 05:07:36", "lastmod": "2023-12-22 23:21:46", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wrobel-Chester-J-J", "name": { "family": "Wrobel", "given": "Chester J. J." }, "orcid": "0000-0001-6047-4644" }, { "id": "Yu-Jingfang", "name": { "family": "Yu", "given": "Jingfang" }, "orcid": "0000-0003-1770-5368" }, { "id": "Rodrigues-Pedro-R", "name": { "family": "Rodrigues", "given": "Pedro R." } }, { "id": "Ludewig-Andreas-H", "name": { "family": "Ludewig", "given": "Andreas H." } }, { "id": "Curtis-Brian-J", "name": { "family": "Curtis", "given": "Brian J." } }, { "id": "Cohen-Sarah-M", "name": { "family": "Cohen", "given": "Sarah M." }, "orcid": "0000-0002-5233-2280" }, { "id": "Fox-Bennett-W", "name": { "family": "Fox", "given": "Bennett W." } }, { "id": "O'Donnell-Michael-P", "name": { "family": "O'Donnell", "given": "Michael P." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Schroeder-Frank-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" } ] }, "title": "Combinatorial Assembly of Modular Glucosides via Carboxylesterases Regulates C. elegans Starvation Survival", "ispublished": "pub", "full_text_status": "public", "keywords": "Peptides and proteins, Carbohydrates, Metabolism, Scaffolds, Biosynthesis", "note": "\u00a9 2021 American Chemical Society. \n\nReceived 7 June 2021. Published online 30 August 2021. \n\nWe thank WormBase for sequences and life stage expression levels data, and D. Kiemle for assistance with NMR spectroscopy, Integrated DNA technologies for CRISPR reagents, and Tsui-Fen Chou for Cas9 protein. \n\nThis research was supported in part by the National Institutes of Health (R35GM131877 and U2CES030167 to F.C.S. and R24OD023041 to P.W.S.) and a National Science Foundation Graduate Research Fellowship (DGE 174301 to S.M.C.). F.C.S. is a Faculty Scholar of the Howard Hughes Medical Institute. \n\nAuthor Contributions: All authors have given approval to the final version of the manuscript.\n\nThe authors declare no competing financial interest.\n\nAccepted Version - nihms-1752617.pdf
Supplemental Material - ja1c05908_si_001.pdf
Supplemental Material - ja1c05908_si_002.xlsx
Supplemental Material - ja1c05908_si_003.xlsx
", "abstract": "The recently discovered modular glucosides (MOGLs) form a large metabolite library derived from combinatorial assembly of moieties from amino acid, neurotransmitter, and lipid metabolism in the model organism C. elegans. Combining CRISPR-Cas9 genome editing, comparative metabolomics, and synthesis, we show that the carboxylesterase homologue Cel-CEST-1.2 is responsible for specific 2-O-acylation of diverse glucose scaffolds with a wide variety of building blocks, resulting in more than 150 different MOGLs. We further show that this biosynthetic role is conserved for the closest homologue of Cel-CEST-1.2 in the related nematode species C. briggsae, Cbr-CEST-2. Expression of Cel-cest-1.2 and MOGL biosynthesis are strongly induced by starvation conditions in C. elegans, one of the premier model systems for mechanisms connecting nutrition and physiology. Cel-cest-1.2-deletion results in early death of adult animals under starvation conditions, providing first insights into the biological functions of MOGLs.", "date": "2021-09-15", "date_type": "published", "publication": "Journal of the American Chemical Society", "volume": "143", "number": "36", "publisher": "American Chemical Society", "pagerange": "14676-14683", "id_number": "CaltechAUTHORS:20210831-200226355", "issn": "0002-7863", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210831-200226355", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R35GM131877" }, { "agency": "NIH", "grant_number": "U2CES030167" }, { "agency": "NIH", "grant_number": "R24OD023041" }, { "agency": "NSF Graduate Research Fellowship", "grant_number": "DGE-174301" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1021/jacs.1c05908", "pmcid": "PMC8594405", "primary_object": { "basename": "ja1c05908_si_002.xlsx", "url": "https://authors.library.caltech.edu/records/79nt9-7vb91/files/ja1c05908_si_002.xlsx" }, "related_objects": [ { "basename": "ja1c05908_si_003.xlsx", "url": "https://authors.library.caltech.edu/records/79nt9-7vb91/files/ja1c05908_si_003.xlsx" }, { "basename": "nihms-1752617.pdf", "url": "https://authors.library.caltech.edu/records/79nt9-7vb91/files/nihms-1752617.pdf" }, { "basename": "ja1c05908_si_001.pdf", "url": "https://authors.library.caltech.edu/records/79nt9-7vb91/files/ja1c05908_si_001.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Wrobel, Chester J. J.; Yu, Jingfang; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/p1prv-6ds73", "eprint_id": 110355, "eprint_status": "archive", "datestamp": "2023-08-20 04:43:48", "lastmod": "2023-12-13 17:16:58", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Banerjee-Navonil", "name": { "family": "Banerjee", "given": "Navonil" } }, { "id": "Shih-Pei-Yin", "name": { "family": "Shih", "given": "Pei-Yin" }, "orcid": "0000-0003-3082-9242" }, { "id": "Rojas-Palato-Elisa-J", "name": { "family": "Rojas Palato", "given": "Elisa J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Hallem-Elissa-A", "name": { "family": "Hallem", "given": "Elissa A." }, "orcid": "0000-0003-0260-3174" } ] }, "title": "Distinct neural circuits establish the same chemosensory behavior in C. elegans", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. \n\nThis version posted August 17, 2021. \n\nWe thank the Caenorhabditis Genetics Centre, the C. elegans Knockout Consortium, Oliver Hobert, Cori Bargmann, Gary Ruvkun, Shai Shaham, Ikue Mori, Yuichi Iino, and Mario de Bono for strains. We thank Astra Bryant, Michelle Castelletto, and Ricardo Frausto for insightful comments on the manuscript. This work was funded by NIH F32 AI147617 (N.B.), NIH MARC T34 GM008563 (E.R.P.), NIH UF1 NS111697 (P.W.S.), and NIH R01 DC017959 and an HHMI Faculty Scholar Award (E.A.H.). \n\nAuthor Contributions: N.B., P.-Y.S., P.W.S., and E.A.H. conceived the study. N.B. and E.R.P. performed experiments. N.B. and E.R.P. analyzed the data. N.B., E.R.P., and E.A.H. wrote the manuscript. All authors read and approved the final manuscript. \n\nThe authors declare no competing interests.\n\nSubmitted - 2021.08.17.456617v1.full.pdf
", "abstract": "Animals frequently exhibit the same behavior under different environmental or physiological conditions. To what extent these behaviors are generated by similar vs. distinct mechanisms is unclear. Moreover, the circumstances under which divergent neural mechanisms establish the same behavior, and the molecular signals that regulate the same behavior across conditions, are poorly understood. We show that in C. elegans, distinct neural mechanisms mediate the same chemosensory behavior at two different life stages. Both dauer larvae and starved adults are attracted to carbon dioxide (CO\u2082), but CO\u2082 attraction is mediated by distinct sets of interneurons at the two life stages. Some interneurons mediate CO\u2082 response only in dauers, some show CO2-evoked activity in adults and dauers but contribute to CO\u2082 response only in adults, and some show CO\u2082-evoked activity that opposes CO\u2082 attraction in adults but promotes CO\u2082 attraction in dauers. We also identify a novel role for insulin signaling in establishing life-stage-specific CO\u2082 responses by modulating interneuron activity. Further, we show that a combinatorial code of both shared and life-stage-specific molecular signals regulate CO\u2082 attraction. Our results identify a mechanism by which the same chemosensory behavior can be generated by distinct neural circuits, revealing an unexpected complexity to chemosensory processing.", "date": "2021-08-21", "date_type": "published", "id_number": "CaltechAUTHORS:20210821-151507927", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210821-151507927", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Postdoctoral Fellowship", "grant_number": "F32 AI147617" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T34 GM008563" }, { "agency": "NIH", "grant_number": "UF1 NS111697" }, { "agency": "NIH", "grant_number": "R01 DC017959" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2021.08.17.456617", "primary_object": { "basename": "2021.08.17.456617v1.full.pdf", "url": "https://authors.library.caltech.edu/records/p1prv-6ds73/files/2021.08.17.456617v1.full.pdf" }, "resource_type": "monograph", "pub_year": "2021", "author_list": "Banerjee, Navonil; Shih, Pei-Yin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/hbjnw-g9h21", "eprint_id": 110810, "eprint_status": "archive", "datestamp": "2023-08-20 04:38:03", "lastmod": "2023-12-22 23:08:58", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dillman-Adler-R", "name": { "family": "Dillman", "given": "Adler R" } }, { "id": "Korff-Wyatt", "name": { "family": "Korff", "given": "Wyatt" }, "orcid": "0000-0001-8396-1533" }, { "id": "Dickinson-M-H", "name": { "family": "Dickinson", "given": "Michael H." }, "orcid": "0000-0002-8587-9936" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Steinernema carpocapsae jumps with greater velocity and acceleration than previously reported", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: May 20, 2021; Revision received: July 22, 2021; Accepted: July 26, 2021; Published: August 2, 2021. \n\nFunding: Was supported by NIH T32GM07616 and the Howard Hughes Medical Institute. \n\nAuthor Contributions: \nAdler R Dillman: Conceptualization, Investigation, Writing - original draft\nWyatt Korff: Formal analysis, Methodology, Investigation, Writing - original draft\nMichael H Dickinson: Formal analysis, Writing - original draft\nPaul W Sternberg: Conceptualization, Writing - original draft.\n\nPublished - Dillman_2021.pdf
Supplemental Material - Dillman_ScarpocapsaeJumping1.mp4
Supplemental Material - Dillman_Scarpocapsae_Jumping2.mp4
", "abstract": "Infective juveniles of the insect-parastic nematode Steinernema carpocapsae can jump greater than 6 times their height, a striking evolved novelty in some species of this genus. Using high-speed videography, we observed the kinematics of Steinernema carpocapsae spontaneous jumping behavior. Our analysis places a lower bound on the velocity and acceleration of these worms.", "date": "2021-08-02", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "Art. No. 000435", "id_number": "CaltechAUTHORS:20210910-200019850", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210910-200019850", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM07616" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.17912/micropub.biology.000435", "pmcid": "PMC8329732", "primary_object": { "basename": "Dillman_2021.pdf", "url": "https://authors.library.caltech.edu/records/hbjnw-g9h21/files/Dillman_2021.pdf" }, "related_objects": [ { "basename": "Dillman_ScarpocapsaeJumping1.mp4", "url": "https://authors.library.caltech.edu/records/hbjnw-g9h21/files/Dillman_ScarpocapsaeJumping1.mp4" }, { "basename": "Dillman_Scarpocapsae_Jumping2.mp4", "url": "https://authors.library.caltech.edu/records/hbjnw-g9h21/files/Dillman_Scarpocapsae_Jumping2.mp4" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Dillman, Adler R; Korff, Wyatt; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/4bsgq-epm73", "eprint_id": 112463, "eprint_status": "archive", "datestamp": "2023-08-20 04:33:37", "lastmod": "2023-12-22 23:21:13", "type": "conference_item", "metadata_visibility": "show", "creators": { "items": [ { "id": "Holman-Elizabeth-A", "name": { "family": "Holman", "given": "Elizabeth A." }, "orcid": "0000-0002-5158-4689" }, { "id": "Fang-Yuan-Sheng", "name": { "family": "Fang", "given": "Yuan-Sheng" }, "orcid": "0000-0003-4643-0084" }, { "id": "Chen-Liang", "name": { "family": "Chen", "given": "Liang" } }, { "id": "DeWeese-Michael-R", "name": { "family": "DeWeese", "given": "Michael" }, "orcid": "0000-0003-2801-5768" }, { "id": "Holman-Hoi-Ying-N", "name": { "family": "Holman", "given": "Hoi-Ying" }, "orcid": "0000-0002-7534-2625" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul" }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Autonomous adaptive data acquisition for scanning hyperspectral imaging", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2021 American Chemical Society.", "abstract": "Non-invasive and label-free spectral microscopy (spectromicroscopy) techniques can provide quant. biochem. information complementary to genomic sequencing, transcriptomic profiling, and proteomic analyses. However, spectromicroscopy techniques generate high-dimensional data; acquisition of a single spectral image can range from tens of minutes to hours, depending on the desired spatial resoln. and the image size. This substantially limits the timescales of observable transient biol. processes. To address this challenge and move spectromicroscopy towards efficient real-time spatiochem. imaging, we developed a grid-less autonomous adaptive sampling method. Our method substantially decreases image acquisition time while increasing sampling d. in regions of steeper physico-chem. gradients. When implemented with scanning Fourier Transform IR spectromicroscopy expts., this grid-less adaptive sampling approach outperformed std. uniform grid sampling in a two-component chem. model system and in a complex biol. sample, Caenorhabditis elegans. We quant. and qual. assess the efficiency of data acquisition using performance metrics and multivariate IR spectral anal., resp.", "date": "2021-08", "date_type": "published", "publisher": "Caltech Library", "id_number": "CaltechAUTHORS:20211215-165045540", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211215-165045540", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "resource_type": "conference_item", "pub_year": "2021", "author_list": "Holman, Elizabeth A.; Fang, Yuan-Sheng; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/2ka04-cv716", "eprint_id": 112496, "eprint_status": "archive", "datestamp": "2023-08-20 04:35:02", "lastmod": "2023-12-22 23:22:08", "type": "conference_item", "metadata_visibility": "show", "creators": { "items": [ { "id": "Holman-Elizabeth-A", "name": { "family": "Holman", "given": "Elizabeth A." }, "orcid": "0000-0002-5158-4689" }, { "id": "Li-Dong", "name": { "family": "Li", "given": "Dong" } }, { "id": "Ashby-Paul-D", "name": { "family": "Ashby", "given": "Paul D." } }, { "id": "Zuckermann-Ronald-N", "name": { "family": "Zuckermann", "given": "Ronald N." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul" }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Designing optically transparent photo-crosslinked peptoid nanosheets for imaging applications", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2021 American Chemical Society.", "abstract": "Peptoid bilayer nanosheets are a new class of biocompatible 2D nanomaterial with broad applications, including sensing,\nmembrane mimicry and pathogen binding. They are formed from the self-assembly of sequence-defined peptoid chains\nand can be readily functionalized to tune their properties. In order to broaden their utility, there is a need to improve their mech. stability. Here, we create nanosheets that can function as a mech. robust, optically transparent interfacial barrier for covering microfluidic channels, microscopy grids and other sample chambers. This barrier would increase hydration control in otherwise open-channel environments, permitting water-sensitive, non-destructive IR spectroscopy to be incorporated into multimodal imaging platforms. Therefore, we explored new peptoid analogs contg. photo-crosslinkable side chains that can form intra-monolayer as well as inter-layer covalent bonds. These constructs can be co-assembled in various ratios to achieve a range of desirable mech. properties to provide a new route to ultrathin, mech. robust, 2D nanomaterials that serve as optically transparent interfacial barriers for a variety of imaging techniques.", "date": "2021-08", "date_type": "published", "publisher": "Caltech Library", "id_number": "CaltechAUTHORS:20211217-000135083", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211217-000135083", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "resource_type": "conference_item", "pub_year": "2021", "author_list": "Holman, Elizabeth A.; Li, Dong; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/172k7-01k12", "eprint_id": 109773, "eprint_status": "archive", "datestamp": "2023-08-20 04:09:39", "lastmod": "2023-12-22 23:30:53", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "da-Veiga-Beltrame-Eduardo", "name": { "family": "da Veiga Beltrame", "given": "Eduardo" }, "orcid": "0000-0002-1529-9207" }, { "id": "Arnaboldi-Valerio", "name": { "family": "Arnaboldi", "given": "Valerio" }, "orcid": "0000-0002-2563-5374" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Single cell tools for WormBase", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder has placed this preprint in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or adapt this material for any purpose without crediting the original authors. \n\nThis version posted July 4, 2021. \n\nThe authors would like to thank Paulo Nuin for reviewing the code, Tom Morrell for assistance with CaltechData, and Valentine Svensson for suggestions on the manuscript. This work was supported by grants NIH U24HG010859 and NIH U24HG002223.\n\nSubmitted - 2021.07.04.451030v1.full.pdf
", "abstract": "We present two web apps for interactively performing common tasks with single cell RNA sequencing data: scdefg for interactive differential expression and wormcells-viz for visualization of gene expression. We made these tools available with public C. elegans datasets curated by WormBase at single-cell.wormbase.org. They can also be readily deployed for use with any other datasets using the source code available at github.com/WormBase/scdefg and at github.com/WormBase/wormcells-viz.", "date": "2021-07-12", "date_type": "published", "id_number": "CaltechAUTHORS:20210712-143510822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210712-143510822", "funders": { "items": [ { "agency": "NIH", "grant_number": "U24HG010859" }, { "agency": "NIH", "grant_number": "U24HG002223" } ] }, "local_group": { "items": [ { "id": "WormBase" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2021.07.04.451030", "primary_object": { "basename": "2021.07.04.451030v1.full.pdf", "url": "https://authors.library.caltech.edu/records/172k7-01k12/files/2021.07.04.451030v1.full.pdf" }, "resource_type": "monograph", "pub_year": "2021", "author_list": "da Veiga Beltrame, Eduardo; Arnaboldi, Valerio; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/40ax5-m3s24", "eprint_id": 109818, "eprint_status": "archive", "datestamp": "2023-08-20 04:12:16", "lastmod": "2023-12-22 23:30:49", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cohen-Sarah-M", "name": { "family": "Cohen", "given": "Sarah M." }, "orcid": "0000-0002-5233-2280" }, { "id": "Le-Henry-H", "name": { "family": "Le", "given": "Henry H." }, "orcid": "0000-0003-2942-2357" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "A Mutation of lips-6 in C. elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 by the authors. This is an open-access article distributed under the terms of the Creative Commons\nAttribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nHistory: Received June 9, 2021 Revision received July 3, 2021 Accepted July 5, 2021 Published July 9, 2021. \n\nWe thank Heenam Park and Frank Schroeder for their helpful discussion and comments. \n\nThis material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE 1745301 to SMC and Grant No. R24OD023041 to PWS. \n\nAuthor Contributions: Sarah M Cohen: Conceptualization, Investigation, Methodology, Writing - original draft, Visualization. Henry H Le: Methodology, Visualization, Writing - review and editing, Investigation. Paul W Sternberg: Funding acquisition, Project administration, Resources, Supervision, Writing - review and editing. \n\nReviewed By: Jennifer Watts.\n\nPublished - micropub-biology-000419.pdf
", "abstract": "The efficient CRISPR/Cas9 genome editing toolkit in the nematode Caenorhabditis elegans has made the creation of null mutants easier than ever. The putative lipid hydrolase lips-6 is known to function in the DAF-12/DIN-1 pathway to promote fat mobilization during periods of starvation in adult worms (Tao et al. 2016). Similarly, it was found to be strongly downregulated in response to dauer ascarosides given during the L1 to L2d decision in larval worms (Cohen et al. 2021). Here, we have created a mutant of the putative lipase lips-6 and studied its lifespan as well as its ascaroside profile.", "date": "2021-07-09", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "Art. No. 000419", "id_number": "CaltechAUTHORS:20210714-172910613", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210714-172910613", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF Graduate Research Fellowship", "grant_number": "DGE-1745301" }, { "agency": "NIH", "grant_number": "R24OD023041" } ] }, "local_group": { "items": [ { "id": "WormBase" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.17912/micropub.biology.000419", "pmcid": "PMC8271349", "primary_object": { "basename": "micropub-biology-000419.pdf", "url": "https://authors.library.caltech.edu/records/40ax5-m3s24/files/micropub-biology-000419.pdf" }, "resource_type": "article", "pub_year": "2021", "author_list": "Cohen, Sarah M.; Le, Henry H.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/rn7z8-cm974", "eprint_id": 107396, "eprint_status": "archive", "datestamp": "2023-08-22 09:55:16", "lastmod": "2023-12-22 23:21:25", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Middelkoop-Teije-C", "name": { "family": "Middelkoop", "given": "Teije C." }, "orcid": "0000-0002-0346-6143" }, { "id": "Garcia-Baucells-J\u00falia", "name": { "family": "Garcia-Baucells", "given": "J\u00falia" }, "orcid": "0000-0001-7874-7671" }, { "id": "Quintero-Cadena-Porfirio", "name": { "family": "Quintero-Cadena", "given": "Porfirio" }, "orcid": "0000-0003-0067-5844" }, { "id": "Pimpale-Lokesh-G", "name": { "family": "Pimpale", "given": "Lokesh G." }, "orcid": "0000-0001-6145-1516" }, { "id": "Yazdi-Shahrzad", "name": { "family": "Yazdi", "given": "Shahrzad" }, "orcid": "0000-0003-1988-4320" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Gross-Peter", "name": { "family": "Gross", "given": "Peter" }, "orcid": "0000-0002-4258-6105" }, { "id": "Grill-Stephan-W", "name": { "family": "Grill", "given": "Stephan W." }, "orcid": "0000-0002-2290-5826" } ] }, "title": "CYK-1/Formin activation in cortical RhoA signaling centers promotes organismal left\u2013right symmetry breaking", "ispublished": "pub", "full_text_status": "public", "keywords": "left\u2013right asymmetry; Formin; RhoA signaling; C. elegans", "note": "\u00a9 2021 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND). \n\nEdited by Timothy J. Mitchison, Harvard Medical School, Boston, MA, and approved March 15, 2021 (received for review October 21, 2020). \n\nWe thank Julie Canman for sharing cyk-1(or596ts); Bob Goldstein for nmy-2(cp8[nmy-2::GFP]) and nmy-2(cp52[nmy-2::mKate2); Tony Hyman for the mCherry-tubulin strain and mlc-4 and ect-2 RNAi clones; Martin Harterink and Sander van den Heuvel for PH-GFP-LOV2 plasmid; the Caenorhabditis Genetics Center for the ect-2(gf) mutant and xsSi5[GFP-ani-1(AH-PH)]; Addgene for pJA281, pJA245, pCM1.36, pCFJ150, and pCFJ1415 plasmids; and Julie Ahringer and Source BioScience for L4440, rga-3, and cyk-1/Formin RNAi clones. We also thank Friederike Thonwart for assistance with molecular biology, GE-Deltavision and its representatives for having the Deltavision OMX SIM-TIRF system available for the 2018 Woods Hole Physiology course, and Sylvia Hurlimann for capturing SIM-TIRF movies during this course. Furthermore, we thank Jonas Neipel for valuable discussion on the hydrodynamic theory and Anne Grapin-Botton, Arghyadip Mukherjee, J\u00e1n Sab\u00f3, Jonas Neipel, and Zden\u011bk L\u00e1nsk\u00fd for critical reading of the manuscript. T.C.M. was supported by a European Molecular Biology Organization long-term fellowship ALTF 1033-2015 and a Nederlandse organisatie voor Wetenschappelijk Onderzoek Rubicon fellowship 825.15.010. L.G.P. was supported by the European Union's Horizon 2020 research under the Marie Sklodowska-Curie Grant 641639. S.W.G. was supported by the Deutsche Forschungsgemeinschaft (SPP 1782, GSC 97, GR 3271/2, GR 3271/3, GR 3271/4) and the European Research Council (Grant 742712). \n\nData Availability: The raw data generated in this study is made publicly available: Speckle microscopy movies can be downloaded from CaltechDATA at https://data.caltech.edu/records/1442 (81). All other movies and micrographs can be downloaded from the Max Planck Society at https://dx.doi.org/10.17617/3.61 (82). \n\nJ.G.-B. and P.Q.-C. contributed equally to this work. \n\nAuthor contributions: T.C.M. and S.W.G. designed research; T.C.M., J.G.-B., P.Q.-C., L.G.P., and S.Y. performed research; T.C.M., J.G.-B., P.Q.-C., and P.G. contributed new reagents/analytic tools; T.C.M., J.G.-B., P.Q.-C., L.G.P., P.W.S., P.G., and S.W.G. analyzed data; and T.C.M. and S.W.G. wrote the paper. \n\nThe authors declare no competing interest. \n\nThis article is a PNAS Direct Submission. \n\nThis article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2021814118/-/DCSupplemental.\n\nPublished - e2021814118.full.pdf
Submitted - 2021.01.08.425924v1.full.pdf
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", "abstract": "Proper left\u2013right symmetry breaking is essential for animal development, and in many cases, this process is actomyosin-dependent. In Caenorhabditis elegans embryos active torque generation in the actomyosin layer promotes left\u2013right symmetry breaking by driving chiral counterrotating cortical flows. While both Formins and Myosins have been implicated in left\u2013right symmetry breaking and both can rotate actin filaments in vitro, it remains unclear whether active torques in the actomyosin cortex are generated by Formins, Myosins, or both. We combined the strength of C. elegans genetics with quantitative imaging and thin film, chiral active fluid theory to show that, while Non-Muscle Myosin II activity drives cortical actomyosin flows, it is permissive for chiral counterrotation and dispensable for chiral symmetry breaking of cortical flows. Instead, we find that CYK-1/Formin activation in RhoA foci is instructive for chiral counterrotation and promotes in-plane, active torque generation in the actomyosin cortex. Notably, we observe that artificially generated large active RhoA patches undergo rotations with consistent handedness in a CYK-1/Formin\u2013dependent manner. Altogether, we conclude that CYK-1/Formin\u2013dependent active torque generation facilitates chiral symmetry breaking of actomyosin flows and drives organismal left\u2013right symmetry breaking in the nematode worm.", "date": "2021-05-18", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "118", "number": "20", "publisher": "National Academy of Sciences", "pagerange": "Art. No. e2021814118", "id_number": "CaltechAUTHORS:20210111-143923766", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210111-143923766", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "European Molecular Biology Organization (EMBO)", "grant_number": "ALTF 1033-2015" }, { "agency": "Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)", "grant_number": "825.15.010" }, { "agency": "Marie Curie Fellowship", "grant_number": "641639" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "SPP 1782" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "GSC 97" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "GR 3271/2" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "GR 3271/3" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "GR 3271/4" }, { "agency": "European Research Council (ERC)", "grant_number": "742712" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1073/pnas.2021814118", "pmcid": "PMC8157923", "primary_object": { "basename": "pnas.2021814118.sm07.avi", "url": "https://authors.library.caltech.edu/records/rn7z8-cm974/files/pnas.2021814118.sm07.avi" }, "related_objects": [ { "basename": "pnas.2021814118.sm25.avi", "url": "https://authors.library.caltech.edu/records/rn7z8-cm974/files/pnas.2021814118.sm25.avi" }, { "basename": "pnas.2021814118.sm30.avi", "url": "https://authors.library.caltech.edu/records/rn7z8-cm974/files/pnas.2021814118.sm30.avi" }, { "basename": "pnas.2021814118.sm20.avi", "url": "https://authors.library.caltech.edu/records/rn7z8-cm974/files/pnas.2021814118.sm20.avi" }, { "basename": "pnas.2021814118.sm29.avi", "url": "https://authors.library.caltech.edu/records/rn7z8-cm974/files/pnas.2021814118.sm29.avi" }, { "basename": 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"pnas.2021814118.sm24.avi", "url": "https://authors.library.caltech.edu/records/rn7z8-cm974/files/pnas.2021814118.sm24.avi" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Middelkoop, Teije C.; Garcia-Baucells, J\u00falia; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/5nj3f-n2p44", "eprint_id": 109146, "eprint_status": "archive", "datestamp": "2023-08-20 03:14:03", "lastmod": "2023-12-22 23:21:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cohen-Sarah-M", "name": { "family": "Cohen", "given": "Sarah M." }, "orcid": "0000-0002-5233-2280" }, { "id": "Sun-Jessica-J", "name": { "family": "Sun", "given": "Jessica J." } }, { "id": "Schroeder-Frank-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Transcriptional Response to a Dauer-Inducing Ascaroside Cocktail in Late L1 in C. elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: April 29, 2021; Revision received: May 6, 2021; Accepted: May 6, 2021; Published: May 12, 2021. \n\nThis work was supported by the Amgen Scholars Program at Caltech, by UF1NS111697 to PWS and by GM0088290 to FCS. \n\nAuthor Contributions: Sarah M Cohen: Conceptualization, Methodology, Formal analysis, Writing - original draft, Writing - review and editing, Data curation. Jessica J Sun: Visualization, Data curation, Formal analysis, Writing - review and editing. Frank C Schroeder: Funding acquisition, Project administration, Resources, Supervision, Writing - review and editing, Conceptualization. Paul W Sternberg: Funding acquisition, Project administration, Resources, Supervision, Writing - review and editing, Conceptualization. \n\nReviewed By: Anonymous.\n\nPublished - Cohen_2021p000397.pdf
", "abstract": "C. elegans larvae choose between dauer diapause and immediate reproductive development in two phases, the first being a choice between L2 and L2d, and the second between dauer and L3 (Golden and Riddle 1984). We used RNA-seq to study the transcriptomic response of well-fed C. elegans when exposed to a cocktail of diapause-inducing ascarosides (ascr#2, ascr#3, and ascr#8) during the L1 larval stage when they first receive cues from their environment and then adapt via developmental programming (Kaplan et al. 2011). This research was performed in N2 wild-type worms and daf-22(ok693) mutants that lack an enzyme necessary for the biosynthesis of ascaroside pheromones (reviewed by Ludewig and Schroeder 2013). We found that early exposure to ascarosides triggers a pervasive transcriptional response that may drive diapause induction within as little as three hours. In N2, 362 genes were significantly differentially expressed at p = 0.001, while in daf-22, 1,007 genes were significantly differentially expressed at p = 0.001. The daf-22 mutant may have more significantly expressed genes when exposed to ascarosides indicating a stronger response as it has never encountered ascaroside signaling previously, even at low levels.", "date": "2021-05-12", "date_type": "published", "publication": "microPublication Biology", "volume": "2021", "publisher": "Caltech Library", "pagerange": "Art. No. 000397", "id_number": "CaltechAUTHORS:20210517-095926181", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210517-095926181", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "AmGen Scholars Program" }, { "agency": "NIH", "grant_number": "UF1NS111697" }, { "agency": "NIH", "grant_number": "GM0088290" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.17912/micropub.biology.000397", "pmcid": "PMC8116936", "primary_object": { "basename": "Cohen_2021p000397.pdf", "url": "https://authors.library.caltech.edu/records/5nj3f-n2p44/files/Cohen_2021p000397.pdf" }, "resource_type": "article", "pub_year": "2021", "author_list": "Cohen, Sarah M.; Sun, Jessica J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/x6d0d-d5m50", "eprint_id": 108628, "eprint_status": "archive", "datestamp": "2023-08-20 02:26:23", "lastmod": "2023-12-22 23:21:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Arnaboldi-Valerio", "name": { "family": "Arnaboldi", "given": "Valerio" }, "orcid": "0000-0002-2563-5374" }, { "id": "Cho-Jaehyoung", "name": { "family": "Cho", "given": "Jaehyoung" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature", "ispublished": "pub", "full_text_status": "public", "note": "Published by Oxford University Press 2021. This work is written by (a) US Government employee(s) and is in the public domain in the US.\n\nReceived 15 December 2020; Revised 19 February 2021; Published: 31 March 2021.\n\nWe thank Ranjana Kishore, Daniela Raciti and Eduardo da Veiga Beltrame for their comments and suggestions on the manuscript.\n\nFunding:\nNational Institutes of Health/National Human Genome Research Institute grants [U24HG002223 (WormBase) and U24HG010859 (Alliance Central)].\n\nThe authors declare that they have no conflict of interest.\n\nPublished - baab015.pdf
Supplemental Material - baab015_supp.zip
", "abstract": "Finding relevant information from newly published scientific papers is becoming increasingly difficult due to the pace at which articles are published every year as well as the increasing amount of information per paper. Biocuration and model organism databases provide a map for researchers to navigate through the complex structure of the biomedical literature by distilling knowledge into curated and standardized information. In addition, scientific search engines such as PubMed and text-mining tools such as Textpresso allow researchers to easily search for specific biological aspects from newly published papers, facilitating knowledge transfer. However, digesting the information returned by these systems\u2014often a large number of documents\u2014still requires considerable effort. In this paper, we present Wormicloud, a new tool that summarizes scientific articles in a graphical way through word clouds. This tool is aimed at facilitating the discovery of new experimental results not yet curated by model organism databases and is designed for both researchers and biocurators. Wormicloud is customized for the Caenorhabditis elegans literature and provides several advantages over existing solutions, including being able to perform full-text searches through Textpresso, which provides more accurate results than other existing literature search engines. Wormicloud is integrated through direct links from gene interaction pages in WormBase. Additionally, it allows analysis on the gene sets obtained from literature searches with other WormBase tools such as SimpleMine and Gene Set Enrichment.", "date": "2021-03-31", "date_type": "published", "publication": "Database : The Journal of Biological Databases and Curation", "volume": "2021", "publisher": "Oxford University Press", "pagerange": "Art. No. baab015", "id_number": "CaltechAUTHORS:20210406-083450889", "issn": "1758-0463", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210406-083450889", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U24HG002223" }, { "agency": "NIH", "grant_number": "U24HG010859" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/database/baab015", "pmcid": "PMC8011436", "primary_object": { "basename": "baab015_supp.zip", "url": "https://authors.library.caltech.edu/records/x6d0d-d5m50/files/baab015_supp.zip" }, "related_objects": [ { "basename": "baab015.pdf", "url": "https://authors.library.caltech.edu/records/x6d0d-d5m50/files/baab015.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Arnaboldi, Valerio; Cho, Jaehyoung; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/b2azw-mtk43", "eprint_id": 109358, "eprint_status": "archive", "datestamp": "2023-08-20 02:07:10", "lastmod": "2023-12-22 23:21:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chai-C-M", "name": { "family": "Chai", "given": "C. M." } }, { "id": "Wen-C", "name": { "family": "Wen", "given": "C." } }, { "id": "Wong-W-R", "name": { "family": "Wong", "given": "W. R." } }, { "id": "Park-H-N", "name": { "family": "Park", "given": "H. N." } }, { "id": "Cohen-S-M", "name": { "family": "Cohen", "given": "S. M." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "P. W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Discovery of a highly-conserved behavioral role for an interneuron neuropeptide receptor", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model). \n\nPublished: 22 February 2021.", "abstract": "[no abstract]", "date": "2021-03", "date_type": "published", "publication": "Integrative and Comparative Biology", "volume": "61", "number": "S1", "publisher": "Oxford University Press", "pagerange": "E124-E125", "id_number": "CaltechAUTHORS:20210603-110650467", "issn": "1540-7063", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210603-110650467", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/icb/icab001", "resource_type": "article", "pub_year": "2021", "author_list": "Chai, C. M.; Wen, C.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/347j4-3qc12", "eprint_id": 107714, "eprint_status": "archive", "datestamp": "2023-08-20 01:24:37", "lastmod": "2023-12-22 23:21:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wong-Wan-Rong", "name": { "family": "Wong", "given": "Wan-Rong" }, "orcid": "0000-0002-9757-8145" }, { "id": "Maher-Shayda", "name": { "family": "Maher", "given": "Shayda" }, "orcid": "0000-0002-1987-6104" }, { "id": "Oh-Jun-Young", "name": { "family": "Oh", "given": "Jun Young" }, "orcid": "0000-0002-5158-9017" }, { "id": "Brugman-Katherine-I", "name": { "family": "Brugman", "given": "Katherine I." }, "orcid": "0000-0003-2625-2903" }, { "id": "Gharib-Shahla", "name": { "family": "Gharib", "given": "Shahla" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Conserved missense variant in ALDH1A3 ortholog impairs fecundity in C. elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: December 29, 2020; Revision received: January 8, 2021; Accepted: January 11, 2021; Published: January 14, 2021. \n\nThis work was supported by Simons Foundation (SFARI award # 367560 to PWS). PWS was an investigator with the Howard Hughes Medical Institute during the initial part of this study. \n\nAuthor Contributions: Wan-Rong Wong: Investigation, Formal analysis, Writing - original draft. Shayda Maher: Methodology, Writing - review and editing Jun Young Oh: Investigation, Writing - review and editing. Katherine I Brugman: Methodology. Shahla Gharib: Methodology. Paul W Sternberg: Conceptualization, Funding acquisition, Writing - review and editing.\n\nPublished - Wong_1-14-21.pdf
", "abstract": "Accumulating evidence demonstrates that mutations in ALDH1A3 (the aldehyde dehydrogenase 1 family, member A3) are associated with developmental defects. The ALDH1A3 enzyme catalyzes retinoic acid biosynthesis and is essential to patterning and neuronal differentiation in the development of embryonic nervous system. Several missense mutations in ALDH1A3 have been identified in family studies of autosomal recessive microphthalmia, autism spectrum disorder, and other neurological disorders. However, there has been no evidence from animal models that verify the functional consequence of missense mutations in ALDH1A3. Here, we introduced the equivalent of the ALDH1A3 C174Y variant into the Caenorhabditis elegans ortholog, alh-1, at the corresponding locus. Mutant animals with this missense mutation exhibited decreased fecundity by 50% compared to wild-type animals, indicating disrupted protein function. To our knowledge, this is the first ALDH1A3 C174Y missense model, which might be used to elucidate the effects of ALDH1A3 C174Y missense mutation in the retinoic acid signaling pathway during development.", "date": "2021-01-14", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "Art. No. 000357", "id_number": "CaltechAUTHORS:20210125-135501460", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210125-135501460", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Simons Foundation", "grant_number": "367560" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.17912/micropub.biology.000357", "primary_object": { "basename": "Wong_1-14-21.pdf", "url": "https://authors.library.caltech.edu/records/347j4-3qc12/files/Wong_1-14-21.pdf" }, "resource_type": "article", "pub_year": "2021", "author_list": "Wong, Wan-Rong; Maher, Shayda; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/vk9jd-bna77", "eprint_id": 107976, "eprint_status": "archive", "datestamp": "2023-08-20 01:21:52", "lastmod": "2023-12-22 23:21:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Carbon-Seth", "name": { "family": "Carbon", "given": "Seth" }, "orcid": "0000-0001-8244-1536" }, { "name": { "family": "Douglass", "given": "Eric" } }, { "name": { "family": "Good", "given": "Benjamin M." } }, { "name": { "family": "Unni", "given": "Deepak R." } }, { "name": { "family": "Harris", "given": "Nomi L." } }, { "name": { "family": "Mungall", "given": "Christopher J." }, "orcid": "0000-0002-6601-2165" }, { "name": { "family": "Basu", "given": "Siddartha" } }, { "name": { "family": "Chisholm", "given": "Rex L." } }, { "name": { "family": "Dodson", "given": "Robert J." } }, { "name": { "family": "Hartline", "given": "Eric" } }, { "name": { "family": "Fey", "given": "Petra" } }, { "name": { "family": "Thomas", "given": "Paul D." }, "orcid": "0000-0002-9074-3507" }, { "name": { "family": "Albou", "given": "Laurent-Philippe" }, "orcid": "0000-0001-5801-1974" }, { "name": { "family": "Ebert", "given": "Dustin" } }, { "name": { "family": "Kesling", "given": "Michael J." } }, { "name": { "family": "Mi", "given": "Huaiyu" }, "orcid": "0000-0001-8721-202X" }, { "name": { "family": "Muruganujan", "given": "Anushya" } }, { "name": { "family": "Huang", "given": "Xiaosong" } }, { "name": { "family": "Mushayahama", "given": "Tremayne" } }, { "name": { "family": "LaBonte", "given": "Sandra A." } }, { "name": { "family": "Siegele", "given": "Deborah A." } }, { "name": { "family": "Antonazzo", "given": "Giulia" } }, { "name": { "family": "Attrill", "given": "Helen" }, "orcid": "0000-0003-3212-6364" }, { "name": { "family": "Brown", "given": "Nick H." } }, { "name": { "family": "Garapati", "given": "Phani" } }, { "name": { "family": "Marygold", "given": "Steven J." } }, { "name": { "family": "Trovisco", "given": "Vitor" } }, { "name": { "family": "dos Santos", "given": "Gil" } }, { "name": { "family": "Falls", "given": "Kathleen" } }, { "name": { "family": "Tabone", "given": "Christopher" } }, { "name": { "family": "Zhou", "given": "Pinglei" } }, { "name": { "family": "Goodman", "given": "Joshua L." } }, { "name": { "family": "Strelets", "given": "Victor B." } }, { "name": { "family": "Thurmond", "given": "Jim" } }, { "name": { "family": "Garmiri", "given": "Penelope" } }, { "name": { "family": "Ishtiaq", "given": "Rizwan" } }, { "name": { "family": "Rodr\u00edguez-L\u00f3pez", "given": "Milagros" } }, { "name": { "family": "Acencio", "given": "Marcio L." } }, { "name": { "family": "Kuiper", "given": "Martin" } }, { "name": { "family": "L\u00e6greid", "given": "Astrid" } }, { "name": { "family": "Logie", "given": "Colin" } }, { "name": { "family": "Lovering", "given": "Ruth C." }, "orcid": "0000-0002-9791-0064" }, { "name": { "family": "Kramarz", "given": "Barbara" } }, { "name": { "family": "Saverimuttu", "given": "Shirin C. C." } }, { "name": { "family": "Pinheiro", "given": "Sandra M." } }, { "name": { "family": "Gunn", "given": "Heather" } }, { "name": { "family": "Su", "given": "Renzhi" } }, { "name": { "family": "Thurlow", "given": "Katherine E." } }, { "name": { "family": "Chibucos", "given": "Marcus C." }, "orcid": "0000-0001-9586-0780" }, { "name": { "family": "Giglio", "given": "Michelle" }, "orcid": "0000-0001-7628-5565" }, { "name": { "family": "Nadendla", "given": "Suvarna" } }, { "name": { "family": "Munro", "given": "James" } }, { "name": { "family": "Jackson", "given": "Rebecca" } }, { "name": { "family": "Duesbury", "given": "Margaret J." } }, { "name": { "family": "Del-Toro", "given": "Noemi" } }, { "name": { "family": "Meldal", "given": "Birgit H. M." } }, { "name": { "family": "Paneerselvam", "given": "Kalpana" } }, { "name": { "family": "Perfetto", "given": "Livia" } }, { "name": { "family": "Porras", "given": "Pablo" } }, { "name": { "family": "Orchard", "given": "Sandra" } }, { "name": { "family": "Shrivastava", "given": "Anjali" } }, { "name": { "family": "Chang", "given": "Hsin-Yu" } }, { "name": { "family": "Finn", "given": "Robert Daniel" } }, { "name": { "family": "Mitchell", "given": "Alexander Lawson" } }, { "name": { "family": "Rawlings", "given": "Neil David" } }, { "name": { "family": "Richardson", "given": "Lorna" } }, { "name": { "family": "Sangrador-Vegas", "given": "Amaia" } }, { "name": { "family": "Blake", "given": "Judith A." } }, { "name": { "family": "Christie", "given": "Karen R." } }, { "name": { "family": "Dolan", "given": "Mary E." }, "orcid": "0000-0001-7732-3295" }, { "name": { "family": "Drabkin", "given": "Harold J." } }, { "name": { "family": "Hill", "given": "David P." }, "orcid": "0000-0001-7476-6306" }, { "name": { "family": "Ni", "given": "Li" } }, { "name": { "family": "Sitnikov", "given": "Dmitry M." } }, { "name": { "family": "Harris", "given": "Midori A." }, "orcid": "0000-0003-4148-4606" }, { "name": { "family": "Oliver", "given": "Stephen G." } }, { "name": { "family": "Rutherford", "given": "Kim M." }, "orcid": "0000-0001-6277-726X" }, { "name": { "family": "Wood", "given": "Valerie" }, "orcid": "0000-0001-6330-7526" }, { "name": { "family": "Hayles", "given": "Jaqueline" } }, { "name": { "family": "B\u00e4hler", "given": "J\u00fcrg" } }, { "name": { "family": "Bolton", "given": "Elizabeth R." } }, { "name": { "family": "De Pons", "given": "Jeffery L." } }, { "name": { "family": "Dwinell", "given": "Melinda R." } }, { "name": { "family": "Hayman", "given": "G. Thomas" } }, { "name": { "family": "Kaldunski", "given": "Mary L." } }, { "name": { "family": "Kwitek", "given": "Anne E." } }, { "name": { "family": "Laulederkind", "given": "Stanley J. F." } }, { "name": { "family": "Plasterer", "given": "Cody" } }, { "name": { "family": "Tutaj", "given": "Marek A." } }, { "name": { "family": "Vedi", "given": "Mahima" } }, { "name": { "family": "Wang", "given": "Shur-Jen" } }, { "name": { "family": "D'Eustachio", "given": "Peter" } }, { "name": { "family": "Matthews", "given": "Lisa" } }, { "name": { "family": "Balhoff", "given": "James P." }, "orcid": "0000-0002-8688-6599" }, { "name": { "family": "Aleksander", "given": "Suzi A." } }, { "name": { "family": "Alexander", "given": "Michael J." } }, { "name": { "family": "Cherry", "given": "J. Michael" }, "orcid": "0000-0001-9163-5180" }, { "name": { "family": "Engel", "given": "Stacia R." }, "orcid": "0000-0001-5472-917X" }, { "name": { "family": "Gondwe", "given": "Felix" } }, { "name": { "family": "Karra", "given": "Kalpana" } }, { "name": { "family": "Miyasato", "given": "Stuart R." } }, { "name": { "family": "Nash", "given": "Robert S." } }, { "name": { "family": "Simison", "given": "Matt" } }, { "name": { "family": "Skrzypek", "given": "Marek S." } }, { "name": { "family": "Weng", "given": "Shuai" } }, { "name": { "family": "Wong", "given": "Edith D." } }, { "name": { "family": "Feuermann", "given": "Marc" }, "orcid": "0000-0002-4187-2863" }, { "name": { "family": "Gaudet", "given": "Pascale" }, "orcid": "0000-0003-1813-6857" }, { "name": { "family": "Morgat", "given": "Anne" } }, { "name": { "family": "Bakker", "given": "Erica" } }, { "name": { "family": "Berardini", "given": "Tanya Z." } }, { "name": { "family": "Reiser", "given": "Leonore" }, "orcid": "0000-0003-0073-0858" }, { "name": { "family": "Subramaniam", "given": "Shabari" } }, { "name": { "family": "Huala", "given": "Eva" } }, { "name": { "family": "Arighi", "given": "Cecilia N." } }, { "name": { "family": "Auchincloss", "given": "Andrea" } }, { "name": { "family": "Axelsen", "given": "Kristian" } }, { "name": { "family": "Argoud-Puy", "given": "Ghislaine" } }, { "name": { "family": "Bateman", "given": "Alex" }, "orcid": "0000-0002-6982-4660" }, { "name": { "family": "Blatter", "given": "Marie-Claude" } }, { "name": { "family": "Boutet", "given": "Emmanuel" } }, { "name": { "family": "Bowler", "given": "Emily" } }, { "name": { "family": "Breuza", "given": "Lionel" } }, { "name": { "family": "Bridge", "given": "Alan" } }, { "name": { "family": "Britto", "given": "Ramona" } }, { "name": { "family": "Bye-A-Jee", "given": "Hema" } }, { "name": { "family": "Casals Casas", "given": "Cristina" } }, { "name": { "family": "Coudert", "given": "Elisabeth" } }, { "name": { "family": "Denny", "given": "Paul" } }, { "name": { "family": "Estreicher", "given": "Anne" } }, { "name": { "family": "Famiglietti", "given": "Maria Livia" } }, { "name": { "family": "Georghiou", "given": "George" }, "orcid": "0000-0001-5067-3199" }, { "name": { "family": "Gos", "given": "Arnaud" } }, { "name": { "family": "Gruaz-Gumowski", "given": "Nadine" } }, { "name": { "family": "Hatton-Ellis", "given": "Emma" } }, { "name": { "family": "Hulo", "given": "Chantal" } }, { "name": { "family": "Ignatchenko", "given": "Alexandr" } }, { "name": { "family": "Jungo", "given": "Florence" } }, { "name": { "family": "Laiho", "given": "Kati" } }, { "name": { "family": "Le Mercier", "given": "Philippe" } }, { "name": { "family": "Lieberherr", "given": "Damien" } }, { "name": { "family": "Lock", "given": "Antonia" }, "orcid": "0000-0003-1179-5999" }, { "name": { "family": "Lussi", "given": "Yvonne" } }, { "name": { "family": "MacDougall", "given": "Alistair" } }, { "name": { "family": "Magrane", "given": "Michele" } }, { "name": { "family": "Martin", "given": "Maria J." } }, { "name": { "family": "Masson", "given": "Patrick" } }, { "name": { "family": "Natale", "given": "Darren A." } }, { "name": { "family": "Hyka-Nouspikel", "given": "Nevila" } }, { "name": { "family": "Orchard", "given": "Sandra" } }, { "name": { "family": "Pedruzzi", "given": "Ivo" } }, { "name": { "family": "Pourcel", "given": "Lucille" } }, { "name": { "family": "Poux", "given": "Sylvain" }, "orcid": "0000-0001-7299-6685" }, { "name": { "family": "Pundir", "given": "Sangya" } }, { "name": { "family": "Rivoire", "given": "Catherine" } }, { "name": { "family": "Speretta", "given": "Elena" } }, { "name": { "family": "Sundaram", "given": "Shyamala" } }, { "name": { "family": "Tyagi", "given": "Nidhi" } }, { "name": { "family": "Warner", "given": "Kate" } }, { "name": { "family": "Zaru", "given": "Rossana" } }, { "name": { "family": "Wu", "given": "Cathy H." } }, { "name": { "family": "Diehl", "given": "Alexander D." } }, { "id": "Chan-Juancarlos-N", "name": { "family": "Chan", "given": "Juancarlos N." }, "orcid": "0000-0002-7259-8107" }, { "id": "Grove-Christian-A", "name": { "family": "Grove", "given": "Christian" }, "orcid": "0000-0001-9076-6015" }, { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "Raymond Y. N." }, "orcid": "0000-0002-8151-7479" }, { "id": "M\u00fcller-Hans-Michael", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } }, { "id": "Raciti-Daniela", "name": { "family": "Raciti", "given": "Daniela" } }, { "id": "Van-Auken-Kimberly", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "name": { "family": "Berriman", "given": "Matthew" }, "orcid": "0000-0002-9581-0377" }, { "name": { "family": "Paulini", "given": "Michael" } }, { "name": { "family": "Howe", "given": "Kevin" }, "orcid": "0000-0002-1751-9226" }, { "name": { "family": "Gao", "given": "Sibyl" } }, { "name": { "family": "Wright", "given": "Adam" } }, { "name": { "family": "Stein", "given": "Lincoln" }, "orcid": "0000-0002-1983-4588" }, { "name": { "family": "Howe", "given": "Douglas G." } }, { "name": { "family": "Toro", "given": "Sabrina" } }, { "name": { "family": "Westerfield", "given": "Monte" } }, { "name": { "family": "Jaiswal", "given": "Pankaj" } }, { "name": { "family": "Cooper", "given": "Laurel" } }, { "name": { "family": "Elser", "given": "Justin" } } ] }, "title": "Gene Ontology resource: enriching a GOld mine", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived: 15 September 2020; Revision received: 22 October 2020; Accepted: 02 December 2020; Published: 08 December 2020. \n\nWe want to thank all the contributors to the GO resource over the last 20 years (http://geneontology.org/page/acknowledgments-contributors), and all the authors of papers represented in the GO knowledgebase (https://pubmed.ncbi.nlm.nih.gov/?term=loprovGeneOntol[SB]). \n\nWe would like to recognize the efforts of two members of the GO Consortium who passed away in early 2020, James C. Hu, professor at Texas A&M Department of Biochemistry and Biophysics, and Mary Ellen Shimoyama, associate professor of biomedical engineering at the Medical College of Wisconsin (MCW). We miss their participation in our meetings and discussions. \n\nFinally, we would like to acknowledge the immense contribution of Suzanna E. Lewis, one of the founders of the GO project, who retired in 2020. Her vision, creativity, enthusiasm and unshakable commitment to the project have been instrumental in creating one of the most useful projects to bioinformatics and keeping it relevant for over two decades. \n\nThe GO resource is supported by grants from the National Human Genome Research Institute [U41 HG02273 to P.D.T., P.W.S., S.E.L., J.M.C., J.A.B., supplements to grant U41 HG001315 to J.M.C., U24 HG002223 to P.W.S.]; GO Consortium members are also supported by diverse funding sources: dictyBase is supported by the National Institute of General Medical Sciences [1R24GM137770-01 to R.L.C.]; The EcoliWiki group is supported by the National Institutes of Health [GM089636]; National Science Foundation [1565146]; EMBL-EBI is funded by EMBL core funds; FlyBase is supported by the UK Medical Research Council [MR/N030117/1]; National Human Genome Research Institute [U41HG000739]; InterPro is funded by the Wellcome Trust [108433/Z/15/Z]; Biotechnology and Biological Sciences Research Council [BB/N00521X/1, BB/N019172/1, BB/L024136/1 to R.D.F.]; The Institute for Genome Sciences GO-related work on ECO is supported by the National Science Foundation [1458400]; The Gene Regulation Consortium (GRECO) is supported by Gene Regulation; Ensemble Effort for the Knowledge Commons (GREEKC) COST Action [CA15205]; A.L. and M.L.A. are also supported by the Research Council of Norway [247727]; Functional Gene Annotation, University College London is supported by Alzheimer's Research UK [ARUK-NAS2017A-1 to R.C.L.]; National Institute for Health Research University College London Hospitals Biomedical Research Centre; IntAct and the Complex Portal are supported by the European Molecular Biology Laboratory core funds, Open Targets [OTAR-044, OTAR02-048]; Wellcome Trust grant INVAR [212925/Z/18/Z]; PomBase is supported by the Wellcome Trust [104967/Z/14/Z to S.G.O.]; MGI is supported by the National Human Genome Research Institute [HG 000330, HG 002273]; RGD is supported by the National Heart, Lung, and Blood Institute [HL 64541]; Reactome is supported by the National Human Genome Research Institute [HG 003751]; the TAIR project is funded by academic institutional, corporate and individual subscriptions; TAIR is administered by the 501(c)(3) non-profit Phoenix Bioinformatics; the UniProt Consortium is supported by the National Eye Institute, National Human Genome Research Institute, National Heart, Lung and Blood Institute, National Institute of Allergy and Infectious Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of General Medical Sciences; National Institute of Mental Health of the National Institutes of Health [U24HG007822]; National Human Genome Research Institute [U41HG007822, U41HG002273]; National Institute of General Medical Sciences [R01GM080646, P20GM103446, U01GM120953]; Swiss Federal Government through the State Secretariat for Education, Research and Innovation SERI; European Molecular Biology Laboratory core funds; Biotechnology and Biological Sciences Research Council [BB/M011674/1]; the Alzheimer's Research UK [ARUK-NAS2017A-1]; WormBase is supported by the US National Human Genome Research Institute [U24-HG002223]; UK Medical Research Council [MR/S000453/1]; UK Biotechnology and Biological Sciences Research Council [BB/P024610, BB/P024602]; ZFIN is supported by the National Human Genome Research Institute [HG002659 to M.W. and HG010859 to P.W.S]. Gramene contributions are supported by the National Science Foundation award [IOS #1127112] and Planteome contributions are supported by National Science Foundation award [IOS #1340112]. The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding agencies. Funding for open access charges: National Human Genome Research Institute [U41 HG02273]. \n\nConflict of interest statement: None declared.\n\nPublished - gkaa1113.pdf
Supplemental Material - gkaa1113_supplemental_file.pdf
", "abstract": "The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations.", "date": "2021-01-08", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "49", "number": "D1", "publisher": "Oxford University Press", "pagerange": "D325-D334", "id_number": "CaltechAUTHORS:20210210-070215975", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210210-070215975", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U41 HG02273" }, { "agency": "NIH", "grant_number": "U41 HG001315" }, { "agency": "NIH", "grant_number": "U24 HG002223" }, { "agency": "NIH", "grant_number": "1R24GM137770-01" }, { "agency": "NIH", "grant_number": "GM089636" }, { "agency": "NSF", "grant_number": "DBI-1565146" }, { "agency": "European Molecular Biology Laboratory (EMBL)" }, { "agency": "Medical Research Council (UK)", "grant_number": "MR/N030117/1" }, { "agency": "NIH", "grant_number": "U41HG000739" }, { "agency": "Wellcome Trust", "grant_number": "108433/Z/15/Z" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/N00521X/1" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/N019172/1" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/L024136/1" }, { "agency": "NSF", "grant_number": "DBI-1458400" }, { "agency": "Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC)", "grant_number": "CA15205" }, { "agency": "Research Council of Norway", "grant_number": "247727" }, { "agency": "Alzheimer's Research UK", "grant_number": "ARUK-NAS2017A-1" }, { "agency": "National Institute for Health Research" }, { "agency": "University College London" }, { "agency": "Open Targets", "grant_number": "OTAR-044" }, { "agency": "Open Targets", "grant_number": "OTAR02-048" }, { "agency": "Wellcome Trust", "grant_number": "212925/Z/18/Z" }, { "agency": "Wellcome Trust", "grant_number": "104967/Z/14/Z" }, { "agency": "NIH", "grant_number": "HG 000330" }, { "agency": "NIH", "grant_number": "HG 002273" }, { "agency": "NIH", "grant_number": "HL 64541" }, { "agency": "NIH", "grant_number": "HG 003751" }, { "agency": "Phoenix Bioinformatics" }, { "agency": "NIH", "grant_number": "U24HG007822" }, { "agency": "NIH", "grant_number": "U41HG007822" }, { "agency": "NIH", "grant_number": "U41HG002273" }, { "agency": "NIH", "grant_number": "R01GM080646" }, { "agency": "NIH", "grant_number": "P20GM103446" }, { "agency": "NIH", "grant_number": "U01GM120953" }, { "agency": "State Secretariat for Education, Research and Innovation (SERI)" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/M011674/1" }, { "agency": "NIH", "grant_number": "U24-HG002223" }, { "agency": "Medical Research Council (UK)", "grant_number": "MR/S000453/1" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/P024610" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/P024602/1" }, { "agency": "NIH", "grant_number": "HG002659" }, { "agency": "NIH", "grant_number": "HG010859" }, { "agency": "NSF", "grant_number": "IOS-1127112" }, { "agency": "NSF", "grant_number": "IOS-1340112" }, { "agency": "NIH", "grant_number": "U41 HG02273" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "corp_creators": { "items": [ "Gene Ontology Consortium" ] }, "doi": "10.1093/nar/gkaa1113", "pmcid": "PMC7779012", "primary_object": { "basename": "gkaa1113.pdf", "url": "https://authors.library.caltech.edu/records/vk9jd-bna77/files/gkaa1113.pdf" }, "related_objects": [ { "basename": "gkaa1113_supplemental_file.pdf", "url": "https://authors.library.caltech.edu/records/vk9jd-bna77/files/gkaa1113_supplemental_file.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Carbon, Seth; Douglass, Eric; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ssdba-vag82", "eprint_id": 107278, "eprint_status": "archive", "datestamp": "2023-08-20 01:20:44", "lastmod": "2023-12-22 23:21:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kato-Mihoko", "name": { "family": "Kato", "given": "Mihoko" }, "orcid": "0000-0003-3827-8879" }, { "id": "Kolotuev-Irina", "name": { "family": "Kolotuev", "given": "Irina" }, "orcid": "0000-0003-1433-8048" }, { "id": "Cunha-Alexandre", "name": { "family": "Cunha", "given": "Alexandre" }, "orcid": "0000-0002-2541-6024" }, { "id": "Gharib-Shahla", "name": { "family": "Gharib", "given": "Shahla" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Extrasynaptic acetylcholine signaling through a muscarinic receptor regulates cell migration", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 The Author(s). Published under the PNAS license. \n\nContributed by Paul W. Sternberg, September 6, 2020 (sent for review March 20, 2019; reviewed by Reinhard W. K\u00f6ster and James B. Rand) Published in issue January 5, 2021. Published first December 23, 2020. \n\nWe thank laboratory members, particularly Pei Yin Shih, Ravi Nath, and Han Wang, for comments on the paper. Some strains were provided by the Caenorhabditis Genetics Center, which is funded by NIH Office of Research Infrastructure Programs (grant P40 OD010440), and by the C. elegans Gene Knockout Project at the Oklahoma Medical Research Foundation, which was part of the International C. elegans Gene Knockout Consortium. For image collection and analysis, we used the Caltech Biological Imaging Facility and the Center for Advanced Methods in Biological Image Analysis. We received microscopy training from Dr. Andres Collazo and Huygens software training from Say-Tar Goh. Dr. Rene Garcia, Dr. Derek Sieburth, and Dr. Kenneth Miller kindly provided strains and reagents. This work was supported by HHMI with whom P.W.S. was an investigator and by US Public Health Service NIH, Eunice Kennedy Shriver Institute of Child Health and Human Development grant R01 HD091327 to P.W.S. and M.K. \n\nData Availability. All study data are included in the article and supporting information. \n\nAuthor contributions: M.K., I.K., and P.W.S. designed research; M.K., I.K., and S.G. performed research; M.K. and A.C. contributed new reagents/analytic tools; M.K., I.K., and A.C. analyzed data; and M.K. and P.W.S. wrote the paper. \n\nReviewers: R.W.K., Technische Universit\u00e4t Braunschweig; and J.B.R., University of Oklahoma Health Sciences Center. \n\nThe authors declare no competing interest. \n\nThis article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1904338118/-/DCSupplemental.\n\nPublished - e1904338118.full.pdf
Supplemental Material - pnas.1904338118.sapp.pdf
Supplemental Material - pnas.1904338118.sd01.xlsx
", "abstract": "Acetylcholine (ACh) promotes various cell migrations in vitro, but there are few investigations into this nonsynaptic role of ACh signaling in vivo. Here we investigate the function of a muscarinic receptor on an epithelial cell migration in Caenorhabditis elegans. We show that the migratory gonad leader cell, the linker cell (LC), uses an M1/M3/M5-like muscarinic ACh receptor GAR-3 to receive extrasynaptic ACh signaling from cholinergic neurons for its migration. Either the loss of the GAR-3 receptor in the LC or the inhibition of ACh release from cholinergic neurons resulted in migratory path defects. The overactivation of the GAR-3 muscarinic receptor caused the LC to reverse its orientation through its downstream effectors G\u03b1q/egl-30, PLC\u03b2/egl-8, and TRIO/unc-73. This reversal response only occurred in the fourth larval stage, which corresponds to the developmental time when the GAR-3::yellow fluorescent protein receptor in the membrane relocalizes from a uniform to an asymmetric distribution. These findings suggest a role for the GAR-3 muscarinic receptor in determining the direction of LC migration.", "date": "2021-01-05", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "118", "number": "1", "publisher": "National Academy of Sciences", "pagerange": "Art. No. e1904338118", "id_number": "CaltechAUTHORS:20201224-085807779", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201224-085807779", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P40 OD010440" }, { "agency": "Oklahoma Medical Research Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)", "grant_number": "047-101" }, { "agency": "NIH", "grant_number": "R01HD091327" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1073/pnas.1904338118", "pmcid": "PMC7817160", "primary_object": { "basename": "e1904338118.full.pdf", "url": "https://authors.library.caltech.edu/records/ssdba-vag82/files/e1904338118.full.pdf" }, "related_objects": [ { "basename": "pnas.1904338118.sapp.pdf", "url": "https://authors.library.caltech.edu/records/ssdba-vag82/files/pnas.1904338118.sapp.pdf" }, { "basename": "pnas.1904338118.sd01.xlsx", "url": "https://authors.library.caltech.edu/records/ssdba-vag82/files/pnas.1904338118.sd01.xlsx" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Kato, Mihoko; Kolotuev, Irina; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/vatm0-d4991", "eprint_id": 106729, "eprint_status": "archive", "datestamp": "2023-08-22 07:38:15", "lastmod": "2023-12-22 23:21:49", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Holman-E-A", "name": { "family": "Holman", "given": "Elizabeth A." }, "orcid": "0000-0002-5158-4689" }, { "id": "Fang-Yuan-Sheng", "name": { "family": "Fang", "given": "Yuan-Sheng" }, "orcid": "0000-0003-4643-0084" }, { "id": "Chen-Liang", "name": { "family": "Chen", "given": "Liang" } }, { "id": "DeWeese-M-R", "name": { "family": "DeWeese", "given": "Michael" }, "orcid": "0000-0003-2801-5768" }, { "id": "Holman-Hoi-Ying-N", "name": { "family": "Holman", "given": "Hoi-Ying N." }, "orcid": "0000-0002-7534-2625" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Autonomous adaptive data acquisition for scanning hyperspectral imaging", "ispublished": "pub", "full_text_status": "public", "keywords": "Data acquisition; Optical imaging", "note": "\u00a9 The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 25 February 2020; Accepted 18 September 2020; Published 18 November 2020. \n\nWe thank Dr. Hans Bechtel and ALS Beamline 1.4.3 staff for their instrumentation support, Drs. Peter Zwart and Derek R. Holman for discussion, and the reviewers for their constructive comments. This research used resources of the Berkeley Synchrotron Infrared Structural Biology (BSISB) Imaging program, the Molecular Foundry, and the Advanced Light Source, DOE Office of Science User Facilities, under contract no. DE-AC02-05CH11231. E.A.H. was supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1745301 and the Howard Hughes Medical Institute under Grant No. 047-101, with which P.W.S. was an investigator. Y.-S.F., L.C., and H.-Y.N.H. were supported by the US Department of Energy, Office of Science, Office of Biological and Environmental Research under contract no. DE-AC02-05CH11231. \n\nData availability: Infrared spectral data are available through the CaltechDATA repository (https://doi.org/10.22002/D1.1609). The 11 high-resolution spectral maps used for calibration simulations are not included in the repository, since they are undergoing spectral analysis and interpretation in a different manuscript. Any remaining data is available from the corresponding author upon reasonable request. \n\nCode availability: This proprietary adaptive sampling code and GUI are specific to the Infrared Beamline 1.4.3 at the Advanced Light Source (https://als.lbl.gov/). They are available to IR beamline users through the DOE-supported Berkeley Synchrotron Infrared Structural Biology (BSISB) Imaging Program (https://bsisb.lbl.gov/wordpress/). Further requests concerning this code can be directed to H.-Y.N.H. \n\nAuthor Contributions: These authors contributed equally: Elizabeth A. Holman, Yuan-Sheng Fang. \n\nH.-Y.N.H. conceived the idea. H.-Y.N.H., and Y.-S.F. designed adaptive data acquisition. Y.-S.F. developed and wrote the algorithm, designed, and performed simulations. Y.-S.F., H.-Y.N.H., and E.A.H. implemented algorithm at ALS Beamline 1.4.3. Y.-S.F. and E.A.H. designed and tested IR processing module. Y.-S.F. wrote IR processing module. E.A.H. designed and performed proof-of-principle experiments. L.C. and E.A.H. performed IR data processing. E.A.H. performed IR spectral analysis, gathered materials from all authors, and wrote the manuscript. M.D., L.C., and H.-Y.N.H. supervised Y.-S.F. P.W.S. supervised E.A.H. \n\nThe authors declare no competing interests.\n\nPublished - s42003-020-01385-3.pdf
Supplemental Material - 42003_2020_1385_MOESM1_ESM.pdf
Supplemental Material - 42003_2020_1385_MOESM2_ESM.pdf
", "abstract": "Non-invasive and label-free spectral microscopy (spectromicroscopy) techniques can provide quantitative biochemical information complementary to genomic sequencing, transcriptomic profiling, and proteomic analyses. However, spectromicroscopy techniques generate high-dimensional data; acquisition of a single spectral image can range from tens of minutes to hours, depending on the desired spatial resolution and the image size. This substantially limits the timescales of observable transient biological processes. To address this challenge and move spectromicroscopy towards efficient real-time spatiochemical imaging, we developed a grid-less autonomous adaptive sampling method. Our method substantially decreases image acquisition time while increasing sampling density in regions of steeper physico-chemical gradients. When implemented with scanning Fourier Transform infrared spectromicroscopy experiments, this grid-less adaptive sampling approach outperformed standard uniform grid sampling in a two-component chemical model system and in a complex biological sample, Caenorhabditis elegans. We quantitatively and qualitatively assess the efficiency of data acquisition using performance metrics and multivariate infrared spectral analysis, respectively.", "date": "2020-11-18", "date_type": "published", "publication": "Communications Biology", "volume": "3", "number": "1", "publisher": "Springer", "pagerange": "Art. No. 684", "id_number": "CaltechAUTHORS:20201118-141320800", "issn": "2399-3642", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201118-141320800", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Energy (DOE)", "grant_number": "DE-AC02-05CH11231" }, { "agency": "NSF Graduate Research Fellowship", "grant_number": "DGE-1745301" }, { "agency": "Howard Hughes Medical Institute (HHMI)", "grant_number": "047-101" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s42003-020-01385-3", "primary_object": { "basename": "s42003-020-01385-3.pdf", "url": "https://authors.library.caltech.edu/records/vatm0-d4991/files/s42003-020-01385-3.pdf" }, "related_objects": [ { "basename": "42003_2020_1385_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/vatm0-d4991/files/42003_2020_1385_MOESM1_ESM.pdf" }, { "basename": "42003_2020_1385_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/vatm0-d4991/files/42003_2020_1385_MOESM2_ESM.pdf" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Holman, Elizabeth A.; Fang, Yuan-Sheng; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/kbtjg-8t517", "eprint_id": 106016, "eprint_status": "archive", "datestamp": "2023-08-19 23:54:15", "lastmod": "2023-12-22 23:21:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Le-Henry-H", "name": { "family": "Le", "given": "Henry H." }, "orcid": "0000-0003-2942-2357" }, { "id": "Wrobel-Chester-J-J", "name": { "family": "Wrobel", "given": "Chester J. J." }, "orcid": "0000-0001-6047-4644" }, { "id": "Cohen-Sarah-M", "name": { "family": "Cohen", "given": "Sarah M." }, "orcid": "0000-0002-5233-2280" }, { "id": "Yu-Jingfang", "name": { "family": "Yu", "given": "Jingfang" }, "orcid": "0000-0003-1770-5368" }, { "id": "Park-Heenam", "name": { "family": "Park", "given": "Heenam" }, "orcid": "0000-0001-7911-5828" }, { "id": "Helf-Maximilian-J", "name": { "family": "Helf", "given": "Maximilian J." }, "orcid": "0000-0002-1393-3999" }, { "id": "Curtis-Brian-J", "name": { "family": "Curtis", "given": "Brian J." } }, { "id": "Kruempel-Joseph-C", "name": { "family": "Kruempel", "given": "Joseph C." } }, { "id": "Reis-Rodrigues-Pedro", "name": { "family": "Reis-Rodrigues", "given": "Pedro" } }, { "id": "Hu-Patrick-John", "name": { "family": "Hu", "given": "Patrick J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Schroeder-F-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" } ] }, "title": "Modular metabolite assembly in Caenorhabditis elegans depends on carboxylesterases and formation of lysosome-related organelles", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 Le et al. This article\nis distributed under the terms of\nthe Creative Commons\nAttribution License, which\npermits unrestricted use and\nredistribution provided that the\noriginal author and source are\ncredited.\n\nReceived: 07 August 2020;\nAccepted: 14 October 2020;\nPublished: 16 October 2020.\n\nThis research was funded by an NIH Chemical Biology Interface (CBI) Training Grant 5T32GM008500\n(to B.C.), National Institutes of Health grants R35 GM131877 (to F.C.S.), and R24OD023041 (to P.W.\nS.). F.C.S. is a Faculty Scholar of the Howard Hughes Medical Institute. We thank WormBase for\nsequences, Tsui-Fen Chou for Cas9 protein, Ying (Kitty) Zhang for assistance with NMR spectroscopy, and Navid Movahed for assistance with mass spectrometry.\n\nThe funders had no role in study design, data collection and interpretation, or the\ndecision to submit the work for publication.\n\nAuthor contributions:\nHenry H Le, Chester JJ Wrobel, Conceptualization, Data curation, Formal analysis, Investigation,\nWriting - original draft, Writing - review and editing; Sarah M Cohen, Conceptualization, Resources,\nMethodology; Jingfang Yu, Resources, Formal analysis; Heenam Park, Resources, Methodology;\nMaximilian J Helf, Software, Methodology; Brian J Curtis, Resources, Investigation; Joseph C Kruempel, Patrick J Hu, Resources; Pedro Reis Rodrigues, Data curation, Investigation; Paul W Sternberg,\nConceptualization, Funding acquisition, Writing - original draft, Project administration, Writing -\nreview and editing; Frank C Schroeder, Conceptualization, Formal analysis, Supervision, Funding\nacquisition, Writing - original draft, Project administration, Writing - review and editing.\n\nData availability:\nAll data generated or analysed during this study are included in the manuscript and supporting files.\nMS/MS data is available via MassIVE under accession number: MSV000086293.\n\nPublished - elife-61886-v2.pdf
Accepted Version - elife-61886-v1.pdf
Submitted - 2020.08.22.262956v2.full.pdf
Supplemental Material - elife-61886-supp-v1.zip
Supplemental Material - elife-61886-supp1-v2.pdf
Supplemental Material - elife-61886-transrepform-v2.docx
", "abstract": "Signaling molecules derived from attachment of diverse metabolic building blocks to ascarosides play a central role in the life history of C. elegans and other nematodes; however, many aspects of their biogenesis remain unclear. Using comparative metabolomics, we show that a pathway mediating formation of intestinal lysosome-related organelles (LROs) is required for biosynthesis of most modular ascarosides as well as previously undescribed modular glucosides. Similar to modular ascarosides, the modular glucosides are derived from highly selective assembly of moieties from nucleoside, amino acid, neurotransmitter, and lipid metabolism, suggesting that modular glucosides, like the ascarosides, may serve signaling functions. We further show that carboxylesterases that localize to intestinal organelles are required for the assembly of both modular ascarosides and glucosides via ester and amide linkages. Further exploration of LRO function and carboxylesterase homologs in C. elegans and other animals may reveal additional new compound families and signaling paradigms.", "date": "2020-10-16", "date_type": "published", "publication": "eLife", "volume": "2020", "number": "9", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e61886", "id_number": "CaltechAUTHORS:20201013-104022895", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201013-104022895", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "5T32GM008500" }, { "agency": "NIH", "grant_number": "R35 GM131877" }, { "agency": "NIH", "grant_number": "R24OD023041" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.7554/eLife.61886", "pmcid": "PMC7641594", "primary_object": { "basename": "elife-61886-v1.pdf", "url": "https://authors.library.caltech.edu/records/kbtjg-8t517/files/elife-61886-v1.pdf" }, "related_objects": [ { "basename": "elife-61886-v2.pdf", "url": "https://authors.library.caltech.edu/records/kbtjg-8t517/files/elife-61886-v2.pdf" }, { "basename": "2020.08.22.262956v2.full.pdf", "url": "https://authors.library.caltech.edu/records/kbtjg-8t517/files/2020.08.22.262956v2.full.pdf" }, { "basename": "elife-61886-supp-v1.zip", "url": "https://authors.library.caltech.edu/records/kbtjg-8t517/files/elife-61886-supp-v1.zip" }, { "basename": "elife-61886-supp1-v2.pdf", "url": "https://authors.library.caltech.edu/records/kbtjg-8t517/files/elife-61886-supp1-v2.pdf" }, { "basename": "elife-61886-transrepform-v2.docx", "url": "https://authors.library.caltech.edu/records/kbtjg-8t517/files/elife-61886-transrepform-v2.docx" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Le, Henry H.; Wrobel, Chester J. J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/pggd9-8pw73", "eprint_id": 106226, "eprint_status": "archive", "datestamp": "2023-08-19 23:39:18", "lastmod": "2023-12-22 23:41:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sun-Simo", "name": { "family": "Sun", "given": "Simo" } }, { "id": "Shinya-Ryoji", "name": { "family": "Shinya", "given": "Ryoji" }, "orcid": "0000-0002-2450-3054" }, { "id": "Dayi-Mehmet", "name": { "family": "Dayi", "given": "Mehmet" }, "orcid": "0000-0002-5367-918X" }, { "id": "Yoshida-Akemi", "name": { "family": "Yoshida", "given": "Akemi" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Kikuchi-Taisei", "name": { "family": "Kikuchi", "given": "Taisei" }, "orcid": "0000-0003-2759-9167" } ] }, "title": "Telomere-to-Telomere Genome Assembly of Bursaphelenchus okinawaensis Strain SH1", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 Sun et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. \n\nReceived 7 September 2020. Accepted 25 September 2020. Published 22 October 2020. \n\nWe thank Asuka Konosu, Melis Konno, Ryusei Tanaka, Igor Antoschechkin, and the Jacobs Genome Facility for their technical assistance. \n\nThis work was funded in part by Japan Society for the Promotion of Science (JSPS) KAKENHI grant numbers 26460510 and 19H03212 and JST CREST grant number JPMJCR18S7. \n\nData availability:\nThe B. okinawaensis v2 assembly has been deposited in DDBJ/EMBL/GenBank under BioProject number PRJEB40023. The raw Illumina, Nanopore, and Hi-C read data are available in the Sequence Read Archive with accession numbers DRR243691, DRR243689, and DRR243690, respectively.\n\nPublished - Microbiology_Resource_Announcements-2020-Sun-e01000-20.full.pdf
", "abstract": "Bursaphelenchus okinawaensis is a self-fertilizing, hermaphroditic, fungus-feeding nematode used as a laboratory model for the genus Bursaphelenchus, which includes the important pathogen Bursaphelenchus xylophilus. Here, we report the nearly complete genome sequence of B. okinawaensis. The 70-Mbp assembly contained six scaffolds (>11 Mbp each) with telomere repeats on their ends, indicating complete chromosomes.", "date": "2020-10", "date_type": "published", "publication": "Microbiology Resource Announcements", "volume": "9", "number": "43", "publisher": "American Society for Microbiology", "pagerange": "Art. No. e01000-20", "id_number": "CaltechAUTHORS:20201022-112712963", "issn": "2576-098X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201022-112712963", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Japan Society for the Promotion of Science (JSPS)", "grant_number": "26460510" }, { "agency": "Japan Society for the Promotion of Science (JSPS)", "grant_number": "19H03212" }, { "agency": "Japan Science and Technology Agency", "grant_number": "JPMJCR18S7" } ] }, "local_group": { "items": [ { "id": "Millard-and-Muriel-Jacobs-Genetics-and-Genomics-Laboratory" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1128/mra.01000-20", "pmcid": "PMC7585841", "primary_object": { "basename": "Microbiology_Resource_Announcements-2020-Sun-e01000-20.full.pdf", "url": "https://authors.library.caltech.edu/records/pggd9-8pw73/files/Microbiology_Resource_Announcements-2020-Sun-e01000-20.full.pdf" }, "resource_type": "article", "pub_year": "2020", "author_list": "Sun, Simo; Shinya, Ryoji; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/gf1c5-jdg33", "eprint_id": 104582, "eprint_status": "archive", "datestamp": "2023-08-19 23:09:26", "lastmod": "2023-12-22 23:21:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Baiocchi-T", "name": { "family": "Baiocchi", "given": "Tiffany" } }, { "id": "Anesko-K", "name": { "family": "Anesko", "given": "Kyle" } }, { "id": "Mercado-N", "name": { "family": "Mercado", "given": "Nathan" } }, { "id": "Park-Heenam", "name": { "family": "Park", "given": "Heenam" } }, { "id": "Kin-Kassandra", "name": { "family": "Kin", "given": "Kassandra" } }, { "id": "Strickhouser-Monzon-B", "name": { "family": "Strickhouser-Monzon", "given": "Brandon" } }, { "id": "Robles-P", "name": { "family": "Robles", "given": "Priscila" } }, { "id": "Bowman-C", "name": { "family": "Bowman", "given": "Christian" } }, { "id": "Wang-Han", "name": { "family": "Wang", "given": "Han" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Dillman-A-R", "name": { "family": "Dillman", "given": "Adler R." }, "orcid": "0000-0001-7171-4332" } ] }, "title": "Signaling by AWC Olfactory Neurons Is Necessary for Caenorhabditis elegans' Response to Prenol, an Odor Associated with Nematode-Infected Insects", "ispublished": "pub", "full_text_status": "public", "keywords": "prenol, 3-methyl-2-buten-1-ol, dcap-1, dcap-2, and clec-39", "note": "\u00a9 2020 Baiocchi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Available freely online through the author-supported open access option. \n\nManuscript received April 21, 2020; accepted for publication July 14, 2020; published Early Online July 17, 2020. \n\nWe thank the C. elegans Natural Diversity Resource (CeNDR) for providing the natural variants used in this study as well as the C. elegans Genetics Center, which is funded by National Institutes of Health Office of Research Infrastructure Programs (P40 OD010440); the Mitani Laboratory at the Tokyo Women's Medical University School of Medicine; and the providers of (lf) mutants from a variety of laboratory (which have been listed in Table S21; resources summary), including the C. elegans gene knockout project at the Oklahoma Medical Research foundation, which is part of the international C. elegans gene knockout consortium and created a large number of the (lf) mutants used in this study. This research was supported by the US Department of Agriculture National Institute of Food and Agriculture Hatch project (accession no. 1011296) to A.R.D., K99 GM126137/National Institute of General Medical Sciences to H.W., R24 OD023041/Office of the Director/National Institutes of Health to P.W.S., and the Graduate Research Mentorship Project from University of California Riverside, which provided support to T.B. \n\nAuthor contributions: T.B. and A.R.D. conceived and designed the behavioral experiments. M.C, K.K., B.S-M, K.A., P.R., and C.B performed behavioral experiments. H.W., H.P., and P.W.S. created CRISPR/Cas9-mediated knockout strains and generated dcap-2 rescue lines for use in behavioral experiments and provided information for the methods on creation of knockout strains, as well as feedback and suggestions for manuscript edits. T.B. and A.R.D. analyzed and interpreted behavioral data. T.B. and A.R.D. wrote and revised the manuscript. The authors declare no competing interests.\n\nPublished - 145.full.pdf
Supplemental Material - 12616691.zip
", "abstract": "Chemosensation plays a role in the behaviors and life cycles of numerous organisms, including nematodes. Many guilds of nematodes exist, ranging from the free-living Caenorhabditis elegans to various parasitic species such as entomopathogenic nematodes (EPNs), which are parasites of insects. Despite ecological differences, previous research has shown that both EPNs and C. elegans respond to prenol (3-methyl-2-buten-1-ol), an odor associated with EPN infections. However, it is unclear how C. elegans responds to prenol. By utilizing natural variation and genetic neuron ablation to investigate the response of C. elegans to prenol, we found that the AWC neurons are involved in the detection of prenol and that several genes (including dcap-1, dcap-2, and clec-39) influence response to this odorant. Furthermore, we identified that the response to prenol is mediated by the canonically proposed pathway required for other AWC-sensed attractants. However, upon testing genetically diverse isolates, we found that the response of some strains to prenol differed from their response to isoamyl alcohol, suggesting that the pathways mediating response to these two odorants may be genetically distinct. Further, evaluations leveraging natural variation and genome wide association revealed specific genes that influence nematode behavior and provide a foundation for future studies to better understand the role of prenol in nematode behavioral ecology.", "date": "2020-09", "date_type": "published", "publication": "Genetics", "volume": "216", "number": "1", "publisher": "Genetics Society of America", "pagerange": "145-157", "id_number": "CaltechAUTHORS:20200727-090420630", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200727-090420630", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P40 OD010440" }, { "agency": "Tokyo Women's Medical University School of Medicine" }, { "agency": "Oklahoma Medical Research Foundation" }, { "agency": "Department of Agriculture", "grant_number": "1011296" }, { "agency": "NIH", "grant_number": "K99 GM126137" }, { "agency": "NIH", "grant_number": "R24 OD023041" }, { "agency": "University of California, Riverside" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1534/genetics.120.303280", "pmcid": "PMC7463287", "primary_object": { "basename": "12616691.zip", "url": "https://authors.library.caltech.edu/records/gf1c5-jdg33/files/12616691.zip" }, "related_objects": [ { "basename": "145.full.pdf", "url": "https://authors.library.caltech.edu/records/gf1c5-jdg33/files/145.full.pdf" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Baiocchi, Tiffany; Anesko, Kyle; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/cfdy6-q9489", "eprint_id": 105100, "eprint_status": "archive", "datestamp": "2023-08-19 23:01:52", "lastmod": "2023-12-13 17:16:12", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Le-Henry-H", "name": { "family": "Le", "given": "Henry H." }, "orcid": "0000-0003-2942-2357" }, { "id": "Wrobel-C-J", "name": { "family": "Wrobel", "given": "Chester J." }, "orcid": "0000-0001-6047-4644" }, { "id": "Cohen-S-M", "name": { "family": "Cohen", "given": "Sarah M." }, "orcid": "0000-0002-5233-2280" }, { "id": "Yu-Jingfang", "name": { "family": "Yu", "given": "Jingfang" }, "orcid": "0000-0003-1770-5368" }, { "id": "Park-Heenam", "name": { "family": "Park", "given": "Heenam" }, "orcid": "0000-0001-7911-5828" }, { "id": "Helf-M-J", "name": { "family": "Helf", "given": "Maximilian J." }, "orcid": "0000-0002-1393-3999" }, { "id": "Curtis-B-J", "name": { "family": "Curtis", "given": "Brian J." } }, { "id": "Rodrigues-P-R", "name": { "family": "Rodrigues", "given": "Pedro R." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Schroeder-F-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" } ] }, "title": "Modular metabolite assembly in C. elegans lysosome-related organelles", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. \n\nPosted August 24, 2020. \n\nThis research was funded by an NIH Chemical Biology Interface (CBI) Training Grant 5T32GM008500 (to B.C.), National Institutes of Health grants R35 GM131877 (to F.C.S.), and R24OD023041 (to P.W.S.). F.C.S. is a Faculty Scholar of the Howard Hughes Medical Institute. We thank WormBase for sequences, Tsui-Fen Chou for Cas9 protein, Ying (Kitty) Zhang for assistance with NMR spectroscopy, and Navid Movahed for assistance with mass spectrometry. \n\nAuthor Contributions: The manuscript was written through contributions of all authors and all authors have given approval to the final version of the manuscript. \n\nThe authors declare no competing interests.\n\nSubmitted - 2020.08.22.262956v1.full.pdf
", "abstract": "Signaling molecules derived from attachment of diverse primary metabolic building blocks to ascarosides play a central role in the life history of C. elegans and other nematodes; however, many aspects of their biogenesis remain unclear. Using comparative metabolomics, we show that lysosome-related organelles (LROs) are required for biosynthesis of most modular ascarosides as well as previously undescribed modular glucosides. Both modular glucosides and ascarosides are derived from highly selective assembly of moieties from nucleoside, amino acid, neurotransmitter, and lipid metabolism. We further show that cholinesterase (cest) homologs that localize to the LROs are required for assembly of both modular ascarosides and glucosides, mediating formation of ester and amide linkages between subsets of building blocks. Their specific biosynthesis suggests that modular glucosides, like ascarosides, serve dedicated signaling functions. Further exploration of LRO function and cest homologs in C. elegans and other animals may reveal additional new compound families and signaling paradigms.", "date": "2020-08-25", "date_type": "published", "id_number": "CaltechAUTHORS:20200825-103646907", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200825-103646907", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "5T32GM008500" }, { "agency": "NIH", "grant_number": "R35 GM131877" }, { "agency": "NIH", "grant_number": "R24OD023041" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2020.08.22.262956", "primary_object": { "basename": "2020.08.22.262956v1.full.pdf", "url": "https://authors.library.caltech.edu/records/cfdy6-q9489/files/2020.08.22.262956v1.full.pdf" }, "resource_type": "monograph", "pub_year": "2020", "author_list": "Le, Henry H.; Wrobel, Chester J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/w5czb-tcf76", "eprint_id": 99484, "eprint_status": "archive", "datestamp": "2023-08-19 22:35:28", "lastmod": "2023-12-22 23:41:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Walton-Sophie-J", "name": { "family": "Walton", "given": "Sophie J." }, "orcid": "0000-0003-1320-1525" }, { "id": "Wang-Han", "name": { "family": "Wang", "given": "Han" }, "orcid": "0000-0002-1933-5762" }, { "id": "Quintero-Cadena-Porfirio", "name": { "family": "Quintero-Cadena", "given": "Porfirio" }, "orcid": "0000-0003-0067-5844" }, { "id": "Bateman-Alex", "name": { "family": "Bateman", "given": "Alex" }, "orcid": "0000-0002-6982-4660" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Caenorhabditis elegans AF4/FMR2 Family Homolog affl-2 Regulates Heat-Shock-Induced Gene Expression", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 by the Genetics Society of America. \n\nManuscript received October 21, 2019; accepted for publication May 27, 2020; published Early Online June 9, 2020. \n\nWe thank Heenam Park for helping create putative affl-1 null mutants using CRISPR/Cas9, and Jean Badroos, Jasmine S. Revanna, and Minyi Tan for technical assistance. We thank Hillel Schwartz, Jonathan Liu, and members of the Sternberg laboratory for insightful discussions. We thank Sarah MacLean and the Sternberg laboratory members for comments on the manuscript. Some strains were provided by the Caenorhabditis Genetics Center (CGC), which is funded by the National Institutes of Science (NIH) Office of Research Infrastructure Programs (P40 OD010440). This work was supported by National Institutes of Heath grant (K99GM126137 to H.W., U24HG002223 to P.W.S., and R240D023041). The Millard and Muriel Jacobs Genetics and Genomics Laboratory at California Institute of Technology performed whole genome sequencing and RNA-sequencing. S.J.W. was supported by the Caltech Student Faculty Programs, the family of Laurence J. Stuppy, Samuel N. Vodopia, and Carol J. Hasson.\n\nAccepted Version - genetics.120.302923.full.pdf
Submitted - 817833.full.pdf
", "abstract": "To mitigate the deleterious effects of temperature increases on cellular organization and proteotoxicity, organisms have developed mechanisms to respond to heat stress. In eukaryotes, HSF1 is the master regulator of the heat shock transcriptional response, but the heat shock response pathway is not yet fully understood. From a forward genetic screen for suppressors of heat-shock-induced gene expression in Caenorhabditis elegans, we found a new allele of hsf-1 that alters its DNA-binding domain, and we found three additional alleles of sup-45, a previously molecularly uncharacterized genetic locus. We identified sup-45 as one of the two hitherto unknown C. elegans orthologs of the human AF4/FMR2 family proteins, which are involved in regulation of transcriptional elongation rate. We thus renamed sup-45 as affl-2 (AF4/FMR2-Like). Through RNA-seq, we demonstrated that affl-2 mutants are deficient in heat-shock-induced transcription. Additionally, affl-2 mutants have herniated intestines, while worms lacking its sole paralog (affl-1) appear wild type. AFFL-2 is a broadly expressed nuclear protein, and nuclear localization of AFFL-2 is necessary for its role in heat shock response. affl-2 and its paralog are not essential for proper HSF-1 expression and localization after heat shock, which suggests that affl-2 may function downstream of, or parallel to, hsf-1. Our characterization of affl-2 provides insights into the regulation of heat-shock-induced gene expression to protect against heat stress.", "date": "2020-08", "date_type": "published", "publication": "Genetics", "volume": "215", "number": "4", "publisher": "Genetics Society of America", "pagerange": "1039-1054", "id_number": "CaltechAUTHORS:20191028-093454817", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191028-093454817", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P40 OD010440" }, { "agency": "NIH", "grant_number": "K99GM126137" }, { "agency": "NIH", "grant_number": "U24HG002223" }, { "agency": "NIH", "grant_number": "R240D023041" }, { "agency": "Caltech" }, { "agency": "Laurence J. Stuppy" }, { "agency": "Samuel N. Vodopia" }, { "agency": "Carol J. Hasson" } ] }, "local_group": { "items": [ { "id": "Millard-and-Muriel-Jacobs-Genetics-and-Genomics-Laboratory" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1534/genetics.120.302923", "pmcid": "PMC7404228", "primary_object": { "basename": "817833.full.pdf", "url": "https://authors.library.caltech.edu/records/w5czb-tcf76/files/817833.full.pdf" }, "related_objects": [ { "basename": "genetics.120.302923.full.pdf", "url": "https://authors.library.caltech.edu/records/w5czb-tcf76/files/genetics.120.302923.full.pdf" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Walton, Sophie J.; Wang, Han; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/41xr7-92q84", "eprint_id": 99592, "eprint_status": "archive", "datestamp": "2023-08-22 05:39:29", "lastmod": "2023-12-22 23:44:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Quintero-Cadena-P", "name": { "family": "Quintero-Cadena", "given": "Porfirio" }, "orcid": "0000-0003-0067-5844" }, { "id": "Lenstra-T-L", "name": { "family": "Lenstra", "given": "Tineke L." }, "orcid": "0000-0002-4440-9962" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting", "ispublished": "pub", "full_text_status": "public", "keywords": "transcriptional bursting; RNA Pol II; CTD length; phase separation; transcription scaling", "note": "\u00a9 2020 Elsevier Inc. \n\nReceived 30 October 2019, Revised 9 April 2020, Accepted 19 May 2020, Available online 15 June 2020. \n\nWe thank Mitchell Guttman, Matt Thomson, and members of the Sternberg laboratory for helpful discussions; Heun J. Lee, Andres Collazo, and Giada Spigolon for imaging assistance; Igor Antoshechkin and Vijaya Kumar for RNA-seq experiments; and Steven Mcknight and Masato Kato for reagents. This work was supported by the Howard Hughes Medical Institute, with which P.W.S. was an investigator; the Gordon Ross Medical Foundation and Benjamin M. Rosen graduate fellowships; the Biological Imaging Center at the Caltech Beckman Institute; and the Millard and Muriel Jacobs Genetics and Genomics Laboratory. \n\nAuthor Contributions: Conceptualization, P.Q.-C. and P.W.S.; Methodology, P.Q.-C., P.W.S., and T.L.L.; Software, P.Q.-C.; Formal Analysis, P.Q.-C. and T.L.L.; Investigation, P.Q.-C.; Data Curation, P.Q.-C.; Writing \u2013 Original Draft, P.Q.-C. and P.W.S.; Writing \u2013 Review & Editing, P.Q.-C., P.W.S., and T.L.L.; Visualization, P.Q.-C.; Supervision, P.W.S.; Funding Acquisition, P.W.S. \n\nThe authors declare no competing interests.\n\nSubmitted - 825299.full.pdf
Supplemental Material - 1-s2.0-S1097276520303506-mmc1.pdf
Supplemental Material - 1-s2.0-S1097276520303506-mmc2.csv
", "abstract": "RNA polymerase II (RNA Pol II) contains a disordered C-terminal domain (CTD) whose length enigmatically correlates with genome size. The CTD is crucial to eukaryotic transcription, yet the functional and evolutionary relevance of this variation remains unclear. Here, we investigate how CTD length and disorder influence transcription. We find that length modulates the size and frequency of transcriptional bursting. Disorder is highly conserved and facilitates CTD-CTD interactions, an ability we show is separable from protein sequence and necessary for efficient transcription. We build a data-driven quantitative model, simulations of which recapitulate experiments and support that CTD length promotes initial polymerase recruitment to the promoter and slows down its release from it and that CTD-CTD interactions enable recruitment of multiple polymerases. Our results reveal how these parameters provide access to a range of transcriptional activity, offering a new perspective for the mechanistic significance of CTD length and disorder in transcription across eukaryotes.", "date": "2020-07-16", "date_type": "published", "publication": "Molecular Cell", "volume": "79", "number": "2", "publisher": "Elsevier", "pagerange": "207-220", "id_number": "CaltechAUTHORS:20191031-131636300", "issn": "1097-2765", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191031-131636300", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Gordon Ross Medical Foundation" }, { "agency": "Donna and Benjamin M. Rosen Bioengineering Center" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Millard and Muriel Jacobs Genetics and Genomics Laboratory" } ] }, "local_group": { "items": [ { "id": "Millard-and-Muriel-Jacobs-Genetics-and-Genomics-Laboratory" }, { "id": "Rosen-Bioengineering-Center" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.molcel.2020.05.030", "primary_object": { "basename": "825299.full.pdf", "url": "https://authors.library.caltech.edu/records/41xr7-92q84/files/825299.full.pdf" }, "related_objects": [ { "basename": "1-s2.0-S1097276520303506-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/41xr7-92q84/files/1-s2.0-S1097276520303506-mmc1.pdf" }, { "basename": "1-s2.0-S1097276520303506-mmc2.csv", "url": "https://authors.library.caltech.edu/records/41xr7-92q84/files/1-s2.0-S1097276520303506-mmc2.csv" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Quintero-Cadena, Porfirio; Lenstra, Tineke L.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/d9g6n-41x24", "eprint_id": 102718, "eprint_status": "archive", "datestamp": "2023-08-19 22:19:51", "lastmod": "2023-12-22 23:21:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Juan", "name": { "family": "Wang", "given": "Juan" } }, { "id": "Nikonorova-Inna-A", "name": { "family": "Nikonorova", "given": "Inna A." } }, { "id": "Gu-Amanda", "name": { "family": "Gu", "given": "Amanda" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Barr-Maureen-M", "name": { "family": "Barr", "given": "Maureen M." }, "orcid": "0000-0003-4483-2952" } ] }, "title": "Release and targeting of polycystin-2-carrying ciliary extracellular vesicles", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 Elsevier Inc. \n\nAvailable online 6 July 2020.\n\nAccepted Version - 2020.04.21.050690v2.full.pdf
Accepted Version - nihms-1639777.pdf
Supplemental Material - 1-s2.0-S0960982220307661-mmc1.pdf
", "abstract": "Extracellular vesicles (EVs) are emerging as a universal means of cell-to-cell communication and hold great potential in diagnostics and regenerative therapies [1]. An urgent need in the field is a fundamental understanding of physiological mechanisms driving EV generation and function. Ciliary EVs act as signaling devices in Chlamydomonas and Caenorhabditis elegans [2, 3, 4]. Mammalian cilia shed EVs to eliminate unwanted receptors [5] or to retract cilia before entering the cell cycle [6]. Here, we used our established C. elegans model to study sensory-evoked ciliary EV release and targeting using a fluorescently labeled EV cargo polycystin-2 (PKD-2). In C. elegans and mammals, the autosomal dominant polycystic kidney disease (ADPKD) gene products polycystin-1 and polycystin-2 localize to cilia and EVs, act in the same genetic pathway, and function in a sensory capacity, suggesting ancient conservation [7]. We find that males deposit PKD-2-carrying EVs onto the vulva of the hermaphrodite during mating. We also show that mechanical stimulation triggers release of PKD-2-carrying EVs from cilia. To our knowledge, this is the first report of mechanoresponsive ciliary EV release and of the directional transfer of ciliary EVs from one animal to another animal. Since the polycystins are evolutionarily conserved ciliary EV cargoes, our findings suggest that similar mechanisms for EV release and targeting may occur in other systems and biological contexts.", "date": "2020-07-06", "date_type": "published", "publication": "Current Biology", "volume": "30", "number": "13", "publisher": "Cell Press", "pagerange": "R755-R756", "id_number": "CaltechAUTHORS:20200422-121506214", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200422-121506214", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P30 DK106912" }, { "agency": "NIH", "grant_number": "DK059418" }, { "agency": "NIH", "grant_number": "DK116606" }, { "agency": "NIH", "grant_number": "P40OD010440" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.cub.2020.05.079", "pmcid": "PMC7668157", "primary_object": { "basename": "1-s2.0-S0960982220307661-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/d9g6n-41x24/files/1-s2.0-S0960982220307661-mmc1.pdf" }, "related_objects": [ { "basename": "2020.04.21.050690v2.full.pdf", "url": "https://authors.library.caltech.edu/records/d9g6n-41x24/files/2020.04.21.050690v2.full.pdf" }, { "basename": "nihms-1639777.pdf", "url": "https://authors.library.caltech.edu/records/d9g6n-41x24/files/nihms-1639777.pdf" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Wang, Juan; Nikonorova, Inna A.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/3fa5v-gdq14", "eprint_id": 104002, "eprint_status": "archive", "datestamp": "2023-08-19 21:55:56", "lastmod": "2023-12-22 23:12:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kishore-R", "name": { "family": "Kishore", "given": "Ranjana" } }, { "id": "Arnaboldi-V", "name": { "family": "Arnaboldi", "given": "Valerio" }, "orcid": "0000-0002-2563-5374" }, { "id": "Van-Slyke-C-E", "name": { "family": "Van Slyke", "given": "Ceri E." }, "orcid": "0000-0002-2244-7917" }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "Nash-R-S", "name": { "family": "Nash", "given": "Robert S." } }, { "id": "Urbano-Jose-M", "name": { "family": "Urbano", "given": "Jose M." } }, { "id": "Dolan-M-E", "name": { "family": "Dolan", "given": "Mary E." }, "orcid": "0000-0001-7732-3295" }, { "id": "Engel-S-R", "name": { "family": "Engel", "given": "Stacia R." }, "orcid": "0000-0001-5472-917X" }, { "id": "Shimoyama-Mary", "name": { "family": "Shimoyama", "given": "Mary" }, "orcid": "0000-0003-1176-0796" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Automated generation of gene summaries at the Alliance of Genome Resources", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2020. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived 14 February 2020; Revised 6 April 2020; Accepted 29 April 2020. \n\nWe thank Daniela Raciti, Constance M. Smith, Doug G. Howe and Sian Gramates for their suggestions for generating gene expression summaries. We thank Susan M. Bello, Yvonne M. Bradford and Jennifer Smith for their help in generating disease relevance summaries. We also thank Kimberly Van Auken, Peter D'Eustachio, Yvonne Bradford, Nomi Harris and Chris Mungall for discussions related to the project and for comments and suggestions on the manuscript. Special thanks to all the Alliance developers and technical staff for helping integrate the gene summaries software into the Alliance portal.\n\nFunding: National Institutes of Health/National Human Genome Research Institute grant (U24HG002223-19S1, 1U24HG010859); National Institutes of Health/National Human Genome Research Institute grants (P41HG002659 (ZFIN), U24HG002223 (WB), U41HG000739 (FB), U41HG001315 (SGD), HG000330 (MGD), U41HG002273 (GOC)); National Institutes of Health/National Heart, Lung and Blood Institute (HL64541 to R.G.D.); Medical Research Council-UK (MR/L001020/1 (WB)). Funding for open access charge: National Institutes of Health/National Human Genome Research Institute grant (1U24HG010859-01).\n\nPublished - baaa037.pdf
", "abstract": "Short paragraphs that describe gene function, referred to as gene summaries, are valued by users of biological knowledgebases for the ease with which they convey key aspects of gene function. Manual curation of gene summaries, while desirable, is difficult for knowledgebases to sustain. We developed an algorithm that uses curated, structured gene data at the Alliance of Genome Resources (Alliance; www.alliancegenome.org) to automatically generate gene summaries that simulate natural language. The gene data used for this purpose include curated associations (annotations) to ontology terms from the Gene Ontology, Disease Ontology, model organism knowledgebase (MOK)-specific anatomy ontologies and Alliance orthology data. The method uses sentence templates for each data category included in the gene summary in order to build a natural language sentence from the list of terms associated with each gene. To improve readability of the summaries when numerous gene annotations are present, we developed a new algorithm that traverses ontology graphs in order to group terms by their common ancestors. The algorithm optimizes the coverage of the initial set of terms and limits the length of the final summary, using measures of information content of each ontology term as a criterion for inclusion in the summary. The automated gene summaries are generated with each Alliance release, ensuring that they reflect current data at the Alliance. Our method effectively leverages category-specific curation efforts of the Alliance member databases to create modular, structured and standardized gene summaries for seven member species of the Alliance. These automatically generated gene summaries make cross-species gene function comparisons tenable and increase discoverability of potential models of human disease. In addition to being displayed on Alliance gene pages, these summaries are also included on several MOK gene pages.", "date": "2020-06-19", "date_type": "published", "publication": "Database : The Journal of Biological Databases and Curation", "volume": "2020", "publisher": "Oxford University Press", "pagerange": "Art. No. baaa037", "id_number": "CaltechAUTHORS:20200624-104212433", "issn": "1758-0463", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200624-104212433", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U24HG002223-19S1" }, { "agency": "NIH", "grant_number": "U24HG010859" }, { "agency": "NIH", "grant_number": "P41HG002659" }, { "agency": "NIH", "grant_number": "U41HG000739" }, { "agency": "NIH", "grant_number": "U41HG001315" }, { "agency": "NIH", "grant_number": "HG000330" }, { "agency": "NIH", "grant_number": "U41HG002273" }, { "agency": "NIH", "grant_number": "HL64541" }, { "agency": "Medical Research Council (UK)", "grant_number": "MR/L001020/1" }, { "agency": "NIH", "grant_number": "1U24HG010859-01" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "corp_creators": { "items": [ "Alliance of Genome Resources Consortium" ] }, "doi": "10.1093/database/baaa037", "pmcid": "PMC7304461", "primary_object": { "basename": "baaa037.pdf", "url": "https://authors.library.caltech.edu/records/3fa5v-gdq14/files/baaa037.pdf" }, "resource_type": "article", "pub_year": "2020", "author_list": "Kishore, Ranjana; Arnaboldi, Valerio; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/hrqf2-ypr42", "eprint_id": 99947, "eprint_status": "archive", "datestamp": "2023-08-19 21:46:52", "lastmod": "2023-12-22 23:21:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bai-Xiaofei", "name": { "family": "Bai", "given": "Xiaofei" }, "orcid": "0000-0001-8179-8162" }, { "id": "Bouffard-J", "name": { "family": "Bouffard", "given": "Jeff" } }, { "id": "Lord-Avery", "name": { "family": "Lord", "given": "Avery" } }, { "id": "Brugman-K-I", "name": { "family": "Brugman", "given": "Katherine" }, "orcid": "0000-0003-2625-2903" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Cram-E-J", "name": { "family": "Cram", "given": "Erin J." }, "orcid": "0000-0002-8129-1326" }, { "id": "Golden-A", "name": { "family": "Golden", "given": "Andy" }, "orcid": "0000-0002-8599-2031" } ] }, "title": "Caenorhabditis elegans PIEZO Channel Coordinates Multiple Reproductive Tissues to Govern Ovulation", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 eLife Sciences Publications Ltd. This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. \n\nReceived: 14 November 2019; Accepted: 02 June 2020; Published: 03 June 2020. \n\nWe thank the Caenorhabditis Genetics Center, which is funded by the National Institutes of Health Office of Research Infrastructure Programs (P40OD010440), for providing strains for this study. We thank Dr Orna Cohen-Fix for generously sharing the SP-12::GFP strain, and Dr Harold Smith for sharing the BA17 fem-1(hc17ts) strain. We also thank Dr David Greenstein for sharing fluorescein-tagged MSP and discussion about mating assays. We are grateful to the members of the Golden laboratory, Dr Peter Kropp, Dr Tao Cai, Rosie Bauer, Isabella Zafra, and Carina Graham for productive discussions and preparing reagents. We thank our summer intern Kyle Wilson for manuscript editing. We especially thank Dr Harold Smith, Dr Orna Cohen-Fix, Dr Kevin O'Connell, Dr Katherine McJunkin and Dan Konzman for critical inputs on the project and feedback on the manuscript. We thank all members of the Baltimore Worm Club for providing feedback and suggestions to our investigations. \n\nFunding: National Institute of General Medical Sciences (GM110268) - Erin J Cram; National Institute of Neurological Disorders and Stroke (R01 NS113119) - Paul W Sternberg; NIH Clinical Center (R24 0D023041) - Paul W Sternberg. \n\nThe funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.\n\nAuthor contributions: Xiaofei Bai, Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Writing - original draft; Jeff Bouffard, Data curation, Formal analysis, Investigation, Methodology; Avery Lord, Data curation, Investigation; Katherine Brugman, Formal analysis, Methodology; Paul W Sternberg, Conceptualization, Supervision, Funding acquisition; Erin J Cram, Conceptualization, Resources, Supervision, Funding acquisition, Investigation, Methodology, Writing - review and editing; Andy Golden, Conceptualization, Supervision, Methodology, Writing - review and editing. \n\nData availability: All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for all Figures and figure supplements.\n\nPublished - elife-53603-v3.pdf
Submitted - 847392.full.pdf
Supplemental Material - elife-53603-supp-v2.zip
Supplemental Material - elife-53603-transrepform-v3.docx
", "abstract": "PIEZO1 and PIEZO2 are newly identified mechanosensitive ion channels that exhibit a preference for calcium in response to mechanical stimuli. In this study, we discovered the vital roles of pezo-1, the sole PIEZO ortholog in Caenorhabditiselegans, in regulating reproduction. A number of deletion alleles, as well as a putative gain-of-function mutant, of PEZO-1 caused a severe reduction in brood size. In vivo observations showed that oocytes undergo a variety of transit defects as they enter and exit the spermatheca during ovulation. Post-ovulation oocytes were frequently damaged during spermathecal contraction. However, the calcium signaling was not dramatically changed in the pezo-1 mutants during ovulation. Loss of PEZO-1 also led to an inability of self-sperm to navigate back to the spermatheca properly after being pushed out of the spermatheca during ovulation. These findings suggest that PEZO-1 acts in different reproductive tissues to promote proper ovulation and fertilization in C. elegans.", "date": "2020-06-03", "date_type": "published", "publication": "eLife", "volume": "9", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e53603", "id_number": "CaltechAUTHORS:20191120-090302713", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191120-090302713", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM110268" }, { "agency": "NIH", "grant_number": "R01 NS113119" }, { "agency": "NIH", "grant_number": "R24 0D023041" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.7554/eLife.53603", "primary_object": { "basename": "847392.full.pdf", "url": "https://authors.library.caltech.edu/records/hrqf2-ypr42/files/847392.full.pdf" }, "related_objects": [ { "basename": "elife-53603-supp-v2.zip", "url": "https://authors.library.caltech.edu/records/hrqf2-ypr42/files/elife-53603-supp-v2.zip" }, { "basename": "elife-53603-transrepform-v3.docx", "url": "https://authors.library.caltech.edu/records/hrqf2-ypr42/files/elife-53603-transrepform-v3.docx" }, { "basename": "elife-53603-v3.pdf", "url": "https://authors.library.caltech.edu/records/hrqf2-ypr42/files/elife-53603-v3.pdf" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Bai, Xiaofei; Bouffard, Jeff; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/yp06p-0by08", "eprint_id": 103989, "eprint_status": "archive", "datestamp": "2023-08-19 21:31:40", "lastmod": "2023-12-22 23:21:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cho-Jaehyoung", "name": { "family": "Cho", "given": "Jaehyoung" } }, { "id": "Gao-Sibyl", "name": { "family": "Gao", "given": "Sibyl" } }, { "id": "Stein-L-D", "name": { "family": "Stein", "given": "Lincoln" }, "orcid": "0000-0002-1983-4588" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Vennter \u2013 An interactive analysis tool for WormBase interaction data using Venn diagrams", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.\n\nReceived: April 28, 2020; Revision received: May 19, 2020; Accepted: May 19, 2020; Published: May 25, 2020.\n\nReagents: All the interactions data are available at the WormBase FTP site\n(ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/species/c_elegans/PRJNA13758/annotation/c_elegans.PRJNA13758.WS###.interactions.txt.gz, where WS### is the database version release, like \"WS275\"). \n\nAt the time of writing, the source code for Vennter is part of the WormBase website source code. The WS276.1 version of the source code is available at the GitHub depository (https://github.com/WormBase/website-public/releases/tag/WS276.1). \n\nThis work was supported by U24-HG002223 to PWS. \n\nAuthor Contributions: \nJaehyoung Cho: Conceptualization, Investigation, Data curation, Visualization, Writing - original draft, Writing - review and editing\nSibyl Gao: Investigation, Methodology, Visualization, Writing - review and editing\nLincoln Stein: Investigation, Writing - review and editing\nPaul W Sternberg: Conceptualization, Investigation, Writing - review and editing, Funding acquisition, Project administration, Supervision. \n\nReviewed By: Sander van den Heuvel.\n\nPublished - 10.17912\uf022micropub.biology.000258.pdf
", "abstract": "WormBase curates four different types of gene-to-gene interaction data: genetic, regulatory, physical, and predicted. These data are found in the Interactions widget in each gene page. Aside from the predicted interactions, the other three types are curated with direct experimental evidence from the literature. In WormBase, genetic interaction data is defined as a phenotypic deviation of double mutants (or any other genetic perturbations) from single mutant phenotypes and the control phenotype. Regulatory interactions are defined by how perturbation of one gene or gene product affects the expression of another gene or the localization of its gene product. Physical interactions represent molecular associations between genes and gene products from C. elegans (Grove et al. 2018). Each type of interaction data is essential to understanding certain aspects of the biological process mediated by the two interacting genes. However, integrating information from these three types of interaction data is critical to reading the biological context. Understanding the logical relations between different types of interaction data provides a vital clue on how to tackle a gene-to-gene interaction within this context. To achieve this goal, we introduce a new tool for analyzing these logical relations among the interaction data using a Venn diagram, named Vennter (Venn diagram for interaction). Venn diagrams are very useful for displaying similarities and distinctions between different data sets of interest, especially when they are area-proportional to the amount of information presented.\nVennter consists of three circles, each representing one of the three different interaction data types. The size of any area within the interactive Venn diagram corresponds to the number of unique interactor genes pertaining to that region. Figure 1A shows an example of a Vennter diagram for selected genes (daf-2, daf-15, daf-16, and let-363) which play key roles in the Insulin/IGF-1 and TOR-dependent signaling pathway. These results exhibit distinct patterns of overlap among their interaction data. In some cases, the differences might reflect differences in prior scientific approaches to studying these genes as well as the availability of annotated interaction data in WormBase.\nVennter is fully interactive for analyzing interactor genes from different sets of interaction data. By clicking on any single or multiple area in combination, one can easily obtain all gene names corresponding to the selected area (represented by hashed lines) in Vennter. The number of selected genes is shown next to the 'View selected genes' button (see arrows). From there, one can open a popup window called 'Browse gene set' which contains a comprehensive list of interactor genes shown in alphabetic order. This list can be copied or downloaded in diverse formats, and for the user's convenience, each gene name is linked to its unique WormBase gene page. Under the same 'Browse gene set' window, Vennter also offers other functions for further analysis of selected genes, such as direct links to the batch analysis tools 'SimpleMine' and 'Gene-set Enrichment Analysis' (Figure 1B) which can help to query the gene list more conveniently and efficiently.\nTo demonstrate yet another aspect of Vennter, we can look at the high-throughput physical protein-protein interaction data, which comprise long lists of genes. To date, WormBase has curated 86.9% of physical protein-protein interaction data from these high-throughput studies (Cho et al. 2018). However, identifying the functional relevance of such large amounts of interacting gene candidates can often be quite challenging to researchers. To improve this, Vennter provides more organized and relevant information to researchers by evaluating overlapping information between physical, genetic, and/or regulatory interactions, which enables researchers to more easily measure the confidence and biological relevance of their gene candidates of interest.\nFor the C. elegans research community, Vennter can help compare and integrate the different types of interaction data available. It also provides hyperlinks to other useful WormBase tools in order to analyze the gene interactor list in a more efficient and automated manner.", "date": "2020-05-25", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "micropub.biology.000258", "id_number": "CaltechAUTHORS:20200624-094841002", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200624-094841002", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U24-HG002223" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.17912/micropub.biology.000258", "pmcid": "PMC7251783", "primary_object": { "basename": "10.17912\uf022micropub.biology.000258.pdf", "url": "https://authors.library.caltech.edu/records/yp06p-0by08/files/10.17912\uf022micropub.biology.000258.pdf" }, "resource_type": "article", "pub_year": "2020", "author_list": "Cho, Jaehyoung; Gao, Sibyl; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/6vcw6-hvw39", "eprint_id": 103265, "eprint_status": "archive", "datestamp": "2023-08-22 05:04:53", "lastmod": "2023-12-22 23:21:41", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Campos-T-L", "name": { "family": "Campos", "given": "Tulio L." } }, { "id": "Korhonen-P-K", "name": { "family": "Korhonen", "given": "Pasi K." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } } ] }, "title": "Predicting gene essentiality in Caenorhabditis elegans by feature engineering and machine-learning", "ispublished": "pub", "full_text_status": "public", "keywords": "Caenorhabditis elegans; Machine-learning; Essential genes; Essentiality predictions", "note": "\u00a9 2020 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). \n\nReceived 23 March 2020, Revised 1 May 2020, Accepted 6 May 2020, Available online 15 May 2020. \n\nThis research was funded by grants from the National Health and Medical Research Council (NHMRC) of Australia and the Australian Research Council (ARC) to RBG, PKK and/or NDY. Other support to RBG was from the Melbourne Water. NDY was supported by a Career Development Fellowship, and PKK by an Early Career Research Fellowship from NHMRC. TLC was a recipient of a Research Training Program Scholarship from the Australian Government and is also supported by the Oswaldo Cruz Foundation (Fiocruz/Brazil). PWS was supported by U.S. National Institutes of Health grant U24-HG002223. \n\nCRediT authorship contribution statement: Tulio L. Campos: Conceptualization, Methodology, Software, Validation, Data curation, Writing - original draft, Visualization, Investigation, Writing - review & editing. Pasi K. Korhonen: Conceptualization, Supervision, Software, Validation, Visualization, Investigation, Writing - review & editing. Paul W. Sternberg: Visualization, Investigation, Writing - review & editing. Robin B. Gasser: Conceptualization, Supervision, Visualization, Investigation, Writing - review & editing. Neil D. Young: Conceptualization, Supervision, Visualization, Investigation, Writing - review & editing. \n\nThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. \n\nData and code availability: The data used herein, the code developed to perform the systematic ML approaches as well as information regarding software versions and attached libraries are available at: https://bitbucket.org/tuliocampos/essential_elegans. A static version linked to this publication is available at: https://doi.org/10.6084/m9.figshare.11533101.\n\nPublished - 1-s2.0-S2001037020302713-main.pdf
Supplemental Material - 1-s2.0-S2001037020302713-mmc1.zip
", "abstract": "Defining genes that are essential for life has major implications for understanding critical biological processes and mechanisms. Although essential genes have been identified and characterised experimentally using functional genomic tools, it is challenging to predict with confidence such genes from molecular and phenomic data sets using computational methods. Using extensive data sets available for the model organism Caenorhabditis elegans, we constructed here a machine-learning (ML)-based workflow for the prediction of essential genes on a genome-wide scale. We identified strong predictors for such genes and showed that trained ML models consistently achieve highly-accurate classifications. Complementary analyses revealed an association between essential genes and chromosomal location. Our findings reveal that essential genes in C. elegans tend to be located in or near the centre of autosomal chromosomes; are positively correlated with low single nucleotide polymorphim (SNP) densities and epigenetic markers in promoter regions; are involved in protein and nucleotide processing; are transcribed in most cells; are enriched in reproductive tissues or are targets for small RNAs bound to the argonaut CSR-1. Based on these results, we hypothesise an interplay between epigenetic markers and small RNA pathways in the germline, with transcription-based memory; this hypothesis warrants testing. From a technical perspective, further work is needed to evaluate whether the present ML-based approach will be applicable to other metazoans (including Drosophila melanogaster) for which comprehensive data set (i.e. genomic, transcriptomic, proteomic, variomic, epigenetic and phenomic) are available.", "date": "2020-05-15", "date_type": "published", "publication": "Computational and Structural Biotechnology Journal", "volume": "18", "publisher": "Elsevier", "pagerange": "1093-1102", "id_number": "CaltechAUTHORS:20200518-091100663", "issn": "2001-0370", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200518-091100663", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Health and Medical Research Council (NHMRC)" }, { "agency": "Australian Research Council" }, { "agency": "Melbourne Water" }, { "agency": "Funda\u00e7\u00e3o Oswaldo Cruz" }, { "agency": "NIH", "grant_number": "U24-HG002223" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.csbj.2020.05.008", "primary_object": { "basename": "1-s2.0-S2001037020302713-main.pdf", "url": "https://authors.library.caltech.edu/records/6vcw6-hvw39/files/1-s2.0-S2001037020302713-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S2001037020302713-mmc1.zip", "url": "https://authors.library.caltech.edu/records/6vcw6-hvw39/files/1-s2.0-S2001037020302713-mmc1.zip" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Campos, Tulio L.; Korhonen, Pasi K.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/t6xph-rw787", "eprint_id": 102036, "eprint_status": "archive", "datestamp": "2023-08-19 20:35:34", "lastmod": "2023-12-22 23:21:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Arnaboldi-Valerio", "name": { "family": "Arnaboldi", "given": "Valerio" }, "orcid": "0000-0002-2563-5374" }, { "id": "Raciti-Daniela", "name": { "family": "Raciti", "given": "Daniela" } }, { "id": "Van-Auken-Kimberly", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Chan-Juancarlos-N", "name": { "family": "Chan", "given": "Juancarlos N." } }, { "id": "M\u00fcller-Hans-Michael", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2020. Published by Oxford University Press.\nThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived 29 October 2019; Revised 8 January 2020; Accepted 14 January 2020. Published: 17 March 2020. \n\nWe would particularly like to thank all authors who participated in testing and all WB curators who helped validate author submissions. We also thank Gary Ruvkun for the permission to use his name in Figure 3. \n\nFunding: National Institutes of Health/National Human Genome Research Institute grants [U24HG002223 (WormBase) and U24HG010859 (Alliance Central)]. \n\nAuthor Notes: Valerio Arnaboldi, Daniela Raciti and Kimberly Van Auken contributed equally. \n\nThe authors declare that they have no conflict of interest.\n\nPublished - baaa006.pdf
Supplemental Material - s1_baaa006.jpeg
", "abstract": "Biological knowledgebases rely on expert biocuration of the research literature to maintain up-to-date collections of data organized in machine-readable form. To enter information into knowledgebases, curators need to follow three steps: (i) identify papers containing relevant data, a process called triaging; (ii) recognize named entities; and (iii) extract and curate data in accordance with the underlying data models. WormBase (WB), the authoritative repository for research data on Caenorhabditis elegans and other nematodes, uses text mining (TM) to semi-automate its curation pipeline. In addition, WB engages its community, via an Author First Pass (AFP) system, to help recognize entities and classify data types in their recently published papers. In this paper, we present a new WB AFP system that combines TM and AFP into a single application to enhance community curation. The system employs string-searching algorithms and statistical methods (e.g. support vector machines (SVMs)) to extract biological entities and classify data types, and it presents the results to authors in a web form where they validate the extracted information, rather than enter it de novo as the previous form required. With this new system, we lessen the burden for authors, while at the same time receive valuable feedback on the performance of our TM tools. The new user interface also links out to specific structured data submission forms, e.g. for phenotype or expression pattern data, giving the authors the opportunity to contribute a more detailed curation that can be incorporated into WB with minimal curator review. Our approach is generalizable and could be applied to additional knowledgebases that would like to engage their user community in assisting with the curation. In the five months succeeding the launch of the new system, the response rate has been comparable with that of the previous AFP version, but the quality and quantity of the data received has greatly improved.", "date": "2020-03-17", "date_type": "published", "publication": "Database : The Journal of Biological Databases and Curation", "volume": "2020", "publisher": "Oxford University Press", "pagerange": "Art. No. baaa006", "id_number": "CaltechAUTHORS:20200323-075540460", "issn": "1758-0463", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200323-075540460", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U24HG002223" }, { "agency": "NIH", "grant_number": "U24HG010859" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/database/baaa006", "pmcid": "PMC7078066", "primary_object": { "basename": "baaa006.pdf", "url": "https://authors.library.caltech.edu/records/t6xph-rw787/files/baaa006.pdf" }, "related_objects": [ { "basename": "s1_baaa006.jpeg", "url": "https://authors.library.caltech.edu/records/t6xph-rw787/files/s1_baaa006.jpeg" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Arnaboldi, Valerio; Raciti, Daniela; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/p9ef8-rt585", "eprint_id": 101045, "eprint_status": "archive", "datestamp": "2023-08-19 19:41:59", "lastmod": "2024-01-14 22:05:56", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ma-Guangxu", "name": { "family": "Ma", "given": "Guangxu" } }, { "id": "Wang-Tao", "name": { "family": "Wang", "given": "Tao" } }, { "id": "Korhonen-P-K", "name": { "family": "Korhonen", "given": "Pasi K." } }, { "id": "Hofmann-A", "name": { "family": "Hofmann", "given": "Andreas" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "Elucidating the molecular and developmental biology of parasitic nematodes: Moving to a multiomics paradigm", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2020 Elsevier Ltd. \n\nAvailable online 31 January 2020.", "abstract": "In the past two decades, significant progress has been made in the sequencing, assembly, annotation and analyses of genomes and transcriptomes of parasitic worms of socioeconomic importance. This progress has somewhat improved our knowledge and understanding of these pathogens at the molecular level. However, compared with the free-living nematode Caenorhabditis elegans, the areas of functional genomics, transcriptomics, proteomics and metabolomics of parasitic nematodes are still in their infancy, and there are major gaps in our knowledge and understanding of the molecular biology of parasitic nematodes. The information on signalling molecules, molecular pathways and microRNAs (miRNAs) that are known to be involved in developmental processes in C. elegans and the availability of some molecular resources (draft genomes, transcriptomes and some proteomes) for selected parasitic nematodes provide a basis to start exploring the developmental biology of parasitic nematodes. Indeed, some studies have identified molecules and pathways that might associate with developmental processes in related, parasitic nematodes, such as Haemonchus contortus (barber's pole worm). However, detailed information is often scant and 'omics resources are limited, preventing a proper integration of 'omic data sets and comprehensive analyses. Moreover, little is known about the functional roles of pheromones, hormones, signalling pathways and post-transcriptional/post-translational regulations in the development of key parasitic nematodes throughout their entire life cycles.\n\nAlthough C. elegans is an excellent model to assist molecular studies of parasitic nematodes, its use is limited when it comes to explorations of processes that are specific to parasitism within host animals. A deep understanding of parasitic nematodes, such as H. contortus, requires substantially enhanced resources and the use of integrative 'omics approaches for analyses. The improved genome and well-established in vitro larval culture system for H. contortus provide unprecedented opportunities for comprehensive studies of the transcriptomes (mRNA and miRNA), proteomes (somatic, excretory/secretory and phosphorylated proteins) and lipidomes (e.g., polar and neutral lipids) of this nematode. Such resources should enable in-depth explorations of its developmental biology at a level, not previously possible.\n\nThe main aims of this review are (i) to provide a background on the development of nematodes, with a particular emphasis on the molecular aspects involved in the dauer formation and exit in C. elegans; (ii) to critically appraise the current state of knowledge of the developmental biology of parasitic nematodes and identify key knowledge gaps; (iii) to cover salient aspects of H. contortus, with a focus on the recent advances in genomics, transcriptomics, proteomics and lipidomics as well as in vitro culturing systems; (iv) to review recent advances in our knowledge and understanding of the molecular and developmental biology of H. contortus using an integrative multiomics approach, and discuss the implications of this approach for detailed explorations of signalling molecules, molecular processes and pathways likely associated with nematode development, adaptation and parasitism, and for the identification of novel intervention targets against these pathogens. Clearly, the multiomics approach established recently is readily applicable to exploring a wide range of interesting and socioeconomically significant parasitic worms (including also trematodes and cestodes) at the molecular level, and to elucidate host\u2013parasite interactions and disease processes.", "date": "2020-01-31", "date_type": "published", "publisher": "Academic Press", "place_of_pub": "London", "pagerange": "175-229", "id_number": "CaltechAUTHORS:20200131-155314220", "isbn": "978-0-12-820750-5", "book_title": "Giardia and Giardiasis, Part A", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200131-155314220", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "contributors": { "items": [ { "id": "Ortega-Pierres-G", "name": { "family": "Ortega-Pierres", "given": "Guadalupe" } } ] }, "doi": "10.1016/bs.apar.2019.12.005", "resource_type": "book_section", "pub_year": "2020", "author_list": "Ma, Guangxu; Wang, Tao; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/jskmd-kqf35", "eprint_id": 102491, "eprint_status": "archive", "datestamp": "2023-08-19 19:31:47", "lastmod": "2023-12-22 23:21:57", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Agapite-J", "name": { "family": "Agapite", "given": "Julie" } }, { "name": { "family": "Albou", "given": "Laurent-Philippe" } }, { "name": { "family": "Aleksander", "given": "Suzi" } }, { "name": { "family": "Argasinska", "given": "Joanna" } }, { "name": { "family": "Arnaboldi", "given": "Valerio" } }, { "name": { "family": "Attrill", "given": "Helen" } }, { "name": { "family": "Bello", "given": "Susan M." } }, { "name": { "family": "Blake", "given": "Judith A." } }, { "name": { "family": "Blodgett", "given": "Olin" } }, { "name": { "family": "Bradford", "given": "Yvonne M." } }, { "name": { "family": "Bult", "given": "Carol J." } }, { "name": { "family": "Cain", "given": "Scott" } }, { "name": { "family": "Calvi", "given": "Brian R." } }, { "name": { "family": "Carbon", "given": "Seth" } }, { "name": { "family": "Chan", "given": "Juancarlos" } }, { "name": { "family": "Chen", "given": "Wen J." } }, { "name": { "family": "Cherry", "given": "J. Michael" } }, { "name": { "family": "Cho", "given": "Jaehyoung" } }, { "name": { "family": "Christie", "given": "Karen R." } }, { "name": { "family": "Crosby", "given": "Madeline A." } }, { "name": { "family": "De Pons", "given": "Jeff" } }, { "name": { "family": "Dolan", "given": "Mary E" } }, { "name": { "family": "dos Santos", "given": "Gilberto" } }, { "name": { "family": "Dunn", "given": "Barbara" } }, { "name": { "family": "Dunn", "given": "Nathan" } }, { "name": { "family": "Eagle", "given": "Anne" } }, { "name": { "family": "Ebert", "given": "Dustin" } }, { "name": { "family": "Engel", "given": "Stacia R." }, "orcid": "0000-0001-5472-917X" }, { "name": { "family": "Fashena", "given": "David" } }, { "name": { "family": "Frazer", "given": "Ken" } }, { "name": { "family": "Gao", "given": "Sibyl" } }, { "name": { "family": "Gondwe", "given": "Felix" } }, { "name": { "family": "Goodman", "given": "Josh" } }, { "name": { "family": "Gramates", "given": "L. Sian" } }, { "name": { "family": "Grove", "given": "Christian A." }, "orcid": "0000-0001-9076-6015" }, { "name": { "family": "Harris", "given": "Todd" } }, { "name": { "family": "Harrison", "given": "Marie-Claire" } }, { "name": { "family": "Howe", "given": "Douglas G." } }, { "name": { "family": "Howe", "given": "Kevin L." } }, { "name": { "family": "Jha", "given": "Sagar" } }, { "name": { "family": "Kadin", "given": "James A." } }, { "name": { "family": "Kaufman", "given": "Thomas C." } }, { "name": { "family": "Kalita", "given": "Patrick" } }, { "name": { "family": "Karra", "given": "Kalpana" } }, { "name": { "family": "Kishore", "given": "Ranjana" } }, { "name": { "family": "Laulederkind", "given": "Stan" } }, { "name": { "family": "Lee", "given": "Raymond" } }, { "name": { "family": "MacPherson", "given": "Kevin A." } }, { "name": { "family": "Marygold", "given": "Steven J." } }, { "name": { "family": "Matthews", "given": "Beverley" } }, { "name": { "family": "Millburn", "given": "Gillian" } }, { "name": { "family": "Miyasato", "given": "Stuart" } }, { "name": { "family": "Moxon", "given": "Sierra" } }, { "name": { "family": "Mueller", "given": "Hans-Michael" } }, { "name": { "family": "Mungall", "given": "Christopher" } }, { "name": { "family": "Muruganujan", "given": "Anushya" } }, { "name": { "family": "Mushayahama", "given": "Tremayne" } }, { "name": { "family": "Nash", "given": "Robert S." } }, { "name": { "family": "Ng", "given": "Patrick" } }, { "name": { "family": "Paulini", "given": "Michael" } }, { "name": { "family": "Perrimon", "given": "Norbert" } }, { "name": { "family": "Pich", "given": "Christian" } }, { "name": { "family": "Raciti", "given": "Daniela" } }, { "name": { "family": "Richardson", "given": "Joel E." } }, { "name": { "family": "Russell", "given": "Matthew" } }, { "name": { "family": "Russo Gelbart", "given": "Susan" } }, { "name": { "family": "Ruzicka", "given": "Leyla" } }, { "name": { "family": "Schaper", "given": "Kevin" } }, { "name": { "family": "Shimoyama", "given": "Mary" } }, { "name": { "family": "Simison", "given": "Matt" } }, { "name": { "family": "Smith", "given": "Cynthia" } }, { "name": { "family": "Shaw", "given": "David R." } }, { "name": { "family": "Shrivatsav", "given": "Ajay" } }, { "name": { "family": "Skrzypek", "given": "Marek" } }, { "name": { "family": "Smith", "given": "Jennifer R." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "name": { "family": "Tabone", "given": "Christopher J." } }, { "name": { "family": "Thomas", "given": "Paul D." }, "orcid": "0000-0002-9074-3507" }, { "name": { "family": "Thota", "given": "Jyothi" } }, { "name": { "family": "Toro", "given": "Sabrina" } }, { "name": { "family": "Tomczuk", "given": "Monika" } }, { "name": { "family": "Tutaj", "given": "Marek" } }, { "name": { "family": "Tutaj", "given": "Monika" } }, { "name": { "family": "Urbano", "given": "Jose-Maria" } }, { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "name": { "family": "Van Slyke", "given": "Ceri E." } }, { "name": { "family": "Wang", "given": "Shur-Jen" } }, { "name": { "family": "Weng", "given": "Shuai" } }, { "name": { "family": "Westerfield", "given": "Monte" } }, { "name": { "family": "Williams", "given": "Gary" } }, { "name": { "family": "Wong", "given": "Edith D." } }, { "name": { "family": "Wright", "given": "Adam" } }, { "name": { "family": "Yook", "given": "Karen" } } ] }, "title": "Alliance of Genome Resources Portal: unified model organism research platform", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived: 31 July 2019; Revision received: 03 September 2019; Accepted: 19 September 2019; Published: 25 September 2019. \n\nThe Alliance platform is designed and implemented by a core group of developers and curators at SGD, WormBase, ZFIN, RGD, MGD, FlyBase and the GOC. We would particularly like to acknowledge other staff at those projects who continue to provide gold-standard curation of model organism data without which the work described here would not be possible. \n\nFunding: National Institutes of Health/National Human Genome Research Institute grant [U24HG002223-19S1]; National Institutes of Health/National Human Genome Research Institute grants [P41HG002659 (ZFIN), U24HG002223 (WormBase), U41HG000739 (FlyBase), U41HG001315 (SGD), HG000330 (MGD), U41HG002273] (GOC, which also provides funding to W.B., M.G.D., S.G.D.); National Institutes of Health/National Heart, Lung and Blood Institute [HL64541 to R.G.D.]; Medical Research Council-UK [MR/L001020/1 (WormBase)]. Funding for open access charge: National Institutes of Health/National Human Genome Research Institute grant [1U24HG010859-01]. \n\nConflict of interest statement. None declared.\n\nPublished - gkz813.pdf
", "abstract": "The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human and well-studied model organisms by providing a highly integrated and comprehensive platform that enables researchers to leverage the extensive body of genetic and genomic studies in these organisms. Initiated in 2016, the Alliance is building a central portal (www.alliancegenome.org) for access to data for the primary model organisms along with gene ontology data and human data. All data types represented in the Alliance portal (e.g. genomic data and phenotype descriptions) have common data models and workflows for curation. All data are open and freely available via a variety of mechanisms. Long-term plans for the Alliance project include a focus on coverage of additional model organisms including those without dedicated curation communities, and the inclusion of new data types with a particular focus on providing data and tools for the non-model-organism researcher that support enhanced discovery about human health and disease. Here we review current progress and present immediate plans for this new bioinformatics resource.", "date": "2020-01-08", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "48", "number": "D1", "publisher": "Oxford University Press", "pagerange": "D650-D658", "id_number": "CaltechAUTHORS:20200413-081503928", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200413-081503928", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U24HG002223-19S1" }, { "agency": "NIH", "grant_number": "P41HG002659" }, { "agency": "NIH", "grant_number": "U24HG002223" }, { "agency": "NIH", "grant_number": "U41HG000739" }, { "agency": "NIH", "grant_number": "U41HG001315" }, { "agency": "NIH", "grant_number": "HG000330" }, { "agency": "NIH", "grant_number": "U41HG002273" }, { "agency": "NIH", "grant_number": "HL64541" }, { "agency": "Medical Research Council (UK)", "grant_number": "MR/L001020/1" }, { "agency": "NIH", "grant_number": "1U24HG010859-01" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "corp_creators": { "items": [ "Alliance of Genome Resources Consortium" ] }, "doi": "10.1093/nar/gkz813", "pmcid": "PMC6943066", "primary_object": { "basename": "gkz813.pdf", "url": "https://authors.library.caltech.edu/records/jskmd-kqf35/files/gkz813.pdf" }, "resource_type": "article", "pub_year": "2020", "author_list": "Agapite, Julie; Albou, Laurent-Philippe; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/scabh-anq11", "eprint_id": 99530, "eprint_status": "archive", "datestamp": "2023-08-19 19:30:58", "lastmod": "2023-12-22 23:12:32", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Harris-Todd-W", "name": { "family": "Harris", "given": "Todd W." }, "orcid": "0000-0003-3406-163X" }, { "id": "Arnaboldi-Valerio", "name": { "family": "Arnaboldi", "given": "Valerio" }, "orcid": "0000-0002-2563-5374" }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "Chen-Wen-J", "name": { "family": "Chen", "given": "Wen J." } }, { "id": "Cho-Jaehyoung", "name": { "family": "Cho", "given": "Jaehyoung" } }, { "id": "Grove-Christian-A", "name": { "family": "Grove", "given": "Christian A." }, "orcid": "0000-0001-9076-6015" }, { "id": "Kishore-Ranjana", "name": { "family": "Kishore", "given": "Ranjana" } }, { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "Y. N." }, "orcid": "0000-0002-8151-7479" }, { "id": "M\u00fcller-Hans-Michael", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } }, { "id": "Nakamura-Cecilia", "name": { "family": "Nakamura", "given": "Cecilia" }, "orcid": "0000-0002-4689-7314" }, { "id": "Raciti-Daniela", "name": { "family": "Raciti", "given": "Daniela" } }, { "id": "Schindelman-Gary", "name": { "family": "Schindelman", "given": "Gary" } }, { "id": "Van-Auken-K", "name": { "family": "V. Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Wang-Qinghua", "name": { "family": "Wang", "given": "Qinghua" } }, { "id": "Yook-Karen-J", "name": { "family": "Yook", "given": "Karen" }, "orcid": "0000-0002-4457-6787" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "WormBase: a modern Model Organism Information Resource", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived: 15 September 2019; Revision received: 02 October 2019; Accepted: 07 October 2019; Published: 23 October 2019. \n\nThe authors wish to thank funding agencies for their ongoing support of WormBase and members of the C. elegans research community whose results form the foundation and purpose of WormBase. \n\nFunding: US National Human Genome Research Institute [U24 HG002223]; UK Medical Research Council [MR/S000453/1]; UK Biotechnology and Biological Sciences Research Council [BB/P024602/1]. Funding for open access charge: US National Human Genome Research Institute [U24 HG002223]. \n\nConflict of interest statement. None declared.\n\nPublished - gkz920.pdf
", "abstract": "WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user interface and architecture. In this update, we describe progress in each of these three areas. In particular, we discuss the status of literature curation and recently added data, detail new features of the web interface and options for users wishing to conduct data mining workflows, and discuss our efforts to build a robust and scalable architecture by leveraging commercial cloud offerings. We conclude with a description of WormBase's role as a founding member of the nascent Alliance of Genome Resources.", "date": "2020-01-08", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "48", "number": "D1", "publisher": "Oxford University Press", "pagerange": "D762-D767", "id_number": "CaltechAUTHORS:20191029-103634272", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191029-103634272", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U24 HG002223" }, { "agency": "Medical Research Council (UK)", "grant_number": "MR/S000453/1" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/P024602/1" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/nar/gkz920", "pmcid": "PMC7145598", "primary_object": { "basename": "gkz920.pdf", "url": "https://authors.library.caltech.edu/records/scabh-anq11/files/gkz920.pdf" }, "resource_type": "article", "pub_year": "2020", "author_list": "Harris, Todd W.; Arnaboldi, Valerio; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/v7apq-gyw11", "eprint_id": 100474, "eprint_status": "archive", "datestamp": "2023-08-22 03:11:06", "lastmod": "2023-10-18 20:34:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bult-C-J", "name": { "family": "Bult", "given": "Carol J." } }, { "id": "Blake-J-A", "name": { "family": "Blake", "given": "Judith A." } }, { "id": "Calvi-B-R", "name": { "family": "Calvi", "given": "Brian R." } }, { "id": "Cherry-J-M", "name": { "family": "Cherry", "given": "J. Michael" } }, { "id": "DiFrancesco-V", "name": { "family": "DiFrancesco", "given": "Valentina" } }, { "id": "Fullem-R", "name": { "family": "Fullem", "given": "Robert" } }, { "id": "Howe-K-L", "name": { "family": "Howe", "given": "Kevin L." } }, { "id": "Kaufman-T-C", "name": { "family": "Kaufman", "given": "Thom" } }, { "id": "Mungall-C-J", "name": { "family": "Mungall", "given": "Christopher" }, "orcid": "0000-0002-6601-2165" }, { "id": "Perrimon-N", "name": { "family": "Perrimon", "given": "Norbert" } }, { "id": "Shimoyama-Mary", "name": { "family": "Shimoyama", "given": "Mary" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Thomas-P-D", "name": { "family": "Thomas", "given": "Paul" }, "orcid": "0000-0002-9074-3507" }, { "id": "Westerfield-M", "name": { "family": "Westerfield", "given": "Monte" } } ] }, "title": "The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases", "ispublished": "pub", "full_text_status": "public", "keywords": "model organism databases; bioinformatics; data stewardship; database sustainability", "note": "\u00a9 2019 Bult et al. Available freely online through the author-supported open access option. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nManuscript received July 15, 2019; accepted for publication October 11, 2019; published Early Online October 17, 2019. \n\nWe thank all members of the Alliance of Genome Resources, the staff of the MODs and GOC, and the Alliance Scientific Advisory Board for their contributions to developing the vision and approach for the Alliance. V.D.F. and R.F. contributed to this manuscript in their official roles as program coordinators for the National Institutes of Health National Human Genome Research Institute.\n\nPublished - 1189.full.pdf
", "abstract": "Model organisms are essential experimental platforms for discovering gene functions, defining protein and genetic networks, uncovering functional consequences of human genome variation, and for modeling human disease. For decades, researchers who use model organisms have relied on Model Organism Databases (MODs) and the Gene Ontology Consortium (GOC) for expertly curated annotations, and for access to integrated genomic and biological information obtained from the scientific literature and public data archives. Through the development and enforcement of data and semantic standards, these genome resources provide rapid access to the collected knowledge of model organisms in human readable and computation-ready formats that would otherwise require countless hours for individual researchers to assemble on their own. Since their inception, the MODs for the predominant biomedical model organisms [Mus sp. (laboratory mouse), Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, Danio rerio, and Rattus norvegicus] along with the GOC have operated as a network of independent, highly collaborative genome resources. In 2016, these six MODs and the GOC joined forces as the Alliance of Genome Resources (the Alliance). By implementing shared programmatic access methods and data-specific web pages with a unified \"look and feel,\" the Alliance is tackling barriers that have limited the ability of researchers to easily compare common data types and annotations across model organisms. To adapt to the rapidly changing landscape for evaluating and funding core data resources, the Alliance is building a modern, extensible, and operationally efficient \"knowledge commons\" for model organisms using shared, modular infrastructure.", "date": "2019-12", "date_type": "published", "publication": "Genetics", "volume": "213", "number": "4", "publisher": "Genetics Society of America", "pagerange": "1189-1196", "id_number": "CaltechAUTHORS:20200102-160631829", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200102-160631829", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" } ] }, "corp_creators": { "items": [ "Alliance of Genome Resources Consortium" ] }, "doi": "10.1534/genetics.119.302523", "pmcid": "PMC6893393", "primary_object": { "basename": "1189.full.pdf", "url": "https://authors.library.caltech.edu/records/v7apq-gyw11/files/1189.full.pdf" }, "resource_type": "article", "pub_year": "2019", "author_list": "Bult, Carol J.; Blake, Judith A.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/7z575-y5v64", "eprint_id": 104150, "eprint_status": "archive", "datestamp": "2023-08-19 18:48:45", "lastmod": "2023-10-20 19:08:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lee-James-Siho", "name": { "family": "Lee", "given": "James S." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Wearable microPosters", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: July 9, 2019; Accepted: November 24, 2019; Published: November 26, 2019. \n\nWe thank our laboratory for sharing their microPosters and for discussions. \n\nFunding: Supported by grant N.I.H. grants U01-LM012672 and R21-MH115454. \n\nAuthor Contributions: \nJames S Lee: Investigation, Writing - review and editing\nPaul W Sternberg: Conceptualization, Funding acquisition, Writing - original draft, Investigation. \n\nReviewed By: Anonymous.\n\nPublished - Lee_11-26-19.pdf
", "abstract": "One barrier to communication at large face-to-face meetings, especially those focusing on scientific or technical topics, is a rapid way to understand what a person knows and thinks about before initiating a conversation. We have devised and reduced to practice an effective way to accomplish this task, the wearable microPoster. \n\nIn our experience, we observed that at most scientific meetings, especially once the number of participants passed 100, it is difficult to get productive conversations started with strangers. Thus, conversations tend to initiate among people that already know one another. This tends to exclude newer participants and those who do not have formal speaking slots. The difficulty increases at informal aspects of meetings: coffee breaks, lines for meals, social events, outdoor events in which a prominent speaker might have different clothes and sunglasses and is thus rendered unknown. \n\nPoster sessions have long provided a venue for rapid communication and finding participants. These are usually the most productive parts of meetings. Our thinking evolved from jokes about sandwich board posters, in which one walks around with large posters on the front and back, to shirts with printed information. The advent of printed cloth posters provides a practical solution in which a microPoster is cut from the larger poster (ideally cloth), or printed on one or more sheets of standard paper, which are then taped together. A microPoster comprises your name, affiliation (with appropriate granularity determined by the meeting), and a graphical abstract. The goal is to identify yourself in a much more informative way than a nametag. \n\nOne convenient way to present the microPoster is pinned on your back like a bib number (e.g., as in marathons or dances). We carried out a pilot with ten microPosters at a meeting of 1500 people (Figure 1), and found them to be effective at attracting useful conversation. \n\nThe addition of a machine readable QR code (e.g., Salt, 2019) is a possible useful addition but we note that the expense in time, money and carbon footprint of a face-to-face meeting is better spent on face-to-face conversations.", "date": "2019-11-26", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "micropub.biology.000192", "id_number": "CaltechAUTHORS:20200629-154039795", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200629-154039795", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U01-LM012672" }, { "agency": "NIH", "grant_number": "R21-MH115454" } ] }, "doi": "10.17912/micropub.biology.000192", "pmcid": "PMC7252233", "primary_object": { "basename": "Lee_11-26-19.pdf", "url": "https://authors.library.caltech.edu/records/7z575-y5v64/files/Lee_11-26-19.pdf" }, "resource_type": "article", "pub_year": "2019", "author_list": "Lee, James S. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/xx3bj-16f36", "eprint_id": 104128, "eprint_status": "archive", "datestamp": "2023-08-19 18:18:51", "lastmod": "2023-10-20 19:06:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gonz\u00e1lez-Cavazos-C", "name": { "family": "Gonz\u00e1lez-Cavazos", "given": "Carolina" } }, { "id": "Cao-Mengyi", "name": { "family": "Cao", "given": "Mengyi" } }, { "id": "Wong-Wan-Rong", "name": { "family": "Wong", "given": "Wan-Rong" } }, { "id": "Chai-Cynthia-M", "name": { "family": "Chai", "given": "Cynthia" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Effects of ASD-associated daf-18/PTEN missense variants on C. elegans dauer development", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: September 30, 2019; Accepted: October 8, 2019; Published: October 16, 2019. \n\nFunding: CGC: Simons Foundation SFARI pilot grant and summer fellowship. MC: NIH-F32 fellowship (1 F32 GM131570-01). WRW, CC, PWS: NIH U01-NS111697. \n\nAuthor Contributions:\nCarolina Gonz\u00e1lez-Cavazos: Investigation, Formal analysis, Writing - original draft\nMengyi Cao: Methodology, Formal analysis, Writing - original draft\nWan-Rong Wong: Methodology, Writing - review and editing\nCynthia Chai: Formal analysis, Writing - review and editing\nPaul W Sternberg: Conceptualization, Resources, Funding acquisition, Project administration, Writing - review and editing.\n\nPublished - Gonz\u00e1lez-Cavazos_2019.pdf
", "abstract": "The relatively simple nervous system and facile genetics of Caenorhabditis elegans makes it a potential model organism to study the genetic basis of complex neural diseases, such as autism spectrum disorder (ASD). Our previously published study identified conserved human ASD-missense variants in C. elegans orthologs that have a role on morphology, locomotion or fecundity, suggesting C. elegans as an efficient phenotypic model to study conserved ASD variants (Wong et al., 2019).\u00a0One of the ASD-associated genes screened in this study is daf-18, an ortholog of PTEN. DAF-18/PTEN is a lipid phosphatase protein that dephosphorylates PIP3, a critical lipid second messenger that mediates downstream kinase cascade signaling of the insulin pathway, that in turn regulates expression of genes involved in C. elegans lifespan and dauer formation (Murphy and Hu, 2013). It is reported that the daf-18(e1375)\u00a0strain, which has a 30\u2013base pairs insertion in the fourth exon, has a dauer defective phenotype (Ogg and Ruvkun, 1998); however, the effect of daf-18/PTEN single amino acid substitution in dauer formation has not been evaluated before. Here, we investigate the dauer entry abilities of previously published ASD-associated daf-18/PTEN missense variants (Wong et al., 2019). \n\nWe performed a dauer-entry assay using crude pheromone as a proxy for high population density and heat-killed bacteria as a limited food source. We first determined the crude pheromone concentration required to induce 50% of wild type (N2) strain to enter dauer stage (EC50). Using the calculated EC50value we evaluated each mutant strain in two independent experiments (Table 1). To control day-to-day variations caused by environmental conditions, N2 controls were used in every trail. Additionally, we used the previously reported daf-18 dauer-defective strain (e1375) as a control (Ogg and Ruvkun, 1998). To analyze the obtained data, we performed one-way ANOVA followed by multiple comparisons test (Dunnett test) (Figure 1A). \n\nTable 1 Evaluated ASD-associated daf-18/PTEN mutant strains.\n\nStrain name\nPS7439\nPS7432\nPS7436\nPS7430\nPS7434\n\n\nC. elegans allele name\ndaf-18(sy879)\ndaf-18(sy887)\ndaf-18(sy881)\ndaf-18(sy885)\ndaf-18(sy882)\n\n\nC. elegans protein change\nD66E\nL115V\nH138R\nH168Q\nT176I\n\n\nHuman protein change\nD22E\nL70V\nH93R\nH123Q\nT131I\n\n\n\nAs expected, we observed statistically significant difference between our wild type and dauer defective control (e1375). Our results show that H138R (PS7436) and T176I (PS7434)\u00a0daf-18 mutant strains have a significant difference from the wild type control, and a non-significant difference from the dauer defective control, suggesting these missense alleles cause dauer defective phenotypes to the same level of the e1375\u00a0strain. In contrast, we found the D66E (PS7439), L115V (PS7432) and H168Q (PS7430) mutant strains are significantly different from the dauer defective control and not significantly different from the wild type control, suggesting these three missense alleles do not cause the same level of dauer defective phenotype as the defective control does. Altogether, our current data show that H138R and T176I are defective in dauer entry, while D66E, L115V and H168Q daf-18 mutant strains are not (Figure 1A).\nThe Conserved Domain Database (Conserved Domain Search) of NCBI (ID: G5EE01) predicts that four of the five missense variations evaluated in this study are located in the phosphatase domain of DAF-18/PTEN(Figure 1B). It is predicted that amino acid Histidine 138 is located in the active site of the protein, suggesting that H138R (PS7436) amino acid change might have an impact on PIP3\u00a0substrate specificity, which could explain the dauer defect phenotype observed. Moreover, it is predicted that both amino acid Histidine 168 and Threonine 176 are located close to the catalytic site of the phosphatase domain. We found a dauer defective phenotype resulting from a T176I substitution (PS7434) but not from a H168Q amino acid substitution (PS7430). \n\nThese data suggest that certain amino acids in the catalytic and active sites of DAF-18/PTEN decrease the function of the protein, in turn regulating\u00a0C. elegans dauer development. Future evaluation of PIP3 phosphorylation levels could confirm the effect of these variations on the phosphatase activity. The results of this study contribute to the knowledge of the mechanisms controlling C. elegans\u00a0dauer entry, and to the C. elegans\u00a0phenotype-screening of conserved ASD variations.", "date": "2019-10-16", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "micropub.biology.000177", "id_number": "CaltechAUTHORS:20200629-120228447", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200629-120228447", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Simons Foundation" }, { "agency": "NIH", "grant_number": "1 F32 GM131570-01" }, { "agency": "NIH", "grant_number": "U01-NS111697" } ] }, "doi": "10.17912/micropub.biology.000177", "pmcid": "PMC7252320", "primary_object": { "basename": "Gonz\u00e1lez-Cavazos_2019.pdf", "url": "https://authors.library.caltech.edu/records/xx3bj-16f36/files/Gonz\u00e1lez-Cavazos_2019.pdf" }, "resource_type": "article", "pub_year": "2019", "author_list": "Gonz\u00e1lez-Cavazos, Carolina; Cao, Mengyi; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/4b8wt-d8q56", "eprint_id": 96671, "eprint_status": "archive", "datestamp": "2023-08-22 02:42:53", "lastmod": "2023-10-20 21:25:26", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shih-Pei-Yin", "name": { "family": "Shih", "given": "Pei-Yin" }, "orcid": "0000-0003-3082-9242" }, { "id": "Lee-James-Siho", "name": { "family": "Lee", "given": "James Siho" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Genetic markers enable the verification and manipulation of the dauer entry decision", "ispublished": "pub", "full_text_status": "public", "keywords": "Diapause; Phenotypic plasticity; Dauer larvae; Genetic marker", "note": "\u00a9 2019 Published by Elsevier Inc. \n\nReceived 15 January 2019, Revised 14 June 2019, Accepted 14 June 2019, Available online 23 June 2019. \n\nWe thank Chun-Hao Chen, Sarah Cohen, and Katherine I. Brugman for critically reading the manuscript; C. Bargmann (Rockefeller University) for sharing reagents; the Caenorhabditis Genetics Center, which is funded by the NIH Office of Research Infrastructure Programs (P40 OD010440); WormBase and the Alliance of Genome Resource for datasets and invaluable information. This research was supported by the Howard Hughes Medical Institute with which PWS was an investigator.\n\nSupplemental Material - 1-s2.0-S0012160618307887-mmc2.xlsx
Supplemental Material - 1-s2.0-S0012160618307887-mmc3.pdf
", "abstract": "Phenotypic plasticity allows animals to survive in changing environments through the alteration of phenotypes or development. One of the best-studied examples of phenotypic plasticity is dauer larval development in the free-living roundworm Caenorhabditis elegans. When faced with hostile environments, C. elegans larvae can exit reproductive development and enter the stress-resistant and spore-like dauer larval stage. However, knowledge about how the dauer entry decision is made, and how the different tissues of the animal coordinate to execute transformation into dauer, is limited. This is because identifying animals that make the entry decision, or that fail to coordinately remodel their tissues during dauer development, is time-consuming and labor-intensive. Utilizing our previously reported RNA-seq of animals going through dauer or reproductive development (Lee et al., 2017), we have identified genetic markers for conveniently tracking and manipulating the dauer entry decision. These include col-183 (which tracks dauer fate in the hypodermis), ets-10 (neurons and intestine), nhr-246 (intestine and hypodermis), and F53F1.4 (reproductive fate in the hypodermis). Using condition shift experiments, we demonstrate that the dauer-specific fluorescent expression of the markers correspond to the commitment event of the dauer entry decision, and therefore label when the decision is made. We show that these markers can be used to manipulate the entry decision by driving the reproduction-promoting gene daf-9 under the control of the dauer-specific marker col-183, through which we could shift animals into non-dauer development. We further demonstrate that the markers can be used to track tissue coordination during the decision. daf-9, daf-15, and daf-18 partial dauers exhibit incomplete expression of the ets-10 marker, with our results indicating that the same gene (e.g. daf-9 or daf-18) can affect dauer development differently in different tissues. Our findings provide molecular tools for studying phenotypic plasticity during a whole animal decision.", "date": "2019-10-15", "date_type": "published", "publication": "Developmental Biology", "volume": "454", "number": "2", "publisher": "Elsevier", "pagerange": "170-180", "id_number": "CaltechAUTHORS:20190624-141107109", "issn": "0012-1606", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190624-141107109", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P40 OD010440" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1016/j.ydbio.2019.06.009", "primary_object": { "basename": "1-s2.0-S0012160618307887-mmc2.xlsx", "url": "https://authors.library.caltech.edu/records/4b8wt-d8q56/files/1-s2.0-S0012160618307887-mmc2.xlsx" }, "related_objects": [ { "basename": "1-s2.0-S0012160618307887-mmc3.pdf", "url": "https://authors.library.caltech.edu/records/4b8wt-d8q56/files/1-s2.0-S0012160618307887-mmc3.pdf" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Shih, Pei-Yin; Lee, James Siho; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/qhs5k-thr67", "eprint_id": 104064, "eprint_status": "archive", "datestamp": "2023-08-19 18:17:18", "lastmod": "2023-10-20 19:02:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cohen-S-M", "name": { "family": "Cohen", "given": "Sarah M." }, "orcid": "0000-0002-5233-2280" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Genome editing of Caenorhabditis briggsae using CRISPR/Cas9 co-conversion marker dpy-10", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: September 12, 2019; Accepted: September 30, 2019; Published: October 11, 2019. \n\nWe thank Heenam Park for her discussion and comments. \n\nFunding:\nThis material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE 1745301 and the NIH under Grant No. R24 0D023041.\n\nAuthor Contributions:\nSarah M Cohen: Conceptualization, Investigation, Methodology, Visualization, Writing - original draft, Writing - review and editing\nPaul W Sternberg: Conceptualization, Funding acquisition, Supervision, Writing - review and editing.\n\nPublished - 10.17912\uf022micropub.biology.000171.pdf
", "abstract": "Genomic editing of the roundworm Caenorhabditis elegans using the CRISPR/Cas9 system has allowed for widespread creation of null mutants \u2013 vital for scientific understanding of this model organism. A closely-related nematode species, Caenorhabditis briggsae, is emerging as an alternative model organism to better understand how findings in C. elegans can broaden and develop the larger field of nematology (Gupta et al. 2007). To that end, we have developed an effective and efficient co-conversion CRISPR/Cas9 system for use in C. briggsae using the gene dpy-10.\nWe modified the universal STOP-IN cassette method, as described by Wang et al. (2018), for use in C. briggsae (Wang et al. 2018). Using the wildtype AF16 strain, we tested the method by choosing the gene Cbr-dpy-10 because of its readily observed predicted phenotype. Cbr-dpy-10 is a predicted one-to-one ortholog of C. elegans dpy-10, which encodes a protein important for cuticle development and has a phenotype characterized by short, fat animals relative to wild type (Brenner 1974).\nA universal STOP-IN allele of Cbr-dpy-10, sy1387, was generated and confirmed by genotype sequencing. The expected phenotype was subsequently observed, consistent with the creation of a null allele (Figure 1). Surprisingly, sy1387 is dominant. Injections of 20 animals produced 15 successful injections; 247 animals from these 15 injections (F1) were singled out and allowed to self-fertilize to produce F2. 81% of the F1 Dumpy progeny were homozygous as evidenced by their segregation of only Dumpy progeny \u2013 one of these candidates became sy1387. 2% of the F1s did not produce progeny. 17% of the 247 F1 Dumpy progeny were heterozygotes and had a mixture of Dumpy and non-Dumpy progeny; these non-Dumpy F2s only produced non-Dumpy progeny. This discovery of a dominant mutation will allow for more effective use of this as a co-conversion marker when screening for other mutations. We used Cbr-dpy-10 as a potential co-CRISPR marker for a second target that will be described elsewhere. We used PCR to detect insertion of a STOP-IN cassette at this other locus; we screened 39 Dumpy strains to obtain 11 candidates for our target gene, from which we have three STOP-IN alleles.", "date": "2019-10-11", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "micropub.biology.000171", "id_number": "CaltechAUTHORS:20200625-134930761", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200625-134930761", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF Graduate Research Fellowship", "grant_number": "DGE-1745301" }, { "agency": "NIH", "grant_number": "R24 0D023041" } ] }, "doi": "10.17912/micropub.biology.000171", "pmcid": "PMC7252229", "primary_object": { "basename": "10.17912\uf022micropub.biology.000171.pdf", "url": "https://authors.library.caltech.edu/records/qhs5k-thr67/files/10.17912\uf022micropub.biology.000171.pdf" }, "resource_type": "article", "pub_year": "2019", "author_list": "Cohen, Sarah M. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ydheb-djt19", "eprint_id": 98870, "eprint_status": "archive", "datestamp": "2023-08-22 02:40:50", "lastmod": "2023-10-18 17:41:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shih-Pei-Yin", "name": { "family": "Shih", "given": "Pei-Yin" }, "orcid": "0000-0003-3082-9242" }, { "id": "Lee-James-Siho", "name": { "family": "Lee", "given": "James Siho" } }, { "id": "Shinya-Ryoji", "name": { "family": "Shinya", "given": "Ryoji" } }, { "id": "Kanzaki-Natsumi", "name": { "family": "Kanzaki", "given": "Natsumi" }, "orcid": "0000-0001-8752-1674" }, { "id": "Pires-daSilva-A", "name": { "family": "Pires-daSilva", "given": "Andre" } }, { "id": "Badroos-J-M", "name": { "family": "Badroos", "given": "Jean Marie" } }, { "id": "Goetz-E", "name": { "family": "Goetz", "given": "Elizabeth" } }, { "id": "Sapir-A", "name": { "family": "Sapir", "given": "Amir" }, "orcid": "0000-0001-9888-1800" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Newly Identified Nematodes from Mono Lake Exhibit Extreme Arsenic Resistance", "ispublished": "pub", "full_text_status": "public", "keywords": "Mono Lake; arsenic; extremophiles; nematodes; preadaptation; resilience", "note": "\u00a9 2019 Elsevier Ltd. \n\nReceived 7 March 2019, Revised 24 May 2019, Accepted 9 August 2019, Available online 26 September 2019. \n\nWe thank Dr. Avi BarMassada for the map of Mono Lake, Dr. Stephanie A. Connon for advice on collecting and preserving samples from Mono Lake, Dr. Tim Hollibaugh for suggestions on replicating Mono Lake conditions in the laboratory, Prof. Joe Parker for suggestions on building phylogenetic trees, Prof. Tsui-Fen Chou for advice on calculating relative arsenic resistance, and Dr. Nathan Dalleska at the Environmental Analysis Center at Caltech for help on soil property measurements. J.M.B. was supported by the Amgen Scholars Program. A.P.-d.S. acknowledges funding by Leverhulme Trust (RPG-2016-089). P.W.S was an investigator with the Howard Hughes Medical Institute, which supported this work. \n\nAuthor Contributions: Conceptualization, P.-Y.S., J.S.L., R.S., A.S., and P.W.S.; Formal Analysis, P.-Y.S., J.S.L., R.S., N.K., A.P.-d.S., and A.S; Investigation, P.-Y.S., J.S.L., R.S., N.K., A.P.-d.S., J.M.B., and A.S.; Resources, A.P.-d.S., E.G., and A.S.; Writing \u2013 Original Draft, P.-Y.S., and J.S.L.; Writing \u2013 Review & Editing, P.-Y.S., J.S.L., R.S., N.K., E.G., A.S., and P.W.S.; Visualization, P.-Y.S., J.S.L., R.S., and N.K.; Supervision, A.S. and P.W.S.; Funding Acquisition, P.W.S. \n\nThe authors declare no competing interests.\n\nSupplemental Material - 1-s2.0-S0960982219310401-mmc1.pdf
Supplemental Material - 1-s2.0-S0960982219310401-mmc2.pdf
", "abstract": "Extremophiles have much to reveal about the biology of resilience, yet their study is limited by sampling and culturing difficulties [1, 2, 3]. The broad success and small size of nematodes make them advantageous for tackling these problems [4, 5, 6]. We investigated the arsenic-rich, alkaline, and hypersaline Mono Lake (CA, US) [7, 8, 9] for extremophile nematodes. Though Mono Lake has previously been described to contain only two animal species (brine shrimp and alkali flies) in its water and sediments [10], we report the discovery of eight nematode species from the lake, including microbe grazers, parasites, and predators. Thus, nematodes are the dominant animals of Mono Lake in species richness. Phylogenetic analysis suggests that the nematodes originated from multiple colonization events, which is striking, given the young history of extreme conditions at Mono Lake [7, 11]. One species, Auanema sp., is new, culturable, and survives 500 times the human lethal dose of arsenic. Comparisons to two non-extremophile sister species [12] reveal that arsenic resistance is a common feature of the genus and a preadaptive trait that likely allowed Auanema to inhabit Mono Lake. This preadaptation may be partly explained by a variant in the gene dbt-1 shared with some Caenorhabditis elegans natural populations and known to confer arsenic resistance [13]. Our findings expand Mono Lake's ecosystem from two known animal species to ten, and they provide a new system for studying arsenic resistance. The dominance of nematodes in Mono Lake and other extreme environments and our findings of preadaptation to arsenic raise the intriguing possibility that nematodes are widely pre-adapted to be extremophiles.", "date": "2019-10-07", "date_type": "published", "publication": "Current Biology", "volume": "29", "number": "19", "publisher": "Cell Press", "pagerange": "3339-3344", "id_number": "CaltechAUTHORS:20190926-092428868", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190926-092428868", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Amgen" }, { "agency": "Leverhulme Trust", "grant_number": "RPG-2016-089" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1016/j.cub.2019.08.024", "primary_object": { "basename": "1-s2.0-S0960982219310401-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/ydheb-djt19/files/1-s2.0-S0960982219310401-mmc1.pdf" }, "related_objects": [ { "basename": "1-s2.0-S0960982219310401-mmc2.pdf", "url": "https://authors.library.caltech.edu/records/ydheb-djt19/files/1-s2.0-S0960982219310401-mmc2.pdf" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Shih, Pei-Yin; Lee, James Siho; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/rxyxy-y4s89", "eprint_id": 104061, "eprint_status": "archive", "datestamp": "2023-08-19 17:29:08", "lastmod": "2023-10-20 19:02:36", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Minor-P-J", "name": { "family": "Minor", "given": "Paul J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "C. elegans LRP-2 functions in vulval precursor cell polarity", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: July 29, 2019; Accepted: August 6, 2019; Published: August 27, 2019. \n\nFunding: Howard Hughes Medical Institute, with whom PWS was an Investigator. The National Institute of Neurological Disorders and Stroke of the National Institutes of Health under award number 1F32NS098658-01A1 awarded to PJM.\n\nPublished - 10.17912\uf022micropub.biology.000152.pdf
", "abstract": "The C. elegans vulva is formed from divisions of three vulval precursor cells (VPCs) \u2013 P5.p, P6.p, and P7.p \u2013 arranged along the anteroposterior axis in the ventral epithelium (Sulston and Horvitz, 1977). Previous analyses show the orientation of P5.p and P7.p descendants is determined by the interaction of multiple Wnt signals. Specifically, in the absence of all Wnts, the VPCs display a randomized orientation, which is likely the default (Green et al., 2008; Minor et al. 2013). Two separate Wnts from the anchor cell, LIN-44 and MOM-2 acting through receptors LIN-17/Frizzled and LIN-18/Ryk, respectively, regulate P7.p orientation (Ferguson et al., 1987; Sternberg and Horvitz, 1988; Sawa et al., 1996; Inoue et al., 2004; Gleason et al., 2006). In the absence of these signals the orientation of the progeny of P7.p mimic those of P5.p and face toward the posterior of the worm, a phenotype referred to as posterior-reversed vulval lineage (P-Rvl). This posterior orientation is dependent on the instructive signal EGL-20, a Wnt expressed in the tail acting through CAM-1/ROR and VANG-1/Van Gogh, and is referred to as \"ground polarity\" (Green et al., 2008). \n\nHere we examine the role of a low-density lipoprotein receptor, lrp-2, and its role in controlling the orientation of P7.p daughter cells. To investigate this interaction double mutants were constructed with both alleles of lrp-2 and lin-17(n671) (Table 1). Much like cam-1(gm122) and vang-1(ok1142), both alleles of lrp-2 suppress the lin-17(n671) phenotype from 74 to approximately 50% P-Rvl leading us to hypothesize that lrp-2 functions in the same pathway as cam-1 and vang-1. Furthering this hypothesis we have shown that, like cam-1 and vang-1, lrp-2 controls the localization of SYS-1/b-catenin (Minor and Sternberg, 2019). To ensure that this phenotype was a result of loss of lrp-2 function as opposed to background effects we injected a fosmid (WRM0617cA02) containing the full-length sequence of lrp-2 and found that it does rescue the double mutant phenotype of lin-17(n671); lrp-2(gk272) from 55 to 73%. In order to better test this hypothesis a triple mutant was constructed between lin-17(n671), lrp-2(gk272), and cam-1(gm122) (Table 1). This triple mutant displays the same P-Rvl penetrance as both the lin-17(n671); lrp-2(gk272) and lin-17(n671); cam-1(gm122) double mutants confirming that lrp-2 functions in the same pathway as cam-1.", "date": "2019-08-27", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "micropub.biology.000152", "id_number": "CaltechAUTHORS:20200625-132530323", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200625-132530323", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "1F32NS098658-01A1" } ] }, "doi": "10.17912/micropub.biology.000152", "pmcid": "PMC7252275", "primary_object": { "basename": "10.17912\uf022micropub.biology.000152.pdf", "url": "https://authors.library.caltech.edu/records/rxyxy-y4s89/files/10.17912\uf022micropub.biology.000152.pdf" }, "resource_type": "article", "pub_year": "2019", "author_list": "Minor, Paul J. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/60w7m-8e330", "eprint_id": 104017, "eprint_status": "archive", "datestamp": "2023-08-19 17:28:59", "lastmod": "2023-10-20 19:00:25", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Minor-P-J", "name": { "family": "Minor", "given": "Paul J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "LRP-2 controls the localization of C. elegans SYS-1/beta-catenin", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: July 29, 2019; Accepted: August 27, 2019; Published: August 27, 2019. \n\nFunding: Howard Hughes Medical Institute, with whom PWS was an Investigator. The National Institute of Neurological Disorders and Stroke of the National Institutes of Health under award number 1F32NS098658-01A1 awarded to PJM. \n\nReviewed By: Hitoshi Sawa.\n\nPublished - 10.17912\uf022micropub.biology.000151.pdf
", "abstract": "The polarity of the C. elegans P7.p cell divisions is controlled by the Wnt/\u03b2-catenin asymmetry pathway (Green et al., 2008; Minor et al., 2013). This pathway includes the \u03b2-catenin-like proteins SYS-1 and WRM-1, POP-1/TCF, and the Nemo-like-kinase, LIT-1 (reviewed by Mizumoto and Sawa, 2007). The Wnt/\u03b2-catenin asymmetry pathway ensures different ratios of SYS-1 to POP-1, controlling the differential transcription of Wnt target genes between daughters of an asymmetric cell division. Because our genetic data indicate an antagonism between LRP-2 and LIN-17 similar to that between CAM-1 and VANG-1 and LIN-17 (Minor and Sternberg, 2019), we wanted to determine if LRP-2 can control the asymmetric localization of SYS-1 between the daughter cells of P7.p during anaphase of the first cell division. The initial establishment of vulval polarity can be observed through the localization of VENUS::SYS-1 (VNS::SYS-1), localized in a high (P7.pa)/low (P7.pp) pattern in the wild-type worm, reciprocal to the localization of POP-1/TCF (Phillips et al., 2007; Green et al., 2008).\nIt was previously reported (Green et al. 2008) that VNS::SYS-1 asymmetry in P7.p daughter cells is often lost in lin-17(n671) and lin-18(e620) mutants. These mutants display two aberrant patterns of VNS::SYS-1 localization as well as the wild-type pattern, though less frequently. The two deviant localization patterns include one in which both P7.pa and P7.pp express equal amounts of VNS::SYS-1 and a reversed VNS::SYS-1 pattern in which P7.pp is enriched with VNS::SYS-1. By observing VNS::SYS-1 localization in a lin-17(n671); lrp-2(gk272) background we see that the aberrant localization of SYS-1 is suppressed to a similar degree to that of lin-17(n671); cam-1(gm122) and lin-17(n671); vang-1(ok1142). This observation confirms LRP-2 controls vulval cell polarity by antagonizing LIN-17 in a similar fashion to CAM-1 and VANG-1, and that the effect of LRP-2 is at the level of P7.p rather than its progeny.", "date": "2019-08-27", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "micropub.biology.000151", "id_number": "CaltechAUTHORS:20200624-134109150", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200624-134109150", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "1F32NS098658-01A1" } ] }, "doi": "10.17912/micropub.biology.000151", "pmcid": "PMC7252296", "primary_object": { "basename": "10.17912\uf022micropub.biology.000151.pdf", "url": "https://authors.library.caltech.edu/records/60w7m-8e330/files/10.17912\uf022micropub.biology.000151.pdf" }, "resource_type": "article", "pub_year": "2019", "author_list": "Minor, Paul J. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/twa83-4q547", "eprint_id": 104060, "eprint_status": "archive", "datestamp": "2023-08-19 17:29:03", "lastmod": "2023-10-20 19:02:32", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Minor-P-J", "name": { "family": "Minor", "given": "Paul J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "LRP-2 likely acts downstream of EGL-20/Wnt", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: July 29, 2019; Accepted: August 26, 2019; Published: August 27, 2019. \n\nFunding: Howard Hughes Medical Institute, with whom PWS was an Investigator. The National Institute of Neurological Disorders and Stroke of the National Institutes of Health under award number 1F32NS098658-01A1 awarded to PJM.\n\nReviewed By:\nDavid Eisenmann.\n\nPublished - 10.17912\uf022micropub.biology.000153.pdf
", "abstract": "The C. elegans vulva is formed from divisions of three vulval precursor cells (VPCs) \u2013 P5.p, P6.p, and P7.p \u2013 arranged along the anteroposterior axis in the ventral epithelium (Sulston and Horvitz, 1977). Previous analyses show the orientation of P5.p and P7.p descendants is determined by the interaction of multiple Wnt signals. egl-20/Wnt is expressed in the tail (Whangbo and Kenyon, 2000) and forms a posterior-to-anterior concentration gradient (Coudreuse et al., 2006). It has previously been shown that EGL-20 acts instructively during vulva development by imparting directional information, as opposed to being permissive, where it would only be required for polarization (Green et al., 2008; Minor et al., 2013). By moving the source of egl-20 expression from the posterior of the worm to the anchor cell, the axis of symmetry of the developing vulva, we can reorient the daughter cells of P5.p and P7.p toward the center in a wild-type configuration. \n\nExpression of egl-20 from the center of the axis of symmetry partially suppresses the lin-17(n671) phenotype (Green et al., 2008; Table 1). To test whether LRP-2 acts downstream of EGL-20, we ectopically expressed egl-20 from the anchor cell in a lin-17(n671); lrp-2(gk272) double mutant background and compared it to a lin-17(n671); lrp-2(+) strain. If LRP-2 acts downstream of EGL-20, then anteriorly-expressed EGL-20 will not be able to suppress the lin-17 phenotype, with is the result observed (Table 1). Thus, like CAM-1 and VANG-1, LRP-2 likely acts downstream of EGL-20.", "date": "2019-08-27", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "micropub.biology.000153", "id_number": "CaltechAUTHORS:20200625-124034164", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200625-124034164", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "1F32NS098658-01A1" } ] }, "doi": "10.17912/micropub.biology.000153", "pmcid": "PMC7252290", "primary_object": { "basename": "10.17912\uf022micropub.biology.000153.pdf", "url": "https://authors.library.caltech.edu/records/twa83-4q547/files/10.17912\uf022micropub.biology.000153.pdf" }, "resource_type": "article", "pub_year": "2019", "author_list": "Minor, Paul J. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/tz066-a5756", "eprint_id": 104062, "eprint_status": "archive", "datestamp": "2023-08-19 17:29:12", "lastmod": "2023-10-20 19:02:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Minor-P-J", "name": { "family": "Minor", "given": "Paul J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Low density lipoprotein receptors LRP-1 and LRP-2 in C. elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: July 29, 2019; Accepted: August 26, 2019; Published: August 27, 2019. \n\nFunding: Howard Hughes Medical Institute, with whom PWS was an Investigator. The National Institute of Neurological Disorders and Stroke of the National Institutes of Health under award number 1F32NS098658-01A1 awarded to PJM. \n\nReviewed By: David Eisenmann.\n\nPublished - 10.17912\uf022micropub.biology.000154.pdf
", "abstract": "The regulation of vulval cell lineage polarity is controlled by Wnt signaling. Previously known components involved in the regulation of vulval cell lineage polarity include LIN-17, LIN-18, CAM-1, and VANG-1 (Inoue et al., 2004; Gleason et al., 2006; Green et al., 2008). A directed bioinformatics screen of known Wnt pathway components was performed to find additional genes involved in directing vulval orientation. A BLAST was run using other known Wnt receptors and it was determined that C. elegans does not contain a true ortholog of Drosophila LRP5/6 (Arrow) (He et al., 2004; Eisenmann, 2005), but does have multiple low-density lipoprotein receptors, including LRP-1 and LRP-2 (Figure 1). Like other low-density lipoprotein receptors, both LRP-1 and LRP-2 contain many LDLR Domain Class A and Class B repeats, EGF-like domains, and a transmembrane domain. However, having approximately three times as many amino acids, LRP-1 and LRP-2 are more similar to megalin than LRP5/6 (Yochem et al., 1999). The absence of LRP5/6 within C. elegans but presence in flies and all other higher order organisms suggests that the gene encoding LRP5/6 arose after nematodes, potentially from either LRP1 or LRP2/megalin, as both receptors contain the entire extracellular portion of LRP5/6 in a single contiguous sequence block (Figure 1).\nOur examination of the protein sequence of LRP-1 and LRP-2 indicates that most nematodes have at least two copies of LRP-like proteins with C. elegans LRP-1 and LRP-2 being highly similar possibly due to a recent duplication and divergence (Figure 2). Comparing the sequences across Caenorhabditis we find that LRP-1 proteins cluster together and LRP-2 proteins also form their own cluster. Based on location in the genome and sequence similarity from protein alignment, we believe that Caenorhabditis lrp-2 is a recent duplication and divergence of lrp-1 (Figure 2).", "date": "2019-08-27", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "micropub.biology.000154", "id_number": "CaltechAUTHORS:20200625-133236952", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200625-133236952", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "1F32NS098658-01A1" } ] }, "doi": "10.17912/micropub.biology.000154", "pmcid": "PMC7252236", "primary_object": { "basename": "10.17912\uf022micropub.biology.000154.pdf", "url": "https://authors.library.caltech.edu/records/tz066-a5756/files/10.17912\uf022micropub.biology.000154.pdf" }, "resource_type": "article", "pub_year": "2019", "author_list": "Minor, Paul J. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/z3v2w-2dm54", "eprint_id": 104149, "eprint_status": "archive", "datestamp": "2023-08-19 17:29:17", "lastmod": "2023-10-20 19:08:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Minor-P-J", "name": { "family": "Minor", "given": "Paul J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The role of lrp-2 in C. elegans vulval cell lineage polarity", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: July 29, 2019; Accepted: August 26, 2019; Published: August 27, 2019. \n\nFunding: Howard Hughes Medical Institute, with whom PWS was an Investigator. The National Institute of Neurological Disorders and Stroke of the National Institutes of Health under award number 1F32NS098658-01A1 awarded to PJM. \n\nReviewed By: David Eisenmann.\n\nPublished - Minor_8-27-19.pdf
", "abstract": "We investigated the role of the low-density lipoprotein receptor lrp-2 in C. elegans vulval cell lineage polarity. We find that despite the high conservation of the Wnt signaling component, LRP5/6, in higher order organisms it appears to have evolved after the split of Nematoda due to its absence in all nematode genomes examined. C. elegans contains multiple low-density lipoprotein receptors within its genome, two of which are lrp-1 and lrp-2. Due to the position in the genome and high sequence similarity we believe that lrp-2 is the product of a recent duplication of lrp-1 within the Caenorhabditis lineage (Minor and Sternberg, 2019d). \nTo understand the potential role of lrp-1 and lrp-2, we sought to score the vulval phenotypes of these mutants during L4 stage. lrp-1(ku156) mutants are sick and arrest during an early larval stage. For this reason we were not able to examine the role of lrp-1 in vulval formation. Despite high sequence similarity and proposed functional redundancy with lrp-1, lrp-2 mutants are remarkably wild-type. lrp-2 is expressed in the developing vulva at the same time as both cam-1 and vang-1. By examining double and triple mutant strains we find that lrp-2 is likely to function downstream of egl-20 along with transmembrane proteins cam-1 and vang-1 (Minor and Sternberg, 2019b; Minor and Sternberg, 2019c). All three genes antagonize the lin-17/Frizzled pathway by directing the aberrant localization of SYS-1 to the posterior daughter cell of P7.p, thereby leading to the posterior orientation of the P7.p lineage (Minor and Sternberg, 2019a). These observations suggest the simple model shown in Figure 1, in which LRP-2 cooperates with CAM-1 and VANG-1 to respond to EGL-20. \n\nThis work provides evidence that despite lacking a true LRP5/6 ortholog, the formation of the C. elegans vulva is controlled by another member of the low-density lipoprotein superfamily, lrp-2. This data could potentially lead to insight into the evolution of both structure and function of the highly important Wnt pathway component, LRP5/6. Despite strong genetic evidence, this work does not describe the physical interaction between LRP-2 and CAM-1, VANG-1, EGL-20. Can LRP-2 bind with the other transmembrane proteins, CAM-1 and VANG-1, involved in this pathway? Can LRP-2 physically bind the Wnt ligand, EGL-20? Future work should focus on the biochemistry of this pathway. Answers to these questions could provide interesting insights into the evolution of low-density lipoprotein receptors, including LRP5/6, as well as how Wnt signaling has evolved within nematodes without the presence of one of the most important and highly conserved transmembrane proteins.", "date": "2019-08-27", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "/micropub.biology.000155", "id_number": "CaltechAUTHORS:20200629-153021156", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200629-153021156", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "National Institute of Neurological Disorders and Stroke (NINDS)" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "1F32NS098658-01A1" } ] }, "doi": "10.17912/micropub.biology.000155", "pmcid": "PMC7252271", "primary_object": { "basename": "Minor_8-27-19.pdf", "url": "https://authors.library.caltech.edu/records/z3v2w-2dm54/files/Minor_8-27-19.pdf" }, "resource_type": "article", "pub_year": "2019", "author_list": "Minor, Paul J. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/weexf-2wz07", "eprint_id": 96649, "eprint_status": "archive", "datestamp": "2023-08-19 16:40:57", "lastmod": "2023-10-20 21:24:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wong-Wan-Rong", "name": { "family": "Wong", "given": "Wan-Rong" }, "orcid": "0000-0002-9757-8145" }, { "id": "Brugman-K-I", "name": { "family": "Brugman", "given": "Katherine I." }, "orcid": "0000-0003-2625-2903" }, { "id": "Maher-S", "name": { "family": "Maher", "given": "Shayda" }, "orcid": "0000-0002-1987-6104" }, { "id": "Oh-Jun-Young", "name": { "family": "Oh", "given": "Jun Young" }, "orcid": "0000-0002-5158-9017" }, { "id": "Howe-Kevin", "name": { "family": "Howe", "given": "Kevin" }, "orcid": "0000-0002-1751-9226" }, { "id": "Kato-Mihoko", "name": { "family": "Kato", "given": "Mihoko" }, "orcid": "0000-0003-3827-8879" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Autism-associated missense genetic variants impact locomotion and neurodevelopment in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "alleles, phenotype, autistic disorder, caenorhabditis elegans, fertility, genes, locomotion, models, genetic, missense mutation, tryptophanase, vertebrates, genetics, pten gene, nervous system development, autism spectrum disorder, inference, crispr", "note": "\u00a9 The Author(s) 2019. Published by Oxford University Press. All rights reserved. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model). \n\nReceived: 06 November 2018; Revision Received: 27 February 2019; Accepted: 04 March 2019; Published: 01 April 2019.", "abstract": "Autism spectrum disorder (ASD) involves thousands of alleles in over 850 genes, but the current functional inference tools are not sufficient to predict phenotypic changes. As a result, the causal relationship of most of these genetic variants in the pathogenesis of ASD has not yet been demonstrated and an experimental method prioritizing missense alleles for further intensive analysis is crucial. For this purpose, we have designed a pipeline that uses Caenorhabditis elegans as a genetic model to screen for phenotype-changing missense alleles inferred from human ASD studies. We identified highly conserved human ASD-associated missense variants in their C. elegans orthologs, used a CRISPR/Cas9-mediated homology-directed knock-in strategy to generate missense mutants and analyzed their impact on behaviors and development via several broad-spectrum assays. All tested missense alleles were predicted to perturb protein function, but we found only 70% of them showed detectable phenotypic changes in morphology, locomotion or fecundity. Our findings indicate that certain missense variants in the C. elegans orthologs of human CACNA1D, CHD7, CHD8, CUL3, DLG4, GLRA2, NAA15, PTEN, SYNGAP1 and TPH2 impact neurodevelopment and movement functions, elevating these genes as candidates for future study into ASD. Our approach will help prioritize functionally important missense variants for detailed studies in vertebrate models and human cells.", "date": "2019-07-01", "date_type": "published", "publication": "Human Molecular Genetics", "volume": "28", "number": "13", "publisher": "Oxford University Press", "pagerange": "2271-2281", "id_number": "CaltechAUTHORS:20190624-075623572", "issn": "0964-6906", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190624-075623572", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Simons Foundation", "grant_number": "367560" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM007616" } ] }, "doi": "10.1093/hmg/ddz051", "pmcid": "PMC6586145", "resource_type": "article", "pub_year": "2019", "author_list": "Wong, Wan-Rong; Brugman, Katherine I.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/4hnv2-na917", "eprint_id": 90532, "eprint_status": "archive", "datestamp": "2023-08-22 01:11:55", "lastmod": "2023-10-23 16:09:09", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Beltran-Toni", "name": { "family": "Beltran", "given": "Toni" }, "orcid": "0000-0002-5949-2615" }, { "id": "Barruso-Consuelo", "name": { "family": "Barruso", "given": "Consuelo" } }, { "id": "Birkle-Timothy-Y", "name": { "family": "Birkle", "given": "Timothy Y." } }, { "id": "Stevens-Lewis", "name": { "family": "Stevens", "given": "Lewis" } }, { "id": "Schwartz-Hillel-T", "name": { "family": "Schwartz", "given": "Hillel T." }, "orcid": "0000-0002-3448-8652" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Fradin-H\u00e9l\u00e8ne", "name": { "family": "Fradin", "given": "H\u00e9l\u00e8ne" }, "orcid": "0000-0003-4110-0983" }, { "id": "Gunsalus-Kristin", "name": { "family": "Gunsalus", "given": "Kristin" }, "orcid": "0000-0001-9769-4624" }, { "id": "Piano-Fabio", "name": { "family": "Piano", "given": "Fabio" } }, { "id": "Sharma-Garima", "name": { "family": "Sharma", "given": "Garima" } }, { "id": "Cerrato-Chiara", "name": { "family": "Cerrato", "given": "Chiara" } }, { "id": "Ahringer-Julie", "name": { "family": "Ahringer", "given": "Julie" }, "orcid": "0000-0002-7074-4051" }, { "id": "Mart\u00ednez-P\u00e9rez-Enrique", "name": { "family": "Mart\u00ednez-P\u00e9rez", "given": "Enrique" }, "orcid": "0000-0001-5813-0383" }, { "id": "Blaxter-Mark", "name": { "family": "Blaxter", "given": "Mark" }, "orcid": "0000-0003-2861-949X" }, { "id": "Sarkies-Peter", "name": { "family": "Sarkies", "given": "Peter" }, "orcid": "0000-0003-0279-6199" } ] }, "title": "Comparative Epigenomics Reveals that RNA Polymerase II Pausing and Chromatin Domain Organization Control Nematode piRNA Biogenesis", "ispublished": "pub", "full_text_status": "public", "keywords": "piwi-interacting small RNAs; C. elegans; evolution; chromatin; epigenetics; nematodes; comparative epigenomics", "note": "\u00a9 2019 The Author(s). Published by Elsevier under a Creative Commons license (Attribution 4.0 International (CC BY 4.0)). \n\nReceived 23 February 2018, Revised 6 December 2018, Accepted 27 December 2018, Available online 31 January 2019. \n\nWork in the Sarkies laboratory is funded by a grant from the Medical Research Council MC-A652-5PY80. P.S. was funded by an Imperial College Research Fellowship. L.S. was funded by a Bailie-Gifford PhD studentship. We thank the London Institute of Medical Sciences Genomics Facility for sequencing. Some sequencing was carried out at Edinburgh Genomics, which has core support from the NERC Biomolecular Analysis Facility award UKSBS PR18037. Work in the Mart\u00ednez-P\u00e9rez laboratory was funded by a grant from the Medical Research Council MC-A652-5PY60. G.S. was funded by a Newton International Fellowship (Royal Society). J.A. was funded by a Wellcome Senior Research Fellowship (101863). T.Y.B. was funded by a Genetics Society Summer Studentship to the Sarkies lab. We thank Christian Eckmann for sharing parn-1 (tm869) mutant worms and Ben Lehner, Matthias Merkenschlager, and Luis Arag\u00f3n for helpful comments on the manuscript. \n\nAuthor Contributions: Conceptualization, P.S., M.B., and T.B.; Methodology, T.B., P.S., E.M.P., and M.B.; Investigation, T.B., P.S., C.B., T.Y.B., and L.S.; Formal Analysis, T.B. and P.S.; Resources, J.A., G.S., C.C., H.S., P.W.S., F.P., K.G., and L.S.; Writing \u2013 Original Draft, P.S. and T.B.; Writing \u2013 Editing, P.S., T.B., M.B., E.M.P., and J.A.; Supervision, P.S., E.M.P., J.A., P.W.S., F.P., K.G., and M.B. \n\nData and Software Availability: Sequencing data has been submitted to the SRA Study SRP117954: Evolution of piRNAs in nematodes. The P. oxycercus and P. sambesii genomes have been uploaded to http://caenorhabditis.org/. \n\nThe authors declare no competing interests.\n\nPublished - 1-s2.0-S1534580718311262-main.pdf
Submitted - 281360.full.pdf
Supplemental Material - 1-s2.0-S1534580718311262-mmc1.pdf
Supplemental Material - 1-s2.0-S1534580718311262-mmc2.xlsx
Supplemental Material - 1-s2.0-S1534580718311262-mmc3.xlsx
Supplemental Material - 1-s2.0-S1534580718311262-mmc4.xlsx
Supplemental Material - 1-s2.0-S1534580718311262-mmc5.xlsx
Supplemental Material - 1-s2.0-S1534580718311262-mmc6.zip
Supplemental Material - 1-s2.0-S1534580718311262-mmc7.pdf
", "abstract": "Piwi-interacting RNAs (piRNAs) are important for genome regulation across metazoans, but their biogenesis evolves rapidly. In Caenorhabditis elegans, piRNA loci are clustered within two 3-Mb regions on chromosome IV. Each piRNA locus possesses an upstream motif that recruits RNA polymerase II to produce an \u223c28 nt primary transcript. We used comparative epigenomics across nematodes to gain insight into the origin, evolution, and mechanism of nematode piRNA biogenesis. We show that the piRNA upstream motif is derived from core promoter elements controlling snRNA transcription. We describe two alternative modes of piRNA organization in nematodes: in C. elegans and closely related nematodes, piRNAs are clustered within repressive H3K27me3 chromatin, while in other species, typified by Pristionchus pacificus, piRNAs are found within introns of active genes. Additionally, we discover that piRNA production depends on sequence signals associated with RNA polymerase II pausing. We show that pausing signals synergize with chromatin to control piRNA transcription.", "date": "2019-03-25", "date_type": "published", "publication": "Developmental Cell", "volume": "48", "number": "6", "publisher": "Cell Press", "pagerange": "793-810", "id_number": "CaltechAUTHORS:20181031-081252031", "issn": "1534-5807", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181031-081252031", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Medical Research Council (UK)", "grant_number": "MC-A652-5PY80" }, { "agency": "Imperial College London" }, { "agency": "University of Oxford" }, { "agency": "Natural Environment Research Council (NERC)", "grant_number": "UKSBS PR18037" }, { "agency": "Medical Research Council (UK)", "grant_number": "MC-A652-5PY60" }, { "agency": "Royal Society" }, { "agency": "Wellcome Trust", "grant_number": "101863" }, { "agency": "Genetics Society" } ] }, "doi": "10.1016/j.devcel.2018.12.026", "pmcid": "PMC6436959", "primary_object": { "basename": "1-s2.0-S1534580718311262-main.pdf", "url": "https://authors.library.caltech.edu/records/4hnv2-na917/files/1-s2.0-S1534580718311262-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S1534580718311262-mmc2.xlsx", "url": "https://authors.library.caltech.edu/records/4hnv2-na917/files/1-s2.0-S1534580718311262-mmc2.xlsx" }, { "basename": "1-s2.0-S1534580718311262-mmc4.xlsx", "url": "https://authors.library.caltech.edu/records/4hnv2-na917/files/1-s2.0-S1534580718311262-mmc4.xlsx" }, { "basename": "1-s2.0-S1534580718311262-mmc5.xlsx", "url": "https://authors.library.caltech.edu/records/4hnv2-na917/files/1-s2.0-S1534580718311262-mmc5.xlsx" }, { "basename": "1-s2.0-S1534580718311262-mmc7.pdf", "url": "https://authors.library.caltech.edu/records/4hnv2-na917/files/1-s2.0-S1534580718311262-mmc7.pdf" }, { "basename": "281360.full.pdf", "url": "https://authors.library.caltech.edu/records/4hnv2-na917/files/281360.full.pdf" }, { "basename": "1-s2.0-S1534580718311262-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/4hnv2-na917/files/1-s2.0-S1534580718311262-mmc1.pdf" }, { "basename": "1-s2.0-S1534580718311262-mmc3.xlsx", "url": "https://authors.library.caltech.edu/records/4hnv2-na917/files/1-s2.0-S1534580718311262-mmc3.xlsx" }, { "basename": "1-s2.0-S1534580718311262-mmc6.zip", "url": "https://authors.library.caltech.edu/records/4hnv2-na917/files/1-s2.0-S1534580718311262-mmc6.zip" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Beltran, Toni; Barruso, Consuelo; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/06yd3-h1j06", "eprint_id": 104015, "eprint_status": "archive", "datestamp": "2023-08-19 14:45:28", "lastmod": "2023-10-20 19:00:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Oh-Jun-Young", "name": { "family": "Oh", "given": "Jun Young" }, "orcid": "0000-0002-5158-9017" }, { "id": "Gharib-Shahla", "name": { "family": "Gharib", "given": "Shahla" } }, { "id": "Liu-Jonathan", "name": { "family": "Liu", "given": "Jonathan" } }, { "id": "Wang-Han", "name": { "family": "Wang", "given": "Han" }, "orcid": "0000-0002-1933-5762" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "DVC interneuron cGAL driver in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.\n\nReceived: December 12, 2018; Accepted: February 26, 2019; Published: March 6, 2019. \n\nFunding: R21 MH115454/MH/NIMH NIH HHS/United States. \n\nAuthor Contributions:\nJun Young Oh: Conceptualization, Methodology, Data curation, Investigation, Validation, Writing - original draft\nShahla Gharib: Investigation\nJonathan Liu: Conceptualization, Methodology, Supervision, Writing - review and editing\nHan Wang: Conceptualization, Methodology, Supervision, Writing - review and editing\nPaul Sternberg: Conceptualization, Methodology, Funding acquisition, Project administration, Supervision, Writing - review and editing.\n\nReviewed By: Ian Hope.\n\nPublished - Oh_2019_DVCcGal.pdf
", "abstract": "cGAL, a recently developed temperature-robust bipartite GAL4-UAS system in C. elegans, consists of two components: a cGAL \"driver\" that expresses the cGAL protein in specific cells using a promoter (i.e. neuron-specific or tissue-specific), and an \"effector\" that carries a gene of interest downstream of UAS (Wang et al., 2017). Crossing or combining a driver with an effector leads to the expression of the gene of interest in a cell-specific or tissue-specific manner.\n\nHere we report a new cGAL driver for the DVC interneuron. The ceh-63 promoter was chosen due to its restricted expression in the DVC neuron (Feng et al. 2012). The DVC interneuron driver construct containing the ceh-63 promoter (646 bp upstream of ATG translation start site) was injected into N2 and an integrated DVC driver line was generated. When crossed with the UAS-GFP effector strain (PS6843), the ceh-63 cGAL driver dictated GFP expression in the single DVC neuron (Figure 1), in addition to GFP in the coelomocyte from Punc-122::gfp co-injection marker. We did not observe GFP expression in uterus as reported by Feng et al., 2012.", "date": "2019-03-06", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "micropub.biology.000082", "id_number": "CaltechAUTHORS:20200624-132515714", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200624-132515714", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R21 MH115454" }, { "agency": "National Institute of Mental Health (NIMH)" } ] }, "doi": "10.17912/micropub.biology.000082", "pmcid": "PMC7255773", "primary_object": { "basename": "Oh_2019_DVCcGal.pdf", "url": "https://authors.library.caltech.edu/records/06yd3-h1j06/files/Oh_2019_DVCcGal.pdf" }, "resource_type": "article", "pub_year": "2019", "author_list": "Oh, Jun Young; Gharib, Shahla; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/3p7xk-8gf53", "eprint_id": 94241, "eprint_status": "archive", "datestamp": "2023-08-19 14:33:09", "lastmod": "2023-10-20 17:48:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chai-C-M", "name": { "family": "Chai", "given": "C. M." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "P. W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Interneuron Control of C. elegans Diapause Entry", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 Oxford University Press. \n\nPublished: 11 February 2019.", "abstract": "[no abstract]", "date": "2019-03", "date_type": "published", "publication": "Integrative and Comparative Biology", "volume": "59", "number": "S1", "publisher": "Oxford University Press", "pagerange": "E34", "id_number": "CaltechAUTHORS:20190328-095430387", "issn": "1540-7063", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190328-095430387", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1093/icb/icz003", "resource_type": "article", "pub_year": "2019", "author_list": "Chai, C. M. and Sternberg, P. W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/hf80x-pmv73", "eprint_id": 92449, "eprint_status": "archive", "datestamp": "2023-08-19 14:12:03", "lastmod": "2023-10-20 22:08:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Ablating the fixed lineage conjecture: Commentary on Kimble 1981", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2018 Published by Elsevier Inc. Under an Elsevier user license. \n\nAvailable online 24 January 2019.", "abstract": "In 1981 Judith Kimble published what became a classic paper in developmental biology (Kimble, 1981). The history of nematode cell lineage dating back to Boveri and zur Strassen in the 19th century indicated that nematodes had a fixed cell lineage. This invariance was confirmed in a modern study by Sulston and Horvitz (1977). Kimble's PhD work confirmed this except for two cases of indeterminate development (Kimble and Hirsh, 1979). As a postdoc, Kimble followed up using a laser microbeam system developed by John White (Sulston and White, 1980a, Sulston and White, 1980b) to selectively remove cells. With this system, if you can see the cell with Nomarski DIC optics, you can kill it. This paper laid the groundwork for analysis of the AC-VU decision, hence for the genetic analysis of LIN-12/Notch signaling (Greenwald, 2012), and for vulval induction, hence for the genetic analysis of the EGFR-RAS pathway (Sternberg, 2006).", "date": "2019-02-01", "date_type": "published", "publication": "Developmental Biology", "volume": "446", "number": "1", "publisher": "Elsevier", "pagerange": "1-16", "id_number": "CaltechAUTHORS:20190124-104128076", "issn": "0012-1606", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190124-104128076", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.ydbio.2018.12.024", "resource_type": "article", "pub_year": "2019", "author_list": "Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/e5cym-w6e82", "eprint_id": 94702, "eprint_status": "archive", "datestamp": "2023-08-19 13:49:17", "lastmod": "2023-10-20 18:11:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "J." }, "orcid": "0000-0002-7259-8107" }, { "id": "Cho-J", "name": { "family": "Cho", "given": "J." } }, { "id": "Gao-S", "name": { "family": "Gao", "given": "S." } }, { "id": "Grove-C-A", "name": { "family": "Grove", "given": "C." }, "orcid": "0000-0001-9076-6015" }, { "id": "Harrison-M-C", "name": { "family": "Harrison", "given": "M. C." } }, { "id": "Howe-K", "name": { "family": "Howe", "given": "K." } }, { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "R." }, "orcid": "0000-0002-8151-7479" }, { "id": "Mendel-J", "name": { "family": "Mendel", "given": "J." } }, { "id": "Muller-H-M", "name": { "family": "Muller", "given": "H.-M." } }, { "id": "Raciti-D", "name": { "family": "Raciti", "given": "D." } }, { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "K." }, "orcid": "0000-0002-1706-4196" }, { "id": "Berriman-M", "name": { "family": "Berriman", "given": "M." }, "orcid": "0000-0002-9581-0377" }, { "id": "Stein-L-D", "name": { "family": "Stein", "given": "L." }, "orcid": "0000-0002-1983-4588" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "P. W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The Gene Ontology Resource: 20 years and still GOing strong", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived September 22, 2018; Revised October 16, 2018; Editorial Decision October 17, 2018; Accepted October 17, 2018. Published: 05 November 2018. \n\nWe would like to thank the domain experts Peter Yurchenco, Sylvie Ricard-Blum, Rachel Lennon, Geoff Meyer, David Sherwood and Jeff Miner for discussions leading to the refinement of the extracellular matrix area. We also want to thank all the contributors to the GO resource over the last 20 years (http://geneontology.org/page/acknowledgments-contributors), and all the authors of papers represented in the GO knowledgebase (https://www.ncbi.nlm.nih.gov/pubmed/?term=loprovGeneOntol[SB]). \n\nThe GO resource is supported by grant from the National Human Genome Research Institute [U41 HG02273 to P.D.T., P.W.S., S.E.L., J.M.C., J.A.B. and supplements to grant U41 HG001315 to J.M.C., U24 HG002223 to P.W.S.]. In addition, GO Consortium members are also supported by diverse funding sources: dictyBase is supported by the National Institute of General Medical Sciences [GM064426, GM087371 to R.L.C.]; The EcoliWiki group is supported by the National Institutes of Health [GM089636]; National Science Foundation [1565146]; EMBL-EBI is funded by EMBL core funds; FlyBase is supported by the UK Medical Research Council [MR/N030117/1]; National Human Genome Research Institute [U41HG000739]; InterPro is funded by the Wellcome Trust [108433/Z/15/Z]; Biotechnology and Biological Sciences Research Council [BB/N00521X/1, BB/N019172/1, BB/L024136/1 to RDF]; The Institute for Genome Sciences GO-related work on ECO is supported by the National Science Foundation [1458400]; The Gene Regulation Consortium (GRECO) is supported by Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC) COST Action [grant CA15205]; A.L. and M.L.A. are also supported by the Research Council of Norway [project 247727]; The Institute of Cardiovascular Science, University College London (R. Lovering's group) is supported by British Heart Foundation [RG/13/5/30112]; Parkinson's UK [G-1307]; National Institute for Health Research University College London Hospitals Biomedical Research Centre; IntAct and the Complex Portal are supported by the European Molecular Biology Laboratory core funds; PomBase is supported by the Wellcome Trust [104967/Z/14/Z to S.G.O.]; MGI is supported by the National Human Genome Research Institute [HG 000330, HG 002273]; RGD is supported by and by the National Heart, Lung, and Blood Institute [HL 64541]; The UniProt Consortium is supported by the National Eye Institute, National Human Genome Research Institute, National Heart, Lung and Blood Institute, National Institute of Allergy and Infectious Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of General Medical Sciences, and National Institute of Mental Health of the National Institutes of Health under Award Number [U24HG007822], National Human Genome Research Institute under Award Numbers [U41HG007822 and U41HG002273]; National Institute of General Medical Sciences under Award Numbers [R01GM080646, P20GM103446 and U01GM120953]; Biotechnology and Biological Sciences Research Council [BB/M011674/1]; the British Heart Foundation [RG/13/5/30112]; Swiss Federal Government through the State Secretariat for Education, Research and Innovation (SERI); European Molecular Biology Laboratory core funds; The TAIR project is funded by academic institutional, corporate, and individual subscriptions. TAIR is administered by the 501(c)(3) non-profit Phoenix Bioinformatics; WormBase is supported by the US National Human Genome Research Institute [U24-HG002223]; UK Medical Research Council [MR/L001220]; UK Biotechnology and Biological Sciences Research Council [BB/K020080]; ZFIN also supported by the National Human Genome Research Institute [U41 HG002659 to M.W.]. The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding agencies. Funding for open access charges: National Human Genome Research Institute [U41 HG02273]. \n\nConflict of interest statement. None declared.\n\nPublished - gky1055.pdf
", "abstract": "The Gene Ontology resource (GO; http://geneontology.org) provides structured, computable knowledge regarding the functions of genes and gene products. Founded in 1998, GO has become widely adopted in the life sciences, and its contents are under continual improvement, both in quantity and in quality. Here, we report the major developments of the GO resource during the past two years. Each monthly release of the GO resource is now packaged and given a unique identifier (DOI), enabling GO-based analyses on a specific release to be reproduced in the future. The molecular function ontology has been refactored to better represent the overall activities of gene products, with a focus on transcription regulator activities. Quality assurance efforts have been ramped up to address potentially out-of-date or inaccurate annotations. New evidence codes for high-throughput experiments now enable users to filter out annotations obtained from these sources. GO-CAM, a new framework for representing gene function that is more expressive than standard GO annotations, has been released, and users can now explore the growing repository of these models. We also provide the 'GO ribbon' widget for visualizing GO annotations to a gene; the widget can be easily embedded in any web page.", "date": "2019-01-08", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "47", "number": "D1", "publisher": "Oxford University Press", "pagerange": "D330-D338", "id_number": "CaltechAUTHORS:20190415-100854557", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190415-100854557", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U41 HG02273" }, { "agency": "NIH", "grant_number": "U41 HG001315" }, { "agency": "NIH", "grant_number": "U24 HG002223" }, { "agency": "NIH", "grant_number": "GM064426" }, { "agency": "NIH", "grant_number": "GM087371" }, { "agency": "NIH", "grant_number": "GM089636" }, { "agency": "NSF", "grant_number": "DBI-1565146" }, { "agency": "European Molecular Biology Laboratory (EMBL)" }, { "agency": "Medical Research Council (UK)", "grant_number": "MR/N030117/1" }, { "agency": "NIH", "grant_number": "U41HG000739" }, { "agency": "Wellcome Trust", "grant_number": "108433/Z/15/Z" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/N00521X/1" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/N019172/1" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/L024136/1" }, { "agency": "NSF", "grant_number": "DBI-1458400" }, { "agency": "Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC)", "grant_number": "CA15205" }, { "agency": "Research Council of Norway", "grant_number": "247727" }, { "agency": "University College London" }, { "agency": "British Heart Foundation", "grant_number": "RG/13/5/30112" }, { "agency": "Parkinson's UK", "grant_number": "G-1307" }, { "agency": "Wellcome Trust", "grant_number": "104967/Z/14/Z" }, { "agency": "NIH", "grant_number": "HG 000330" }, { "agency": "NIH", "grant_number": "HG 002273" }, { "agency": "NIH", "grant_number": "HL 64541" }, { "agency": "National Eye Institute" }, { "agency": "National Institute of Allergy and Infectious Diseases" }, { "agency": "National Institute of Diabetes and Digestive and Kidney Diseases" }, { "agency": "National Institute of General Medical Sciences" }, { "agency": "NIH", "grant_number": "U24HG007822" }, { "agency": "NIH", "grant_number": "U41HG007822" }, { "agency": "NIH", "grant_number": "U41HG002273" }, { "agency": "NIH", "grant_number": "R01GM080646" }, { "agency": "NIH", "grant_number": "P20GM103446" }, { "agency": "NIH", "grant_number": "U01GM120953" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/M011674/1" }, { "agency": "Swiss Federal Government" }, { "agency": "State Secretariat for Education, Research and Innovation (SERI)" }, { "agency": "Medical Research Council (UK)", "grant_number": "MR/L001220" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/K020080" }, { "agency": "NIH", "grant_number": "U41 HG002659" } ] }, "corp_creators": { "items": [ "Gene Ontology Consortium" ] }, "doi": "10.1093/nar/gky1055", "pmcid": "PMC6323945", "primary_object": { "basename": "gky1055.pdf", "url": "https://authors.library.caltech.edu/records/e5cym-w6e82/files/gky1055.pdf" }, "resource_type": "article", "pub_year": "2019", "author_list": "Chan, J.; Cho, J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/16kyp-tr088", "eprint_id": 91435, "eprint_status": "archive", "datestamp": "2023-08-19 13:36:02", "lastmod": "2023-10-19 22:30:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Opening up a large can of worms", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2018 Springer Nature Publishing AG. \n\nPublished 04 December 2018. \n\nThe author declares no competing interests.", "abstract": "The genomes for essentially all worm parasites of humans are in hand thanks to a new study. Now we have to use them.", "date": "2019-01", "date_type": "published", "publication": "Nature Genetics", "volume": "51", "number": "1", "publisher": "Nature Publishing Group", "pagerange": "10-11", "id_number": "CaltechAUTHORS:20181204-114817167", "issn": "1061-4036", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181204-114817167", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1038/s41588-018-0317-3", "resource_type": "article", "pub_year": "2019", "author_list": "Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/bb1ps-94z46", "eprint_id": 104105, "eprint_status": "archive", "datestamp": "2023-08-19 12:49:22", "lastmod": "2023-10-20 19:05:08", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cho-Jaehyoung", "name": { "family": "Cho", "given": "Jaehyoung" } }, { "id": "Grove-Christian-A", "name": { "family": "Grove", "given": "Christian A." }, "orcid": "0000-0001-9076-6015" }, { "id": "Van-Auken-Kimberly", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "Gao-Sibyl", "name": { "family": "Gao", "given": "Sibyl" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "2018 Update on Protein-Protein Interaction Data in WormBase", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2018 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.\n\nReceived: October 9, 2018;\nAccepted: November 21, 2018;\nPublished: November 26, 2018.\n\nFunding:\nSupported by NIH U24 HG002223 (to PWS).\n\nReviewed By:\nWeiwei Zhong.\n\nPublished - 10.17912\uf022micropub.biology.000074.pdf
", "abstract": "Protein interaction is an important data type to understand the biological function of proteins involved in the interaction, and helps researchers to deduce the biological nature of unknown proteins from the well-characterized functions of their interaction partners. High-throughput studies, coupled with the aggregation of individual experiments, provides a global 'snapshot' of the protein interactions occurring at all levels of biological processes or circumstances. This snapshot of the interaction network, the interactome, is important to understand the overall events up to the level of comparison between species or pathway simulation, or to find new factors yet undefined in the processes, or to add details to the biological processes and pathways. \n\n As of September 2018, WormBase (www.wormbase.org) (Lee et al. 2018) contains 28,279 physical protein-protein interactions for the roundworm Caenorhabditis elegans. Among these, 1500 protein-protein interactions have been curated by BioGRID as a collaboration with WormBase. Within the data set, 17,990 protein-protein interactions are unique, and 6,079 unique genes are involved in these interactions. In order to visualize the overall interaction map, a network diagram for all the unique interactions was generated by using the 'Cytoscape' program, version 3.6.1 (Shannon et al. 2003) (Figure 1A). These numbers represent a 108% increase in the number of interaction annotations since last year, 2017. These interaction data were curated from 1,251 peer-reviewed papers, which were selected from the literature by 'Textpresso Central' using automatic SVM (Support Vector Machine)-based text mining approaches (Fang et al. 2012; M\u00fcller et al. 2018) and manual verification. Compared to other databases providing C. elegans protein-protein interaction, WormBase now presents the largest data set, which has 1.72-fold more interaction annotations than IMEx (Orchard et al. 2012) and 4.51-fold more than BioGRID (Chatr-Aryamontri et al. 2017) (Figure 1B). Most significantly, WormBase now houses the complete protein interaction data from almost all of the C. elegans literature published from 1993 to 2018. The data sets presented at IMEx and BioGRID are annotated from 253 and 174 papers, respectively. All the physical interaction data in WormBase are supported by experimental evidence from original research papers. The statistics of the detection methods used as experimental evidence are shown in Figure 1C. The majority of the interaction data came from high throughput analysis such as large-scale yeast two-hybrid assays or mass-spectrometry, however, a significant portion of the data (13.1%) are supported by more direct detection methods using small-scale, low throughput methods such as co-immunoprecipitation or co-crystallography (Figure 1C). \n\n In WormBase, protein-protein interaction data can be found as a subclass of physical interaction data in the 'Interactions widget' on the gene report page. The Interactions widget provides all types of interaction data related to the gene of interest, such as physical, genetic, regulatory, and predicted interactions. All the interaction data are represented together in a graph created with 'Cytoscape.js' and a table. In the table, the gene names of interaction partners (bait-target) in the interaction are displayed along with the publication. The interaction details including the detection method are also captured in the summary and the remark field in the Interactions page. Users can query the data by using the search bar on the WormBase front page or download all the available data files from the WormBase FTP site (ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/species/c_elegans/PRJNA13758\n/annotation/c_elegans.PRJNA13758.WSXXX.interactions.txt.gz, where WSXXX is the database version release, like \"WS267\"). \n \n All the interaction data in WormBase will be available soon at the new information resource for multiple model organisms, the Alliance of Genome Resources (https://www.alliancegenome.org/). This site will integrate all the interaction data from human and from model organisms C. elegans, budding yeast (Saccharomyces cerevisiae), fruit fly (Drosophila melanogaster), zebrafish (Danio rerio), mouse (Mus musculus) and rat (Rattus norvegicus). Integrated views of interaction data from diverse model organisms will be extremely helpful to build interaction databases for species-to-species comparison, and to establish a disease model quickly based on the database. For the most efficient analysis of the interaction data in WormBase, we are now working on developing a new 'Venn diagram tool' and integrating the 'Gene Set Enrichment Analysis tool' (https://wormbase.org/tools/enrichment/tea/tea.cgi) into the Interactions widget. We will continue to curate other types of macro-molecular interactions including protein-DNA, protein-RNA and RNA-RNA interactions, as well as newly reported protein-protein interaction data to serve our research community.", "date": "2018-11-26", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "micropub.biology.000074", "id_number": "CaltechAUTHORS:20200629-072302491", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200629-072302491", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U24 HG002223" } ] }, "doi": "10.17912/micropub.biology.000074", "pmcid": "PMC7255808", "primary_object": { "basename": "10.17912\uf022micropub.biology.000074.pdf", "url": "https://authors.library.caltech.edu/records/bb1ps-94z46/files/10.17912\uf022micropub.biology.000074.pdf" }, "resource_type": "article", "pub_year": "2018", "author_list": "Cho, Jaehyoung; Grove, Christian A.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ygyrq-wfa17", "eprint_id": 89891, "eprint_status": "archive", "datestamp": "2023-08-19 12:34:15", "lastmod": "2023-10-23 15:44:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Han", "name": { "family": "Wang", "given": "Han" }, "orcid": "0000-0002-1933-5762" }, { "id": "Park-Heenam", "name": { "family": "Park", "given": "Heenam" }, "orcid": "0000-0001-7911-5828" }, { "id": "Liu-Jonathan", "name": { "family": "Liu", "given": "Jonathan" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "An Efficient Genome Editing Strategy To Generate Putative Null Mutants in Caenorhabditis elegans Using CRISPR/Cas9", "ispublished": "pub", "full_text_status": "public", "keywords": "CRISPR/Cas9, C. elegans, null allele, STOP-IN, genome editing", "note": "\u00a9 2018 Wang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived August 10, 2018; Accepted September 9, 2018; Early online September 17, 2018. \n\nWe thank Tsui-Fen Chou for providing Cas9 protein, Shohei Mitani for the balancer strain FX30236, and Michael Nonet for the plasmid pHO4d-Cas9. We thank Behnon Farboud and Barbara Meyer for sharing unpublished results and Hillel Schwartz for discussion. We also thank the members from the Sternberg lab for comments on the manuscript. Some strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). WormBase annotations were crucial for choosing target genes and location of guide sequences. This work was supported NIH (K99GM126137 to H.W., R24OD023041 to P.W.S., and T32GM007616, which supported J.L.).\n\nPublished - 3607.full.pdf
Submitted - 391243.full.pdf
Supplemental Material - 7086647.zip
", "abstract": "Null mutants are essential for analyzing gene function. Here, we describe a simple and efficient method to generate Caenorhabditis elegans null mutants using CRISPR/Cas9 and short single stranded DNA oligo repair templates to insert a universal 43-nucleotide-long knock-in cassette (STOP-IN) into the early exons of target genes. This STOP-IN cassette has stop codons in all three reading frames and leads to frameshifts, which will generate putative null mutations regardless of the reading frame of the insertion position in exons. The STOP-IN cassette also contains an exogenous Cas9 target site that allows further genome editing and provides a unique sequence that simplifies the identification of successful insertion events via PCR. As a proof of concept, we inserted the STOP-IN cassette right at a Cas9 target site in aex\u20112 to generate new putative null alleles by injecting preassembled Cas9 ribonucleoprotein and a short synthetic single stranded DNA repair template containing the STOP-IN cassette and two \u223c35-nucleotide-long homology arms identical to the sequences flanking the Cas9 cut site. We showed that these new aex\u20112 alleles phenocopied an existing loss-of-function allele of aex-2. We further showed that the new aex\u20112 null alleles could be reverted back to the wild-type sequence by targeting the exogenous Cas9 cut site included in the STOP-IN cassette and providing a single stranded wild-type DNA repair oligo. We applied our STOP-IN method to generate new putative null mutants for 20 additional genes, including three pharyngeal muscle-specific genes (clik-1, clik-2, and clik-3), and reported a high insertion rate (46%) based on the animals we screened. We showed that null mutations of clik-2 cause recessive lethality with a severe pumping defect and clik-3 null mutants have a mild pumping defect, while clik-1 is dispensable for pumping. We expect that the knock-in method using the STOP-IN cassette will facilitate the generation of new null mutants to understand gene function in C. elegans and other genetic model organisms.", "date": "2018-11-01", "date_type": "published", "publication": "G3", "volume": "8", "number": "11", "publisher": "Genetics Society of America", "pagerange": "3607-3616", "id_number": "CaltechAUTHORS:20180924-133547145", "issn": "2160-1836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180924-133547145", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P40 OD010440" }, { "agency": "NIH", "grant_number": "K99GM126137" }, { "agency": "NIH", "grant_number": "R24OD023041" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM007616" } ] }, "doi": "10.1534/g3.118.200662", "pmcid": "PMC6222585", "primary_object": { "basename": "7086647.zip", "url": "https://authors.library.caltech.edu/records/ygyrq-wfa17/files/7086647.zip" }, "related_objects": [ { "basename": "3607.full.pdf", "url": "https://authors.library.caltech.edu/records/ygyrq-wfa17/files/3607.full.pdf" }, { "basename": "391243.full.pdf", "url": "https://authors.library.caltech.edu/records/ygyrq-wfa17/files/391243.full.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Wang, Han; Park, Heenam; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/cp9d4-0j504", "eprint_id": 88352, "eprint_status": "archive", "datestamp": "2023-08-21 23:54:08", "lastmod": "2023-10-23 15:55:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Angeles-Albores-David", "name": { "family": "Angeles-Albores", "given": "David" }, "orcid": "0000-0001-5497-8264" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Using Transcriptomes as Mutant Phenotypes Reveals Functional Regions of a Mediator Subunit in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "Genetic interactions; Transcriptome; Mediator; Wnt; Ras; Dominance; Cdk8", "note": "\u00a9 2018 Genetics Society of America. \n\nReceived May 12, 2018. Revision received June 29, 2018. Accepted July 5, 2018. \n\nThis article would not be possible without help from Igor Antoshechkin and Vijaya Kumar who performed the library preparation and sequencing. Han Wang, Hillel Schwartz, Erich Schwarz, and Carmie Puckett Robinson provided valuable input throughout the project. This work was supported by National Institutes of Health (NIH) grant U41 HG002223, by the Millard and Muriel Jacobs Genetics and Genomics Laboratory at California Institute of Technology, and by the Howard Hughes Medical Institute, with which Paul W. Sternberg was an investigator.\n\nSubmitted - 210724.full.pdf
Supplemental Material - SI1_dpy_22_results.csv
", "abstract": "Although transcriptomes have recently been used as phenotypes with which to perform epistasis analyses, they are not yet used to study intragenic function/structure relationships. We developed a theoretical framework to study allelic series using transcriptomic phenotypes. As a proof-of-concept, we apply our methods to an allelic series of dpy-22, a highly pleiotropic Caenorhabditis elegans gene orthologous to the human gene MED12, which encodes a subunit of the Mediator complex. Our methods identify functional units within dpy-22 that modulate Mediator activity upon various genetic programs, including the Wnt and Ras modules.", "date": "2018-09", "date_type": "published", "publication": "Genetics", "volume": "210", "number": "1", "publisher": "Genetics Society of America", "pagerange": "15-24", "id_number": "CaltechAUTHORS:20180730-102625156", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180730-102625156", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U41 HG002223" }, { "agency": "Millard and Muriel Jacobs Genetics and Genomics Laboratory" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1534/genetics.118.301133", "pmcid": "PMC6116950", "primary_object": { "basename": "210724.full.pdf", "url": "https://authors.library.caltech.edu/records/cp9d4-0j504/files/210724.full.pdf" }, "related_objects": [ { "basename": "SI1_dpy_22_results.csv", "url": "https://authors.library.caltech.edu/records/cp9d4-0j504/files/SI1_dpy_22_results.csv" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Angeles-Albores, David and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ppf0y-z0a57", "eprint_id": 104154, "eprint_status": "archive", "datestamp": "2023-08-19 11:11:02", "lastmod": "2023-10-20 19:08:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cao-Mengyi", "name": { "family": "Cao", "given": "Mengyi" } }, { "id": "Chai-Cynthia-M", "name": { "family": "Chai", "given": "Cynthia" } }, { "id": "Liu-Jonathan", "name": { "family": "Liu", "given": "Jonathan" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Application of the red-shifted channelrhodopsin Chrimson for the Caenorhabditis elegans cGAL bipartite system", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2018 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: August 7, 2018; Accepted: August 21, 2018; Published: August 22, 2018. \n\nWe thank Dr. Han Wang for his comments, suggestions, and support. \n\nFunding: R21 MH115454/MH/NIMH NIH HHS/United States\n\nPublished - cao_v3_2018_chrimson.pdf
", "abstract": "Channelrhodopsins are light-gated ion channels that serve as photoreceptors in photosynthetic microbes and have been applied as crucial optogenetic tools in genetic model organisms. When expressed in animals, they enable light-inducible control of ionic membrane permeability, which directly manipulates the activity of neurons expressing the protein. The application of channelrhodopsin-based optogenetics is particularly powerful when used in conjugation with the cGAL (GAL4-UAS) bipartite system (Wang, 2017). The mating of neuron-specific GAL4 driver lines to new channelrhodopsin effector lines could expand the genetic toolkit to perturb and manipulate neural circuits in the organism. \n\nBlue light-gated channelrhodopsins have been widely used in C. elegans neurobiology but often have to be performed in lite-1(ce314) mutant backgrounds because short-wavelength blue light is an aversive cue in wild-type animals and directly affects C. elegans neuronal physiology. Previously, a red light-gated variant of channelrhodopsin, termed Chrimson, has been successfully applied in Drosophila and mice, and has recently been codon-optimized for use in C. elegans (Klapoetke, 2014; Schild, 2015). \n\nHere, we constructed a Chrimson (15xUAS::chrimson::gfp) cGAL effector line. We introduced the UAS::chrimson::gfp effector DNA construct as an extrachromosomal array into a previously published cGAL pan-neuronal driver line (PS6961 syIs334) and generated integrants on chromosome II (PS8023, syIs503) and chromosome V (PS8024, syIs504) (Table 1) via standard X-ray irradiation. We showed Chrimson-GFP expression in the C. elegans head and tail neurons (Fig. 1A-1D). We also showed that red light could induce a seizure-like motility phenotype in C. elegans expressing Chrimson-GFP in a pan-neuronal manner (videos), while the negative controls expressing only the effector, or without light induction showed regular motility as expected (Table 2). The body curvature maps from normal and seizure-like motilities showed distinct patterns (Fig. 1E and 1F). We report the effector construct of red-light-gated channelrhodopsin Chrimson as an addition to our cGAL toolkit, which could be widely used in future research to overcome the technical restrictions of blue light-gated channelrhodopsins in C. elegans.", "date": "2018-08-22", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "10.17912/2JGW-FJ52", "id_number": "CaltechAUTHORS:20200630-074613816", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200630-074613816", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R21 MH115454" }, { "agency": "National Institute of Mental Health (NIMH)" } ] }, "doi": "10.17912/2JGW-FJ52", "pmcid": "PMC7282527", "primary_object": { "basename": "cao_v3_2018_chrimson.pdf", "url": "https://authors.library.caltech.edu/records/ppf0y-z0a57/files/cao_v3_2018_chrimson.pdf" }, "resource_type": "article", "pub_year": "2018", "author_list": "Cao, Mengyi; Chai, Cynthia; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/r5mrq-0dw90", "eprint_id": 88806, "eprint_status": "archive", "datestamp": "2023-08-19 11:03:06", "lastmod": "2023-10-18 22:19:32", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kanzaki-Natsumi", "name": { "family": "Kanzaki", "given": "Natsumi" }, "orcid": "0000-0001-8752-1674" }, { "id": "Tsai-Isheng-J", "name": { "family": "Tsai", "given": "Isheng J." }, "orcid": "0000-0002-2123-5058" }, { "id": "Tanaka-Ryusei", "name": { "family": "Tanaka", "given": "Ryusei" } }, { "id": "Hunt-Vicky-L", "name": { "family": "Hunt", "given": "Vicky L." } }, { "id": "Liu-Dang", "name": { "family": "Liu", "given": "Dang" }, "orcid": "0000-0002-7805-889X" }, { "id": "Tsuyama-Kenji", "name": { "family": "Tsuyama", "given": "Kenji" }, "orcid": "0000-0003-4698-9961" }, { "id": "Maeda-Yasunobu", "name": { "family": "Maeda", "given": "Yasunobu" } }, { "id": "Namai-Satoshi", "name": { "family": "Namai", "given": "Satoshi" } }, { "id": "Kumagai-Ryohei", "name": { "family": "Kumagai", "given": "Ryohei" } }, { "id": "Tracey-Alan", "name": { "family": "Tracey", "given": "Alan" } }, { "id": "Holroyd-Nancy", "name": { "family": "Holroyd", "given": "Nancy" } }, { "id": "Doyle-Stephen-R", "name": { "family": "Doyle", "given": "Stephen R." }, "orcid": "0000-0001-9167-7532" }, { "id": "Woodruff-G-C", "name": { "family": "Woodruff", "given": "Gavin C." } }, { "id": "Murase-Kazunori", "name": { "family": "Murase", "given": "Kazunori" } }, { "id": "Kitazume-Hiromi", "name": { "family": "Kitazume", "given": "Hiromi" } }, { "id": "Chai-Cynthia-M", "name": { "family": "Chai", "given": "Cynthia" } }, { "id": "Akagi-Allison", "name": { "family": "Akagi", "given": "Allison" } }, { "id": "Panda-Oishika", "name": { "family": "Panda", "given": "Oishika" }, "orcid": "0000-0002-1217-8231" }, { "id": "Ke-Huei-Mien", "name": { "family": "Ke", "given": "Huei-Mien" } }, { "id": "Schroeder-Frank-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" }, { "id": "Wang-John", "name": { "family": "Wang", "given": "John" } }, { "id": "Berriman-Matthew", "name": { "family": "Berriman", "given": "Matthew" }, "orcid": "0000-0002-9581-0377" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Sugimoto-Asako", "name": { "family": "Sugimoto", "given": "Asako" }, "orcid": "0000-0001-6001-4293" }, { "id": "Kikuchi-Taisei", "name": { "family": "Kikuchi", "given": "Taisei" }, "orcid": "0000-0003-2759-9167" } ] }, "title": "Biology and genome of a newly discovered sibling species of Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2018. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 08 December 2017; Accepted 19 July 2018; Published\n10 August 2018. \n\nThis work was supported by Japan Society for the Promotion of Science (JSPS) KAKENHI Grant Numbers 26292178, 16H04722, and 15K14503. V.L.H. was supported by JSPS International Research Fellowship, A.T., N.H., S.R.D., and M.B. by the core funding at the Wellcome Trust Sanger Institute (grant no. 206194), P.W.S. by Howard Hughes Medical Institute. Genome data analyses were partly performed using the DDBJ supercomputer system. We thank Akemi Yoshida, Mark Bligh, Mohammad-Masum Billah, Tanzila Afrin, Aya Adachi, Shakhinur Islam Mondal, Arzuba Akter, Haruhiko Maruyama, Tzu-hao Kuo, Karen Brooks, Michelle Smith for assistance and comments. \n\nAuthor Contributions: T.K. and N.K. conceived the study. P.W.S., A.S., F.S., I.J.T., N.K., and T.K. contributed to study design. V.L.H., A.S., I.J.T., P.W.S., N.K., and T.K. wrote the manuscript with inputs from others. N.K., R.T., K.T., S.N., R.K., H.K., H.T., C.C., A.A., O.P., and J.W. conducted experiments. N.K. and G.C.W. provided the strains. I.J.T., A.T., S.R.D., N.H., T.K., and M.B. completed genome assembly. V.L.H., Y.M., K.M., D.L., I.J.T., and T.K. analysed genome data. \n\nThe authors declare no competing interests. \n\nData availability: All sequence data from the C. elegans sibling genome project have been deposited at DDBJ/ENA/GenBank under BioProject accession PRJDB5687. Taxonomic descriptions were deposited at Zoobank. Nematode specimen and strains are available from T. Kikuchi or N. Kanzaki on request. All relevant data are available from the corresponding authors upon reasonable request.\n\nPublished - 41467_2018_Article_5712.pdf
Supplemental Material - 41467_2018_5712_MOESM1_ESM.pdf
Supplemental Material - 41467_2018_5712_MOESM2_ESM.pdf
Supplemental Material - 41467_2018_5712_MOESM3_ESM.xlsx
", "abstract": "A 'sibling' species of the model organism Caenorhabditis elegans has long been sought for use in comparative analyses that would enable deep evolutionary interpretations of biological phenomena. Here, we describe the first sibling species of C. elegans, C. inopinata n. sp., isolated from fig syconia in Okinawa, Japan. We investigate the morphology, developmental processes and behaviour of C. inopinata, which differ significantly from those of C. elegans. The 123-Mb C. inopinata genome was sequenced and assembled into six nuclear chromosomes, allowing delineation of Caenorhabditis genome evolution and revealing unique characteristics, such as highly expanded transposable elements that might have contributed to the genome evolution of C. inopinata. In addition, C. inopinata exhibits massive gene losses in chemoreceptor gene families, which could be correlated with its limited habitat area. We have developed genetic and molecular techniques for C. inopinata; thus C. inopinata provides an exciting new platform for comparative evolutionary studies.", "date": "2018-08-10", "date_type": "published", "publication": "Nature Communications", "volume": "9", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 3216", "id_number": "CaltechAUTHORS:20180815-073051892", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180815-073051892", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Japan Society for the Promotion of Science (JSPS)", "grant_number": "26292178" }, { "agency": "Japan Society for the Promotion of Science (JSPS)", "grant_number": "16H04722" }, { "agency": "Japan Society for the Promotion of Science (JSPS)", "grant_number": "15K14503" }, { "agency": "Wellcome Trust", "grant_number": "206194" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1038/s41467-018-05712-5", "pmcid": "PMC6086898", "primary_object": { "basename": "41467_2018_5712_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/r5mrq-0dw90/files/41467_2018_5712_MOESM1_ESM.pdf" }, "related_objects": [ { "basename": "41467_2018_5712_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/r5mrq-0dw90/files/41467_2018_5712_MOESM2_ESM.pdf" }, { "basename": "41467_2018_5712_MOESM3_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/r5mrq-0dw90/files/41467_2018_5712_MOESM3_ESM.xlsx" }, { "basename": "41467_2018_Article_5712.pdf", "url": "https://authors.library.caltech.edu/records/r5mrq-0dw90/files/41467_2018_Article_5712.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Kanzaki, Natsumi; Tsai, Isheng J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/1kst0-m8x45", "eprint_id": 90238, "eprint_status": "archive", "datestamp": "2023-08-19 10:05:49", "lastmod": "2023-10-18 23:18:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cho-Julie-Y", "name": { "family": "Cho", "given": "Julie" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul" }, "orcid": "0000-0002-7699-0173" }, { "id": "Colon-Ramos-D", "name": { "family": "Colon-Ramos", "given": "Daniel" } }, { "id": "Teng-Christopher", "name": { "family": "Teng", "given": "Christopher" } } ] }, "title": "Microfluidic platform to study pressure-induced changes in neurons", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2018 The Authors. This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.\n\nPublished - Microfluidic_platform_to_study_pressure-induced_changes_in_neurons___IOVS___.pdf
", "abstract": "Purpose : Explore a model for glaucoma by developing methods to image Caenorhabditis elegans neuronal function in response to controlled pressure modulation. \n\nMethods : Microfluidic devices have been developed for imaging behavior and cellular processes in C. elegans. These devices are fabricated using polydimethylsiloxane (PDMS), an inert polymer. External pressure is adjusted to immobilize the animal as well as to control flow of solutions in the devices (Figure 1a). Here we developed and tested modified versions of microfluidic devices (Hulme et al 2007, Cho et al 2014, Figure 1). These devices use pressure to hold the animals and allow for fluorescent imaging (Figure 2). The chips were designed in AutoCAD (Autodesk). Previously published protocols were used to make the PDMS replicas. Devices were controlled using an external valve system to regulate pressure in these channels. External components were built according to published protocols to automate the valve system (Rafael Gomez-Sjoberg, Microfluidics Lab, Lawrence Berkeley National Laboratory). Animals were imaged on a Zeiss 710 or Zeiss Axioscope inverted microscope. GCamP3 signals was used to confirm the function of the sensory neurons and prab-3 driven mcherry was used to visualize vesicles in axons. \n\nResults : Animals were successfully immobilized and intermittently imaged up to 6 hours in tapered microfluidic devices (n=15). All animal survived and there was no significant change in the function of the sensory neurons following immobilization at 5 psi in the tapered channels. Pressures of 20psi were tested in these devices without malfunction of the devices. Vesicular markers were visualized these devices, which is promising for the further characterization of dynamics of axonal transport in the model. \n\nConclusions : Glaucoma is associated with high intraocular pressures and characterized by accelerated loss of retinal ganglion cells and their axons. Impaired axonal transport has been implicated as a pathogenic mechanism in glaucoma and impaired axonal transport along retinal ganglion cells has been demonstrated in animal and human glaucoma studies (Knox et. Al 2007). Here we show that external pressure can be modulated in these devices while allowing for simultaneous neuronal imaging. Caenorhabditis elegans provides a tractable nervous system with accessible genetic tools that can be used to study real-time neuronal and axonal response to direct pressure modulation.", "date": "2018-07", "date_type": "published", "publication": "Investigative Ophthalmology and Visual Science", "volume": "59", "number": "9", "publisher": "Association for Research in Vision and Ophthalmology", "pagerange": "Art. No. 5842", "id_number": "CaltechAUTHORS:20181010-154605049", "issn": "0146-0404", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181010-154605049", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "primary_object": { "basename": "Microfluidic_platform_to_study_pressure-induced_changes_in_neurons___IOVS___.pdf", "url": "https://authors.library.caltech.edu/records/1kst0-m8x45/files/Microfluidic_platform_to_study_pressure-induced_changes_in_neurons___IOVS___.pdf" }, "resource_type": "article", "pub_year": "2018", "author_list": "Cho, Julie; Sternberg, Paul; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/jyk45-vam12", "eprint_id": 85435, "eprint_status": "archive", "datestamp": "2023-08-21 23:09:29", "lastmod": "2023-10-18 18:13:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Han", "name": { "family": "Wang", "given": "Han" }, "orcid": "0000-0002-1933-5762" }, { "id": "Liu-Jonathan", "name": { "family": "Liu", "given": "Jonathan" } }, { "id": "Yuet-Kai-P", "name": { "family": "Yuet", "given": "Kai P." }, "orcid": "0000-0002-1381-8923" }, { "id": "Hill-Andrew-J", "name": { "family": "Hill", "given": "Andrew J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Split cGAL, an intersectional strategy using a split intein for refined spatiotemporal transgene control in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "split cGAL; intein; GAL4-UAS; Caenorhabditis elegans; PKA", "note": "\u00a9 2018 National Academy of Sciences. Published under the PNAS license. \n\nContributed by Paul W. Sternberg, March 1, 2018 (sent for review November 20, 2017; reviewed by Thomas R. Clandinin and Yishi Jin) \n\nWe thank D. Tirrell and H. Schwartz for insightful discussion; S. J. Walton and S. Gharib for technical help; members of the P.W.S. laboratory and H. Chiu for editorial comments on the manuscript; and V. Gradinaru and D. Sieburth for sharing reagents. This work was supported by National Institute of Mental Health Grant R21MH115454 (to P.W.S.); National Institute of General Medical Sciences Grant K99GM126137 (to H.W.); a Della Martin Fellowship in Mental Illness (to H.W.); and the Howard Hughes Medical Institute, with which P.W.S. was an investigator. J.L. and A.J.H. were supported by National Institute of General Medical Sciences training Grant T32GM007616, and K.P.Y. was supported by U.S. Army Research Office, Institute for Collaborative Biotechnologies Grant W911NF-09-0001. \n\nH.W. and J.L. contributed equally to this work. \n\nAuthor contributions: H.W., J.L., K.P.Y., and P.W.S. designed research; H.W. and J.L. performed research; K.P.Y. and A.J.H. contributed new reagents/analytic tools; H.W. and J.L. analyzed data; and H.W., J.L., and P.W.S. wrote the paper. \n\nData deposition: Some of the plasmids used in this study have been deposited in Addgene (catalog nos. 107130\u2013107137, and 107139, available at https://www.addgene.org/ Paul_Sternberg/). \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1720063115/-/DCSupplemental. \n\nThe authors declare no conflict of interest.\n\nPublished - 3900.full.pdf
Supplemental Material - pnas.1720063115.sapp.pdf
Supplemental Material - pnas.201720063SI.pdf
", "abstract": "Bipartite expression systems, such as the GAL4-UAS system, allow fine manipulation of gene expression and are powerful tools for interrogating gene function. Recently, we established cGAL, a GAL4-based bipartite expression system for transgene control in Caenorhabditis elegans, where a single promoter dictates the expression pattern of a cGAL driver, which then binds target upstream activation sequences to drive expression of a downstream effector gene. Here, we report a split strategy for cGAL using the split intein gp41-1 for intersectional control of transgene expression. Split inteins are protein domains that associate, self-excise, and covalently ligate their flanking peptides together. We split the DNA binding domain and transcriptional activation domain of cGAL and fused them to the N terminal of gp41-1-N-intein and the C terminal of gp41-1-C-intein, respectively. In cells where both halves of cGAL are expressed, a functional cGAL driver is reconstituted via intein-mediated protein splicing. This reconstitution allows expression of the driver to be dictated by two promoters for refined spatial control or spatiotemporal control of transgene expression. We apply the split cGAL system to genetically access the single pair of MC neurons (previously inaccessible with a single promoter), and reveal an important role of protein kinase A in rhythmic pharyngeal pumping in C. elegans. Thus, the split cGAL system gives researchers a greater degree of spatiotemporal control over transgene expression, and will be a valuable genetic tool in C. elegans for dissecting gene function with finer cell-specific resolution.", "date": "2018-04-10", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "115", "number": "15", "publisher": "National Academy of Sciences", "pagerange": "3900-3905", "id_number": "CaltechAUTHORS:20180326-161144190", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180326-161144190", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R21MH115454" }, { "agency": "National Institute of Mental Health (NIMH)" }, { "agency": "NIH", "grant_number": "K99GM126137" }, { "agency": "National Institute of General Medical Sciences" }, { "agency": "Della Martin Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM007616" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-09-0001" } ] }, "doi": "10.1073/pnas.1720063115", "pmcid": "PMC5899461", "primary_object": { "basename": "3900.full.pdf", "url": "https://authors.library.caltech.edu/records/jyk45-vam12/files/3900.full.pdf" }, "related_objects": [ { "basename": "pnas.1720063115.sapp.pdf", "url": "https://authors.library.caltech.edu/records/jyk45-vam12/files/pnas.1720063115.sapp.pdf" }, { "basename": "pnas.201720063SI.pdf", "url": "https://authors.library.caltech.edu/records/jyk45-vam12/files/pnas.201720063SI.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Wang, Han; Liu, Jonathan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/f2dt8-q9n52", "eprint_id": 84615, "eprint_status": "archive", "datestamp": "2023-08-21 23:02:34", "lastmod": "2023-10-18 16:24:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schwartz-Hillel-T", "name": { "family": "Schwartz", "given": "Hillel T." }, "orcid": "0000-0002-3448-8652" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "A Toolkit of Engineered Recombinational Balancers in C. elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "Caenorhabditis elegans; CRISPR; Cas9; balancer; recombinational suppression", "note": "\u00a9 2018 Elsevier. \n\nAvailable online 31 January 2018.\n\nAccepted Version - nihms938823.pdf
", "abstract": "Dejima and colleagues report using CRISPR/Cas9 to generate a new collection of greatly improved balancer chromosomes in the standard laboratory nematode Caenorhabditis elegans, using methods previously reported by the same laboratory, expanding the set of C. elegans balancers to cover nearly 90% of coding genes.", "date": "2018-04", "date_type": "published", "publication": "Trends in Genetics", "volume": "34", "number": "4", "publisher": "Cell Press", "pagerange": "253-255", "id_number": "CaltechAUTHORS:20180201-080049478", "issn": "0168-9525", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180201-080049478", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.tig.2018.01.009", "pmcid": "PMC5878134", "primary_object": { "basename": "nihms938823.pdf", "url": "https://authors.library.caltech.edu/records/f2dt8-q9n52/files/nihms938823.pdf" }, "resource_type": "article", "pub_year": "2018", "author_list": "Schwartz, Hillel T. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/gaq7b-6h936", "eprint_id": 78613, "eprint_status": "archive", "datestamp": "2023-08-21 23:00:55", "lastmod": "2023-10-23 15:54:18", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Angeles-Albores-David", "name": { "family": "Angeles-Albores", "given": "David" }, "orcid": "0000-0001-5497-8264" }, { "id": "Puckett-Robinson-Carmie", "name": { "family": "Puckett Robinson", "given": "Carmie" } }, { "id": "Williams-Brian-A", "name": { "family": "Williams", "given": "Brian A." } }, { "id": "Wold-B-J", "name": { "family": "Wold", "given": "Barbara J." }, "orcid": "0000-0003-3235-8130" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Reconstructing a metazoan genetic pathway with transcriptome-wide epistasis measurements", "ispublished": "pub", "full_text_status": "public", "keywords": "hypoxia; transcriptomics; epistasis; genetics; gene expression", "note": "\u00a9 2018 National Academy of Sciences. Published under the PNAS license. \n\nContributed by Paul W. Sternberg, February 6, 2018 (sent for review July 13, 2017; reviewed by Erik C. Andersen and Aviv Regev). Published ahead of print March 12, 2018. \n\nWe thank Hillel Schwartz, Erich Schwarz, Jonathan Liu, Han Wang, and Porfirio Quintero for their advice throughout this project. This work was supported by the Howard Hughes Medical Institute, with whom P.W.S. is an investigator, and by the Millard and Muriel Jacobs Genetics and Genomics Laboratory at Caltech. Strains were provided by the Caenorhabditis Genetics Center, which is funded by the NIH Office of Research Infrastructure Programs (P40 OD010440). \n\nAuthor contributions: D.A.-A., C.P.R., and P.W.S. designed research; D.A.-A., C.P.R., and B.A.W. performed research; D.A.-A., B.A.W., and B.J.W. contributed new reagents/analytic tools; D.A.-A. analyzed data; and D.A.-A., C.P.R., and P.W.S. wrote the paper. \n\nReviewers: E.C.A., Northwestern University; and A.R., Broad Institute. \n\nThe authors declare no conflict of interest.\n\nData deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, https://www.ncbi.nlm.nih.gov/geo (accession no. GSE97355). Raw reads were deposited in the Short Read Archive (accession no. SRP100886). All code and processed data are available in the GitHub database, https://github.com/WormLabCaltech/mprsq. Our Jupyter Notebook and interactive graphs for this project can be found at https://wormlabcaltech.github.io/mprsq/, or in SI Appendix. \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1712387115/-/DCSupplemental.\n\nPublished - E2930.full.pdf
Submitted - 112920.1.full.pdf
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Supplemental Material - pnas.1712387115.sd01.csv
Supplemental Material - pnas.1712387115.sd01.xlsx
", "abstract": "RNA-sequencing (RNA-seq) is commonly used to identify genetic modules that respond to perturbations. In single cells, transcriptomes have been used as phenotypes, but this concept has not been applied to whole-organism RNA-seq. Also, quantifying and interpreting epistatic effects using expression profiles remains a challenge. We developed a single coefficient to quantify transcriptome-wide epistasis that reflects the underlying interactions and which can be interpreted intuitively. To demonstrate our approach, we sequenced four single and two double mutants of Caenorhabditis elegans. From these mutants, we reconstructed the known hypoxia pathway. In addition, we uncovered a class of 56 genes with HIF-1\u2013dependent expression that have opposite changes in expression in mutants of two genes that cooperate to negatively regulate HIF-1 abundance; however, the double mutant of these genes exhibits suppression epistasis. This class violates the classical model of HIF-1 regulation but can be explained by postulating a role of hydroxylated HIF-1 in transcriptional control.", "date": "2018-03-27", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "115", "number": "13", "publisher": "National Academy of Sciences", "pagerange": "E2930-E2939", "id_number": "CaltechAUTHORS:20170627-111146177", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170627-111146177", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Millard and Muriel Jacobs Genetics and Genomics Laboratory" }, { "agency": "NIH", "grant_number": "P40 OD010440" } ] }, "doi": "10.1073/pnas.1712387115", "pmcid": "PMC5879656", "primary_object": { "basename": "112920.1.full.pdf", "url": "https://authors.library.caltech.edu/records/gaq7b-6h936/files/112920.1.full.pdf" }, "related_objects": [ { "basename": "E2930.full.pdf", "url": "https://authors.library.caltech.edu/records/gaq7b-6h936/files/E2930.full.pdf" }, { "basename": "pnas.1712387115.sapp.pdf", "url": "https://authors.library.caltech.edu/records/gaq7b-6h936/files/pnas.1712387115.sapp.pdf" }, { "basename": "pnas.1712387115.sd01.csv", "url": "https://authors.library.caltech.edu/records/gaq7b-6h936/files/pnas.1712387115.sd01.csv" }, { "basename": "pnas.1712387115.sd01.xlsx", "url": "https://authors.library.caltech.edu/records/gaq7b-6h936/files/pnas.1712387115.sd01.xlsx" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Angeles-Albores, David; Puckett Robinson, Carmie; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/aqn19-wwt76", "eprint_id": 88127, "eprint_status": "archive", "datestamp": "2023-08-19 08:26:12", "lastmod": "2023-10-20 21:52:36", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Angeles-Albores-David", "name": { "family": "Angeles-Albores", "given": "David" }, "orcid": "0000-0001-5497-8264" }, { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "Raymond Y. N." }, "orcid": "0000-0002-8151-7479" }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Two new functions in the WormBase Enrichment Suite", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2018. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived 02/07/2018, Accepted 02/28/2018. Available starting WormBase release WS266, Published Online 03/27/2018. \n\nThis work was supported by the NIH grant U41 HG002223.\n\nPublished - angeles-albores_2018_enrichment.2.pdf
Submitted - 106369.full.pdf
", "abstract": "Genome-wide experiments routinely generate large amounts of data that can be hard to interpret biologically. A common approach to interpreting these results is to employ enrichment analyses of controlled languages, known as ontologies, that describe various biological parameters such as gene molecular or biological function. In C. elegans, three distinct ontologies, the Gene Ontology (GO), Anatomy Ontology (AO), and the Worm Phenotype Ontology (WPO) are used to annotate gene function, expression and phenotype, respectively (Ashburner et al. 2000; Lee and Sternberg, 2003; Schindelman et al. 2011). Previously, we developed software to test datasets for enrichment of anatomical terms, called the Tissue Enrichment Analysis (TEA) tool (Angeles-Albores and Sternberg, 2016). Using the same hypergeometric statistical method, we extend enrichment testing to include WPO and GO, offering a unified approach to enrichment testing in C. elegans. The WormBase Enrichment Suite can be accessed via a user-friendly interface at http://www.wormbase.org/tools/enrichment/tea/tea.cgi. To validate the tools, we analyzed a previously published extracellular vesicle (EV)-releasing neuron (EVN) signature gene set derived from dissociated ciliated EV neurons (Wang et al. 2015) using WormBase Enrichment Suite based on the WS262 WormBase release. TEA correctly identified the CEM, hook sensillum and IL2 neuron as enriched tissues. The top phenotype associated with the EVN signature was chemosensory behavior. Gene Ontology enrichment analysis showed that cell projection and cell body were the most enriched cellular components in this gene set, followed by the biological processes neuropeptide signaling pathway and vesicle localization further down. The tutorial script used to generate the figure above can be viewed at: https://github.com/dangeles/TissueEnrichmentAnalysis/blob/master/tutorial/Tutorial.ipynb The addition of Gene Enrichment Analysis (GEA) and Phenotype Enrichment Analysis (PEA) to WormBase marks an important step towards a unified set of analyses that can help researchers to understand genomic datasets. These enrichment analyses will allow the community to fully benefit from the data curation ongoing at WormBase.", "date": "2018-03-27", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "W25Q2N", "id_number": "CaltechAUTHORS:20180723-110009269", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180723-110009269", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U41 HG002223" } ] }, "doi": "10.17912/W25Q2N", "pmcid": "PMC7255849", "primary_object": { "basename": "106369.full.pdf", "url": "https://authors.library.caltech.edu/records/aqn19-wwt76/files/106369.full.pdf" }, "related_objects": [ { "basename": "angeles-albores_2018_enrichment.2.pdf", "url": "https://authors.library.caltech.edu/records/aqn19-wwt76/files/angeles-albores_2018_enrichment.2.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Angeles-Albores, David; Lee, Raymond Y. N.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/x2hqk-1c354", "eprint_id": 85218, "eprint_status": "archive", "datestamp": "2023-08-19 08:17:29", "lastmod": "2023-10-18 17:58:50", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "M\u00fcller-Hans-Michael", "name": { "family": "M\u00fcller", "given": "H.-M." } }, { "id": "Van-Auken-Kimberly-M", "name": { "family": "Van Auken", "given": "Kimberly M." }, "orcid": "0000-0002-1706-4196" }, { "id": "Li-Y", "name": { "family": "Li", "given": "Y." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "P. W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature", "ispublished": "pub", "full_text_status": "public", "keywords": "Literature curation - Text mining - Information retrieval - Information extraction - Literature search engine - Ontology - Model organism databases", "note": "\u00a9 2018 The Author(s). Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver\n(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. \n\nReceived: 13 July 2017. Accepted: 1 March 2018. Published: 9 March 2018. \n\nWe would like to thank Daniela Raciti, Christian Grove, and Valerio Arnaboldi for testing the system and helpful discussion, and Seth Carbon and Chris Mungall for assistance with the Noctua-Textpresso Central communication protocol. \n\nThis work was supported by USPHS grant U41-HG002223 (WormBase) and U41-HG002273 (Gene Ontology Consortium). Paul W. Sternberg is an investigator of the Howard Hughes Medical Institute. \n\nAuthors' contributions: HMM designed the system, developed the software, implemented the system and wrote the paper. KVA designed and tested the system, and wrote the paper. YL developed the software and implemented the system. PWS designed and tested the system, and supervised the project. All authors read and approved the final manuscript. \n\nThe authors declare that they have no competing interests.\n\nPublished - 10.1186_2Fs12859-018-2103-8.pdf
", "abstract": "Background: The biomedical literature continues to grow at a rapid pace, making the challenge of knowledge retrieval and extraction ever greater. Tools that provide a means to search and mine the full text of literature thus represent an important way by which the efficiency of these processes can be improved. \n\nResults: We describe the next generation of the Textpresso information retrieval system, Textpresso Central (TPC). TPC builds on the strengths of the original system by expanding the full text corpus to include the PubMed Central Open Access Subset (PMC OA), as well as the WormBase C. elegans bibliography. In addition, TPC allows users to create a customized corpus by uploading and processing documents of their choosing. TPC is UIMA compliant, to facilitate compatibility with external processing modules, and takes advantage of Lucene indexing and search technology for efficient handling of millions of full text documents. \n\nLike Textpresso, TPC searches can be performed using keywords and/or categories (semantically related groups of terms), but to provide better context for interpreting and validating queries, search results may now be viewed as highlighted passages in the context of full text. To facilitate biocuration efforts, TPC also allows users to select text spans from the full text and annotate them, create customized curation forms for any data type, and send resulting annotations to external curation databases. As an example of such a curation form, we describe integration of TPC with the Noctua curation tool developed by the Gene Ontology (GO) Consortium. \n\nConclusion: Textpresso Central is an online literature search and curation platform that enables biocurators and biomedical researchers to search and mine the full text of literature by integrating keyword and category searches with viewing search results in the context of the full text. It also allows users to create customized curation interfaces, use those interfaces to make annotations linked to supporting evidence statements, and then send those annotations to any database in the world.", "date": "2018-03-09", "date_type": "published", "publication": "BMC Bioinformatics", "volume": "19", "publisher": "BioMed Central", "pagerange": "Art. No. 94", "id_number": "CaltechAUTHORS:20180309-075052784", "issn": "1471-2105", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180309-075052784", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U41-HG002223" }, { "agency": "NIH", "grant_number": "U41-HG002273" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1186/s12859-018-2103-8", "pmcid": "PMC5845379", "primary_object": { "basename": "10.1186_2Fs12859-018-2103-8.pdf", "url": "https://authors.library.caltech.edu/records/x2hqk-1c354/files/10.1186_2Fs12859-018-2103-8.pdf" }, "resource_type": "article", "pub_year": "2018", "author_list": "M\u00fcller, H.-M.; Van Auken, Kimberly M.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/w5amy-tm274", "eprint_id": 85236, "eprint_status": "archive", "datestamp": "2023-08-19 08:13:14", "lastmod": "2023-10-18 18:00:04", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Raciti-Daniela", "name": { "family": "Raciti", "given": "Daniela" } }, { "id": "Yook-Karen-J", "name": { "family": "Yook", "given": "Karen" }, "orcid": "0000-0002-4457-6787" }, { "id": "Harris-Todd-W", "name": { "family": "Harris", "given": "Todd W." }, "orcid": "0000-0003-3406-163X" }, { "id": "Schedl-Tim", "name": { "family": "Schedl", "given": "Tim" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Micropublication: incentivizing community curation and placing unpublished data into the public domain", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2018 The Author(s). Published by Oxford University Press.\nThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived: 08 November 2017; Revision Received: 10 January 2018; Accepted: 18 January 2018; Published: 02 March 2018. \n\nThe authors would like to thank members of the C. elegans research community and representatives from other model organisms databases such as TAIR (The Arabidopsis Information Resource, Phoenix Bioinformatics), Xenbase and ZFIN for their feedback on submission forms and workflow and to the Collaborative Knowledge Foundation for facilitating this community input. The authors would also like to thanks Juancarlos Chan for initial implementation of the submission forms. \n\nFunding: National Institute of Health (U01-LM012672 to P.W.S. and T.S.) for the Micropublication project. US National Human Genome Research Institute (U41-HG002223 to P.W.S.) for WormBase. Funding for open access charge: National Institute of Health U01-LM012672. \n\nConflict of interest. None declared.\n\nPublished - bay013.pdf
", "abstract": "Large volumes of data generated by research laboratories coupled with the required effort and cost of curation present a significant barrier to inclusion of these data in authoritative community databases. Further, many publicly funded experimental observations remain invisible to curation simply because they are never published: results often do not fit within the scope of a standard publication; trainee-generated data are forgotten when the experimenter (e.g. student, post-doc) leaves the lab; results are omitted from science narratives due to publication bias where certain results are considered irrelevant for the publication. While authors are in the best position to curate their own data, they face a steep learning curve to ensure that appropriate referential tags, metadata, and ontologies are applied correctly to their observations, a task sometimes considered beyond the scope of their research and other numerous responsibilities. Getting researchers to adopt a new system of data reporting and curation requires a fundamental change in behavior among all members of the research community. To solve these challenges, we have created a novel scholarly communication platform that captures data from researchers and directly delivers them to information resources via Micropublication. This platform incentivizes authors to publish their unpublished observations along with associated metadata by providing a deliberately fast and lightweight but still peer-reviewed process that results in a citable publication. Our long-term goal is to develop a data ecosystem that improves reproducibility and accountability of publicly funded research and in turn accelerates both basic and translational discovery.", "date": "2018-03-02", "date_type": "published", "publication": "Database : The Journal of Biological Databases and Curation", "volume": "2018", "publisher": "Oxford University Press", "pagerange": "Art. No. bay013", "id_number": "CaltechAUTHORS:20180312-073358675", "issn": "1758-0463", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180312-073358675", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U01-LM012672" }, { "agency": "NIH", "grant_number": "U41-HG002223" }, { "agency": "NIH", "grant_number": "U01-LM012672" } ] }, "doi": "10.1093/database/bay013", "pmcid": "PMC5836261", "primary_object": { "basename": "bay013.pdf", "url": "https://authors.library.caltech.edu/records/w5amy-tm274/files/bay013.pdf" }, "resource_type": "article", "pub_year": "2018", "author_list": "Raciti, Daniela; Yook, Karen; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/x41s9-0f425", "eprint_id": 84888, "eprint_status": "archive", "datestamp": "2023-08-19 07:57:07", "lastmod": "2023-10-18 16:48:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Artyukhin-A-B", "name": { "family": "Artyukhin", "given": "Alexander B." } }, { "id": "Zhang-Ying-K", "name": { "family": "Zhang", "given": "Ying K." } }, { "id": "Akagi-Allison-E", "name": { "family": "Akagi", "given": "Allison E." }, "orcid": "0000-0002-7233-6190" }, { "id": "Panda-Oishika", "name": { "family": "Panda", "given": "Oishika" }, "orcid": "0000-0002-1217-8231" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Schroeder-F-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" } ] }, "title": "Metabolomic \"Dark Matter\" Dependent on Peroxisomal \u03b2-Oxidation in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2018 American Chemical Society. \n\nReceived 8 November 2017. Published online 5 February 2018. \n\nWe are grateful to David Kiemle for help with acquiring NMR spectra. This work was supported in part by the NIH (GM113692, GM088290 to FCS, and T32GM007616 to A.E.A.) and HHMI.\n\nAccepted Version - nihms953485.pdf
Supplemental Material - ja7b11811_si_001.pdf
Supplemental Material - ja7b11811_si_002.xlsx
Supplemental Material - ja7b11811_si_003.xlsx
", "abstract": "Peroxisomal \u03b2-oxidation (p\u03b2o) is a highly conserved fat metabolism pathway involved in the biosynthesis of diverse signaling molecules in animals and plants. In Caenorhabditis elegans, p\u03b2o is required for the biosynthesis of the ascarosides, signaling molecules that control development, lifespan, and behavior in this model organism. Via comparative mass spectrometric analysis of p\u03b2o mutants and wildtype, we show that p\u03b2o in C. elegans and the satellite model P. pacificus contributes to life stage-specific biosynthesis of several hundred previously unknown metabolites. The p\u03b2o-dependent portion of the metabolome is unexpectedly diverse, e.g., intersecting with nucleoside and neurotransmitter metabolism. Cell type-specific restoration of p\u03b2o in p\u03b2o-defective mutants further revealed that p\u03b2o-dependent submetabolomes differ between tissues. These results suggest that interactions of fat, nucleoside, and other primary metabolism pathways can generate structural diversity reminiscent of that arising from combinatorial strategies in microbial natural product biosynthesis.", "date": "2018-02-28", "date_type": "published", "publication": "Journal of the American Chemical Society", "volume": "140", "number": "8", "publisher": "American Chemical Society", "pagerange": "2841-2852", "id_number": "CaltechAUTHORS:20180220-093417995", "issn": "0002-7863", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180220-093417995", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM113692" }, { "agency": "NIH", "grant_number": "GM088290" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM007616" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1021/jacs.7b11811", "pmcid": "PMC5890438", "primary_object": { "basename": "ja7b11811_si_001.pdf", "url": "https://authors.library.caltech.edu/records/x41s9-0f425/files/ja7b11811_si_001.pdf" }, "related_objects": [ { "basename": "ja7b11811_si_002.xlsx", "url": "https://authors.library.caltech.edu/records/x41s9-0f425/files/ja7b11811_si_002.xlsx" }, { "basename": "ja7b11811_si_003.xlsx", "url": "https://authors.library.caltech.edu/records/x41s9-0f425/files/ja7b11811_si_003.xlsx" }, { "basename": "nihms953485.pdf", "url": "https://authors.library.caltech.edu/records/x41s9-0f425/files/nihms953485.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Artyukhin, Alexander B.; Zhang, Ying K.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/nctet-yw153", "eprint_id": 82767, "eprint_status": "archive", "datestamp": "2023-08-19 07:18:02", "lastmod": "2023-10-17 22:39:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "Raymond Y. N." }, "orcid": "0000-0002-8151-7479" }, { "id": "Arnaboldi-Valerio", "name": { "family": "Arnaboldi", "given": "Valerio" }, "orcid": "0000-0002-2563-5374" }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "Chen-Wen-J", "name": { "family": "Chen", "given": "Wen J." } }, { "id": "Grove-Christian-A", "name": { "family": "Grove", "given": "Christian" }, "orcid": "0000-0001-9076-6015" }, { "id": "Kishore-Ranjana", "name": { "family": "Kishore", "given": "Ranjana" }, "orcid": "0000-0002-1478-7671" }, { "id": "M\u00fcller-Hans-Michael", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } }, { "id": "Nakamura-Cecilia", "name": { "family": "Nakamura", "given": "Cecilia" }, "orcid": "0000-0002-4689-7314" }, { "id": "Raciti-Daniela", "name": { "family": "Raciti", "given": "Daniela" } }, { "id": "Schindelman-Gary", "name": { "family": "Schindelman", "given": "Gary" } }, { "id": "Tuli-Mary-Ann", "name": { "family": "Tuli", "given": "Mary Ann" } }, { "id": "Van-Auken-Kimberly-M", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Wang-Qinghua", "name": { "family": "Wang", "given": "Qinghua" } }, { "id": "Yook-Karen-J", "name": { "family": "Yook", "given": "Karen" }, "orcid": "0000-0002-4457-6787" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "WormBase 2017: molting into a new stage", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived September 29, 2017; Revised October 10, 2017; Editorial Decision October 11, 2017; Accepted October 11, 2017. Published: 24 October 2017. \n\nFunding: US National Human Genome Research Institute [U41-HG002223]; UK Medical Research Council [MR/L001220]; UK Biotechnology and Biological Sciences Research Council [BB/K020080]. Funding for open access charge: US National Human Genome Research Institute [U41-HG002223]. \n\nConflict of interest statement. None declared.\n\nPublished - gkx998.pdf
", "abstract": "WormBase (http://www.wormbase.org) is an important knowledge resource for biomedical researchers worldwide. To accommodate the ever increasing amount and complexity of research data, WormBase continues to advance its practices on data acquisition, curation and retrieval to most effectively deliver comprehensive knowledge about Caenorhabditis elegans, and genomic information about other nematodes and parasitic flatworms. Recent notable enhancements include user-directed submission of data, such as micropublication; genomic data curation and presentation, including additional genomes and JBrowse, respectively; new query tools, such as SimpleMine, Gene Enrichment Analysis; new data displays, such as the Person Lineage browser and the Summary of Ontology-based Annotations. Anticipating more rapid data growth ahead, WormBase continues the process of migrating to a cutting-edge database technology to achieve better stability, scalability, reproducibility and a faster response time. To better serve the broader research community, WormBase, with five other Model Organism Databases and The Gene Ontology project, have begun to collaborate formally as the Alliance of Genome Resources.", "date": "2018-01-04", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "46", "number": "D1", "publisher": "Oxford University Press", "pagerange": "D869-D874", "id_number": "CaltechAUTHORS:20171030-085417622", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171030-085417622", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U41-HG002223" }, { "agency": "Medical Research Council (UK)", "grant_number": "MR/L001220" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/K020080" } ] }, "local_group": { "items": [ { "id": "WormBase" } ] }, "doi": "10.1093/nar/gkx998", "pmcid": "PMC5753391", "primary_object": { "basename": "gkx998.pdf", "url": "https://authors.library.caltech.edu/records/nctet-yw153/files/gkx998.pdf" }, "resource_type": "article", "pub_year": "2018", "author_list": "Lee, Raymond Y. N.; Arnaboldi, Valerio; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/91v5b-cwc77", "eprint_id": 83434, "eprint_status": "archive", "datestamp": "2023-08-21 22:22:20", "lastmod": "2023-10-17 23:07:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lee-James-Siho", "name": { "family": "Lee", "given": "James Siho" } }, { "id": "Shih-Pei-Yin", "name": { "family": "Shih", "given": "Pei-Yin" }, "orcid": "0000-0003-3082-9242" }, { "id": "Schaedel-Oren-N", "name": { "family": "Schaedel", "given": "Oren N." } }, { "id": "Quintero-Cadena-Porfirio", "name": { "family": "Quintero-Cadena", "given": "Porfirio" }, "orcid": "0000-0003-0067-5844" }, { "id": "Rogers-Alicia-K", "name": { "family": "Rogers", "given": "Alicia K." }, "orcid": "0000-0001-5525-6095" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "FMRFamide-like peptides expand the behavioral repertoire of a densely connected nervous system", "ispublished": "pub", "full_text_status": "public", "keywords": "phenotypic plasticity; RNA-seq; dauer; neuropeptide; FMRFamide", "note": "\u00a9 2017 National Academy of Sciences. Published under the PNAS license. \n\nContributed by Paul W. Sternberg, October 31, 2017 (sent for review June 8, 2017; reviewed by Junho Lee and Chris Li). Published online before print November 22, 2017. \n\nWe thank Daehan Lee for providing the nictation microchip design; Elissa Hallem for advice on CO_2 assays; Christopher Cronin for advice on behavioral assay setups; Mihoko Kato, Hillel Schwartz, Igor Antoshechkin, Ryoji Shinya, Han Wang, Animesh Ray, and Jonathan Liu for critically reading the manuscript; the Caenorhabditis Genetics Center, which is funded by the NIH Office of Research Infrastructure Programs (Grant P40 OD010440), and Adam Antebi, Mario de Bono, and H. Robert Horvitz for providing animal strains; WormBase and WormBase SPELL for tools, datasets, and invaluable information; and the Millard and Muriel Jacobs Genetics and Genomics Laboratory for support with library construction and sequencing. \n\nAuthor contributions: J.S.L., P.-Y.S., O.N.S., and P.W.S. designed research; J.S.L., P.-Y.S., and O.N.S. performed research; J.S.L., P.-Y.S., O.N.S., and P.Q.-C. contributed new reagents/analytic tools; J.S.L., P.-Y.S., O.N.S., P.Q.-C., and A.K.R. analyzed data; and J.S.L., P.-Y.S., O.N.S., P.Q.-C., and P.W.S. wrote the paper. \n\nReviewers: J.L., Seoul National University; and C.L., City College of New York. \n\nThe authors declare no conflict of interest. \n\nData deposition: The RNA-seq data in this paper have been deposited in the National Center for Biotechnology Information Sequence Read Archive (SRA) database (accession no. SRP116980). Codes used for data analysis have been deposited in GitHub and are available at https://github.com/WormLabCaltech/dauerRNAseq. \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1710374114/-/DCSupplemental.\n\nPublished - PNAS-2017-Lee-E10726-35.pdf
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", "abstract": "Animals, including humans, can adapt to environmental stress through phenotypic plasticity. The free-living nematode Caenorhabditis elegans can adapt to harsh environments by undergoing a whole-animal change, involving exiting reproductive development and entering the stress-resistant dauer larval stage. The dauer is a dispersal stage with dauer-specific behaviors for finding and stowing onto carrier animals, but how dauers acquire these behaviors, despite having a physically limited nervous system of 302 neurons, is poorly understood. We compared dauer and reproductive development using whole-animal RNA sequencing at fine time points and at sufficient depth to measure transcriptional changes within single cells. We detected 8,042 genes differentially expressed during dauer and reproductive development and observed striking up-regulation of neuropeptide genes during dauer entry. We knocked down neuropeptide processing using sbt-1 mutants and demonstrate that neuropeptide signaling promotes the decision to enter dauer rather than reproductive development. We also demonstrate that during dauer neuropeptides modulate the dauer-specific nictation behavior (carrier animal-hitchhiking) and are necessary for switching from repulsion to CO_2 (a carrier animal cue) in nondauers to CO_2 attraction in dauers. We tested individual neuropeptides using CRISPR knockouts and existing strains and demonstrate that the combined effects of flp-10 and flp-17 mimic the effects of sbt-1on nictation and CO_2 attraction. Through meta-analysis, we discovered similar up-regulation of neuropeptides in the dauer-like infective juveniles of diverse parasitic nematodes, suggesting the antiparasitic target potential of SBT-1. Our findings reveal that, under stress, increased neuropeptide signaling in C. elegans enhances their decision-making accuracy and expands their behavioral repertoire.", "date": "2017-12-12", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "114", "number": "50", "publisher": "National Academy of Sciences", "pagerange": "E10726-E10735", "id_number": "CaltechAUTHORS:20171127-073708419", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171127-073708419", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P40 OD010440" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" } ] }, "doi": "10.1073/pnas.1710374114", "pmcid": "PMC5740649", "primary_object": { "basename": "pnas.1710374114.sd01.xlsx", "url": "https://authors.library.caltech.edu/records/91v5b-cwc77/files/pnas.1710374114.sd01.xlsx" }, "related_objects": [ { "basename": "pnas.1710374114.sd04.xlsx", "url": "https://authors.library.caltech.edu/records/91v5b-cwc77/files/pnas.1710374114.sd04.xlsx" }, { "basename": "pnas.1710374114.sm04.avi", "url": "https://authors.library.caltech.edu/records/91v5b-cwc77/files/pnas.1710374114.sm04.avi" }, { "basename": "PNAS-2017-Lee-E10726-35.pdf", "url": "https://authors.library.caltech.edu/records/91v5b-cwc77/files/PNAS-2017-Lee-E10726-35.pdf" }, { "basename": "pnas.1710374114.sd02.xlsx", "url": "https://authors.library.caltech.edu/records/91v5b-cwc77/files/pnas.1710374114.sd02.xlsx" }, { "basename": "pnas.1710374114.sm01.wmv", "url": "https://authors.library.caltech.edu/records/91v5b-cwc77/files/pnas.1710374114.sm01.wmv" }, { "basename": "pnas.1710374114.sm06.avi", "url": "https://authors.library.caltech.edu/records/91v5b-cwc77/files/pnas.1710374114.sm06.avi" }, { "basename": "pnas.1710374114.sm05.avi", "url": "https://authors.library.caltech.edu/records/91v5b-cwc77/files/pnas.1710374114.sm05.avi" }, { "basename": "pnas.201710374SI.pdf", "url": "https://authors.library.caltech.edu/records/91v5b-cwc77/files/pnas.201710374SI.pdf" }, { "basename": "pnas.1710374114.sd03.xlsx", "url": "https://authors.library.caltech.edu/records/91v5b-cwc77/files/pnas.1710374114.sd03.xlsx" }, { "basename": "pnas.1710374114.sd05.xlsx", "url": "https://authors.library.caltech.edu/records/91v5b-cwc77/files/pnas.1710374114.sd05.xlsx" }, { "basename": "pnas.1710374114.sm02.wmv", "url": "https://authors.library.caltech.edu/records/91v5b-cwc77/files/pnas.1710374114.sm02.wmv" }, { "basename": "pnas.1710374114.sm03.avi", "url": "https://authors.library.caltech.edu/records/91v5b-cwc77/files/pnas.1710374114.sm03.avi" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Lee, James Siho; Shih, Pei-Yin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/e44fx-42d23", "eprint_id": 82769, "eprint_status": "archive", "datestamp": "2023-08-19 06:15:52", "lastmod": "2023-10-17 22:40:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ho-Margaret-C-W", "name": { "family": "Ho", "given": "Margaret C. W." }, "orcid": "0000-0002-2007-2226" }, { "id": "Quintero-Cadena-Porfirio", "name": { "family": "Quintero-Cadena", "given": "Porfirio" }, "orcid": "0000-0003-0067-5844" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Genome-wide discovery of active regulatory elements and transcription factor footprints in Caenorhabditis elegans using DNase-seq", "ispublished": "pub", "full_text_status": "public", "keywords": "cis-regulatory modules, gene regulation, enhancers, nematode development, transcription, DNase, hypersensitivity", "note": "\u00a9 2017 Ho et al.; Published by Cold Spring Harbor Laboratory Press This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/. \n\nReceived April 6, 2017; Accepted October 18, 2017; Published in Advance October 26, 2017. \n\nData access: The DNase-seq data from this study have been submitted to the NCBI Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE97425. Additional analysis files, including DNase I signal data, all DHSs and nearest genes, putative TF footprints, novel motifs, motif-associated genes, and GO analysis, are available from WormBase (detailed list of files in Supplemental Table S3). \n\nWe thank WormBase, especially Xiaodong Wang and James Done. This research was supported by NIH (National Institute of General Medical Sciences) grant GM084389 to P.W.S. and the Howard Hughes Medical Institute (047101), with which P.W.S. is an investigator. M.C.W.H. was supported by a National Science Foundation GRFP predoctoral fellowship. We would like to thank Ali Mortazavi, Igor Antoshechkin, John DeModena, Steven Kuntz, Erich Schwarz, Jim McGhee, and Erin Osborne Nishimura for assistance and advice on experimental design, sequence library construction, and analysis and interpretation of data. We thank David Angeles for help performing anatomy enrichment analysis. We thank Mark Wu, Mihoko Kato, and Hillel Schwartz for helpful suggestions on the manuscript.\n\nPublished - Genome_Res.-2017-Ho-2108-19.pdf
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", "abstract": "Deep sequencing of size-selected DNase I\u2013treated chromatin (DNase-seq) allows high-resolution measurement of chromatin accessibility to DNase I cleavage, permitting identification of de novo active cis-regulatory modules (CRMs) and individual transcription factor (TF) binding sites. We adapted DNase-seq to nuclei isolated from C. elegans embryos and L1 arrest larvae to generate high-resolution maps of TF binding. Over half of embryonic DNase I hypersensitive sites (DHSs) were annotated as noncoding, with 24% in intergenic, 12% in promoters, and 28% in introns, with similar statistics observed in L1 arrest larvae. Noncoding DHSs are highly conserved and enriched in marks of enhancer activity and transcription. We validated noncoding DHSs against known enhancers from myo-2, myo-3, hlh-1, elt-2, and lin-26/lir-1 and recapitulated 15 of 17 known enhancers. We then mined DNase-seq data to identify putative active CRMs and TF footprints. Using DNase-seq data improved predictions of tissue-specific expression compared with motifs alone. In a pilot functional test, 10 of 15 DHSs from pha-4, icl-1, and ceh-13 drove reporter gene expression in transgenic C. elegans. Overall, we provide experimental annotation of 26,644 putative CRMs in the embryo containing 55,890 TF footprints, as well as 15,841 putative CRMs in the L1 arrest larvae containing 32,685 TF footprints.", "date": "2017-12", "date_type": "published", "publication": "Genome Research", "volume": "27", "number": "12", "publisher": "Cold Spring Harbor Laboratory Press", "pagerange": "2108-2119", "id_number": "CaltechAUTHORS:20171030-102102638", "issn": "1088-9051", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171030-102102638", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM084389" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NSF Graduate Research Fellowship" } ] }, "local_group": { "items": [ { "id": "WormBase" } ] }, "doi": "10.1101/gr.223735.117", "pmcid": "PMC5741056", "primary_object": { "basename": "Supplemental_Fig_S11.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Fig_S11.pdf" }, "related_objects": [ { "basename": "Supplemental_Fig_S6.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Fig_S6.pdf" }, { "basename": "Supplemental_Table_S3.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Table_S3.pdf" }, { "basename": "Supplemental_Table_S8.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Table_S8.pdf" }, { "basename": "Supplemental_Table_S5.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Table_S5.pdf" }, { "basename": "Supplemental_Table_S7.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Table_S7.pdf" }, { "basename": "Genome_Res.-2017-Ho-2108-19.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Genome_Res.-2017-Ho-2108-19.pdf" }, { "basename": "Supplemental_Fig_S1.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Fig_S1.pdf" }, { "basename": "Supplemental_Fig_S2.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Fig_S2.pdf" }, { "basename": "Supplemental_Fig_S5.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Fig_S5.pdf" }, { "basename": "Supplemental_Fig_S9.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Fig_S9.pdf" }, { "basename": "Supplemental_Table_S2.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Table_S2.pdf" }, { "basename": "Supplemental_Fig_S8.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Fig_S8.pdf" }, { "basename": "Supplemental_Table_S4.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Table_S4.pdf" }, { "basename": "Supplemental_Table_S6.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Table_S6.pdf" }, { "basename": "Supplemental_Table_S9.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Table_S9.pdf" }, { "basename": "Supplementary_Text.docx", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplementary_Text.docx" }, { "basename": "Supplemental_Fig_S10.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Fig_S10.pdf" }, { "basename": "Supplemental_Fig_S3.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Fig_S3.pdf" }, { "basename": "Supplemental_Fig_S4.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Fig_S4.pdf" }, { "basename": "Supplemental_Fig_S7.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Fig_S7.pdf" }, { "basename": "Supplemental_Table_S1.pdf", "url": "https://authors.library.caltech.edu/records/e44fx-42d23/files/Supplemental_Table_S1.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Ho, Margaret C. W.; Quintero-Cadena, Porfirio; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/5z1j1-4fj26", "eprint_id": 83946, "eprint_status": "archive", "datestamp": "2023-08-19 06:02:27", "lastmod": "2023-10-18 14:32:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ghosh-Srimoyee", "name": { "family": "Ghosh", "given": "Srimoyee" }, "orcid": "0000-0002-7820-6741" }, { "id": "Vetrone-Sylvia-A", "name": { "family": "Vetrone", "given": "Sylvia A." }, "orcid": "0000-0002-5521-0959" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Non-neuronal cell outgrowth in C. elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "cell outgrowth, genetic analysis, gonad development, postembryonic development", "note": "\u00a9 2017 Taylor & Francis. \n\nReceived 11 Sep 2017, Accepted 30 Oct 2017, Accepted author version posted online: 14 Nov 2017, Published online: 14 Nov 2017. \n\nWe thank Mihoko Kato and reviewers for critical reading of the manuscript. P.W.S. is an investigator of the Howard Hughes Medical Institute. \n\nS.G. was supported by National Institutes of Health training grant GM07616. S. V. was supported by the American Society of Cell Biology Minorities Affairs Committee Visiting Professor's Program, which was funded by the Howard Hughes Medical Institute grant number 047101. \n\nNo potential conflicts of interest were disclosed.\n\nPublished - kwrm-06-3-4-1405212.pdf
Supplemental Material - kwrm_a_1405212_sm6270.xlsx
", "abstract": "Cell outgrowth is a hallmark of some non-migratory developing cells during morphogenesis. Understanding the mechanisms that control cell outgrowth not only increases our knowledge of tissue and organ development, but can also shed light on disease pathologies that exhibit outgrowth-like behavior. C. elegans is a highly useful model for the analysis of genes and the function of their respective proteins. In addition, C. elegans also has several cells and tissues that undergo outgrowth during development. Here we discuss the outgrowth mechanisms of nine different C. elegans cells and tissues. We specifically focus on how these cells and tissues grow outward and the interactions they make with their environment. Through our own identification, and a meta-analysis, we also identify gene families involved in multiple cell outgrowth processes, which defined potential C. elegans core components of cell outgrowth, as well as identify a potential stepwise cell behavioral cascade used by cells undergoing outgrowth.", "date": "2017-11-14", "date_type": "published", "publication": "Worm", "volume": "6", "number": "3-4", "publisher": "Taylor & Francis", "pagerange": "Art. No. e1405212", "id_number": "CaltechAUTHORS:20171218-070748557", "issn": "2162-4054", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171218-070748557", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)", "grant_number": "047101" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "GM07616" }, { "agency": "American Society of Cell Biology" } ] }, "doi": "10.1080/21624054.2017.1405212", "pmcid": "PMC5721946", "primary_object": { "basename": "kwrm-06-3-4-1405212.pdf", "url": "https://authors.library.caltech.edu/records/5z1j1-4fj26/files/kwrm-06-3-4-1405212.pdf" }, "related_objects": [ { "basename": "kwrm_a_1405212_sm6270.xlsx", "url": "https://authors.library.caltech.edu/records/5z1j1-4fj26/files/kwrm_a_1405212_sm6270.xlsx" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Ghosh, Srimoyee; Vetrone, Sylvia A.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/10yc6-0bs64", "eprint_id": 104127, "eprint_status": "archive", "datestamp": "2023-08-19 06:00:16", "lastmod": "2023-10-20 19:06:23", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Whittaker-A-J", "name": { "family": "Whittaker", "given": "Allyson" } }, { "id": "Schindelman-G", "name": { "family": "Schindelman", "given": "Gary" } }, { "id": "Gharib-Shahla", "name": { "family": "Gharib", "given": "Shahla" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "A new mutation with a polycystin phenotypic spectrum in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: October 17, 2017; Accepted: November 6, 2017; Published: November 9, 2017. \n\nFunding: Howard Hughes Medical Institute, with whom PWS was an Investigator. \n\nReviewed By: Sreejiit Ramakrishnan.\n\nPublished - microPublication.biology.10.17912-W2N37P.pdf
", "abstract": "lov-1 and pkd-2, which encode the C. elegans orthologs of human polycystin-1 and -2, are necessary for three particular aspects of male mating behavior. In a screen for male mating defective mutants with similar spectrum of mating defects, we identified a mutation that apparently defines a new locus, lov-3. \n \nWe isolated the sy682 mutation in an ethyl-methane sulphonate (EMS)-screen of Caenorhabditis elegans strain PS1395 [genotype: plg-1(e2001d); him-5(e1490)] for mutant males that do not mate efficiently and hence do not form plugs on hermaphrodites (Liu et al, 2017). sy682 is defective in the males' response to contact with hermaphrodite and in vulval location (Table 1). The vulval location defect is failing to stop at the vulva. These two phenotypes are associated with lov-1 (Barr, 1999) and pkd-2 loss-of-function mutations (Barr et al. 2001; Whittaker et al., 2017). sy682 maps to the X chromosome and thus is distinct from lov-1 and pkd-2, so it defines a likely new locus, lov-3.", "date": "2017-11-09", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "10.17912/W2N37P", "id_number": "CaltechAUTHORS:20200629-104910389", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200629-104910389", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.17912/W2N37P", "pmcid": "PMC7255857", "primary_object": { "basename": "microPublication.biology.10.17912-W2N37P.pdf", "url": "https://authors.library.caltech.edu/records/10yc6-0bs64/files/microPublication.biology.10.17912-W2N37P.pdf" }, "resource_type": "article", "pub_year": "2017", "author_list": "Whittaker, Allyson; Schindelman, Gary; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/whddq-2nr50", "eprint_id": 104107, "eprint_status": "archive", "datestamp": "2023-08-19 05:56:51", "lastmod": "2023-10-20 19:05:14", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hajdu-Cronin-Y-M", "name": { "family": "Hajdu-Cronin", "given": "Yvonne M." } }, { "id": "Liu-Katharine-S", "name": { "family": "Liu", "given": "Katharine S." } }, { "id": "Barber-Leslie", "name": { "family": "Barber", "given": "Leslie" } }, { "id": "Chamberlin-H-M", "name": { "family": "Chamberlin", "given": "Helen M." } }, { "id": "Boorstein-W", "name": { "family": "Boorstein", "given": "William" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Copulation defective mutants of C. elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: October 9, 2017; Accepted: November 1, 2017; Published: November 2, 2017. \n\nThis screen was supported by an NSF Presidential Young Investigator Award to PWS (1988) and by the Howard Hughes Medical Institute, with which PWS was an Investigator. \n\nReviewed By: Douglas Portman and Ray Hong\n\nPublished - microPublication.biology-10.17912-W2XH3S.pdf
", "abstract": "To identify genes involved in male copulatory behavior, we carried out an F2 clonal screen in a him-5 mutant background. We identified 20 mutations that affect male mating behavior without causing gross defects in morphology. \n\nMale mating in C. elegans comprises at least five steps (Liu and Sternberg, 1995). (l) The male responds to the hermaphrodite by backing his tail along the length of the hermaphrodite, (2) he turns over or under her body before reaching the head or tail, (3) he locates the vulva with his tail, at which point he stops backing, (4) he inserts his spicules into the vulva, and (5) he transfers sperm. To study the genetic basis for male mating behavior, we are isolating and characterizing Copulation Defective (Cod) mutations. We screened for mutant strains defective in this behavior using the screen described by Hodgkin (1983). him-5(e1490) worms are mutagenized with ethyl methane sulfonate (EMS); 20 P0 L4 hermaphrodites are picked singly to Petri plates; ten F1 worms are picked per mutagenized P0; and ten F2 L4 hermaphrodites are singled per P0 and their male progeny tested for mating efficiency via a qualitative mating test (six males crossed with six unc-52(e444) hermaphrodites, which are paralyzed at adulthood (Brenner, 1974). Mutants with phenotypes that are likely to reduce mating efficiency in a non-specific manner (such as those causing an Unc, Dpy, or Lon phenotype) were discarded. Those strains that appear morphologically normal under the dissecting microscope yet fail to mate or mate at a very low efficiency (1-5% cross progeny compared to wild type) were screened under Nomarski optics for defects in male reproductive structures. We screened over 3000 haploid genomes, and picked over 100 strains with reproduction defects. Nineteen strains were successfully backcrossed, which represents about 25% of the total strains attempted. This result suggests that most strains harbor two or more mutations that contribute to the mating-deficiency defect. Preliminary analysis of behavior suggests that every major step in the wild-type mating pathway has at least one corresponding Cod mutation blocking the behavior, with several mutations blocking at the spicule insertion step. The screen also yielded morphological mutants, whose phenotypes include crumpled spicules, abnormal rays, and a gonad migration defect; some of these will be described elsewhere (Chamberlin & Sternberg; micropublication in preparation).", "date": "2017-11-02", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "10.17912/W2XH3S", "id_number": "CaltechAUTHORS:20200629-073648893", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200629-073648893", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.17912/W2XH3S", "pmcid": "PMC7255866", "primary_object": { "basename": "microPublication.biology-10.17912-W2XH3S.pdf", "url": "https://authors.library.caltech.edu/records/whddq-2nr50/files/microPublication.biology-10.17912-W2XH3S.pdf" }, "resource_type": "article", "pub_year": "2017", "author_list": "Hajdu-Cronin, Yvonne M.; Liu, Katharine S.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/0e3mz-arn34", "eprint_id": 104106, "eprint_status": "archive", "datestamp": "2023-08-19 05:56:47", "lastmod": "2023-10-20 19:05:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Liu-Katharine-S", "name": { "family": "Liu", "given": "Katharine" } }, { "id": "Hajdu-Cronin-Y-M", "name": { "family": "Hajdu-Cronin", "given": "Yvonne" } }, { "id": "Chen-Ann", "name": { "family": "Chen", "given": "Ann" } }, { "id": "Schindelman-G", "name": { "family": "Schindelman", "given": "Gary" } }, { "id": "Whittaker-A-J", "name": { "family": "Whittaker", "given": "Allyson" } }, { "id": "Gharib-Shahla", "name": { "family": "Gharib", "given": "Shahla" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Screening for C. elegans male copulation-defective mutants by the mating plug phenotype", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: October 9, 2017; Accepted: November 1, 2017; Published: November 2, 2017. \n\nFunding: Howard Hughes Medical Institute, with whom PWS was an Investigator. \n\nReviewed By: Douglas Portman and Ray Hong.\n\nPublished - microPublication.biology-10.17912-W2SS9K.pdf
", "abstract": "We describe an efficient screen for male mating defective mutants in Caenorhabditis elegans. We report the isolation of 20 alleles that confer specific mating defects. In a previously reported screen (Hajdu-Cronin et al, 2017), we isolated 19 Cod (for copulation defective) strains in which morphologically wild-type males fail to mate. Failure to mate could conceivably result from defects in any step of the mating process: response, turning, vulva location, spicule insertion, and sperm transfer. By observation, we identified mutants defective in each of these steps except for vulva location. We believe that this was due to both redundancy of sensory structures mediating this step and our stringent screening conditions. To address this, we modified the Cod screen, using the strain plg-1(e2001d); him-5(e1490), in which the presence of a copulatory \"plug\" over the hermaphrodite vulva provides a visible marker for successful mating (Hodgkin and Doniach, 1997). We backcrossed plg-1(e2001d) four times into him-5(e1490) to make strain PS1395, the parent of our initial screen (sy4xx series). We subsequently repeated our screen after re-isolating a plg-1(e2001d); him-5(e1490) strain PS3696 that had consistent mating behavior and brood size (PS3696 is the parental background for the sy6xx series). Since we select for whether males are able to mate with their moving siblings as opposed to paralyzed hermaphrodites, we expected to isolate more subtle Cod mutants (such as incompletely penetrant vulva location defects). The screen would also allow for the identification of plug formation defective and hermaphrodite-specific mating defective strains. In one PS3696 screen, of 1400 F2 clones, 5% were non-Plg, 280 were then examined for behavior; we kept 69 as candidates; eight had strong phenotypes and normal morphology and were given allele names (sy678, sy680, sy681, sy682, sy683, sy684, sy685, and sy678). sy681 turned out to have the same molecular lesion as sy680 and was discarded. Overall, we isolated 20 Cod mutants from several screens including several pilot screens (Table 1). sy671 was isolated in this screen and found to be an allele of unc-18 (Schindelman et al., 2006).", "date": "2017-11-02", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "10.17912/W2SS9K", "id_number": "CaltechAUTHORS:20200629-072917595", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200629-072917595", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.17912/W2SS9K", "pmcid": "PMC7255882", "primary_object": { "basename": "microPublication.biology-10.17912-W2SS9K.pdf", "url": "https://authors.library.caltech.edu/records/0e3mz-arn34/files/microPublication.biology-10.17912-W2SS9K.pdf" }, "resource_type": "article", "pub_year": "2017", "author_list": "Liu, Katharine; Hajdu-Cronin, Yvonne; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/29vxt-a9e22", "eprint_id": 78318, "eprint_status": "archive", "datestamp": "2023-08-21 22:03:48", "lastmod": "2023-10-26 00:00:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Stroehlein-A-J", "name": { "family": "Stroehlein", "given": "Andreas J." } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Korhonen-P-K", "name": { "family": "Korhonen", "given": "Pasi K." } }, { "id": "Chang-Bill-C-H", "name": { "family": "Chang", "given": "Bill C. H." } }, { "id": "Nejsum-P", "name": { "family": "Nejsum", "given": "Peter" } }, { "id": "Pozio-E", "name": { "family": "Pozio", "given": "Edoardo" } }, { "id": "La-Rosa-G", "name": { "family": "La Rosa", "given": "Giuseppe" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "Whipworm kinomes reflect a unique biology and adaptation to the host animal", "ispublished": "pub", "full_text_status": "public", "keywords": "Kinome; Gene curation; Nematodes; Kinase signalling; Host\u2013parasite interactions", "note": "\u00a9 2017 Australian Society for Parasitology. Published by Elsevier Ltd. \n\nReceived 21 February 2017, Revised 14 April 2017, Accepted 20 April 2017, Available online 10 June 2017.", "abstract": "Roundworms belong to a diverse phylum (Nematoda) which is comprised of many parasitic species including whipworms (genus Trichuris). These worms have adapted to a biological niche within the host and exhibit unique morphological characteristics compared with other nematodes. Although these adaptations are known, the underlying molecular mechanisms remain elusive. The availability of genomes and transcriptomes of some whipworms now enables detailed studies of their molecular biology. Here, we defined and curated the full complement of an important class of enzymes, the protein kinases (kinomes) of two species of Trichuris, using an advanced and integrated bioinformatic pipeline. We investigated the transcription of Trichuris suis kinase genes across developmental stages, sexes and tissues, and reveal that selectively transcribed genes can be linked to central roles in developmental and reproductive processes. We also classified and functionally annotated the curated kinomes by integrating evidence from structural modelling and pathway analyses, and compared them with other curated kinomes of phylogenetically diverse nematode species. Our findings suggest unique adaptations in signalling processes governing worm morphology and biology, and provide an important resource that should facilitate experimental investigations of kinases and the biology of signalling pathways in nematodes.", "date": "2017-11", "date_type": "published", "publication": "International Journal for Parasitology", "volume": "47", "number": "13", "publisher": "Elsevier", "pagerange": "857-866", "id_number": "CaltechAUTHORS:20170619-081556369", "issn": "0020-7519", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170619-081556369", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.ijpara.2017.04.005", "resource_type": "article", "pub_year": "2017", "author_list": "Stroehlein, Andreas J.; Young, Neil D.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/psp7j-nmv35", "eprint_id": 81662, "eprint_status": "archive", "datestamp": "2023-08-21 21:57:37", "lastmod": "2023-10-17 20:56:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nath-Ravi-D", "name": { "family": "Nath", "given": "Ravi D." } }, { "id": "Bedbrook-Claire-N", "name": { "family": "Bedbrook", "given": "Claire N." }, "orcid": "0000-0003-3973-598X" }, { "id": "Abrams-Michael-J", "name": { "family": "Abrams", "given": "Michael J." }, "orcid": "0000-0003-1864-1706" }, { "id": "Basinger-Ty", "name": { "family": "Basinger", "given": "Ty" } }, { "id": "Bois-J-S", "name": { "family": "Bois", "given": "Justin S." }, "orcid": "0000-0001-7137-8746" }, { "id": "Prober-D-A", "name": { "family": "Prober", "given": "David A." }, "orcid": "0000-0002-7371-4675" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Gradinaru-V", "name": { "family": "Gradinaru", "given": "Viviana" }, "orcid": "0000-0001-5868-348X" }, { "id": "Goentoro-L-A", "name": { "family": "Goentoro", "given": "Lea" }, "orcid": "0000-0002-3904-0195" } ] }, "title": "The Jellyfish Cassiopea Exhibits a Sleep-like State", "ispublished": "pub", "full_text_status": "public", "keywords": "evolution of sleep; sleep; Cnidaria; jellyfish; Cassiopea", "note": "\u00a9 2017 Elsevier. \n\nReceived 30 April 2017, Revised 17 July 2017, Accepted 4 August 2017, Available online 21 September 2017. Published: September 21, 2017. \n\nWe thank Chris Blair from the National Aquarium, MD; Monica Medina and Aki Ohdera from Pennsylvania State University, PA; and Wyatt Patry from the Monterey Bay Aquarium, CA, for generously supplying Cassiopea medusa and polyps and Dr. John Bedbrook for critical reading of the manuscript. We thank Kiersten Darrow and Michael Schaadt of the Cabrillo Marine Aquarium, CA, for input on husbandry. We thank http://dryades.units.it/jelly for an image of Cassiopea (CC 3.01 NC-BY-SA) that was adapted in Figure 3 and Figure S1. This work was supported by the NIH Director's New Innovator Award/PECASE (IDP20D017782-01; to V.G.), the James S. McDonnell Foundation for Complex Systems Science (220020365; to L.G.), the NIMH under a Ruth L. Kirschstein National Research Service Award (F31MH102913; to C.N.B.), the NINDS under a Ruth L. Kirschstein National Research Service Award (F31NS100519; to R.D.N.), a National Science Foundation Graduate Research Fellowship (1144469; to M.J.A.), and an NIH training grant (T32GM007616; to C.N.B. and R.D.N.). V.G. is a Heritage Principal Investigator supported by the Heritage Medical Research Institute; P.W.S. is an investigator with the HHMI (047-101), which supported this research. \n\nData and Software Availability: Code used for tracking jellyfish activity and analysis is available at https://github.com/GradinaruLab/Jellyfish. \n\nAuthor Contributions: R.D.N., C.N.B., and M.J.A. conceived the project. V.G., P.W.S., and L.G. oversaw the project. R.D.N., C.N.B., and M.J.A. performed experiments and data analysis. R.D.N., C.N.B., M.J.A., and T.B. conceptualized, designed, and built experimental setups. C.N.B. and R.D.N. wrote image-processing and data-analysis scripts with J.S.B.'s oversight. D.A.P. provided input on experimental design. R.D.N., C.N.B., and M.J.A. wrote the paper with input from J.S.B., D.A.P., V.G., P.W.S., and L.G.\n\nAccepted Version - nihms907190.pdf
Supplemental Material - mmc1.pdf
Supplemental Material - mmc2.mp4
Supplemental Material - mmc3.mp4
Supplemental Material - mmc4.zip
", "abstract": "Do all animals sleep? Sleep has been observed in many vertebrates, and there is a growing body of evidence for sleep-like states in arthropods and nematodes. Here we show that sleep is also present in Cnidaria, an earlier-branching metazoan lineage. Cnidaria and Ctenophora are the first metazoan phyla to evolve tissue-level organization and differentiated cell types, such as neurons and muscle. In Cnidaria, neurons are organized into a non-centralized radially symmetric nerve net that nevertheless shares fundamental properties with the vertebrate nervous system: action potentials, synaptic transmission, neuropeptides, and neurotransmitters . It was reported that cnidarian soft corals and box jellyfish exhibit periods of quiescence, a pre-requisite for sleep-like states, prompting us to ask whether sleep is present in Cnidaria. Within Cnidaria, the upside-down jellyfish Cassiopea spp. displays a quantifiable pulsing behavior, allowing us to perform long-term behavioral tracking. Monitoring of Cassiopea pulsing activity for consecutive days and nights revealed behavioral quiescence at night that is rapidly reversible, as well as a delayed response to stimulation in the quiescent state. When deprived of nighttime quiescence, Cassiopea exhibited decreased activity and reduced responsiveness to a sensory stimulus during the subsequent day, consistent with homeostatic regulation of the quiescent state. Together, these results indicate that Cassiopea has a sleep-like state, supporting the hypothesis that sleep arose early in the metazoan lineage, prior to the emergence of a centralized nervous system.", "date": "2017-10-09", "date_type": "published", "publication": "Current Biology", "volume": "27", "number": "19", "publisher": "Cell Press", "pagerange": "2984-2990", "id_number": "CaltechAUTHORS:20170921-075913502", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170921-075913502", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "IDP20D017782-01" }, { "agency": "James S. McDonnell Foundation", "grant_number": "220020365" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "F31MH102913" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "F31NS100519" }, { "agency": "NSF Graduate Research Fellowship", "grant_number": "DGE-1144469" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM007616" }, { "agency": "Heritage Medical Research Institute" }, { "agency": "Howard Hughes Medical Institute (HHMI)", "grant_number": "047-101" } ] }, "local_group": { "items": [ { "id": "Heritage-Medical-Research-Institute" }, { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" } ] }, "doi": "10.1016/j.cub.2017.08.014", "pmcid": "PMC5653286", "primary_object": { "basename": "nihms907190.pdf", "url": "https://authors.library.caltech.edu/records/psp7j-nmv35/files/nihms907190.pdf" }, "related_objects": [ { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/psp7j-nmv35/files/mmc1.pdf" }, { "basename": "mmc2.mp4", "url": "https://authors.library.caltech.edu/records/psp7j-nmv35/files/mmc2.mp4" }, { "basename": "mmc3.mp4", "url": "https://authors.library.caltech.edu/records/psp7j-nmv35/files/mmc3.mp4" }, { "basename": "mmc4.zip", "url": "https://authors.library.caltech.edu/records/psp7j-nmv35/files/mmc4.zip" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Nath, Ravi D.; Bedbrook, Claire N.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/e85cc-1bk22", "eprint_id": 79128, "eprint_status": "archive", "datestamp": "2023-08-21 21:50:40", "lastmod": "2023-10-26 14:36:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Preston-S", "name": { "family": "Preston", "given": "Sarah" } }, { "id": "Korhonen-P-K", "name": { "family": "Korhonen", "given": "Pasi K." } }, { "id": "Mouchiroud-L", "name": { "family": "Mouchiroud", "given": "Laurent" } }, { "id": "Cornaglia-M", "name": { "family": "Cornaglia", "given": "Matteo" } }, { "id": "McGee-S-L", "name": { "family": "McGee", "given": "Sean L." } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Davis-R-A", "name": { "family": "Davis", "given": "Rohan A." } }, { "id": "Crawford-S", "name": { "family": "Crawford", "given": "Simon" } }, { "id": "Nowell-C", "name": { "family": "Nowell", "given": "Cameron" } }, { "id": "Ansell-B-R-E", "name": { "family": "Ansell", "given": "Brendan R. E." } }, { "id": "Fisher-G-M", "name": { "family": "Fisher", "given": "Gillian M." } }, { "id": "Andrews-K-T", "name": { "family": "Andrews", "given": "Katherine T." } }, { "id": "Chang-Bill-C-H", "name": { "family": "Chang", "given": "Bill C. H." } }, { "id": "Gijs-M-A-M", "name": { "family": "Gijs", "given": "Martin A. M." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Auwerx-J", "name": { "family": "Auwerx", "given": "Johan" } }, { "id": "Baell-J", "name": { "family": "Baell", "given": "Jonathan" } }, { "id": "Hofmann-A", "name": { "family": "Hofmann", "given": "Andreas" } }, { "id": "Jabbar-A", "name": { "family": "Jabbar", "given": "Abdul" } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "Deguelin exerts potent nematocidal activity via the mitochondrial respiratory chain", "ispublished": "pub", "full_text_status": "public", "keywords": "natural product; anthelmintic activity; transcriptomics; oxidative phosphorylation; nematode", "note": "\u00a9 2017 FASEB. \n\nReceived April 5, 2017; Accepted June 12, 2017; Published online before print July 7, 2017. \n\nThis study was supported by the Australian Research Council\nand the National Health and Medical Research Council (NHMRC) of Australia, as well as by the Medicines for Malaria Venture, Yourgene Bioscience, the University of Melbourne (to R.B.G. S.P., A.J., J.B., B.C.H.C., and A.H.), the \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne, and the Gebert R\u00fcf Stiftung (GRS-025/16) and the AgingX program of the Swiss Initiative for Systems Biology (to J.A. and L.H.). Some work was supported by the EU Ideas Program (ERC-2012-AdG-320404; to M.A.M.G and M.C.). G.M.F. was supported by a postdoctoral fellowship and a new researcher grant from Griffith University. P.K.K. was supported by an early career research fellowship, and N.D.Y. by a career development fellowship (CDF1) from NHMRC. Funding bodies played no role in the design of the study or collection, analysis, or interpretation of data, or in the\nwriting of the manuscript. The authors thank Compounds\nAustralia (http://www.griffith.edu.au/science-aviation/compoundsaustralia) for access to the Davis open-access natural product library, which forms part of the Open Access Compound Collection. The authors declare no conflicts of interest. \n\nAuthor Contributions: S. Preston, L. Mouchiroud, S. L. McGee, K. T. Andrews, B. Chang, M.A. M. Gijs, P. W. Sternberg, J. Auwerx, J. Baell, A. Hofmann, A. Jabbar, and R. B. Gasser designed research; S. Preston, P. K. Korhonen, L. Mouchiroud, M. Cornaglia, and B. R. E.Ansell analyzed data; S. Preston, L.Mouchiroud, M. Cornaglia, S. L.McGee, N. D. Young, S. Crawford, and G. M. Fisher performed research; S. Preston, L. Mouchiroud, andR. B. Gasser wrote thepaper; R. A. Davis contributed reagents; and C. Nowell developed\nsoftware to analyze data.\n\nSupplemental Material - Supplemental_Table1.xlsx
Supplemental Material - Supplemental_Table2.xlsx
Supplemental Material - Supplemental_Table3.xlsx
Supplemental Material - Supplemental_Table4.xlsx
Supplemental Material - Supplemental_Table5.xlsx
", "abstract": "As a result of limited classes of anthelmintics and an over-reliance on chemical control, there is a great need to discover new compounds to combat drug resistance in parasitic nematodes. Here, we show that deguelin, a plant-derived rotenoid, selectively and potently inhibits the motility and development of nematodes, which supports its potential as a lead candidate for drug development. Furthermore, we demonstrate that deguelin treatment significantly increases gene transcription that is associated with energy metabolism, particularly oxidative phosphorylation and mito-ribosomal protein production before inhibiting motility. Mitochondrial tracking confirmed enhanced oxidative phosphorylation. In accordance, real-time measurements of oxidative phosphorylation in response to deguelin treatment demonstrated an immediate decrease in oxygen consumption in both parasitic (Haemonchus contortus) and free-living (Caenorhabditis elegans) nematodes. Consequently, we hypothesize that deguelin is exerting its toxic effect on nematodes as a modulator of oxidative phosphorylation. This study highlights the dynamic biologic response of multicellular organisms to deguelin perturbation.\u2014Preston, S., Korhonen, P. K., Mouchiroud, L., Cornaglia, M., McGee, S. L., Young, N. D., Davis, R. A., Crawford, S., Nowell, C., Ansell, B. R. E., Fisher, G. M., Andrews, K. T., Chang, B. C. H., Gijs, M. A. M., Sternberg, P. W., Auwerx, J., Baell, J., Hofmann, A., Jabbar, A., Gasser, R. B. Deguelin exerts potent nematocidal activity via the mitochondrial respiratory chain.", "date": "2017-10", "date_type": "published", "publication": "FASEB Journal", "volume": "31", "number": "10", "publisher": "Federation of American Societies for Experimental Biology", "pagerange": "4515-4532", "id_number": "CaltechAUTHORS:20170717-103000121", "issn": "0892-6638", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170717-103000121", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council" }, { "agency": "National Health and Medical Research Council (NHMRC)" }, { "agency": "Medicines for Malaria Venture" }, { "agency": "Yourgene Bioscience" }, { "agency": "University of Melbourne" }, { "agency": "\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne" }, { "agency": "Gebert R\u00fcf Stiftung", "grant_number": "GRS-025/16" }, { "agency": "Swiss Initiative for Systems Biology" }, { "agency": "European Research Council (ERC)", "grant_number": "320404" }, { "agency": "Griffith University" } ] }, "doi": "10.1096/fj.201700288R", "primary_object": { "basename": "Supplemental_Table1.xlsx", "url": "https://authors.library.caltech.edu/records/e85cc-1bk22/files/Supplemental_Table1.xlsx" }, "related_objects": [ { "basename": "Supplemental_Table2.xlsx", "url": "https://authors.library.caltech.edu/records/e85cc-1bk22/files/Supplemental_Table2.xlsx" }, { "basename": "Supplemental_Table3.xlsx", "url": "https://authors.library.caltech.edu/records/e85cc-1bk22/files/Supplemental_Table3.xlsx" }, { "basename": "Supplemental_Table4.xlsx", "url": "https://authors.library.caltech.edu/records/e85cc-1bk22/files/Supplemental_Table4.xlsx" }, { "basename": "Supplemental_Table5.xlsx", "url": "https://authors.library.caltech.edu/records/e85cc-1bk22/files/Supplemental_Table5.xlsx" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Preston, Sarah; Korhonen, Pasi K.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/bnycs-z1x20", "eprint_id": 104155, "eprint_status": "archive", "datestamp": "2023-08-19 05:13:27", "lastmod": "2023-10-20 19:08:30", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Whittaker-A-J", "name": { "family": "Whittaker", "given": "Allyson" } }, { "id": "Schindelman-G", "name": { "family": "Schindelman", "given": "Gary" } }, { "id": "Gharib-Shahla", "name": { "family": "Gharib", "given": "Shahla" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "sy680 is a novel allele of pkd-2", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: September 13, 2017; Accepted: September 28, 2017; Published: September 28, 2017. \n\nFunding: Supported by the Howard Hughes Medical Institute (047-101), with which PWS is an investigator. \n\nReviewed By: Bob O'Hagan.\n\nPublished - microPublication.biology.10.17912-W2SW9M.pdf
", "abstract": "A new allele of pkd-2 was isolated in a behavioral genetic screen for male mating defects, and found to result in a substitution of Arginine for Glycine in the equivalent of human PKD2 alanine 615. \n \nThe C. elegans ortholog of polcystin-2 is encoded by pkd-2 (Barr et al., 2001). From an EMS screen of a plg-1; him-5 strain for male mating defective mutants and a secondary behavioral screen for defects in discrete steps of male mating behavior, namely response to contact to hermaphrodites and vulval location (described in Schindelman et al., 2006), we identified a new allele of pkd-2 based on mapping and complementation. sy680 fails to complement pkd-2(sy606) for defects in response to contact with hermaphrodite and vulval location. Here we report the sequence of this allele. PCR amplification and sequencing of pkd-2 exons indicated that there was a c-->t transition in the transcribed DNA strand (g-->a in the pkd-2 sense strand; Figure 1A). This change leads to an altered codon, a Glycine to Arginine substitution the PKD-2 protein. This position corresponds to A615 of the human protein (Figure 1B).", "date": "2017-09-28", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "10.17912/W2SW9M", "id_number": "CaltechAUTHORS:20200630-075434730", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200630-075434730", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.17912/W2SW9M", "pmcid": "PMC7255874", "primary_object": { "basename": "microPublication.biology.10.17912-W2SW9M.pdf", "url": "https://authors.library.caltech.edu/records/bnycs-z1x20/files/microPublication.biology.10.17912-W2SW9M.pdf" }, "resource_type": "article", "pub_year": "2017", "author_list": "Whittaker, Allyson; Schindelman, Gary; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/5vt3w-07j30", "eprint_id": 74065, "eprint_status": "archive", "datestamp": "2023-08-21 21:41:41", "lastmod": "2023-10-23 16:05:23", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Angeles-Albores-David", "name": { "family": "Angeles-Albores", "given": "David" }, "orcid": "0000-0001-5497-8264" }, { "id": "Leighton-Daniel-H-W", "name": { "family": "Leighton", "given": "Daniel H. W." }, "orcid": "0000-0002-1379-0078" }, { "id": "Tsou-Tiffany", "name": { "family": "Tsou", "given": "Tiffany" }, "orcid": "0000-0002-5651-2879" }, { "id": "Khaw-Tiffany-H", "name": { "family": "Khaw", "given": "Tiffany H." } }, { "id": "Antoshechkin-Igor-A", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The Caenorhabditis elegans Female State: Decoupling the Transcriptomic Effects of Aging and Sperm-Status", "ispublished": "pub", "full_text_status": "public", "keywords": "epistasis; genetic interactions; ageing; life cycle; RNA-seq; germline sex determination", "note": "\u00a9 2017 Genetics Society of America. \n\nReceived March 13, 2017; Accepted July 4, 2017; Early online July 27, 2017. \n\nWe thank the Caenorhabditis Genetics Center for providing worm strains. This work would not be possible without the central repository of C. elegans information generated by WormBase, with out which mining the genetic data would not have been possible. DHWL was supported by a National Institutes of Health US Public Health Service Training Grant (T32GM07616). This research was supported by the Howard Hughes Medical Institute, for which PWS is an investigator. \n\nAuthor Contributions: DA, DHWL and PWS designed all experiments. DHWL and THK collected RNA for library preparation. IA generated libraries and performed sequencing. DA performed all bioinformatics and statistical analyses. DA, TT and DHWL performed all screens. DA, DHWL and PWS wrote the paper.\n\nPublished - 2969.pdf
Submitted - 083113.full.pdf
Supplemental Material - FileS1.csv
Supplemental Material - FileS2.csv
Supplemental Material - FileS3.csv
", "abstract": "Understanding genome and gene function in a whole organism requires us to fully comprehend the life cycle and the physiology of the organism in question. Caenorhabditis elegans XX animals are hermaphrodites that exhaust their sperm after 3 d of egg-laying. Even though C. elegans can live for many days after cessation of egg-laying, the molecular physiology of this state has not been as intensely studied as other parts of the life cycle, despite documented changes in behavior and metabolism. To study the effects of sperm depletion and aging of C. elegans during the first 6 d of adulthood, we measured the transcriptomes of first-day adult hermaphrodites and sixth-day sperm-depleted adults, and, at the same time points, mutant fog-2(lf) worms that have a feminized germline phenotype. We found that we could separate the effects of biological aging from sperm depletion. For a large subset of genes, young adult fog-2(lf) animals had the same gene expression changes as sperm-depleted sixth-day wild-type hermaphrodites, and these genes did not change expression when fog-2(lf) females reached the sixth day of adulthood. Taken together, this indicates that changing sperm status causes a change in the internal state of the worm, which we call the female-like state. Our data provide a high-quality picture of the changes that happen in global gene expression throughout the period of early aging in the worm.", "date": "2017-09-01", "date_type": "published", "publication": "G3", "volume": "7", "number": "9", "publisher": "Genetics Society of America", "pagerange": "2969-2977", "id_number": "CaltechAUTHORS:20170206-085209419", "issn": "2160-1836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170206-085209419", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM07616" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1534/g3.117.300080", "pmcid": "PMC5592924", "primary_object": { "basename": "FileS2.csv", "url": "https://authors.library.caltech.edu/records/5vt3w-07j30/files/FileS2.csv" }, "related_objects": [ { "basename": "FileS3.csv", "url": "https://authors.library.caltech.edu/records/5vt3w-07j30/files/FileS3.csv" }, { "basename": "083113.full.pdf", "url": "https://authors.library.caltech.edu/records/5vt3w-07j30/files/083113.full.pdf" }, { "basename": "2969.pdf", "url": "https://authors.library.caltech.edu/records/5vt3w-07j30/files/2969.pdf" }, { "basename": "FileS1.csv", "url": "https://authors.library.caltech.edu/records/5vt3w-07j30/files/FileS1.csv" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Angeles-Albores, David; Leighton, Daniel H. W.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/48dyn-2z690", "eprint_id": 81478, "eprint_status": "archive", "datestamp": "2023-08-19 04:28:04", "lastmod": "2023-10-17 19:53:18", "type": "conference_item", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shinya-Ryoji", "name": { "family": "Shinya", "given": "Ryoji" } }, { "id": "Gronquist-M", "name": { "family": "Gronquist", "given": "Mathew" } }, { "id": "Leighton-D-H-W", "name": { "family": "Leighton", "given": "Daniel H. W." }, "orcid": "0000-0002-1379-0078" }, { "id": "Hsueh-Yen-Ping", "name": { "family": "Hsueh", "given": "Yen-Ping" } }, { "id": "Schroeder-F-C", "name": { "family": "Schroeder", "given": "Frank" }, "orcid": "0000-0002-4420-0237" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul" }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Volatile nematode sex pheromones", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2017 American Chemical Society.", "abstract": "Nematodes produce a staggering array of sol. social cues, glycosides of dideoxy-sugars such as the ascarylose\n(ascarosides), that are secondary metabolites and communicate information such as population d. and location\nof sex partners. We found that predatory fungi respond to certain ascarosides by making sticky traps that trap\nand kill nematodes. This finding suggested that one driver of the evolution of ascaroside prodn. is avoiding\npredation. We have recently identified using GC-MS of the head-space of cultures of two distant genera of\nnematodes - the fungal-feeding and tree-parasitic Bursaphelenchus and the fruit-assocd., free-living\nCaenorhabditis - a set of volatile compds. that are produced by nematodes and attract sex partners. These\ncompds. are hexenyl acetates and relatives. The prodn. of, and response to, these volatiles are genus specific,\nsuggesting that the volatile pheromones might be under similar selective pressures as the sol. pheromones.\nIndeed, the same predatory fungi that senses ascarosides as a proxy for nematodes attract nematodes by prodn. of volatile org. compds. One of these, methyl-2 methyl-3 butenoate, is a potent attractor of hermaphrodite (female) nematodes but not males, suggesting that it mimics endogenous volatile pheromones. The prodn. of volatile pheromones by females is regulated by their sperm status: only unmated females produce the pheromone, suggesting a way to identify candidate genes that control pheromone\nprodn.", "date": "2017-08", "date_type": "published", "publisher": "Caltech Library", "id_number": "CaltechAUTHORS:20170915-080841696", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170915-080841696", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "resource_type": "conference_item", "pub_year": "2017", "author_list": "Shinya, Ryoji; Gronquist, Mathew; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/csx79-98a80", "eprint_id": 79583, "eprint_status": "archive", "datestamp": "2023-08-19 04:08:24", "lastmod": "2023-10-26 16:57:47", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chai-Cynthia-M", "name": { "family": "Chai", "given": "Cynthia M." } }, { "id": "Cronin-C-J", "name": { "family": "Cronin", "given": "Christopher J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Automated Analysis of a Nematode Population-based Chemosensory Preference Assay", "ispublished": "pub", "full_text_status": "public", "keywords": "Behavior, Issue 125, Nematode, Caenorhabditis elegans, automated behavior analysis, population-based assay, chemosensory\npreference, neurobiology", "note": "\u00a9 2017 Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. \n\nDate Published: 7/13/2017. \n\nSome strains were provided by the Caenorhabditis Genetics Center (CGC), which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). This work is supported by the Howard Hughes Medical Institute, with which P.W.S. is an investigator.\n\nPublished - jove-protocol-55963-automated-analysis-nematode-population-based-chemosensory-preference.pdf
Supplemental Material - JoVE_template.pptx
Supplemental Material - Supplementary_Video_1.mp4
Supplemental Material - Supplementary_video_2.mp4
", "abstract": "The nematode, Caenorhabditis elegans' compact nervous system of only 302 neurons underlies a diverse repertoire of behaviors. To facilitate the dissection of the neural circuits underlying these behaviors, the development of robust and reproducible behavioral assays is necessary. Previous C. elegans behavioral studies have used variations of a \"drop test\", a \"chemotaxis assay\", and a \"retention assay\" to investigate the response of C. elegans to soluble compounds. The method described in this article seeks to combine the complementary strengths of the three aforementioned assays. Briefly, a small circle in the middle of each assay plate is divided into four quadrants with the control and experimental solutions alternately placed. After the addition of the worms, the assay plates are loaded into a behavior chamber where microscope cameras record the worms' encounters with the treated regions. Automated video analysis is then performed and a preference index (PI) value for each video is generated. The video acquisition and automated analysis features of this method minimizes the experimenter's involvement and any associated errors. Furthermore, minute amounts of the experimental compound are used per assay and the behavior chamber's multi-camera setup increases experimental throughput. This method is particularly useful for conducting behavioral screens of genetic mutants and novel chemical compounds. However, this method is not appropriate for studying stimulus gradient navigation due to the close proximity of the control and experimental solution regions. It should also not be used when only a small population of worms is available. While suitable for assaying responses only to soluble compounds in its current form, this method can be easily modified to accommodate multimodal sensory interaction and optogenetic studies. This method can also be adapted to assay the chemosensory responses of other nematode species.", "date": "2017-07-13", "date_type": "published", "publication": "Journal of Visualized Experiments", "number": "125", "publisher": "Journal of Visualized Experiments (JoVE)", "pagerange": "e55963", "id_number": "CaltechAUTHORS:20170731-091632206", "issn": "1940-087X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170731-091632206", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P40 OD010440" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.3791/55963", "pmcid": "PMC5612354", "primary_object": { "basename": "JoVE_template.pptx", "url": "https://authors.library.caltech.edu/records/csx79-98a80/files/JoVE_template.pptx" }, "related_objects": [ { "basename": "Supplementary_Video_1.mp4", "url": "https://authors.library.caltech.edu/records/csx79-98a80/files/Supplementary_Video_1.mp4" }, { "basename": "Supplementary_video_2.mp4", "url": "https://authors.library.caltech.edu/records/csx79-98a80/files/Supplementary_video_2.mp4" }, { "basename": "jove-protocol-55963-automated-analysis-nematode-population-based-chemosensory-preference.pdf", "url": "https://authors.library.caltech.edu/records/csx79-98a80/files/jove-protocol-55963-automated-analysis-nematode-population-based-chemosensory-preference.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Chai, Cynthia M.; Cronin, Christopher J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/hmaqy-ejx33", "eprint_id": 104156, "eprint_status": "archive", "datestamp": "2023-08-19 04:04:03", "lastmod": "2023-10-20 19:08:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Walton-S-J", "name": { "family": "Walton", "given": "Sophie J." } }, { "id": "Wang-Han", "name": { "family": "Wang", "given": "Han" }, "orcid": "0000-0002-1933-5762" }, { "id": "Liu-Jonathan", "name": { "family": "Liu", "given": "Jonathan" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Mapping results for a set of cGAL effectors and drivers", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: June 1, 2017; Accepted: June 26, 2017; Published: July 6, 2017. \n\nFunding: Howard Hughes Medical Institute (grant number 047-101) \n\nReviewed By: Michael Ailion.\n\nPublished - microPublication.biology.10.17912-W2Q947.pdf
", "abstract": "Recently, the GAL4-UAS system (cGAL) has been adapted for use in C. elegans for control of gene expression across 15\u00b0C - 25\u00b0C (Wang et al., 2017). In order to create a desired gene expression pattern, one crosses a transgenic strain containing a driver construct with another strain containing an effector gene. Here we mapped several cGAL driver and effector integrations. We first crossed each of the cGAL driver and effector strains with N2 males, picked the heterozygous male progeny, crossed them with hermaphrodites of the mapping strain (DA438), picked L4 hermaphrodites with the corresponding transgenic marker of the driver or effector strain and scored the progeny in the next generation. The DA438 strain contains six recessive mutations, each of which locates on one of the six chromosomes and produces visible phenotypes (Bli on chromosome I, Rol on II, Vab on III, Unc on IV, Dpy on V, and Lon on X (Avery, 1993). F2 progeny with each of the six phenotypes were selected and examined for the presence or absence of the dominant marker associated with the transgene. In the cases where the dominant transgene marker is unlinked to the recessive phenotypic marker, about three quarters of the F2 progeny will have the dominant marker. If the two markers are linked, very few or no animals are expected to have the dominant transgenic marker. The following tables summarize the mapping results for each cGAL strain, stating the ratios of the F2 mutant progeny with and without the dominant transgenic marker.", "date": "2017-07-06", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "10.17912/W2Q947", "id_number": "CaltechAUTHORS:20200630-080605772", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200630-080605772", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)", "grant_number": "047-101" } ] }, "doi": "10.17912/W2Q947", "pmcid": "PMC7255865", "primary_object": { "basename": "microPublication.biology.10.17912-W2Q947.pdf", "url": "https://authors.library.caltech.edu/records/hmaqy-ejx33/files/microPublication.biology.10.17912-W2Q947.pdf" }, "resource_type": "article", "pub_year": "2017", "author_list": "Walton, Sophie J.; Wang, Han; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/24xg2-d1c46", "eprint_id": 77564, "eprint_status": "archive", "datestamp": "2023-08-19 03:34:24", "lastmod": "2023-10-25 23:15:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhang-Ying-K", "name": { "family": "Zhang", "given": "Ying K." } }, { "id": "Sanchez-Ayala-Marcos-A", "name": { "family": "Sanchez-Ayala", "given": "Marco A." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Srinivasan-Jagan", "name": { "family": "Srinivasan", "given": "Jagan" }, "orcid": "0000-0001-5449-7938" }, { "id": "Schroeder-Frank-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" } ] }, "title": "Improved Synthesis for Modular Ascarosides Uncovers Biological Activity", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 American Chemical Society. \n\nReceived: April 3, 2017; Published: May 17, 2017. \n\nThis work was supported in part by the NIH (GM113692 and GM088290 to FCS) and the Howard Hughes Medical Institute. We thank Robert J. Micikas (University of Pennsylvania) for helpful comments and Alexander Artyukhin (Boyce Thompson Institute) for assistance with mass spectrometry.\n\nAccepted Version - nihms877819.pdf
Supplemental Material - ol7b01009_si_001.pdf
", "abstract": "A versatile synthesis of modular ascarosides, a family of signaling molecules from Caenorhabditis elegans and other nematodes, via hydrogenolysis of a cyclic sulfate derived from methyl-\u03b1-l-rhamnopyranoside is reported. The route enables selective introduction of different side chains at the 1, 2, and 4 positions of the sugar, as demonstrated for ascarosides from C. elegans and Pristionchus pacificus. Bioassays with synthetic samples of 4\u2032-tigloyl ascaroside mbas#3 revealed its role as an avoidance or dispersal signal.", "date": "2017-06-02", "date_type": "published", "publication": "Organic Letters", "volume": "19", "number": "11", "publisher": "American Chemical Society", "pagerange": "2837-2840", "id_number": "CaltechAUTHORS:20170518-101558193", "issn": "1523-7060", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170518-101558193", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM113692" }, { "agency": "NIH", "grant_number": "GM088290" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1021/acs.orglett.7b01009", "pmcid": "PMC5533076", "primary_object": { "basename": "nihms877819.pdf", "url": "https://authors.library.caltech.edu/records/24xg2-d1c46/files/nihms877819.pdf" }, "related_objects": [ { "basename": "ol7b01009_si_001.pdf", "url": "https://authors.library.caltech.edu/records/24xg2-d1c46/files/ol7b01009_si_001.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Zhang, Ying K.; Sanchez-Ayala, Marco A.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/fmt8z-0gq52", "eprint_id": 76471, "eprint_status": "archive", "datestamp": "2023-08-19 02:38:45", "lastmod": "2023-10-25 16:01:55", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Panda-Oishika", "name": { "family": "Panda", "given": "Oishika" }, "orcid": "0000-0002-1217-8231" }, { "id": "Akagi-Allison-E", "name": { "family": "Akagi", "given": "Allison E." }, "orcid": "0000-0002-7233-6190" }, { "id": "Artyukhin-A-B", "name": { "family": "Artyukhin", "given": "Alexander B." } }, { "id": "Judkins-J-C", "name": { "family": "Judkins", "given": "Joshua C." } }, { "id": "Le-Henry-H", "name": { "family": "Le", "given": "Henry H." } }, { "id": "Mahanti-P", "name": { "family": "Mahanti", "given": "Parag" } }, { "id": "Cohen-S-M", "name": { "family": "Cohen", "given": "Sarah M." }, "orcid": "0000-0002-5233-2280" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Schroeder-F-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" } ] }, "title": "Biosynthesis of Modular Ascarosides in C. elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. \n\nManuscript received: January 4, 2017; Revised: February 20, 2017; Final Article published: March 28, 2017. \n\nStrains used in this work were provided by NBRP (Japan) and CGC which is funded by NIH (P40 OD010440). This work was supported in part by the NIH (GM113692, GM088290 to F.C.S., T32-GM007616 to A.A., T32 GM008500 to J.C.J.), NSF (DBI-0618969 to BTI), and HHMI. \n\nThe authors declare no conflict of interest.\n\nSupplemental Material - anie201700103-sup-0001-misc_information.pdf
", "abstract": "The nematode Caenorhabditis elegans uses simple building blocks from primary metabolism and a strategy of modular assembly to build a great diversity of signaling molecules, the ascarosides, which function as a chemical language in this model organism. In the ascarosides, the dideoxysugar ascarylose serves as a scaffold to which diverse moieties from lipid, amino acid, neurotransmitter, and nucleoside metabolism are attached. However, the mechanisms that underlie the highly specific assembly of ascarosides are not understood. We show that the acyl-CoA synthetase ACS-7, which localizes to lysosome-related organelles, is specifically required for the attachment of different building blocks to the 4\u2032-position of ascr#9. We further show that mutants lacking lysosome-related organelles are defective in the production of all 4\u2032-modified ascarosides, thus identifying the waste disposal system of the cell as a hotspot for ascaroside biosynthesis.", "date": "2017-04-18", "date_type": "published", "publication": "Angewandte Chemie International Edition", "volume": "56", "number": "17", "publisher": "Wiley", "pagerange": "4729-4733", "id_number": "CaltechAUTHORS:20170410-105746372", "issn": "1433-7851", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170410-105746372", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National BioResource Project" }, { "agency": "NIH", "grant_number": "P40 OD010440" }, { "agency": "NIH", "grant_number": "GM113692" }, { "agency": "NIH", "grant_number": "GM088290" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32-GM007616" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 GM008500" }, { "agency": "NSF", "grant_number": "DBI-0618969" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1002/anie.201700103", "pmcid": "PMC5486983", "primary_object": { "basename": "anie201700103-sup-0001-misc_information.pdf", "url": "https://authors.library.caltech.edu/records/fmt8z-0gq52/files/anie201700103-sup-0001-misc_information.pdf" }, "resource_type": "article", "pub_year": "2017", "author_list": "Panda, Oishika; Akagi, Allison E.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/nc3b7-e8x73", "eprint_id": 77295, "eprint_status": "archive", "datestamp": "2023-08-19 02:25:41", "lastmod": "2023-10-25 22:03:25", "type": "conference_item", "metadata_visibility": "show", "creators": { "items": [ { "id": "Akagi-Allison-E", "name": { "family": "Akagi", "given": "Allison E." }, "orcid": "0000-0002-7233-6190" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul" }, "orcid": "0000-0002-7699-0173" }, { "id": "Schroeder-F-C", "name": { "family": "Schroeder", "given": "Frank" }, "orcid": "0000-0002-4420-0237" } ] }, "title": "Tissue-specific ascaroside production in the nematode Caenorhabditis elegans", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2017 American Chemical Society.", "abstract": "Ascarosides are a family of small mols. used as signals in a variety of important behaviors in C. elegans and other nematodes; these include mate attraction, aggression, repulsion, and entry into dauer diapause under stressful conditions. Structurally, ascarosides are modular glycosides of the dideoxysugar ascarylose. Small structural changes in the fatty add moiety attached to the first position of the sugar as well as the addn. of other metabolically-derived components to the fourth position have been shown to elicit different behaviors. DAF-22, a thiolase responsible for the last step of peroxisomal beta-oxidn. of the ascaroside lipid side chain, is necessary for the prodn. of biol. active ascarosides and is normally expressed in the intestine, body wall muscle, and hypodermis of the worm. After transgenically rescuing the expression of DAF-22 in each tissue individually in a DAF-22 knockout background, HPLC-MS anal. revealed that all three tissues are capable of producing ascarosides, but in different quantities. Furthermore, the expression of DAF-22 in any of the three tissues rescues the ability of the worm to enter dauer diapause, but to varying degrees. By studying these site-specific activity relationships, we highlight the roles of multiple tissues in worm communication via ascarosides.", "date": "2017-04", "date_type": "published", "publisher": "Caltech Library", "id_number": "CaltechAUTHORS:20170509-100756135", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170509-100756135", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "resource_type": "conference_item", "pub_year": "2017", "author_list": "Akagi, Allison E.; Sternberg, Paul; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/n6zdg-qdy23", "eprint_id": 75648, "eprint_status": "archive", "datestamp": "2023-08-19 02:12:41", "lastmod": "2023-10-25 15:11:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "In Retrospect: Forty years of cellular clues from worms", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2017 Macmillan Publishers Limited, part of Springer Nature. \n\nPublished online 29 March 2017.", "abstract": "The cell divisions that occur when a larva develops into an adult Caenorhabditis elegans worm were described in a cell-lineage map in 1977. The work has provided the foundation for many discoveries about developmental mechanisms.", "date": "2017-03-30", "date_type": "published", "publication": "Nature", "volume": "543", "number": "7647", "publisher": "Nature Publishing Group", "pagerange": "628-630", "id_number": "CaltechAUTHORS:20170403-140239429", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170403-140239429", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1038/543628a", "resource_type": "article", "pub_year": "2017", "author_list": "Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/p8673-79f98", "eprint_id": 72124, "eprint_status": "archive", "datestamp": "2023-08-19 01:13:47", "lastmod": "2023-10-23 17:56:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Han", "name": { "family": "Wang", "given": "Han" }, "orcid": "0000-0002-1933-5762" }, { "id": "Liu-Jonathan", "name": { "family": "Liu", "given": "Jonathan" } }, { "id": "Gharib-Shahla", "name": { "family": "Gharib", "given": "Shahla" } }, { "id": "Chai-Cynthia-M", "name": { "family": "Chai", "given": "Cynthia M." } }, { "id": "Schwarz-E-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Pokala-N", "name": { "family": "Pokala", "given": "Navin" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "cGAL, a temperature-robust GAL4\u2013UAS system for Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 Macmillan Publishers Limited. \n\nReceived 22 May; Accepted 18 November; Published online 19 December 2016. \n\nWe are grateful to A. Fire (Stanford University) for sharing unpublished results and to C.T. Hittinger (University of Wisconsin-Madison), D. Sieburth (University of Southern California), E.M. Jorgensen (University of Utah), C. Bargmann (Rockefeller University) and A. Fire (Stanford University) for reagents. We thank H. Korswagen (Hubrecht Institute) for thoughtful discussion. N.P. thanks C. Bargmann for her support. We thank M. Bao, Y.M. Kim, D. Leighton, J. DeModena and G. Medina for technical assistance; and WormBase for technical support. We also thank M. Kato, H. Schwartz, D. Angeles-Albores and other members of the Sternberg lab for editorial comments on the manuscript. Some strains were provided by the CGC, which is funded by the NIH Office of Research Infrastructure Programs (grant P40 OD010440). Some imaging was performed at the Caltech Biological Imaging Facility with the support of the Caltech Beckman Institute and the Arnold and Mabel Beckman Foundation. H.W. is supported by the Della Martin Fellowship. J.L. was supported by NIH grant T32GM007616. This work is supported by the Howard Hughes Medical Institute, with which P.W.S. is an investigator. \n\nData availability: The source data used for the plots in the main and supplementary figures are included in the supplementary materials. Other data are also available from the corresponding author upon request. The coding sequence of Gal4p from Saccharomyces kudriavzevii is in GenBank (GU299177.1). The plasmids for cGAL driver (pHW393, plasmid no. 85583) and effector (pHW394, plasmid no. 85584) are available from Addgene. Source data for Figures 1, 2, 3 and Supplementary Figures 1 and 2 are available online. \n\nAuthor Contributions: H.W., J.L. and P.W.S. conceived the project. H.W. and J.L. performed the experiments, analyzed the data and wrote the paper. S.G. helped with molecular cloning and strain handling. E.M.S. devised the idea of trying Gal4p from yeast species with lower growth temperatures. C.M.C. and N.P. contributed reagents. \n\nThe authors declare no competing financial interests.\n\nAccepted Version - nihms831958.pdf
Supplemental Material - nmeth.4109-S1.pdf
Supplemental Material - nmeth.4109-S2.xlsx
Supplemental Material - nmeth.4109-S3.xlsx
Supplemental Material - nmeth.4109-SF1.jpg
Supplemental Material - nmeth.4109-SF2.jpg
Supplemental Material - nmeth.4109-SF3.jpg
Supplemental Material - nmeth.4109-sv1.mp4
Supplemental Material - nmeth.4109-sv2.mp4
Supplemental Material - nmeth.4109-sv3.mp4
Supplemental Material - nmeth.4109-sv4.mp4
Supplemental Material - nmeth.4109-sv5.mp4
", "abstract": "The GAL4\u2013UAS system is a powerful tool for manipulating gene expression, but its application in Caenorhabditis elegans has not been described. Here we systematically optimize the system's three main components to develop a temperature-optimized GAL4\u2013UAS system (cGAL) that robustly controls gene expression in C. elegans from 15 to 25 \u00b0C. We demonstrate this system's utility in transcriptional reporter analysis, site-of-action experiments and exogenous transgene expression; and we provide a basic driver and effector toolkit.", "date": "2017-02", "date_type": "published", "publication": "Nature Methods", "volume": "14", "number": "2", "publisher": "Nature Publishing Group", "pagerange": "145-148", "id_number": "CaltechAUTHORS:20161117-125604575", "issn": "1548-7091", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161117-125604575", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P40 OD010440" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Arnold and Mabel Beckman Foundation" }, { "agency": "Della Martin Foundation" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM007616" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "collection": "CaltechAUTHORS", "doi": "10.1038/nmeth.4109", "pmcid": "PMC5693259", "primary_object": { "basename": "nmeth.4109-sv5.mp4", "url": "https://authors.library.caltech.edu/records/p8673-79f98/files/nmeth.4109-sv5.mp4" }, "related_objects": [ { "basename": "nmeth.4109-S3.xlsx", "url": "https://authors.library.caltech.edu/records/p8673-79f98/files/nmeth.4109-S3.xlsx" }, { "basename": "nmeth.4109-S2.xlsx", "url": "https://authors.library.caltech.edu/records/p8673-79f98/files/nmeth.4109-S2.xlsx" }, { "basename": "nmeth.4109-sv1.mp4", "url": "https://authors.library.caltech.edu/records/p8673-79f98/files/nmeth.4109-sv1.mp4" }, { "basename": "nmeth.4109-SF2.jpg", "url": "https://authors.library.caltech.edu/records/p8673-79f98/files/nmeth.4109-SF2.jpg" }, { "basename": "nmeth.4109-SF3.jpg", "url": "https://authors.library.caltech.edu/records/p8673-79f98/files/nmeth.4109-SF3.jpg" }, { "basename": "nihms831958.pdf", "url": "https://authors.library.caltech.edu/records/p8673-79f98/files/nihms831958.pdf" }, { "basename": "nmeth.4109-SF1.jpg", "url": "https://authors.library.caltech.edu/records/p8673-79f98/files/nmeth.4109-SF1.jpg" }, { "basename": "nmeth.4109-S1.pdf", "url": "https://authors.library.caltech.edu/records/p8673-79f98/files/nmeth.4109-S1.pdf" }, { "basename": "nmeth.4109-sv3.mp4", "url": "https://authors.library.caltech.edu/records/p8673-79f98/files/nmeth.4109-sv3.mp4" }, { "basename": "nmeth.4109-sv4.mp4", "url": "https://authors.library.caltech.edu/records/p8673-79f98/files/nmeth.4109-sv4.mp4" }, { "basename": "nmeth.4109-sv2.mp4", "url": "https://authors.library.caltech.edu/records/p8673-79f98/files/nmeth.4109-sv2.mp4" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Wang, Han; Liu, Jonathan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/s4931-80158", "eprint_id": 73619, "eprint_status": "archive", "datestamp": "2023-08-19 01:07:29", "lastmod": "2023-10-24 15:32:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hsueh-Yen-Ping", "name": { "family": "Hsueh", "given": "Yen-Ping" } }, { "id": "Gronquist-M-R", "name": { "family": "Gronquist", "given": "Matthew R." } }, { "id": "Schwarz-E-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Nath-R-D", "name": { "family": "Nath", "given": "Ravi David" } }, { "id": "Lee-Ching-Han", "name": { "family": "Lee", "given": "Ching-Han" } }, { "id": "Gharib-S", "name": { "family": "Gharib", "given": "Shalha" } }, { "id": "Schroeder-F-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Nematophagous fungus Arthrobotrys oligospora mimics olfactory cues of sex and food to lure its nematode prey", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 Hsueh et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. \n\nReceived: 24 July 2016; Accepted: 28 December 2016; Published: 18 January 2017. \n\nWe thank Marie-Anne Felix (IBENS), Cori Bargmann (The Rockefeller University), Ryoji Shinya (Sternberg lab), Vivian Chiu (then in Sternberg lab) and the Caenorhabditis Genetics Center (University of Minnesota) for providing the nematode strains used in this study. We also thank Valerie Knowlton (NCSU) for acquiring the SEM image and Clay Wang (USC) for providing the Aspergillus strains. Michael Milligan (SUNY Fredonia) provided invaluable assistance with GC x GC-TOFMS analyses and Chris Cronin and Sreekanth Chalasani (Salk Institute) provided advices for the calcium imaging set-up. We thank Gladys Medina, Sarah Kim, Chiang Yu Shi and Ka-Naam Heung for providing technical assistance and members of the Sternberg laboratory for helpful discussion. This work was supported by HHMI, with which PWS is an investigator, by the NIH K99 award 1 K99GM108867-1 to YPH, by NIH GM084389 to PWS, and startup funds from Academia Sinica to YPH. RN was supported by T32-GM007616. \n\nAuthor contributions: Y-PH, Conceptualization, Data curation, Formal analysis, Supervision, Funding acquisition, Validation, Investigation, Writing\u2014original draft, Writing\u2014review and editing; MRG, Data curation, Formal analysis, Writing\u2014original draft; EMS, Data curation, Formal analysis, Methodology, Writing\u2014original draft, Writing\u2014review and editing; RDN, C-HL, Data curation, Formal analysis; SG, Data curation, Validation; FCS, Formal analysis, Supervision, Writing\u2014review and editing; PWS, Conceptualization, Resources, Supervision, Funding acquisition, Writing\u2014review and editing. \n\nThe funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. \n\nThe authors declare that no competing interests exist.\n\nPublished - e20023-download.pdf
", "abstract": "To study the molecular basis for predator-prey coevolution, we investigated how Caenorhabditis elegans responds to the predatory fungus Arthrobotrys oligospora. C. elegans and other nematodes were attracted to volatile compounds produced by A. oligospora. Gas-chromatographic mass-spectral analyses of A. oligospora-derived volatile metabolites identified several odors mimicking food cues attractive to nematodes. One compound, methyl 3-methyl-2-butenoate (MMB) additionally triggered strong sex- and stage-specific attraction in several Caenorhabditis species. Furthermore, when MMB is present, it interferes with nematode mating, suggesting that MMB might mimic sex pheromone in Caenorhabditis species. Forward genetic screening suggests that multiple receptors are involved in sensing MMB. Response to fungal odors involves the olfactory neuron AWCs. Single-cell RNA-seq revealed the GPCRs expressed in AWC. We propose that A. oligospora likely evolved the means to use olfactory mimicry to attract its nematode prey through the olfactory neurons in C. elegans and related species.", "date": "2017-01-18", "date_type": "published", "publication": "eLife", "volume": "6", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e20023", "id_number": "CaltechAUTHORS:20170123-103744458", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170123-103744458", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "1 K99GM108867-1" }, { "agency": "NIH", "grant_number": "GM084389" }, { "agency": "Academia Sinica" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32-GM007616" } ] }, "collection": "CaltechAUTHORS", "doi": "10.7554/eLife.20023", "pmcid": "PMC5243009", "primary_object": { "basename": "e20023-download.pdf", "url": "https://authors.library.caltech.edu/records/s4931-80158/files/e20023-download.pdf" }, "resource_type": "article", "pub_year": "2017", "author_list": "Hsueh, Yen-Ping; Gronquist, Matthew R.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/syfat-c2914", "eprint_id": 75569, "eprint_status": "archive", "datestamp": "2023-08-19 00:59:27", "lastmod": "2023-10-25 15:09:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Carbon-S", "name": { "family": "Carbon", "given": "S." }, "orcid": "0000-0001-8244-1536" }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "J." }, "orcid": "0000-0002-7259-8107" }, { "id": "Kishore-R", "name": { "family": "Kishore", "given": "R." } }, { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "R." }, "orcid": "0000-0002-8151-7479" }, { "id": "M\u00fcller-H-M", "name": { "family": "Muller", "given": "H.-M." } }, { "id": "Raciti-D", "name": { "family": "Raciti", "given": "D." } }, { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "K." }, "orcid": "0000-0002-1706-4196" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "P. W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Expansion of the Gene Ontology knowledgebase and resources", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived October 25, 2016; Editorial Decision October 26, 2016; Accepted November 16, 2016. \n\nWe want to acknowledge the broad community of scientists who have contributed to the GO knowledgebase, as biocurators and software developers (see http://geneontology.org/page/acknowledgments-contributors), and as authors of published papers that provide the basis for GO annotations (see http://geneontology.org/page/acknowledgments-authors). \n\nFUNDING: National Institutes of Health/National Human Genome Research Institute [HG002273] awarded to the PI group formed by (alphabetically) Judith A. Blake, J. Michael Cherry, Suzanna E. Lewis, Paul W. Sternberg and Paul D. Thomas, as well as additional funding awarded to each participating institution. For more details please visit: http://geneontology.org/page/go-consortium-contributors-list. Funding for open access charge: National Institutes of Health/National Human Genome Research Institute [HG002273]. \n\nConflict of interest statement. None declared.\n\nPublished - gkw1108.pdf
", "abstract": "The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics and related data. Our continued focus is on improving the quality and utility of the GO resources, and we welcome and encourage input from researchers in all areas of biology. In this update, we summarize the current contents of the GO knowledgebase, and present several new features and improvements that have been made to the ontology, the annotations and the tools. Among the highlights are 1) developments that facilitate access to, and application of, the GO knowledgebase, and 2) extensions to the resource as well as increasing support for descriptions of causal models of biological systems and network biology. To learn more, visit http://geneontology.org/.", "date": "2017-01-04", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "45", "number": "D1", "publisher": "Oxford University Press", "pagerange": "D331-D338", "id_number": "CaltechAUTHORS:20170331-093423187", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170331-093423187", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HG002273" } ] }, "corp_creators": { "items": [ "Gene Ontology Consortium" ] }, "doi": "10.1093/nar/gkw1108", "pmcid": "PMC5210579", "primary_object": { "basename": "gkw1108.pdf", "url": "https://authors.library.caltech.edu/records/syfat-c2914/files/gkw1108.pdf" }, "resource_type": "article", "pub_year": "2017", "author_list": "Carbon, S.; Chan, J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/03f4p-hqz26", "eprint_id": 69342, "eprint_status": "archive", "datestamp": "2023-08-22 19:15:52", "lastmod": "2023-10-23 20:11:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Quintero-Cadena-Porfirio", "name": { "family": "Quintero-Cadena", "given": "Porfirio" }, "orcid": "0000-0003-0067-5844" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Enhancer sharing promotes neighborhoods of transcriptional regulation across eukaryotes", "ispublished": "pub", "full_text_status": "public", "keywords": "enhancer sharing; gene coexpression; gene neighbors; enhancer specificity; transcriptional domains", "note": "\u00a9 2016 Quintero-Cadena, Sternberg. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\n\nReceived June 28, 2016. Accepted October 15, 2016. Early Online October 31, 2016. \n\nWe thank Zhiping Wang and Yishi Jin for plasmids for CRISPR-Cas9 single-copy insertion; Carmie Robinson for discussions, experimental suggestions, and comments on the manuscript; Han Wang for discussions, technical advice, and comments on the manuscript; Hillel Schwartz, Mitchell Guttman, Mihoko Kato, David Angeles-Albores, Jonathan Liu, Barbara Wold, Isabelle Peter, and Angelike Stathopoulos for discussions and comments on the manuscript; the Encode and ModEncode consortiums, FlyBase, WormBase, and Ensembl databases, the Wold Lab, and the Guigo Lab for data accessibility. Our work was supported by the Howard Hughes Medical Institute, of which P.W.S. is an investigator. \n\nAuthor contributions: P.Q.C. performed the experiments and analyzed the data. P.Q.C. and P.W.S. designed the experiments and wrote the paper. \n\nThe authors declare no competing financial interests.\n\nPublished - 4167.full.pdf
Submitted - 061218.full.pdf
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Supplemental Material - FigureS6.eps
Supplemental Material - FileS1.zip
Supplemental Material - FileS2.pdf
Supplemental Material - TableS1.csv
Supplemental Material - TableS2.csv
", "abstract": "Enhancers physically interact with transcriptional promoters, looping over distances that can span multiple regulatory elements. Given that enhancer\u2013promoter (EP) interactions generally occur via common protein complexes, it is unclear whether EP pairing is predominantly deterministic or proximity guided. Here, we present cross-organismic evidence suggesting that most EP pairs are compatible, largely determined by physical proximity rather than specific interactions. By reanalyzing transcriptome datasets, we find that the transcription of gene neighbors is correlated over distances that scale with genome size. We experimentally show that nonspecific EP interactions can explain such correlation, and that EP distance acts as a scaling factor for the transcriptional influence of an enhancer. We propose that enhancer sharing is commonplace among eukaryotes, and that EP distance is an important layer of information in gene regulation.", "date": "2016-12-01", "date_type": "published", "publication": "G3", "volume": "6", "number": "12", "publisher": "Genetics Society of America", "pagerange": "4167-4174", "id_number": "CaltechAUTHORS:20160801-083326464", "issn": "2160-1836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160801-083326464", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1534/g3.116.036228", "pmcid": "PMC5144984", "primary_object": { "basename": "FigureS1.eps", "url": "https://authors.library.caltech.edu/records/03f4p-hqz26/files/FigureS1.eps" }, "related_objects": [ { "basename": "FigureS3.eps", "url": "https://authors.library.caltech.edu/records/03f4p-hqz26/files/FigureS3.eps" }, { "basename": "FigureS5.jpg", "url": "https://authors.library.caltech.edu/records/03f4p-hqz26/files/FigureS5.jpg" }, { "basename": "FigureS6.eps", "url": "https://authors.library.caltech.edu/records/03f4p-hqz26/files/FigureS6.eps" }, { "basename": "4167.full.pdf", "url": "https://authors.library.caltech.edu/records/03f4p-hqz26/files/4167.full.pdf" }, { "basename": "FigureS2.jpg", "url": "https://authors.library.caltech.edu/records/03f4p-hqz26/files/FigureS2.jpg" }, { "basename": "FigureS4.jpg", "url": "https://authors.library.caltech.edu/records/03f4p-hqz26/files/FigureS4.jpg" }, { "basename": "FileS1.zip", "url": "https://authors.library.caltech.edu/records/03f4p-hqz26/files/FileS1.zip" }, { "basename": "FileS2.pdf", "url": "https://authors.library.caltech.edu/records/03f4p-hqz26/files/FileS2.pdf" }, { "basename": "TableS1.csv", "url": "https://authors.library.caltech.edu/records/03f4p-hqz26/files/TableS1.csv" }, { "basename": "TableS2.csv", "url": "https://authors.library.caltech.edu/records/03f4p-hqz26/files/TableS2.csv" }, { "basename": "061218.full.pdf", "url": "https://authors.library.caltech.edu/records/03f4p-hqz26/files/061218.full.pdf" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Quintero-Cadena, Porfirio and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/erz2g-k0970", "eprint_id": 75592, "eprint_status": "archive", "datestamp": "2023-08-19 00:19:17", "lastmod": "2023-10-25 15:09:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Angeles-Albores-David", "name": { "family": "Angeles-Albores", "given": "D." }, "orcid": "0000-0001-5497-8264" }, { "id": "Puckett-Robinson-Carmie", "name": { "family": "Robinson", "given": "C. P." } }, { "id": "Williams-B", "name": { "family": "Williams", "given": "B." } }, { "id": "Antoshechkin-Igor-A", "name": { "family": "Antoshechkin", "given": "I." }, "orcid": "0000-0002-9934-3040" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "P. W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Reconstruction of a Genetic Pathway Using Transcriptome Mapping in a Metazoan", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 American Society for Cell Biology.\n\nPublished - Angeles-Albore_2016pP888.pdf
", "abstract": "RNA\u2010seq is a technique that is commonly used to identify downstream elements to a genetic or chemical perturbation. In theory, global transcriptomes contain enough information to perform a full\u2010fledged genetic analysis of a pathway. Early attempts to do this using microarrays in single celled organisms reported partial reconstruction of a genetic pathway. \nUsing the hypoxia pathway, we show that genetic reconstructions can be performed using global\ntranscriptome data. We obtained the transcriptomes of 5 C. elegans single mutants and 2 double mutants at the young adult stage. We show that in a blinded computational study, we were able to identify relevant genetic relationships between all genes in a pathway. \nIn addition, we identified a core set of ~500 genes that make up the bulk of the C. elegans hypoxia response. Multiple of these genes are directly implicated in the Electron Transport Chain (ETC),\nmetabolism regulation or chemical damage responses.", "date": "2016-12", "date_type": "published", "publication": "Molecular Biology of the Cell", "volume": "27", "publisher": "American Society for Cell Biology", "pagerange": "Art. No. P888", "id_number": "CaltechAUTHORS:20170331-130937502", "issn": "1059-1524", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170331-130937502", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "primary_object": { "basename": "Angeles-Albore_2016pP888.pdf", "url": "https://authors.library.caltech.edu/records/erz2g-k0970/files/Angeles-Albore_2016pP888.pdf" }, "resource_type": "article", "pub_year": "2016", "author_list": "Angeles-Albores, D.; Robinson, C. P.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/wyea6-ewr42", "eprint_id": 70835, "eprint_status": "archive", "datestamp": "2023-08-19 00:03:17", "lastmod": "2023-10-20 23:25:08", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lockhead-Dean", "name": { "family": "Lockhead", "given": "Dean" } }, { "id": "Schwarz-Erich-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "O'Hagan-Robert", "name": { "family": "O'Hagan", "given": "Robert" } }, { "id": "Bellotti-Sebastian", "name": { "family": "Bellotti", "given": "Sebastian" } }, { "id": "Krieg-Michael", "name": { "family": "Krieg", "given": "Michael" } }, { "id": "Barr-Maureen-M", "name": { "family": "Barr", "given": "Maureen M." }, "orcid": "0000-0003-4483-2952" }, { "id": "Dunn-Alexander-R", "name": { "family": "Dunn", "given": "Alexander R." }, "orcid": "0000-0001-6096-4600" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Goodman-Miriam-B", "name": { "family": "Goodman", "given": "Miriam B." } } ] }, "title": "The tubulin repertoire of C. elegans sensory neurons and its context-dependent role in process outgrowth", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 The American Society for Cell Biology. Under the License and Publishing Agreement, authors grant to the general public, effective two months after publication of (i.e.,. the appearance of) the edited manuscript in an online issue of MBoC, the nonexclusive right to copy, distribute, or display the manuscript subject to the terms of the Creative Commons\u2013Noncommercial\u2013Share Alike 3.0 Unported license (http://creativecommons.org/licenses/by-nc-sa/3.0). \n\nSubmitted July 1, 2016. Revised September 12, 2016. Accepted September 15, 2016. This article was published online ahead of print in MBoC in Press (http://www.molbiolcell.org/cgi/doi/10.1091/mbc.E16-06-0473) on September 21, 2016. \n\nThis work was funded by: NIH research grants K99NS089942 (to M.K), R01NS047715 (to M.B.G.), R01GM084389 (to P.W.S.), R01DK059418 and R56DK074746 (to M.M.B); The New Jersey Commission on Spinal Cord Research Grant CSCR15IRG014 (to R.O.); and The Stanford Graduate Fellowship and the NIH's Cellular and Molecular Biology Training Program T32GM007276 (to D.L). P.W.S. is an investigator of the Howard Hughes Medical Institute. We thank the following: Beth Pruitt and Maria Gallegos for discussion and feedback, Zhiwen Liao for numerous microinjections; Chlo\u00e9 Girard for technical consultation; the Japanese Knockout Consortium, Martin Chalfie, and Chaogu Zheng for strains; Igor Antoshechkin at the Jacobs Genomics Laboratory (California Institute of Technology) for RNA-seq; WormBase; and the Goodman, Pruitt, and Dunn groups for insightful discussions regarding this work. \n\nData availability: Sequence files for raw RNA-seq reads have been deposited in the National Center for Biotechnology Information Sequence Read Archive (www.ncbi.nlm.nih.gov/sra) under the accession numbers SRR3481679 (PLM neuron pool), SRR3481680 (AFD neuron pool), and SRR3481678 (ASER neuron pool). \n\nThe authors declare no conflicting financial interests.\n\nPublished - 3717.full.pdf
Submitted - 075879.full.pdf
Supplemental Material - CombinedSupMats.pdf
Supplemental Material - mc-E16-06-0473-s02.xlsx
", "abstract": "Microtubules contribute to many cellular processes, including transport, signaling, and chromosome separation during cell division (Kapitein and Hoogenraad, 2015). They are comprised of \u03b1\u03b2\u2010tubulin heterodimers arranged into linear protofilaments and assembled into tubes. Eukaryotes express multiple tubulin isoforms (Gogonea et al., 1999), and there has been a longstanding debate as to whether the isoforms are redundant or perform specialized roles as part of a tubulin code (Fulton and Simpson, 1976). Here, we use the well\u2010characterized touch receptor neurons (TRNs) of Caenorhabditis elegans to investigate this question, through genetic dissection of process outgrowth both in vivo and in vitro. With single\u2010cell RNA-seq, we compare transcription profiles for TRNs with those of two other sensory neurons, and present evidence that each sensory neuron expresses a distinct palette of tubulin genes. In the TRNs, we analyze process outgrowth and show that four tubulins (tba\u20101, tba\u20102, tbb\u20101, and tbb\u20102) function partially or fully redundantly, while two others (mec\u20107 and mec\u201012) perform specialized, context\u2010dependent roles. Our findings support a model in which sensory neurons express overlapping subsets of tubulin genes whose functional redundancy varies between cell types and in vivo and in vitro contexts.", "date": "2016-11-15", "date_type": "published", "publication": "Molecular Biology of the Cell", "volume": "27", "number": "23", "publisher": "American Society for Cell Biology", "pagerange": "3717-3728", "id_number": "CaltechAUTHORS:20161004-135532696", "issn": "1059-1524", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161004-135532696", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "K99NS089942" }, { "agency": "NIH", "grant_number": "R01NS047715" }, { "agency": "NIH", "grant_number": "R01GM084389" }, { "agency": "NIH", "grant_number": "R01DK059418" }, { "agency": "NIH", "grant_number": "R56DK074746" }, { "agency": "New Jersey Commission on Spinal Cord Research", "grant_number": "CSCR15IRG014" }, { "agency": "Stanford Graduate Fellowship" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM007276" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1091/mbc.E16-06-0473", "pmcid": "PMC5170555", "primary_object": { "basename": "mc-E16-06-0473-s02.xlsx", "url": "https://authors.library.caltech.edu/records/wyea6-ewr42/files/mc-E16-06-0473-s02.xlsx" }, "related_objects": [ { "basename": "075879.full.pdf", "url": "https://authors.library.caltech.edu/records/wyea6-ewr42/files/075879.full.pdf" }, { "basename": "3717.full.pdf", "url": "https://authors.library.caltech.edu/records/wyea6-ewr42/files/3717.full.pdf" }, { "basename": "CombinedSupMats.pdf", "url": "https://authors.library.caltech.edu/records/wyea6-ewr42/files/CombinedSupMats.pdf" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Lockhead, Dean; Schwarz, Erich M.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/z27p8-phb40", "eprint_id": 70986, "eprint_status": "archive", "datestamp": "2023-08-22 18:50:54", "lastmod": "2023-10-23 15:14:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Choi-Harry-M-T", "name": { "family": "Choi", "given": "Harry M. T." }, "orcid": "0000-0002-1530-0773" }, { "id": "Calvert-Colby-R", "name": { "family": "Calvert", "given": "Colby R." } }, { "id": "Husain-Naeem", "name": { "family": "Husain", "given": "Naeem" }, "orcid": "0000-0003-4962-7237" }, { "id": "Barsi-Julius-C", "name": { "family": "Barsi", "given": "Julius C." }, "orcid": "0000-0002-5161-6708" }, { "id": "Deverman-Benjamin-E", "name": { "family": "Deverman", "given": "Benjamin E." }, "orcid": "0000-0002-6223-9303" }, { "id": "Hunter-Ryan-C", "name": { "family": "Hunter", "given": "Ryan C." }, "orcid": "0000-0003-3841-1676" }, { "id": "Kato-Mihoko", "name": { "family": "Kato", "given": "Mihoko" }, "orcid": "0000-0003-3827-8879" }, { "id": "Lee-S-Melanie", "name": { "family": "Lee", "given": "S. Melanie" } }, { "id": "Abelin-Anna-C-T", "name": { "family": "Abelin", "given": "Anna C. T." } }, { "id": "Rosenthal-Adam-Z", "name": { "family": "Rosenthal", "given": "Adam Z." }, "orcid": "0000-0002-6936-3665" }, { "id": "Akbari-Omar-S", "name": { "family": "Akbari", "given": "Omar S." }, "orcid": "0000-0002-6853-9884" }, { "id": "Li-Yuwei", "name": { "family": "Li", "given": "Yuwei" }, "orcid": "0000-0001-7753-4869" }, { "id": "Hay-B-A", "name": { "family": "Hay", "given": "Bruce A." }, "orcid": "0000-0002-5486-0482" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Patterson-P-H", "name": { "family": "Patterson", "given": "Paul H." } }, { "id": "Davidson-E-H", "name": { "family": "Davidson", "given": "Eric H." } }, { "id": "Mazmanian-S-K", "name": { "family": "Mazmanian", "given": "Sarkis K." }, "orcid": "0000-0003-2713-1513" }, { "id": "Prober-D-A", "name": { "family": "Prober", "given": "David A." }, "orcid": "0000-0002-7371-4675" }, { "id": "Leadbetter-J-R", "name": { "family": "Leadbetter", "given": "Jared R." }, "orcid": "0000-0002-7033-0844" }, { "id": "Newman-D-K", "name": { "family": "Newman", "given": "Dianne K." }, "orcid": "0000-0003-1647-1918" }, { "id": "Readhead-Carol", "name": { "family": "Readhead", "given": "Carol" } }, { "id": "Bronner-M-E", "name": { "family": "Bronner", "given": "Marianne E." }, "orcid": "0000-0003-4274-1862" }, { "id": "Wold-B-J", "name": { "family": "Wold", "given": "Barbara" }, "orcid": "0000-0003-3235-8130" }, { "id": "Fraser-S-E", "name": { "family": "Fraser", "given": "Scott E." }, "orcid": "0000-0002-5377-0223" }, { "id": "Pierce-N-A", "name": { "family": "Pierce", "given": "Niles A." }, "orcid": "0000-0003-2367-4406" } ] }, "title": "Mapping a multiplexed zoo of mRNA expression", "ispublished": "pub", "full_text_status": "public", "keywords": "In situ hybridization, In situ amplification, Hybridization chain reaction (HCR), Multiplexing, Deep sample penetration, High contrast, Subcellular resolution, Bacteria, Whole-mount embryos and larvae, Tissue sections", "note": "\u00a9 2016. Published by The Company of Biologists Ltd. \n\nReceived May 20, 2016. Accepted August 1, 2016.\n\nThis work was funded by the National Institutes of Health (NIH) [5R01EB006192]; the National Science Foundation Molecular Programming Project [NSF-CCF-1317694]; the Gordon and Betty Moore Foundation [GBMF2809]; the Beckman Institute at Caltech (PMTC); the Translational Biomedical Imaging Laboratory at CHLA; the Translational Imaging Center at USC; a Christensen Fellowship at St Catherine's College, University of Oxford; and by the John Simon Guggenheim Memorial Foundation. Deposited in PMC for release after 12 months. \n\nCompeting interests: The authors declare competing financial interests in the form of patents and pending patent applications. \n\nAuthor contributions: Study conceived by N.A.P. in consultation with M.E.B., E.H.D., S.E.F., B.A.H., J.R.L., D.K.N., P.H.P., M.v.d.R., B.W. Experiments designed by H.M.T.C. and N.A.P. Preliminary studies and protocol adaptation performed by S.M.L., R.C.H., A.Z.R., H.M.T.C. (bacteria), C.R.C. (nematode), N.H. (fly), J.C.B., C.R.C. (urchin), H.M.T.C. (zebrafish), T.S.-S., C.R.C. (chicken), A.C.T.A., B.E.D., D.H., H.M.T.C. (mouse), and H.M.T.C., N.H. (human), in consultation with D.K.N., J.R.L. (bacteria), M.K. (nematode), R.L., S.E.F. (chicken), R.L., C.R.C., S.E.F., B.W. (mouse), M.v.d.R. (human), and H.M.T.C., N.A.P. (all organisms). Final protocols optimized and final data collected by H.M.T.C. (bacteria, zebrafish, mouse), C.R.C. (nematode, urchin, chicken) and N.H. (fly, human). Final data analyzed by: S.M.L., S.K.M., R.C.H., D.K.N., A.Z.R., J.R.L. (bacteria), M.K., P.S., C.R.C. (nematode), O.S.A., B.A.H., N.H. (fly), J.C.B., C.R.C. (urchin), D.A.P., S.E.F. (fish), T.S.-S., M.E.B., C.R.C. (chicken), A.C.T.A., B.W., B.E.D., D.H., Y.L., C.R., R.L., S.E.F. (mouse), A.C.M., M.v.d.R., N.H. (human) and H.M.T.C and N.A.P. (all organisms). Paper and supplementary information written by H.M.T.C. and N.A.P. Paper was edited and approved by all coauthors.\n\nPublished - 3632.full.pdf
Supplemental Material - DEV140137supp.pdf
", "abstract": "In situ hybridization methods are used across the biological sciences to map mRNA expression within intact specimens. Multiplexed experiments, in which multiple target mRNAs are mapped in a single sample, are essential for studying regulatory interactions, but remain cumbersome in most model organisms. Programmable in situ amplifiers based on the mechanism of hybridization chain reaction (HCR) overcome this longstanding challenge by operating independently within a sample, enabling multiplexed experiments to be performed with an experimental timeline independent of the number of target mRNAs. To assist biologists working across a broad spectrum of organisms, we demonstrate multiplexed in situ HCR in diverse imaging settings: bacteria, whole-mount nematode larvae, whole-mount fruit fly embryos, whole-mount sea urchin embryos, whole-mount zebrafish larvae, whole-mount chicken embryos, whole-mount mouse embryos and formalin-fixed paraffin-embedded human tissue sections. In addition to straightforward multiplexing, in situ HCR enables deep sample penetration, high contrast and subcellular resolution, providing an incisive tool for the study of interlaced and overlapping expression patterns, with implications for research communities across the biological sciences.", "date": "2016-10-01", "date_type": "published", "publication": "Development", "volume": "143", "number": "19", "publisher": "Company of Biologists", "pagerange": "3632-3637", "id_number": "CaltechAUTHORS:20161011-070233463", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161011-070233463", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "5R01EB006192" }, { "agency": "NSF", "grant_number": "CCF-1317694" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "Caltech Beckman Institute" }, { "agency": "CHLA Translational Biomedical Imaging Laboratory" }, { "agency": "USC Translational Imaging Center" }, { "agency": "St. Catharine's College" }, { "agency": "University of Oxford" }, { "agency": "John Simon Guggenheim Memorial Foundation" } ] }, "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1242/dev.140137", "pmcid": "PMC5087610", "primary_object": { "basename": "3632.full.pdf", "url": "https://authors.library.caltech.edu/records/z27p8-phb40/files/3632.full.pdf" }, "related_objects": [ { "basename": "DEV140137supp.pdf", "url": "https://authors.library.caltech.edu/records/z27p8-phb40/files/DEV140137supp.pdf" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Choi, Harry M. T.; Calvert, Colby R.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/s640m-9hj35", "eprint_id": 69749, "eprint_status": "archive", "datestamp": "2023-08-22 18:45:29", "lastmod": "2023-10-20 20:33:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nath-Ravi-D", "name": { "family": "Nath", "given": "Ravi D." } }, { "id": "Chow-Elly", "name": { "family": "Chow", "given": "Elly S." } }, { "id": "Wang-Han", "name": { "family": "Wang", "given": "Han" }, "orcid": "0000-0002-1933-5762" }, { "id": "Schwarz-Erich-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "C. elegans Stress-Induced Sleep Emerges from the Collective Action of Multiple Neuropeptides", "ispublished": "pub", "full_text_status": "public", "keywords": "sleep regulation; RFamides; neuropeptide modulation; single-neuron RNA-seq; genetic redundancy", "note": "\u00a9 2016 Elsevier Ltd. \n\nReceived 14 April 2016, Revised 15 June 2016, Accepted 19 July 2016, Available online 18 August 2016, Published: August 18, 2016. \n\nWe thank the Caenorhabditis Genetics Center (NIH P40OD010440) and S. Mitani for strains, WormBase for bioinformatics support, Gladys Medina for technical support, the Millard and Muriel Jacobs Genetics and Genomics Laboratory for sequencing, and members of our laboratories for discussions. We thank Cheryl Van Buskirk for sharing unpublished observations and Dr. Daniel Lee, Dr. David Prober, Dr. John Bedbrook, Claire Bedbrook, Dr. Hillel Schwartz, and Dr. Mihoko Kato for comments and discussions. We thank Monica Savasta for generating graphics. This work was supported by the Howard Hughes Medical Institute(147-101), of which P.W.S. is an investigator, and NIH grant GM084389 to P.W.S. R.D.N. was supported by NIH grant T32GM007616. H.W. is supported by a Della Martin Postdoctoral Fellowship. The strain carrying the tm2427 allele is available through the National BioResource Project, subject to a materials transfer agreement. \n\nAuthor Contributions: E.S.C., E.M.S., R.D.N., and P.W.S. conceived the project. E.S.C. dissected ALA neurons and sequenced their amplified cDNA. E.M.S. performed the ALA transcriptome analysis. R.D.N., E.S.C., and H.W. performed C. elegans behavior experiments. E.S.C., H.W., and R.D.N. generated reagents. R.D.N., E.S.C., H.W., E.M.S., and P.W.S. wrote the paper. \n\nAccession Numbers: The accession number for the RNA-seq reads for the two pools of wild-type mid-L4 ALA neurons reported in this paper is NCBI Sequence Read Archive (SRA): SRP038903. The accession number for the RNA-seq reads for the two pools of whole C. elegans mixed-stage wild-type N2 larvae reused in this paper is SRA: SRP015688.\n\nAccepted Version - nihms811541.pdf
Supplemental Material - mmc1.pdf
Supplemental Material - mmc2.xlsx
Supplemental Material - mmc3.xlsx
Supplemental Material - mmc4.mp4
Supplemental Material - mmc5.mp4
Supplemental Material - mmc6.mp4
", "abstract": "The genetic basis of sleep regulation remains poorly understood. In C. elegans, cellular stress induces sleep through epidermal growth factor (EGF)-dependent activation of the EGF receptor in the ALA neuron. The downstream mechanism by which this neuron promotes sleep is unknown. Single-cell RNA sequencing of ALA reveals that the most highly expressed, ALA-enriched genes encode neuropeptides. Here we have systematically investigated the four most highly enriched neuropeptides: flp-7, nlp-8, flp-24, and flp-13. When individually removed by null mutation, these peptides had little or no effect on stress-induced sleep. However, stress-induced sleep was abolished in nlp-8; flp-24; flp-13 triple-mutant animals, indicating that these neuropeptides work collectively in controlling stress-induced sleep. We tested the effect of overexpression of these neuropeptide genes on five behaviors modulated during sleep\u2014pharyngeal pumping, defecation, locomotion, head movement, and avoidance response to an aversive stimulus\u2014and we found that, if individually overexpressed, each of three neuropeptides (nlp-8, flp-24, or flp-13) induced a different suite of sleep-associated behaviors. These overexpression results raise the possibility that individual components of sleep might be specified by individual neuropeptides or combinations of neuropeptides.", "date": "2016-09-26", "date_type": "published", "publication": "Current Biology", "volume": "26", "number": "18", "publisher": "Cell Press", "pagerange": "2446-2455", "id_number": "CaltechAUTHORS:20160818-085530875", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160818-085530875", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P40OD010440" }, { "agency": "Millard and Muriel Jacobs Genetics and Genomics Laboratory" }, { "agency": "Howard Hughes Medical Institute (HHMI)", "grant_number": "147-101" }, { "agency": "NIH", "grant_number": "GM084389" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM007616" }, { "agency": "Della Martin Postdoctoral Fellowship" } ] }, "local_group": { "items": [ { "id": "Millard-and-Muriel-Jacobs-Genetics-and-Genomics-Laboratory" } ] }, "doi": "10.1016/j.cub.2016.07.048", "pmcid": "PMC5694219", "primary_object": { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/s640m-9hj35/files/mmc1.pdf" }, "related_objects": [ { "basename": "mmc2.xlsx", "url": "https://authors.library.caltech.edu/records/s640m-9hj35/files/mmc2.xlsx" }, { "basename": "mmc3.xlsx", "url": "https://authors.library.caltech.edu/records/s640m-9hj35/files/mmc3.xlsx" }, { "basename": "mmc4.mp4", "url": "https://authors.library.caltech.edu/records/s640m-9hj35/files/mmc4.mp4" }, { "basename": "mmc5.mp4", "url": "https://authors.library.caltech.edu/records/s640m-9hj35/files/mmc5.mp4" }, { "basename": "mmc6.mp4", "url": "https://authors.library.caltech.edu/records/s640m-9hj35/files/mmc6.mp4" }, { "basename": "nihms811541.pdf", "url": "https://authors.library.caltech.edu/records/s640m-9hj35/files/nihms811541.pdf" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Nath, Ravi D.; Chow, Elly S.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/jz2r1-r5261", "eprint_id": 70328, "eprint_status": "archive", "datestamp": "2023-08-20 13:48:21", "lastmod": "2023-10-20 22:10:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Angeles-Albores-David", "name": { "family": "Angeles-Albores", "given": "David" }, "orcid": "0000-0001-5497-8264" }, { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "Raymond Y. N." }, "orcid": "0000-0002-8151-7479" }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Tissue enrichment analysis for C. elegans genomics", "ispublished": "pub", "full_text_status": "public", "keywords": "Gene ontology \u2013 Anatomy ontology \u2013 WormBase \u2013 RNA-seq \u2013 High-throughput biology", "note": "\u00a9 2016 The Author(s). Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0\nInternational License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and\nreproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the\nCreative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver\n(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. \n\nReceived: 30 April 2016; Accepted: 26 August 2016; Published online: 13 September 2016. \n\nWe thank Justin Bois for his help and support. We would like to acknowledge all members of the Sternberg lab for helpful discussion. \n\nThis work was supported by HG002223 from the National Human Genome Research Institute to PWS., and H.H.M.I., with which PWS is an investigator. The funding agencies had no input into the design, execution or interpretation of our experiments, nor into the writing of this manuscript. \n\nAvailability of data and materials: \nOur web implementation is available at http://www.wormbase.org/tools/enrichment/tea/tea.cgi. Our software can also be downloaded using Python's pip installer via the command\n\npip install tissue_enrichment_analysis \n\nAlternatively, our software is available for download at: http://dangeles.github.io/TissueEnrichmentAnalysis \n\nAll benchmark gene sets, benchmarking code and Figures can also be found at the same address, under the 'tests' folder. \n\nAuthors' contributions: DA and PWS conceived of the project; DA developed algorithm; RYL made intellectual contributions to the project; RYL and JC developed the web GUI. All authors read and approved the final manuscript. \n\nThe authors declare that they have no competing interests.\n\nConsent for publication: Not applicable. \n\nEthics approval and consent to participate: Not applicable.\n\nPublished - art_10.1186_s12859-016-1229-9.pdf
Supplemental Material - 12859_2016_1229_MOESM1_ESM.pdf
Supplemental Material - 12859_2016_1229_MOESM2_ESM.pdf
Supplemental Material - 12859_2016_1229_MOESM3_ESM.zip
Supplemental Material - 12859_2016_1229_MOESM4_ESM.zip
", "abstract": "Background: Over the last ten years, there has been explosive development in methods for measuring gene expression. These methods can identify thousands of genes altered between conditions, but understanding these datasets and forming hypotheses based on them remains challenging. One way to analyze these datasets is to associate ontologies (hierarchical, descriptive vocabularies with controlled relations between terms) with genes and to look for enrichment of specific terms. Although Gene Ontology (GO) is available for Caenorhabditis elegans, it does not include anatomical information. \n\nResults: We have developed a tool for identifying enrichment of C. elegans tissues among gene sets and generated a website GUI where users can access this tool. Since a common drawback to ontology enrichment analyses is its verbosity, we developed a very simple filtering algorithm to reduce the ontology size by an order of magnitude. We adjusted these filters and validated our tool using a set of 30 gold standards from Expression Cluster data in WormBase. We show our tool can even discriminate between embryonic and larval tissues and can even identify tissues down to the single-cell level. We used our tool to identify multiple neuronal tissues that are down-regulated due to pathogen infection in C. elegans. \n\nConclusions: Our Tissue Enrichment Analysis (TEA) can be found within WormBase, and can be downloaded using Python's standard pip installer. It tests a slimmed-down C. elegans tissue ontology for enrichment of specific terms and provides users with a text and graphic representation of the results.", "date": "2016-09-13", "date_type": "published", "publication": "BMC Bioinformatics", "volume": "17", "publisher": "BioMed Central", "pagerange": "Art. No. 366", "id_number": "CaltechAUTHORS:20160914-074709906", "issn": "1471-2105", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160914-074709906", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HG002223" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1186/s12859-016-1229-9", "pmcid": "PMC5020436", "primary_object": { "basename": "art_10.1186_s12859-016-1229-9.pdf", "url": "https://authors.library.caltech.edu/records/jz2r1-r5261/files/art_10.1186_s12859-016-1229-9.pdf" }, "related_objects": [ { "basename": "12859_2016_1229_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/jz2r1-r5261/files/12859_2016_1229_MOESM1_ESM.pdf" }, { "basename": "12859_2016_1229_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/jz2r1-r5261/files/12859_2016_1229_MOESM2_ESM.pdf" }, { "basename": "12859_2016_1229_MOESM3_ESM.zip", "url": "https://authors.library.caltech.edu/records/jz2r1-r5261/files/12859_2016_1229_MOESM3_ESM.zip" }, { "basename": "12859_2016_1229_MOESM4_ESM.zip", "url": "https://authors.library.caltech.edu/records/jz2r1-r5261/files/12859_2016_1229_MOESM4_ESM.zip" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Angeles-Albores, David; Lee, Raymond Y. N.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/r768j-hqk19", "eprint_id": 69202, "eprint_status": "archive", "datestamp": "2023-08-20 13:34:02", "lastmod": "2023-10-20 16:39:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Stroehlein-Andreas-J", "name": { "family": "Stroehlein", "given": "Andreas J." }, "orcid": "0000-0001-9432-9816" }, { "id": "Young-Neil-D", "name": { "family": "Young", "given": "Neil D." }, "orcid": "0000-0001-8756-229X" }, { "id": "Korhonen-Pasi-K", "name": { "family": "Korhonen", "given": "Pasi K." }, "orcid": "0000-0002-9957-4674" }, { "id": "Chang-Bill-C-H", "name": { "family": "Chang", "given": "Bill C. H." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "La-Rosa-Giuseppe", "name": { "family": "La Rosa", "given": "Giuseppe" }, "orcid": "0000-0002-9906-3137" }, { "id": "Pozio-Eoardo", "name": { "family": "Pozio", "given": "Edoardo" }, "orcid": "0000-0003-3317-4704" }, { "id": "Gasser-Robin-B", "name": { "family": "Gasser", "given": "Robin B." }, "orcid": "0000-0002-4423-1690" } ] }, "title": "Analyses of Compact Trichinella Kinomes Reveal a MOS-like Protein Kinase with a Unique N-terminal Domain", "ispublished": "pub", "full_text_status": "public", "keywords": "Trichinella kinome parasitic worms protein annotation protein kinases", "note": "\u00a9 2016 Stroehlein et al. Published by the Genetics Society of America. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nManuscript received May 19, 2016; accepted for publication July 7, 2016; published Early Online July 13, 2016. \n\nResearch funding from the National Health and Medical Research Council (NHMRC), Australian Research Council, Wellcome Trust, and The University of Melbourne Business Improvement Program is gratefully acknowledged (R.B.G.). Support from the Australian Academy of Science, the Australian-American Fulbright Commission, Alexander von Humboldt Foundation, and Melbourne Water Corporation, as well as the Victorian Life Sciences Computation Initiative and WormBase (www.wormbase.org), is gratefully acknowledged. P.W.S. acknowledges support from the Howard Hughes Medical Institute and the National Institutes of Health. A.J.S. is a recipient of a Melbourne International Research Scholarship and a Melbourne International Fee Remission Scholarship from the University of Melbourne. N.D.Y. holds an NHMRC Career Development Fellowship.\n\nPublished - 2847.full.pdf
Submitted - TableS4.xlsx
Supplemental Material - FigureS1.pdf
Supplemental Material - FigureS2.pdf
Supplemental Material - TableS1.xlsx
Supplemental Material - TableS10.xlsx
Supplemental Material - TableS2.xlsx
Supplemental Material - TableS3.xlsx
Supplemental Material - TableS5.xlsx
Supplemental Material - TableS6.xlsx
Supplemental Material - TableS7.xlsx
Supplemental Material - TableS8.xlsx
Supplemental Material - TableS9.xlsx
", "abstract": "Parasitic worms of the genus Trichinella (phylum Nematoda; class Enoplea) represent a complex of at least twelve taxa that infect a range of different host animals, including humans, around the world. They are foodborne, intracellular nematodes, and their life cycles differ substantially from those of other nematodes. The recent characterization of the genomes and transcriptomes of all twelve recognized taxa of Trichinella now allows, for the first time, detailed studies of their molecular biology. In the present study, we defined, curated, and compared the protein kinase complements (kinomes) of Trichinella spiralis and T. pseudospiralis using an integrated bioinformatic workflow employing transcriptomic and genomic data sets. We examined how variation in the kinome might link to unique aspects of Trichinella morphology, biology, and evolution. Furthermore, we utilized in silico structural modeling to discover and characterize a novel, MOS-like kinase with an unusual, previously undescribed N-terminal domain. Taken together, the present findings provide a basis for comparative investigations of nematode kinomes, and might facilitate the identification of Enoplea-specific intervention and diagnostic targets. Importantly, the in silico modeling approach assessed here provides an exciting prospect of being able to identify and classify currently unknown (orphan) kinases, as a foundation for their subsequent structural and functional investigation.", "date": "2016-09", "date_type": "published", "publication": "G3", "volume": "6", "number": "9", "publisher": "Genetics Society of America", "pagerange": "2847-2856", "id_number": "CaltechAUTHORS:20160725-131922343", "issn": "2160-1836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160725-131922343", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Health and Medical Research Council (NHMRC)" }, { "agency": "Australian Research Council" }, { "agency": "Wellcome Trust" }, { "agency": "University of Melbourne" }, { "agency": "Australian Academy of Science" }, { "agency": "Australian-American Fulbright Commission" }, { "agency": "Alexander von Humboldt Foundation" }, { "agency": "Melbourne Water Corporation" }, { "agency": "Victorian Life Sciences Computation Initiative (VLSCI)" }, { "agency": "WormBase" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH" } ] }, "doi": "10.1534/g3.116.032961", "pmcid": "PMC5015942", "primary_object": { "basename": "TableS2.xlsx", "url": "https://authors.library.caltech.edu/records/r768j-hqk19/files/TableS2.xlsx" }, "related_objects": [ { "basename": "TableS8.xlsx", "url": "https://authors.library.caltech.edu/records/r768j-hqk19/files/TableS8.xlsx" }, { "basename": "TableS6.xlsx", "url": "https://authors.library.caltech.edu/records/r768j-hqk19/files/TableS6.xlsx" }, { "basename": "FigureS1.pdf", "url": "https://authors.library.caltech.edu/records/r768j-hqk19/files/FigureS1.pdf" }, { "basename": "FigureS2.pdf", "url": "https://authors.library.caltech.edu/records/r768j-hqk19/files/FigureS2.pdf" }, { "basename": "TableS3.xlsx", "url": "https://authors.library.caltech.edu/records/r768j-hqk19/files/TableS3.xlsx" }, { "basename": "TableS7.xlsx", "url": "https://authors.library.caltech.edu/records/r768j-hqk19/files/TableS7.xlsx" }, { "basename": "TableS9.xlsx", "url": "https://authors.library.caltech.edu/records/r768j-hqk19/files/TableS9.xlsx" }, { "basename": "2847.full.pdf", "url": "https://authors.library.caltech.edu/records/r768j-hqk19/files/2847.full.pdf" }, { "basename": "TableS10.xlsx", "url": "https://authors.library.caltech.edu/records/r768j-hqk19/files/TableS10.xlsx" }, { "basename": "TableS4.xlsx", "url": "https://authors.library.caltech.edu/records/r768j-hqk19/files/TableS4.xlsx" }, { "basename": "TableS5.xlsx", "url": "https://authors.library.caltech.edu/records/r768j-hqk19/files/TableS5.xlsx" }, { "basename": "TableS1.xlsx", "url": "https://authors.library.caltech.edu/records/r768j-hqk19/files/TableS1.xlsx" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Stroehlein, Andreas J.; Young, Neil D.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/2p0ym-10d71", "eprint_id": 68535, "eprint_status": "archive", "datestamp": "2023-08-20 13:14:19", "lastmod": "2023-10-19 22:16:49", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Grimbert-S", "name": { "family": "Grimbert", "given": "St\u00e9phanie" } }, { "id": "Tietze-K", "name": { "family": "Tietze", "given": "Kyria" } }, { "id": "Barkoulas-M", "name": { "family": "Barkoulas", "given": "Michalis" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "F\u00e9lix-M-A", "name": { "family": "F\u00e9lix", "given": "Marie-Anne" } }, { "id": "Braendle-C", "name": { "family": "Braendle", "given": "Christian" } } ] }, "title": "Anchor cell signaling and vulval precursor cell positioning establish a reproducible spatial context during C. elegans vulval induction", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 Elsevier Inc. \n\nReceived date: 22 February 2016; Revised date: 5 April 2016; Accepted date: 31 May 2016. \n\nCB acknowledges financial support by the Centre National de la Recherche Scientifique (CNRS), the Agence Nationale de la Recherche, the Fondation ARC pour la Recherche sur le Cancer, and the Fondation Schlumberger pour l'Education et la Recherche. SG was supported by fellowships from the Minist\u00e8re de l'Enseignement Sup\u00e9rieur et de la Recherche and the Fondation ARC pour la Recherche sur le Cancer. MAF acknowledges funding provided by the Agence Nationale de la Recherche (ANR12-BSV2-0004-01 and ANR10-LABX-54 MEMOLIFE) and the Bettencourt Schueller Foundation (Coup d'Elan 2011). MB was supported by a postdoctoral fellowship from the Fondation pour la Recherche M\u00e9dicale. \n\nAuthor contributions: Conceived and designed the experiments: CB, MAF, PWS. Performed the experiments: SG, KT, MB. Analyzed the data: CB, SG. Wrote the paper: CB, MAF, SG. \n\nCompeting Interests: None.\n\nSupplemental Material - mmc1.pdf
Supplemental Material - mmc2.pdf
Supplemental Material - mmc3.xlsx
Supplemental Material - mmc4.xlsx
", "abstract": "How cells coordinate their spatial positioning to successfully communicate is poorly understood. Here we address this topic using C. elegans vulval patterning during which hypodermal vulval precursor cells (VPCs) adopt distinct cell fates determined by their relative positions to the gonadal anchor cell (AC). LIN-3/EGF signaling by the AC induces the central VPC, P6.p, to adopt a 1\u00b0 vulval fate. Exact alignment of AC and VPCs is thus critical for correct fate patterning, yet, as we show here, the initial AC-VPC positioning is both highly variable and asymmetric among individuals, with AC and P6.p only becoming aligned at the early L3 stage. Cell ablations and mutant analysis indicate that VPCs, most prominently 1\u00b0 cells, move towards the AC. We identify AC-released LIN-3/EGF as a major attractive signal, which therefore plays a dual role in vulval patterning (cell alignment and fate induction). Additionally, compromising Wnt pathway components also induces AC-VPC alignment errors, with loss of posterior Wnt signaling increasing stochastic vulval centering on P5.p. Our results illustrate how intercellular signaling reduces initial spatial variability in cell positioning to generate reproducible interactions across tissues.", "date": "2016-08-01", "date_type": "published", "publication": "Developmental Biology", "volume": "416", "number": "1", "publisher": "Elsevier", "pagerange": "123-135", "id_number": "CaltechAUTHORS:20160620-132014255", "issn": "0012-1606", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160620-132014255", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Centre National de la Recherche Scientifique (CNRS)" }, { "agency": "Fondation ARC pour la Recherche sur le Cancer" }, { "agency": "Fondation Schlumberger pour l'Education et la Recherche" }, { "agency": "Minist\u00e8re de l'Enseignement Sup\u00e9rieur et de la Recherche" }, { "agency": "Agence Nationale de la Recherche (ANR)", "grant_number": "ANR12-BSV2-0004-01" }, { "agency": "Agence Nationale de la Recherche (ANR)", "grant_number": "ANR10-LABX-54 MEMOLIFE" }, { "agency": "Bettencourt Schueller Foundation" }, { "agency": "Fondation pour la Recherche M\u00e9dicale" } ] }, "doi": "10.1016/j.ydbio.2016.05.036", "primary_object": { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/2p0ym-10d71/files/mmc1.pdf" }, "related_objects": [ { "basename": "mmc2.pdf", "url": "https://authors.library.caltech.edu/records/2p0ym-10d71/files/mmc2.pdf" }, { "basename": "mmc3.xlsx", "url": "https://authors.library.caltech.edu/records/2p0ym-10d71/files/mmc3.xlsx" }, { "basename": "mmc4.xlsx", "url": "https://authors.library.caltech.edu/records/2p0ym-10d71/files/mmc4.xlsx" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Grimbert, St\u00e9phanie; Tietze, Kyria; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/j6wh6-82t76", "eprint_id": 68852, "eprint_status": "archive", "datestamp": "2023-09-15 05:28:58", "lastmod": "2023-10-23 21:18:04", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Stroehlein-A-J", "name": { "family": "Stroehlein", "given": "Andreas J." } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Hall-R-S", "name": { "family": "Hall", "given": "Ross S." } }, { "id": "Korhonen-P-K", "name": { "family": "Korhonen", "given": "Pasi K." } }, { "id": "Hofmann-A", "name": { "family": "Hofmann", "given": "Andreas" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Jabbar-A", "name": { "family": "Jabbar", "given": "Abdul" } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "CAP protein superfamily members in Toxocara canis", "ispublished": "pub", "full_text_status": "public", "keywords": "Nematodes, Toxocara canis, CAP (SCP/TAPS) protein genes, Transcription profiles, Genetic interactions", "note": "\u00a9 2016 The Author(s). This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. \n\nReceived: 2 May 2016. Accepted: 13 June 2016. Published: 24 June 2016. \n\nSupport from the Victorian Life Sciences Computation Initiative, Australia (VLSCI; grant no. VR0007) on its Peak Computing Facility at the University of Melbourne, Australia, an initiative of the Victorian Government, Australia, is gratefully acknowledged (RBG), as is other support from the Medicines for Malaria Venture (MMV), YourGene Bioscience (Taiwan) and Melbourne Water (RBG). We acknowledge the contributions of all of the staff members at WormBase (www.wormbase.org). \n\nThe present study was funded by the Australian Research Council (ARC), the National Health and Medical Research Council of Australia (NHMRC) and the Wellcome Trust (Pathfinder) (RBG). NDY is a NHMRC Career Development Fellow (CDF). AJS is a recipient of a Melbourne International Research Scholarship (MIRS) and a Melbourne International Fee Remission Scholarship (MIFRS) from The University of Melbourne. Funding bodies had no role in the design of the study or collection, analysis or interpretation of data, or in writing the manuscript. \n\nAvailability of data and material: The datasets supporting the conclusions of this article are included within the article and the additional file. \n\nAuthors' contributions: Conceived and designed the study and supervised the project: AJS and RBG. Undertook the study and data analysis: AJS and RSH. Contributed to analysis using various tools: NDY and PKK. Wrote the paper: AJS and RBG. Contributed to the interpretation of findings, drafting of the manuscript and funding: NDY, AJ, AH, PWS and RBG. All authors read and approved the final version of the manuscript. \n\nThe authors declare that they have no competing interests. \n\nConsent for publication: Not applicable. \n\nEthics approval and consent to participate: Not applicable.\n\nPublished - parasites360.pdf
Supplemental Material - 13071_2016_1642_MOESM1_ESM.xlsx
", "abstract": "Background: Proteins of the cysteine-rich secretory proteins, antigen 5 and pathogenesis-related 1 (CAP) superfamily are recognized or proposed to play roles in parasite development and reproduction, and in modulating host immune attack and infection processes. However, little is known about these proteins for most parasites. \n\nResults: In the present study, we explored CAP proteins of Toxocara canis, a socioeconomically important zoonotic roundworm. To do this, we mined and curated transcriptomic and genomic data, predicted and curated full-length protein sequences (n\u2009=\u200928), conducted analyses of these data and studied the transcription of respective genes in different developmental stages of T. canis. In addition, based on information available for Caenorhabditis elegans, we inferred that selected genes (including lon-1, vap-1, vap-2, scl-1, scl-8 and scl-11 orthologs) of T. canis and their interaction partners likely play central roles in this parasite's development and/or reproduction via TGF-beta and/or insulin-like signaling pathways, or via host interactions. \n\nConclusion: In conclusion, this study could provide a foundation to guide future studies of CAP proteins of T. canis and related parasites, and might assist in finding new interventions against diseases caused by these parasites.", "date": "2016-06-24", "date_type": "published", "publication": "Parasites and Vectors", "volume": "9", "number": "1", "publisher": "BioMed Central", "pagerange": "Art. No. 360", "id_number": "CaltechAUTHORS:20160706-100101575", "issn": "1756-3305", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160706-100101575", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Victorian Life Sciences Computation Initiative (VLSCI)", "grant_number": "VR0007" }, { "agency": "Australian Research Council" }, { "agency": "National Health and Medical Research Council (NHMRC)" }, { "agency": "Wellcome Trust" }, { "agency": "University of Melbourne" } ] }, "doi": "10.1186/s13071-016-1642-y", "pmcid": "PMC4921028", "primary_object": { "basename": "13071_2016_1642_MOESM1_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/j6wh6-82t76/files/13071_2016_1642_MOESM1_ESM.xlsx" }, "related_objects": [ { "basename": "parasites360.pdf", "url": "https://authors.library.caltech.edu/records/j6wh6-82t76/files/parasites360.pdf" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Stroehlein, Andreas J.; Young, Neil D.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/rvpfs-47f04", "eprint_id": 67490, "eprint_status": "archive", "datestamp": "2023-08-20 11:49:25", "lastmod": "2023-10-18 21:14:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Leighton-D-H-W", "name": { "family": "Leighton", "given": "Daniel H. W." }, "orcid": "0000-0002-1379-0078" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Mating pheromones of Nematoda: olfactory signaling with physiological consequences", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2016 Elsevier Ltd. \n\nAvailable online 21 May 2016. \n\nConflict of interest statement: Nothing declared.", "abstract": "Secreted pheromones have long been known to influence mating in the phylum Nematoda. The study of nematode sexual behavior has greatly benefited in the last decade from the genetic and neurobiological tools available for the model nematode Caenorhabditis elegans, as well as from the chemical identification of many pheromones secreted by this species. The discovery that nematodes can influence one another's physiological development and stress responsiveness through the sharing of pheromones, in addition to simply triggering sexual attraction, is particularly striking. Here we review recent research on nematode mating pheromones, which has been conducted predominantly on C. elegans, but there are beginning to be parallel studies in other species.", "date": "2016-06", "date_type": "published", "publication": "Current Opinion in Neurobiology", "volume": "38", "publisher": "Elsevier", "pagerange": "119-124", "id_number": "CaltechAUTHORS:20160531-100813515", "issn": "0959-4388", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160531-100813515", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.conb.2016.04.008", "resource_type": "article", "pub_year": "2016", "author_list": "Leighton, Daniel H. W. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/fe2fn-gfe83", "eprint_id": 64670, "eprint_status": "archive", "datestamp": "2023-08-22 17:33:54", "lastmod": "2023-10-17 21:35:30", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Narayan-Anusha", "name": { "family": "Narayan", "given": "Anusha" } }, { "id": "Venkatachalam-Vivek", "name": { "family": "Venkatachalam", "given": "Vivek" }, "orcid": "0000-0002-2414-7416" }, { "id": "Durak-Omer", "name": { "family": "Durak", "given": "Omer" }, "orcid": "0000-0001-8426-6188" }, { "id": "Reilly-Douglas-K", "name": { "family": "Reilly", "given": "Douglas K." }, "orcid": "0000-0001-8260-8690" }, { "id": "Bose-Neelanjan", "name": { "family": "Bose", "given": "Neelanjan" }, "orcid": "0000-0002-3817-4757" }, { "id": "Schroeder-Frank-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" }, { "id": "Samuel-Aravinthan-D-T", "name": { "family": "Samuel", "given": "Aravinthan D. T." } }, { "id": "Srinivasan-Jagan", "name": { "family": "Srinivasan", "given": "Jagan" }, "orcid": "0000-0001-5449-7938" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Contrasting responses within a single neuron class enable sex-specific attraction in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "population coding; electrophysiology; chemosensation; calcium imaging; animal behavior", "note": "\u00a9 2016 National Academy of Sciences.\n\nContributed by Paul W. Sternberg, January 22, 2016 (sent for review July 5, 2015; reviewed by Mala Murthy and Douglas Portman). Published online before print February 22, 2016. \n\nWe thank Ofer Mazor, Michale Fee, and Vivek Jayaraman for helpful suggestions; Scott Emmons for sharing unpublished information on the male connectome; and Robyn Lints for the generous gift of the ppkd-2::GCAMP6 strain. This work was supported in part by National Science Foundation Grant PHY-0957185 and National Institutes of Health (NIH) Grant 8DP1GM105383-05 (to A.D.T.S.), startup funds from Worcester Polytechnic Institute (to J.S.), NIH Grant GM085285 (to F.C.S. and P.W.S.), and the Howard Hughes Medical Institute, with which P.W.S. is an Investigator. \n\nAuthor contributions: A.N. and J.S. designed research; A.N., O.D., D.K.R., N.B., F.C.S., and J.S. performed research; A.N., V.V., A.D.T.S., J.S., and P.W.S. analyzed data; A.N., V.V., A.D.T.S., J.S., and P.W.S. wrote the paper; and N.B. and F.C.S. synthesized ascr#3 and #8. \n\nReviewers: M.M., Princeton University; and D.P., University of Rochester Medical Center. \n\nThe authors declare no conflict of interest. \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1600786113/-/DCSupplemental.\n\nPublished - PNAS-2016-Narayan-E1392-401.pdf
Supplemental Material - pnas.1600786113.sapp.pdf
Supplemental Material - pnas.1600786113.sm01.mp4
Supplemental Material - pnas.1600786113.sm02.mp4
Supplemental Material - pnas.201600786SI.pdf
", "abstract": "Animals find mates and food, and avoid predators, by navigating to regions within a favorable range of available sensory cues. How are these ranges set and recognized? Here we show that male Caenorhabditis elegans exhibit strong concentration preferences for sex-specific small molecule cues secreted by hermaphrodites, and that these preferences emerge from the collective dynamics of a single male-specific class of neurons, the cephalic sensory neurons (CEMs). Within a single worm, CEM responses are dissimilar, not determined by anatomical classification and can be excitatory or inhibitory. Response kinetics vary by concentration, suggesting a mechanism for establishing preferences. CEM responses are enhanced in the absence of synaptic transmission, and worms with only one intact CEM show nonpreferential attraction to all concentrations of ascaroside for which CEM is the primary sensor, suggesting that synaptic modulation of CEM responses is necessary for establishing preferences. A heterogeneous concentration-dependent sensory representation thus appears to allow a single neural class to set behavioral preferences and recognize ranges of sensory cues.", "date": "2016-03-08", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "113", "number": "10", "publisher": "National Academy of Sciences", "pagerange": "E1392-E1401", "id_number": "CaltechAUTHORS:20160223-073624632", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160223-073624632", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "PHY-0957185" }, { "agency": "NIH", "grant_number": "8DP1GM105383-05" }, { "agency": "Worcester Polytechnic Institute" }, { "agency": "NIH", "grant_number": "GM085285" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1073/pnas.1600786113", "pmcid": "PMC4791020", "primary_object": { "basename": "pnas.1600786113.sm01.mp4", "url": "https://authors.library.caltech.edu/records/fe2fn-gfe83/files/pnas.1600786113.sm01.mp4" }, "related_objects": [ { "basename": "pnas.1600786113.sm02.mp4", "url": "https://authors.library.caltech.edu/records/fe2fn-gfe83/files/pnas.1600786113.sm02.mp4" }, { "basename": "pnas.201600786SI.pdf", "url": "https://authors.library.caltech.edu/records/fe2fn-gfe83/files/pnas.201600786SI.pdf" }, { "basename": "PNAS-2016-Narayan-E1392-401.pdf", "url": "https://authors.library.caltech.edu/records/fe2fn-gfe83/files/PNAS-2016-Narayan-E1392-401.pdf" }, { "basename": "pnas.1600786113.sapp.pdf", "url": "https://authors.library.caltech.edu/records/fe2fn-gfe83/files/pnas.1600786113.sapp.pdf" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Narayan, Anusha; Venkatachalam, Vivek; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/z1x7p-8zh69", "eprint_id": 104157, "eprint_status": "archive", "datestamp": "2023-08-20 10:48:03", "lastmod": "2023-10-20 19:08:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ghosh-Srimoyee", "name": { "family": "Ghosh", "given": "Srimoyee" } }, { "id": "Inoue-Takao", "name": { "family": "Inoue", "given": "Takao" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "ina-1 expression in the somatic gonad during late larval development", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 by the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: July 1, 2015; Accepted: August 1, 2015; Published: March 1, 2016. \n\nFunding: National Institutes of Health USPHS training grant. \n\nReviewed By: Bhagwati Gupta.\n\nPublished - microPublication.biology.10.17912-W2159J.pdf
", "abstract": "ina-1 is expressed throughout uterine toroids. At mid L4, expression is seen in uterine toroid 1 and 4 (ut1, ut4) and in the anterior uterine toroids 2 and 3 (ut2, ut3). In addition, ina-1::GFP is detected in the spermathecal-uterine junction and spermatheca. At the L4 lethargus stage, bright expression is observed in uterine toroids 1 and 4, the spermathecal-uterine junction, and spermatheca. Dimmer expression is present in uterine toroid 2 and posterior toroid 3. Fluorescence is also detected in vulE.\nReagents: gmIs5", "date": "2016-03-01", "date_type": "published", "publication": "microPublication Biology", "publisher": "Caltech Library", "pagerange": "10.17912/W2159J", "id_number": "CaltechAUTHORS:20200630-081142712", "issn": "2578-9430", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200630-081142712", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship" } ] }, "doi": "10.17912/W2159J", "pmcid": "PMC7255860", "primary_object": { "basename": "microPublication.biology.10.17912-W2159J.pdf", "url": "https://authors.library.caltech.edu/records/z1x7p-8zh69/files/microPublication.biology.10.17912-W2159J.pdf" }, "resource_type": "article", "pub_year": "2016", "author_list": "Ghosh, Srimoyee; Inoue, Takao; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ntwsq-57q51", "eprint_id": 64632, "eprint_status": "archive", "datestamp": "2023-08-20 10:17:55", "lastmod": "2023-10-17 21:33:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Druzinsky-R-E", "name": { "family": "Druzinsky", "given": "Robert E." } }, { "id": "Balhoff-J-E", "name": { "family": "Balhoff", "given": "James P." } }, { "id": "Crompton-A-W", "name": { "family": "Crompton", "given": "Alfred W." } }, { "id": "Done-J", "name": { "family": "Done", "given": "James" } }, { "id": "German-R-Z", "name": { "family": "German", "given": "Rebecca Z." } }, { "id": "Haendel-M-A", "name": { "family": "Haendel", "given": "Melissa A." } }, { "id": "Herrel-A", "name": { "family": "Herrel", "given": "Anthony" } }, { "id": "Herring-S-W", "name": { "family": "Herring", "given": "Susan W." } }, { "id": "Lapp-H", "name": { "family": "Lapp", "given": "Hilmar" } }, { "id": "Mabee-P-M", "name": { "family": "Mabee", "given": "Paula M." } }, { "id": "Muller-H-M", "name": { "family": "Muller", "given": "Hans-Michael" } }, { "id": "Mungall-C-J", "name": { "family": "Mungall", "given": "Christopher J." }, "orcid": "0000-0002-6601-2165" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Vinyard-C-J", "name": { "family": "Vinyard", "given": "Christopher J." } }, { "id": "Williams-S-H", "name": { "family": "Williams", "given": "Susan H." } }, { "id": "Wall-C-E", "name": { "family": "Wall", "given": "Christine E." } } ] }, "title": "Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 The Authors. This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. \n\nReceived: August 14, 2015. Accepted: January 27, 2016. Published: February 12, 2016. \n\nEditor: Sharon Swartz, Brown University. \n\nThis work received support from the following sources: National Science Foundation (nsf.gov) to RED DBI-1062350; to SHW DBI-1062327; to CEW DBI-1062333; to RZG DBI-1343588; to CJV DBI-1062332; to PMM DBI-1062542 and DEB-0956049; National Evolutionary Synthesis Center (https://www.nescent.org/; NESCent; NSF EF-0905606). NESCent hosted FEED Workshops in May, 2012, and May, 2014. CJM was supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 (http://energy.gov/eere/vehicles/downloads/office-science-basic-energy-sciences). PMM acknowledges funding from the National Science Foundation (DBI-1062542) and the Phenotype Ontology Research Coordination Network (DEB-0956049). Phenotype RCN (www.phenotypercn.org/) also provided support for RED and CJM. National Institutes of Health (www.nih.gov/; U41-HG002223) to PWS. PWS is also an investigator of the Howard Hughes Medical Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. \n\nGowri Ramachandran and Matt O'Neill provided support to help organize and enter data on muscle anatomy and terminology. Kun Peng and Elizabeth Ro performed data entry for the Textpresso for FEED project. Work on the MFMO is supported by the National Science Foundation (DBI-1062350 to Robert Druzinsky). We thank Wasila Dahdul for all of her advice and support. We would like to thank Kathleen Smith, Allen Rodrigo, Susan Alberts, and the National Evolutionary Synthesis Center (NESCent; NSF EF-0905606). NESCent hosted FEED Workshops in May, 2012, and May, 2014. Chris Mungall was supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Paula Mabee and Wasila Dahdul acknowledge funding from the National Science Foundation (DBI-1062542) and the Phenotype Ontology Research Coordination Network (DEB-0956049). The Phenotype RCN (NSF DEB-0956049) also provided support for Robert Druzinsky and Chris Mungall. Paul Sternberg is an investigator of the Howard Hughes Medical Institute. \n\nAuthor Contributions: Conceived and designed the experiments: RED MAH HL PMM CJM CEW. Performed the experiments: RED. Analyzed the data: RED HL PMM CEW. Contributed reagents/materials/analysis tools: RED JPB AWC JD RZG MAH AH SWH HL PMM HMM CJM PWS KVA CJV SHW CEW. Wrote the paper: RED JPB MAH AH SWH HL PMM HMM CJM PWS KVA CJV SHW CEW. \n\nAll relevant data are within the paper and its Supporting Information files or can be found via the URLs in the paper.\n\nPublished - journal.pone.0149102.pdf
Supplemental Material - journal.pone.0149102.s001.PNG
Supplemental Material - journal.pone.0149102.s002.PNG
Supplemental Material - journal.pone.0149102.s003.PNG
Supplemental Material - journal.pone.0149102.s004.PNG
Supplemental Material - journal.pone.0149102.s005.PNG
Supplemental Material - journal.pone.0149102.s006.PNG
Supplemental Material - journal.pone.0149102.s007.PNG
", "abstract": "Background:\nIn recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic searches are limited. To enable searches that deliver the results expected by comparative anatomists, an underlying logical structure known as an ontology is required.\nDevelopment and Testing of the Ontology:\nHere we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repository for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). We compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar.\nResults and Significance:\nOur tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities.", "date": "2016-02-12", "date_type": "published", "publication": "PLoS ONE", "volume": "11", "number": "2", "publisher": "Public Library of Science", "pagerange": "Art. No. e0149102", "id_number": "CaltechAUTHORS:20160222-104844651", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160222-104844651", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "DBI-1062350" }, { "agency": "NSF", "grant_number": "DBI-1062327" }, { "agency": "NSF", "grant_number": "DBI-1062333" }, { "agency": "NSF", "grant_number": "DBI-1343588" }, { "agency": "NSF", "grant_number": "DBI-1062332" }, { "agency": "NSF", "grant_number": "DBI-1062542" }, { "agency": "NSF", "grant_number": "DEB-0956049" }, { "agency": "National Evolutionary Synthesis Center (NESCent)" }, { "agency": "NSF", "grant_number": "EF-0905606" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-AC02-05CH11231" }, { "agency": "NIH", "grant_number": "U41-HG002223" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1371/journal.pone.0149102", "pmcid": "PMC4752357", "primary_object": { "basename": "journal.pone.0149102.s003.PNG", "url": "https://authors.library.caltech.edu/records/ntwsq-57q51/files/journal.pone.0149102.s003.PNG" }, "related_objects": [ { "basename": "journal.pone.0149102.s004.PNG", "url": "https://authors.library.caltech.edu/records/ntwsq-57q51/files/journal.pone.0149102.s004.PNG" }, { "basename": "journal.pone.0149102.s005.PNG", "url": "https://authors.library.caltech.edu/records/ntwsq-57q51/files/journal.pone.0149102.s005.PNG" }, { "basename": "journal.pone.0149102.s006.PNG", "url": "https://authors.library.caltech.edu/records/ntwsq-57q51/files/journal.pone.0149102.s006.PNG" }, { "basename": "journal.pone.0149102.s007.PNG", "url": "https://authors.library.caltech.edu/records/ntwsq-57q51/files/journal.pone.0149102.s007.PNG" }, { "basename": "journal.pone.0149102.pdf", "url": "https://authors.library.caltech.edu/records/ntwsq-57q51/files/journal.pone.0149102.pdf" }, { "basename": "journal.pone.0149102.s001.PNG", "url": "https://authors.library.caltech.edu/records/ntwsq-57q51/files/journal.pone.0149102.s001.PNG" }, { "basename": "journal.pone.0149102.s002.PNG", "url": "https://authors.library.caltech.edu/records/ntwsq-57q51/files/journal.pone.0149102.s002.PNG" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Druzinsky, Robert E.; Balhoff, James P.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/5cgge-hrv29", "eprint_id": 64510, "eprint_status": "archive", "datestamp": "2023-08-20 10:14:17", "lastmod": "2023-10-17 21:27:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "McNulty-Samantha-N", "name": { "family": "McNulty", "given": "Samantha N." }, "orcid": "0000-0003-0004-0697" }, { "id": "Str\u00fcbe-Christina", "name": { "family": "Str\u00fcbe", "given": "Christina" }, "orcid": "0000-0002-9093-1006" }, { "id": "Rosa-Bruce-A", "name": { "family": "Rosa", "given": "Bruce A." }, "orcid": "0000-0002-6820-446X" }, { "id": "Martin-John-C", "name": { "family": "Martin", "given": "John C." } }, { "id": "Tyagi-Rahul", "name": { "family": "Tyagi", "given": "Rahul" } }, { "id": "Choi-Young-Jun", "name": { "family": "Choi", "given": "Young-Jun" } }, { "id": "Wang-Qi", "name": { "family": "Wang", "given": "Qi" } }, { "id": "Hallsworth-Pepin-Kymberlie", "name": { "family": "Hallsworth Pepin", "given": "Kymberlie" }, "orcid": "0000-0002-2771-309X" }, { "id": "Zhang-Xu", "name": { "family": "Zhang", "given": "Xu" }, "orcid": "0000-0002-6491-3234" }, { "id": "Ozersky-Philip", "name": { "family": "Ozersky", "given": "Philip" }, "orcid": "0000-0002-8942-0524" }, { "id": "Wilson-Richard-K", "name": { "family": "Wilson", "given": "Richard K." }, "orcid": "0000-0002-1992-1358" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Gasser-Robin-B", "name": { "family": "Gasser", "given": "Robin B." }, "orcid": "0000-0002-4423-1690" }, { "id": "Mitreva-Makedonka", "name": { "family": "Mitreva", "given": "Makedonka" }, "orcid": "0000-0001-9572-3436" } ] }, "title": "Dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 Macmillan Publishers Limited. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ \n\nReceived: 10 July 2015. Accepted: 26 October 2015. Published: 09 February 2016. \n\nThis article is dedicated to the memory of Professor Thomas Schnieder. The genome sequencing and annotation work was funded by US National Institutes of Health (NIH)\u2013National Human Genome Research Institute grant U54HG003079 to R.K.W. Comparative genome analysis was funded by NIH/NIAID grant AI081803 to M.M and by Agriculture and Food Research Initiative Competitive Grant no. (2013-67015-21230) from the USDA National Institute of Food and Agriculture. R.B.G's research was supported by the Australian Research Council (ARC), the National Health and Medical Research Council (NHMRC) of Australia, Alexander von Humboldt Foundation as well as by a Victorian Life Sciences Computation Initiative (VLSCI) grant number VR0007 on its Peak Computing Facility at the University of Melbourne, an initiative of the Victorian Government. We thank the faculty and staff of The McDonnell Genome Institute at Washington University who contributed to this study. \n\nAuthor Contributions: M.M., R.B.G., P.W.S., R.K.W. and C.S. conceived and planned the project. S.N.M. and M.M. led the project, analysis, and manuscript preparation. C.S. provided materials. K.H.P., X.Z., J.C.M. and P.O. were involved in sequence data production, genome assembly, annotation, and data submission to relevant repositories. S.N.M., B.A.R., R.T., Y.C. and Q.W. performed genome-based comparative analyses, host-parasite interaction analyses, variome analyses, and differential expression analyses. S.N.M., B.A.R., R.B.G. and M.M. drafted and edited the manuscript. \n\nThe authors declare no competing financial interests.\n\nPublished - srep20316.pdf
Supplemental Material - srep20316-s1.pdf
Supplemental Material - srep20316-s2.xls
", "abstract": "The bovine lungworm, Dictyocaulus viviparus (order Strongylida), is an important parasite of livestock that causes substantial economic and production losses worldwide. Here we report the draft genome, variome, and developmental transcriptome of D. viviparus. The genome (161\u2009Mb) is smaller than those of related bursate nematodes and encodes fewer proteins (14,171 total). In the first genome-wide assessment of genomic variation in any parasitic nematode, we found a high degree of sequence variability in proteins predicted to be involved host-parasite interactions. Next, we used extensive RNA sequence data to track gene transcription across the life cycle of D. viviparus, and identified genes that might be important in nematode development and parasitism. Finally, we predicted genes that could be vital in host-parasite interactions, genes that could serve as drug targets, and putative RNAi effectors with a view to developing functional genomic tools. This extensive, well-curated dataset should provide a basis for developing new anthelmintics, vaccines, and improved diagnostic tests and serve as a platform for future investigations of drug resistance and epidemiology of the bovine lungworm and related nematodes.", "date": "2016-02-09", "date_type": "published", "publication": "Scientific Reports", "volume": "6", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 20316", "id_number": "CaltechAUTHORS:20160216-122511118", "issn": "2045-2322", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160216-122511118", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U54HG003079" }, { "agency": "NIH", "grant_number": "AI081803" }, { "agency": "Department of Agriculture", "grant_number": "2013-67015-21230" }, { "agency": "Australian Research Council" }, { "agency": "National Health and Medical Research Council (NHMRC)" }, { "agency": "Alexander von Humboldt Foundation" }, { "agency": "Victorian Life Sciences Computation Initiative (VLSCI)", "grant_number": "VR0007" } ] }, "doi": "10.1038/srep20316", "pmcid": "PMC4746573", "primary_object": { "basename": "srep20316-s1.pdf", "url": "https://authors.library.caltech.edu/records/5cgge-hrv29/files/srep20316-s1.pdf" }, "related_objects": [ { "basename": "srep20316-s2.xls", "url": "https://authors.library.caltech.edu/records/5cgge-hrv29/files/srep20316-s2.xls" }, { "basename": "srep20316.pdf", "url": "https://authors.library.caltech.edu/records/5cgge-hrv29/files/srep20316.pdf" } ], "resource_type": "article", "pub_year": "2016", "author_list": "McNulty, Samantha N.; Str\u00fcbe, Christina; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/c7xbx-49316", "eprint_id": 64297, "eprint_status": "archive", "datestamp": "2023-08-20 10:05:45", "lastmod": "2023-10-17 20:49:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Korhonen-Pasi-K", "name": { "family": "Korhonen", "given": "Pasi K." }, "orcid": "0000-0002-9957-4674" }, { "id": "Pozio-Edoardo", "name": { "family": "Pozio", "given": "Edoardo" }, "orcid": "0000-0003-3317-4704" }, { "id": "La-Rosa-Giuseppe", "name": { "family": "La Rosa", "given": "Giuseppe" }, "orcid": "0000-0002-9906-3137" }, { "id": "Chang-Bill-C-H", "name": { "family": "Chang", "given": "Bill C. H." } }, { "id": "Koehler-Anson-V", "name": { "family": "Koehler", "given": "Anson V." }, "orcid": "0000-0001-8330-6416" }, { "id": "Hoberg-Eric-P", "name": { "family": "Hoberg", "given": "Eric P." }, "orcid": "0000-0003-0819-7437" }, { "id": "Boag-Peter-R", "name": { "family": "Boag", "given": "Peter R." }, "orcid": "0000-0002-0889-0859" }, { "id": "Tan-Patrick", "name": { "family": "Tan", "given": "Patrick" } }, { "id": "Jex-Aaron-R", "name": { "family": "Jex", "given": "Aaron R." }, "orcid": "0000-0002-1285-7947" }, { "id": "Hofmann-Andreas", "name": { "family": "Hofmann", "given": "Andreas" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Young-Neil-D", "name": { "family": "Young", "given": "Neil D." }, "orcid": "0000-0001-8756-229X" }, { "id": "Gasser-Robin-B", "name": { "family": "Gasser", "given": "Robin B." }, "orcid": "0000-0002-4423-1690" } ] }, "title": "Phylogenomic and biogeographic reconstruction of the Trichinella complex", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 Nature Publishing Group. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ \n\nReceived 05 May 2015. Accepted 18 December 2015. Published 01 February 2016. \n\nFunding from the Australian Research Council, the National Health and Medical Research Council (NHMRC) of Australia, Yourgene Bioscience and Melbourne Water Corporation is gratefully acknowledged (R.B.G. et al.). This project was funded in part through DG SANCO of the European Commission and Istituto Superiore di Sanit\u00e0, Rome (E.P.). This project was also supported by a Victorian Life Sciences Computation Initiative (grant number VR0007) on its Peak Computing Facility at the University of Melbourne, an initiative of the Victorian Government (R.B.G.). N.D.Y. holds an NHMRC Early Career Research Fellowship. P.W.S. thanks the Howard Hughes Medical Institute (HHMI) and the National Institutes of Health (NIH). We thank the staff of Yourgene Bioscience for their contributions. We would specifically like to acknowledge all scientists who developed the programmes used in this study. Given restrictions on the number of articles that could be cited, we were unable to include all original articles in the Methods section. Instead, we have included links to respective websites. P.K.K. is the recipient of a scholarship (STRAPA) from the University of Melbourne. \n\nThese authors contributed equally to this work: Pasi K. Korhonen, Edoardo Pozio & Giuseppe La Rosa. \n\nContributions: P.K.K., N.D.Y. and R.B.G. wrote the paper with inputs from all other co-authors including B.C.H.C., A.R.J., P.T. and P.R.B. G.L.R., E.P. and colleagues produced parasite material. G.L.R. prepared all nucleic acids and undertook laboratory-based evaluations. P.K.K. undertook the genome assembly and all bioinformatic analyses, with support from N.D.Y. and R.B.G. A.V.K. provided initial support with phylogeny. A.H. provided support with structural modelling. E.P.H. explored aspects of historical biogeography and faunal assembly. With support from G.L.R. and E.P., R.B.G. led the project. \n\nThe authors declare no competing financial interests.\n\nPublished - ncomms10513.pdf
Supplemental Material - ncomms10513-s1.pdf
Supplemental Material - ncomms10513-s2.xlsx
Supplemental Material - ncomms10513-s3.xlsx
Supplemental Material - ncomms10513-s4.xlsx
", "abstract": "Trichinellosis is a globally important food-borne parasitic disease of humans caused by roundworms of the Trichinella complex. Extensive biological diversity is reflected in substantial ecological and genetic variability within and among Trichinella taxa, and major controversy surrounds the systematics of this complex. Here we report the sequencing and assembly of 16 draft genomes representing all 12 recognized Trichinella species and genotypes, define protein-coding gene sets and assess genetic differences among these taxa. Using thousands of shared single-copy orthologous gene sequences, we fully reconstruct, for the first time, a phylogeny and biogeography for the Trichinella complex, and show that encapsulated and non-encapsulated Trichinella taxa diverged from their most recent common ancestor ~21 million years ago (mya), with taxon diversifications commencing ~10\u22127\u2009mya.", "date": "2016-02", "date_type": "published", "publication": "Nature Communications", "volume": "7", "number": "2", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 10513", "id_number": "CaltechAUTHORS:20160208-092710363", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160208-092710363", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council" }, { "agency": "National Health and Medical Research Council (NHMRC)" }, { "agency": "Directorate-General for Health and Consumers" }, { "agency": "Victorian Life Sciences Computation Initiative (VLSCI)", "grant_number": "VR0007" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH" }, { "agency": "University of Melbourne" }, { "agency": "Istituto Superiore di Sanita" }, { "agency": "Yourgene Bioscience" }, { "agency": "Melbourne Water Corporation" } ] }, "doi": "10.1038/ncomms10513", "pmcid": "PMC4740406", "primary_object": { "basename": "ncomms10513-s1.pdf", "url": "https://authors.library.caltech.edu/records/c7xbx-49316/files/ncomms10513-s1.pdf" }, "related_objects": [ { "basename": "ncomms10513-s2.xlsx", "url": "https://authors.library.caltech.edu/records/c7xbx-49316/files/ncomms10513-s2.xlsx" }, { "basename": "ncomms10513-s3.xlsx", "url": "https://authors.library.caltech.edu/records/c7xbx-49316/files/ncomms10513-s3.xlsx" }, { "basename": "ncomms10513-s4.xlsx", "url": "https://authors.library.caltech.edu/records/c7xbx-49316/files/ncomms10513-s4.xlsx" }, { "basename": "ncomms10513.pdf", "url": "https://authors.library.caltech.edu/records/c7xbx-49316/files/ncomms10513.pdf" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Korhonen, Pasi K.; Pozio, Edoardo; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/gw8j8-4sh52", "eprint_id": 64311, "eprint_status": "archive", "datestamp": "2023-08-20 09:54:31", "lastmod": "2023-10-17 20:49:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mohandas-N", "name": { "family": "Mohandas", "given": "Namitha" } }, { "id": "Hu-Min", "name": { "family": "Hu", "given": "Min" } }, { "id": "Stroehlein-A-J", "name": { "family": "Stroehlein", "given": "Andreas J." } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Lok-James-B", "name": { "family": "Lok", "given": "James B." } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "Reconstruction of the insulin-like signalling pathway of Haemonchus contortus", "ispublished": "pub", "full_text_status": "public", "keywords": "Nematode, Haemonchus contortus, Insulin-like signalling pathway", "note": "\u00a9 Mohandas et al. 2016. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. \n\nReceived: 12 January 2016. Accepted: 26 January 2016. Published: 3 February 2016. \n\nFunding from the Australian Research Council (ARC) and the National Health and Medical Research Council of Australia (NHMRC) is gratefully acknowledged, as is support from the Victorian Life Sciences Computation Initiative (VLSCI; grant number VR0007) (RBG). Other support was from grants from the National Key Basic Research Program (973 program) of China (no. 2015CB150300), the National Natural Science Foundation of China (NSFC) (no. 31172310) (MH) and from the National Institute of Health (NIH), USA (AI-50688) (JBL). We acknowledge the contributions of staff at WormBase (www.wormbase.org). AJS is a recipient of a Melbourne International Research Scholarship (MIRS) and a Melbourne International Fee Remission Scholarship (MIFRS) from The University of Melbourne. \n\nAuthors' contributions: Conceived and designed the study and supervised the project: RBG. Undertook the study and data analysis: NM and RBG. Contributed to developing bioinformatic tools: NM, NDY and RBG. Contributed to the interpretation of findings, and drafting or formatting of the manuscript: NM, RBG, JBL, MH, AJS and PWS. Planned and wrote the paper: NM, RBG, JBL and MH. All authors read and approved the final version of the manuscript. \n\nThe authors declare that they have no competing interests.\n\nPublished - art_3A10.1186_2Fs13071-016-1341-8.pdf
Supplemental Material - 13071_2016_1341_MOESM1_ESM.pdf
", "abstract": "Background: In the present study, we reconstructed the insulin/insulin-like growth factor 1 signalling (IIS) pathway for Haemonchus contortus, which is one of the most important eukaryotic pathogens of livestock worldwide and is related to the free-living nematode Caenorhabditis elegans.\nMethods: We curated full-length open-reading frames from assembled transcripts, defined the complement of genes that encode proteins involved in this pathway and then investigated the transcription profiles of these genes for all key developmental stages of H. contortus.\nResults: The core components of the IIS pathway are similar to their respective homologs in C. elegans. However, there is considerable variation in the numbers of isoforms between H. contortus and C. elegans and an absence of AKT-2 and DDL-2 homologs from H. contortus. Interestingly, DAF-16 has a single isoform in H. contortus compared with 12 in C. elegans, suggesting novel functional roles in the parasitic nematode. Some IIS proteins, such as DAF-18 and SGK-1, vary in their functional domains, indicating distinct roles from their homologs in C. elegans.\nConclusions: This study paves the way for the further characterization of key signalling pathways in other socioeconomically important parasites and should help understand the complex mechanisms involved in developmental processes.", "date": "2016-01-12", "date_type": "published", "publication": "Parasites and Vectors", "volume": "9", "number": "1", "publisher": "BioMed Central", "pagerange": "Art. No. 64", "id_number": "CaltechAUTHORS:20160208-142115902", "issn": "1756-3305", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160208-142115902", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council" }, { "agency": "National Health and Medical Research Council (NHMRC)" }, { "agency": "Victorian Life Sciences Computation Initiative (VLSCI)", "grant_number": "VR0007" }, { "agency": "National Key Basic Research Program of China", "grant_number": "2015CB150300" }, { "agency": "National Natural Science Foundation of China (NSFC)", "grant_number": "31172310" }, { "agency": "NIH", "grant_number": "AI-50688" } ] }, "doi": "10.1186/s13071-016-1341-8", "pmcid": "PMC4741068", "primary_object": { "basename": "13071_2016_1341_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/gw8j8-4sh52/files/13071_2016_1341_MOESM1_ESM.pdf" }, "related_objects": [ { "basename": "art_3A10.1186_2Fs13071-016-1341-8.pdf", "url": "https://authors.library.caltech.edu/records/gw8j8-4sh52/files/art_3A10.1186_2Fs13071-016-1341-8.pdf" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Mohandas, Namitha; Hu, Min; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/h3xnc-tha73", "eprint_id": 62374, "eprint_status": "archive", "datestamp": "2023-08-20 09:51:36", "lastmod": "2023-10-23 15:13:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Howe-Kevin-L", "name": { "family": "Howe", "given": "Kevin L." } }, { "id": "Bolt-Bruce-J", "name": { "family": "Bolt", "given": "Bruce J." } }, { "id": "Cain-Scott", "name": { "family": "Cain", "given": "Scott" } }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "Chen-Wen-J", "name": { "family": "Chen", "given": "Wen J." } }, { "id": "Davis-Paul-M", "name": { "family": "Davis", "given": "Paul" } }, { "id": "Done-James", "name": { "family": "Done", "given": "James" } }, { "id": "Down-Thomas", "name": { "family": "Down", "given": "Thomas" } }, { "id": "Gao-Sibyl", "name": { "family": "Gao", "given": "Sibyl" } }, { "id": "Grove-Christian-A", "name": { "family": "Grove", "given": "Christian" }, "orcid": "0000-0001-9076-6015" }, { "id": "Harris-Todd-W", "name": { "family": "Harris", "given": "Todd W." }, "orcid": "0000-0003-3406-163X" }, { "id": "Kishore-Ranjana", "name": { "family": "Kishore", "given": "Ranjana" }, "orcid": "0000-0002-1478-7671" }, { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "Raymond" }, "orcid": "0000-0002-8151-7479" }, { "id": "Lomax-Jane", "name": { "family": "Lomax", "given": "Jane" } }, { "id": "Li-Yuling", "name": { "family": "Li", "given": "Yuling" } }, { "id": "M\u00fcller-Hans-Michael", "name": { "family": "Muller", "given": "Hans-Michael" } }, { "id": "Nakamura-Cecilia", "name": { "family": "Nakamura", "given": "Cecilia" }, "orcid": "0000-0002-4689-7314" }, { "id": "Nuin-Paul", "name": { "family": "Nuin", "given": "Paulo" } }, { "id": "Paulini-Michael-G", "name": { "family": "Paulini", "given": "Michael" } }, { "id": "Raciti-Daniela", "name": { "family": "Raciti", "given": "Daniela" } }, { "id": "Schindelman-Gary", "name": { "family": "Schindelman", "given": "Gary" } }, { "id": "Stanley-Eleanor", "name": { "family": "Stanley", "given": "Eleanor" } }, { "id": "Tuli-Mary-Ann", "name": { "family": "Tuli", "given": "Mary Ann" } }, { "id": "Van-Auken-Kimberly-M", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Wang-Daniel-L", "name": { "family": "Wang", "given": "Daniel" } }, { "id": "Wang-Xiaodong", "name": { "family": "Wang", "given": "Xiaodong" } }, { "id": "Williams-Gary-L", "name": { "family": "Williams", "given": "Gary" } }, { "id": "Wright-Adam", "name": { "family": "Wright", "given": "Adam" } }, { "id": "Yook-Karen-J", "name": { "family": "Yook", "given": "Karen" }, "orcid": "0000-0002-4457-6787" }, { "id": "Berriman-Matthew", "name": { "family": "Berriman", "given": "Matthew" }, "orcid": "0000-0002-9581-0377" }, { "id": "Kersey-Paul", "name": { "family": "Kersey", "given": "Paul" } }, { "id": "Schedl-Tim", "name": { "family": "Schedl", "given": "Tim" } }, { "id": "Stein-Lincoln-D", "name": { "family": "Stein", "given": "Lincoln D." }, "orcid": "0000-0002-1983-4588" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "WormBase 2016: expanding to enable helminth genomic research", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived September 30, 2015; Revised October 26, 2015; Accepted October 28, 2015. Nucleic Acids Research Advance Access published November 17, 2015. \n\nAfter many years working closely with WormBase as the guardian and authority for C. elegans genetic nomenclature, Jonathan Hodgkin has now stepped down from this role. We would like to thank him for his guidance and leadership. \n\nUS National Human Genome Research Institute [U41-HG002223]; UK Medical Research Council [MR/L001220]; UK Biotechnology and Biological Sciences Research Council [BB/K020080 to WormBase]; P.W.S. is an investigator with the Howard Hughes Medical Institute. Funding for open access charge: US National Human Genome Research Institute [U41-HG002223]. \n\nConflict of interest statement. None declared.\n\nPublished - Nucl._Acids_Res.-2016-Howe-D774-80.pdf
", "abstract": "WormBase (www.wormbase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project has evolved from its original remit to collect and integrate all data for a single species, and now extends to numerous nematodes, ranging from evolutionary comparators of C. elegans to parasitic species that threaten plant, animal and human health. Research activity using C. elegans as a model system is as vibrant as ever, and we have created new tools for community curation in response to the ever-increasing volume and complexity of data. To better allow users to navigate their way through these data, we have made a number of improvements to our main website, including new tools for browsing genomic features and ontology annotations. Finally, we have developed a new portal for parasitic worm genomes. WormBase ParaSite (parasite.wormbase.org) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research.", "date": "2016-01-04", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "44", "number": "D1", "publisher": "Oxford University Press", "pagerange": "D774-D780", "id_number": "CaltechAUTHORS:20151124-111442659", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151124-111442659", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U41-HG002223" }, { "agency": "Medical Research Council (MRC)", "grant_number": "MR/L00122" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/K020080" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "National Human Genome Research Institute" } ] }, "doi": "10.1093/nar/gkv1217", "pmcid": "PMC4702863", "primary_object": { "basename": "Nucl._Acids_Res.-2016-Howe-D774-80.pdf", "url": "https://authors.library.caltech.edu/records/h3xnc-tha73/files/Nucl._Acids_Res.-2016-Howe-D774-80.pdf" }, "resource_type": "article", "pub_year": "2016", "author_list": "Howe, Kevin L.; Bolt, Bruce J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/wjkk3-pxy11", "eprint_id": 62920, "eprint_status": "archive", "datestamp": "2023-08-20 09:27:23", "lastmod": "2023-10-25 21:59:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Stroehlein-A-J", "name": { "family": "Stroehlein", "given": "Andreas J." } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Korhonen-P-K", "name": { "family": "Korhonen", "given": "Pasi K." } }, { "id": "Jabbar-A", "name": { "family": "Jabbar", "given": "Abdul" } }, { "id": "Hofmann-A", "name": { "family": "Hofmann", "given": "Andreas" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "The Haemonchus contortus kinome - a resource for fundamental molecular investigations and drug discovery", "ispublished": "pub", "full_text_status": "public", "keywords": "Haemonchus contortus, Protein kinases, Kinome, Caenorhabditis elegans, Bioinformatics", "note": "\u00a9 2015 Stroehlein et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. \n\nReceived: 4 November 2015. Accepted: 25 November 2015. Published online: 08 December 2015. \n\nResearch funding from the National Health and Medical Research Council (NHMRC) and Australian Research Council (ARC) is gratefully acknowledged. Other support from the Australian Academy of Science, the Australian-American Fulbright Commission, Alexander von Humboldt Foundation, Melbourne Water Corporation as well as the Victorian Life Sciences Computation Initiative (VLSCI) and WormBase (www.wormbase.org) is gratefully acknowledged. PWS thanks the Howard Hughes Medical Institute (HHMI) and the National Institutes of Health (NIH). AJS is a recipient of a Melbourne International Research Scholarships (MIRS) and a Melbourne International Fee Remission Scholarship (MIFRS) from the University of Melbourne. NDY is an NHMRC Early Career Research (ECR) Fellow. \n\nAuthors' contributions: Conceived and designed the study and supervised the project: AJS, RBG and NDY. Undertook the study and data analysis: AJS and NDY. Contributed to analysis using various tools: NDY and PKK. Wrote the paper: AJS, NDY and RBG. Contributed to the interpretation of findings and drafting of the manuscript: AJ, AH and PWS. All authors read and approved the final version of the manuscript. \n\nThe authors declare that they have no competing interests.\n\nPublished - art_3A10.1186_2Fs13071-015-1231-5.pdf
Supplemental Material - s13071-015-1231-5-s1.xlsx
Supplemental Material - s13071-015-1231-5-s2.docx
", "abstract": "Background:\nProtein kinases regulate a plethora of essential signalling and other biological pathways in all eukaryotic organisms, but very little is known about them in most parasitic nematodes. \n\nMethods:\nHere, we defined, for the first time, the entire complement of protein kinases (kinome) encoded in the barber's pole worm (Haemonchus contortus) through an integrated analysis of transcriptomic and genomic datasets using an advanced bioinformatic workflow. \n\nResults:\nWe identified, curated and classified 432 kinases representing ten groups, 103 distinct families and 98 subfamilies. A comparison of the kinomes of H. contortus and Caenorhabditis elegans (a related, free-living nematode) revealed considerable variation in the numbers of casein kinases, tyrosine kinases and Ca^(2+) /calmodulin-dependent protein kinases, which likely relate to differences in biology, habitat and life cycle between these worms. Moreover, a suite of kinase genes was selectively transcribed in particular developmental stages of H. contortus, indicating central roles in developmental and reproductive processes. In addition, using a ranking system, drug targets (n\u2009=\u200913) and associated small-molecule effectors (n\u2009=\u20091517) were inferred. \n\nConclusions:\nThe H. contortus kinome will provide a useful resource for fundamental investigations of kinases and signalling pathways in this nematode, and should assist future anthelmintic discovery efforts; this is particularly important, given current drug resistance problems in parasitic nematodes.", "date": "2015-12-08", "date_type": "published", "publication": "Parasites and Vectors", "volume": "8", "number": "1", "publisher": "BioMed Central", "pagerange": "Art. No. 623", "id_number": "CaltechAUTHORS:20151215-091610309", "issn": "1756-3305", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151215-091610309", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Health and Medical Research Council (NHMRC)" }, { "agency": "Australian Research Council" }, { "agency": "Australian Academy of Science" }, { "agency": "Australian-American Fulbright Commission" }, { "agency": "Alexander von Humboldt Foundation" }, { "agency": "Melbourne Water Corporation" }, { "agency": "Victorian Life Sciences Computation Initiative (VLSCI)" }, { "agency": "WormBase" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH" }, { "agency": "University of Melbourne" } ] }, "doi": "10.1186/s13071-015-1231-5", "pmcid": "PMC4672506", "primary_object": { "basename": "art_3A10.1186_2Fs13071-015-1231-5.pdf", "url": "https://authors.library.caltech.edu/records/wjkk3-pxy11/files/art_3A10.1186_2Fs13071-015-1231-5.pdf" }, "related_objects": [ { "basename": "s13071-015-1231-5-s1.xlsx", "url": "https://authors.library.caltech.edu/records/wjkk3-pxy11/files/s13071-015-1231-5-s1.xlsx" }, { "basename": "s13071-015-1231-5-s2.docx", "url": "https://authors.library.caltech.edu/records/wjkk3-pxy11/files/s13071-015-1231-5-s2.docx" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Stroehlein, Andreas J.; Young, Neil D.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/yryvc-rp329", "eprint_id": 62957, "eprint_status": "archive", "datestamp": "2023-08-20 09:26:22", "lastmod": "2023-10-25 22:58:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Stroehlein-A-J", "name": { "family": "Stroehlein", "given": "Andreas J." } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Jex-A-R", "name": { "family": "Jex", "given": "Aaron R." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Tan-Patrick", "name": { "family": "Tan", "given": "Patrick" } }, { "id": "Boag-P-R", "name": { "family": "Boag", "given": "Peter R." } }, { "id": "Hofmann-A", "name": { "family": "Hofmann", "given": "Andreas" } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "Defining the Schistosoma haematobium kinome enables the prediction of essential kinases as anti-schistosome drug targets", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2015 Macmillan Publishers Limited. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ \n\nReceived: 06 May 2015; Accepted: 26 August 2015; Published online: 04 December 2015. \n\nTThis project was funded by the National Health and Medical Research Council (NHMRC) of Australia and the Australian Research Council (ARC), and supported by a Victorian Life Sciences Computation Initiative (VLSCI) grant number VR0007 on its Peak Computing Facility at the University of Melbourne, an initiative of the Victorian Government. Other support from the Australian Academy of Science, the Australian-American Fulbright Commission, Alexander von Humboldt Foundation and Melbourne Water Corporation (R.B.G.) is gratefully acknowledged. A.J.S. is a recipient of a Melbourne International Research Scholarships (MIRS) and a Melbourne International Fee Remission Scholarship (MIFRS) from the University of Melbourne. N.D.Y. is an NHMRC Early Career Research (ECR) Fellow. We thank Stefano Mangiola for help with preliminary data analysis. \n\nAuthor Contributions: A.J.S., R.B.G. and N.D.Y. were involved in the experimental design. A.J.S., R.B.G. and N.D.Y. were responsible for writing and editing of the manuscript. A.J.S. and N.D.Y. conducted bioinformatic analyses. Other authors (A.R.J., P.W.S., P.T., P.R.B. and A.H.) contributed to the writing of the manuscript. \n\nThe authors declare no competing financial interests.\n\nPublished - srep17759.pdf
Supplemental Material - srep17759-s1.pdf
Supplemental Material - srep17759-s2.xls
Supplemental Material - srep17759-s3.xls
Supplemental Material - srep17759-s4.xls
Supplemental Material - srep17759-s5.xls
Supplemental Material - srep17759-s6.xls
Supplemental Material - srep17759-s7.xls
", "abstract": "The blood fluke Schistosoma haematobium causes urogenital schistosomiasis, a neglected tropical disease (NTD) that affects more than 110 million people. Treating this disease by targeted or mass administration with a single chemical, praziquantel, carries the risk that drug resistance will develop in this pathogen. Therefore, there is an imperative to search for new drug targets in S. haematobium and other schistosomes. In this regard, protein kinases have potential, given their essential roles in biological processes and as targets for drugs already approved by the US Food and Drug Administration (FDA) for use in humans. In this context, we defined here the kinome of S. haematobium using a refined bioinformatic pipeline. We classified, curated and annotated predicted kinases, and assessed the developmental transcription profiles of kinase genes. Then, we prioritised a panel of kinases as potential drug targets and inferred chemicals that bind to them using an integrated bioinformatic pipeline. Most kinases of S. haematobium are very similar to those of its congener, S. mansoni, offering the prospect of designing chemicals that kill both species. Overall, this study provides a global insight into the kinome of S. haematobium and should assist the repurposing or discovery of drugs against schistosomiasis.", "date": "2015-12-04", "date_type": "published", "publication": "Scientific Reports", "volume": "5", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 17759", "id_number": "CaltechAUTHORS:20151215-155916318", "issn": "2045-2322", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151215-155916318", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Health and Medical Research Council (NHMRC)" }, { "agency": "Australian Research Council" }, { "agency": "Victorian Life Sciences Computation Initiative (VLSCI)", "grant_number": "VR0007" }, { "agency": "Australian Academy of Science" }, { "agency": "Australian-American Fulbright Commission" }, { "agency": "Alexander von Humboldt Foundation" }, { "agency": "Melbourne Water Corporation" }, { "agency": "University of Melbourne" } ] }, "doi": "10.1038/srep17759", "pmcid": "PMC4669435", "primary_object": { "basename": "srep17759-s6.xls", "url": "https://authors.library.caltech.edu/records/yryvc-rp329/files/srep17759-s6.xls" }, "related_objects": [ { "basename": "srep17759-s7.xls", "url": "https://authors.library.caltech.edu/records/yryvc-rp329/files/srep17759-s7.xls" }, { "basename": "srep17759.pdf", "url": "https://authors.library.caltech.edu/records/yryvc-rp329/files/srep17759.pdf" }, { "basename": "srep17759-s1.pdf", "url": "https://authors.library.caltech.edu/records/yryvc-rp329/files/srep17759-s1.pdf" }, { "basename": "srep17759-s2.xls", "url": "https://authors.library.caltech.edu/records/yryvc-rp329/files/srep17759-s2.xls" }, { "basename": "srep17759-s3.xls", "url": "https://authors.library.caltech.edu/records/yryvc-rp329/files/srep17759-s3.xls" }, { "basename": "srep17759-s4.xls", "url": "https://authors.library.caltech.edu/records/yryvc-rp329/files/srep17759-s4.xls" }, { "basename": "srep17759-s5.xls", "url": "https://authors.library.caltech.edu/records/yryvc-rp329/files/srep17759-s5.xls" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Stroehlein, Andreas J.; Young, Neil D.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/pnde9-31x37", "eprint_id": 59425, "eprint_status": "archive", "datestamp": "2023-08-20 09:12:43", "lastmod": "2023-10-23 20:34:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mohandas-N", "name": { "family": "Mohandas", "given": "Namitha" } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Jabbar-A", "name": { "family": "Jabbar", "given": "Abdul" } }, { "id": "Korhonen-P-K", "name": { "family": "Korhonen", "given": "Pasi K." } }, { "id": "Koehler-A-V", "name": { "family": "Koehler", "given": "Anson V." } }, { "id": "Amani-P", "name": { "family": "Amani", "given": "Parisa" } }, { "id": "Hall-R-S", "name": { "family": "Hall", "given": "Ross S." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Jex-A-R", "name": { "family": "Jex", "given": "Aaron R." } }, { "id": "Hofmann-A", "name": { "family": "Hofmann", "given": "Andreas" } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "The barber's pole worm CAP protein superfamily - A basis for fundamental discovery and biotechnology advances", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2015 Elsevier.\n\nReceived date: 26 May 2015; Revised date: 2 July 2015; Accepted date: 11 July 2015; Available online 31 July 2015. \n\nResearch funding from the National Health and Medical Research Council and Australian Research Council is gratefully acknowledged; support from the Victorian Life Sciences Computation Initiative (VLSCI) is also acknowledged (RBG). We acknowledge the contributions of all staff at WormBase (www.wormbase.org). P.W.S. thanks the Howard Hughes Medical Institute (HHMI) and the National Institutes of Health (NIH). The authors thank Christopher Lee for some assistance with bioinformatics and the collection of some articles.\n\nAccepted Version - MOHANDAS_2015.pdf
", "abstract": "Parasitic worm proteins that belong to the cysteine-rich secretory proteins, antigen 5 and pathogenesis-related 1 (CAP) superfamily are proposed to play key roles in the infection process and the modulation of immune responses in host animals. However, there is limited information on these proteins for most socio-economically important worms. Here, we review the CAP protein superfamily of Haemonchus contortus (barber's pole worm), a highly significant parasitic roundworm (order Strongylida) of small ruminants. To do this, we mined genome and transcriptomic datasets, predicted and curated full-length amino acid sequences (n = 45), undertook systematic phylogenetic analyses of these data and investigated transcription throughout the life cycle of H. contortus. We inferred functions for selected C. elegans orthologs (including vap-1, vap-2, scl-5 and lon-1) based on genetic networking and by integrating data and published information, and were able to infer that a subset of orthologs and their interaction partners play pivotal roles in growth and development via the insulin-like and/or the TGF-beta signaling pathways. The identification of the important and conserved growth regulator LON-1 led us to appraise the three-dimensional structure of this CAP protein by comparative modelling. This model revealed the presence of different topological moieties on the canonical fold of the CAP domain, which coincide with an overall charge separation as indicated by the electrostatic surface potential map. These observations suggest the existence of separate sites for effector binding and receptor interactions, and thus support the proposal that these worm molecules act in similar ways as venoms act as ligands for chemokine receptors or G protein-coupled receptor effectors. In conclusion, this review should guide future molecular studies of these molecules, and could support the development of novel interventions against haemonchosis.", "date": "2015-12", "date_type": "published", "publication": "Biotechnology Advances", "volume": "33", "number": "8", "publisher": "Elsevier", "pagerange": "1744-1754", "id_number": "CaltechAUTHORS:20150811-133012832", "issn": "0734-9750", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150811-133012832", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Health and Medical Research Council (NHMRC)" }, { "agency": "Australian Research Council" }, { "agency": "Victorian Life Sciences Computation Initiative (VLSCI)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH" } ] }, "doi": "10.1016/j.biotechadv.2015.07.003", "primary_object": { "basename": "MOHANDAS_2015.pdf", "url": "https://authors.library.caltech.edu/records/pnde9-31x37/files/MOHANDAS_2015.pdf" }, "resource_type": "article", "pub_year": "2015", "author_list": "Mohandas, Namitha; Young, Neil D.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/spyag-d6k71", "eprint_id": 63748, "eprint_status": "archive", "datestamp": "2023-08-22 16:57:16", "lastmod": "2023-10-17 16:05:58", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mohandas-N", "name": { "family": "Mohandas", "given": "Namitha" } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Jabbar-A", "name": { "family": "Jabbar", "given": "Abdul" } }, { "id": "Korhonen-P-K", "name": { "family": "Korhonen", "given": "Pasi K." } }, { "id": "Koehler-A-V", "name": { "family": "Koehler", "given": "Anson V." } }, { "id": "Amani-P", "name": { "family": "Amani", "given": "Parisa" } }, { "id": "Hall-R-S", "name": { "family": "Hall", "given": "Ross S." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Jex-A-R", "name": { "family": "Jex", "given": "Aaron R." } }, { "id": "Hofmann-A", "name": { "family": "Hofmann", "given": "Andreas" } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "The barber's pole worm CAP protein superfamily \u2014 A basis for fundamental discovery and biotechnology advances", "ispublished": "pub", "full_text_status": "public", "keywords": "Nematodes; Haemonchus contortus; Genome; Transcriptome; CAP (SCP/TAPS) proteins; Genetic networking; Transcription profiles; Structure models", "note": "\u00a9 2015 Elsevier Inc.", "abstract": "Parasitic worm proteins that belong to the cysteine-rich secretory proteins, antigen 5 and pathogenesis-related 1 (CAP) superfamily are proposed to play key roles in the infection process and the modulation of immune responses in host animals. However, there is limited information on these proteins for most socio-economically important worms. Here, we review the CAP protein superfamily of Haemonchus contortus (barber's pole worm), a highly significant parasitic roundworm (order Strongylida) of small ruminants. To do this, we mined genome and transcriptomic datasets, predicted and curated full-length amino acid sequences (n = 45), undertook systematic phylogenetic analyses of these data and investigated transcription throughout the life cycle of H. contortus. We inferred functions for selected Caenorhabditis elegans orthologs (including vap-1, vap-2, scl-5 and lon-1) based on genetic networking and by integrating data and published information, and were able to infer that a subset of orthologs and their interaction partners play pivotal roles in growth and development via the insulin-like and/or the TGF-beta signalling pathways. The identification of the important and conserved growth regulator LON-1 led us to appraise the three-dimensional structure of this CAP protein by comparative modelling. This model revealed the presence of different topological moieties on the canonical fold of the CAP domain, which coincide with an overall charge separation as indicated by the electrostatic surface potential map. These observations suggest the existence of separate sites for effector binding and receptor interactions, and thus support the proposal that these worm molecules act in similar ways as venoms act as ligands for chemokine receptors or G protein-coupled receptor effectors. In conclusion, this review should guide future molecular studies of these molecules, and could support the development of novel interventions against haemonchosis.", "date": "2015-12", "date_type": "published", "publication": "Biotechnology Advances", "volume": "33", "number": "8", "publisher": "Elsevier", "pagerange": "1744-1754", "id_number": "CaltechAUTHORS:20160119-083737138", "issn": "0734-9750", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160119-083737138", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.biotechadv.2015.07.003", "resource_type": "article", "pub_year": "2015", "author_list": "Mohandas, Namitha; Young, Neil D.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/jw921-ga551", "eprint_id": 61759, "eprint_status": "archive", "datestamp": "2023-08-22 16:48:07", "lastmod": "2023-10-25 15:42:40", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tyagi-Rahul", "name": { "family": "Tyagi", "given": "Rahul" } }, { "id": "Joachim-Anja", "name": { "family": "Joachim", "given": "Anja" } }, { "id": "Ruttkowski-B\u00e4rbel", "name": { "family": "Ruttkowski", "given": "B\u00e4rbel" } }, { "id": "Rosa-Bruce-A", "name": { "family": "Rosa", "given": "Bruce A." }, "orcid": "0000-0002-6820-446X" }, { "id": "Martin-John-C", "name": { "family": "Martin", "given": "John C." } }, { "id": "Hallsworth-Pepin-Kymberlie", "name": { "family": "Hallsworth-Pepin", "given": "Kymberlie" } }, { "id": "Zhang-Xu", "name": { "family": "Zhang", "given": "Xu" }, "orcid": "0000-0002-6491-3234" }, { "id": "Ozersky-Philip", "name": { "family": "Ozersky", "given": "Philip" }, "orcid": "0000-0002-8942-0524" }, { "id": "Wilson-Richard-K", "name": { "family": "Wilson", "given": "Richard K." }, "orcid": "0000-0002-1992-1358" }, { "id": "Ranganathan-Shoba", "name": { "family": "Ranganathan", "given": "Shoba" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Gasser-Robin-B", "name": { "family": "Gasser", "given": "Robin B." }, "orcid": "0000-0002-4423-1690" }, { "id": "Mitreva-Makedonka", "name": { "family": "Mitreva", "given": "Makedonka" }, "orcid": "0000-0001-9572-3436" } ] }, "title": "Cracking the nodule worm code advances knowledge of parasite biology and biotechnology to tackle major diseases of livestock", "ispublished": "pub", "full_text_status": "public", "keywords": "Biotechnology; Genomics; Transcriptomics; Bioinformatics; Nodule worm disease; Livestock", "note": "\u00a9 2015 Elsevier Inc. \n\nReceived 13 April 2015, Accepted 23 May 2015, Available online 27 May 2015. \n\nThe authors thank the faculty and staff of the Genome Institute at Washington University who contributed the work described in this article. The genome sequencing and annotation work was funded by US National Institutes of Health grant U54HG003079 to R.K.W. Comparative genome analysis was funded by grants AI081803 and GM097435 to M.M. P.W.S. is an investigator with the Howard Hughes Medical Institute. RBG's research was supported by the Australian Research Council (SRC), the National Health & Medical Research Council of Australia (NHMRC) and the Victorian Life Sciences Computation Initiative (VR0007).\n\nAccepted Version - nihms743744.pdf
", "abstract": "Many infectious diseases caused by eukaryotic pathogens have a devastating, long-term impact on animal health and welfare. Hundreds of millions of animals are affected by parasitic nematodes of the order Strongylida. Unlocking the molecular biology of representatives of this order, and understanding nematode\u2013host interactions, drug resistance and disease using advanced technologies could lead to entirely new ways of controlling the diseases that they cause. Oesophagostomum dentatum (nodule worm; superfamily Strongyloidea) is an economically important strongylid nematode parasite of swine worldwide. The present article reports recent advances made in biology and animal biotechnology through the draft genome and developmental transcriptome of O. dentatum, in order to support biological research of this and related parasitic nematodes as well as the search for new and improved interventions. This first genome of any member of the Strongyloidea is 443 Mb in size and predicted to encode 25,291 protein-coding genes. Here, we review the dynamics of transcription throughout the life cycle of O. dentatum, describe double-stranded RNA interference (RNAi) machinery and infer molecules involved in development and reproduction, and in inducing or modulating immune responses or disease. The secretome predicted for O. dentatum is particularly rich in peptidases linked to interactions with host tissues and/or feeding activity, and a diverse array of molecules likely involved in immune responses. This research progress provides an important resource for future comparative genomic and molecular biological investigations as well as for biotechnological research toward new anthelmintics, vaccines and diagnostic tests.", "date": "2015-11-01", "date_type": "published", "publication": "Biotechnology Advances", "volume": "33", "number": "6", "publisher": "Elsevier", "pagerange": "980-991", "id_number": "CaltechAUTHORS:20151102-085546701", "issn": "0734-9750", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151102-085546701", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U54HG003079" }, { "agency": "NIH", "grant_number": "AI081803" }, { "agency": "NIH", "grant_number": "GM097435" }, { "agency": "Australian Research Council" }, { "agency": "National Health and Medical Research Council (NHMRC)" }, { "agency": "Victorian Life Sciences Computation Initiative (VLSCI)", "grant_number": "VR0007" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1016/j.biotechadv.2015.05.004", "pmcid": "PMC4746232", "primary_object": { "basename": "nihms743744.pdf", "url": "https://authors.library.caltech.edu/records/jw921-ga551/files/nihms743744.pdf" }, "resource_type": "article", "pub_year": "2015", "author_list": "Tyagi, Rahul; Joachim, Anja; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/qqcae-19a15", "eprint_id": 60578, "eprint_status": "archive", "datestamp": "2023-08-20 08:15:29", "lastmod": "2023-10-24 16:41:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dillman-Adler-R", "name": { "family": "Dillman", "given": "Adler R." }, "orcid": "0000-0001-7171-4332" }, { "id": "Macchietto-Marissa-G", "name": { "family": "Macchietto", "given": "Marissa" }, "orcid": "0000-0002-9877-6020" }, { "id": "Porter-Camille-F", "name": { "family": "Porter", "given": "Camille F." }, "orcid": "0000-0001-7620-258X" }, { "id": "Rogers-Alicia-K", "name": { "family": "Rogers", "given": "Alicia" }, "orcid": "0000-0001-5525-6095" }, { "id": "Williams-Brian", "name": { "family": "Williams", "given": "Brian" } }, { "id": "Antoshechkin-Igor-A", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Lee-Ming-Min", "name": { "family": "Lee", "given": "Ming-Min" } }, { "id": "Goodwin-Zane", "name": { "family": "Goodwin", "given": "Zane" } }, { "id": "Lu-Xiaojun", "name": { "family": "Lu", "given": "Xiaojun" } }, { "id": "Lewis-Edwin-E", "name": { "family": "Lewis", "given": "Edwin E." }, "orcid": "0000-0002-8825-1562" }, { "id": "Goodrich-Blair-Heidi", "name": { "family": "Goodrich-Blair", "given": "Heidi" }, "orcid": "0000-0003-1934-2636" }, { "id": "Stock-S-Patricia", "name": { "family": "Stock", "given": "S. Patricia" }, "orcid": "0000-0003-0175-9839" }, { "id": "Adams-Byron-J", "name": { "family": "Adams", "given": "Byron J." }, "orcid": "0000-0002-7815-3352" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Mortazavi-A", "name": { "family": "Mortazavi", "given": "Ali" }, "orcid": "0000-0002-4259-6362" } ] }, "title": "Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2015 Dillman et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0\nInternational License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and\nreproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to\nthe Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver\n(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.\n\nReceived: 1 June 2015 Accepted: 10 August.\nPublished online: 21 September 2015.\n\nThis research was supported by grants from the US National Institutes of\nHealth (NIH) and the Howard Hughes Medical Institute, for which PWS is\nan investigator. ARD was supported by NIH training grants (5T32GM007616\nand 5T32HG000044). AM and MM were supported by an NIH New Innovator\nAward to AM (DP2 GM111100). XL was supported by the UW-Madison\nGraduate School research funds.\n\nAuthors' contributions:\nARD, MM, PWS, and AM conceived the project. ARD and MM carried out all\nexperiments. IA, BW and MM built as well as sequenced all libraries. MM and\nAM did the primary genome assemblies and gene annotations. ARD and BJA\ndid the phylogenetic analysis. ARD and MM did all comparative analyses. ARD,\nMM, PWS, and AM wrote the manuscript. All authors read and approved the\nfinal manuscript.\n\nPublished - s13059-015-0746-6.pdf
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", "abstract": "Background: Parasitism is a major ecological niche for a variety of nematodes. Multiple nematode lineages have specialized as pathogens, including deadly parasites of insects that are used in biological control. We have sequenced and analyzed the draft genomes and transcriptomes of the entomopathogenic nematode Steinernema carpocapsae and four congeners (S. scapterisci, S. monticolum, S. feltiae, and S. glaseri). \n\nResults: We used these genomes to establish phylogenetic relationships, explore gene conservation across species, and identify genes uniquely expanded in insect parasites. Protein domain analysis in Steinernema revealed a striking expansion of numerous putative parasitism genes, including certain protease and protease inhibitor families, as well as fatty acid- and retinol-binding proteins. Stage-specific gene expression of some of these expanded families further supports the notion that they are involved in insect parasitism by Steinernema. We show that sets of novel conserved non-coding regulatory motifs are associated with orthologous genes in Steinernema and Caenorhabditis. \n\nConclusions: We have identified a set of expanded gene families that are likely to be involved in parasitism. We have also identified a set of non-coding motifs associated with groups of orthologous genes in Steinernema and Caenorhabditis involved in neurogenesis and embryonic development that are likely part of conserved protein\u2013DNA relationships shared between these two genera.", "date": "2015-09-21", "date_type": "published", "publication": "Genome Biology", "volume": "16", "publisher": "BioMed Central", "pagerange": "Art. No. 200", "id_number": "CaltechAUTHORS:20150928-125105151", "issn": "1474-760X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150928-125105151", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "5T32GM007616-37" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "5T32HG000044" }, { "agency": "NIH", "grant_number": "DP2 GM111100" }, { "agency": "University of Wisconsin" } ] }, "doi": "10.1186/s13059-015-0746-6", "pmcid": "PMC4578762", "primary_object": { "basename": "s13059-015-0746-6-s5.txt", "url": "https://authors.library.caltech.edu/records/qqcae-19a15/files/s13059-015-0746-6-s5.txt" }, "related_objects": [ { "basename": "s13059-015-0746-6-s7.htm", "url": "https://authors.library.caltech.edu/records/qqcae-19a15/files/s13059-015-0746-6-s7.htm" }, { "basename": "s13059-015-0746-6-s1.pdf", "url": "https://authors.library.caltech.edu/records/qqcae-19a15/files/s13059-015-0746-6-s1.pdf" }, { "basename": "s13059-015-0746-6-s11.txt", "url": "https://authors.library.caltech.edu/records/qqcae-19a15/files/s13059-015-0746-6-s11.txt" }, { "basename": "s13059-015-0746-6-s3.txt", "url": "https://authors.library.caltech.edu/records/qqcae-19a15/files/s13059-015-0746-6-s3.txt" }, { "basename": "s13059-015-0746-6.pdf", "url": "https://authors.library.caltech.edu/records/qqcae-19a15/files/s13059-015-0746-6.pdf" }, { "basename": "s13059-015-0746-6-s4.txt", "url": "https://authors.library.caltech.edu/records/qqcae-19a15/files/s13059-015-0746-6-s4.txt" }, { "basename": "s13059-015-0746-6-s8.txt", "url": "https://authors.library.caltech.edu/records/qqcae-19a15/files/s13059-015-0746-6-s8.txt" }, { "basename": "s13059-015-0746-6-s2.pdf", "url": "https://authors.library.caltech.edu/records/qqcae-19a15/files/s13059-015-0746-6-s2.pdf" }, { "basename": "s13059-015-0746-6-s6.txt", "url": "https://authors.library.caltech.edu/records/qqcae-19a15/files/s13059-015-0746-6-s6.txt" }, { "basename": "s13059-015-0746-6-s9.png", "url": "https://authors.library.caltech.edu/records/qqcae-19a15/files/s13059-015-0746-6-s9.png" }, { "basename": "s13059-015-0746-6-s10.txt", "url": "https://authors.library.caltech.edu/records/qqcae-19a15/files/s13059-015-0746-6-s10.txt" }, { "basename": "s13059-015-0746-6-s12.txt", "url": "https://authors.library.caltech.edu/records/qqcae-19a15/files/s13059-015-0746-6-s12.txt" }, { "basename": "s13059-015-0746-6-s13.txt", "url": "https://authors.library.caltech.edu/records/qqcae-19a15/files/s13059-015-0746-6-s13.txt" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Dillman, Adler R.; Macchietto, Marissa; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/92h1r-z8v71", "eprint_id": 61973, "eprint_status": "archive", "datestamp": "2023-08-20 08:01:03", "lastmod": "2023-10-25 16:07:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shinya-Ryoji", "name": { "family": "Shinya", "given": "Ryoji" }, "orcid": "0000-0002-2450-3054" }, { "id": "Chen-Anthony", "name": { "family": "Chen", "given": "Anthony" }, "orcid": "0000-0002-9578-4893" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Sex Attraction and Mating in Bursaphelenchus okinawaensis and B. xylophilus", "ispublished": "pub", "full_text_status": "public", "keywords": "behavior, mating behavior, reproductive isolation, sex pheromone, sperm status", "note": "\u00a9 2015 The Society of Nematologists.\n\nReceived for publication November 21, 2014.\n\nWe thank Daniel Leighton and other members of our laboratory for discussions and Gladys Medina for assistance. R. S. is a fellow of the Japan Society for the Promotion of Science. P. W. S. is an investigator with the Howard Hughes Medical Institute, which supported this work.\n\nPublished - 176.pdf
", "abstract": "The fungal feeding, hermaphroditic Bursaphelenchus okinawaensis is a laboratory model to understand the biology of Bursaphelenchus. The extent to which B. okinawaensis can be used to model Bursaphelenchus xylophilus mating was investigated. A chemotaxis assay was conducted to examine whether B. xylophilus and B. okinawaensis produce and respond to volatile sex attractants. Unmated B. xylophilus females were found to attract B. xylophilus males. Similarly, old (sperm depleted) but not young (sperm repleted) B. okinawaensis hermaphrodites attract B. okinawaensis males. Thus, in both species, sperm status corresponds to its ability to attract males. B. xylophilus males also produce a volatile pheromone that attracts both mated and unmated females. A second assay, in which the behavior of males on petri plates in the presence of different females or hermaphrodites of Bursaphelenchus was observed, revealed that B. xylophilus unmated females attract B. okinawaensis males, and B. okinawaensis old hermaphrodites attract B. xylophilus males. These observations suggested that the pheromones of Bursaphelenchus work to some extent across species. Mating behavior through spicule insertion occurs across species, suggesting that postcopulatory mechanisms prevent production of interspecific progeny. The hermaphroditic B. okinawaensis will be a useful model to conduct genetic studies for the understanding of the molecular mechanisms underlying mating behavior in Bursaphelenchus nematodes.", "date": "2015-09", "date_type": "published", "publication": "Journal of Nematology", "volume": "47", "number": "3", "publisher": "Society of Nematologists", "pagerange": "176-183", "id_number": "CaltechAUTHORS:20151109-084413604", "issn": "0022-300X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151109-084413604", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Japan Society for the Promotion of Science (JSPS)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "pmcid": "PMC4612187", "primary_object": { "basename": "176.pdf", "url": "https://authors.library.caltech.edu/records/92h1r-z8v71/files/176.pdf" }, "resource_type": "article", "pub_year": "2015", "author_list": "Shinya, Ryoji; Chen, Anthony; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/746rc-19032", "eprint_id": 59026, "eprint_status": "archive", "datestamp": "2023-08-20 07:49:01", "lastmod": "2023-10-23 19:58:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bedbrook-Claire-N", "name": { "family": "Bedbrook", "given": "Claire N." }, "orcid": "0000-0003-3973-598X" }, { "id": "Kato-Mihoko", "name": { "family": "Kato", "given": "Mihoko" }, "orcid": "0000-0003-3827-8879" }, { "id": "Ravindra-Kumar-Sripriya", "name": { "family": "Ravindra Kumar", "given": "Sripriya" }, "orcid": "0000-0001-6033-7631" }, { "id": "Lakshmanan-Anupama", "name": { "family": "Lakshmanan", "given": "Anupama" }, "orcid": "0000-0002-6702-837X" }, { "id": "Nath-Ravi-D", "name": { "family": "Nath", "given": "Ravi D." } }, { "id": "Sun-Fei", "name": { "family": "Sun", "given": "Fei" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Arnold-F-H", "name": { "family": "Arnold", "given": "Frances H." }, "orcid": "0000-0002-4027-364X" }, { "id": "Gradinaru-V", "name": { "family": "Gradinaru", "given": "Viviana" }, "orcid": "0000-0001-5868-348X" } ] }, "title": "Genetically Encoded Spy Peptide Fusion System to Detect Plasma Membrane-Localized Proteins In Vivo", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2015 Elsevier Ltd. \n\nReceived: February 10, 2015. Revised: May 19, 2015. Accepted: June 15, 2015. Published: July 23, 2015. \n\nWe thank the Gradinaru and Arnold labs for helpful discussions, and Han Wang of the Sternberg lab for assistance with behavioral assays. We also thank Sheri McKinney for assistance with cultured neurons, and Dr. John Bedbrook for critical reading of the manuscript. This work was funded by the NIH/NINDS New Innovator (NIH IDP20D017782-01), the Beckman Institute for Optogenetics and CLARITY, the Gordon and Betty Moore Foundation through Grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative (to V.G. and F.H.A.); by NIH 1R21MH103824-01 (to V.G. and F.H.A.); and by the Institute for Collaborative Biotechnologies through grant W911NF-09-0001 from the U.S. Army Research Office (to F.H.A.). The content of the information does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred. P.W.S. is an investigator with the HHMI, which supported this research. C.N.B. acknowledges support from the NIMH of the NIH for the NRSA fellowship under Award Number F31MH102913.\n\nAccepted Version - nihms711085.pdf
Supplemental Material - mmc1.pdf
Supplemental Material - mmc2.mp4
", "abstract": "Membrane proteins are the main gatekeepers of cellular state, especially in neurons, serving either to maintain homeostasis or instruct response to synaptic input or other external signals. Visualization of membrane protein localization and trafficking in live cells facilitates understanding the molecular basis of cellular dynamics. We describe here a method for specifically labeling the plasma membrane-localized fraction of heterologous membrane protein expression using channelrhodopsins as a case study. We show that the genetically encoded, covalent binding SpyTag and SpyCatcher pair from the Streptococcus pyogenes fibronectin-binding protein FbaB can selectively label membrane-localized proteins in living cells in culture and in vivo in Caenorhabditis elegans. The SpyTag/SpyCatcher covalent labeling method is highly specific, modular, and stable in living cells. We have used the binding pair to develop a channelrhodopsin membrane localization assay that is amenable to high-throughput screening for opsin discovery and engineering.", "date": "2015-08-20", "date_type": "published", "publication": "Chemistry and Biology", "volume": "22", "number": "8", "publisher": "Cell Press", "pagerange": "1108-1121", "id_number": "CaltechAUTHORS:20150728-090618874", "issn": "1074-5521", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150728-090618874", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "IDP20D017782-01" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "NIH", "grant_number": "1R21MH103824-01" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-09-0001" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "F31MH102913" }, { "agency": "National Institute of Mental Health (NIMH)" } ] }, "doi": "10.1016/j.chembiol.2015.06.020", "pmcid": "PMC4546540", "primary_object": { "basename": "mmc2.mp4", "url": "https://authors.library.caltech.edu/records/746rc-19032/files/mmc2.mp4" }, "related_objects": [ { "basename": "nihms711085.pdf", "url": "https://authors.library.caltech.edu/records/746rc-19032/files/nihms711085.pdf" }, { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/746rc-19032/files/mmc1.pdf" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Bedbrook, Claire N.; Kato, Mihoko; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/frahn-56y54", "eprint_id": 59788, "eprint_status": "archive", "datestamp": "2023-08-20 07:06:04", "lastmod": "2023-10-23 22:42:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Manosalva-Patricia", "name": { "family": "Manosalva", "given": "Patricia" }, "orcid": "0000-0003-2580-6521" }, { "id": "Manohar-Murli", "name": { "family": "Manohar", "given": "Murli" } }, { "id": "von-Reuss-Stephen-H", "name": { "family": "von Reuss", "given": "Stephan H." }, "orcid": "0000-0003-4325-5495" }, { "id": "Chen-Shiyan", "name": { "family": "Chen", "given": "Shiyan" }, "orcid": "0000-0002-6730-8216" }, { "id": "Koch-Aline", "name": { "family": "Koch", "given": "Aline" }, "orcid": "0000-0003-3536-5344" }, { "id": "Kaplan-Fatma", "name": { "family": "Kaplan", "given": "Fatma" }, "orcid": "0000-0002-9565-0211" }, { "id": "Choe-Andrea", "name": { "family": "Choe", "given": "Andrea" } }, { "id": "Micikas-Robert-J", "name": { "family": "Micikas", "given": "Robert J." } }, { "id": "Wang-Xiaohong", "name": { "family": "Wang", "given": "Xiaohong" } }, { "id": "Kogel-Karl-Heinz", "name": { "family": "Kogel", "given": "Karl-Heinz" }, "orcid": "0000-0003-1226-003X" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Williamson-Valerie-M", "name": { "family": "Williamson", "given": "Valerie M." }, "orcid": "0000-0002-1437-4439" }, { "id": "Schroeder-Frank-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" }, { "id": "Klessig-Daniel-F", "name": { "family": "Klessig", "given": "Daniel F." } } ] }, "title": "Conserved nematode signalling molecules elicit plant defenses and pathogen resistance", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2015 Macmillan Publishers Limited. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 24 November 2014; Accepted 10 June 2015; Published 23 July 2015.\n\nWe thank William E. Fry for providing P. infestans strains and laboratory space for P. infestans inoculations, Neelanjan Bose, Alexander Artyukhin and Sydney Campbell for assistance with HPLC-MS analyses, Anshu Kumari for the greenhouse support and Patrick Boyle for helpful discussions. This work was supported in part by the USDA (AFRI 2011-68004-30154 to D.F.K., AFRI 2013-02577 to V.M.W. and AFRI 2014-04823 to F.K.), the NSF (IOS-0820405, to D.F.K.), the Triad Foundation (D.F.K. and F.C.S.) and BASF SE. \n\nContributions: P.M., M.M., D.F.K. and F.C.S. designed the research; P.M., M.M., A.K., S.H.v.R., F.K., and S.C. performed the research; F.K., A.C., and V.M.W. contributed reagents, S.H.v.R., F.K. and F.C.S. analyzed nematode metabolomes, R.J.M and S.H.v.R. synthesized ascarosides; P.M., M.M., S.H.v.R., D.F.K., A.K., S.C., X.W., K.-H.K. and F.C.S. analyzed the data; and D.F.K., P.M., M.M., F.K., V.M.W., and F.C.S. wrote the paper. \n\nThe authors declare no competing financial interests.\n\nPublished - ncomms8795.pdf
Supplemental Material - ncomms8795-s1.pdf
", "abstract": "Plant-defense responses are triggered by perception of conserved microbe-associated molecular patterns (MAMPs), for example, flagellin or peptidoglycan. However, it remained unknown whether plants can detect conserved molecular patterns derived from plant-parasitic animals, including nematodes. Here we show that several genera of plant-parasitic nematodes produce small molecules called ascarosides, an evolutionarily conserved family of nematode pheromones. Picomolar to micromolar concentrations of ascr#18, the major ascaroside in plant-parasitic nematodes, induce hallmark defense responses including the expression of genes associated with MAMP-triggered immunity, activation of mitogen-activated protein kinases, as well as salicylic acid- and jasmonic acid-mediated defense signalling pathways. Ascr#18 perception increases resistance in Arabidopsis, tomato, potato and barley to viral, bacterial, oomycete, fungal and nematode infections. These results indicate that plants recognize ascarosides as a conserved molecular signature of nematodes. Using small-molecule signals such as ascarosides to activate plant immune responses has potential utility to improve economic and environmental sustainability of agriculture.", "date": "2015-07", "date_type": "published", "publication": "Nature Communications", "volume": "6", "number": "7", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 7795", "id_number": "CaltechAUTHORS:20150820-104302919", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150820-104302919", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Agriculture", "grant_number": "AFRI 2011-68004-30154" }, { "agency": "Department of Agriculture", "grant_number": "AFRI 2013-02577" }, { "agency": "Department of Agriculture", "grant_number": "AFRI 2014-04823" }, { "agency": "NSF", "grant_number": "IOS-0820405" }, { "agency": "Triad Foundation" }, { "agency": "BASF SE" } ] }, "doi": "10.1038/ncomms8795", "pmcid": "PMC4525156", "primary_object": { "basename": "ncomms8795-s1.pdf", "url": "https://authors.library.caltech.edu/records/frahn-56y54/files/ncomms8795-s1.pdf" }, "related_objects": [ { "basename": "ncomms8795.pdf", "url": "https://authors.library.caltech.edu/records/frahn-56y54/files/ncomms8795.pdf" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Manosalva, Patricia; Manohar, Murli; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/qj540-2qa60", "eprint_id": 58845, "eprint_status": "archive", "datestamp": "2023-08-20 06:53:46", "lastmod": "2023-10-23 19:48:34", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mok-Darren-Z-L", "name": { "family": "Mok", "given": "Darren Z. L." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Inoue-Takao", "name": { "family": "Inoue", "given": "Takao" } } ] }, "title": "Morphologically defined sub-stages of C. elegans vulval development in the fourth larval stage", "ispublished": "pub", "full_text_status": "public", "keywords": "C. elegans, Vulval development, Developmental timing, Gene expression", "note": "\u00a9 2015 Mok et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.\n\nReceived: 18 February 2015. Accepted:\t3 June 2015. Published online: 12 June 2015. \n\nWe thank Goh Kah Yee for preliminary analysis of best-13:gfp expression. We thank Marie-Anne Felix for the daf-6:cfp plasmid and strain. Some strains used in this study were provided by the Caenorhabditis Genetics Center,\nwhich is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). This work was supported by the Singapore Ministry of Education Academic Research Fund Tier 1 grant (T13-1001-P02). PWS is an Investigator of the Howard Hughes Medical Institute. \n\nAuthors' contributions:\n\nTI and PWS developed the L4 sub-staging scheme. DZLM determined the\ntiming of sub-stages and the expression of reporters in sub-stages. TI and\nDZLM determined the correlation with other developmental events. The\nmanuscript was drafted by DZLM and edited by all authors. All authors read\nand approved the final manuscript.\n\nPublished - s12861-015-0076-7.pdf
", "abstract": "Background: During the fourth larval (L4) stage, vulval cells of C. elegans undergo extensive morphogenesis accompanied by changes in gene expression. This phase of vulval development, occurring after the well-studied induction of vulval cells, is not well understood but is potentially a useful context in which to study how a complex temporal sequence of events is regulated during development. However, a system for precisely describing different phases of vulval development in the L4 stage has been lacking.\nResults: We defined ten sub-stages of L4 based on morphological criteria as observed using Nomarski microscopy (L4.0\u2009~\u2009L4.9). Precise timing of each sub-stage at 20 \u00b0C was determined. We also re-examined the timing of expression for several gene expression markers, and correlated the sub-stages with the timing of other developmental events in the vulva and the uterus.\nConclusions: This scheme allows the developmental timing of an L4 individual to be determined at approximately one-hour resolution without the need to resort to time course experiments. These well-defined developmental stages will enable more precise description of gene expression and other developmental events.", "date": "2015-06-12", "date_type": "published", "publication": "BMC Developmental Biology", "volume": "15", "publisher": "BioMed Central", "pagerange": "Art. No. 26", "id_number": "CaltechAUTHORS:20150710-104105215", "issn": "1471-213X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150710-104105215", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P40 OD010440" }, { "agency": "Ministry of Education (Singapore)", "grant_number": "T13-1001-P02" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1186/s12861-015-0076-7", "pmcid": "PMC4464634", "primary_object": { "basename": "s12861-015-0076-7.pdf", "url": "https://authors.library.caltech.edu/records/qj540-2qa60/files/s12861-015-0076-7.pdf" }, "resource_type": "article", "pub_year": "2015", "author_list": "Mok, Darren Z. L.; Sternberg, Paul W.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/tyxay-7df83", "eprint_id": 58441, "eprint_status": "archive", "datestamp": "2023-08-20 06:03:53", "lastmod": "2023-10-23 19:21:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Breugelmans-B", "name": { "family": "Breugelmans", "given": "Bert" } }, { "id": "Ansell-B-R-E", "name": { "family": "Ansell", "given": "Brendan R. E." } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Amani-P", "name": { "family": "Amani", "given": "Parisa" } }, { "id": "Stroehlein-A-J", "name": { "family": "Stroehlein", "given": "Andreas J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Jex-A-R", "name": { "family": "Jex", "given": "Aaron R." } }, { "id": "Boag-P-R", "name": { "family": "Boag", "given": "Peter R." } }, { "id": "Hofmann-A", "name": { "family": "Hofmann", "given": "Andreas" } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "Flatworms have lost the right open reading frame kinase 3 gene during evolution", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2015 The Authors. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder in order to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ \n\nReceived 28 November 2014; Accepted 26 February 2015; Published 15 May 2015.\n\nThis project was funded by the National Health and Medical Research Council (NHMRC) of Australia and the Australian Research Council (ARC). This project was also supported by a Victorian Life Sciences Computation Initiative (VLSCI) grant number VR0007 on its Peak Computing Facility at the University of Melbourne, an initiative of the Victorian Government. Other support from the Australian Academy of Science, the Australian-American Fulbright Commission, Alexander von Humboldt Foundation, Melbourne Water Corporation (R.B.G.) is gratefully acknowledged, as is funding from the Howard Hughes Medical Institute (HHMI) and National Institutes of Health (NIH) (P.W.S.). N.D.Y. is an NHMRC Early Career Research (ECR) Fellow. We acknowledge the staff at WormBase (www.wormbase.org) and Wellcome Trust Sanger Institute (http://www.ebi.ac.uk/ena/data/view/PRJEB2709) for their support or provision of data. We acknowledge the use of the program I-TASSER \u2013 \u00a9 2013 The Regents of the University of Michigan.\n\nPublished - srep09417.pdf
Supplemental Material - srep09417-s1.docx
", "abstract": "All multicellular organisms studied to date have three right open reading frame kinase genes (designated riok-1, riok-2 and riok-3). Current evidence indicates that riok-1 and riok-2 have essential roles in ribosome biosynthesis, and that the riok-3 gene assists this process. In the present study, we conducted a detailed bioinformatic analysis of the riok gene family in 25 parasitic flatworms (platyhelminths) for which extensive genomic and transcriptomic data sets are available. We found that none of the flatworms studied have a riok-3 gene, which is unprecedented for multicellular organisms. We propose that, unlike in other eukaryotes, the loss of RIOK-3 from flatworms does not result in an evolutionary disadvantage due to the unique biology and physiology of this phylum. We show that the loss of RIOK-3 coincides with a loss of particular proteins associated with essential cellular pathways linked to cell growth and apoptosis. These findings indicate multiple, key regulatory functions of RIOK-3 in other metazoan species. Taking advantage of a known partial crystal structure of human RIOK-1, molecular modelling revealed variability in nucleotide binding sites between flatworm and human RIOK proteins.", "date": "2015-05", "date_type": "published", "publication": "Scientific Reports", "volume": "5", "number": "5", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 9417", "id_number": "CaltechAUTHORS:20150623-103133027", "issn": "2045-2322", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150623-103133027", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Health and Medical Research Council (NHMRC) (Australia)" }, { "agency": "Australian Research Council (ARC)" }, { "agency": "Victorian Life Sciences Computation Initiative (VLSCI)", "grant_number": "VR0007" }, { "agency": "Australian Academy of Science" }, { "agency": "Australian-American Fulbright Commission" }, { "agency": "Alexander von Humboldt Foundation" }, { "agency": "MelbourneWater Corporation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH" } ] }, "doi": "10.1038/srep09417", "pmcid": "PMC4894443", "primary_object": { "basename": "srep09417-s1.docx", "url": "https://authors.library.caltech.edu/records/tyxay-7df83/files/srep09417-s1.docx" }, "related_objects": [ { "basename": "srep09417.pdf", "url": "https://authors.library.caltech.edu/records/tyxay-7df83/files/srep09417.pdf" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Breugelmans, Bert; Ansell, Brendan R. E.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/qazpc-zzp98", "eprint_id": 55529, "eprint_status": "archive", "datestamp": "2023-08-20 05:35:19", "lastmod": "2023-10-20 22:20:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schwarz-E-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Hu-Yan", "name": { "family": "Hu", "given": "Yan" } }, { "id": "Antoshechkin-I-A", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Miller-M-M", "name": { "family": "Miller", "given": "Melanie M." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Aroian-R-V", "name": { "family": "Aroian", "given": "Raffi V." } } ] }, "title": "The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2015 Macmillan Publishers Limited. This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/. \n\nReceived 12 January 2014; Accepted 05 February 2015; Published online 02 March 2015. \n\nWe thank C.T. Brown, P.K. Korhonen, S. Kumar and J.E. Stajich for advice on bioinformatics, T.A. Aydin, J. Liu and A.H.K. Roeder for comments on the manuscript, L. Schaeffer and V. Kumar for genome and RNA sequencing, and C.T. Brown for use of the Michigan State University High-Performance Computing Center (supported by grant 2010-65205-20361 from the US Department of Agriculture and grant IOS-0923812 from the National Institute of Food and Agriculture and the National Science Foundation). \n\nAuthor Contributions: E.M.S., P.W.S. and R.V.A. conceived of and managed the project. Y.H. isolated genomic DNA and RNA from all infection stages of A. ceylanicum and converted RNA to cDNA for sequencing. M.M.M. maintained A. ceylanicum and golden hamster cultures through full life cycles and performed the photography for\nFigure 1. I.A. constructed large-insert paired-end and jumping Illumina libraries and supervised both genomic and RNA-seq Illumina sequencing. E.M.S. conducted all bioinformatics and biological analyses. Writing was primarily carried out by E.M.S. but with input from all authors.\n\nPublished - ng.3237.pdf
Accepted Version - nihms681025.pdf
Supplemental Material - ng.3237-S1.pdf
Supplemental Material - ng.3237-S10.xlsx
Supplemental Material - ng.3237-S11.xlsx
Supplemental Material - ng.3237-S2.xlsx
Supplemental Material - ng.3237-S3.xlsx
Supplemental Material - ng.3237-S4.xlsx
Supplemental Material - ng.3237-S5.xlsx
Supplemental Material - ng.3237-S6.xlsx
Supplemental Material - ng.3237-S7.xlsx
Supplemental Material - ng.3237-S8.xlsx
Supplemental Material - ng.3237-S9.xlsx
", "abstract": "Hookworms infect over 400 million people, stunting and impoverishing them. Sequencing hookworm genomes and finding which genes they express during infection should help in devising new drugs or vaccines against hookworms. Unlike other hookworms, Ancylostoma ceylanicum infects both humans and other mammals, providing a laboratory model for hookworm disease. We determined an A. ceylanicum genome sequence of 313 Mb, with transcriptomic data throughout infection showing expression of 30,738 genes. Approximately 900 genes were upregulated during early infection in vivo, including ASPRs, a cryptic subfamily of activation-associated secreted proteins (ASPs). Genes downregulated during early infection included ion channels and G protein\u2013coupled receptors; this downregulation was observed in both parasitic and free-living nematodes. Later, at the onset of heavy blood feeding, C-lectin genes were upregulated along with genes for secreted clade V proteins (SCVPs), encoding a previously undescribed protein family. These findings provide new drug and vaccine targets and should help elucidate hookworm pathogenesis.", "date": "2015-04", "date_type": "published", "publication": "Nature Genetics", "volume": "47", "number": "4", "publisher": "Nature Publishing Group", "pagerange": "416-422", "id_number": "CaltechAUTHORS:20150305-080922455", "issn": "1061-4036", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150305-080922455", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Agriculture", "grant_number": "2010-65205-20361" }, { "agency": "NSF", "grant_number": "IOS-0923812" } ] }, "doi": "10.1038/ng.3237", "pmcid": "PMC4617383", "primary_object": { "basename": "ng.3237-S3.xlsx", "url": "https://authors.library.caltech.edu/records/qazpc-zzp98/files/ng.3237-S3.xlsx" }, "related_objects": [ { "basename": "ng.3237-S7.xlsx", "url": "https://authors.library.caltech.edu/records/qazpc-zzp98/files/ng.3237-S7.xlsx" }, { "basename": "ng.3237-S9.xlsx", "url": "https://authors.library.caltech.edu/records/qazpc-zzp98/files/ng.3237-S9.xlsx" }, { "basename": "nihms681025.pdf", "url": "https://authors.library.caltech.edu/records/qazpc-zzp98/files/nihms681025.pdf" }, { "basename": "ng.3237-S1.pdf", "url": "https://authors.library.caltech.edu/records/qazpc-zzp98/files/ng.3237-S1.pdf" }, { "basename": "ng.3237-S11.xlsx", "url": "https://authors.library.caltech.edu/records/qazpc-zzp98/files/ng.3237-S11.xlsx" }, { "basename": "ng.3237-S2.xlsx", "url": "https://authors.library.caltech.edu/records/qazpc-zzp98/files/ng.3237-S2.xlsx" }, { "basename": "ng.3237-S4.xlsx", "url": "https://authors.library.caltech.edu/records/qazpc-zzp98/files/ng.3237-S4.xlsx" }, { "basename": "ng.3237-S8.xlsx", "url": "https://authors.library.caltech.edu/records/qazpc-zzp98/files/ng.3237-S8.xlsx" }, { "basename": "ng.3237.pdf", "url": "https://authors.library.caltech.edu/records/qazpc-zzp98/files/ng.3237.pdf" }, { "basename": "ng.3237-S10.xlsx", "url": "https://authors.library.caltech.edu/records/qazpc-zzp98/files/ng.3237-S10.xlsx" }, { "basename": "ng.3237-S5.xlsx", "url": "https://authors.library.caltech.edu/records/qazpc-zzp98/files/ng.3237-S5.xlsx" }, { "basename": "ng.3237-S6.xlsx", "url": "https://authors.library.caltech.edu/records/qazpc-zzp98/files/ng.3237-S6.xlsx" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Schwarz, Erich M.; Hu, Yan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/aw203-fcg20", "eprint_id": 54160, "eprint_status": "archive", "datestamp": "2023-08-22 15:07:55", "lastmod": "2023-10-19 23:42:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yuet-Kai-P", "name": { "family": "Yuet", "given": "Kai P." }, "orcid": "0000-0002-1381-8923" }, { "id": "Doma-M-K", "name": { "family": "Doma", "given": "Meenakshi K." } }, { "id": "Ngo-John-T", "name": { "family": "Ngo", "given": "John T." } }, { "id": "Sweredoski-M-J", "name": { "family": "Sweredoski", "given": "Michael J." }, "orcid": "0000-0003-0878-3831" }, { "id": "Graham-R-L-J", "name": { "family": "Graham", "given": "Robert L. J." } }, { "id": "Moradian-A", "name": { "family": "Moradian", "given": "Annie" }, "orcid": "0000-0002-0407-2031" }, { "id": "Hess-S", "name": { "family": "Hess", "given": "Sonja" }, "orcid": "0000-0002-5904-9816" }, { "id": "Schuman-E-M", "name": { "family": "Schuman", "given": "Erin M." }, "orcid": "0000-0002-7053-1005" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Tirrell-D-A", "name": { "family": "Tirrell", "given": "David A." }, "orcid": "0000-0003-3175-4596" } ] }, "title": "Cell-Specific Proteomic Analysis in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "click chemistry; protein engineering; proteomics; cell-specific protein expression; nematode pharyngeal muscle", "note": "\u00a9 2015 National Academy of Sciences.\n\nEdited by Carolyn R. Bertozzi, University of California, Berkeley, CA, and approved January 22, 2015 (received for review November 10, 2014).\nPublished online before print February 17, 2015.\n\nWe thank past and present members of the P.W.S.\nand D.A.T. laboratories for fruitful discussions and suggestions, and Roxana\nEggleston-Rangel and Geoffrey T. Smith (Proteome Exploration Laboratory,\nBeckman Institute, California Institute of Technology) for technical assistance.\nThis work was supported by National Institutes of Health (NIH) Grant\nR01 GM062523. K.P.Y. was supported in part by a National Science Foundation\ngraduate fellowship. P.W.S. is an Investigator of the Howard Hughes\nMedical Institute, which supported this work. The Proteome Exploration\nLaboratory is supported by Gordon and Betty Moore Foundation Grant\nGBMF775, the Beckman Institute, and NIH Grant 1S10RR029594-01A1.\n\nAuthor contributions: K.P.Y., M.K.D., J.T.N., E.M.S., P.W.S., and D.A.T. designed research;\nK.P.Y., M.K.D., and J.T.N. performed research; M.J.S., R.L.J.G., A.M., and S.H. contributed\nnew reagents/analytic tools; K.P.Y., M.J.S., P.W.S., and D.A.T. analyzed data; and K.P.Y.,\nP.W.S., and D.A.T. wrote the paper.\n\nThe authors declare no conflict of interest.\n\nThis article is a PNAS Direct Submission.\n\nData deposition: The vectors generated in this study have been deposited in the Addgene\ndatabase, www.addgene.org (Addgene nos. 62598 and 62599).\n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1421567112/-/DCSupplemental.\n\nPublished - PNAS-2015-Yuet-2705-10.pdf
Supplemental Material - pnas.1421567112.sapp.pdf
", "abstract": "Proteomic analysis of rare cells in heterogeneous environments presents difficult challenges. Systematic methods are needed to enrich, identify, and quantify proteins expressed in specific cells in complex biological systems including multicellular plants and animals. Here, we have engineered a Caenorhabditis elegans phenylalanyl-tRNA synthetase capable of tagging proteins with the reactive noncanonical amino acid p-azido-L-phenylalanine. We achieved spatiotemporal selectivity in the labeling of C. elegans proteins by controlling expression of the mutant synthetase using cell-selective (body wall muscles, intestinal epithelial cells, neurons, and pharyngeal muscle) or state-selective (heat-shock) promoters in several transgenic lines. Tagged proteins are distinguished from the rest of the protein pool through bioorthogonal conjugation of the azide side chain to probes that permit visualization and isolation of labeled proteins. By coupling our methodology with stable-isotope labeling of amino acids in cell culture (SILAC), we successfully profiled proteins expressed in pharyngeal muscle cells, and in the process, identified proteins not previously known to be expressed in these cells. Our results show that tagging proteins with spatiotemporal selectivity can be achieved in C. elegans and illustrate a convenient and effective approach for unbiased discovery of proteins expressed in targeted subsets of cells.", "date": "2015-03-03", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "112", "number": "9", "publisher": "National Academy of Sciences", "pagerange": "2705-2710", "id_number": "CaltechAUTHORS:20150127-223214858", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150127-223214858", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 GM062523" }, { "agency": "NSF Graduate Fellowship" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF775" }, { "agency": "Caltech Beckman Institute" }, { "agency": "NIH", "grant_number": "1S10RR029594-01A1" } ] }, "doi": "10.1073/pnas.1421567112", "pmcid": "PMC4352802", "primary_object": { "basename": "PNAS-2015-Yuet-2705-10.pdf", "url": "https://authors.library.caltech.edu/records/aw203-fcg20/files/PNAS-2015-Yuet-2705-10.pdf" }, "related_objects": [ { "basename": "pnas.1421567112.sapp.pdf", "url": "https://authors.library.caltech.edu/records/aw203-fcg20/files/pnas.1421567112.sapp.pdf" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Yuet, Kai P.; Doma, Meenakshi K.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/5424d-3f426", "eprint_id": 56167, "eprint_status": "archive", "datestamp": "2023-08-20 04:53:00", "lastmod": "2023-10-20 23:44:03", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhu-Xing-Quan", "name": { "family": "Zhu", "given": "Xing-Quan" } }, { "id": "Korhonen-P-K", "name": { "family": "Korhonen", "given": "Pasi K." } }, { "id": "Cai-Huimin", "name": { "family": "Cai", "given": "Huimin" } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Nejsum-P", "name": { "family": "Nejsum", "given": "Peter" } }, { "id": "von-Samson-Himmelstjerna-G", "name": { "family": "von Samson-Himmelstjerna", "given": "Georg" } }, { "id": "Boag-P-R", "name": { "family": "Boag", "given": "Peter R." } }, { "id": "Tan-Patrick", "name": { "family": "Tan", "given": "Patrick" } }, { "id": "Li-Qiye", "name": { "family": "Li", "given": "Qiye" } }, { "id": "Min-Jiumeng", "name": { "family": "Min", "given": "Jiumeng" } }, { "id": "Yang-Yulan", "name": { "family": "Yang", "given": "Yulan" } }, { "id": "Wang-Xiuhua", "name": { "family": "Wang", "given": "Xiuhua" } }, { "id": "Fang-Xiaodong", "name": { "family": "Fang", "given": "Xiaodong" } }, { "id": "Hall-R-S", "name": { "family": "Hall", "given": "Ross S." } }, { "id": "Hofmann-A", "name": { "family": "Hofmann", "given": "Andreas" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Jex-A-R", "name": { "family": "Jex", "given": "Aaron R." } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "Genetic blueprint of the zoonotic pathogen Toxocara canis", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2015 Macmillan Publishers Limited. This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/\n\nReceived: 16 August 2014; Accepted: 11 December 2014;\nPublished: 04 February 2015.\n\nThis project was funded by the International Science & Technology Cooperation Program of China (grant no. 2013DFA31840; X.-Q.Z. and R.B.G.), the Australian Research Council (ARC) and the National Health and Medical Research Council (NHMRC) of Australia (R.B.G.); it was also supported by a Victorian Life Sciences Computation Initiative (VLSCI) grant (VR0007; R.B.G.) on its Peak Computing Facility at the University of Melbourne, an initiative of the Victorian Government. Other support from the Australian Academy of Science, Alexander von Humboldt Foundation and Melbourne Water Corporation is gratefully acknowledged. N.D.Y. is an NHMRC Early Career Research (ECRF) Fellow. We acknowledge the contributions of all the staff members at WormBase (www.wormbase.org). We thank the Howard Hughes Medical Institute (HHMI) and the National Institutes of Health (NIH; P.W.S.). We thank BGI-Shenzhen for providing a commercial service for the construction of RNA-seq and genomic libraries, and for sequencing.\n\nPublished - ncomms7145.pdf
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", "abstract": "Toxocara canis is a zoonotic parasite of major socioeconomic importance worldwide. In humans, this nematode causes disease (toxocariasis) mainly in the under-privileged communities in developed and developing countries. Although relatively well studied from clinical and epidemiological perspectives, to date, there has been no global investigation of the molecular biology of this parasite. Here we use next-generation sequencing to produce a draft genome and transcriptome of T. canis to support future biological and biotechnological investigations. This genome is 317\u2009Mb in size, has a repeat content of 13.5% and encodes at least 18,596 protein-coding genes. We study transcription in a larval, as well as adult female and male stages, characterize the parasite's gene-silencing machinery, explore molecules involved in development or host\u2013parasite interactions and predict intervention targets. The draft genome of T. canis should provide a useful resource for future molecular studies of this and other, related parasites.", "date": "2015-02-04", "date_type": "published", "publication": "Nature Communications", "volume": "6", "number": "2", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 6145", "id_number": "CaltechAUTHORS:20150327-092534533", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150327-092534533", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "International Science & Technology Cooperation Program of China", "grant_number": "2013DFA31840" }, { "agency": "Australian Research Council" }, { "agency": "National Health and Medical Research Council (NHMRC)" }, { "agency": "Victorian Life Sciences Computation Initiative (VLSCI)", "grant_number": "VR0007" }, { "agency": "Australian Academy of Science" }, { "agency": "Alexander von Humboldt Foundation" }, { "agency": "Melbourne Water Corporation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH" } ] }, "doi": "10.1038/ncomms7145", "pmcid": "PMC4327413", "primary_object": { "basename": "ncomms7145-s5.xlsx", "url": "https://authors.library.caltech.edu/records/5424d-3f426/files/ncomms7145-s5.xlsx" }, "related_objects": [ { "basename": "ncomms7145-s9.xlsx", "url": "https://authors.library.caltech.edu/records/5424d-3f426/files/ncomms7145-s9.xlsx" }, { "basename": "ncomms7145-s1.xlsx", "url": "https://authors.library.caltech.edu/records/5424d-3f426/files/ncomms7145-s1.xlsx" }, { "basename": "ncomms7145-s12.xlsx", "url": "https://authors.library.caltech.edu/records/5424d-3f426/files/ncomms7145-s12.xlsx" }, { "basename": "ncomms7145-s8.xlsx", "url": "https://authors.library.caltech.edu/records/5424d-3f426/files/ncomms7145-s8.xlsx" }, { "basename": "ncomms7145.pdf", "url": "https://authors.library.caltech.edu/records/5424d-3f426/files/ncomms7145.pdf" }, { "basename": "ncomms7145-s10.xlsx", "url": "https://authors.library.caltech.edu/records/5424d-3f426/files/ncomms7145-s10.xlsx" }, { "basename": "ncomms7145-s11.xlsx", "url": "https://authors.library.caltech.edu/records/5424d-3f426/files/ncomms7145-s11.xlsx" }, { "basename": "ncomms7145-s7.xlsx", "url": "https://authors.library.caltech.edu/records/5424d-3f426/files/ncomms7145-s7.xlsx" }, { "basename": "ncomms7145-s3.xlsx", "url": "https://authors.library.caltech.edu/records/5424d-3f426/files/ncomms7145-s3.xlsx" }, { "basename": "ncomms7145-s4.xlsx", "url": "https://authors.library.caltech.edu/records/5424d-3f426/files/ncomms7145-s4.xlsx" }, { "basename": "ncomms7145-s6.xlsx", "url": "https://authors.library.caltech.edu/records/5424d-3f426/files/ncomms7145-s6.xlsx" }, { "basename": "ncomms7145-s13.xlsx", "url": "https://authors.library.caltech.edu/records/5424d-3f426/files/ncomms7145-s13.xlsx" }, { "basename": "ncomms7145-s2.xlsx", "url": "https://authors.library.caltech.edu/records/5424d-3f426/files/ncomms7145-s2.xlsx" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Zhu, Xing-Quan; Korhonen, Pasi K.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/zq9t9-gte91", "eprint_id": 56560, "eprint_status": "archive", "datestamp": "2023-08-20 04:41:43", "lastmod": "2023-10-23 15:33:34", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Blake-J-A", "name": { "family": "Blake", "given": "J. A." } }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "J." }, "orcid": "0000-0002-7259-8107" }, { "id": "Kishore-R", "name": { "family": "Kishore", "given": "R." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "P. W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "K." }, "orcid": "0000-0002-1706-4196" }, { "id": "M\u00fcller-H-M", "name": { "family": "M\u00fcller", "given": "H. M." } }, { "id": "Done-J", "name": { "family": "Done", "given": "J." } }, { "id": "Li-Y", "name": { "family": "Li", "given": "Y." } } ] }, "title": "Gene Ontology Consortium: going forward", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.\nThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which\npermits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.\n\nReceived September 24, 2014; Revised October 30, 2014; Accepted October 31, 2014.\nPublished online 26 November 2014.\n\nWe gratefully acknowledge the many other contributors to\nGO annotation efforts: Gramene, Department of Botany\nand Plant Pathology, Oregon State University, Corvallis,\nOR, USA; The J. Craig Venter Institute, Rockville,\nMD, USA; PAMGO, Wells College, Aurora, NY, USA\nand PAMGO, Virginia Bioinformatics Institute, VA, USA;\nAspGD, Stanford, CA, USA; CGD, Stanford, CA, USA;\nSanger GeneDB, Hinxton, UK; InterPro European Molecular\nBiology Laboratory-European Bioinformatics Institute\n(EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK; IntAct, (EMBL-EBI), Hinxton, UK; seudo-\nCAP, British Columbia, Canada; SGN, Ithaca, NY, USA.\n\nFunding:\nNational Institutes of Health/National Human Genome\nResearch Institute grant [HG002273] awarded to the PI\ngroup formed by Judith A. Blake, J. Michael Cherry,\nSuzanna E. Lewis, PaulW. Sternberg, and Paul D. Thomas,\nas well as additional funding awarded to each participating\ninstitution. For more details please visit: http:\n//geneontology.org/page/go-consortium-contributors-list.\nFunding for open access charge: National Institutes of\nHealth/National Human Genome Research Institute\n[HG002273].\n\nPublished - Nucl._Acids_Res.-2015--D1049-56.pdf
", "abstract": "The Gene Ontology (GO; http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions. The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data. Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser. We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology.", "date": "2015-01-28", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "43", "number": "D1", "publisher": "Oxford University Press", "pagerange": "D1049-D1056", "id_number": "CaltechAUTHORS:20150409-154316585", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150409-154316585", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HG002273" }, { "agency": "National Human Genome Research Institute" } ] }, "doi": "10.1093/nar/gku1179", "pmcid": "PMC4383973", "primary_object": { "basename": "Nucl._Acids_Res.-2015--D1049-56.pdf", "url": "https://authors.library.caltech.edu/records/zq9t9-gte91/files/Nucl._Acids_Res.-2015--D1049-56.pdf" }, "resource_type": "article", "pub_year": "2015", "author_list": "Blake, J. A.; Chan, J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/frvbz-9rv86", "eprint_id": 53772, "eprint_status": "archive", "datestamp": "2023-08-22 14:47:56", "lastmod": "2023-10-23 17:53:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zaslaver-A", "name": { "family": "Zaslaver", "given": "Alon" } }, { "id": "Liani-I", "name": { "family": "Liani", "given": "Idan" } }, { "id": "Shtangel-O", "name": { "family": "Shtangel", "given": "Oshrat" } }, { "id": "Ginzburg-S", "name": { "family": "Ginzburg", "given": "Shira" } }, { "id": "Yee-Lisa", "name": { "family": "Yee", "given": "Lisa" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Hierarchical sparse coding in the sensory system of Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "neural circuits; calcium imagaing; sensory coding", "note": "\u00a9 2015 National Academy of Sciences.\n\nPublished ahead of print January 12, 2015.\n\nWe thank Piali Sengupta for sharing the genetically ablated AWCON strain (PY7502). The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013) and European Research Council Grant Agreement 336803. Initial stages of this research were supported by the Caltech Center for Biological Circuit Design. P.W.S. is an investigator of the Howard Hughes Medical Institute, which supported this work.\n\nAuthor contributions: A.Z. and P.W.S. designed research; A.Z., I.L., O.S., S.G., and L.Y. performed research; A.Z. contributed new reagents/analytic tools; A.Z. analyzed data; and A.Z. and P.W.S. wrote the paper.\n\nThe authors declare no conflict of interest.\n\nFreely available online through the PNAS open access option.\n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1423656112/-/DCSupplemental.\n\nCorrection for Zaslaver et al., Hierarchical sparse coding in the sensory system of Caenorhabditis elegans\nPNAS 2015 112 (13) E1688-E1689; published ahead of print March 11, 2015, doi:10.1073/pnas.1504344112\n\nPublished - PNAS-2015-Zaslaver-1185-9.pdf
Supplemental Material - pnas.201423656SI.pdf
", "abstract": "Animals with compact sensory systems face an encoding problem\nwhere a small number of sensory neurons are required to encode\ninformation about its surrounding complex environment. Using\nCaenorhabditis elegans worms as a model, we ask how chemical\nstimuli are encoded by a small and highly connected sensory system.\nWe first generated a comprehensive library of transgenic\nworms where each animal expresses a genetically encoded calcium\nindicator in individual sensory neurons. This library includes the\nvast majority of the sensory system in C. elegans. Imaging from\nindividual sensory neurons while subjecting the worms to various\nstimuli allowed us to compile a comprehensive functional map of\nthe sensory system at single neuron resolution. The functional\nmap reveals that despite the dense wiring, chemosensory neurons\nrepresent the environment using sparse codes. Moreover, although\nanatomically closely connected, chemo- and mechano-sensory\nneurons are functionally segregated. In addition, the code is hierarchical,\nwhere few neurons participate in encoding multiple cues,\nwhereas other sensory neurons are stimulus specific. This encoding\nstrategy may have evolved to mitigate the constraints of\na compact sensory system.", "date": "2015-01-27", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "112", "number": "4", "publisher": "National Academy of Sciences", "pagerange": "1185-1189", "id_number": "CaltechAUTHORS:20150115-102430590", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150115-102430590", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "European Research Council (ERC)", "grant_number": "336803" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1073/pnas.1423656112", "pmcid": "PMC4313814", "primary_object": { "basename": "PNAS-2015-Zaslaver-1185-9.pdf", "url": "https://authors.library.caltech.edu/records/frvbz-9rv86/files/PNAS-2015-Zaslaver-1185-9.pdf" }, "related_objects": [ { "basename": "pnas.201423656SI.pdf", "url": "https://authors.library.caltech.edu/records/frvbz-9rv86/files/pnas.201423656SI.pdf" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Zaslaver, Alon; Liani, Idan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/jjhgg-b1717", "eprint_id": 52337, "eprint_status": "archive", "datestamp": "2023-08-22 14:30:17", "lastmod": "2023-10-18 19:46:44", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Leighton-D-H-W", "name": { "family": "Leighton", "given": "Daniel H. W." }, "orcid": "0000-0002-1379-0078" }, { "id": "Choe-Andrea", "name": { "family": "Choe", "given": "Andrea" } }, { "id": "Wu-Shannon-Y", "name": { "family": "Wu", "given": "Shannon Y" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Communication between oocytes and somatic cells regulates volatile pheromone production in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "fertilization; sex pheromones; egg\u2013soma communication", "note": "Copyright \u00a9 2014 National Academy of Sciences. \n\nContributed by Paul W. Sternberg, November 8, 2014 (sent for review March 16, 2014).\n\nPublished online before print December 1, 2014, doi: 10.1073/pnas.1420439111 \nPNAS December 1, 2014.\n\nWe thank Asher Cutter and Eric Haag for communicating unpublished results; Ashley Hebard for assisting with some of the experiments; Mihoko Kato and Hillel Schwartz for helpful discussions; and H. Robert Horvitz, Paul Minor, and the Caenorhabditis Genetics Center for sharing worm strains. D.H.W.L. was supported by a National Institutes of Health US Public Health Service Training Grant (T32GM07616). This research was supported by the Howard Hughes Medical Institute, for which P.W.S. is an investigator.\n\nAuthor contributions: D.H.W.L., A.C., and P.W.S. designed research; D.H.W.L., A.C., and S.Y.W. performed research; D.H.W.L. analyzed data; and D.H.W.L., A.C., and P.W.S. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1420439111/-/DCSupplemental.\n\nPublished - 17905.full.pdf
Supplemental Material - pnas.201420439SI.pdf
", "abstract": "Males of the androdioecious species Caenorhabditis elegans are more likely to attempt to mate with and successfully inseminate C. elegans hermaphrodites that do not concurrently harbor sperm. Although a small number of genes have been implicated in this effect, the mechanism by which it arises remains unknown. In the context of the battle of the sexes, it is also unknown whether this effect is to the benefit of the male, the hermaphrodite, or both. We report that successful contact between mature sperm and oocyte in the C. elegans gonad at the start of fertilization causes the oocyte to release a signal that is transmitted to somatic cells in its mother, with the ultimate effect of reducing her attractiveness to males. Changes in hermaphrodite attractiveness are tied to the production of a volatile pheromone, the first such pheromone described in C. elegans.", "date": "2014-12-16", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "111", "number": "50", "publisher": "National Academy of Sciences", "pagerange": "17905-17910", "id_number": "CaltechAUTHORS:20141203-130630817", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141203-130630817", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "T32GM07616" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1073/pnas.1420439111", "pmcid": "PMC4273420", "primary_object": { "basename": "17905.full.pdf", "url": "https://authors.library.caltech.edu/records/jjhgg-b1717/files/17905.full.pdf" }, "related_objects": [ { "basename": "pnas.201420439SI.pdf", "url": "https://authors.library.caltech.edu/records/jjhgg-b1717/files/pnas.201420439SI.pdf" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Leighton, Daniel H. W.; Choe, Andrea; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/qc0ec-yqr06", "eprint_id": 52399, "eprint_status": "archive", "datestamp": "2023-08-20 03:56:21", "lastmod": "2023-10-18 19:49:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kato-Mihoko", "name": { "family": "Kato", "given": "Mihoko" }, "orcid": "0000-0003-3827-8879" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Yu-Collin-Z", "name": { "family": "Yu", "given": "Collin Z." } }, { "id": "DeModena-J-A", "name": { "family": "DeModena", "given": "John A." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "LINKIN, a new transmembrane protein necessary for cell adhesion", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 eLife Sciences Publications.\n\nReceived: 21 August 2014;\nAccepted: 28 November 2014;\nPublished: 1 December 2014.\n\nWe are grateful to Amir Sapir, Hillel Schwartz, and Srimoyee Ghosh for critical reading of the manuscript, and to TFC's postdocs, Xiaoyi Zhaang and Lin Gui, for assistance with IP/Western blot analysis experiments. Caltech protein expression facility expressed and purified LNKN-1 extracellular domain. Mass spectrometry experiments were performed at the Caltech protein exploration laboratory directed by Dr. Sonja Hess and Prof. Ray Deshaies. Wormbase (wormbase.org) was a valuable resource for C. elegans information as was the British Columbia C. elegans Gene Expression Consortium (http://elegans.bcgsc.ca/home/ge_consortium.html) GFP expression pattern database. The monoclonal antibody developed by Frankel, J. and Nelsen, E.M. was obtained from the Developmental Studies Hydridoma Bank, created by the NICHD of the NIH and maintained at the University of Iowa. Nematode strains were provided by the Caenorhabditis Genetics Center, which is funded by the NIH National Center for Research Resources. C.Z.Y. was funded by a CIRM pre-doctoral training grant. P.W.S. in an investigator with the Howard Hughes Medical Institute, which supported this work.\n\nAuthor contributions:\n\nMK, T-FC, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting\nor revising the article; CZY, JD, Acquisition of data, Analysis and interpretation of data; PWS,\nConception and design, Analysis and interpretation of data, Drafting or revising the article.\n\nSupplemental Material - elife04449_Supplemental_files.zip
", "abstract": "In epithelial collective migration, leader and follower cells migrate while maintaining cell-cell adhesion and tissue polarity. We have identified a conserved protein and interactors required for maintaining cell adhesion during a simple collective migration in the developing C. elegans male gonad. LINKIN is a previously uncharacterized, transmembrane protein conserved throughout Metazoa. We identified seven atypical FG-GAP domains in the extracellular domain, which potentially folds into a \u03b2-propeller structure resembling the \u03b1-integrin ligand-binding domain. C. elegans LNKN-1 localizes to the plasma membrane of all gonadal cells, with apical and lateral bias. We identified the LINKIN interactors RUVBL1, RUVBL2, and \u03b1-tubulin by using SILAC mass spectrometry on human HEK 293T cells and testing candidates for lnkn-1-like function in C. elegans male gonad. We propose that LINKIN promotes adhesion between neighboring cells through its extracellular domain and regulates microtubule dynamics through RUVBL proteins at its intracellular domain.", "date": "2014-12-01", "date_type": "published", "publication": "eLife", "volume": "2014", "number": "3", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e04449", "id_number": "CaltechAUTHORS:20141204-125558317", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141204-125558317", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "California Institute for Regenerative Medicine (CIRM)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.7554/eLife.04449", "pmcid": "PMC4275582", "primary_object": { "basename": "elife04449_Supplemental_files.zip", "url": "https://authors.library.caltech.edu/records/qc0ec-yqr06/files/elife04449_Supplemental_files.zip" }, "resource_type": "article", "pub_year": "2014", "author_list": "Kato, Mihoko; Chou, Tsui-Fen; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/yckan-agz47", "eprint_id": 50294, "eprint_status": "archive", "datestamp": "2023-08-22 14:24:35", "lastmod": "2023-10-17 22:54:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ghosh-Srimoyee", "name": { "family": "Ghosh", "given": "Srimoyee" }, "orcid": "0000-0002-7820-6741" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Spatial and molecular cues for cell outgrowth during C. elegans uterine development", "ispublished": "pub", "full_text_status": "public", "keywords": "Trio; Nav; Rab; C. elegans; Cell outgrowth; Nuclear migration", "note": "\u00a9 2014 Published by Elsevier Inc.\n\nReceived 4 June 2014;\nReceived in revised form\n19 September 2014;\nAccepted 22 September 2014;\nAvailable online 2 October 2014.\n\nWe thank Matthew Buechner (University of Kansas), David Sherwood (Duke University), Ian Hope (University of Leeds), Nathalie Pujol (Centre d'Immunologie de Marseille-Luminy) and the Caenorhabditis Genetics Center (University of Minnesota) for worm strains; Sang Nguyen for verification of uterine toroid genes; Barbara Perry and Gladys Medina for technical assistance; Wendy Hanna-Rose, Marianne Bronner, Bruce Hay, David Chan, Amir Sapir, Mihoko Kato, Paul Minor and Hillel Schwartz for helpful discussions and critically reading the manuscript. S.G. was supported by National Institutes of Health USPHS training grant GM07616. This work was supported by the Howard Hughes Medical Institute, with which P.W.S. is an investigator.\n\nSupplemental Material - mmc1.pdf
", "abstract": "The Caenorhabditis elegans uterine seam cell (utse) is an H-shaped syncytium that connects the uterus to the body wall. Comprising nine nuclei that move outward in a bidirectional manner, this synctium undergoes remarkable shape change during development. Using cell ablation experiments, we show that three surrounding cell types affect utse development: uterine toroids, the anchor cell and the sex myoblasts. The presence of the anchor cell (AC) nucleus within the utse is necessary for proper utse development and AC invasion genes fos-1, cdh-3, him-4, egl-43, zmp-1 and mig-10 promote utse cell outgrowth. Two types of uterine lumen epithelial cells, uterine toroid 1 (ut1) and uterine toroid 2 (ut2), mediate proper utse outgrowth and we show roles in utse development two genes expressed in the uterine toroids: RASEF ortholog rsef-1 and Trio/unc-73. The SM expressed gene unc-53/NAV regulates utse cell shape; ablation of sex myoblasts (SMs), which generate uterine and vulval muscles, cause defects in utse morphology. Our results clarify the nature of the interactions that exist between utse and surrounding tissue, identify new roles for genes involved in cell outgrowth, and present the utse as a new model system for understanding cell shape change and, putatively, diseases associated with cell shape change.", "date": "2014-12-01", "date_type": "published", "publication": "Developmental Biology", "volume": "396", "number": "1", "publisher": "Elsevier", "pagerange": "121-135", "id_number": "CaltechAUTHORS:20141009-082402427", "issn": "0012-1606", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141009-082402427", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM07616" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1016/j.ydbio.2014.09.028", "primary_object": { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/yckan-agz47/files/mmc1.pdf" }, "resource_type": "article", "pub_year": "2014", "author_list": "Ghosh, Srimoyee and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/thqw3-x1580", "eprint_id": 50097, "eprint_status": "archive", "datestamp": "2023-08-22 14:18:32", "lastmod": "2023-10-17 22:30:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mohandas-N", "name": { "family": "Mohandas", "given": "Namitha" } }, { "id": "Pozio-E", "name": { "family": "Pozio", "given": "Edoardo" } }, { "id": "La-Rosa-G", "name": { "family": "La Rosa", "given": "Giuseppe" } }, { "id": "Korhonen-P-K", "name": { "family": "Korhonen", "given": "Pasi K." } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Koehler-A-V", "name": { "family": "Koehler", "given": "Anson V." } }, { "id": "Hall-R-S", "name": { "family": "Hall", "given": "Ross S." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Boag-P-R", "name": { "family": "Boag", "given": "Peter R." } }, { "id": "Jex-A-R", "name": { "family": "Jex", "given": "Aaron R." } }, { "id": "Chang-B", "name": { "family": "Chang", "given": "Bill" } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "Mitochondrial genomes of Trichinella species and genotypes \u2013 a basis for diagnosis, and systematic and epidemiological explorations", "ispublished": "pub", "full_text_status": "public", "keywords": "Trichinella/trichinellosis; Deep sequencing; Bioinformatics; Mitochondrial genome; Genetic relationships; Systematics; Population genetics; Epidemiology", "note": "\u00a9 2014 Published by Elsevier Ltd. on behalf of Australian Society for Parasitology Inc. \n\nReceived 24 June 2014; Received in revised form 8 August 2014; Accepted 11 August 2014; Available online 21 September 2014.\n\nThis project was funded through the Australian Research Council (ARC), the National Health and Medical Research Council (NHMRC) of Australia (R.B.G. et al.) and DG SANCO of the European Commission; it was also supported by a Victorian Life Sciences Computation Initiative (VLSCI) grant number VR0007 on its Peak Computing Facility at the University of Melbourne, an initiative of the Victorian Government, Australia. Other support from the Australian Academy of Science, Alexander von Humboldt Foundation, Germany, and Melbourne Water Corporation, Australia, is gratefully acknowledged. PWS is an Investigator with the Howard Hughes Medical Institute, USA. N.D.Y. is an NHMRC Early Career Research Fellow (ECRF).\n\nSupplemental Material - mmc1.xlsx
Supplemental Material - mmc2.xlsx
Supplemental Material - mmc3.xlsx
Supplemental Material - mmc4.xlsx
Supplemental Material - mmc5.xlsx
", "abstract": "In the present study we sequenced or re-sequenced, assembled and annotated 15 mitochondrial genomes representing the 12 currently recognised taxa of Trichinella using a deep sequencing-coupled approach. We then defined and compared the gene order in individual mitochondrial genomes (\u223c14 to 17.7 kb), evaluated genetic differences among species/genotypes and re-assessed the relationships among these taxa using the mitochondrial nucleic acid or amino acid sequence data sets. In addition, a rich source of mitochondrial genetic markers was defined that could be used in future systematic, epidemiological and population genetic studies of Trichinella. The sequencing-bioinformatic approach employed herein should be applicable to a wide range of eukaryotic parasites.", "date": "2014-12", "date_type": "published", "publication": "International Journal for Parasitology", "volume": "44", "number": "14", "publisher": "Elsevier", "pagerange": "1073-1080", "id_number": "CaltechAUTHORS:20140929-115146927", "issn": "0020-7519", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140929-115146927", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council (ARC)" }, { "agency": "National Health and Medical Research Council (NHMRC) of Australia" }, { "agency": "European Commission DG SANCO" }, { "agency": "Victorian Life Sciences Computation Initiative (VLSCI)", "grant_number": "VR0007" }, { "agency": "Australian Academy of Science" }, { "agency": "Alexander von Humboldt Foundation" }, { "agency": "Melbourne Water Corporation, Australia" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1016/j.ijpara.2014.08.010", "primary_object": { "basename": "mmc1.xlsx", "url": "https://authors.library.caltech.edu/records/thqw3-x1580/files/mmc1.xlsx" }, "related_objects": [ { "basename": "mmc2.xlsx", "url": "https://authors.library.caltech.edu/records/thqw3-x1580/files/mmc2.xlsx" }, { "basename": "mmc3.xlsx", "url": "https://authors.library.caltech.edu/records/thqw3-x1580/files/mmc3.xlsx" }, { "basename": "mmc4.xlsx", "url": "https://authors.library.caltech.edu/records/thqw3-x1580/files/mmc4.xlsx" }, { "basename": "mmc5.xlsx", "url": "https://authors.library.caltech.edu/records/thqw3-x1580/files/mmc5.xlsx" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Mohandas, Namitha; Pozio, Edoardo; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/m2xx8-q5512", "eprint_id": 61032, "eprint_status": "archive", "datestamp": "2023-08-20 03:33:15", "lastmod": "2023-10-24 23:19:44", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kato-Mihoko", "name": { "family": "Kato", "given": "Mihoko" }, "orcid": "0000-0003-3827-8879" }, { "id": "Liu-Jonathan", "name": { "family": "Liu", "given": "Jonathan" } }, { "id": "Power-O-B", "name": { "family": "Power", "given": "Olivia Box" } }, { "id": "Upadhyaya-A", "name": { "family": "Upadhyaya", "given": "Anand" } }, { "id": "Yim-John", "name": { "family": "Yim", "given": "John" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul" }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Comparison of genes upregulated in metastasis with three C. elegans cell migrations", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2014 American Association for Cancer Research.", "abstract": "Cell migration is an important process occurring during normal animal development but also in the early stages of metastatic cancer when cells invasively migrate out of the primary tumor. It is therefore likely that some of the same genes function in both migrations. Although transcriptional profiling has identified many genes differentially expressed between metastases and primary tumors, we do not understand the function of most of these genes in either normal or disease states. Our goal has been to identify conserved genes used in migration of mammalian metastasis and normal C. elegans development to further characterize their function in both systems. From two published transcriptional profile datasets, we selected genes that were upregulated in metastases compared to primary tumors, and then identified the C. elegans orthologs of those genes to generate a list of 107 genes.", "date": "2014-11", "date_type": "published", "publication": "Molecular Cancer Research", "volume": "12", "number": "S11", "publisher": "American Association for Cancer Research", "pagerange": "Art. No. A46", "id_number": "CaltechAUTHORS:20151013-102856013", "issn": "1541-7786", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151013-102856013", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1158/1557-3125.MODORG-A46", "resource_type": "article", "pub_year": "2014", "author_list": "Kato, Mihoko; Liu, Jonathan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/hs36b-h6b78", "eprint_id": 47534, "eprint_status": "archive", "datestamp": "2023-08-22 13:51:10", "lastmod": "2023-10-26 20:41:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Breugelmans-B", "name": { "family": "Breugelmans", "given": "Bert" } }, { "id": "Jex-A-R", "name": { "family": "Jex", "given": "Aaron R." } }, { "id": "Korhonen-P-K", "name": { "family": "Korhonen", "given": "Pasi K." } }, { "id": "Mangiola-S", "name": { "family": "Mangiola", "given": "Stefano" } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Boag-P-R", "name": { "family": "Boag", "given": "Peter R." } }, { "id": "Hofmann-A", "name": { "family": "Hofmann", "given": "Andreas" } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "Bioinformatic exploration of RIO protein kinases of parasitic and free-living nematodes", "ispublished": "pub", "full_text_status": "public", "keywords": "Parasitic nematode; RIO kinase; Structure; Function", "note": "\u00a9 2014 Published by Elsevier Ltd. on behalf of Australian Society for Parasitology Inc. \n\nReceived 1 May 2014, Revised 17 June 2014, Accepted 18 June 2014, Available online 17 July 2014. \n\nThis project was funded by the National Health and Medical \nResearch Council (NHMRC) of Australia, and the Australian \nResearch Council (ARC). This project was also supported by a Victorian Life Sciences Computation Initiative (VLSCI), Australia, grant number VR0007 on its Peak Computing Facility at the University of Melbourne, Australia an initiative of the Victorian Government. Other support from the Australian Academy of Science, the Australian-American Fulbright Commission, Alexander von Humboldt Foundation, Germany, Melbourne Water Corporation, Australia (R.B.G.) is gratefully acknowledged, as is funding from the Howard Hughes Medical Institute (HHMI), USA, and National Institutes of Health (NIH), USA (P.W.S.). N.D.Y is an NHMRC Early Career Research Fellow (ECRF). Thanks to Brendan Ansell for discussions and advice on the use of i-TASSER. We also acknowledge the contributions of all staff at WormBase (www.wormbase.org). Data for S. ratti (GenBank assembly ID: GCA_000208845.1) and B. malayi (RNA-seq, PRJEB2709) were kindly provided by the Wellcome Trust Sanger Institute, UK (http://www.ebi.ac.uk/ena/data/view/PRJEB2709). We acknowledge the use of the program I-TASSER \u2013 \u00a9 2013 The Regents of the University of Michigan, USA.\n\nSupplemental Material - mmc1.docx
Supplemental Material - mmc2.docx
Supplemental Material - mmc3.docx
Supplemental Material - mmc4.docx
Supplemental Material - mmc5.docx
Supplemental Material - mmc6.pdb
Supplemental Material - mmc7.pdb
Supplemental Material - mmc8.pdb
", "abstract": "Despite right open reading frame kinases being essential for life, their functions, substrates and cellular pathways remain enigmatic. In the present study, gene structures were characterised for 26 right open reading frame kinase from draft genomes of parasitic and free-living nematodes. RNA-seq transcription profiles of right open reading frame kinase genes were investigated for selected parasitic nematodes and showed that these kinases are transcribed in developmental stages that infect their mammalian host. Three-dimensional structural models of Caenorhabditis elegans right open reading frame kinases were predicted, and elucidated functional domains and conserved regions in nematode homologs. These findings provide prospects for functional studies of RIO kinase genes in C. elegans and an opportunity for the design and validation of nematode-specific inhibitors of these enzymes in socioeconomic parasitic worms.", "date": "2014-10-01", "date_type": "published", "publication": "International Journal for Parasitology", "volume": "44", "number": "11", "publisher": "Elsevier", "pagerange": "827-836", "id_number": "CaltechAUTHORS:20140728-143519002", "issn": "0020-7519", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140728-143519002", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Health and Medical Research Council (NHMRC) of Australia" }, { "agency": "Australian Research Council (ARC)" }, { "agency": "Victorian Life Sciences Computation Initiative (VLSCI), Australia, grant", "grant_number": "VR0007" }, { "agency": "Australian Academy of Science" }, { "agency": "Australian-American Fulbright Commission" }, { "agency": "Alexander von Humboldt Foundation" }, { "agency": "Melbourne Water Corporation, Australia" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH" }, { "agency": "NHMRC Early Career Research Fellow (ECRF)" } ] }, "doi": "10.1016/j.ijpara.2014.06.005", "primary_object": { "basename": "mmc6.pdb", "url": "https://authors.library.caltech.edu/records/hs36b-h6b78/files/mmc6.pdb" }, "related_objects": [ { "basename": "mmc7.pdb", "url": "https://authors.library.caltech.edu/records/hs36b-h6b78/files/mmc7.pdb" }, { "basename": "mmc8.pdb", "url": "https://authors.library.caltech.edu/records/hs36b-h6b78/files/mmc8.pdb" }, { "basename": "mmc1.docx", "url": "https://authors.library.caltech.edu/records/hs36b-h6b78/files/mmc1.docx" }, { "basename": "mmc2.docx", "url": "https://authors.library.caltech.edu/records/hs36b-h6b78/files/mmc2.docx" }, { "basename": "mmc3.docx", "url": "https://authors.library.caltech.edu/records/hs36b-h6b78/files/mmc3.docx" }, { "basename": "mmc4.docx", "url": "https://authors.library.caltech.edu/records/hs36b-h6b78/files/mmc4.docx" }, { "basename": "mmc5.docx", "url": "https://authors.library.caltech.edu/records/hs36b-h6b78/files/mmc5.docx" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Breugelmans, Bert; Jex, Aaron R.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/tb6b9-3xq53", "eprint_id": 48708, "eprint_status": "archive", "datestamp": "2023-08-20 03:13:52", "lastmod": "2023-10-17 20:22:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shinya-Ryoji", "name": { "family": "Shinya", "given": "Ryoji" } }, { "id": "Hasegawa-Koichi", "name": { "family": "Hasegawa", "given": "Koichi" } }, { "id": "Chen-Anthony", "name": { "family": "Chen", "given": "Anthony" }, "orcid": "0000-0002-9578-4893" }, { "id": "Kanzaki-Natsumi", "name": { "family": "Kanzaki", "given": "Natsumi" }, "orcid": "0000-0001-8752-1674" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Evidence of hermaphroditism and sex ratio distortion in the fungal feeding nematode Bursaphelenchus okinawaensis", "ispublished": "pub", "full_text_status": "public", "keywords": "hermaphroditism, nematode, early embryogenesis, genetics, satellite model", "note": "\u00a9 2014 Author et al. This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.\n\nReceived May 28, 2014. Accepted August 1, 2014. Early Online August 12, 2014. \n\nWe thank Gladys Medina for technical assistance; Kazuki Sato and Sota Ozawa\nfor help in collecting insects on Ishigaki Island; members of the Sternberg laboratory for helpful discussions; Hillel Schwartz and Daniel Leighton for critical review and helpful comments; Andres Collazo for help in confocal imaging; and Jonathan Hodgkin and Tim Schedl for nomenclature discussions. Imaging was performed in the Biological Imaging Facility, with the support of the Caltech Beckman Institute and the Beckman Foundation. This work was supported by a Grant-in-Aid for the Japan Society for the Promotion of Science Fellows (to R. S.), the Howard Hughes Medical Institute (with which P. W. S. is an investigator), and a Caltech Summer Undergraduate Research\nFellowship (to A. C.).\n\nPublished - 1907.full.pdf
", "abstract": "Nematodes have many different reproductive strategies along with their divergent life-histories; the ability of hermaphrodite to self- and cross-fertilize is useful for genetic manipulation. Here, we demonstrate the hermaphroditism of the fungal feeding nematode Bursaphelenchus okinawaensis, which was formerly described as a parthenogenetic nematode, and we show its other unique sexual characteristics. To determine that it is hermaphroditic, we performed the following experiments: 1) observation of the pronuclear and chromosome behavior during oogenesis and early embryogenesis; 2) observation of spermatogenesis during the fourth larval stage; 3) investigation of sperm utilization; and 4) investigation of phenotypic segregation after cross-mating using an chemically-induced visible mutant. We then investigated the mating preferences and spermatid size difference between males and hermaphrodites. B. okinawaensis males successfully mated only with sperm-depleted old hermaphrodites, and the spermatid sizes of males were almost the same as those of hermaphrodites. Moreover, the sex ratio of cross-fertilized progeny was highly skewed toward hermaphrodites. B. okinawaensis is phylogenetically distant from established model nematodes such as C. elegans and is more closely related to some economically relevant parasitic nematodes. This newly discovered hermaphroditic nematode has great potential for evolutionary and parasitological research.", "date": "2014-10-01", "date_type": "published", "publication": "G3", "volume": "4", "number": "10", "publisher": "Genetics Society of America", "pagerange": "1907-1917", "id_number": "CaltechAUTHORS:20140820-084833184", "issn": "2160-1836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140820-084833184", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech Beckman Institute" }, { "agency": "Arnold and Mabel Beckman Foundation" }, { "agency": "Japan Society for the Promotion of Science (JSPS)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Caltech Summer Undergraduate Research Fellowship (SURF)" } ] }, "doi": "10.1534/g3.114.012385", "pmcid": "PMC4199697", "primary_object": { "basename": "1907.full.pdf", "url": "https://authors.library.caltech.edu/records/tb6b9-3xq53/files/1907.full.pdf" }, "resource_type": "article", "pub_year": "2014", "author_list": "Shinya, Ryoji; Hasegawa, Koichi; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/d6fcr-wag21", "eprint_id": 49244, "eprint_status": "archive", "datestamp": "2023-08-22 13:41:08", "lastmod": "2023-10-17 21:14:46", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sapir-A", "name": { "family": "Sapir", "given": "Amir" }, "orcid": "0000-0001-9888-1800" }, { "id": "Tsur-A", "name": { "family": "Tsur", "given": "Assaf" } }, { "id": "Koorman-T", "name": { "family": "Koorman", "given": "Thijs" }, "orcid": "0000-0002-6064-3353" }, { "id": "Ching-Kaitlin", "name": { "family": "Ching", "given": "Kaitlin" }, "orcid": "0000-0002-0517-2421" }, { "id": "Mishra-P", "name": { "family": "Mishra", "given": "Prashant" } }, { "id": "Bardenheier-A", "name": { "family": "Bardenheier", "given": "Annabelle" } }, { "id": "Podolsky-L", "name": { "family": "Podolsky", "given": "Lisa" } }, { "id": "Bening-Abu-Schach-U", "name": { "family": "Bening-Abu-Schach", "given": "Ulrike" } }, { "id": "Boxem-M", "name": { "family": "Boxem", "given": "Mike" }, "orcid": "0000-0003-3966-4173" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Broday-L", "name": { "family": "Broday", "given": "Limor" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Controlled sumoylation of the mevalonate pathway enzyme HMGS-1 regulates metabolism during aging", "ispublished": "pub", "full_text_status": "public", "keywords": "HMG-CoA synthase; sterol synthesis; yeast two-hybrid", "note": "\u00a9 2014 National Academy of Sciences. \n\nContributed by Paul W. Sternberg, August 6, 2014 (sent for review July 3, 2014). Published online before print September 3, 2014, doi: 10.1073/pnas.1414748111. \n\nWe thank Shohei Mitani for a knockout allele, Ann Wang for the ulp-4 RNAi in the ulp-4::gfp experiments, Adam Kolawa and Kevin Yu for their help with worm functional assays, Robyn Branicky and William Schafer for sharing the clh-3::mCherry worms, Brian Williams for total human RNA, David Chan for use of his Seahorse oxygen consumption analyzer, Domenico Fasci for his help with in vitro sumoylation assays, and Jennifer Watt for fat measurements. We also thank WormBase and the Caenorhabditis Genetics Center for C. elegans genetic annotation and strains. The Henry L. Guenther Foundation supported the Q-Exactive mass spectrometer. This research was supported by the Howard Hughes Medical Institute (of which P.W.S. is an Investigator), the Israel Cancer Research Fund PG -11-3086 (to L.B.), and Israel Science Foundation Grant ISF 1617/11 (to L.B.). A.T. was supported by the Ori Foundation-In Memory of Ori Levi, the Israeli Mitochondrial Disease Foundation (www.orifund.org). T.-F.C. is a member of University of California, Los Angeles's Jonsson Comprehensive Cancer Center. P.M. is supported by a Baxter Senior Postdoctoral Fellowship. \n\nAuthor contributions: A.S., M.B., T.-F.C., L.B., and P.W.S. designed research; A.S., A.T., T.K., K.C., P.M., A.B., L.P., U.B.-A.-S., T.-F.C., and L.B. performed research; A.S., A.T., T.K., P.M., M.B., T.-F.C., and L.B. analyzed data; and A.S., K.C., L.B., and P.W.S. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1414748111/-/DCSupplemental.\n\nPublished - E3880.full.pdf
Supplemental Material - pnas.1414748111.sd01.xlsx
Supplemental Material - pnas.1414748111.sm01.avi
Supplemental Material - pnas.1414748111.sm02.avi
Supplemental Material - pnas.201414748SI.pdf
", "abstract": "Many metabolic pathways are critically regulated during development and aging but little is known about the molecular mechanisms underlying this regulation. One key metabolic cascade in eukaryotes is the mevalonate pathway. It catalyzes the synthesis of sterol and nonsterol isoprenoids, such as cholesterol and ubiquinone, as well as other metabolites. In humans, an age-dependent decrease in ubiquinone levels and changes in cholesterol homeostasis suggest that mevalonate pathway activity changes with age. However, our knowledge of the mechanistic basis of these changes remains rudimentary. We have identified a regulatory circuit controlling the sumoylation state of Caenorhabditis elegans HMG-CoA synthase (HMGS-1). This protein is the ortholog of human HMGCS1 enzyme, which mediates the first committed step of the mevalonate pathway. In vivo, HMGS-1 undergoes an age-dependent sumoylation that is balanced by the activity of ULP-4 small ubiquitin-like modifier protease. ULP-4 exhibits an age-regulated expression pattern and a dynamic cytoplasm-to-mitochondria translocation. Thus, spatiotemporal ULP-4 activity controls the HMGS-1 sumoylation state in a mechanism that orchestrates mevalonate pathway activity with the age of the organism. To expand the HMGS-1 regulatory network, we combined proteomic analyses with knockout studies and found that the HMGS-1 level is also governed by the ubiquitin\u2013proteasome pathway. We propose that these conserved molecular circuits have evolved to govern the level of mevalonate pathway flux during aging, a flux whose dysregulation is associated with numerous age-dependent cardiovascular and cancer pathologies.", "date": "2014-09-16", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "111", "number": "37", "publisher": "National Academy of Sciences", "pagerange": "E3880-E3889", "id_number": "CaltechAUTHORS:20140904-122954030", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140904-122954030", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Henry L. Guenther Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Israel Cancer Research Fund", "grant_number": "PG-11-3086" }, { "agency": "Israel Science Foundation", "grant_number": "ISF 1617/11" }, { "agency": "Ori Foundation" }, { "agency": "Israeli Mitochondrial Disease Foundation" }, { "agency": "Baxter Foundation" } ] }, "doi": "10.1073/pnas.1414748111", "pmcid": "PMC4169931", "primary_object": { "basename": "E3880.full.pdf", "url": "https://authors.library.caltech.edu/records/d6fcr-wag21/files/E3880.full.pdf" }, "related_objects": [ { "basename": "pnas.1414748111.sd01.xlsx", "url": "https://authors.library.caltech.edu/records/d6fcr-wag21/files/pnas.1414748111.sd01.xlsx" }, { "basename": "pnas.1414748111.sm01.avi", "url": "https://authors.library.caltech.edu/records/d6fcr-wag21/files/pnas.1414748111.sm01.avi" }, { "basename": "pnas.1414748111.sm02.avi", "url": "https://authors.library.caltech.edu/records/d6fcr-wag21/files/pnas.1414748111.sm02.avi" }, { "basename": "pnas.201414748SI.pdf", "url": "https://authors.library.caltech.edu/records/d6fcr-wag21/files/pnas.201414748SI.pdf" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Sapir, Amir; Tsur, Assaf; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/70kmm-8py90", "eprint_id": 47673, "eprint_status": "archive", "datestamp": "2023-08-22 13:40:29", "lastmod": "2023-10-26 21:09:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Flytzanis-N-C", "name": { "family": "Flytzanis", "given": "Nicholas C." }, "orcid": "0000-0002-7921-9392" }, { "id": "Bedbrook-C-N", "name": { "family": "Bedbrook", "given": "Claire N." }, "orcid": "0000-0003-3973-598X" }, { "id": "Chiu-Hui", "name": { "family": "Chiu", "given": "Hui" } }, { "id": "Engqvist-M-K-M", "name": { "family": "Engqvist", "given": "Martin K. M." } }, { "id": "Xiao-Cheng", "name": { "family": "Xiao", "given": "Cheng" }, "orcid": "0000-0001-9649-7450" }, { "id": "Chan-Ken-Y", "name": { "family": "Chan", "given": "Ken Y." }, "orcid": "0000-0002-8853-5186" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Arnold-F-H", "name": { "family": "Arnold", "given": "Frances H." }, "orcid": "0000-0002-4027-364X" }, { "id": "Gradinaru-V", "name": { "family": "Gradinaru", "given": "Viviana" }, "orcid": "0000-0001-5868-348X" } ] }, "title": "Archaerhodopsin variants with enhanced voltage-sensitive fluorescence in mammalian and Caenorhabditis elegans neurons", "ispublished": "pub", "full_text_status": "public", "keywords": "Biological sciences; Neuroscience", "note": "\u00a9 2014, Nature Publishing Group. \n\nReceived 21 June 2014. Accepted 04 August 2014. Published 15 September 2014. \n\nWe thank the entire Gradinaru lab for helpful discussions. We also thank Prof. David Anderson for helpful discussions and suggestions; Dr Benjamin Judkewitz for valuable input on the optical setup for imaging; Bin Yang for assistance with optical setup and cultured neurons; Christopher Cronin and Ravi Nath for assistance with C. elegans experiments; and Dr John Bedbrook and Dr Jennifer Treweek for critical reading of the manuscript. This work was funded by the NIH/NINDS New Innovator (NIH IDP20D017782-01); startup funds from the President and Provost of California Institute of Technology and the Biology and Biological Engineering Division of California Institute of Technology; the Beckman Institute of Caltech; the Gordon and Betty Moore Foundation through Grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative (to V.G.); by NIH 1R21MH103824-01 (to V.G. and F.H.A.); and by the Institute for Collaborative Biotechnologies through grant W911NF-09-0001 from the U.S. Army Research Office (to F.H.A.). The content of the information does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred. V.G. is also supported by Human Frontiers in Science Program, the Mallinckrodt Foundation, the Pew Charitable Trust, the Michael J. Fox Foundation, the Kimmel Foundation, Caltech-GIST, NIH 1R01NS085910-01, NIH 1R01AG047664-01. P.W.S. is an investigator with the HHMI, which supported this research. N.C.F., C.N.B. and K.Y.C. acknowledge support from the Caltech Biology Division Training grant (NIH/NRSA 5T32GM07616). M.K.M.E. acknowledges support from the German Research Foundation (DFG) under programme EN 957/1-1. \n\nNicholas C. Flytzanis & Claire N. Bedbrook: These authors contributed equally to this work. \n\nAuthor Contributions: N.C.F., M.K.M.E., F.H.A. and V.G. conceived the project. N.C.F., C.N.B., H.C., P.S.W. and V.G. designed the experiments. N.C.F., C.N.B., H.C., C.X. and K.Y.C. performed the experiments. N.C.F. and C.N.B. analysed all of the data. N.C.F., C.N.B. and V.G. wrote the manuscript with support from all authors. V.G. supervised all aspects of the work. \n\nThe authors declare no competing financial interests.\n\nAccepted Version - nihms619133.pdf
Supplemental Material - ncomms5894-s1.pdf
Supplemental Material - ncomms5894-s2.mov
Supplemental Material - ncomms5894-s3.mov
", "abstract": "Probing the neural circuit dynamics underlying behaviour would benefit greatly from improved genetically encoded voltage indicators. The proton pump Archaerhodopsin-3 (Arch), an optogenetic tool commonly used for neuronal inhibition, has been shown to emit voltage-sensitive fluorescence. Here we report two Arch variants with enhanced radiance (Archers) that in response to 655\u2009nm light have 3\u20135 times increased fluorescence and 55\u201399 times reduced photocurrents compared with Arch WT. The most fluorescent variant, Archer1, has 25\u201340% fluorescence change in response to action potentials while using 9 times lower light intensity compared with other Arch-based voltage sensors. Archer1 is capable of wavelength-specific functionality as a voltage sensor under red light and as an inhibitory actuator under green light. As a proof-of-concept for the application of Arch-based sensors in vivo, we show fluorescence voltage sensing in behaving Caenorhabditis elegans. Archer1's characteristics contribute to the goal of all-optical detection and modulation of activity in neuronal networks in vivo.", "date": "2014-09-15", "date_type": "published", "publication": "Nature Communications", "volume": "5", "number": "9", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 4894", "id_number": "CaltechAUTHORS:20140730-113211664", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140730-113211664", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "IDP20D017782-01" }, { "agency": "President and Provost of Caltech" }, { "agency": "Caltech Biology and Biological Engineering Division" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "NIH", "grant_number": "1R21MH103824-01" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-09-0001" }, { "agency": "Human Frontier Science Program" }, { "agency": "Edward Mallinckrodt, Jr. Foundation" }, { "agency": "Pew Charitable Trust" }, { "agency": "Michael J. Fox Foundation" }, { "agency": "Sidney Kimmel Foundation for Cancer Research" }, { "agency": "Caltech-GIST" }, { "agency": "NIH", "grant_number": "1R01NS085910-01" }, { "agency": "NIH", "grant_number": "1R01AG047664-01" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "5T32GM07616" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "EN 957/1-1" }, { "agency": "National Institute of Neurological Disorders and Stroke (NINDS)" } ] }, "doi": "10.1038/ncomms5894", "pmcid": "PMC4166526", "primary_object": { "basename": "ncomms5894-s1.pdf", "url": "https://authors.library.caltech.edu/records/70kmm-8py90/files/ncomms5894-s1.pdf" }, "related_objects": [ { "basename": "ncomms5894-s2.mov", "url": "https://authors.library.caltech.edu/records/70kmm-8py90/files/ncomms5894-s2.mov" }, { "basename": "ncomms5894-s3.mov", "url": "https://authors.library.caltech.edu/records/70kmm-8py90/files/ncomms5894-s3.mov" }, { "basename": "nihms619133.pdf", "url": "https://authors.library.caltech.edu/records/70kmm-8py90/files/nihms619133.pdf" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Flytzanis, Nicholas C.; Bedbrook, Claire N.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/anhyp-4bb78", "eprint_id": 50317, "eprint_status": "archive", "datestamp": "2023-08-20 02:44:47", "lastmod": "2023-10-17 22:55:26", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Veesenmeyer-J-L", "name": { "family": "Veesenmeyer", "given": "Jeff L." } }, { "id": "Andersen-A-W", "name": { "family": "Andersen", "given": "Aaron W." } }, { "id": "Lu-Xiaojun", "name": { "family": "Lu", "given": "Xiaojun" } }, { "id": "Hussa-E-A", "name": { "family": "Hussa", "given": "Elizabeth A." } }, { "id": "Murfin-K-E", "name": { "family": "Murfin", "given": "Kristen E." } }, { "id": "Chaston-J-M", "name": { "family": "Chaston", "given": "John M." } }, { "id": "Dillman-A-R", "name": { "family": "Dillman", "given": "Adler R." }, "orcid": "0000-0001-7171-4332" }, { "id": "Wassarman-K-M", "name": { "family": "Wassarman", "given": "Karen M." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Goodrich-Blair-H", "name": { "family": "Goodrich-Blair", "given": "Heidi" } } ] }, "title": "NilD CRISPR RNA contributes to Xenorhabdus nematophila colonization of symbiotic host nematodes", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 John Wiley & Sons Ltd.\n\nIssue published online: 29 AUG 2014; Article first published online: 6 AUG 2014; Accepted manuscript online: 14 JUL 2014 02:49AM EST; Manuscript Accepted: 10 JUL 2014.\n\nWe wish to thank Amy Cavanagh (UW-Madison) for technical\nsupport on Northerns and RPAs, and Jonathan Klassen\n(UConn-Storrs) and the Magnifying Genome team for their\nassistance in genome analysis and annotation. We gratefully\nacknowledge former and current members of the Goodrich-\nBlair lab: Dr Kurt Heungens for preliminary data on the nilD\nlocus, James Weger and Nick Feirer for contributions to cas\nmutant phenotypic analyses, and \u00c1ngel Casanova-Torres for\nquantitative reverse transcriptase PCR analysis of putative\ntarget genes. We thank Dr Brian Tjaden (Wellesley College)\nfor providing the Target RNA program for X. nematophila, S.\nPatricia Stock and S. Forst for collaborative work on S. anatoliense and S. websteri, and Caitilyn Allen and Katrina\nForest (UW-Madison) for helpful discussions. Work in the\nGoodrich-Blair lab was funded by a grant from the National\nScience Foundation IOS-0950873. X.L. was supported by the\nUW-Madison Graduate School research funds. J.M.C. and\nK.E.M. were supported by a National Institutes of Health\n(NIH) National Research Service Award T32 (AI55397)\n'Microbes in Health and Disease'. J.M.C. was also supported\nby a National Science Foundation (NSF) Graduate Research\nFellowship. E.A.H. was supported by the National Institutes\nof Health grant 1F32AI084441. A.R.D. was supported by a\nUnited States Public Health Service Training Grant\n(T32GM07616), and the Howard Hughes Medical Institute,\nwith which P.W.S. is an investigator. The authors have no\nconflict of interest to declare.\n\nAccepted Version - nihms614057.pdf
Supplemental Material - mmi12715-sup-0001-si.pdf
", "abstract": "The bacterium Xenorhabdus nematophila is a mutualist of entomopathogenic Steinernema carpocapsae nematodes and facilitates infection of insect hosts. X. nematophila colonizes the intestine of S. carpocapsae which carries it between insects. In the X. nematophila colonization-defective mutant nilD6::Tn5, the transposon is inserted in a region lacking obvious coding potential. We demonstrate that the transposon disrupts expression of a single CRISPR RNA, NilD RNA. A variant NilD RNA also is expressed by X. nematophila strains from S. anatoliense and S. websteri nematodes. Only nilD from the S. carpocapsae strain of X. nematophila rescued the colonization defect of the nilD6::Tn5 mutant, and this mutant was defective in colonizing all three nematode host species. NilD expression depends on the presence of the associated Cas6e but not Cas3, components of the Type I-E CRISPR-associated machinery. While cas6e deletion in the complemented strain abolished nematode colonization, its disruption in the wild-type parent did not. Likewise, nilD deletion in the parental strain did not impact colonization of the nematode, revealing that the requirement for NilD is evident only in certain genetic backgrounds. Our data demonstrate that NilD RNA is conditionally necessary for mutualistic host colonization and suggest that it functions to regulate endogenous gene expression.", "date": "2014-09", "date_type": "published", "publication": "Molecular Microbiology", "volume": "93", "number": "5", "publisher": "Wiley", "pagerange": "1026-1042", "id_number": "CaltechAUTHORS:20141009-141146108", "issn": "0950-382X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141009-141146108", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "IOS-0950873" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 (AI55397)" }, { "agency": "NSF Graduate Research Fellowship" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "1F32AI084441" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM07616" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1111/mmi.12715", "pmcid": "PMC4152777", "primary_object": { "basename": "mmi12715-sup-0001-si.pdf", "url": "https://authors.library.caltech.edu/records/anhyp-4bb78/files/mmi12715-sup-0001-si.pdf" }, "related_objects": [ { "basename": "nihms614057.pdf", "url": "https://authors.library.caltech.edu/records/anhyp-4bb78/files/nihms614057.pdf" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Veesenmeyer, Jeff L.; Andersen, Aaron W.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/y9y8b-sz397", "eprint_id": 49073, "eprint_status": "archive", "datestamp": "2023-08-20 02:00:47", "lastmod": "2023-10-17 21:07:18", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Schaeffer-M-L", "name": { "family": "Schaeffer", "given": "Mary L." } }, { "id": "McQuilton-P", "name": { "family": "McQuilton", "given": "Peter" } }, { "id": "Laulederkind-S-J-F", "name": { "family": "Laulederkind", "given": "Stanley J. F." } }, { "id": "Li-Donghui", "name": { "family": "Li", "given": "Donghui" } }, { "id": "Wang-Shur-Jen", "name": { "family": "Wang", "given": "Shur-Jen" } }, { "id": "Hayman-G-T", "name": { "family": "Hayman", "given": "G. Thomas" } }, { "id": "Tweedie-S", "name": { "family": "Tweedie", "given": "Susan" } }, { "id": "Arighi-C-N", "name": { "family": "Arighi", "given": "Cecilia N." } }, { "id": "Done-J", "name": { "family": "Done", "given": "James" } }, { "id": "M\u00fcller-H-M", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Mao-Yuqing", "name": { "family": "Mao", "given": "Yuqing" } }, { "id": "Wei-Chih-Hsuan", "name": { "family": "Wei", "given": "Chih-Hsuan" } }, { "id": "Lu-Zhiyong", "name": { "family": "Lu", "given": "Zhiyong" } } ] }, "title": "BC4GO: a full-text corpus for the BioCreative IV GO task", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 Oxford University Press. This work is written by US Government employees and is in the public domain in the US. Received 1 February 2014; Revised 1 July 2014; Accepted 3 July 2014. We would like to thank Don Comeau, Rezarta Dogan and John Wilbur for general discussion and technical assistance in using BioC, and in particular to Don Comeau for providing us source PMC articles in the BioC XML format. We also thank Lynette Hirschman, Cathy Wu, Kevin Cohen, Martin Krallinger and Thomas Wiegers from the BioCreative IV organizing committee for their support, and\nJudith Blake, Andrew Chatr-aryamontri, Sherri Matis, Fiona\nMcCarthy, Sandra Orchard and Phoebe Roberts from the\nBioCreative IV User Advisory Group for their helpful discussions. Funding Intramural Research Program of the NIH, National Library of Medicine (to C.W., Y.M. and Z.L.), the USDA ARS (to M.L.S.), the National Human Genome Research Institute at the US National Institutes of Health (# HG004090, # HG002223 and # HG002273) and National Science Foundation (ABI-1062520, ABI-1147029 and\nDBI-0850319). Conflict of interest. None declared.\n\nPublished - Database-2014-Van_Auken-database_bau074.pdf
", "abstract": "Gene function curation via Gene Ontology (GO) annotation is a common task among Model Organism Database groups. Owing to its manual nature, this task is considered one of the bottlenecks in literature curation. There have been many previous attempts at automatic identification of GO terms and supporting information from full text. However, few systems have delivered an accuracy that is comparable with humans. One recognized challenge in developing such systems is the lack of marked sentence-level evidence text that provides the basis for making GO annotations. We aim to create a corpus that includes the GO evidence text along with the three core elements of GO annotations: (i) a gene or gene product, (ii) a GO term and (iii) a GO evidence code. To ensure our results are consistent with real-life GO data, we recruited eight professional GO curators and asked them to follow their routine GO annotation protocols. Our annotators marked up more than 5000 text passages in 200 articles for 1356 distinct GO terms. For evidence sentence selection, the inter-annotator agreement (IAA) results are 9.3% (strict) and 42.7% (relaxed) in F1-measures. For GO term selection, the IAAs are 47% (strict) and 62.9% (hierarchical). Our corpus analysis further shows that abstracts contain \u223c10% of relevant evidence sentences and 30% distinct GO terms, while the Results/Experiment section has nearly 60% relevant sentences and >70% GO terms. Further, of those evidence sentences found in abstracts, less than one-third contain enough experimental detail to fulfill the three core criteria of a GO annotation. This result demonstrates the need of using full-text articles for text mining GO annotations. Through its use at the BioCreative IV GO (BC4GO) task, we expect our corpus to become a valuable resource for the BioNLP research community.", "date": "2014-07-28", "date_type": "published", "publication": "Database : The Journal of Biological Databases and Curation", "volume": "2014", "publisher": "Oxford University Press", "pagerange": "Art. No. 74", "id_number": "CaltechAUTHORS:20140829-131503355", "issn": "1758-0463", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140829-131503355", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Agriculture" }, { "agency": "NIH", "grant_number": "HG004090" }, { "agency": "NIH", "grant_number": "HG002223" }, { "agency": "NIH", "grant_number": "HG002273" }, { "agency": "NSF", "grant_number": "ABI-1062520" }, { "agency": "NSF", "grant_number": "ABI-1147029" }, { "agency": "NSF", "grant_number": "DBI-0850319" } ] }, "doi": "10.1093/database/bau074", "pmcid": "PMC4112614", "primary_object": { "basename": "Database-2014-Van_Auken-database_bau074.pdf", "url": "https://authors.library.caltech.edu/records/y9y8b-sz397/files/Database-2014-Van_Auken-database_bau074.pdf" }, "resource_type": "article", "pub_year": "2014", "author_list": "Van Auken, Kimberly; Schaeffer, Mary L.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/1k8eq-b2v46", "eprint_id": 45935, "eprint_status": "archive", "datestamp": "2023-08-22 13:11:40", "lastmod": "2023-10-26 18:33:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Davenport-A-M", "name": { "family": "Davenport", "given": "Andrew M." } }, { "id": "Collins-L-N", "name": { "family": "Collins", "given": "Leslie N." } }, { "id": "Chiu-Hui", "name": { "family": "Chiu", "given": "Hui" } }, { "id": "Minor-P-J", "name": { "family": "Minor", "given": "Paul J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Hoelz-A", "name": { "family": "Hoelz", "given": "Andr\u00e9" }, "orcid": "0000-0003-1726-0127" } ] }, "title": "Structural and Functional Characterization of the \u03b1-Tubulin Acetyltransferase MEC-17", "ispublished": "pub", "full_text_status": "public", "keywords": "X-ray crystallography; Tubulin acetyltransferase; Substrate recognition; C. elegans; Mechanosensation", "note": "\u00a9 2014 Published by Elsevier Ltd. Received date: 28 March 2014. Revised date: 5 May 2014. Accepted date: 6 May 2014. We thank Daniel H. Lin, Alina Patke, Tobias Stuwe, Karsten Thierbach, and Yunji Wu for critical reading of the manuscript, David King for mass spectrometry analysis, Maxene Nachury and Irini Topalidou for providing material, Jens Kaiser and the scientific staff of SSRL beamline 12-2 for their support with X-ray diffraction measurements. We acknowledge the Gordon and Betty Moore Foundation for their support of the Molecular Observatory at the California Institute of Technology. The operations at the SSRL are supported by the Department of Energy and by the National Institutes of Health. AMD and PJM are supported by a National Institutes of Health Research Service Award (5 T32 GM07616). AH was supported by the Albert Wyrick V Scholar Award of the V Foundation for Cancer Research, the 54th Mallinckrodt Scholar Award of the Edward Mallinckrodt, Jr. Foundation, and a Kimmel Scholar Award of the Sidney Kimmel Foundation for Cancer Research. Research supported in part by the Howard Hughes Medical Institute, with which P.W.S. is an investigator.\n\nSupplemental Material - mmc1__1_.doc
Supplemental Material - mmc2.docx
Supplemental Material - mmc3.mp4
Supplemental Material - mmc4.mp4
Supplemental Material - mmc5.mp4
Supplemental Material - mmc6.mp4
", "abstract": "Tubulin protomers undergo an extensive array of post-translational modifications to tailor microtubules to specific tasks. One such modification, the acetylation of lysine-40 of \u03b1-tubulin, located in the lumen of microtubules, is associated with stable, long-living microtubule structures. MEC-17 was recently identified as the acetyltransferase that mediates this event. We have determined the crystal structure of the catalytic core of human MEC-17 in complex with its cofactor acetyl-CoA at 1.7 \u00c5 resolution. The structure reveals that the MEC-17 core adopts a canonical Gcn5-related N-acetyltransferase (GNAT) fold that is decorated with extensive surface loops. An enzymatic analysis of 33 MEC-17 surface mutants identifies hot-spot residues for catalysis and substrate recognition. A large, evolutionarily conserved hydrophobic surface patch is identified that is critical for enzymatic activity, suggesting that specificity is achieved by interactions with the \u03b1-tubulin substrate that extend outside of the modified surface loop. An analysis of MEC-17 mutants in C. elegans shows that enzymatic activity is dispensable for touch sensitivity.", "date": "2014-07-15", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "426", "number": "14", "publisher": "Elsevier", "pagerange": "2605-2616", "id_number": "CaltechAUTHORS:20140528-103912267", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140528-103912267", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Department of Energy (DOE)" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "5 T32 GM07616" }, { "agency": "V Foundation for Cancer Research" }, { "agency": "Edward Mallinckrodt, Jr. Foundation" }, { "agency": "Sidney Kimmel Foundation for Cancer Research" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1016/j.jmb.2014.05.009", "pmcid": "PMC4259157", "primary_object": { "basename": "mmc4.mp4", "url": "https://authors.library.caltech.edu/records/1k8eq-b2v46/files/mmc4.mp4" }, "related_objects": [ { "basename": "mmc5.mp4", "url": "https://authors.library.caltech.edu/records/1k8eq-b2v46/files/mmc5.mp4" }, { "basename": "mmc6.mp4", "url": "https://authors.library.caltech.edu/records/1k8eq-b2v46/files/mmc6.mp4" }, { "basename": "mmc1__1_.doc", "url": "https://authors.library.caltech.edu/records/1k8eq-b2v46/files/mmc1__1_.doc" }, { "basename": "mmc2.docx", "url": "https://authors.library.caltech.edu/records/1k8eq-b2v46/files/mmc2.docx" }, { "basename": "mmc3.mp4", "url": "https://authors.library.caltech.edu/records/1k8eq-b2v46/files/mmc3.mp4" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Davenport, Andrew M.; Collins, Leslie N.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/9czqj-n7339", "eprint_id": 47692, "eprint_status": "archive", "datestamp": "2023-08-20 01:37:42", "lastmod": "2024-01-31 19:57:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chen-Zhen-Xia", "name": { "family": "Chen", "given": "Zhen-Xia" }, "orcid": "0000-0003-0474-902X" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Comparative validation of the D. melanogaster modENCODE transcriptome annotation", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 Chen et al. Published by Cold Spring Harbor Laboratory Press. Freely available online through the Genome Research Open Access option. This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/. \n\nPublished in Advance July 1, 2014. Received April 29, 2013; accepted in revised form December 2, 2013. \n\nWe thank modENCODE and laboratory members for discussion.\nThis research was supported by the Intramural Research Programs of the National Institutes of Health, NIDDK (DK015600-18 to B.O.) and by the extramural National Institutes of Health program (1ROIGM082843 to A.K.; U01HB004271 to S.E.C.). This study utilized the high-performance computational capabilities of the\nBiowulf Linux cluster at the National Institutes of Health,\nBethesda, Maryland (http://biowulf.nih.gov).\n\nPublished - Genome_Res.-2014-Chen-1209-23.pdf
Supplemental Material - Supp_File_S1_CAGE_Dmel_FM_carcass.bed
Supplemental Material - Supp_File_S2_CAGE_Dmel_ovary.bed
Supplemental Material - Supp_File_S3_CAGE_Dmel_testis_rep1.bed
Supplemental Material - Supp_File_S4_CAGE_Dmel_testis_rep2.bed
Supplemental Material - Supp_File_S5_CAGE_Dpse_F_carcass.bed
Supplemental Material - Supp_File_S6_CAGE_Dpse_M_carcass.bed
Supplemental Material - Supp_File_S7_CAGE_Dpse_ovary.bed
Supplemental Material - Supp_File_S8_CAGE_Dpse_testes.bed
Supplemental Material - Supplemental_Material.docx
Supplemental Material - Table_S10_intergenic_validation.xls
Supplemental Material - Table_S12_promoter_summary.xls
Supplemental Material - Table_S13_splice_junction_validation.xls
Supplemental Material - Table_S15_splicing_events.xls
Supplemental Material - Table_S16_editing_validation.xls
Supplemental Material - Table_S4_sample_identifiers.xls
Supplemental Material - Table_S5_first_CDS_RPKM.xls
Supplemental Material - Table_S6_CDS_exon_validation.xls
Supplemental Material - Table_S7_UTR_validation.xls
Supplemental Material - Table_S8_ncRNA_validation.xls
Supplemental Material - Table_S9_intron_validation.xls
", "abstract": "Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.", "date": "2014-07", "date_type": "published", "publication": "Genome Research", "volume": "24", "number": "7", "publisher": "Cold Spring Harbor Laboratory Press", "pagerange": "1209-1223", "id_number": "CaltechAUTHORS:20140731-083814156", "issn": "1088-9051", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140731-083814156", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "DK015600-18" }, { "agency": "NIH", "grant_number": "1ROIGM082843" }, { "agency": "NIH", "grant_number": "U01HB004271" } ] }, "doi": "10.1101/gr.159384.113", "pmcid": "PMC4079975", "primary_object": { "basename": "Table_S16_editing_validation.xls", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Table_S16_editing_validation.xls" }, "related_objects": [ { "basename": "Table_S5_first_CDS_RPKM.xls", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Table_S5_first_CDS_RPKM.xls" }, { "basename": "Table_S9_intron_validation.xls", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Table_S9_intron_validation.xls" }, { "basename": "Supp_File_S2_CAGE_Dmel_ovary.bed", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Supp_File_S2_CAGE_Dmel_ovary.bed" }, { "basename": "Supp_File_S6_CAGE_Dpse_M_carcass.bed", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Supp_File_S6_CAGE_Dpse_M_carcass.bed" }, { "basename": "Table_S10_intergenic_validation.xls", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Table_S10_intergenic_validation.xls" }, { "basename": "Supp_File_S5_CAGE_Dpse_F_carcass.bed", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Supp_File_S5_CAGE_Dpse_F_carcass.bed" }, { "basename": "Supp_File_S8_CAGE_Dpse_testes.bed", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Supp_File_S8_CAGE_Dpse_testes.bed" }, { "basename": "Table_S4_sample_identifiers.xls", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Table_S4_sample_identifiers.xls" }, { "basename": "Table_S12_promoter_summary.xls", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Table_S12_promoter_summary.xls" }, { "basename": "Table_S15_splicing_events.xls", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Table_S15_splicing_events.xls" }, { "basename": "Table_S7_UTR_validation.xls", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Table_S7_UTR_validation.xls" }, { "basename": "Table_S8_ncRNA_validation.xls", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Table_S8_ncRNA_validation.xls" }, { "basename": "Genome_Res.-2014-Chen-1209-23.pdf", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Genome_Res.-2014-Chen-1209-23.pdf" }, { "basename": "Supp_File_S3_CAGE_Dmel_testis_rep1.bed", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Supp_File_S3_CAGE_Dmel_testis_rep1.bed" }, { "basename": "Supp_File_S7_CAGE_Dpse_ovary.bed", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Supp_File_S7_CAGE_Dpse_ovary.bed" }, { "basename": "Table_S13_splice_junction_validation.xls", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Table_S13_splice_junction_validation.xls" }, { "basename": "Table_S6_CDS_exon_validation.xls", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Table_S6_CDS_exon_validation.xls" }, { "basename": "Supp_File_S1_CAGE_Dmel_FM_carcass.bed", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Supp_File_S1_CAGE_Dmel_FM_carcass.bed" }, { "basename": "Supp_File_S4_CAGE_Dmel_testis_rep2.bed", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Supp_File_S4_CAGE_Dmel_testis_rep2.bed" }, { "basename": "Supplemental_Material.docx", "url": "https://authors.library.caltech.edu/records/9czqj-n7339/files/Supplemental_Material.docx" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Chen, Zhen-Xia and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/m7xew-y2c97", "eprint_id": 46436, "eprint_status": "archive", "datestamp": "2023-08-20 01:36:19", "lastmod": "2023-10-26 19:44:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jex-A-R", "name": { "family": "Jex", "given": "Aaron R." } }, { "id": "Nejsum-P", "name": { "family": "Nejsum", "given": "Peter" } }, { "id": "Schwarz-E-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Hu-Li", "name": { "family": "Hu", "given": "Li" } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Hall-R-S", "name": { "family": "Hall", "given": "Ross S." } }, { "id": "Korhonen-P-K", "name": { "family": "Korhonen", "given": "Pasi K." } }, { "id": "Liao-Shengguang", "name": { "family": "Liao", "given": "Shengguang" } }, { "id": "Thamsborg-S", "name": { "family": "Thamsborg", "given": "Stig" } }, { "id": "Xia-Jinquan", "name": { "family": "Xia", "given": "Jinquan" } }, { "id": "Xu-Pengwei", "name": { "family": "Xu", "given": "Pengwei" } }, { "id": "Wang-Shaowei", "name": { "family": "Wang", "given": "Shaowei" } }, { "id": "Scheerlinck-J-P-Y", "name": { "family": "Scheerlinck", "given": "Jean-Pierre Y." } }, { "id": "Hofmann-A", "name": { "family": "Hofmann", "given": "Andreas" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Wang-Jun", "name": { "family": "Wang", "given": "Jun" } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "Genome and transcriptome of the porcine whipworm Trichuris suis", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 Macmillan Publishers Limited.\n\nThis work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/.\n\nReceived 15 December 2013; Accepted 22 May 2014; Published online 15 June 2014.\n\nWe are indebted to the staff of the BGI-Shenzhen who assisted this study but whose names are not included in the authorship. We also acknowledge the continued contributions of staff at WormBase. This project was funded by the Australian Research\nCouncil (ARC), the National Health and Medical Research Council (NHMRC) of Australia and BGI-Shenzhen. This research was supported by a Victorian Life Sciences Computation Initiative (VLSCI) grant number VR0007 on its Peak Computing Facility at the University of Melbourne, an initiative of the Victorian Government (A.R.J.\nand R.B.G.). Other support to R.B.G. from the Alexander von Humboldt Foundation, Australian Academy of Science, the Australian-American Fulbright Commission, Melbourne Water Corporation and the IBM Research Collaboratory for Life Sciences \u2013\nMelbourne is gratefully acknowledged. P.N. was supported by Danish Agency for Science, Technology and Innovation. N.D.Y. holds an NHMRC Early Career Research Fellowship. E.M.S. was supported by startup funds from Cornell University. P.W.S. is an investigator with the Howard Hughes Medical Institute (HHMI) and acknowledges support from the US National Institutes of Health (NIH).\n\nAuthor Contributions: P.N. and S.T. provided T. suis, and N.D.Y. purified nucleic acids for sequencing. L.H. and S.W. coordinated sequencing. A.R.J., S.L., P.K.K., R.S.H., J.X. and P.X. undertook the assembly, annotation and analyses of genomic and transcriptomic data. A.R.J., R.S.H., A.H., P.K.K. and E.M.S. planned and performed additional, detailed bioinformatic analyses. A.R.J., P.W.S., J.-P.Y.S. and R.B.G. drafted and edited the manuscript, tables, figures and supplementary information. A.R.J., N.D.Y., J.W. and R.B.G. conceived and planned the project. A.R.J., N.D.Y. and R.B.G. supervised and coordinated the research.\n\nPublished - ng.3012.pdf
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", "abstract": "Trichuris (whipworm) infects 1 billion people worldwide and causes a disease (trichuriasis) that results in major socioeconomic losses in both humans and pigs. Trichuriasis relates to an inflammation of the large intestine manifested in bloody diarrhea, and chronic disease can cause malnourishment and stunting in children. Paradoxically, Trichuris of pigs has shown substantial promise as a treatment for human autoimmune disorders, including inflammatory bowel disease (IBD) and multiple sclerosis. Here we report whole-genome sequencing at ~140-fold coverage of adult male and female T. suis and ~80-Mb draft assemblies. We explore stage-, sex- and tissue-specific transcription of mRNAs and small noncoding RNAs.", "date": "2014-07", "date_type": "published", "publication": "Nature Genetics", "volume": "46", "number": "7", "publisher": "Nature Publishing Group", "pagerange": "701-706", "id_number": "CaltechAUTHORS:20140623-125424513", "issn": "1061-4036", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140623-125424513", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council (ARC)" }, { "agency": "National Health and Medical Research Council (NHMRC) (Australia)" }, { "agency": "BGI-Shenzhen" }, { "agency": "Victorian Life Sciences Computation Initiative (VLSCI)", "grant_number": "VR0007" }, { "agency": "Alexander von Humboldt Foundation" }, { "agency": "Australian Academy of Science" }, { "agency": "Australian-American Fulbright Commission" }, { "agency": "Melbourne Water Corporation" }, { "agency": "IBM Research Collaboratory for Life Sciences-Melbourne" }, { "agency": "Danish Agency for Science, Technology and Innovation" }, { "agency": "NHMRC Early Career Research Fellowship" }, { "agency": "Cornell University" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH" } ] }, "doi": "10.1038/ng.3012", "pmcid": "PMC4105696", "primary_object": { "basename": "Table_18.xlsx", "url": "https://authors.library.caltech.edu/records/m7xew-y2c97/files/Table_18.xlsx" }, "related_objects": [ { "basename": "Table_9.xlsx", "url": "https://authors.library.caltech.edu/records/m7xew-y2c97/files/Table_9.xlsx" }, { "basename": "Table_10.xlsx", "url": "https://authors.library.caltech.edu/records/m7xew-y2c97/files/Table_10.xlsx" }, { "basename": "Table_13.xlsx", "url": "https://authors.library.caltech.edu/records/m7xew-y2c97/files/Table_13.xlsx" }, { "basename": "Table_14.xlsx", "url": "https://authors.library.caltech.edu/records/m7xew-y2c97/files/Table_14.xlsx" }, { "basename": "Table_5.xlsx", "url": "https://authors.library.caltech.edu/records/m7xew-y2c97/files/Table_5.xlsx" }, { "basename": "Table_17.xlsx", "url": "https://authors.library.caltech.edu/records/m7xew-y2c97/files/Table_17.xlsx" }, { "basename": "Table_21.xlsx", "url": "https://authors.library.caltech.edu/records/m7xew-y2c97/files/Table_21.xlsx" }, { "basename": "Table_22.xlsx", "url": "https://authors.library.caltech.edu/records/m7xew-y2c97/files/Table_22.xlsx" }, { "basename": "Table_12.xlsx", "url": "https://authors.library.caltech.edu/records/m7xew-y2c97/files/Table_12.xlsx" }, { "basename": "Table_6.xlsx", "url": "https://authors.library.caltech.edu/records/m7xew-y2c97/files/Table_6.xlsx" }, { "basename": "ng.3012-S1.pdf", "url": "https://authors.library.caltech.edu/records/m7xew-y2c97/files/ng.3012-S1.pdf" }, { "basename": "Table_8.xlsx", "url": "https://authors.library.caltech.edu/records/m7xew-y2c97/files/Table_8.xlsx" }, { "basename": "ng.3012.pdf", "url": "https://authors.library.caltech.edu/records/m7xew-y2c97/files/ng.3012.pdf" }, { "basename": "Table_11.xlsx", "url": "https://authors.library.caltech.edu/records/m7xew-y2c97/files/Table_11.xlsx" }, { "basename": "Table_15.xlsx", "url": "https://authors.library.caltech.edu/records/m7xew-y2c97/files/Table_15.xlsx" }, { "basename": "Table_16.xlsx", "url": "https://authors.library.caltech.edu/records/m7xew-y2c97/files/Table_16.xlsx" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Jex, Aaron R.; Nejsum, Peter; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/2adzc-qdb58", "eprint_id": 49646, "eprint_status": "archive", "datestamp": "2023-08-22 13:06:17", "lastmod": "2023-10-17 21:36:25", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Nagarajan-Niranjan", "name": { "family": "Nagarajan", "given": "Niranjan" } }, { "id": "Lin-Suling-Joyce", "name": { "family": "Lin", "given": "Suling Joyce" } }, { "id": "Korhonen-P-K", "name": { "family": "Korhonen", "given": "Pasi K." } }, { "id": "Jex-A-R", "name": { "family": "Jex", "given": "Aaron R." } }, { "id": "Hall-R-S", "name": { "family": "Hall", "given": "Ross S." } }, { "id": "Safavi-Hemami-H", "name": { "family": "Safavi-Hemami", "given": "Helena" } }, { "id": "Kaewkong-Worasak", "name": { "family": "Kaewkong", "given": "Worasak" } }, { "id": "Bertrand-Denis", "name": { "family": "Bertrand", "given": "Denis" } }, { "id": "Gao-Song", "name": { "family": "Gao", "given": "Song" }, "orcid": "0000-0001-7427-6681" }, { "id": "Seet-Qihui", "name": { "family": "Seet", "given": "Qihui" } }, { "id": "Wongkham-Sopit", "name": { "family": "Wongkham", "given": "Sopit" } }, { "id": "Teh-Bin-Tean", "name": { "family": "Teh", "given": "Bin Tean" }, "orcid": "0000-0003-1743-4158" }, { "id": "Wongkham-Chaisiri", "name": { "family": "Wongkham", "given": "Chaisiri" } }, { "id": "Intapan-Pewpan-Maleewong", "name": { "family": "Intapan", "given": "Pewpan Maleewong" } }, { "id": "Maleewong-Wanchai", "name": { "family": "Maleewong", "given": "Wanchai" } }, { "id": "Yang-Xinhua", "name": { "family": "Yang", "given": "Xinhua" } }, { "id": "Hu-Min", "name": { "family": "Hu", "given": "Min" } }, { "id": "Wang-Zuo", "name": { "family": "Wang", "given": "Zuo" } }, { "id": "Hofmann-Andreas", "name": { "family": "Hofmann", "given": "Andreas" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Tan-Patrick", "name": { "family": "Tan", "given": "Patrick" } }, { "id": "Wang-Jun", "name": { "family": "Wang", "given": "Jun" } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "The Opisthorchis viverrini genome provides insights into life in the bile duct", "ispublished": "pub", "full_text_status": "public", "keywords": "Biological sciences; Evolution; Genetics", "note": "\u00a9 2014 The Authors. This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. \n\nReceived 3 March 2014; Accepted 11 June 2014; Published 9 July 2014.\n\nWe thank the staff of BGI-Shenzhen for their contributions. This project was funded by the Australian Research Council, the National Health and Medical Research Council\n(NHMRC) of Australia and BGI-Shenzhen (R.B.G.). Other support from the Alexander von Humboldt Foundation, Melbourne Water Corporation (R.B.G.) and Genome Institute of Singapore (P.T.) is gratefully acknowledged. This project was also supported by a Victorian Life Sciences Computation Initiative (grant number VR0007) on its Peak\nComputing Facility at the University of Melbourne, an initiative of the Victorian Government. N.D.Y. holds an NHMRC Early Career Research Fellowship. P.W.S. thanks the\nHoward Hughes Medical Institute (HHMI) and the National Institutes of Health (NIH). We would specifically like to acknowledge the research scientists that developed the\nprograms used in this study. Given restrictions on the number of publications that could be cited, we were unable to include all original articles in the methods section. Instead, we have included links to their respective websites. This paper is dedicated to the memory of Eduard Gasser.\n\nPublished - ncomms5378.pdf
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", "abstract": "Opisthorchiasis is a neglected, tropical disease caused by the carcinogenic Asian liver fluke, Opisthorchis viverrini. This hepatobiliary disease is linked to malignant cancer (cholangiocarcinoma, CCA) and affects millions of people in Asia. No vaccine is available, and only one drug (praziquantel) is used against the parasite. Little is known about O. viverrini biology and the diseases that it causes. Here we characterize the draft genome (634.5\u2009Mb) and transcriptomes of O. viverrini, elucidate how this fluke survives in the hostile environment within the bile duct and show that metabolic pathways in the parasite are highly adapted to a lipid-rich diet from bile and/or cholangiocytes. We also provide additional evidence that O. viverrini and other flukes secrete proteins that directly modulate host cell proliferation. Our molecular resources now underpin profound explorations of opisthorchiasis/CCA and the design of new interventions.", "date": "2014-07", "date_type": "published", "publication": "Nature Communications", "volume": "5", "number": "7", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 4378", "id_number": "CaltechAUTHORS:20140912-092833842", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140912-092833842", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council" }, { "agency": "National Health and Medical Research Council (NHMRC)" }, { "agency": "BGI-Shenzhen" }, { "agency": "Alexander von Humboldt Foundation" }, { "agency": "Melbourne Water Corporation" }, { "agency": "Genome Institute of Singapore" }, { "agency": "Victorian Life Sciences Computation Initiative", "grant_number": "VR0007" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH" } ] }, "doi": "10.1038/ncomms5378", "pmcid": "PMC4104445", "primary_object": { "basename": "ncomms5378-s6.xlsx", "url": "https://authors.library.caltech.edu/records/2adzc-qdb58/files/ncomms5378-s6.xlsx" }, "related_objects": [ { "basename": "ncomms5378-s7.xlsx", "url": "https://authors.library.caltech.edu/records/2adzc-qdb58/files/ncomms5378-s7.xlsx" }, { "basename": "ncomms5378.pdf", "url": "https://authors.library.caltech.edu/records/2adzc-qdb58/files/ncomms5378.pdf" }, { "basename": "ncomms5378-s1.pdf", "url": "https://authors.library.caltech.edu/records/2adzc-qdb58/files/ncomms5378-s1.pdf" }, { "basename": "ncomms5378-s2.xlsx", "url": "https://authors.library.caltech.edu/records/2adzc-qdb58/files/ncomms5378-s2.xlsx" }, { "basename": "ncomms5378-s3.xlsx", "url": "https://authors.library.caltech.edu/records/2adzc-qdb58/files/ncomms5378-s3.xlsx" }, { "basename": "ncomms5378-s4.xlsx", "url": "https://authors.library.caltech.edu/records/2adzc-qdb58/files/ncomms5378-s4.xlsx" }, { "basename": "ncomms5378-s5.xlsx", "url": "https://authors.library.caltech.edu/records/2adzc-qdb58/files/ncomms5378-s5.xlsx" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Young, Neil D.; Nagarajan, Niranjan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/kbj3x-q3p86", "eprint_id": 44616, "eprint_status": "archive", "datestamp": "2023-08-22 12:33:07", "lastmod": "2023-10-26 14:49:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mason-Lyndel", "name": { "family": "Mason", "given": "Lyndel" } }, { "id": "Tribolet-L", "name": { "family": "Tribolet", "given": "Leon" } }, { "id": "Simon-Anne", "name": { "family": "Simon", "given": "Anne" } }, { "id": "von-Gnielinksi-N", "name": { "family": "von Gnielinksi", "given": "Natascha" } }, { "id": "Nienaber-L", "name": { "family": "Nienaber", "given": "Lisa" } }, { "id": "Taylor-Paul", "name": { "family": "Taylor", "given": "Paul" } }, { "id": "Willis-Charlene", "name": { "family": "Willis", "given": "Charlene" } }, { "id": "Jones-M-K", "name": { "family": "Jones", "given": "Malcolm K." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } }, { "id": "Loukas-A", "name": { "family": "Loukas", "given": "Alex" } }, { "id": "Hofmann-Andreas", "name": { "family": "Hofmann", "given": "Andreas" } } ] }, "title": "Probing the equatorial groove of the hookworm protein and vaccine candidate antigen, Na-ASP-2", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Activation-associated secreted proteins; Host\u2013parasite interactions; Pathogenesis-related proteins; Protein structure; SCP/TAPS proteins", "note": "\u00a9 2014 Elsevier Ltd.\n\nReceived 19 December 2013; Received in revised form 23 February 2014; Accepted 4 March 2014; Available online 13 March 2014.\n\nThis study was supported by the Australian Research Council (ARC LP100100092 to RBG, AH, AL and PWS). We also gratefully acknowledge funding of our laboratories by the National Health and Medical Research Council (AH, MKJ, AL, RBG). LT is the recipient of an Australian Postgraduate Award. AL is the recipient of a principal research fellowship from NHMRC. Parts of this research were undertaken on the MX1 beamline at the Australian Synchrotron, Victoria, Australia.", "abstract": "Hookworm activation-associated secreted proteins can be structurally classified into at least three different groups. The hallmark feature of Group 1 activation-associated secreted proteins is a prominent equatorial groove, which is inferred to form a ligand binding site. Furthermore, a conserved tandem histidine motif is located in the centre of the groove and believed to provide or support a yet to be determined catalytic activity.\n\nHere, we report three-dimensional crystal structures of Na-ASP-2, an L3-secreted activation-associated secreted protein from the human hookworm Necator americanus, which demonstrate transition metal binding ability of the conserved tandem histidine motif. We further identified moderate phosphohydrolase activity of recombinant Na-ASP-2, which relates to the tandem histidine motif. By panning a random 12-mer peptide phage library, we identified a peptide with high similarity to the human calcium-activated potassium channel SK3, and confirm binding of the synthetic peptide to recombinant Na-ASP-2 by differential scanning fluorimetry. Potential binding modes of the peptide to Na-ASP-2 were studied by molecular dynamics simulations which clearly identify a preferred topology of the Na-ASP-2:SK3 peptide complex.", "date": "2014-05", "date_type": "published", "publication": "International Journal of Biochemistry & Cell Biology", "volume": "50", "publisher": "Elsevier", "pagerange": "146-155", "id_number": "CaltechAUTHORS:20140402-161040827", "issn": "1357-2725", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140402-161040827", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council", "grant_number": "ARC LP100100092" }, { "agency": "National Health and Medical Research Council (NHMRC)" } ] }, "doi": "10.1016/j.biocel.2014.03.003", "resource_type": "article", "pub_year": "2014", "author_list": "Mason, Lyndel; Tribolet, Leon; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/cp2jb-pda61", "eprint_id": 54422, "eprint_status": "archive", "datestamp": "2023-08-20 00:16:17", "lastmod": "2023-10-20 16:26:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Druzinsky-R", "name": { "family": "Druzinsky", "given": "Robert" } }, { "id": "Done-J", "name": { "family": "Done", "given": "James" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul" }, "orcid": "0000-0002-7699-0173" }, { "id": "Mueller-H-M", "name": { "family": "Mueller", "given": "Hans-Michael" } } ] }, "title": "Textpresso for oro-pharyngeal anatomy: a system for searching the full text of anatomy literatures", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2014 Federation of American Societies for Experimental Biology.", "abstract": "Biological databases are a useful resource for parlaying existing data into new experimental hypotheses. Populating such databases with information from the published literature, however, can be labor intensive and thus is aided greatly by text mining tools capable of retrieving key facts from full text. The Textpresso information retrieval system (http://www.textpresso.org) is used by several Model Organism Database (MOD) communities to assist in curation [M\u00fcller HM, Kenny EE, Sternberg PW. 2004. PLoS Biol. Nov;2(11):e309; Van Auken KM, Fey P, Berardini TZ, et al. 2012. Database (Oxford). Nov 17;2012:bas040.] Textpresso searches the full text of literature using keywords and/or categories, groups of semantically related words, to identify sentences within a paper that describe specific aspects of biology. Using the anatomy ontology of oro-pharyngeal structures developed in the FEED project [Druzinsky R, et al., in prep ], we are constructing a Textpresso site to aid in curation of the oro-pharyngeal muscle literature. At this time, we have amassed a database of over 2000 searchable references. We will present a demonstration of Textpresso for Oro-Pharyngeal Anatomy and show how it can be used to construct meaningful queries on the full text of the literature.", "date": "2014-04", "date_type": "published", "publication": "FASEB Journal", "volume": "28", "number": "1", "publisher": "Federation of American Societies for Experimental Biology", "pagerange": "338.3", "id_number": "CaltechAUTHORS:20150205-104258509", "issn": "0892-6638", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150205-104258509", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "resource_type": "article", "pub_year": "2014", "author_list": "Van Auken, Kimberly; Druzinsky, Robert; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/qp7fj-1pn93", "eprint_id": 43743, "eprint_status": "archive", "datestamp": "2023-08-22 11:49:11", "lastmod": "2023-10-25 23:50:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mangiola-S", "name": { "family": "Mangiola", "given": "Stefano" } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Strube-C", "name": { "family": "Strube", "given": "Christina" } }, { "id": "Korhonen-P-K", "name": { "family": "Korhonen", "given": "Pasi K." } }, { "id": "Mitreva-M", "name": { "family": "Mitreva", "given": "Makedonka" } }, { "id": "Scheerlinck-J-P", "name": { "family": "Scheerlinck", "given": "Jean-Pierre" } }, { "id": "Hofmann-A", "name": { "family": "Hofmann", "given": "Andreas" } }, { "id": "Jex-A-R", "name": { "family": "Jex", "given": "Aaron R." } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "Analysis of the transcriptome of adult Dictyocaulus filaria and comparison with Dictyocaulus viviparus, with a focus on molecules involved in host\u2013parasite interactions", "ispublished": "pub", "full_text_status": "public", "keywords": "Lungworms; Dictyocaulus spp.; Transcriptome; Host\u2013parasite interactions", "note": "\u00a9 2014 Australian Society for Parasitology Inc. Published by Elsevier Ltd. \n\nReceived 1 October 2013; Received in revised form 11 December 2013; Accepted 18 December 2013; Available online 31 January 2014. \n\nThis project was funded by the Australian Research Council (ARC) and Australian National Health & Medical Research Council (NHMRC). This project was also supported by a Victorian Life Sciences Computation Initiative (VLSCI) grant number VR0007 on its Peak Computing Facility at the University of Melbourne, an initiative of the Victorian Government, Australia. Other support from the Alexander von Humboldt Foundation, Germany, and the Melbourne Water Corporation, Australia, is gratefully acknowledged (R.B.G), as is funding from and the Howard Hughes Medical Institute (HHMI), USA and National Institutes of Health (NIH), USA (P.W.S.). M.M. also received funds from NIH. N.D.Y is an NHMRC Early Career Research (ECR) Fellow. We also acknowledge the continued contributions of staff at WormBase (www.wormbase.org).\n\nAccepted Version - nihms569958.pdf
", "abstract": "Parasitic nematodes cause diseases of major economic importance in animals. Key representatives are species of Dictyocaulus (=lungworms), which cause bronchitis (=dictyocaulosis, commonly known as \"husk\") and have a major adverse impact on the health of livestock. In spite of their economic importance, very little is known about the immunomolecular biology of these parasites. Here, we conducted a comprehensive investigation of the adult transcriptome of Dictyocaulus filaria of small ruminants and compared it with that of Dictyocaulus viviparus of bovids. We then identified a subset of highly transcribed molecules inferred to be linked to host\u2013parasite interactions, including cathepsin B peptidases, fatty-acid and/or retinol-binding proteins, \u03b2-galactoside-binding galectins, secreted protein 6 precursors, macrophage migration inhibitory factors, glutathione peroxidases, a transthyretin-like protein and a type 2-like cystatin. We then studied homologues of D. filaria type 2-like cystatin encoded in D. viviparus and 24 other nematodes representing seven distinct taxonomic orders, with a particular focus on their proposed role in immunomodulation and/or metabolism. Taken together, the present study provides new insights into nematode\u2013host interactions. The findings lay the foundation for future experimental studies and could have implications for designing new interventions against lungworms and other parasitic nematodes. The future characterisation of the genomes of Dictyocaulus spp. should underpin these endeavours.", "date": "2014-03", "date_type": "published", "publication": "International Journal for Parasitology", "volume": "44", "number": "3-4", "publisher": "Elsevier", "pagerange": "251-261", "id_number": "CaltechAUTHORS:20140210-115459871", "issn": "0020-7519", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140210-115459871", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council" }, { "agency": "Australian National Health and Medical Research Council (NHMRC)" }, { "agency": "Victorian Life Sciences Computation Initiative (VLSCI)", "grant_number": "VR0007" }, { "agency": "Alexander von Humboldt Foundation" }, { "agency": "Melbourne Water Corporation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH" } ] }, "doi": "10.1016/j.ijpara.2013.12.003", "pmcid": "PMC4040346", "primary_object": { "basename": "nihms569958.pdf", "url": "https://authors.library.caltech.edu/records/qp7fj-1pn93/files/nihms569958.pdf" }, "resource_type": "article", "pub_year": "2014", "author_list": "Mangiola, Stefano; Young, Neil D.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/jdfw8-dtj05", "eprint_id": 43523, "eprint_status": "archive", "datestamp": "2023-08-19 23:35:26", "lastmod": "2023-10-25 23:37:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tang-Yat-T", "name": { "family": "Tang", "given": "Yat T." } }, { "id": "Gao-Xin", "name": { "family": "Gao", "given": "Xin" } }, { "id": "Rosa-B-A", "name": { "family": "Rosa", "given": "Bruce A." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Genome of the human hookworm Necator americanus", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 Nature Publishing Group, a division of Macmillan Publishers Limited. This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/.\n\nReceived 10 June 2013; accepted 18 December 2013; published online 19 January 2014. \n\nWe thank the faculty and staff of the Genome Institute at Washington University and the Protein Microarray Laboratory at the University of California\u2013Irvine (U54AI065359) who contributed to this study. The genome sequencing and annotation work was funded by US National Institutes of Health (NIH)\u2013National Human Genome Research Institute grant U54HG003079 to R.K.W. Comparative genome analysis was funded by grants NIH\u2013National Institute of Allergy and Infectious Diseases AI081803 and NIH\u2013National Institute of General Medical Sciences GM097435 to M.M. Funds from the Australian Research Council and Australia's National Health and Medical Research Council to R.B.G. are gratefully acknowledged. P.W.S. is an investigator with the Howard Hughes Medical Institute. We thank the faculty and staff of The Genome Institute at Washington University who contributed to this study. \n\nThese authors contributed equally to this work: Yat T Tang, Xin Gao & Bruce A Rosa \n\nAuthor Contributions: Y.T.T., X.G. and B.A.R. contributed equally to this work. M.M., R.B.G., P.W.S., R.K.W. and S.R. conceived and planned the project. M.M. led the project, analysis and manuscript preparation. B.Z., P.J.H., J.M.H., P.L.F., J.B. and E.M.R. provided material. K.H.-P., X.Z., V.B.-P., P.M., W.C.W., J. Martin and S.A. produced sequence data and constructed, annotated and submitted the assembly. M.M., Y.T.T., X.G., B.A.R., R.T., Q.W., S.A., J. Martin, E.H., A.L., S.T.G., P.L.F., J. Mulvenna, J.S. and A.D. performed genome-based comparative studies, differential transcription, host-parasite interaction analysis, and proteomics and protein-array analysis. M.M., R.B.G., A.L. and J.M.H. drafted, edited and wrote the manuscript. \n\nThe authors declare no competing financial interests.\n\nPublished - Tang_2014.pdf
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Supplemental Material - ng.2875-S1.pdf
", "abstract": "The hookworm Necator americanus is the predominant soil-transmitted human parasite. Adult worms feed on blood in the small intestine, causing iron-deficiency anemia, malnutrition, growth and development stunting in children, and severe morbidity and mortality during pregnancy in women. We report sequencing and assembly of the N. americanus genome (244 Mb, 1 19,151 1 genes). Characterization of this first hookworm genome sequence identified genes orchestrating the hookworm's invasion of the human host, genes involved in blood feeding and development, and genes encoding proteins that represent new potential drug targets against hookworms. N. americanus has undergone a considerable and unique expansion of immunomodulator proteins, some of which we highlight as potential treatments against inflammatory diseases. We also used a protein microarray to demonstrate a postgenomic application of the hookworm genome sequence. This genome provides an invaluable resource to boost ongoing efforts toward fundamental and applied postgenomic research, including the development of new methods to control hookworm and human immunological diseases.", "date": "2014-03", "date_type": "published", "publication": "Nature Genetics", "volume": "46", "number": "3", "publisher": "Nature Publishing Group", "pagerange": "261-269", "id_number": "CaltechAUTHORS:20140127-101549521", "issn": "1061-4036", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140127-101549521", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U54HG003079" }, { "agency": "NIH", "grant_number": "AI081803" }, { "agency": "NIH", "grant_number": "GM097435" }, { "agency": "Australian Research Council" }, { "agency": "National Health and Medical Research Council (NHMRC)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1038/ng.2875", "pmcid": "PMC3950333", "primary_object": { "basename": "Table14.xlsx", "url": "https://authors.library.caltech.edu/records/jdfw8-dtj05/files/Table14.xlsx" }, "related_objects": [ { "basename": "Table15.xlsx", "url": "https://authors.library.caltech.edu/records/jdfw8-dtj05/files/Table15.xlsx" }, { "basename": "Table5.xlsx", "url": "https://authors.library.caltech.edu/records/jdfw8-dtj05/files/Table5.xlsx" }, { "basename": "Table12.xlsx", "url": "https://authors.library.caltech.edu/records/jdfw8-dtj05/files/Table12.xlsx" }, { "basename": "Table3.xlsx", "url": "https://authors.library.caltech.edu/records/jdfw8-dtj05/files/Table3.xlsx" }, { "basename": "Table4.xlsx", "url": "https://authors.library.caltech.edu/records/jdfw8-dtj05/files/Table4.xlsx" }, { "basename": "Table6.xlsx", "url": "https://authors.library.caltech.edu/records/jdfw8-dtj05/files/Table6.xlsx" }, { "basename": "Table8.xlsx", "url": "https://authors.library.caltech.edu/records/jdfw8-dtj05/files/Table8.xlsx" }, { "basename": "Table13.xlsx", "url": "https://authors.library.caltech.edu/records/jdfw8-dtj05/files/Table13.xlsx" }, { "basename": "Table9.xlsx", "url": "https://authors.library.caltech.edu/records/jdfw8-dtj05/files/Table9.xlsx" }, { "basename": "Table10.xlsx", "url": "https://authors.library.caltech.edu/records/jdfw8-dtj05/files/Table10.xlsx" }, { "basename": "Table7.xlsx", "url": "https://authors.library.caltech.edu/records/jdfw8-dtj05/files/Table7.xlsx" }, { "basename": "Tang_2014.pdf", "url": "https://authors.library.caltech.edu/records/jdfw8-dtj05/files/Tang_2014.pdf" }, { "basename": "ng.2875-S1.pdf", "url": "https://authors.library.caltech.edu/records/jdfw8-dtj05/files/ng.2875-S1.pdf" }, { "basename": "Table11.xlsx", "url": "https://authors.library.caltech.edu/records/jdfw8-dtj05/files/Table11.xlsx" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Tang, Yat T.; Gao, Xin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/sybzw-cvw76", "eprint_id": 44218, "eprint_status": "archive", "datestamp": "2023-08-22 11:42:23", "lastmod": "2023-10-26 00:18:04", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sapir-A", "name": { "family": "Sapir", "given": "Amir" }, "orcid": "0000-0001-9888-1800" }, { "id": "Dillman-A-R", "name": { "family": "Dillman", "given": "Adler R." }, "orcid": "0000-0001-7171-4332" }, { "id": "Connon-S-A", "name": { "family": "Connon", "given": "Stephanie A." } }, { "id": "Grupe-B-M", "name": { "family": "Grupe", "given": "Benjamin M." }, "orcid": "0000-0002-5421-7278" }, { "id": "Ingels-J", "name": { "family": "Ingels", "given": "Jeroen" }, "orcid": "0000-0001-8342-2222" }, { "id": "Mundo-Ocampo-M", "name": { "family": "Mundo-Ocampo", "given": "Manuel" } }, { "id": "Levin-L-A", "name": { "family": "Levin", "given": "Lisa A." }, "orcid": "0000-0002-2858-8622" }, { "id": "Baldwin-J-G", "name": { "family": "Baldwin", "given": "James G." }, "orcid": "0000-0001-6468-0285" }, { "id": "Orphan-V-J", "name": { "family": "Orphan", "given": "Victoria J." }, "orcid": "0000-0002-5374-6178" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Microsporidia-nematode associations in methane seeps reveal basal fungal parasitism in the deep sea", "ispublished": "pub", "full_text_status": "public", "keywords": "deep-sea methane seeps, nematodes hosts, deep-sea microsporidia parasitism, muscle decomposition, basal fungi in the deep sea", "note": "\u00a9 2014 Sapir, Dillman, Connon, Grupe, Ingels, Mundo-Ocampo, Levin, Baldwin, Orphan and Sternberg. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. \n\nReceived: 29 November 2013; Paper pending published: 14 December 2013; Accepted: 21 January 2014; Published online: 10 February 2014.\n\nWe thank captain, crew, Alvin and Jason II pilots, and cruise participants of Atlantis legs 15-68 and 18-10 for assistance with sample collection. We thank Alasdair McDowall for excellent TEM assistance, Nathalie De Hauwere and the Flanders Marine Institute for drawing the HR map, Stephen Meisenhelter for worm picking, Emily Troemel for sharing reagents, John Curington for Latin grammar advice, Katja Guilini for sharing samples, slides, published data about HR nematodes, James Becnel for comments on the manuscript, and Greg Rouse for E4 rock photo. This work was supported by the Howard Hughes Medical Institute, with which PWS is an investigator, sample collection was supported by NSF OCE 0826254 to LAL and NSF\nOCE-0825791 to VJO, and an NIH USPHS Training Grant (T32GM07616) to A.R.D. JI is supported by a Marie Curie Intra-European Fellowship within the 7th European Community\nFramework Programme (Grant Agreement FP7-PEOPLE-2011-IEF No 300879).\nRunning title: Microsporidia parasitism in deep-sea methane seeps\n\nPublished - fmicb-05-00043.pdf
Supplemental Material - Data_Sheet_1.DOCX
Supplemental Material - Movie_1.AVI
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Supplemental Material - Presentation_1.PDF
", "abstract": "The deep sea is Earth's largest habitat but little is known about the nature of deep-sea parasitism. In contrast to a few characterized cases of bacterial and protistan parasites, the existence and biological significance of deep-sea parasitic fungi is yet to be understood. Here we report the discovery of a fungus-related parasitic microsporidium, Nematocenator marisprofundi n. gen. n. sp. that infects benthic nematodes at methane seeps on the Pacific Ocean floor. This infection is species-specific and has been temporally and spatially stable over 2 years of sampling, indicating an ecologically consistent host-parasite interaction. A high distribution of spores in the reproductive tracts of infected males and females and their absence from host nematodes' intestines suggests a sexual transmission strategy in contrast to the fecal-oral transmission of most microsporidia. N. marisprofundi targets the host's body wall muscles causing cell lysis, and in severe infection even muscle filament degradation. Phylogenetic analyses placed N. marisprofundi in a novel and basal clade not closely related to any described microsporidia clade, suggesting either that microsporidia-nematode parasitism occurred early in microsporidia evolution or that host specialization occurred late in an ancient deep-sea microsporidian lineage. Our findings reveal that methane seeps support complex ecosystems involving interkingdom interactions between bacteria, nematodes, and parasitic fungi and that microsporidia parasitism exists also in the deep-sea biosphere.", "date": "2014-02-10", "date_type": "published", "publication": "Frontiers in Microbiology", "volume": "5", "publisher": "Frontiers Research Foundation", "pagerange": "Art. No. 43", "id_number": "CaltechAUTHORS:20140310-102130554", "issn": "1664-302X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140310-102130554", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NSF", "grant_number": "OCE 0826254" }, { "agency": "NSF", "grant_number": "OCE-0825791" }, { "agency": "NIH", "grant_number": "T32GM07616" }, { "agency": "Marie Curie Fellowship", "grant_number": "300879" } ] }, "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.3389/fmicb.2014.00043", "pmcid": "PMC3918590", "primary_object": { "basename": "Data_Sheet_1.DOCX", "url": "https://authors.library.caltech.edu/records/sybzw-cvw76/files/Data_Sheet_1.DOCX" }, "related_objects": [ { "basename": "Movie_1.AVI", "url": "https://authors.library.caltech.edu/records/sybzw-cvw76/files/Movie_1.AVI" }, { "basename": "Movie_2.AVI", "url": "https://authors.library.caltech.edu/records/sybzw-cvw76/files/Movie_2.AVI" }, { "basename": "Presentation_1.PDF", "url": "https://authors.library.caltech.edu/records/sybzw-cvw76/files/Presentation_1.PDF" }, { "basename": "fmicb-05-00043.pdf", "url": "https://authors.library.caltech.edu/records/sybzw-cvw76/files/fmicb-05-00043.pdf" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Sapir, Amir; Dillman, Adler R.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/00qkp-ey978", "eprint_id": 47292, "eprint_status": "archive", "datestamp": "2023-08-22 11:39:20", "lastmod": "2023-10-26 20:28:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dillman-A-R", "name": { "family": "Dillman", "given": "Adler R." }, "orcid": "0000-0001-7171-4332" }, { "id": "Cronin-C-J", "name": { "family": "Cronin", "given": "Christopher J." } }, { "id": "Tang-Joseph", "name": { "family": "Tang", "given": "Joseph" } }, { "id": "Gray-D-A", "name": { "family": "Gray", "given": "David A." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "A Modified Mole Cricket Lure and Description of Scapteriscus borellii (Orthoptera: Gryllotalpidae) Range Expansion and Calling Song in California", "ispublished": "pub", "full_text_status": "public", "keywords": "Scapteriscus borellii; mole cricket; cricket trap; calling song", "note": "\u00a9 2014 Entomological Society of America.\n\nReceived 17 May 2013; accepted 13 December 2013.\nPublication date: February 1, 2014.\n\nWe thank John Rodriguez and the Rio Hondo Golf Club\nfor the cooperation and help in our sampling efforts; John\nDeModena for fruitful discussions, advice, and critical reading\nof the manuscript; Benjamin Cronin for trap design discussions\nand recommendations; and J. Howard Frank for\nmany suggestions, discussion, critical reading of the manuscript,\nand sharing his mole cricket expertise. Wet hank Brian\nAnderson, Michael E. Castillo, and Esther Thompson for help\nwith mole cricket collection. We also appreciate the time and\nsuggestions of anonymous reviewers. This work was supported\nby a National Institutes of Health (NIH) United States\nPublic Health Service Training Grant (5T32GM07616) to\nA.R.D. and by the Howard Hughes Medical Institute (with\nwhich P.W.S. is an investigator).\n\nAccepted Version - nihms648075.pdf
", "abstract": "Invasive mole cricket species in the genus Scapteriscus have become significant agricultural pests and are continuing to expand their range in North America. Though largely subterranean, adults of some species, such as Scapteriscus borellii Giglio-Tos 1894, are capable of long dispersive flights and phonotaxis to male calling songs to find suitable habitats and mates. Mole crickets in the genus Scapteriscus are known to be attracted to and can be caught by audio lure traps that broadcast synthesized or recorded calling songs. We report improvements in the design and production of electronic controllers for the automation of semipermanent mole cricket trap lures as well as highly portable audio trap collection designs. Using these improved audio lure traps, we collected the first reported individuals of the pest mole cricket S. borellii in California. We describe several characteristic features of the calling song of the California population including that the pulse rate is a function of soil temperature, similar to Florida populations of S. borellii. Further, we show that other calling song characteristics (carrier frequency, intensity, and pulse rate) are significantly different between the populations.", "date": "2014-02", "date_type": "published", "publication": "Environmental Entomology", "volume": "43", "number": "1", "publisher": "Entomological Society of America", "pagerange": "146-156", "id_number": "CaltechAUTHORS:20140717-110304913", "issn": "0046-225X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140717-110304913", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH/NRSA", "grant_number": "5T32GM07616" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1603/EN13152", "pmcid": "PMC4289669", "primary_object": { "basename": "nihms648075.pdf", "url": "https://authors.library.caltech.edu/records/00qkp-ey978/files/nihms648075.pdf" }, "resource_type": "article", "pub_year": "2014", "author_list": "Dillman, Adler R.; Cronin, Christopher J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/py410-sb611", "eprint_id": 43481, "eprint_status": "archive", "datestamp": "2023-08-19 23:09:01", "lastmod": "2023-10-25 23:35:03", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cho-Julie-Y", "name": { "family": "Cho", "given": "Julie Y." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Multilevel Modulation of a Sensory Motor Circuit during C. elegans Sleep and Arousal", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 Elsevier Inc.\n\nReceived: May 25, 2013; Revised: September 26, 2013;\nAccepted: November 15, 2013; Published: January 16, 2014.\n\nWe thank William Schafer (University of Cambridge), Alexander Gottschalk\n(Johann Wolfgang Goethe University), Elissa Hallem (University of California,\nLos Angeles), and the Caenorhabditis Genetics Center (University of\nMinnesota) for worm strains and Karl Deisseroth (Stanford University) for channelrhodopsin\nconstructs. We also thank David Anderson, David Prober, Alon\nZaslaver, Trevor Fowler, and Lauren Lebon for their input and Meenakshi\nDoma, Yen-ping Hsueh, Mihoko Kato, Hillel Schwartz, and members of our\nlab for editorial comments. J.Y.C. was supported by National Institutes of\nHealth USPHS training grant GM07616. This work was supported by the\nHoward Hughes Medical Institute, with which P.W.S. is an investigator, and\nby NIH grant DA018341 to P.W.S.\n\nAccepted Version - nihms552435.pdf
", "abstract": "Sleep is characterized by behavioral quiescence, homeostasis, increased arousal threshold, and rapid reversibility. Understanding how these properties are encoded by a neuronal circuit has been difficult, and no single molecular or neuronal pathway has been shown to be responsible for the regulation of sleep. Taking advantage of the well-mapped neuronal connections of Caenorhabditis elegans and the sleep-like states in this animal, we demonstrate the changed properties of both sensory neurons and downstream interneurons that mediate sleep and arousal. The ASH sensory neuron displays reduced sensitivity to stimuli in the sleep-like state, and the activity of the corresponding interneurons in ASH's motor circuit becomes asynchronous. Restoration of interneuron synchrony is sufficient for arousal. The multilevel circuit depression revealed provides an elegant strategy to promote a robust decrease in arousal while allowing for rapid reversibility of the sleep state.", "date": "2014-01-16", "date_type": "published", "publication": "Cell", "volume": "156", "number": "1-2", "publisher": "Elsevier", "pagerange": "249-260", "id_number": "CaltechAUTHORS:20140123-085452909", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140123-085452909", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH USPHS Training Grant", "grant_number": "GM07616" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "DA018341" } ] }, "doi": "10.1016/j.cell.2013.11.036", "pmcid": "PMC3962823", "primary_object": { "basename": "nihms552435.pdf", "url": "https://authors.library.caltech.edu/records/py410-sb611/files/nihms552435.pdf" }, "resource_type": "article", "pub_year": "2014", "author_list": "Cho, Julie Y. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/5bvvw-w4486", "eprint_id": 42405, "eprint_status": "archive", "datestamp": "2023-08-19 22:59:24", "lastmod": "2023-10-25 15:54:26", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Harris-T-W", "name": { "family": "Harris", "given": "Todd W." }, "orcid": "0000-0003-3406-163X" }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "Chen-Wen-J", "name": { "family": "Chen", "given": "Wen J." } }, { "id": "Done-J", "name": { "family": "Done", "given": "James" } }, { "id": "Grove-C-A", "name": { "family": "Grove", "given": "Christian" }, "orcid": "0000-0001-9076-6015" }, { "id": "Kishore-R", "name": { "family": "Kishore", "given": "Ranjana" } }, { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "Raymond" }, "orcid": "0000-0002-8151-7479" }, { "id": "Li-Yuling", "name": { "family": "Li", "given": "Yuling" } }, { "id": "M\u00fcller-H-M", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } }, { "id": "Nakamura-Cecilia", "name": { "family": "Nakamura", "given": "Cecilia" }, "orcid": "0000-0002-4689-7314" }, { "id": "Raciti-D", "name": { "family": "Raciti", "given": "Daniela" } }, { "id": "Schindelman-G", "name": { "family": "Schindelman", "given": "Gary" } }, { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Wang-Daniel", "name": { "family": "Wang", "given": "Daniel" } }, { "id": "Wang-Xiaodong", "name": { "family": "Wang", "given": "Xiaodong" } }, { "id": "Yook-Karen-J", "name": { "family": "Yook", "given": "Karen" }, "orcid": "0000-0002-4457-6787" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "WormBase 2014: new views of curated biology", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 The Author(s). Published by Oxford University Press. \nThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which\npermits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.\n\nReceived October 10, 2013; Accepted October 12, 2013. \nFirst published online: November 4, 2013.\n\nThe US National Human Genome Research Institute\n[U41-HG002223] to WormBase and British Medical\nResearch Council [G070119] to WormBase; P.W.S. is an\ninvestigator with the Howard Hughes Medical Institute.\nFunding for open access charge: US National Human\nGenome Research Institute [U41-HG002223].\nConflict of interest statement. None declared.\n\nPublished - Harris_2013.pdf
", "abstract": "WormBase (http://www.wormbase.org/) is a highly curated resource dedicated to supporting research using the model organism Caenorhabditis elegans. With an electronic history predating the World Wide Web, WormBase contains information ranging from the sequence and phenotype of individual alleles to genome-wide studies generated using next-generation sequencing technologies. In recent years, we have expanded the contents to include data on additional nematodes of agricultural and medical significance, bringing the knowledge of C. elegans to bear on these systems and providing support for underserved research communities. Manual curation of the primary literature remains a central focus of the WormBase project, providing users with reliable, up-to-date and highly cross-linked information. In this update, we describe efforts to organize the original atomized and highly contextualized curated data into integrated syntheses of discrete biological topics. Next, we discuss our experiences coping with the vast increase in available genome sequences made possible through next-generation sequencing platforms. Finally, we describe some of the features and tools of the new WormBase Web site that help users better find and explore data of interest.", "date": "2014-01-01", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "42", "publisher": "Oxford University Press", "pagerange": "D789-D793", "id_number": "CaltechAUTHORS:20131112-152912465", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131112-152912465", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U41-HG002223" }, { "agency": "Medical Research Council (UK)", "grant_number": "G070119" } ] }, "doi": "10.1093/nar/gkt1063", "pmcid": "PMC3965043", "primary_object": { "basename": "Harris_2013.pdf", "url": "https://authors.library.caltech.edu/records/5bvvw-w4486/files/Harris_2013.pdf" }, "resource_type": "article", "pub_year": "2014", "author_list": "Harris, Todd W.; Chan, Juancarlos; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/eydq4-rj487", "eprint_id": 57201, "eprint_status": "archive", "datestamp": "2023-08-19 22:46:32", "lastmod": "2023-10-23 17:09:14", "type": "conference_item", "metadata_visibility": "show", "creators": { "items": [ { "id": "Vetrone-S-A", "name": { "family": "Vetrone", "given": "S. A." }, "orcid": "0000-0002-5521-0959" }, { "id": "Kato-Mihoko", "name": { "family": "Kato", "given": "M." }, "orcid": "0000-0003-3827-8879" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "P." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Metastasis Upregulated Genes Have Distinct Function in C. elegans Cell Migrations", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2014 American Society for Cell Biology. POSTER PRESENTATIONS- Sunday, December 7.\n\nPublished - Vetrone_2014pP258.pdf
", "abstract": "Cell migration is vital for normal animal development but also contributes to the invasive spreading of\nearly stage metastatic cancer. From two published databases, we complied 107 genes unregulated in\neither breast cancer or melanoma metastases and investigated their requirement in two Caenorhabditis\nelegans cell migrations: the male linker cell (LC) and hermaphrodite distal tip cells (DTC) which have\nsimilar functions as gonadal leader cells that undergo a complex migration while pulling non-motile\nfollowers. We performed an RNAi screen to identify genes implicated in normal LC and DTC migrations.\nThirty-two genes from the metastasis list were required for the cell migration of which 13 genes\neffected the migration of both LC and DTC, 18 genes effected only LC migration, and 4 genes only DTC\nmigration. The genes used by both cell types corresponded to genes involved in cell cycle activity,\nadhesion, cytoskeleton organization, protein degradation activity, spliceosome activity, ubiquitin-like\nmodification and function, and peptidase inhibition. The genes used by only the LC corresponded to\ngenes involved in adhesion, cytoskeletal organization, methyltransferase activity, metalloproteinase\nactivity, and signaling. Those genes used by only DTC corresponded to genes involved in signaling,\npeptidase inhibition, and utrophin activity. The significant differences among the developmental cell\nmigrations and the overlap in genes shared between the two metastases underscores the value of\ncharacterizing diverse genes and considering cell type in developing treatments.", "date": "2014", "date_type": "published", "publisher": "Caltech Library", "id_number": "CaltechAUTHORS:20150504-132426990", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150504-132426990", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Lippincott-Schwartz-J", "name": { "family": "Lippincott-Schwartz", "given": "Jennifer" } }, { "id": "Marshall-W", "name": { "family": "Marshall", "given": "Wallace" } }, { "id": "Marks-M", "name": { "family": "Marks", "given": "Michael" } } ] }, "primary_object": { "basename": "Vetrone_2014pP258.pdf", "url": "https://authors.library.caltech.edu/records/eydq4-rj487/files/Vetrone_2014pP258.pdf" }, "resource_type": "conference_item", "pub_year": "2014", "author_list": "Vetrone, S. A.; Kato, M.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/hpe1r-7yn34", "eprint_id": 52082, "eprint_status": "archive", "datestamp": "2023-08-22 11:12:09", "lastmod": "2024-01-13 16:12:35", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schwartz-H-T", "name": { "family": "Schwartz", "given": "Hillel T." }, "orcid": "0000-0002-3448-8652" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Transgene-Free Genome Editing by Germline Injection of CRISPR/Cas RNA", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "Caenorhabditis elegans; Nematode; CRISPR; Cas9; Engineered nuclease; Gene targeting; Germline injection; RNA injection; Transgene-free", "note": "\u00a9 2014 Elsevier Inc.", "abstract": "Genome modification by CRISPR/Cas offers its users the ability to target endogenous sites in the genome for cleavage and for engineering precise genomic changes using template-directed repair, all with unprecedented ease and flexibility of targeting. As such, CRISPR/Cas is just part of a set of recently developed and rapidly improving tools that offer great potential for researchers to functionally access the genomes of organisms that have not previously been extensively used in a laboratory setting. We describe in detail protocols for using CRISPR/Cas to target genes of experimental organisms, in a manner that does not require transformation to obtain transgenic lines and that should be readily applicable to a wide range of previously little-studied species.", "date": "2014", "date_type": "published", "publisher": "Elsevier", "pagerange": "441-457", "id_number": "CaltechAUTHORS:20141124-081534463", "isbn": "9780128011850", "book_title": "The Use of CRISPR/Cas9, ZFNs, and TALENs in Generating Site-Specific Genome Alterations", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141124-081534463", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Doudna-J-A", "name": { "family": "Doudna", "given": "Jennifer A." } }, { "id": "Sontheimer-E-J", "name": { "family": "Sontheimer", "given": "Erik J." } } ] }, "doi": "10.1016/B978-0-12-801185-0.00021-0", "resource_type": "book_section", "pub_year": "2014", "author_list": "Schwartz, Hillel T. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/6qf9w-wq378", "eprint_id": 44079, "eprint_status": "archive", "datestamp": "2023-08-19 22:24:34", "lastmod": "2023-10-26 00:09:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Grewal-P-S", "name": { "family": "Grewal", "given": "Parwinder S." } }, { "id": "Bai-X", "name": { "family": "Bai", "given": "Xiaodong" } }, { "id": "Adams-B-J", "name": { "family": "Adams", "given": "Byron J." } }, { "id": "Ciche-T-A", "name": { "family": "Ciche", "given": "Todd A." } }, { "id": "Clifton-S", "name": { "family": "Clifton", "given": "Sandra" } }, { "id": "Gaugler-R", "name": { "family": "Gaugler", "given": "Randy" } }, { "id": "Kim-K-S", "name": { "family": "Kim", "given": "Kwi-suk" } }, { "id": "Spieth-J", "name": { "family": "Spieth", "given": "John" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Wilson-R-K", "name": { "family": "Wilson", "given": "Richard K." } } ] }, "title": "First Complete Genome Sequence of an Entomopathogenic Nematode Goes Public", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2013 The Society of Nematologists.", "abstract": "Entomopathogenic nematodes (Steinernematidae and Heterorhabditidae) have a fascinating biology as they form mutualistic\nsymbioses with bacteria (Enterobacteriacae) and together they serve as important biological control agents of insect\npests. Here we reveal the first complete genome sequence of an athogenic nematode species that will serve as a model for\nfuture genetic studies in this group and in the phylum Nematoda.", "date": "2013-12", "date_type": "published", "publication": "Journal of Nematology", "volume": "45", "number": "4", "publisher": "Society of Nematologists", "pagerange": "291-291", "id_number": "CaltechAUTHORS:20140303-101418706", "issn": "0022-300X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140303-101418706", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "resource_type": "article", "pub_year": "2013", "author_list": "Grewal, Parwinder S.; Bai, Xiaodong; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/fxsce-6v668", "eprint_id": 43825, "eprint_status": "archive", "datestamp": "2023-08-22 11:01:05", "lastmod": "2023-10-25 23:55:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mangiola-S", "name": { "family": "Mangiola", "given": "Stefano" } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Korhonen-P-K", "name": { "family": "Korhonen", "given": "Pasi" } }, { "id": "Mondal-A", "name": { "family": "Mondal", "given": "Alinda" } }, { "id": "Scheerlinck-J-P", "name": { "family": "Scheerlinck", "given": "Jean-Pierre" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Cantacessi-C", "name": { "family": "Cantacessi", "given": "Cinzia" } }, { "id": "Hall-R-S", "name": { "family": "Hall", "given": "Ross S." } }, { "id": "Jex-A-R", "name": { "family": "Jex", "given": "Aaron R." } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "Getting the most out of parasitic helminth transcriptomes using HelmDB: Implications for biology and biotechnology", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Parasitic helminths (nematode and trematode); Systems biology; Transcriptomics; Annotation-improvement; Genomics; Bioinformatics", "note": "\u00a9 2012 Elsevier Inc. Received 11 October 2012. Received in revised form 8 December 2012. Accepted 13 December 2012. Available online 21 December 2012. This research was supported largely through grants from the\nAustralian Research Council (ARC) and the National Health and\nMedical Research Council (NHMRC) (RBG). Other support from the\nAustralian Academy of Science, the Australian\u2013American Fulbright\nCommission, Melbourne Water Corporation and the Victorian Life\nSciences Computation Initiative (VLSCI) is gratefully acknowledged.\nSM is the grateful recipient of scholarships from the University of\nMelbourne and a special scholarship from VLSCI. NDY holds an Early\nCareer Research Fellowship (ECRF) from (NHMRC). PWS is an investigator\nwith the Howard Hughes Medical Institute (HHMI).", "abstract": "Compounded by a massive global food shortage, many parasitic diseases have a devastating, long-term impact on animal and human health and welfare worldwide. Parasitic helminths (worms) affect the health of billions of animals. Unlocking the systems biology of these neglected pathogens will underpin the design of new and improved interventions against them. Currently, the functional annotation of genomic and transcriptomic sequence data for socio-economically important parasitic worms relies almost exclusively on comparative bioinformatic analyses using model organism- and other databases. However, many genes and gene products of parasitic helminths (often > 50%) cannot be annotated using this approach, because they are specific to parasites and/or do not have identifiable homologs in other organisms for which sequence data are available. This inability to fully annotate transcriptomes and predicted proteomes is a major challenge and constrains our understanding of the biology of parasites, interactions with their hosts and of parasitism and the pathogenesis of disease on a molecular level. In the present article, we compiled transcriptomic data sets of key, socioeconomically important parasitic helminths, and constructed and validated a curated database, called HelmDB (www.helmdb.org). We demonstrate how this database can be used effectively for the improvement of functional annotation by employing data integration and clustering. Importantly, HelmDB provides a practical and user-friendly toolkit for sequence browsing and comparative analyses among divergent helminth groups (including nematodes and trematodes), and should be readily adaptable and applicable to a wide range of other organisms. This web-based, integrative database should assist 'systems biology' studies of parasitic helminths, and the discovery and prioritization of novel drug and vaccine targets. This focus provides a pathway toward developing new and improved approaches for the treatment and control of parasitic diseases, with the potential for important biotechnological outcomes.", "date": "2013-12", "date_type": "published", "publication": "Biotechnology Advances", "volume": "31", "number": "8", "publisher": "Elsevier", "pagerange": "1109-1119", "id_number": "CaltechAUTHORS:20140214-073210680", "issn": "0734-9750", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140214-073210680", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council (ARC)" }, { "agency": "National Health and Medical Research Council (NHMRC)" }, { "agency": "Australian Academy of Science" }, { "agency": "Australian\u2013American Fulbright Commission" }, { "agency": "Melbourne Water Corporation" }, { "agency": "Victorian Life Sciences Computation Initiative (VLSCI)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "University of Melbourne" } ] }, "doi": "10.1016/j.biotechadv.2012.12.004", "resource_type": "article", "pub_year": "2013", "author_list": "Mangiola, Stefano; Young, Neil D.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/zdr7b-c4t77", "eprint_id": 43830, "eprint_status": "archive", "datestamp": "2023-08-22 11:01:13", "lastmod": "2023-10-25 23:55:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ansell-B-R-E", "name": { "family": "Ansell", "given": "Brendan R. E." } }, { "id": "Schnyder-M", "name": { "family": "Schnyder", "given": "Manuela" } }, { "id": "Deplazes-P", "name": { "family": "Deplazes", "given": "Peter" } }, { "id": "Korhonen-P-K", "name": { "family": "Korhonen", "given": "Pasi K." } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Hall-R-S", "name": { "family": "Hall", "given": "Ross S." } }, { "id": "Mangiola-S", "name": { "family": "Mangiola", "given": "Stefano" } }, { "id": "Boag-P-R", "name": { "family": "Boag", "given": "Peter R." } }, { "id": "Hofmann-A", "name": { "family": "Hofmann", "given": "Andreas" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Jex-A-R", "name": { "family": "Jex", "given": "Aaron R." } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "Insights into the immuno-molecular biology of Angiostrongylus vasorum through transcriptomics\u2014Prospects for new interventions", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Angiostrongylus vasorum; Canine lungworm; Transcriptome; Bioinformatics; Molecular biology; Immunity; Intervention targets", "note": "\u00a9 2013 Elsevier Inc.\n\nReceived 2 May 2013; Received in revised form 28 June 2013;\nAccepted 16 July 2013; Available online 27 July 2013.\n\nThis project was funded by the Australian Research Council and National Health and Medical Research Council (NHMRC) (R.B.G.), Howard Hughes Medical Institute (HHMI) and the National Institutes of Health (NIH) (P.W.S.). This project was also supported by a Victorian Life Sciences Computation Initiative (VLSCI) grant number VR0007 on its Peak Computing Facility at the University of Melbourne, an initiative of the Victorian Government. Other support from the Australian Academy of Science, the Australian\u2013American Fulbright Commission, Alexander von Humboldt Foundation, Melbourne Water Corporation and the IBM Research Collaboratory for Life Sciences\u2014Melbourne is gratefully acknowledged (R.B.G.). N.D.Y. is an NHMRC Early Career Research (ECR) Fellow. We also acknowledge the continued contributions of all staff at WormBase (www.wormbase.org).\nNucleotide sequence data reported in this article are available in HelmDB (www.helmdb.org).", "abstract": "Angiostrongylus vasorum is a metastrongyloid nematode of dogs and other canids of major clinical importance in many countries. In order to gain first insights into the molecular biology of this worm, we conducted the first large-scale exploration of its transcriptome, and predicted essential molecules linked to metabolic and biological processes as well as host immune responses. We also predicted and prioritized drug targets and drug candidates. Following Illumina sequencing (RNA-seq), 52.3 million sequence reads representing adult A. vasorum were assembled and annotated. The assembly yielded 20,033 contigs, which encoded proteins with 11,505 homologues in Caenorhabditis elegans, and additional 2252 homologues in various other parasitic helminths for which curated data sets were publicly available. Functional annotation was achieved for 11,752 (58.6%) proteins predicted for A. vasorum, including peptidases (4.5%) and peptidase inhibitors (1.6%), protein kinases (1.7%), G protein-coupled receptors (GPCRs) (1.5%) and phosphatases (1.2%). Contigs encoding excretory/secretory and immuno-modulatory proteins represented some of the most highly transcribed molecules, and encoded enzymes that digest haemoglobin were conserved between A. vasorum and other blood-feeding nematodes. Using an essentiality-based approach, drug targets, including neurotransmitter receptors, an important chemosensory ion channel and cysteine proteinase-3 were predicted in A. vasorum, as were associated small molecular inhibitors/activators. Future transcriptomic analyses of all developmental stages of A. vasorum should facilitate deep explorations of the molecular biology of this important parasitic nematode and support the sequencing of its genome. These advances will provide a foundation for exploring immuno-molecular aspects of angiostrongylosis and have the potential to underpin the discovery of new methods of intervention.", "date": "2013-12", "date_type": "published", "publication": "Biotechnology Advances", "volume": "31", "number": "8", "publisher": "Elsevier", "pagerange": "1486-1500", "id_number": "CaltechAUTHORS:20140214-093158107", "issn": "0734-9750", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140214-093158107", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council" }, { "agency": "National Health and Medical Research Council (NHMRC)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH" }, { "agency": "Victorian Life Sciences Computation Initiative (VLSCI)", "grant_number": "VR0007" }, { "agency": "Australian Academy of Science" }, { "agency": "Australian\u2013American Fulbright Commission" }, { "agency": "Alexander von Humboldt Foundation" }, { "agency": "Melbourne Water Corporation" }, { "agency": "IBM Research Collaboratory for Life Sciences\u2014Melbourne" }, { "agency": "NHMRC Early Career Research (ECR) Fellow" } ] }, "doi": "10.1016/j.biotechadv.2013.07.006", "resource_type": "article", "pub_year": "2013", "author_list": "Ansell, Brendan R. E.; Schnyder, Manuela; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/8mpzk-dgr21", "eprint_id": 43810, "eprint_status": "archive", "datestamp": "2023-08-22 10:46:03", "lastmod": "2023-10-25 23:54:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chiu-Hui", "name": { "family": "Chiu", "given": "Hui" } }, { "id": "Schwartz-H-T", "name": { "family": "Schwartz", "given": "Hillel T." }, "orcid": "0000-0002-3448-8652" }, { "id": "Antoshechkin-I-A", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Transgene-Free Genome Editing in Caenorhabditis elegans Using CRISPR-Cas", "ispublished": "pub", "full_text_status": "public", "keywords": "CRISPR; targeted nuclease; reverse genetics; Caenorhabditis elegans; genome resequencing", "note": "\u00a9 2013 Genetics Society of America.\n\nManuscript received July 29, 2013; accepted for publication August 13, 2013; Early Online August 26, 2013.\n\nWe thank Mihoko Kato and David Greenstein for helpful\ncomments on the manuscript, participants in the Engineered\nNucleases workshop at the 2013 International C. elegans\nmeeting for collegial discussions, and WormBase. Highthroughput\nDNA sequencing was performed at the Millard and\nMuriel Jacobs Genetics and Genomics Laboratory at California\nInstitute of Technology. P.W.S. is an investigator of the\nHoward Hughes Medical Institute, which supported this work.\n\nSupplemental Material - FileS1.pdf
Supplemental Material - SI.pdf
Supplemental Material - TableS1.pdf
Supplemental Material - TableS2.pdf
Supplemental Material - TableS3.pdf
Supplemental Material - TableS4.pdf
", "abstract": "CRISPR-Cas is an efficient method for genome editing in organisms from bacteria to human cells. We describe a transgene-free method for CRISPR-Cas-mediated cleavage in nematodes, enabling RNA-homology-targeted deletions that cause loss of gene function; analysis of whole-genome sequencing indicates that the nuclease activity is highly specific.", "date": "2013-11", "date_type": "published", "publication": "Genetics", "volume": "195", "number": "3", "publisher": "Genetics Society of America", "pagerange": "1167-1171", "id_number": "CaltechAUTHORS:20140213-100046738", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140213-100046738", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1534/genetics.113.155879", "pmcid": "PMC3813845", "primary_object": { "basename": "SI.pdf", "url": "https://authors.library.caltech.edu/records/8mpzk-dgr21/files/SI.pdf" }, "related_objects": [ { "basename": "TableS1.pdf", "url": "https://authors.library.caltech.edu/records/8mpzk-dgr21/files/TableS1.pdf" }, { "basename": "TableS2.pdf", "url": "https://authors.library.caltech.edu/records/8mpzk-dgr21/files/TableS2.pdf" }, { "basename": "TableS3.pdf", "url": "https://authors.library.caltech.edu/records/8mpzk-dgr21/files/TableS3.pdf" }, { "basename": "TableS4.pdf", "url": "https://authors.library.caltech.edu/records/8mpzk-dgr21/files/TableS4.pdf" }, { "basename": "FileS1.pdf", "url": "https://authors.library.caltech.edu/records/8mpzk-dgr21/files/FileS1.pdf" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Chiu, Hui; Schwartz, Hillel T.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/fyqfn-5z174", "eprint_id": 42236, "eprint_status": "archive", "datestamp": "2023-08-22 10:34:04", "lastmod": "2023-10-25 15:46:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Rakowski-F", "name": { "family": "Rakowski", "given": "Franciszek" } }, { "id": "Srinivasan-J", "name": { "family": "Srinivasan", "given": "Jagan" }, "orcid": "0000-0001-5449-7938" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Karbowski-J", "name": { "family": "Karbowski", "given": "Jan" } } ] }, "title": "Synaptic polarity of the interneuron circuit controlling C. elegans locomotion", "ispublished": "pub", "full_text_status": "public", "keywords": "C. elegans; locomotory interneurons; synaptic polarity; locomotion; neural circuit modeling; optimization; laser ablations", "note": "\u00a9 2013 Rakowski, Srinivasan, Sternberg and Karbowski. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. \n\nReceived: 07 May 2013; Accepted: 07 September 2013;\nPublished online: 02 October 2013.\n\nWe thank Cori Bargmann for comments on the manuscript.\nThe work was supported by the EU grant POIG.02.01.00-14-122/09 \"Physics as the basis for new technologie\u2014development\nof modern research infrastructure at the Faculty of Physics of the University of Warsaw\" (Franciszek Rakowski), by the Marie Curie Actions EU grant FP7-PEOPLE-2007-IRG-210538 (Jan\nKarbowski), and by the grant from the Polish Ministry of Science and Education NN 518 409238(Jan Karbowski).\n\nPublished - fncom-07-00128.pdf
Supplemental Material - 55552_Karbowski_Presentation1.PDF
", "abstract": "Caenorhabditis elegans is the only animal for which a detailed neural connectivity diagram has been constructed. However, synaptic polarities in this diagram, and thus, circuit functions are largely unknown. Here, we deciphered the likely polarities of seven pre-motor neurons implicated in the control of worm's locomotion, using a combination of experimental and computational tools. We performed single and multiple laser ablations in the locomotor interneuron circuit and recorded times the worms spent in forward and backward locomotion. We constructed a theoretical model of the locomotor circuit and searched its all possible synaptic polarity combinations and sensory input patterns in order to find the best match to the timing data. The optimal solution is when either all or most of the interneurons are inhibitory and forward interneurons receive the strongest input, which suggests that inhibition governs the dynamics of the locomotor interneuron circuit. From the five pre-motor interneurons, only AVB and AVD are equally likely to be excitatory, i.e., they have probably similar number of inhibitory and excitatory connections to distant targets. The method used here has a general character and thus can be also applied to other neural systems consisting of small functional networks.", "date": "2013-10-02", "date_type": "published", "publication": "Frontiers in Computational Neuroscience", "volume": "7", "publisher": "Frontiers Research Foundation", "pagerange": "Art. No. 128", "id_number": "CaltechAUTHORS:20131104-162133423", "issn": "1662-5188", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131104-162133423", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "European Union", "grant_number": "POIG.02.01.00-14-122/09" }, { "agency": "Marie Curie Fellowship", "grant_number": "FP7-PEOPLE-2007-IRG-210538" }, { "agency": "Ministry of Science and Education (Poland)", "grant_number": "NN 518 409238" } ] }, "doi": "10.3389/fncom.2013.00128", "pmcid": "PMC3788333", "primary_object": { "basename": "55552_Karbowski_Presentation1.PDF", "url": "https://authors.library.caltech.edu/records/fyqfn-5z174/files/55552_Karbowski_Presentation1.PDF" }, "related_objects": [ { "basename": "fncom-07-00128.pdf", "url": "https://authors.library.caltech.edu/records/fyqfn-5z174/files/fncom-07-00128.pdf" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Rakowski, Franciszek; Srinivasan, Jagan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/y9mk3-39f03", "eprint_id": 42444, "eprint_status": "archive", "datestamp": "2023-08-19 21:38:33", "lastmod": "2023-10-25 16:03:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Feeny-B-F", "name": { "family": "Feeny", "given": "B. F." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "P. W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Cronin-C-J", "name": { "family": "Cronin", "given": "C. J." } }, { "id": "Coppola-C-A", "name": { "family": "Coppola", "given": "C. A." } } ] }, "title": "Complex Orthogonal Decomposition Applied to Nematode Posturing", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 by ASME.\n\nContributed by the Design Engineering Division of ASME for publication in the\nJOURNAL OF COMPUTATIONAL AND NONLINEAR DYNAMICS. Manuscript received October\n12, 2011; final manuscript received September 15, 2012; published online May 14,\n2013. Assoc. Editor: D. Dane Quinn.\n\nThis work was supported in part by the National Institutes of\nHealth (Grant No. USPHS DA018341) and was related in part to a\nproject with the National Science Foundation (CMMI-0727838).\nAny opinions, findings, and conclusions or recommendations are\nthose of the authors and do not necessarily reflect the views of the\nNSF.\n\nPublished - cnd_008_04_041010.pdf
", "abstract": "The complex orthogonal decomposition (COD), a process of extracting complex modes from complex ensemble data, is summarized, as is the use of complex modal coordinates. A brief assessment is made on how small levels of noise affect the decomposition. The decomposition is applied to the posturing of Caenorhabditis elegans, an intensively studied nematode. The decomposition indicates that the worm has a multimodal posturing behavior, involving a dominant forward locomotion mode, a secondary, steering mode, and likely a mode for reverse motion. The locomotion mode is closer to a pure traveling waveform than the steering mode. The characteristic wavelength of the primary mode is estimated in the complex plane. The frequency is obtained from the complex modal coordinate's complex whirl rate of the complex modal coordinate, and from its fast Fourier transform. Short-time decompositions indicate the variation of the wavelength and frequency through the time record.", "date": "2013-10", "date_type": "published", "publication": "Journal of Computational and Nonlinear Dynamics", "volume": "8", "number": "4", "publisher": "American Society of Mechanical Engineers", "pagerange": "Art. No. 041010", "id_number": "CaltechAUTHORS:20131114-073305975", "issn": "1555-1423", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131114-073305975", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "USPHS DA018341" }, { "agency": "NSF", "grant_number": "CMMI-0727838" } ] }, "doi": "10.1115/1.4023548", "primary_object": { "basename": "cnd_008_04_041010.pdf", "url": "https://authors.library.caltech.edu/records/y9mk3-39f03/files/cnd_008_04_041010.pdf" }, "resource_type": "article", "pub_year": "2013", "author_list": "Feeny, B. F.; Sternberg, P. W.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/0hccr-s0w89", "eprint_id": 52622, "eprint_status": "archive", "datestamp": "2023-08-19 21:43:32", "lastmod": "2023-10-18 21:02:46", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Han-Chao", "name": { "family": "Han", "given": "Chao" } }, { "id": "Pang-Shuo", "name": { "family": "Pang", "given": "Shuo" } }, { "id": "Kato-Mihoko", "name": { "family": "Kato", "given": "Mihoko" }, "orcid": "0000-0003-3827-8879" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul" }, "orcid": "0000-0002-7699-0173" }, { "id": "Yang-Changhuei", "name": { "family": "Yang", "given": "Changhuei" }, "orcid": "0000-0001-8791-0354" } ] }, "title": "On-Chip Fluorescence Microscopy for Wide Field-of-View High-Throughput Phynotype Screening of Caenorhabditis elegans", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "on-chip fluorescence microscopy, wide field-of-view, Caenorhabditis elegans", "note": "\u00a9 2013 CBMS.\n\nThis project is funded by National Institute of Health under Grant No. 1R01AI09622601.", "abstract": "We developed a low-cost compact on-chip fluorescence imaging platform, termed the Fluorescence Talbot\nMicroscopy (FTM), which utilizes the Talbot self-imaging effect to enable efficient fluorescence imaging over a large\nand directly-scalable field-of-view (FOV). The FTM prototype has a resolution of 1.2 \u03bcm and an FOV of 3.9\u00d73.5mm^2. We demonstrate the use of the FTM prototype in performing high-throughput imaging of live Caenorhabditis elegans (C. elegans), and RNA interference (RNAi) phenotyping of distal tip cell (DTC) migration defects in C. elegans.", "date": "2013-10", "date_type": "published", "publisher": "Caltech Library", "pagerange": "257-259", "id_number": "CaltechAUTHORS:20141212-093902623", "isbn": "978-0-9798064-6-9", "book_title": "17th International Conference on Miniaturized Systems for Chemistry and Life Sciences", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141212-093902623", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "1R01AI09622601" } ] }, "resource_type": "book_section", "pub_year": "2013", "author_list": "Han, Chao; Pang, Shuo; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/pw7df-cvf06", "eprint_id": 41431, "eprint_status": "archive", "datestamp": "2023-08-19 21:27:49", "lastmod": "2023-10-24 23:44:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Minor-P-J", "name": { "family": "Minor", "given": "Paul J." } }, { "id": "He-Ting-Fang", "name": { "family": "He", "given": "Ting-Fang" } }, { "id": "Sohn-Chang-Ho", "name": { "family": "Sohn", "given": "Chang Ho" } }, { "id": "Asthagiri-A-R", "name": { "family": "Asthagiri", "given": "Anand R." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "FGF signaling regulates Wnt ligand expression to control vulval cell lineage polarity in C. elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "FGF, Wnt, C. elegans, Vulval development, Cell polarity", "note": "\u00a9 2013. Published by The Company of Biologists Ltd.\n\nAccepted 3 July 2013.\n\nPosted online before print August 14, 2013.\nWe thank Takao Inoue, Jennifer Green, Wendy Katz, Adeline Seah and Michael\nStern for insightful comments and laying the groundwork for this project;\nLong Cai for use of his microscope for FISH; Gladys Medina and Barbara Perry\nfor technical assistance; and members of the Sternberg laboratory, especially\nMihoko Kato, Amir Sapir, James Lee and Hillel Schwartz, for helpful discussions\nand critically reading the manuscript. We thank WormBase and the\nCaenorhabditis Genetics Center.\n\nFunding:\nP.J.M. was supported by a National Institutes of Health (NIH) United States\nPublic Health Service Training Grant [T32GM07616]; and the Howard Hughes\nMedical Institute (HHMI). P.W.S. is an HHMI investigator. T.-F.H. and C.H.S.\nwere supported by the NIH [R01 HD075605 to Long Cai]. Deposited in PMC\nfor release after 6 months.\n\nAuthor contributions:\nP.J.M., A.A. and P.W.S. conceived the experiments. P.J.M. carried out all the\nexperiments with help from T.-F.H. and C.H.S. for the FISH experiments. P.J.M.\nand P.W.S. wrote the manuscript.\n\nPublished - Development-2013-Minor-3882-91.pdf
Supplemental Material - DEV095687_si.pdf
", "abstract": "The interpretation of extracellular cues leading to the polarization of intracellular components and asymmetric cell divisions is a\nfundamental part of metazoan organogenesis. The Caenorhabditis elegans vulva, with its invariant cell lineage and interaction of\nmultiple cell signaling pathways, provides an excellent model for the study of cell polarity within an organized epithelial tissue. Here,\nwe show that the fibroblast growth factor (FGF) pathway acts in concert with the Frizzled homolog LIN-17 to influence the localization\nof SYS-1, a component of the Wnt/\u03b2-catenin asymmetry pathway, indirectly through the regulation of cwn-1. The source of the FGF\nligand is the primary vulval precursor cell (VPC) P6.p, which controls the orientation of the neighboring secondary VPC P7.p by\nsignaling through the sex myoblasts (SMs), activating the FGF pathway. The Wnt CWN-1 is expressed in the posterior body wall muscle\nof the worm as well as in the SMs, making it the only Wnt expressed on the posterior and anterior sides of P7.p at the time of the\npolarity decision. Both sources of cwn-1 act instructively to influence P7.p polarity in the direction of the highest Wnt signal. Using\nsingle molecule fluorescence in situ hybridization, we show that the FGF pathway regulates the expression of cwn-1 in the SMs. These\nresults demonstrate an interaction between FGF and Wnt in C. elegans development and vulval cell lineage polarity, and highlight\nthe promiscuous nature of Wnts and the importance of Wnt gradient directionality within C. elegans.", "date": "2013-09-15", "date_type": "published", "publication": "Development", "volume": "140", "number": "18", "publisher": "Company of Biologists", "pagerange": "3882-3891", "id_number": "CaltechAUTHORS:20130920-074404035", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130920-074404035", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM07616" }, { "agency": "NIH", "grant_number": "R01 HD075605" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1242/dev.095687", "pmcid": "PMC3754481", "primary_object": { "basename": "DEV095687_si.pdf", "url": "https://authors.library.caltech.edu/records/pw7df-cvf06/files/DEV095687_si.pdf" }, "related_objects": [ { "basename": "Development-2013-Minor-3882-91.pdf", "url": "https://authors.library.caltech.edu/records/pw7df-cvf06/files/Development-2013-Minor-3882-91.pdf" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Minor, Paul J.; He, Ting-Fang; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/hst8f-h1f88", "eprint_id": 43881, "eprint_status": "archive", "datestamp": "2023-08-19 21:25:46", "lastmod": "2023-10-25 23:58:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Paul W. Sternberg", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2013 Published by Elsevier Ltd.", "abstract": "Paul W. Sternberg was born on Long Island, New York. He was an undergraduate at Hampshire\nCollege, obtaining his B.A. in 1978. He received his Ph.D. in Biology from MIT in 1984 for work on nematode\ndevelopment with Robert Horvitz, and pursued postdoctoral research in yeast molecular genetics with Ira\nHerskowitz at UCSF. He joined the faculty of the California Institute of Technology, where he is now the T.H.\nMorgan Professor of Biology. He has been an Investigator with the Howard Hughes Medical Institute since 1989,\nFellow of the American Academy of Arts and Sciences since 2000, and a member of the National Academy of\nSciences since 2009. He is also PI of WormBase, a PI of the Gene Ontology Consortium, and was 2011 President\nof the Genetics Society of America. In addition to his research on many aspects of biology in Caenorhabditis\nelegans and other nematode biology, he co-founded WormBase, WormBook and Textpresso.", "date": "2013-09-09", "date_type": "published", "publication": "Current Biology", "volume": "23", "number": "17", "publisher": "Cell Press", "pagerange": "R704-R705", "id_number": "CaltechAUTHORS:20140220-084528438", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140220-084528438", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.cub.2013.07.023", "resource_type": "article", "pub_year": "2013", "author_list": "Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/g2sr8-v5g41", "eprint_id": 43333, "eprint_status": "archive", "datestamp": "2023-08-19 21:11:02", "lastmod": "2023-10-25 23:28:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schwarz-E-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Korhonen-P-K", "name": { "family": "Korhonen", "given": "Pasi K." } }, { "id": "Campbell-B-E", "name": { "family": "Campbell", "given": "Bronwyn E." } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Jex-A-R", "name": { "family": "Jex", "given": "Aaron R." } }, { "id": "Jabbar-A", "name": { "family": "Jabbar", "given": "Abdul" } }, { "id": "Hall-R-S", "name": { "family": "Hall", "given": "Ross S." } }, { "id": "Mondal-A", "name": { "family": "Mondal", "given": "Alinda" } }, { "id": "Howe-A-C", "name": { "family": "Howe", "given": "Adina C." } }, { "id": "Pell-J", "name": { "family": "Pell", "given": "Jason" } }, { "id": "Hofmann-A", "name": { "family": "Hofmann", "given": "Andreas" } }, { "id": "Boag-P-R", "name": { "family": "Boag", "given": "Peter R." } }, { "id": "Zhu-Xing-Quan", "name": { "family": "Zhu", "given": "Xing-Quan" } }, { "id": "Gregory-T-R", "name": { "family": "Gregory", "given": "T. Ryan" } }, { "id": "Loukas-A", "name": { "family": "Loukas", "given": "Alex" } }, { "id": "Williams-B-A", "name": { "family": "Williams", "given": "Brian A." } }, { "id": "Antoshechkin-I-A", "name": { "family": "Antoshechkin", "given": "Igor A." }, "orcid": "0000-0002-9934-3040" }, { "id": "Brown-C-T", "name": { "family": "Brown", "given": "C. Titus" }, "orcid": "0000-0001-6001-2677" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 Schwarz et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http//creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any\nmedium, provided the original work is properly cited. \n\nReceived: 10 April 2013 Revised: 8 August 2013\nAccepted: 28 August 2013 Published: 28 August 2013.\n\nThis paper is dedicated to the memories of Sue Newton and Paul J Presidente. We thank Sujai Kumar and Mark Blaxter for providing methods for removing contaminant sequences, and Ali Mortazavi for early sequence analyses. We are grateful to Jody Zawadzki and the late Paul Presidente for\noriginally providing us with the McMaster and Haecon-5 strains of H. contortus. This project was funded by the Australian Research Council (RBG and PWS), National Health and Medical Research Council (NHMRC), Howard Hughes Medical Institute, and the National Institutes of Health. This project was also supported by a Victorian Life Sciences Computation Initiative (grant number VR0007) on its Peak Computing Facility at the University of\nMelbourne, an initiative of the Victorian Government. Other support from\nthe Australian Academy of Science, the Australian-American Fulbright\nCommission, Alexander von Humboldt Foundation, Melbourne Water\nCorporation, and the IBM Research Collaboratory for Life Sciences -\nMelbourne is gratefully acknowledged. NDY is an NHMRC Early Career\nResearch Fellow. We also acknowledge the contributions of all staff at\nWormBase. We thank the anonymous reviewers for their very constructive\nreports on our original manuscript.\n\nPublished - Schwarz_2013pR89.pdf
Supplemental Material - gb-2013-14-8-r89-s1.xls
", "abstract": "Background: The barber's pole worm, Haemonchus contortus, is one of the most economically important parasites of small ruminants worldwide. Although this parasite can be controlled using anthelmintic drugs, resistance against most drugs in common use has become a widespread problem. We provide a draft of the genome and the transcriptomes of all key developmental stages of H. contortus to support biological and biotechnological research areas of this and related parasites.\nResults: The draft genome of H. contortus is 320 Mb in size and encodes 23,610 protein-coding genes. On a fundamental level, we elucidate transcriptional alterations taking place throughout the life cycle, characterize the parasite's gene silencing machinery, and explore molecules involved in development, reproduction, host-parasite interactions, immunity, and disease. The secretome of H. contortus is particularly rich in peptidases linked to blood-feeding activity and interactions with host tissues, and a diverse array of molecules is involved in complex immune responses. On an applied level, we predict drug targets and identify vaccine molecules.\nConclusions: The draft genome and developmental transcriptome of H. contortus provide a major resource to the scientific community for a wide range of genomic, genetic, proteomic, metabolomic, evolutionary, biological, ecological, and epidemiological investigations, and a solid foundation for biotechnological outcomes, including new anthelmintics, vaccines and diagnostic tests. This first draft genome of any strongylid nematode paves the way for a rapid acceleration in our understanding of a wide range of socioeconomically important parasites of one of the largest nematode orders.", "date": "2013-08-28", "date_type": "published", "publication": "Genome Biology", "volume": "14", "number": "8", "publisher": "BioMed Central", "pagerange": "Art. No. R89", "id_number": "CaltechAUTHORS:20140113-100602079", "issn": "1465-6906", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140113-100602079", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council" }, { "agency": "National Health and Medical Research Council (NHMRC)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH" }, { "agency": "Victorian Life Sciences Computation Initiative (VLSCI)", "grant_number": "VR0007" }, { "agency": "Victorian Government" }, { "agency": "Australian Academy of Science" }, { "agency": "Australian-American Fulbright Commission" }, { "agency": "Alexander von Humboldt Foundation" }, { "agency": "Melbourne Water Corporation" }, { "agency": "IBM Research Collaboratory for Life Sciences - Melbourne" } ] }, "doi": "10.1186/gb-2013-14-8-r89", "pmcid": "PMC4053716", "primary_object": { "basename": "Schwarz_2013pR89.pdf", "url": "https://authors.library.caltech.edu/records/g2sr8-v5g41/files/Schwarz_2013pR89.pdf" }, "related_objects": [ { "basename": "gb-2013-14-8-r89-s1.xls", "url": "https://authors.library.caltech.edu/records/g2sr8-v5g41/files/gb-2013-14-8-r89-s1.xls" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Schwarz, Erich M.; Korhonen, Pasi K.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ygn7y-ezz55", "eprint_id": 78575, "eprint_status": "archive", "datestamp": "2023-08-19 21:08:28", "lastmod": "2023-10-26 00:11:38", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hsueh-Yen-Ping", "name": { "family": "Hsueh", "given": "Yen-Ping" } }, { "id": "Leighton-D-H-W", "name": { "family": "Leighton", "given": "Daniel H. W." }, "orcid": "0000-0002-1379-0078" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Nematode Communication", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2014 Springer. \n\nDate: 21 August 2013. \n\nWe thank our many collaborators and colleagues for making the study of nematode communication exciting and enjoyable, and for many conversations. We thank Hillel Schwartz for critical comments on the manuscript. PWS is an investigator with the Howard Hughes Medical Institute. D. L. is supported by National Institutes of Health USPHS training grant, GM07616.", "abstract": "Nematodes, a diverse animal phylum that comprises an estimated million species, inhabit very broad ranges of ecological niches throughout earth. These animals, ranging from microscopic to a meter in size, are extremely successful in adapting different environments and have different lifestyles as free-living or parasitic to plants, animals and humans. As a result, nematodes have evolved to communicate with a wide variety of organisms that they live and interact with, including microbes, plants, insects, other animals, and nematodes of the same and different species. These communications play a key role in the mutualism, parasitism, predatory and prey, host and pathogen relationships between nematodes and other organisms and are critical to the ecological fitness of nematodes. In this chapter, we highlight examples of different types of communication among the nematodes and\nbetween nematodes and their natural trophic partners, and discuss their implications in nematode evolution.", "date": "2013-08-21", "date_type": "published", "publisher": "Springer", "pagerange": "383-407", "id_number": "CaltechAUTHORS:20170626-140737808", "isbn": "978-94-007-7413-1", "book_title": "Biocommunication of Animals", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170626-140737808", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "GM07616" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "contributors": { "items": [ { "id": "Witzany-G", "name": { "family": "Witzany", "given": "Guenther" } } ] }, "doi": "10.1007/978-94-007-7414-8_21", "resource_type": "book_section", "pub_year": "2013", "author_list": "Hsueh, Yen-Ping; Leighton, Daniel H. W.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/92fqd-1ew52", "eprint_id": 41695, "eprint_status": "archive", "datestamp": "2023-08-19 20:48:00", "lastmod": "2023-10-24 23:56:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bai-Xiaodong", "name": { "family": "Bai", "given": "Xiaodong" } }, { "id": "Adams-B-J", "name": { "family": "Adams", "given": "Byron J." } }, { "id": "Ciche-T-A", "name": { "family": "Ciche", "given": "Todd A." } }, { "id": "Clifton-S", "name": { "family": "Clifton", "given": "Sandra" } }, { "id": "Gaugler-R", "name": { "family": "Gaugler", "given": "Randy" } }, { "id": "Kim-Kwi-suk", "name": { "family": "Kim", "given": "Kwi-suk" } }, { "id": "Spieth-J", "name": { "family": "Spieth", "given": "John" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Wilson-R-K", "name": { "family": "Wilson", "given": "Richard K." } }, { "id": "Grewal-P-S", "name": { "family": "Grewal", "given": "Parwinder S." } } ] }, "title": "A Lover and a Fighter: The Genome Sequence of an Entomopathogenic Nematode Heterorhabditis bacteriophora", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 Bai et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: April 7, 2013; Accepted: June 12, 2013; Published: July 18, 2013. \n\nThis project was supported by grants from the United States Department of Agriculture (www.usda.gov) and National Science Foundation (www.nsf.gov) Microbial Genome Sequence Program under the grant #2006-35600-16665. P.W.S. is an investigator with the Howard Hughes Medical Institute (www.hhmi.org) with reference number of 047\u2013101. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. \n\nWe thank the members of the EPN and EPB International Genome\nSequence Consortium for support and the Washington University School of Medicine's Genome Institute, St. Louis, MO, USA for sequencing the genome.\n\nPublished - journal.pone.0069618.pdf
", "abstract": "Heterorhabditis bacteriophora are entomopathogenic nematodes that have evolved a mutualism with Photorhabdus luminescens bacteria to function as highly virulent insect pathogens. The nematode provides a safe harbor for intestinal symbionts in soil and delivers the symbiotic bacteria into the insect blood. The symbiont provides virulence and toxins, metabolites essential for nematode reproduction, and antibiotic preservation of the insect cadaver. Approximately half of the 21,250 putative protein coding genes identified in the 77 Mbp high quality draft H. bacteriophora genome sequence were novel proteins of unknown function lacking homologs in Caenorhabditis elegans or any other sequenced organisms. Similarly, 317 of the 603 predicted secreted proteins are novel with unknown function in addition to 19 putative peptidases, 9 peptidase inhibitors and 7 C-type lectins that may function in interactions with insect hosts or bacterial symbionts. The 134 proteins contained mariner transposase domains, of which there are none in C. elegans, suggesting an invasion and expansion of mariner transposons in H. bacteriophora. Fewer Kyoto Encyclopedia of Genes and Genomes Orthologies in almost all metabolic categories were detected in the genome compared with 9 other sequenced nematode genomes, which may reflect dependence on the symbiont or insect host for these functions. The H. bacteriophora genome sequence will greatly facilitate genetics, genomics and evolutionary studies to gain fundamental knowledge of nematode parasitism and mutualism. It also elevates the utility of H. bacteriophora as a bridge species between vertebrate parasitic nematodes and the C. elegans model.", "date": "2013-07-18", "date_type": "published", "publication": "PLoS ONE", "volume": "8", "number": "7", "publisher": "Public Library of Science", "pagerange": "Art. No. e69618", "id_number": "CaltechAUTHORS:20131004-161442725", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131004-161442725", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Agriculture" }, { "agency": "NSF" }, { "agency": "Howard Hughes Medical Institute (HHMI)", "grant_number": "047\u2013101" } ] }, "doi": "10.1371/journal.pone.0069618", "pmcid": "PMC3715494", "primary_object": { "basename": "journal.pone.0069618.pdf", "url": "https://authors.library.caltech.edu/records/92fqd-1ew52/files/journal.pone.0069618.pdf" }, "resource_type": "article", "pub_year": "2013", "author_list": "Bai, Xiaodong; Adams, Byron J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/m9q61-st292", "eprint_id": 41088, "eprint_status": "archive", "datestamp": "2023-08-22 09:54:34", "lastmod": "2023-10-24 23:26:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yu-Hui", "name": { "family": "Yu", "given": "Hui" } }, { "id": "Aleman-Meza-B", "name": { "family": "Aleman-Meza", "given": "Boanerges" } }, { "id": "Gharib-Shahla", "name": { "family": "Gharib", "given": "Shahla" } }, { "id": "Labocha-M-K", "name": { "family": "Labocha", "given": "Marta K." } }, { "id": "Cronin-C-J", "name": { "family": "Cronin", "given": "Christopher J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Zhong-Weiwei", "name": { "family": "Zhong", "given": "Weiwei" } } ] }, "title": "Systematic profiling of Caenorhabditis elegans locomotive behaviors reveals additional components in G-protein G\u03b1q signaling", "ispublished": "pub", "full_text_status": "public", "keywords": "gene network; high-content screening; locomotion", "note": "\u00a9 2013 National Academy of Sciences.\n\nContributed by Paul W. Sternberg, June 4, 2013 (sent for review March 8, 2013).\n\nPublished online before print July 1, 2013.\n\nWe thank the Caenorhabditis Genetics Center (CGC),\nErin Cram, and Shohei Mitani for strains, Illya Hicks for helpful discussions,\nJoaquina Nunez, Barbara Perry, and Julie Nguyen for technical assistance,\nRanjana Kishore for a critical reading of the manuscript, and WormBase. This\nwork was supported by National Institutes of Health Grant HG004724 and\na Searle Scholar grant from the Kinship Foundation (to W.Z.), by National\nInstitutes of Health Grant DA018341 (to P.W.S. and W.Z.), and by the\nHoward Hughes Medical Institute, with which P.W.S. is an investigator. CGC\nis funded by National Institutes of Health Office of Research Infrastructure\nPrograms Grant P40 OD010440.\n\nAuthor contributions: H.Y., B.A.-M., P.W.S., and W.Z. designed research; H.Y., B.A.-M.,\nS.G., and W.Z. performed research; C.J.C. contributed new reagents/analytic tools;\nB.A.-M., M.K.L., and W.Z. analyzed data; and P.W.S. and W.Z. wrote the paper.\n\nPublished - PNAS-2013-Yu-11940-5.pdf
Supplemental Material - TableS1.doc
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Supplemental Material - pnas.201310468SI.pdf
", "abstract": "Genetic screens have been widely applied to uncover genetic mechanisms of movement disorders. However, most screens rely on human observations of qualitative differences. Here we demonstrate the application of an automatic imaging system to conduct a quantitative screen for genes regulating the locomotive behavior in Caenorhabditis elegans. Two hundred twenty-seven neuronal signaling genes with viable homozygous mutants were selected for this study. We tracked and recorded each animal for 4 min and analyzed over 4,400 animals of 239 genotypes to obtain a quantitative, 10-parameter behavioral profile for each genotype. We discovered 87 genes whose inactivation causes movement defects, including 50 genes that had never been associated with locomotive defects. Computational analysis of the high-content behavioral profiles predicted 370 genetic interactions among these genes. Network partition revealed several functional modules regulating locomotive behaviors, including sensory genes that detect environmental conditions, genes that function in multiple types of excitable cells, and genes in the signaling pathway of the G protein G\u03b1q, a protein that is essential for animal life and behavior. We developed quantitative epistasis analysis methods to analyze the locomotive profiles and validated the prediction of the \u03b3 isoform of phospholipase C as a component in the G\u03b1q pathway. These results provided a system-level understanding of how neuronal signaling genes coordinate locomotive behaviors. This study also demonstrated the power of quantitative approaches in genetic studies.", "date": "2013-07-16", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "110", "number": "29", "publisher": "National Academy of Sciences", "pagerange": "11940-11945", "id_number": "CaltechAUTHORS:20130904-135424352", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130904-135424352", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HG004724" }, { "agency": "Kinship Foundation Searle Scholar Grant" }, { "agency": "NIH", "grant_number": "DA018341" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH Office of Research Infrastructure Programs", "grant_number": "P40 OD010440" } ] }, "doi": "10.1073/pnas.1310468110", "pmcid": "PMC3718121", "primary_object": { "basename": "TableS7.doc", "url": "https://authors.library.caltech.edu/records/m9q61-st292/files/TableS7.doc" }, "related_objects": [ { "basename": "pnas.201310468SI.pdf", "url": "https://authors.library.caltech.edu/records/m9q61-st292/files/pnas.201310468SI.pdf" }, { "basename": "PNAS-2013-Yu-11940-5.pdf", "url": "https://authors.library.caltech.edu/records/m9q61-st292/files/PNAS-2013-Yu-11940-5.pdf" }, { "basename": "TableS1.doc", "url": "https://authors.library.caltech.edu/records/m9q61-st292/files/TableS1.doc" }, { "basename": "TableS2.doc", "url": "https://authors.library.caltech.edu/records/m9q61-st292/files/TableS2.doc" }, { "basename": "TableS5.doc", "url": "https://authors.library.caltech.edu/records/m9q61-st292/files/TableS5.doc" }, { "basename": "TableS6.doc", "url": "https://authors.library.caltech.edu/records/m9q61-st292/files/TableS6.doc" }, { "basename": "TableS3.doc", "url": "https://authors.library.caltech.edu/records/m9q61-st292/files/TableS3.doc" }, { "basename": "TableS4.doc", "url": "https://authors.library.caltech.edu/records/m9q61-st292/files/TableS4.doc" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Yu, Hui; Aleman-Meza, Boanerges; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/y08zm-vk116", "eprint_id": 39905, "eprint_status": "archive", "datestamp": "2023-08-19 20:30:25", "lastmod": "2023-10-24 17:18:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Artyukhin-A-B", "name": { "family": "Artyukhin", "given": "Alexander B." } }, { "id": "Yim-Joshua-J", "name": { "family": "Yim", "given": "Joshua J." } }, { "id": "Srinivasan-J", "name": { "family": "Srinivasan", "given": "Jagan" }, "orcid": "0000-0001-5449-7938" }, { "id": "Izrayelit-Y", "name": { "family": "Izrayelit", "given": "Yevgeniy" } }, { "id": "Bose-N", "name": { "family": "Bose", "given": "Neelanjan" } }, { "id": "von-Reuss-S-H", "name": { "family": "von Reuss", "given": "Stephan H." } }, { "id": "Jo-Yeara", "name": { "family": "Jo", "given": "Yeara" } }, { "id": "Jordan-J-M", "name": { "family": "Jordan", "given": "James M." } }, { "id": "Baugh-L-R", "name": { "family": "Baugh", "given": "L. Ryan" } }, { "id": "Cheong-Micheong", "name": { "family": "Cheong", "given": "Micheong" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Avery-L", "name": { "family": "Avery", "given": "Leon" } }, { "id": "Schroeder-F-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" } ] }, "title": "Succinylated Octopamine Ascarosides and a New Pathway of Biogenic Amine Metabolism in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 by The American Society for Biochemistry and Molecular Biology, Inc.\nReceived for publication, April 12, 2013, and in revised form, May 13, 2013\nPublished, JBC Papers in Press, May 20, 2013.\n\nThis work was supported in part by National Institutes of Health Grants\nGM088290 (to F. C. S.), GM008500 (to Y. I.), DK83593 (to L. A.), and\nGM085285 (to F. C. S. and P. W. S.), and National Science Foundation Grant\nIOS1120206 (to L. R. B.), as well as the Vassar College Mary Landon Sague\nFellowship (to Y. I.).\n\nWe thank Maciej Kukula for help with high resolution\nMS analysis.\n\nPublished - J._Biol._Chem.-2013-Artyukhin-18778-83.pdf
Supplemental Material - jbc.C113.477000-1.pdf
", "abstract": "The ascarosides, small-molecule signals derived from combinatorial\nassembly of primary metabolism-derived building\nblocks, play a central role in Caenorhabditis elegans biology and\nregulate many aspects of development and behavior in this\nmodel organism as well as in other nematodes. Using HPLCMS/\nMS-based targeted metabolomics, we identified novel ascarosides\nincorporating a side chain derived from succinylation of\nthe neurotransmitter octopamine. These compounds, named\nosas#2, osas#9, and osas#10, are produced predominantly by L1\nlarvae, where they serve as part of a dispersal signal, whereas\nthese ascarosides are largely absent from the metabolomes of\nother life stages. Investigating the biogenesis of these octopamine-\nderived ascarosides, we found that succinylation represents\na previously unrecognized pathway of biogenic amine\nmetabolism. At physiological concentrations, the neurotransmitters\nserotonin, dopamine, and octopamine are converted to a\nlarge extent into the corresponding succinates, in addition to\nthe previously described acetates. Chemically, bimodal deactivation\nof biogenic amines via acetylation and succinylation parallels\nposttranslational modification of proteins via acetylation\nand succinylation of L-lysine. Our results reveal a small-molecule\nconnection between neurotransmitter signaling and\ninterorganismal regulation of behavior and suggest that ascaroside\nbiosynthesis is based in part on co-option of degradative\nbiochemical pathways.", "date": "2013-06-28", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "288", "number": "26", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "18778-18783", "id_number": "CaltechAUTHORS:20130814-081450157", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130814-081450157", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM088290" }, { "agency": "NIH", "grant_number": "GM008500" }, { "agency": "NIH", "grant_number": "DK83593" }, { "agency": "NIH", "grant_number": "GM085285" }, { "agency": "NSF", "grant_number": "IOS1120206" }, { "agency": "Vassar College Mary Landon Sague Fellowship" } ] }, "doi": "10.1074/jbc.C113.477000", "pmcid": "PMC3696653", "primary_object": { "basename": "J._Biol._Chem.-2013-Artyukhin-18778-83.pdf", "url": "https://authors.library.caltech.edu/records/y08zm-vk116/files/J._Biol._Chem.-2013-Artyukhin-18778-83.pdf" }, "related_objects": [ { "basename": "jbc.C113.477000-1.pdf", "url": "https://authors.library.caltech.edu/records/y08zm-vk116/files/jbc.C113.477000-1.pdf" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Artyukhin, Alexander B.; Yim, Joshua J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/repc0-pbd96", "eprint_id": 39723, "eprint_status": "archive", "datestamp": "2023-08-23 16:50:04", "lastmod": "2023-10-24 17:07:56", "type": "conference_item", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yuet-Kai-P", "name": { "family": "Yuet", "given": "Kai P." }, "orcid": "0000-0002-1381-8923" }, { "id": "Doma-M-K", "name": { "family": "Doma", "given": "Meenakshi K." } }, { "id": "Ngo-John-T", "name": { "family": "Ngo", "given": "John T." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Tirrell-D-A", "name": { "family": "Tirrell", "given": "David A." }, "orcid": "0000-0003-3175-4596" } ] }, "title": "Cell type-specific proteomic profiling in Caenorhabditis elegans", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2013 American Chemical Society.", "abstract": "In a complex eukaryote like C. Elegans, cell and tissue heterogeneity restricts the usefulness of large-scale, mass spectrometrybased anal. of an organism's proteome. As worm cell lines are not available and enriching for specific cells or tissues is challenging, researchers cannot systematically identify low abundance proteins expressed in specific cells or tissues from wholeworm lysates. To isolate protein from specific cells, we have engineered C. Elegans phenylalanyl-tRNA synthetases capable of appending azide- or alkynyl-bearing analogs of phenylalanine to tRNA^(Phe). As these analogs are not substrates for any of the wild-type aminoacyl-tRNA synthetases in C. Elegans, we achieved cell type selectivity by spatially restricting the expression of a mutant synthetase using cell type-specific promoters. Because proteins from those cells that express the mutant synthetase - and only those cells - contain the analogs, they can be enriched by treatment with alkyne- or azide-functionalized biotin reagents and subsequent affinity chromatog. for identification by LC/MS-MS.", "date": "2013-04", "date_type": "published", "publisher": "Caltech Library", "id_number": "CaltechAUTHORS:20130802-084724182", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130802-084724182", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "resource_type": "conference_item", "pub_year": "2013", "author_list": "Yuet, Kai P.; Doma, Meenakshi K.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/w9346-xa951", "eprint_id": 38318, "eprint_status": "archive", "datestamp": "2023-08-22 09:00:12", "lastmod": "2023-10-23 20:03:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Srinivasan-J", "name": { "family": "Srinivasan", "given": "Jagan" }, "orcid": "0000-0001-5449-7938" }, { "id": "Dillman-A-R", "name": { "family": "Dillman", "given": "Adler R." }, "orcid": "0000-0001-7171-4332" }, { "id": "Macchietto-M-G", "name": { "family": "Macchietto", "given": "Marissa G." } }, { "id": "Heikkinen-L", "name": { "family": "Heikkinen", "given": "Liisa" } }, { "id": "Lakso-M", "name": { "family": "Lakso", "given": "Merja" } }, { "id": "Fracchia-K-M", "name": { "family": "Fracchia", "given": "Kelley M." } }, { "id": "Antoshechkin-I-A", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Mortazavi-A", "name": { "family": "Mortazavi", "given": "Ali" }, "orcid": "0000-0002-4259-6362" }, { "id": "Wong-Garry", "name": { "family": "Wong", "given": "Garry" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The Draft Genome and Transcriptome of Panagrellus redivivus Are Shaped by the Harsh Demands of a Free-Living Lifestyle", "ispublished": "pub", "full_text_status": "public", "keywords": "Panagrellus redivivus; microRNA; BTB domain; F-box; eRF1; cullin", "note": "\u00a9 2013 Genetics Society of America. Available freely online through the author-supported open access option. \n\nManuscript received December 15, 2012; accepted for publication January 8, 2013. \n\nWe thank Hillel Schwartz, Margaret C. Ho, Alexei Aravin,\nClaire C. de la Cova, Iva Greenwald, Kay Hofmann, and\nRaymond Deshaies for discussions. We thank Alicia Rogers\nand Zane Goodwin for their patience and help with some of\nthe computations. This work was supported by a National\nInstitutes of Health U.S. Public Health Service Training\nGrant (T32GM07616) to A.R.D. and by the Howard Hughes\nMedical Institute (with which P.W.S. is an Investigator).\nSequencing was carried out at the Millard and Muriel Jacobs\nGenome Facility at the California Institute of Technology.\n\nPublished - 1279.full.pdf
Supplemental Material - 148809SI.pdf
", "abstract": "Nematodes compose an abundant and diverse invertebrate phylum with members inhabiting nearly every ecological niche. Panagrellus redivivus (the \"microworm\") is a free-living nematode frequently used to understand the evolution of developmental and behavioral processes given its phylogenetic distance to Caenorhabditis elegans. Here we report the de novo sequencing of the genome, transcriptome, and small RNAs of P. redivivus. Using a combination of automated gene finders and RNA-seq data, we predict 24,249 genes and 32,676 transcripts. Small RNA analysis revealed 248 microRNA (miRNA) hairpins, of which 63 had orthologs in other species. Fourteen miRNA clusters containing 42 miRNA precursors were found. The RNA interference, dauer development, and programmed cell death pathways are largely conserved. Analysis of protein family domain abundance revealed that P. redivivus has experienced a striking expansion of BTB domain-containing proteins and an unprecedented expansion of the cullin scaffold family of proteins involved in multi-subunit ubiquitin ligases, suggesting proteolytic plasticity and/or tighter regulation of protein turnover. The eukaryotic release factor protein family has also been dramatically expanded and suggests an ongoing evolutionary arms race with viruses and transposons. The P. redivivus genome provides a resource to advance our understanding of nematode evolution and biology and to further elucidate the genomic architecture leading to free-living lineages, taking advantage of the many fascinating features of this worm revealed by comparative studies.", "date": "2013-04", "date_type": "published", "publication": "Genetics", "volume": "193", "number": "4", "publisher": "Genetics Society of America", "pagerange": "1279-1295", "id_number": "CaltechAUTHORS:20130507-103412407", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130507-103412407", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM07616" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1534/genetics.112.148809", "pmcid": "PMC3606103", "primary_object": { "basename": "1279.full.pdf", "url": "https://authors.library.caltech.edu/records/w9346-xa951/files/1279.full.pdf" }, "related_objects": [ { "basename": "148809SI.pdf", "url": "https://authors.library.caltech.edu/records/w9346-xa951/files/148809SI.pdf" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Srinivasan, Jagan; Dillman, Adler R.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/s6t64-49e09", "eprint_id": 37566, "eprint_status": "archive", "datestamp": "2023-08-22 08:39:29", "lastmod": "2023-10-23 17:48:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dillman-A-R", "name": { "family": "Dillman", "given": "Adler R." }, "orcid": "0000-0001-7171-4332" }, { "id": "Minor-P-J", "name": { "family": "Minor", "given": "Paul J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Origin and Evolution of Dishevelled", "ispublished": "pub", "full_text_status": "public", "keywords": "dishevelled; protein evolution; Nematoda; Wnt; C. elegans", "note": "\u00a9 2013 Dillman et al. This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nManuscript received October 23, 2012; accepted for publication December 9, 2012. \n\nWe thank Byron J. Adams, Geoffrey T. Smith, and Christian A. Grove\nfor their critical reading of the manuscript and Art Vandelay for\nhelpful insights into the details of importing and exporting. This work was supported by a National Institutes of Health (NIH) United States Public Health Service Training Grant (T32GM07616) to A.R.D. and P.J.M., and by the Howard Hughes Medical Institute (with which P.W.S. is an investigator).\n\nPublished - 251.full.pdf
Supplemental Material - 005314SI.pdf
Supplemental Material - FigureS1.pdf
Supplemental Material - FigureS2.pdf
Supplemental Material - FigureS3.pdf
Supplemental Material - FileS1.pdf
", "abstract": "Dishevelled (Dsh or Dvl) is an important signaling protein, playing a key role in Wnt signaling and relaying cellular information for several developmental pathways. Dsh is highly conserved among metazoans and has expanded into a multigene family in most bilaterian lineages, including vertebrates, planarians, and nematodes. These orthologs, where explored, are known to have considerable overlap in function, but evidence for functional specialization continues to mount. We performed a comparative analysis of Dsh across animals to explore protein architecture and identify conserved and divergent features that could provide insight into functional specialization with an emphasis on invertebrates, especially nematodes. We find evidence of dynamic evolution of Dsh, particularly among nematodes, with taxa varying in ortholog number from one to three. We identify a new domain specific to some nematode lineages and find an unexpected nuclear localization signal conserved in many Dsh orthologs. Our findings raise questions of protein evolution in general and provide clues as to how animals have dealt with the complex intricacies of having a protein, such as Dsh, act as a central messenger hub connected to many different and vitally important pathways. We discuss our findings in the context of functional specialization and bring many testable hypotheses to light.", "date": "2013-02-01", "date_type": "published", "publication": "G3", "volume": "3", "number": "2", "publisher": "Genetics Society of America", "pagerange": "251-262", "id_number": "CaltechAUTHORS:20130319-132644894", "issn": "2160-1836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130319-132644894", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM07616" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1534/g3.112.005314", "pmcid": "PMC3564985", "primary_object": { "basename": "FileS1.pdf", "url": "https://authors.library.caltech.edu/records/s6t64-49e09/files/FileS1.pdf" }, "related_objects": [ { "basename": "005314SI.pdf", "url": "https://authors.library.caltech.edu/records/s6t64-49e09/files/005314SI.pdf" }, { "basename": "251.full.pdf", "url": "https://authors.library.caltech.edu/records/s6t64-49e09/files/251.full.pdf" }, { "basename": "FigureS1.pdf", "url": "https://authors.library.caltech.edu/records/s6t64-49e09/files/FigureS1.pdf" }, { "basename": "FigureS2.pdf", "url": "https://authors.library.caltech.edu/records/s6t64-49e09/files/FigureS2.pdf" }, { "basename": "FigureS3.pdf", "url": "https://authors.library.caltech.edu/records/s6t64-49e09/files/FigureS3.pdf" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Dillman, Adler R.; Minor, Paul J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/7c8gt-a0c07", "eprint_id": 37611, "eprint_status": "archive", "datestamp": "2023-08-19 14:27:07", "lastmod": "2023-10-23 17:51:09", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Robinson-C-P", "name": { "family": "Robinson", "given": "Carmie Puckett" } }, { "id": "Schwarz-E-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Identification of DVA Interneuron Regulatory Sequences in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 Puckett Robinson et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which\npermits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.\n\nReceived August 12, 2010; Accepted December 21, 2012; Published January 28, 2013.\n\nFunding: Howard Hughes Medical Institute, with which PWS is an investigator; National Institutes of Health GM084389 (to PWS). The funders had no role in study\ndesign, data collection and analysis, decision to publish, or preparation of the manuscript.\n\nWe thank L. Ryan Baugh for his constructs and methods of PCR fusion\nand ballistics; Steven Kuntz for help with MUSSA; Cheryl Van Buskirk for\nidentification of RID; Jagan Srinivasan, Amir Sapir, Adler Dillman and\nChristopher Cronin for technical help with illustration; and anonymous\nreviewers for comments. We thank L. Salkoff for the twk-16 construct A3\n(pRxn4) for WT2000, and Bruce Wightman for the MU1147 line\nexpressing fax-1::GFP.\nAuthor Contributions:\nConceived and designed the experiments: CPR PWS. Performed the\nexperiments: CPR. Analyzed the data: CPR EMS. Wrote the paper: CPR\nEMS PWS. Conceived and designed the experiments: CPR, EMS, PWS.\nPerformed the experiments: CPR. Analyzed the data: CPR, EMS, PWS.\nContributed reagents/materials/analysis tools: EMS. Wrote the paper:\nCPR, EMS, PWS.\n\nPublished - journal.pone.0054971.pdf
Supplemental Material - FigureS1.tif
Supplemental Material - FigureS2.tif
Supplemental Material - TableS1.xlsx
Supplemental Material - TableS2.docx
", "abstract": "Background:\n \nThe identity of each neuron is determined by the expression of a distinct group of genes comprising its terminal gene battery. The regulatory sequences that control the expression of such terminal gene batteries in individual neurons is largely unknown. The existence of a complete genome sequence for C. elegans and draft genomes of other nematodes let us use comparative genomics to identify regulatory sequences directing expression in the DVA interneuron.\n\nMethodology/Principal Findings:\n \nUsing phylogenetic comparisons of multiple Caenorhabditis species, we identified conserved non-coding sequences in 3 of 10 genes (fax-1, nmr-1, and twk-16) that direct expression of reporter transgenes in DVA and other neurons. The conserved region and flanking sequences in an 85-bp intronic region of the twk-16 gene directs highly restricted expression in DVA. Mutagenesis of this 85 bp region shows that it has at least four regions. The central 53 bp region contains a 29 bp region that represses expression and a 24 bp region that drives broad neuronal expression. Two short flanking regions restrict expression of the twk-16 gene to DVA. A shared GA-rich motif was identified in three of these genes but had opposite effects on expression when mutated in the nmr-1 and twk-16 DVA regulatory elements.\n\nConclusions/Significance:\n \nWe identified by multi-species conservation regulatory regions within three genes that direct expression in the DVA neuron. We identified four contiguous regions of sequence of the twk-16 gene enhancer with positive and negative effects on expression, which combined to restrict expression to the DVA neuron. For this neuron a single binding site may thus not achieve sufficient specificity for cell specific expression. One of the positive elements, an 8-bp sequence required for expression was identified in silico by sequence comparisons of seven nematode species, demonstrating the potential resolution of expanded multi-species phylogenetic comparisons.", "date": "2013-01-28", "date_type": "published", "publication": "PLoS ONE", "volume": "8", "number": "1", "publisher": "Public Library of Science", "pagerange": "Art. No. e54971", "id_number": "CaltechAUTHORS:20130325-134216106", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130325-134216106", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "GM084389" } ] }, "doi": "10.1371/journal.pone.0054971", "pmcid": "PMC3557239", "primary_object": { "basename": "FigureS2.tif", "url": "https://authors.library.caltech.edu/records/7c8gt-a0c07/files/FigureS2.tif" }, "related_objects": [ { "basename": "TableS1.xlsx", "url": "https://authors.library.caltech.edu/records/7c8gt-a0c07/files/TableS1.xlsx" }, { "basename": "TableS2.docx", "url": "https://authors.library.caltech.edu/records/7c8gt-a0c07/files/TableS2.docx" }, { "basename": "journal.pone.0054971.pdf", "url": "https://authors.library.caltech.edu/records/7c8gt-a0c07/files/journal.pone.0054971.pdf" }, { "basename": "FigureS1.tif", "url": "https://authors.library.caltech.edu/records/7c8gt-a0c07/files/FigureS1.tif" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Robinson, Carmie Puckett; Schwarz, Erich M.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/zxkfq-p7338", "eprint_id": 37531, "eprint_status": "archive", "datestamp": "2023-08-19 14:18:35", "lastmod": "2023-10-23 17:43:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hsueh-Yen-Ping", "name": { "family": "Hsueh", "given": "Yen-Ping" } }, { "id": "Mahanti-P", "name": { "family": "Mahanti", "given": "Parag" } }, { "id": "Schroeder-F-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Nematode-Trapping Fungi Eavesdrop on Nematode Pheromones", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 Elsevier Ltd. \n\nReceived: November 2, 2012. Revised: November 19, 2012. Accepted: November 19, 2012. Published: December 13, 2012. \n\nWe thank American Type Culture Collection, Centraalbureau voor Schimmelcultures, and S.S. Tzean for providing fungal strains; A. Dillman for assisting with the construction of the phylogenetic tree; and J. Leadbetter, H. Schwartz, M. Kato, J. Cho, S. von Reuss, and anonymous reviewers for valuable comments and suggestions. This work was supported by the National Institutes of Health (GM088290 to F.C.S.) and the Howard Hughes Medical Institute, of which P.W.S. is an Investigator.\n\nAccepted Version - nihms429942.pdf
Supplemental Material - mmc1.pdf
Supplemental Material - mmc2.avi
", "abstract": "The recognition of molecular patterns associated with specific pathogens or food sources is fundamental to ecology and plays a major role in the evolution of predator-prey relationships. Recent studies showed that nematodes produce an evolutionarily highly conserved family of small molecules, the ascarosides, which serve essential functions in regulating nematode development and behavior. Here, we show that nematophagous fungi, natural predators of soil-dwelling nematodes, can detect and respond to ascarosides. Nematophagous fungi use specialized trapping devices to catch and consume nematodes, and previous studies demonstrated that most fungal species do not produce traps constitutively but rather initiate trap formation in response to their prey. We found that ascarosides, which are constitutively secreted by many species of soil-dwelling nematodes, represent a conserved molecular pattern used by nematophagous fungi to detect prey and trigger trap formation. Ascaroside-induced morphogenesis is conserved in several closely related species of nematophagous fungi and occurs only under nutrient-deprived conditions. Our results demonstrate that microbial predators eavesdrop on chemical communication among their metazoan prey to regulate morphogenesis, providing a striking example of predator-prey coevolution. We anticipate that these findings will have broader implications for understanding other interkingdom interactions involving nematodes, which are found in almost any ecological niche on Earth.", "date": "2013-01-07", "date_type": "published", "publication": "Current Biology", "volume": "23", "number": "1", "publisher": "Cell Press", "pagerange": "83-86", "id_number": "CaltechAUTHORS:20130315-093313407", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130315-093313407", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM088290" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1016/j.cub.2012.11.035", "pmcid": "PMC4047969", "primary_object": { "basename": "nihms429942.pdf", "url": "https://authors.library.caltech.edu/records/zxkfq-p7338/files/nihms429942.pdf" }, "related_objects": [ { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/zxkfq-p7338/files/mmc1.pdf" }, { "basename": "mmc2.avi", "url": "https://authors.library.caltech.edu/records/zxkfq-p7338/files/mmc2.avi" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Hsueh, Yen-Ping; Mahanti, Parag; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/m0h9d-qk991", "eprint_id": 36766, "eprint_status": "archive", "datestamp": "2023-08-19 14:09:17", "lastmod": "2023-10-23 15:45:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Blake-J-A", "name": { "family": "Blake", "given": "J. A." } }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "J." }, "orcid": "0000-0002-7259-8107" }, { "id": "Kishore-R", "name": { "family": "Kishore", "given": "R." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "P." }, "orcid": "0000-0002-7699-0173" }, { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "K." }, "orcid": "0000-0002-1706-4196" } ] }, "title": "Gene Ontology Annotations and Resources", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 The Author(s). Published by Oxford University Press.\nThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which\npermits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited.\n\nPublished online 17 November 2012.\n\nThe GO acknowledges the annotation effort from the\nannotators at: Gramene, Department of Botany and\nPlant Pathology, Oregon State University, Corvallis,\nOR, USA; The J. Craig Venter Institute, Rockville, MD,\nUSA; PAMGO, Wells College, Aurora, NY, USA and\nPAMGO, Virginia Bioinformatics Institute, VA, USA;\nAspGD, Stanford, CA, USA; CGD, Stanford, CA,\nUSA; Sanger GeneDB, Hinxton, UK; InterPro\nEBI, Hinxton, UK; IntAct, EBI, Hinxton, UK;\nseudoCAP, British Columbia, Canada; SGN, Ithaca,\nNY, USA.\n\nFunding:\nNational Human Genome Research Institute (NHGRI)\n[U41HG002273 to the Gene Ontology Consortium,\n1U41HG006104-03 to the European Bioinformatics\nInstitute]; British Heart Foundation [SP/07/007/23671].\nFunding for open access charge: NHGRI.\n\nPublished - Nucl._Acids_Res.-2013--D530-5.pdf
", "abstract": "The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.", "date": "2013-01", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "41", "number": "D1", "publisher": "Oxford University Press", "pagerange": "D530-D535", "id_number": "CaltechAUTHORS:20130204-141831710", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130204-141831710", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U41HG002273" }, { "agency": "NIH", "grant_number": "1U41HG006104-03" }, { "agency": "British Heart Foundation", "grant_number": "SP/07/007/23671" }, { "agency": "National Human Genome Research Institute" } ] }, "corp_creators": { "items": [ "Gene Ontology Consortium" ] }, "doi": "10.1093/nar/gks1050", "pmcid": "PMC3531070", "primary_object": { "basename": "Nucl._Acids_Res.-2013--D530-5.pdf", "url": "https://authors.library.caltech.edu/records/m0h9d-qk991/files/Nucl._Acids_Res.-2013--D530-5.pdf" }, "resource_type": "article", "pub_year": "2013", "author_list": "Blake, J. A.; Chan, J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/f970w-y8g42", "eprint_id": 36828, "eprint_status": "archive", "datestamp": "2023-08-22 07:57:32", "lastmod": "2023-10-23 15:49:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Choe-Andrea", "name": { "family": "Choe", "given": "Andrea" } }, { "id": "Chuman-Tatsuji", "name": { "family": "Chuman", "given": "Tatsuji" } }, { "id": "von-Reuss-S-H", "name": { "family": "von Reuss", "given": "Stephan H." } }, { "id": "Dossey-A-T", "name": { "family": "Dossey", "given": "Aaron T." } }, { "id": "Yim-Joshua-J", "name": { "family": "Yim", "given": "Joshua J." } }, { "id": "Ajredini-R", "name": { "family": "Ajredini", "given": "Ramadan" } }, { "id": "Kolawa-A-A", "name": { "family": "Kolawa", "given": "Adam A." } }, { "id": "Kaplan-F", "name": { "family": "Kaplan", "given": "Fatma" }, "orcid": "0000-0002-9565-0211" }, { "id": "Alborn-H-T", "name": { "family": "Alborn", "given": "Hans T." }, "orcid": "0000-0003-3918-5041" }, { "id": "Teal-P-E-A", "name": { "family": "Teal", "given": "Peter E. A." } }, { "id": "Schroeder-F-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Edison-A-S", "name": { "family": "Edison", "given": "Arthur S." }, "orcid": "0000-0002-5686-2350" } ] }, "title": "Sex-specific mating pheromones in the nematode Panagrellus redivivus", "ispublished": "pub", "full_text_status": "public", "keywords": "chemical ecology; chemical signaling; peroxisomal \u03b2-oxidation; metabolomics", "note": "\u00a9 2012 National Academy of Sciences. \n\nContributed by Paul W. Sternberg, October 23, 2012 (sent for review July 5, 2012).\nPublished online before print December 3, 2012.\n\nWe thank James R. Rocca for expert assistance in NMR\ndata collection and interpretation. NMR data were collected in the University of Florida Advanced Magnetic Resonance Imaging and Spectroscopy (AMRIS) Facility, which is supported in part by the National Science Foundation-funded National High Magnetic Field Laboratory. Support for this study was from National Institutes of Health Grant R01GM085285.\n\nAuthor contributions: A.C., T.C., S.H.v.R., A.T.D., R.A., F.C.S., P.W.S., and A.S.E. designed\nresearch; A.C., T.C., S.H.v.R., A.T.D., J.J.Y., R.A., A.A.K., and F.K. performed research; J.J.Y.,\nA.A.K., H.T.A., and P.E.A.T. contributed new reagents/analytic tools; A.C., T.C., S.H.v.R.,\nA.T.D., F.C.S., P.W.S., and A.S.E. analyzed data; A.C., T.C., S.H.v.R., F.C.S., P.W.S., and A.S.E.\nwrote the paper; A.C., P.W.S., and A.S.E. conceived of purification of Panagrellus redivivus\ncues; A.C. performed the behavior assays for the activity-guided fractionation; A.C. and\nA.A.K. performed the behavior assays for the synthesized ascarosides; T.C., S.H.v.R., A.T.D.,\nand R.A. conducted activity-guided fractionation, purification, and structural elucidation\nof dhas#18 and ascr#1; S.H.v.R. and F.C.S. conducted targeted screening of ascarosides and\nthe Mosher analysis for absolute configuration of dhas#18; J.J.Y. and F.C.S. synthesized\ndhas#18; R.A. grew large-scale liquid cultures of P. redivivus and performed solid-phase\nextractions; and F.K., H.T.A., and P.E.A.T. trained T.C. for the activity-guided purification\nof Panagrellus mating pheromone and developed methods for LC-MS to analyze and\npurify the fractions.\n\nPublished - PNAS-2012-Choe-20949-54.pdf
Supplemental Material - pnas.201218302SI.pdf
Supplemental Material - sfig01.pdf
Supplemental Material - sfig02.pdf
Supplemental Material - sfig03.pdf
Supplemental Material - sfig04.pdf
Supplemental Material - sfig05.pdf
", "abstract": "Nematodes use an extensive chemical language based on glycosides of the dideoxysugar ascarylose for developmental regulation (dauer formation), male sex attraction, aggregation, and dispersal. However, no examples of a female- or hermaphrodite-specific sex attractant have been identified to date. In this study, we investigated the pheromone system of the gonochoristic sour paste nematode Panagrellus redivivus, which produces sex-specific attractants of the opposite sex. Activity-guided fractionation of the P. redivivus exometabolome revealed that males are strongly attracted to ascr#1 (also known as daumone), an ascaroside previously identified from Caenorhabditis elegans hermaphrodites. Female P. redivivus are repelled by high concentrations of ascr#1 but are specifically attracted to a previously unknown ascaroside that we named dhas#18, a dihydroxy derivative of the known ascr#18 and an ascaroside that features extensive functionalization of the lipid-derived side chain. Targeted profiling of the P. redivivus exometabolome revealed several additional ascarosides that did not induce strong chemotaxis. We show that P. redivivus females, but not males, produce the male-attracting ascr#1, whereas males, but not females, produce the female-attracting dhas#18. These results show that ascaroside biosynthesis in P. redivivus is highly sex-specific. Furthermore, the extensive side chain functionalization in dhas#18, which is reminiscent of polyketide-derived natural products, indicates unanticipated biosynthetic capabilities in nematodes.", "date": "2012-12-18", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "109", "number": "51", "publisher": "National Academy of Sciences", "pagerange": "20949-20954", "id_number": "CaltechAUTHORS:20130208-132151908", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130208-132151908", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01GM085285" } ] }, "doi": "10.1073/pnas.1218302109", "pmcid": "PMC3529029", "primary_object": { "basename": "sfig01.pdf", "url": "https://authors.library.caltech.edu/records/f970w-y8g42/files/sfig01.pdf" }, "related_objects": [ { "basename": "sfig02.pdf", "url": "https://authors.library.caltech.edu/records/f970w-y8g42/files/sfig02.pdf" }, { "basename": "sfig03.pdf", "url": "https://authors.library.caltech.edu/records/f970w-y8g42/files/sfig03.pdf" }, { "basename": "sfig04.pdf", "url": "https://authors.library.caltech.edu/records/f970w-y8g42/files/sfig04.pdf" }, { "basename": "sfig05.pdf", "url": "https://authors.library.caltech.edu/records/f970w-y8g42/files/sfig05.pdf" }, { "basename": "PNAS-2012-Choe-20949-54.pdf", "url": "https://authors.library.caltech.edu/records/f970w-y8g42/files/PNAS-2012-Choe-20949-54.pdf" }, { "basename": "pnas.201218302SI.pdf", "url": "https://authors.library.caltech.edu/records/f970w-y8g42/files/pnas.201218302SI.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Choe, Andrea; Chuman, Tatsuji; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/xdex8-t5s39", "eprint_id": 36213, "eprint_status": "archive", "datestamp": "2023-08-19 13:45:46", "lastmod": "2023-10-20 22:53:04", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Pang-Shuo", "name": { "family": "Pang", "given": "Shuo" } }, { "id": "Han-Chao", "name": { "family": "Han", "given": "Chao" } }, { "id": "Kato-Mihoko", "name": { "family": "Kato", "given": "Mihoko" }, "orcid": "0000-0003-3827-8879" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Yang-Changhuei", "name": { "family": "Yang", "given": "Changhuei" }, "orcid": "0000-0001-8791-0354" } ] }, "title": "Wide and scalable field-of-view Talbot-grid-based fluorescence microscopy", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Optical Society of America. \n\nReceived September 18, 2012; revised October 24, 2012; accepted November 5, 2012. \n\nWe thank Danielle V. Bower (Biological Imaging Center, Caltech) for the help in sample preparation. This project is funded by NIH under the grant 1R01AI096226-01.\n\nPublished - ol-37-23-5018.pdf
Accepted Version - nihms491195.pdf
", "abstract": "Here we report a low-cost and simple wide field-of-view (FOV) on-chip fluorescence-imaging platform, termed fluorescence Talbot microscopy (FTM), which utilizes the Talbot self-imaging effect to enable efficient fluorescence imaging over a large and directly scalable FOV. The FTM prototype has a resolution of 1.2 \u03bcm and an FOV of 3.9\u2009\u2009mm\u00d73.5\u2009\u2009mm. We demonstrate the imaging capability of FTM on fluorescently labeled breast cancer cells (SK-BR-3) and human embryonic kidney 293 (HEK) cells expressing green fluorescent protein.", "date": "2012-12-01", "date_type": "published", "publication": "Optics Letters", "volume": "37", "number": "23", "publisher": "Optical Society of America", "pagerange": "5018-5020", "id_number": "CaltechAUTHORS:20130107-153250959", "issn": "0146-9592", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130107-153250959", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "1R01AI096226-01" } ] }, "doi": "10.1364/OL.37.005018", "pmcid": "PMC3718313", "primary_object": { "basename": "nihms491195.pdf", "url": "https://authors.library.caltech.edu/records/xdex8-t5s39/files/nihms491195.pdf" }, "related_objects": [ { "basename": "ol-37-23-5018.pdf", "url": "https://authors.library.caltech.edu/records/xdex8-t5s39/files/ol-37-23-5018.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Pang, Shuo; Han, Chao; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/d5ejf-cjf86", "eprint_id": 40994, "eprint_status": "archive", "datestamp": "2023-08-19 13:41:59", "lastmod": "2023-10-24 23:21:50", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dillman-A-R", "name": { "family": "Dillman", "given": "Adler R." }, "orcid": "0000-0001-7171-4332" }, { "id": "Mortazavi-A", "name": { "family": "Mortazavi", "given": "Ali" }, "orcid": "0000-0002-4259-6362" }, { "id": "Hallem-E-A", "name": { "family": "Hallem", "given": "Elissa A." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Host-Seeking, Olfaction, Foraging Strategies, and the Genomic Architecture of Parasitisim among Steinernema Nematodes", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2012 Society of Nematologists.", "abstract": "Many parasitic nematodes actively seek out hosts to infect and thus complete their lifecycles. Olfaction is thought to\nplay an important role in the host-seeking process, with parasites following a chemical trail toward host-associated odors.\nSteinernema is a diverse genus of entomopathogenic nematodes, with over 60 described species. The host-seeking behaviors\nof Steinernema include chemotaxis and jumping behavior and vary along a foraging strategy continuum between cruise and\nambush strategies. Little is known about the odors that stimulate host-seeking behavior or how olfactory information is\ninterpreted in these agriculturally important parasitic nematodes. We explored the host-seeking responses of several Steinernema\nspecies to CO_2 and volatile organic compounds produced by laboratory and ecologically relevant potential hosts.\nWe show that all Steinernema species tested are attracted to CO_2, but display varying behavioral responses to different\npotential hosts, suggesting that they can differentiate between potential hosts based on odor alone. CO_2 seems to play a key\nrole in the host-seeking process for steinernematids, though this varies for different parasite-host combinations and for\ndifferent host-seeking behaviors. Further, we used gas chromatography-mass spectrometry and solid-phase microextractiongas\nchromatography-mass spectrometry to identify odorants emitted by seven potential hosts. We found that these odorants\nstimulate host-seeking behaviors in a species-specific manner, suggesting that parasitic nematodes have evolved highly\nspecialized olfactory systems to enable their navigation through complex environments and make appropriate host selection\ndecisions. To pursue these observations further, we sequenced the genomes and transcriptomes of five Steinernema species\n(S. carpocapsae, S. scapterisci, S. monticolum, S. feltiae, and S. glaseri). In an unbiased search through the vast genomic\ndata, we found striking evidence of expansions in protease, protease inhibitor, and G-protein coupled receptor families. Our\nresults indicate that Steinernema species have experienced significant evolution of these protein families, provocatively suggesting that the repertoire of olfactory receptors and armory of proteases underlie niche partitioning and the evolution of\nforaging strategy and host range among Steinernema nematodes.", "date": "2012-12", "date_type": "published", "publication": "Journal of Nematology", "volume": "44", "number": "4", "publisher": "Society of Nematologists", "pagerange": "460-461", "id_number": "CaltechAUTHORS:20130829-111020625", "issn": "0022-300X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130829-111020625", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "resource_type": "article", "pub_year": "2012", "author_list": "Dillman, Adler R.; Mortazavi, Ali; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/4w26n-pk771", "eprint_id": 95439, "eprint_status": "archive", "datestamp": "2023-08-19 13:35:43", "lastmod": "2023-10-20 20:14:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gupta-B-P", "name": { "family": "Gupta", "given": "Bhagwati P." } }, { "id": "Hanna-Rose-W", "name": { "family": "Hanna-Rose", "given": "Wendy" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Morphogenesis of the vulva and the vulval-uterine connection", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Gupta et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nEdited by Barbara Meyer. Last revised June 8, 2012. Published November 30, 2012. \n\nWe thank members of our laboratories for discussion and feedback. BPG is supported by funds from NSERC, CIHR and Ministry of Research and Innovation (through ERA program). WHR is supported by R01 GM086786 from the NIH and IOS-071867 from the NSF. PWS is an investigator of the Howard Hughes Medical Institute.\n\nPublished - vulvamorph.pdf
", "abstract": "The C. elegans hermaphrodite vulva is an established model system to study mechanisms of cell fate specification and tissue morphogenesis. The adult vulva is a tubular shaped organ composed of seven concentric toroids that arise from selective fusion between differentiated vulval progeny. The dorsal end of the vulval tubule is connected to the uterus via a multinucleate syncytium utse (uterine-seam) cell. The vulval tubule and utse are formed as a result of changes in morphogenetic processes such as cell polarity, adhesion, and invagination. A number of genes controlling these processes are conserved all the way up to human and function in similar developmental contexts. This makes it possible to extend the findings to other metazoan systems. Gene expression studies in the vulval and uterine cells have revealed the presence of regulatory networks specifying distinct cell fates. Thus, these two cell types serve as a good system to understand how gene networks confer unique cell identities both experimentally and computationally. This chapter focuses on morphogenetic processes during the formation of the vulva and its connection to uterus.", "date": "2012-11-30", "date_type": "published", "publication": "WormBook: the online review of C. elegans biology", "publisher": "WormBase", "pagerange": "Art. No. 1.152.1", "id_number": "CaltechAUTHORS:20190513-132517279", "issn": "1551-8507", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190513-132517279", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)" }, { "agency": "Canadian Institutes of Health Research (CIHR)" }, { "agency": "Ontario Ministry of Research and Innovation" }, { "agency": "NIH", "grant_number": "R01 GM086786" }, { "agency": "NSF", "grant_number": "IOS-071867" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1895/wormbook.1.152.1", "pmcid": "PMC5402222", "primary_object": { "basename": "vulvamorph.pdf", "url": "https://authors.library.caltech.edu/records/4w26n-pk771/files/vulvamorph.pdf" }, "resource_type": "article", "pub_year": "2012", "author_list": "Gupta, Bhagwati P.; Hanna-Rose, Wendy; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/rg8k3-d3369", "eprint_id": 36475, "eprint_status": "archive", "datestamp": "2023-08-19 13:31:35", "lastmod": "2023-10-20 23:11:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Fey-P", "name": { "family": "Fey", "given": "Petra" } }, { "id": "Berardini-T-Z", "name": { "family": "Berardini", "given": "Tanya Z." } }, { "id": "Dodson-R", "name": { "family": "Dodson", "given": "Robert" } }, { "id": "Cooper-L", "name": { "family": "Cooper", "given": "Laurel" } }, { "id": "Li-Donghui", "name": { "family": "Li", "given": "Donghui" } }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "Li-Yuling", "name": { "family": "Li", "given": "Yuling" } }, { "id": "Basu-Siddhartha", "name": { "family": "Basu", "given": "Siddhartha" } }, { "id": "Muller-H-M", "name": { "family": "Muller", "given": "Hans-Michael" } }, { "id": "Chisolm-R", "name": { "family": "Chisholm", "given": "Rex" } }, { "id": "Huala-E", "name": { "family": "Huala", "given": "Eva" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 The Author(s). Published by Oxford University Press.\nThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com.\n\nSubmitted 18 June 2012; Revised 30 September 2012; Accepted 2 October 2012.\n\nWe would like to thank the BioCreative Workshop 2012\nSteering Committee for the opportunity to participate in\nthe workshop and, in particular, C. Arighi for advice and\nsupport regarding the Task III evaluation. We also thank\nC Grove, K Howe, R Kishore, D Raciti, MA Tuli, X Wang,\nG Williams and K Yook for their helpful comments on the\nmanuscript and gratefully acknowledge S. Wimpfheimer for assistance with the figures. The members of the WormBase Consortium are M. Berriman and R. Durbin (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK); T. Bieri, P. Ozersky and J. Spieth (The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA); A. Cabunoc, A. Duong, T.W. Harris and L. Stein (Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, ON, Canada M5G0A); J. Chan, W.J. Chen, J. Done, C. Grove, R. Kishore, R. Lee, Y. Li, H.M. Muller, C. Nakamura, D. Raciti, G. Schindelman, K. Van Auken, D. Wang, X. Wang, K. Yook and P.W. Sternberg (Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA); J. Hodgkin (Genetics Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom); P. Davis, K. Howe, M. Paulini, M.A. Tuli, G. Williams and P. Kersey\n(EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK).\n\nFunding:\nThe US National Human Genome Research Institute\n(HG02223 to WormBase) and the British Medical Research\nCouncil (G070119 to WormBase); The US National Human\nGenome Research Institute (HG004090 to Textpresso); The\nUS National Institute of Health (GM64426 to dictyBase);\nThe National Science Foundation (DBI-0850219 to TAIR],\nwith additional support from TAIR sponsors (http://www.\narabidopsis.org/doc/about/tair_sponsors/413); The National\nScience Foundation (0822201 to The Plant Ontology); US\nNational Human Genome Research Institute (HG002273 to\nThe Gene Ontology Consortium). PWS is an investigator\nwith the Howard Hughes Medical Institute. Funding for\nopen access charge: US National Human Genome\nResearch Institute [Grant no. HG002273].\n\nPublished - VanAuken_2012pbas040.pdf
", "abstract": "WormBase, dictyBase and The Arabidopsis Information Resource (TAIR) are model organism databases containing information about Caenorhabditis elegans and other nematodes, the social amoeba Dictyostelium discoideum and related Dictyostelids and the flowering plant Arabidopsis thaliana, respectively. Each database curates multiple data types from the primary research literature. In this article, we describe the curation workflow at WormBase, with particular emphasis on our use of text-mining tools (BioCreative 2012, Workshop Track II). We then describe the application of a specific component of that workflow, Textpresso for Cellular Component Curation (CCC), to Gene Ontology (GO) curation at dictyBase and TAIR (BioCreative 2012, Workshop Track III). We find that, with organism-specific modifications, Textpresso can be used by dictyBase and TAIR to annotate gene productions to GO's Cellular Component (CC) ontology.", "date": "2012-11-17", "date_type": "published", "publication": "Database : The Journal of Biological Databases and Curation", "volume": "2012", "publisher": "Oxford University Press", "pagerange": "Art. No. bas040", "id_number": "CaltechAUTHORS:20130118-102637703", "issn": "1758-0463", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130118-102637703", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HG02223" }, { "agency": "Medical Research Council (UK)", "grant_number": "G070119" }, { "agency": "NIH", "grant_number": "HG004090" }, { "agency": "NIH", "grant_number": "GM64426" }, { "agency": "NSF", "grant_number": "DBI-0850219" }, { "agency": "NSF", "grant_number": "IOS-0822201" }, { "agency": "NIH", "grant_number": "HG002273" }, { "agency": "National Human Genome Research Institute" } ] }, "corp_creators": { "items": [ "WormBase Consortium" ] }, "doi": "10.1093/database/bas040", "pmcid": "PMC3500519", "primary_object": { "basename": "VanAuken_2012pbas040.pdf", "url": "https://authors.library.caltech.edu/records/rg8k3-d3369/files/VanAuken_2012pbas040.pdf" }, "resource_type": "article", "pub_year": "2012", "author_list": "Van Auken, Kimberly; Fey, Petra; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/8sdz3-tab27", "eprint_id": 34313, "eprint_status": "archive", "datestamp": "2023-08-22 07:07:35", "lastmod": "2023-10-19 14:49:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schwarz-E-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Kato-Mihoko", "name": { "family": "Kato", "given": "Mihoko" }, "orcid": "0000-0003-3827-8879" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Functional transcriptomics of a migrating cell in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "major sperm protein; nematode development; transcriptional profiling; twin pore potassium channels; conserved uncharacterized proteins", "note": "\u00a9 2012 by the National Academy of Sciences.\n\nEdited by Ruth Lehmann, New York University Medical Center, New York, NY, and approved August 24, 2012 (received for review February 22, 2012). Published online before print September 18, 2012. \n\nWe thank M. Goodman, M. Chalfie, and A. Mortazavi for early support in developing single-cell RT-PCR; B. Williams for providing\ncontrol spike poly(A)+ RNAs; L. Schaeffer, D. Trout, and I. Antoshechkin of the Jacobs Genome Center for Illumina sequencing; A. Narayan for help setting up the dissection rig; J. Downes for scoring linker cell migration phenotypes; J. Thomas for his list of transcription factors; WormBase for gene annotations; and T. Brown, Y.-P. Hsueh, A. Roeder, K. Yook, and A. Zaslaver for comments. This work was supported by National Institutes of Health Grant GM084389 and by the Howard Hughes Medical Institute, with which P.W.S. is an Investigator. \n\nAuthor contributions: E.M.S. and M.K. designed research; E.M.S. and M.K. performed research; E.M.S., M.K., and P.W.S. analyzed data; and E.M.S., M.K., and P.W.S. wrote the paper. \n\nThe authors declare no conflict of interest.\n\nPublished - PNAS-2012-Schwarz-16246-51.pdf
Supplemental Material - sapp.doc
Supplemental Material - sd01.xlsx
", "abstract": "In both metazoan development and metastatic cancer, migrating\ncells must carry out a detailed, complex program of sensing cues,\nbinding substrates, and moving their cytoskeletons. The linker cell\nin Caenorhabditis elegans males undergoes a stereotyped migration\nthat guides gonad organogenesis, occurs with precise timing,\nand requires the nuclear hormone receptor NHR-67. To better understand\nhow this occurs, we performed RNA-seq of individually\nstaged and dissected linker cells, comparing transcriptomes from\nlinker cells of third-stage (L3) larvae, fourth-stage (L4) larvae, and\nnhr-67-RNAi\u2013treated L4 larvae. We observed expression of 8,000\u2013\n10,000 genes in the linker cell, 22\u201325% of which were up- or downregulated\n20-fold during development by NHR-67. Of genes that\nwe tested by RNAi, 22% (45 of 204) were required for normal\nshape and migration, suggesting that many NHR-67\u2013dependent,\nlinker cell-enriched genes play roles in this migration. One unexpected\nclass of genes up-regulated by NHR-67 was tandem pore\npotassium channels, which are required for normal linker-cell migration.\nWe also found phenotypes for genes with human orthologs\nbut no previously described migratory function. Our results\nprovide an extensive catalog of genes that act in a migrating cell,\nidentify unique molecular functions involved in nematode cell migration,\nand suggest similar functions in humans.", "date": "2012-10-02", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "109", "number": "40", "publisher": "National Academy of Sciences", "pagerange": "16246-16251", "id_number": "CaltechAUTHORS:20120924-131548711", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120924-131548711", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM084389" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1073/pnas.1203045109", "pmcid": "PMC3479585", "primary_object": { "basename": "PNAS-2012-Schwarz-16246-51.pdf", "url": "https://authors.library.caltech.edu/records/8sdz3-tab27/files/PNAS-2012-Schwarz-16246-51.pdf" }, "related_objects": [ { "basename": "sapp.doc", "url": "https://authors.library.caltech.edu/records/8sdz3-tab27/files/sapp.doc" }, { "basename": "sd01.xlsx", "url": "https://authors.library.caltech.edu/records/8sdz3-tab27/files/sd01.xlsx" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Schwarz, Erich M.; Kato, Mihoko; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/sxp8z-vw703", "eprint_id": 35269, "eprint_status": "archive", "datestamp": "2023-08-19 12:57:57", "lastmod": "2023-10-20 15:55:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kuntz-S-G", "name": { "family": "Kuntz", "given": "Steven G." } }, { "id": "Williams-B-A", "name": { "family": "Williams", "given": "Brian A." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Wold-B-J", "name": { "family": "Wold", "given": "Barbara J." }, "orcid": "0000-0003-3235-8130" } ] }, "title": "Transcription factor redundancy and tissue-specific regulation: Evidence from functional and physical network connectivity", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Published by Cold Spring Harbor Laboratory Press.\n\nReceived November 11, 2011; accepted in revised form May 24, 2012.\nPublished in Advance June 22, 2012.\nSome nematode strains used in this work were provided by the the\nCaenorhabditis Genetics Center, funded by the NIH National\nCenter for Research Resources (NCRR).We thank M. Krause for the\nanti-HLH-1 antibody, K. Fisher for her assistance in generating\ndensity graphs, S. Pepke for her assistance in generating conservation\ngraphs, A. Kirilusha for his motif counter, H. Amrhein\nfor assistance in managing genomic databases, M. Anaya and\nJ. Vielmetter for purification of the antibody, I. Antoshechkin and\nL. Schaeffer for library making and sequencing, J. DeModena for\nassistance in obtaining reagents and helping grow worms, and\nWormbase. This work was supported by NIGMS (GM084389 to\nP.W.S. and B.J.W.), the HHMI, with which P.W.S. is an investigator,\nthe National Human Genome Research Institute (NHGRI),\nthe Beckman Institute at Caltech, and the NCRR.\n\nPublished - Genome_Res.-2012-Kuntz-1907-19.pdf
Supplemental Material - KuntzSupplementaryMaterial.pdf
", "abstract": "Two major transcriptional regulators of Caenorhabditis elegans bodywall muscle (BWM) differentiation, hlh-1 and unc-120, are expressed in muscle where they are known to bind and regulate several well-studied muscle-specific genes. Simultaneously mutating both factors profoundly inhibits formation of contractile BWM. These observations were consistent with a simple network model in which the muscle regulatory factors drive tissue-specific transcription by binding selectively near muscle-specific targets to activate them. We tested this model by measuring the number, identity, and tissue-specificity of functional regulatory targets for each factor. Some joint regulatory targets (218) are BWM-specific and enriched for nearby HLH-1 binding. However, contrary to the simple model, the majority of genes regulated by one or both muscle factors are also expressed significantly in non-BWM tissues. We also mapped global factor occupancy by HLH-1, and created a genetic interaction map that identifies hlh-1 collaborating transcription factors. HLH-1 binding did not predict proximate regulatory action overall, despite enrichment for binding among BWM-specific positive regulatory targets of hlh-1. We conclude that these tissue-specific factors contribute much more broadly to the transcriptional output of muscle tissue than previously thought, offering a partial explanation for widespread HLH-1 occupancy. We also identify a novel regulatory connection between the BWM-specific hlh-1 network and the hlh-8/twist nonstriated muscle network. Finally, our results suggest a molecular basis for synthetic lethality in which hlh-1 and unc-120 mutant phenotypes are mutually buffered by joint additive regulation of essential target genes, with additional buffering suggested via newly identified hlh-1 interacting factors.", "date": "2012-10", "date_type": "published", "publication": "Genome Research", "volume": "22", "number": "10", "publisher": "Cold Spring Harbor Laboratory Press", "pagerange": "1907-1919", "id_number": "CaltechAUTHORS:20121102-133341484", "issn": "1088-9051", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121102-133341484", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Institute of General Medical Sciences (NIGMS)", "grant_number": "GM084389" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "National Human Genome Research Institute (NHGRI)" }, { "agency": "Caltech Beckman Institute" }, { "agency": "National Center for Research Resources (NCRR)" } ] }, "doi": "10.1101/gr.133306.111", "pmcid": "PMC3460186", "primary_object": { "basename": "KuntzSupplementaryMaterial.pdf", "url": "https://authors.library.caltech.edu/records/sxp8z-vw703/files/KuntzSupplementaryMaterial.pdf" }, "related_objects": [ { "basename": "Genome_Res.-2012-Kuntz-1907-19.pdf", "url": "https://authors.library.caltech.edu/records/sxp8z-vw703/files/Genome_Res.-2012-Kuntz-1907-19.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Kuntz, Steven G.; Williams, Brian A.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/f1g05-e9056", "eprint_id": 33957, "eprint_status": "archive", "datestamp": "2023-08-22 06:24:47", "lastmod": "2023-10-18 21:40:04", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dillman-A-R", "name": { "family": "Dillman", "given": "Adler R." }, "orcid": "0000-0001-7171-4332" }, { "id": "Guillermin-M-L", "name": { "family": "Guillermin", "given": "Manon L." } }, { "id": "Lee-Joon-Ha", "name": { "family": "Lee", "given": "Joon Ha" } }, { "id": "Kim-Brian", "name": { "family": "Kim", "given": "Brian" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Hallem-E-A", "name": { "family": "Hallem", "given": "Elissa A." } } ] }, "title": "Olfaction shapes host\u2013parasite interactions in parasitic nematodes", "ispublished": "pub", "full_text_status": "public", "keywords": "entomopathogens; chemosensation; Heterorhabditis; Steinernema", "note": "\u00a9 2012 National Academy of Sciences. \n\nContributed by Paul W. Sternberg, July 9, 2012 (sent for review May 8, 2012). \n\nWe thank Todd Ciche, Heidi Goodrich-Blair, S. Patricia Stock, Byron Adams, and the Caenorhabditis Genetics Center for nematode and bacterial stocks; Nathan Dalleska and the California Institute of Technology Environmental Analysis Center for help with TD-GC-MS, SPMEGC-MS, and subsequent analysis; Richard Menking for help in collecting insects around the California Institute of Technology campus; John Rodriguez and the Rio Hondo golf course grounds crew for access to the grounds and help in setting up mole cricket traps; Chris Cronin for help with the design and maintenance of mole cricket sound traps and mole cricket collection; Joseph Tang, John DeModena, Brian Anderson, Michael Castillo, Esther Thompson, and Beth Dillman for help with mole cricket collection; Joseph Vanderwaart and the University of California, Los Angeles Statistical Consulting Center for help with statistical analysis; and James Baldwin and Jagan Srinivasan for critical reading of the manuscript. We also thank the reviewers of this manuscript for their insightful comments. This work was supported by National Institutes of Health US Public Health Service Training Grant T32GM07616 (to A.R.D.), the Howard Hughes Medical Institute (of which P.W.S. is an investigator), and a Summer Undergraduate Research Fellowship (to B.K.). E.A.H. is an Alfred P. Sloan Research Fellow and a Rita Allen Foundation Scholar.\n\nPublished - PNAS-2012-Dillman-E2324-33.pdf
Supplemental Material - pnas.201211436SI.pdf
Supplemental Material - sd01.xlsx
", "abstract": "Many parasitic nematodes actively seek out hosts in which to complete their lifecycles. Olfaction is thought to play an important role in the host-seeking process, with parasites following a chemical trail toward host-associated odors. However, little is known about the olfactory cues that attract parasitic nematodes to hosts or the behavioral responses these cues elicit. Moreover, what little is known focuses on easily obtainable laboratory hosts rather than on natural or other ecologically relevant hosts. Here we investigate the olfactory responses of six diverse species of entomopathogenic nematodes (EPNs) to seven ecologically relevant potential invertebrate hosts, including one known natural host and other potential hosts collected from the environment. We show that EPNs respond differentially to the odor blends emitted by live potential hosts as well as to individual host-derived odorants. In addition, we show that EPNs use the universal host cue CO_2 as well as host-specific odorants for host location, but the relative importance of CO_2 versus host-specific odorants varies for different parasite\u2013host combinations and for different host-seeking behaviors. We also identified host-derived odorants by gas chromatography-mass spectrometry and found that many of these odorants stimulate host-seeking behaviors in a species-specific manner. Taken together, our results demonstrate that parasitic nematodes have evolved specialized olfactory systems that likely contribute to appropriate host selection.", "date": "2012-08-28", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "109", "number": "35", "publisher": "National Academy of Sciences", "pagerange": "E2324-E2333", "id_number": "CaltechAUTHORS:20120910-104141784", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120910-104141784", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM07616" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Caltech Summer Undergraduate Research Fellowship (SURF)" }, { "agency": "Alfred P. Sloan Foundation" }, { "agency": "Rita Allen Foundation" } ] }, "doi": "10.1073/pnas.1211436109", "pmcid": "PMC3435218", "primary_object": { "basename": "PNAS-2012-Dillman-E2324-33.pdf", "url": "https://authors.library.caltech.edu/records/f1g05-e9056/files/PNAS-2012-Dillman-E2324-33.pdf" }, "related_objects": [ { "basename": "pnas.201211436SI.pdf", "url": "https://authors.library.caltech.edu/records/f1g05-e9056/files/pnas.201211436SI.pdf" }, { "basename": "sd01.xlsx", "url": "https://authors.library.caltech.edu/records/f1g05-e9056/files/sd01.xlsx" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Dillman, Adler R.; Guillermin, Manon L.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/45m6e-way58", "eprint_id": 33587, "eprint_status": "archive", "datestamp": "2023-08-19 11:54:27", "lastmod": "2023-10-18 20:27:03", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yuet-Kai-P", "name": { "family": "Yuet", "given": "Kai" }, "orcid": "0000-0002-1381-8923" }, { "id": "Doma-M-K", "name": { "family": "Doma", "given": "Meenakshi" } }, { "id": "Ngo-John-T", "name": { "family": "Ngo", "given": "John" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul" }, "orcid": "0000-0002-7699-0173" }, { "id": "Tirrell-D-A", "name": { "family": "Tirrell", "given": "David" }, "orcid": "0000-0003-3175-4596" } ] }, "title": "Cell type-specific proteomic profiling in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "restricted", "abstract": "Caenorhabditis elegans is a small, free-living soil\nnematode. For several decades. this multi-cellular\norganism has been used to study intricate biological\nand molecular processes in fields ranging from\ndevelopmental biology to neurobiology. In a complex\neukaryote like C. elegans, cell and tissue heterogeneity\nrestricts the usefulness oflarge-scale, mass spectrometrybased\nanalysis of an organism's proteome. As worm cell\nlines are not available and enriching for specific cells or\ntissues is challenging, researchers cannot systematically\nidentify low abundance proteins expressed in specifc\ncells or tissues from whole-worm lysates. To isolate\nprotein from specific cells, we have engineered a family of mutant C. elegans phenylalanyl-tRNA synthetases\ncapable of appending azide- or alkynyl-bearing analogs\nof phenylalanine to tRNAPhe. As these analogs are\nnot substrates for any of the wild-type aminoacyltRNA\nsynthetases in C. elegans, we achieved cell type\nselectivity by spatially restricting the expression of a\nmutant synthetase using cell type-specific promoters.\nBecause proteins from those cells that express the\nmutant synthetase - and only those cells - contain the\nanalogs, they can be enriched by treatment with alkyneor\nazide-functionalized biotin reagents and subsequent\naffinity chromatography for identification by LC/MSMS.", "date": "2012-08", "date_type": "published", "publication": "Protein Science", "volume": "21", "number": "S1", "publisher": "Wiley", "pagerange": "126", "id_number": "CaltechAUTHORS:20120828-072510427", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120828-072510427", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "resource_type": "article", "pub_year": "2012", "author_list": "Yuet, Kai; Doma, Meenakshi; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/18t9y-bva41", "eprint_id": 102784, "eprint_status": "archive", "datestamp": "2023-08-19 12:00:25", "lastmod": "2023-10-20 00:30:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Murfin-K-E", "name": { "family": "Murfin", "given": "Kristen E." } }, { "id": "Dillman-A-R", "name": { "family": "Dillman", "given": "Adler R." }, "orcid": "0000-0001-7171-4332" }, { "id": "Foster-J-M", "name": { "family": "Foster", "given": "Jeremy M." } }, { "id": "Bulgheresi-S", "name": { "family": "Bulgheresi", "given": "Silvia" } }, { "id": "Slatko-B-E", "name": { "family": "Slatko", "given": "Barton E." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Goodrich-Blair-H", "name": { "family": "Goodrich-Blair", "given": "Heidi" } } ] }, "title": "Nematode-Bacterium Symbioses\u2014Cooperation and Conflict Revealed in the \"Omics\" Age", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Marine Biological Laboratory. \n\nReceived 24 January 2012; accepted 24 May 2012. \n\nDiscussions relevant to this paper were facilitated by the NEMASYM (Nematode-Bacterium Symbioses) Research Coordination Network (NSF- IOS 0840932 to SPS), which was also used to support publication costs. ARD was supported by a United States Public Health Service Training Grant (T32GM07616). KEM was supported by National Institutes of Health (NIH) National Research Service Award T32 AI55397. JMF and BES are supported by New England Biolabs, Inc. PWS is an Investigator with the Howard Hughes Medical Institute. HGB was supported by NSF (IOS-0920631 and IOS-0950873). SB is very grateful to Mark Blaxter and Stephen Bridgett for sequencing, assembling, and making publicly available the Laxus oneistus transcriptome. SB is supported by the Austrian Science Fund (FWF) grant P224701.\n\nPublished - BBLv223n1p85.pdf
Accepted Version - nihms414070.pdf
Supplemental Material - Supplemental_Table_1_BIOLBULL-D-12-00014.docx
Supplemental Material - Supplemental_Table_2_BIOLBULL-D-12-00014.docx
", "abstract": "Nematodes are ubiquitous organisms that have a significant global impact on ecosystems, economies, agriculture, and human health. The applied importance of nematodes and the experimental tractability of many species have promoted their use as models in various research areas, including developmental biology, evolutionary biology, ecology, and animal-bacterium interactions. Nematodes are particularly well suited for the investigation of host associations with bacteria because all nematodes have interacted with bacteria during their evolutionary history and engage in a variety of association types. Interactions between nematodes and bacteria can be positive (mutualistic) or negative (pathogenic/parasitic) and may be transient or stably maintained (symbiotic). Furthermore, since many mechanistic aspects of nematode-bacterium interactions are conserved, their study can provide broader insights into other types of associations, including those relevant to human diseases. Recently, genome-scale studies have been applied to diverse nematode-bacterial interactions and have helped reveal mechanisms of communication and exchange between the associated partners. In addition to providing specific information about the system under investigation, these studies also have helped inform our understanding of genome evolution, mutualism, and innate immunity. In this review we discuss the importance and diversity of nematodes, \"omics\"' studies in nematode-bacterial systems, and the wider implications of the findings.", "date": "2012-08", "date_type": "published", "publication": "Biological Bulletin", "volume": "223", "number": "1", "publisher": "Marine Biological Laboratory", "pagerange": "85-102", "id_number": "CaltechAUTHORS:20200427-082904476", "issn": "0006-3185", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200427-082904476", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "IOS-0840932" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM07616" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 AI55397" }, { "agency": "New England Biolabs, Inc." }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NSF", "grant_number": "IOS-0920631" }, { "agency": "NSF", "grant_number": "IOS-0950873" }, { "agency": "FWF Der Wissenschaftsfonds", "grant_number": "P224701" } ] }, "doi": "10.1086/bblv223n1p85", "pmcid": "PMC3508788", "primary_object": { "basename": "BBLv223n1p85.pdf", "url": "https://authors.library.caltech.edu/records/18t9y-bva41/files/BBLv223n1p85.pdf" }, "related_objects": [ { "basename": "Supplemental_Table_1_BIOLBULL-D-12-00014.docx", "url": "https://authors.library.caltech.edu/records/18t9y-bva41/files/Supplemental_Table_1_BIOLBULL-D-12-00014.docx" }, { "basename": "Supplemental_Table_2_BIOLBULL-D-12-00014.docx", "url": "https://authors.library.caltech.edu/records/18t9y-bva41/files/Supplemental_Table_2_BIOLBULL-D-12-00014.docx" }, { "basename": "nihms414070.pdf", "url": "https://authors.library.caltech.edu/records/18t9y-bva41/files/nihms414070.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Murfin, Kristen E.; Dillman, Adler R.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/w2p7g-6cr80", "eprint_id": 35277, "eprint_status": "archive", "datestamp": "2023-08-19 11:57:10", "lastmod": "2023-10-20 15:55:32", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Murfin-K-E", "name": { "family": "Murfin", "given": "Kristen E." } }, { "id": "Dillman-A-R", "name": { "family": "Dillman", "given": "Adler R." }, "orcid": "0000-0001-7171-4332" }, { "id": "Foster-J-M", "name": { "family": "Foster", "given": "Jeremy M." } }, { "id": "Bulgheresi-S", "name": { "family": "Bulgheresi", "given": "Silvia" } }, { "id": "Slatko-B-E", "name": { "family": "Slatko", "given": "Barton E." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Goodrich-Blair-H", "name": { "family": "Goodrich-Blair", "given": "Heidi" } } ] }, "title": "Nematode-Bacterium Symbioses\u2014Cooperation and Conflict Revealed in the \"Omics\" Age", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Marine Biological Laboratory. \n\nReceived 24 January 2012; accepted 24 May 2012. \n\nDiscussions relevant to this paper were facilitated by the NEMASYM (Nematode-Bacterium Symbioses) Research Coordination Network (NSF- IOS 0840932 to SPS), which was also used to support publication costs. ARD was supported by a United States Public Health Service Training Grant (T32GM07616). KEM was supported by National Institutes of Health (NIH) National Research Service Award T32 AI55397. JMF and BES are supported by New England Biolabs, Inc. PWS is an Investigator with the Howard Hughes Medical Institute. HGB was supported by NSF (IOS-0920631 and IOS-0950873). SB is very grateful to Mark Blaxter and Stephen Bridgett for sequencing, assembling, and making publicly available the Laxus oneistus transcriptome. SB is supported by the Austrian Science Fund (FWF) grant P224701.\n\nAccepted Version - nihms414070.pdf
", "abstract": "Nematodes are ubiquitous organisms that have a significant global impact on ecosystems, economies, agriculture, and human health. The applied importance of nematodes and the experimental tractability of many species have promoted their use as models in various research areas, including developmental biology, evolutionary biology, ecology, and animal-bacterium interactions. Nematodes are particularly well suited for the investigation of host associations with bacteria because all nematodes have interacted with bacteria during their evolutionary history and engage in a variety of association types. Interactions between nematodes and bacteria can be positive (mutualistic) or negative (pathogenic/parasitic) and may be transient or stably maintained (symbiotic). Furthermore, since many mechanistic aspects of nematode-bacterium interactions are conserved, their study can provide broader insights into other types of associations, including those relevant to human diseases. Recently, genome-scale studies have been applied to diverse nematode-bacterial interactions and have helped reveal mechanisms of communication and exchange between the associated partners. In addition to providing specific information about the system under investigation, these studies also have helped inform our understanding of genome evolution, mutualism, and innate immunity. In this review we discuss the importance and diversity of nematodes, \"omics\"' studies in nematode-bacterial systems, and the wider implications of the findings.", "date": "2012-08", "date_type": "published", "publication": "Biological Bulletin", "volume": "223", "number": "1", "publisher": "Marine Biological Laboratory", "pagerange": "85-102", "id_number": "CaltechAUTHORS:20121105-085733081", "issn": "0006-3185", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121105-085733081", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM07616" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 AI55397" }, { "agency": "New England Biolabs, Inc." }, { "agency": "NSF", "grant_number": "IOS-0920631" }, { "agency": "NSF", "grant_number": "IOS-0950873" }, { "agency": "FWF Der Wissenschaftsfonds", "grant_number": "P224701" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1086/BBLv223n1p85", "pmcid": "PMC3508788", "primary_object": { "basename": "nihms414070.pdf", "url": "https://authors.library.caltech.edu/records/w2p7g-6cr80/files/nihms414070.pdf" }, "resource_type": "article", "pub_year": "2012", "author_list": "Murfin, Kristen E.; Dillman, Adler R.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/33jns-8sc61", "eprint_id": 35519, "eprint_status": "archive", "datestamp": "2023-08-19 11:57:48", "lastmod": "2023-10-20 16:26:41", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Izrayelit-Y", "name": { "family": "Izrayelit", "given": "Yevgeniy" } }, { "id": "Srinivasan-J", "name": { "family": "Srinivasan", "given": "Jagan" }, "orcid": "0000-0001-5449-7938" }, { "id": "Campbell-S-L", "name": { "family": "Campbell", "given": "Sydney L." } }, { "id": "Jo-Yeara", "name": { "family": "Jo", "given": "Yeara" } }, { "id": "von-Reuss-S-H", "name": { "family": "von Reuss", "given": "Stephan H." } }, { "id": "Genoff-M-C", "name": { "family": "Genoff", "given": "Margaux-C" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Schroeder-F-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" } ] }, "title": "Targeted Metabolomics Reveals a Male Pheromone and Sex-Specific Ascaroside Biosynthesis in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 American Chemical Society.\n\nReceived: April 11, 2012; Accepted: June 4, 2012; Published: June 5, 2012.\n\nWe thank S. Lee (Cornell University) for helpful discussions\nand J. Liu (Cornell University) for providing strain CB4856.\nThis work was supported in part by the National Institutes of Health (GM088290 to F.C.S., GM008500 to Y.I., and\nGM085285 to F.C.S. and P.W.S.); the Howard Hughes\nMedical Institute, with which P.W.S. is an Investigator; and\nthe Vassar College Mary Landon Sague Fellowship (to Y.I.).\n\nPublished - cb300169c.pdf
Accepted Version - nihms385140.pdf
Supplemental Material - cb300169c_si_001.pdf
", "abstract": "In the model organism Caenorhabditis elegans, a class of small molecule signals called ascarosides regulate development, mating, and social behaviors. Ascaroside production has been studied in the predominant sex, the hermaphrodite, but not in males, which account for less than 1% of wild-type worms grown under typical laboratory conditions. Using HPLC\u2013MS-based targeted metabolomics, we show that males also produce ascarosides and that their ascaroside profile differs markedly from that of hermaphrodites. Whereas hermaphrodite ascaroside profiles are dominated by ascr#3, containing an \u03b1,\u03b2-unsaturated fatty acid, males predominantly produce the corresponding dihydro-derivative ascr#10. This small structural modification profoundly affects signaling properties: hermaphrodites are retained by attomole-amounts of male-produced ascr#10, whereas hermaphrodite-produced ascr#3 repels hermaphrodites and attracts males. Male production of ascr#10 is population density-dependent, indicating sensory regulation of ascaroside biosynthesis. Analysis of gene expression data supports a model in which sex-specific regulation of peroxisomal \u03b2-oxidation produces functionally different ascaroside profiles.", "date": "2012-08", "date_type": "published", "publication": "ACS Chemical Biology", "volume": "7", "number": "8", "publisher": "American Chemical Society", "pagerange": "1321-1325", "id_number": "CaltechAUTHORS:20121116-132822383", "issn": "1554-8929", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121116-132822383", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM088290" }, { "agency": "NIH", "grant_number": "GM008500" }, { "agency": "NIH", "grant_number": "GM085285" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Vassar College Mary Landon Sague Fellowship" } ] }, "doi": "10.1021/cb300169c", "pmcid": "PMC3423530", "primary_object": { "basename": "cb300169c.pdf", "url": "https://authors.library.caltech.edu/records/33jns-8sc61/files/cb300169c.pdf" }, "related_objects": [ { "basename": "cb300169c_si_001.pdf", "url": "https://authors.library.caltech.edu/records/33jns-8sc61/files/cb300169c_si_001.pdf" }, { "basename": "nihms385140.pdf", "url": "https://authors.library.caltech.edu/records/33jns-8sc61/files/nihms385140.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Izrayelit, Yevgeniy; Srinivasan, Jagan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/11f5j-yqq75", "eprint_id": 32273, "eprint_status": "archive", "datestamp": "2023-08-19 11:18:18", "lastmod": "2023-10-17 23:05:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dillman-A-R", "name": { "family": "Dillman", "given": "Adler R." }, "orcid": "0000-0001-7171-4332" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Entomopathogenic nematodes", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Elsevier. Available online 4 June 2012.\n\nAccepted Version - nihms737513.pdf
", "abstract": "What are entomopathogenic nematodes? Nematodes seem to have evolved to occupy nearly every niche imaginable, including a wide diversity of parasitic niches. Among the vast variety of parasitic nematodes, some have evolved an association with insect-pathogenic bacteria. Together the bacteria and nematode are a lethal duo. These nematodes are called 'entomopathogenic nematodes'. Essentially the nematodes serve as mobile vectors for their insect-pathogenic bacteria cargo, like little Typhoid Marys. The nematodes seek out and invade potential hosts and release their pathogenic payload into the nutrient-rich hemolymph. Infected insect hosts die quickly, the bacteria proliferate, the nematodes feed on bacteria and insect tissues, and reproduce. When the host cadaver is depleted of resources, nematodes associated with pathogenic bacteria emerge and search for new hosts to infect (Figure 1). The cooperation with bacteria and the speed with which they kill set entomopathogenic nematodes apart from other nematode parasites.", "date": "2012-06-05", "date_type": "published", "publication": "Current Biology", "volume": "22", "number": "11", "publisher": "Cell Press", "pagerange": "R430-R431", "id_number": "CaltechAUTHORS:20120706-082800053", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120706-082800053", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.cub.2012.03.047", "pmcid": "PMC4662870", "primary_object": { "basename": "nihms737513.pdf", "url": "https://authors.library.caltech.edu/records/11f5j-yqq75/files/nihms737513.pdf" }, "resource_type": "article", "pub_year": "2012", "author_list": "Dillman, Adler R. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/t4p80-dcm43", "eprint_id": 95462, "eprint_status": "archive", "datestamp": "2023-08-19 11:15:20", "lastmod": "2023-10-20 20:15:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dillman-A-R", "name": { "family": "Dillman", "given": "Adler R." }, "orcid": "0000-0001-7171-4332" }, { "id": "Mortazavi-A", "name": { "family": "Mortazavi", "given": "Ali" }, "orcid": "0000-0002-4259-6362" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Incorporating Genomics into the Toolkit of Nematology", "ispublished": "pub", "full_text_status": "public", "keywords": "ecological genomics, evolution, genomics, nematodes, phylogenetics, proteomics, sequencing", "note": "\u00a9 2012 The Society of Nematologists. \n\nWe would like to thank all the researchers who have contributed to the wealth of literature from which we have drawn and from which we have been stimulated, enlightened, and encouraged. We also wish to thank Ganpati Jagdale and Parwinder Grewal for organizing the \"EPNs as model systems in stress physiology and evolutionary biology\" symposium at the 2011 Society of Nematologists annual meeting, and for inviting the authors to contribute. We express gratitude to Hillel Schwartz, Jagan Srinivasan, James Baldwin, Mihoko Kato, Margaret Ho, and two reviewers for helpful comments and discussion on the manuscript. ARD was supported by a United States Public Health Service Training Grant (T32GM07616). PWS is an investigator with the Howard Hughes Medical Institute.\n\nPublished - 191.pdf
", "abstract": "The study of nematode genomes over the last three decades has relied heavily on the model organism Caenorhabditis elegans, which remains the best-assembled and annotatedmetazoan genome. This is now changing as a rapidly expanding number of nematodes of medical and economic importance have been sequenced in recent years. The advent of sequencing technologies to achieve the equivalent of the $1000 human genome promises that every nematode genome of interest will eventually be sequenced at a reasonable cost. As the sequencing of species spanning the nematode phylumbecomes a routine part of characterizing nematodes, the comparative approach and the increasing use of ecological context will help us to further understand the evolution and functional specializations of any given species by comparing its genome to that of other closely and more distantly related nematodes.We review the current state of nematode genomics and discuss some of the highlights that these genomes have revealed and the trend and benefits of ecological genomics, emphasizing the potential for new genomes and the exciting opportunities this provides for nematological studies.", "date": "2012-06", "date_type": "published", "publication": "Journal of Nematology", "volume": "44", "number": "2", "publisher": "Society of Nematologists", "pagerange": "191-205", "id_number": "CaltechAUTHORS:20190514-074932646", "issn": "0022-300X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-074932646", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM07616" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "pmcid": "PMC3578471", "primary_object": { "basename": "191.pdf", "url": "https://authors.library.caltech.edu/records/t4p80-dcm43/files/191.pdf" }, "resource_type": "article", "pub_year": "2012", "author_list": "Dillman, Adler R.; Mortazavi, Ali; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/swak1-15p28", "eprint_id": 31813, "eprint_status": "archive", "datestamp": "2023-08-19 10:55:44", "lastmod": "2023-10-17 21:21:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Choe-Andrea", "name": { "family": "Choe", "given": "Andrea" } }, { "id": "von-Reuss-S-H", "name": { "family": "von Reuss", "given": "Stephan H." } }, { "id": "Kogan-D", "name": { "family": "Kogan", "given": "Dima" } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } }, { "id": "Platzer-E-G", "name": { "family": "Platzer", "given": "Edward G." } }, { "id": "Schroeder-F-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Ascaroside Signaling Is Widely Conserved among Nematodes", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Elsevier Ltd. \n\nReceived: December 14, 2011; Revised: February 16, 2012;\nAccepted: March 12, 2012; Published online: April 12, 2012.\n\nWe thank the Caenorhabditis Genetics Center, Marie-Anne Felix, Antoon Ploeg, S. Patricia Stock, J. Scott Cameron, Teresa Mullens, Jennifer Becker, Scott Edwards, John Darsow, Adler R. Dillman, and Hillel T. Schwartz for their contribution of nematodes to this study. We further thank Adler R. Dillman for assembling a phylogenetic tree for the species used in this study. We thank Moises Garcia for his help in manufacturing the copper chambers used in the attraction assay. We thank Arthur S. Edison, Adler R. Dillman, Hillel T. Schwartz, Jagan Srinivasan, David A. Prober, and Bruce A. Hay for their valuable suggestions. This work was supported in part by a National Institutes of Health grant (GM088290 to F.C.S. and GM085285 to A.S. Edison, F.C.S., and P.W.S.), and the Howard Hughes Medical\nInstitute, with which P.W.S. is an Investigator.\n\nAccepted Version - nihms365633.pdf
Supplemental Material - mmc1.pdf
", "abstract": "Background: Nematodes are among the most successful animals on earth and include important human pathogens, yet little is known about nematode pheromone systems. A group of small molecules called ascarosides has been found to mediate mate finding, aggregation, and developmental diapause in Caenorhabditis elegans, but it is unknown whether ascaroside signaling exists outside of the genus Caenorhabditis.\nResults: To determine whether ascarosides are used as signaling molecules by other nematode species, we performed a mass spectrometry-based screen for ascarosides in secretions from a variety of both free-living and parasitic (plant, insect, and animal) nematodes. We found that most of the species analyzed, including nematodes from several different clades, produce species-specific ascaroside mixtures. In some cases, ascaroside biosynthesis patterns appear to correlate with phylogeny, whereas in other cases, biosynthesis seems to correlate with lifestyle and ecological niche. We further show that ascarosides mediate distinct nematode behaviors, such as retention, avoidance, and long-range attraction, and that different nematode species respond to distinct, but overlapping, sets of ascarosides.\nConclusions: Our findings indicate that nematodes utilize a conserved family of signaling molecules despite having evolved to occupy diverse ecologies. Their structural features and level of conservation are evocative of bacterial quorum sensing, where acyl homoserine lactones (AHLs) are both produced and sensed by many species of gram-negative bacteria. The identification of species-specific ascaroside profiles may enable pheromone-based approaches to interfere with reproduction and survival of parasitic nematodes, which are responsible for significant agricultural losses and many human diseases worldwide.", "date": "2012-05-08", "date_type": "published", "publication": "Current Biology", "volume": "22", "number": "9", "publisher": "Cell Press", "pagerange": "772-780", "id_number": "CaltechAUTHORS:20120605-104715210", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120605-104715210", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM088290" }, { "agency": "NIH", "grant_number": "GM085285" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1016/j.cub.2012.03.024", "pmcid": "PMC3360977", "primary_object": { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/swak1-15p28/files/mmc1.pdf" }, "related_objects": [ { "basename": "nihms365633.pdf", "url": "https://authors.library.caltech.edu/records/swak1-15p28/files/nihms365633.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Choe, Andrea; von Reuss, Stephan H.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/m17qb-ern29", "eprint_id": 32348, "eprint_status": "archive", "datestamp": "2023-08-19 10:43:15", "lastmod": "2023-10-17 23:20:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kroetz-S-M", "name": { "family": "Kroetz", "given": "Silvina M." } }, { "id": "Srinivasan-J", "name": { "family": "Srinivasan", "given": "Jagan" }, "orcid": "0000-0001-5449-7938" }, { "id": "Yaghoobian-J", "name": { "family": "Yaghoobian", "given": "Jonathan" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Hong-Ray-L", "name": { "family": "Hong", "given": "Ray L." } } ] }, "title": "The cGMP Signaling Pathway Affects Feeding Behavior in the Necromenic Nematode Pristionchus pacificus", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Kroetz et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.\n\nReceived October 13, 2011; Accepted March 5, 2012; Published April 26, 2012\nEditor: Anne C. Hart, Brown University, United States of America.\nFunding: This work was supported by Minority Access to Research Careers (MARC) and Caltech's MURF (Minority Undergraduate Research Fellowship) to SMK,\nHHMI to JS and PWS, and National Institutes of Health grant SC2GM089602 awarded to RLH. The funders had no role in study design, data collection and analysis,\ndecision to publish, or preparation of the manuscript.\nWe thank S. Murray for help with C. crescentus and B. subtilis strains as well as C. van Buskirk for critically reading the manuscript.\nAuthor Contributions:\nConceived and designed the experiments: RLH JS. Performed the\nexperiments: SMK JY JS. Analyzed the data: SMK RLH JY JS.\nContributed reagents/materials/analysis tools: RLH PWS. Wrote the\npaper: RLH JS PWS.\n\nPublished - Kroetz2012p18736PLoS_ONE.pdf
", "abstract": "Background: The genetic tractability and the species-specific association with beetles make the nematode Pristionchus pacificus an exciting emerging model organism for comparative studies in development and behavior. P. pacificus differs from Caenorhabditis elegans (a bacterial feeder) by its buccal teeth and the lack of pharyngeal grinders, but almost nothing is known about which genes coordinate P. pacificus feeding behaviors, such as pharyngeal pumping rate, locomotion, and fat storage.\nMethodology/Principal Findings:\n\nWe analyzed P. pacificus pharyngeal pumping rate and locomotion behavior on and off food, as well as on different species of bacteria (Escherichia coli, Bacillus subtilis, and Caulobacter crescentus). We found that the cGMP-dependent protein kinase G (PKG) Ppa-EGL-4 in P. pacificus plays an important role in regulating the pumping rate, mouth form dimorphism, the duration of forward locomotion, and the amount of fat stored in intestine. In addition, Ppa-EGL-4 interacts with Ppa-OBI-1, a recently identified protein involved in chemosensation, to influence feeding and locomotion behavior. We also found that C. crescentus NA1000 increased pharyngeal pumping as well as fat storage in P. pacificus.\nConclusions:\n\nThe PKG EGL-4 has conserved functions in regulating feeding behavior in both C. elegans and P. pacificus nematodes. The Ppa-EGL-4 also has been co-opted during evolution to regulate P. pacificus mouth form dimorphism that indirectly affect pharyngeal pumping rate. Specifically, the lack of Ppa-EGL-4 function increases pharyngeal pumping, time spent in forward locomotion, and fat storage, in part as a result of higher food intake. Ppa-OBI-1 functions upstream or parallel to Ppa-EGL-4. The beetle-associated omnivorous P. pacificus respond differently to changes in food state and food quality compared to the exclusively bacteriovorous C. elegans.", "date": "2012-04-26", "date_type": "published", "publication": "PLoS ONE", "volume": "7", "number": "4", "publisher": "Public Library of Science", "pagerange": "Art. No. e34464", "id_number": "CaltechAUTHORS:20120711-101659347", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120711-101659347", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Minority Access to Research Careers (MARC)" }, { "agency": "Caltech Minority Undergraduate Research Fellowship (MURF)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "SC2GM089602" } ] }, "doi": "10.1371/journal.pone.0034464", "pmcid": "PMC3338501", "primary_object": { "basename": "Kroetz2012p18736PLoS_ONE.pdf", "url": "https://authors.library.caltech.edu/records/m17qb-ern29/files/Kroetz2012p18736PLoS_ONE.pdf" }, "resource_type": "article", "pub_year": "2012", "author_list": "Kroetz, Silvina M.; Srinivasan, Jagan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/hhebr-gf491", "eprint_id": 95463, "eprint_status": "archive", "datestamp": "2023-08-19 10:36:30", "lastmod": "2023-10-20 20:15:40", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Howe-K-L", "name": { "family": "Howe", "given": "Kevin" } }, { "id": "Davis-P-M", "name": { "family": "Davis", "given": "Paul" } }, { "id": "Paulini-M-G", "name": { "family": "Paulini", "given": "Michael" } }, { "id": "Tuli-M-A", "name": { "family": "Tuli", "given": "Mary Ann" } }, { "id": "Williams-G", "name": { "family": "Williams", "given": "Gary" } }, { "id": "Yook-Karen-J", "name": { "family": "Yook", "given": "Karen" }, "orcid": "0000-0002-4457-6787" }, { "id": "Durbin-R", "name": { "family": "Durbin", "given": "Richard" } }, { "id": "Kersey-P", "name": { "family": "Kersey", "given": "Paul" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "WormBase - Annotating many nematode genomes", "ispublished": "pub", "full_text_status": "public", "keywords": "Caenorhabditis elegans , annotation, community resource, genome, model organism database, nematode, parasitic nematode, sequence curation", "note": "\u00a9 2012 Landes Bioscience. \n\nSubmitted: 11/02/11; Revised: 02/02/12; Accepted: 02/02/12. \n\nThis work is supported by the US National Institutes of Health (Grant no. P41 HG02223); US National Human Genome Research Institute (Grant no. P41-HG02223); and British Medical Research Council (Grant no. G070119); P.W.S. is an investigator with the Howard Hughes Medical Institute. Funding for open access charge: US National Human Genome Research Institute (Grant no. P41-HG02223).\n\nPublished - worm-1-15.pdf
", "abstract": "WormBase (www.wormbase.org) has been serving the scientific community for over 11 years as the central repository for genomic and genetic information for the soil nematode Caenorhabditis elegans. The resource has evolved from its beginnings as a database housing the genomic sequence and genetic and physical maps of a single species, and now represents the breadth and diversity of nematode research, currently serving genome sequence and annotation for around 20 nematodes. In this article, we focus on WormBase's role of genome sequence annotation, describing how we annotate and integrate data from a growing collection of nematode species and strains. We also review our approaches to sequence curation, and discuss the impact on annotation quality of large functional genomics projects such as modENCODE.", "date": "2012-04-04", "date_type": "published", "publication": "Worm", "volume": "1", "number": "1", "publisher": "Taylor & Francis", "pagerange": "15-21", "id_number": "CaltechAUTHORS:20190514-075525922", "issn": "2162-4054", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-075525922", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P41 HG02223" }, { "agency": "Medical Research Council (UK)", "grant_number": "G070119" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.4161/worm.19574", "pmcid": "PMC3670165", "primary_object": { "basename": "worm-1-15.pdf", "url": "https://authors.library.caltech.edu/records/hhebr-gf491/files/worm-1-15.pdf" }, "resource_type": "article", "pub_year": "2012", "author_list": "Howe, Kevin; Davis, Paul; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/bqek9-1qk59", "eprint_id": 31678, "eprint_status": "archive", "datestamp": "2023-08-19 10:29:52", "lastmod": "2023-10-17 18:46:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schaedel-O-N", "name": { "family": "Schaedel", "given": "Oren N." } }, { "id": "Gerisch-B", "name": { "family": "Gerisch", "given": "Birgit" } }, { "id": "Antebi-A", "name": { "family": "Antebi", "given": "Adam" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Hormonal Signal Amplification Mediates Environmental Conditions during Development and Controls an Irreversible Commitment to Adulthood", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Schaedel et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.\n\nReceived September 2, 2011; Accepted March 2, 2012; Published April 10, 2012.\nAcademic Editor: Gary Ruvkun, Massachusetts General Hospital Havard Medical School, United States of America.\n\nFunding: P.W.S is an investigator with the Howard Hughes Medical Institute; O.N.S. was supported by training grant GM07676 and the Caltech Center for Biological Circuit Design. AA was supported by the NIA/NIH (RO1AG027498), the Ellison Medical Foundation, the Max Planck Society, BMBF, and CECAD. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. \n\nWe thank Gladys Medina, Barbara Perry, and John DeModena for technical assistance; WormBase; members of the Sternberg laboratory for\nhelpful discussions; and Dr. Amir Sapir, Dr. Hillel Schwartz, and Dr. Andrea Choe for critically reading the manuscript and Dr. Axel Bethke for helpful discussions. Some nematode strains were provided by the Caenorhabditis Genetics Center, which is funded by the NIH National\nCenter for Research Resources. qPCR was performed in the Millard and Muriel Jacobs Genetics and Genomics Laboratory at the California Institute of Technology.\nAuthor Contributions:\nThe author(s) have made the following declarations about their\ncontributions: Conceived and designed the experiments: OS BG AA.\nPerformed the experiments: OS BG. Analyzed the data: OS BG AA PWS.\nContributed reagents/materials/analysis tools: OS BG. Wrote the paper:\nOS BG AA PWS.\n\nPublished - Schaedel2012p18239Plos_Biol.pdf
Supplemental Material - journal.pbio.1001306.s001.tif
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Supplemental Material - journal.pbio.1001306.s009.rtf
", "abstract": "Many animals can choose between different developmental fates to maximize fitness. Despite the complexity of environmental cues and life history, different developmental fates are executed in a robust fashion. The nematode Caenorhabditis elegans serves as a powerful model to examine this phenomenon because it can adopt one of two developmental fates (adulthood or diapause) depending on environmental conditions. The steroid hormone dafachronic acid (DA) directs development to adulthood by regulating the transcriptional activity of the nuclear hormone receptor DAF-12. The known role of DA suggests that it may be the molecular mediator of environmental condition effects on the developmental fate decision, although the mechanism is yet unknown. We used a combination of physiological and molecular biology techniques to demonstrate that commitment to reproductive adult development occurs when DA levels, produced in the neuroendocrine XXX cells, exceed a threshold. Furthermore, imaging and cell ablation experiments demonstrate that the XXX cells act as a source of DA, which, upon commitment to adult development, is amplified and propagated in the epidermis in a DAF-12 dependent manner. This positive feedback loop increases DA levels and drives adult programs in the gonad and epidermis, thus conferring the irreversibility of the decision. We show that the positive feedback loop canalizes development by ensuring that sufficient amounts of DA are dispersed throughout the body and serves as a robust fate-locking mechanism to enforce an organism-wide binary decision, despite noisy and complex environmental cues. These mechanisms are not only relevant to C. elegans but may be extended to other hormonal-based decision-making mechanisms in insects and mammals.", "date": "2012-04", "date_type": "published", "publication": "PLoS Biology", "volume": "10", "number": "4", "publisher": "Public Library of Science", "pagerange": "Art. No. e1001306", "id_number": "CaltechAUTHORS:20120529-114112675", "issn": "1544-9173", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120529-114112675", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Caltech Center for Biological Circuit Design" }, { "agency": "NIH", "grant_number": "RO1AG027498" }, { "agency": "Ellison Medical Foundation" }, { "agency": "Max Planck Society" }, { "agency": "Bundesministerium f\u00fcr Bildung und Forschung (BMBF)" }, { "agency": "CECAD" }, { "agency": "NIH", "grant_number": "GM07676" } ] }, "doi": "10.1371/journal.pbio.1001306", "pmcid": "PMC3323525", "primary_object": { "basename": "Schaedel2012p18239Plos_Biol.pdf", "url": "https://authors.library.caltech.edu/records/bqek9-1qk59/files/Schaedel2012p18239Plos_Biol.pdf" }, "related_objects": [ { "basename": "journal.pbio.1001306.s003.tif", "url": "https://authors.library.caltech.edu/records/bqek9-1qk59/files/journal.pbio.1001306.s003.tif" }, { "basename": "journal.pbio.1001306.s004.tif", "url": "https://authors.library.caltech.edu/records/bqek9-1qk59/files/journal.pbio.1001306.s004.tif" }, { "basename": "journal.pbio.1001306.s006.tif", "url": "https://authors.library.caltech.edu/records/bqek9-1qk59/files/journal.pbio.1001306.s006.tif" }, { "basename": "journal.pbio.1001306.s009.rtf", "url": "https://authors.library.caltech.edu/records/bqek9-1qk59/files/journal.pbio.1001306.s009.rtf" }, { "basename": "journal.pbio.1001306.s001.tif", "url": "https://authors.library.caltech.edu/records/bqek9-1qk59/files/journal.pbio.1001306.s001.tif" }, { "basename": "journal.pbio.1001306.s002.tif", "url": "https://authors.library.caltech.edu/records/bqek9-1qk59/files/journal.pbio.1001306.s002.tif" }, { "basename": "journal.pbio.1001306.s005.tif", "url": "https://authors.library.caltech.edu/records/bqek9-1qk59/files/journal.pbio.1001306.s005.tif" }, { "basename": "journal.pbio.1001306.s007.rtf", "url": "https://authors.library.caltech.edu/records/bqek9-1qk59/files/journal.pbio.1001306.s007.rtf" }, { "basename": "journal.pbio.1001306.s008.rtf", "url": "https://authors.library.caltech.edu/records/bqek9-1qk59/files/journal.pbio.1001306.s008.rtf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Schaedel, Oren N.; Gerisch, Birgit; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/zj54j-mqt78", "eprint_id": 32285, "eprint_status": "archive", "datestamp": "2023-08-19 10:20:10", "lastmod": "2023-10-17 23:06:21", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bandrowski-A-E", "name": { "family": "Bandrowski", "given": "A. E." } }, { "id": "Cachat-J", "name": { "family": "Cachat", "given": "J." } }, { "id": "Li-Y", "name": { "family": "Li", "given": "Y." } }, { "id": "M\u00fcller-H-M", "name": { "family": "M\u00fcller", "given": "H. M." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "P. W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Ciccarase-P", "name": { "family": "Ciccarase", "given": "P." } }, { "id": "Clark-T", "name": { "family": "Clark", "given": "T." } }, { "id": "Marenco-L", "name": { "family": "Marenco", "given": "L." } }, { "id": "Wang-R", "name": { "family": "Wang", "given": "R." } }, { "id": "Astakhov-V", "name": { "family": "Astakhov", "given": "V." } }, { "id": "Grethe-J-S", "name": { "family": "Grethe", "given": "J. S." } }, { "id": "Martone-M-E", "name": { "family": "Martone", "given": "M. E." } } ] }, "title": "A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 The Author(s). Published by Oxford University Press. Submitted 19 October 2011; Revised 6 January 2012; Accepted 9 January 2012. We thank Mrs Andrea Stagg and many assistant curators for their hard work on the NIF Registry. This work was supported by and has been funded in whole\nor in part through the NIH Blueprint for Neuroscience\nResearch with Federal funds from the National Institute\non Drug Abuse, National Institutes of Health, Department\nof Health and Human Services [Contract Number\nHHSN271200577531C]. P.W.S. is an Investigator with the\nHoward Hughes Medical Institute. Conflict of interest. None declared.\n\nPublished - Bandrowski2012p18676Database-Oxford.pdf
", "abstract": "The breadth of information resources available to researchers on the Internet continues to expand, particularly in light of recently implemented data-sharing policies required by funding agencies. However, the nature of dense, multifaceted neuroscience data and the design of contemporary search engine systems makes efficient, reliable and relevant discovery of such information a significant challenge. This challenge is specifically pertinent for online databases, whose dynamic content is 'hidden' from search engines. The Neuroscience Information Framework (NIF; http://www.neuinfo.org) was funded by the NIH Blueprint for Neuroscience Research to address the problem of finding and utilizing neuroscience-relevant resources such as software tools, data sets, experimental animals and antibodies across the Internet. From the outset, NIF sought to provide an accounting of available resources, whereas developing technical solutions to finding, accessing and utilizing them. The curators therefore, are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping the contents current. In the initial phases of the project, all aspects of the registration and curation processes were manual. However, as the number of resources grew, manual curation became impractical. This report describes our experiences and successes with developing automated resource discovery and semiautomated type characterization with text-mining scripts that facilitate curation team efforts to discover, integrate and display new content. We also describe the DISCO framework, a suite of automated web services that significantly reduce manual curation efforts to periodically check for resource updates. Lastly, we discuss DOMEO, a semi-automated annotation tool that improves the discovery and curation of resources that are not necessarily website-based (i.e. reagents, software tools). Although the ultimate goal of automation was to reduce the workload of the curators, it has resulted in valuable analytic by-products that address accessibility, use and citation of resources that can now be shared with resource owners and the larger scientific community.", "date": "2012-03-20", "date_type": "published", "publication": "Database : The Journal of Biological Databases and Curation", "volume": "2012", "publisher": "Oxford University Press", "pagerange": "Art. No. bas005-", "id_number": "CaltechAUTHORS:20120706-134849278", "issn": "1758-0463", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120706-134849278", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Institute on Drug Abuse" }, { "agency": "NIH", "grant_number": "HHSN271200577531C" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1093/database/bas005", "pmcid": "PMC3308161", "primary_object": { "basename": "Bandrowski2012p18676Database-Oxford.pdf", "url": "https://authors.library.caltech.edu/records/zj54j-mqt78/files/Bandrowski2012p18676Database-Oxford.pdf" }, "resource_type": "article", "pub_year": "2012", "author_list": "Bandrowski, A. E.; Cachat, J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/4kw1x-aza95", "eprint_id": 31260, "eprint_status": "archive", "datestamp": "2023-08-19 10:06:47", "lastmod": "2023-10-17 15:43:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dillman-A-R", "name": { "family": "Dillman", "given": "Adler R." }, "orcid": "0000-0001-7171-4332" }, { "id": "Chaston-J-M", "name": { "family": "Chaston", "given": "John M." } }, { "id": "Adams-B-J", "name": { "family": "Adams", "given": "Byron J." } }, { "id": "Ciche-T-A", "name": { "family": "Ciche", "given": "Todd A." } }, { "id": "Goodrich-Blair-H", "name": { "family": "Goodrich-Blair", "given": "Heidi" } }, { "id": "Stock-S-P", "name": { "family": "Stock", "given": "S. Patricia" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "An Entomopathogenic Nematode by Any Other Name", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Dillman et al. This is an open-access article distributed under the terms of the Creative\nCommons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium,\nprovided the original author and source are credited.\nPublished March 1, 2012.\nEditor: Glenn F. Rall, The Fox Chase Cancer Center, United States of America.\nFunding: The NEMASYM (Nematode-Bacterium Symbioses) Research Coordination Network (NSF-IOS 0840932\nto S. Patricia Stock) provided funding to attend the 3rd NEAMSYM Meeting in Corvallis, Oregon. ARD was\nsupported by a United States Public Health Service Training Grant (T32GM07616). PWS is an investigator with\nthe Howard Hughes Medical Institute. The funders had no role in study design, data collection and analysis,\ndecision to publish, or preparation of the manuscript.\n\nWe would like to thank collaborators and\ncolleagues who have contributed to the wealth\nof knowledge on this subject. We also wish to\nthank Hillel Schwartz and Jagan Srinivasan for\ncritical review of the manuscript and stimulating\ndiscussion, David Fitch for taxonomic and\nnomenclatural suggestions, and for anonymous\nreviewers whose comments significantly improved\nthis manuscript.\n\nPublished - Dillman2012p17890Plos_Pathog.pdf
", "abstract": "Among the diversity of insect-parasitic nematodes, entomopathogenic nematodes (EPNs) are distinct, cooperating with insect-pathogenic bacteria to kill insect hosts. EPNs have adapted specific mechanisms to associate with and transmit bacteria to insect hosts. New discoveries have expanded this guild of nematodes and refine our understanding of the nature and evolution of insect\u2013nematode associations. Here, we clarify the meaning of \"entomopathogenic\" in nematology and argue that EPNs must rapidly kill their hosts with the aid of bacterial partners and must pass on the associated bacteria to future generations.", "date": "2012-03", "date_type": "published", "publication": "PLoS Pathogens", "volume": "8", "number": "3", "publisher": "Public Library of Science", "pagerange": "Art. No. e1002527", "id_number": "CaltechAUTHORS:20120501-144648190", "issn": "1553-7366", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120501-144648190", "rights": "This is an open-access article distributed under the terms of the Creative\nCommons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium,\nprovided the original author and source are credited.", "funders": { "items": [ { "agency": "NSF", "grant_number": "IOS-0840932" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM07616" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1371/journal.ppat.1002527", "pmcid": "PMC3291613", "primary_object": { "basename": "Dillman2012p17890Plos_Pathog.pdf", "url": "https://authors.library.caltech.edu/records/4kw1x-aza95/files/Dillman2012p17890Plos_Pathog.pdf" }, "resource_type": "article", "pub_year": "2012", "author_list": "Dillman, Adler R.; Chaston, John M.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/vqqr6-a0w45", "eprint_id": 29784, "eprint_status": "archive", "datestamp": "2023-08-19 09:42:35", "lastmod": "2023-10-24 22:27:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Fang-Ruihua", "name": { "family": "Fang", "given": "Ruihua" } }, { "id": "Schindelman-G", "name": { "family": "Schindelman", "given": "Gary" } }, { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Fernandes-J", "name": { "family": "Fernandes", "given": "Jolene" } }, { "id": "Chen-Wen", "name": { "family": "Chen", "given": "Wen" } }, { "id": "Wang-Xiaodong", "name": { "family": "Wang", "given": "Xiaodong" } }, { "id": "Davis-P", "name": { "family": "Davis", "given": "Paul" } }, { "id": "Tuli-M-A", "name": { "family": "Tuli", "given": "Mary Ann" } }, { "id": "Marygold-S-J", "name": { "family": "Marygold", "given": "Steven J." } }, { "id": "Millburn-G", "name": { "family": "Millburn", "given": "Gillian" } }, { "id": "Matthews-B", "name": { "family": "Matthews", "given": "Beverley" } }, { "id": "Zhang-Haiyan", "name": { "family": "Zhang", "given": "Haiyan" } }, { "id": "Brown-N", "name": { "family": "Brown", "given": "Nick" } }, { "id": "Gelbart-W-M", "name": { "family": "Gelbart", "given": "William M." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Automatic categorization of diverse experimental information in the bioscience literature", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Fang et al; licensee BioMed Central Ltd.\nThis is an Open Access article distributed under the terms of the Creative Commons\nAttribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in\nany medium, provided the original work is properly cited.\nReceived: 5 October 2011 Accepted: 26 January 2012. Published: 26 January 2012. This work was supported by grants P41 HG002223, P41 HG002223-10S1, P41 HG000739 and R01 HG004090 from the National Human Genome Research Institute (NHGRI) at the United States National Institutes of Health. We thank\nthe past and present members of WormBase and FlyBase for curating the papers used in this study. We gratefully acknowledge Karen Yook for making the WormBase data type definition available on the WormBase Wiki page;\nJuancarlos Chan for help with getting WormBase training data from the WormBase curation status tracking database; and Hans-Michael M\u00fcller for the full text WormBase papers. PWS is an Investigator with the Howard Hughes Medical Institute.\n\nAuthors' contributions:\nRF developed the algorithm, wrote the program and analyzed all the\ndatasets. GS contributed to the comprehensive SVM scheme and validated\nRNAi results. KVA validated gene product (GO) and mutant allele sequence\nresults. JF validated phenotype analysis results. WC validated gene\nexpression and antibody results. XW validated gene regulation results. PD\nvalidated the training set used for the gene structure correction data type.\nMAT validated mutant allele sequence results. SM and GM provided the\nFlyBase Cambridge datasets. BM and HZ provided the FlyBase Harvard\ndatasets. RF wrote the paper with valuable discussion and critical\ncontributions at all stages of the project from PWS. PWS, GS, KVA, GM, BM, and SM edited the manuscript. All authors read and approved the final\nmanuscript.\n\nPublished - Fang2012p17506BMC_Bioinformatics.pdf
Supplemental Material - 1471-2105-13-16-s1.pdf
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Supplemental Material - 1471-2105-13-16-s11.xlsx
Supplemental Material - 1471-2105-13-16-s12.xlsx
Supplemental Material - 1471-2105-13-16-s13.xlsx
Supplemental Material - 1471-2105-13-16-s14.zip
Supplemental Material - 1471-2105-13-16-s2.pdf
Supplemental Material - 1471-2105-13-16-s3.xls
Supplemental Material - 1471-2105-13-16-s4.xls
Supplemental Material - 1471-2105-13-16-s5.xls
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Supplemental Material - 1471-2105-13-16-s7.xls
Supplemental Material - 1471-2105-13-16-s8.xlsx
Supplemental Material - 1471-2105-13-16-s9.xlsx
", "abstract": "Background:\nCuration of information from bioscience literature into biological knowledge databases is a crucial way of capturing experimental information in a computable form. During the biocuration process, a critical first step is to identify from all published literature the papers that contain results for a specific data type the curator is interested in annotating. This step normally requires curators to manually examine many papers to ascertain which few contain information of interest and thus, is usually time consuming. We developed an automatic method for identifying papers containing these curation data types among a large pool of published scientific papers based on the machine learning method Support Vector Machine (SVM). This classification system is completely automatic and can be readily applied to diverse experimental data types. It has been in use in production for automatic categorization of 10 different experimental datatypes in the biocuration process at WormBase for the past two years and it is in the process of being adopted in the biocuration process at FlyBase and the Saccharomyces Genome Database (SGD). We anticipate that this method can be readily adopted by various databases in the biocuration community and thereby greatly reducing time spent on an otherwise laborious and demanding task. We also developed a simple, readily automated procedure to utilize training papers of similar data types from different bodies of literature such as C. elegans and D. melanogaster to identify papers with any of these data types for a single database. This approach has great significance because for some data types, especially those of low occurrence, a single corpus often does not have enough training papers to achieve satisfactory performance.\nResults:\nWe successfully tested the method on ten data types from WormBase, fifteen data types from FlyBase and three data types from Mouse Genomics Informatics (MGI). It is being used in the curation work flow at WormBase for automatic association of newly published papers with ten data types including RNAi, antibody, phenotype, gene regulation, mutant allele sequence, gene expression, gene product interaction, overexpression phenotype, gene interaction, and gene structure correction.\nConclusions:\nOur methods are applicable to a variety of data types with training set containing several hundreds to a few thousand documents. It is completely automatic and, thus can be readily incorporated to different workflow at different literature-based databases. We believe that the work presented here can contribute greatly to the tremendous task of automating the important yet labor-intensive biocuration effort.", "date": "2012-01-26", "date_type": "published", "publication": "BMC Bioinformatics", "volume": "13", "publisher": "BioMed Central", "pagerange": "Art. No. 16", "id_number": "CaltechAUTHORS:20120320-105305942", "issn": "1471-2105", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120320-105305942", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P41-HG002223" }, { "agency": "NIH", "grant_number": "P41 HG02273-1051" }, { "agency": "NIH", "grant_number": "P41 HG000739" }, { "agency": "NIH", "grant_number": "R01 HG004090" } ] }, "doi": "10.1186/1471-2105-13-16", "pmcid": "PMC3305665", "primary_object": { "basename": "1471-2105-13-16-s1.pdf", "url": "https://authors.library.caltech.edu/records/vqqr6-a0w45/files/1471-2105-13-16-s1.pdf" }, "related_objects": [ { "basename": "1471-2105-13-16-s12.xlsx", "url": "https://authors.library.caltech.edu/records/vqqr6-a0w45/files/1471-2105-13-16-s12.xlsx" }, { "basename": "1471-2105-13-16-s14.zip", "url": "https://authors.library.caltech.edu/records/vqqr6-a0w45/files/1471-2105-13-16-s14.zip" }, { "basename": "1471-2105-13-16-s2.pdf", "url": "https://authors.library.caltech.edu/records/vqqr6-a0w45/files/1471-2105-13-16-s2.pdf" }, { "basename": "1471-2105-13-16-s5.xls", "url": "https://authors.library.caltech.edu/records/vqqr6-a0w45/files/1471-2105-13-16-s5.xls" }, { "basename": "1471-2105-13-16-s6.xls", "url": "https://authors.library.caltech.edu/records/vqqr6-a0w45/files/1471-2105-13-16-s6.xls" }, { "basename": "1471-2105-13-16-s9.xlsx", "url": "https://authors.library.caltech.edu/records/vqqr6-a0w45/files/1471-2105-13-16-s9.xlsx" }, { "basename": "1471-2105-13-16-s13.xlsx", "url": "https://authors.library.caltech.edu/records/vqqr6-a0w45/files/1471-2105-13-16-s13.xlsx" }, { "basename": "1471-2105-13-16-s4.xls", "url": "https://authors.library.caltech.edu/records/vqqr6-a0w45/files/1471-2105-13-16-s4.xls" }, { "basename": "1471-2105-13-16-s8.xlsx", "url": "https://authors.library.caltech.edu/records/vqqr6-a0w45/files/1471-2105-13-16-s8.xlsx" }, { "basename": "1471-2105-13-16-s10.xlsx", "url": "https://authors.library.caltech.edu/records/vqqr6-a0w45/files/1471-2105-13-16-s10.xlsx" }, { "basename": "1471-2105-13-16-s11.xlsx", "url": "https://authors.library.caltech.edu/records/vqqr6-a0w45/files/1471-2105-13-16-s11.xlsx" }, { "basename": "1471-2105-13-16-s3.xls", "url": "https://authors.library.caltech.edu/records/vqqr6-a0w45/files/1471-2105-13-16-s3.xls" }, { "basename": "Fang2012p17506BMC_Bioinformatics.pdf", "url": "https://authors.library.caltech.edu/records/vqqr6-a0w45/files/Fang2012p17506BMC_Bioinformatics.pdf" }, { "basename": "1471-2105-13-16-s7.xls", "url": "https://authors.library.caltech.edu/records/vqqr6-a0w45/files/1471-2105-13-16-s7.xls" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Fang, Ruihua; Schindelman, Gary; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/w9b5e-t7y60", "eprint_id": 29976, "eprint_status": "archive", "datestamp": "2023-08-19 09:41:18", "lastmod": "2023-10-24 22:38:18", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "von-Reuss-S-H", "name": { "family": "von Reuss", "given": "Stephan H." } }, { "id": "Bose-N", "name": { "family": "Bose", "given": "Neelanjan" } }, { "id": "Srinivasan-J", "name": { "family": "Srinivasan", "given": "Jagan" }, "orcid": "0000-0001-5449-7938" }, { "id": "Yim-Joshua-J", "name": { "family": "Yim", "given": "Joshua J." } }, { "id": "Judkins-J-C", "name": { "family": "Judkins", "given": "Joshua C." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Schroeder-F-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" } ] }, "title": "Comparative Metabolomics Reveals Biogenesis of Ascarosides, a\n Modular Library of Small-Molecule Signals in C. elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 American Chemical Society. \n\nReceived: October 30, 2011. Publication Date (Web): January 5, 2012. \n\nWe thank Arthur Edison (University of Florida, Gainesville) for\nhelpful suggestions, the Caenorhabditis Genetics Center, Ho Yi Mak (Stowers Institute), and Shohei Mitani (Tokyo Women's\nMedical University) for providing C. elegans mutant strains, and Maciej Kukula (BTI Mass Spectrometry Facility) and Wei\nChen (Proteomics and Mass Spectrometry Core Facility,\nCornell University) for assistance with HR-MS. This work\nwas supported in part by the National Institutes of Health\n(GM088290, GM085285, and T32GM008500) and the\nCornell/Rockefeller/Sloan-Kettering Training Program in\nChemical Biology.\n\nAccepted Version - nihms350942.pdf
Supplemental Material - ja210202y_si_001.pdf
", "abstract": "In the model organism Caenorhabditis elegans, a family of endogenous small molecules, the ascarosides function as key regulators of developmental timing and behavior that act upstream of conserved signaling pathways. The ascarosides are based on the dideoxysugar ascarylose, which is linked to fatty-acid-like side chains of varying lengths derived from peroxisomal \u03b2-oxidation. Despite the importance of ascarosides for many aspects of C. elegans biology, knowledge of their structures, biosynthesis, and homeostasis remains incomplete. We used an MS/MS-based screen to profile ascarosides in C. elegans wild-type and mutant metabolomes, which revealed a much greater structural diversity of ascaroside derivatives than previously reported. Comparison of the metabolomes from wild-type and a series of peroxisomal \u03b2-oxidation mutants showed that the enoyl CoA-hydratase MAOC-1 serves an important role in ascaroside biosynthesis and clarified the functions of two other enzymes, ACOX-1 and DHS-28. We show that, following peroxisomal \u03b2-oxidation, the ascarosides are selectively derivatized with moieties of varied biogenetic origin and that such modifications can dramatically affect biological activity, producing signaling molecules active at low femtomolar concentrations. Based on these results, the ascarosides appear as a modular library of small-molecule signals, integrating building blocks from three major metabolic pathways: carbohydrate metabolism, peroxisomal \u03b2-oxidation of fatty acids, and amino acid catabolism. Our screen further demonstrates that ascaroside biosynthesis is directly affected by nutritional status and that excretion of the final products is highly selective.", "date": "2012-01-25", "date_type": "published", "publication": "Journal of the American Chemical Society", "volume": "134", "number": "3", "publisher": "American Chemical Society", "pagerange": "1817-1824", "id_number": "CaltechAUTHORS:20120404-104142772", "issn": "0002-7863", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120404-104142772", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM088290" }, { "agency": "NIH", "grant_number": "GM085285" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM008500" }, { "agency": "Cornell/Rockefeller/Sloan-Kettering Training Program in Chemical Biology" } ] }, "doi": "10.1021/ja210202y", "pmcid": "PMC3269134", "primary_object": { "basename": "nihms350942.pdf", "url": "https://authors.library.caltech.edu/records/w9b5e-t7y60/files/nihms350942.pdf" }, "related_objects": [ { "basename": "ja210202y_si_001.pdf", "url": "https://authors.library.caltech.edu/records/w9b5e-t7y60/files/ja210202y_si_001.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "von Reuss, Stephan H.; Bose, Neelanjan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/4nkkb-7nk63", "eprint_id": 29738, "eprint_status": "archive", "datestamp": "2023-08-19 09:24:16", "lastmod": "2023-10-24 22:24:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Srinivasan-J", "name": { "family": "Srinivasan", "given": "Jagan" }, "orcid": "0000-0001-5449-7938" }, { "id": "von-Reuss-S-H", "name": { "family": "von Reuss", "given": "Stephan H." } }, { "id": "Bose-N", "name": { "family": "Bose", "given": "Neelanjan" } }, { "id": "Zaslaver-A", "name": { "family": "Zaslaver", "given": "Alon" } }, { "id": "Mahanti-P", "name": { "family": "Mahanti", "given": "Parag" } }, { "id": "Ho-Margaret-C", "name": { "family": "Ho", "given": "Margaret C." } }, { "id": "O'Doherty-O-G", "name": { "family": "O'Doherty", "given": "Oran G." } }, { "id": "Edison-A-S", "name": { "family": "Edison", "given": "Arthur S." }, "orcid": "0000-0002-5686-2350" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Schroeder-F-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" } ] }, "title": "A Modular Library of Small Molecule Signals Regulates Social Behaviors in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Srinivasan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.\n\nReceived August 22, 2011; Accepted November 22, 2011; Published January 10, 2012.\n\nThis work was supported in part by a National Institutes of Health grant (GM088290 to FCS and GM085285 to ASE, FCS, and PWS), and the Howard Hughes Medical Institute, with which PWS is an Investigator. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. \n\nWe thank Hillel Schwartz, David Prober, and Fatma Kaplan for helpful discussions; Christopher J. Cronin and Yang Hu for help with tracker\nexperiments; and Cornelia Bargmann, Takeshi Ishihara, and Tokumitsu Wakabayashi for sharing worm strains.\nAuthor Contributions:\nThe author(s) have made the following declarations about their\ncontributions: Conceived and designed the experiments: JS SHV ASE\nPWS FCS. Performed the experiments: JS SHV NB AZ PM FCS.\nAnalyzed the data: JS SHVR NB AZ PM FCS. Contributed reagents/\nmaterials/analysis tools: OGO MCH. Wrote the paper: JS SHV PWS\nFCS.\n\nPublished - Srinivasan2012p17375Plos_Biol.pdf
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", "abstract": "The nematode C. elegans is an important model for the study of social behaviors. Recent investigations have shown that a family of small molecule signals, the ascarosides, controls population density sensing and mating behavior. However, despite extensive studies of C. elegans aggregation behaviors, no intraspecific signals promoting attraction or aggregation of wild-type hermaphrodites have been identified. Using comparative metabolomics, we show that the known ascarosides are accompanied by a series of derivatives featuring a tryptophan-derived indole moiety. Behavioral assays demonstrate that these indole ascarosides serve as potent intraspecific attraction and aggregation signals for hermaphrodites, in contrast to ascarosides lacking the indole group, which are repulsive. Hermaphrodite attraction to indole ascarosides depends on the ASK amphid sensory neurons. Downstream of the ASK sensory neuron, the interneuron AIA is required for mediating attraction to indole ascarosides instead of the RMG interneurons, which previous studies have shown to integrate attraction and aggregation signals from ASK and other sensory neurons. The role of the RMG interneuron in mediating aggregation and attraction is thought to depend on the neuropeptide Y-like receptor NPR-1, because solitary and social C. elegans strains are distinguished by different npr-1 variants. We show that indole ascarosides promote attraction and aggregation in both solitary and social C. elegans strains. The identification of indole ascarosides as aggregation signals reveals unexpected complexity of social signaling in C. elegans, which appears to be based on a modular library of ascarosides integrating building blocks derived from lipid \u03b2-oxidation and amino-acid metabolism. Variation of modules results in strongly altered signaling content, as addition of a tryptophan-derived indole unit to repellent ascarosides produces strongly attractive indole ascarosides. Our findings show that the library of ascarosides represents a highly developed chemical language integrating different neurophysiological pathways to mediate social communication in C. elegans.", "date": "2012-01", "date_type": "published", "publication": "PLoS Biology", "volume": "10", "number": "1", "publisher": "Public Library of Science", "pagerange": "e1001237", "id_number": "CaltechAUTHORS:20120315-161720438", "issn": "1544-9173", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120315-161720438", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM088290" }, { "agency": "NIH", "grant_number": "GM085285" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1371/journal.pbio.1001237", "pmcid": "PMC3254649", "primary_object": { "basename": "Srinivasan2012p17375Plos_Biol.pdf", "url": "https://authors.library.caltech.edu/records/4nkkb-7nk63/files/Srinivasan2012p17375Plos_Biol.pdf" }, "related_objects": [ { "basename": "journal.pbio.1001237.s001.mov", "url": "https://authors.library.caltech.edu/records/4nkkb-7nk63/files/journal.pbio.1001237.s001.mov" }, { "basename": "journal.pbio.1001237.s012.avi", "url": "https://authors.library.caltech.edu/records/4nkkb-7nk63/files/journal.pbio.1001237.s012.avi" }, { "basename": "journal.pbio.1001237.s007.tif", "url": "https://authors.library.caltech.edu/records/4nkkb-7nk63/files/journal.pbio.1001237.s007.tif" }, { "basename": "journal.pbio.1001237.s008.avi", "url": "https://authors.library.caltech.edu/records/4nkkb-7nk63/files/journal.pbio.1001237.s008.avi" }, { "basename": "journal.pbio.1001237.s013.pdf", "url": "https://authors.library.caltech.edu/records/4nkkb-7nk63/files/journal.pbio.1001237.s013.pdf" }, { "basename": "journal.pbio.1001237.s004.tif", "url": "https://authors.library.caltech.edu/records/4nkkb-7nk63/files/journal.pbio.1001237.s004.tif" }, { "basename": "journal.pbio.1001237.s005.tif", "url": "https://authors.library.caltech.edu/records/4nkkb-7nk63/files/journal.pbio.1001237.s005.tif" }, { "basename": "journal.pbio.1001237.s010.avi", "url": "https://authors.library.caltech.edu/records/4nkkb-7nk63/files/journal.pbio.1001237.s010.avi" }, { "basename": "journal.pbio.1001237.s002.mov", "url": "https://authors.library.caltech.edu/records/4nkkb-7nk63/files/journal.pbio.1001237.s002.mov" }, { "basename": "journal.pbio.1001237.s003.tif", "url": "https://authors.library.caltech.edu/records/4nkkb-7nk63/files/journal.pbio.1001237.s003.tif" }, { "basename": "journal.pbio.1001237.s006.tif", "url": "https://authors.library.caltech.edu/records/4nkkb-7nk63/files/journal.pbio.1001237.s006.tif" }, { "basename": "journal.pbio.1001237.s009.avi", "url": "https://authors.library.caltech.edu/records/4nkkb-7nk63/files/journal.pbio.1001237.s009.avi" }, { "basename": "journal.pbio.1001237.s011.avi", "url": "https://authors.library.caltech.edu/records/4nkkb-7nk63/files/journal.pbio.1001237.s011.avi" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Srinivasan, Jagan; von Reuss, Stephan H.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/2r5mt-k5833", "eprint_id": 29233, "eprint_status": "archive", "datestamp": "2023-08-19 09:21:38", "lastmod": "2023-10-24 22:01:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "J." }, "orcid": "0000-0002-7259-8107" }, { "id": "Kishore-R", "name": { "family": "Kishore", "given": "R." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "P." }, "orcid": "0000-0002-7699-0173" }, { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "K." }, "orcid": "0000-0002-1706-4196" } ] }, "title": "The Gene Ontology: enhancements for 2011", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 The Author(s). Published by Oxford University Press.\nThis is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.\n\nReceived September 15, 2011; Revised October 4, 2011; Accepted October 21, 2011.\n\nNational Human Genome Research Institute (NHGRI) (P41 grant 5P41HG002273-09 to Gene Ontology Consortium) and European Union RTD Programme 'Quality of Life and Management of Living Resources' (QLRI-CT-2001-00981 and QLRI-CT-2001-00015 to GO and UniProtKB-GOA groups at EMBL-EBI).\nFunding for open access charge: National Human Genome Research Institute (NHGRI) (P41 grant 5P41HG002273-09).\nConflict of interest statement. None declared.\n\nPublished - Blake2012p17054Nucleic_Acids_Res.pdf
", "abstract": "The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. The number of GO annotations of gene products has increased due to curation efforts among GO Consortium (GOC) groups, including focused literature-based annotation and ortholog-based functional inference. The GO ontologies continue to expand and improve as a result of targeted ontology development, including the introduction of computable logical definitions and development of new tools for the streamlined addition of terms to the ontology. The GOC continues to support its user community through the use of e-mail lists, social media and web-based resources.", "date": "2012-01", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "40", "number": "D1", "publisher": "Oxford University Press", "pagerange": "D559-D564", "id_number": "CaltechAUTHORS:20120210-100230074", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120210-100230074", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "5P41HG002273-09" }, { "agency": "European Union RTD Programme", "grant_number": "QLRI-CT-2001-00981" }, { "agency": "European Union RTD Programme", "grant_number": "QLRI-CT-2001-00015" }, { "agency": "National Human Genome Research Institute" } ] }, "corp_creators": { "items": [ "Gene Ontology Consortium" ] }, "doi": "10.1093/nar/gkr1028", "pmcid": "PMC3245151", "primary_object": { "basename": "Blake2012p17054Nucleic_Acids_Res.pdf", "url": "https://authors.library.caltech.edu/records/2r5mt-k5833/files/Blake2012p17054Nucleic_Acids_Res.pdf" }, "resource_type": "article", "pub_year": "2012", "author_list": "Chan, J.; Kishore, R.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/0n2cz-r1v80", "eprint_id": 29264, "eprint_status": "archive", "datestamp": "2023-08-19 09:21:43", "lastmod": "2023-10-24 22:03:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yook-Karen-J", "name": { "family": "Yook", "given": "Karen" }, "orcid": "0000-0002-4457-6787" }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "Chen-Wen-J", "name": { "family": "Chen", "given": "Wen J." } }, { "id": "Fang-Ruihua", "name": { "family": "Fang", "given": "Ruihua" } }, { "id": "Ganesan-U", "name": { "family": "Ganesan", "given": "Uma" } }, { "id": "Grove-C-A", "name": { "family": "Grove", "given": "Christian" }, "orcid": "0000-0001-9076-6015" }, { "id": "Kadam-S", "name": { "family": "Kadam", "given": "Snehalata" } }, { "id": "Kishore-R", "name": { "family": "Kishore", "given": "Ranjana" } }, { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "Raymond" }, "orcid": "0000-0002-8151-7479" }, { "id": "Li-Yuling", "name": { "family": "Li", "given": "Yuling" } }, { "id": "M\u00fcller-H-M", "name": { "family": "Muller", "given": "Hans-Michael" } }, { "id": "Nakamura-Cecilia", "name": { "family": "Nakamura", "given": "Cecilia" }, "orcid": "0000-0002-4689-7314" }, { "id": "Rangarajan-A", "name": { "family": "Rangarajan", "given": "Arun" } }, { "id": "Schindelman-G", "name": { "family": "Schindelman", "given": "Gary" } }, { "id": "Schwarz-E-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Wang-Xiaodong", "name": { "family": "Wang", "given": "Xiaodong" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Raciti-D", "name": { "family": "Raciti", "given": "Daniela" } }, { "id": "Wang-Daniel", "name": { "family": "Wang", "given": "Daniel" } } ] }, "title": "WormBase 2012: more genomes, more data, new website", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 The Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.\nReceived September 14, 2011; Accepted October 12, 2011. \nFirst published online: November 8, 2011.\nThis work is supported by the US National Institutes of\nHealth (Grant no. P41 HG02223); US National Human\nGenome Research Institute (Grant no. P41-HG02223) to\nWormBase; and British Medical Research Council (Grant\nno. G070119) to WormBase; P.W.S. is an investigator\nwith the Howard Hughes Medical Institute. Funding for\nopen access charge: US National Human Genome\nResearch Institute (Grant no. P41-HG02223). Conflict of interest statement. None declared.\n\nPublished - Yook2012p17053Nucleic_Acids_Res.pdf
", "abstract": "Since its release in 2000, WormBase (http://www.wormbase.org) has grown from a small resource focusing on a single species and serving a dedicated research community, to one now spanning 15 species essential to the broader biomedical and agricultural research fields. To enhance the rate of curation, we have automated the identification of key data in the scientific literature and use similar methodology for data extraction. To ease access to the data, we are collaborating with journals to link entities in research publications to their report pages at WormBase. To facilitate discovery, we have added new views of the data, integrated large-scale datasets and expanded descriptions of models for human disease. Finally, we have introduced a dramatic overhaul of the WormBase website for public beta testing. Designed to balance complexity and usability, the new site is species-agnostic, highly customizable, and interactive. Casual users and developers alike will be able to leverage the public RESTful application programming interface (API) to generate custom data mining solutions and extensions to the site. We report on the growth of our database and on our work in keeping pace with the growing demand for data, efforts to anticipate the requirements of users and new collaborations with the larger science community.", "date": "2012-01", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "40", "number": "D1", "publisher": "Oxford University Press", "pagerange": "D735-D741", "id_number": "CaltechAUTHORS:20120214-071150526", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120214-071150526", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P41 HG02223" }, { "agency": "Medical Research Council (UK)", "grant_number": "G070119" }, { "agency": "NIH", "grant_number": "P41-HG02223" } ] }, "doi": "10.1093/nar/gkr954", "pmcid": "PMC3245152", "primary_object": { "basename": "Yook2012p17053Nucleic_Acids_Res.pdf", "url": "https://authors.library.caltech.edu/records/0n2cz-r1v80/files/Yook2012p17053Nucleic_Acids_Res.pdf" }, "resource_type": "article", "pub_year": "2012", "author_list": "Yook, Karen; Chan, Juancarlos; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ref04-4jj96", "eprint_id": 28532, "eprint_status": "archive", "datestamp": "2023-08-19 08:43:00", "lastmod": "2023-10-24 17:57:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jex-A-R", "name": { "family": "Jex", "given": "Aaron R." } }, { "id": "Schwarz-E-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Ascaris suum draft genome", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Macmillan Publishers Limited. This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar licence. \n\nReceived 16 June 2011. Accepted 12 September 2011. Published online 26 October 2011. \n\nThis project was funded by the Australian Research Council. This\nresearch was supported by a Victorian Life Sciences Computation Initiative (grant\nnumber VR0007) on its Peak Computing Facility at the University of Melbourne, an\ninitiative of the Victorian Government. Other support from the Australian Academy of\nScience, the Australian-American Fulbright Commission, Melbourne Water\nCorporation, and the IBM Research Collaboratory for Life Sciences\u2014Melbourne is\ngratefully acknowledged. P.W.S. is an investigator with the Howard Hughes Medical\nInstitute. A.R.J. held a CDA1 (Industry) from the National Health and Medical Research\nCouncil of Australia. We are indebted to the faculty and staff of the BGI-Shenzhen, who\ncontributed to this study. We also acknowledge the contributions of staff at WormBase\n(www.wormbase.org). \nAuthor Contributions: R.B.G., N.D.Y., B.E.C., J.V., T.W. and P.G. provided the samples and\npurified nucleic acids for sequencing, X.X. performed the whole genomic amplification\nof genomic DNA for the large insert libraries. S.L., L.Y., N.Z., A.R.J., Z.X., R.S.H., Y.K. and\nF.C. undertook the sequencing, assembly and annotation of genomic and\ntranscriptomicdata. A.R.J., B.L., Z.X., N.D.Y., Y.L., R.S.H., E.M.S., G.Z., X.F., S.L., F.C. and C.C.\nplanned and performed additional bioinformatic analyses. A.R.J., B.L., N.D.Y. and G.A.A.\nassisted with statistical analyses, A.R.J., P.N., E.M.S., P.W.S. and R.B.G. drafted and\nedited the manuscript, tables, figures and Supplementary Information. A.R.J., N.D.Y.,\nS.R., J.W. and R.B.G. conceived andplanned the project. A.R.J., B.L., N.D.Y., G.Z., X.F., X.W.,\nJ.W., Y.L., H.Y., J.W. and R.B.G. supervised and/or coordinated the research. T.W.H.\ncurated the browsable genome.\n\nPublished - Jex2011p16499Nature.pdf
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", "abstract": "Parasitic diseases have a devastating, long-term impact on human health, welfare and food production worldwide. More than two billion people are infected with geohelminths, including the roundworms Ascaris (common roundworm), Necator and Ancylostoma (hookworms), and Trichuris (whipworm), mainly in developing or impoverished nations of Asia, Africa and Latin America. In humans, the diseases caused by these parasites result in about 135,000 deaths annually, with a global burden comparable with that of malaria or tuberculosis in disability-adjusted life years. Ascaris alone infects around 1.2 billion people and, in children, causes nutritional deficiency, impaired physical and cognitive development and, in severe cases, death. Ascaris also causes major production losses in pigs owing to reduced growth, failure to thrive and mortality. The Ascaris\u2013swine model makes it possible to study the parasite, its relationship with the host, and ascariasis at the molecular level. To enable such molecular studies, we report the 273 megabase draft genome of Ascaris suum and compare it with other nematode genomes. This genome has low repeat content (4.4%) and encodes about 18,500 protein-coding genes. Notably, the A. suum secretome (about 750 molecules) is rich in peptidases linked to the penetration and degradation of host tissues, and an assemblage of molecules likely to modulate or evade host immune responses. This genome provides a comprehensive resource to the scientific community and underpins the development of new and urgently needed interventions (drugs, vaccines and diagnostic tests) against ascariasis and other nematodiases.", "date": "2011-11-24", "date_type": "published", "publication": "Nature", "volume": "479", "number": "7374", "publisher": "Nature Publishing Group", "pagerange": "529-533", "id_number": "CaltechAUTHORS:20111220-101512736", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111220-101512736", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council" }, { "agency": "Victorian Life Sciences Computation Initiative (VLSCI)", "grant_number": "VR0007" }, { "agency": "Australian Academy of Science" }, { "agency": "Australian-American Fulbright Commission" }, { "agency": "Melbourne Water Corporation" }, { "agency": "IBM Research Collaboratory for Life Sciences" } ] }, "doi": "10.1038/nature10553", "primary_object": { "basename": "nature10553-s2.xls", "url": "https://authors.library.caltech.edu/records/ref04-4jj96/files/nature10553-s2.xls" }, "related_objects": [ { "basename": "nature10553-s4.xls", "url": "https://authors.library.caltech.edu/records/ref04-4jj96/files/nature10553-s4.xls" }, { "basename": "nature10553-s6.xls", "url": "https://authors.library.caltech.edu/records/ref04-4jj96/files/nature10553-s6.xls" }, { "basename": "nature10553-s7.xls", "url": "https://authors.library.caltech.edu/records/ref04-4jj96/files/nature10553-s7.xls" }, { "basename": "nature10553-s8.zip", "url": "https://authors.library.caltech.edu/records/ref04-4jj96/files/nature10553-s8.zip" }, { "basename": "nature10553-s9.zip", "url": "https://authors.library.caltech.edu/records/ref04-4jj96/files/nature10553-s9.zip" }, { "basename": "Jex2011p16499Nature.pdf", "url": "https://authors.library.caltech.edu/records/ref04-4jj96/files/Jex2011p16499Nature.pdf" }, { "basename": "nature10553-s1.pdf", "url": "https://authors.library.caltech.edu/records/ref04-4jj96/files/nature10553-s1.pdf" }, { "basename": "nature10553-s5.xls", "url": "https://authors.library.caltech.edu/records/ref04-4jj96/files/nature10553-s5.xls" }, { "basename": "nature10553-s10.xls", "url": "https://authors.library.caltech.edu/records/ref04-4jj96/files/nature10553-s10.xls" }, { "basename": "nature10553-s3.xls", "url": "https://authors.library.caltech.edu/records/ref04-4jj96/files/nature10553-s3.xls" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Jex, Aaron R.; Schwarz, Erich M.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/np9bj-t9476", "eprint_id": 29926, "eprint_status": "archive", "datestamp": "2023-08-19 08:32:25", "lastmod": "2023-10-24 22:35:23", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schwartz-H-T", "name": { "family": "Schwartz", "given": "Hillel T." }, "orcid": "0000-0002-3448-8652" }, { "id": "Antoshechkin-I-A", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Applications of high-throughput sequencing to symbiotic nematodes of the genus Heterorhabditis", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2012 Springer Science+Business Media B.V. \n\nReceived: 8 October 2011; Accepted: 4 January 2012; Published online: 18 January 2012.", "abstract": "Entomopathogenic nematodes of the genus Heterorhabditis live in symbiosis with pathogenic Photorhabdus bacteria. Heterorhabditis nematodes are entirely dependent on these bacteria for their food source; in return, the nematodes offer the bacteria a way to infect and kill insects. For their part, Photorhabdus bacteria are lethal to a broad range of insect hosts, to other nematodes, and to other microorganisms, but not to their Heterorhabditis hosts. These nematodes offer the potential to provide a robust experimental system for the in\u2022depth study of a mutually beneficial symbiotic relationship, with both members of the partnership accessible to molecular and genetic studies. New genomic technologies offer the possibility for this potential to be realized, and for Heterorhabditis nematodes to become a standard model system for the investigation of host\u2022symbiote relationships. We present a perspective on the application of these technologies to nematode\u2022bacterial symbiosis and an update on our efforts to sequence three Heterorhabditis species reported at the recent NemaSym meeting.", "date": "2011-11", "date_type": "published", "publication": "Symbiosis", "volume": "55", "number": "3", "publisher": "Springer Verlag", "pagerange": "111-118", "id_number": "CaltechAUTHORS:20120402-082627418", "issn": "0334-5114", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120402-082627418", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1007/s13199-012-0151-9", "resource_type": "article", "pub_year": "2011", "author_list": "Schwartz, Hillel T.; Antoshechkin, Igor; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/vrv8d-gh153", "eprint_id": 27673, "eprint_status": "archive", "datestamp": "2023-08-19 08:06:44", "lastmod": "2023-10-24 17:19:44", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chung-Kwanghun", "name": { "family": "Chung", "given": "Kwanghun" }, "orcid": "0000-0002-8167-3340" }, { "id": "Zhan-Mei", "name": { "family": "Zhan", "given": "Mei" } }, { "id": "Srinivasan-J", "name": { "family": "Srinivasan", "given": "Jagan" }, "orcid": "0000-0001-5449-7938" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Gong-Emily", "name": { "family": "Gong", "given": "Emily" } }, { "id": "Schroeder-F-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" }, { "id": "Lu-Hang", "name": { "family": "Lu", "given": "Hang" } } ] }, "title": "Microfluidic chamber arrays for whole-organism behavior-based chemical screening", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Royal Society of Chemistry. \n\nReceived 10 May 2011, Accepted 30 Aug 2011. First published on the web 20 Sep 2011. \n\nThis paper was supported by the following grant(s):\n\nNational Institute of General Medical Sciences : NIGMS R01 GM088290 || GM.\n\nPublished - Chung2011p16163Lab_on_a_Chip.pdf
Supplemental Material - c1lc20400a.avi
Supplemental Material - c1lc20400a.pdf
Supplemental Material - c1lc20400a.wmv
", "abstract": "The nematode Caenorhabditis elegans is an important model organism in genetic research and drug screening because of its relative simplicity, ease of maintenance, amenability to simple genetic manipulation, and relevance to human biology. However, their small size and mobility make nematodes difficult to physically manipulate, particularly with spatial and temporal precision. We have developed a microfluidic device to overcome these challenges and enable fast behavior-based chemical screening in C. elegans. The key components of this easy-to-use device allow rapid loading and housing of C. elegans in a chamber array for chemical screening. A simple two-step loading process enables simultaneous loading of a large number of animals within a few minutes without using any expensive/active off-chip components. In addition, chemicals can be precisely delivered to the worms and exchanged with high temporal precision. To demonstrate this feature and the ability to measure time dependent responses to chemicals, we characterize the transient response of worms exposed to different concentrations of anesthetics. We then use the device to study the effect of chemical signals from hermaphrodite worms on male behavior. The ability of the device to maintain a large number of free moving animals in one field of view over a long period of time permits us to demonstrate an increase in the incidence of a specific behavior in males subjected to worm-conditioned medium. Because our device allows monitoring of a large number of worms with single-animal resolution, we envision that this platform will greatly expedite chemical screening in C. elegans.", "date": "2011-09-20", "date_type": "published", "publication": "Lab on a Chip", "volume": "11", "number": "21", "publisher": "Royal Society of Chemistry", "pagerange": "3689-3697", "id_number": "CaltechAUTHORS:20111108-112517299", "issn": "1473-0197", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111108-112517299", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 GM088290" } ] }, "doi": "10.1039/c1lc20400a", "pmcid": "PMC3924777", "primary_object": { "basename": "Chung2011p16163Lab_on_a_Chip.pdf", "url": "https://authors.library.caltech.edu/records/vrv8d-gh153/files/Chung2011p16163Lab_on_a_Chip.pdf" }, "related_objects": [ { "basename": "c1lc20400a.avi", "url": "https://authors.library.caltech.edu/records/vrv8d-gh153/files/c1lc20400a.avi" }, { "basename": "c1lc20400a.pdf", "url": "https://authors.library.caltech.edu/records/vrv8d-gh153/files/c1lc20400a.pdf" }, { "basename": "c1lc20400a.wmv", "url": "https://authors.library.caltech.edu/records/vrv8d-gh153/files/c1lc20400a.wmv" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Chung, Kwanghun; Zhan, Mei; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/8wc5w-kyh59", "eprint_id": 95464, "eprint_status": "archive", "datestamp": "2023-08-19 07:59:52", "lastmod": "2023-10-20 20:15:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Andrews-B-J", "name": { "family": "Andrews", "given": "Brenda J." } }, { "id": "Johnston-M", "name": { "family": "Johnston", "given": "Mark" } }, { "id": "Hawley-R-S", "name": { "family": "Hawley", "given": "R. Scott" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Hieter-P", "name": { "family": "Hieter", "given": "Phillip" } }, { "id": "Schedl-T", "name": { "family": "Schedl", "given": "Tim" } } ] }, "title": "G3, GENETICS, and the GSA: Two Journals, One Mission", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Andrews et al. This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.\n\nPublished - 245.pdf
", "abstract": "With the June launch of its open-access journal G3: Genes | Genomes | Genetics, the Genetics Society of America (GSA) now offers two peer-edited journals. The missions of G3 and GENETICS are fundamentally the same: to provide a forum for timely communication of the latest findings in genetics, selected by editors who are the authors' peers. But the scopes of the two journals are different. Why offer two journals?", "date": "2011-09-01", "date_type": "published", "publication": "G3", "volume": "1", "number": "4", "publisher": "Genetics Society of America", "pagerange": "245-246", "id_number": "CaltechAUTHORS:20190514-080119211", "issn": "2160-1836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-080119211", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1534/g3.111.000877", "pmcid": "PMC3276146", "primary_object": { "basename": "245.pdf", "url": "https://authors.library.caltech.edu/records/8wc5w-kyh59/files/245.pdf" }, "resource_type": "article", "pub_year": "2011", "author_list": "Andrews, Brenda J.; Johnston, Mark; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/jgr6d-4ac45", "eprint_id": 95466, "eprint_status": "archive", "datestamp": "2023-08-19 07:59:57", "lastmod": "2023-10-20 20:15:49", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Johnston-M", "name": { "family": "Johnston", "given": "Mark" } }, { "id": "Andrews-B-J", "name": { "family": "Andrews", "given": "Brenda J." } }, { "id": "Hawley-R-S", "name": { "family": "Hawley", "given": "R. Scott" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Hieter-P", "name": { "family": "Hieter", "given": "Phillip" } }, { "id": "Schedl-T", "name": { "family": "Schedl", "given": "Tim" } } ] }, "title": "G3, GENETICS, and the GSA: Two Journals, One Mission", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 by the Genetics Society of America. Available freely online through the author-supported open access option.\n\nPublished - 1.pdf
", "abstract": "With the June launch of its open access journal G3: Genes | Genomes | Genetics, the Genetics Society of America (GSA) now offers two peer-edited journals. The missions of G3 and GENETICS are fundamentally the same: to provide a forum for timely communication of the latest findings in genetics, selected by editors who are the authors' peers. But the scopes of the two journals are different. Why offer two journals?", "date": "2011-09-01", "date_type": "published", "publication": "Genetics", "volume": "189", "number": "1", "publisher": "Genetics Society of America", "pagerange": "1-2", "id_number": "CaltechAUTHORS:20190514-081520002", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-081520002", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1534/genetics.111.133777", "pmcid": "PMC3176113", "primary_object": { "basename": "1.pdf", "url": "https://authors.library.caltech.edu/records/jgr6d-4ac45/files/1.pdf" }, "resource_type": "article", "pub_year": "2011", "author_list": "Johnston, Mark; Andrews, Brenda J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/66fhg-xfa02", "eprint_id": 24209, "eprint_status": "archive", "datestamp": "2023-08-19 07:08:16", "lastmod": "2023-10-23 20:23:23", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zaslaver-A", "name": { "family": "Zaslaver", "given": "Alon" } }, { "id": "Baugh-L-R", "name": { "family": "Baugh", "given": "L. Ryan" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Metazoan Operons Accelerate Recovery from Growth-Arrested States", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Elsevier Inc.\n\nReceived 19 December 2010; revised 3 April 2011; accepted 9 May 2011. Published: June 9, 2011. Available online 9 June 2011. \n\nWe are grateful to Tom Blumenthal, Erich Schwarz, Hillel Schwartz, Shalev Itzkovitz, Ronen Zaidel-Bar, and Ron Milo for critical review and helpful comments. We thank Elodie Ghedin for sharing the list of operon genes in B. malayi, the Mitani laboratory and the Caenorhabditis Genetics Center for deletion strains, WormBase, and the Genome BC C. elegans Gene Expression Consortium http://elegans.bcgsc.bc.ca/ for SAGE data (produced at the\nMichael Smith Genome Sciences Centre with funding from Genome Canada). A.Z. was supported by the European Molecular Biology Organization (EMBO), the Human Frontier Science Program (HFSP), and the Caltech Center for Biological Circuit Design. L.R.B. was an ACS postdoctoral fellow. P.W.S. is an Investigator with the HHMI, which supported this work. A.Z. conceived the idea of this study, designed and performed all of the experiments and the mathematical modeling, and carried out all of the data and bioinformatics analyses. L.R.B. contributed experimental tools, shared unpublished data, and helped to analyze and interpret the data. A.Z. and P.W.S. wrote the paper.\n\nAccepted Version - nihms-304806.pdf
", "abstract": "Existing theories explain why operons are advantageous in prokaryotes, but their occurrence in metazoans is an enigma. Nematode operon genes, typically consisting of growth genes, are significantly upregulated during recovery from growth-arrested states. This expression pattern is anticorrelated to nonoperon genes, consistent with a competition for transcriptional resources. We find that transcriptional resources are initially limiting during recovery and that recovering animals are highly sensitive to any additional decrease in transcriptional resources. We provide evidence that operons become advantageous because, by clustering growth genes into operons, fewer promoters compete for the limited transcriptional machinery, effectively increasing the concentration of transcriptional resources and accelerating recovery. Mathematical modeling reveals how a moderate increase in transcriptional resources can substantially enhance transcription rate and recovery. This design principle occurs in different nematodes and the chordate C. intestinalis. As transition from arrest to rapid growth is shared by many metazoans, operons could have evolved to facilitate these processes.", "date": "2011-06-10", "date_type": "published", "publication": "Cell", "volume": "145", "number": "6", "publisher": "Elsevier", "pagerange": "981-992", "id_number": "CaltechAUTHORS:20110624-135516788", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110624-135516788", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Genome Canada" }, { "agency": "European Molecular Biology Organization (EMBO)" }, { "agency": "Human Frontier Science Program" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1016/j.cell.2011.05.013", "pmcid": "PMC3152313", "primary_object": { "basename": "nihms-304806.pdf", "url": "https://authors.library.caltech.edu/records/66fhg-xfa02/files/nihms-304806.pdf" }, "resource_type": "article", "pub_year": "2011", "author_list": "Zaslaver, Alon; Baugh, L. Ryan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/qd558-gf760", "eprint_id": 24063, "eprint_status": "archive", "datestamp": "2023-08-19 07:06:14", "lastmod": "2023-10-23 20:17:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Narayan-Anusha", "name": { "family": "Narayan", "given": "Anusha" } }, { "id": "Laurent-G", "name": { "family": "Laurent", "given": "Gilles" }, "orcid": "0000-0002-2296-114X" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Transfer characteristics of a thermosensory synapse in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 National Academy of Sciences.\n\nContributed by Paul W. Sternberg, April 27, 2011 (sent for review February 13, 2011). Published online before print May 23, 2011. \n\nWe thank Serge Faumont, Thad Lindsay, and Shawn Lockery for their generous aid with the C. elegans preparation and helpful discussions. We thank Vivek Jayaraman, Glenn Turner, and members of the G.L. and P.W.S. laboratories for helpful discussions, the Caenorhabditis Genetics Center for strains, and WormBase. This work was supported by the Howard Hughes Medical Institute, with which P.W.S. is an investigator. \n\nAuthor contributions: A.N., G.L., and P.W.S. designed research; A.N. performed research; A.N. analyzed data; and A.N., G.L., and P.W.S. wrote the paper.\n\nPublished - Narayan2011p14118P_Natl_Acad_Sci_Usa.pdf
Supplemental Material - pnas.201106617SI.pdf
", "abstract": "Caenorhabditis elegans is a compact, attractive system for neural circuit analysis. An understanding of the functional dynamics of neural computation requires physiological analyses. We undertook the characterization of transfer at a central synapse in C. elegans by combining optical stimulation of targeted neurons with electrophysiological recordings. We show that the synapse between AFD and AIY, the first stage in the thermotactic circuit, exhibits excitatory, tonic, and graded release. We measured the linear range of the input-output curve and estimate the static synaptic gain as 0.056 (<0.1). Release showed no obvious facilitation or depression. Transmission at this synapse is peptidergic. The AFD/AIY synapse thus seems to have evolved for reliable transmission of a scaled-down temperature signal from AFD, enabling AIY to monitor and integrate temperature with other sensory input. Combining optogenetics with electrophysiology is a powerful way to analyze C. elegans' neural function.", "date": "2011-06-07", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "108", "number": "23", "publisher": "National Academy of Sciences", "pagerange": "9667-9672", "id_number": "CaltechAUTHORS:20110620-134743597", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-134743597", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1073/pnas.1106617108", "pmcid": "PMC3111291", "primary_object": { "basename": "Narayan2011p14118P_Natl_Acad_Sci_Usa.pdf", "url": "https://authors.library.caltech.edu/records/qd558-gf760/files/Narayan2011p14118P_Natl_Acad_Sci_Usa.pdf" }, "related_objects": [ { "basename": "pnas.201106617SI.pdf", "url": "https://authors.library.caltech.edu/records/qd558-gf760/files/pnas.201106617SI.pdf" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Narayan, Anusha; Laurent, Gilles; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/b4756-fgr86", "eprint_id": 95467, "eprint_status": "archive", "datestamp": "2023-08-19 07:04:51", "lastmod": "2023-10-20 20:15:52", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Andrews-B-J", "name": { "family": "Andrews", "given": "Brenda J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "DePellegrin-Connelly-T", "name": { "family": "DePellegrin Connelly", "given": "Tracey" } } ] }, "title": "GSA Launches G3: Genes | Genomes | Genetics", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Andrews et al. This is an open access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/ ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.\n\nPublished - Untitled.pdf
", "abstract": "We are proud to present the inaugural issue of G3: Genes | Genomes | Genetics, an open-access journal published by the Genetics Society of America (GSA). The journal's team of over 60 associate editors and 4 section editors, all practicing scientists\u2014your peers\u2014have come together to form a new, open-access journal with a unique mission and vision. The Editorial Board of G3 taps the expertise of the community of geneticists in the widest sense, from microbes to humans, from individuals to populations, and from classic \"wet lab\" experimentation to the most recent innovations in bioinformatics.", "date": "2011-06-01", "date_type": "published", "publication": "G3", "volume": "1", "number": "1", "publisher": "Genetics Society of America", "pagerange": "1-1", "id_number": "CaltechAUTHORS:20190514-082200653", "issn": "2160-1836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-082200653", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1534/g3.111.000414", "pmcid": "PMC3276121", "primary_object": { "basename": "Untitled.pdf", "url": "https://authors.library.caltech.edu/records/b4756-fgr86/files/Untitled.pdf" }, "resource_type": "article", "pub_year": "2011", "author_list": "Andrews, Brenda J.; Sternberg, Paul W.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/0ts58-chw79", "eprint_id": 23711, "eprint_status": "archive", "datestamp": "2023-08-22 02:37:38", "lastmod": "2023-10-23 19:52:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Campbell-B-E", "name": { "family": "Campbell", "given": "Bronwyn E." } }, { "id": "Boag-P-R", "name": { "family": "Boag", "given": "Peter R." } }, { "id": "Hofmann-A", "name": { "family": "Hofmann", "given": "Andreas" } }, { "id": "Cantacessi-C", "name": { "family": "Cantacessi", "given": "Cinzia" } }, { "id": "Wang-Conan-K", "name": { "family": "Wang", "given": "Conan K." } }, { "id": "Taylor-P", "name": { "family": "Taylor", "given": "Paul" } }, { "id": "Hu-Min", "name": { "family": "Hu", "given": "Min" } }, { "id": "Sindhu-Z-D", "name": { "family": "Sindhu", "given": "Zia-ud-Din" } }, { "id": "Loukas-A", "name": { "family": "Loukas", "given": "Alex" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "Atypical (RIO) protein kinases from Haemonchus contortus \u2014 Promise as new targets for nematocidal drugs", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Parasite; Haemonchus contortus; RIO kinases; Structure; Relationships; Inferred function; Drug targets", "note": "\u00a9 2011 Elsevier Inc. Received 6 September 2010; revised 28 December 2010; accepted 14 January 2011. Available online 22 January 2011. Funding from the Australian Research Council (ARC) is gratefully acknowledged (RBG). PRB is supported by funding from the National Health and Medical Research Council (NHMRC).", "abstract": "Almost nothing is known about atypical kinases in multicellular organisms, including parasites. Supported by information and data available for the free-living nematode, Caenorhabditis elegans, and other eukaryotes, the present article describes three RIO kinase genes, riok-1, riok-2 and riok-3, from Haemonchus contortus, one of the most important parasitic nematodes of small ruminants. Analyses of these genes and their products predict that they each play critical roles in the developmental pathways of parasitic nematodes. The findings of this review indicate prospects for functional studies of these genes in C. elegans (as a surrogate) and opportunities for the design of a novel class of nematode-specific inhibitors of RIO kinases. The latter aspect is of paramount importance, given the serious problems linked to anthelmintic resistance in parasitic nematode populations of livestock.", "date": "2011-05", "date_type": "published", "publication": "Biotechnology Advances", "volume": "29", "number": "3", "publisher": "Elsevier", "pagerange": "338-350", "id_number": "CaltechAUTHORS:20110518-104531775", "issn": "0734-9750", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110518-104531775", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council" }, { "agency": "National Health and Medical Research Council (NHMRC)" } ] }, "doi": "10.1016/j.biotechadv.2011.01.006", "resource_type": "article", "pub_year": "2011", "author_list": "Campbell, Bronwyn E.; Boag, Peter R.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/tg694-2h707", "eprint_id": 23697, "eprint_status": "archive", "datestamp": "2023-08-22 02:37:30", "lastmod": "2023-10-23 19:52:03", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cantacessi-C", "name": { "family": "Cantacessi", "given": "Cinzia" } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } }, { "id": "Strube-C", "name": { "family": "Strube", "given": "Christina" } }, { "id": "Schnieder-T", "name": { "family": "Schnieder", "given": "Thomas" } }, { "id": "Jex-A-R", "name": { "family": "Jex", "given": "Aaron R." } }, { "id": "Hall-R-S", "name": { "family": "Hall", "given": "Ross S." } }, { "id": "Campbell-B-E", "name": { "family": "Campbell", "given": "Bronwyn E." } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Ranganathan-S", "name": { "family": "Ranganathan", "given": "Shoba" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Mitreva-M", "name": { "family": "Mitreva", "given": "Makedonka" } } ] }, "title": "Deep insights into Dictyocaulus viviparus transcriptomes provides unique prospects for new drug targets and disease intervention", "ispublished": "pub", "full_text_status": "public", "keywords": "Dictyocaulus viviparus; Bovine lungworm; Next-generation sequencing; Bioinformatics; Transcriptome; Ancylostoma-secreted proteins; Drug target prediction", "note": "\u00a9 2010 Elsevier Inc. \n\nReceived 6 September 2010; accepted 22 November 2010. Available online 21 December 2010. \n\nThis research was supported by grants from the Australian Research Council, the Australian Academy of Science, the Australian\u2013American Fulbright Commission (RBG) as well as the National Human Genome Research Institute and National Institutes of Health (MM). CC is the grateful recipient of an International Postgraduate Research Scholarship from the Australian Government and a fee-remission scholarship through the University of Melbourne as well as the Clunies Ross (2008) and Sue Newton (2009) awards from the School of Veterinary Science of the same university. ARJ is the recipient of a Career Developmental Award (CDA1) from the National Health and Medical Research Council (NHMRC).\nSupport from the Victorian Life Sciences Computation Initiative (VLSCI) and IBM 'Collaboratory' is gratefully acknowledged (RBG).\n\nAccepted Version - nihms311933.pdf
", "abstract": "The lungworm, Dictyocaulus viviparus, causes parasitic bronchitis in cattle, and is responsible for substantial economic losses in temperate regions of the world. Here, we undertake the first large-scale exploration of available transcriptomic data for this lungworm, examine differences in transcription between different stages/both genders and identify and prioritize essential molecules linked to fundamental metabolic pathways, which could represent novel drug targets. Approximately 3 million expressed sequence tags (ESTs), generated by 454 sequencing from third-stage larvae (L3s) as well as adult females and males of D. viviparus, were assembled and annotated. The assembly of these sequences yielded ~61,000 contigs, of which relatively large proportions encoded collagens (4.3%), ubiquitins (2.1%) and serine/threonine protein kinases (1.9%). Subtractive analysis in silico identified 6928 nucleotide sequences as being uniquely transcribed in L3, and 5203 and 7889 transcripts as being exclusive to the adult female and male, respectively. Most peptides predicted from the conceptual translations were nucleoplasmins (L3), serine/threonine protein kinases (female) and major sperm proteins (male). Additional analyses allowed the prediction of three drug target candidates, whose Caenorhabditis elegans homologues were linked to a lethal RNA interference phenotype. This detailed exploration, combined with future transcriptomic sequencing of all developmental stages of D. viviparus, will facilitate future investigations of the molecular biology of this parasitic nematode as well as genomic sequencing. These advances will underpin the discovery of new drug and/or vaccine targets, focused on biotechnological outcomes.", "date": "2011-05", "date_type": "published", "publication": "Biotechnology Advances", "volume": "29", "number": "3", "publisher": "Elsevier", "pagerange": "261-271", "id_number": "CaltechAUTHORS:20110517-151915276", "issn": "0734-9750", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110517-151915276", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council" }, { "agency": "Australian Academy of Science" }, { "agency": "Australian\u2013American Fulbright Commission" }, { "agency": "Human Genome Research Institute" }, { "agency": "NIH" }, { "agency": "Australian Government" }, { "agency": "University of Melbourne" }, { "agency": "National Health and Medical Research Council (NHMRC)" }, { "agency": "Victorian Life Sciences Computation Initiative (VLSCI)" }, { "agency": "IBM Collaboratory" } ] }, "doi": "10.1016/j.biotechadv.2010.11.005", "pmcid": "PMC3827682", "primary_object": { "basename": "nihms311933.pdf", "url": "https://authors.library.caltech.edu/records/tg694-2h707/files/nihms311933.pdf" }, "resource_type": "article", "pub_year": "2011", "author_list": "Cantacessi, Cinzia; Gasser, Robin B.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/gb1kw-yfp70", "eprint_id": 23353, "eprint_status": "archive", "datestamp": "2023-08-19 05:55:26", "lastmod": "2023-10-23 19:02:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Baugh-L-R", "name": { "family": "Baugh", "given": "L. Ryan" } }, { "id": "Kurhanewicz-N", "name": { "family": "Kurhanewicz", "given": "Nicole" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Sensitive and Precise Quantification of Insulin-Like mRNA Expression in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Baugh et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived August 20, 2010; Accepted February 24, 2011; Published March 22, 2011. \n\nEditor: Simon Melov, Buck Institute for Age Research, United States of America. \n\nThis work was funded by the Howard Hughes Medical Institute (P.W.S.), the American Cancer Society (L.R.B. PF-06-028-01-DDC) and start up funds from Duke University (L.R.B.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. \n\nWe would like to thank Eric Davidson for use of the nCounter instrument, and Stefan Materna for advice and help processing samples for nCounter analysis. We would also like to thank the Mitani Lab and the National BioResource Project for providing deletion alleles of insulin-like genes. \n\nAuthor Contributions: Conceived and designed the experiments: LRB. Performed the experiments: LRB NK. Analyzed the data: LRB. Contributed reagents/materials/analysis tools: PWS. Wrote the paper: LRB PWS.\n\nPublished - Baugh2011p13447PLoS_ONE.pdf
Supplemental Material - journal.pone.0018086.s001.xls
Supplemental Material - journal.pone.0018086.s002.xls
Supplemental Material - journal.pone.0018086.s003.xls
", "abstract": "Insulin-like signaling regulates developmental arrest, stress resistance and lifespan in the nematode Caenorhabditis elegans. However, the genome encodes 40 insulin-like peptides, and the regulation and function of individual peptides is largely uncharacterized. We used the nCounter platform to measure mRNA expression of all 40 insulin-like peptides as well as the insulin-like receptor daf-2, its transcriptional effector daf-16, and the daf-16 target gene sod-3. We validated the platform using 53 RNA samples previously characterized by high density oligonucleotide microarray analysis. For this set of genes and the standard nCounter protocol, sensitivity and precision were comparable between the two platforms. We optimized conditions of the nCounter assay by varying the mass of total RNA used for hybridization, thereby increasing sensitivity up to 50-fold and reducing the median coefficient of variation as much as 4-fold. We used deletion mutants to demonstrate specificity of the assay, and we used optimized conditions to assay insulin-like gene expression throughout the C. elegans life cycle. We detected expression for nearly all insulin-like genes and find that they are expressed in a variety of distinct patterns suggesting complexity of regulation and specificity of function. We identified insulin-like genes that are specifically expressed during developmental arrest, larval development, adulthood and embryogenesis. These results demonstrate that the nCounter platform provides a powerful approach to analyzing insulin-like gene expression dynamics, and they suggest hypotheses about the function of individual insulin-like genes.", "date": "2011-03-22", "date_type": "published", "publication": "PLoS ONE", "volume": "6", "number": "3", "publisher": "Public Library of Science", "pagerange": "Art. No. e18086", "id_number": "CaltechAUTHORS:20110418-095304718", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110418-095304718", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "American Cancer Society", "grant_number": "PF-06-028-01-DDC" }, { "agency": "Duke University" } ] }, "doi": "10.1371/journal.pone.0018086", "pmcid": "PMC3062572", "primary_object": { "basename": "journal.pone.0018086.s002.xls", "url": "https://authors.library.caltech.edu/records/gb1kw-yfp70/files/journal.pone.0018086.s002.xls" }, "related_objects": [ { "basename": "journal.pone.0018086.s003.xls", "url": "https://authors.library.caltech.edu/records/gb1kw-yfp70/files/journal.pone.0018086.s003.xls" }, { "basename": "Baugh2011p13447PLoS_ONE.pdf", "url": "https://authors.library.caltech.edu/records/gb1kw-yfp70/files/Baugh2011p13447PLoS_ONE.pdf" }, { "basename": "journal.pone.0018086.s001.xls", "url": "https://authors.library.caltech.edu/records/gb1kw-yfp70/files/journal.pone.0018086.s001.xls" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Baugh, L. Ryan; Kurhanewicz, Nicole; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/wep2c-cdx11", "eprint_id": 23276, "eprint_status": "archive", "datestamp": "2023-08-19 05:51:46", "lastmod": "2023-10-23 18:58:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kaplan-F", "name": { "family": "Kaplan", "given": "Fatma" }, "orcid": "0000-0002-9565-0211" }, { "id": "Srinivasan-J", "name": { "family": "Srinivasan", "given": "Jagan" }, "orcid": "0000-0001-5449-7938" }, { "id": "Mahanti-P", "name": { "family": "Mahanti", "given": "Parag" } }, { "id": "Ajredini-R", "name": { "family": "Ajredini", "given": "Ramadan" } }, { "id": "Durak-O", "name": { "family": "Durak", "given": "Omer" } }, { "id": "Nimalendran-R", "name": { "family": "Nimalendran", "given": "Rathika" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Teal-P-E-A", "name": { "family": "Teal", "given": "Peter E. A." } }, { "id": "Schroeder-F-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" }, { "id": "Edison-A-S", "name": { "family": "Edison", "given": "Arthur S." }, "orcid": "0000-0002-5686-2350" }, { "id": "Alborn-H-T", "name": { "family": "Alborn", "given": "Hans T." }, "orcid": "0000-0003-3918-5041" } ] }, "title": "Ascaroside Expression in Caenorhabditis elegans Is Strongly Dependent on Diet and Developmental Stage", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Kaplan et al. This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. \n\nReceived October 26, 2010; Accepted February 11, 2011; Published March 15, 2011. \n\nEditor: Paulo Ho, Instituto Butantan, Brazil. \n\nPartially funded by National Institutes of Health (1R01GM085285-01A1, 3R01GM085285-01A1S1, and GM088290). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. No additional external funding received for this study. \n\nAuthor Contributions:\nConceived and designed the experiments: FK HTA JS PWS ASE FCS. Performed the experiments: FK HTA JS PM RA OD RN. Analyzed the data: FK JS HTA FCS ASE PEAT PWS. Contributed reagents/materials/ analysis tools: ASE FCS PWS HTA PEAT. Wrote the paper: FK JS HTA FCS ASE PEAT PWS. Collected nematode secretions in water or M9 buffer: FK RA RN. Collected nematode secretions in liquid culture: RA\nRN. Performed ascaroside extraction from nematodes: FK. Performed quantification of ascarosides by LC-MS: FK HTA. Designed the biological experiments: JS PWS. Performed all the biological experiments: JS OMD. Synthesized ascr#1, ascr#2, ascr#3, ascr#4 and ascr#8: FCS PM.\n\nPublished - Kaplan2011p13347PLoS_ONE.pdf
Supplemental Material - journal.pone.0017804.s001.eps
Supplemental Material - journal.pone.0017804.s002.eps
", "abstract": "Background:\nThe ascarosides form a family of small molecules that have been isolated from cultures of the nematode Caenorhabditis elegans. They are often referred to as \"dauer pheromones\" because most of them induce formation of long-lived and highly stress resistant dauer larvae. More recent studies have shown that ascarosides serve additional functions as social signals and mating pheromones. Thus, ascarosides have multiple functions. Until now, it has been generally assumed that ascarosides are constitutively expressed during nematode development.\n\nMethodology/Principal Findings:\nCultures of C. elegans were developmentally synchronized on controlled diets. Ascarosides released into the media, as well as stored internally, were quantified by LC/MS. We found that ascaroside biosynthesis and release were strongly dependent on developmental stage and diet. The male attracting pheromone was verified to be a blend of at least four ascarosides, and peak production of the two most potent mating pheromone components, ascr#3 and asc#8 immediately preceded or coincided with the temporal window for mating. The concentration of ascr#2 increased under starvation conditions and peaked during dauer formation, strongly supporting ascr#2 as the main population density signal (dauer pheromone). After dauer formation, ascaroside production largely ceased and dauer larvae did not release any ascarosides. These findings show that both total ascaroside production and the relative proportions of individual ascarosides strongly correlate with these compounds' stage-specific biological functions.\n\nConclusions/Significance:\nAscaroside expression changes with development and environmental conditions. This is consistent with multiple functions of these signaling molecules. Knowledge of such differential regulation will make it possible to associate ascaroside production to gene expression profiles (transcript, protein or enzyme activity) and help to determine genetic pathways that control ascaroside biosynthesis. In conjunction with findings from previous studies, our results show that the pheromone system of C. elegans mimics that of insects in many ways, suggesting that pheromone signaling in C. elegans may exhibit functional homology also at the sensory level. In addition, our results provide a strong foundation for future behavioral modeling studies.", "date": "2011-03-15", "date_type": "published", "publication": "PLoS ONE", "volume": "6", "number": "3", "publisher": "Public Library of Science", "pagerange": "Art. No. e17804", "id_number": "CaltechAUTHORS:20110411-105726989", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110411-105726989", "rights": "This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.", "funders": { "items": [ { "agency": "NIH", "grant_number": "1R01GM085285-01A1" }, { "agency": "NIH", "grant_number": "3R01GM085285-01A1S1" }, { "agency": "NIH", "grant_number": "GM088290" } ] }, "doi": "10.1371/journal.pone.0017804", "pmcid": "PMC3058051", "primary_object": { "basename": "Kaplan2011p13347PLoS_ONE.pdf", "url": "https://authors.library.caltech.edu/records/wep2c-cdx11/files/Kaplan2011p13347PLoS_ONE.pdf" }, "related_objects": [ { "basename": "journal.pone.0017804.s001.eps", "url": "https://authors.library.caltech.edu/records/wep2c-cdx11/files/journal.pone.0017804.s001.eps" }, { "basename": "journal.pone.0017804.s002.eps", "url": "https://authors.library.caltech.edu/records/wep2c-cdx11/files/journal.pone.0017804.s002.eps" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Kaplan, Fatma; Srinivasan, Jagan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/73396-x4t96", "eprint_id": 23160, "eprint_status": "archive", "datestamp": "2023-08-19 05:50:16", "lastmod": "2023-10-23 18:00:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hallem-E-A", "name": { "family": "Hallem", "given": "Elissa A." } }, { "id": "Dillman-A-R", "name": { "family": "Dillman", "given": "Adler R." }, "orcid": "0000-0001-7171-4332" }, { "id": "Hong-Annie-V", "name": { "family": "Hong", "given": "Annie V." } }, { "id": "Zhang-Yuanjun", "name": { "family": "Zhang", "given": "Yuanjun" } }, { "id": "Yano-J-M", "name": { "family": "Yano", "given": "Jessica M." } }, { "id": "DeMarco-S-F", "name": { "family": "DeMarco", "given": "Stephanie F." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "A Sensory Code for Host Seeking in Parasitic Nematodes", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Elsevier Ltd. \n\nReceived 3 November 2010; revised 29 December 2010; accepted 20 January 2011. Published online: February 24, 2011. Available online 25 February 2011. \n\nWe thank Todd Ciche, Heidi Goodrich-Blair, Patrick McGrath, and Cori Bargmann for nematode and bacterial stocks; Nathan Dalleska, the Caltech Environmental Analysis Center, and Andrea Choe for help with TD-GC-MS; Scott Peat and Byron Adams for help with phylogenetic analysis; and Jagan Srinivasan, David Prober, Byron Adams, Bruce Hay, Hillel Schwartz, and laboratory members for critical reading of the manuscript. This work was supported by the Howard Hughes Medical Institute (with which P.W.S. is an investigator), a Helen Hay Whitney postdoctoral fellowship and National Institutes of Health (NIH) Pathway to Independence award to E.A.H., an NIH United States Public Health Service Training Grant (T32GM07616) to A.R.D., and Summer Undergraduate Research Fellowships to A.V.H., Y.Z., and J.M.Y.\n\nAccepted Version - nihms281017.pdf
", "abstract": "Parasitic nematode species often display highly specialized\nhost-seeking behaviors that reflect their specific host preferences. Many such behaviors are triggered by host odors, but little is known about either the specific olfactory cues that trigger these behaviors or the underlying neural circuits. Heterorhabditis bacteriophora and Steinernema carpocapsae are phylogenetically distant insect-parasitic nematodes whose host-seeking and host-invasion behavior resembles that of some devastating human- and plant-parasitic nematodes. We compare the olfactory responses of Heterorhabditis and Steinernema infective juveniles (IJs) to those of Caenorhabditis elegans dauers, which are analogous life stages [1]. The broad host range of these parasites results from their ability to respond to the universally produced signal carbon dioxide (CO_2), as well as a wide array of odors,\nincluding host-specific odors that we identified using\nthermal desorption-gas chromatography-mass spectroscopy.\nWe find that CO_2 is attractive for the parasitic IJs and\nC. elegans dauers despite being repulsive for C. elegans\nadults [2\u20134], and we identify a sensory neuron that mediates\nCO_2 response in both parasitic and free-living species,\nregardless of whether CO_2 is attractive or repulsive. The\nparasites' odor response profiles are more similar to each\nother than to that of C. elegans despite their greater phylogenetic distance, likely reflecting evolutionary convergence to insect parasitism.", "date": "2011-03-08", "date_type": "published", "publication": "Current Biology", "volume": "21", "number": "5", "publisher": "Cell Press", "pagerange": "377-383", "id_number": "CaltechAUTHORS:20110329-141518846", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110329-141518846", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Helen Hay Whitney Foundation" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM07616" }, { "agency": "Caltech Summer Undergraduate Research Fellowship (SURF)" } ] }, "doi": "10.1016/j.cub.2011.01.048", "pmcid": "PMC3152378", "primary_object": { "basename": "nihms281017.pdf", "url": "https://authors.library.caltech.edu/records/73396-x4t96/files/nihms281017.pdf" }, "resource_type": "article", "pub_year": "2011", "author_list": "Hallem, Elissa A.; Dillman, Adler R.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/zvbcq-98903", "eprint_id": 23208, "eprint_status": "archive", "datestamp": "2023-08-19 05:42:25", "lastmod": "2023-10-23 18:03:55", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Davison-E-M", "name": { "family": "Davison", "given": "Ewa M." } }, { "id": "Saffer-A-M", "name": { "family": "Saffer", "given": "Adam M." } }, { "id": "Huang-Linda-S", "name": { "family": "Huang", "given": "Linda S." } }, { "id": "DeModena-J", "name": { "family": "DeModena", "given": "John" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Horvitz-H-R", "name": { "family": "Horvitz", "given": "H. Robert" } } ] }, "title": "The LIN-15A and LIN-56 Transcriptional Regulators Interact to Negatively Regulate EGF/Ras Signaling in Caenorhabditis elegans Vulval Cell-Fate Determination", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Genetics Society of America. \n\nManuscript received October 21, 2010. Accepted for publication December 21, 2010. Originally published as Genetics Advance Online Publication on December 31, 2010. \n\nCommunicating editor: D. I. Greenstein. \n\nWe thank Erik Andersen, Craig Ceol, Alison Frand, and Niels Ringstad for editorial comments; Melissa Harrison for help with yeast two-hybrid analysis; Erik Andersen for construction of lin-15A and lin-56 Gateway entry clones; Beth Castor for help with DNA sequence determination; Na An for strain management; Yuji Kohara for EST cDNA clones; Alan Coulson and the C. elegans Sequencing Consortium for cosmid clones and sequences; and Steve Bell for use of the ABI PRISM 7000 Sequence Detection System. The deficiency strains were provided by Theresa Stiernagle of the Caenorhabditis Genetics Center, which is supported by the National Institutes of Health (NIH) National Center for Research Resources. This work was supported by NIH grant GM24663 (to H.R.H.) and a Howard Hughes Medical Institute predoctoral fellowship (to E.M.D.). L.S.H. was supported by a March of Dimes Birth Defects Foundation grant (to P.W.S.). H.R.H. and P.W.S. are Investigators of the Howard Hughes Medical Institute.\n\nPublished - Davison2011p13311Genetics.pdf
Supplemental Material - Fig_S1.pdf
", "abstract": "The restricted expression of epidermal growth factor (EGF) family ligands is important for proper development and for preventing cancerous growth in mammals. In Caenorhabditis elegans, the class A and B synthetic multivulva (synMuv) genes redundantly repress expression of lin-3 EGF to negatively regulate Ras-mediated vulval development. The class B synMuv genes encode proteins homologous to components of the NuRD and Myb-MuvB/dREAM transcriptional repressor complexes, indicating that they likely silence lin-3 EGF through chromatin remodeling. The two class A synMuv genes cloned thus far, lin-8 and lin-15A, both encode novel proteins. The LIN-8 protein is nuclear. We have characterized the class A synMuv gene lin-56 and found it to encode a novel protein that shares a THAP-like C_2CH motif with LIN-15A. Both the LIN-56 and LIN-15A proteins localize to nuclei. Wild-type levels of LIN-56 require LIN-15A, and wild-type levels and/or localization of LIN-15A requires LIN-56. Furthermore, LIN-56 and LIN-15A interact in the yeast two-hybrid system. We propose that LIN-56 and LIN-15A associate in a nuclear complex that inhibits vulval specification by repressing lin-3 EGF expression.", "date": "2011-03", "date_type": "published", "publication": "Genetics", "volume": "187", "number": "3", "publisher": "Genetics Society of America", "pagerange": "803-815", "id_number": "CaltechAUTHORS:20110401-135236894", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110401-135236894", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM24663" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "March of Dimes Birth Defects Foundation" } ] }, "doi": "10.1534/genetics.110.124487", "pmcid": "PMC3063674", "primary_object": { "basename": "Davison2011p13311Genetics.pdf", "url": "https://authors.library.caltech.edu/records/zvbcq-98903/files/Davison2011p13311Genetics.pdf" }, "related_objects": [ { "basename": "Fig_S1.pdf", "url": "https://authors.library.caltech.edu/records/zvbcq-98903/files/Fig_S1.pdf" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Davison, Ewa M.; Saffer, Adam M.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/66zys-5hv18", "eprint_id": 22420, "eprint_status": "archive", "datestamp": "2023-08-19 05:19:20", "lastmod": "2023-10-23 16:00:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schindelman-G", "name": { "family": "Schindelman", "given": "Gary" } }, { "id": "Fernandes-J-S", "name": { "family": "Fernandes", "given": "Jolene S." } }, { "id": "Bastiani-C-A", "name": { "family": "Bastiani", "given": "Carol A." } }, { "id": "Yook-Karen-J", "name": { "family": "Yook", "given": "Karen" }, "orcid": "0000-0002-4457-6787" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Schindelman et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived: 12 August 2010 Accepted: 24 January 2011. Published: 24 January 2011. \n\nWe thank Raymond Lee and Christian Grove for helpful discussions and advice; Igor Antoshechkin for assistance with RNAi phenotype curation tools and advice; Juancarlos Chan for assistance with curation tools for alleles and transgene overexpression; Chris Mungall and Amina Abdullah for the impetus to include equivalences for the WPO; Kris Gunsalus for input on early embryonic lethal phenotype suggestions; Norie de la Cruz for his work on the phenotype ontology search tool and fellow curators at WormBase for their valuable input. We also thank Christian Grove, Ranjana Kishore, Raymond Lee, Chris Mungall, Kimberly Van Auken, Cheryl Van Buskirk, and Xiaodong Wang for comments on the manuscript. Supported by U.S.P.H.S grant P41HG0223 to PWS, an investigator of the Howard Hughes Medical Institute. \n\nAuthors' contributions: CAB and PWS initiated this project. CAB, GS, JSF and KY further developed the WPO, namely creating, defining and placing terms in the ontology. JSF and GS generated and maintained the WPO-GO XP ontology. GS, JSF and CAB wrote the paper with valuable discussions and critical contributions at all stages of the project from KY and PWS. All authors read and approved the final manuscript.\n\nPublished - Schindelman2011p12667BMC_Bioinformatics.pdf
Supplemental Material - 1471-2105-12-32-s1_1_.pdf
Supplemental Material - 1471-2105-12-32-s2_1_.pdf
Supplemental Material - 1471-2105-12-32-s3_1_.pdf
Supplemental Material - 1471-2105-12-32-s4_1_.pdf
", "abstract": "Background: Caenorhabditis elegans gene-based phenotype information dates back to the 1970's, beginning with\nSydney Brenner and the characterization of behavioral and morphological mutant alleles via classical genetics in\norder to understand nervous system function. Since then C. elegans has become an important genetic model\nsystem for the study of basic biological and biomedical principles, largely through the use of phenotype analysis.\nBecause of the growth of C. elegans as a genetically tractable model organism and the development of large-scale\nanalyses, there has been a significant increase of phenotype data that needs to be managed and made accessible\nto the research community. To do so, a standardized vocabulary is necessary to integrate phenotype data from\ndiverse sources, permit integration with other data types and render the data in a computable form.\nResults: We describe a hierarchically structured, controlled vocabulary of terms that can be used to standardize\nphenotype descriptions in C. elegans, namely the Worm Phenotype Ontology (WPO). The WPO is currently\ncomprised of 1,880 phenotype terms, 74% of which have been used in the annotation of phenotypes associated\nwith greater than 18,000 C. elegans genes. The scope of the WPO is not exclusively limited to C. elegans biology,\nrather it is devised to also incorporate phenotypes observed in related nematode species. We have enriched the\nvalue of the WPO by integrating it with other ontologies, thereby increasing the accessibility of worm phenotypes\nto non-nematode biologists. We are actively developing the WPO to continue to fulfill the evolving needs of the\nscientific community and hope to engage researchers in this crucial endeavor.\nConclusions: We provide a phenotype ontology (WPO) that will help to facilitate data retrieval, and cross-species\ncomparisons within the nematode community. In the larger scientific community, the WPO will permit data\nintegration, and interoperability across the different Model Organism Databases (MODs) and other biological\ndatabases. This standardized phenotype ontology will therefore allow for more complex data queries and enhance\nbioinformatic analyses.", "date": "2011-01-24", "date_type": "published", "publication": "BMC Bioinformatics", "volume": "12", "publisher": "BioMed Central", "pagerange": "Art. No. 32", "id_number": "CaltechAUTHORS:20110222-110252067", "issn": "1471-2105", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110222-110252067", "rights": "This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P41HG0223" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1186/1471-2105-12-32", "pmcid": "PMC3039574", "primary_object": { "basename": "1471-2105-12-32-s1_1_.pdf", "url": "https://authors.library.caltech.edu/records/66zys-5hv18/files/1471-2105-12-32-s1_1_.pdf" }, "related_objects": [ { "basename": "1471-2105-12-32-s2_1_.pdf", "url": "https://authors.library.caltech.edu/records/66zys-5hv18/files/1471-2105-12-32-s2_1_.pdf" }, { "basename": "1471-2105-12-32-s3_1_.pdf", "url": "https://authors.library.caltech.edu/records/66zys-5hv18/files/1471-2105-12-32-s3_1_.pdf" }, { "basename": "1471-2105-12-32-s4_1_.pdf", "url": "https://authors.library.caltech.edu/records/66zys-5hv18/files/1471-2105-12-32-s4_1_.pdf" }, { "basename": "Schindelman2011p12667BMC_Bioinformatics.pdf", "url": "https://authors.library.caltech.edu/records/66zys-5hv18/files/Schindelman2011p12667BMC_Bioinformatics.pdf" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Schindelman, Gary; Fernandes, Jolene S.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/6ayvh-r3107", "eprint_id": 22472, "eprint_status": "archive", "datestamp": "2023-08-22 01:49:51", "lastmod": "2023-10-23 16:04:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hallem-E-A", "name": { "family": "Hallem", "given": "Elissa A." } }, { "id": "Spencer-W-C", "name": { "family": "Spencer", "given": "W. Clay" } }, { "id": "McWhirter-R-D", "name": { "family": "McWhirter", "given": "Rebecca D." } }, { "id": "Zeller-G", "name": { "family": "Zeller", "given": "Georg" } }, { "id": "Henz-S-R", "name": { "family": "Henz", "given": "Stefan R." } }, { "id": "R\u00e4tsch-G", "name": { "family": "R\u00e4tsch", "given": "Gunnar" } }, { "id": "Miller-D-M-III", "name": { "family": "Miller", "given": "David M., III" } }, { "id": "Horvitz-H-R", "name": { "family": "Horvitz", "given": "H. Robert" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Ringstad-N", "name": { "family": "Ringstad", "given": "Niels" } } ] }, "title": "Receptor-type guanylate cyclase is required for\n carbon dioxide sensation by Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "guanylyl cyclase; olfaction; transcriptional profiling; regulator of G protein signaling; chemosensation", "note": "\u00a9 2011 National Academy of Sciences. Freely available online through the PNAS open access option. \n\nContributed by Paul W. Sternberg, November 22, 2010 (sent for review August 2, 2010). Published online before print December 20, 2010. \n\nWe thank Aravi Samuel, Chris Gabel, and Harrison Gabel (Harvard University, Cambridge, MA); Cori Bargmann (Rockefeller University, New York); Leon Avery (University of Texas Southwestern Medical Center, Dallas); Ikue Mori and Atsushi Kuhara (Nagoya University, Nagoya, Japan); Denise Ferkey (SUNY Buffalo, Buffalo, NY); Larry Salkoff (Washington University School of Medicine, St. Louis); Shohei Mitani (Tokyo Women's Medical University School of Medicine, Tokyo); Anne Hart (Brown University, Providence, RI); and the Caenorhabditis Genetics Center for strains and reagents. We thank the Vanderbilt Flow Cytometry Core and Vanderbilt Functional Genomics Shared Resource (VFGSR) for help with microarray experiments. We thank Julia Brandt and Sonya Aziz-Zaman for assistance in cloning the gcy-9 cDNA. H.R.H. and P.W.S. are Investigators of the Howard Hughes Medical Institute. This work was supported by a Helen Hay Whitney postdoctoral fellowship (to E.A.H.), a National Institutes of Health Pathway to Independence award (to E.A.H.), National Institutes of Health Grants U01\nHG004263 (to D.M.M.), R01 NS26115 (to D.M.M.), and R01 GM24663 (to H.R.H.), the Howard HughesMedical Institute (P.W.S.), a Whitehead Fellowship for Junior Faculty in Biomedical and Biological Sciences (to N.R.), and funds from the Helen L. and Martin S. Kimmel Center for Biology and Medicine (to N.R.). Data deposition: The sequence reported in this paper has been deposited in the GenBank database (accession no. HQ636455). The gene expression data have been deposited in the Gene Expression Omnibus database (accession no. GSE23769). \n\nAuthor contributions: E.A.H., D.M.M., H.R.H., P.W.S., and N.R. designed research; E.A.H., N.R., W.C.S., and R.D.M. performed research; E.A.H., G.Z., S.R.H., G.R., and N.R. analyzed data; and E.A.H., H.R.H., P.W.S., and N.R. wrote the paper.\n\nPublished - Hallem2011p12638P_Natl_Acad_Sci_Usa.pdf
Supplemental Material - pnas.201017354SI.pdf
Supplemental Material - sd01.xlsx
Supplemental Material - sd02.xlsx
", "abstract": "CO_2 is both a critical regulator of animal physiology and an important sensory cue for many animals for host detection, food location, and mate finding. The free-living soil nematode Caenorhabditis elegans shows CO_2 avoidance behavior, which requires a pair of ciliated sensory neurons, the BAG neurons. Using in vivo calcium imaging, we show that CO_2 specifically activates the BAG neurons and that the CO_2-sensing function of BAG neurons requires TAX-2/TAX-4 cyclic nucleotide-gated ion channels and the receptor-type guanylate cyclase GCY-9. Our results delineate a molecular pathway for CO_2 sensing and suggest that activation of a receptor-type guanylate cyclase is an evolutionarily conserved mechanism by which animals detect environmental CO_2.", "date": "2011-01-04", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "108", "number": "1", "publisher": "National Academy of Sciences", "pagerange": "254-259", "id_number": "CaltechAUTHORS:20110224-100625385", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110224-100625385", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Helen Hay Whitney Foundation" }, { "agency": "NIH", "grant_number": "U01 HG004263" }, { "agency": "NIH", "grant_number": "R01 NS26115" }, { "agency": "NIH", "grant_number": "R01 GM24663" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Whitehead Fellowship for Junior Faculty in Biomedical and Biological Sciences" } ] }, "doi": "10.1073/pnas.1017354108", "pmcid": "PMC3017194", "primary_object": { "basename": "Hallem2011p12638P_Natl_Acad_Sci_Usa.pdf", "url": "https://authors.library.caltech.edu/records/6ayvh-r3107/files/Hallem2011p12638P_Natl_Acad_Sci_Usa.pdf" }, "related_objects": [ { "basename": "pnas.201017354SI.pdf", "url": "https://authors.library.caltech.edu/records/6ayvh-r3107/files/pnas.201017354SI.pdf" }, { "basename": "sd01.xlsx", "url": "https://authors.library.caltech.edu/records/6ayvh-r3107/files/sd01.xlsx" }, { "basename": "sd02.xlsx", "url": "https://authors.library.caltech.edu/records/6ayvh-r3107/files/sd02.xlsx" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Hallem, Elissa A.; Spencer, W. Clay; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/1xgxv-zg755", "eprint_id": 24540, "eprint_status": "archive", "datestamp": "2023-08-19 04:53:10", "lastmod": "2023-10-23 23:26:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Rangarajan-A", "name": { "family": "Rangarajan", "given": "Arun" } }, { "id": "Schedl-T", "name": { "family": "Schedl", "given": "Tim" } }, { "id": "Yook-Karen-J", "name": { "family": "Yook", "given": "Karen" }, "orcid": "0000-0002-4457-6787" }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "Haenel-S", "name": { "family": "Haenel", "given": "Stephen" } }, { "id": "Otis-L", "name": { "family": "Otis", "given": "Lolly" } }, { "id": "Faelten-S", "name": { "family": "Faelten", "given": "Sharon" } }, { "id": "DePellegrin-Connelly-T", "name": { "family": "DePellegrin-Connelly", "given": "Tracey" } }, { "id": "Isaacson-R", "name": { "family": "Isaacson", "given": "Ruth" } }, { "id": "Skyzypek-S", "name": { "family": "Skyzypek", "given": "Marek S." } }, { "id": "Marygold-S-J", "name": { "family": "Marygold", "given": "Steven J." } }, { "id": "Stefancsik-R", "name": { "family": "Stefancsik", "given": "Raymund" } }, { "id": "Cherry-J-M", "name": { "family": "Cherry", "given": "J. Michael" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "M\u00fcller-H-M", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } } ] }, "title": "Toward an interactive article: integrating journals and biological databases", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Rangarajan et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived: 13 August 2010; Accepted: 19 May 2011; Published: 19 May 2011. \n\nWe thank members of WormBase, SGD, the GSA editorial board, Dartmouth Journal Services and FlyBase for helpful discussions and collaborations. We thank the anonymous reviewers for helpful critiques of the manuscript. This work was funded in part by grants #R01-HG004090, #P41-HG002223, #P41-HG000739 and #P41-HG001315 from the National Human Genome Research Institute (NHGRI) at the United States National Institutes of Health. Work by TS was funded by GM63310 and GM085150. PWS is an investigator with the Howard Hughes Medical Institute. \n\nAuthors' contributions: AR developed, maintains and runs the linking software and the software for obtaining the entities from the biological databases. TS initiated the project, provided the workflow, did initial manual quality control and oversees the project. KY does the manual quality control for WormBase and provides feedback to correct the linking software and the pipeline, and designed the author form for declaring new entities. JC set up the author form, integrated author data to forms used by WormBase curators and provides access to WormBase data. SH runs the source XML composition software. LO, SF send article source files to databases and receive the returned, linked article, and communicate with the authors at the proof stage. TDC helped to initiate and oversees the project. RI obtains a WormBase paper ID for each new article published by Genetics and sends authors the new author form. MSS\ndoes manual QC for SGD. JMC initiated the project at SGD, provided access to SGD data and oversees the project for SGD. RS does manual QC for FlyBase. SJM initiated the project at FlyBasae, provided access to FlyBase data and oversees the project for FlyBase. PWS oversees the project at WormBase, and helps with QC. HMM provided the textpresso software used as part of the linking software, and also helps run the software. All the authors read and approved the final manuscript.\n\nPublished - Rangarajan2011p15330BMC_Bioinformatics.pdf
", "abstract": "Background: Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five years and have resulted in the development of automated tools that can recognize entities within a document and link those entities to a relevant database. Unfortunately, automated tools cannot resolve ambiguities that arise from one term being used to signify entities that are quite distinct from one another. Instead, resolving these ambiguities requires some manual oversight. Finding the right balance between the speed and portability of automation and the accuracy and flexibility of manual effort is a crucial goal to making text markup a successful venture.\n\nResults: We have established a journal article mark-up pipeline that links GENETICS journal articles and the model organism database (MOD) WormBase. This pipeline uses a lexicon built with entities from the database as a first step. The entity markup pipeline results in links from over nine classes of objects including genes, proteins, alleles, phenotypes and anatomical terms. New entities and ambiguities are discovered and resolved by a database curator through a manual quality control (QC) step, along with help from authors via a web form that is provided to them by the journal. New entities discovered through this pipeline are immediately sent to an appropriate curator at the database. Ambiguous entities that do not automatically resolve to one link are resolved by hand ensuring an accurate link. This pipeline has been extended to other databases, namely Saccharomyces Genome Database (SGD) and FlyBase, and has been implemented in marking up a paper with links to multiple databases.\n\nConclusions: Our semi-automated pipeline hyperlinks articles published in GENETICS to model organism databases such as WormBase. Our pipeline results in interactive articles that are data rich with high accuracy. The use of a manual quality control step sets this pipeline apart from other hyperlinking tools and results in benefits to authors, journals, readers and databases.", "date": "2011", "date_type": "published", "publication": "BMC Bioinformatics", "volume": "12", "publisher": "BioMed Central", "pagerange": "Art. No. 175", "id_number": "CaltechAUTHORS:20110726-095513577", "issn": "1471-2105", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110726-095513577", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01-HG004090" }, { "agency": "NIH", "grant_number": "P41-HG002223" }, { "agency": "NIH", "grant_number": "P41 HG000739" }, { "agency": "NIH", "grant_number": "P41-HG001315" }, { "agency": "NIH", "grant_number": "GM63310" }, { "agency": "NIH", "grant_number": "GM085150" }, { "agency": "National Human Genome Research Institute" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1186/1471-2105-12-175", "pmcid": "PMC3213741", "primary_object": { "basename": "Rangarajan2011p15330BMC_Bioinformatics.pdf", "url": "https://authors.library.caltech.edu/records/1xgxv-zg755/files/Rangarajan2011p15330BMC_Bioinformatics.pdf" }, "resource_type": "article", "pub_year": "2011", "author_list": "Rangarajan, Arun; Schedl, Tim; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/3rz0v-v0135", "eprint_id": 21459, "eprint_status": "archive", "datestamp": "2023-08-19 04:30:39", "lastmod": "2023-10-21 00:03:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mortazavi-A", "name": { "family": "Mortazavi", "given": "Ali" }, "orcid": "0000-0002-4259-6362" }, { "id": "Schwarz-E-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Williams-B-A", "name": { "family": "Williams", "given": "Brian" } }, { "id": "Schaeffer-L-V", "name": { "family": "Schaeffer", "given": "Lorian" } }, { "id": "Antoshechkin-I-A", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Wold-B-J", "name": { "family": "Wold", "given": "Barbara J." }, "orcid": "0000-0003-3235-8130" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Scaffolding a Caenorhabditis nematode genome with RNA-seq", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2010 Cold Spring Harbor Laboratory Press. The Authors acknowledge that six months after the full-issue publication date, the Article will be distributed under a Creative Commons CC-BY-NC License (Attribution-NonCommercial 4.0 International License, http://creativecommons.org/licenses/by-nc/4.0/). \n\nReceived May 26, 2010; accepted in revised form August 24, 2010.\nPublished in Advance October 27, 2010. \n\nWe thank Robin Giblin-Davis for providing PS1010 in 1991, Oren\nSchaedel for use of his C. elegans L3 RNA-seq data, Todd Ciche and\nKarin Kiontke for advice on worm culture and RNA extractions,\nHenry Amrhein and Diane Trout for computational support, and\nAdler Dillman, Karin Kiontke, Adrienne Roeder, Hillel Schwartz,\nand Allyson Whittaker for comments on the manuscript. Sequencing\nwas performed in the Millard and Muriel Jacobs Genetics\nand Genomics Laboratory at Caltech (I.A., L.S.). This work was\nsupported by the Howard Hughes Medical Institute, with which\nP.W.S. is an Investigator, the Beckman Institute Functional Genomics\nCenter, the Caltech Moore Cell Center, grants HG02223 and\nHG003162 from the National Human Genome Research Institute,\nand grant GM084389 from the National Institute of General\nMedical Sciences.\n\nPublished - Mortazavi2010p12233Genome_Res.pdf
Supplemental Material - Mortazavi_FigS1.pdf
Supplemental Material - Mortazavi_FigS2.pdf
Supplemental Material - Mortazavi_Table_S6.xls
Supplemental Material - Supp_Material.doc
Supplemental Material - Supplemental_Files.zip
", "abstract": "Efficient sequencing of animal and plant genomes by next-generation technology should allow many neglected organisms of biological and medical importance to be better understood. As a test case, we have assembled a draft genome of Caenorhabditis sp. 3 PS1010 through a combination of direct sequencing and scaffolding with RNA-seq. We first sequenced genomic DNA and mixed-stage cDNA using paired 75-nt reads from an Illumina GAII. A set of 230 million genomic reads yielded an 80-Mb assembly, with a supercontig N50 of 5.0 kb, covering 90% of 429 kb from previously published genomic contigs. Mixed-stage poly(A)+ cDNA gave 47.3 million mappable 75-mers (including 5.1 million spliced reads), which separately assembled into 17.8 Mb of cDNA, with an N50 of 1.06 kb. By further scaffolding our genomic supercontigs with cDNA, we increased their N50 to 9.4 kb, nearly double the average gene size in C. elegans. We predicted 22,851 protein-coding genes, and detected expression in 78% of them. Multigenome alignment and data filtering identified 2672 DNA elements conserved between PS1010 and C. elegans that are likely to encode regulatory sequences or previously unknown ncRNAs. Genomic and cDNA sequencing followed by joint assembly is a rapid and useful strategy for biological analysis.", "date": "2010-12", "date_type": "published", "publication": "Genome Research", "volume": "20", "number": "12", "publisher": "Cold Spring Harbor Laboratory Press", "pagerange": "1740-1747", "id_number": "CaltechAUTHORS:20101220-153301188", "issn": "1088-9051", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101220-153301188", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Caltech Moore Cell Center" }, { "agency": "NIH", "grant_number": "HG02223" }, { "agency": "NIH", "grant_number": "HG003162" }, { "agency": "NIH", "grant_number": "GM084389" } ] }, "doi": "10.1101/gr.111021.110", "pmcid": "PMC2990000", "primary_object": { "basename": "Mortazavi_FigS2.pdf", "url": "https://authors.library.caltech.edu/records/3rz0v-v0135/files/Mortazavi_FigS2.pdf" }, "related_objects": [ { "basename": "Mortazavi_Table_S6.xls", "url": "https://authors.library.caltech.edu/records/3rz0v-v0135/files/Mortazavi_Table_S6.xls" }, { "basename": "Supp_Material.doc", "url": "https://authors.library.caltech.edu/records/3rz0v-v0135/files/Supp_Material.doc" }, { "basename": "Supplemental_Files.zip", "url": "https://authors.library.caltech.edu/records/3rz0v-v0135/files/Supplemental_Files.zip" }, { "basename": "Mortazavi2010p12233Genome_Res.pdf", "url": "https://authors.library.caltech.edu/records/3rz0v-v0135/files/Mortazavi2010p12233Genome_Res.pdf" }, { "basename": "Mortazavi_FigS1.pdf", "url": "https://authors.library.caltech.edu/records/3rz0v-v0135/files/Mortazavi_FigS1.pdf" } ], "resource_type": "article", "pub_year": "2010", "author_list": "Mortazavi, Ali; Schwarz, Erich M.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/c7sy1-jtw80", "eprint_id": 19833, "eprint_status": "archive", "datestamp": "2023-08-22 00:47:10", "lastmod": "2023-10-20 21:57:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yu-Hui", "name": { "family": "Yu", "given": "Hui" } }, { "id": "Seah-A", "name": { "family": "Seah", "given": "Adeline" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Re-programming of C. elegans male epidermal precursor fates by Wnt, Hox, and LIN-12/Notch activities", "ispublished": "pub", "full_text_status": "public", "keywords": "Pattern formation; Fate transformation; Axin; \u03b2-catenin; Hox; WNT; Notch", "note": "\u00a9 2010 Elsevier Inc. \n\nReceived 12 December 2009; revised 26 April 2010; accepted 10 May 2010. Available online 15 May 2010. \n\nWe thank Cynthia Kenyon for the muIs9 and muIs16 strains, John Murray and Rob Waterston for the Ex [MAB-5\u2013GFP] strain (RW10320), Takao Inoue, Mihoko Kato, Gary Schindelman and Amir Sapir for helpful discussions and critical reading of this manuscript. We thank the Caenorhabditis Genetic Center for providing some strains used in this study. This work was supported by the HHMI, with which P.W. S. is an Investigator, and USPHS grant #1P50DK57325 to G. Germino (co-PI, P.W.S.).\n\nAccepted Version - nihms231435.pdf
Supplemental Material - f.doc
", "abstract": "In Caenorhabditis elegans males, different subsets of ventral epidermal precursor (Pn.p) cells adopt distinct fates in a position-specific manner: three posterior cells, P(9\u201311).p, comprise the hook sensillum competence group (HCG) with three potential fates (1\u00b0, 2\u00b0, or 3\u00b0), while eight anterior cells, P(1\u20138).p, fuse with the hyp7 epidermal syncytium. Here we show that activation of the canonical BAR-1 \u03b2-catenin pathway of Wnt signaling alters the competence of P(3\u20138).p and specifies ectopic HCG-like fates. This fate transformation requires the Hox gene mab-5. In addition, misexpression of mab-5 in P(1\u20138).p is sufficient to establish HCG competence among these cells, as well as to generate ectopic HCG fates in combination with LIN-12 or EGF signaling. While increased Wnt signaling induces predominantly 1\u00b0 HCG fates, increased LIN-12 or EGF signaling in combination with MAB-5 overexpression promotes 2\u00b0 HCG fates in anterior Pn.p cells, suggesting distinctive functions of Wnt, LIN-12, and EGF signaling in specification of HCG fates. Lastly, wild-type mab-5 function is necessary for normal P(9\u201311).p fate specification, indicating that regulation of ectopic HCG fate formation revealed in anterior Pn.p cells reflect mechanisms of pattern formation during normal hook development.", "date": "2010-09-01", "date_type": "published", "publication": "Developmental Biology", "volume": "345", "number": "1", "publisher": "Elsevier", "pagerange": "1-11", "id_number": "CaltechAUTHORS:20100908-113218717", "issn": "0012-1606", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100908-113218717", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "1P50DK57325" } ] }, "doi": "10.1016/j.ydbio.2010.05.008", "pmcid": "PMC3326348", "primary_object": { "basename": "f.doc", "url": "https://authors.library.caltech.edu/records/c7sy1-jtw80/files/f.doc" }, "related_objects": [ { "basename": "nihms231435.pdf", "url": "https://authors.library.caltech.edu/records/c7sy1-jtw80/files/nihms231435.pdf" } ], "resource_type": "article", "pub_year": "2010", "author_list": "Yu, Hui; Seah, Adeline; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/krrbk-xns98", "eprint_id": 20463, "eprint_status": "archive", "datestamp": "2023-08-19 03:39:27", "lastmod": "2023-10-20 23:04:52", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cantacessi-C", "name": { "family": "Cantacessi", "given": "Cinzia" } }, { "id": "Jex-A-R", "name": { "family": "Jex", "given": "Aaron R." } }, { "id": "Hall-R-S", "name": { "family": "Hall", "given": "Ross S." } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Campbell-B-E", "name": { "family": "Campbell", "given": "Bronwyn E." } }, { "id": "Joachim-A", "name": { "family": "Joachim", "given": "Anja" } }, { "id": "Nolan-M-J", "name": { "family": "Nolan", "given": "Matthew J." } }, { "id": "Abubucker-S", "name": { "family": "Abubucker", "given": "Sahar" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Ranganathan-S", "name": { "family": "Ranganathan", "given": "Shoba" } }, { "id": "Mitreva-M", "name": { "family": "Mitreva", "given": "Makedonka" } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2010. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived June 2, 2010; Revised July 11, 2010; Accepted July 15, 2010. \n\nStaff at WormBase are gratefully acknowledged. The Austrian Ministry for Science and Research approved the animal experimentation (BMWF-68.205/0103-II/10b/2008) and is also acknowledged. C.C. is in receipt of an International Postgraduate Research Scholarship from the Australian Government and a fee-remission scholarship from The University of Melbourne as well as the Clunies Ross (2008) and Sue Newton (2009) awards from the School of Veterinary Science of the same university. \n\nFunding: The Australian Research Council; Australian Academy of\nScience; the Australian-American Fulbright Commission (to R.B.G.); National Human Genome Research Institute and National Institutes of Health (to M.M.).\n\nPublished - Cantacessi2010p11548Nucleic_Acids_Res.pdf
Supplemental Material - NAR-01194-Met-N-2010_R1_Legends_to_supplementary_material.doc
Supplemental Material - Supplementary_Figure_1.ppt
Supplemental Material - Supplementary_Figure_2_R1.ppt
Supplemental Material - Supplementary_Figure_3_R1.ppt
Supplemental Material - Supplementary_Figure_4_R1.ppt
Supplemental Material - Supplementary_data_file_1_R1.doc
Supplemental Material - Supplementary_data_file_2.xls
Supplemental Material - Supplementary_data_file_3.xls
", "abstract": "Transcriptomics (at the level of single cells, tissues and/or whole organisms) underpins many fields of biomedical science, from understanding the basic cellular function in model organisms, to the elucidation of the biological events that govern the development and progression of human diseases, and the exploration of the mechanisms of survival, drug-resistance and virulence of pathogens. Next-generation sequencing (NGS) technologies are contributing to a massive expansion of transcriptomics in all fields and are reducing the cost, time and performance barriers presented by conventional approaches. However, bioinformatic tools for the analysis of the sequence data sets produced by these technologies can be daunting to researchers with limited or no expertise in bioinformatics. Here, we constructed a semi-automated, bioinformatic workflow system, and critically evaluated it for the analysis and annotation of large-scale sequence data sets generated by NGS. We demonstrated its utility for the exploration of differences in the transcriptomes among various stages and both sexes of an economically important parasitic worm (Oesophagostomum dentatum) as well as the prediction and prioritization of essential molecules (including GTPases, protein kinases and phosphatases) as novel drug target candidates. This workflow system provides a practical tool for the assembly, annotation and analysis of NGS data sets, also to researchers with a limited bioinformatic expertise. The custom-written Perl, Python and Unix shell computer scripts used can be readily modified or adapted to suit many different applications. This system is now utilized routinely for the analysis of data sets from pathogens of major socio-economic importance and can, in principle, be applied to transcriptomics data sets from any organism.", "date": "2010-09", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "38", "number": "17", "publisher": "Oxford University Press", "pagerange": "Art. No. e171", "id_number": "CaltechAUTHORS:20101021-094944627", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101021-094944627", "rights": "This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.", "funders": { "items": [ { "agency": "Australian Research Council" }, { "agency": "Australian Academy of Science" }, { "agency": "Australian-American Fulbright Commission" }, { "agency": "National Human Genome Research Institute" }, { "agency": "NIH" }, { "agency": "Australian Government" }, { "agency": "University of Melbourne" }, { "agency": "School of Veterinary Science of the University of Melbourne" } ] }, "doi": "10.1093/nar/gkq667", "pmcid": "PMC2943614", "primary_object": { "basename": "Supplementary_Figure_2_R1.ppt", "url": "https://authors.library.caltech.edu/records/krrbk-xns98/files/Supplementary_Figure_2_R1.ppt" }, "related_objects": [ { "basename": "Supplementary_Figure_3_R1.ppt", "url": "https://authors.library.caltech.edu/records/krrbk-xns98/files/Supplementary_Figure_3_R1.ppt" }, { "basename": "Supplementary_Figure_4_R1.ppt", "url": "https://authors.library.caltech.edu/records/krrbk-xns98/files/Supplementary_Figure_4_R1.ppt" }, { "basename": "Supplementary_data_file_1_R1.doc", "url": "https://authors.library.caltech.edu/records/krrbk-xns98/files/Supplementary_data_file_1_R1.doc" }, { "basename": "Supplementary_data_file_3.xls", "url": "https://authors.library.caltech.edu/records/krrbk-xns98/files/Supplementary_data_file_3.xls" }, { "basename": "Cantacessi2010p11548Nucleic_Acids_Res.pdf", "url": "https://authors.library.caltech.edu/records/krrbk-xns98/files/Cantacessi2010p11548Nucleic_Acids_Res.pdf" }, { "basename": "NAR-01194-Met-N-2010_R1_Legends_to_supplementary_material.doc", "url": "https://authors.library.caltech.edu/records/krrbk-xns98/files/NAR-01194-Met-N-2010_R1_Legends_to_supplementary_material.doc" }, { "basename": "Supplementary_Figure_1.ppt", "url": "https://authors.library.caltech.edu/records/krrbk-xns98/files/Supplementary_Figure_1.ppt" }, { "basename": "Supplementary_data_file_2.xls", "url": "https://authors.library.caltech.edu/records/krrbk-xns98/files/Supplementary_data_file_2.xls" } ], "resource_type": "article", "pub_year": "2010", "author_list": "Cantacessi, Cinzia; Jex, Aaron R.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/19mpp-g5087", "eprint_id": 19405, "eprint_status": "archive", "datestamp": "2023-08-22 00:27:02", "lastmod": "2023-10-20 20:39:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hu-Min", "name": { "family": "Hu", "given": "Min" } }, { "id": "He-Li", "name": { "family": "He", "given": "Li" } }, { "id": "Campbell-B-E", "name": { "family": "Campbell", "given": "Bronwyn E." } }, { "id": "Zhong-Weiwei", "name": { "family": "Zhong", "given": "Weiwei" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "A vacuolar-type proton (H^+) translocating ATPase \u03b1 subunit encoded by the Hc-vha-6 gene of Haemonchus contortus", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Vacuolar-type proton (H+); translocating ATPase; Nematode; Haemonchus contortus; Caenorhabditis elegans; Transcription", "note": "\u00a9 2010 Elsevier Ltd.\nReceived 3 January 2010; \naccepted 22 March 2010. \nAvailable online 31 March 2010.\nNucleotide sequence data reported in this paper are available in the EMBL,\nGenBank and DDJB databases under accession numbers FN601335 and FN601336.\n\nFunding from the Australian Research Council, the Australian\nAcademy of Science, the Australian-American Fulbright Commission\nare gratefully acknowledged. PWS is an Investigator with the\nHoward Hughes Medical Institute.", "abstract": "In the present study, a full-length cDNA (designated Hc-vha-6) inferred to encode an \u03b1 subunit of\na vacuolar-type proton translocating adenosine triphosphatase (V-ATPase) was isolated from the parasitic\nnematode Haemonchus contortus, and characterized. The transcript for Hc-vha-6 was detected in all\ndevelopmental stages and both sexes of H. contortus. Elements, including two TATA box (TATAA), two\ninverted CAAT box (ATTGG), five E box (CANNTG) and six GATA as well as five inverse GATA (TTATC)\ntranscription factor motifs, were identified in the non-coding region upstream of Hc-vha-6. The open\nreading frame (ORF) of 2601 nucleotides encoded a protein (Hc-VHA-6) of 866 amino acids and\na molecular weight of ~98.7 kDa. Comparison with a published protein sequence for a homologue\n(VPH1P) from yeast showed that Hc-VHA-6 had nine transmembrane domains and the 14 essential\namino acid residues associated with enzyme activity, assembly, intracellular and/or membrane targeting.\nPhylogenetic analyses of selected amino acid sequence data revealed Hc-VHA-6 to be most closely related\nto VHA-6 of Caenorhabditis elegans. A predictive network analysis inferred that vha-6 interacts with at\nleast seven other genes encoding V-ATPase subunits and a small Rab GTPase. This study provides the first\ninsight into a V-ATPase of parasitic nematodes and a sound basis for future functional genomic work.", "date": "2010-08", "date_type": "published", "publication": "Molecular and Cellular Probes", "volume": "24", "number": "4", "publisher": "Elsevier", "pagerange": "196-203", "id_number": "CaltechAUTHORS:20100812-082444037", "issn": "0890-8508", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100812-082444037", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council" }, { "agency": "Australian Academy of Science" }, { "agency": "Australian-American Fulbright Commission" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1016/j.mcp.2010.03.002", "resource_type": "article", "pub_year": "2010", "author_list": "Hu, Min; He, Li; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/sxypc-4pt11", "eprint_id": 18690, "eprint_status": "archive", "datestamp": "2023-08-22 00:07:34", "lastmod": "2023-10-20 16:40:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Van-Buskirk-C", "name": { "family": "Van Buskirk", "given": "Cheryl" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Paired and LIM class homeodomain proteins coordinate differentiation of the C. elegans ALA neuron", "ispublished": "pub", "full_text_status": "public", "keywords": "EGFR; Axon migration; Gene battery; Homeodomain; Sleep; C. elegans", "note": "\u00a9 2010 Published by The Company of Biologists Ltd. \n\nAccepted April 20, 2010. \n\nWe are grateful to N. Pujol for reporter constructs and insightful comments and to H. Kagoshima and T. B\u00fcrglin for sharing unpublished observations. We thank M. Nonet, M. Treinin, S. Xu, G. Schindelman, R. Roubin, I. Hope, C. Li and T. Cai for reporter constructs, the Caenorhabditis Genetics Center for strains, members of the Sternberg lab for helpful discussions and O. Hobert and A. Wright for critical reading of the manuscript. This work was supported by a grant from the US National Institute on Drug Abuse (DA018341) to P.W.S., an investigator of the HHMI. \n\nDeposited in PMC for release after 6 months.\n\nPublished - VanBuskirk2010p10343Development.pdf
", "abstract": "The ancient origin of sleep is evidenced by deeply conserved signaling pathways regulating sleep-like behavior, such as signaling through the Epidermal growth factor receptor (EGFR). In Caenorhabditis elegans, a sleep-like state can be induced at any time during development or adulthood through conditional expression of LIN-3/EGF. The behavioral response to EGF is mediated by EGFR activity within a single cell, the ALA neuron, and mutations that impair ALA differentiation are expected to confer EGF-resistance. Here we describe three such EGF-resistant mutants. One of these corresponds to the LIM class homeodomain (HD) protein CEH-14/Lhx3, and the other two correspond to Paired-like HD proteins CEH-10/Chx10 and CEH-17/Phox2. Whereas CEH-14 is required for ALA-specific gene expression throughout development, the Prd-like proteins display complementary temporal contributions to gene expression, with the requirement for CEH-10 decreasing as that of CEH-17 increases. We present evidence that CEH-17 participates in a positive autoregulatory loop with CEH-14 in ALA, and that CEH-10, in addition to its role in ALA differentiation, functions in the generation of the ALA neuron. Similarly to CEH-17, CEH-10 is required for the posterior migration of the ALA axons, but CEH-14 appears to regulate an aspect of ALA axon outgrowth that is distinct from that of the Prd-like proteins. Our findings reveal partial modularity among the features of a neuronal differentiation program and their coordination by Prd and LIM class HD proteins.", "date": "2010-06-15", "date_type": "published", "publication": "Development", "volume": "137", "number": "12", "publisher": "Company of Biologists", "pagerange": "2065-2074", "id_number": "CaltechAUTHORS:20100615-133523696", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100615-133523696", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "DA018341" }, { "agency": "National Institute on Drug Abuse" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1242/dev.040881", "pmcid": "PMC2875845", "primary_object": { "basename": "VanBuskirk2010p10343Development.pdf", "url": "https://authors.library.caltech.edu/records/sxypc-4pt11/files/VanBuskirk2010p10343Development.pdf" }, "resource_type": "article", "pub_year": "2010", "author_list": "Van Buskirk, Cheryl and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/1skpx-x6t87", "eprint_id": 18917, "eprint_status": "archive", "datestamp": "2023-08-19 02:22:05", "lastmod": "2023-10-20 19:11:36", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cantacessi-C", "name": { "family": "Cantacessi", "given": "Cinzia" } }, { "id": "Mitreva-M", "name": { "family": "Mitreva", "given": "Makedonka" } }, { "id": "Jex-A-R", "name": { "family": "Jex", "given": "Aaron R." } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Campbell-B-E", "name": { "family": "Campbell", "given": "Bronwyn E." } }, { "id": "Hall-R-S", "name": { "family": "Hall", "given": "Ross S." } }, { "id": "Doyle-M-A", "name": { "family": "Doyle", "given": "Maria A." } }, { "id": "Ralph-S-A", "name": { "family": "Ralph", "given": "Stuart A." } }, { "id": "Rabelo-E-M", "name": { "family": "Rabelo", "given": "Elida M." } }, { "id": "Ranganathan-S", "name": { "family": "Ranganathan", "given": "Shoba" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Loukas-A", "name": { "family": "Loukas", "given": "Alex" } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "Massively Parallel Sequencing and Analysis of the Necator americanus Transcriptome", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2010 Cantacessi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived January 11, 2010; Accepted March 25, 2010; Published May 11, 2010. \n\nEditor: Matty Knight, Biomedical Research Institute, United States of America. \n\nThis research was supported by grants from the National Human Genome Research Institute (NHGRI) and National Institutes of Health (MM) and the Australian Research Council, the Australian Academy of Science and the Australian-American Fulbright Commission (RBG). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. \n\nCC is the grateful recipient of International Postgraduate Research\nScholarship (IPRS) from the Australian Government and a fee-remission scholarship through the University of Melbourne as well as the Clunies Ross (2008) and Sue Newton (2009) awards from the School of Veterinary Science of the same university. The contribution of staff at WormBase is gratefully acknowledged.\n\nAuthor Contributions: Conceived and designed the experiments: CC MM RBG. Performed the experiments: CC MM. Analyzed the data: CC ARJ NDY BEC RSH MAD SAR SR AL RBG. Contributed reagents/materials/analysis tools: MM EMR. Wrote the paper: CC PWS RBG.\n\nPublished - Cantacessi2010p10522Plos_Neglect_Trop_D.pdf
Supplemental Material - journal.pntd.0000684.s001.xls
Supplemental Material - journal.pntd.0000684.s002.xls
Supplemental Material - journal.pntd.0000684.s003.xls
Supplemental Material - journal.pntd.0000684.s004.xls
", "abstract": "Background: \nThe blood-feeding hookworm Necator americanus infects hundreds of millions of people worldwide. In order to elucidate fundamental molecular biological aspects of this hookworm, the transcriptome of the adult stage of Necator americanus was explored using next-generation sequencing and bioinformatic analyses.\nMethodology/Principal Findings: \nA total of 19,997 contigs were assembled from the sequence data; 6,771 of these contigs had known orthologues in the free-living nematode Caenorhabditis elegans, and most of them encoded proteins with WD40 repeats (10.6%), proteinase inhibitors (7.8%) or calcium-binding EF-hand proteins (6.7%). Bioinformatic analyses inferred that the C. elegans homologues are involved mainly in biological pathways linked to ribosome biogenesis (70%), oxidative phosphorylation (63%) and/or proteases (60%); most of these molecules were predicted to be involved in more than one biological pathway. Comparative analyses of the transcriptomes of N. americanus and the canine hookworm, Ancylostoma caninum, revealed qualitative and quantitative differences. For instance, proteinase inhibitors were inferred to be highly represented in the former species, whereas SCP/Tpx-1/Ag5/PR-1/Sc7 proteins (=SCP/TAPS or Ancylostoma-secreted proteins) were predominant in the latter. In N. americanus, essential molecules were predicted using a combination of orthology mapping and functional data available for C. elegans. Further analyses allowed the prioritization of 18 predicted drug targets which did not have homologues in the human host. These candidate targets were inferred to be linked to mitochondrial (e.g., processing proteins) or amino acid metabolism (e.g., asparagine t-RNA synthetase).\nConclusions: \nThis study has provided detailed insights into the transcriptome of the adult stage of N. americanus and examines similarities and differences between this species and A. caninum. Future efforts should focus on comparative transcriptomic and proteomic investigations of the other predominant human hookworm, A. duodenale, for both fundamental and applied purposes, including the prevalidation of anti-hookworm drug targets.", "date": "2010-05", "date_type": "published", "publication": "PLoS Neglected Tropical Diseases", "volume": "4", "number": "5", "publisher": "Public Library of Science", "pagerange": "Art. No. e684", "id_number": "CaltechAUTHORS:20100707-095001420", "issn": "1935-2735", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100707-095001420", "rights": "\u00a9 2010 Cantacessi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits\nunrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.", "funders": { "items": [ { "agency": "National Human Genome Research Institute" }, { "agency": "NIH" }, { "agency": "Australian Research Council" }, { "agency": "Australian Academy of Science" }, { "agency": "Australian-American Fulbright Commission" } ] }, "doi": "10.1371/journal.pntd.0000684", "pmcid": "PMC2867931", "primary_object": { "basename": "Cantacessi2010p10522Plos_Neglect_Trop_D.pdf", "url": "https://authors.library.caltech.edu/records/1skpx-x6t87/files/Cantacessi2010p10522Plos_Neglect_Trop_D.pdf" }, "related_objects": [ { "basename": "journal.pntd.0000684.s001.xls", "url": "https://authors.library.caltech.edu/records/1skpx-x6t87/files/journal.pntd.0000684.s001.xls" }, { "basename": "journal.pntd.0000684.s002.xls", "url": "https://authors.library.caltech.edu/records/1skpx-x6t87/files/journal.pntd.0000684.s002.xls" }, { "basename": "journal.pntd.0000684.s003.xls", "url": "https://authors.library.caltech.edu/records/1skpx-x6t87/files/journal.pntd.0000684.s003.xls" }, { "basename": "journal.pntd.0000684.s004.xls", "url": "https://authors.library.caltech.edu/records/1skpx-x6t87/files/journal.pntd.0000684.s004.xls" } ], "resource_type": "article", "pub_year": "2010", "author_list": "Cantacessi, Cinzia; Mitreva, Makedonka; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/27p5c-pyt41", "eprint_id": 18382, "eprint_status": "archive", "datestamp": "2023-08-21 23:35:10", "lastmod": "2023-10-20 16:10:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hu-Min", "name": { "family": "Hu", "given": "Min" } }, { "id": "Lok-James-B", "name": { "family": "Lok", "given": "James B." } }, { "id": "Ranjit-N", "name": { "family": "Ranjit", "given": "Najju" } }, { "id": "Massey-H-C", "name": { "family": "Massey", "given": "Holman C., Jr." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "Structural and functional characterisation of the fork head transcription factor-encoding gene, Hc-daf-16, from the parasitic nematode Haemonchus contortus (Strongylida)", "ispublished": "pub", "full_text_status": "public", "keywords": "Daf-16; Fork head transcription factor; Dauer; Haemonchus contortus; Caenorhabditis elegans; Transgenesis", "note": "\u00a9 2009 Australian Society for Parasitology Inc. Published by Elsevier Ltd. \n\nReceived 13 August 2009; revised 20 September 2009; accepted 21 September 2009. Available online 29 September 2009. \n\nThis work was supported by grants from the Australian Research Council (ARC) (LP0667795 and LX0882231), Genetic Technologies Limited, Meat and Livestock Australia, the Australian Academy of Science, the Australian-American Fulbright Commission (R.B.G.), the National Institutes of Health (AI-50688 to J.B.L.) and The Ellison Medical Foundation (ID-IA-0037-02 to J.B.L.). The authors thank Ben Datu for sharing primers DAF-16F100 and DAF-16R100. The C. elegans strains used in this study were originally provided by the Caenorhabditis Genetics Center, University of Minnesota, which is funded by the NIH National Center for Research Resources.\n\nAccepted Version - nihms190381.pdf
", "abstract": "Despite their phylogenetic diversity, parasitic nematodes share attributes of longevity and developmental arrest (=hypobiosis) with free-living nematodes at key points in their life cycles, particularly in larval stages responsible for establishing infection in the host. Insulin-like signalling plays crucial roles in the regulation of life span and arrest (=dauer formation) in the free-living nematode, Caenorhabditis elegans. Insulin-like signalling in C. elegans negatively regulates the fork head boxO (FoxO) transcription factor encoded by daf-16, which is linked to initiating a dauer-specific pattern of gene expression. Orthologues of daf-16 have been identified in several species of parasitic nematode. Although function has been demonstrated for an orthologue from the parasitic nematode Strongyloides stercoralis (Rhabditida), the functional capabilities of homologues/orthologues in bursate nematodes (Strongylida) are unknown. In the present study, we used a genomic approach to determine the structures of two complete daf-16 orthologues (designated Hc-daf-16.1 and Hc-daf-16.2) and their transcripts in the parasitic nematode Haemonchus contortus, and assessed their function(s) using C. elegans as a genetic surrogate. Unlike the multiple isoforms of Ce-DAF-16 and Ss-DAF-16, which are encoded by a single gene and produced by alternative splicing, mRNAs encoding the proteins Hc-DAF-16.1 and Hc-DAF-16.2 are transcribed from separate and distinct loci. Both orthologues are transcribed in all developmental stages and both sexes of H. contortus, and the inferred proteins (603 and 556 amino acids) each contain a characteristic, highly conserved fork head domain. In spite of distinct differences in genomic organisation compared with orthologues in C. elegans and S. stercoralis, genetic complementation studies demonstrated here that Hc-daf-16.2, but not Hc-daf-16.1, could restore daf-16 function to a C. elegans strain carrying a null mutation at this locus. These findings are consistent with previous results for S. stercoralis and demonstrate functional conservation of the daf-16b orthologue between key parasitic nematodes from two different taxonomic orders and C. elegans. We conclude from these experiments that the fork head transcription factor DAF-16 and, by inference, other insulin-like signalling elements, are conserved in H. contortus, a parasitic nematode of paramount economic importance. We demonstrate that functionality is sufficiently conserved in Hc-DAF-16.2 that it can replace Ce-DAF-16 in promoting dauer arrest in C. elegans.", "date": "2010-03-15", "date_type": "published", "publication": "International Journal for Parasitology", "volume": "40", "number": "4", "publisher": "Elsevier", "pagerange": "405-415", "id_number": "CaltechAUTHORS:20100521-080935136", "issn": "0020-7519", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100521-080935136", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council", "grant_number": "LP0667795" }, { "agency": "Australian Research Council", "grant_number": "LX0882231" }, { "agency": "Genetic Technologies Limited" }, { "agency": "Meat and Livestock Australia" }, { "agency": "Australian Academy of Science" }, { "agency": "Australian-American Fulbright Commission" }, { "agency": "NIH", "grant_number": "AI-50688" }, { "agency": "Ellison Medical Foundation", "grant_number": "ID-IA-0037-02" } ] }, "doi": "10.1016/j.ijpara.2009.09.005", "pmcid": "PMC2853935", "primary_object": { "basename": "nihms190381.pdf", "url": "https://authors.library.caltech.edu/records/27p5c-pyt41/files/nihms190381.pdf" }, "resource_type": "article", "pub_year": "2010", "author_list": "Hu, Min; Lok, James B.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/creg9-s5854", "eprint_id": 17489, "eprint_status": "archive", "datestamp": "2023-08-19 01:41:29", "lastmod": "2023-10-19 23:56:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Pang-Shuo", "name": { "family": "Pang", "given": "Shuo" } }, { "id": "Cui-Xiquan", "name": { "family": "Cui", "given": "Xiquan" } }, { "id": "DeModena-J", "name": { "family": "DeModena", "given": "John" } }, { "id": "Wang-Ying-Min", "name": { "family": "Wang", "given": "Ying Min" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Yang-Changhuei", "name": { "family": "Yang", "given": "Changhuei" }, "orcid": "0000-0001-8791-0354" } ] }, "title": "Implementation of a color-capable optofluidic microscope on a RGB CMOS color sensor chip substrate", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2010 Royal Society of Chemistry.\nReceived 15th September 2009, Accepted 14th December 2009.\nFirst published as an Advance Article on the web 5th January 2010.\nWe would like to express our thanks to Dr Sri Rama Prasanna\nPavani for the assistance of the experiments, Lap Man Lee and Dr JigangWu for constructive discussions. This work is supported by\nthe Coulter Foundation and NIH R21EB008867.\n\nPublished - Pang2010p7023Lab_on_a_Chip.pdf
", "abstract": "We report the implementation of a color-capable on-chip lensless microscope system, termed color optofluidic microscope (color OFM), and demonstrate imaging of double stained Caenorhabditis elegans with lacZ gene expression at a light intensity about 10 mW/cm^2.", "date": "2010-02-21", "date_type": "published", "publication": "Lab on a Chip", "volume": "10", "number": "4", "publisher": "Royal Society of Chemistry", "pagerange": "411-414", "id_number": "CaltechAUTHORS:20100216-140439313", "issn": "1473-0197", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100216-140439313", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Coulter Foundation" }, { "agency": "NIH", "grant_number": "R21EB008867" } ] }, "doi": "10.1039/b919004j", "primary_object": { "basename": "Pang2010p7023Lab_on_a_Chip.pdf", "url": "https://authors.library.caltech.edu/records/creg9-s5854/files/Pang2010p7023Lab_on_a_Chip.pdf" }, "resource_type": "article", "pub_year": "2010", "author_list": "Pang, Shuo; Cui, Xiquan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/amfrq-hc195", "eprint_id": 17860, "eprint_status": "archive", "datestamp": "2023-08-19 01:41:12", "lastmod": "2023-10-20 15:21:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Rivard-L", "name": { "family": "Rivard", "given": "Laura" } }, { "id": "Srinivasan-J", "name": { "family": "Srinivasan", "given": "Jagan" }, "orcid": "0000-0001-5449-7938" }, { "id": "Stone-A", "name": { "family": "Stone", "given": "Allison" } }, { "id": "Ochoa-S", "name": { "family": "Ochoa", "given": "Stacy" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Loer-C-M", "name": { "family": "Loer", "given": "Curtis M." } } ] }, "title": "A comparison of experience-dependent locomotory behaviors and biogenic amine neurons in nematode relatives of Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2010 Rivard et al; licensee BioMed Central Ltd.\nThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.\nReceived: 19 August 2009.\nAccepted: 19 February 2010 Published: 19 February 2010.\n\nWe thank David Fitch for strains and advice, and Karin Kiontke for discussions\nabout nematode sensilla evolution. Some strains were obtained from the\nCaenorhabditis Genetics Center, an NIH Research Resource. We thank Kris\nCarter and Jason Kehrer (USD) who also contributed to the project. CL is\nsupported by an endowment from the Fletcher Jones Foundation; some of\nthis work was also supported by NIGMS Grant R15GM60203 (to CL). We also\nthank Christopher Cronin for assistance in worm locomotion scripts and\nmembers of the Sternberg lab for comments and discussions on the\nmanuscript. JS is an Associate and PWS is an Investigator of the Howard\nHughes Medical Institute, which supported this research.\nAuthors' contributions: \nLR, AS, and SO performed manual locomotion studies, LR, AS and CL\nperformed anti-serotonin staining studies, CL performed FIF and 5HTP/antiserotonin\nstudies, JS and PWS designed tracker experiments and JS\nperformed automated tracker locomotion experiments, and LR, JS, CL and\nPWS wrote the paper. All the authors have read and approved the final\nmanuscript.\n\nPublished - Rivard2010p7383Bmc_Neurosci.pdf
", "abstract": "Background: \n\nSurvival of an animal depends on its ability to match its responses to environmental conditions. To generate an optimal behavioral output, the nervous system must process sensory information and generate a directed motor output in response to stimuli. The nervous system should also store information about experiences to use in the future. The diverse group of free-living nematodes provides an excellent system to study macro- and microevolution of molecular, morphological and behavioral character states associated with such nervous system function. We asked whether an adaptive behavior would vary among bacterivorous nematodes and whether differences in the neurotransmitter systems known to regulate the behavior in one species would reflect differences seen in the adaptive behavior among those species. Caenorhabditis elegans worms slow in the presence of food; this 'basal' slowing is triggered by dopaminergic mechanosensory neurons that detect bacteria. Starved worms slow more dramatically; this 'enhanced' slowing is regulated by serotonin.\nResults: \n\nWe examined seven nematode species with known phylogenetic relationship to C. elegans for locomotory behaviors modulated by food (E. coli), and by the worm's recent history of feeding (being well-fed or starved). We found that locomotory behavior in some species was modulated by food and recent feeding experience in a manner similar to C. elegans, but not all the species tested exhibited these food-modulated behaviors. We also found that some worms had different responses to bacteria other than E. coli. Using histochemical and immunological staining, we found that dopaminergic neurons were very similar among all species. For instance, we saw likely homologs of four bilateral pairs of dopaminergic cephalic and deirid neurons known from C. elegans in all seven species examined. In contrast, there was greater variation in the patterns of serotonergic neurons. The presence of presumptive homologs of dopaminergic and serotonergic neurons in a given species did not correlate with the observed differences in locomotory behaviors.\nConclusions: \n\nThis study demonstrates that behaviors can differ significantly between species that appear morphologically very similar, and therefore it is important to consider factors, such as ecology of a species in the wild, when formulating hypotheses about the adaptive significance of a behavior. Our results suggest that evolutionary changes in locomotory behaviors are less likely to be caused by changes in neurotransmitter expression of neurons. Such changes could be caused either by subtle changes in neural circuitry or in the function of the signal transduction pathways mediating these behaviors.", "date": "2010-02-19", "date_type": "published", "publication": "BMC Neuroscience", "volume": "11", "publisher": "BioMed Central", "pagerange": "Art. No. 22", "id_number": "CaltechAUTHORS:20100406-091844958", "issn": "1471-2202", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100406-091844958", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Fletcher Jones Foundation" }, { "agency": "NIH", "grant_number": "R15GM60203" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "collection": "CaltechAUTHORS", "doi": "10.1186/1471-2202-11-22", "pmcid": "PMC2836364", "primary_object": { "basename": "Rivard2010p7383Bmc_Neurosci.pdf", "url": "https://authors.library.caltech.edu/records/amfrq-hc195/files/Rivard2010p7383Bmc_Neurosci.pdf" }, "resource_type": "article", "pub_year": "2010", "author_list": "Rivard, Laura; Srinivasan, Jagan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/9b58m-tbm85", "eprint_id": 17638, "eprint_status": "archive", "datestamp": "2023-08-21 23:23:35", "lastmod": "2023-10-20 00:05:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Inoue-Takao", "name": { "family": "Inoue", "given": "Takao" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "C. elegans BED domain transcription factor BED-3 controls lineage-specific cell proliferation during organogenesis", "ispublished": "pub", "full_text_status": "public", "keywords": "C. elegans; Organogenesis; Cell cycle regulation; Cell division; Cell proliferation; BED domain; Zinc finger; Transcription; Gene regulatory network (GRN)", "note": "\u00a9 2009 Elsevier Inc. \n\nReceived 22 April 2009; revised 9 November 2009; accepted 4 December 2009. Available online 17 December 2009. \n\nWe thank J. Gruber, Ng L.F., B. Halliwell, Shen Y.Q. and Fu X.Y. for assistance and resources at NUS. We thank J. Fernandes and T. Ririe for comments on the manuscript, and members of the Sternberg laboratory for helpful discussions. T.I. was supported by fellowship DRG-1646 from the Damon Runyon Cancer Research Foundation. This work was supported by the HHMI, with which P.W.S. is an investigator. Some nematode strains used in this work were provided by the Caenorhabditis Genetics Center, which is funded by the NIH National Center for Research Resources (NCRR).\n\nAccepted Version - nihms177815.pdf
", "abstract": "The control of cell division is critical to organogenesis, but how this control is achieved is not fully understood. We found that mutations in bed-3, encoding a BED Zn-finger domain transcription factor, confer a phenotype where a specific set of cell divisions during vulval organogenesis is lost. Unlike general cell cycle regulators in Caenorhabditis elegans, the function of bed-3 is restricted to specific lineages. Transcriptional reporters suggest that bed-3 is expressed in a limited number of cell types including vulval cells whose divisions are affected in bed-3 mutants. A bed-3 mutation also affects the expression pattern of the cdh-3 cadherin gene in the vulva. The phenotype of bed-3 mutants is similar to the phenotype caused by mutations in cog-1 (Nkx6), a component of a gene regulatory network controlling cell type specific gene expression in the vulval lineage. These results suggest that bed-3 is a key component linking the gene regulatory network controlling cell-type specification to control of cell division during vulval organogenesis.", "date": "2010-02-15", "date_type": "published", "publication": "Developmental Biology", "volume": "338", "number": "2", "publisher": "Elsevier", "pagerange": "226-236", "id_number": "CaltechAUTHORS:20100303-094838992", "issn": "0012-1606", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100303-094838992", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Damon Runyon Cancer Research Foundation", "grant_number": "DRG-1646" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH" } ] }, "doi": "10.1016/j.ydbio.2009.12.005", "pmcid": "PMC2862168", "primary_object": { "basename": "nihms177815.pdf", "url": "https://authors.library.caltech.edu/records/9b58m-tbm85/files/nihms177815.pdf" }, "resource_type": "article", "pub_year": "2010", "author_list": "Inoue, Takao and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/yp3fy-wk708", "eprint_id": 17654, "eprint_status": "archive", "datestamp": "2023-08-21 23:09:57", "lastmod": "2023-10-20 00:06:47", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hu-Min", "name": { "family": "Hu", "given": "Min" } }, { "id": "Zhong-Weiwei", "name": { "family": "Zhong", "given": "Weiwei" } }, { "id": "Campbell-B-E", "name": { "family": "Campbell", "given": "Bronwyn E." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Pellegrino-M-W", "name": { "family": "Pellegrino", "given": "Mark W." } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "Elucidating ANTs in worms using genomic and bioinformatic tools \u2014 Biotechnological prospects?", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Adenine nucleotide translocator; ADP/ATP translocase; Nematodes; Caenorhabditis elegans; Haemonchus contortus; Genomics; Bioinformatics; Genetic interactions", "note": "\u00a9 2009 Elsevier Inc.\nReceived 2 July 2009; \nrevised 11 August 2009; \naccepted 3 September 2009. \nAvailable online 19 September 2009.\n\nFunding support to RBG from the Australian Research Council\n(LX0882231 and LX0989150), Genetic Technologies Limited and Meat\nand Livestock Australia are gratefully acknowledged. The authors thank\nDrs Warwick Grant, Kirsten Grant and Jagan Srinivasan for discussions\nand support as well as Alon Zaslaver for technical assistance.", "abstract": "Adenine nucleotide translocators (ANTs) belong to the mitochondrial carrier family (MCF) of proteins. ATP production and consumption are tightly linked to ANTs, the kinetics of which have been proposed to play a key regulatory role in mitochondrial oxidative phosphorylation. ANTs are also recognized as a central component of the mitochondrial permeability transition pore associated with apoptosis. Although ANTs have been investigated in a range of vertebrates, including human, mouse and cattle, and invertebrates, such as Drosophila melanogaster (vinegar fly), Saccharomyces cerevisiae (yeast) and Caenorhabditis elegans (free-living nematode), there has been a void of information on these molecules for parasitic nematodes of socio-economic importance. Exploring ANTs in nematodes has the potential lead to a better understanding of their fundamental roles in key biological pathways and might provide an avenue for the identification of targets for the rational design of nematocidal drugs. In the present article, we describe the discovery of an ANT from Haemonchus contortus (one of the most economically important parasitic nematodes of sheep and goats), conduct a comparative analysis of key ANTs and their genes (particularly ant-1.1) in nematodes and other organisms, predict the functional roles utilizing a combined genomic-bioinformatic approach and propose ANTs and associated molecules as possible drug targets, with the potential for biotechnological outcomes.", "date": "2010-01", "date_type": "published", "publication": "Biotechnology Advances", "volume": "28", "number": "1", "publisher": "Elsevier", "pagerange": "49-60", "id_number": "CaltechAUTHORS:20100303-151930574", "issn": "0734-9750", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100303-151930574", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council", "grant_number": "LX0882231" }, { "agency": "Australian Research Council", "grant_number": "LX0989150" }, { "agency": "Genetic Technologies Limited" }, { "agency": "Meat and Livestock Australia" } ] }, "doi": "10.1016/j.biotechadv.2009.09.001", "resource_type": "article", "pub_year": "2010", "author_list": "Hu, Min; Zhong, Weiwei; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/sra62-q7n63", "eprint_id": 18482, "eprint_status": "archive", "datestamp": "2023-08-19 01:17:45", "lastmod": "2023-10-20 16:26:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Harris-T-W", "name": { "family": "Harris", "given": "Todd W." }, "orcid": "0000-0003-3406-163X" }, { "id": "Antoshechkin-I-A", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Bieri-T", "name": { "family": "Bieri", "given": "Tamberlyn" } }, { "id": "Blasiar-D", "name": { "family": "Blasiar", "given": "Darin" } }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "Chen-Wen-J", "name": { "family": "Chen", "given": "Wen J." } }, { "id": "De-La-Cruz-N", "name": { "family": "De La Cruz", "given": "Norie" } }, { "id": "Davis-P-M", "name": { "family": "Davis", "given": "Paul" } }, { "id": "Duesbury-M", "name": { "family": "Duesbury", "given": "Margaret" } }, { "id": "Fang-Ruihua", "name": { "family": "Fang", "given": "Ruihua" } }, { "id": "Fernandes-J-S", "name": { "family": "Fernandes", "given": "Jolene" } }, { "id": "Han-Michael", "name": { "family": "Han", "given": "Michael" } }, { "id": "Kishore-R", "name": { "family": "Kishore", "given": "Ranjana" } }, { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "Raymond" }, "orcid": "0000-0002-8151-7479" }, { "id": "M\u00fcller-H-M", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } }, { "id": "Nakamura-Cecilia", "name": { "family": "Nakamura", "given": "Cecilia" }, "orcid": "0000-0002-4689-7314" }, { "id": "Ozersky-P", "name": { "family": "Ozersky", "given": "Philip" } }, { "id": "Petcherski-A", "name": { "family": "Petcherski", "given": "Andrei" } }, { "id": "Rangarajan-A", "name": { "family": "Rangarajan", "given": "Arun" } }, { "id": "Rogers-A", "name": { "family": "Rogers", "given": "Anthony" } }, { "id": "Schindelman-G", "name": { "family": "Schindelman", "given": "Gary" } }, { "id": "Schwarz-E-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Tuli-M-A", "name": { "family": "Tuli", "given": "Mary Ann" } }, { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Wang-Daniel", "name": { "family": "Wang", "given": "Daniel" } }, { "id": "Wang-Xiaodong", "name": { "family": "Wang", "given": "Xiaodong" } }, { "id": "Williams-G", "name": { "family": "Williams", "given": "Gary" } }, { "id": "Yook-Karen-J", "name": { "family": "Yook", "given": "Karen" }, "orcid": "0000-0002-4457-6787" }, { "id": "Durbin-R", "name": { "family": "Durbin", "given": "Richard" } }, { "id": "Stein-L-D", "name": { "family": "Stein", "given": "Lincoln D." }, "orcid": "0000-0002-1983-4588" }, { "id": "Spieth-J", "name": { "family": "Spieth", "given": "John" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "WormBase: a comprehensive resource for nematode research", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2009. Published by Oxford University Press. \n\nReceived September 15, 2009; Revised October 11, 2009; Accepted October 12, 2009. \n\nUS National Institutes of Health (Grant no. P41 HG02223); US National Human Genome Research Institute (Grant no. P41-HG02223 to WormBase); British Medical Research Council (to WormBase); P.W.S. is an investigator with the Howard HughesMedical Institute. Funding for open access charge: US National Human Genome Research Institute (Grant P41-HG02223).\n\nPublished - Harris2010p9889Nucleic_Acids_Res.pdf
", "abstract": "WormBase (http://www.wormbase.org) is a central data repository for nematode biology. Initially created as a service to the Caenorhabditis elegans research field, WormBase has evolved into a powerful research tool in its own right. In the past 2 years, we expanded WormBase to include the complete genomic sequence, gene predictions and orthology assignments from a range of related nematodes. This comparative data enrich the C. elegans data with improved gene predictions and a better understanding of gene function. In turn, they bring the wealth of experimental knowledge of C. elegans to other systems of medical and agricultural importance. Here, we describe new species and data types now available at WormBase. In addition, we detail enhancements to our curatorial pipeline and website infrastructure to accommodate new genomes and an extensive user base.", "date": "2010-01", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "38", "number": "D1", "publisher": "Oxford University Press", "pagerange": "D463-D467", "id_number": "CaltechAUTHORS:20100527-134537612", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100527-134537612", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P41HG02223" }, { "agency": "National Human Genome Research Institute", "grant_number": "P41-HG02223" }, { "agency": "Medical Research Council (MRC)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "collection": "CaltechAUTHORS", "doi": "10.1093/nar/gkp952", "pmcid": "PMC2808986", "primary_object": { "basename": "Harris2010p9889Nucleic_Acids_Res.pdf", "url": "https://authors.library.caltech.edu/records/sra62-q7n63/files/Harris2010p9889Nucleic_Acids_Res.pdf" }, "resource_type": "article", "pub_year": "2010", "author_list": "Harris, Todd W.; Antoshechkin, Igor; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/4x55w-q4b03", "eprint_id": 18785, "eprint_status": "archive", "datestamp": "2023-08-19 00:58:01", "lastmod": "2023-10-20 16:46:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cantacessi-C", "name": { "family": "Cantacessi", "given": "Cinzia" } }, { "id": "Campbell-B-E", "name": { "family": "Campbell", "given": "Bronwyn E." } }, { "id": "Young-N-D", "name": { "family": "Young", "given": "Neil D." } }, { "id": "Jex-A-R", "name": { "family": "Jex", "given": "Aaron R." } }, { "id": "Hall-R-S", "name": { "family": "Hall", "given": "Ross S." } }, { "id": "Presidente-P-J-A", "name": { "family": "Presidente", "given": "Paul J. A." } }, { "id": "Zawadzki-J-L", "name": { "family": "Zawadzki", "given": "Jodi L." } }, { "id": "Zhong-Weiwei", "name": { "family": "Zhong", "given": "Weiwei" } }, { "id": "Aleman-Meza-B", "name": { "family": "Aleman-Meza", "given": "Boanerges" } }, { "id": "Loukas-A", "name": { "family": "Loukas", "given": "Alex" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "Differences in transcription between free-living and CO_2-activated third-stage larvae of Haemonchus contortus", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2010 Cantacessi et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived: 15 December 2009. Accepted: 27 April 2010. Published: 27 April 2010. \n\nThis work was supported by grants from the Australian Research Council (RBG, AL, PWS) and the Australian-American Fulbright Commission (RBG). CC is the grateful recipient of International Postgraduate Research Scholarship (IPRS) from the Australian Government and a fee-remission scholarship through the University of Melbourne as well as the Clunies Ross (2008) and Sue Newton (2009) awards from the School of Veterinary Science of the same university. The staff of WormBase is acknowledged for their contributions. This article is dedicated to the late Paul JA Presidente.\n\nAuthors' contributions: CC performed the bioinformatic analyses, analysed the results and drafted the manuscript, BEC, NDY, ARJ and RSH also participated in the bioinformatic analyses, PJAP and JLZ provided the parasite material, WZ and BAM assisted in the probabilistic genetic interaction network predictions, AL and PWS contributed to the drafting of the manuscript. RBG conceived and designed the study, coordinated and supervised the project and drafted the manuscript with CC. All authors read and approved the final manuscript.\n\nPublished - Cantacessi2010p10462Bmc_Genomics.pdf
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Supplemental Material - 1471-2164-11-266-s4.xls
Supplemental Material - 1471-2164-11-266-s5.doc
Supplemental Material - 1471-2164-11-266-s6.doc
Supplemental Material - 1471-2164-11-266-s7.xls
Supplemental Material - 1471-2164-11-266-s8.doc
", "abstract": "Background: \n\nThe disease caused by Haemonchus contortus, a blood-feeding nematode of small ruminants, is of major economic importance worldwide. The infective third-stage larva (L3) of this gastric nematode is enclosed in a cuticle (sheath) and, once ingested with herbage by the host, undergoes an exsheathment process that marks the transition from the free-living (L3) to the parasitic (xL3) stage. This study explored changes in gene transcription associated with this transition and predicted, based on comparative analysis, functional roles for key transcripts in the metabolic pathways linked to larval development.\nResults: \n\nTotals of 101,305 (L3) and 105,553 (xL3) expressed sequence tags (ESTs) were determined using 454 sequencing technology, and then assembled and annotated; the most abundant transcripts encoded transthyretin-like, calcium-binding EF-hand, NAD(P)-binding and nucleotide-binding proteins as well as homologues of Ancylostoma-secreted proteins (ASPs). Using an in silico-subtractive analysis, 560 and 685 sequences were shown to be uniquely represented in the L3 and xL3 stages, respectively; the transcripts encoded ribosomal proteins, collagens and elongation factors (in L3), and mainly peptidases and other enzymes of amino acid catabolism (in xL3). Caenorhabditis elegans orthologues of transcripts that were uniquely transcribed in each L3 and xL3 were predicted to interact with a total of 535 other genes, all of which were involved in embryonic development.\nConclusion: \n\nThe present study indicated that some key transcriptional alterations taking place during the transition from the L3 to the xL3 stage of H. contortus involve genes predicted to be linked to the development of neuronal tissue (L3 and xL3), formation of the cuticle (L3) and digestion of host haemoglobin (xL3). Future efforts using next-generation sequencing and bioinformatic technologies should provide the efficiency and depth of coverage required for the determination of the complete transcriptomes of different developmental stages and/or tissues of H. contortus as well as the genome of this important parasitic nematode. Such advances should lead to a significantly improved understanding of the molecular biology of H. contortus and, from an applied perspective, to novel methods of intervention.", "date": "2010", "date_type": "published", "publication": "BMC Genomics", "volume": "11", "publisher": "BioMed Central", "pagerange": "266-279", "id_number": "CaltechAUTHORS:20100624-080447987", "issn": "1471-2164", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100624-080447987", "rights": "This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.", "funders": { "items": [ { "agency": "Australian Research Council" }, { "agency": "Australian-American Fulbright Commission" } ] }, "collection": "CaltechAUTHORS", "doi": "10.1186/1471-2164-11-266", "pmcid": "PMC2880303", "primary_object": { "basename": "1471-2164-11-266-s4.xls", "url": "https://authors.library.caltech.edu/records/4x55w-q4b03/files/1471-2164-11-266-s4.xls" }, "related_objects": [ { "basename": "1471-2164-11-266-s5.doc", "url": "https://authors.library.caltech.edu/records/4x55w-q4b03/files/1471-2164-11-266-s5.doc" }, { "basename": "1471-2164-11-266-s2.xls", "url": "https://authors.library.caltech.edu/records/4x55w-q4b03/files/1471-2164-11-266-s2.xls" }, { "basename": "1471-2164-11-266-s1.xls", "url": "https://authors.library.caltech.edu/records/4x55w-q4b03/files/1471-2164-11-266-s1.xls" }, { "basename": "1471-2164-11-266-s6.doc", "url": "https://authors.library.caltech.edu/records/4x55w-q4b03/files/1471-2164-11-266-s6.doc" }, { "basename": "1471-2164-11-266-s8.doc", "url": "https://authors.library.caltech.edu/records/4x55w-q4b03/files/1471-2164-11-266-s8.doc" }, { "basename": "1471-2164-11-266-s3.xls", "url": "https://authors.library.caltech.edu/records/4x55w-q4b03/files/1471-2164-11-266-s3.xls" }, { "basename": "Cantacessi2010p10462Bmc_Genomics.pdf", "url": "https://authors.library.caltech.edu/records/4x55w-q4b03/files/Cantacessi2010p10462Bmc_Genomics.pdf" }, { "basename": "1471-2164-11-266-s7.xls", "url": "https://authors.library.caltech.edu/records/4x55w-q4b03/files/1471-2164-11-266-s7.xls" } ], "resource_type": "article", "pub_year": "2010", "author_list": "Cantacessi, Cinzia; Campbell, Bronwyn E.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/s8hzm-z2a70", "eprint_id": 17703, "eprint_status": "archive", "datestamp": "2023-08-19 00:56:30", "lastmod": "2023-10-20 00:09:57", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Seah-A", "name": { "family": "Seah", "given": "Adeline" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The roles of EGF and Wnt signaling during patterning of the C. elegans B\u03b3/\u03b4 Equivalence Group", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2009 Seah and Sternberg; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived: 18 September 2009. Accepted: 31 December 2009. Published: 31 December 2009. \n\nWe thank Fritz Muller for pMF1, Cheryl Van Buskirk for the HS::EGF strain, Helen Chamberlin for discussions and unpublished data, Erich Schwarz for discussions on motif enrichment, Mihoko Kato and Cheryl Van Buskirk for discussions and helpful comments on the manuscript. PWS is an Investigator of the Howard Hughes Medical Institute, which supported this work. AS was supported by a HHMI Pre-Doctoral Fellowship. \n\nAuthors' contributions: AS participated in the design of the study, carried out all experimental procedures and drafted the manuscript.\nPWS conceived of the study and helped to draft the manuscript. Both authors have read and approved the final manuscript.\n\nPublished - Seah2009p7009BMC_Dev_Biol.pdf
Supplemental Material - 1471-213x-9-74-s1.doc
", "abstract": "Background: \nDuring development, different signaling pathways interact to specify cell fate by regulating transcription factors necessary for fate specification and morphogenesis. In Caenorhabditis elegans, the EGF-Ras and Wnt signaling pathways have been shown to interact to specify cell fate in three equivalence groups: the vulval precursor cells (VPCs), the hook competence group (HCG) and P11/12. In the VPCs, HCG and P11/12 pair, EGF and Wnt signaling positively regulate different Hox genes, each of which also functions during fate specification. In the male, EGF-Ras signaling is required to specify the B\u03b3 fate within the B\u03b3/\u03b4 equivalence pair, while Notch signaling is required for B\u03b4 fate specification. In addition, TGF-\u03b2 signaling by dbl-1/dpp controls ceh-13/labial/Hox1 expression in B\u03b3.\n\nResults: \nWe show that EGF-Ras signaling is required for B\u03b3 expression of ceh-13/labial/Hox1. The transcription factors lin-1/ETS and lin-31/Forkhead, functioning downstream of the EGF pathway, as well as sur-2/MED23 (a component of the Mediator complex) also control ceh-13 expression in B\u03b3. In addition, our results indicate that lin-44/Wnt, mom-2/Wnt and lin-17/Fz are necessary to maintain the division of B\u03b3 along a longitudinal axis. We also show that dbl-1/dpp acts either in parallel or downstream of EGF pathway to regulate ceh-13/Hox1 expression in B\u03b3. Lastly, we find that a dbl-1/dpp null mutation did not cause any vulval or P12 defects and did not enhance vulval and P12 defects of reduction-of-function mutations of components of the EGF pathway.\n\nConclusions: \nceh-13/labial/Hox1 expression in B\u03b3 is regulated by the EGF pathway and downstream factors lin-1/ETS lin-31/Forkhead and sur-2/MED23. Wnt signaling is required for proper B\u03b3 division, perhaps to orient the B\u03b3 mitotic spindle. Our results suggest that dbl-1/dpp is not required for VPC and P12 specification, highlighting another difference among these EGF-dependent equivalence groups.", "date": "2009-12-31", "date_type": "published", "publication": "BMC Developmental Biology", "volume": "9", "publisher": "BioMed Central", "pagerange": "Art. No. 74", "id_number": "CaltechAUTHORS:20100309-100907034", "issn": "1471-213X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100309-100907034", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1186/1471-213X-9-74", "pmcid": "PMC2813230", "primary_object": { "basename": "1471-213x-9-74-s1.doc", "url": "https://authors.library.caltech.edu/records/s8hzm-z2a70/files/1471-213x-9-74-s1.doc" }, "related_objects": [ { "basename": "Seah2009p7009BMC_Dev_Biol.pdf", "url": "https://authors.library.caltech.edu/records/s8hzm-z2a70/files/Seah2009p7009BMC_Dev_Biol.pdf" } ], "resource_type": "article", "pub_year": "2009", "author_list": "Seah, Adeline and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/fjdty-x3778", "eprint_id": 17427, "eprint_status": "archive", "datestamp": "2023-08-19 00:51:07", "lastmod": "2023-10-19 23:53:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Adhikari-B-N", "name": { "family": "Adhikari", "given": "Bishwo N." } }, { "id": "Lin-Chin-Yo", "name": { "family": "Lin", "given": "Chin-Yo" } }, { "id": "Bai-Xiaodong", "name": { "family": "Bai", "given": "Xiaodong" } }, { "id": "Ciche-T-A", "name": { "family": "Ciche", "given": "Todd A." } }, { "id": "Grewal-P-S", "name": { "family": "Grewal", "given": "Parwinder S." } }, { "id": "Dillman-A-R", "name": { "family": "Dillman", "given": "Adler R." }, "orcid": "0000-0001-7171-4332" }, { "id": "Chaston-J-M", "name": { "family": "Chaston", "given": "John M." } }, { "id": "Shapiro-Ilan-D-I", "name": { "family": "Shapiro-Ilan", "given": "David I." } }, { "id": "Bilgrami-A-L", "name": { "family": "Bilgrami", "given": "Anwar L." } }, { "id": "Gaugler-R", "name": { "family": "Gaugler", "given": "Randy" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Adams-B-J", "name": { "family": "Adams", "given": "Byron J." } } ] }, "title": "Transcriptional profiling of trait deterioration in the insect\n pathogenic nematode Heterorhabditis bacteriophora", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2009 Adhikari et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived: 16 October 2009. Accepted: 15 December 2009. Published: 15 December 2009. \n\nThis work was supported by a grant from the United States Department of Agriculture (USDA)/National Science Foundation (NSF) Microbial Genome Sequence Program and the National Human Genome Research Institute (NHGRI) awarded to PSG, TAC, RG, PWS and BJA, and a USDA National Research Initiative (NRI) grant to DIS, RG and BJA. W. E. Johnson provided important advice concerning microarray data analysis.\n\nPublished - Adhikari2009p6994Bmc_Genomics.pdf
Supplemental Material - 1471-2164-10-609-s1.pdf
Supplemental Material - 1471-2164-10-609-s2.pdf
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Supplemental Material - 1471-2164-10-609-s4.pdf
Supplemental Material - 1471-2164-10-609-s5.pdf
", "abstract": "Background: \nThe success of a biological control agent depends on key traits, particularly reproductive potential, environmental tolerance, and ability to be cultured. These traits can deteriorate rapidly when the biological control agent is reared in culture. Trait deterioration under laboratory conditions has been widely documented in the entomopathogenic nematode (EPN) Heterorhabditis bacteriophora (Hb) but the specific mechanisms behind these genetic processes remain unclear. This research investigates the molecular mechanisms of trait deterioration of two experimental lines of Hb, an inbred line (L5M) and its original parental line (OHB). We generated transcriptional profiles of two experimental lines of Hb, identified the differentially expressed genes (DEGs) and validated their differential expression in the deteriorated line.\n\nResults: \nAn expression profiling study was performed between experimental lines L5M and OHB of Hb with probes for 15,220 ESTs from the Hb transcriptome. Microarray analysis showed 1,185 DEGs comprising of 469 down- and 716 up-regulated genes in trait deteriorated nematodes. Analysis of the DEGs showed that trait deterioration involves massive changes of the transcripts encoding enzymes involved in metabolism, signal transduction, virulence and longevity. We observed a pattern of reduced expression of enzymes related to primary metabolic processes and induced secondary metabolism. Expression of sixteen DEGs in trait deteriorated nematodes was validated by quantitative reverse transcription-PCR (qRT-PCR) which revealed similar expression kinetics for all the genes tested as shown by microarray.\n\nConclusion: \nAs the most closely related major entomopathogen to C. elegans, Hb provides an attractive near-term application for using a model organism to better understand interspecies interactions and to enhance our understanding of the mechanisms underlying trait deterioration in biological control agents. This information could also be used to improve the beneficial traits of biological control agents and better understand fundamental aspects of nematode parasitism and mutualism.", "date": "2009-12-15", "date_type": "published", "publication": "BMC Genomics", "volume": "10", "publisher": "BioMed Central", "pagerange": "Art. No. 609", "id_number": "CaltechAUTHORS:20100209-084317670", "issn": "1471-2164", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100209-084317670", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Agriculture (USDA)" }, { "agency": "NSF" }, { "agency": "National Human Genome Research Institute" } ] }, "collection": "CaltechAUTHORS", "doi": "10.1186/1471-2164-10-609", "pmcid": "PMC2805696", "primary_object": { "basename": "1471-2164-10-609-s1.pdf", "url": "https://authors.library.caltech.edu/records/fjdty-x3778/files/1471-2164-10-609-s1.pdf" }, "related_objects": [ { "basename": "1471-2164-10-609-s2.pdf", "url": "https://authors.library.caltech.edu/records/fjdty-x3778/files/1471-2164-10-609-s2.pdf" }, { "basename": "1471-2164-10-609-s3.xlsx", "url": "https://authors.library.caltech.edu/records/fjdty-x3778/files/1471-2164-10-609-s3.xlsx" }, { "basename": "1471-2164-10-609-s4.pdf", "url": "https://authors.library.caltech.edu/records/fjdty-x3778/files/1471-2164-10-609-s4.pdf" }, { "basename": "Adhikari2009p6994Bmc_Genomics.pdf", "url": "https://authors.library.caltech.edu/records/fjdty-x3778/files/Adhikari2009p6994Bmc_Genomics.pdf" }, { "basename": "1471-2164-10-609-s5.pdf", "url": "https://authors.library.caltech.edu/records/fjdty-x3778/files/1471-2164-10-609-s5.pdf" } ], "resource_type": "article", "pub_year": "2009", "author_list": "Adhikari, Bishwo N.; Lin, Chin-Yo; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/e55v9-ccs28", "eprint_id": 17026, "eprint_status": "archive", "datestamp": "2023-08-21 22:51:22", "lastmod": "2023-10-19 22:44:47", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kato-Mihoko", "name": { "family": "Kato", "given": "Mihoko" }, "orcid": "0000-0003-3827-8879" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The C. elegans tailless/Tlx homolog nhr-67 regulates a stage-specific program of linker cell migration in male gonadogenesis", "ispublished": "pub", "full_text_status": "public", "keywords": "C. elegans males; Gonadogenesis; Cell migration; nhr-67/tailless; Timing", "note": "\u00a9 2009 The Company of Biologists Ltd. \n\nAccepted September 22, 2009. \n\nWe thank the Andrew Fire laboratory for reagents; Gladys Medina and Barbara Perry for technical assistance; members of our laboratory for helpful discussions; and, in particular, Jolene Fernandes, Jennifer Green, Amir Sapir, Erich Schwarz, Adeline Seah, Jagan Srinivasan, Cheryl Van Buskirk and Allyson Whittaker for critically reading the manuscript; Elyse Blum for help with scoring LC death; and Sumeet Sarin for discussions on nhr-67 binding site sequence alignment. Some nematode strains were provided by the Caenorhabditis Genetics Center, which is funded by the NIH National Center for Research Resources. Confocal images were acquired at the Caltech Biological Imaging Center. P.W.S. is an investigator with the Howard Hughes Medical Institute and M.K. was supported by an NIH postdoctoral fellowship. Deposited in PMC for release after 6 months.\n\nPublished - Kato2009p6455Development.pdf
", "abstract": "Cell migration is a common event during organogenesis, yet little is known about how migration is temporally coordinated with organ development. We are investigating stage-specific programs of cell migration using the linker cell (LC), a migratory cell crucial for male gonadogenesis of C. elegans. During the L3 and L4 larval stages of wild-type males, the LC undergoes changes in its position along the migratory route, in transcriptional regulation of the unc-5 netrin receptor and zmp-1 zinc matrix metalloprotease, and in cell morphology. We have identified the tailless homolog nhr-67 as a cell-autonomous, stage-specific regulator of timing in LC migration programs. In nhr-67-deficient animals, each of the L3 and L4 stage changes is either severely delayed or never occurs, yet LC development before the early L3 stage or after the mid-L4 stage occurs with normal timing. We propose that there is a basal migration program utilized throughout LC migration that is modified by stage-specific regulators such as nhr-67.", "date": "2009-12-01", "date_type": "published", "publication": "Development", "volume": "136", "number": "23", "publisher": "Company of Biologists", "pagerange": "3907-3915", "id_number": "CaltechAUTHORS:20091223-100126934", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20091223-100126934", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Postdoctoral Fellowship" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1242/dev.035477", "pmcid": "PMC2778740", "primary_object": { "basename": "Kato2009p6455Development.pdf", "url": "https://authors.library.caltech.edu/records/e55v9-ccs28/files/Kato2009p6455Development.pdf" }, "resource_type": "article", "pub_year": "2009", "author_list": "Kato, Mihoko and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/6et5c-pz165", "eprint_id": 16635, "eprint_status": "archive", "datestamp": "2023-08-21 22:40:03", "lastmod": "2023-10-19 22:26:21", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Klerkx-E-P-F", "name": { "family": "Klerkx", "given": "Elke P. F." } }, { "id": "Alarc\u00f3n-P", "name": { "family": "Alarc\u00f3n", "given": "Pilar" } }, { "id": "Waters-K", "name": { "family": "Waters", "given": "Katherine" } }, { "id": "Reinke-V", "name": { "family": "Reinke", "given": "Valerie" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Askjaer-P", "name": { "family": "Askjaer", "given": "Peter" } } ] }, "title": "Protein kinase VRK-1 regulates cell invasion and EGL-17/FGF signaling in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "Anchor cell; Caenorhabditis elegans; Cell invasion; Cell polarity; Cell signaling; FGF; Uterus; Vaccinia-related kinase; vrk-1; Vulva", "note": "\u00a9 2009 Elsevier Inc. \n\nReceived 19 March 2009; revised 3 August 2009; accepted 3 August 2009. Available online 11 August 2009. \n\nThis work was funded by grants from the Spanish Ministry of\nScience (RYC-2003-001521, BFU-2004-01096, BFU-2007-60116) to PA. In addition, we wish to acknowledge EMBO and the Boehringer Ingelheim Foundation for support to EK and Junta de Andaluc\u00eda for institutional support. PWS is an investigator with the Howard Hughes Medical Institute. We are grateful to C. Ayuso for excellent technical assistance. We wish to thank D. Sherwood and S. Tuck for providing strains, C. R. Dombecki for corrections on the manuscript, and two anonymous reviewers for constructive criticism. Some nematode strains used in this work were provided by the International C. elegans Gene Knockout Consortium and the Caenorhabditis Genetics Center, which is funded by the NIH National Center for Research Resources (NCRR).\n\nAccepted Version - nihms382120.pdf
Supplemental Material - Klerkx2009p6280Dev_Biol_fig_1.pdf
Supplemental Material - Klerkx2009p6280Dev_Biol_fig_2.pdf
Supplemental Material - Klerkx2009p6280Dev_Biol_fig_3.pdf
Supplemental Material - Klerkx2009p6280Dev_Biol_fig_4.pdf
Supplemental Material - Klerkx2009p6280Dev_Biol_supp.pdf
", "abstract": "The vaccinia-related kinases (VRKs) are highly conserved throughout the animal kingdom and phosphorylate several chromatin proteins and transcription factors. In early Caenorhabditis elegans embryos, VRK-1 is required for proper nuclear envelope formation. In this work, we present the first investigation of the developmental role of VRKs by means of a novel C. elegans vrk-1 mutant allele. We found that VRK-1 is essential in hermaphrodites for formation of the vulva, uterus, and utse and for development and maintenance of the somatic gonad and thus the germ line. VRK-1 regulates anchor cell polarity and the timing of anchor cell invasion through the basement membranes separating vulval and somatic gonadal cells during the L3 larval stage. VRK-1 is also required for proper specification and proliferation of uterine cells and sex myoblasts. Expression of the fibroblast growth factor-like protein EGL-17 and its receptor EGL-15 is reduced in vrk-1 mutants, suggesting that VRK-1 might act at least partially through activation of FGF signaling. Expression of a translational VRK-1::GFP fusion protein in the ventral nerve cord and vulva precursor cells restores vulva and uterus formation, suggesting both cell autonomous and non-autonomous roles of VRK-1.", "date": "2009-11-01", "date_type": "published", "publication": "Developmental Biology", "volume": "335", "number": "1", "publisher": "Elsevier", "pagerange": "12-21", "id_number": "CaltechAUTHORS:20091110-085633287", "issn": "0012-1606", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20091110-085633287", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Ministerio de Ciencia Y Tecnologia (MCYT)", "grant_number": "RYC-2003-001521" }, { "agency": "Ministerio de Ciencia Y Tecnologia (MCYT)", "grant_number": "BFU-2004-01096" }, { "agency": "Ministerio de Ciencia Y Tecnologia (MCYT)", "grant_number": "BFU-2007-60116" }, { "agency": "NIH" }, { "agency": "European Molecular Biology Organization (EMBO)" }, { "agency": "Boehringer-Ingelheim" }, { "agency": "Junta de Andaluc\u00eda" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1016/j.ydbio.2009.08.007", "pmcid": "PMC3378332", "primary_object": { "basename": "Klerkx2009p6280Dev_Biol_fig_1.pdf", "url": "https://authors.library.caltech.edu/records/6et5c-pz165/files/Klerkx2009p6280Dev_Biol_fig_1.pdf" }, "related_objects": [ { "basename": "Klerkx2009p6280Dev_Biol_fig_2.pdf", "url": "https://authors.library.caltech.edu/records/6et5c-pz165/files/Klerkx2009p6280Dev_Biol_fig_2.pdf" }, { "basename": "Klerkx2009p6280Dev_Biol_fig_3.pdf", "url": "https://authors.library.caltech.edu/records/6et5c-pz165/files/Klerkx2009p6280Dev_Biol_fig_3.pdf" }, { "basename": "Klerkx2009p6280Dev_Biol_fig_4.pdf", "url": "https://authors.library.caltech.edu/records/6et5c-pz165/files/Klerkx2009p6280Dev_Biol_fig_4.pdf" }, { "basename": "Klerkx2009p6280Dev_Biol_supp.pdf", "url": "https://authors.library.caltech.edu/records/6et5c-pz165/files/Klerkx2009p6280Dev_Biol_supp.pdf" }, { "basename": "nihms382120.pdf", "url": "https://authors.library.caltech.edu/records/6et5c-pz165/files/nihms382120.pdf" } ], "resource_type": "article", "pub_year": "2009", "author_list": "Klerkx, Elke P. F.; Alarc\u00f3n, Pilar; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/a4px6-9fb42", "eprint_id": 15582, "eprint_status": "archive", "datestamp": "2023-08-21 22:24:24", "lastmod": "2023-10-19 14:36:03", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cantacessi-C", "name": { "family": "Cantacessi", "given": "C." } }, { "id": "Zou-F-C", "name": { "family": "Zou", "given": "F. C." } }, { "id": "Hall-R-S", "name": { "family": "Hall", "given": "R. S." } }, { "id": "Zhong-W", "name": { "family": "Zhong", "given": "W." } }, { "id": "Jex-A-R", "name": { "family": "Jex", "given": "A. R." } }, { "id": "Campbell-B-E", "name": { "family": "Campbell", "given": "B. E." } }, { "id": "Ranganathan-S", "name": { "family": "Ranganathan", "given": "S." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "P. W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Zhu-X-Q", "name": { "family": "Zhu", "given": "X. Q." } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "R. B." } } ] }, "title": "Bioinformatic analysis of abundant, gender-enriched transcripts of adult Ascaris suum (Nematoda) using a semi-automated workflow platform", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Ascaris suum; Gender-enriched; Suppressive-subtractive hybridization; Caenorhabditis elegans; Bioinformatics; Gene ontology; Genetic interactions", "note": "\u00a9 2009 Elsevier B.V. \n\nReceived 27 January 2009; accepted 16 March 2009. Available online 8 April 2009. \n\nThis workwas supported by the Australian Research Council, the\nAustralian Academy of Science and the Australian\u2013American Fulbright\nCommission (RBG), the Howard Hughes Medical Institute\nand WormBase (PWS), the China National Science Funds for\nDistinguished Young Scientists (grant no. 30225033), the National\nNatural Science Foundation of China (grant no. 30671578), and the\nNatural Science Foundation of Guangdong Province (key project,\ngrant no. 36835) (XQZ). CC is the grateful recipient of International\nPostgraduate Research Scholarship (IPRS) from the Australian\nGovernment and a fee-remission scholarship through the University\nof Melbourne, and the Sir Ian Clunies Ross Prize (2008) and\nDr Sue Newton (2009) Award from the Faculty of Veterinary\nScience, The University of Melbourne.\n\nNote: New nucleotide sequence data used in this paper have been deposited in the GenBank database under accession numbers GO254595\u2013GO254953.", "abstract": "Expressed sequence tag (EST) data representing transcripts with a high level of differential hybridization in suppressive-subtractive hybridization (SSH)-based microarray analysis between adult female and male Ascaris suum were subjected to detailed bioinformatic analysis. A total of 361 ESTs clustered into 209 sequences, of which 52 and 157 represented transcripts that were enriched in female and male A. suum, respectively. Thirty (57.7%) of the 'female' subset of 52 sequences had orthologues/homologues in other parasitic nematodes and/or Caenorhabditis elegans, 13 (25%) exclusively in other parasitic nematodes and nine (17.3%) had no match in any other organism for which sequence data are currently available; the C. elegans orthologues encoded molecules involved in reproduction as well as embryonic and gamete development, such as vitellogenins and chitin-binding proteins. Of the 'male' subset of 157 sequences, 73 (46.5%) had orthologues/homologues in other parasitic nematodes and/or C. elegans, 57 (37.5%) in other parasitic nematodes only, and 22 (14.5%) had no significant similarity match in any other organism; the C. elegans orthologues encoded predominantly major sperm proteins (MSPs), kinases and phosphatases, actins, myosins and an Ancylostoma secreted protein-like molecule. The findings of the present study should support further genomic investigations of A. suum.", "date": "2009-10", "date_type": "published", "publication": "Molecular and Cellular Probes", "volume": "23", "number": "5", "publisher": "Elsevier", "pagerange": "205-217", "id_number": "CaltechAUTHORS:20090903-140152794", "issn": "0890-8508", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090903-140152794", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council" }, { "agency": "Australian Academy of Science" }, { "agency": "Australian-American Fullbright Commission" }, { "agency": "Howard Hughes Medical Institute and WormBase" }, { "agency": "China National Science Funds for Distinguished Young Scientists", "grant_number": "30225033" }, { "agency": "National Natural Science Foundation of China", "grant_number": "30671578" }, { "agency": "Natural Science Foundation of Guangdong Province", "grant_number": "36835" }, { "agency": "International Postgraduate Research Scholarship, Australian Government" }, { "agency": "University of Melbourne" } ] }, "doi": "10.1016/j.mcp.2009.03.003", "resource_type": "article", "pub_year": "2009", "author_list": "Cantacessi, C.; Zou, F. C.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/awdg9-mdr65", "eprint_id": 14899, "eprint_status": "archive", "datestamp": "2023-08-20 02:33:56", "lastmod": "2023-10-18 20:22:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Broitman-Maduro-G", "name": { "family": "Broitman-Maduro", "given": "Gina" } }, { "id": "Owraghi-M", "name": { "family": "Owraghi", "given": "Melissa" } }, { "id": "Hung-Wendy-W-K", "name": { "family": "Hung", "given": "Wendy W. K." } }, { "id": "Kuntz-S-G", "name": { "family": "Kuntz", "given": "Steven G." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Maduro-M-F", "name": { "family": "Maduro", "given": "Morris F." } } ] }, "title": "The NK-2 class homeodomain factor CEH-51 and the T-box factor TBX-35 have overlapping function in C. elegans mesoderm development", "ispublished": "pub", "full_text_status": "public", "keywords": "Mesoderm, C. elegans, tbx-35, ceh-51, Tissue specification", "note": "\u00a9 The Company of Biologists Ltd 2009. \n\nAccepted 12 June 2009. First published online 15 July 2009. \n\nWe are grateful to Shohei Mitani for tm2123; L. Ryan Baugh and Craig Hunter for sharing embryo transcriptome data prior to publication; Ian Hope, Michael Krause, Craig Hunter, Johnny Fares, Jeb Gaudet, Peter Okkema, Jenny Hsieh and Andy Fire for sending GFP reporter strains; Yuji Kohara for ceh-51 ESTs; Christian Fr\u00f8kj\u00e6r-Jensen, Erik Jorgensen, Attila Stetak, Andy Fire and David Miller for plasmids; Serena Cervantes for preliminary characterization of the tbx-35 elongation defects; and two anonymous reviewers for helpful comments. Some nematode strains used in this work were provided by the Caenorhabditis Genetics Center, which is funded by the NIH National Center for Research Resources (NCRR). This work was funded by grants from the NSF (IBN#0416922 and IOS#0643325) and NIH (1R03HD054589-01) to M.F.M. P.W.S. is an Investigator with the Howard Hughes Medical Institute, which supported this work. Deposited in PMC for release after 6 months.\n\nPublished - BroitmanMaduro2009p5557Development.pdf
", "abstract": "The C. elegans MS blastomere, born at the 7-cell stage of embryogenesis, generates primarily mesodermal cell types, including pharynx cells, body muscles and coelomocytes. A presumptive null mutation in the T-box factor gene tbx-35, a target of the MED-1 and MED-2 divergent GATA factors, was previously found to result in a profound decrease in the production of MS-derived tissues, although the tbx-35(-) embryonic arrest phenotype was variable. We report here that the NK-2 class homeobox gene ceh-51 is a direct target of TBX-35 and at least one other factor, and that CEH-51 and TBX-35 share functions. Embryos homozygous for a ceh-51 null mutation arrest as larvae with pharynx and muscle defects, although these tissues appear to be specified correctly. Loss of tbx-35 and ceh-51 together results in a synergistic phenotype resembling loss of med-1 and med-2. Overexpression of ceh-51 causes embryonic arrest and generation of ectopic body muscle and coelomocytes. Our data show that TBX-35 and CEH-51 have overlapping function in MS lineage development. As T-box regulators and NK-2 homeodomain factors are both important for heart development in Drosophila and vertebrates, our results suggest that these regulators function in a similar manner in C. elegans to specify a major precursor of mesoderm.", "date": "2009-08-15", "date_type": "published", "publication": "Development", "volume": "136", "number": "16", "publisher": "Company of Biologists", "pagerange": "2735-2746", "id_number": "CaltechAUTHORS:20090808-142503838", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090808-142503838", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "IBN-0416922" }, { "agency": "NSF", "grant_number": "IOS-0643325" }, { "agency": "NIH", "grant_number": "1R03HD054589-01" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1242/dev.038307", "pmcid": "PMC2730403", "primary_object": { "basename": "BroitmanMaduro2009p5557Development.pdf", "url": "https://authors.library.caltech.edu/records/awdg9-mdr65/files/BroitmanMaduro2009p5557Development.pdf" }, "resource_type": "article", "pub_year": "2009", "author_list": "Broitman-Maduro, Gina; Owraghi, Melissa; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/e1v4q-cd929", "eprint_id": 15819, "eprint_status": "archive", "datestamp": "2023-08-20 02:19:34", "lastmod": "2023-10-19 17:16:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Jaffery-J", "name": { "family": "Jaffery", "given": "Joshua" } }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "M\u00fcller-H-M", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2009 Van Auken et al; licensee BioMed Central Ltd.\nThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived:\t29 January 2009. Accepted:\t21 July 2009. Published:\t21 July 2009. \n\nWe gratefully acknowledge helpful comments on the manuscript from Tanya Berardini, Kara Dolinski, Ranjana Kishore, Mike Livstone, and Tracy Teal, and Seth Carbon for assistance with GO database queries. We also thank David Botstein, Kara Dolinski, and Mike Livstone at the Lewis-Sigler Institute for Integrative Genomics at Princeton University for generously providing space to KV while this work was being completed. This work was supported by grants #P41-HG02223, #R01-HG004090, and #P41-HG02273 from the National Human Genome Research Institute (NHGRI) at the United States National Institutes of Health. PWS is an Investigator with the Howard Hughes Medical Institute. \n\nKV and JJ identified training set sentences and developed the categories. KV performed and analyzed the recall and precision tests. KV, JJ, and PWS performed the curation efficiency tests. JC developed all curation tools for the project. HMM developed and maintained the Textpresso for Cellular Component Curation site. KV wrote the paper with valuable discussions and critical contributions at all stages of the project from HMM and PWS.\n\nPublished - VanAuken2009p5888BMC_Bioinformatics.pdf
Supplemental Material - 1471-2105-10-228-s1.txt
Supplemental Material - 1471-2105-10-228-s2.txt
Supplemental Material - 1471-2105-10-228-s3.txt
Supplemental Material - 1471-2105-10-228-s4.txt
Supplemental Material - 1471-2105-10-228-s5.ppt
", "abstract": "Background: Manual curation of experimental data from the biomedical literature is an expensive and time-consuming endeavor. Nevertheless, most biological knowledge bases still rely heavily on manual curation for data extraction and entry. Text mining software that can semi- or fully automate information retrieval from the literature would thus provide a significant boost to manual curation efforts. \n\nResults: We employ the Textpresso category-based information retrieval and extraction system http://www.textpresso.org webcite, developed by WormBase to explore how Textpresso might improve the efficiency with which we manually curate C. elegans proteins to the Gene Ontology's Cellular Component Ontology. Using a training set of sentences that describe results of localization experiments in the published literature, we generated three new curation task-specific categories (Cellular Components, Assay Terms, and Verbs) containing words and phrases associated with reports of experimentally determined subcellular localization. We compared the results of manual curation to that of Textpresso queries that searched the full text of articles for sentences containing terms from each of the three new categories plus the name of a previously uncurated C. elegans protein, and found that Textpresso searches identified curatable papers with recall and precision rates of 79.1% and 61.8%, respectively (F-score of 69.5%), when compared to manual curation. Within those documents, Textpresso identified relevant sentences with recall and precision rates of 30.3% and 80.1% (F-score of 44.0%). From returned sentences, curators were able to make 66.2% of all possible experimentally supported GO Cellular Component annotations with 97.3% precision (F-score of 78.8%). Measuring the relative efficiencies of Textpresso-based versus manual curation we find that Textpresso has the potential to increase curation efficiency by at least 8-fold, and perhaps as much as 15-fold, given differences in individual curatorial speed. \n\nConclusion: Textpresso is an effective tool for improving the efficiency of manual, experimentally based curation. Incorporating a Textpresso-based Cellular Component curation pipeline at WormBase has allowed us to transition from strictly manual curation of this data type to a more efficient pipeline of computer-assisted validation. Continued development of curation task-specific Textpresso categories will provide an invaluable resource for genomics databases that rely heavily on manual curation.", "date": "2009-07-21", "date_type": "published", "publication": "BMC Bioinformatics", "volume": "10", "number": "228", "publisher": "BioMed Central", "id_number": "CaltechAUTHORS:20090911-153603785", "issn": "1471-2105", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090911-153603785", "rights": "This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P41-HG02223" }, { "agency": "NIH", "grant_number": "R01-HG004090" }, { "agency": "NIH", "grant_number": "P41-HG02273" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "National Human Genome Research Institute" } ] }, "doi": "10.1186/1471-2105-10-228", "pmcid": "PMC2719631", "primary_object": { "basename": "1471-2105-10-228-s3.txt", "url": "https://authors.library.caltech.edu/records/e1v4q-cd929/files/1471-2105-10-228-s3.txt" }, "related_objects": [ { "basename": "1471-2105-10-228-s4.txt", "url": "https://authors.library.caltech.edu/records/e1v4q-cd929/files/1471-2105-10-228-s4.txt" }, { "basename": "1471-2105-10-228-s5.ppt", "url": "https://authors.library.caltech.edu/records/e1v4q-cd929/files/1471-2105-10-228-s5.ppt" }, { "basename": "VanAuken2009p5888BMC_Bioinformatics.pdf", "url": "https://authors.library.caltech.edu/records/e1v4q-cd929/files/VanAuken2009p5888BMC_Bioinformatics.pdf" }, { "basename": "1471-2105-10-228-s1.txt", "url": "https://authors.library.caltech.edu/records/e1v4q-cd929/files/1471-2105-10-228-s1.txt" }, { "basename": "1471-2105-10-228-s2.txt", "url": "https://authors.library.caltech.edu/records/e1v4q-cd929/files/1471-2105-10-228-s2.txt" } ], "resource_type": "article", "pub_year": "2009", "author_list": "Van Auken, Kimberly; Jaffery, Joshua; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/bswkt-43j69", "eprint_id": 14784, "eprint_status": "archive", "datestamp": "2023-08-21 21:41:27", "lastmod": "2023-10-18 19:53:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cantacessi-C", "name": { "family": "Cantacessi", "given": "C." } }, { "id": "Campbell-B-E", "name": { "family": "Campbell", "given": "B. E." } }, { "id": "Visser-A", "name": { "family": "Visser", "given": "A." } }, { "id": "Geldhof-P", "name": { "family": "Geldhof", "given": "P." } }, { "id": "Nolan-M-J", "name": { "family": "Nolan", "given": "M. J." } }, { "id": "Nisbet-A-J", "name": { "family": "Nisbet", "given": "A. J." } }, { "id": "Matthews-J-B", "name": { "family": "Matthews", "given": "J. B." } }, { "id": "Loukas-A", "name": { "family": "Loukas", "given": "A." } }, { "id": "Hofmann-A", "name": { "family": "Hofmann", "given": "A." } }, { "id": "Otranto-D", "name": { "family": "Otranto", "given": "D." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "P. W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "R. B." } } ] }, "title": "A portrait of the \"SCP/TAPS\" proteins of eukaryotes -- developing a framework for fundamental research and biotechnological outcomes", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Sperm coating protein-extracellular domain; SCP/TAPS; Activation-associated secreted proteins; Hookworms; Classification; Nomenclature; Bayesian inference; Venom allergen; Pathogenesis-related proteins", "note": "\u00a9 2009 Elsevier B.V.\nReceived 10 December 2008; revised 5 February 2009; accepted 11 February 2009. Available online 21 February 2009. \nThe research was supported by the Australian Research Council\n(ARC) (DP0665230; RBG and AL), the Australian Academy of Science and\nthe Australian\u2013American Fulbright Commission (RBG). JBM and AJN are\nfunded by the Scottish Government RERAD. CC was the grateful\nrecipient of a Dr Sue Newton Scholarship and an International\nPostgraduate Research Scholarship (IPRS) from the Australian Government\nvia The University of Melbourne. PG is a Postdoctoral Fellow of the\nFund for Scientific Research \u2013 Flanders (Belgium) (F.W.O. \u2013 Vlaanderen).", "abstract": "A wide range of proteins belonging to the SCP/TAPS \"family\" has been described for various eukaryotic organisms, including plants and animals (vertebrates and invertebrates, such as helminths). Although SCP/TAPS proteins have been proposed to play key roles in a number of fundamental biological processes, such as host\u2013pathogen interactions and defence mechanisms, there is a paucity of information on their genetic relationships, structures and functions, and there is no standardised nomenclature for these proteins. A detailed analysis of the relationships of members of the SCP/TAPS family of proteins, based on key protein signatures, could provide a foundation for investigating these areas. In this article, we review the current state of knowledge of key SCP/TAPS proteins of eukaryotes, with an emphasis on those from parasitic helminths, and undertake a comprehensive, systematic phylogenetic analysis of currently available full-length protein sequence data (considering characteristic protein signatures or motifs) to infer relationships and provide a framework (based on statistical support) for the naming of these proteins. This framework is intended to guide genomic and molecular biological explorations of key SCP/TAPS molecules associated with infectious diseases of plants and animals. In particular, fundamental investigations of these molecules in parasites and the integration of structural and functional data could lead to new and innovative approaches for the control of parasitic diseases, with important biotechnological outcomes.", "date": "2009-07", "date_type": "published", "publication": "Biotechnology Advances", "volume": "27", "number": "4", "publisher": "Elsevier", "pagerange": "376-388", "id_number": "CaltechAUTHORS:20090804-100455850", "issn": "0734-9750", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090804-100455850", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council", "grant_number": "DP0665230" }, { "agency": "Australian Academy of Science" }, { "agency": "Australian\u2013American Fulbright Commission" }, { "agency": "Scottish Government RERAD" }, { "agency": "University of Melbourne" }, { "agency": "Fund for Scientific Research \u2013 Flanders (Belgium)" } ] }, "doi": "10.1016/j.biotechadv.2009.02.005", "resource_type": "article", "pub_year": "2009", "author_list": "Cantacessi, C.; Campbell, B. E.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/2vd71-54a56", "eprint_id": 14902, "eprint_status": "archive", "datestamp": "2023-08-20 02:06:45", "lastmod": "2023-10-18 20:22:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Whittaker-A-J", "name": { "family": "Whittaker", "given": "Allyson J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Coordination of opposing sex-specific and core muscle groups regulates male tail posture during Caenorhabditis elegans male mating behavior", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2009 Whittaker and Sternberg; et al; licensee BioMed Central Ltd.\nThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nWe would like to thank members of the Sternberg laboratory for critical reading of this manuscript. This research was supported by the Howard Hughes Medical Institute of which PWS is an investigator. AJW was supported by NIH postdoctoral fellowship NS042497. \n\nAuthors' contributions: AJW and PWS conceived the study and designed the experiments. AJW carried out the experiments. AJW wrote the manuscript and PWS provided input and revised the manuscript.\n\nPublished - Whittaker2009p5552Bmc_Biol.pdf
", "abstract": "Background \nTo survive and reproduce, animals must be able to modify their motor behavior in response to changes in the environment. We studied a complex behavior of Caenorhabditis elegans, male mating behavior, which provided a model for understanding motor behaviors at the genetic, molecular as well as circuit level. C. elegans male mating behavior consists of a series of six sub-steps: response to contact, backing, turning, vulva location, spicule insertion, and sperm transfer. The male tail contains most of the sensory structures required for mating, in addition to the copulatory structures, and thus to carry out the steps of mating behavior, the male must keep his tail in contact with the hermaphrodite. However, because the hermaphrodite does not play an active role in mating and continues moving, the male must modify his tail posture to maintain contact. We provide a better understanding of the molecular and neuro-muscular pathways that regulate male tail posture during mating.\n\nResults\nGenetic and laser ablation analysis, in conjunction with behavioral assays were used to determine neurotransmitters, receptors, neurons and muscles required for the regulation of male tail posture. We showed that proper male tail posture is maintained by the coordinated activity of opposing muscle groups that curl the tail ventrally and dorsally. Specifically, acetylcholine regulates both ventral and dorsal curling of the male tail, partially through anthelmintic levamisole-sensitive, nicotinic receptor subunits. Male-specific muscles are required for acetylcholine-driven ventral curling of the male tail but dorsal curling requires the dorsal body wall muscles shared by males and hermaphrodites. Gamma-aminobutyric acid activity is required for both dorsal and ventral acetylcholine-induced curling of the male tail and an inhibitory gamma-aminobutyric acid receptor, UNC-49, prevents over-curling of the male tail during mating, suggesting that cross-inhibition of muscle groups helps maintain proper tail posture.\n\nConclusion\nOur results demonstrated that coordination of opposing sex-specific and core muscle groups, through the activity of multiple neurotransmitters, is required for regulation of male tail posture during mating. We have provided a simple model for regulation of male tail posture that provides a foundation for studies of how genes, molecular pathways, and neural circuits contribute to sensory regulation of this motor behavior.", "date": "2009-06-22", "date_type": "published", "publication": "BMC Biology", "volume": "7", "publisher": "BioMed Central", "pagerange": "Art. No. 33", "id_number": "CaltechAUTHORS:20090808-142504550", "issn": "1741-7007", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090808-142504550", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "NS042497" } ] }, "doi": "10.1186/1741-7007-7-33", "pmcid": "PMC2715377", "primary_object": { "basename": "Whittaker2009p5552Bmc_Biol.pdf", "url": "https://authors.library.caltech.edu/records/2vd71-54a56/files/Whittaker2009p5552Bmc_Biol.pdf" }, "resource_type": "article", "pub_year": "2009", "author_list": "Whittaker, Allyson J. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/0dkfd-se656", "eprint_id": 14945, "eprint_status": "archive", "datestamp": "2023-08-21 21:26:56", "lastmod": "2023-10-18 20:24:03", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Pungaliya-C", "name": { "family": "Pungaliya", "given": "Chirag" } }, { "id": "Srinivasan-J", "name": { "family": "Srinivasan", "given": "Jagan" }, "orcid": "0000-0001-5449-7938" }, { "id": "Fox-B-W", "name": { "family": "Fox", "given": "Bennett W." } }, { "id": "Malik-R-U", "name": { "family": "Malik", "given": "Rabia U." } }, { "id": "Ludewig-A-H", "name": { "family": "Ludewig", "given": "Andreas H." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Schroeder-F-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" } ] }, "title": "A shortcut to identifying small molecule signals that regulate behavior and development in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "dauer formation; differential analysis; metabolomics; NMR spectroscopy; sex pheromone", "note": "\u00a9 2009 by the National Academy of Sciences.\nEdited by Jerrold Meinwald, Cornell University, Ithaca, NY, and approved March 3, 2009 (received for review November 22, 2008).\nAuthor contributions: C.P., J.S., P.W.S., and F.C.S. designed research; C.P., J.S., B.W.F.,\nR.U.M., and F.C.S. performed research; B.W.F., R.U.M., and A.H.L. contributed new reagents/\nanalytic tools; C.P., J.S., P.W.S., and F.C.S. analyzed data; and C.P., J.S., P.W.S., and\nF.C.S. wrote the paper.\nWe thank Art Edison and Fatma Kaplan for helpful\ndiscussions, Olena Vatamaniuk for assistance with C. elegans liquid cultures,\nand Ivan Keresztes for assistance with NMR spectroscopy. This work was\nsupported in part by National Institutes of Health Grant P41 GM079571 (to\nF.C.S.) and by the Howard Hughes Medical Institute (J.S., P.W.S.).\n\nPublished - Pungaliya2009p4254P_Natl_Acad_Sci_Usa.pdf
Supplemental Material - Pungaliya2009p4254P_Natl_Acad_Sci_Usa_supp.pdf
", "abstract": "Small molecule metabolites play important roles in Caenorhabditis elegans biology, but effective approaches for identifying their chemical structures are lacking. Recent studies revealed that a family of glycosides, the ascarosides, differentially regulate C. elegans development and behavior. Low concentrations of ascarosides attract males and thus appear to be part of the C. elegans sex pheromone, whereas higher concentrations induce developmental arrest at the dauer stage, an alternative, nonaging larval stage. The ascarosides act synergistically, which presented challenges for their identification via traditional activity-guided fractionation. As a result the chemical characterization of the dauer and male attracting pheromones remained incomplete. Here, we describe the identification of several additional pheromone components by using a recently developed NMR-spectroscopic approach, differential analysis by 2D NMR spectroscopy (DANS), which simplifies linking small molecule metabolites with their biological function. DANS-based comparison of wild-type C. elegans and a signaling-deficient mutant, daf-22, enabled identification of 3 known and 4 previously undescribed ascarosides, including a compound that features a p-aminobenzoic acid subunit. Biological testing of synthetic samples of these compounds revealed additional evidence for synergy and provided insights into structure\u2013activity relationships. Using a combination of the three most active ascarosides allowed full reconstitution of the male-attracting activity of wild-type pheromone extract. Our results highlight the efficacy of DANS as a method for identifying small-molecule metabolites and placing them within a specific genetic context. This study further supports the hypothesis that ascarosides represent a structurally diverse set of nematode signaling molecules regulating major life history traits.", "date": "2009-05-12", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "106", "number": "19", "publisher": "National Academy of Sciences", "pagerange": "7708-7713", "id_number": "CaltechAUTHORS:20090811-093016588", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090811-093016588", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P41 GM079571" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1073/pnas.0811918106", "pmcid": "PMC2683085", "primary_object": { "basename": "Pungaliya2009p4254P_Natl_Acad_Sci_Usa.pdf", "url": "https://authors.library.caltech.edu/records/0dkfd-se656/files/Pungaliya2009p4254P_Natl_Acad_Sci_Usa.pdf" }, "related_objects": [ { "basename": "Pungaliya2009p4254P_Natl_Acad_Sci_Usa_supp.pdf", "url": "https://authors.library.caltech.edu/records/0dkfd-se656/files/Pungaliya2009p4254P_Natl_Acad_Sci_Usa_supp.pdf" } ], "resource_type": "article", "pub_year": "2009", "author_list": "Pungaliya, Chirag; Srinivasan, Jagan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/4s2rw-71k82", "eprint_id": 14496, "eprint_status": "archive", "datestamp": "2023-08-20 01:33:21", "lastmod": "2023-10-18 18:03:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bai-Xiaodong", "name": { "family": "Bai", "given": "Xiaodong" } }, { "id": "Adams-B-J", "name": { "family": "Adams", "given": "Byron J." } }, { "id": "Ciche-T-A", "name": { "family": "Ciche", "given": "Todd A." } }, { "id": "Clifton-S", "name": { "family": "Clifton", "given": "Sandra" } }, { "id": "Gaugler-R", "name": { "family": "Gaugler", "given": "Randy" } }, { "id": "Hogenhout-S-A", "name": { "family": "Hogenhout", "given": "Saskia A." } }, { "id": "Spieth-J", "name": { "family": "Spieth", "given": "John" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Wilson-R-K", "name": { "family": "Wilson", "given": "Richard K." } }, { "id": "Grewal-P-S", "name": { "family": "Grewal", "given": "Parwinder S." } } ] }, "title": "Transcriptomic analysis of the entomopathogenic nematode Heterorhabditis bacteriophora TTO1", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 Bai et al; licensee BioMed Central Ltd. 2009. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived: 21 July 2008; accepted: 30 April 2009; published: 30 April 2009. \n\nThis project was supported by grants from the United States Department of Agriculture (USDA)/National Science Foundation (NSF) Microbial Genome Sequence Program and National Human Genome Research Institute (NHGRI) awarded to PSG, BJA, TAC, RG, and PWS. We thank teams of scientists led by Lucinda Fulton, Makedonka Mitreva, Kimberly Delehaunty, Michael Becker, and Brenda Theising at the Genome Center at Washington University School of Medicine in St. Louis, MO who produced and curated EST data.\n\nPublished - 1471-2164-10-205.pdf
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Supplemental Material - 1471-2164-10-205-s5.xls
Supplemental Material - 1471-2164-10-205-s6.xls
", "abstract": "Background:\nThe entomopathogenic nematode Heterorhabditis bacteriophora and its symbiotic bacterium, Photorhabdus luminescens, are important biological control agents of insect pests. This nematode-bacterium-insect association represents an emerging tripartite model for research on mutualistic and parasitic symbioses. Elucidation of mechanisms underlying these biological processes may serve as a foundation for improving the biological control potential of the nematode-bacterium complex. This large-scale expressed sequence tag (EST) analysis effort enables gene discovery and development of microsatellite markers. These ESTs will also aid in the annotation of the upcoming complete genome sequence of H. bacteriophora.\n\nResults:\nA total of 31,485 high quality ESTs were generated from cDNA libraries of the adult H. bacteriophora TTO1 strain. Cluster analysis revealed the presence of 3,051 contigs and 7,835 singletons, representing 10,886 distinct EST sequences. About 72% of the distinct EST sequences had significant matches (E value < 1e-5) to proteins in GenBank's non-redundant (nr) and Wormpep190 databases. We have identified 12 ESTs corresponding to 8 genes potentially involved in RNA interference, 22 ESTs corresponding to 14 genes potentially involved in dauer-related processes, and 51 ESTs corresponding to 27 genes potentially involved in defense and stress responses. Comparison to ESTs and proteins of free-living nematodes led to the identification of 554 parasitic nematode-specific ESTs in H. bacteriophora, among which are those encoding F-box-like/WD-repeat protein theromacin, Bax inhibitor-1-like protein, and PAZ domain containing protein. Gene Ontology terms were assigned to 6,685 of the 10,886 ESTs. A total of 168 microsatellite loci were identified with primers designable for 141 loci.\n\nConclusion:\nA total of 10,886 distinct EST sequences were identified from adult H. bacteriophora cDNA libraries. BLAST searches revealed ESTs potentially involved in parasitism, RNA interference, defense responses, stress responses, and dauer-related processes. The putative microsatellite markers identified in H. bacteriophora ESTs will enable genetic mapping and population genetic studies. These genomic resources provide the material base necessary for genome annotation, microarray development, and in-depth gene functional analysis.", "date": "2009-04-30", "date_type": "published", "publication": "BMC Genomics", "volume": "10", "publisher": "BioMed Central", "pagerange": "Art. No. 205", "id_number": "CaltechAUTHORS:20090706-113251763", "issn": "1471-2164", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090706-113251763", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Agriculture" }, { "agency": "NSF" }, { "agency": "National Human Genome Research Institute" } ] }, "doi": "10.1186/1471-2164-10-205", "pmcid": "PMC2686736", "primary_object": { "basename": "1471-2164-10-205-s4.xls", "url": "https://authors.library.caltech.edu/records/4s2rw-71k82/files/1471-2164-10-205-s4.xls" }, "related_objects": [ { "basename": "1471-2164-10-205-s5.xls", "url": "https://authors.library.caltech.edu/records/4s2rw-71k82/files/1471-2164-10-205-s5.xls" }, { "basename": "1471-2164-10-205-s6.xls", "url": "https://authors.library.caltech.edu/records/4s2rw-71k82/files/1471-2164-10-205-s6.xls" }, { "basename": "1471-2164-10-205.pdf", "url": "https://authors.library.caltech.edu/records/4s2rw-71k82/files/1471-2164-10-205.pdf" }, { "basename": "1471-2164-10-205-s1.xls", "url": "https://authors.library.caltech.edu/records/4s2rw-71k82/files/1471-2164-10-205-s1.xls" }, { "basename": "1471-2164-10-205-s2.xls", "url": "https://authors.library.caltech.edu/records/4s2rw-71k82/files/1471-2164-10-205-s2.xls" }, { "basename": "1471-2164-10-205-s3.xls", "url": "https://authors.library.caltech.edu/records/4s2rw-71k82/files/1471-2164-10-205-s3.xls" } ], "resource_type": "article", "pub_year": "2009", "author_list": "Bai, Xiaodong; Adams, Byron J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/sr8as-jn944", "eprint_id": 14186, "eprint_status": "archive", "datestamp": "2023-08-20 01:24:57", "lastmod": "2023-10-18 16:19:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Baugh-L-R", "name": { "family": "Baugh", "given": "L. Ryan" } }, { "id": "DeModena-J", "name": { "family": "DeModena", "given": "John" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "RNA Pol II accumulates at promoters of growth genes during developmental arrest", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2009 American Association for the Advancement of Science.\nReceived for publication 11 December 2008; accepted for publication 17 February 2009.\nWe thank L. Schaeffer, D. Trout, A. Mortazavi, J. L. Riechmann, and B. Wold for assistance and discussions. We thank E. H. Davidson for sharing his COPAS Biosorter and B. Hwang for sharing his destabilized YFP plasmid. L.R.B. was supported by the American Cancer Society. P.W.S. is an investigator with the Howard Hughes Medical Institute, which supported this work. Microarray analysis and sequencing were performed in the Millard and Muriel Jacobs Genetics and Genomics Laboratory at Caltech. Data and analysis available for download from NCBI Gene Expression Omnibus (accession GSE14009) at www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14009.", "abstract": "When Caenorhabditis elegans larvae hatch from the egg case in the absence of food, their development is arrested (L1 arrest), and they show increased stress resistance until food becomes available. To study nutritional control of larval development, we analyzed growth and gene expression profiles during L1 arrest and recovery. Larvae that were fed responded relatively slowly to starvation compared with the rapid response of arrested larvae to feeding. Chromatin immunoprecipitation of RNA polymerase II (Pol II) followed by deep sequencing showed that during L1 arrest, Pol II continued transcribing starvation-response genes, but the enzyme accumulated on the promoters of growth and development genes. In response to feeding, promoter accumulation decreased, and elongation and messenger RNA levels increased. Therefore, accumulation of Pol II at promoters anticipates nutritionally controlled gene expression during C. elegans development.", "date": "2009-04-03", "date_type": "published", "publication": "Science", "volume": "324", "number": "5923", "publisher": "American Association for the Advancement of Science", "pagerange": "92-94", "id_number": "CaltechAUTHORS:20090508-105122714", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090508-105122714", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "American Cancer Society" }, { "agency": "Howard Hughes Medical Institute" } ] }, "doi": "10.1126/science.1169628", "resource_type": "article", "pub_year": "2009", "author_list": "Baugh, L. Ryan; DeModena, John; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/3h5gp-w8n91", "eprint_id": 15194, "eprint_status": "archive", "datestamp": "2023-08-20 01:20:32", "lastmod": "2023-10-18 21:04:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Giurumescu-C-A", "name": { "family": "Giurumescu", "given": "Claudiu A." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Asthagiri-A-R", "name": { "family": "Asthagiri", "given": "Anand R." } } ] }, "title": "Predicting Phenotypic Diversity and the Underlying Quantitative Molecular Transitions", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2009 Giurumescu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nThis work was supported by the Institute for Collaborative Biotechnologies Grant DAAD 19-03-D-0004 from the U.S. Army Research Office (to A.R.A.), the Center for Biological Circuit Design at Caltech, and the Jacobs Institute for Molecular Engineering for Medicine. P.W.S. is an investigator with the Howard Hughes Medical Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. \n\nAuthor Contributions: Conceived and designed the experiments: CAG. Performed the experiments: CAG. Analyzed the data: CAG PWS ARA. Contributed reagents/materials/analysis tools: PWS. Wrote the paper: CAG ARA. \n\nThe authors have declared that no competing interests exist.\n\nPublished - Giurumescu2009p4253Plos_Comput_Biol.pdf
Supplemental Material - journal.pcbi.1000354.s001.pdf
Supplemental Material - journal.pcbi.1000354.s002.pdf
Supplemental Material - journal.pcbi.1000354.s003.pdf
Supplemental Material - journal.pcbi.1000354.s004.pdf
Supplemental Material - journal.pcbi.1000354.s005.pdf
Supplemental Material - journal.pcbi.1000354.s006.pdf
Supplemental Material - journal.pcbi.1000354.s007.pdf
Supplemental Material - journal.pcbi.1000354.s008.pdf
Supplemental Material - journal.pcbi.1000354.s009.pdf
Supplemental Material - journal.pcbi.1000354.s010.pdf
Supplemental Material - journal.pcbi.1000354.s011.pdf
Supplemental Material - journal.pcbi.1000354.s012.pdf
", "abstract": "During development, signaling networks control the formation of multicellular patterns. To what extent quantitative fluctuations in these complex networks may affect multicellular phenotype remains unclear. Here, we describe a computational approach to predict and analyze the phenotypic diversity that is accessible to a developmental signaling network. Applying this framework to vulval development in C. elegans, we demonstrate that quantitative changes in the regulatory network can render ~500 multicellular phenotypes. This phenotypic capacity is an order-of-magnitude below the theoretical upper limit for this system but yet is large enough to demonstrate that the system is not restricted to a select few outcomes. Using metrics to gauge the robustness of these phenotypes to parameter perturbations, we identify a select subset of novel phenotypes that are the most promising for experimental validation. In addition, our model calculations provide a layout of these phenotypes in network parameter space. Analyzing this landscape of multicellular phenotypes yielded two significant insights. First, we show that experimentally well-established mutant phenotypes may be rendered using non-canonical network perturbations. Second, we show that the predicted multicellular patterns include not only those observed in C. elegans, but also those occurring exclusively in other species of the Caenorhabditis genus. This result demonstrates that quantitative diversification of a common regulatory network is indeed demonstrably sufficient to generate the phenotypic differences observed across three major species within the Caenorhabditis genus. Using our computational framework, we systematically identify the quantitative changes that may have occurred in the regulatory network during the evolution of these species. Our model predictions show that significant phenotypic diversity may be sampled through quantitative variations in the regulatory network without overhauling the core network architecture. Furthermore, by comparing the predicted landscape of phenotypes to multicellular patterns that have been experimentally observed across multiple species, we systematically trace the quantitative regulatory changes that may have occurred during the evolution of the Caenorhabditis genus.", "date": "2009-04", "date_type": "published", "publication": "PLoS Computational Biology", "volume": "5", "number": "4", "publisher": "Public Library of Science", "pagerange": "Art. No. e1000354", "id_number": "CaltechAUTHORS:20090820-142952457", "issn": "1553-734X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090820-142952457", "rights": "This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.", "funders": { "items": [ { "agency": "Army Research Office (ARO)", "grant_number": "DAAD 19-03-D-0004" }, { "agency": "Jacobs Institute for Molecular Engineering for Medicine" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Jacobs-Institute-for-Molecular-Engineering-for-Medicine" } ] }, "doi": "10.1371/journal.pcbi.1000354", "pmcid": "PMC2661366", "primary_object": { "basename": "journal.pcbi.1000354.s002.pdf", "url": "https://authors.library.caltech.edu/records/3h5gp-w8n91/files/journal.pcbi.1000354.s002.pdf" }, "related_objects": [ { "basename": "journal.pcbi.1000354.s003.pdf", "url": "https://authors.library.caltech.edu/records/3h5gp-w8n91/files/journal.pcbi.1000354.s003.pdf" }, { "basename": "journal.pcbi.1000354.s007.pdf", "url": "https://authors.library.caltech.edu/records/3h5gp-w8n91/files/journal.pcbi.1000354.s007.pdf" }, { "basename": "journal.pcbi.1000354.s009.pdf", "url": "https://authors.library.caltech.edu/records/3h5gp-w8n91/files/journal.pcbi.1000354.s009.pdf" }, { "basename": "journal.pcbi.1000354.s012.pdf", "url": "https://authors.library.caltech.edu/records/3h5gp-w8n91/files/journal.pcbi.1000354.s012.pdf" }, { "basename": "journal.pcbi.1000354.s001.pdf", "url": "https://authors.library.caltech.edu/records/3h5gp-w8n91/files/journal.pcbi.1000354.s001.pdf" }, { "basename": "journal.pcbi.1000354.s004.pdf", "url": "https://authors.library.caltech.edu/records/3h5gp-w8n91/files/journal.pcbi.1000354.s004.pdf" }, { "basename": "journal.pcbi.1000354.s005.pdf", "url": "https://authors.library.caltech.edu/records/3h5gp-w8n91/files/journal.pcbi.1000354.s005.pdf" }, { "basename": "journal.pcbi.1000354.s008.pdf", "url": "https://authors.library.caltech.edu/records/3h5gp-w8n91/files/journal.pcbi.1000354.s008.pdf" }, { "basename": "journal.pcbi.1000354.s006.pdf", "url": "https://authors.library.caltech.edu/records/3h5gp-w8n91/files/journal.pcbi.1000354.s006.pdf" }, { "basename": "Giurumescu2009p4253Plos_Comput_Biol.pdf", "url": "https://authors.library.caltech.edu/records/3h5gp-w8n91/files/Giurumescu2009p4253Plos_Comput_Biol.pdf" }, { "basename": "journal.pcbi.1000354.s010.pdf", "url": "https://authors.library.caltech.edu/records/3h5gp-w8n91/files/journal.pcbi.1000354.s010.pdf" }, { "basename": "journal.pcbi.1000354.s011.pdf", "url": "https://authors.library.caltech.edu/records/3h5gp-w8n91/files/journal.pcbi.1000354.s011.pdf" } ], "resource_type": "article", "pub_year": "2009", "author_list": "Giurumescu, Claudiu A.; Sternberg, Paul W.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/0t0q0-8b675", "eprint_id": 14506, "eprint_status": "archive", "datestamp": "2023-08-21 21:02:08", "lastmod": "2023-10-18 18:03:44", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yu-Hui", "name": { "family": "Yu", "given": "Hui" } }, { "id": "Seah-A", "name": { "family": "Seah", "given": "Adeline" } }, { "id": "Herman-M-A", "name": { "family": "Herman", "given": "Michael A." } }, { "id": "Ferguson-E-L", "name": { "family": "Ferguson", "given": "Edwin L." } }, { "id": "Horvitz-H-R", "name": { "family": "Horvitz", "given": "H. Robert" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Wnt and EGF pathways act together to induce C. elegans male hook development", "ispublished": "pub", "full_text_status": "public", "keywords": "Pattern formation; EGF signaling; Wnt signaling", "note": "\u00a9 2009 Elsevier. \n\nReceived 16 July 2008; revised 26 November 2008; accepted 19 December 2008. Available online 30 December 2008. \n\nWe thank Jennifer Green for the HS::CAM-1 strain, Bhagwati Gupta\nfor the lin-17::GFP construct, David Eisenmann for the BAR-1\u2013 GFP\nstrain, Helen Chamberlin for unpublished data the Caenorhabditis\nGenetic Center for providing some strains used in this study, Raymond Lee for suggesting eat-4::GFP as a neuronal marker and Takao Inoue for the cwn-1::GFP and cwn-2::GFP reporters. We thank Mihoko Kato, Cheryl Van Buskirk, Jennifer Green, Takao Inoue, Weiwei Zhong, Jolene Fernandes, Iva Greenwald, William Fixsen, Victor Ambros and Elissa Hallem for helpful discussions and critical reading of this manuscript. P.W.S. and H.R.H. are Investigators of the Howard Hughes Medical Institute. H.R.H. was supported by NIH grant GM24663. A.S. was supported by a HHMI Pre-Doctoral Fellowship. While at MIT, M.A.H., P.W.S. and E.L.F. were supported by USPHS training grant GM07287. \n\nSupplementary data associated with this article can be found, in\nthe online version, at doi:10.1016/j.ydbio.2008.12.023.\n\nAccepted Version - nihms102170.pdf
Supplemental Material - Yu2009p1028Dev_Biol_supp.doc
", "abstract": "Comparative studies of vulva development between Caenorhabditis elegans and other nematode species have provided some insight into the evolution of patterning networks. However, molecular genetic details are available only in C. elegans and Pristionchus pacificus. To extend our knowledge on the evolution of patterning networks, we studied the C. elegans male hook competence group (HCG), an equivalence group that has similar developmental origins to the vulval precursor cells (VPCs), which generate the vulva in the hermaphrodite. Similar to VPC fate specification, each HCG cell adopts one of three fates (1\u00b0, 2\u00b0, 3\u00b0), and 2\u00b0 HCG fate specification is mediated by LIN-12/Notch. We show that 2\u00b0 HCG specification depends on the presence of a cell with the 1\u00b0 fate. We also provide evidence that Wnt signaling via the Frizzled-like Wnt receptor LIN-17 acts to specify the 1\u00b0 and 2\u00b0 HCG fate. A requirement for EGF signaling during 1\u00b0 fate specification is seen only when LIN-17 activity is compromised. In addition, activation of the EGF pathway decreases dependence on LIN-17 and causes ectopic hook development. Our results suggest that WNT plays a more significant role than EGF signaling in specifying HCG fates, whereas in VPC specification EGF signaling is the major inductive signal. Nonetheless, the overall logic is similar in the VPCs and the HCG: EGF and/or WNT induce a 1\u00b0 lineage, and LIN-12/NOTCH induces a 2\u00b0 lineage. Wnt signaling is also required for execution of the 1\u00b0 and 2\u00b0 HCG lineages. lin-17 and bar-1/\u03b2-catenin are preferentially expressed in the presumptive 1\u00b0 cell P11.p. The dynamic subcellular localization of BAR-1\u2013GFP in P11.p is concordant with the timing of HCG fate determination.", "date": "2009-03-15", "date_type": "published", "publication": "Developmental Biology", "volume": "327", "number": "2", "publisher": "Elsevier", "pagerange": "419-432", "id_number": "CaltechAUTHORS:20090707-095026171", "issn": "0012-1606", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090707-095026171", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM24663" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "GM07287" } ] }, "doi": "10.1016/j.ydbio.2008.12.023", "pmcid": "PMC2695933", "primary_object": { "basename": "Yu2009p1028Dev_Biol_supp.doc", "url": "https://authors.library.caltech.edu/records/0t0q0-8b675/files/Yu2009p1028Dev_Biol_supp.doc" }, "related_objects": [ { "basename": "nihms102170.pdf", "url": "https://authors.library.caltech.edu/records/0t0q0-8b675/files/nihms102170.pdf" } ], "resource_type": "article", "pub_year": "2009", "author_list": "Yu, Hui; Seah, Adeline; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/n0q4v-e2e07", "eprint_id": 14086, "eprint_status": "archive", "datestamp": "2023-08-21 20:33:35", "lastmod": "2023-10-18 16:06:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cantacessi-C", "name": { "family": "Cantacessi", "given": "C." } }, { "id": "Loukas-A", "name": { "family": "Loukas", "given": "A." } }, { "id": "Campbell-B-E", "name": { "family": "Campbell", "given": "B. E." } }, { "id": "Mulvenna-J", "name": { "family": "Mulvenna", "given": "J." } }, { "id": "Ong-E-K", "name": { "family": "Ong", "given": "E. K." } }, { "id": "Zhong-W", "name": { "family": "Zhong", "given": "W." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Otranto-D", "name": { "family": "Otranto", "given": "D." } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "R. B." } } ] }, "title": "Exploring transcriptional conservation between Ancylostoma caninum and Haemonchus contortus by oligonucleotide microarray and bioinformatic analyses", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Cross-species hybridization (CSH); Parasitic nematodes; Haemonchus contortus; Ancylostoma caninum; Microarray; Expressed sequence tags (ESTs); Caenorhabditis elegans; Bioinformatics; Genetic interactions; Gene ontology", "note": "\u00a9 2008 Elsevier Ltd.\nReceived 18 March 2008; revised 13 August 2008; accepted 3 September 2008. Available online 11 October 2008.\nThis study was supported by the Australian Research Council\n(ARC) (DP0665230). The authors thank Bennett Datu for\nproducing and providing RNA from A. caninum used in the present study. CC is the recipient of scholarships from the University of Melbourne. The Australian-American Fulbright Commission and Australian Academy of Science are gratefully acknowledged (RBG).", "abstract": "In this study, we identified, using an established oligonucleotide microarray platform for the parasitic nematode Haemonchus contortus, transcripts that are 'conserved' between serum-activated and non-activated L3s of Ancylostoma caninum (aL3 and L3, respectively) and H. contortus by cross-species hybridization (CSH) at high stringency and conducted extensive bioinformatic analyses of the cross-hybridizing expressed sequence tags (ESTs). The microarray analysis revealed significant differential hybridization between aL3 and L3 for 32 molecules from A. caninum, of which 29 were shown to have homologues/orthologues in the free-living nematode Caenorhabditis elegans and/or A. caninum and the other three molecules had no homologues in current gene databases. 'Non-wildtype' RNAi phenotypes were recorded for 13 of the C. elegans homologues. A subset of 16 C. elegans homologues/orthologues (i.e. genes abce-1, act-2, C08H9.2, C55F2.1, calu-1, col-181, cpr-6, elo-2, asp-1, K07E3.4, rpn-2, sel-9, T28C12.4, hsb-1, Y57G11C.15 and ZK593.1) were predicted to interact genetically with a total of 156 (range 1\u201388) other genes. Gene ontology (GO) analysis of the interacting genes revealed that the most common subcategories were signal transduction (7%), intracellular protein transport and glycolysis (6.2%) within 'biological process'; nuclear (25.7%) and intracellular (19.8%) within 'cellular component'; and ATP-binding (14.4%) and protein-binding (8.4%) within 'molecular function'. The potential roles of key molecules in the two blood-feeding parasitic nematodes are discussed in relation to the known roles of their homologues/orthologues in C. elegans. The CSH approach used may provide a tool for the screening of genes conserved across a range of different taxa of parasites for which DNA microarray platforms are not available.", "date": "2009-02", "date_type": "published", "publication": "Molecular and Cellular Probes", "volume": "23", "number": "1", "publisher": "Elsevier", "pagerange": "1-9", "id_number": "CaltechAUTHORS:20090427-112942718", "issn": "0890-8508", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090427-112942718", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Research Council", "grant_number": "DP0665230" } ] }, "doi": "10.1016/j.mcp.2008.09.004", "resource_type": "article", "pub_year": "2009", "author_list": "Cantacessi, C.; Loukas, A.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/8b5sx-gtx94", "eprint_id": 42510, "eprint_status": "archive", "datestamp": "2023-08-20 00:26:46", "lastmod": "2023-10-25 16:43:54", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Feeny-B-F", "name": { "family": "Feeny", "given": "B. F." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "P. W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Cronin-C-J", "name": { "family": "Cronin", "given": "C. J." } } ] }, "title": "Complex Modal Decomposition Applied to Nematode Posturing", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2009 ASME.\n\nPublished - Feeny_2010p247.pdf
", "abstract": "The complex orthogonal decomposition (COD), a process of\nextracting complex modes from complex ensemble data, is summarized,\nas is the use of complex modal coordinates. A brief\nassessment is made on how small levels of noise affect the decomposition.\nThe decomposition is applied to the posturing of\na wild Caenorhabditis elegans nematode. The decomposition\nindicates that the worm has a multi-modal posturing behavior,\ninvolving at least a dominant locomotion mode and a secondary,\nsteering mode. The locomotion mode is closer to a pure traveling\nwaveform than the steering mode. The characteristic wavelength\nof the primary mode was estimated in the complex plane.\nFrequency was obtained from the complex modal coordinate's\ncomplex whirl rate of the complex modal coordinate, and from\nits fast Fourier transform.", "date": "2009", "date_type": "published", "publisher": "American Society of Mechanical Engineers", "place_of_pub": "New York, NY", "pagerange": "247-254", "id_number": "CaltechAUTHORS:20131115-154737239", "isbn": "978-0-7918-4898-2", "book_title": "Proceedings of the ASME 2009 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference: IDETC/CIE 2009", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131115-154737239", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "primary_object": { "basename": "Feeny_2010p247.pdf", "url": "https://authors.library.caltech.edu/records/8b5sx-gtx94/files/Feeny_2010p247.pdf" }, "resource_type": "book_section", "pub_year": "2009", "author_list": "Feeny, B. F.; Sternberg, P. W.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/h4n7g-hef88", "eprint_id": 13010, "eprint_status": "archive", "datestamp": "2023-08-22 13:55:05", "lastmod": "2023-10-17 21:42:32", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ririe-T-O", "name": { "family": "Ririe", "given": "Ted O." } }, { "id": "Fernandes-J-S", "name": { "family": "Fernandes", "given": "Jolene S." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The Caenorhabditis elegans vulva: A post-embryonic gene regulatory network controlling organogenesis", "ispublished": "pub", "full_text_status": "public", "keywords": "genetic regulatory networks; nematode; transcriptional regulation", "note": "\u00a9 2008 by The National Academy of Sciences of the USA. \n\nEdited by Michael S. Levine, University of California, Berkeley, CA, and approved August 25, 2008 (received for review July 10, 2008). Published online before print December 22, 2008, doi: 10.1073/pnas.0806377105 \n\nWe thank A. Mortazavi for help with comparative genomics, H. Chamberlin (Ohio State University, Columbus, OH) for guEx877; A. Fire (Stanford University, Palo Alto, CA) for GFP vectors; S.-H. Kim for his assistance with the zmp-1::GFP RNAi screen; M. Kato, S. Kuntz, E. Schwarz and X. Wang for comments on the manuscript; and T. Inoue for discussions. T.O.R. was supported by National Institutes of Health Grant T32-GM007616. P.W.S. is an investigator with the Howard Hughes Medical Institute. \n\nAuthor contributions: T.O.R., J.S.F., and P.W.S. designed research; T.O.R. and J.S.F. performed research; T.O.R., J.S.F., and P.W.S. analyzed data; and T.O.R., J.S.F., and P.W.S. wrote the paper. \n\nThis paper results from the Arthur M. Sackler Colloquium of the National Academy of Sciences, \"Gene Networks in Animal Development and Evolution,\" held February 15\u201316, 2008, at the Arnold and Mabel Beckman Center of the National Academies of Sciences and Engineering in Irvine, CA. The complete program and audio files of most presentations are available on the NAS web site at http://www.nasonline.org/SACKLER_Gene_Networks. \n\nThe authors declare no conflict of interest. \n\nThis article is a PNAS Direct Submission. \n\nThis article contains supporting information online at www.pnas.org/cgi/content/full/0806377105/DCSupplemental.\n\nPublished - RIRpnas08.pdf
Supplemental Material - RIRpnas08supp.pdf
Supplemental Material - RIRpnas08tableS1.pdf
Supplemental Material - RIRpnas08tableS2.pdf
Supplemental Material - RIRpnas08tableS3.pdf
", "abstract": "The Caenorhabditis elegans vulva is an elegant model for dissecting a gene regulatory network (GRN) that directs postembryonic organogenesis. The mature vulva comprises seven cell types (vulA, vulB1, vulB2, vulC, vulD, vulE, and vulF), each with its own unique pattern of spatial and temporal gene expression. The mechanisms that specify these cell types in a precise spatial pattern are not well understood. Using reverse genetic screens, we identified novel components of the vulval GRN, including nhr-113 in vulA. Several transcription factors (lin-11, lin-29, cog-1, egl-38, and nhr-67) interact with each other and act in concert to regulate target gene expression in the diverse vulval cell types. For example, egl-38 (Pax2/5/8) stabilizes the vulF fate by positively regulating vulF characteristics and by inhibiting characteristics associated with the neighboring vulE cells. nhr-67 and egl-38 regulate cog-1, helping restrict its expression to vulE. Computational approaches have been successfully used to identify functional cis-regulatory motifs in the zmp-1 (zinc metalloproteinase) promoter. These results provide an overview of the regulatory network architecture for each vulval cell type.", "date": "2008-12-23", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "105", "number": "51", "publisher": "National Academy of Sciences", "pagerange": "20095-20099", "id_number": "CaltechAUTHORS:RIRpnas08", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:RIRpnas08", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32-GM007616" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1073/pnas.0806377105", "pmcid": "PMC2629251", "primary_object": { "basename": "RIRpnas08.pdf", "url": "https://authors.library.caltech.edu/records/h4n7g-hef88/files/RIRpnas08.pdf" }, "related_objects": [ { "basename": "RIRpnas08supp.pdf", "url": "https://authors.library.caltech.edu/records/h4n7g-hef88/files/RIRpnas08supp.pdf" }, { "basename": "RIRpnas08tableS1.pdf", "url": "https://authors.library.caltech.edu/records/h4n7g-hef88/files/RIRpnas08tableS1.pdf" }, { "basename": "RIRpnas08tableS2.pdf", "url": "https://authors.library.caltech.edu/records/h4n7g-hef88/files/RIRpnas08tableS2.pdf" }, { "basename": "RIRpnas08tableS3.pdf", "url": "https://authors.library.caltech.edu/records/h4n7g-hef88/files/RIRpnas08tableS3.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Ririe, Ted O.; Fernandes, Jolene S.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/fnpp7-azk86", "eprint_id": 14019, "eprint_status": "archive", "datestamp": "2023-08-22 13:53:09", "lastmod": "2023-10-18 16:02:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Srinivasan-J", "name": { "family": "Srinivasan", "given": "Jagan" }, "orcid": "0000-0001-5449-7938" }, { "id": "Durak-O", "name": { "family": "Durak", "given": "Omer" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Evolution of a polymodal sensory response network", "ispublished": "pub", "full_text_status": "public", "keywords": "nematode caenorhabditis-elegans; stercoralis infective larvae; sodium-chloride gradient; strongyloides-stercoralis; c-elegans; amphidial neurons; pristionchus-pacificus; haemonchus-contortus; parasitic nematode; ash neurons", "note": "\u00a9 2008 Srinivasan et al; licensee BioMed Central Ltd. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\n\nReceived: 26 September 2008. Accepted: 15 December 2008. Published: 15 December 2008. \n\nWe thank the Bargmann Lab and the Hart Lab for advice, and Krisha Begalla and Dorota Korta for help with the behavioral assays, Alon Zaslaver for suggesting the cluster analysis and help in generating Figure 7. We thank Karin Kiontke for the C. tripartitum (SB202) strain and advice on phylogeny. Some nematode strains were provided by the Caenorhabditis Genetics Center. We also thank Cori Bargmann, Ryan Baugh, Takao Inoue, Elissa Hallem, Marie-Anne Felix, Ralf J. Sommer and Karin Kiontke for discussions and comments on the manuscript. JS is an Associate and PWS is an Investigator of the Howard Hughes Medical Institute, which supported this research. OD was supported in part by a Summer Undergraduate Fellowship from Caltech.\n\nPublished - Srinivasan2008p1026Bmc_Biol.pdf
Supplemental Material - 1741-7007-6-52-S1.pdf
Supplemental Material - 1741-7007-6-52-S2.pdf
", "abstract": "Background: Avoidance of noxious stimuli is essential for the survival of an animal in its natural habitat. Some avoidance responses require polymodal sensory neurons, which sense a range of diverse stimuli, whereas other stimuli require a unimodal sensory neuron, which senses a single stimulus. Polymodality might have evolved to help animals quickly detect and respond to diverse noxious stimuli. Nematodes inhabit diverse habitats and most nematode nervous systems are composed of a small number of neurons, despite a wide assortment in nematode sizes. Given this observation, we speculated that cellular contribution to stereotyped avoidance behaviors would also be conserved between nematode species. The ASH neuron mediates avoidance of three classes of noxious stimuli in Caenorhabditis elegans. Two species of parasitic nematodes also utilize the ASH neuron to avoid certain stimuli. We wanted to extend our knowledge of avoidance behaviors by comparing multiple stimuli in a set of free-living nematode species.\n\nResults: We used comparative behavioral analysis and laser microsurgery to examine three avoidance behaviors in six diverse species of free-living nematodes. We found that all species tested exhibit avoidance of chemo-, mechano- and osmosensory stimuli. In C. elegans, the bilaterally symmetric polymodal ASH neurons detect all three classes of repellant. We identified the putative ASH neurons in different nematode species by their anatomical positions and showed that in all six species ablation of the ASH neurons resulted in an inability to avoid noxious stimuli. However, in the nematode Pristionchus pacificus, the ADL neuron in addition to the ASH neuron contributed to osmosensation. In the species Caenorhabditis sp. 3, only the ASH neuron was required to mediate nose touch avoidance instead of three neurons in C. elegans. These data suggest that different species can increase or decrease the contribution of additional, non-ASH sensory neurons mediating osmosensation and mechanosensation.\n\nConclusion: The overall conservation of ASH mediated polymodal nociception suggests that it is an ancestral evolutionarily stable feature of sensation. However, the finding that contribution from non-ASH sensory neurons mediates polymodal nociception in some nematode species suggests that even in conserved sensory behaviors, the cellular response network is dynamic over evolutionary time, perhaps shaped by adaptation of each species to its environment.", "date": "2008-12-15", "date_type": "published", "publication": "BMC Biology", "volume": "6", "publisher": "Biomed Central", "pagerange": "Art. No. 52", "id_number": "CaltechAUTHORS:20090419-212757124", "issn": "1741-7007", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090419-212757124", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Caltech Summer Undergraduate Research Fellowship (SURF)" } ] }, "doi": "10.1186/1741-7007-6-52", "pmcid": "PMC2636771", "primary_object": { "basename": "Srinivasan2008p1026Bmc_Biol.pdf", "url": "https://authors.library.caltech.edu/records/fnpp7-azk86/files/Srinivasan2008p1026Bmc_Biol.pdf" }, "related_objects": [ { "basename": "1741-7007-6-52-S1.pdf", "url": "https://authors.library.caltech.edu/records/fnpp7-azk86/files/1741-7007-6-52-S1.pdf" }, { "basename": "1741-7007-6-52-S2.pdf", "url": "https://authors.library.caltech.edu/records/fnpp7-azk86/files/1741-7007-6-52-S2.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Srinivasan, Jagan; Durak, Omer; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/75mk8-pwx10", "eprint_id": 12867, "eprint_status": "archive", "datestamp": "2023-08-20 00:02:23", "lastmod": "2023-10-17 20:58:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kuntz-S-G", "name": { "family": "Kuntz", "given": "Steven G." } }, { "id": "Schwarz-E-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "DeModena-J-A", "name": { "family": "DeModena", "given": "John A." } }, { "id": "De-Buysscher-T", "name": { "family": "De Buysscher", "given": "Tristan" } }, { "id": "Trout-D", "name": { "family": "Trout", "given": "Diane" } }, { "id": "Shizuya-Hiroaki", "name": { "family": "Shizuya", "given": "Hiroaki" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Wold-B-J", "name": { "family": "Wold", "given": "Barbara J." }, "orcid": "0000-0003-3235-8130" } ] }, "title": "Multigenome DNA sequence conservation identifies Hox cis-regulatory elements", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2008, Cold Spring Harbor Laboratory Press. \n\nReceived August 26, 2008; accepted in revised form September 17, 2008. Published in Advance November 3, 2008, doi:10.1101/gr.085472.108 \n\nWe dedicate this study to the memory of E.B. Lewis, who pioneered the analysis of Hox clusters at Caltech. We thank C.T. Brown for discussions, N. Mullaney for work on an early version of MUSSA, E. Moon for aid in fosmid library construction, and E. Rubin and his colleagues at the DOE JGI for fosmid sequencing and assembly. We thank L.R. Baugh, C.T. Brown, C. Dalal, J. Green, M. Kato, K. Kiontke, A. Mortazavi, A. Seah, and B. Williams for comments on the manuscript. Some nematode strains used in this work were provided by the Caenorhabditis Genetics Center, which is funded by the NIH National Center for Research Resources (NCRR). Unpublished metazoan genomic sequences were generously provided by the DOE JGI and GeneDB. This work was supported by grants from DOE to B.J.W. and P.W.S., from NASA to B.J.W., from NIH to B.J.W., and from the HHMI, with which P.W.S. is an Investigator. \n\nSupplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GenBank (http://www.ncbi.nlm.nih.gov/Genbank/) under accession nos. FJ362353\u2013FJ36238.\n\nPublished - KUNgr08.pdf
", "abstract": "To learn how well ungapped sequence comparisons of multiple species can predict cis-regulatory elements in Caenorhabditis elegans, we made such predictions across the large, complex ceh-13/lin-39 locus and tested them transgenically. We also examined how prediction quality varied with different genomes and parameters in our comparisons. Specifically, we sequenced \u223c0.5% of the C. brenneri and C. sp. 3 PS1010 genomes, and compared five Caenorhabditis genomes (C. elegans, C. briggsae, C. brenneri, C. remanei, and C. sp. 3 PS1010) to find regulatory elements in 22.8 kb of noncoding sequence from the ceh-13/lin-39 Hox subcluster. We developed the MUSSA program to find ungapped DNA sequences with N-way transitive conservation, applied it to the ceh-13/lin-39 locus, and transgenically assayed 21 regions with both high and low degrees of conservation. This identified 10 functional regulatory elements whose activities matched known ceh-13/lin-39 expression, with 100% specificity and a 77% recovery rate. One element was so well conserved that a similar mouse Hox cluster sequence recapitulated the native nematode expression pattern when tested in worms. Our findings suggest that ungapped sequence comparisons can predict regulatory elements genome-wide.", "date": "2008-12", "date_type": "published", "publication": "Genome Research", "volume": "18", "number": "12", "publisher": "Cold Spring Harbor Laboratory Press", "pagerange": "1955-1968", "id_number": "CaltechAUTHORS:KUNgr08", "issn": "1088-9051", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:KUNgr08", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Energy (DOE)" }, { "agency": "NASA" }, { "agency": "NIH" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1101/gr.085472.108", "pmcid": "PMC2593573", "primary_object": { "basename": "KUNgr08.pdf", "url": "https://authors.library.caltech.edu/records/75mk8-pwx10/files/KUNgr08.pdf" }, "resource_type": "article", "pub_year": "2008", "author_list": "Kuntz, Steven G.; Schwarz, Erich M.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/5hkct-9kc56", "eprint_id": 23642, "eprint_status": "archive", "datestamp": "2023-08-19 23:59:07", "lastmod": "2023-10-23 19:49:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Karp-P-D", "name": { "family": "Karp", "given": "Peter D." } }, { "id": "Sherlock-G", "name": { "family": "Sherlock", "given": "Gavin" } }, { "id": "Gerlt-J-A", "name": { "family": "Gerlt", "given": "John A." } }, { "id": "Sim-I", "name": { "family": "Sim", "given": "Ida" } }, { "id": "Paulsen-I", "name": { "family": "Paulsen", "given": "Ian" } }, { "id": "Babbitt-P-C", "name": { "family": "Babbitt", "given": "Patricia C." } }, { "id": "Laderoute-K", "name": { "family": "Laderoute", "given": "Keith" } }, { "id": "Hunter-L", "name": { "family": "Hunter", "given": "Lawrence" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul" }, "orcid": "0000-0002-7699-0173" }, { "id": "Wooley-J", "name": { "family": "Wooley", "given": "John" } }, { "id": "Bourne-P-E", "name": { "family": "Bourne", "given": "Philip E." } } ] }, "title": "Changes to NIH Grant System May Backfire", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2008 American Association for the Advancement of Science.", "abstract": "Although we appreciate the many challenges facing the current NIH grant system and applaud attempts at reform, we believe that several of the changes planned (News of the Week, \"Changes in peer review target young scientists, heavyweights,\" J. Kaiser, 13 June, p. 1404) will cause more harm than good.", "date": "2008-11-21", "date_type": "published", "publication": "Science", "volume": "322", "number": "5905", "publisher": "American Association for the Advancement of Science", "pagerange": "1187-1188", "id_number": "CaltechAUTHORS:20110511-110728873", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110511-110728873", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1126/science.322.5905.1187c", "resource_type": "article", "pub_year": "2008", "author_list": "Karp, Peter D.; Sherlock, Gavin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/n34bv-t6094", "eprint_id": 12526, "eprint_status": "archive", "datestamp": "2023-08-22 13:27:20", "lastmod": "2023-10-17 17:02:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Green-J-L", "name": { "family": "Green", "given": "Jennifer L." } }, { "id": "Kuntz-S-G", "name": { "family": "Kuntz", "given": "Steven G." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Ror receptor tyrosine kinases: orphans no more", "ispublished": "pub", "full_text_status": "public", "note": "Copyright \u00a9 2008 Elsevier. \n\nAvailable online 9 October 2008. \n\nP.W.S. is an investigator with the HHMI. J.L.G. was supported by the Thomas Hunt Morgan Fellowship for graduate study toward the Doctor of Philosophy degree in Biology at the California Institute of Technology. S.G.K. was supported by NIH training grant GM07616.\n\nAccepted Version - nihms-737512.pdf
", "abstract": "Receptor tyrosine kinase-like orphan receptor (Ror) proteins are a conserved family of tyrosine kinase receptors that function in developmental processes including skeletal and neuronal development, cell movement and cell polarity. Although Ror proteins were originally named because the associated ligand and signaling pathway were unknown, recent studies in multiple species have now established that Ror proteins are Wnt receptors. Depending on the cellular context, Ror proteins can either activate or repress transcription of Wnt target genes and can modulate Wnt signaling by sequestering Wnt ligands. New evidence implicates Ror proteins in planar cell polarity, an alternative Wnt pathway. Here, we review the progress made in understanding these mysterious proteins and, in particular, we focus on their function as Wnt receptors.", "date": "2008-11", "date_type": "published", "publication": "Trends in Cell Biology", "volume": "18", "number": "11", "publisher": "Elsevier", "pagerange": "536-544", "id_number": "CaltechAUTHORS:GREtcb08", "issn": "0962-8924", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:GREtcb08", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Thomas Hunt Morgan Fellowship, Caltech" }, { "agency": "NIH", "grant_number": "GM07616" } ] }, "collection": "CaltechAUTHORS", "doi": "10.1016/j.tcb.2008.08.006", "pmcid": "PMC4672995", "primary_object": { "basename": "nihms-737512.pdf", "url": "https://authors.library.caltech.edu/records/n34bv-t6094/files/nihms-737512.pdf" }, "resource_type": "article", "pub_year": "2008", "author_list": "Green, Jennifer L.; Kuntz, Steven G.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/91wa9-wvs66", "eprint_id": 13362, "eprint_status": "archive", "datestamp": "2023-08-22 13:12:12", "lastmod": "2023-10-17 23:50:14", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Srinivasan-J", "name": { "family": "Srinivasan", "given": "Jagan" }, "orcid": "0000-0001-5449-7938" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Pristionchus pacificus: an appropriate fondness for beetles", "ispublished": "pub", "full_text_status": "restricted", "keywords": "nematodes; genome", "note": "\u00a9 2008 Nature Publishing Group.", "abstract": "The nematode Pristionchus pacificus associates with one particular beetle and eats its rotting corpse. The report of the genome sequence of P. pacificus, the fifth nematode to be sequenced and a useful secondary nematode genetic model system, highlights genes that may have influenced the route to parasitism.", "date": "2008-10", "date_type": "published", "publication": "Nature Genetics", "volume": "40", "number": "10", "publisher": "Nature Publishing Group", "pagerange": "1146-1147", "id_number": "CaltechAUTHORS:SRIng08", "issn": "1061-4036", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:SRIng08", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1038/ng1008-1146", "resource_type": "article", "pub_year": "2008", "author_list": "Srinivasan, Jagan and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/2twtg-5dh22", "eprint_id": 11941, "eprint_status": "archive", "datestamp": "2023-08-22 13:07:28", "lastmod": "2023-10-17 16:00:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hu-Min", "name": { "family": "Hu", "given": "Min" } }, { "id": "LaRonde-LeBlanc-N", "name": { "family": "LaRonde-LeBlanc", "given": "Nicole" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } } ] }, "title": "Tv-RIO1 \u2013 an atypical protein kinase from the parasitic nematode Trichostrongylus vitrinus", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2008 Hu et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived: 31 July 2008. Accepted: 22 September 2008. Published: 22 September 2008. \n\nThis work was supported by the Australian Research Council (LP0667795 and LX0882231), Genetic Technologies Limited, Meat and Livestock Australia, the Australian Academy of Science, the Australian-American Fulbright Commission (RBG), and the Howard Hughes Medical Institute (PWS). \n\nAuthors' contributions: RBG and MH conceived the project, collected the parasite material, analysed the data and drafted the manuscript. MH carried out the molecular work. NLL and PWS assisted in analyses, interpretation and the drafting of the manuscript. All authors read and approved the final manuscript. \n\nThe authors declare that they have no competing interests.\n\nPublished - HUMpv08.pdf
", "abstract": "Background: Protein kinases are key enzymes that regulate a wide range of cellular processes, including cell-cycle progression, transcription, DNA replication and metabolic functions. These enzymes catalyse the transfer of phosphates to serine, threonine and tyrosine residues, thus playing functional roles in reversible protein phosphorylation. There are two main groups, namely eukaryotic protein kinases (ePKs) and atypical protein kinases (aPKs); RIO kinases belong to the latter group. While there is some information about RIO kinases and their roles in animals, nothing is known about them in parasites. This is the first study to characterise a RIO1 kinase from any parasite. \n\nResults: A full-length cDNA (Tv-rio-1) encoding a RIO1 protein kinase (Tv-RIO1) was isolated from the economically important parasitic nematode Trichostrongylus vitrinus (Order Strongylida). The uninterrupted open reading frame (ORF) of 1476 nucleotides encoded a protein of 491 amino acids, containing the characteristic RIO1 motif LVHADLSEYNTL. Tv-rio-1 was transcribed at the highest level in the third-stage larva (L3), and a higher level in adult females than in males. Comparison with homologues from other organisms showed that protein Tv-RIO1 had significant homology to related proteins from a range of metazoans and plants. Amino acid sequence identity was most pronounced in the ATP-binding motif, active site and metal binding loop. Phylogenetic analyses of selected amino acid sequence data revealed Tv-RIO1 to be most closely related to the proteins in the species of Caenorhabditis. A structural model of Tv-RIO1 was constructed and compared with the published crystal structure of RIO1 of Archaeoglobus fulgidus (Af-Rio1). \n\nConclusion: This study provides the first insights into the RIO1 protein kinases of nematodes, and a foundation for further investigations into the biochemical and functional roles of this molecule in biological processes in parasitic nematodes.", "date": "2008-09-22", "date_type": "published", "publication": "Parasites and Vectors", "volume": "1", "publisher": "BioMed Central", "pagerange": "Art. No. 34", "id_number": "CaltechAUTHORS:HUMpv08", "issn": "1756-3305", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:HUMpv08", "rights": "This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.", "funders": { "items": [ { "agency": "Australian Research Council", "grant_number": "LP0667795" }, { "agency": "Australian Research Council", "grant_number": "LX0882231" }, { "agency": "Genetic Technologies Limited" }, { "agency": "Meat and Livestock Australia" }, { "agency": "Australian Academy of Science" }, { "agency": "Australian-American Fulbright Commission" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1186/1756-3305-1-34", "pmcid": "PMC2564912", "primary_object": { "basename": "HUMpv08.pdf", "url": "https://authors.library.caltech.edu/records/2twtg-5dh22/files/HUMpv08.pdf" }, "resource_type": "article", "pub_year": "2008", "author_list": "Hu, Min; LaRonde-LeBlanc, Nicole; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/v1tbn-60t59", "eprint_id": 13884, "eprint_status": "archive", "datestamp": "2023-08-22 12:54:34", "lastmod": "2023-10-18 14:32:16", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gupta-A", "name": { "family": "Gupta", "given": "Amarnath" } }, { "id": "Bug-W", "name": { "family": "Bug", "given": "William" } }, { "id": "Marenco-L", "name": { "family": "Marenco", "given": "Luis" } }, { "id": "Qian-Xufei", "name": { "family": "Qian", "given": "Xufei" } }, { "id": "Condit-C", "name": { "family": "Condit", "given": "Christopher" } }, { "id": "Rangarajan-A", "name": { "family": "Rangarajan", "given": "Arun" } }, { "id": "M\u00fcller-H-M", "name": { "family": "M\u00fcller", "given": "Hans Michael" } }, { "id": "Miller-P-L", "name": { "family": "Miller", "given": "Perry L." } }, { "id": "Sanders-B", "name": { "family": "Sanders", "given": "Brian" } }, { "id": "Grethe-J-S", "name": { "family": "Grethe", "given": "Jeffrey S." } }, { "id": "Astakhov-V", "name": { "family": "Astakhov", "given": "Vadim" } }, { "id": "Shepherd-G-M", "name": { "family": "Shepherd", "given": "Gordon" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Martone-M-E", "name": { "family": "Martone", "given": "Maryann E." } } ] }, "title": "Federated access to heterogeneous information resources in the Neuroscience Information Framework (NIF)", "ispublished": "pub", "full_text_status": "public", "keywords": "ontology; data federation; neuroscience resource", "note": "\u00a9 The Author(s) 2008. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.\n\n\nReceived: 6 September 2008 Accepted: 8 September 2008 Published online: 29 October 2008.\n\n\nThis project has been funded in whole or in part\nthrough the NIH Blueprint for Neuroscience Research with Federal\nfunds from the National Institute on Drug Abuse, National Institutes of Health, Department of Health and Human Services, under Contract\nNo. HHSN271200577531C. The mediator and concept mapping tools\nwere adopted from the Biomedical Informatics Research Network,\nsupported by an award from the National Center for Research\nResources (U24-RR019701).\nOpen Access: This article is distributed under the terms of the\nCreative Commons Attribution Noncommercial License which permits\nany noncommercial use, distribution, and reproduction in any\nmedium, provided the original author(s) and source are credited.\n\nPublished - GUPni08.pdf
Accepted Version - nihms97995.pdf
", "abstract": "The overarching goal of the NIF (Neuroscience Information Framework) project is to be a one-stop-shop for Neuroscience. This paper provides a technical overview of how the system is designed. The technical goal of the first version of the NIF system was to develop an information system that a neuroscientist can use to locate relevant information from a wide variety of information sources by simple keyword queries. Although the user would provide only keywords to retrieve information, the NIF system is designed to treat them as concepts whose meanings are interpreted by the system. Thus, a search for term should find a record containing synonyms of the term. The system is targeted to find information from web pages, publications, databases, web sites built upon databases, XML documents and any other modality in which such information may be published. We have designed a system to achieve this functionality. A central element in the system is an ontology called NIFSTD (for NIF Standard) constructed by amalgamating a number of known and newly developed ontologies. NIFSTD is used by our ontology management module, called OntoQuest to perform ontology-based search over data sources. The NIF architecture currently provides three different mechanisms for searching heterogeneous data sources including relational databases, web sites, XML documents and full text of publications. Version 1.0 of the NIF system is currently in beta test and may be accessed through http://nif.nih.gov.", "date": "2008-09", "date_type": "published", "publication": "Neuroinformatics", "volume": "6", "number": "3", "publisher": "Springer", "pagerange": "205-217", "id_number": "CaltechAUTHORS:20090407-152558990", "issn": "1539-2791", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090407-152558990", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Institute on Drug Abuse" }, { "agency": "NIH", "grant_number": "HHSN271200577531C" }, { "agency": "NIH", "grant_number": "U24-RR019701" } ] }, "doi": "10.1007/s12021-008-9033-y", "pmcid": "PMC2689790", "primary_object": { "basename": "GUPni08.pdf", "url": "https://authors.library.caltech.edu/records/v1tbn-60t59/files/GUPni08.pdf" }, "related_objects": [ { "basename": "nihms97995.pdf", "url": "https://authors.library.caltech.edu/records/v1tbn-60t59/files/nihms97995.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Gupta, Amarnath; Bug, William; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/acxer-4dy24", "eprint_id": 22936, "eprint_status": "archive", "datestamp": "2023-08-22 12:55:40", "lastmod": "2023-10-23 17:40:50", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Marenco-L", "name": { "family": "Marenco", "given": "Luis" } }, { "id": "Li-Yuli", "name": { "family": "Li", "given": "Yuli" } }, { "id": "Martone-M-E", "name": { "family": "Martone", "given": "Maryann E." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Shepherd-G-M", "name": { "family": "Shepherd", "given": "Gordon M." } }, { "id": "Miller-P-L", "name": { "family": "Miller", "given": "Perry L." } } ] }, "title": "Issues in the Design of a Pilot Concept-Based Query Interface for the Neuroinformatics Information Framework", "ispublished": "pub", "full_text_status": "public", "keywords": "Data search; Web search; Ontologies; Database mediation; Data federation; Text search; Neuroscience", "note": "\u00a9 The Author(s) 2008. This article is published with open access at Springerlink.com. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. \n\nPublished online: 25 October 2008. \n\nThis project has been funded in whole or in part through the NIH Blueprint for Neuroscience Research with Federal funds from the National Institute on Drug Abuse, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN271200577531C. This research was also supported by NIH grants P01 DC04732 and R01 DA021253, Volunteer consultant-collaborators and friends, and The Society for Neuroscience.\n\nPublished - Marenco2008p3000Neuroinformatics.pdf
Accepted Version - nihms97990.pdf
", "abstract": "This paper describes a pilot query interface that has been constructed to help us explore a \"concept-based\" approach for searching the\n Neuroscience Information Framework (NIF). The query interface is\n concept-based in the sense that the search terms submitted through the\n interface are selected from a standardized vocabulary of terms\n (concepts) that are structured in the form of an ontology. The NIF\n contains three primary resources: the NIF Resource Registry, the NIF\n Document Archive, and the NIF Database Mediator. These NIF resources\n are very different in their nature and therefore pose challenges when\n designing a single interface from which searches can be automatically\n launched against all three resources simultaneously. The paper first\n discusses briefly several background issues involving the use of\n standardized biomedical vocabularies in biomedical information\n retrieval, and then presents a detailed example that illustrates how\n the pilot concept-based query interface operates. The paper concludes\n by discussing certain lessons learned in the development of the current\n version of the interface.", "date": "2008-09", "date_type": "published", "publication": "Neuroinformatics", "volume": "6", "number": "3", "publisher": "Humana Press Inc.", "pagerange": "229-239", "id_number": "CaltechAUTHORS:20110316-131549531", "issn": "1539-2791", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110316-131549531", "rights": "This article is distributed under the terms of the\nCreative Commons Attribution Noncommercial License which permits\nany noncommercial use, distribution, and reproduction in any\nmedium, provided the original author(s) and source are credited.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HHSN271200577531C" }, { "agency": "NIH", "grant_number": "P01 DC04732" }, { "agency": "NIH", "grant_number": "R01 DA021253" }, { "agency": "Society for Neuroscience" }, { "agency": "National Institute on Drug Abuse" } ] }, "doi": "10.1007/s12021-008-9035-9", "pmcid": "PMC2664632", "primary_object": { "basename": "Marenco2008p3000Neuroinformatics.pdf", "url": "https://authors.library.caltech.edu/records/acxer-4dy24/files/Marenco2008p3000Neuroinformatics.pdf" }, "related_objects": [ { "basename": "nihms97990.pdf", "url": "https://authors.library.caltech.edu/records/acxer-4dy24/files/nihms97990.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Marenco, Luis; Li, Yuli; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/xekfm-eqr22", "eprint_id": 22937, "eprint_status": "archive", "datestamp": "2023-08-22 12:55:47", "lastmod": "2023-10-23 17:40:52", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mueller-H-M", "name": { "family": "Mueller", "given": "Hans-Michael" } }, { "id": "Rangarajan-A", "name": { "family": "Rangarajan", "given": "Arun" } }, { "id": "Teal-T-K", "name": { "family": "Teal", "given": "Tracy K." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Textpresso for Neuroscience: Searching the Full Text of Thousands of Neuroscience Research Papers", "ispublished": "pub", "full_text_status": "public", "keywords": "Literature search engine; Information retrieval; Full text; Information extraction; Ontology; Semantic searches", "note": "\u00a9 The Author(s) 2008. This article is published with open access at Springerlink.com. This article is distributed under the terms of the\nCreative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. \n\nPublished online: 24 October 2008. \n\nTextpresso is supported by a grant from the National Human Genome Research Institute at the US National Institutes of Health # HG004090. The Textpresso for Neuroscience site has been funded in whole or in part through the NIH Blueprint for Neuroscience Research with Federal funds from the National Institute on Drug Abuse, National Institutes of Health, Department of Health and Human Services, under contract No. HHSN271200577531C. PWS is an Investigator of the Howard Hughes Medical Institute.\n\nPublished - Mueller2008p2992Neuroinformatics.pdf
Accepted Version - nihms96840.pdf
", "abstract": "Textpresso is a text-mining system for scientific literature. Its two major features are access to the full text of research papers and the development and use of categories of biological concepts as well as categories that describe or relate objects. A search engine enables the user to search for one or a combination of these categories and/or keywords within an entire literature. Here we describe Textpresso for\n Neuroscience, part of the core Neuroscience Information Framework\n (NIF). The Textpresso site currently consists of 67,500 full text\n papers and 131,300 abstracts. We show that using categories in\n literature can make a pure keyword query more refined and meaningful.\n We also show how semantic queries can be formulated with categories\n only. We explain the build and content of the database and describe the\n main features of the web pages and the advanced search options. We also\n give detailed illustrations of the web service developed to provide\n programmatic access to Textpresso. This web service is used by the NIF\n interface to access Textpresso. The standalone website of Textpresso\n for Neuroscience can be accessed at\n http://www.textpresso.org/neuroscience.", "date": "2008-09", "date_type": "published", "publication": "Neuroinformatics", "volume": "6", "number": "3", "publisher": "Humana Press Inc.", "pagerange": "195-204", "id_number": "CaltechAUTHORS:20110316-132400869", "issn": "1539-2791", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110316-132400869", "rights": "This article is distributed under the terms of the\nCreative Commons Attribution Noncommercial License which permits\nany noncommercial use, distribution, and reproduction in any\nmedium, provided the original author(s) and source are credited.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HG004090" }, { "agency": "NIH", "grant_number": "HHSN271200577531C" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "National Human Genome Research Institute" }, { "agency": "National Institute on Drug Abuse" } ] }, "doi": "10.1007/s12021-008-9031-0", "pmcid": "PMC2666735", "primary_object": { "basename": "Mueller2008p2992Neuroinformatics.pdf", "url": "https://authors.library.caltech.edu/records/xekfm-eqr22/files/Mueller2008p2992Neuroinformatics.pdf" }, "related_objects": [ { "basename": "nihms96840.pdf", "url": "https://authors.library.caltech.edu/records/xekfm-eqr22/files/nihms96840.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Mueller, Hans-Michael; Rangarajan, Arun; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ptsmx-j9a64", "eprint_id": 14132, "eprint_status": "archive", "datestamp": "2023-08-22 12:54:47", "lastmod": "2023-10-18 16:09:03", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gardner-D", "name": { "family": "Gardner", "given": "Daniel" } }, { "id": "Akil-H", "name": { "family": "Akil", "given": "Huda" } }, { "id": "Ascoli-G-A", "name": { "family": "Ascoli", "given": "Giorgio A." } }, { "id": "Bowden-D-M", "name": { "family": "Bowden", "given": "Douglas M." } }, { "id": "Bug-W", "name": { "family": "Bug", "given": "William" } }, { "id": "Donohue-D-E", "name": { "family": "Donohue", "given": "Duncan E." } }, { "id": "Goldberg-D-H", "name": { "family": "Goldberg", "given": "David H." } }, { "id": "Grafstein-B", "name": { "family": "Grafstein", "given": "Bernice" } }, { "id": "Grethe-J-S", "name": { "family": "Grethe", "given": "Jeffrey S." } }, { "id": "Gupta-A", "name": { "family": "Gupta", "given": "Amarnath" } }, { "id": "Halavi-M", "name": { "family": "Halavi", "given": "Maryam" } }, { "id": "Kennedy-D-N", "name": { "family": "Kennedy", "given": "David N." } }, { "id": "Marenco-L", "name": { "family": "Marenco", "given": "Luis" } }, { "id": "Martone-M-E", "name": { "family": "Martone", "given": "Maryann E." } }, { "id": "Miller-P-L", "name": { "family": "Miller", "given": "Perry L." } }, { "id": "M\u00fcller-H-M", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } }, { "id": "Robert-A", "name": { "family": "Robert", "given": "Adrian" } }, { "id": "Shepherd-G-M", "name": { "family": "Shepherd", "given": "Gordon M." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Van-Essen-D-C", "name": { "family": "Van Essen", "given": "David C." }, "orcid": "0000-0001-7044-4721" }, { "id": "Williams-R-W", "name": { "family": "Williams", "given": "Robert W." } } ] }, "title": "The Neuroscience Information Framework: A Data and Knowledge Environment for Neuroscience", "ispublished": "pub", "full_text_status": "public", "keywords": "neurodatabases; data sharing; terminologies; portals", "note": "\u00a9 The Author(s) 2008. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. \n\nReceived: 15 August 2008 Accepted: 26 August 2008 Published online: 23 October 2008. \n\nThis project has been funded in whole or in part through the NIH Blueprint for Neuroscience Research with Federal funds from the National Institute on Drug Abuse, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN271200577531C. The Neuroscience Information Framework team gratefully acknowledges the support of volunteer consultant-collaborators and friends, and The Society for Neuroscience.\nEarly development of the SfN Neuroscience Database Gateway\nwas supported by the Society for Neuroscience by means of a\ngenerous gift from Paul Allen and Jody Patton and by contract (NIH\nOrder No. 263-MD-409125-1) from NIMH, NINDS, and NIDA. We\nthank C. Wren for the epitaph adaptable as the Information Sharing\nStatement. The Advisory Committee consists of Huda Akil, Giorgio\nAscoli, Daniel Gardner, Bernice Grafstein, Maryann E. Martone,\nGordon Shepherd, Paul Sternberg, David C. Van Essen, and Robert W. Williams.\n\nPublished - GARni08.pdf
Accepted Version - nihms94457.pdf
", "abstract": "With support from the Institutes and Centers forming the NIH Blueprint for Neuroscience Research, we have designed and implemented a new initiative for integrating access to and use of Web-based neuroscience resources: the Neuroscience Information Framework. The Framework arises from the expressed need of the neuroscience community for neuroinformatic tools and resources to aid scientific inquiry, builds upon prior development of neuroinformatics by the Human Brain Project and others, and directly derives from the Society for Neuroscience's Neuroscience Database Gateway. Partnered with the Society, its Neuroinformatics Committee, and volunteer consultant-collaborators, our multi-site consortium has developed: (1) a comprehensive, dynamic, inventory of Web-accessible neuroscience resources, (2) an extended and integrated terminology describing resources and contents, and (3) a framework accepting and aiding concept-based queries. Evolving instantiations of the Framework may be viewed at http://nif.nih.gov, http://neurogateway.org, and other sites as they come on line.", "date": "2008-09", "date_type": "published", "publication": "Neuroinformatics", "volume": "6", "number": "3", "publisher": "Humana Press Inc.", "pagerange": "149-160", "id_number": "CaltechAUTHORS:20090501-121556840", "issn": "1539-2791", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090501-121556840", "rights": "Springer Open Choice articles are protected by the Springer Open Choice license, which is compatible with the Creative Commons Attribution License. ", "funders": { "items": [ { "agency": "National Institute on Drug Abuse" }, { "agency": "NIH", "grant_number": "HHSN271200577531C" }, { "agency": "Society for Neuroscience" } ] }, "doi": "10.1007/s12021-008-9024-z", "pmcid": "PMC2661130", "primary_object": { "basename": "GARni08.pdf", "url": "https://authors.library.caltech.edu/records/ptsmx-j9a64/files/GARni08.pdf" }, "related_objects": [ { "basename": "nihms94457.pdf", "url": "https://authors.library.caltech.edu/records/ptsmx-j9a64/files/nihms94457.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Gardner, Daniel; Akil, Huda; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/612sy-wgs82", "eprint_id": 95469, "eprint_status": "archive", "datestamp": "2023-08-19 23:32:10", "lastmod": "2023-10-20 20:16:03", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Srinivasan-J", "name": { "family": "Srinivasan", "given": "Jagan" }, "orcid": "0000-0001-5449-7938" }, { "id": "Kaplan-F", "name": { "family": "Kaplan", "given": "Fatma" }, "orcid": "0000-0002-9565-0211" }, { "id": "Ajredini-R", "name": { "family": "Ajredini", "given": "Ramadan" } }, { "id": "Zachariah-C", "name": { "family": "Zachariah", "given": "Cherian" } }, { "id": "Alborn-H-T", "name": { "family": "Alborn", "given": "Hans T." }, "orcid": "0000-0003-3918-5041" }, { "id": "Teal-P-E-A", "name": { "family": "Teal", "given": "Peter E. A." } }, { "id": "Malik-R-U", "name": { "family": "Malik", "given": "Rabia U." } }, { "id": "Edison-A-S", "name": { "family": "Edison", "given": "Arthur S." }, "orcid": "0000-0002-5686-2350" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Schroeder-F-C", "name": { "family": "Schroeder", "given": "Frank C." }, "orcid": "0000-0002-4420-0237" } ] }, "title": "A blend of small molecules regulates both mating and development in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2008 Macmillan Publishers Limited. \n\nReceived 17 January 2008; Accepted 13 June 2008; Published\n23 July 2008. \n\nThis work was supported by the Human Frontiers Science Program (A.S.E., P.W.S. and P.E.A.T.), a US National Institutes of Health grant (P41 GM079571) to F.C.S., and the Howard Hughes Medical Institute, of which J.S. is an associate and P.W.S. an investigator. NMR data were collected in the UF-AMRIS facility; we thank J. Rocca for assistance. We thank E. Peden and D. Xue for the ceh-30 strains, C. J. Cronin and A. Choe for advice on behavioural assays, L. R. Baugh for liquid-culture dauer formation assays, B. Fox for assistance with the synthesis of ascr#2, ascr#3 and ascr#4, and M. de Bono, A. Dossey and M. Stadler for discussions. E. Hallem, J. Bungert and D. Hutchinson provided comments on the manuscript. \n\nAuthor Contributions J.S. and P.W.S. designed the biological experiments and J.S. performed all the biological experiments; F.K. developed the procedure for collecting secreted worm metabolites and designed the chemical experiments and fractionation; F.K. and R.A. produced worm-conditioned water and performed chromatography; F.K., F.C.S., R.U.M., C.Z. and A.S.E. performed structure elucidation by NMR; H.T.A. performed structure elucidation by LC-MS; F.C.S. synthesized ascr#2, ascr#3 and ascr#4; and J.S., F.K., F.C.S., A.S.E., P.E.A.T. and P.W.S. analysed the data and wrote the paper. \n\nJagan Srinivasan & Fatma Kaplan: These authors contributed equally to this work.\n\nAccepted Version - nihms-128366.pdf
Supplemental Material - nature07168-s1.pdf
Supplemental Material - nature07168-s2.mov
Supplemental Material - nature07168-s3.mov
", "abstract": "In many organisms, population-density sensing and sexual attraction rely on small-molecule-based signalling systems. In the nematode Caenorhabditis elegans, population density is monitored through specific glycosides of the dideoxysugar ascarylose (the 'ascarosides') that promote entry into an alternative larval stage, the non-feeding and highly persistent dauer stage. In addition, adult C. elegans males are attracted to hermaphrodites by a previously unidentified small-molecule signal. Here we show, by means of combinatorial activity-guided fractionation of the C. elegans metabolome, that the mating signal consists of a synergistic blend of three dauer-inducing ascarosides, which we call ascr#2, ascr#3 and ascr#4. This blend of ascarosides acts as a potent male attractant at very low concentrations, whereas at the higher concentrations required for dauer formation the compounds no longer attract males and instead deter hermaphrodites. The ascarosides ascr#2 and ascr#3 carry different, but overlapping, information, as ascr#3 is more potent as a male attractant than ascr#2, whereas ascr#2 is slightly more potent than ascr#3 in promoting dauer formation7. We demonstrate that ascr#2, ascr#3 and ascr#4 are strongly synergistic, and that two types of neuron, the amphid single-ciliated sensory neuron type K (ASK) and the male-specific cephalic companion neuron (CEM), are required for male attraction by ascr#3. On the basis of these results, male attraction and dauer formation in C. elegans appear as alternative behavioural responses to a common set of signalling molecules. The ascaroside signalling system thus connects reproductive and developmental pathways and represents a unique example of structure- and concentration-dependent differential activity of signalling molecules.", "date": "2008-08-28", "date_type": "published", "publication": "Nature", "volume": "454", "number": "7208", "publisher": "Nature Publishing Group", "pagerange": "1115-1118", "id_number": "CaltechAUTHORS:20190514-083519984", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-083519984", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Human Frontier Science Program" }, { "agency": "NIH", "grant_number": "P41 GM079571" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1038/nature07168", "pmcid": "PMC2774729", "primary_object": { "basename": "nature07168-s1.pdf", "url": "https://authors.library.caltech.edu/records/612sy-wgs82/files/nature07168-s1.pdf" }, "related_objects": [ { "basename": "nature07168-s2.mov", "url": "https://authors.library.caltech.edu/records/612sy-wgs82/files/nature07168-s2.mov" }, { "basename": "nature07168-s3.mov", "url": "https://authors.library.caltech.edu/records/612sy-wgs82/files/nature07168-s3.mov" }, { "basename": "nihms-128366.pdf", "url": "https://authors.library.caltech.edu/records/612sy-wgs82/files/nihms-128366.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Srinivasan, Jagan; Kaplan, Fatma; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ck4rk-fb013", "eprint_id": 95468, "eprint_status": "archive", "datestamp": "2023-08-22 12:46:57", "lastmod": "2023-10-20 20:15:55", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Green-J-L", "name": { "family": "Green", "given": "Jennifer L." } }, { "id": "Inoue-Takao", "name": { "family": "Inoue", "given": "Takao" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Opposing Wnt Pathways Orient Cell Polarity during Organogenesis", "ispublished": "pub", "full_text_status": "public", "keywords": "CELLBIO; DEVBIO; SIGNALING", "note": "\u00a9 2008 Elsevier Inc. \n\nReceived 30 October 2007, Revised 23 April 2008, Accepted 10 June 2008, Available online 21 August 2008. \n\nWe thank Gladys Medina, Barbara Perry, and Shahla Gharib for technical assistance, members of our lab for helpful discussions, Andrea Choe for artistic input, and Marianne Bronner-Fraser, Scott Fraser, Cheryl Van Buskirk, Mihoko Kato, Elissa Hallem, and Adeline Seah for critically reading the manuscript. Many strains used in this study were provided by the Caenorhabditis Genetics Center, funded by the National Institutes of Health, National Center for Research Resources. We are grateful to the late Peter Snow for his valuable assistance in making our CAM-1 antibody. P.W.S. is an investigator with the Howard Hughes Medical Institute, who supported this work, and J.L.G. was supported by the Moore Foundation Fellowship for graduate study toward the Doctor of Philosophy degree in Biology at the California Institute of Technology.\n\nAccepted Version - nihms67892.pdf
Supplemental Material - 1-s2.0-S0092867408007782-mmc1.pdf
", "abstract": "The orientation of asymmetric cell division contributes to the organization of cells within a tissue or organ. For example, mirror-image symmetry of the C. elegans vulva is achieved by the opposite division orientation of the vulval precursor cells (VPCs) flanking the axis of symmetry. We characterized the molecular mechanisms contributing to this division pattern. Wnts MOM-2 and LIN-44 are expressed at the axis of symmetry and orient the VPCs toward the center. These Wnts act via Fz/LIN-17 and Ryk/LIN-18, which control \u03b2-catenin localization and activate gene transcription. In addition, VPCs on both sides of the axis of symmetry possess a uniform underlying \"ground\" polarity, established by the instructive activity of Wnt/EGL-20. EGL-20 establishes ground polarity via a novel type of signaling involving the Ror receptor tyrosine kinase CAM-1 and the planar cell polarity component Van Gogh/VANG-1. Thus, tissue polarity is determined by the integration of multiple Wnt pathways.", "date": "2008-08-22", "date_type": "published", "publication": "Cell", "volume": "134", "number": "4", "publisher": "Elsevier", "pagerange": "646-656", "id_number": "CaltechAUTHORS:20190514-082856223", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-082856223", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1016/j.cell.2008.06.026", "pmcid": "PMC2603076", "primary_object": { "basename": "1-s2.0-S0092867408007782-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/ck4rk-fb013/files/1-s2.0-S0092867408007782-mmc1.pdf" }, "related_objects": [ { "basename": "nihms67892.pdf", "url": "https://authors.library.caltech.edu/records/ck4rk-fb013/files/nihms67892.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Green, Jennifer L.; Inoue, Takao; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/f640y-5p079", "eprint_id": 11361, "eprint_status": "archive", "datestamp": "2023-08-22 12:41:25", "lastmod": "2023-10-16 23:44:50", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cui-Xiquan", "name": { "family": "Cui", "given": "Xiquan" } }, { "id": "Lee-Lap-Man", "name": { "family": "Lee", "given": "Lap Man" } }, { "id": "Heng-Xin", "name": { "family": "Heng", "given": "Xin" } }, { "id": "Zhong-Weiwei", "name": { "family": "Zhong", "given": "Weiwei" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Psaltis-D", "name": { "family": "Psaltis", "given": "Demetri" } }, { "id": "Yang-Changhuei", "name": { "family": "Yang", "given": "Changhuei" }, "orcid": "0000-0001-8791-0354" } ] }, "title": "Lensless high-resolution on-chip optofluidic microscopes for Caenorhabditis elegans and cell imaging", "ispublished": "pub", "full_text_status": "public", "keywords": "optofluidic microscopy; phenotype characterization; microfluidic", "note": "\u00a9 2008 by the National Academy of Sciences. Freely available online through the PNAS open access option. \n\nCommunicated by Amnon Yariv, California Institute of Technology, Pasadena, CA, May 13, 2008 (received for review March 31, 2008). Published online before print July 28, 2008, doi: 10.1073/pnas.0804612105. \n\nWe are grateful for the constructive discussions with and the generous help from Professor Axel Scherer, Jigang Wu, Dr. Zahid Yaqoob, Dr. Claudiu Giurumescu, Oren Schaedel and Dr. Xiaoyan Robert Bao. We appreciate the assistance of the Caltech Watson clean-room. This work is funded by DARPA's Center of Optofluidic Integration, the Wallace Coulter Foundation, National Science Foundation Career Award BES-0547657, and National Institutes of Health Grant R21 PA03-107. L.M.L. thanks the Croucher Scholarship for financial support. P.W.S. is an Investigator of the Howard Hughes Medical Institute. \n\nAuthor contributions: X.C., P.W.S., D.P., and C.Y. designed research; X.C., L.M.L., X.H., and W.Z. performed research; X.C. and L.M.L. analyzed data; and X.C., L.M.L., X.H., W.Z., P.W.S., D.P., and C.Y. wrote the paper. X.C. and L.M.L. contributed equally to this work. \n\nThe authors declare no conflict of interest.\n\nPublished - CUIpnas08.pdf
", "abstract": "Low-cost and high-resolution on-chip microscopes are vital for reducing cost and improving efficiency for modern biomedicine and bioscience. Despite the needs, the conventional microscope design has proven difficult to miniaturize. Here, we report the implementation and application of two high-resolution (\u22480.9 \u03bcm for the first and \u22480.8 \u03bcm for the second), lensless, and fully on-chip microscopes based on the optofluidic microscopy (OFM) method. These systems abandon the conventional microscope design, which requires expensive lenses and large space to magnify images, and instead utilizes microfluidic flow to deliver specimens across array(s) of micrometer-size apertures defined on a metal-coated CMOS sensor to generate direct projection images. The first system utilizes a gravity-driven microfluidic flow for sample scanning and is suited for imaging elongate objects, such as Caenorhabditis elegans; and the second system employs an electrokinetic drive for flow control and is suited for imaging cells and other spherical/ellipsoidal objects. As a demonstration of the OFM for bioscience research, we show that the prototypes can be used to perform automated phenotype characterization of different Caenorhabditis elegans mutant strains, and to image spores and single cellular entities. The optofluidic microscope design, readily fabricable with existing semiconductor and microfluidic technologies, offers low-cost and highly compact imaging solutions. More functionalities, such as on-chip phase and fluorescence imaging, can also be readily adapted into OFM systems. We anticipate that the OFM can significantly address a range of biomedical and bioscience needs, and engender new microscope applications.", "date": "2008-08-05", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "105", "number": "31", "publisher": "National Academy of Sciences", "pagerange": "10670-10675", "id_number": "CaltechAUTHORS:CUIpnas08", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:CUIpnas08", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "Wallace Coulter Foundation" }, { "agency": "NSF", "grant_number": "BES-0547657" }, { "agency": "NIH", "grant_number": "R21 PA03-107" }, { "agency": "Croucher Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Kavli-Nanoscience-Institute" } ] }, "doi": "10.1073/pnas.0804612105", "pmcid": "PMC2488383", "primary_object": { "basename": "CUIpnas08.pdf", "url": "https://authors.library.caltech.edu/records/f640y-5p079/files/CUIpnas08.pdf" }, "resource_type": "article", "pub_year": "2008", "author_list": "Cui, Xiquan; Lee, Lap Man; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/z9s1c-gmk30", "eprint_id": 11012, "eprint_status": "archive", "datestamp": "2023-08-22 11:58:02", "lastmod": "2023-10-16 23:13:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hallem-E-A", "name": { "family": "Hallem", "given": "Elissa A." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Acute carbon dioxide avoidance in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "behavioral genetics; cGMP signaling; chemosensation", "note": "\u00a9 2008 by The National Academy of Sciences of the USA. Freely available online through the PNAS open access option. \n\nEdited by Martin Chalfie, Columbia University, New York, NY, and approved February 20, 2008 (received for review August 8, 2007). This article is a PNAS Direct Submission. \n\nWe thank M. de Bono (MRC Laboratory of Molecular Biology, Cambridge, U.K.), C. Bargmann (HHMI and The Rockefeller University, New York, NY), J. Thomas (University of Washington, Seattle, WA), and the Caenorhabditis Genetics Center (University of Minnesota, Minneapolis, MN) for strains; D. Anderson (California Institute of Technology, Pasadena, CA) and members of our laboratory for insightful discussions; and J. Srinivasan (California Institute of Technology, Pasadena, CA) for discussion of other species. This work was supported by the Howard Hughes Medical Institute, of which P.W.S. is an investigator, and a Helen Hay Whitney postdoctoral fellowship (to E.A.H.). \n\nAuthor contributions: E.A.H. and P.W.S. designed research; E.A.H. performed research; E.A.H. analyzed data; and E.A.H. and P.W.S. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nThis article contains supporting information online at www.pnas.org/cgi/content/full/0707469105/DCSupplemental.\n\nPublished - HALpnas08.pdf
Supplemental Material - HALpnas08movie1.mpg
Supplemental Material - HALpnas08movie2.mpg
Supplemental Material - HALpnas08sup.pdf
", "abstract": "Carbon dioxide is produced as a by-product of cellular respiration by all aerobic organisms and thus serves for many animals as an important indicator of food, mates, and predators. However, whether free-living terrestrial nematodes such as Caenorhabditis elegans respond to CO2 was unclear. We have demonstrated that adult C. elegans display an acute avoidance response upon exposure to CO2 that is characterized by the cessation of forward movement and the rapid initiation of backward movement. This response is mediated by a cGMP signaling pathway that includes the cGMP-gated heteromeric channel TAX-2/TAX-4. CO2 avoidance is modulated by multiple signaling molecules, including the neuropeptide Y receptor NPR-1 and the calcineurin subunits TAX-6 and CNB-1. Nutritional status also modulates CO2 responsiveness via the insulin and TGF\u03b2 signaling pathways. CO2 response is mediated by a neural circuit that includes the BAG neurons, a pair of sensory neurons of previously unknown function. TAX-2/TAX-4 function in the BAG neurons to mediate acute CO2 avoidance. Our results demonstrate that C. elegans senses and responds to CO2 using multiple signaling pathways and a neural network that includes the BAG neurons and that this response is modulated by the physiological state of the worm.", "date": "2008-06-10", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "105", "number": "23", "publisher": "National Academy of Sciences", "pagerange": "8038-8043", "id_number": "CaltechAUTHORS:HALpnas08", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:HALpnas08", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Helen Hay Whitney Foundation" } ] }, "doi": "10.1073/pnas.0707469105", "pmcid": "PMC2430355", "primary_object": { "basename": "HALpnas08.pdf", "url": "https://authors.library.caltech.edu/records/z9s1c-gmk30/files/HALpnas08.pdf" }, "related_objects": [ { "basename": "HALpnas08movie1.mpg", "url": "https://authors.library.caltech.edu/records/z9s1c-gmk30/files/HALpnas08movie1.mpg" }, { "basename": "HALpnas08movie2.mpg", "url": "https://authors.library.caltech.edu/records/z9s1c-gmk30/files/HALpnas08movie2.mpg" }, { "basename": "HALpnas08sup.pdf", "url": "https://authors.library.caltech.edu/records/z9s1c-gmk30/files/HALpnas08sup.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Hallem, Elissa A. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/3wwmx-n3x66", "eprint_id": 12907, "eprint_status": "archive", "datestamp": "2023-08-19 22:47:52", "lastmod": "2023-10-17 21:14:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Huang-Cui-Qin", "name": { "family": "Huang", "given": "Cui-Qin" } }, { "id": "Gasser-R-B", "name": { "family": "Gasser", "given": "Robin B." } }, { "id": "Cantacessi-C", "name": { "family": "Cantacessi", "given": "Cinzia" } }, { "id": "Nisbet-A-J", "name": { "family": "Nisbet", "given": "Alasdair J." } }, { "id": "Zhong-Weiwei", "name": { "family": "Zhong", "given": "Weiwei" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Loukas-A", "name": { "family": "Loukas", "given": "Alex" } }, { "id": "Mulvenna-J", "name": { "family": "Mulvenna", "given": "Jason" } }, { "id": "Lin-Rui-Qing", "name": { "family": "Lin", "given": "Rui-Qing" } }, { "id": "Chen-Ning", "name": { "family": "Chen", "given": "Ning" } }, { "id": "Zhu-Xing-Quan", "name": { "family": "Zhu", "given": "Xing-Quan" } } ] }, "title": "Genomic-Bioinformatic Analysis of Transcripts Enriched in the Third-Stage Larva of the Parasitic Nematode Ascaris suum", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2008 Huang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: January 8, 2008; Accepted: May 13, 2008; Published: June 18, 2008. Editor: Michael Cappello, Yale Child Health Research Center, United States of America. \n\nThis work was supported by the National Natural Science Foundation of China (grant no. 36071578), International Foundation for Science (grant no. B/4018-1), the Scientific and Technological Programme of Guangdong Province (grant no. 2004B50201020) (XQZ), the Australian Research Council (RBG and AL), the Howard Hughes Medical Institute (PWS), and the National Health and Medical Research Council of Australia (AL and JM). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. \n\nXQZ, RBG, and CC conceived and planned the research, and participated in data collection and analysis. CQH, RBG, CC, AJN, WZ, PWS, AL, JM, RQL, NC, and XQZ analysed the data, and RBG, CC, AJN, WZ, PWS, AL, and JM interpreted the data. All authors contributed to the analyses and to the manuscript. All authors read and approved the final version of the manuscript. \n\nCompeting Interests: The authors have declared that no competing interests exist.\n\nPublished - HUAplosntd08.pdf
Supplemental Material - HUAplosntd08table1.xls
Supplemental Material - HUAplosntd08table2.xls
", "abstract": "Differential transcription in Ascaris suum was investigated using a genomic-bioinformatic approach. A cDNA archive enriched for molecules in the infective third-stage larva (L3) of A. suum was constructed by suppressive-subtractive hybridization (SSH), and a subset of cDNAs from 3075 clones subjected to microarray analysis using cDNA probes derived from RNA from different developmental stages of A. suum. The cDNAs (n = 498) shown by microarray analysis to be enriched in the L3 were sequenced and subjected to bioinformatic analyses using a semi-automated pipeline (ESTExplorer). Using gene ontology (GO), 235 of these molecules were assigned to 'biological process' (n = 68), 'cellular component' (n = 50), or 'molecular function' (n = 117). Of the 91 clusters assembled, 56 molecules (61.5%) had homologues/orthologues in the free-living nematodes Caenorhabditis elegans and C. briggsae and/or other organisms, whereas 35 (38.5%) had no significant similarity to any sequences available in current gene databases. Transcripts encoding protein kinases, protein phosphatases (and their precursors), and enolases were abundantly represented in the L3 of A. suum, as were molecules involved in cellular processes, such as ubiquitination and proteasome function, gene transcription, protein\u2013protein interactions, and function. In silico analyses inferred the C. elegans orthologues/homologues (n = 50) to be involved in apoptosis and insulin signaling (2%), ATP synthesis (2%), carbon metabolism (6%), fatty acid biosynthesis (2%), gap junction (2%), glucose metabolism (6%), or porphyrin metabolism (2%), although 34 (68%) of them could not be mapped to a specific metabolic pathway. Small numbers of these 50 molecules were predicted to be secreted (10%), anchored (2%), and/or transmembrane (12%) proteins. Functionally, 17 (34%) of them were predicted to be associated with (non-wild-type) RNAi phenotypes in C. elegans, the majority being embryonic lethality (Emb) (13 types; 58.8%), larval arrest (Lva) (23.5%) and larval lethality (Lvl) (47%). A genetic interaction network was predicted for these 17 C. elegans orthologues, revealing highly significant interactions for nine molecules associated with embryonic and larval development (66.9%), information storage and processing (5.1%), cellular processing and signaling (15.2%), metabolism (6.1%), and unknown function (6.7%). The potential roles of these molecules in development are discussed in relation to the known roles of their homologues/orthologues in C. elegans and some other nematodes. The results of the present study provide a basis for future functional genomic studies to elucidate molecular aspects governing larval developmental processes in A. suum and/or the transition to parasitism.", "date": "2008-06", "date_type": "published", "publication": "PLoS Neglected Tropical Diseases", "volume": "2", "number": "6", "publisher": "Public Library of Science", "pagerange": "e246", "id_number": "CaltechAUTHORS:HUAplosntd08", "issn": "1935-2735", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:HUAplosntd08", "rights": "This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.", "funders": { "items": [ { "agency": "National Natural Science Foundation of China", "grant_number": "36071578" }, { "agency": "International Foundation for Science", "grant_number": "B/4018-1" }, { "agency": "Scientific and Technological Programme, Guangdong Province", "grant_number": "2004B50201020" }, { "agency": "Australian Research Council" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "National Health and Medical Research Council of Australia" } ] }, "doi": "10.1371/journal.pntd.0000246", "pmcid": "PMC2398786", "primary_object": { "basename": "HUAplosntd08table2.xls", "url": "https://authors.library.caltech.edu/records/3wwmx-n3x66/files/HUAplosntd08table2.xls" }, "related_objects": [ { "basename": "HUAplosntd08.pdf", "url": "https://authors.library.caltech.edu/records/3wwmx-n3x66/files/HUAplosntd08.pdf" }, { "basename": "HUAplosntd08table1.xls", "url": "https://authors.library.caltech.edu/records/3wwmx-n3x66/files/HUAplosntd08table1.xls" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Huang, Cui-Qin; Gasser, Robin B.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/53y4e-rzy84", "eprint_id": 97951, "eprint_status": "archive", "datestamp": "2023-08-22 11:54:54", "lastmod": "2023-10-18 16:54:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Karbowski-J", "name": { "family": "Karbowski", "given": "Jan" } }, { "id": "Schindelman-G", "name": { "family": "Schindelman", "given": "Gary" } }, { "id": "Cronin-C-J", "name": { "family": "Cronin", "given": "Christopher J." } }, { "id": "Seah-A", "name": { "family": "Seah", "given": "Adeline" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Systems level circuit model of C. elegans undulatory locomotion: mathematical modeling and molecular genetics", "ispublished": "pub", "full_text_status": "public", "keywords": "C. elegans; Circuit model for movement; Oscillations; Mechanosensory feedback; GABA; Acetylcholine; Calcium; Myosin; Mutants", "note": "\u00a9 2007 Springer Science+Business Media, LLC. \n\nReceived: 20 April 2007; Revised: 6 July 2007; Accepted: 26 July 2007; Published online: 1 September 2007. \n\nWe thank A. Davies and S. McIntire for slo-1 strains, and J. Kramer for advice on cuticle mutants. The work was supported by the Sloan-Swartz Fellowship (J.K.), by NIH Fellowship (NS043037 to G.S.), by USPHS grant R01-DA018341 (P.W.S.), and by the Howard Hughes Medical Institute, with which P.W.S. is an Investigator.\n\nSupplemental Material - 10827_2007_54_MOESM1_ESM.pdf
", "abstract": "To establish the relationship between locomotory behavior and dynamics of neural circuits in the nematode C. elegans we combined molecular and theoretical approaches. In particular, we quantitatively analyzed the motion of C. elegans with defective synaptic GABA and acetylcholine transmission, defective muscle calcium signaling, and defective muscles and cuticle structures, and compared the data with our systems level circuit model. The major experimental findings are: (1) anterior-to-posterior gradients of body bending flex for almost all strains both for forward and backward motion, and for neuronal mutants, also analogous weak gradients of undulatory frequency, (2) existence of some form of neuromuscular (stretch receptor) feedback, (3) invariance of neuromuscular wavelength, (4) biphasic dependence of frequency on synaptic signaling, and (5) decrease of frequency with increase of the muscle time constant. Based on (1) we hypothesize that the Central Pattern Generator (CPG) is located in the head both for forward and backward motion. Points (1) and (2) are the starting assumptions for our theoretical model, whose dynamical patterns are qualitatively insensitive to the details of the CPG design if stretch receptor feedback is sufficiently strong and slow. The model reveals that stretch receptor coupling in the body wall is critical for generation of the neuromuscular wave. Our model agrees with our behavioral data (3), (4), and (5), and with other pertinent published data, e.g., that frequency is an increasing function of muscle gap-junction coupling.", "date": "2008-06", "date_type": "published", "publication": "Journal of Computational Neuroscience", "volume": "24", "number": "3", "publisher": "Springer", "pagerange": "253-276", "id_number": "CaltechAUTHORS:20190816-110714287", "issn": "0929-5313", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190816-110714287", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech Division of Biology" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "NS043037" }, { "agency": "NIH", "grant_number": "R01-DA018341" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Sloan-Swartz Foundation" } ] }, "doi": "10.1007/s10827-007-0054-6", "primary_object": { "basename": "10827_2007_54_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/53y4e-rzy84/files/10827_2007_54_MOESM1_ESM.pdf" }, "resource_type": "article", "pub_year": "2008", "author_list": "Karbowski, Jan; Schindelman, Gary; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/sn0ag-5wc68", "eprint_id": 9640, "eprint_status": "archive", "datestamp": "2023-08-22 10:51:49", "lastmod": "2023-10-16 22:24:04", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Rogers-A", "name": { "family": "Rogers", "given": "Anthony" } }, { "id": "Antoshechkin-I-A", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Bieri-T", "name": { "family": "Bieri", "given": "Tamberlyn" } }, { "id": "Blasiar-D", "name": { "family": "Blasiar", "given": "Darin" } }, { "id": "Bastiani-C-A", "name": { "family": "Bastiani", "given": "Carol" } }, { "id": "Canaran-P", "name": { "family": "Canaran", "given": "Payan" } }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "Chen-Wen-J", "name": { "family": "Chen", "given": "Wen J." } }, { "id": "Davis-P-M", "name": { "family": "Davis", "given": "Paul" } }, { "id": "Fernandes-J-S", "name": { "family": "Fernandes", "given": "Jolene" } }, { "id": "Fiedler-T-J", "name": { "family": "Fiedler", "given": "Tristan J." } }, { "id": "Han-Michael", "name": { "family": "Han", "given": "Michael" } }, { "id": "Harris-T-W", "name": { "family": "Harris", "given": "Todd W." }, "orcid": "0000-0003-3406-163X" }, { "id": "Kishore-R", "name": { "family": "Kishore", "given": "Ranjana" } }, { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "Raymond" }, "orcid": "0000-0002-8151-7479" }, { "id": "McKay-S", "name": { "family": "McKay", "given": "Sheldon" } }, { "id": "M\u00fcller-H-M", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } }, { "id": "Nakamura-Cecilia", "name": { "family": "Nakamura", "given": "Cecilia" }, "orcid": "0000-0002-4689-7314" }, { "id": "Ozersky-P", "name": { "family": "Ozersky", "given": "Philip" } }, { "id": "Petcherski-A", "name": { "family": "Petcherski", "given": "Andrei" } }, { "id": "Schindelman-G", "name": { "family": "Schindelman", "given": "Gary" } }, { "id": "Schwarz-E-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Spooner-W", "name": { "family": "Spooner", "given": "Will" } }, { "id": "Tuli-M-A", "name": { "family": "Tuli", "given": "Mary Ann" } }, { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Wang-Daniel", "name": { "family": "Wang", "given": "Daniel" } }, { "id": "Wang-Xiaodong", "name": { "family": "Wang", "given": "Xiaodong" } }, { "id": "Williams-G", "name": { "family": "Williams", "given": "Gary" } }, { "id": "Yook-Karen-J", "name": { "family": "Yook", "given": "Karen" }, "orcid": "0000-0002-4457-6787" }, { "id": "Durbin-R", "name": { "family": "Durbin", "given": "Richard" } }, { "id": "Stein-L-D", "name": { "family": "Stein", "given": "Lincoln D." }, "orcid": "0000-0002-1983-4588" }, { "id": "Spieth-J", "name": { "family": "Spieth", "given": "John" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "WormBase 2007", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2007 The Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived September 13, 2007. Revised October 18, 2007. Accepted October 18, 2007. Nucleic Acids Research Advance Access originally published online on November 8, 2007. \n\nWormBase is supported by grant P41-HG02223 from the US National Human Genome Research Institute and the British Medical Research Council. P.W.S. is an investigator with the Howard Hughes Medical Institute. Funding to pay the Open Access publication charges for this article was provided by grant P41-HG02223 from the US National Human Genome Research Institute. \n\nConflict of interest statement. None declared.\n\nPublished - ROGnar08.pdf
", "abstract": "WormBase (www.wormbase.org) is the major publicly available database of information about Caenorhabditis elegans, an important system for basic biological and biomedical research. Derived from the initial ACeDB database of C. elegans genetic and sequence information, WormBase now includes the genomic, anatomical and functional information about C. elegans, other Caenorhabditis species and other nematodes. As such, it is a crucial resource not only for C. elegans biologists but the larger biomedical and bioinformatics communities. Coverage of core areas of C. elegans biology will allow the biomedical community to make full use of the results of intensive molecular genetic analysis and functional genomic studies of this organism. Improved search and display tools, wider cross-species comparisons and extended ontologies are some of the features that will help scientists extend their research and take advantage of other nematode species genome sequences.", "date": "2008-01", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "36", "number": "Supple", "publisher": "Oxford University Press", "pagerange": "D612-D617", "id_number": "CaltechAUTHORS:ROGnar08", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:ROGnar08", "rights": "This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P41-HG02223" }, { "agency": "Medical Research Council (UK)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1093/nar/gkm975", "pmcid": "PMC2238927", "primary_object": { "basename": "ROGnar08.pdf", "url": "https://authors.library.caltech.edu/records/sn0ag-5wc68/files/ROGnar08.pdf" }, "resource_type": "article", "pub_year": "2008", "author_list": "Rogers, Anthony; Antoshechkin, Igor; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ab6f9-jy197", "eprint_id": 18033, "eprint_status": "archive", "datestamp": "2023-08-22 10:27:20", "lastmod": "2023-10-20 15:31:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Green-J-L", "name": { "family": "Green", "given": "Jennifer L." } }, { "id": "Inoue-T", "name": { "family": "Inoue", "given": "Takao" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The C. Elegans ROR receptor tyrosine kinase, CAM-1, non-autonomously inhibits the Wnt pathway", "ispublished": "pub", "full_text_status": "public", "keywords": "ROR, CAM-1; Wnt; Vulva; Patterning; CRD; Organogenesis; Morphogen", "note": "\u00a9 2007 Company of Biologists. \n\nAccepted August 25, 2007.\n\nWe thank Gladys Medina and Barbara Perry for technical assistance and members of the Sternberg laboratory for helpful discussions. For reagents and worms we thank W. Forrester, C. Wu, A. Fire, A. V. Maricq, M. Francis, D.\nSherwood, I. Greenwald and H. Sawa. Some Nematode strains were from the Caenorhabditis Genetics Center, funded by the NIH National Center for Research Resources. We thank Cheryl Van Buskirk, Ryan Baugh, Jagan Srinivasan and Mihoko Kato for critically reading the manuscript; the Benzer laboratory (especially Gil Carvallo) for use of their microplate spectrophotometer; the Hay laboratory for use of their tissue culture hood; Jost Vielmetter and Inderjit Nangiana of the Caltech Protein Expression Facility\nfor production of CRD-AP conditioned media; and Julie Gleason for kindly exchanging lin-17 and mom-5 mutant alleles. P.W.S. is an investigator with the Howard Hughes Medical Institute and J.L.G. was supported by the Thomas\nHunt Morgan Fellowship for graduate study toward the doctor of philosophy degree in biology at the California Institute of Technology.\n\nPublished - GREdev07.pdf
Supplemental Material - DEV005363-FigS1.jpg
Supplemental Material - DEV005363tables_1-3.pdf
", "abstract": "Inhibitors of Wnt signaling promote normal development and prevent cancer by restraining when and where the Wnt pathway is activated. ROR proteins, a class of Wnt-binding receptor tyrosine kinases, inhibit Wnt signaling by an unknown mechanism. To clarify how RORs inhibit the Wnt pathway, we examined the relationship between Wnts and the sole C. elegans ROR homolog, cam-1, during C. elegans vulval development, a Wnt-regulated process. We found that loss and overexpression of cam-1 causes reciprocal defects in Wnt-mediated cell-fate specification. Our molecular and genetic analyses revealed that the CAM-1 extracellular domain (ECD) is sufficient to non-autonomously antagonize multiple Wnts, suggesting that the CAM-1/ROR ECD sequesters Wnts. A sequestration model is supported by our findings that the CAM-1 ECD binds to several Wnts in vitro. These results demonstrate how ROR proteins help to refine the spatial pattern of Wnt activity in a complex multicellular environment.", "date": "2007-11-15", "date_type": "published", "publication": "Development", "volume": "134", "number": "22", "publisher": "Company of Biologists", "pagerange": "4053-4062", "id_number": "CaltechAUTHORS:20100421-095202544", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100421-095202544", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Thomas Hunt Morgan Fellowship" } ] }, "doi": "10.1242/dev.005363", "primary_object": { "basename": "DEV005363-FigS1.jpg", "url": "https://authors.library.caltech.edu/records/ab6f9-jy197/files/DEV005363-FigS1.jpg" }, "related_objects": [ { "basename": "DEV005363tables_1-3.pdf", "url": "https://authors.library.caltech.edu/records/ab6f9-jy197/files/DEV005363tables_1-3.pdf" }, { "basename": "GREdev07.pdf", "url": "https://authors.library.caltech.edu/records/ab6f9-jy197/files/GREdev07.pdf" }, { "basename": "medium.png", "url": "https://authors.library.caltech.edu/records/ab6f9-jy197/files/medium.png" }, { "basename": "small.png", "url": "https://authors.library.caltech.edu/records/ab6f9-jy197/files/small.png" } ], "resource_type": "article", "pub_year": "2007", "author_list": "Green, Jennifer L.; Inoue, Takao; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/7hg5y-3v977", "eprint_id": 95470, "eprint_status": "archive", "datestamp": "2023-08-19 21:04:53", "lastmod": "2023-10-20 20:16:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Inoue-Takao", "name": { "family": "Inoue", "given": "Takao" } }, { "id": "Ailion-M", "name": { "family": "Ailion", "given": "Michael" } }, { "id": "Poon-S", "name": { "family": "Poon", "given": "Shirley" } }, { "id": "Kim-Hannah-K", "name": { "family": "Kim", "given": "Hannah K." } }, { "id": "Thomas-J-H", "name": { "family": "Thomas", "given": "James H." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Genetic Analysis of Dauer Formation in Caenorhabditis briggsae", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2007 by the Genetics Society of America. \n\nManuscript received July 13, 2007; Accepted for publication July 18, 2007. \n\nWe thank R. Johnsen and D. Baillie for C. briggsae mutants and mapping data. We thank S. Gharib and B. P. Gupta for technical assistance and useful reagents. We thank E. Hallem, X. Wang, and J. Srinivasan for comments on the manuscript. T.I. was supported by fellowship DRG-1646 from the Damon Runyon Cancer Research Foundation. This work was supported by HHMI, where P.W.S. is an investigator. Some nematode strains used in this work were provided by the Caenorhabditis Genetics Center, which is funded by the National Institutes of Health National Center for Research Resources (NCRR).\n\nPublished - GEN1772809.pdf
", "abstract": "Molecular changes that underlie evolutionary changes in behavior and physiology are not well understood. Dauer formation in Caenorhabditis elegans is a temperature-sensitive process controlled through a network of signaling pathways associated with sensory neurons and is potentially an excellent system in which to investigate molecular changes in neuronal function during evolution. To begin to investigate the evolution of dauer formation in the genus Caenorhabditis at the molecular level, we isolated dauer-formation mutations in C. briggsae, a species closely related to the model organism C. elegans. We identified mutations in orthologs of C. elegans genes daf-2 (insulin receptor), daf-3 (Smad), and daf-4 (TGF-\u03b2 type 2 receptor), as well as genes required for formation of sensory cilia. Phenotypic analyses revealed that functions of these genes are conserved between C. elegans and C. briggsae. Analysis of C. briggsae mutations also revealed a significant difference between the two species in their responses to high temperatures (>26\u00b0). C. elegans is strongly induced to form dauers at temperatures above 26\u00b0, near the upper limit for growth of C. elegans. In contrast, C. briggsae, which is capable of growth at higher temperatures than C. elegans, lacks this response.", "date": "2007-10-01", "date_type": "published", "publication": "Genetics", "volume": "177", "number": "2", "publisher": "Genetics Society of America", "pagerange": "809-818", "id_number": "CaltechAUTHORS:20190514-084400196", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-084400196", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Damon Runyon Cancer Research Foundation", "grant_number": "DRG-1646" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH" } ] }, "doi": "10.1534/genetics.107.078857", "pmcid": "PMC2034645", "primary_object": { "basename": "GEN1772809.pdf", "url": "https://authors.library.caltech.edu/records/7hg5y-3v977/files/GEN1772809.pdf" }, "resource_type": "article", "pub_year": "2007", "author_list": "Inoue, Takao; Ailion, Michael; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/9f1e3-zee81", "eprint_id": 55862, "eprint_status": "archive", "datestamp": "2023-08-19 21:02:44", "lastmod": "2023-10-20 23:19:16", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Van-Buskirk-C", "name": { "family": "Van Buskirk", "given": "Cheryl" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Epidermal growth factor signaling induces behavioral quiescence in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2007 Nature Publishing Group;\n\nReceived 9 July; accepted 17 August; published online 23 September 2007.\n\nWe thank the Caenorhabditis Genetics Center for providing strains, S. Kim\n(Stanford University School of Medicine) for anti-LET-23 antibody, J. DeModena for antibody staining, S. Xu (Univ. Michigan) for the plc-3(sy698) allele, S. Mitani (Tokyo Women's Medical University School of Medicine) for the\nplc-3(tm1340) allele, N. Moghal, M. Kato, and S. Xu for critical reading of the\nmanuscript, and C.J. Cronin for help with the automated tracking system and\nlocomotion data analysis. This work was supported by a California Breast Cancer Research Program fellowship to C.V.B., by a US National Institute on Drug Abuse grant (DA018341) to P.W.S., and by the Howard Hughes Medical Institute, with which C.V.B. is an Associate and P.W.S. is an Investigator.\n\nAuthor Contributions: C.V.B. designed and conducted the experiments and wrote the manuscript; P.W.S. supervised the project.", "abstract": "The epidermal growth factor receptor (EGFR)/ErbB receptor tyrosine kinases regulate several aspects of development, including the development of the mammalian nervous system. ErbB signaling also has physiological effects on neuronal function, with influences on synaptic plasticity and daily cycles of activity. However, little is known about the effectors of EGFR activation in neurons. Here we show that EGF signaling has a nondevelopmental effect on behavior in Caenorhabditis elegans. Ectopic expression of the EGF-like ligand LIN-3 at any stage induces a reversible cessation of feeding and locomotion. These effects are mediated by neuronal EGFR (also called LET-23) and phospholipase C-\u03b3 (PLC-\u03b3), diacylglycerol-binding proteins, and regulators of synaptic vesicle release. Activation of EGFR within a single neuron, ALA, is sufficient to induce a quiescent state. This pathway modulates the cessation of pharyngeal pumping and locomotion that normally occurs during the lethargus period that precedes larval molting. Our results reveal an evolutionarily conserved role for EGF signaling in the regulation of behavioral quiescence.", "date": "2007-10", "date_type": "published", "publication": "Nature Neuroscience", "volume": "10", "number": "10", "publisher": "Nature Publishing Group", "pagerange": "1300-1307", "id_number": "CaltechAUTHORS:20150317-140501183", "issn": "1097-6256", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150317-140501183", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "California Breast Cancer Research Program" }, { "agency": "National Institute on Drug Abuse (NIDA)", "grant_number": "DA018341" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1038/nn1981", "resource_type": "article", "pub_year": "2007", "author_list": "Van Buskirk, Cheryl and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/3rg9x-web04", "eprint_id": 12698, "eprint_status": "archive", "datestamp": "2023-08-19 20:58:00", "lastmod": "2023-10-17 20:26:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhong-W", "name": { "family": "Zhong", "given": "Weiwei" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Automated data integration for developmental biological research", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Company of Biologists Ltd 2007. \n\nMany of the model organism databases and the Gene Ontology Consortium that are crucial to data integration are supported by the National Human Genome Research Institute (e.g. WormBase grant HG02223 to P.W.S. and Gene Ontology Consortium grant HG002273 to Judith Blake). We thank Min Han for communicating unpublished results, and Alok Saldanha, Erich Schwarz, Xiaodong Wang and anonymous reviewers for comments on the manuscript. Relevant genetics research in our laboratory is supported by the Howard Hughes Medical Institute, with which P.W.S. is an Investigator and W.Z. an Associate.\n\nPublished - ZHOdev07.pdf
", "abstract": "In an era exploding with genome-scale data, a major challenge for developmental biologists is how to extract significant clues from these publicly available data to benefit our studies of individual genes, and how to use them to improve our understanding of development at a systems level. Several studies have successfully demonstrated new approaches to classic developmental questions by computationally integrating various genome-wide data sets. Such computational approaches have shown great potential for facilitating research: instead of testing 20,000 genes, researchers might test 200 to the same effect. We discuss the nature and state of this art as it applies to developmental research.", "date": "2007-09-15", "date_type": "published", "publication": "Development", "volume": "134", "number": "18", "publisher": "Company of Biologists", "pagerange": "3227-3238", "id_number": "CaltechAUTHORS:ZHOdev07", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:ZHOdev07", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Human Genome Research Institute", "grant_number": "HG02223" }, { "agency": "National Human Genome Research Institute", "grant_number": "HG002273" }, { "agency": "Howard Hughes Medical Institute" } ] }, "doi": "10.1242/dev.001073", "primary_object": { "basename": "ZHOdev07.pdf", "url": "https://authors.library.caltech.edu/records/3rg9x-web04/files/ZHOdev07.pdf" }, "resource_type": "article", "pub_year": "2007", "author_list": "Zhong, Weiwei and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/gd7gx-m1q67", "eprint_id": 8693, "eprint_status": "archive", "datestamp": "2023-08-22 09:58:26", "lastmod": "2023-10-16 21:39:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ciche-T-A", "name": { "family": "Ciche", "given": "Todd A." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Postembryonic RNAi in Heterorhabditis bacteriophora: a nematode insect parasite and host for insect pathogenic symbionts", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2007 Ciche and Sternberg, licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nWe graciously thank Prof. Ann Burnell (National University of Ireland-Maynooth) for communicating her then unpublished EST data. T.A. Ciche was supported by a fellowship from the Gordon Ross Foundation. Supported by the Howard Hughes Medical Institute, with which P.W. Sternberg is an Investigator. \n\nAuthors' contributions: T.A. Ciche designed and performed all experiments and wrote the paper. P.W. Sternberg mentored T.A. Ciche during these experiments by providing valuable advice, laboratory space and resources, and edited the paper. Both authors have read and approved the final version. \n\nAccession numbers: The accession numbers (Genbank, dbEST) for H. bacteriophora ESTs used in this study are: EE724174 (Hba-cct-2); EE724171-73 (Hba-daf-21); EE724162, EE724228 (Hba-icd-1); EE724163-64 (Hba-nol-5); EE724167-68 (Hba-W01G7.3); EE724169-70 (Hba-arf-1); EE724158-61, EE724188, EE724199, EE7241206-09 (Hba-rack-1); EE724165-66 (Hba-ben-1); EE724176 (Hba-mrp-4); EE724175 (Hba-nhr-47).\n\nPublished - CICbmcdb07.pdf
", "abstract": "Background: Heterorhabditis bacteriophora is applied throughout the world for the biological control of insects and is an animal model to study interspecies interactions, e.g. mutualism, parasitism and vector-borne disease. H. bacteriophora nematodes are mutually associated with the insect pathogen, Photorhabdus luminescens. The developmentally arrested infective juvenile (IJ) stage nematode (vector) specifically transmits Photorhabdus luminescens bacteria (pathogen) in its gut mucosa to the haemocoel of insects (host). The nematode vector and pathogen alone are not known to cause insect disease. RNA interference is an excellent reverse genetic tool to study gene function in C. elegans, and it would be useful in H. bacteriophora to exploit the H. bacteriophora genome project, currently in progress. \n\nResults: Soaking L1 stage H. bacteriophora with seven dsRNAs of genes whose C. elegans orthologs had severe RNAi phenotypes resulted in highly penetrant and obvious developmental and reproductive abnormalities. The efficacy of postembryonic double strand RNA interference (RNAi) was evident by abnormal gonad morphology and sterility of adult H. bacteriophora and C. elegans presumable due to defects in germ cell proliferation and gonad development. The penetrance of RNAi phenotypes in H. bacteriophora was high for five genes (87-100%; Hba-cct-2, Hba-daf-21, Hba-icd-1; Hba-nol-5, and Hba-W01G7.3) and moderate for two genes (usually 30-50%; Hba-rack-1 and Hba-arf-1). RNAi of three additional C. elegans orthologs for which RNAi phenotypes were not previously detected in C. elegans, also did not result in any apparent phenotypes in H. bacteriophora. Specific and severe reduction in transcript levels in RNAi treated L1s was determined by quantitative real-time RT-PCR. These results suggest that postembryonic RNAi by soaking is potent and specific. \n\nConclusion: Although RNAi is conserved in animals and plants, RNAi using long dsRNA is not. These results demonstrate that RNAi can be used effectively in H. bacteriophora and can be applied for analyses of nematode genes involved in symbiosis and parasitism. It is likely that RNAi will be an important tool for functional genomics utilizing the high quality draft H. bacteriophora genome sequence.", "date": "2007-09-05", "date_type": "published", "publication": "BMC Developmental Biology", "volume": "7", "publisher": "BioMed Central", "pagerange": "Art. No. 101", "id_number": "CaltechAUTHORS:CICbmcdb07", "issn": "1471-213X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:CICbmcdb07", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Gordon Ross Medical Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1186/1471-213X-7-101", "pmcid": "PMC2014770", "primary_object": { "basename": "CICbmcdb07.pdf", "url": "https://authors.library.caltech.edu/records/gd7gx-m1q67/files/CICbmcdb07.pdf" }, "resource_type": "article", "pub_year": "2007", "author_list": "Ciche, Todd A. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/qnwkd-1xs68", "eprint_id": 55861, "eprint_status": "archive", "datestamp": "2023-08-19 20:32:24", "lastmod": "2023-10-20 23:19:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Antoshechkin-I-A", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The versatile worm: genetic and genomic resources for Caenorhabditis elegans research", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2007 Nature Publishing Group.\n\nPublished online 5 June 2007.\n\nWe thank G. Schindelman for helpful discussions and assistance. I.A. is supported by a grant to WormBase from the US National Human Genome Research Institute (P41-HG02223). P.W.S. is an investigator with the Howard Hughes Medical Institute, Pasadena, USA.", "abstract": "Since its establishment as a model organism, Caenorhabditis elegans has been an invaluable tool for biological research. An immense spectrum of questions can be addressed using this small nematode, making it one of the most versatile and exciting model organisms. Although the many tools and resources developed by the C. elegans community greatly facilitate new discoveries, they can also overwhelm newcomers to the field. This Review aims to familiarize new worm researchers with the main resources, and help them to select the tools that are best suited for their needs. We also hope that it will be helpful in identifying new research opportunities and will promote the development of additional resources.", "date": "2007-07", "date_type": "published", "publication": "Nature Reviews. Genetics", "volume": "8", "number": "7", "publisher": "Nature Publishing Group", "pagerange": "518-532", "id_number": "CaltechAUTHORS:20150317-133558278", "issn": "1471-0056", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150317-133558278", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P41-HG02223" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "National Human Genome Research Institute" } ] }, "doi": "10.1038/nrg2105", "resource_type": "article", "pub_year": "2007", "author_list": "Antoshechkin, Igor and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/k26bk-rza26", "eprint_id": 8378, "eprint_status": "archive", "datestamp": "2023-08-22 08:56:45", "lastmod": "2023-10-16 21:27:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Modzelewska-K", "name": { "family": "Modzelewska", "given": "Katarzyna" } }, { "id": "Elgort-M-G", "name": { "family": "Elgort", "given": "Marc G." } }, { "id": "Huang-Jingyu", "name": { "family": "Huang", "given": "Jingyu" } }, { "id": "Jongeward-G", "name": { "family": "Jongeward", "given": "Gregg" } }, { "id": "Lauritzen-A", "name": { "family": "Lauritzen", "given": "Amara" } }, { "id": "Yoon-Charles-H", "name": { "family": "Yoon", "given": "Charles H." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Moghal-N", "name": { "family": "Moghal", "given": "Nadeem" } } ] }, "title": "An Activating Mutation in sos-1 Identifies Its Dbl Domain as a Critical Inhibitor of the Epidermal Growth Factor Receptor Pathway during Caenorhabditis elegans Vulval Development", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2007, American Society for Microbiology. \n\nReceived 1 September 2006/ Returned for modification 7 November 2006/ Accepted 15 February 2007 / Published ahead of print on 5 March 2007. \n\nWe thank Ben Neel for the hSOS1 cDNA clone and the hemagglutinin (HA)-ERK1 expression vector, Steve Lessnick for HEK 293 EBNA cells and polyethylenimine, and David Virshup for NIH 3T3 cells. We also thank Steve Lessnick, Don Ayer, Scott Kuwada, and members of the Moghal laboratory for critically reading the manuscript and Tommy Wong and Suzanne Elgort for help with figures. We also thank the reviewers for their insightful comments/criticisms about the manuscript. Some nematode strains used in this work were provided by the Caenorhabditis Genetics Center, which is funded by the NIH National Center for Research Resources (NCRR). We thank the C. elegans Reverse Genetics Core Facility at the University of British Columbia, which is part of the International C. elegans Gene Knockout Consortium, for providing the rac-2(ok326) deletion mutant. \n\nThis research was supported by Public Health Services grant R01 GM073184 from the National Institutes of Health to N.M. and the Howard Hughes Medical Institute, for which P.W.S. is an Investigator.\n\nPublished - MODmcb07.pdf
", "abstract": "Proper regulation of receptor tyrosine kinase (RTK)-Ras-mitogen-activated protein kinase (MAPK) signaling pathways is critical for normal development and the prevention of cancer. SOS is a dual-function guanine nucleotide exchange factor (GEF) that catalyzes exchange on Ras and Rac. Although the physiologic role of SOS and its CDC25 domain in RTK-mediated Ras activation is well established, the in vivo function of its Dbl Rac GEF domain is less clear. We have identified a novel gain-of-function missense mutation in the Dbl domain of Caenorhabditis elegans SOS-1 that promotes epidermal growth factor receptor (EGFR) signaling in vivo. Our data indicate that a major developmental function of the Dbl domain is to inhibit EGF-dependent MAPK activation. The amount of inhibition conferred by the Dbl domain is equal to that of established trans-acting inhibitors of the EGFR pathway, including c-Cbl and RasGAP, and more than that of MAPK phosphatase. In conjunction with molecular modeling, our data suggest that the C. elegans mutation, as well as an equivalent mutation in human SOS1, activates the MAPK pathway by disrupting an autoinhibitory function of the Dbl domain on Ras activation. Our work suggests that functionally similar point mutations in humans could directly contribute to disease.", "date": "2007-05", "date_type": "published", "publication": "Molecular and Cellular Biology", "volume": "27", "number": "10", "publisher": "American Society for Microbiology", "pagerange": "3695-3707", "id_number": "CaltechAUTHORS:MODmcb07", "issn": "0270-7306", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:MODmcb07", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 GM073184" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1128/MCB.01630-06", "pmcid": "PMC1899997", "primary_object": { "basename": "MODmcb07.pdf", "url": "https://authors.library.caltech.edu/records/k26bk-rza26/files/MODmcb07.pdf" }, "resource_type": "article", "pub_year": "2007", "author_list": "Modzelewska, Katarzyna; Elgort, Marc G.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/mrn24-f4h91", "eprint_id": 8063, "eprint_status": "archive", "datestamp": "2023-08-22 08:46:45", "lastmod": "2023-10-23 16:21:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Fernandes-J-S", "name": { "family": "Fernandes", "given": "Jolene S." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The tailless Ortholog nhr-67 Regulates Patterning of Gene Expression and Morphogenesis in the C. elegans Vulva", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2007 Fernandes and Sternberg. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: December 1, 2006; Accepted: March 16, 2007; Published: April 27, 2007. \n\nWe thank Minqin Wang for strain constructions; Helen Chamberlin for the guEx64 strain; the Fire lab for GFP vectors; Nathalie Pujol for the pNP10 plasmid; and Andrew Udit, Mihoko Kato, Gladys Medina, and Barbara Perry for technical assistance. The nhr-67 deletion allele (ok631) and kuIs36 was provided by the C. elegans Genetic Center. We also thank Elissa Hallem, Takao Inoue, Steven Kuntz, Ted Ririe, Erich Schwarz, Adeline Seah, and Weiwei Zhong for comments on the manuscript. \n\nAuthor contributions. JSF and PWS conceived and designed the experiments, analyzed the data, and wrote the paper. JSF performed the experiments. \n\nThe authors were supported by the Howard Hughes Medical Institute of which PWS is an investigator. \n\nThe authors have declared that no competing interests exist. \n\nThe WormBase Gene IDs (www.wormbase.org) as well as the Refseq accession numbers (www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide) for the genes described in this study are ajm-1:WBGene00000100 (NM_077135; NM_077137; NM_077136; NM_171966); cdh-3:WBGene00000395 (NM_066286); ceh-2:WBGene00000429 (NM_059345); cog-1:WBGene00000584 (NM_182115); eff-1:WBGene00001159 (NM_001026819); egl-17:WBGene00001185( NM_075706); egl-26:WBGene00001193 (NM_061251); egl-38:WBGene00001204 (NM_069435); lin-3:WBGene00002992 (NM_171418;NM_171919;NM_171918); lin-11:WBGene00003000 (NM_060295); nhr-67: WBGene00003657 (NM_069693); pax-2:WBGene00003938 (NM_068112); unc-53: WBGene00006788 (NM_001027000;NM_001026999); and zmp-1:WBGene00006987 (NM_171138).\n\nPublished - FERplosg07.pdf
", "abstract": "Regulation of spatio-temporal gene expression in diverse cell and tissue types is a critical aspect of development. Progression through Caenorhabditis elegans vulval development leads to the generation of seven distinct vulval cell types (vulA, vulB1, vulB2, vulC, vulD, vulE, and vulF), each with its own unique gene expression profile. The mechanisms that establish the precise spatial patterning of these mature cell types are largely unknown. Dissection of the gene regulatory networks involved in vulval patterning and differentiation would help us understand how cells generate a spatially defined pattern of cell fates during organogenesis. We disrupted the activity of 508 transcription factors via RNAi and assayed the expression of ceh-2, a marker for vulB fate during the L4 stage. From this screen, we identified the tailless ortholog nhr-67 as a novel regulator of gene expression in multiple vulval cell types. We find that one way in which nhr-67 maintains cell identity is by restricting inappropriate cell fusion events in specific vulval cells, namely vulE and vulF. nhr-67 exhibits a dynamic expression pattern in the vulval cells and interacts with three other transcriptional regulators cog-1 (Nkx6.1/6.2), lin-11 (LIM), and egl-38 (Pax2/5/8) to generate the composite expression patterns of their downstream targets. We provide evidence that egl-38 regulates gene expression in vulB1, vulC, vulD, vulE, as well as vulF cells. We demonstrate that the pairwise interactions between these regulatory genes are complex and vary among the seven cell types. We also discovered a striking regulatory circuit that affects a subset of the vulval lineages: cog-1 and nhr-67 inhibit both one another and themselves. We postulate that the differential levels and combinatorial patterns of lin-11, cog-1, and nhr-67 expression are a part of a regulatory code for the mature vulval cell types.", "date": "2007-04", "date_type": "published", "publication": "PLoS Genetics", "volume": "3", "number": "4", "publisher": "Public Library of Science", "pagerange": "603-616", "id_number": "CaltechAUTHORS:FERplosg07", "issn": "1553-7390", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:FERplosg07", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "pmcid": "PMC1857733", "primary_object": { "basename": "FERplosg07.pdf", "url": "https://authors.library.caltech.edu/records/mrn24-f4h91/files/FERplosg07.pdf" }, "resource_type": "article", "pub_year": "2007", "author_list": "Fernandes, Jolene S. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/rfg8t-zs711", "eprint_id": 11719, "eprint_status": "archive", "datestamp": "2023-08-22 08:32:24", "lastmod": "2023-10-17 15:30:18", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hwang-B-J", "name": { "family": "Hwang", "given": "Byung Joon" } }, { "id": "Meruelo-A-D", "name": { "family": "Meruelo", "given": "Alejandro D." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "C. elegans EVI1 proto-oncogene, EGL-43, is necessary for Notch-mediated cell fate specification and regulates cell invasion", "ispublished": "pub", "full_text_status": "public", "keywords": "EGL-43, HLH-2, FOS-1, LIN-12/Notch, Cell fate specification, Cell invasion", "note": "Published by The Company of Biologists 2007. \n\nAccepted 30 November 2006. First published online 10 January 2007. \n\nWe thank C. Van Buskirk, G.B. Choi, J. Fernandes, E. Hallem, M. Kato, C. Robinson, and G. Schindelman for carefully reading the manuscript; J. DeModena for Ab staining; S. Gharib for help with the RNAi screen; S. Mitani at Tokyo Women's Medical University for the egl-43(tm1802) strain; J. Kimble at the University of Wisconsin-Madison and Michael Krause at NIH for LAG-3 (SEL-8) and HLH-2 antibodies; M. H. Lee at the University of Wisconsin-Madison for helping with the ChIP assay; and B. Gupta, H.-M. Muller, A. Saldanha, E. Schwarz, and L. Warren for discussions about ClusterSearch. P.W.S. is an investigator of the Howard Hughes Medical Institute. B.J.H. is supported by a NHGRI/NIH Genome Scholar Development and Faculty Transition Award (K22HG02907-02). The development of ClusterSearch was supported in part by the Caltech/SURF award from Dr Ashley to A.D.M. \n\nSupplementary material for this article is available at http://dev.biologists.org/cgi/content/full/134/4/669.\n\nPublished - HWAdev07.pdf
Supplemental Material - HWAdev07supp.pdf
", "abstract": "During C. elegans development, LIN-12 (Notch) signaling specifies the anchor cell (AC) and ventral uterine precursor cell (VU) fates from two equivalent pre-AC/pre-VU cells in the hermaphrodite gonad. Once specified, the AC induces patterned proliferation of vulva via expression of LIN-3 (EGF) and then invades into the vulval epithelium. Although these cellular processes are essential for the proper organogenesis of vulva and appear to be temporally regulated, the mechanisms that coordinate the processes are not well understood. We computationally identified egl-43 as a gene likely to be expressed in the pre-AC/pre-VU cells and the AC, based on the presence of an enhancer element similar to the one that transcribes lin-3 in the same cells. Genetic epistasis analyses reveal that egl-43 acts downstream of or parallel to lin-12 in AC/VU cell fate specification at an early developmental stage, and functions downstream of fos-1 as well as upstream of zmp-1 and him-4 to regulate AC invasion at a later developmental stage. Characterization of the egl-43 regulatory region suggests that EGL-43 is a direct target of LIN-12 and HLH-2 (E12/47), which is required for the specification of the VU fate during AC/VU specification. EGL-43 also regulates basement membrane breakdown during AC invasion through a FOS-1-responsive regulatory element that drives EGL-43 expression in the AC and VU cells at the later stage. Thus, egl-43 integrates temporally distinct upstream regulatory events and helps program cell fate specification and cell invasion.", "date": "2007-02-15", "date_type": "published", "publication": "Development", "volume": "134", "number": "4", "publisher": "Company of Biologists", "pagerange": "669-679", "id_number": "CaltechAUTHORS:HWAdev07", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:HWAdev07", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute" }, { "agency": "National Institutes of Health", "grant_number": "K22HG02907-02" }, { "agency": "Summer Ungraduate Research Fund (SURF), Caltech" } ] }, "doi": "10.1242/dev.02769", "primary_object": { "basename": "HWAdev07.pdf", "url": "https://authors.library.caltech.edu/records/rfg8t-zs711/files/HWAdev07.pdf" }, "related_objects": [ { "basename": "HWAdev07supp.pdf", "url": "https://authors.library.caltech.edu/records/rfg8t-zs711/files/HWAdev07supp.pdf" } ], "resource_type": "article", "pub_year": "2007", "author_list": "Hwang, Byung Joon; Meruelo, Alejandro D.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/wkfr0-csh30", "eprint_id": 64115, "eprint_status": "archive", "datestamp": "2023-08-19 19:41:53", "lastmod": "2023-10-17 19:31:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kee-Yun", "name": { "family": "Kee", "given": "Yun" } }, { "id": "Hwang-Byung-Joon", "name": { "family": "Hwang", "given": "Byung Joon" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Bronner-M-E", "name": { "family": "Bronner-Fraser", "given": "Marianne" }, "orcid": "0000-0003-4274-1862" } ] }, "title": "Evolutionary conservation of cell migration genes: from nematode neurons to vertebrate neural crest", "ispublished": "pub", "full_text_status": "public", "keywords": "Neural crest, cell migration, C. elegans HSN, comparative genomic analysis", "note": "\u00a9 2007 by Cold Spring Harbor Laboratory Press. The Authors acknowledge that six months after the full-issue publication date, the Article will be distributed under a Creative Commons CC-BY-NC License (Attribution-NonCommercial 4.0 International License, http://creativecommons.org/licenses/by-nc/4.0/). \n\nReceived November 7, 2006; revised version accepted January 9, 2007.\n\nWe thank Samuel Ki for technical assistance and colleagues in the M.B.-F. laboratory for technical advice and discussion. We especially thank Drs. Titus Brown, Scott Fraser, Mihoko Kato, Daniel Meulemans, Ellen Rothenberg, Tatjana Sauka-Spengler, Erich Schwarz, and J.K. Sky\nYu for helpful discussions on the manuscript, and Drs. Dominique Alfandari, Tamara Allison, Rik Derynck, Todd Evans, Cees Oudejans, and Richard Harland for sharing the constructs. This work was supported by NIH grants NS36585 and NS051051 (to M.B.-F.); by the Howard Hughes Medical Institute, of which P.W.S. is an Investigator; and by\nNHGRI Genome Scholar Development and Faculty Transition Award (K22) (to B.J.H.).\n\nPublished - 391.full.pdf
Supplemental Material - KeeSuppMat.doc
", "abstract": "Because migratory cells in all animals share common properties, we hypothesized that genetic networks involved in cell migration may be conserved between nematodes and vertebrates. To explore this, we performed comparative genomic analysis to identify vertebrate orthologs of genes required for hermaphrodite-specific neuron (HSN) migration in Caenoryhabditis elegans, and then examined their expression and function in the vertebrate neural crest. The results demonstrate high conservation of regulatory components involved in long-range migrations across diverse species. Although the neural crest is a vertebrate innovation, the results suggest that its migratory properties evolved by utilizing programs already present in the common vertebrate\u2013invertebrate ancestor.", "date": "2007-02-15", "date_type": "published", "publication": "Genes and Development", "volume": "21", "number": "4", "publisher": "Cold Spring Harbor Laboratory Press", "pagerange": "391-396", "id_number": "CaltechAUTHORS:20160201-085752814", "issn": "0890-9369", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160201-085752814", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "NS36585" }, { "agency": "NIH", "grant_number": "NS051051" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "National Human Genome Research Institute (NHGRI)" }, { "agency": "Faculty Transition Award", "grant_number": "K22" } ] }, "doi": "10.1101/gad.1509307", "pmcid": "PMC1804327", "primary_object": { "basename": "KeeSuppMat.doc", "url": "https://authors.library.caltech.edu/records/wkfr0-csh30/files/KeeSuppMat.doc" }, "related_objects": [ { "basename": "391.full.pdf", "url": "https://authors.library.caltech.edu/records/wkfr0-csh30/files/391.full.pdf" } ], "resource_type": "article", "pub_year": "2007", "author_list": "Kee, Yun; Hwang, Byung Joon; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/a37xs-xwg66", "eprint_id": 16676, "eprint_status": "archive", "datestamp": "2023-08-19 19:25:52", "lastmod": "2023-10-19 22:28:30", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Girard-L-R", "name": { "family": "Girard", "given": "Lisa R." } }, { "id": "Fiedler-T-J", "name": { "family": "Fiedler", "given": "Tristan J." } }, { "id": "Harris-T-W", "name": { "family": "Harris", "given": "Todd W." }, "orcid": "0000-0003-3406-163X" }, { "id": "Carvalho-F", "name": { "family": "Carvalho", "given": "Felicia" } }, { "id": "Antoshechkin-I-A", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Han-Michael", "name": { "family": "Han", "given": "Michael" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Stein-L-D", "name": { "family": "Stein", "given": "Lincoln D." }, "orcid": "0000-0002-1983-4588" }, { "id": "Chalfie-M", "name": { "family": "Chalfie", "given": "Martin" } } ] }, "title": "WormBook: the online review of Caenorhabditis elegans biology", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 The Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived August 14, 2006; Revised October 9, 2006; Accepted October 10, 2006. Nucleic Acids Research Advance Access originally published online on November 11, 2006. \n\nWe would like to thank the members of WormBase for helpful discussions and assistance. Funding for WormBook has been provided by a grant to WormBase from the US National Human Genome Research Institute (P41 HG02223), the Genetics Society, the Society for Developmental Biology, as well as the generous support of the editors of C.elegans II. Funding to pay the Open Access publication charges for this article was provided by a grant to WormBase from the US National Human Genome Research Institute (P41 HG02223).\n\nPublished - GIRnar07.pdf
", "abstract": "WormBook (www.wormbook.org) is an open-access, online collection of original, peer-reviewed chapters on the biology of Caenorhabditis elegans and related nematodes. Since WormBook was launched in June 2005 with 12 chapters, it has grown to over 100 chapters, covering nearly every aspect of C.elegans research, from Cell Biology and Neurobiology to Evolution and Ecology. WormBook also serves as the text companion to WormBase, the C.elegans model organism database. Objects such as genes, proteins and cells are linked to the relevant pages in WormBase, providing easily accessible background information. Additionally, WormBook chapters contain links to other relevant topics in WormBook, and the in-text citations are linked to their abstracts in PubMed and full-text references, if available. Since WormBook is online, its chapters are able to contain movies and complex images that would not be possible in a print version. WormBook is designed to keep up with the rapid pace of discovery in the field of C.elegans research and continues to grow. WormBook represents a generic publishing infrastructure that is easily adaptable to other research communities to facilitate the dissemination of knowledge in the field.", "date": "2007-01", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "35", "number": "Databa", "publisher": "Oxford University Press", "pagerange": "D472-D475", "id_number": "CaltechAUTHORS:20091112-084251306", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20091112-084251306", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Human Genome Research Institute" }, { "agency": "Genetics Society" }, { "agency": "Society for Developmental Biology" }, { "agency": "NIH", "grant_number": "P41 HG02223" } ] }, "doi": "10.1093/nar/gkl894", "pmcid": "PMC1669767", "primary_object": { "basename": "GIRnar07.pdf", "url": "https://authors.library.caltech.edu/records/a37xs-xwg66/files/GIRnar07.pdf" }, "resource_type": "article", "pub_year": "2007", "author_list": "Girard, Lisa R.; Fiedler, Tristan J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/1p2jn-fwh08", "eprint_id": 6044, "eprint_status": "archive", "datestamp": "2023-08-22 07:13:35", "lastmod": "2023-10-16 20:02:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bieri-T", "name": { "family": "Bieri", "given": "Tamberlyn" } }, { "id": "Blasiar-D", "name": { "family": "Blasiar", "given": "Darin" } }, { "id": "Ozersky-P", "name": { "family": "Ozersky", "given": "Philip" } }, { "id": "Antoshechkin-I-A", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Bastiani-C-A", "name": { "family": "Bastiani", "given": "Carol" } }, { "id": "Canaran-P", "name": { "family": "Canaran", "given": "Payan" } }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "Chen-Nansheng", "name": { "family": "Chen", "given": "Nansheng" } }, { "id": "Chen-Wen-J", "name": { "family": "Chen", "given": "Wen J." } }, { "id": "Davis-P-M", "name": { "family": "Davis", "given": "Paul" } }, { "id": "Fiedler-T-J", "name": { "family": "Fiedler", "given": "Tristan J." } }, { "id": "Girard-L-R", "name": { "family": "Girard", "given": "Lisa" } }, { "id": "Han-Michael", "name": { "family": "Han", "given": "Michael" } }, { "id": "Harris-T-W", "name": { "family": "Harris", "given": "Todd W." }, "orcid": "0000-0003-3406-163X" }, { "id": "Kishore-R", "name": { "family": "Kishore", "given": "Ranjana" } }, { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "Raymond" }, "orcid": "0000-0002-8151-7479" }, { "id": "McKay-S", "name": { "family": "McKay", "given": "Sheldon" } }, { "id": "M\u00fcller-H-M", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } }, { "id": "Nakamura-Cecilia", "name": { "family": "Nakamura", "given": "Cecilia" }, "orcid": "0000-0002-4689-7314" }, { "id": "Petcherski-A", "name": { "family": "Petcherski", "given": "Andrei" } }, { "id": "Rangarajan-A", "name": { "family": "Rangarajan", "given": "Arun" } }, { "id": "Rogers-A", "name": { "family": "Rogers", "given": "Anthony" } }, { "id": "Schindelman-G", "name": { "family": "Schindelman", "given": "Gary" } }, { "id": "Schwarz-E-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Spooner-W", "name": { "family": "Spooner", "given": "Will" } }, { "id": "Tuli-M-A", "name": { "family": "Tuli", "given": "Mary Ann" } }, { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Wang-Daniel", "name": { "family": "Wang", "given": "Daniel" } }, { "id": "Wang-Xiaodong", "name": { "family": "Wang", "given": "Xiaodong" } }, { "id": "Williams-G", "name": { "family": "Williams", "given": "Gary" } }, { "id": "Durbin-R", "name": { "family": "Durbin", "given": "Richard" } }, { "id": "Stein-L-D", "name": { "family": "Stein", "given": "Lincoln D." }, "orcid": "0000-0002-1983-4588" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Spieth-J", "name": { "family": "Spieth", "given": "John" } } ] }, "title": "WormBase: new content and better access", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 The Author(s)\nThis is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived September 14, 2006. Revised October 3, 2006. Accepted October 4, 2006. Nucleic Acids Research Advance Access published online on November 11, 2006 \n\nP.W.S. is an investigator with the Howard Hughes Medical Institute. WormBase is supported by grant P41-HG02223 from the US National Human Genome Research Institute and by the British Medical Research Council. Funding to pay the Open Access publication charges for this article was provided by grant P41-HG02223 from the US National Human Genome Research Institute. \n\nConflict of interest statement. None declared. \n\nSupplementary Data are available at NAR Online.\n\nPublished - BIEnar07.pdf
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Supplemental Material - BIEnar06-data-e-2006-File011.pdf
", "abstract": "WormBase (http://wormbase.org), a model organism database for Caenorhabditis elegans and other related nematodes, continues to evolve and expand. Over the past year WormBase has added new data on C.elegans, including data on classical genetics, cell biology and functional genomics; expanded the annotation of closely related nematodes with a new genome browser for Caenorhabditis remanei; and deployed new hardware for stronger performance. Several existing datasets including phenotype descriptions and RNAi experiments have seen a large increase in new content. New datasets such as the C.remanei draft assembly and annotations, the Vancouver Fosmid library and TEC-RED 5' end sites are now available as well. Access to and searching WormBase has become more dependable and flexible via multiple mirror sites and indexing through Google.", "date": "2006-11-11", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "35", "number": "Databa", "publisher": "Oxford University Press", "pagerange": "D1-D5", "id_number": "CaltechAUTHORS:BIEnar06advacc", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:BIEnar06advacc", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1093/nar/gkl818", "pmcid": "PMC1669750", "primary_object": { "basename": "BIEnar06-data-e-2006-File006.pdf", "url": "https://authors.library.caltech.edu/records/1p2jn-fwh08/files/BIEnar06-data-e-2006-File006.pdf" }, "related_objects": [ { "basename": "BIEnar06-data-e-2006-File007.pdf", "url": "https://authors.library.caltech.edu/records/1p2jn-fwh08/files/BIEnar06-data-e-2006-File007.pdf" }, { "basename": "BIEnar06-data-e-2006-File010.pdf", "url": "https://authors.library.caltech.edu/records/1p2jn-fwh08/files/BIEnar06-data-e-2006-File010.pdf" }, { "basename": "BIEnar07.pdf", "url": "https://authors.library.caltech.edu/records/1p2jn-fwh08/files/BIEnar07.pdf" }, { "basename": "BIEnar06-data-e-2006-File004.pdf", "url": "https://authors.library.caltech.edu/records/1p2jn-fwh08/files/BIEnar06-data-e-2006-File004.pdf" }, { "basename": "BIEnar06-data-e-2006-File005.pdf", "url": "https://authors.library.caltech.edu/records/1p2jn-fwh08/files/BIEnar06-data-e-2006-File005.pdf" }, { "basename": "BIEnar06-data-e-2006-File011.pdf", "url": "https://authors.library.caltech.edu/records/1p2jn-fwh08/files/BIEnar06-data-e-2006-File011.pdf" }, { "basename": "BIEnar06-data-e-2006-File008.pdf", "url": "https://authors.library.caltech.edu/records/1p2jn-fwh08/files/BIEnar06-data-e-2006-File008.pdf" }, { "basename": "BIEnar06-data-e-2006-File009.pdf", "url": "https://authors.library.caltech.edu/records/1p2jn-fwh08/files/BIEnar06-data-e-2006-File009.pdf" } ], "resource_type": "article", "pub_year": "2006", "author_list": "Bieri, Tamberlyn; Blasiar, Darin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/fnctc-wb061", "eprint_id": 95471, "eprint_status": "archive", "datestamp": "2023-08-19 18:50:43", "lastmod": "2023-10-20 20:16:09", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Feng-Zhaoyang", "name": { "family": "Feng", "given": "Zhaoyang" } }, { "id": "Li-Wei", "name": { "family": "Li", "given": "Wei" }, "orcid": "0000-0003-2543-2558" }, { "id": "Ward-A", "name": { "family": "Ward", "given": "Alex" } }, { "id": "Piggott-B-J", "name": { "family": "Piggott", "given": "Beverly J." } }, { "id": "Larkspur-E-R", "name": { "family": "Larkspur", "given": "Erin R." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Xu-X-Z-Shawn", "name": { "family": "Xu", "given": "X. Z. Shawn" } } ] }, "title": "A C. elegans Model of Nicotine-Dependent Behavior: Regulation by TRP-Family Channels", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 Elsevier Inc. \n\nReceived 21 November 2005, Revised 16 July 2006, Accepted 15 September 2006, Available online 2 November 2006. \n\nWe thank William Schafer, Gary Schindelman, Patrick Hu, Raad Nashmi, and Craig Montell for comments and advice; Junichi Nakai for the G-CaMP plasmid; Millet Treinin for the deg-3 strain; Henry Lester for mouse nAChR cDNA plasmids; and Barbara Perry and Rahul Mahapatra for technical assistance. Z.F. was inspired to study nicotine by previous training with W.S. Some strains were obtained from the CGC and C. elegans Gene Knockout Consortium. P.W.S. is an HHMI investigator. This work was supported by USPHS training grants T32EY017878 (A.W.) and T32GM008322 (B.J.P.), the Howard Hughes Medical Institute (HHMI) (P.W.S.), NIDA grant 7R01DA018341-02 (P.W.S.), the University of Michigan BSSP program (X.Z.S.X.), and grants from the American Legacy Foundation via UMTRN and NIGMS (X.Z.S.X.). \n\nZ.F. and X.Z.S.X. conceived and designed the experiments. Z.F. and W.L. performed the experiments and analyzed the data. A.W., B.J.P., and E.R.L. helped perform some experiments and paper writing. P.W.S. contributed critical reagents, intellectual input, and help with paper writing. X.Z.S.X. and Z.F. wrote the paper.\n\nAccepted Version - nihms194149.pdf
Supplemental Material - 1-s2.0-S0092867406012955-mmc1.pdf
", "abstract": "Nicotine, the primary addictive substance in tobacco, induces profound behavioral responses in mammals, but the underlying genetic mechanisms are not well understood. Here we develop a C. elegans model of nicotine-dependent behavior. We show that worms exhibit behavioral responses to nicotine that parallel those observed in mammals, including acute response, tolerance, withdrawal, and sensitization. These nicotine responses require nicotinic acetylcholine receptor (nAChR) family genes that are known to mediate nicotine dependence in mammals, suggesting functional conservation of nAChRs in nicotine responses. Importantly, we find that mutant worms lacking TRPC (transient receptor potential canonical) channels are defective in their response to nicotine and that such a defect can be rescued by a human TRPC channel, revealing an unexpected role for TRPC channels in regulating nicotine-dependent behavior. Thus, C. elegans can be used to characterize known genes as well as to identify new genes regulating nicotine responses.", "date": "2006-11-03", "date_type": "published", "publication": "Cell", "volume": "127", "number": "3", "publisher": "Elsevier", "pagerange": "621-633", "id_number": "CaltechAUTHORS:20190514-085132111", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-085132111", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32EY017878" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM008322" }, { "agency": "NIH", "grant_number": "7R01DA018341-02" }, { "agency": "American Legacy Foundation" }, { "agency": "University of Michigan Tobacco Research Network" }, { "agency": "National Institute of General Medical Sciences" }, { "agency": "National Institute on Drug Abuse" } ] }, "doi": "10.1016/j.cell.2006.09.035", "pmcid": "PMC2859215", "primary_object": { "basename": "1-s2.0-S0092867406012955-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/fnctc-wb061/files/1-s2.0-S0092867406012955-mmc1.pdf" }, "related_objects": [ { "basename": "nihms194149.pdf", "url": "https://authors.library.caltech.edu/records/fnctc-wb061/files/nihms194149.pdf" } ], "resource_type": "article", "pub_year": "2006", "author_list": "Feng, Zhaoyang; Li, Wei; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/8x82s-dez63", "eprint_id": 95472, "eprint_status": "archive", "datestamp": "2023-08-19 18:49:46", "lastmod": "2023-10-20 20:16:14", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gupta-B-P", "name": { "family": "Gupta", "given": "Bhagwati P." } }, { "id": "Liu-Jing", "name": { "family": "Liu", "given": "Jing" } }, { "id": "Hwang-Byung-J", "name": { "family": "Hwang", "given": "Byung J." } }, { "id": "Moghal-N", "name": { "family": "Moghal", "given": "Nadeem" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "sli-3 Negatively Regulates the LET-23/Epidermal Growth Factor Receptor-Mediated Vulval Induction Pathway in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 by the Genetics Society of America.\n\nManuscript received July 26, 2006; Accepted for publication August 21, 2006. \n\nWe thank Neil Hopper, Chieh Chang, Giovanni Lisa, Maureen Barr, and Minqin Wang for insights in this project. We also thank the anonymous reviewers for helpful comments on a draft of this article. This work was supported by the U.S. Public Health Service (USHS) grant HD23690 to P.W.S., the Canada Research Chair and McMaster research funds to B.P.G., and National Institutes of Health grant R01 GM073184 to N.M. Additional support was provided by the Howard Hughes Medical Institute, with which P.W.S. is an investigator and B.J.H. and B.P.G. were associates. J.L. was supported by a U.S.H.S. training grant. B.P.G. was a postdoctoral fellow of the Human Frontier Science Foundation. N.M. was a fellow of the California Breast Cancer Research Foundation. Some strains were provided by the Caenorhabditis Genetics Center.\n\nPublished - GEN17431315.pdf
", "abstract": "The LIN-3\u2013LET-23-mediated inductive signaling pathway plays a major role during vulval development in C. elegans. Studies on the components of this pathway have revealed positive as well as negative regulators that function to modulate the strength and specificity of the signal transduction cascade. We have carried out genetic screens to identify new regulators of this pathway by screening for suppressors of lin-3 vulvaless phenotype. The screens recovered three loci including alleles of gap-1 and a new gene represented by sli-3. Our genetic epistasis experiments suggest that sli-3 functions either downstream or in parallel to nuclear factors lin-1 and sur-2. sli-3 synergistically interacts with the previously identified negative regulators of the let-23 signaling pathway and causes excessive cell proliferation. However, in the absence of any other mutation sli-3 mutant animals display wild-type vulval induction and morphology. We propose that sli-3 functions as a negative regulator of vulval induction and defines a branch of the inductive signaling pathway. We provide evidence that sli-3 interacts with the EGF signaling pathway components during vulval induction but not during viability and ovulation processes. Thus, sli-3 helps define specificity of the EGF signaling to induce the vulva.", "date": "2006-11-01", "date_type": "published", "publication": "Genetics", "volume": "174", "number": "3", "publisher": "Genetics Society of America", "pagerange": "1315-1326", "id_number": "CaltechAUTHORS:20190514-090058420", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-090058420", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HD23690" }, { "agency": "Canada Research Chairs Program" }, { "agency": "McMaster University" }, { "agency": "NIH", "grant_number": "R01 GM073184" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Human Frontier Science Foundation" }, { "agency": "California Breast Cancer Research Foundation" } ] }, "doi": "10.1534/genetics.106.063990", "pmcid": "PMC1667086", "primary_object": { "basename": "GEN17431315.pdf", "url": "https://authors.library.caltech.edu/records/8x82s-dez63/files/GEN17431315.pdf" }, "resource_type": "article", "pub_year": "2006", "author_list": "Gupta, Bhagwati P.; Liu, Jing; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/r8heh-n5r16", "eprint_id": 87887, "eprint_status": "archive", "datestamp": "2023-08-19 18:36:38", "lastmod": "2024-01-14 20:26:10", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Heng-Xin", "name": { "family": "Heng", "given": "Xin" } }, { "id": "Cui-Xiquan", "name": { "family": "Cui", "given": "Xiquan" } }, { "id": "Erickson-D", "name": { "family": "Erickson", "given": "David" } }, { "id": "Baugh-L-R", "name": { "family": "Baugh", "given": "Larry R." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Psaltis-D", "name": { "family": "Psaltis", "given": "Demetri" } }, { "id": "Yang-Changhuei", "name": { "family": "Yang", "given": "Changhuei" }, "orcid": "0000-0001-8791-0354" } ] }, "title": "A compact optofluidic microscope", "ispublished": "unpub", "full_text_status": "public", "keywords": "Microfluidics, Nanophootnics, C elegans phenotyping", "note": "\u00a9 2006 Society of Photo-Optical Instrumentation Engineers (SPIE). \n\nWe are grateful for the generous help from Professor Axel Scherer, Dr. Joerg Schilling in fabrication. We thank Dr. Zahid Yaqoob, Jigang Wu for constructive discussions. The assistance from Cornell Nanofabrication Facility and Caltech Watson cleanroom is appreciated. This project is funded by DARPA's center for optofluidic integration\n\nPublished - 632908.pdf
", "abstract": "We demonstrate a novel optical imaging device that can be directly integrated into a microfluidic network, and therefore enables on-chip imaging in a microfluidic system. This micro imaging device, termed optofluidic microscope (OFM) is free of bulk optics and is based on a nanohole array defined in a non-transmissive metallic layer that is patterned onto the floor of the microfluidic channel. The operation of the optofluidic microscope will be explained in details and its performance is examined by using a popular animal model, Caenorhabditis elegans (C. elegans). Images from a large population of nematode worms are efficiently acquired within a short time frame. The quality of the OFM images of C. elegans and the morphological characteristics revealed therein are evaluated. Two groups of early-stage C. elegans larvae, wild-type and dpy-24 are successfully separated even though their morphological difference at the larval stage is subtle. The experimental results support our claim that the methodology described therein can be effectively used to develop a powerful tool for fulfilling high-resolution, high-throughput imaging task in microfluidics-based systems.", "date": "2006-09-13", "date_type": "published", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_pub": "Bellingham, WA", "pagerange": "Art. no. 632908", "id_number": "CaltechAUTHORS:20180716-113829146", "isbn": "0819464082", "book_title": "Optofluidics", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-113829146", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Defense Advanced Research Projects Agency (DARPA)" } ] }, "contributors": { "items": [ { "id": "Psaltis-D", "name": { "family": "Psaltis", "given": "Demetri" } }, { "id": "Fainman-Y", "name": { "family": "Fainman", "given": "Yeshaiahu" } } ] }, "doi": "10.1117/12.678940", "primary_object": { "basename": "632908.pdf", "url": "https://authors.library.caltech.edu/records/r8heh-n5r16/files/632908.pdf" }, "resource_type": "book_section", "pub_year": "2006", "author_list": "Heng, Xin; Cui, Xiquan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/eec0d-grs21", "eprint_id": 4396, "eprint_status": "archive", "datestamp": "2023-08-22 06:20:24", "lastmod": "2023-10-16 17:44:18", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schindelman-G", "name": { "family": "Schindelman", "given": "Gary" } }, { "id": "Whittaker-A-J", "name": { "family": "Whittaker", "given": "Allyson J." } }, { "id": "Thum-Jian-Yuan", "name": { "family": "Thum", "given": "Jian Yuan" } }, { "id": "Gharib-Shahla", "name": { "family": "Gharib", "given": "Shahla" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Initiation of male sperm-transfer behavior in Caenorhabditis elegans requires input from the ventral nerve cord", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 Schindelman et al., licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nSubmission date 17 January 2006; Acceptance date 15 August 2006; Publication date 15 August 2006. \n\nGS, AJW and PWS conceived the study. GS, AJW, JYT, and SG all contributed to the genetic screening and the initial characterization of isolated male mating-behavior mutants. GS performed laser ablations, genetic manipulations, and behavioral assays on transformants. JYT was involved in the behavioral assays on transformants. GS drafted the manuscript, with AJW, JYT, SG, and PWS revising it critically for important intellectual content. All authors read and approved the final manuscript. \n\nWe thank Cheryl Van Buskirk, Jagan Srinivasan and Rene Garcia and members of his laboratory for critical reading of this manuscript. We thank Ryuji Hosono, Erik Jorgensen and James Rand for additional alleles of unc-18. This research was supported by the Howard Hughes Medical Institute, with which P.W.S. is an investigator. G.S. and A.J.W. were supported by NIH postdoctoral fellowships NS043037 and NS042497, respectively.\n\nPublished - SCHIbmcbiol06.pdf
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", "abstract": "Background: The Caenorhabditis elegans male exhibits a stereotypic behavioral pattern when attempting to mate. This behavior has been divided into the following steps: response, backing, turning, vulva location, spicule insertion, and sperm transfer. We and others have begun in-depth analyses of all these steps in order to understand how complex behaviors are generated. Here we extend our understanding of the sperm-transfer step of male mating behavior. \n\nResults: Based on observation of wild-type males and on genetic analysis, we have divided the sperm-transfer step of mating behavior into four sub-steps: initiation, release, continued transfer, and cessation. To begin to understand how these sub-steps of sperm transfer are regulated, we screened for ethylmethanesulfonate (EMS)-induced mutations that cause males to transfer sperm aberrantly. We isolated an allele of unc-18, a previously reported member of the Sec1/Munc-18 (SM) family of proteins that is necessary for regulated exocytosis in C. elegans motor neurons. Our allele, sy671, is defective in two distinct sub-steps of sperm transfer: initiation and continued transfer. By a series of transgenic site-of-action experiments, we found that motor neurons in the ventral nerve cord require UNC-18 for the initiation of sperm transfer, and that UNC-18 acts downstream or in parallel to the SPV sensory neurons in this process. In addition to this neuronal requirement, we found that non-neuronal expression of UNC-18, in the male gonad, is necessary for the continuation of sperm transfer. \n\nConclusions: Our division of sperm-transfer behavior into sub-steps has provided a framework for the further detailed analysis of sperm transfer and its integration with other aspects of mating behavior. By determining the site of action of UNC-18 in sperm-transfer behavior, and its relation to the SPV sensory neurons, we have further defined the cells and tissues involved in the generation of this behavior. We have shown both a neuronal and non-neuronal requirement for UNC-18 in distinct sub-steps of sperm-transfer behavior. The definition of circuit components is a crucial first step toward understanding how genes specify the neural circuit and hence the behavior.", "date": "2006-08-15", "date_type": "published", "publication": "BMC Biology", "volume": "4", "publisher": "BioMed Central", "pagerange": "Art. no. 26", "id_number": "CaltechAUTHORS:SCHIbmcbiol06", "issn": "1741-7007", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:SCHIbmcbiol06", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "NS043037" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "NS042497" } ] }, "doi": "10.1186/1741-7007-4-26", "pmcid": "PMC1564418", "primary_object": { "basename": "SCHIbmcbiol06.pdf", "url": "https://authors.library.caltech.edu/records/eec0d-grs21/files/SCHIbmcbiol06.pdf" }, "related_objects": [ { "basename": "SCHIbmcbiol06movie1.mov", "url": "https://authors.library.caltech.edu/records/eec0d-grs21/files/SCHIbmcbiol06movie1.mov" }, { "basename": "SCHIbmcbiol06movie2.mov", "url": "https://authors.library.caltech.edu/records/eec0d-grs21/files/SCHIbmcbiol06movie2.mov" }, { "basename": "SCHIbmcbiol06movie3.mov", "url": "https://authors.library.caltech.edu/records/eec0d-grs21/files/SCHIbmcbiol06movie3.mov" } ], "resource_type": "article", "pub_year": "2006", "author_list": "Schindelman, Gary; Whittaker, Allyson J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/xtqga-f4t53", "eprint_id": 4376, "eprint_status": "archive", "datestamp": "2023-08-22 06:17:24", "lastmod": "2023-10-16 17:43:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chen-David", "name": { "family": "Chen", "given": "David" } }, { "id": "M\u00fcller-H-M", "name": { "family": "Muller", "given": "Hans-Michael" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Automatic document classification of biological literature", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 Chen et al., licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nSubmission date 28 March 2006; Acceptance date 7 August 2006; Publication date 7 August 2006 \n\nAuthors' contributions: DC devised and developed all aspects of the algorithm, performed the computational experiments and analyzed them, implemented the web-interface and its underlying data-processing and wrote the manuscript. HMM initiated the project, provided the Textpresso database and infrastructure, suggested ideas and edited the manuscript. PWS edited the manuscript, provided materials and supervised the project. All authors read and approved the final manuscript. \n\nWe thank the Caltech WormBase group for discussions. This project was funded by the generosity of Dr. Anthony Skjellum via the SURF program at the California Institute of Technology, and the National Human Genome Research Institute at the US National Institutes of Health # P41 HG02223 and # HG004090.\n\nPublished - CHEbmcbioinf06.pdf
Supplemental Material - CHEbmcbioinf06sup1.pdf
", "abstract": "Background: Document classification is a wide-spread problem with many applications, from organizing search engine snippets to spam filtering. We previously described Textpresso, a text-mining system for biological literature, which marks up full text according to a shallow ontology that includes terms of biological interest. This project investigates document classification in the context of biological literature, making use of the Textpresso markup of a corpus of Caenorhabditis elegans literature. \n\nResults: We present a two-step text categorization algorithm to classify a corpus of C. elegans papers. Our classification method first uses a support vector machine-trained classifier, followed by a novel, phrase-based clustering algorithm. This clustering step autonomously creates cluster labels that are descriptive and understandable by humans. This clustering engine performed better on a standard test-set (Reuters 21578) compared to previously published results (F-value of 0.55 vs. 0.49), while producing cluster descriptions that appear more useful. A web interface allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept. \n\nConclusions: We have demonstrated a simple method to classify biological documents that embodies an improvement over current methods. While the classification results are currently optimized for Caenorhabditis elegans papers by human-created rules, the classification engine can be adapted to different types of documents. We have demonstrated this by presenting a web interface that allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept.", "date": "2006-08-07", "date_type": "published", "publication": "BMC Bioinformatics", "volume": "7", "publisher": "BMC Bioinformatics", "pagerange": "Art. No. 370", "id_number": "CaltechAUTHORS:CHEbmcbioinf06", "issn": "1471-2105", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:CHEbmcbioinf06", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech Summer Undergraduate Research Fellowship (SURF)" }, { "agency": "NIH", "grant_number": "P41 HG02223" }, { "agency": "NIH", "grant_number": "HG004090" }, { "agency": "National Human Genome Research Institute" } ] }, "doi": "10.1186/1471-2105-7-370", "pmcid": "PMC1559726", "primary_object": { "basename": "CHEbmcbioinf06.pdf", "url": "https://authors.library.caltech.edu/records/xtqga-f4t53/files/CHEbmcbioinf06.pdf" }, "related_objects": [ { "basename": "CHEbmcbioinf06sup1.pdf", "url": "https://authors.library.caltech.edu/records/xtqga-f4t53/files/CHEbmcbioinf06sup1.pdf" } ], "resource_type": "article", "pub_year": "2006", "author_list": "Chen, David; Muller, Hans-Michael; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/52pv9-7kx62", "eprint_id": 95458, "eprint_status": "archive", "datestamp": "2023-08-19 18:01:47", "lastmod": "2023-10-20 20:15:30", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Huang-Linda-S", "name": { "family": "Huang", "given": "Linda S." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Genetic dissection of developmental pathways", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 WormBase. All WormBook content, except where otherwise noted, is licensed under a Creative Commons Attribution License. \n\nEdited by David Fay. WormMethods editor, Victor Ambros. Last revised April 22, 2005. Published June 14, 2006. \n\nThe authors would like to thank Paul Garrity, Wendy Katz, Ralf Sommer, John DeModena, Marie-Anne F\u00e9lix, Yvonne Hadju-Cronin, Howard Lipshitz, Katharine Liu, Anna Newman, and the editors for critical comments. Research in our laboratory discussed here was supported by the U. S .P. H. S, the March of Dimes Birth Defects Foundation, and the Howard Hughes Medical Institute, with which P. W. S. is an Investigator.\n\nPublished - epistasis.pdf
", "abstract": "A major tool of developmental geneticists is the ordering of genes in functional pathways. In this chapter, we explain the logic behind constructing pathways, starting from the knowledge of the relevant phenotypes associated with the genes of interest, assuming that careful analysis of the phenotype has been carried out. We discuss the construction and interpretation of phenotypes of double mutants, screening for and analysis of extragenic suppressors, as well as issues regarding complex pathways and genetic redundancy. Avery and Wasserman (1992) have provided a brief theoretical discussion of epistasis analysis; here we explain the more practical aspects of how models of developmental pathways are built in C. elegans.", "date": "2006-06-14", "date_type": "published", "publication": "WormBook: the online review of C. elegans biology", "publisher": "WormBase", "pagerange": "Art. No. 1.88.2", "id_number": "CaltechAUTHORS:20190513-161611318", "issn": "1551-8507", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190513-161611318", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "March of Dimes Birth Defects Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1895/wormbook.1.88.2", "primary_object": { "basename": "epistasis.pdf", "url": "https://authors.library.caltech.edu/records/52pv9-7kx62/files/epistasis.pdf" }, "resource_type": "article", "pub_year": "2006", "author_list": "Huang, Linda S. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/gfw4w-56818", "eprint_id": 3788, "eprint_status": "archive", "datestamp": "2023-08-22 05:52:54", "lastmod": "2023-10-16 16:09:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gonzalez-Serricchio-A-S", "name": { "family": "Gonzalez-Serricchio", "given": "Aidyl S." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Visualization of C. elegans transgenic arrays by GFP", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 Gonzalez-Serricchio and Sternberg, licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nSubmission date 14 March 2006; Acceptance date 7 June 2006; Publication date 7 June 2006 \n\nWe greatly thank Andrew Belmont for the fusion protein GFP-LacI and lacO repeat constructs as well for invaluable help developing this system, and Linda Huang for suggesting its use in mosaic analysis. We also thank Barbara Meyer for the dpy-30 promoter, Shahla Gharib for help with transgene integration, members of our laboratory for discussions and encouragement, and anonymous reviewers for helpful suggestions. The Caenorhabditis Genetic Center provided some strains. This work was supported USPHS (grant HD23690 to PWS) and by the Howard Hughes Medical Institute, with which P.W.S. is an Investigator. A.S.G-S. was a Howard Hughes Medical Institute Graduate Fellow. \n\nAuthors' contributions: AG-S designed and executed all the experiments. AG-S and PWS analyzed the data and wrote the paper. \n\nArticle URL http://www.biomedcentral.com/1471-2156/7/36\n\nPublished - GONbmcgen06.pdf
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", "abstract": "Background: Targeting the green fluorescent protein (GFP) via the E. coli lac repressor (LacI) to a specific DNA sequence, the lac operator (lacO), allows visualization of chromosomes in yeast and mammalian cells. In principle this method of visualization could be used for genetic mosaic analysis, which requires cell-autonomous markers that can be scored easily and at single cell resolution. The C. elegans lin-3 gene encodes an epidermal growth factor family (EGF) growth factor. lin-3 is expressed in the gonadal anchor cell and acts through LET-23 (transmembrane protein tyrosine kinase and ortholog of EGF receptor) to signal the vulval precursor cells to generate vulval tissue. lin-3 is expressed in the vulval cells later, and recent evidence raises the possibility that lin-3 acts in the vulval cells as a relay signal during vulval induction. It is thus of interest to test the site of action of lin-3 by mosaic analysis. \n\nResults: We visualized transgenes in living C. elegans by targeting the green fluorescent protein (GFP) via the E. coli lac repressor (LacI) to a specific 256 sequence repeat of the lac operator (lacO) incorporated into transgenes. We engineered animals to express a nuclear-localized GFP-LacI fusion protein. C. elegans cells having a lacO transgene result in nuclear-localized bright spots (i.e., GFP-LacI bound to lacO). Cells with diffuse nuclear fluorescence correspond to unbound nuclear localized GFP-LacI. We detected chromosomes in living animals by chromosomally integrating the array of the lacO repeat sequence and visualizing the integrated transgene with GFP-LacI. This detection system can be applied to determine polyploidy as well as investigating chromosome segregation. To assess the GFP-LacI-lacO system as a marker for mosaic analysis, we conducted genetic mosaic analysis of the epidermal growth factor lin-3, expressed in the anchor cell. We establish that lin-3 acts in the anchor cell to induce vulva development, demonstrating this methods utility in detecting the presence of a transgene. \n\nConclusions: The GFP-LacIlacO transgene detection system works in C. elegans for visualization of chromosomes and extrachromosomal transgenes. It can be used as a marker for genetic mosaic analysis. The lacO repeat sequence as an extrachromosomal array becomes a valuable technique allowing rapid, accurate determination of spontaneous loss of the array, thereby allowing high-resolution mosaic analysis. The lin-3 gene is required in the anchor cell to induce the epidermal vulval precursors cells to undergo vulval development.", "date": "2006-06-07", "date_type": "published", "publication": "BMC Genetics", "volume": "7", "publisher": "BioMed Central", "pagerange": "Art. No. 36", "id_number": "CaltechAUTHORS:GONbmcgen06", "issn": "1471-2156", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:GONbmcgen06", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HD23690" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1186/1471-2156-7-36", "pmcid": "PMC1539001", "primary_object": { "basename": "12863_2006_459_MOESM1_ESM.png", "url": "https://authors.library.caltech.edu/records/gfw4w-56818/files/12863_2006_459_MOESM1_ESM.png" }, "related_objects": [ { "basename": "12863_2006_459_MOESM2_ESM.png", "url": "https://authors.library.caltech.edu/records/gfw4w-56818/files/12863_2006_459_MOESM2_ESM.png" }, { "basename": "12863_2006_459_MOESM3_ESM.png", "url": "https://authors.library.caltech.edu/records/gfw4w-56818/files/12863_2006_459_MOESM3_ESM.png" }, { "basename": "GONbmcgen06.pdf", "url": "https://authors.library.caltech.edu/records/gfw4w-56818/files/GONbmcgen06.pdf" } ], "resource_type": "article", "pub_year": "2006", "author_list": "Gonzalez-Serricchio, Aidyl S. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/xwb7j-rw379", "eprint_id": 56073, "eprint_status": "archive", "datestamp": "2023-08-19 17:35:19", "lastmod": "2023-10-20 23:37:16", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Li-Wei", "name": { "family": "Li", "given": "Wei" }, "orcid": "0000-0003-2543-2558" }, { "id": "Feng-Zhaoyang", "name": { "family": "Feng", "given": "Zhaoyang" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Xu-X-Z-S", "name": { "family": "Xu", "given": "X. Z. Shawn" } } ] }, "title": "A C-elegans stretch receptor neuron revealed by a mechanosensitive TRP channel homologue", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 Nature Publishing Group.\n\nReceived 7 July 2005; Accepted 19 December 2005.\n\nWe thank J. Nakai for the G-CaMP plasmid; B. Perry for help with deletion libraries; C. Cronin for assistance with data analysis; G. Schindelman, N. Moghal, C. Montell and A. Ward for comments; and G. Medina, E. Larkspur and R. Mahapatra for technical assistance. Some strains were obtained from the Caenorhabditis Genetics Center. This work was supported by the University of Michigan BSSP Scholar Program (X.Z.S.X.), the Helen Hay Whitney Foundation (X.Z.S.X), and the Howard Hughes Medical Institute, of which P.W.S. is an investigator.\n\nAccepted Version - nihms196026.pdf
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Supplemental Material - Methods.doc
", "abstract": "The nematode Caenorhabditis elegans is commonly used as a genetic model organism for dissecting integration of the sensory and motor systems. Despite extensive genetic and behavioural analyses that have led to the identification of many genes and neural circuits involved in regulating C. elegans locomotion behaviour, it remains unclear whether and how somatosensory feedback modulates motor output during locomotion. In particular, no stretch receptors have been identified in C. elegans, raising the issue of whether stretch-receptor-mediated proprioception is used by C. elegans to regulate its locomotion behaviour. Here we have characterized TRP-4, the C. elegans homologue of the mechanosensitive TRPN channel. We show that trp-4 mutant worms bend their body abnormally, exhibiting a body posture distinct from that of wild-type worms during locomotion, suggesting that TRP-4 is involved in stretch-receptor-mediated proprioception. We show that TRP-4 acts in a single neuron, DVA, to mediate its function in proprioception, and that the activity of DVA can be stimulated by body stretch. DVA both positively and negatively modulates locomotion, providing a unique mechanism whereby a single neuron can fine-tune motor activity. Thus, DVA represents a stretch receptor neuron that regulates sensory\u2013motor integration during C. elegans locomotion.", "date": "2006-03-30", "date_type": "published", "publication": "Nature", "volume": "440", "number": "7084", "publisher": "Nature Publishing Group", "pagerange": "684-687", "id_number": "CaltechAUTHORS:20150325-111101940", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150325-111101940", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "University of Michigan BSSP Scholar Program" }, { "agency": "Helen Hay Whitney Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1038/nature04538", "pmcid": "PMC2865900", "primary_object": { "basename": "Fig4.pdf", "url": "https://authors.library.caltech.edu/records/xwb7j-rw379/files/Fig4.pdf" }, "related_objects": [ { "basename": "Methods.doc", "url": "https://authors.library.caltech.edu/records/xwb7j-rw379/files/Methods.doc" }, { "basename": "nihms196026.pdf", "url": "https://authors.library.caltech.edu/records/xwb7j-rw379/files/nihms196026.pdf" }, { "basename": "Fig1.pdf", "url": "https://authors.library.caltech.edu/records/xwb7j-rw379/files/Fig1.pdf" }, { "basename": "Fig2.pdf", "url": "https://authors.library.caltech.edu/records/xwb7j-rw379/files/Fig2.pdf" }, { "basename": "Fig3.pdf", "url": "https://authors.library.caltech.edu/records/xwb7j-rw379/files/Fig3.pdf" } ], "resource_type": "article", "pub_year": "2006", "author_list": "Li, Wei; Feng, Zhaoyang; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/d4b17-v6651", "eprint_id": 51980, "eprint_status": "archive", "datestamp": "2023-08-19 17:30:13", "lastmod": "2023-10-18 19:13:16", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhong-W", "name": { "family": "Zhong", "given": "Weiwei" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Genome-Wide Prediction of C. elegans Genetic Interactions", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 American Association for the Advancement of Science.\n\n1 December 2005; Accepted 26 January 2006.\n\nWe thank the Caenorhabditis Genetics Center for strains;\nWormBase staff for discussions; L. Chen for advice on\nstatistical analysis; B. Perry for maintaining reagents; and\nC. Van Buskirk, E. Hallem, B. Hwang, M. Kato, E. Kipreos,\nR. Kishore, A. Petcherski, and E. Schwarz for critical\nreading of the manuscript. P.W.S. is an investigator and\nW.Z. is an associate of the Howard Hughes Medical Institute.\n\nSupplemental Material - ZhongW.SOM.pdf
", "abstract": "To obtain a global view of functional interactions among genes in a metazoan genome, we computationally integrated interactome data, gene expression data, phenotype data, and functional annotation data from three model organisms\u2014Saccharomyces cerevisiae, Caenorhabditis elegans, and Drosophila melanogaster\u2014and predicted genome-wide genetic interactions in C. elegans. The resulting genetic interaction network (consisting of 18,183 interactions) provides a framework for system-level understanding of gene functions. We experimentally tested the predicted interactions for two human disease-related genes and identified 14 new modifiers.", "date": "2006-03-10", "date_type": "published", "publication": "Science", "volume": "311", "number": "5766", "publisher": "American Association for the Advancement of Science", "pagerange": "1481-1484", "id_number": "CaltechAUTHORS:20141119-151713868", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141119-151713868", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1126/science.1123287", "primary_object": { "basename": "ZhongW.SOM.pdf", "url": "https://authors.library.caltech.edu/records/d4b17-v6651/files/ZhongW.SOM.pdf" }, "resource_type": "article", "pub_year": "2006", "author_list": "Zhong, Weiwei and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/g6kwr-58m76", "eprint_id": 95473, "eprint_status": "archive", "datestamp": "2023-08-19 17:18:56", "lastmod": "2023-10-20 20:16:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Pathway to RAS", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 by the Genetics Society of America. \n\nI thank Bob Horvitz for showing me my first C. elegans cell division and for his generosity when I returned as a ''ghost'' to work on the vulva. I especially thank my many colleagues for making the pathway to RAS so exhilarating, productive, and fun.\n\nPublished - GEN1722727.pdf
", "abstract": "When I started my laboratory at Caltech in 1987, I hung on my door a wall chart from Oncogene Sciences with all the known proto-oncogenes and their cellular locations and regulatory relationships. One of these, ras, was identified by viral and cancer genetics as a dominant oncogene in many tumors and in transforming retroviruses. The RAS protein is a small GTPase, which undergoes a cycle of guanine nucleotide exchange and hydrolysis. RAS was known to be active when bound to GTP, but its normal role in the cell was not known, nor was how it became activated and what it did once it was. RAS and epidermal growth factor receptor (EGFR) resided on opposite sides of the wall chart. The molecular genetics of Caenorhabditis elegans vulval development allowed us to draw a big arrow between RAS and EGFR in 1990 and other arrows in 1992. The intellectual pathway to RAS is a genetic story, the highlight being 15 years ago when we described the initial genetic pathway from a cell surface receptor to the ras proto-oncogene let-60 in C. elegans (Han et al. 1990). This article places this genetic analysis in perspective.", "date": "2006-02-01", "date_type": "published", "publication": "Genetics", "volume": "172", "number": "2", "publisher": "Genetics Society of America", "pagerange": "727-731", "id_number": "CaltechAUTHORS:20190514-091015642", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-091015642", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "pmcid": "PMC1456259", "primary_object": { "basename": "GEN1722727.pdf", "url": "https://authors.library.caltech.edu/records/g6kwr-58m76/files/GEN1722727.pdf" }, "resource_type": "article", "pub_year": "2006", "author_list": "Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/x9ems-cms15", "eprint_id": 3042, "eprint_status": "archive", "datestamp": "2023-08-22 05:02:13", "lastmod": "2023-10-16 15:34:44", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Giurumescu-C-A", "name": { "family": "Giurumescu", "given": "Claudiu A." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Asthagiri-A-R", "name": { "family": "Asthagiri", "given": "Anand R." } } ] }, "title": "Intercellular coupling amplifies fate segregation during Caenorhabditis elegans vulval development", "ispublished": "pub", "full_text_status": "public", "keywords": "multicellular patterning; signal transduction; mitogen-activated protein kinase; gradient amplification; mathematical model", "note": "\u00a9 2006 by The National Academy of Sciences of the USA. \n\nPublished online before print January 23, 2006, 10.1073/pnas.0506476103. \n\nEdited by Scott W. Emmons, Albert Einstein College of Medicine, Bronx, NY, and accepted by the Editorial Board December 19, 2005 (received for review July 28, 2005). \n\nThis paper was submitted directly (Track II) to the PNAS office. S.W.E. is a guest editor invited by the Editorial Board. \n\nThis work was supported by Institute for Collaborative Biotechnologies Grant DAAD 19-03-D-0004 from the U.S. Army Research Office (to A.R.A.) and a start-up grant from the California Institute of Technology (to A.R.A.). P.W.S. is an investigator with the Howard Hughes Medical Institute.\n\nPublished - GIUpnas06.pdf
", "abstract": "During vulval development in Caenorhabditis elegans, six precursor cells acquire a spatial pattern of distinct cell fates. This process is guided by a gradient in the soluble factor, LIN-3, and by direct interactions between neighboring cells mediated by the Notch-like receptor, LIN-12. Genetic evidence has revealed that these two extracellular signals are coupled: lateral cell-cell interactions inhibit LIN-3-mediated signaling, whereas LIN-3 regulates the extent of lateral signaling. To elucidate the quantitative implications of this coupled network topology for cell patterning during vulval development, we developed a mathematical model of LIN-3/LIN12-mediated signaling in the vulval precursor cell array. Our analysis reveals that coupling LIN-3 and LIN-12 amplifies cellular perception of the LIN-3 gradient and polarizes lateral signaling, both of which enhance fate segregation beyond that achievable by an uncoupled system.", "date": "2006-01-31", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "103", "number": "5", "publisher": "National Academy of Sciences", "pagerange": "1331-1336", "id_number": "CaltechAUTHORS:GIUpnas06", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:GIUpnas06", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Army Research Office (ARO)", "grant_number": "DAAD 19-03-D-0004" }, { "agency": "Caltech" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1073/pnas.0506476103", "pmcid": "PMC1360524", "primary_object": { "basename": "GIUpnas06.pdf", "url": "https://authors.library.caltech.edu/records/x9ems-cms15/files/GIUpnas06.pdf" }, "resource_type": "article", "pub_year": "2006", "author_list": "Giurumescu, Claudiu A.; Sternberg, Paul W.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/m1wgk-4j062", "eprint_id": 1221, "eprint_status": "archive", "datestamp": "2023-08-22 04:56:15", "lastmod": "2023-10-13 22:41:26", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schwarz-E-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Antoshechkin-I-A", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Bastiani-C-A", "name": { "family": "Bastiani", "given": "Carol" } }, { "id": "Bieri-T", "name": { "family": "Bieri", "given": "Tamberlyn" } }, { "id": "Blasiar-D", "name": { "family": "Blasiar", "given": "Darin" } }, { "id": "Canaran-P", "name": { "family": "Canaran", "given": "Payan" } }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "Chen-Nansheng", "name": { "family": "Chen", "given": "Nansheng" } }, { "id": "Chen-Wen-J", "name": { "family": "Chen", "given": "Wen J." } }, { "id": "Davis-P-M", "name": { "family": "Davis", "given": "Paul" } }, { "id": "Fiedler-T-J", "name": { "family": "Fiedler", "given": "Tristan J." } }, { "id": "Girard-L-R", "name": { "family": "Girard", "given": "Lisa" } }, { "id": "Harris-T-W", "name": { "family": "Harris", "given": "Todd W." }, "orcid": "0000-0003-3406-163X" }, { "id": "Kenny-E-E", "name": { "family": "Kenny", "given": "Eimear E." } }, { "id": "Kishore-R", "name": { "family": "Kishore", "given": "Ranjana" } }, { "id": "Lawson-D", "name": { "family": "Lawson", "given": "Dan" } }, { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "Raymond" }, "orcid": "0000-0002-8151-7479" }, { "id": "M\u00fcller-H-M", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } }, { "id": "Nakamura-Cecilia", "name": { "family": "Nakamura", "given": "Cecilia" }, "orcid": "0000-0002-4689-7314" }, { "id": "Ozersky-P", "name": { "family": "Ozersky", "given": "Phil" } }, { "id": "Petcherski-A", "name": { "family": "Petcherski", "given": "Andrei" } }, { "id": "Rogers-A", "name": { "family": "Rogers", "given": "Anthony" } }, { "id": "Spooner-W", "name": { "family": "Spooner", "given": "Will" } }, { "id": "Tuli-M-A", "name": { "family": "Tuli", "given": "Mary Ann" } }, { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Wang-Daniel", "name": { "family": "Wang", "given": "Daniel" } }, { "id": "Durbin-R", "name": { "family": "Durbin", "given": "Richard" } }, { "id": "Spieth-J", "name": { "family": "Spieth", "given": "John" } }, { "id": "Stein-L-D", "name": { "family": "Stein", "given": "Lincoln D." }, "orcid": "0000-0002-1983-4588" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "WormBase: better software, richer content", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author 2006. Published by Oxford University Press. All rights reserved. \n\nThe online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. \n\nReceived September 13, 2005. Revised October 6, 2005. Accepted October 6, 2005. \n\nP.W.S. is an investigator with the Howard Hughes Medical Institute. WormBase is supported by grant P41-HG02223 from the US National Human Genome Research Institute, and by the British Medical Research Council. Funding to pay the Open Access publication charges for this article was provided by grant P41-HG02223 from the US National Human Genome Research Institute. \n\nConflict of interest statement. None declared.\n\nPublished - SCHWnar06.pdf
", "abstract": "WormBase (http://wormbase.org), the public database for genomics and biology of Caenorhabditis elegans, has been restructured for stronger performance and expanded for richer biological content. Performance was improved by accelerating the loading of central data pages such as the omnibus Gene page, by rationalizing internal data structures and software for greater portability, and by making the Genome Browser highly customizable in how it views and exports genomic subsequences. Arbitrarily complex, user-specified queries are now possible through Textpresso (for all available literature) and through WormMart (for most genomic data). Biological content was enriched by reconciling all available cDNA and expressed sequence tag data with gene predictions, clarifying single nucleotide polymorphism and RNAi sites, and summarizing known functions for most genes studied in this organism.", "date": "2006-01-01", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "34", "number": "Databa", "publisher": "Oxford University Press", "pagerange": "D475-D478", "id_number": "CaltechAUTHORS:SCHWnar06", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:SCHWnar06", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1093/nar/gkj061", "pmcid": "PMC1347424", "primary_object": { "basename": "SCHWnar06.pdf", "url": "https://authors.library.caltech.edu/records/m1wgk-4j062/files/SCHWnar06.pdf" }, "resource_type": "article", "pub_year": "2006", "author_list": "Schwarz, Erich M.; Antoshechkin, Igor; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/fmz09-54128", "eprint_id": 95474, "eprint_status": "archive", "datestamp": "2023-08-19 16:47:37", "lastmod": "2023-10-20 20:16:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bird-D-McK", "name": { "family": "Bird", "given": "David McK." } }, { "id": "Blaxter-M-L", "name": { "family": "Blaxter", "given": "Mark L." } }, { "id": "McCarter-J-P", "name": { "family": "McCarter", "given": "James P." } }, { "id": "Mitreva-M", "name": { "family": "Mitreva", "given": "Makedonka" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Thomas-W-K", "name": { "family": "Thomas", "given": "W. Kelley" } } ] }, "title": "A White Paper on Nematode Comparative Genomics", "ispublished": "pub", "full_text_status": "public", "keywords": "Caenorhabditis elegans, comparative genomics, genome sequencing, systematics", "note": "\u00a9 2005 Society of Nematologists. \n\nReceived for publication 19 July 2005. \n\nThe authors are grateful for discussions with and comments from many colleagues, especially during the Genome Workshop at the 2004 Society of Nematology annual meeting, Estes Park, CO, August 2004 (Bird, 2004), and the Helminth Genome Sequencing Meeting organized by Prof. R. Maizels and held at the Sanger Institute, Cambridge, UK, March, 2004. In particular, we thank Prof. Maizels for allowing us to draw from his report of that meeting in preparing this document.\n\nPublished - 408.pdf
", "abstract": "In response to the new opportunities for genome sequencing and comparative genomics, the Society of Nematology (SON) formed a committee to develop a white paper in support of the broad scientific needs associated with this phylum and interests of SON members. Although genome sequencing is expensive, the data generated are unique in biological systems in that genomes have the potential to be complete (every base of the genome can be accounted for), accurate (the data are digital and not subject to stochastic variation), and permanent (once obtained, the genome of a species does not need to be experimentally re-sampled). The availability of complete, accurate, and permanent genome sequences from diverse nematode species will underpin future studies into the biology and evolution of this phylum and the ecological associations (particularly parasitic) nematodes have with other organisms. We anticipate that upwards of 100 nematode genomes will be solved to varying levels of completion in the coming decade and suggest biological and practical considerations to guide the selection of the most informative taxa for sequencing.", "date": "2005-12", "date_type": "published", "publication": "Journal of Nematology", "volume": "37", "number": "4", "publisher": "Society of Nematologists", "pagerange": "408-416", "id_number": "CaltechAUTHORS:20190514-091645302", "issn": "0022-300X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-091645302", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "pmcid": "PMC2620993", "primary_object": { "basename": "408.pdf", "url": "https://authors.library.caltech.edu/records/fmz09-54128/files/408.pdf" }, "resource_type": "article", "pub_year": "2005", "author_list": "Bird, David McK.; Blaxter, Mark L.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/80b3x-n4967", "eprint_id": 95465, "eprint_status": "archive", "datestamp": "2023-08-19 15:59:54", "lastmod": "2023-10-20 20:15:46", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Vulval development", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2005 Paul W. Sternberg. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nEdited by Barbara J. Meyer. Last revised June 18, 2005. Published June, 25 2005. \n\nI am grateful to all my colleagues over the past 25 years who have studied vulval development or at least been willing to discuss it, especially Bob Horvitz, John Sulston, Judith Kimble, Chip Ferguson, Iva Greenwald, Victor Ambros, John White, Bill Fixsen, Jim Thomas, Tim Schedl, Stuart Kim, Meera Sundaram, Hitoshi Sawa, Alex Hajnal, Ira Herskowitz, Geraldine Seydoux, David Eisenmann, and in my laboratory, Raffi Aroian, Russell Hill, Gregg Jongeward, Min Han, Hiroyuki Mori, Andy Golden, Paul Kayne, Linda Huang, Helen Chamberlin, Jane Mendel, Junho Lee, Kyria Tietze, Robert Palmer, Wendy Katz, Ralf Sommer, Anna Newman, Giovanni Lesa, Jing Liu, Tom Clandinin, Marie-Anne Felix, Keith Brown, Minqin Wang, Pheobe Tzou, Yvonne Hajdu-Cronin, Chris Lacenere, Charles Yoon, Neil Hopper, Chieh Chang, Nadeem Moghal, Rene Garcia, Aidyl Gonzalez-Serricchio, Martha Kirouac, Shahla Gharib, Bhagwati Gupta, David Sherwood, Byung Hwang, Takao Inoue, Cheryl Van Buskirk, Jolene Fernandes, Ted Ririe, David Goulet, and Edo Israeli. I thank Cheryl Van Buskirk and Iva Greenwald for helpful editorial comments. \n\nI am grateful to the following sources that funded vulval development research in my laboratory: Searle Foundation (1988-1991); National Institutes of Health HD23690 (1988 -2000), March of Dimes (1988-1994), National Science Foundation (1988-1991), U.S. Army Breast Cancer Research Program (1992-1997) and the Howard Hughes Medical Institute (1989-present), as well as postdoctoral fellowships from American Cancer Society, Human Frontier Science Program, Life Sciences Research Foundation, Lymphoma and Leukemia Society, Damon Runyon Cancer Research Foundation, California Breast Cancer Research Program, European Molecular Biology Organization, National Institutes of Health, U.S.A. I am an Investigator with the Howard Hughes Medical Institute.\n\nPublished - vulvaldev.pdf
", "abstract": "C. elegans vulval development is an intensively studied example of animal organogenesis. A network of intercellular signaling, signal transduction, and transcriptional regulation underlies the precise formation of this organ, which is the connection between the hermaphrodite uterus and the outside of the nematode. A single cell of the somatic gonad, the anchor cell, organizes the development of the vulva from epidermal precursors as well as the physical connection of the epidermis with the uterus. WNT signaling acting via the HOX gene lin-39 renders six epidermal precursor cells competent to respond to other developmental signals. The anchor cell induces nearby epidermal precursor cells to generate vulval cells via an epidermal growth factor (EGF) signaling pathway. The precise pattern of vulval precursor cell fates involves the graded action of the EGF signaling and LIN-12 (Notch) mediated lateral signaling. EGF promotes the 1\u00b0 fate while LIN-12 promotes the 2\u00b0 fate. Both EGF and LIN-12 prevent precursor cells from adopting the 3\u00b0 fate, which generates non-specialized epidermis. EGF-receptor and Notch signaling are antagonistic: EGF-receptor signaling leads to down-regulation of the Notch-like receptor LIN-12, while LIN-12 signaling induces negative regulators of EGF-receptor signaling such as MAP kinase phosphatase LIP-1 and the tyrosine kinase ARK-1. The 1\u00b0 precursor cell generates vulE and vulF mature vulval cells; the pattern of vulE and vulF cells requires an additional signal from the anchor cell as well as WNT signaling. The two 2\u00b0 precursor cells generate vulA, vulB1, vulB2, vulC and vulD cells but in mirror symmetric polar patterns: ABCD and DCBA. The reversed polarity of the posterior 2\u00b0 precursor cell lineage requires WNT signaling mediated by both Frizzled class and Ryk class WNT-receptors LIN-17 and LIN-18, respectively. A network of transcription factors controls the seven mature adult cell types; these include the LIM domain protein LIN-11, the Pax2/5/8 protein EGL-38, the zinc finger protein LIN-29, and the Nkx6.1/6.2 protein COG-1. The anchor cell also patterns nearby uterine cells, via the DSL ligand LAG-2 and LIN-12, to generate the four uv1 cells that form the tight connection with the vulva. This connection is initiated by the anchor cell, which invades between the vulF cells in a process analogous to invasive behavior of metastatic tumor cells. During this invasion process, the basement membranes between the gonad and body wall are degraded. The extensive information about vulval development in C. elegans has helped it become a paradigmatic case for identifying and studying a variety of regulatory pathways.", "date": "2005-06-25", "date_type": "published", "publication": "WormBook: the online review of C. elegans biology", "publisher": "WormBase", "pagerange": "Art. No. 1.6.1", "id_number": "CaltechAUTHORS:20190514-080615692", "issn": "1551-8507", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-080615692", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Searle Foundation" }, { "agency": "NIH", "grant_number": "HD23690" }, { "agency": "March of Dimes Foundation" }, { "agency": "NSF" }, { "agency": "Army Breast Cancer Research Program" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "American Cancer Society" }, { "agency": "Human Frontier Science Program" }, { "agency": "Life Sciences Research Foundation" }, { "agency": "Lymphoma and Leukemia Society" }, { "agency": "Damon Runyon Cancer Research Foundation" }, { "agency": "California Breast Cancer Research Program" }, { "agency": "European Molecular Biology Organization (EMBO)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1895/wormbook.1.6.1", "primary_object": { "basename": "vulvaldev.pdf", "url": "https://authors.library.caltech.edu/records/80b3x-n4967/files/vulvaldev.pdf" }, "resource_type": "article", "pub_year": "2005", "author_list": "Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/7em6p-tj508", "eprint_id": 1165, "eprint_status": "archive", "datestamp": "2023-08-22 03:28:29", "lastmod": "2023-10-13 22:39:32", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Inoue-Takao", "name": { "family": "Inoue", "given": "Takao" } }, { "id": "Wang-Minqin", "name": { "family": "Wang", "given": "Minqin" } }, { "id": "Ririe-T-O", "name": { "family": "Ririe", "given": "Ted O." } }, { "id": "Fernandes-J-S", "name": { "family": "Fernandes", "given": "Jolene S." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Transcriptional network underlying Caenorhabditis elegans vulval development", "ispublished": "pub", "full_text_status": "public", "keywords": "ORGANOGENESIS, SIGNALING PATHWAYS, TRANSCRIPTION, HOMEOBOX GENE LIN-11, VENTRAL NEURAL-TUBE, C-ELEGANS, CELL MORPHOGENESIS, NEURONAL FATE, PROTEIN, ENCODES, DIFFERENTIATION, HOMEODOMAIN, EXPRESSION", "note": "\u00a9 2005 by the National Academy of Sciences. \n\nEdited by Eric H. Davidson, California Institute of Technology, Pasadena, CA, and approved February 1, 2005 (received for review November 11, 2004). \n\nWe thank A. Fire (Stanford University, Stanford, CA) for providing GFP vectors, and I. Hope (University of Leeds, Leeds, U.K.) for providing the C55C3.5::gfp construct. We thank Ryan Baugh, Jennifer Sanders, Mihoko Kato, Steven Kuntz, Alok Saldanha, and reviewers for comments on the manuscript. We thank the Caenorhabditis Genetics Center (University of Minnesota, Minneapolis) for C. elegans strains. T.I. was supported by fellowship DRG-1646 from the Damon Runyon Cancer Research Foundation. Research was supported by the Howard Hughes Medical Institute, with which P.W.S. is an investigator. \n\nThis paper was submitted directly (Track II) to the PNAS office.\n\nPublished - INOpnas05.pdf
", "abstract": "The vulval development of Caenorhabditis elegans provides an opportunity to investigate genetic networks that control gene expression during organogenesis. During the fourth larval stage (L4), seven vulval cell types are produced, each of which executes a distinct gene expression program. We analyze how the expression of cell-type-specific genes is regulated. Ras and Writ signaling pathways play major roles in generating the spatial pattern of cell types and regulate gene expression through a network of transcription factors. One transcription factor (lin-29) primarily controls the temporal expression pattern. Other transcription factors (lin-11, cog-1, and egl-38) act in combination to control cell-type-specific gene expression. The complexity of the network arises in part because of the dynamic nature of gene expression, in part because of the presence of seven cell types, and also because there are multiple regulatory paths for gene expression within each cell type.", "date": "2005-04-05", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "102", "number": "14", "publisher": "National Academy of Sciences", "pagerange": "4972-4977", "id_number": "CaltechAUTHORS:INOpnas05", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:INOpnas05", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Damon Runyon Cancer Research Foundation", "grant_number": "DRG-1646" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1073/pnas.0408122102", "pmcid": "PMC555976", "primary_object": { "basename": "INOpnas05.pdf", "url": "https://authors.library.caltech.edu/records/7em6p-tj508/files/INOpnas05.pdf" }, "resource_type": "article", "pub_year": "2005", "author_list": "Inoue, Takao; Wang, Minqin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/mbs8e-rsm97", "eprint_id": 989, "eprint_status": "archive", "datestamp": "2023-08-22 03:11:00", "lastmod": "2023-10-13 22:04:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cronin-C-J", "name": { "family": "Cronin", "given": "Christopher J." } }, { "id": "Mendel-J-E", "name": { "family": "Mendel", "given": "Jane E." } }, { "id": "Mukhtar-S", "name": { "family": "Mukhtar", "given": "Saleem" } }, { "id": "Kim-Young-Mee", "name": { "family": "Kim", "given": "Young-Mee" } }, { "id": "Stirbl-R-C", "name": { "family": "Stirbl", "given": "Robert C." } }, { "id": "Bruck-J", "name": { "family": "Bruck", "given": "Jehoshua" }, "orcid": "0000-0001-8474-0812" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "An automated system for measuring parameters of nematode sinusoidal movement", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2005 Cronin et al; licensee BioMed Central Ltd.\nThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nAvailability of source code: Source code is available through a GPL at http://wormlab.caltech.edu/publications/download.html \n\nDocumentation of this software is available as a pdf from http://wormlab.caltech.edu/publications/download.html \n\nContributions of authors: SM, JB, JM and PS conceived and designed the original automated system for tracking and movement measurement. SM developed a working prototype system and brought in the key algorithms used. CC wrote most of the code in the current release. JM developed the protocol for the plate assay, and devised the dose-response and genetic experiments. RS conceived of applying automated analysis of C. elegans movement for toxicology studies, YK performed most of the toxicology experiments. JM, CC, RS and PS analyzed the data. CC, JM, and PS wrote the paper. All authors read and approved the final manuscript. \n\nAcknowledgements: We thank X. Xu for suggesting length normalization, Jonathan Shewchuk for Triangle, and anonymous reviewers for many helpful suggestions. Supported by grants from the ONR (S.B.), DARPA (R. S.) and Howard Hughes Medical Institute, with which PWS is an Investigator.\n\nPublished - CRObmcg05.pdf
", "abstract": "Background: Nematode sinusoidal movement has been used as a phenotype in many studies of C. elegans development, behavior and physiology. A thorough understanding of the ways in which genes control these aspects of biology depends, in part, on the accuracy of phenotypic analysis. While worms that move poorly are relatively easy to describe, description of hyperactive movement and movement modulation presents more of a challenge. An enhanced capability to analyze all the complexities of nematode movement will thus help our understanding of how genes control behavior.\n\nResults: We have developed a user-friendly system to analyze nematode movement in an automated and quantitative manner. In this system nematodes are automatically recognized and a computer-controlled microscope stage ensures that the nematode is kept within the camera field of view while video images from the camera are stored on videotape. In a second step, the images from the videotapes are processed to recognize the worm and to extract its changing position and posture over time. From this information, a variety of movement parameters are calculated. These parameters include the velocity of the worm's centroid, the velocity of the worm along its track, the extent and frequency of body bending, the amplitude and wavelength of the sinusoidal movement, and the propagation of the contraction wave along the body. The length of the worm is also determined and used to normalize the amplitude and wavelength measurements. \n\nTo demonstrate the utility of this system, we report here a comparison of movement parameters for a small set of mutants affecting the Go/Gq mediated signaling network that controls acetylcholine release at the neuromuscular junction. The system allows comparison of distinct genotypes that affect movement similarly (activation of Gq-alpha versus loss of Go-alpha function), as well as of different mutant alleles at a single locus (null and dominant negative alleles of the goa-1 gene, which encodes Go-alpha). We also demonstrate the use of this system for analyzing the effects of toxic agents. Concentration-response curves for the toxicants arsenite and aldicarb, both of which affect motility, were determined for wild-type and several mutant strains, identifying P-glycoprotein mutants as not significantly more sensitive to either compound, while cat-4 mutants are more sensitive to arsenite but not aldicarb. \n\nConclusions: Automated analysis of nematode movement facilitates a broad spectrum of experiments. Detailed genetic analysis of multiple alleles and of distinct genes in a regulatory network is now possible. These studies will facilitate quantitative modeling of C. elegans movement, as well as a comparison of gene function. Concentration-response curves will allow rigorous analysis of toxic agents as well as of pharmacological agents. This type of system thus represents a powerful analytical tool that can be readily coupled with the molecular genetics of nematodes.", "date": "2005-02-07", "date_type": "published", "publication": "BMC Genetics", "volume": "6", "publisher": "BMC Genetics", "pagerange": "Art. No. 5", "id_number": "CaltechAUTHORS:CRObmcg05", "issn": "1471-2156", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:CRObmcg05", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Office of Naval Research (ONR)" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1186/1471-2156-6-5", "pmcid": "PMC549551", "primary_object": { "basename": "CRObmcg05.pdf", "url": "https://authors.library.caltech.edu/records/mbs8e-rsm97/files/CRObmcg05.pdf" }, "resource_type": "article", "pub_year": "2005", "author_list": "Cronin, Christopher J.; Mendel, Jane E.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/mzz80-z1b49", "eprint_id": 26098, "eprint_status": "archive", "datestamp": "2023-08-19 15:20:56", "lastmod": "2023-10-24 16:13:59", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cronin-C-J", "name": { "family": "Cronin", "given": "Christopher J." } }, { "id": "Mendel-J-E", "name": { "family": "Mendel", "given": "Jane E." } }, { "id": "Mukhtar-S", "name": { "family": "Mukhtar", "given": "Saleem" } }, { "id": "Kim-Y-M", "name": { "family": "Kim", "given": "Young-Mee" } }, { "id": "Stirbl-R-C", "name": { "family": "Stirbl", "given": "Robert C." } }, { "id": "Bruck-J", "name": { "family": "Bruck", "given": "Jehoshua" }, "orcid": "0000-0001-8474-0812" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "An automated system for measuring parameters of nematode sinusoidal movement", "ispublished": "unpub", "full_text_status": "public", "note": "Availability of source code \nSource code is available through a GPL at http://wormlab.caltech.edu/publications/download.html\nDocumentation of this software is available as a pdf from\nhttp://wormlab.caltech.edu/publications/download.html\n\nContributions of authors \nSM, JB, JM and PS conceived and designed the original\nautomated system for tracking and movement measurement.\nSM developed a working prototype system and brought in the key algorithms used. CC wrote most of the code in the current release. JM developed the protocol for the plate assay, and devised the dose-response and genetic experiments. RS conceived of applying automated analysis\nof C. elegans movement for toxicology studies, YK performed\nmost of the toxicology experiments. JM, CC, RS and PS analyzed the data. CC, JM, and PS wrote the paper. All authors read and approved the final manuscript. \n\nAcknowledgements \nWe thank X. Xu for suggesting length normalization, Jonathan Shewchuk for Triangle, and anonymous reviewers for many helpful suggestions. Supported by grants from the ONR (S.B.), DARPA (R. S.) and Howard Hughes Medical Institute, with which PWS is an Investigator. \n\nhttp://www.paradise.caltech.edu/papers/etr066.pdf", "abstract": "Background: Nematode sinusoidal movement has been used as a phenotype in many studies of C. elegans development, behavior and physiology. A thorough understanding of the ways in which genes control these aspects of biology depends, in part, on the accuracy of phenotypic analysis. While worms that move poorly are relatively easy to describe, description of hyperactive movement and movement modulation presents more of a challenge. An enhanced capability to analyze all the complexities of nematode movement will thus help our understanding of how genes control behavior.\n\nResults: We have developed a user-friendly system to analyze nematode movement in an automated and quantitative manner. In this system nematodes are automatically recognized and a computer-controlled microscope stage ensures that the nematode is kept within the camera field of view while video images from the camera are stored on videotape. In a second step, the images from the videotapes are processed to recognize the worm and to extract its changing position and posture over time. From this information, a variety of movement parameters are calculated. These parameters include the velocity of the worm's centroid, the velocity of the worm along its track, the extent and frequency of body bending, the amplitude and wavelength of the sinusoidal movement, and the propagation of the contraction wave along the body. The length of the worm is also determined and used to normalize the amplitude and wavelength measurements. \n\nTo demonstrate the utility of this system, we report here a comparison of movement parameters for a small set of mutants\naffecting the Go/Gq mediated signaling network that controls acetylcholine release at the neuromuscular junction. The system allows comparison of distinct genotypes that affect movement similarly (activation of Gq-alpha versus loss of Go-alpha function), as well as of different mutant alleles at a single locus (null and dominant negative alleles of the goa-1 gene, which encodes Goalpha). We also demonstrate the use of this system for analyzing the effects of toxic agents. Concentration-response curves for the toxicants arsenite and aldicarb, both of which affect motility, were determined for wild-type and several mutant strains,\nidentifying P-glycoprotein mutants as not significantly more sensitive to either compound, while cat-4 mutants are more sensitive to arsenite but not aldicarb.\n\nConclusions: Automated analysis of nematode movement facilitates a broad spectrum of experiments. Detailed genetic analysis of multiple alleles and of distinct genes in a regulatory network is now possible. These studies will facilitate quantitative modeling of C. elegans movement, as well as a comparison of gene function. Concentration-response curves will allow rigorous analysis\nof toxic agents as well as of pharmacological agents. This type of system thus represents a powerful analytical tool that can be readily coupled with the molecular genetics of nematodes.", "date": "2005-02-07", "date_type": "published", "publisher": "California Institute of Technology", "id_number": "CaltechPARADISE:2005.ETR066", "official_url": "https://resolver.caltech.edu/CaltechPARADISE:2005.ETR066", "rights": "You are granted permission for individual, educational, research and non-commercial reproduction, distribution, display and performance of this work in any format.", "local_group": { "items": [ { "id": "Parallel-and-Distributed-Systems-Group" } ] }, "primary_object": { "basename": "etr066.pdf", "url": "https://authors.library.caltech.edu/records/mzz80-z1b49/files/etr066.pdf" }, "resource_type": "monograph", "pub_year": "2005", "author_list": "Cronin, Christopher J.; Mendel, Jane E.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/wx1mf-4a394", "eprint_id": 818, "eprint_status": "archive", "datestamp": "2023-08-22 02:52:47", "lastmod": "2023-10-13 21:59:09", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chen-Nansheng", "name": { "family": "Chen", "given": "Nansheng" } }, { "id": "Harris-T-W", "name": { "family": "Harris", "given": "Todd W." }, "orcid": "0000-0003-3406-163X" }, { "id": "Antoshechkin-I-A", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Bastiani-C-A", "name": { "family": "Bastiani", "given": "Carol" } }, { "id": "Bieri-T", "name": { "family": "Bieri", "given": "Tamberlyn" } }, { "id": "Blasiar-D", "name": { "family": "Blasiar", "given": "Darin" } }, { "id": "Bradnam-K", "name": { "family": "Bradnam", "given": "Keith" } }, { "id": "Canaran-P", "name": { "family": "Canaran", "given": "Payan" } }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "Chen-Chao-Kung", "name": { "family": "Chen", "given": "Chao-Kung" } }, { "id": "Chen-Wen-J", "name": { "family": "Chen", "given": "Wen J." } }, { "id": "Cunningham-F", "name": { "family": "Cunningham", "given": "Fiona" } }, { "id": "Davis-P-M", "name": { "family": "Davis", "given": "Paul" } }, { "id": "Kenny-E-E", "name": { "family": "Kenny", "given": "Eimear" } }, { "id": "Kishore-R", "name": { "family": "Kishore", "given": "Ranjana" } }, { "id": "Lawson-D", "name": { "family": "Lawson", "given": "Daniel" } }, { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "Raymond" }, "orcid": "0000-0002-8151-7479" }, { "id": "M\u00fcller-H-M", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } }, { "id": "Nakamura-Cecilia", "name": { "family": "Nakamura", "given": "Cecilia" }, "orcid": "0000-0002-4689-7314" }, { "id": "Pai-S", "name": { "family": "Pai", "given": "Shraddha" } }, { "id": "Ozersky-P", "name": { "family": "Ozersky", "given": "Philip" } }, { "id": "Petcherski-A", "name": { "family": "Petcherski", "given": "Andrei" } }, { "id": "Rogers-A", "name": { "family": "Rogers", "given": "Anthony" } }, { "id": "Sabo-Aniko", "name": { "family": "Sabo", "given": "Aniko" } }, { "id": "Schwarz-E-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Wang-Qinghua", "name": { "family": "Wang", "given": "Qinghua" } }, { "id": "Durbin-R", "name": { "family": "Durbin", "given": "Richard" } }, { "id": "Spieth-J", "name": { "family": "Spieth", "given": "John" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Stein-L-D", "name": { "family": "Stein", "given": "Lincoln D." }, "orcid": "0000-0002-1983-4588" } ] }, "title": "WormBase: a comprehensive data resource for Caenorhabditis biology and genomics", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2005, the authors. Nucleic Acids Research, Vol. 33, Database issue \u00a9 Oxford University Press 2005; all rights reserved \n\nReceived August 21, 2004; Revised and Accepted October 5, 2004 \n\nP.W.S. is an Investigator with the Howard Hughes Medical Institute. We thank Sheldon McKay and Kris Gunsalus for critical reading of the manuscript. WormBase is supported by grant P41-HG02223 from the US National Human Genome Research Institute and the British Medical Research Council. \n\nAs always, we welcome comments, questions, corrections and data submissions (wormbase-help@wormbase.org). \n\nThe authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors. \n\nThe online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions@oupjournals.org.\n\nPublished - CHEnar05.pdf
", "abstract": "WormBase (http://www.wormbase.org), the model organism database for information about Caenorhabditis elegans and related nematodes, continues to expand in breadth and depth. Over the past year, WormBase has added multiple large-scale datasets including SAGE, interactome, 3D protein structure datasets and NCBI KOGs. To accommodate this growth, the International WormBase Consortium has improved the user interface by adding new features to aid in navigation, visualization of large-scale datasets, advanced searching and data mining. Internally, we have restructured the database models to rationalize the representation of genes and to prepare the system to accept the genome sequences of three additional Caenorhabditis species over the coming year.", "date": "2005", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "33", "number": "Databa", "publisher": "Oxford University Press", "pagerange": "D383-D389", "id_number": "CaltechAUTHORS:CHEnar05", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:CHEnar05", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1093/nar/gki066", "pmcid": "PMC540020", "primary_object": { "basename": "CHEnar05.pdf", "url": "https://authors.library.caltech.edu/records/wx1mf-4a394/files/CHEnar05.pdf" }, "resource_type": "article", "pub_year": "2005", "author_list": "Chen, Nansheng; Harris, Todd W.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ww2rn-1xk35", "eprint_id": 95475, "eprint_status": "archive", "datestamp": "2023-08-19 14:49:29", "lastmod": "2023-10-20 20:16:23", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hajdu-Cronin-Y-M", "name": { "family": "Hajdu-Cronin", "given": "Yvonne M." } }, { "id": "Chen-Wen-J", "name": { "family": "Chen", "given": "Wen J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The L-Type Cyclin CYL-1 and the Heat-Shock-Factor HSF-1 Are Required for Heat-Shock-Induced Protein Expression in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2004 by the Genetics Society of America. \n\nManuscript received March 10, 2004; Accepted for publication July 29, 2004. \n\nWe thank C. Bastiani for C. elegans GOA-1 antibody, M. C. Hresko and R. Waterston for MH16 anti-paramyosin antibody, the C. elegans Genetics Center for strains, A. Coulson for cosmids used in positional cloning, and Y. Kohara for cDNA clones. We thank H. Yu, G. Schindelman, E. Schwarz, N. Moghal, L. R. Garcia, C. van Buskirk, C. Bastiani, R. Lee, B. Gupta, and T. Inoue for advice and helpful discussions. We thank E.-S. David, R. Pant, and C. Dionne for guidance and E. Rothenberg for use of her facility for Q-PCR. C. Cronin provided the software for analyzing the length of worms. Most mapping information was obtained from WormBase (http://www.wormbase.org). Research was supported by the Howard Hughes Medical Institute, with which P.W.S. is an investigator. W.J.C. was an Amgen graduate Fellow. \n\nSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY557405, AY559747, and AY559748.\n\nPublished - 8423.pdf
", "abstract": "In a screen for suppressors of activated GOA-1 (G\u03b1_o) under the control of the hsp-16.2heat-shock promoter, we identified three genetic loci that affected heat-shock-induced GOA-1 expression. The cyl-1 mutants are essentially wild type in appearance, while hsf-1and sup-45 mutants have egg-laying defects. The hsf-1 mutation also causes a temperature-sensitive developmental arrest, and hsf-1 mutants have decreased life span. Western analysis indicated that mutations in all three loci suppressed the activated GOA-1 transgene by decreasing its expression. Heat-shock-induced expression of hsp-16.2 mRNA was reduced in cyl-1 mutants and virtually eliminated in hsf-1 and sup-45 mutants, as compared to wild-type expression. The mutations could also suppress other transgenes under heat-shock control. cyl-1 and sup-45, but not hsf-1, mutations suppressed a defect caused by a transgene not under heat-shock control, suggesting a role in general transcription or a post-transcriptional aspect of gene expression. hsf-1 encodes the C. elegans homolog of the human heat-shock factor HSF1, and cyl-1 encodes a cyclin most similar to cyclin L. We believe HSF-1 acts in heat-shock-inducible transcription and CYL-1 acts more generally in gene expression.", "date": "2004-12-01", "date_type": "published", "publication": "Genetics", "volume": "168", "number": "4", "publisher": "Genetics Society of America", "pagerange": "1937-1949", "id_number": "CaltechAUTHORS:20190514-092613986", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-092613986", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Amgen" } ] }, "doi": "10.1534/genetics.104.028423", "pmcid": "PMC1448743", "primary_object": { "basename": "8423.pdf", "url": "https://authors.library.caltech.edu/records/ww2rn-1xk35/files/8423.pdf" }, "resource_type": "article", "pub_year": "2004", "author_list": "Hajdu-Cronin, Yvonne M.; Chen, Wen J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/xts0b-1kr77", "eprint_id": 295, "eprint_status": "archive", "datestamp": "2023-08-22 02:36:57", "lastmod": "2023-10-13 20:36:41", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "M\u00fcller-H-M", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } }, { "id": "Kenny-E-E", "name": { "family": "Kenny", "given": "Eimear E." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Textpresso: An Ontology-Based Information Retrieval and Extraction System for Biological Literature", "ispublished": "pub", "full_text_status": "public", "keywords": "CGC, Caenorhabditis Genetics Center; GMOD, Generic Model Organism Database; GO, Gene Ontology; PERL, Practical Extraction and Report Language; PMID, PubMed unique identifier; SNOMED, Systemized Nomenclature of Medicine; UMLS, Unified Medical Language System; XML, eXtensible Markup Language; XPDF, a PDF viewer for X", "note": "Copyright: 2004 Muller et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived November 17, 2003; Accepted July 19, 2004; Published September 21, 2004. \n\nThis work was supported in part by a grant (# P41 HG02223) from the National Human Genome Research Institute at the United States National Institutes of Health. HMM was a participant in the Initiative in Computational Molecular Biology, which was funded by the Burroughs Wellcome Fund Interfaces program, and was a Howard Hughes Medical Institute Associate, with which Paul W. Sternberg is an Investigator. We thank Juancarlos Chan for programming help, Andrei Petcherski for his help with evaluating the Textpresso system, Robert Li for developing the PDF-to-text conversion software package, and Daniel Wang for the continued acquisition of papers. We thank Igor Antoshechkin, Kimberly Van Auken, Carol Bastiani, Ranjana Kishore, Raymond Lee, Alok Saldanha, Erich Schwarz, Weiwei Zhong, and the anonymous referees for helpful comments on the manuscript. \n\nConflicts of interest: The authors have declared that no conflicts of interest exist. \n\nAuthor contributions: HMM, EEK, and PWS conceived and designed the experiments. HMM, EEK, and PWS performed the experiments. HMM, EEK, and PWS analyzed the data. HMM, EEK, PWS contributed reagents/materials/analysis tools. HMM, EEK, and PWS wrote the paper.\n\nPublished - MULpb04.pdf
", "abstract": "We have developed Textpresso, a new text-mining system for scientific literature whose capabilities go far beyond those of a simple keyword search engine. Textpresso's two major elements are a collection of the full text of scientific articles split into individual sentences, and the implementation of categories of terms for which a database of articles and individual sentences can be searched. The categories are classes of biological concepts (e.g., gene, allele, cell or cell group, phenotype, etc.) and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., biological process, etc.). Together they form a catalog of types of objects and concepts called an ontology. After this ontology is populated with terms, the whole corpus of articles and abstracts is marked up to identify terms of these categories. The current ontology comprises 33 categories of terms. A search engine enables the user to search for one or a combination of these tags and/or keywords within a sentence or document, and as the ontology allows word meaning to be queried, it is possible to formulate semantic queries. Full text access increases recall of biological data types from 45% to 95%. Extraction of particular biological facts, such as gene-gene interactions, can be accelerated significantly by ontologies, with Textpresso automatically performing nearly as well as expert curators to identify sentences; in searches for two uniquely named genes and an interaction term, the ontology confers a 3-fold increase of search efficiency. Textpresso currently focuses on Caenorhabditis elegans literature, with 3,800 full text articles and 16,000 abstracts. The lexicon of the ontology contains 14,500 entries, each of which includes all versions of a specific word or phrase, and it includes all categories of the Gene Ontology database. Textpresso is a useful curation tool, as well as search engine for researchers, and can readily be extended to other organism-specific corpora of text. Textpresso can be accessed at http://www.textpresso.org or via WormBase at http://www.wormbase.org.", "date": "2004-11", "date_type": "published", "publication": "PLoS Biology", "volume": "2", "number": "11", "publisher": "Public Library of Science", "pagerange": "1984-1998", "id_number": "CaltechAUTHORS:MULpb04", "issn": "1544-9173", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:MULpb04", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P41 HG02223" }, { "agency": "National Human Genome Research Institute" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1371/journal.pbio.0020309", "pmcid": "PMC517822", "primary_object": { "basename": "MULpb04.pdf", "url": "https://authors.library.caltech.edu/records/xts0b-1kr77/files/MULpb04.pdf" }, "resource_type": "article", "pub_year": "2004", "author_list": "M\u00fcller, Hans-Michael; Kenny, Eimear E.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/7ce86-88h06", "eprint_id": 95477, "eprint_status": "archive", "datestamp": "2023-08-22 02:32:04", "lastmod": "2023-10-20 20:16:26", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Broday-L", "name": { "family": "Broday", "given": "Limor" } }, { "id": "Kolotuev-I", "name": { "family": "Kolotuev", "given": "Irina" } }, { "id": "Didier-C", "name": { "family": "Didier", "given": "Christine" } }, { "id": "Bhoumik-A", "name": { "family": "Bhoumik", "given": "Anindita" } }, { "id": "Gupta-B-P", "name": { "family": "Gupta", "given": "Bhagwati P." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Podbilewicz-B", "name": { "family": "Podbilewicz", "given": "Benjamin" } }, { "id": "Ronai-Z", "name": { "family": "Ronai", "given": "Ze'ev" } } ] }, "title": "The small ubiquitin-like modifier (SUMO) is required for gonadal and uterine-vulval morphogenesis in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "SUMO; somatic gonad; smo-1; lin-11; uterine\u2013vulval connection", "note": "\u00a9 2004 by Cold Spring Harbor Laboratory Press. \n\nReceived May 28, 2004; revised version accepted August 9, 2004. \n\nWe thank the C. elegans Gene Knockout Project team at OMRF for generating the smo-1 null strain. We thank the Caernorhabditis Genetics Center (CGC) for providing strains, Reuven Agami for the kind gift of the pSUPER construct, Ke Shuai for the PIAS3 plasmid, Susan Strome for the SP56 antibody, and Chelly Hresko and Bob Waterston for the MH27 antibody. We also thank the members of the Ronai and Podbilewicz Labs for discussions. P.W.S. is an Investigator and P.B.G. was an Associate with the HHMI. Support from NCI grant CA59908 (to Z.R.), HFSP, and the Israel Science Foundation (to B.P.) is gratefully acknowledged.\n\nPublished - 0182380.pdf
Supplemental Material - BrodaySuppFig1.pdf
Supplemental Material - BrodaySuppFig2.pdf
Supplemental Material - BrodaySuppFig3.pdf
Supplemental Material - BrodaySuppFig4.pdf
Supplemental Material - BrodaySuppFig5.pdf
Supplemental Material - BrodaySuppFigureLegends.doc
Supplemental Material - Broday_Fig6.pdf
", "abstract": "The small ubiquitin-like modifier (SUMO) modification alters the subcellular distribution and function of its substrates. Here we show the major role of SUMO during the development of the Caenorhabditis elegans reproductive system. smo-1 deletion mutants develop into sterile adults with abnormal somatic gonad, germ line, and vulva. SMO-1::GFP reporter is highly expressed in the somatic reproductive system. smo-1 animals lack a vulval-uterine connection as a result of impaired ventral uterine \u03c0-cell differentiation and anchor cell fusion. Mutations in the LIN-11 LIM domain transcription factor lead to a uterine phenotype that resembles the smo-1 phenotype. LIN-11 is sumoylated, and its sumoylation is required for its activity during uterine morphogenesis. Expression of a SUMO-modified LIN-11 in the smo-1 background partially rescued \u03c0-cell differentiation and retained LIN-11 in nuclear bodies. Thus, our results identify the reproductive system as the major SUMO target during postembryonic development and highlight LIN-11 as a physiological substrate whose sumoylation is associated with the formation of a functional vulval-uterine connection.", "date": "2004-10-01", "date_type": "published", "publication": "Genes and Development", "volume": "18", "number": "19", "publisher": "Cold Spring Harbor Laboratory Press", "pagerange": "2380-2391", "id_number": "CaltechAUTHORS:20190514-100517710", "issn": "0890-9369", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-100517710", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "CA59908" }, { "agency": "Human Frontier Science Program" }, { "agency": "Israel Science Foundation" } ] }, "doi": "10.1101/gad.1227104", "pmcid": "PMC522988", "primary_object": { "basename": "BrodaySuppFig1.pdf", "url": "https://authors.library.caltech.edu/records/7ce86-88h06/files/BrodaySuppFig1.pdf" }, "related_objects": [ { "basename": "BrodaySuppFig2.pdf", "url": "https://authors.library.caltech.edu/records/7ce86-88h06/files/BrodaySuppFig2.pdf" }, { "basename": "BrodaySuppFig3.pdf", "url": "https://authors.library.caltech.edu/records/7ce86-88h06/files/BrodaySuppFig3.pdf" }, { "basename": "BrodaySuppFig4.pdf", "url": "https://authors.library.caltech.edu/records/7ce86-88h06/files/BrodaySuppFig4.pdf" }, { "basename": "BrodaySuppFig5.pdf", "url": "https://authors.library.caltech.edu/records/7ce86-88h06/files/BrodaySuppFig5.pdf" }, { "basename": "BrodaySuppFigureLegends.doc", "url": "https://authors.library.caltech.edu/records/7ce86-88h06/files/BrodaySuppFigureLegends.doc" }, { "basename": "Broday_Fig6.pdf", "url": "https://authors.library.caltech.edu/records/7ce86-88h06/files/Broday_Fig6.pdf" }, { "basename": "0182380.pdf", "url": "https://authors.library.caltech.edu/records/7ce86-88h06/files/0182380.pdf" } ], "resource_type": "article", "pub_year": "2004", "author_list": "Broday, Limor; Kolotuev, Irina; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/vjfw3-xy107", "eprint_id": 76137, "eprint_status": "archive", "datestamp": "2023-08-19 14:17:05", "lastmod": "2023-10-25 15:32:30", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Inoue-Takao", "name": { "family": "Inoue", "given": "Takao" } }, { "id": "Oz-H-S", "name": { "family": "Oz", "given": "Helieh S." } }, { "id": "Wiland-D", "name": { "family": "Wiland", "given": "Debra" } }, { "id": "Gharib-S", "name": { "family": "Gharib", "given": "Shahla" } }, { "id": "Deshpande-R", "name": { "family": "Deshpande", "given": "Rashmi" } }, { "id": "Hill-R-J", "name": { "family": "Hill", "given": "Russell J." } }, { "id": "Katz-W-S", "name": { "family": "Katz", "given": "Wendy S." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "C. elegans LIN-18 Is a Ryk Ortholog and Functions in Parallel to LIN-17/Frizzled in Wnt Signaling", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2004 Cell Press. \n\nReceived 16 March 2004, Revised 14 July 2004, Accepted 24 July 2004, Available online 16 September 2004. Published: September 16, 2004. \n\nWe thank J. Goodwin for technical assistance, X.Z.S. Xu for DsRed2 plasmids, and B.P. Gupta for lin-17 plasmids. We thank A. Fire, S. Xu, J. Ahnn, and G. Seydoux for gfp vectors, D. Eisenmann and S. Kim for ga75, and Y. Kohara for cDNA clones and in situ data. Some strains were obtained from Caenorhabditis Genetics Center, funded by NIH, National Center for Research Resources. P.W.S. is an Investigator with and W.S.K. was an Associate with the HHMI, which supported this work. T.I. was supported by fellowship DRG-1646 from the Damon Runyon Cancer Research Foundation. W.S.K. was also supported by grants: March of Dimes 5-FY97-0674, ACS IRG-163H, and EPSCoR OSR-9452895. R.J.H. was supported by March of Dimes 5-FY00-550.\n\nSupplemental Material - mmc1.pdf
", "abstract": "Wnt proteins are intercellular signals that regulate various aspects of animal development. In Caenorhabditis elegans, mutations in lin-17, a Frizzled-class Wnt receptor, and in lin-18 affect cell fate patterning in the P7.p vulval lineage. We found that lin-18 encodes a member of the Ryk/Derailed family of tyrosine kinase-related receptors, recently found to function as Wnt receptors. Members of this family have nonactive kinase domains. The LIN-18 kinase domain is dispensable for LIN-18 function, while the Wnt binding WIF domain is required. We also found that Wnt proteins LIN-44, MOM-2, and CWN-2 redundantly regulate P7.p patterning. Genetic interactions indicate that LIN-17 and LIN-18 function independently of each other in parallel pathways, and different ligands display different receptor specificities. Thus, two independent Wnt signaling pathways, one employing a Ryk receptor and the other a Frizzled receptor, function in parallel to regulate cell fate patterning in the C. elegans vulva.", "date": "2004-09-17", "date_type": "published", "publication": "Cell", "volume": "118", "number": "6", "publisher": "Elsevier", "pagerange": "795-806", "id_number": "CaltechAUTHORS:20170408-160853586", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170408-160853586", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Damon Runyon Cancer Research Foundation", "grant_number": "DRG-1646" }, { "agency": "March of Dimes", "grant_number": "5-FY97-0674" }, { "agency": "American Cancer Society", "grant_number": "IRG-163H" }, { "agency": "NSF", "grant_number": "OSR-9452895" }, { "agency": "March of Dimes", "grant_number": "5-FY00-550" } ] }, "doi": "10.1016/j.cell.2004.09.001", "primary_object": { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/vjfw3-xy107/files/mmc1.pdf" }, "resource_type": "article", "pub_year": "2004", "author_list": "Inoue, Takao; Oz, Helieh S.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/rwm63-gpv06", "eprint_id": 264, "eprint_status": "archive", "datestamp": "2023-08-22 02:19:12", "lastmod": "2023-10-13 20:35:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Feng-Zhaoyang", "name": { "family": "Feng", "given": "Zhaoyang" } }, { "id": "Cronin-C-J", "name": { "family": "Cronin", "given": "Christopher J." } }, { "id": "Wittig-J-H-Jr", "name": { "family": "Wittig", "given": "John H., Jr." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Schafer-W-R", "name": { "family": "Schafer", "given": "William R." } } ] }, "title": "An imaging system for standardized quantitative analysis of C.\n elegans behavior", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2004 Feng et al; licensee BioMed Central Ltd.\nThis is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),\nwhich permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived: 12 May 2004; Accepted: 26 August 2004; Published: 26 August 2004. \n\nThis article is available from: http://www.biomedcentral.com/1471-2105/5/115 \n\nThis work was supported by research grants from the National Institutes of Health (to W.R.S. and P.W.S.) and the Howard Hughes Medical Institute (P.W.S.). Zhaoyang Feng is a postdoctoral fellow of the Burroughs-Wellcome Fund/La Jolla Interfaces in Science interdisciplinary training program. The authors thank Anthony Kempf for critical discussion. \n\nZF and CJC jointly wrote the software and developed the system described here. JHW developed an early version of the system and designed the hardware configuration. PWS and WRS jointly conceived of this project, and participated in its design and coordination. WRS drafted the manuscript, CJC drafted the supplemental guide to the algorithms, and ZF drafted the supplemental hardware list. All authors read and approved the final version.\n\nPublished - FENbmcb04.pdf
Supplemental Material - 1471-2105-5-115-S1.doc
Supplemental Material - 1471-2105-5-115-S2.pdf
Supplemental Material - 1471-2105-5-115-S3.zip
Supplemental Material - 1471-2105-5-115-S4.doc
", "abstract": "Background: The nematode Caenorhabditis elegans is widely used for the genetic analysis of neuronal cell biology, development, and behavior. Because traditional methods for evaluating behavioral phenotypes are qualitative and imprecise, there is a need for tools that allow quantitation and standardization of C. elegans behavioral assays.\nResults: Here we describe a tracking and imaging system for the automated analysis of C. elegans morphology and behavior. Using this system, it is possible to record the behavior of individual nematodes over long time periods and quantify 144 specific phenotypic parameters.\nConclusions: These tools for phenotypic analysis will provide reliable, comprehensive scoring of a wide range of behavioral abnormalities, and will make it possible to standardize assays such that behavioral data from different labs can readily be compared. In addition, this system will facilitate high-throughput collection of phenotypic data that can ultimately be used to generate a comprehensive database of C. elegans phenotypic information.\nAvailability: The hardware configuration and software for the system are available from wschafer AT ucsd.edu.", "date": "2004-08-26", "date_type": "published", "publication": "BMC Bioinformatics", "volume": "5", "publisher": "BioMed Central", "pagerange": "Art. No. 115", "id_number": "CaltechAUTHORS:FENbmcb04", "issn": "1471-2105", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:FENbmcb04", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Burroughs Wellcome Fund" } ] }, "doi": "10.1186/1471-2105-5-115", "pmcid": "PMC517925", "primary_object": { "basename": "1471-2105-5-115-S1.doc", "url": "https://authors.library.caltech.edu/records/rwm63-gpv06/files/1471-2105-5-115-S1.doc" }, "related_objects": [ { "basename": "1471-2105-5-115-S2.pdf", "url": "https://authors.library.caltech.edu/records/rwm63-gpv06/files/1471-2105-5-115-S2.pdf" }, { "basename": "1471-2105-5-115-S3.zip", "url": "https://authors.library.caltech.edu/records/rwm63-gpv06/files/1471-2105-5-115-S3.zip" }, { "basename": "1471-2105-5-115-S4.doc", "url": "https://authors.library.caltech.edu/records/rwm63-gpv06/files/1471-2105-5-115-S4.doc" }, { "basename": "FENbmcb04.pdf", "url": "https://authors.library.caltech.edu/records/rwm63-gpv06/files/FENbmcb04.pdf" } ], "resource_type": "article", "pub_year": "2004", "author_list": "Feng, Zhaoyang; Cronin, Christopher J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/dbdc2-ha641", "eprint_id": 95478, "eprint_status": "archive", "datestamp": "2023-08-19 14:04:09", "lastmod": "2023-10-20 20:16:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Miley-G-R", "name": { "family": "Miley", "given": "Ginger R." } }, { "id": "Fantz-D", "name": { "family": "Fantz", "given": "Douglas" } }, { "id": "Glossip-D", "name": { "family": "Glossip", "given": "Danielle" } }, { "id": "Lu-Xiaowei", "name": { "family": "Lu", "given": "Xiaowei" } }, { "id": "Saito-R-Mako", "name": { "family": "Saito", "given": "R. Mako" } }, { "id": "Palmer-R-E", "name": { "family": "Palmer", "given": "Robert E." } }, { "id": "Inoue-Takao", "name": { "family": "Inoue", "given": "Takao" } }, { "id": "van-den-Heuvel-S", "name": { "family": "van den Heuvel", "given": "Sander" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Kornfeld-K", "name": { "family": "Kornfeld", "given": "Kerry" } } ] }, "title": "Identification of Residues of the Caenorhabditis elegans LIN-1 ETS Domain That Are Necessary for DNA Binding and Regulation of Vulval Cell Fates", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2004 by the Genetics Society of America. \n\nManuscript received April 7, 2004; Accepted for publication May 6, 2004. \n\nWe are grateful to the following individuals for providing lin-1 alleles: Bob Horvitz and members of his lab including Greg Beitel, Jeff Thomas, Chip Ferguson, Erik Jorgenson, Scott Clark, Craig Ceol, Frank Stegmeier, Melissa Harrison, and Na An as well as Joseph Lee, Dave Eisenmann, and Stuart Kim. We thank Parie Garg and Andrew Turk for assistance with experiments. Some strains were provided by the Caenorhabditis Genetics Center, which is funded by the National Center for Research Resources of the National Institutes of Health (NIH). This work was supported by grants from the NIH to K.K. (CA-84271). K.K. is a scholar of the Leukemia and Lymphoma Society. P.W.S is an Investigator and R.E.P. was an associate with the Howard Hughes Medical Institute. D.F. was supported by an NIH grant (GM20450-01). R.M.S. has a postdoctoral fellowship from the American Cancer Society and the Massachusetts General Hospital Fund for Medical Discovery.\n\nPublished - 15342509.pdf
", "abstract": "LIN-1 is an ETS domain protein. A receptor tyrosine kinase/Ras/mitogen-activated protein kinase signaling pathway regulates LIN-1 in the P6.p cell to induce the primary vulval cell fate during Caenorhabditis elegans development. We identified 23 lin-1 loss-of-function mutations by conducting several genetic screens. We characterized the molecular lesions in these lin-1 alleles and in several previously identified lin-1 alleles. Nine missense mutations and 10 nonsense mutations were identified. All of these lin-1 missense mutations affect highly conserved residues in the ETS domain. These missense mutations can be arranged in an allelic series; the strongest mutations eliminate most or all lin-1 functions, and the weakest mutation partially reduces lin-1 function. An electrophoretic mobility shift assay was used to demonstrate that purified LIN-1 protein has sequence-specific DNA-binding activity that required the core sequence GGAA. LIN-1 mutant proteins containing the missense substitutions had dramatically reduced DNA binding. These experiments identify eight highly conserved residues of the ETS domain that are necessary for DNA binding. The identification of multiple mutations that reduce the function of lin-1 as an inhibitor of the primary vulval cell fate and also reduce DNA binding suggest that DNA binding is essential for LIN-1 function in an animal.", "date": "2004-08-01", "date_type": "published", "publication": "Genetics", "volume": "167", "number": "4", "publisher": "Genetics Society of America", "pagerange": "1697-1709", "id_number": "CaltechAUTHORS:20190514-101613052", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-101613052", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "CA-84271" }, { "agency": "Leukemia and Lymphoma Society" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "GM20450-01" }, { "agency": "American Cancer Society" }, { "agency": "Massachusetts General Hospital" } ] }, "doi": "10.1534/genetics.104.029017", "pmcid": "PMC1471005", "primary_object": { "basename": "15342509.pdf", "url": "https://authors.library.caltech.edu/records/dbdc2-ha641/files/15342509.pdf" }, "resource_type": "article", "pub_year": "2004", "author_list": "Miley, Ginger R.; Fantz, Douglas; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/v4mec-z2551", "eprint_id": 27227, "eprint_status": "archive", "datestamp": "2023-08-19 13:39:11", "lastmod": "2023-10-24 16:58:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Levchenko-A", "name": { "family": "Levchenko", "given": "A." } }, { "id": "Bruck-J", "name": { "family": "Bruck", "given": "J." }, "orcid": "0000-0001-8474-0812" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "P. W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Regulatory modules that generate biphasic signal\n response in biological systems", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2004 IEE.\nPaper first received 5th April and in revised form 15th May 2004.", "abstract": "Biochemical networks might be composed of modules. It is still not clear how biochemical modules can be defined and characterised. Here we propose a functional approach to\nmodule definition, considering different classes of biphasic regulation modules, which effect optimal cell response to intermediate signal strength. Each regulation class might possess unique properties that make it especially suitable for particular biological functions.", "date": "2004-06", "date_type": "published", "publication": "Systems Biology", "volume": "1", "number": "1", "publisher": "Institution of Engineering and Technology", "pagerange": "139-148", "id_number": "CaltechAUTHORS:20111014-095736081", "issn": "1741-2471", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111014-095736081", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1049/sb:20045014", "resource_type": "article", "pub_year": "2004", "author_list": "Levchenko, A.; Bruck, J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/p1vh2-tfh30", "eprint_id": 1337, "eprint_status": "archive", "datestamp": "2023-08-22 01:32:39", "lastmod": "2023-10-13 22:45:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hwang-Byung-Joon", "name": { "family": "Hwang", "given": "Byung Joon" } }, { "id": "M\u00fcller-H-M", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Genome annotation by high-throughput 5' RNA end determination", "ispublished": "pub", "full_text_status": "public", "keywords": "pre-messenger-RNA, C-elegans, spliced leader, gene, expression, sequences, operons, sage", "note": "\u00a9 2004 by the National Academy of Sciences. \n\nCommunicated by Philip P. Green, University of Washington School of Medicine, Seattle, WA, December 16, 2003 (received for review November 20, 2003). Published online before print February 2, 2004, 10.1073/pnas.0308384100 \n\nWe thank S. Gharib for DNA preparation, T. Blumenthal for discussions about operons, and C. Bastiani, T. Blumenthal, Y. Kee, E. Schwarz, and S. Vernooy for careful reading of the manuscript. This work was supported by the Howard Hughes Medical Institute, with which P.W.S. is an Investigator and B.J.H. and H.-M.M. were Associates, by a W. M. Keck Foundation/California Institute of Technology discovery award (to B.J.H. and P.W.S.), and by National Human Genome Research Institute/National Institutes of Health Genome Scholar and Faculty Transition Award K22HG02907-01 (to B.J.H.).\n\nPublished - HWApnas04b.pdf
", "abstract": "Complete gene identification and annotation, including alternative transcripts, remains a challenge in understanding genome organization. Such annotation can be achieved by a combination of computational analysis and experimental confirmation. Here, we describe a high-throughput technique, trans-spliced exon coupled RNA end determination (TEC-RED), that identifies 5' ends of expressed genes in nematodes. TEC-RED can distinguish coding regions from regulatory regions and identify genes as well as their alternative transcripts that have different 5' ends. Application of TEC-RED to approximate to 10% of the Caenorhabditis elegans genome yielded tags 75% of which experimentally verified predicted 5'-RNA ends and 25% of which provided previously unknown information about 5'-RNA ends, including the identification of 99 previously unknown genes and 32 previously unknown operons. This technique will be applicable in any organisms that have a trans-splicing reaction from spliced leader RNA. We also describe an efficient sequential method for concatenating short sequence tags for any serial analysis of gene expression-like techniques.", "date": "2004-02-10", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "101", "number": "6", "publisher": "National Academy of Sciences", "pagerange": "1650-1655", "id_number": "CaltechAUTHORS:HWApnas04b", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:HWApnas04b", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "W. M. Keck Foundation" }, { "agency": "Caltech" }, { "agency": "National Human Genome Research Institute" }, { "agency": "NIH", "grant_number": "K22HG02907-01" } ] }, "doi": "10.1073/pnas.0308384100", "pmcid": "PMC341809", "primary_object": { "basename": "HWApnas04b.pdf", "url": "https://authors.library.caltech.edu/records/p1vh2-tfh30/files/HWApnas04b.pdf" }, "resource_type": "article", "pub_year": "2004", "author_list": "Hwang, Byung Joon; M\u00fcller, Hans-Michael; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/rsa3t-kj257", "eprint_id": 51941, "eprint_status": "archive", "datestamp": "2023-08-19 13:01:00", "lastmod": "2023-10-18 18:43:52", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "A pattern of precision", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2004 American Association for the Advancement of Science.", "abstract": "The amazing precision with which different cell types find their correct locations in developing tissues has fascinated\nbiologists for decades. Models of cell fate patterning during development emphasize the contrast between spatial\ngradients of developmental signals that act at long range and cell-to-cell signaling events that act locally. Development of the vulva in the nematode Caenorhabditis elegans provides an elegant model system for examining the patterning of cell fate in an animal. There is strong evidence that two different intercellular signals contribute to the relatively simple induction of cell fate\namong vulval precursor cells (VPCs): a long-range spatial gradient of epidermal growth factor (EGF) mediated by the EGF receptor (1, 2) and a cell-to-cell lateral signal\nmediated by the Notch-like receptor LIN-12 (3\u20135).", "date": "2004-01-30", "date_type": "published", "publication": "Science", "volume": "303", "number": "5658", "publisher": "American Association for the Advancement of Science", "pagerange": "637-638", "id_number": "CaltechAUTHORS:20141119-085927005", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141119-085927005", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1126/science.1094409", "resource_type": "article", "pub_year": "2004", "author_list": "Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/g6x4n-1cb18", "eprint_id": 11718, "eprint_status": "archive", "datestamp": "2023-08-22 01:26:22", "lastmod": "2023-10-17 15:30:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hwang-B-J", "name": { "family": "Hwang", "given": "Byung Joon" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "A cell-specific enhancer that specifies lin-3 expression in the C. elegans anchor cell for vulval development", "ispublished": "pub", "full_text_status": "public", "keywords": "EGF, LIN-3, HLH-2, E-protein/Daughterless, Nuclear hormone receptor, Anchor cell, Vulval induction", "note": "Published by The Company of Biologists 2004. \n\nAccepted 23 September 2003. \n\nWe are grateful to X. Karp and I. Greenwald for communicating unpublished data on hlh-2; to Y Kohara for nhr-25 cDNA; and to A. Fire for gfp constructs. We thank J. Lee and H. Y. Yoon in W. Dunphy's laboratory for helping with phosphoimager analysis and expressing proteins in insect cells. Great appreciation for carefully reading the manuscript is given to C. Bastiani, B. Gupta, T. Inoue, Y. Kee, J. S. Kim, N. Moghal and S. Vernooy. This work was supported by the Howard Hughes Medical Institute with which P.W.S. is an investigator and B.J.H. was an associate.\n\nPublished - HWAdev04.pdf
", "abstract": "During C. elegans vulval development, the anchor cell (AC) in the somatic gonad expresses lin-3, activating the EGF receptor signaling pathway in vulval precursor cells (VPCs) and thereby inducing and patterning VPCs. Previous studies with lin-3 mutants and transgene expression have revealed that the level of LIN-3 in the AC must be precisely regulated for proper vulval development. To understand how lin-3 expression is achieved in the AC, we identified a 59 bp lin-3 enhancer sufficient to activate lin-3 transcription solely in the AC. The enhancer contains two E-box elements, and one FTZ-F1 nuclear hormone receptor (NHR) binding site that is mutated in a vulvaless mutant, lin-3(e1417). Mutagenesis studies show that both E-boxes and the NHR binding site are necessary to express lin-3 in the AC. In vitro DNA-binding studies and in vivo functional assays indicate that distinct trans-acting factors, including the E-protein/Daughterless homolog HLH-2 and unidentified nuclear hormone receptor(s), are necessary for lin-3 transcription in the AC and thus are involved in vulval development.", "date": "2004-01-01", "date_type": "published", "publication": "Development", "volume": "131", "number": "1", "publisher": "Company of Biologists", "pagerange": "143-151", "id_number": "CaltechAUTHORS:HWAdev04", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:HWAdev04", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute" } ] }, "doi": "10.1242/dev.00924", "primary_object": { "basename": "HWAdev04.pdf", "url": "https://authors.library.caltech.edu/records/g6x4n-1cb18/files/HWAdev04.pdf" }, "resource_type": "article", "pub_year": "2004", "author_list": "Hwang, Byung Joon and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/qtxb1-thm72", "eprint_id": 814, "eprint_status": "archive", "datestamp": "2023-08-22 01:17:41", "lastmod": "2023-10-13 21:59:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Harris-T-W", "name": { "family": "Harris", "given": "Todd W." }, "orcid": "0000-0003-3406-163X" }, { "id": "Chen-Nansheng", "name": { "family": "Chen", "given": "Nansheng" } }, { "id": "Cunningham-F", "name": { "family": "Cunningham", "given": "Fiona" } }, { "id": "Tello-Ruiz-M", "name": { "family": "Tello-Ruiz", "given": "Marcela" } }, { "id": "Antoshechkin-I-A", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Bastiani-C-A", "name": { "family": "Bastiani", "given": "Carol" } }, { "id": "Bieri-T", "name": { "family": "Bieri", "given": "Tamberlyn" } }, { "id": "Blasiar-D", "name": { "family": "Blasiar", "given": "Darin" } }, { "id": "Bradnam-K", "name": { "family": "Bradnam", "given": "Keith" } }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "Chen-Chao-Kung", "name": { "family": "Chen", "given": "Chao-Kung" } }, { "id": "Chen-Wen-J", "name": { "family": "Chen", "given": "Wen J." } }, { "id": "Davis-P", "name": { "family": "Davis", "given": "Paul" } }, { "id": "Kenny-E-E", "name": { "family": "Kenny", "given": "Eimear" } }, { "id": "Kishore-R", "name": { "family": "Kishore", "given": "Ranjana" } }, { "id": "Lawson-D", "name": { "family": "Lawson", "given": "Daniel" } }, { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "Raymond Y. N." }, "orcid": "0000-0002-8151-7479" }, { "id": "M\u00fcller-H-M", "name": { "family": "M\u00fcller", "given": "Hans-Michael" } }, { "id": "Nakamura-Cecilia", "name": { "family": "Nakamura", "given": "Cecilia" }, "orcid": "0000-0002-4689-7314" }, { "id": "Ozersky-P", "name": { "family": "Ozersky", "given": "Philip" } }, { "id": "Petcherski-A", "name": { "family": "Petcherski", "given": "Andrei" } }, { "id": "Rogers-A", "name": { "family": "Rogers", "given": "Anthony" } }, { "id": "Sabo-Aniko", "name": { "family": "Sabo", "given": "Aniko" } }, { "id": "Schwarz-E-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Van-Auken-K", "name": { "family": "Van Auken", "given": "Kimberly" }, "orcid": "0000-0002-1706-4196" }, { "id": "Wang-Qinghua", "name": { "family": "Wang", "given": "Qinghua" } }, { "id": "Durbin-R", "name": { "family": "Durbin", "given": "Richard" } }, { "id": "Spieth-J", "name": { "family": "Spieth", "given": "John" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Stein-L-D", "name": { "family": "Stein", "given": "Lincoln D." }, "orcid": "0000-0002-1983-4588" } ] }, "title": "WormBase: a multi-species resource for nematode biology and genomics", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2004 Oxford University Press \n\nReceived September 15, 2003; Revised and Accepted September 25, 2003 \n\nWormBase is supported by grant P41-HG02223 from the US National Human Genome Research Institute and the British Medical Research Council. P.W.S. is an Investigator with the Howard Hughes Medical Institute. \n\nThe authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.\n\nOn a closing note, we welcome the submission of data sets, corrections to existing data, and your comments, questions and suggestions (wormbase-help@wormbase.org).\n\nPublished - HARnar04.pdf
", "abstract": "WormBase (http://www.wormbase.org/) is the central data repository for information about Caenorhabditis elegans and related nematodes. As a model organism database, WormBase extends beyond the genomic sequence, integrating experimental results with extensively annotated views of the genome. The WormBase Consortium continues to expand the biological scope and utility of WormBase with the inclusion of large-scale genomic analyses, through active data and literature curation, through new analysis and visualization tools, and through refinement of the user interface. Over the past year, the nearly complete genomic sequence and comparative analyses of the closely related species Caenorhabditis briggsae have been integrated into WormBase, including gene predictions, ortholog assignments and a new synteny viewer to display the relationships between the two species. Extensive site-wide refinement of the user interface now provides quick access to the most frequently accessed resources and a consistent browsing experience across the site. Unified single-page views now provide complete summaries of commonly accessed entries like genes. These advances continue to increase the utility of WormBase for C.elegans researchers, as well as for those researchers exploring problems in functional and comparative genomics in the context of a powerful genetic system.", "date": "2004", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "32", "number": "Databa", "publisher": "Oxford University Press", "pagerange": "D411-D417", "id_number": "CaltechAUTHORS:HARnar04", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:HARnar04", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1093/nar/gkh066", "pmcid": "PMC308800", "primary_object": { "basename": "HARnar04.pdf", "url": "https://authors.library.caltech.edu/records/qtxb1-thm72/files/HARnar04.pdf" }, "resource_type": "article", "pub_year": "2004", "author_list": "Harris, Todd W.; Chen, Nansheng; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/rtakw-47r94", "eprint_id": 95479, "eprint_status": "archive", "datestamp": "2023-08-19 12:37:20", "lastmod": "2023-10-20 20:16:32", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bastiani-C-A", "name": { "family": "Bastiani", "given": "Carol A." } }, { "id": "Gharib-Shahla", "name": { "family": "Gharib", "given": "Shahla" } }, { "id": "Simon-M-I", "name": { "family": "Simon", "given": "Melvin I." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Caenorhabditis elegans G\u03b1_q Regulates Egg-Laying Behavior via a PLC\u03b2-Independent and Serotonin-Dependent Signaling Pathway and Likely Functions Both in the Nervous System and in Muscle", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2003 by the Genetics Society of America. \n\nManuscript received August 20, 2002; Accepted for publication September 8, 2003. \n\nWe thank members of the Sternberg and Simon labs for stimulating discussion and review of this manuscript. We also thank the Iwasaki laboratory for providing egl-30(tg26), the Miller laboratory for providing EGL-8 antibody, the Tsien laboratory for providing the RSET vector, Lorna Brundage for providing syIs36 and for injecting pLB24, and the Caenorhabditis Genetics Center for providing strains. This research was supported by the Howard Hughes Medical Institute with which P.W.S. is an investigator and by National Institute of General Medical Science grant no. GM34236 to M.I.S. C.A.B. was supported by a Department of Health and Human Services National Research Service Award (GM18704).\n\nPublished - 14704167.pdf
", "abstract": "egl-30 encodes the single C. elegans ortholog of vertebrate G\u03b1_q family members. We analyzed the expression pattern of EGL-30 and found that it is broadly expressed, with highest expression in the nervous system and in pharyngeal muscle. We isolated dominant, gain-of-function alleles of egl-30 as intragenic revertants of an egl-30reduction-of-function mutation. Using these gain-of-function mutants and existing reduction-of-function mutants, we examined the site and mode of action of EGL-30. On the basis of pharmacological analysis, it has been determined that egl-30 functions both in the nervous system and in the vulval muscles for egg-laying behavior. Genetic epistasis over mutations that eliminate detectable levels of serotonin reveals that egl-30requires serotonin to regulate egg laying. Furthermore, pharmacological response assays strongly suggest that EGL-30 may directly couple to a serotonin receptor to mediate egg laying. We also examined genetic interactions with mutations in the gene that encodes the single C. elegans homolog of PLC\u03b2 and mutations in genes that encode signaling molecules downstream of PLC\u03b2. We conclude that PLC\u03b2 functions in parallel with egl-30 with respect to egg laying or is not the major effector of EGL-30. In contrast, PLC\u03b2-mediated signaling is likely downstream of EGL-30 with respect to pharyngeal-pumping behavior. Our data indicate that there are multiple signaling pathways downstream of EGL-30 and that different pathways could predominate with respect to the regulation of different behaviors.", "date": "2003-12-01", "date_type": "published", "publication": "Genetics", "volume": "165", "number": "4", "publisher": "Genetics Society of America", "pagerange": "1805-1822", "id_number": "CaltechAUTHORS:20190514-102529225", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-102529225", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "GM34236" }, { "agency": "NIH", "grant_number": "GM18704" } ] }, "pmcid": "PMC1462877", "primary_object": { "basename": "14704167.pdf", "url": "https://authors.library.caltech.edu/records/rtakw-47r94/files/14704167.pdf" }, "resource_type": "article", "pub_year": "2003", "author_list": "Bastiani, Carol A.; Gharib, Shahla; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/69wq6-31744", "eprint_id": 819, "eprint_status": "archive", "datestamp": "2023-08-22 01:07:33", "lastmod": "2023-10-13 21:59:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gupta-B-P", "name": { "family": "Gupta", "given": "Bhagwati P." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The draft genome sequence of the nematode Caenorhabditis briggsae, a companion to C. elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "Genome studies, Model organisms, Evolution, Development, Genetics", "note": "\u00a9 BioMed Central Ltd 2003. \n\nThe electronic version of this article is the complete one and can be found online at: http://genomebiology.com/2003/4/12/238\n\nPublished - GUPgb03.pdf
", "abstract": "The publication of the draft genome sequence of Caenorhabditis briggsae improves the annotation of the genome of its close relative Caenorhabditis elegans and will facilitate comparative genomics and the study of the evolutionary changes during development.", "date": "2003-11-18", "date_type": "published", "publication": "Genome Biology", "volume": "4", "number": "12", "publisher": "BioMed Central", "pagerange": "Art. No. 238", "id_number": "CaltechAUTHORS:GUPgb03", "issn": "1465-6906", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:GUPgb03", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1186/gb-2003-4-12-238", "pmcid": "PMC329410", "primary_object": { "basename": "GUPgb03.pdf", "url": "https://authors.library.caltech.edu/records/69wq6-31744/files/GUPgb03.pdf" }, "resource_type": "article", "pub_year": "2003", "author_list": "Gupta, Bhagwati P. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/jw7hg-fa950", "eprint_id": 12708, "eprint_status": "archive", "datestamp": "2023-08-19 12:29:28", "lastmod": "2023-10-17 20:26:58", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yu-Hui", "name": { "family": "Yu", "given": "Hui" } }, { "id": "Pr\u00e9t\u00f4t-R-F", "name": { "family": "Pr\u00e9t\u00f4t", "given": "Ren\u00e9 F." } }, { "id": "B\u00fcrglin-T-R", "name": { "family": "B\u00fcrglin", "given": "Thomas R." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Distinct roles of transcription factors EGL-46 and DAF-19 in specifying the functionality of a polycystin-expressing sensory neuron necessary for C. elegans male vulva location behavior", "ispublished": "pub", "full_text_status": "public", "keywords": "Transcriptional regulation, Cell specification, Zinc finger proteins, TEF, RFX factors, Polycystins", "note": "Copyright \u00a9 2003 The Company of Biologists Limited. \n\nAccepted 19 June 2003. First published online 3 September 2003. \n\nWe thank Ji Wu, Martin Chalfie, Peter Swoboda, Maureen Barr, Hillel Schwartz, H. Robert Horvitz, Ann Hart and Joan Collet for GFP, CFP, and YFP plasmids and strains. We thank Alan Coulson for providing cosmids, the Caenorhabditis Genetic Center for providing some strains used in this study, and the C. elegans Genome Sequencing Consortium and WormBase for sequence information. We thank L. Rene Garcia, Takao Inoue, Gary Schindelman, Allyson Whittaker and X.Z. Shawn Xu for helpful discussions and critical reading of this manuscript. This work was supported by USPHS grant #1P50DK57325 to G. Germino (co-PI, P.W.S.). P.W.S. is an Investigator with the HHMI. H.Y. was a recipient of a Gordon Ross graduate fellowship. R.F.P. and T.R.B. were supported by grants from the Swiss National Science Foundation. T.R.B. was recipient of a START Fellowship (NF. 3130-038786.93) and is now supported by the Swedish Foundation for Strategic Research (SSF).\n\nPublished - YUHdev03.pdf
", "abstract": "Caenorhabditis elegans polycystins LOV-1 and PKD-2 are expressed in the male-specific HOB neuron, and are necessary for sensation of the hermaphrodite vulva during mating. We demonstrate that male vulva location behavior and expression of lov-1 and pkd-2 in the ciliated sensory neuron HOB require the activities of transcription factor EGL-46 and to some extent also EGL-44. This EGL-46- regulated program is specific to HOB and is distinct from a general ciliogenic pathway functioning in all ciliated neurons. The ciliogenic pathway regulator DAF-19 affects downstream components of the HOB-specific program indirectly and is independent of EGL-46 activity. The sensory function of HOB requires the combined action of these two distinct regulatory pathways.", "date": "2003-11-01", "date_type": "published", "publication": "Development", "volume": "130", "number": "21", "publisher": "Company of Biologists", "pagerange": "5217-5227", "id_number": "CaltechAUTHORS:YUHdev03", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:YUHdev03", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Public Health Service", "grant_number": "1P50DK57325" }, { "agency": "Howard Hughes Medical Institute" }, { "agency": "Gordon Ross Medical Foundation" }, { "agency": "Swiss National Science Foundation", "grant_number": "NF. 3130-038786.93" }, { "agency": "Swedish Foundation for Strategic Research (SSF)" } ] }, "doi": "10.1242/dev.00678", "primary_object": { "basename": "YUHdev03.pdf", "url": "https://authors.library.caltech.edu/records/jw7hg-fa950/files/YUHdev03.pdf" }, "resource_type": "article", "pub_year": "2003", "author_list": "Yu, Hui; Pr\u00e9t\u00f4t, Ren\u00e9 F.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/5cpq0-09p94", "eprint_id": 12899, "eprint_status": "archive", "datestamp": "2023-09-14 18:45:29", "lastmod": "2023-10-23 20:44:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Moghal-N", "name": { "family": "Moghal", "given": "Nadeem" } }, { "id": "Garcia-L-R", "name": { "family": "Garcia", "given": "L. Rene" } }, { "id": "Khan-L-A", "name": { "family": "Khan", "given": "Liakot A." } }, { "id": "Iwasaki-K", "name": { "family": "Iwasaki", "given": "Kouichi" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Modulation of EGF receptor-mediated vulva development by the heterotrimeric G-protein G{alpha}q and excitable cells in C. elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "EGF, Muscle, Neurons, Behavior, Vulva, G protein", "note": "Copyright \u00a9 2003 The Company of Biologists Limited. \n\nAccepted 12 June 2003. First published online August 18, 2003. \n\nSome nematode strains used in this work were provided by the Caenorhabditis Genetics Center, which is funded by the NIH National Center for Research Resources (NCRR). We thank A. Fire, S. Xu and C. Van Buskirk for providing plasmids, and B. Neel, C. Bastiani, R. Lee and G. Schindelman for discussions. This research was supported by the Howard Hughes Medical Institute of which P.W.S. is an investigator, and L.R.G. was an associate, and by grants from the Ministry of International Trading and Industry to K.I. N.M. was supported by postdoctoral fellowships from the Leukemia and Lymphoma Society, and the California Breast Cancer Research Program. L.R.G. was supported by a Department of Health and Human Services National Research Award (GM18857).\n\nPublished - MOGdev03b.pdf
", "date": "2003-10-01", "date_type": "published", "publication": "Development", "volume": "130", "number": "19", "publisher": "Company of Biologists", "pagerange": "4553-4566", "id_number": "CaltechAUTHORS:MOGdev03b", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:MOGdev03b", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute" }, { "agency": "Ministry of International Trading and Industry (Japan)" }, { "agency": "Leukemia and Lymphoma Society" }, { "agency": "California Breast Cancer Research Program" }, { "agency": "Department of Health and Human Services", "grant_number": "GM18857" } ] }, "doi": "10.1242/10.1242/dev.00670", "primary_object": { "basename": "MOGdev03b.pdf", "url": "https://authors.library.caltech.edu/records/5cpq0-09p94/files/MOGdev03b.pdf" }, "resource_type": "article", "pub_year": "2003", "author_list": "Moghal, Nadeem; Garcia, L. Rene; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/t4w9w-sg275", "eprint_id": 12787, "eprint_status": "archive", "datestamp": "2023-08-19 11:37:28", "lastmod": "2023-10-17 20:55:26", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gupta-B-P", "name": { "family": "Gupta", "given": "Bhagwati P." } }, { "id": "Wang-Minqin", "name": { "family": "Wang", "given": "Minqin" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The C. elegans LIM homeobox gene lin-11 specifies multiple cell fates during vulval development", "ispublished": "pub", "full_text_status": "public", "keywords": "C. elegans, lin-11, ldb-1, LIM homeodomain, Vulva, Differentiation", "note": "\u00a9 2003 The Company of Biologists Limited. \n\nAccepted 17 March 2003. \n\nWe thank S. Cameron, D. Sherwood and T. Inoue for integrated strains. Robert Oania provided assistance in two-hybrid experiments. Some of the strains were obtained from Caenorhabditis Genetics Center. We also thank D. Sherwood, T. Inoue and anonymous reviewers for comments on the manuscript. This work was supported by funds from the HHMI and USPHS grant HD23690 to P.W.S. B.P.G. was supported by a long-term fellowship from HFSP and as an associate of the HHMI. M.W. was an AMGEN fellow. P.W.S. is an investigator of the HHMI.\n\nPublished - GUPdev03.pdf
", "abstract": "LIM homeobox family members regulate a variety of cell fate choices during animal development. In C. elegans, mutations in the LIM homeobox gene lin-11 have previously been shown to alter the cell division pattern of a subset of the 2\u00b0 lineage vulval cells. We demonstrate multiple functions of lin-11 during vulval development. We examined the fate of vulval cells in lin-11 mutant animals using five cellular markers and found that lin-11 is necessary for the patterning of both 1\u00b0 and 2\u00b0 lineage cells. In the absence of lin-11 function, vulval cells fail to acquire correct identity and inappropriately fuse with each other. The expression pattern of lin-11 reveals dynamic changes during development. Using a temporally controlled overexpression system, we show that lin-11 is initially required in vulval cells for establishing the correct invagination pattern. This process involves asymmetric expression of lin-11 in the 2\u00b0 lineage cells. Using a conditional RNAi approach, we show that lin-11 regulates vulval morphogenesis. Finally, we show that LDB-1, a NLI/Ldb1/CLIM2 family member, interacts physically with LIN-11, and is necessary for vulval morphogenesis. Together, these findings demonstrate that temporal regulation of lin-11 is crucial for the wild-type vulval patterning.", "date": "2003-06-15", "date_type": "published", "publication": "Development", "volume": "130", "number": "12", "publisher": "Company of Biologists", "pagerange": "2589-2601", "id_number": "CaltechAUTHORS:GUPdev03", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:GUPdev03", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "HD23690" }, { "agency": "Human Frontier Science Program" }, { "agency": "Amgen Corp." } ] }, "doi": "10.1242/10.1242/dev.00500", "primary_object": { "basename": "GUPdev03.pdf", "url": "https://authors.library.caltech.edu/records/t4w9w-sg275/files/GUPdev03.pdf" }, "resource_type": "article", "pub_year": "2003", "author_list": "Gupta, Bhagwati P.; Wang, Minqin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/5j23f-rwj88", "eprint_id": 99021, "eprint_status": "archive", "datestamp": "2023-08-22 00:23:22", "lastmod": "2023-10-18 17:47:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Garcia-L-Rene", "name": { "family": "Garcia", "given": "L. Rene" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Caenorhabditis elegans UNC-103 ERG-Like Potassium Channel Regulates Contractile Behaviors of Sex Muscles in Males before and during Mating", "ispublished": "pub", "full_text_status": "public", "keywords": "Caenorhabditis elegans; mating behavior; unc-103; ERG; K+ channel; L-type voltage-gated calcium channels", "note": "\u00a9 2003 Society for Neuroscience. \n\nReceived Nov. 13, 2002; revised Jan. 9, 2003; accepted Jan. 13, 2003. \n\nThe Howard Hughes Medical Institute with which P.W.S. is an investigator and L.R.G. was an associate supported this research. L.R.G. was supported by a Department of Health and Human Services National Research Service Award (GM18857). Strains were provided by the Caenorhabditis Genetics Center, which is supported by National Institutes of Health National Center for Research Resources. We thank David Reiner and James Thomas for communicating to us the molecular lesions in unc-103(e1597gf ) and unc-103(n1213). We also thank Karin Doerr for writing software used in this work and Gary Schindelman for comments on this manuscript.\n\nPublished - 2696.full.pdf
", "abstract": "During mating behavior the Caenorhabditis elegansmale must regulate periodic and prolonged protractor muscle contractions to insert his copulatory spicules into his mate. The protractors undergo periodic contractions to allow the spicules to reattempt insertion if a previous thrust failed to breach the vulva. When the spicule tips penetrate the vulva, the protractors undergo prolonged contraction to keep the spicules inside the hermaphrodite until sperm transfer is complete. To understand how these contractions are regulated, we isolated EMS-induced mutations that cause males to execute prolonged contraction inappropriately. Loss-of-function mutations in the unc-103 ERG-like K+channel gene cause the protractor muscles to contract in the absence of mating stimulation. unc-103-induced spicule protraction can be suppressed by killing the SPC motor neurons and the anal depressor muscle: cells that directly contact the protractors. Also, reduction in acetylcholine suppresses unc-103-induced protraction, suggesting that UNC-103 keeps cholinergic neurons from stimulating the protractors before mating behavior. UNC-103 also regulates the timing of spicule protraction during mating behavior.unc-103 males that do not display mating-independent spicule protraction show abnormal spicule insertion behavior during sex. In contrast to wild-type males, unc-103 mutants execute prolonged contractions spontaneously within sequences of periodic protractor contractions. The premature prolonged contractions cause the spicules to extend from the male tail before the spicule tips penetrate the vulva. These observations demonstrate thatunc-103 controls various aspects of spicule function.", "date": "2003-04-01", "date_type": "published", "publication": "Journal of Neuroscience", "volume": "23", "number": "7", "publisher": "Society for Neuroscience", "pagerange": "2696-2705", "id_number": "CaltechAUTHORS:20191002-113744979", "issn": "0270-6474", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191002-113744979", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "GM18857" } ] }, "doi": "10.1523/jneurosci.23-07-02696.2003", "pmcid": "PMC6742059", "primary_object": { "basename": "2696.full.pdf", "url": "https://authors.library.caltech.edu/records/5j23f-rwj88/files/2696.full.pdf" }, "resource_type": "article", "pub_year": "2003", "author_list": "Garcia, L. Rene and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/qvpah-ktz80", "eprint_id": 27335, "eprint_status": "archive", "datestamp": "2023-08-22 00:11:24", "lastmod": "2023-10-24 17:04:41", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "Raymond Y. N." }, "orcid": "0000-0002-8151-7479" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Building a cell and anatomy ontology of Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "Caenorhabditis elegans; ontology; cell and anatomy; information technology", "note": "\u00a9 2003 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived 11 November 2002; Accepted 2 December 2002.\n\nPublished - LEEcfg03hindawi.pdf
", "abstract": "We are endowed with a rich knowledge about Caenorhabditis elegans. Its stereotyped anatomy and development has stimulated research and resulted in the accumulation of cell-based information concerning gene expression, and the role of specific cells in developmental signalling and behavioural circuits. To make the information more\naccessible to sophisticated queries and automated retrieval systems, WormBase has begun to construct a C. elegans cell and anatomy ontology. Here we present our strategies and progress.", "date": "2003-02", "date_type": "published", "publication": "Comparative and Functional Genomics", "volume": "4", "number": "1", "publisher": "John Wiley & Sons, Ltd", "pagerange": "121-126", "id_number": "CaltechAUTHORS:20111020-154253383", "issn": "1531-6912", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111020-154253383", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1002/cfg.248", "pmcid": "PMC2447384", "primary_object": { "basename": "LEEcfg03hindawi.pdf", "url": "https://authors.library.caltech.edu/records/qvpah-ktz80/files/LEEcfg03hindawi.pdf" }, "resource_type": "article", "pub_year": "2003", "author_list": "Lee, Raymond Y. N. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/6p04k-ggj31", "eprint_id": 12898, "eprint_status": "archive", "datestamp": "2023-08-19 10:46:36", "lastmod": "2023-10-17 21:13:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Moghal-N", "name": { "family": "Moghal", "given": "Nadeem" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "A component of the transcriptional mediator complex inhibits RAS-dependent vulval fate specification in C. elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "EGF, RAS, LET-23, SOP-1, DPY-22, Mediator, Vulva, C. elegans", "note": "Copyright \u00a9 2003 The Company of Biologists Limited. \n\nAccepted 4 October 2002. \n\nSome nematode strains used in this work were provided by the Caenorhabditis Genetics Center, which is funded by the NIH National Center for Research Resources (NCRR). We thank S. Emmons and C. Kenyon for providing strains, and A. Fire for plasmids. We thank J. Maloof and C. Kenyon for help in identifying the bar-1(mu63) mutation; H. Sawa for communicating unpublished results; and L.R. Garcia, R. Lee, B.P. Gupta, H. Yu, G. Schindelman and C. Van Buskirk for helpful discussions. This research was supported by the Howard Hughes Medical Institute, of which P.W.S. is an investigator. N.M. was supported by postdoctoral fellowships from the Leukemia and Lymphoma Society, and the California Breast Cancer Research Program.\n\nPublished - MOGdev03a.pdf
", "abstract": "Negative regulation of receptor tyrosine kinase (RTK)/RAS signaling pathways is important for normal development and the prevention of disease in humans. We have used a genetic screen in C. elegans to identify genes that antagonize the activity of activated LET-23, a member of the EGFR family of RTKs. We identified two loss-of-function mutations in dpy-22, previously cloned as sop-1, that promote the ability of activated LET-23 to induce ectopic vulval fates. DPY-22 is a glutamine-rich protein that is most similar to human TRAP230, a component of a transcriptional mediator complex. DPY-22 has previously been shown to regulate WNT responses through inhibition of the \u00df-catenin-like protein BAR-1. We provide evidence that DPY-22 also inhibits RAS-dependent vulval fate specification independently of BAR-1, and probably regulates the activities of multiple transcription factors during development. Furthermore, we demonstrate that although inhibition of BAR-1-dependent gene expression has been shown to require the C-terminal glutamine-rich region, this region is dispensable for inhibition of RAS-dependent cell differentiation. Thus, the glutamine-rich region contributes to specificity of this class of mediator protein.", "date": "2003-01-01", "date_type": "published", "publication": "Development", "volume": "130", "number": "1", "publisher": "Company of Biologists", "pagerange": "57-69", "id_number": "CaltechAUTHORS:MOGdev03a", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:MOGdev03a", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute" }, { "agency": "Leukemia and Lymphoma Society" }, { "agency": "California Breast Cancer Research Program" } ] }, "doi": "10.1242/10.1242/dev.00189", "primary_object": { "basename": "MOGdev03a.pdf", "url": "https://authors.library.caltech.edu/records/6p04k-ggj31/files/MOGdev03a.pdf" }, "resource_type": "article", "pub_year": "2003", "author_list": "Moghal, Nadeem and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/fp5xk-4rq02", "eprint_id": 2162, "eprint_status": "archive", "datestamp": "2023-08-22 00:07:39", "lastmod": "2023-10-13 23:14:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Harris-T-W", "name": { "family": "Harris", "given": "Todd W." }, "orcid": "0000-0003-3406-163X" }, { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "Raymond" }, "orcid": "0000-0002-8151-7479" }, { "id": "Schwarz-E-M", "name": { "family": "Schwarz", "given": "Erich M." }, "orcid": "0000-0003-3151-4381" }, { "id": "Bradnam-K", "name": { "family": "Bradnam", "given": "Keith" } }, { "id": "Lawson-D", "name": { "family": "Lawson", "given": "Daniel" } }, { "id": "Chen-Wen", "name": { "family": "Chen", "given": "Wen" } }, { "id": "Blasiar-D", "name": { "family": "Blasier", "given": "Darin" } }, { "id": "Kenny-E-E", "name": { "family": "Kenny", "given": "Eimear" } }, { "id": "Cunningham-F", "name": { "family": "Cunningham", "given": "Fiona" } }, { "id": "Kishore-R", "name": { "family": "Kishore", "given": "Ranjana" } }, { "id": "Chan-Juancarlos", "name": { "family": "Chan", "given": "Juancarlos" }, "orcid": "0000-0002-7259-8107" }, { "id": "M\u00fcller-H-M", "name": { "family": "Muller", "given": "Hans-Michael" } }, { "id": "Petcherski-A", "name": { "family": "Petcherski", "given": "Andrei" } }, { "id": "Thorisson-G", "name": { "family": "Thorisson", "given": "Gudmundur" } }, { "id": "Day-Allen", "name": { "family": "Day", "given": "Allen" } }, { "id": "Bieri-T", "name": { "family": "Bieri", "given": "Tamberlyn" } }, { "id": "Rogers-A", "name": { "family": "Rogers", "given": "Anthony" } }, { "id": "Chen-Chao-Kung", "name": { "family": "Chen", "given": "Chao-Kung" } }, { "id": "Spieth-J", "name": { "family": "Spieth", "given": "John" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul" }, "orcid": "0000-0002-7699-0173" }, { "id": "Durbin-R", "name": { "family": "Durbin", "given": "Richard" } }, { "id": "Stein-L-D", "name": { "family": "Stein", "given": "Lincoln D." }, "orcid": "0000-0002-1983-4588" } ] }, "title": "WormBase: a cross-species database for comparative genomics", "ispublished": "pub", "full_text_status": "public", "keywords": "NEMATODE CAENORHABDITIS-ELEGANS; MAP", "note": "\u00a9 2003 Oxford University Press. Reprinted with permission. \n\nReceived September 18, 2002; Accepted September 27, 2002. \n\nWormBase is supported by grant P41-HG02223 from the US National Human Genome Research Institute and the British Medical Research Council. P.W.S. is an investigator with the Howard Hughes Medical Institute.\n\nPublished - HARnar03.pdf
", "abstract": "WormBase (http://www.wormbase.org/) is a web-accessible central data repository for information about Caenorhabditis elegans and related nematodes. The past two years have seen a significant expansion in the biological scope of WormBase, including the integration of large-scale, genome-wide data sets, the inclusion of genome sequence and gene predictions from related species and active literature curation. This expansion of data has also driven the development and refinement of user interfaces and operability, including a new Genome Browser, new searches and facilities for data access and the inclusion of extensive documentation. These advances have expanded WormBase beyond the obvious target audience of C. elegans researchers, to include researchers wishing to explore problems in functional and comparative genomics within the context of a powerful genetic system.", "date": "2003-01-01", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "31", "number": "1", "publisher": "Oxford University Press", "pagerange": "133-137", "id_number": "CaltechAUTHORS:HARnar03", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:HARnar03", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P41-HG02223" }, { "agency": "Medical Research Council (UK)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1093/nar/gkg053", "pmcid": "PMC165500", "primary_object": { "basename": "HARnar03.pdf", "url": "https://authors.library.caltech.edu/records/fp5xk-4rq02/files/HARnar03.pdf" }, "resource_type": "article", "pub_year": "2003", "author_list": "Harris, Todd W.; Lee, Raymond; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/x4ve5-m8s54", "eprint_id": 101483, "eprint_status": "archive", "datestamp": "2023-08-22 00:04:21", "lastmod": "2023-10-19 22:47:11", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chen-Nansheng", "name": { "family": "Chen", "given": "Nansheng" } }, { "id": "Lee-Raymond-Y-N", "name": { "family": "Lee", "given": "Raymond Y. N." }, "orcid": "0000-0002-8151-7479" }, { "id": "Altun-Z-F", "name": { "family": "Altun", "given": "Zeynep F." } }, { "id": "Boulin-T", "name": { "family": "Boulin", "given": "Thomas" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Stein-L-D", "name": { "family": "Stein", "given": "Lincoln D." }, "orcid": "0000-0002-1983-4588" } ] }, "title": "Neuroinformatics for C. elegans: Relating Mind and Body in Wormbase", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "C. elegans; ACeDB; Wormbase; Database; Neuroscience; Wiring; Gene Ontology", "note": "\u00a9 2003 Springer Science+Business Media New York.", "abstract": "In this chapter, we have described how neuroscience data for the nematode C. elegans are deposited to and accessed from database. Research on neuroscience of C. elegans has attracted tremendous attention primarily because of its simple nervous system with 302 neurons. Data generated by comprehensive reconstruction and other efforts were initially deposited to and retrieved from ACeDB. More recently, Wormbase was created, which allows users to access data remotely and easily.", "date": "2003", "date_type": "published", "publisher": "Springer", "place_of_pub": "Boston, MA", "pagerange": "1-17", "id_number": "CaltechAUTHORS:20200224-084507495", "isbn": "978-1-4613-5384-3", "book_title": "Neuroscience Databases: A Practical Guide", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200224-084507495", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "K\u00f6tter-R", "name": { "family": "K\u00f6tter", "given": "Rolf" } } ] }, "doi": "10.1007/978-1-4615-1079-6_1", "resource_type": "book_section", "pub_year": "2003", "author_list": "Chen, Nansheng; Lee, Raymond Y. N.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/z7ga3-tev10", "eprint_id": 79156, "eprint_status": "archive", "datestamp": "2023-08-19 10:38:23", "lastmod": "2023-10-26 14:38:25", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Moghal-N", "name": { "family": "Moghal", "given": "Nadeem" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The epidermal growth factor system in Caenorhabditis elegans", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2003 Elsevier Inc.", "abstract": "The single known epidermal growth factor-like growth factor and single epidermal growth factor receptor in Caenorhabditis elegans mediate two types of processes, each via a distinct signal transduction pathway. This pathway is subject to multiple redundantly acting positive and negative modulatory signals and, in addition, virtually, every step of signaling from receptor localization to communication to RNA Pol II is regulated in a precise manner. Several instances of cell fate specification during organogenesis require the RAS\u2013MAP kinase pathway, as well as multiple nuclear factors. In contrast, appropriate myoepithelial contractions during ovulation involve IP3-mediated signal transduction. Positive modulators of the RAS pathway include KSR, SUR-8, phosphatase PP2A, and a zinc cation diffusion facilitator. Negative regulators of the RAS pathway include homologs of CBL, GAP-1, ACK, and MAP kinase phosphatase, while negative regulators of the IP3 pathway are enzymes that modify IP3. In addition to its stimulation of RAS activity, the GRB2 homolog SEM-5 acts negatively on both signaling pathways, as does the Ack-related kinase ARK-1.", "date": "2003", "date_type": "published", "publisher": "Elsevier", "place_of_pub": "Amsterdam", "pagerange": "157-166", "id_number": "CaltechAUTHORS:20170718-111119634", "isbn": "978-0-12-160281-9", "book_title": "The EGF Receptor Family: Biologic Mechanisms and Role in Cancer", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170718-111119634", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Carpenter-G", "name": { "family": "Carpenter", "given": "Graham" } } ] }, "doi": "10.1016/B978-012160281-9/50014-1", "resource_type": "book_section", "pub_year": "2003", "author_list": "Moghal, Nadeem and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/d736n-fyj73", "eprint_id": 56260, "eprint_status": "archive", "datestamp": "2023-08-19 10:26:23", "lastmod": "2023-10-23 15:14:34", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gilman-A-G", "name": { "family": "Gilman", "given": "Alfred G." } }, { "id": "Simon-M-I", "name": { "family": "Simon", "given": "Melvin I." } }, { "id": "Choi-Sangdun", "name": { "family": "Choi", "given": "Sangdun" } }, { "id": "Eversole-Cire-P", "name": { "family": "Eversole-Cire", "given": "Pamela" } }, { "id": "Fraser-I-D-C", "name": { "family": "Fraser", "given": "Iain" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Doyle-J-C", "name": { "family": "Doyle", "given": "John" }, "orcid": "0000-0002-1828-2486" } ] }, "title": "Overview of the Alliance for Cellular Signaling", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2002 Nature Publishing Group. This article was written by R. Taussig, R. Ranganathan, E. M. Ross and A. G. Gilman (University of Texas Southwestern Medical Center) on behalf of the participating investigators and scientists of the AfCS. R.R. is an Associate Investigator of the Howard Hughes Medical Institute.", "abstract": "The Alliance for Cellular Signaling is a large-scale collaboration designed to answer global questions about signalling networks. Pathways will be studied intensively in two cells \u2014 B lymphocytes (the cells of the immune system) and cardiac myocytes \u2014 to facilitate quantitative modelling. One goal is to catalyse complementary research in individual laboratories; to facilitate this, all alliance data are freely available for use by the entire research community.", "date": "2002-12-12", "date_type": "published", "publication": "Nature", "volume": "420", "number": "6916", "publisher": "Nature Publishing Group", "pagerange": "703-706", "id_number": "CaltechAUTHORS:20150401-065047086", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150401-065047086", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1038/nature01304", "resource_type": "article", "pub_year": "2002", "author_list": "Gilman, Alfred G.; Simon, Melvin I.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/40657-znb79", "eprint_id": 76364, "eprint_status": "archive", "datestamp": "2023-09-28 01:20:11", "lastmod": "2023-10-24 15:24:52", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gupta-B-P", "name": { "family": "Gupta", "given": "Bhagwati P." }, "orcid": "0000-0001-8572-7054" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Tissue-Specific Regulation of the LIM Homeobox Gene lin-11 during Development of the Caenorhabditis elegans Egg-Laying System", "ispublished": "pub", "full_text_status": "restricted", "keywords": "C. elegans; egg-laying; vulva; uterus; LIN-11; Wnt; Notch", "note": "\u00a9 2002 Elsevier. \n\nReceived 7 January 2002, Revised 3 April 2002, Accepted 8 April 2002, Available online 21 June 2002. \n\nWe thank S. Cameron for the nIs96 strain and Plin-11gfp plasmid, Y. Kohara for the lin-11 cDNA clone, J. Kimble for the lag-1 plasmid, and Fire Lab for GFP vectors. Some of the strains were provided by the C. elegans Genetics Center. We also thank B. Hwang for advice on the RNAi experiment and R. Garcia, D. Sherwood, and B. Hwang for comments on the manuscript. B.P.G. was supported by a long-term HFSP fellowship. P.W.S. is an Investigator and B.P.G. an Associate with the Howard Hughes Medical Institute, which funded this research.", "abstract": "The egg-laying system of Caenorhabditis elegans hermaphrodites requires development of the vulva and its precise connection with the uterus. This process is regulated by LET-23-mediated epidermal growth factor signaling and LIN-12-mediated lateral signaling pathways. Among the nuclear factors that act downstream of these pathways, the LIM homeobox gene lin-11 plays a major role. lin-11 mutant animals are egg-laying defective because of the abnormalities in vulval lineage and uterine seam\u2013cell formation. However, the mechanisms providing specificity to lin-11 function are not understood. Here, we examine the regulation of lin-11 during development of the egg-laying system. Our results demonstrate that the tissue-specific expression of lin-11 is controlled by two distinct regulatory elements that function as independent modules and together specify a wild-type egg-laying system. A uterine \u03c0 lineage module depends on the LIN-12/Notch signaling, while a vulval module depends on the LIN-17-mediated Wnt signaling. These results provide a unique example of the tissue-specific regulation of a LIM homeobox gene by two evolutionarily conserved signaling pathways. Finally, we provide evidence that the regulation of lin-11 by LIN-12/Notch signaling is directly mediated by the Su(H)/CBF1 family member LAG-1.", "date": "2002-07-01", "date_type": "published", "publication": "Developmental Biology", "volume": "247", "number": "1", "publisher": "Elsevier", "pagerange": "102-115", "id_number": "CaltechAUTHORS:20170408-192830845", "issn": "0012-1606", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170408-192830845", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Human Frontier Science Program" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1006/dbio.2002.0688", "resource_type": "article", "pub_year": "2002", "author_list": "Gupta, Bhagwati P. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/0w91k-0ne16", "eprint_id": 5003, "eprint_status": "archive", "datestamp": "2023-08-21 23:15:19", "lastmod": "2023-10-16 18:03:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bui-Yen-Kim", "name": { "family": "Bui", "given": "Yen Kim" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Caenorhabditis elegans Inositol 5-Phosphatase Homolog Negatively Regulates Inositol 1,4,5-Triphosphate Signaling in Ovulation", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2002 by The American Society for Cell Biology. Under the License and Publishing Agreement, authors grant to the general public, effective two months after publication of (i.e.,. the appearance of) the edited manuscript in an online issue of MBoC, the nonexclusive right to copy, distribute, or display the manuscript subject to the terms of the Creative Commons\u2013Noncommercial\u2013Share Alike 3.0 Unported license (http://creativecommons.org/licenses/by-nc-sa/3.0). \n\nSubmitted October 3, 2001; Revised January 18, 2002; Accepted February 1, 2002. Monitoring Editor: Judith Kimble. Originally published as MBC in Press, 10.1091/mbc.02-01-0008 on April 3, 2002 \n\nWe thank Y. Hadju-Cronin, J. Copeland, and B. Bingol for help isolating sy605; Y. Kohara for cDNA; J. Thomas for sa62 and sa73; A. Fire for GFP and HS vectors; A. Parker for the pCeh promoter and strain KR3738; A. Hart for the nlp-8 promoter and strain PT4; L.R. Garcia, E. Schwarz, other members of our laboratory, and an anonymous reviewer for valuable discussion and comments on the manuscript; and L. Maxfield (Caltech Digital Media Center) for help making web movies. The Caenorhabditis Genetics Center provided some strains. This project was supported by the Howard Hughes Medical Institute, with which P.W.S is an investigator. Y.K.B. is a National Institutes of Health trainee supported by National Institutes of Health grant 5T32GM07737.\n\nPublished - BUImbc02.pdf
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", "abstract": "Ovulation in Caenorhabditis elegans requires inositol 1,4,5-triphosphate (IP3) signaling activated by the epidermal growth factor (EGF)-receptor homolog LET-23. We generated a deletion mutant of a type I 5-phosphatase, ipp-5, and found a novel ovulation phenotype whereby the spermatheca hyperextends to engulf two oocytes per ovulation cycle. The temporal and spatial expression of IPP-5 is consistent with its proposed inhibition of IP3 signaling in the adult spermatheca. ipp-5 acts downstream of let-23, and interacts with let-23-mediated IP3 signaling pathway genes. We infer that IPP-5 negatively regulates IP3 signaling to ensure proper spermathecal contraction.", "date": "2002-05", "date_type": "published", "publication": "Molecular Biology of the Cell", "volume": "13", "number": "5", "publisher": "American Society for Cell Biology", "pagerange": "1641-1651", "id_number": "CaltechAUTHORS:BUImbc02", "issn": "1059-1524", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:BUImbc02", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1091/mbc.02-01-0008", "pmcid": "PMC111133", "primary_object": { "basename": "BUImbc02fig3.jpg", "url": "https://authors.library.caltech.edu/records/0w91k-0ne16/files/BUImbc02fig3.jpg" }, "related_objects": [ { "basename": "BUImbc02fig4.jpg", "url": "https://authors.library.caltech.edu/records/0w91k-0ne16/files/BUImbc02fig4.jpg" }, { "basename": "BUImbc02fig5.jpg", "url": "https://authors.library.caltech.edu/records/0w91k-0ne16/files/BUImbc02fig5.jpg" }, { "basename": "BUImbc02table1.htm", "url": "https://authors.library.caltech.edu/records/0w91k-0ne16/files/BUImbc02table1.htm" }, { "basename": "BUImbc02table2.jpg", "url": "https://authors.library.caltech.edu/records/0w91k-0ne16/files/BUImbc02table2.jpg" }, { "basename": "medium.png", "url": "https://authors.library.caltech.edu/records/0w91k-0ne16/files/medium.png" }, { "basename": "BUImbc02.pdf", "url": "https://authors.library.caltech.edu/records/0w91k-0ne16/files/BUImbc02.pdf" }, { "basename": "BUImbc02fig1.jpg", "url": "https://authors.library.caltech.edu/records/0w91k-0ne16/files/BUImbc02fig1.jpg" }, { "basename": "BUImbc02fig2.jpg", "url": "https://authors.library.caltech.edu/records/0w91k-0ne16/files/BUImbc02fig2.jpg" }, { "basename": "small.png", "url": "https://authors.library.caltech.edu/records/0w91k-0ne16/files/small.png" } ], "resource_type": "article", "pub_year": "2002", "author_list": "Bui, Yen Kim and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/9c5kn-mj396", "eprint_id": 1470, "eprint_status": "archive", "datestamp": "2023-08-21 23:02:38", "lastmod": "2023-10-13 22:50:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Simon-J-M", "name": { "family": "Simon", "given": "Jasper M." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Evidence of a mate-finding cue in the hermaphrodite nematode Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "SENSORY BEHAVIOR; MATING BEHAVIOR; KINESIS; MALE MATING-BEHAVIOR; DROSOPHILA-MELANOGASTER; NATURAL VARIATION; CELL LINEAGES; C-ELEGANS; PHEROMONES; OLFACTION; RESPONSES; MUTANTS; ODOR", "note": "\u00a9 2002 by the National Academy of Sciences. \n\nEdited by H. Robert Horvitz, Massachusetts Institute of Technology, Cambridge, MA, and approved December 4, 2001 (received for review May 7, 2001). Published online before print January 29, 2002, 10.1073/pnas.032225799. \n\nWe thank R. Garcia and N. Moghal for discussions, J. DeModena for experimental suggestions, S. Mukhtar for setting up the video-tracking system, and members of the Sternberg and Benzer laboratories for experimental guidance and reading drafts of our manuscript. The Caenorhabditis Genetics Center provided strains. This work was supported by the Howard Hughes Medical Institute, with which P.W.S. is an investigator. This paper was submitted directly (Track II) to the PNAS office. \n\nThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked \"advertisement\" in accordance with 18 U.S.C.\n\u00a71734 solely to indicate this fact.\n\nPublished - SIMpnas02.pdf
", "abstract": "When males of the roundworm Caenorhabditis elegans come into association with their hermaphroditic counterparts they cease foraging behavior and begin to mate. Here we detail several assays used to demonstrate that a diffusible cue is correlated with this process. This cue is sexually dimorphic, given off only by the hermaphrodite and eliciting a response only in the male. Males are attracted to, reverse direction of movement frequently, and remain in regions of agar conditioned with hermaphrodites. From our studies we suggest a form of kinesis that works by attracting males to their mating partners from a distance and functions, once males arrive, in holding attracted males in close proximity. The hermaphrodite vulva is not required for the cue. Males from general sensory mutants osm-5 and osm-6 fail to respond to the cue, whereas male-specific mutants lov-1 and pkd-2 respond. Finally, that males from multiple isolates of C elegans also respond similarly to this cue indicates that this cue is robust and has been maintained during recent evolution.", "date": "2002-02-05", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "99", "number": "3", "publisher": "National Academy of Sciences", "pagerange": "1598-1603", "id_number": "CaltechAUTHORS:SIMpnas02", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:SIMpnas02", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1073/pnas.032225799", "pmcid": "PMC122236", "primary_object": { "basename": "SIMpnas02.pdf", "url": "https://authors.library.caltech.edu/records/9c5kn-mj396/files/SIMpnas02.pdf" }, "resource_type": "article", "pub_year": "2002", "author_list": "Simon, Jasper M. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/q6xba-jm793", "eprint_id": 95480, "eprint_status": "archive", "datestamp": "2023-08-19 07:52:27", "lastmod": "2023-10-20 20:16:34", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "van-Swinderen-B", "name": { "family": "van Swinderen", "given": "Bruno" } }, { "id": "Metz-L-B", "name": { "family": "Metz", "given": "Laura B." } }, { "id": "Shebester-L-D", "name": { "family": "Shebester", "given": "Laynie D." } }, { "id": "Mendel-J-E", "name": { "family": "Mendel", "given": "Jane E." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Crowder-C-M", "name": { "family": "Crowder", "given": "C. Michael" } } ] }, "title": "Go\u03b1 Regulates Volatile Anesthetic Action in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2001 by the Genetics Society of America. \n\nManuscript received October 20, 2000; Accepted for publication March 7, 2001. \n\nWe thank Yvonne Hajdu-Cronin and Shahla Gharib for technical assistance in sequencing goa-1(sy192) and Yvonne Hajdu-Cronin, Wen Chen, and Russell Roberson for communication of unpublished results. This work was supported by National Institutes of Health RO1 GM-55832-01 and RO1 GM-59781-02 (C.M.C.), the Foundation for Anesthesia Education and Research (C.M.C.). P.W.S. is an investigator of the Howard Hughes Medical Institute. Some of the C. elegans strains used in this work were provided by the Caenorhabditis Genetics Center, which is funded by the National Institutes of Health National Center for Research Resources.\n\nPublished - 11404329.pdf
", "abstract": "To identify genes controlling volatile anesthetic (VA) action, we have screened through existing Caenorhabditis elegans mutants and found that strains with a reduction in Go signaling are VA resistant. Loss-of-function mutants of the gene goa-1, which codes for the \u03b1-subunit of Go, have EC_(50)s for the VA isoflurane of 1.7- to 2.4-fold that of wild type. Strains overexpressing egl-10, which codes for an RGS protein negatively regulating goa-1, are also isoflurane resistant. However, sensitivity to halothane, a structurally distinct VA, is differentially affected by Go pathway mutants. The RGS overexpressing strains, a goa-1 missense mutant found to carry a novel mutation near the GTP-binding domain, and eat-16(rf) mutants, which suppress goa-1(gf) mutations, are all halothane resistant; goa-1(null) mutants have wild-type sensitivities. Double mutant strains carrying mutations in both goa-1 and unc-64, which codes for a neuronal syntaxin previously found to regulate VA sensitivity, show that the syntaxin mutant phenotypes depend in part on goa-1 expression. Pharmacological assays using the cholinesterase inhibitor aldicarb suggest that VAs and GOA-1 similarly downregulate cholinergic neurotransmitter release in C. elegans. Thus, the mechanism of action of VAs in C. elegans is regulated by Go\u03b1, and presynaptic Go\u03b1-effectors are candidate VA molecular targets.", "date": "2001-06-01", "date_type": "published", "publication": "Genetics", "volume": "158", "number": "2", "publisher": "Genetics Society of America", "pagerange": "643-655", "id_number": "CaltechAUTHORS:20190514-103243544", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-103243544", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "RO1 GM-55832-01" }, { "agency": "NIH", "grant_number": "RO1 GM-59781-02" }, { "agency": "Foundation for Anesthesia Education and Research" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "pmcid": "PMC1461665", "primary_object": { "basename": "11404329.pdf", "url": "https://authors.library.caltech.edu/records/q6xba-jm793/files/11404329.pdf" }, "resource_type": "article", "pub_year": "2001", "author_list": "van Swinderen, Bruno; Metz, Laura B.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/0mcy1-kqt03", "eprint_id": 95481, "eprint_status": "archive", "datestamp": "2023-08-19 07:11:54", "lastmod": "2023-10-20 20:16:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dichtel-M-L", "name": { "family": "Dichtel", "given": "Marie-Laure" } }, { "id": "Louvet-Vall\u00e9e-S", "name": { "family": "Louvet-Vall\u00e9e", "given": "Sophie" } }, { "id": "Viney-M-E", "name": { "family": "Viney", "given": "Mark E." } }, { "id": "F\u00e9lix-M-A", "name": { "family": "F\u00e9lix", "given": "Marie-Anne" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Control of Vulval Cell Division Number in the Nematode Oscheius/Dolichorhabditis sp. CEW1", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2001 by the Genetics Society of America. \n\nManuscript received July 24, 2000; Accepted for publication September 18, 2000. \n\nWe thank Marie Delattre and Ralf Sommer for discussions and reading of the manuscript. We are very grateful to G. Medina, M. Khairy, E. Delattre, and S. Boeuf for preparing the many worm plates that were used. P.W.S. is an Investigator with the Howard Hughes Medical Institute. M.-A.F. was supported during the course of this work by the Howard Hughes Medical Institute and the Centre National de la Recherche Scientifique. M.E.V. was supported by a Medical Research Council Career Development Award. Work in the M.-A.F. laboratory is supported by an ATIPE of Centre National de la Recherche Scientifique, the Fondation pour la Recherche M\u00e9dicale and the Association pour la Recherche sur le Cancer.\n\nPublished - 11139501.pdf
", "abstract": "Spatial patterning of vulval precursor cell fates is achieved through a different two-stage induction mechanism in the nematode Oscheius/Dolichorhabditis sp. CEW1 compared with Caenorhabditis elegans. We therefore performed a genetic screen for vulva mutants in Oscheius sp. CEW1. Most mutants display phenotypes unknown in C. elegans. Here we present the largest mutant category, which affects division number of the vulva precursors P(4-8).p without changing their fate. Among these mutations, some reduce the number of divisions of P4.p and P8.p specifically. Two mutants omit the second cell cycle of all vulval lineages. A large subset of mutants undergo additional rounds of vulval divisions. We also found precocious and retarded heterochronic mutants. Whereas the C. elegans vulval lineage mutants can be interpreted as overall (homeotic) changes in precursor cell fates with concomitant cell cycle changes, the mutants described in Oscheius sp. CEW1 do not affect overall precursor fate and thereby dissociate the genetic mechanisms controlling vulval cell cycle and fate. Laser ablation experiments in these mutants reveal that the two first vulval divisions in Oscheius sp. CEW1 appear to be redundantly controlled by a gonad-independent mechanism and by a gonadal signal that operates partially independently of vulval fate induction.", "date": "2001-01-01", "date_type": "published", "publication": "Genetics", "volume": "157", "number": "1", "publisher": "Genetics Society of America", "pagerange": "183-197", "id_number": "CaltechAUTHORS:20190514-103856899", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-103856899", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Centre National de la Recherche Scientifique (CNRS)" }, { "agency": "Medical Research Council (UK)" }, { "agency": "Fondation pour la Recherche M\u00e9dicale" }, { "agency": "Association pour la Recherche sur le Cancer" } ] }, "pmcid": "PMC1461485", "primary_object": { "basename": "11139501.pdf", "url": "https://authors.library.caltech.edu/records/0mcy1-kqt03/files/11139501.pdf" }, "resource_type": "article", "pub_year": "2001", "author_list": "Dichtel, Marie-Laure; Louvet-Vall\u00e9e, Sophie; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/nme8v-z0v53", "eprint_id": 790, "eprint_status": "archive", "datestamp": "2023-08-21 21:55:08", "lastmod": "2023-10-13 21:58:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Stein-L-D", "name": { "family": "Stein", "given": "Lincoln" }, "orcid": "0000-0002-1983-4588" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Durbin-R", "name": { "family": "Durbin", "given": "Richard" } }, { "id": "Thierry-Mieg-J", "name": { "family": "Thierry-Mieg", "given": "Jean" } }, { "id": "Spieth-J", "name": { "family": "Spieth", "given": "John" } } ] }, "title": "WormBase: network access to the genome and biology of Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2001 Oxford University Press \n\nReceived September 18, 2000; Accepted October 4, 2000 \n\nThis work was supported in part by NIH grant P41HG02223, as well as funding from the UK Medical Research Council and the National Library of Medicine.", "abstract": "WormBase (http://www.wormbase.org) is a web-based resource for the Caenorhabditis elegans genome and its biology. It builds upon the existing ACeDB database of the C.elegans genome by providing data curation services, a significantly expanded range of subject areas and a user-friendly front end.", "date": "2001-01-01", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "29", "number": "1", "publisher": "Nucleic Acids Research", "pagerange": "82-86", "id_number": "CaltechAUTHORS:STEnar01", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:STEnar01", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1093/nar/29.1.82", "primary_object": { "basename": "STEnar01.pdf", "url": "https://authors.library.caltech.edu/records/nme8v-z0v53/files/STEnar01.pdf" }, "resource_type": "article", "pub_year": "2001", "author_list": "Stein, Lincoln; Sternberg, Paul W.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/y5xm3-gcb90", "eprint_id": 28394, "eprint_status": "archive", "datestamp": "2023-08-19 06:52:11", "lastmod": "2023-10-24 17:51:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Minqin", "name": { "family": "Wang", "given": "Minqin" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Patterning of the C. elegans 1\u00b0 vulval lineage by RAS and Wnt pathways", "ispublished": "pub", "full_text_status": "public", "keywords": "Pattern formation, 1\u00b0 lineage, Execution, Asymmetric\ncell division, C. elegans", "note": "\u00a9 2000 The Company of Biologists. Accepted 8 September; published on WWW 2 November 2000. We are grateful to Jim Butler and Jim Kramer for zmp-1::GFP DNA, Carola Sigrist and Ralf Sommer for Pristionchus hs-ras(dn) DNA, and Bhagwati Gupta and Martha Kirouac for integrating syEx282. We thank Tom Clandinin, Dave Sherwood, Nadeem Moghal, Takao Inoue, Bhagwati Gupta, Byung Joon Hwang, and Lisa Girard for critically reading the manuscript. Some of the strains were provided by the C. elegans Genetics Center. This work was supported by USPHS (grant HD23690) to P.W.S., an Investigator with the Howard Hughes Medical Institute.\n\nPublished - WANdev00.pdf
", "abstract": "In C. elegans, the descendants of the 1\u00b0 vulval precursor\ncell (VPC) establish a fixed spatial pattern of two different cell fates: E-F-F-E. The two inner granddaughters attach to the somatic gonadal anchor cell (AC) and generate four vulF cells, while the two outer granddaughters produce\nfour vulE progeny. zmp-1::GFP, a molecular marker that\ndistinguishes these two fates, is expressed in vulE cells, but not vulF cells. We demonstrate that a short-range AC signal is required to ensure that the pattern of vulE and vulF fates is properly established. In addition, signaling between the inner and outer 1\u00b0 VPC descendants, as well as intrinsic polarity of the 1\u00b0 VPC daughters, is involved in the asymmetric divisions of the 1\u00b0 VPC daughters and the\nproper orientation of the outcome. Finally, we provide\nevidence that RAS signaling is used during this new AC\nsignaling event, while the Wnt receptor LIN-17 appears to\nmediate signaling between the inner and outer 1\u00b0 VPC\ndescendants.", "date": "2000-12-01", "date_type": "published", "publication": "Development", "volume": "127", "number": "23", "publisher": "Company of Biologists", "pagerange": "5047-5058", "id_number": "CaltechAUTHORS:20111209-102248415", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111209-102248415", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HD23690" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "primary_object": { "basename": "WANdev00.pdf", "url": "https://authors.library.caltech.edu/records/y5xm3-gcb90/files/WANdev00.pdf" }, "resource_type": "article", "pub_year": "2000", "author_list": "Wang, Minqin and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/f8h3k-hwp23", "eprint_id": 7036, "eprint_status": "archive", "datestamp": "2023-08-21 21:40:53", "lastmod": "2023-10-23 15:51:52", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yoon-Charles-H", "name": { "family": "Yoon", "given": "Charles H." } }, { "id": "Chang-Chieh", "name": { "family": "Chang", "given": "Chieh" } }, { "id": "Hopper-N-A", "name": { "family": "Hopper", "given": "Neil A." } }, { "id": "Lesa-G-M", "name": { "family": "Lesa", "given": "Giovanni M." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Requirements of Multiple Domains of SLI-1, a Caenorhabditis elegans Homologue of c-Cbl, and an Inhibitory Tyrosine in LET-23 in Regulating Vulval Differentiation", "ispublished": "pub", "full_text_status": "public", "note": "Copyright \u00a9 2000 by The American Society for Cell Biology. Under the License and Publishing Agreement, authors grant to the general public, effective two months after publication of (i.e.,. the appearance of) the edited manuscript in an online issue of MBoC, the nonexclusive right to copy, distribute, or display the manuscript subject to the terms of the Creative Commons\u2013Noncommercial\u2013Share Alike 3.0 Unported license (http://creativecommons.org/licenses/by-nc-sa/3.0). \n\nSubmitted June 28, 2000; Revised August 21, 2000; Accepted September 15, 2000. \n\nWe thank Michael Stern for providing the sem-5(ay73) and the sem-5(n1619) alleles, Wally Langdon for providing the human c-cbl cDNA. We also thank Raffi Aroian for critical reading of this manuscript; Pepe Alberola-I1a, David Chan, Maureen Barr, anonymous reviewers, and members of the Sternberg laboratory for helpful comments. This work was supported by a grant from the US Army Breast Cancer Program (grant DAMD-95-1-5003) to P.W.S., an investigator with the Howard Hughes Medical Institute. C.H.Y. and C.C. were funded with a National Institutes of Health predoctoral training grant (GM07616). Some strains were provided by the Caenorhabditis Genetic Center.\n\nPublished - YOOmbc00.pdf
Supplemental Material - YOOmbc00fig1.jpg
", "abstract": "SLI-1, a Caenorhabditis elegans homologue of the proto-oncogene product c-Cbl, is a negative regulator of LET-23-mediated vulval differentiation. Lack of SLI-1 activity can compensate for decreased function of the LET-23 epidermal growth factor receptor, the SEM-5 adaptor, but not the LET-60 RAS, suggesting that SLI-1 acts before RAS activation. SLI-1 and c-Cbl comprise an N-terminal region (termed SLI-1:N/Cbl-N, containing a four-helix bundle, an EF hand calcium-binding domain, and a divergent SH2 domain) followed by a RING finger domain and a proline-rich C-terminus. In a transgenic functional assay, the proline-rich C-terminal domain is not essential for sli-1(+) function. A protein lacking the SH2 and RING finger domains has no activity, but a chimeric protein with the SH2 and RING finger domains of SLI-1 replaced by the equivalent domains of c-Cbl has activity. The RING finger domain of c-Cbl has been shown recently to enhance ubiquitination of active RTKs by acting as an E3 ubiquitin-protein ligase. We find that the RING finger domain of SLI-1 is partially dispensable. Further, we identify an inhibitory tyrosine of LET-23 requiring sli-1(+) for its effects: removal of this tyrosine closely mimics the loss of sli-1 but not of another negative regulator, ark-1. Thus, we suggest that this inhibitory tyrosine mediates its effects through SLI-1, which in turn inhibits signaling upstream of LET-60 RAS in a manner not wholly dependent on the ubiquitin-ligase domain.", "date": "2000-11", "date_type": "published", "publication": "Molecular Biology of the Cell", "volume": "11", "number": "11", "publisher": "American Society for Cell Biology", "pagerange": "4019-4031", "id_number": "CaltechAUTHORS:YOOmbc00", "issn": "1059-1524", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:YOOmbc00", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Army Research Office (ARO)", "grant_number": "DAMD-95-1-5003" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH Predoctoral Fewllowship", "grant_number": "GM07616" } ] }, "pmcid": "PMC15054", "primary_object": { "basename": "YOOmbc00fig1.jpg", "url": "https://authors.library.caltech.edu/records/f8h3k-hwp23/files/YOOmbc00fig1.jpg" }, "related_objects": [ { "basename": "medium.png", "url": "https://authors.library.caltech.edu/records/f8h3k-hwp23/files/medium.png" }, { "basename": "small.png", "url": "https://authors.library.caltech.edu/records/f8h3k-hwp23/files/small.png" }, { "basename": "YOOmbc00.pdf", "url": "https://authors.library.caltech.edu/records/f8h3k-hwp23/files/YOOmbc00.pdf" } ], "resource_type": "article", "pub_year": "2000", "author_list": "Yoon, Charles H.; Chang, Chieh; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/g7kw5-1pf16", "eprint_id": 65287, "eprint_status": "archive", "datestamp": "2023-08-19 06:10:18", "lastmod": "2023-10-18 14:29:50", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bronner-M-E", "name": { "family": "Bronner-Fraser", "given": "Marianne" }, "orcid": "0000-0003-4274-1862" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Pattern formation and developmental mechanisms: The cell biological basis of inductive signaling", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2000 Elsevier Science Ltd. \n\nAvailable online 14 July 2000.", "abstract": "A central issue in developmental biology is how a complex organism arises from a single cell. In both plant and animal development, this occurs by a combination of intrinsic information within cells as well as signals transmitted between cells that result in proper patterning of the embryo. Because of the central role of cell communication, intercellular signaling and signal transduction is an important consideration for understanding development as well as the interplay of signaling and transcription. The transcriptional state of the cell depends upon its prior history and the signals it receives. In turn, the signals produced by a cell and its ability to respond to signals are programmed to a large extent by its transcriptional state. The particular wiring of these signals\u2192transcription\u2192signals circuits determines how cells communicate to specify their fates in particular patterns.", "date": "2000-08-01", "date_type": "published", "publication": "Current Opinion in Genetics and Development", "volume": "10", "number": "4", "publisher": "Current Biology Ltd", "pagerange": "347-349", "id_number": "CaltechAUTHORS:20160311-065659955", "issn": "0959-437X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160311-065659955", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/S0959-437X(00)00094-0", "resource_type": "article", "pub_year": "2000", "author_list": "Bronner-Fraser, Marianne and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/jpvk3-yq546", "eprint_id": 28388, "eprint_status": "archive", "datestamp": "2023-08-19 06:08:34", "lastmod": "2023-10-24 17:51:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shim-Jaegal", "name": { "family": "Shim", "given": "Jaegal" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Lee-Junho", "name": { "family": "Lee", "given": "Junho" } } ] }, "title": "Distinct and Redundant Functions of \u00b51 Medium Chains of the AP-1 Clathrin-Associated Protein Complex in the Nematode Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2000 by The American Society for Cell Biology. Under the License and Publishing Agreement, authors grant to the general public, effective two months after publication of (i.e.,. the appearance of) the edited manuscript in an online issue of MBoC, the nonexclusive right to copy, distribute, or display the manuscript subject to the terms of the Creative Commons\u2013Noncommercial\u2013Share Alike 3.0 Unported license (http://creativecommons.org/licenses/by-nc-sa/3.0). \n\nSubmitted May 12, 2000; Revised May 15, 2000; Accepted June 2, 2000. Monitoring Editor: Juan Bonifacino. We thank Drs. A. Fire, A. Coulson, and Y. Kohara, and the Caenorhabditis Genetics Center (St. Paul, MN) for providing the nematode vectors, strains, and genomic and cDNA clones. We also thank S.\nYoo and Dr. D. Jeoung for the dendrogram of the medium chain\nhomologs. This study was supported in part by the Korean /U.S. Cooperative Science Program (KOSEF 965-0504-001\u20132), by the Molecular Medicine Research Group Program (98-J03\u2013 01-01-A-05) from the Ministry of Science and Technology (Korea) to J.L., and by USPHS grant HD23690 to P.W.S. P.W.S. is an investigator with the H. H. M. I.\n\nPublished - SHImbc00.pdf
", "abstract": "In the nematode Caenorhabditis elegans, there exist two \u03bc1 medium chains of the AP-1 clathrin-associated protein complex. Mutations of unc-101, the gene that encodes one of the \u03bc1 chains, cause pleiotropic effects (Lee et al., 1994 blue right-pointing triangle). In this report, we identified and analyzed the second \u03bc1 chain gene, apm-1. Unlike the mammalian homologs, the two medium chains are expressed ubiquitously throughout development. RNA interference (RNAi) experiments with apm-1 showed that apm-1 and unc-101 were redundant in embryogenesis and in vulval development. Consistent with this, a hybrid protein containing APM-1, when overexpressed, rescued the phenotype of an unc-101 mutant. However, single disruptions of apm-1 or unc-101 have distinct phenotypes, indicating that the two medium chains may have distinct functions. RNAi of any one of the small or large chains of AP-1 complex (\u03c31, \u03b21, or \u03b3) showed a phenotype identical to that caused by the simultaneous disruption of unc-101 and apm-1, but not that by single disruption of either gene. This suggests that the two medium chains may share large and small chains in the AP-1 complexes. Thus, apm-1 and unc-101 encode two highly related \u03bc1 chains that share redundant and distinct functions within AP-1 clathrin-associated protein complexes of the same tissue.", "date": "2000-08", "date_type": "published", "publication": "Molecular Biology of the Cell", "volume": "11", "number": "8", "publisher": "American Society for Cell Biology", "pagerange": "2743-2756", "id_number": "CaltechAUTHORS:20111209-094319607", "issn": "1059-1524", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111209-094319607", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Korean/U.S. Cooperative Science Program", "grant_number": "KOSEF 965-0504-001-2" }, { "agency": "Molecular Medicine Research Group Program", "grant_number": "98-J03-01-01-A-05" }, { "agency": "Ministry of Science and Technology (Korea)" }, { "agency": "USPHS", "grant_number": "HD23690" } ] }, "doi": "10.1091/mbc.11.8.2743", "pmcid": "PMC14953", "primary_object": { "basename": "SHImbc00.pdf", "url": "https://authors.library.caltech.edu/records/jpvk3-yq546/files/SHImbc00.pdf" }, "resource_type": "article", "pub_year": "2000", "author_list": "Shim, Jaegal; Sternberg, Paul W.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/d80wc-xt057", "eprint_id": 95485, "eprint_status": "archive", "datestamp": "2023-08-21 21:22:07", "lastmod": "2023-10-20 20:16:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chang-Chieh", "name": { "family": "Chang", "given": "Chieh" } }, { "id": "Hopper-N-A", "name": { "family": "Hopper", "given": "Neil A." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Caenorhabditis elegans SOS-1 is necessary for multiple RAS-mediated developmental signals", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Caenorhabditis Elegans; Proto\u2010Oncogene; Ras Pathway; Tyrosine Kinase; Vulval Development", "note": "\u00a9 2000 European Molecular Biology Organization. \n\nReceived January 20, 2000; revised and accepted May 15, 2000. \n\nWe thank M. Stern for providing his unpublished let\u2010341(n2183) and sem\u20105(ay73) alleles and for discussion of FGF receptor signaling; Z. Chen and M. Han for their generosity in providing their unpublished let\u2010341(ku231) allele; and N. Moghal and J. Alberola\u2010Ila for critical reading of this manuscript. Some strains were provided by the Caenorhabditis Genetics Center, supported by the National Center for Research Resources of the National Institutes of Health. This work has been supported by US Public Health Service grant (HD23690) to P.W.S., an investigator with the Howard Hughes Medical Institute. C.C. is funded by a NIH predoctoral training grant (GM07616).", "abstract": "Vulval induction in Caenorhabditis elegans has helped define an evolutionarily conserved signal transduction pathway from receptor tyrosine kinases (RTKs) through the adaptor protein SEM\u20105 to RAS. One component present in other organisms, a guanine nucleotide exchange factor for Ras, has been missing in C.elegans. To understand the regulation of this pathway it is crucial to have all positive\u2010acting components in hand. Here we describe the identification, cloning and genetic characterization of C.elegans SOS\u20101, a putative guanine nucleotide exchanger for LET\u201060 RAS. RNA interference experiments suggest that SOS\u20101 participates in RAS\u2010dependent signaling events downstream of LET\u201023 EGFR, EGL\u201015 FGFR and an unknown RTK. We demonstrate that the previously identified let\u2010341 gene encodes SOS\u20101. Analyzing vulval development in a let\u2010341 null mutant, we find an SOS\u20101\u2010independent pathway involved in the activation of RAS signaling. This SOS\u20101\u2010independent signaling is not inhibited by SLI\u20101/Cbl and is not mediated by PTP\u20102/SHP, raising the possibility that there could be another RasGEF.", "date": "2000-07-03", "date_type": "published", "publication": "EMBO Journal", "volume": "19", "number": "13", "publisher": "European Molecular Biology Organization", "pagerange": "3283-3294", "id_number": "CaltechAUTHORS:20190514-110311949", "issn": "1460-2075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-110311949", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HD23690" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "GM07616" } ] }, "doi": "10.1093/emboj/19.13.3283", "pmcid": "PMC313952", "resource_type": "article", "pub_year": "2000", "author_list": "Chang, Chieh; Hopper, Neil A.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/pv9g2-e7t51", "eprint_id": 1220, "eprint_status": "archive", "datestamp": "2023-08-21 21:12:42", "lastmod": "2023-10-23 16:06:03", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Levchenko-A", "name": { "family": "Levchenko", "given": "Andre" } }, { "id": "Bruck-J", "name": { "family": "Bruck", "given": "Jehoshua" }, "orcid": "0000-0001-8474-0812" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties", "ispublished": "pub", "full_text_status": "public", "keywords": "MAP-KINASE, SACCHAROMYCES-CEREVISIAE, SWITCH-LIKE, CASCADE, PATHWAYS, COMPLEX, YEAST, BINDING, STE5, KSR", "note": "\u00a9 2000 by the National Academy of Sciences. \n\nEdited by Mark Ptashne, Memorial Sloan\u2013Kettering Cancer Center, New York, NY, and approved March 22, 2000 (received for review October 14, 1999). \n\nWe thank B. J. Wold and three anonymous reviewers for discussion and critical review. This work was supported by Office of Naval Research Grant N00014\u201397-1\u20130293 and by a Jet Propulsion Laboratory grant to J.B. and P.W.S. (an investigator with the Howard Hughes Medical Institute), by a Sloan Research Fellowship to J.B., and by Burroughs\u2013Wellcome Fund Computational Molecular Biology Postdoctoral Fellowship to A.L. This paper was submitted directly (Track II) to the PNAS office. \n\nThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked \"advertisement\" in accordance with 18 U.S.C. \u00a71734 solely to indicate this fact.\n\nPublished - LEVpnas00.pdf
", "abstract": "In addition to preventing crosstalk among related signaling pathways, scaffold proteins might facilitate signal transduction by preforming multimolecular complexes that can be rapidly activated by incoming signal. In many cases, such as mitogen-activated protein kinase (MAPK) cascades, scaffold proteins are necessary for full activation of a signaling pathway. To date, however, no detailed biochemical model of scaffold action has been suggested. Here we describe a quantitative computer model of MAPK cascade with a generic scaffold protein. Analysis of this model reveals that formation of scaffold-kinase complexes can be used effectively to regulate the specificity, efficiency, and amplitude of signal propagation. In particular, for any generic scaffold there exists a concentration value optimal for signal amplitude. The location of the optimum is determined by the concentrations of the kinases rather than their binding constants and in this way is scaffold independent. This effect and the alteration of threshold properties of the signal propagation at high scaffold concentrations might alter local signaling properties at different subcellular compartments. Different scaffold levels and types might then confer specialized properties to tune evolutionarily conserved signaling modules to specific cellular contexts.", "date": "2000-05-23", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "97", "number": "11", "publisher": "National Academy of Sciences", "pagerange": "5818-5823", "id_number": "CaltechAUTHORS:LEVpnas00", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:LEVpnas00", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Office of Naval Research (ONR)", "grant_number": "N00014\u201397-1\u20130293" }, { "agency": "JPL" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Alfred P. Sloan Foundation" }, { "agency": "Burroughs Wellcome Fund" } ] }, "pmcid": "PMC18517", "primary_object": { "basename": "LEVpnas00.pdf", "url": "https://authors.library.caltech.edu/records/pv9g2-e7t51/files/LEVpnas00.pdf" }, "resource_type": "article", "pub_year": "2000", "author_list": "Levchenko, Andre; Bruck, Jehoshua; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/vg37a-vzt72", "eprint_id": 12032, "eprint_status": "archive", "datestamp": "2023-08-22 14:12:18", "lastmod": "2023-10-17 16:29:04", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Newman-A-P", "name": { "family": "Newman", "given": "Anna P." } }, { "id": "Acton-G-Z", "name": { "family": "Acton", "given": "Gwen Z." } }, { "id": "Hartwieg-E", "name": { "family": "Hartwieg", "given": "Erika" } }, { "id": "Horvitz-H-R", "name": { "family": "Horvitz", "given": "H. Robert" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The lin-11 LIM domain transcription factor is necessary for morphogenesis of C. elegans uterine cells", "ispublished": "pub", "full_text_status": "public", "keywords": "Caenorhabditis elegans, lin-11, Uterus, Hermaphrodite", "note": "Copyright \u00a9 1999 by Company of Biologists. \n\nAccepted 10 September; published on WWW 9 November 1999. \n\nThis work was supported by NIH grant GM24663 to H.R.H. and\nby the Howard Hughes Medical Institute. H.R.H. and P.W.S. are Investigators and A.P.N. was an Associate of the Howard Hughes Medical Institute. We are grateful to Maureen Barr and Marie-Anne Felix for their comments concerning the manuscript. We thank Jonathan Pettitt for strains NL1000 and NL1008, Wendy Hanna-Rose and Min Han for the integrated cog-2::GFP transcriptional fusion kuIs28, and Nese Cinar for constructing the strain containing kuIs28 in a lin-11(n389) mutant background. The inability of lin-11 mutant animals without 2\u00b0 cells to lay eggs was first observed by Jim Thomas. lin-11(sy251) was isolated by Bino Palmer and P.W.S.; lin-11(ty6) was isolated by N. Cinar and A.P.N.\n\nPublished - NEWdev99.pdf
", "abstract": "The Caenorhabditis elegans hermaphrodite egg-laying system comprises several tissues, including the uterus and vulva. lin-11 encodes a LIM domain transcription factor needed for certain vulval precursor cells to divide asymmetrically. Based on lin-11 expression studies and the lin-11 mutant phenotype, we find that lin-11 is also required for C. elegans uterine morphogenesis. Specifically, lin-11 is expressed in the ventral uterine intermediate precursor (pi) cells and their progeny (the utse and uv1 cells), which connect the uterus to the vulva. Like (pi) cell induction, the uterine lin-11 expression responds to the uterine anchor cell and the lin-12-encoded receptor. In wild type animals, the utse, which forms the planar process at the uterine-vulval interface, fuses with the anchor cell. We found that, in lin-11 mutants, utse differentiation was abnormal, the utse failed to fuse with the anchor cell and a functional uterine-vulval connection was not made. These findings indicate that lin-11 is essential for uterine-vulval morphogenesis.", "date": "1999-12-01", "date_type": "published", "publication": "Development", "volume": "126", "number": "23", "publisher": "Company of Biologists", "pagerange": "5319-5326", "id_number": "CaltechAUTHORS:NEWdev99", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:NEWdev99", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Institutes of Health", "grant_number": "GM24663" }, { "agency": "Howard Hughes Medical Institute" } ] }, "primary_object": { "basename": "NEWdev99.pdf", "url": "https://authors.library.caltech.edu/records/vg37a-vzt72/files/NEWdev99.pdf" }, "resource_type": "article", "pub_year": "1999", "author_list": "Newman, Anna P.; Acton, Gwen Z.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/0va3g-9xv83", "eprint_id": 95486, "eprint_status": "archive", "datestamp": "2023-08-22 14:09:43", "lastmod": "2023-10-20 20:16:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hsieh-Jenny", "name": { "family": "Hsieh", "given": "Jenny" } }, { "id": "Liu-Jing", "name": { "family": "Liu", "given": "Jing" } }, { "id": "Kostas-S-A", "name": { "family": "Kostas", "given": "Stephen A." } }, { "id": "Chang-Chieh", "name": { "family": "Chang", "given": "Chieh" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Fire-A", "name": { "family": "Fire", "given": "Andrew" } } ] }, "title": "The RING finger/B-Box factor TAM-1 and a retinoblastoma-like protein LIN-35 modulate context-dependent gene silencing in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "TAM-1; Chromatin Silencing; RING finger; C. elegans; Rb; RAS Pathway", "note": "\u00a9 1999 by Cold Spring Harbor Laboratory Press. \n\nReceived June 30 1999; revised version accepted September 28 1999. \n\nWe thank K. Liu, S. Parrish, B. Kelly, L. Timmons, J. Goodliffe, C. Lee, C. Ceol, E. Davison, B. Horvitz, M. Bellini, V. Guacci, P. McGee, E. Jorgensen, and A. Shearn for help and advice; M. Edgley, D. Riddle, H. Hutter, L. Huang, J. DeModena, S. Xu, J. Fleenor, J. Mendel, Y. Kohara, and K. Dej for useful materials; and R. Feldman for isolating several tam-1 alleles. This work was supported by U.S. Public Health Service grants GM37706 (A.F.); HD23690 (P.W.S.); T32GM07231 (J.H., S.K.); GM07616 (J.L., C.C.); and by the Carnegie Institution of Washington. P.W.S. is an investigator of the Howard Hughes Medical Institute. Some nematode strains used in this work were provided by the Caenorhabditis Genetics Center, which is supported by National Institutes of Health's National Center for Research Resources. \n\nThe publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked \"advertisement\" in accordance with 18 USC section 1734 solely to indicate this fact.\n\nPublished - x6.pdf
", "abstract": "Context-dependent gene silencing is used by many organisms to stably modulate gene activity for large chromosomal regions. We have used tandem array transgenes as a model substrate in a screen for Caenorhabditis elegans mutants that affect context-dependent gene silencing in somatic tissues. This screen yielded multiple alleles of a previously uncharacterized gene, designated tam-1 (fortandem-array-modifier). Loss-of-function mutations in tam-1 led to a dramatic reduction in the activity of numerous highly repeated transgenes. These effects were apparently context dependent, as nonrepetitive transgenes retained activity in a tam-1 mutant background. In addition to the dramatic alterations in transgene activity, tam-1 mutants showed modest alterations in expression of a subset of endogenous cellular genes. These effects include genetic interactions that place tam-1 into a group called the class B synMuv genes (for aSynthetic Multivulva phenotype); this family plays a negative role in the regulation of RAS pathway activity in C. elegans. Loss-of-function mutants in other members of the class-B synMuv family, including lin-35, which encodes a protein similar to the tumor suppressor Rb, exhibit a hypersilencing in somatic transgenes similar to that of tam-1 mutants. Molecular analysis reveals that tam-1 encodes a broadly expressed nuclear protein with RING finger and B-box motifs.", "date": "1999-11-15", "date_type": "published", "publication": "Genes and Development", "volume": "13", "number": "22", "publisher": "Cold Spring Harbor Laboratory Press", "pagerange": "2958-2970", "id_number": "CaltechAUTHORS:20190514-110944071", "issn": "0890-9369", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-110944071", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM37706" }, { "agency": "NIH", "grant_number": "HD23690" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM07231" }, { "agency": "NIH", "grant_number": "GM07616" }, { "agency": "Carnegie Institution of Washington" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "pmcid": "PMC317160", "primary_object": { "basename": "x6.pdf", "url": "https://authors.library.caltech.edu/records/0va3g-9xv83/files/x6.pdf" }, "resource_type": "article", "pub_year": "1999", "author_list": "Hsieh, Jenny; Liu, Jing; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/q4paj-db842", "eprint_id": 95487, "eprint_status": "archive", "datestamp": "2023-08-19 04:51:46", "lastmod": "2023-10-20 20:16:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Liu-Jing", "name": { "family": "Liu", "given": "Jing" } }, { "id": "Tzou-Phoebe", "name": { "family": "Tzou", "given": "Phoebe" } }, { "id": "Hill-R-J", "name": { "family": "Hill", "given": "Russell J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Structural Requirements for the Tissue-Specific and Tissue-General Functions of the Caenorhabditis elegans Epidermal Growth Factor LIN-3", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1999 by the Genetics Society of America. \n\nManuscript received August 31, 1998; Accepted for publication July 14, 1999. \n\nWe thank the Caenorhabditis Genetics Center for providing some of the strains, and T. Clandinin for commenting on the manuscript. This work was supported by a grant from U.S. Public Health Service (HD23690) to P.W.S., who is an Investigator with the Howard Hughes Medical Institute.\n\nPublished - 10545457.pdf
", "abstract": "Caenorhabditis elegans lin-3 encodes a homolog of the epidermal growth factor (EGF) family of growth factors. LIN-3 is the inductive signal for hermaphrodite vulval differentiation, and it is required for animal viability, hermaphrodite fertility, and the specification of anterior cell fates in the male B cell lineage. We describe the cloning of a lin-3 homolog from C. briggsae, sequence comparison of C. elegans lin-3 with C. briggsae lin-3, and the determination of molecular lesions in alleles of C. elegans lin-3, including three new alleles. We also analyzed the severity of phenotypes caused by the new and existing alleles of lin-3. Correlation of mutant phenotypes and their molecular lesions, as well as sequence comparison between two species, reveal that the EGF motif and the N-terminal portion of the cytoplasmic domain are important for the functions of LIN-3 in all tissues, while the C-terminal portion of the cytoplasmic domain is involved in the tissue-specific functions of lin-3. We discuss how the structure of lin-3 contributes to its functions in multiple developmental processes.", "date": "1999-11-01", "date_type": "published", "publication": "Genetics", "volume": "153", "number": "3", "publisher": "Genetics Society of America", "pagerange": "1257-1269", "id_number": "CaltechAUTHORS:20190514-112200944", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-112200944", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HD23690" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "pmcid": "PMC1460807", "primary_object": { "basename": "10545457.pdf", "url": "https://authors.library.caltech.edu/records/q4paj-db842/files/10545457.pdf" }, "resource_type": "article", "pub_year": "1999", "author_list": "Liu, Jing; Tzou, Phoebe; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/a7ce1-1mh95", "eprint_id": 95488, "eprint_status": "archive", "datestamp": "2023-08-19 04:46:38", "lastmod": "2023-10-20 20:16:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chamberlin-H-M", "name": { "family": "Chamberlin", "given": "Helen M." } }, { "id": "Brown-K-B", "name": { "family": "Brown", "given": "Keith B." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Thomas-J-H", "name": { "family": "Thomas", "given": "James H." } } ] }, "title": "Characterization of Seven Genes Affecting Caenorhabditis elegans Hindgut Development", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1999 by the Genetics Society of America. \n\nManuscript received April 14, 1999; Accepted for publication June 21, 1999. \n\nWe thank Michael Ailion, Takao Inoue, Duncan Johnstone, and Elizabeth Newton for comments on the manuscript. Many of the strains used in this study were provided by the Caenorhabditis Genetics Center, which is funded by the National Institutes of Health National Center for Research Resources. This work was supported by a Public Health Service Grant (R01 NS30187) to J.H.T. and by the Howard Hughes Medical Institute, with which P.W.S. is an Investigator and K.B.B. is a Predoctoral Fellow. H.M.C. was a fellow of the Helen Hay Whitney Foundation.\n\nPublished - 10511553.pdf
", "abstract": "We have identified and characterized 12 mutations in seven genes that affect the development of the Caenorhabditis elegans hindgut. We find that the mutations can disrupt the postembryonic development of the male-specific blast cells within the hindgut, the hindgut morphology in both males and hermaphrodites, and in some cases, the expression of a hindgut marker in hermaphrodite animals. Mutations in several of the genes also affect viability. On the basis of their mutant phenotypes, we propose that the genes fall into four distinct classes: (1) egl-5 is required for regional identity of the tail; (2) sem-4 is required for a variety of ectodermal and mesodermal cell types, including cells in the hindgut; (3) two genes, lin-49 and lin-59, affect development of many cells, including hindgut; and (4) three genes, mab-9, egl-38, and lin-48, are required for patterning fates within the hindgut, making certain hindgut cells different from others. We also describe a new allele of the Pax gene egl-38 that is temperature sensitive and affects the conserved \u03b2-hairpin of the EGL-38 paired domain. Our results suggest that a combination of different factors contribute to normal C. elegans hindgut development.", "date": "1999-10-01", "date_type": "published", "publication": "Genetics", "volume": "153", "number": "2", "publisher": "Genetics Society of America", "pagerange": "731-742", "id_number": "CaltechAUTHORS:20190514-112709230", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-112709230", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 NS30187" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Helen Hay Whitney Foundation" } ] }, "pmcid": "PMC1460777", "primary_object": { "basename": "10511553.pdf", "url": "https://authors.library.caltech.edu/records/a7ce1-1mh95/files/10511553.pdf" }, "resource_type": "article", "pub_year": "1999", "author_list": "Chamberlin, Helen M.; Brown, Keith B.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/2ncv8-3c054", "eprint_id": 58043, "eprint_status": "archive", "datestamp": "2023-08-19 04:43:57", "lastmod": "2023-10-23 18:01:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Barr-M-M", "name": { "family": "Barr", "given": "Maureen M." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "A polycystic kidney-disease gene homologue required for male mating behaviour in C-elegans", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1999 Macmillan Magazines Ltd.\n\nReceived 23 April; accepted 16 July 1999.\n\nWe thank J. Copeland for help isolating lov-1(sy582\u0394); L. Jiang, R. Garcia and R. Ballester for discussions and constructive criticisms; members of our lab, S. Myers and M. Snow for experimental suggestions; D. Sherwood and B. Smith for assistance with confocal microscopy; A. Fire for vectors; and R. Herman for osm-6::gfp. The Caenorhabditis Genetics stock Center and Sanger Center provided numerous strains, cosmids and sequencing data. This work was supported by the Howard Hughes Medical Institute, with which P.W.S. is an investigator and M.M.B. is an associate, and by the Seaver Institute.", "abstract": "The stereotyped mating behaviour of the Caenorhabditis elegans male is made up of several substeps: response, backing, turning, vulva location, spicule insertion and sperm transfer. The complexity of this behaviour is reflected in the sexually dimorphic anatomy and nervous system. Behavioural functions have been assigned to most of the male-specific sensory neurons by means of cell ablations; for example, the hook sensory neurons HOA and HOB are specifically required for vulva location. We have investigated how sensory perception of the hermaphrodite by the C. elegans male controls mating behaviours. Here we identify a gene, lov-1 (for location of vulva), that is required for two male sensory behaviours: response and vulva location. lov-1 encodes a putative membrane protein with a mucin-like, serine\u2013threonine-rich amino terminus followed by two blocks of homology to human polycystins, products of the autosomal dominant polycystic kidney-disease loci PKD1 and PKD2 (ref 4). LOV-1 is the closest C. elegans homologue of PKD1. lov-1 is expressed in adult males in sensory neurons of the rays, hook and head, which mediate response, vulva location, and potentially chemotaxis to hermaphrodites, respectively. PKD-2, the C. elegans homologue of PKD2, is localized to the same neurons as LOV-1, suggesting that they function in the same pathway.", "date": "1999-09-23", "date_type": "published", "publication": "Nature", "volume": "401", "number": "6751", "publisher": "Nature Publishing Group", "pagerange": "386-389", "id_number": "CaltechAUTHORS:20150605-111134546", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150605-111134546", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Seaver Institute" } ] }, "doi": "10.1038/43916", "resource_type": "article", "pub_year": "1999", "author_list": "Barr, Maureen M. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/wmpqy-tdm98", "eprint_id": 95489, "eprint_status": "archive", "datestamp": "2023-08-22 13:57:55", "lastmod": "2023-10-20 20:16:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "F\u00e9lix-M-A", "name": { "family": "F\u00e9lix", "given": "Marie-Anne" } }, { "id": "Hill-R-J", "name": { "family": "Hill", "given": "Russell J." } }, { "id": "Schwarz-H", "name": { "family": "Schwarz", "given": "Heinz" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Sudhaus-W", "name": { "family": "Sudhaus", "given": "Walter" } }, { "id": "Sommer-R-J", "name": { "family": "Sommer", "given": "Ralf J." } } ] }, "title": "Pristionchus pacificus, a nematode with only three juvenile stages, displays major heterochronic changes relative to Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Pristionchus; Caenorhabditis; nematodes; juvenile stages; heterochrony", "note": "\u00a9 1999 The Royal Society. \n\nReceived 8 April 1999; Accepted 28 May 1999. \n\nWe thank Dr. M. M\u00fcller, ETH Z\u00fcrich, for high-pressure freezing of the nematode samples and I. Zimmermann for preparing samples for TEM. P.W.S. is an HHMI investigator, M.A.F. was supported by the Human Frontier Science Program and the Centre National de Recherche Scientifique (France.)", "abstract": "The nematode Pristionchus pacificus (Diplogastridae) has been described as a satellite organism for a functional comparative approach to the model organism Caenorhabditis elegans because genetic, molecular, and cell\u2013biological tools can be used in a similar way in both species. Here we show that P. pacificus has three juvenile stages, instead of the usual four found in other nematodes. Embryogenesis is lengthened and many developmental events that take place during the first juvenile stage in C. elegans occur during late embryogenesis in P. pacificus. Video imaging and transmission electron microscopy revealed no embryonic moult. The timing of later developmental events relative to the moults differs between P. pacificus and C. elegans. In addition, the post\u2013embryonic blast\u2013cell divisions display a specific change in timing between the two species, resulting in heterochrony between different cell lineages, such as vulval and gonadal lineages. Developmental events appear to come into register during the last larval stage. Thus, differences in developmental timing between P. pacificus and C. elegans represent a deep heterochronic change. We designate the three juvenile stages of P. pacificus as J1 to J3. Comparison with other species of the family Diplogastridae indicates that this pattern represents an apomorphic character for the monophylum Diplogastridae.", "date": "1999-08-22", "date_type": "published", "publication": "Proceedings of the Royal Society of London. Series B: Biological Sciences", "volume": "266", "number": "1429", "publisher": "The Royal Society", "pagerange": "1617-1621", "id_number": "CaltechAUTHORS:20190514-113356568", "issn": "1471-2954", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-113356568", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Human Frontier Science Program" }, { "agency": "Centre National de la Recherche Scientifique (CNRS)" } ] }, "doi": "10.1098/rspb.1999.0823", "pmcid": "PMC1690183", "resource_type": "article", "pub_year": "1999", "author_list": "F\u00e9lix, Marie-Anne; Hill, Russell J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/kjkf8-r9v12", "eprint_id": 95490, "eprint_status": "archive", "datestamp": "2023-08-22 13:53:57", "lastmod": "2023-10-20 20:17:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hajdu-Cronin-Y-M", "name": { "family": "Hajdu-Cronin", "given": "Yvonne M." } }, { "id": "Chen-Wen-J", "name": { "family": "Chen", "given": "Wen J." } }, { "id": "Patikoglou-G", "name": { "family": "Patikoglou", "given": "Georgia" } }, { "id": "Koelle-M-R", "name": { "family": "Koelle", "given": "Michael R." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Antagonism between G_o\u03b1 and G_q\u03b1 in Caenorhabditis elegans: the RGS protein EAT-16 is necessary for G_o\u03b1 signaling and regulates G_q\u03b1 activity", "ispublished": "pub", "full_text_status": "public", "keywords": "C. elegans; G_o protein; G_q protein; RGS protein; signaling; regulation", "note": "\u00a9 1999 by Cold Spring Harbor Laboratory Press. \n\nReceived April 26, 1999; revised version accepted June 2, 1999. \n\nWe thank Jane Mendel for the locomotion assay conditions; Hou-Pu Chou and Chieh Chang for writing software used to record locomotion data; John DeModena for technical assistance; Yuji Kohara for cDNA; Andrew Fire, Joohong Ahnn, Geraldine Seydoux, and Siqun Xu for GFP vectors; Merrilee Robatzek and James Thomas for sa609 andsa735; Bo Yu, Jennifer Gu, and Valeria Mancino for assistance with COS-7 cell assays; Lorna Brundage, Carol Bastiani, Stephen Nurrish, Laurant S\u00e9galat, Joshua Kaplan, Ron Ellis, and Jo Anne Powell-Coffman for sharing strains and communicating unpublished results; and Lorna Brundage, L. Ren\u00e9 Garcia, Jane Mendel, Carol Bastiani, Maureen Barr, Nadeem Moghal, Henry Lester, Mel Simon, and members of our laboratories for stimulating discussions and critical reading of this manuscript. Some of the strains used in this study were provided by the Caenorhabditis Genetics Center. This project is supported by HHMI, with which P.W.S. is an investigator. \n\nThe publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked 'advertisement' in accordance with 18 USC section 1734 solely to indicate this fact.\n\nPublished - x7.pdf
", "abstract": "To elucidate the cellular role of the heterotrimeric G protein G_o, we have taken a molecular genetic approach inCaenorhabditis elegans. We screened for suppressors of activated GOA-1 (G_o\u03b1) that do not simply decrease its expression and found mutations in only two genes, sag-1 andeat-16. Animals defective in either gene display a hyperactive phenotype similar to that of goa-1 loss-of-function mutants. Double-mutant analysis indicates that both sag-1 andeat-16act downstream of, or parallel to, Go\u03b1 and negatively regulate EGL-30 (G_q\u03b1) signaling. eat-16encodes a regulator of G protein signaling (RGS) most similar to the mammalian RGS7 and RGS9 proteins and can inhibit endogenous mammalian G_q/G_(11) in COS-7 cells. Animals defective in both sag-1 and eat-16 are inviable, but reducing function in egl-30 restores viability, indicating that the lethality of the eat-16; sag-1 double mutant is due to excessive G_q\u03b1 activity. Analysis of these mutations indicates that the G_o and G_q pathways function antagonistically in C. elegans, and that G_o\u03b1 negatively regulates the G_q pathway, possibly via EAT-16 or SAG-1. We propose that a major cellular role of G_o is to antagonize signaling by G_q.", "date": "1999-07-15", "date_type": "published", "publication": "Genes and Development", "volume": "13", "number": "14", "publisher": "Cold Spring Harbor Laboratory Press", "pagerange": "1780-1793", "id_number": "CaltechAUTHORS:20190514-115053085", "issn": "0890-9369", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-115053085", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "pmcid": "PMC316886", "primary_object": { "basename": "x7.pdf", "url": "https://authors.library.caltech.edu/records/kjkf8-r9v12/files/x7.pdf" }, "resource_type": "article", "pub_year": "1999", "author_list": "Hajdu-Cronin, Yvonne M.; Chen, Wen J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/nk1yq-26270", "eprint_id": 57504, "eprint_status": "archive", "datestamp": "2023-08-19 04:24:01", "lastmod": "2023-10-23 17:28:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Schmid-S-L", "name": { "family": "Schmid", "given": "Sandra L." } } ] }, "title": "Caveolin, cholesterol and Ras signalling", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1999 Macmillan Magazines Ltd.", "abstract": "Studies on the role of cholesterol- and caveolin-rich membrane microdomains in localizing Ras to the plasma membrane and enabling its signalling activity reveal intriguing differences both between mammalian H-Ras and K-Ras and between requirements for Ras signalling in mammalian and nematode cells.", "date": "1999-06", "date_type": "published", "publication": "Nature Cell Biology", "volume": "1", "number": "2", "publisher": "Nature Publishing Group", "pagerange": "E35-E37", "id_number": "CaltechAUTHORS:20150513-124356266", "issn": "1465-7392", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150513-124356266", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1038/10028", "resource_type": "article", "pub_year": "1999", "author_list": "Sternberg, Paul W. and Schmid, Sandra L." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ccbkx-kyb37", "eprint_id": 95509, "eprint_status": "archive", "datestamp": "2023-08-22 13:42:36", "lastmod": "2023-10-20 20:18:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jiang-Lily-I", "name": { "family": "Jiang", "given": "Lily I." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "An HMG1-like protein facilitates Wnt signaling in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "Wnt; HMG-1; TCF/LEF; cell fate specification; C. elegans", "note": "\u00a9 1999 by Cold Spring Harbor Laboratory Press. \n\nReceived December 28, 1998; revised version accepted February 19, 1999. \n\nWe thank Jane Mendel for the syIs20 him-5 strain, Mike Herman for the lin-17(n698) allele and the hs-lin44constructs, Helen Stewart for the sDf strains and sDfbreak-point mapping data, Rueyling Lin for the hs-pop-1construct, Jennifer Whangbo for the bar-1(mu349) allele, the CGC for strains, and the Sanger center for cosmids and sequencing information. We thank members of our laboratory for discussion and comments on the manuscript. This work was supported by a U.S. Public Health Service grant HD23690 to P.W.S. and by the Howard Hughes Medical Institute, with which P.W.S. is an investigator. \n\nThe publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked 'advertisement' in accordance with 18 USC section 1734 solely to indicate this fact.\n\nPublished - x14.pdf
", "abstract": "We show that during Caenorhabditis elegans male spicule development, the specification of a glial versus neuronal cell fate in a canonical neurogenic sublineage is dependent on Wnt signaling. Inactivation of a Wnt signaling pathway mediated by the Wnt receptor LIN-17 transforms the SPD sheath cell into its sister, the SPD neuron. We discovered a new mutant, son-1, that displays this same cell fate transformation. The son-1 mutation enhances the phenotypes of reduction-of-function lin-17 mutants in several developmental processes, including vulva development, somatic gonad development, and male tail patterning. son-1 encodes an HMG1/2-like DNA-binding protein and is localized in all cell nuclei through development as revealed by a GFP reporter construct. Disruption of son-1 function by RNA-mediated interference results in the same spicule defect as caused by overexpression of POP-1, a TCF/LEF class HMG protein known to act downstream of the Wnt signaling pathway. Our results provide in vivo evidence for the functional involvement of an HMG1/2-like protein, SON-1, in Wnt signaling. The sequence nonspecific HMG protein SON-1 and the sequence specific HMG protein POP-1 might both act in the Wnt responding cells to regulate gene transcription in opposite directions.", "date": "1999-04-01", "date_type": "published", "publication": "Genes and Development", "volume": "13", "number": "7", "publisher": "Cold Spring Harbor Laboratory Press", "pagerange": "877-889", "id_number": "CaltechAUTHORS:20190515-103610812", "issn": "0890-9369", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190515-103610812", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HD23690" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "pmcid": "PMC316596", "primary_object": { "basename": "x14.pdf", "url": "https://authors.library.caltech.edu/records/ccbkx-kyb37/files/x14.pdf" }, "resource_type": "article", "pub_year": "1999", "author_list": "Jiang, Lily I. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/p2z19-c2a84", "eprint_id": 12788, "eprint_status": "archive", "datestamp": "2023-08-19 03:01:21", "lastmod": "2023-10-17 20:55:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jiang-L-I", "name": { "family": "Jiang", "given": "Lily I." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Interactions of EGF, Wnt and HOM-C genes specify the P12 neuroectoblast fate in C. elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "EGF, HOM-C, Wnt, Cell fate specification, Gene interactions, Ceanorhabditis elegans", "note": "Copyright \u00a9 1998 by Company of Biologists. \n\nAccepted 3 April; published on WWW 19 May 1998. \n\nWe are grateful to Craig Hunter for sending us the egl-5 cDNA clone and the muIs13 strain. We thank Michael Herman for the lin-17(n671) lin-44(n1792) strain and for many stimulating discussions. We thank Michael Herman, Howard Lipshitz, Kai Zinn, Tom Clandinin, Maureen Barr, Jing Liu, Minqin Wang, Peter Becker, Marie-Anne F\u00e9lix, Giovanni Lesa, Aidyl Gonzalez-Serrichio, Chris Lacenere, Ren\u00e9 Garcia and Bhagwati Gupta for comments on the manuscript. This work was supported by a USPHS grant HD23690 to P.W.S. and by the HHMI, with which P.W.S. is an investigator.\n\nPublished - JIAdev98.pdf
", "abstract": "We investigate how temporal and spatial interactions between multiple intercellular and intracellular factors specify the fate of a single cell in Caenorhabditis elegans. P12, which is a ventral cord neuroectoblast, divides postembryonically to generate neurons and a unique epidermal cell. Three classes of proteins are involved in the specification of P12 fate: the LIN-3/LET-23 epidermal growth factor signaling pathway, a Wnt protein LIN-44 and its candidate receptor LIN-17, and a homeotic gene product EGL-5. We show that LIN-3 is an inductive signal sufficient to promote the P12 fate, and the conserved EGF signaling pathway is utilized for P12 fate specification; egl-5 is a downstream target of the lin-3/let-23 pathway in specifying P12 fate; and LIN-44 and LIN-17 act synergistically with lin-3 in the specification of the P12 fate. The Wnt pathway may function early in development to regulate the competence of the cells to respond to the LIN-3 inductive signal.", "date": "1998-06-15", "date_type": "published", "publication": "Development", "volume": "125", "number": "12", "publisher": "Company of Biologists", "pagerange": "2337-2347", "id_number": "CaltechAUTHORS:JIAdev98", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:JIAdev98", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Public Health Service", "grant_number": "HD23690" }, { "agency": "Howard Hughes Medical Institute" } ] }, "primary_object": { "basename": "JIAdev98.pdf", "url": "https://authors.library.caltech.edu/records/p2z19-c2a84/files/JIAdev98.pdf" }, "resource_type": "article", "pub_year": "1998", "author_list": "Jiang, Lily I. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/8hm3y-9f765", "eprint_id": 6101, "eprint_status": "archive", "datestamp": "2023-08-22 11:39:36", "lastmod": "2023-10-23 19:42:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lesa-G-M", "name": { "family": "Lesa", "given": "Giovanni M." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Positive and negative tissue-specific signaling by a nematode epidermal growth factor receptor", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1997 by The American Society for Cell Biology. Under the License and Publishing Agreement, authors grant to the general public, effective two months after publication of (i.e.,. the appearance of) the edited manuscript in an online issue of MBoC, the nonexclusive right to copy, distribute, or display the manuscript subject to the terms of the Creative Commons\u2013Noncommercial\u2013Share Alike 3.0 Unported license (http://creativecommons.org/licenses/by-nc-sa/3.0). \n\nSubmitted December 11, 1996; Accepted February 3, 1997 \n\nWe thank Raffi Aroian whose contribution was invaluable to the completion of this work. We are also deeply indebted to Tom Clandinin for suggestions and discussions. We thank Raffi Aroian, Tom Clandinin, Marie-Anne Felix, Neil Hopper, Giovanna Lalli, and Robert Palmer for critical reading of the manuscript. This work was supported by United States National Institutes of Health grant HD23690 to P.W.S. P.W.S. is an investigator with the Howard Hughes Medical Institute. G.M.L. was a Merck Graduate Fellow.\n\nPublished - LESmbc97.pdf
", "abstract": "The major determinants of receptor tissue tyrosine kinase (RTK) signaling specificity have been proposed to be Src homology 2 (SH2) binding sites, phosphotyrosine-containing oligopeptides in the cytoplasmic domain of the receptor. The Caenorhabditis elegans epidermal growth factor receptor homologue LET-23 has multiple functions during development and has eight potential SH2-binding sites in a region carboxyl terminal to its kinase domain. By analyzing transgenic nematodes for three distinct LET-23 functions, we show that six of eight potential sites function in vivo and that they are required for most, but not all, of LET-23 activity. A single site is necessary and sufficient to promote wild-type fertility. Three other sites activate the RAS pathway and are involved only in viability and vulval differentiation. A fifth site is promiscuous and can mediate all three LET-23 functions. An additional site mediates tissue-specific negative regulation. Putative SH2 binding sites are thus key effectors of both cell-specific and negative regulation in an intact organism. We suggest two distinct mechanisms for tissue-specific RTK-mediated signaling. A positive mechanism would promote RTK function through effectors present only in certain cell types. A negative mechanism would inhibit RTK function through tissue-specific negative regulators.", "date": "1997-05", "date_type": "published", "publication": "Molecular Biology of the Cell", "volume": "8", "number": "5", "publisher": "American Society for Cell Biology", "pagerange": "779-793", "id_number": "CaltechAUTHORS:LESmbc97", "issn": "1059-1524", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:LESmbc97", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HD23690" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Merck" } ] }, "pmcid": "PMC276129", "primary_object": { "basename": "LESmbc97.pdf", "url": "https://authors.library.caltech.edu/records/8hm3y-9f765/files/LESmbc97.pdf" }, "resource_type": "article", "pub_year": "1997", "author_list": "Lesa, Giovanni M. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/d0fd6-nkp71", "eprint_id": 95510, "eprint_status": "archive", "datestamp": "2023-08-19 01:07:18", "lastmod": "2023-10-20 20:18:14", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zwaal-R-R", "name": { "family": "Zwaal", "given": "Richard R." } }, { "id": "Mendel-J-E", "name": { "family": "Mendel", "given": "Jane E." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Plasterk-R-H-A", "name": { "family": "Plasterk", "given": "Ronald H. A." } } ] }, "title": "Two Neuronal G Proteins are Involved in Chemosensation of the Caenorhabditis elegans Dauer-Inducing Pheromone", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1997 by the Genetics Society of America. \n\nManuscript received August 8, 1996; Accepted for publication December 2, 1996. \n\nWe thank Betsy Malone and Jim Thomas for help and advice on\nthe pheromone response assays and for sending us the strain JT6130, and Andy Fire for providing us with the lacZ and GFP expression vectors. We thank Cori Bargmann and Ikue More for additional phenotypic analysis of deletion mutants, Henri Van Luenen for help in preparing the manuscript and Rik Korswagen, Lorna Brundage and Dave Sonnenborn for critical reading of the manuscript. Some of the swains were provided by the Caenorhabditis Genetic Center. This work was supported by a Pioneer grant from the Netherlands Organization for Scientific Research (NWO) to R.H.A.P. and from the Human Frontiers in Science Program (HFSP) to R.H.A.P. and P.W.S., an investigator with the Howard Hughes Medical Institute. The transposon mutant library from which the Tcl mutants were isolated is currently supported by grant 5 RO1 RR10082 from the National Institutes of Health National Center for Research Resources.\n\nPublished - ge1453715.pdf
", "abstract": "Caenorhabditis elegans uses chemosensation to determine its course of development. Young larvae can arrest as dauer larvae in response to increasing population density, which they measure by a nematode-excreted pheromone, and decreasing food supply. Dauer larvae can resume development in response to a decrease in pheromone and increase in food concentration. We show here that two novel G protein alpha subunits (GPA-2 and GPA-3) show promoter activity in subsets of chemosensory neurons and are involved in the decision to form dauer larvae primarily through the response to dauer pheromone. Dominant activating mutations in these G proteins result in constitutive, pheromone-independent dauer formation, whereas inactivation results in reduced sensitivity to pheromone, and, under certain conditions, an alteration in the response to food. Interactions between gpa-2, gpa-3 and other genes controlling dauer formation suggest that these G proteins may act in parallel to regulate the neuronal decision making that precedes dauer formation.", "date": "1997-03-01", "date_type": "published", "publication": "Genetics", "volume": "145", "number": "3", "publisher": "Genetics Society of America", "pagerange": "715-727", "id_number": "CaltechAUTHORS:20190515-104420137", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190515-104420137", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)" }, { "agency": "Human Frontier Science Program" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "5 RO1 RR10082" } ] }, "collection": "CaltechAUTHORS", "pmcid": "PMC1207856", "primary_object": { "basename": "ge1453715.pdf", "url": "https://authors.library.caltech.edu/records/d0fd6-nkp71/files/ge1453715.pdf" }, "resource_type": "article", "pub_year": "1997", "author_list": "Zwaal, Richard R.; Mendel, Jane E.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/f30ds-bbx39", "eprint_id": 28827, "eprint_status": "archive", "datestamp": "2023-08-22 11:29:46", "lastmod": "2023-10-24 18:10:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "F\u00e9lix-M-A", "name": { "family": "F\u00e9lix", "given": "Marie-Anne" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Two nested gonadal inductions of the vulva in nematodes", "ispublished": "pub", "full_text_status": "public", "keywords": "nematode; evolution; vulva; patterning; induction; gonad; anchor cell", "note": "\u00a9 1997 The Company of Biologists Limited.\nAccepted 23 September 1996. We thank L. Carta, J. DeModena, D. Fitch, W. Sudhaus and W. Wood for worm strains, R. Sommer, K. Tietze and M. Wang for sharing unpublished observations, and T. Clandinin, D. Dimster-Denk, M. Friedrich, J. Liu and R. Sommer for comments on the manuscript. M.-A. F. is supported by an HFSP fellowship. P. W. S. is an investigator with the Howard Hughes Medical Institute.\n\nPublished - FELdev97.pdf
", "abstract": "How do intercellular signals that pattern cell fates vary in\nevolution? During nematode vulva development, precursor\ncells acquire one of three fates in a pattern centered around the gonadal anchor cell. Non-vulval fates are at the\nperiphery, outer and inner vulval fates are towards the\ncenter. In Caenorhabditis elegans, the three fates are\nspecified around the same time by an induction by the\nanchor cell and lateral signaling between the vulva\nprecursor cells. We find that, in three other nematode\nspecies (Panagrolaimus, Oscheius and Rhabditella spp.)\nspanning two families, the centered pattern is obtained by\ntwo temporally distinct gonadal inductions. The first\ninduction specifies vulval fates; the second induction\nspecifies the inner vulval fates in a subset of the precursors' daughters. This evolutionary change in the spatiotemporal connectivity of cell interactions allows centering of the pattern between two precursors in Panagrolaimus.", "date": "1997-01", "date_type": "published", "publication": "Development", "volume": "124", "number": "1", "publisher": "Company of Biologists", "pagerange": "253-259", "id_number": "CaltechAUTHORS:20120118-110011891", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120118-110011891", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "HFSP Fellowship" } ] }, "primary_object": { "basename": "FELdev97.pdf", "url": "https://authors.library.caltech.edu/records/f30ds-bbx39/files/FELdev97.pdf" }, "resource_type": "article", "pub_year": "1997", "author_list": "F\u00e9lix, Marie-Anne and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/x4a09-07921", "eprint_id": 12033, "eprint_status": "archive", "datestamp": "2023-08-22 11:18:00", "lastmod": "2023-10-17 16:29:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Newman-A-P", "name": { "family": "Newman", "given": "Anna P." } }, { "id": "White-J-G", "name": { "family": "White", "given": "John G." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Morphogenesis of the C. elegans hermaphrodite uterus", "ispublished": "pub", "full_text_status": "public", "keywords": "Caenorhabditis elegans, hermaphrodite uterus, cell fate, morphogenesis, anchor cell", "note": "Copyright \u00a9 1996 by Company of Biologists. \n\n(Accepted 17 July 1996) \n\nThis work was supported by the MRC and the Howard Hughes Medical Institute, with which P.W.S. is an investigator and A.P.N. is an associate. We thank E. Southgate and D. Kershaw for undertaking the electron microscopy, R.H. Waterston for his generous gift of the MH27 antibody, S. Crittendon for help with MH27 antibody staining, and T. Clandinin, M.-A. Felix, A. Gonzalez-Serricchio, and B. Palmer for their comments on the manuscript.\n\nPublished - NEWdev96.pdf
", "abstract": "We have undertaken electron micrographic reconstruction of the Caenorhabditis elegans hermaphrodite uterus and determined the correspondence between cells defined by their lineage history and differentiated cell types. In this organ, many cells do not move during morphogenesis and the cell lineage may function to put cells where they are needed. Differentiated uterine cell types include the toroidal ut cells that make structural epithelium, and specialized utse and uv cells that make the connection between the uterus and the vulva. A cell fate decision in which the anchor cell (AC) induces adjacent ventral uterine intermediate precursor cells to adopt the pi fate, rather than the ground state rho, has profound consequences for terminal differentiation: all pi progeny are directly involved in making the uterine-vulval connection whereas all rho progeny contribute to ut toroids or the uterine-spermathecal valve. In addition to specifying certain uterine cell fates, the AC also induces the vulva. Its multiple inductions thereby function to coordinate the connection of an internal to an external epithelium. The AC induces the pi cells and ultimately fuses with a subset of their progeny. This is an example of reciprocal cell-cell interaction that can be studied at single cell resolution. The AC is thus a transitory cell type that plays a pivotal role in organizing the morphogenesis of the uterine-vulval connection.", "date": "1996-11", "date_type": "published", "publication": "Development", "volume": "122", "number": "11", "publisher": "Company of Biologists", "pagerange": "3617-3626", "id_number": "CaltechAUTHORS:NEWdev96", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:NEWdev96", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Medical Research Council (UK)" }, { "agency": "Howard Hughes Medical Institute" } ] }, "primary_object": { "basename": "NEWdev96.pdf", "url": "https://authors.library.caltech.edu/records/x4a09-07921/files/NEWdev96.pdf" }, "resource_type": "article", "pub_year": "1996", "author_list": "Newman, Anna P.; White, John G.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/n15t8-1p352", "eprint_id": 956, "eprint_status": "archive", "datestamp": "2023-08-22 11:13:30", "lastmod": "2023-10-23 17:39:30", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Newman-A-P", "name": { "family": "Newman", "given": "Anna P." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Coordinated morphogenesis of epithelia during development of the Caenorhabditis elegans uterine-vulval connection", "ispublished": "pub", "full_text_status": "public", "keywords": "CELL FATE DECISION, C-ELEGANS, SIGNALING PATHWAYS, NEGATIVE REGULATOR, TYROSINE KINASE, LET-23 GENE, INDUCTION, LIN-12, ENCODES, NOTCH", "note": "\u00a9 1996 by the National Academy of Sciences. \n\nThis paper was presented at a colloquium entitled \"Biology of Developmental Transcription Control,\" organized by Eric H. Davidson, Roy J. Britten, and Gary Felsenfeld, held October 26-28, 1995, at the National Academy of Sciences in Irvine, CA. \n\nWe thank members of our laboratory for discussion, Gwendolyn Acton and Bob Horvitz for discussions about lin-11, and John White for his many contributions to our thinking about uterine and vulval morphogenesis. Marie-Anne Felix and Dago Dimster Denk provided important editorial comments. This work was supported by the Howard Hughes Medical Institute, with which P.W.S. is an investigator and A.P.N. is an associate.\n\nPublished - NEWpnas96.pdf
", "abstract": "Development of the nematode egg-laying system requires the formation of a connection between the uterine lumen acid the developing vulval lumen, thus allowing a passage for eggs and sperm. This relatively simple process serves as a model for certain aspects of organogenesis. Such a connection demands that cells in both tissues become specialized to participate in the connection, and that the specialized cells are brought in register. A single cell, the anchor cell, acts to induce and to organize specialization of the epidermal and uterine epithelia, and registrates these tissues. The inductions act via evolutionarily conserved intercellular signaling pathways. The anchor cell induces the vulva from ventral epithelial cells via the LIN-3 growth factor and LET-23 transmembrane tyrosine kinase. It then induces surrounding uterine intermediate precursors via the receptor LIN-12, a founding member of the Notch family of receptors. Both signaling pathways are used multiple times during development of Caenorhabditis elegans. The outcome of the signaling is context-dependent. Both inductions are reciprocated. After the anchor cell has induced the vulva, it stretches toward the induced vulval cells. After the anchor cell has induced specialized uterine intermediate precursor cells, it fuses with a subset of their progeny.", "date": "1996-09-03", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "93", "number": "18", "publisher": "National Academy of Sciences", "pagerange": "9329-9333", "id_number": "CaltechAUTHORS:NEWpnas96", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:NEWpnas96", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "pmcid": "PMC38427", "primary_object": { "basename": "NEWpnas96.pdf", "url": "https://authors.library.caltech.edu/records/n15t8-1p352/files/NEWpnas96.pdf" }, "resource_type": "article", "pub_year": "1996", "author_list": "Newman, Anna P. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/tk3p7-eyz42", "eprint_id": 29091, "eprint_status": "archive", "datestamp": "2023-08-22 11:06:24", "lastmod": "2023-10-24 18:21:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "F\u00e9lix-M-A", "name": { "family": "F\u00e9lix", "given": "Marie-Anne" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Symmetry breakage in the development of one-armed gonads in nematodes", "ispublished": "pub", "full_text_status": "public", "keywords": "gonad; evolution; nematodes; cell lineage; apoptosis; lateral signalling", "note": "\u00a9 1996 The Company of Biologists Limited. Accepted 23 April 1996. We are very grateful to L. Carta and W. Sudhaus for strains, to P. De Ley for species identifications, and to all those who collected soil\nsamples for the Caltech worm collection. We thank members of the\nlaboratory for discussions, and D. Anderson, T. Clandinin, J. Liu, A.\nNewman, R. Palmer and R. Sommer for comments on the manuscript.\nThis work was supported by fellowships from the European\nMolecular Biology Organisation and the Human Frontier Science\nProgram. P.W.S. is an investigator with the Howard Hughes Medical\nInstitute.\n\nPublished - FELdev96.pdf
", "abstract": "Whereas the hermaphrodite gonad of Caenorhabditis elegans has two symmetric arms (didelphy), the female/hermaphrodite gonad of many nematode species features a single anterior arm (monodelphy). We examined how gonadal cell lineages and intercellular signalling evolve to generate these diverse structures. In C. elegans, the two arms develop symmetrically from two somatic precursor cells, Z1 (anterior) and Z4 (posterior). Each first gives rise to one distal tip cell (which promotes arm growth and germ line proliferation), two ovary precursors and three uterine precursors in the center of the developing gonad. In monodelphic species, Z1 and Z4 have different fates. The first visible asymmetry between them is in the relative timing of their divisions, followed by asymmetric cell movements. The putative posterior distal tip cell is then eliminated in all but one species by programmed cell death. In some species the posterior ovary precursors form a small vestigial posterior arm, the post-vulval sac; in other species, they stay undivided, or die. In Cephalobus sp. PS1197, the specific fate of Z4 progeny is induced by Z1 (or its daughters). In the uterus in C. elegans, symmetric lateral signalling between Z1.ppp and Z4.aaa renders them equally likely to become the anchor cell, which links the uterus to the vulva. In the different monodelphic species, anchor cell specification is biased, or fully fixed, to a descendant of either Z1 or Z4. Replacement regulation upon anchor cell ablation is conserved in some species, but lost in others, leading to a mosaic-type development. Differentiation between Z1 and Z4 is thus manifested at this later stage in the breakage of symmetry of cell interactions in the ventral uterus.", "date": "1996-07", "date_type": "published", "publication": "Development", "volume": "122", "number": "7", "publisher": "Company of Biologists", "pagerange": "2129-2142", "id_number": "CaltechAUTHORS:20120202-101716190", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120202-101716190", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "European Molecular Biology Organisation" }, { "agency": "Human Frontier Science Program (HFSP)" } ] }, "primary_object": { "basename": "FELdev96.pdf", "url": "https://authors.library.caltech.edu/records/tk3p7-eyz42/files/FELdev96.pdf" }, "resource_type": "article", "pub_year": "1996", "author_list": "F\u00e9lix, Marie-Anne and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/7agqb-dwp90", "eprint_id": 58170, "eprint_status": "archive", "datestamp": "2023-08-18 23:52:51", "lastmod": "2023-10-23 19:07:47", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "F\u00e9lix-M-A", "name": { "family": "F\u00e9lix", "given": "Marie-Anne" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "De-Ley-P", "name": { "family": "De Ley", "given": "Paul" } } ] }, "title": "Sinistral nematode population", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1996 Nature Publishing Group.", "abstract": "Sir-Several animal taxa display a consistent left-right asymmetry of the body plan. In nematodes, dextrality predominates. However, we have now found a nematode species that has sinistral populations.", "date": "1996-05-09", "date_type": "published", "publication": "Nature", "volume": "381", "number": "6578", "publisher": "Nature Publishing Group", "pagerange": "122", "id_number": "CaltechAUTHORS:20150610-141430033", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150610-141430033", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "collection": "CaltechAUTHORS", "doi": "10.1038/381122a0", "resource_type": "article", "pub_year": "1996", "author_list": "F\u00e9lix, Marie-Anne; Sternberg, Paul W.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/dnqmx-1c903", "eprint_id": 79263, "eprint_status": "archive", "datestamp": "2023-08-20 07:33:34", "lastmod": "2023-10-26 14:44:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Brundage-L", "name": { "family": "Brundage", "given": "Lorna" } }, { "id": "Avery-L", "name": { "family": "Avery", "given": "Leon" } }, { "id": "Katz-A", "name": { "family": "Katz", "given": "Arieh" }, "orcid": "0000-0003-3487-7049" }, { "id": "Kim-Ung-Jin", "name": { "family": "Kim", "given": "Ung-Jin" } }, { "id": "Mendel-J-E", "name": { "family": "Mendel", "given": "Jane E." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Simon-M-I", "name": { "family": "Simon", "given": "Melvin I." } } ] }, "title": "Mutations in a C. elegans G_q\u03b1 Gene Disrupt Movement, Egg Laying, and Viability", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1996 Cell Press. \n\nReceived 6 November 1995, Revised 22 March 1996. \n\nWe thank Harry Duttweiler, who selected and partially backcrossed the eat-11 suppressors, and Steve Marsh and Rick Colayco (Caltech DNA sequencing core facility) for assistance in determining the egl-30 lesions. The C. elegans Genetic Stock Center provided some of the strains described here. This work was funded by a grant from the Human Frontiers in Science Organization to M. I. S and P. W. S., research grant HL46154 from the United States Public Health Service to L. A., and National Research Service Award F32NS09541\u201303 to L. B. \n\nThe costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked \"advertisement\" in accordance with 18 USC Section 1734 solely to indicate this fact.\n\nAccepted Version - nihms691804.pdf
", "abstract": "We find that C. elegans egl-30 encodes a heterotrimeric G protein \u03b1 subunit more than 80% identical to mammalian G_q\u03b1 family proteins, and which can function as a G_q\u03b1 subunit in COS-7 cells. We have identified new egl-30 alleles in a selection for genes involved in the C. elegans acetylcholine response. Two egl-30 alleles specify premature termination of G_q\u03b1 and are essentially lethal in homozygotes. Animals homozygous for six other egl-30 alleles are viable and fertile, but exhibit delayed egg laying and leave flattened tracks. Overexpression of the wild-type egl-30 gene produces the opposite behavior. Analysis of these mutants suggest that their phenotypes reflect defects in the muscle or neuromuscular junction.", "date": "1996-05", "date_type": "published", "publication": "Neuron", "volume": "16", "number": "5", "publisher": "Elsevier", "pagerange": "999-1009", "id_number": "CaltechAUTHORS:20170721-070445218", "issn": "0896-6273", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170721-070445218", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Human Frontier Science Program" }, { "agency": "NIH", "grant_number": "HL46154" }, { "agency": "NIH Postodoctoral Fellowship", "grant_number": "F32NS09541\u201303" } ] }, "doi": "10.1016/S0896-6273(00)80123-3", "pmcid": "PMC4444781", "primary_object": { "basename": "nihms691804.pdf", "url": "https://authors.library.caltech.edu/records/dnqmx-1c903/files/nihms691804.pdf" }, "resource_type": "article", "pub_year": "1996", "author_list": "Brundage, Lorna; Avery, Leon; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/yt50h-p0s91", "eprint_id": 3413, "eprint_status": "archive", "datestamp": "2023-08-22 10:50:00", "lastmod": "2023-10-23 17:38:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Katz-W-S", "name": { "family": "Katz", "given": "Wendy S." } }, { "id": "Lesa-G-M", "name": { "family": "Lesa", "given": "Giovanni M." } }, { "id": "Yannoukakos-D", "name": { "family": "Yannoukakos", "given": "Drakoulis" } }, { "id": "Clandinin-T-R", "name": { "family": "Clandinin", "given": "Thomas R." } }, { "id": "Schlessinger-J", "name": { "family": "Schlessinger", "given": "Joseph" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "A point mutation in the extracellular domain activates LET-23, the Caenorhabditis elegans epidermal growth factor receptor homolog", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1996, American Society for Microbiology \n\nReceived 10 May 1995/Returned for modification 27 September 1995/Accepted 7 November 1995 \n\nWe are grateful to Jim Thomas for providing sa62. We thank Giuseppe Tocchini-Valentini for providing an in vitro mutagenesis protocol, Lily Jiang and Katharine Liu for help in scoring sa62 phenotypes, and Raffi Aroian for many suggestions and stimulating discussions. Some strains were provided by the Caenorhabditis Genetics Center. \n\nThis work was supported by a grant to P.W.S. from USPHS and by the HHMI, of which P.W.S. is an investigator and W.S.K. is an associate. G.M.L. is a Merck Graduate Fellow. T.R.C. was supported by an Amgen Fund fellowship.\n\nPublished - KATmcb96.pdf
", "abstract": "The let-23 gene encodes a Caenorhabditis elegans homolog of the epidermal growth factor receptor (EGFR) necessary for vulval development. We have characterized a mutation of let-23 that activates the receptor and downstream signal transduction, leading to excess vulval differentiation. This mutation alters a conserved cysteine residue in the extracellular domain and is the first such point mutation in the EGFR subfamily of tyrosine kinases. Mutation of a different cysteine in the same subdomain causes a strong loss-of- function phenotype, suggesting that cysteines in this region are important for function and nonequivalent. Vulval precursor cells can generate either of two subsets of vulval cells (distinct fates) in response to sa62 activity. The fates produced depended on the copy number of the mutation, suggesting that quantitative differences in receptor activity influence the decision between these two fates.", "date": "1996-02", "date_type": "published", "publication": "Molecular and Cellular Biology", "volume": "16", "number": "2", "publisher": "American Society for Microbiology", "pagerange": "529-537", "id_number": "CaltechAUTHORS:KATmcb96", "issn": "0270-7306", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:KATmcb96", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Merck" }, { "agency": "Amgen" } ] }, "pmcid": "PMC231031", "primary_object": { "basename": "KATmcb96.pdf", "url": "https://authors.library.caltech.edu/records/yt50h-p0s91/files/KATmcb96.pdf" }, "resource_type": "article", "pub_year": "1996", "author_list": "Katz, Wendy S.; Lesa, Giovanni M.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/zanqz-n6r86", "eprint_id": 76438, "eprint_status": "archive", "datestamp": "2023-09-28 19:35:20", "lastmod": "2023-10-24 15:25:50", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sommer-R-J", "name": { "family": "Sommer", "given": "Ralf J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Apoptosis and change of competence limit the size of the vulva equivalence group in Pristionchus pacificus: a genetic analysis", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1996 Elsevier. \n\nReceived 13 October 1995, Revised 10 November 1995, Accepted 10 November 1995. \n\nWe thank members of the Sternberg lab for discussion. P.W.S. is an investigator with the Howard Hughes Medical Institute. R.J.S. is a young investigator with the Max-Planck Society and was supported by an EMBO longterm-fellowship during much of this work.\n\nPublished - 1-s20-S0960982202004219-main.pdf
", "abstract": "Background: To understand how alterations in the molecular mechanisms underlying developmental processes generate a diversity of biological forms, comparative developmental biology can be combined with genetic analysis. The formation of the nematode vulva is one tractable system for such evolutionary developmental analysis, as much is understood about its development in Caenorhabditis elegans. In Caenorhabditis, six of twelve ventral epidermal cells form the 'vulva equivalence group'; although all six cells are competent to adopt vulval cell fates in response to an inductive signal, only three of these cells are induced to form vulval tissue. \n\nResults: In some species of the nematode families Rhabditidae, Neodiplogastridae and Panagrolaimidae, the number of cells in the vulva equivalence group is limited by apoptosis and decreased responsiveness to inductive signals (competence). We have initiated a genetic analysis in one of these species, Pristionchus pacificus, to understand the evolution of the specification of ventral epidermal cells that are competent to generate the vulva. A ped-4 mutation restores competence to an incompetent cell. Mutation of either of two other genes of Pristionchus cause two anterior cells that die in wild-type to survive. A ped-5 mutation causes these cells to be competent to respond to inductive signals, expanding the equivalence group. A ped-6 mutation causes these cells to form ectopic, anterior vulva-like invaginations. \n\nConclusion: During nematode evolution, apoptosis and change of competence alter the number and potency of ventral epidermal cells. The phenotypes of Pristionchus mutants suggest that alterations in homeotic gene control of anteroposterior patterning is involved in creating this cellular diversity.", "date": "1996-01", "date_type": "published", "publication": "Current Biology", "volume": "6", "number": "1", "publisher": "Cell Press", "pagerange": "52-59", "id_number": "CaltechAUTHORS:20170409-073751073", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170409-073751073", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Max Planck Society" }, { "agency": "European Molecular Biology Organization (EMBO)" } ] }, "doi": "10.1016/S0960-9822(02)00421-9", "primary_object": { "basename": "1-s20-S0960982202004219-main.pdf", "url": "https://authors.library.caltech.edu/records/zanqz-n6r86/files/1-s20-S0960982202004219-main.pdf" }, "resource_type": "article", "pub_year": "1996", "author_list": "Sommer, Ralf J. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/w17dm-jab36", "eprint_id": 52632, "eprint_status": "archive", "datestamp": "2023-08-20 06:13:44", "lastmod": "2023-10-18 21:03:23", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yoon-C-H", "name": { "family": "Yoon", "given": "Charles H." } }, { "id": "Lee-J", "name": { "family": "Lee", "given": "Junho" } }, { "id": "Jongeward-G-D", "name": { "family": "Jongeward", "given": "Gregg D." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Similarity of sli-1, a regulator of vulval development in C. elegans, to the mammalian proto-oncogene c-cbl", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1995 American Association for the Advancement of Science.\n\nReceived 13 April 1995; accepted 2 June 1995.\n\nWe thank G. Lesa, N. Hopper, and R. Sommer\nfor comments on the manuscript; G. Medina and\nother members of the Sternberg laboratory for\ntechnical assistance; J. Mendel for pJMG3BP.11;\nand W. Langdon for discussions. Supported by a\ngrant from the U.S. Public Health Service to\nP.W.S., who is an investigator with the Howard\nHughes Medical Institute.", "abstract": "Vulval induction during Caenorhabditis elegans development is mediated by LET-23, a homolog of the mammalian epidermal growth factor receptor tyrosine kinase. The sli-1 gene is a negative regulator of LET-23 and is shown here to encode a protein similar to c-Cbl, a mammalian proto-oncoprotein. SLI-1 and c-Cbl share approximately 55 percent amino acid identity over a stretch of 390 residues, which includes a C_3HC_4 zinc-binding motif known as the RING finger, and multiple consensus binding sites for Src homology 3 (SH3) domains. SLI-1 and c-Cbl may define a new class of proteins that modify receptor tyrosine kinase-mediated signal transduction.", "date": "1995-08-25", "date_type": "published", "publication": "Science", "volume": "269", "number": "5227", "publisher": "American Association for the Advancement of Science", "pagerange": "1102-1105", "id_number": "CaltechAUTHORS:20141212-124138923", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141212-124138923", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "U.S. Public Health Service (USPHS)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1126/science.7652556", "resource_type": "article", "pub_year": "1995", "author_list": "Yoon, Charles H.; Lee, Junho; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/bkpwn-at561", "eprint_id": 54013, "eprint_status": "archive", "datestamp": "2023-08-20 06:11:51", "lastmod": "2023-10-19 23:12:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Loomis-W-F", "name": { "family": "Loomis", "given": "William F." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Genetic Networks", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1995 American Association for the Advancement of Science.", "abstract": "The interactions of biological macromolecules and the flow of regulatory information that controls development, behavior, and homeostasis can be considered a genetic network. The nodes in such networks are genes or their RNA and protein products. The connections are the regulatory and physical interactions among the RNAs, proteins, and\ncis-regulatory DNA sequences of each gene. Modem molecular genetic techniques have greatly increased the rate at which genes are being recognized and their primary sequences\ndetermined. The challenge is to link the genes and their products into functional pathways, circuits, and networks. Analyses of regulatory networks (such as those involving\nsignal transduction and transcriptional regulation cascades) illustrate combinatorial action that implements, for example, digital logic, analog-digital conversions, cross-talk and insulation, and signal integration. Although\nthe existence of sophisticated network elements has been suggested by decades of physiological studies, what is new is the scale and detail becoming available for\nthe components. Much of current molecular biology focuses on identifying new components, defining the regulatory in puts and outputs of each node, and delineating the\nphysiologically relevant pathways.", "date": "1995-08-04", "date_type": "published", "publication": "Science", "volume": "269", "number": "5224", "publisher": "American Association for the Advancement of Science", "pagerange": "649-649", "id_number": "CaltechAUTHORS:20150123-093352728", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150123-093352728", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1126/science.7624792", "resource_type": "article", "pub_year": "1995", "author_list": "Loomis, William F. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/sga8p-cjk12", "eprint_id": 95511, "eprint_status": "archive", "datestamp": "2023-08-20 05:41:56", "lastmod": "2023-10-20 20:18:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jongeward-G-D", "name": { "family": "Jongeward", "given": "Gregg D." } }, { "id": "Clandinin-T-R", "name": { "family": "Clandinin", "given": "Thomas R." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "sli-1, a negative regulator of let-23-mediated signaling in C. elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1995 by the Genetics Society of America. \n\nManuscript received August 30, 1994; Accepted for publication December 19, 1994. \n\nWe are grateful to Gladys Medina for superb media preparation. We thank Andy Golden, Junho Lee, Bino Palmer, and other members of our laboratory for comments on the manuscript. Supported by U.S. Public Health Service grant HD-23690 to P.W.S., an investigator of the Howard Hughes Medical Institute. T.R.C. was supported in part by an Amgen Fund Fellowship. Some strains were supplied by the Caenorhabditis Genetics Center.\n\nPublished - ge13941553.pdf
", "abstract": "By screening for suppressors of hypomorphic mutations of let-23, a receptor tyrosine kinase necessary for vulval induction in Caenorhabditis elegans, we recovered > or = 12 mutations defining the sli-1 (suppressor of lineage defect) locus. sli-1 mutations suppress four of five phenotypes associated with hypomorphic alleles of let-23 but do not suppress let-23 null alleles. Thus, a sli-1 mutation does not bypass the requirement for functional let-23 but rather allows more potent LET-23-dependent signaling. Mutations at the sli-1 locus are otherwise silent with respect to vulval differentiation and cause only a low-penetrance abnormal head phenotype. Mutations at sli-1 also suppress the vulval defects but not other defects associated with mutations of sem-5, whose product likely interacts with LET-23 protein during vulval induction. Mutations at sli-1 suppress lin-2, lin-7 and lin-10 mutations but only partially suppress lin-3 and let-60 mutations and do not suppress a lin-45 mutation. The sli-1 locus displays dosage sensitivity: severe reduction of function alleles of sli-1 are semidominant suppressors; a duplication of the sli-1(+) region enhances the vulvaless phenotype of hypomorphic mutations of let-23. We propose that sli-1 is a negative regulator that acts at or near the LET-23-mediated step of the vulval induction pathway. Our analysis suggests that let-23 can activate distinct signaling pathways in different tissues: one pathway is required for vulval induction; another pathway is involved in hermaphrodite fertility and is not regulated by sli-1.", "date": "1995-04-01", "date_type": "published", "publication": "Genetics", "volume": "139", "number": "4", "publisher": "Genetics Society of America", "pagerange": "1553-1566", "id_number": "CaltechAUTHORS:20190515-110430955", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190515-110430955", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HD23690" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Amgen" } ] }, "pmcid": "PMC1206484", "primary_object": { "basename": "ge13941553.pdf", "url": "https://authors.library.caltech.edu/records/sga8p-cjk12/files/ge13941553.pdf" }, "resource_type": "article", "pub_year": "1995", "author_list": "Jongeward, Gregg D.; Clandinin, Thomas R.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/x338p-prz30", "eprint_id": 54065, "eprint_status": "archive", "datestamp": "2023-08-20 05:38:18", "lastmod": "2023-10-19 23:36:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mendel-J-E", "name": { "family": "Mendel", "given": "Jane E." } }, { "id": "Korswagen-H-C", "name": { "family": "Korswagen", "given": "Hendrik C." } }, { "id": "Liu-K-S", "name": { "family": "Liu", "given": "Katharine S." } }, { "id": "Hajdu-Cronin-Y-M", "name": { "family": "Hajdu-Cronin", "given": "Yvonne M." } }, { "id": "Simon-M-I", "name": { "family": "Simon", "given": "Melvin I." } }, { "id": "Plasterk-R-H-A", "name": { "family": "Plasterk", "given": "Ronald H. A." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Participation of the protein G_o in multiple aspects of behavior in C. elegans", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1995 American Association for the Advancement of Science.\n\n8 October 1994; accepted 19 January 1995.\n\nWe thank S. Gharib for technical assistance and members of our laboratories for critical reading of the manuscript. Some strains were from the Caenorhabditis Genetics Center. Supported by a grant from the Human Frontier Science Program to M.I.S., R.H.A.P., and P.W.S., and by the Howard Hughes\nMedical Institute of which P.W.S. is an investigator.", "abstract": "The goa-1 gene encoding the alpha subunit of the heterotrimeric guanosine triphosphatebinding protein (G protein) G_o. from Caenorhabditis elegans is expressed in most neurons, and in the muscles involved in egg laying and male mating. Reduction-of-function mutations in goa-1 caused a variety of behavioral defects including hyperactive movement, premature egg laying, and male impotence. Expression of the activated G_o alpha subunit\n(G\u03b1_o) in transgenic nematodes resulted in lethargic movement, delayed egg laying, and reduced mating efficiency. Induced expression of activated G\u03b1_o in adults was sufficient to cause these phenotypes, indicating that G\u03b1_o mediates behavior through its role in neuronal function and the functioning of specialized muscles.", "date": "1995-03-17", "date_type": "published", "publication": "Science", "volume": "267", "number": "5204", "publisher": "American Association for the Advancement of Science", "pagerange": "1652-1655", "id_number": "CaltechAUTHORS:20150126-093856927", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150126-093856927", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Human Frontier Science Program" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1126/science.7886455", "resource_type": "article", "pub_year": "1995", "author_list": "Mendel, Jane E.; Korswagen, Hendrik C.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/d35qr-s2d62", "eprint_id": 12031, "eprint_status": "archive", "datestamp": "2023-08-22 10:18:04", "lastmod": "2023-10-17 16:29:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Newman-A-P", "name": { "family": "Newman", "given": "Anna P." } }, { "id": "White-J-G", "name": { "family": "White", "given": "John G." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The Caenorhabditis elegans lin-12 gene mediates induction of ventral uterine specialization by the anchor cell", "ispublished": "pub", "full_text_status": "public", "keywords": "Caenorhabditis, lin-12, anchor cell, uterine development, induction", "note": "Copyright \u00a9 1995 by Company of Biologists. \n\n(Accepted 31 October 1994) \n\nWe thank Eileen Southgate and Douglas Kershaw for the EM reconstructions of the lin-12 mutant animals. Thanks to D. Anderson, N. Bonini, H. Lester, H. Lipshitz and members of our laboratories for their comments on the manuscript. We are grateful to M. Han, J. Kimble, E. Lambie and T. Schedl for sending us strains. This research was supported by the Howard Hughes Medical Institute. P.W.S. is an investigator of the Howard Hughes Medical Institute. A.P.N. was a USPHS postdoctoral fellow.\n\nPublished - NEWdev95.pdf
", "abstract": "The anchor cell (AC) of the Caenorhabditis elegans gonad has a critical role in the development of a functional egg-laying system, which is accomplished through cell-cell interactions. Lateral inhibitory lin-12-mediated signaling among two bipotential cells causes one to adopt the ventral uterine precursor (VU) cell fate while the other becomes the AC. The AC then induces formation of vulval tissue. We find that the AC also induces a particular ventral uterine intermediate precursor fate (pi) by a mechanism that is genetically and temporally distinct from vulval induction. This process requires lin-12, but unlike previously described lin-12-mediated decisions, signaling is unidirectional, is between dissimilar cells and does not involve lateral inhibition. The pi fates are necessary for egg laying and appear to produce a distinct specialized cell type. Thus, patterning of the ventral uterus by the AC is crucial to the development of a functional egg-laying system.", "date": "1995-02", "date_type": "published", "publication": "Development", "volume": "121", "number": "2", "publisher": "Company of Biologists", "pagerange": "263-271", "id_number": "CaltechAUTHORS:NEWdev95", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:NEWdev95", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute" }, { "agency": "Public Health Service" } ] }, "primary_object": { "basename": "NEWdev95.pdf", "url": "https://authors.library.caltech.edu/records/d35qr-s2d62/files/NEWdev95.pdf" }, "resource_type": "article", "pub_year": "1995", "author_list": "Newman, Anna P.; White, John G.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/pdzcm-jr411", "eprint_id": 29376, "eprint_status": "archive", "datestamp": "2023-08-20 04:44:23", "lastmod": "2023-10-24 22:08:52", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chamberlin-H-M", "name": { "family": "Chamberlin", "given": "Helen M." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The lin-3/let-23 pathway mediates inductive signalling during male spicule development in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "cell lineage, cell interaction, cell fate specification,\npattern formation", "note": "\u00a9 1994 The Company of Biologists Limited.\n\nAccepted 29 June 1994.\nWe thank T. R. Clandinin, A. Golden, R. J. Hill, L. S. Huang, G.\nD. Jongeward, W. Katz, P. Kayne, H. D. Lipshitz, J. Liu, A. Newman,\nR. Palmer and R. Sommer for comments on the manuscript, and G.\nMedina and Y. Hajdu-Cronin for technical assistance. We also thank\nR. J. Hill for providing syEx21 and syEx23 and S. Clark for providing\nlet-23(n2020) prior to publication. Some of the strains used in this\nstudy were provided by the Caenorhabditis Genetics Center, which\nis funded by the NIH National Center for Research Resources\n(NCRR). This research was supported by the Howard Hughes Medical\nInstitute and an NSF Presidential Young Investigator Award to P. W.\nS.; H. M. C. was an NSF predoctoral fellow; P. W. S. is an investigator\nof the HHMI.\n\nPublished - CHAdev94.pdf
", "abstract": "During Caenorhabditis elegans male spicule development, four pairs of precursor cells respond to multiple positional cues and establish a pattern of fates that correlates with relative anterior-posterior cell position. One of the extracellular cues is provided by the F and U cells, which promote anterior fates. We show that the genes in the lin-3/let-23 signalling pathway required for hermaphrodite vulval induction also mediate this F/U signal. Reduction-of-function mutations in lin-3, let-23, sem-5, let-60 or lin-45 disrupt the fate of anterior cells. Likewise, activation of the pathway with ubiquitously produced signal results in posterior cells inappropriately adopting the anterior fates even in the absence of F and U. We have further used this genetic pathway to begin to understand how multiple positional cues are integrated to specify cell fate. We demonstrate that lin-15 acts in spicule development as it does in vulval induction, as a negative regulator of let-23 receptor activity. A second extracellular cue, from Y.p, also acts antagonistically to the lin-3/let-23 pathway. However, this signal is apparently integrated into the lin-3/let-23 pathway at some step after lin-45 raf and is thus functionally distinct from lin-15. We have also investigated the role of lin-12 in forming the anterior/posterior pattern of fates. A lin-12 gain-of-function defect is masked by redundant positional information from F and U.", "date": "1994-10", "date_type": "published", "publication": "Development", "volume": "120", "number": "10", "publisher": "Company of Biologists", "pagerange": "2713-2721", "id_number": "CaltechAUTHORS:20120217-153949429", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120217-153949429", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH National Center for Research Resources (NCRR)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NSF Presidential Young Investigator Award" } ] }, "primary_object": { "basename": "CHAdev94.pdf", "url": "https://authors.library.caltech.edu/records/pdzcm-jr411/files/CHAdev94.pdf" }, "resource_type": "article", "pub_year": "1994", "author_list": "Chamberlin, Helen M. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/g2dxs-ygf34", "eprint_id": 53894, "eprint_status": "archive", "datestamp": "2023-08-20 04:28:23", "lastmod": "2023-10-19 22:21:16", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sommer-R-J", "name": { "family": "Sommer", "given": "Ralf J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Changes of induction and competence during the evolution of vulva development in nematodes", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1994 American Association for the Advancement of Science.\n\n14 February 1994; accepted 10 May 1994.\n\nWe thank L. Carta and D. Fitch for strains and E. Davidson, S. Fraser, E. Meyerowitz, L. Zimmer, and members of our laboratory for detailed discussion. P.W.S. is an investigator of the Howard Hughes Medical Institute. Supported by a Presidential Young Investigator Program award from the NSF (to P.W.S.). R.J.S. is supported by an EMBO long-term fellowship.", "abstract": "In Caenorhabditis, the vulva is formed in the central body region from three of six equivalent cells and is induced by the gonad. In some nematodes, however, the vulva is located in the posterior body region. Vulval development has been analyzed in three such genera. The same precursor cells give rise to the vulva in Caenorhabditis and in the posterior vulva species, but in the latter the cells first migrate posteriorly. In two such species, the vulva is not induced by the gonad, but instead relies on intrinsic properties of precursor cells. Thus, evolution of organ position involves changes in induction and competence.", "date": "1994-07-01", "date_type": "published", "publication": "Science", "volume": "265", "number": "5168", "publisher": "American Association for the Advancement of Science", "pagerange": "114-118", "id_number": "CaltechAUTHORS:20150120-140508773", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150120-140508773", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF" }, { "agency": "EMBO" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1126/science.8016644", "resource_type": "article", "pub_year": "1994", "author_list": "Sommer, Ralf J. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/8ksgj-za220", "eprint_id": 3896, "eprint_status": "archive", "datestamp": "2023-08-22 09:50:41", "lastmod": "2023-10-23 16:54:34", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Huang-Linda-S", "name": { "family": "Huang", "given": "Linda S." } }, { "id": "Tzou-Phoebe", "name": { "family": "Tzou", "given": "Phoebe" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The lin-15 locus encodes two negative regulators of Caenorhabditis elegans vulval development", "ispublished": "pub", "full_text_status": "public", "note": "Copyright \u00a9 1994 by The American Society for Cell Biology. Under the License and Publishing Agreement, authors grant to the general public, effective two months after publication of (i.e.,. the appearance of) the edited manuscript in an online issue of MBoC, the nonexclusive right to copy, distribute, or display the manuscript subject to the terms of the Creative Commons\u2013Noncommercial\u2013Share Alike 3.0 Unported license (http://creativecommons.org/licenses/by-nc-sa/3.0). \n\nSubmitted December 21, 1993; Accepted February 7, 1994. Monitoring Editor: Judith Kimble \n\nWe are greatly indebted to the generosity of Min Han, Jane Mendel, and Russell Hill for assistance with the microinjections; Jane Mendel for isolating PS#74B3; Andrea Holboke for help in mapping the lin-15 region; Alan Coulson for numerous discussions and assistance with correlating the physical and genetic maps around lin-15, Monica Driscoll and Marty Chalfie for TU#W1723; Mike Nonet and Barbara Meyer for communicating the cloning of sdc-1 before publication; Mimi Sengupta for help with the lin-15B(n744) mutagenesis; Tom Blumenthal for discussions regarding SL2 trans-splicing; Junho Lee for lin-15A(syl97); Russell Hill for lin-15AB(n767sy222); the Horvitz lab for lin-36B(n766) and the lin-15 alleles n765, n377, n309, el 763, and nl 139; Chris Martin, Stuart Kim, and Bob Barstead for cDNA libraries; and Paul Garrity for hints on LMPCR and gifts of primers LMPCR.1 and LMPCR.2. We are grateful to Helen Chamberlin, Tom Clandinin, Paul Garrity, Wendy Katz, Andy Golden, Yvonne Hajdu, Paul Kayne, and Bino Palmer for critically reading this manuscript. Some nematode strains used in this study were provided by the Caenorhabditis Genetics Center, which is funded by the National Institutes of Health (NIH) National Center for Research Resources. This work was supported by a grant from the March of Dimes Birth Defects Foundation to P.W.S. and NIH award GM-07616 to L.S.H. P.W.S. is an investigator of the Howard Hughes Medical Institute.\n\nPublished - huambc94.pdf
", "abstract": "During Caenorhabditis elegans vulval development, an inductive signal from the anchor cell stimulates three of the six vulval precursor cells (VPCs) to adopt vulval rather than nonvulval epidermal fates. Genes necessary for this induction include the lin-3 growth factor, the let-23 receptor tyrosine kinase, and let-60 ras. lin-15 is a negative regulator of this inductive pathway. In lin-15 mutant animals, all six VPCs adopt vulval fates, even in the absence of inductive signal. Previous genetic studies suggested that lin-15 is a complex locus with two independently mutable activities, A and B. We have cloned the lin-15 locus by germline transformation and find that it encodes two nonoverlapping transcripts that are transcribed in the same direction. The downstream transcript encodes the lin-15A function; the upstream transcript encodes the lin-15B function. The predicted lin-15A and lin- 15B proteins are novel and hydrophilic. We have identified a molecular null allele of lin-15 and have used it to analyze the role of lin-15 in the signaling pathway. We find that lin-15 acts upstream of let-23 and in parallel to the inductive signal.", "date": "1994-04", "date_type": "published", "publication": "Molecular Biology of the Cell", "volume": "5", "number": "4", "publisher": "American Society for Cell Biology", "pagerange": "395-412", "id_number": "CaltechAUTHORS:HUAmbc94", "issn": "1059-1524", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:HUAmbc94", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM-07616" }, { "agency": "March of Dimes Birth Defects Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "pmcid": "PMC301050", "primary_object": { "basename": "huambc94.pdf", "url": "https://authors.library.caltech.edu/records/8ksgj-za220/files/huambc94.pdf" }, "resource_type": "article", "pub_year": "1994", "author_list": "Huang, Linda S.; Tzou, Phoebe; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/y75cd-f6y46", "eprint_id": 95512, "eprint_status": "archive", "datestamp": "2023-08-20 03:52:25", "lastmod": "2023-10-20 20:18:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Aroian-R-V", "name": { "family": "Aroian", "given": "Raffi V." } }, { "id": "Lesa-G-M", "name": { "family": "Lesa", "given": "Giovanni M." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Mutations in the Caenorhabditis elegans let-23 EGFR-like gene define elements important for cell-type specificity and function", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1994 European Molecular Biology Organization. \n\nReceived on September 1, 1993. \n\nWe thank Makota Koga for unpublished let-23 genomic sequence. We also thank Pantelis Tsoulfas, Wendy Fantl, Andr\u00e9 Br\u00e4ndli, Helen Chamberlin, Andy Golden, Becky Kellum, Bin Liu, Michelle Moritz, Naomi Robinson, Tim Steams and Yixian Zheng for critical reading of this manuscript. G.M.L. was supported by a Merck pre-doctoral fellowship. This research was supported by USPHS grant HD23690 to P.W.S. P.W.S. is an investigator of the Howard Hughes Medical Institute.", "abstract": "The Caenorhabditis elegans let-23 gene is a genetically characterized member of the epidermal growth factor receptor (EGFR) tyrosine kinase family. Mutations in let-23 can produce five phenotypes in the nematode. Alleles of let-23 include null alleles, reduction-of-function alleles and alleles that disrupt function in some cell types and not others. We have sequenced some of these mutations to identify sequences and regions important for overall let-23 function and for let-23 function in specific cell types. Our data indicate that in vivo, the receptor's C-terminus can be partitioned into at least three domains that each contribute to receptor function in different cell types. In particular, we find distinct domains that mediate hermaphrodite fertility and vulval induction. Our data also demonstrate for the first time that a single, conserved residue in the ligand binding domain is critical for function in vivo and that mutations in the extracellular cysteines characteristic of the EGFR family can lead to a partial or a complete reduction of receptor function.", "date": "1994-01-15", "date_type": "published", "publication": "EMBO Journal", "volume": "13", "number": "2", "publisher": "European Molecular Biology Organization", "pagerange": "360-366", "id_number": "CaltechAUTHORS:20190515-111211560", "issn": "0261-4189", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190515-111211560", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Merck" }, { "agency": "NIH", "grant_number": "HD23690" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "pmcid": "PMC394816", "resource_type": "article", "pub_year": "1994", "author_list": "Aroian, Raffi V.; Lesa, Giovanni M.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/0hd09-kns18", "eprint_id": 71511, "eprint_status": "archive", "datestamp": "2023-08-20 03:23:10", "lastmod": "2023-10-23 15:51:14", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Intercellular Signaling and Signal Transduction in C. Elegans", "ispublished": "pub", "full_text_status": "restricted", "keywords": "protein kinase, cell migration, cell fate specification, redundancy, tissue-specificity", "note": "\u00a9 1993 Annual Reviews. \n\nI thank the C. elegans community for graciously sending reprints and preprints and for discussions and H. Chamberlin, A. Golden, L. Huang, G. Lesa, and R. Palmer for editorial comments. PWS is an investigator of the Howard Hughes Medical Institute. Research in my laboratory reviewed here was supported by the National Institutes of Health (HD23690), the March of Dimes Birth Defects Foundation, the Howard Hughes Medical Institute, and a Presidential Young Investigator Award from the National Science Foundation.", "abstract": "Intercellular signaling and signal transduction underlie most aspects of development and behavior. To understand any specific case we must identify the ligands, receptors and transducers, as well as regulators that modulate the activity of the signaling pathway. To understand more general aspects of signaling, we have to address the questions: To what extent are there modular signaling pathways, i.e. pathways that act as coherent units? How many such pathways are there? What factors affect the action of a universal pathway in particular cases? How widely is a given component or pathway used? How are the effects of multiple signaling pathways integrated? Here\nI discuss the use of Caenorhabditis elegans molecular genetics to study problems of intercellular signaling and signal transduction.", "date": "1993-12", "date_type": "published", "publication": "Annual Review of Genetics", "volume": "27", "publisher": "Annual Reviews", "pagerange": "497-521", "id_number": "CaltechAUTHORS:20161026-144839265", "issn": "0066-4197", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161026-144839265", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "HD23690" }, { "agency": "March of Dimes Birth Defects Foundation" }, { "agency": "NSF" } ] }, "doi": "10.1146/annurev.ge.27.120193.002433", "resource_type": "article", "pub_year": "1993", "author_list": "Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/6cd61-87p08", "eprint_id": 95513, "eprint_status": "archive", "datestamp": "2023-08-20 03:06:34", "lastmod": "2023-10-20 20:18:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Aroian-R-V", "name": { "family": "Aroian", "given": "Raffi V." } }, { "id": "Carta-L", "name": { "family": "Carta", "given": "Lynn" } }, { "id": "Kaloshian-Isgouhi", "name": { "family": "Kaloshian", "given": "Isgouhi" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "A Free-living Panagrolaimus sp. from Armenia Can Survive in Anhydrobiosis for 8.7 Years", "ispublished": "pub", "full_text_status": "public", "keywords": "anhydrobiosis, Armenia, free-living nematode, Panagrolaimus, survival", "note": "\u00a9 1993 The Society of Nematologists. \n\nReceived for publication 27 July 1992. \n\nFunded by an NSF-PYI award to P. W. S. \n\nThe authors thank Diana Freckman and John Crowe for discussions. Soil texture analysis was provided by the DANR Analytical Laboratory, University of California Cooperative Extension, Davis, CA. Live cultures of PS443 (hy-1) are available upon request.\n\nPublished - 500.pdf
", "abstract": "Although the ability of plant-parasitic nematodes to survive in a dehydrated or anhydrobiotic state for long periods of time has been well documented, the ability of free-living nematodes has not. Here we report on the survival of a free-living nematode, Panagrolaimus sp., from Armenia in the anhydrobiotic state for 8.7 years. This Panagrolaimus sp. can be cultured and maintained readily and may provide a good system for studying anhydrobiosis in nematodes. Key words: anhydrobiosis, Armenia, free-living nematode, Panagrolaimus, survival.", "date": "1993-09", "date_type": "published", "publication": "Journal of Nematology", "volume": "25", "number": "3", "publisher": "Society of Nematologists", "pagerange": "500-502", "id_number": "CaltechAUTHORS:20190515-112911463", "issn": "0022-300X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190515-112911463", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF" } ] }, "pmcid": "PMC2619395", "primary_object": { "basename": "500.pdf", "url": "https://authors.library.caltech.edu/records/6cd61-87p08/files/500.pdf" }, "resource_type": "article", "pub_year": "1993", "author_list": "Aroian, Raffi V.; Carta, Lynn; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/g6k2k-2s449", "eprint_id": 53265, "eprint_status": "archive", "datestamp": "2023-08-20 02:52:02", "lastmod": "2023-10-19 14:42:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Golden-A", "name": { "family": "Golden", "given": "Andy" }, "orcid": "0000-0002-8599-2031" }, { "id": "Han-M", "name": { "family": "Han", "given": "Min" } } ] }, "title": "Role of a raf Proto-Oncogene during Caenorhabditis elegans Vulval Development", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1993 The Royal Society and the authors.\n\nWe are grateful to Phoebe Tzou for technical assistance.\nThis research was supported by the USPHS grants to\nP.W.S. and M.H., and by the Howard Hughes Medical\nInstitute. P.W.S. is investigator of the Howard Hughes\nMedical Institute. A.G. is USPHS postdoctoral fellow.\nM.H. is a Lucille P. Markey Scholar. Strains were provided\nby the Caenorhabditis Genetics Center.", "abstract": "During Caenorhabditise legans vulval induction, multipotent precursors respond to an inductive signal by\ngenerating vulval cells as opposed to non-specialized epidermal cells. Both classical and 'reverse' genetic\napproaches have revealed that a cascade of nematode homologues of mammalian proto-oncogenes is\nnecessary for induction of the vulva. The inductive signal is a growth factor encoded by the lin-3 gene\nand its candidate receptor is a tyrosine kinase encoded by the let-23 gene. let-23 acts via a Ras protein\nencoded by the let-60 gene. A nematode homologue of mammalian raf family protein serine/threonine\nkinases has been cloned and found to be encoded by the lin-45 gene. Dominant negative lin-45 raf\nmutants prevent vulval induction. A recessive lin-45 raf mutation prevents the excessive vulval\ndifferentiation caused by activated ras, indicating that raf might act downstream of ras during vulval\ninduction.", "date": "1993-06-29", "date_type": "published", "publication": "Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences", "volume": "340", "number": "1293", "publisher": "Royal Society of London", "pagerange": "259-265", "id_number": "CaltechAUTHORS:20150107-102655698", "issn": "0962-8436", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150107-102655698", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "USPHS" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Lucille P. Markey Charitable Trust" } ] }, "resource_type": "article", "pub_year": "1993", "author_list": "Sternberg, Paul W.; Golden, Andy; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/jqge3-g2293", "eprint_id": 29525, "eprint_status": "archive", "datestamp": "2023-08-20 02:44:51", "lastmod": "2023-10-24 22:16:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chamberlin-H-M", "name": { "family": "Chamberlin", "given": "Helen M." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Multiple cell interactions are required for fate specification during male spicule development in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "keywords": "C. elegans, cell lineage, cell interactions, cell fate\nspecification, redundancy, pattern formation", "note": "\u00a9 1993 The Company of Biologists Limited.\n\nAccepted 10 March 1993.\nWe thank Leon Avery, Eric Davidson, Scott Fraser, Andy\nGolden, Russell Hill, Linda Huang, Gregg Jongeward, Paul\nKayne, Howard Lipshitz, and Anna Newman for comments on the\nmanuscript, and Gladys Medina for technical assistance. CB1490\nwas provided by the Caenorhabditis Genetics Center. This\nresearch was supported by the Howard Hughes Medical Institute.\nH. M. C. was an NSF predoctoral fellow. P. W. S. is an investigator\nof HHMI.\n\nPublished - CHAdev93.pdf
", "abstract": "The B blast cell divides postembryonically in C. elegans males to produce 47 progeny that include all of the cells of the copulatory spicules. During the early development of the B lineage, the anterior daughter of B, B.a, generates eight cells. These cells migrate to form four pairs of cells that flank the developing cloaca (ventral, dorsal, and two identical lateral pairs). For each pair, the more anterior cell produces a distinct lineage ('anterior fate') from the posterior cell ('posterior fate'). For the ventral and dorsal pairs, either cell can migrate to the anterior position and produce the anterior lineage, and the other cell migrates posterior and produces the posterior lineage (Sulston and Horvitz, 1977, Dev. Biol. 56, 110\u2013156). The migration is variable, although the resultant fate pattern is invariant. In the two lateral pairs, both the migration and fate pattern are invariant. Using a laser microbeam to selectively ablate neighboring cells we have found that the cells of the lateral pair also respond to positional cues. For all four pairs other male-specific blast cells provide extracellular cues. In general, F and U promote anterior fates, Y promotes some posterior fates, and the B.a progeny promote posterior fates. Several of these cues are redundant. By ablating combinations of cells we have deduced how these signals may act in concert to specify the fates of the B.a progeny. We propose that fate specification in these pairs depends on three general classes of extracellular cues: positional cues, modulators of positional cues, and lateral signals. The B lineage thus provides an opportunity to study with single cell resolution the integration of multiple intercellular signals.", "date": "1993-06", "date_type": "published", "publication": "Development", "volume": "118", "number": "2", "publisher": "Company of Biologists", "pagerange": "297-324", "id_number": "CaltechAUTHORS:20120229-094019491", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120229-094019491", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NSF" } ] }, "primary_object": { "basename": "CHAdev93.pdf", "url": "https://authors.library.caltech.edu/records/jqge3-g2293/files/CHAdev93.pdf" }, "resource_type": "article", "pub_year": "1993", "author_list": "Chamberlin, Helen M. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/f15fx-avp64", "eprint_id": 56579, "eprint_status": "archive", "datestamp": "2023-08-20 02:43:34", "lastmod": "2023-10-23 15:34:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Han-Min", "name": { "family": "Han", "given": "Min" } }, { "id": "Golden-A", "name": { "family": "Golden", "given": "Andy" }, "orcid": "0000-0002-8599-2031" }, { "id": "Han-Yuming", "name": { "family": "Han", "given": "Yuming" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "C. elegans lin-45 raf gene participates in let-60 ras-stimulated vulval differentiation", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1993 Nature Publishing Group.\n\nWe thank P. Tzou, R. Rogge, H. Mori and Y. Hajdu for technical contributions;\nA. Coulson and the MRC group for cosmids; R. Barstead and R. Waterston for the deb-1 strain, the\ncDNA library and the YAC clones; the Caltech Biopolymer Synthesis and Analysis Resource Center\nfor oligonucleotides; N. Bonini, H. Lipshitz, M. Kennedy, A. Valsamakis, D. Weigel and members of our\nlaboratories for discussion and editorial comments. Some nematode strains were provided by the\nCaenorhabditis Genetic Center, which is funded by the NIH National Center for Research Resources.\nM.H. thanks W. Wood for support. M.H. is a Lucille P. Markey Scholar in Biomedical Science. A. G. is\na postdoctoral fellow of the USPHS. P.W.S. is an investigator of the Howard Hughes Medical Institute.\nThis research has been supported by US Public Health Service grants to M.H. and to P.W.S., and has\nbeen partly supported by the Lucille P. Markey Charitable Trust. GenBank Accession Number for lin-45\nraf is L15347.", "abstract": "Vulval differentiation in Caenorhabditis elegans is controlled by intercellular signalling mediated by a receptor tyrosine kinase and a ras gene product. The lin-45 gene encodes a homologue of the raf family of serine/threonine kinases and is necessary for vulval differentiation. The lin-45 raf gene product appears to act downstream of the ras protein in this pathway. A proto-oncogene-mediated signalling pathway may be a common feature of metazoan development.", "date": "1993-05-13", "date_type": "published", "publication": "Nature", "volume": "363", "number": "6425", "publisher": "Nature Publishing Group", "pagerange": "133-140", "id_number": "CaltechAUTHORS:20150410-153910302", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150410-153910302", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH National Center for Research Resources (NCRR)" }, { "agency": "Lucille P. Markey Charitable Trust" }, { "agency": "U.S. Public Health Service (USPHS)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1038/363133a0", "resource_type": "article", "pub_year": "1993", "author_list": "Han, Min; Golden, Andy; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/f9z29-33t68", "eprint_id": 1727, "eprint_status": "archive", "datestamp": "2023-08-22 09:10:56", "lastmod": "2023-10-23 16:20:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Aroian-R-V", "name": { "family": "Aroian", "given": "Raffi V." } }, { "id": "Levy-A-D", "name": { "family": "Levy", "given": "Adam D." } }, { "id": "Koga-Makoto", "name": { "family": "Koga", "given": "Makoto" } }, { "id": "Ohshima-Yasumi", "name": { "family": "Ohshima", "given": "Yasumi" } }, { "id": "Kramer-J-M", "name": { "family": "Kramer", "given": "James M." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Splicing in Caenorhabditis elegans does not require an AG at the 3' splice acceptor site", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1993, American Society for Microbiology \n\nReceived 5 May 1992/Returned for modification 5 August 1992/Accepted 28 October 1992 \n\nWe thank Gregg Jongeward for the mutant let-23(sy97sy122), Tom Blumenthal for discussions on splicing in C. elegans, and Bob Horvitz for suggesting promiscuous splicing as a mechanism for generating diversity. We thank James Deshler, Andy Golden, Paul Kayne, and John Rossi for discussions and comments. We thank Jeff Miner for help with RNase protection and Sean Tavtigian and the Dervan Laboratory for help with Phosphorlmager quantitation. We thank Jane Mendel for wild-type RNA, Mike Krause for plasmid pT7/T3-18-103, Joseph LaRusso for help with sequencing, and Paul Kayne, Russell Hill, and Giovanni Lesa for technical advice. \n\nP.W.S. is an investigator of the Howard Hughes Medical Institute. This research was supported by grants HD23690 to P.W.S. and HD22028 to J.M.K.\n\nPublished - AROmcb93.pdf
", "abstract": "The dinucleotide AG, found at the 3' end of virtually all eukaryotic pre-mRNA introns, is thought to be essential for splicing. Reduction-of- function mutations in two Caenorhabditis elegans genes, the receptor tyrosine kinase gene let-23 and the collagen gene dpy-10, both alter the AG at the end of a short (ca. 50-nucleotide) intron to AA. The in vivo effects of these mutations were studied by sequencing polymerase chain reaction-amplified reverse-transcribed RNA isolated from the two mutants. As expected, we find transcripts that splice to a cryptic AG, skip an exon, and retain an unspliced intron. However, we also find significant levels of splicing at the mutated 3' splice site (AA) and at nearby non-AG dinucleotides. Our results indicate that for short C. elegans introns an AG is not required for splicing at either the correct 3' splice site or incorrect sites. Analysis of a splice site mutant involving a longer, 316-nucleotide C. elegans intron indicates that an AG is also not required there for splicing. We hypothesize that elements besides the invariant AG, e.g., an A-U-rich region, a UUUC motif, and/or a potential branch point sequence, are directing the selection of the 3' splice site and that in wild-type genes these elements cooperate so that proper splicing occurs.", "date": "1993-01", "date_type": "published", "publication": "Molecular and Cellular Biology", "volume": "13", "number": "1", "publisher": "American Society for Microbiology", "pagerange": "626-637", "id_number": "CaltechAUTHORS:AROmcb93", "issn": "0270-7306", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:AROmcb93", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "HD23690" }, { "agency": "NIH", "grant_number": "HD22028" } ] }, "pmcid": "PMC358941", "primary_object": { "basename": "AROmcb93.pdf", "url": "https://authors.library.caltech.edu/records/f9z29-33t68/files/AROmcb93.pdf" }, "resource_type": "article", "pub_year": "1993", "author_list": "Aroian, Raffi V.; Levy, Adam D.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/tcbv4-9q554", "eprint_id": 65768, "eprint_status": "archive", "datestamp": "2023-08-22 09:10:23", "lastmod": "2023-10-18 16:46:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hill-R-J", "name": { "family": "Hill", "given": "Russell J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Cell fate patterning during C. elegans vulval development", "ispublished": "pub", "full_text_status": "public", "keywords": "development; genetics; C. elegans; vulva; EGF; inter-cellular signalling", "note": "\u00a9 1993 Company of Biologists.\n\nPublished - 9.full.pdf
", "abstract": "Precursor cells of the vulva of the C. elegans hermaphrodite choose between two vulval cell fates (1\u00b0 and 2\u00b0) and a non-vulval epidermal fate (3\u00b0) in response to three intercellular signals. An inductive signal produced by the anchor cell induces the vulval precursors to assume the 1\u00b0 and 2\u00b0 vulval fates. This inductive signal is an EGF-like growth factor encoded by the gene lin-3. An inhibitory signal mediated by lin-15, and which may originate from the surrounding epidermis, prevents the vulval precursors from assuming vulval fates in the absence of the inductive signal. A short range lateral signal, which acts through the gene lin-12, regulates the pattern of 1\u00b0 and 2\u00b0 fates assumed by the induced vulval precursors.\n\nThe combined action of the three signals precisely directs the six vulval precursors to adopt a 3\u00b0 3\u00b0 2\u00b0 1\u00b0 2 \u00b0 3\u00b0 pattern of fates. The amount of inductive signal produced by the anchor cell appears to determine the number or vulval precursors that assume vulval fates. The three induced vulval precursors most proximal to the anchor cell are proposed to adopt the 2\u00b0 1\u00b0 2\u00b0 pattern of fates in response to a gradient of the inductive signal and also in response to lateral signalling that inhibits adjacent vulval precursor cells from both assuming the 1\u00b0 fate.", "date": "1993", "date_type": "published", "publication": "Development", "volume": "119", "number": "S", "publisher": "Company of Biologists", "pagerange": "9-18", "id_number": "CaltechAUTHORS:20160330-133817838", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160330-133817838", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "primary_object": { "basename": "9.full.pdf", "url": "https://authors.library.caltech.edu/records/tcbv4-9q554/files/9.full.pdf" }, "resource_type": "article", "pub_year": "1993", "author_list": "Hill, Russell J. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/6m2rq-ve016", "eprint_id": 80499, "eprint_status": "archive", "datestamp": "2023-08-20 02:10:19", "lastmod": "2023-10-17 16:02:37", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Aroian-R-V", "name": { "family": "Aroian", "given": "Raffi V." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Signal Transduction during Caenorhabditis elegans Vulval Determination", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 1993 Academic Press, Inc. Published by Elsevier Inc.", "abstract": "[no abstract]", "date": "1993", "date_type": "published", "publisher": "Academic Press", "place_of_pub": "Boston, MA", "pagerange": "391-447", "id_number": "CaltechAUTHORS:20170816-142138416", "isbn": "978-0-12-429350-2", "book_title": "Signal Transduction: Prokaryotic and Simple Eukaryotic Systems", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170816-142138416", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Taylor-B-L", "name": { "family": "Taylor", "given": "Barry L." } } ] }, "doi": "10.1016/B978-0-12-429350-2.50020-6", "resource_type": "book_section", "pub_year": "1993", "author_list": "Aroian, Raffi V. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/2e1yc-q3795", "eprint_id": 57457, "eprint_status": "archive", "datestamp": "2023-08-20 01:36:28", "lastmod": "2023-10-23 17:24:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hill-R-J", "name": { "family": "Hill", "given": "Russell J." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The gene lin-3 encodes an inductive signal for vulval development in C. elegans", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1992 Nature Publishing Group.\n\nReceived 7 May: accepted 25 June 1992.\n\nWe thank P. Tzou for technical assistance, A. Coulson and J. Sulston for the\n\u03bb2001 genomic library and cosmids near the lin-3 locus; R. Waterston for YAC clones grids; I. Mori for RW7096; M. Chalfie for TU355; A. Rose and O. Bailie for map data; A. Fire for lacZ expression vectors and protocols; R. Barstead, C. Martin and S. Kim for cDNA libraries; P. Bjorkman. L. Kozar and E. Schwarz for help with sequence analysis; L. Carta and L. Huang for sharing unpublished results; and members of our laboratory, O. Anderson and E. Schwarz for their comments on the manuscript. This work was supported by a USPHS grant and a Searle Scholar Award to P.W.S. P.W.S. is an investigator of the Howard Hughes Medical Institute. R.J.H. was an NSF predoctoral fellow.", "abstract": "The lin-3 gene is necessary for induction of the Caenorhabditis elegans vulva by the anchor cell. It encodes a molecule similar to epidermal growth factor and to transforming growth factor-a and acts through the epidermal growth factor receptor homologue let-23. Expression of lin-3 in the anchor cell stimulates vulval induction; lin-3 may encode the vulval inducing signal.", "date": "1992-08-06", "date_type": "published", "publication": "Nature", "volume": "358", "number": "6386", "publisher": "Nature Publishing Group", "pagerange": "470-476", "id_number": "CaltechAUTHORS:20150512-124029795", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150512-124029795", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "U.S. Public Health Service (USPHS)" }, { "agency": "Searle Scholars Program" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NSF Predoctoral Fellowship" } ] }, "doi": "10.1038/358470a0", "resource_type": "article", "pub_year": "1992", "author_list": "Hill, Russell J. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/949bk-ya978", "eprint_id": 76057, "eprint_status": "archive", "datestamp": "2023-08-22 08:33:13", "lastmod": "2023-10-25 15:29:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Han-Min", "name": { "family": "Han", "given": "Min" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Analysis of dominant-negative mutations of the Caenorhabditis elegans let-60 ras gene", "ispublished": "pub", "full_text_status": "public", "keywords": "ras; Caenorhabditis elegans; dominant-negative mutations; vulval induction", "note": "\u00a9 1991 Cold Spring Harbor Laboratory Press. The Authors acknowledge that six months after the full-issue publication date, the Article will be distributed under a Creative Commons CC-BY-NC License (Attribution-NonCommercial 4.0 International License, http://creativecommons.org/licenses/by-nc/4.0/). \n\nReceived July 30, 1991; revised version accepted September 2, 1991. \n\nWe thank S. Clark, G. Beitel, and R. Horvitz for strains containing let-60(n2301 dn), let-60(n1531 dn), and nDp5, and D. Clark and D. Baillie for information on the dpy-20 gene. We thank P. Tzou and Y. Hajdu for their assistance during the study; R. Aroian, G. Beitel, W. Boorstein, J. Colicelli, A. Golden, I. Greenwald, G. Jongeward, W. Katz, P. Kayne, H. Lipshitz, and S. Parkhust for comments on the manuscript; and H. Bourne, F. McCormick, S. Powers, and members of our laboratory for helpful discussions. Some nematode strains used in this study were provided by the Caenorhabditis Genetic Center, which is funded by the National Institutes of Health National Center for Research Resources (NCRR). M.H. was a Genentech Fellow of the Life Science Research Foundation and is a Lucille P. Markey Scholar in Biomedical Science. P.W.S. is an investigator of the Howard Hughes Medical Institute. This research has been supported by grants to P.W.S. from the U.S. Public Health Service and March of Dimes Birth Defects Foundation. \n\nThe publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked \"advertisement\" in accordance with 18 USC section 1734 solely to indicate this fact.\n\nPublished - 2188.full.pdf
", "abstract": "The let-60 gene of Caenorhabditis elegans controls the choice between vulval and hypodermal differentiation in response to an inductive signal from the gonad. let-60 encodes a ras protein that acts downstream of the let-23 receptor tyrosine kinase in a signal transduction pathway. Dominant-negative mutations of let-60 [let-60(dn)] cause a reduction of the gene activity in let-60(dn)/+ heterozygotes and a vulva-less mutant phenotype. We have found that nine let-60(dn) mutations cause replacements of conserved residues. Four are in two novel positions; others are in positions known previously to cause dominant-negative mutations in mammalian cells. The locations of these lesions suggest that they disrupt the ability of the ras protein to bind guanine nucleotides. Four let-60(dn) mutant genes were introduced into wild-type animals in the form of extrachromosomal arrays and were found to generate three dominant phenotypes--lethality, vulva-less, or multivulva--depending on gene dose and alleles. The dominant lethality caused by high-dose transgenic let-60(dn) genes suggests a toxic effect of these mutant genes in early development. The dominant-negative effects of these mutations in heterozygotes are likely to be caused by competition between let-60(dn) and let-60(+) protein for a positive regulator. All let-60(dn) mutations interfere with let-60(+) activity, but some alleles have partial constitutive activity, suggesting that the ability to interact with the activator is separable from the ability to exert a physiological effect (stimulation of vulval differentiation). These dn mutations might be useful for interfering with ras-mediated signal transduction pathways in other multicellular organisms.", "date": "1991-12", "date_type": "published", "publication": "Genes and Development", "volume": "5", "number": "12a", "publisher": "Cold Spring Harbor Laboratory Press", "pagerange": "2188-2198", "id_number": "CaltechAUTHORS:20170408-154353782", "issn": "0890-9369", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170408-154353782", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Life Sciences Research Foundation" }, { "agency": "Lucille P. Markey Charitable Trust" }, { "agency": "NIH" }, { "agency": "March of Dimes Birth Defects Foundation" } ] }, "doi": "10.1101/gad.5.12a.2188", "primary_object": { "basename": "2188.full.pdf", "url": "https://authors.library.caltech.edu/records/949bk-ya978/files/2188.full.pdf" }, "resource_type": "article", "pub_year": "1991", "author_list": "Han, Min and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/vc43r-5zj40", "eprint_id": 56577, "eprint_status": "archive", "datestamp": "2023-08-20 00:10:25", "lastmod": "2023-10-23 15:34:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Horvitz-H-R", "name": { "family": "Horvitz", "given": "H. Robert" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Multiple intercellular signalling systems control the development of the Caenorhabditis elegans vulva", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1991 Nature Publishing Group.\n\nWe thank the members of our laboratories, particularly C. Bargmann and E.\nJorgensen. and L. Avery, M. Chalfie. E. Davidson. C. Ferguson, I. Greenwald, B. Herman, I. Herskowltz,\nC. Kenyon. S. Kim, J. Kimble, K. Struhl and J. White for many helpful suggestions. The work done in\nour laboratories was supported by the US Public Health Service. H.R.H. and P.W.S. are Investigators\nof the Howard Hughes Medical Institute.", "abstract": "Developmental, genetic and molecular studies indicate that multiple intercellular signalling systems interact to specify the types and spatial patterns of cells generated during the formation of the vulva of the nematode Caenorhabditis elegans. Two classes of evolutionary conserved transmembrane receptors and a Ras protein function in these signalling systems. The biology of vulval development provides a framework for understanding how cell interactions control the development of animals as diverse as nematodes, insects and mammals.", "date": "1991-06-13", "date_type": "published", "publication": "Nature", "volume": "351", "number": "6327", "publisher": "Nature Publishing Group", "pagerange": "535-541", "id_number": "CaltechAUTHORS:20150410-150918176", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150410-150918176", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "U.S. Public Health Service (USPHS)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1038/351535a0", "resource_type": "article", "pub_year": "1991", "author_list": "Horvitz, H. Robert and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/8d4eh-hej75", "eprint_id": 95493, "eprint_status": "archive", "datestamp": "2023-08-20 00:09:43", "lastmod": "2023-10-20 20:17:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Aroian-R-V", "name": { "family": "Aroian", "given": "Raffi V." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Multiple functions of let-23, a Caenorhabditis elegans receptor tyrosine kinase gene required for vulval induction", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1991 by the Genetics Society of America. \n\nManuscript received December 5, 1990; Accepted for publication February 14, 1991. \n\nWe are grateful for the encouragement of Bob Horvitz in whose laboratory P.W.S. made the initial observations of the n1045 phenotypes. We thank Helen Chamberlin, Gregg Jongeward and Min Han for unpublished observations and Chip Ferguson, Will Boorstein, Nancy Bonini, Howard Lipshitz, Barbara Wold, Min Han, Andy Golden, Russell Hill, Susan Parkhurst, Tom Wilkie, Wendy Katz, Paul Kayne, Nagesh Mahanthappa, and other members of our laboratory for helpful comments and critical reading of this manuscript. Some nematode strains used in this work were provided by the Caenorhabditis Genetic Center, which is funded by the National Institutes of Health National Center for Research Resources (NCRR). We also thank Helen Chamberlin for strains and Andrea Holboke and Yvonne Hajdu for maintenance of our C. elegans strain collection. R.V.A. is a U.S. Public Health Service trainee. P.W.S. is an investigator of the Howard Hughes Medical Institute. This research has been supported by a grant to P.W.S. from the U.S. Public Health Service (HD23690).\n\nPublished - ge1282251.pdf
", "abstract": "The let-23 gene, which encodes a putative tyrosine kinase of the epidermal growth factor (EGF) receptor subfamily, has multiple functions during Caenorhabditis elegans development. We show that let-23 function is required for vulval precursor cells (VPCs) to respond to the signal that induces vulval differentiation: a complete loss of let-23 function results in no induction. However, some let-23 mutations that genetically reduce but do not eliminate let-23 function result in VPCs apparently hypersensitive to inductive signal: as many as five of six VPCs can adopt vulval fates, in contrast to the three that normally do. These results suggest that the let-23 receptor tyrosine kinase controls two opposing pathways, one that stimulates vulval differentiation and another that negatively regulates vulval differentiation. Furthermore, analysis of 16 new let-23 mutations indicates that the let-23 kinase functions in at least five tissues. Since various let-23 mutant phenotypes can be obtained independently, the let-23 gene is likely to have tissue-specific functions.", "date": "1991-06-01", "date_type": "published", "publication": "Genetics", "volume": "128", "number": "2", "publisher": "Genetics Society of America", "pagerange": "251-267", "id_number": "CaltechAUTHORS:20190514-121726625", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190514-121726625", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "HD23690" } ] }, "pmcid": "PMC1204464", "primary_object": { "basename": "ge1282251.pdf", "url": "https://authors.library.caltech.edu/records/8d4eh-hej75/files/ge1282251.pdf" }, "resource_type": "article", "pub_year": "1991", "author_list": "Aroian, Raffi V. and Sternberg, Paul W." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/kxcyd-zx758", "eprint_id": 3903, "eprint_status": "archive", "datestamp": "2023-08-22 07:58:20", "lastmod": "2023-10-23 19:32:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lochrie-M-A", "name": { "family": "Lochrie", "given": "Michael A." } }, { "id": "Mendel-J-E", "name": { "family": "Mendel", "given": "Jane E." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Simon-M-I", "name": { "family": "Simon", "given": "Melvin I." } } ] }, "title": "Homologous and unique G protein alpha subunits in the nematode Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1991 by The American Society for Cell Biology \n\nReceived: October 5, 1990. Revised and accepted: November 16, 1990. \n\nWe thank Mike Strathmann for advice on PCR reactions and for the provision of materials for the \u03b3\u03b4 transposon-based sequencing method, the Caltech Microchemical Facility for oligonucleotide synthesis, Andrea Holboke for C. elegans genomic DNA, Alan Coulson and John Sulston for gene mapping data, Eva Neer and Graeme Milligan for G0\u03b1 antibodies, Stuart Kim and Russell Hill for the C. elegans cDNA library, and Yasumi Ohshima and Ron Plasterk for generous communication of results before publication. P.W.S. is an investigator of the Howard Hughes Medical Institute. Supported by a Developmental Biology Grant from the Lucille P. Markey Foundation and by USPHS grants GM34236 to M.I.S. and HD23690 to P.W.S.\n\nPublished - LOCcr91.pdf
", "abstract": "A cDNA corresponding to a known G protein alpha subunit, the alpha subunit of Go (Go alpha), was isolated and sequenced. The predicted amino acid sequence of C. elegans Go alpha is 80-87% identical to other Go alpha sequences. An mRNA that hybridizes to the C. elegans Go alpha cDNA can be detected on Northern blots. A C. elegans protein that crossreacts with antibovine Go alpha antibody can be detected on immunoblots. A cosmid clone containing the C. elegans Go alpha gene (goa-1) was isolated and mapped to chromosome I. The genomic fragments of three other C. elegans G protein alpha subunit genes (gpa-1, gpa-2, and gpa-3) have been isolated using the polymerase chain reaction. The corresponding cosmid clones were isolated and mapped to disperse locations on chromosome V. The sequences of two of the genes, gpa-1 and gpa-3, were determined. The predicted amino acid sequences of gpa-1 and gpa-3 are only 48% identical to each other. Therefore, they are likely to have distinct functions. In addition they are not homologous enough to G protein alpha subunits in other organisms to be classified. Thus C. elegans has G proteins that are identifiable homologues of mammalian G proteins as well as G proteins that appear to be unique to C. elegans. Study of identifiable G proteins in C. elegans may result in a further understanding of their function in other organisms, whereas study of the novel G proteins may provide an understanding of unique aspects of nematode physiology.", "date": "1991-02", "date_type": "published", "publication": "Cell Regulation", "volume": "2", "number": "2", "publisher": "American Society for Cell Biology", "pagerange": "135-154", "id_number": "CaltechAUTHORS:LOCcr91", "issn": "1044-2030", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:LOCcr91", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Lucille P. Markey Charitable Trust" }, { "agency": "NIH", "grant_number": "GM34236" }, { "agency": "NIH", "grant_number": "HD23690" } ] }, "pmcid": "PMC361731", "primary_object": { "basename": "LOCcr91.pdf", "url": "https://authors.library.caltech.edu/records/kxcyd-zx758/files/LOCcr91.pdf" }, "resource_type": "article", "pub_year": "1991", "author_list": "Lochrie, Michael A.; Mendel, Jane E.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/rb14x-1ys27", "eprint_id": 57497, "eprint_status": "archive", "datestamp": "2023-08-19 23:24:30", "lastmod": "2023-10-23 17:28:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Aroian-R-V", "name": { "family": "Aroian", "given": "Raffi V." } }, { "id": "Koga-Makoto", "name": { "family": "Koga", "given": "Makoto" } }, { "id": "Mendel-J-E", "name": { "family": "Mendel", "given": "Jane E." } }, { "id": "Ohshima-Yasumi", "name": { "family": "Ohshima", "given": "Yasumi" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The let-23 gene necessary for Caenorhabditis elegans vulval induction encodes a tyrosine kinase of the EGF receptor subfamily", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1990 Nature Publishing Group. Received 5 November; accepted 14 November 1990.\n\nWe thank J. Sulston and A. Coulson (MRC, United Kingdom) for physical mapping of kin-7 and the gifts of cosmid clones, C. Link for the genomic library. R. Barstead for the cDNA library and protocols, R. Waterston for YACs, A. Papp for a mapping strain, J. Kramer and J. Park for mapping information, I Mori, t. Tani, P. Tsoulfas, M. Han and members of our laboratories for suggestions and discussions, and A. Holboke, J. Luxemburg and P. Tzou for technical assistance. This work was supported by US Public Health Service (P.W.S.) and the Ministry of Education, Science and Culture of Japan (Y.O.)", "abstract": "The let-23 gene is required for induction of the Caenorhabditis elegans vulva. It is shown that let-23 encodes a putative tyrosine kinase of the epidermal growth factor receptor subfamily. Thus, let-23 might encode the receptor for the inductive signal required for vulval development. Because let-23 acts upstream of let-60 ras in the vulval determination pathway, the identification of the let-23 product provides support for a link in vivo between tyrosine kinase growth factor receptors and ras proteins in a pathway of cell-type determination.", "date": "1990-12-27", "date_type": "published", "publication": "Nature", "volume": "348", "number": "6303", "publisher": "Nature Publishing Group", "pagerange": "693-699", "id_number": "CaltechAUTHORS:20150513-111306779", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150513-111306779", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "U.S. Public Health Service (USPHS)" }, { "agency": "Ministry of Education, Science and Culture (Japan)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1038/348693a0", "resource_type": "article", "pub_year": "1990", "author_list": "Aroian, Raffi V.; Koga, Makoto; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/pe5d0-d6432", "eprint_id": 95521, "eprint_status": "archive", "datestamp": "2023-08-19 23:22:50", "lastmod": "2023-10-20 20:18:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Han-Min", "name": { "family": "Han", "given": "Min" } }, { "id": "Aroian-R-V", "name": { "family": "Aroian", "given": "Raffi V." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The let-60 locus controls the switch between vulval and nonvulval cell fates in Caenorhabditis elegans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1990 by the Genetics Society of America. \n\nManuscript received July 5, 1990; Accepted for publication August 23, 1990. \n\nWe thank R. Rogge for isolating several of the lin-15 suppressors, Y. Hadju and A. Holboke for handling our strain collection, G. Beitel, S. Clark, R. Horvitz, G. Jongeward, and H. Chamberlin for communicating unpublished results on let-60 and lin-34, R. Herman and E. Hedgecock for communicating results on mosaic analysis on lin-15, D. Clark and D. Baillie for providing us with strains with let-60 and other lethal alleles, the Caenorhabditis elegans Genetic Center (supported by a contract between the National Institutes of Health Division of Research Resources and Curators of the University of Missouri) and R. Horvitz's laboratory for many useful strains, and R. Hill, G. Jongeward, and others in our laboratory for strains and stimulating discussions. We thank H. Lipshitz, S. Parkhurst, J. Hodgkin, S. Kim, R. Herman, R. Horvitz, I. Greenwald, C. Kenyon, H. Mori, H. Chamberlin and other members of our laboratory for comments on the manuscript. M.H. is a Genentech Fellow of the Life Science Research Foundation. R.V.A. was a U.S. Public Health Service trainee. P.W.S. is an investigator of the Howard Hughes Medical Institute, a Searle Scholar, and a Presidential Young Investigator of the National Science Foundation. This research has been supported by grants to P.W.S. from the U.S. Public Health Service (HD23690) and the March of Dimes Birth Defects Foundation.\n\nPublished - ge1264899.pdf
", "abstract": "During induction of the Caenorhabditis elegans hermaphrodite vulva by the anchor cell of the gonad, six multipotent vulval precursor cells (VPCs) have two distinct fates: three VPCs generate the vulva and the other three VPCs generate nonspecialized hypodermis. Genes that control the fates of the VPCs in response to the anchor cell signal are defined by mutations that cause all six VPCs to generate vulval tissue (Multivulva or Muv) or that cause all six VPCs to generate hypodermis (Vulvaless or Vul). Seven dominant Vul mutations were isolated as dominant suppressors of a lin-15 Muv mutation. These mutations are dominant alleles of the gene let-60, previously identified only by recessive lethal mutations. Our genetic studies of these dominant Vul recessive lethal mutations, recessive lethal mutations, intragenic revertants of the dominant Vul mutations, and the closely mapping semi-dominant multivulva lin-34 mutations suggest that: (1) loss-of-function mutations of let-60 are recessive lethal at a larval stage, but they also cause a Vul phenotype if the lethality is rescued maternally by a lin-34 gain-of-function mutation. (2) The dominant Vul alleles of let-60 are dominant negative mutations whose gene products compete with wild-type activity. (3) lin-34 semidominant Muv alleles are either gain-of-function mutations of let-60 or gain-of-function mutations of an intimately related gene that elevates let-60 activity. We propose that let-60 activity controls VPC fates. In a wild-type animal, reception by a VPC of inductive signal activates let-60, and it generates into a vulval cell type; in absence of inductive signal, let-60 activity is low and the VPC generates hypodermal cells. Our genetic interaction studies suggest that let-60 acts downstream of let-23 and lin-15 and upstream of lin-1 and lin-12 in the genetic pathway specifying the switch between vulval and nonvulval cell types.", "date": "1990-12-01", "date_type": "published", "publication": "Genetics", "volume": "126", "number": "4", "publisher": "Genetics Society of America", "pagerange": "899-913", "id_number": "CaltechAUTHORS:20190515-145312907", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190515-145312907", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Life Science Research Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Searle Scholars Program" }, { "agency": "NSF" }, { "agency": "NIH", "grant_number": "HD23690" }, { "agency": "March of Dimes Birth Defects Foundation" } ] }, "pmcid": "PMC1204287", "primary_object": { "basename": "ge1264899.pdf", "url": "https://authors.library.caltech.edu/records/pe5d0-d6432/files/ge1264899.pdf" }, "resource_type": "article", "pub_year": "1990", "author_list": "Han, Min; Aroian, Raffi V.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/6fhmq-e0x59", "eprint_id": 95514, "eprint_status": "archive", "datestamp": "2023-08-19 14:59:40", "lastmod": "2023-10-20 20:18:26", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Horvitz-H-R", "name": { "family": "Horvitz", "given": "H. Robert" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Nematode Postembryonic Cell Lineages", "ispublished": "pub", "full_text_status": "public", "keywords": "Caenorhabditis elegans, Panagrellus redivivus, anatomy, development, taxonomy, evolution", "note": "\u00a9 1982 The Society of Nematologists. \n\nReceived for publication 22 September 1981. \n\nSymposium presented at the annual meeting of the Society of Nematologists, Seattle, Washington, August 1981.\n\nPublished - 240.pdf
", "abstract": "The complete postembryonic ceil lineages of the free-living nentatodes Caenorhabditis elegans and Panagrellus redivivus are known. Postembryonic cell divisions lead to substantial increases in the number of cells and, in most cases, in the number of types of cells in the neuronal, muscular, hypodermal, and digestive systems. The patterns of postembyronic cell divisions are essentially invariant and generate a fixed number of progeny cells of strictly specified fates. Cell fates depend upon both lineage history and cell-cell interactions: lineage limits the developmental potential of each cell and, for certain cells, cell-cell interactions specify which of a small number of alternative potential fates is acquired. Relatively simple differences in cell lineage account for some of the striking differences in gross morphology both between sexes and between species. Genetic studies indicate that these cell lineage differences reflect one or a few relatively simple mutational events. Interspecific differences in cell lineage are likely to be good indicators of evolutionary distance and may be helpful in defining taxonomic relationships. Both the techniques utilized in, and the information acquired from, studies of cell lineages in C. elegam and P. redivivus may prove useful to other hematologists. Key words: Caenorhabditis elegans, Panagrellus redivivus, anatomy, development, taxonomy, evolution.", "date": "1982-04", "date_type": "published", "publication": "Journal of Nematology", "volume": "14", "number": "2", "publisher": "Society of Nematologists", "pagerange": "240-248", "id_number": "CaltechAUTHORS:20190515-113500751", "issn": "0022-300X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190515-113500751", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "pmcid": "PMC2618157", "primary_object": { "basename": "240.pdf", "url": "https://authors.library.caltech.edu/records/6fhmq-e0x59/files/240.pdf" }, "resource_type": "article", "pub_year": "1982", "author_list": "Horvitz, H. Robert and Sternberg, Paul W." } ]