[ { "id": "https://authors.library.caltech.edu/records/p39kv-fgh08", "eprint_id": 122522, "eprint_status": "archive", "datestamp": "2023-08-20 16:55:23", "lastmod": "2023-12-22 23:39:19", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tran-Martin", "name": { "family": "Tran", "given": "Martin" }, "orcid": "0000-0001-9882-7230" }, { "id": "Askary-Amjad", "name": { "family": "Askary", "given": "Amjad" }, "orcid": "0000-0002-2913-8498" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Lineage motifs: developmental modules for control of cell type proportions", "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 Duncan Chadly, Ben Emert, Jacob Parres-Gold, Yodai Takei, and other members of the Elowitz lab for scientific input and feedback. We thank Mykel Barrett, Marianne Bronner, Rusty Lansford, Carlos Lois, Magda Zernicka-Goetz, and Meng Zhu for helpful discussion and feedback. This research was supported by Paul G. Allen Frontiers Group and Prime Awarding Agency under Award No. UWSC10142 and the National Institute of Health grant R01MH116508. M.T. was supported with funding from the Tianqiao and Chrissy Chen Institute for Neuroscience at Caltech and by the National Eye Institute of the National Institutes of Health under Award Number F31EY033220. A.A. was supported with funding from National Eye Institute of NIH under Award Number R00EY031782. M.B.E. is a Howard Hughes Medical Institute investigator. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. This article is subject to HHMI's Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author-accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication. \n\nAuthor contributions: Conceptualization, M.T., A.A., and M.B.E.; Methodology, M.T., A.A., and M.B.E.; Software, M.T. and A.A.; Formal Analysis, M.T. and A.A.; Writing \u2013 Original Draft, M.T.; Writing \u2013 Review & Editing, M.T., A.A., and M.B.E.; Visualization, M.T.; Supervision, A.A. and M.B.E.; Funding Acquisition, M.T., A.A., and M.B.E. \n\nThe authors declare no competing interests.\n\n
Submitted - 2023.06.06.543925v1.full.pdf
Supplemental Material - media-1.pdf
", "abstract": "In multicellular organisms, cell types must be produced and maintained in appropriate proportions. One way this is achieved is through committed progenitor cells that produce specific sets of descendant cell types. However, cell fate commitment is probabilistic in most contexts, making it difficult to infer progenitor states and understand how they establish overall cell type proportions. Here, we introduce Lineage Motif Analysis (LMA), a method that recursively identifies statistically overrepresented patterns of cell fates on lineage trees as potential signatures of committed progenitor states. Applying LMA to published datasets reveals spatial and temporal organization of cell fate commitment in zebrafish and rat retina and early mouse embryo development. Comparative analysis of vertebrate species suggests that lineage motifs facilitate adaptive evolutionary variation of retinal cell type proportions. LMA thus provides insight into complex developmental processes by decomposing them into simpler underlying modules.", "date": "2023-08-17", "date_type": "published", "id_number": "CaltechAUTHORS:20230725-706037000.28", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230725-706037000.28", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Paul G. Allen Frontiers Group", "grant_number": "UWSC10142" }, { "agency": "NIH", "grant_number": "R01MH116508" }, { "agency": "Tianqiao and Chrissy Chen Institute for Neuroscience" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "F31EY033220" }, { "agency": "NIH", "grant_number": "R00EY031782" }, { "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": "10.1101/2023.06.06.543925", "pmcid": "PMC10274800", "primary_object": { "basename": "media-1.pdf", "url": "https://authors.library.caltech.edu/records/p39kv-fgh08/files/media-1.pdf" }, "related_objects": [ { "basename": "2023.06.06.543925v1.full.pdf", "url": "https://authors.library.caltech.edu/records/p39kv-fgh08/files/2023.06.06.543925v1.full.pdf" } ], "resource_type": "monograph", "pub_year": "2023", "author_list": "Tran, Martin; Askary, Amjad; et el." }, { "id": "https://authors.library.caltech.edu/records/mt2za-c6023", "eprint_id": 120355, "eprint_status": "archive", "datestamp": "2023-08-20 08:27:24", "lastmod": "2024-01-19 20:40:21", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Granados-Alejandro-A", "name": { "family": "Granados", "given": "Alejandro A." }, "orcid": "0000-0002-6275-9800" }, { "id": "Kanrar-Nivedita", "name": { "family": "Kanrar", "given": "Nivedita" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Combinatorial expression motifs in signaling pathways", "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 would like to thank Heidi Klumpe, Rachael Kuintzle, Matthew Langley, James Linton, Benjamin Emert, Nicolas Pelaez-Restrapo, and other members of the Elowitz lab for suggestions and critical feedback on this work, as well as critical feedback from Matt Thomson, Kai Zinn, Yaron Antebi, and Miri Adler. This research was supported by the Allen Discovery Center program under Award No. UWSC10142, a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation, and by the National Institutes of Health grant R01 HD075335A. N.K. was supported in the summer of 2020 by the Samuel N. Vodopia and Carol J. Hasson SURF Endowment. \n\nThe authors have declared no competing interest.\n\nSubmitted - 2022.08.21.504714v1.full.pdf
", "abstract": "Cell-cell signaling pathways comprise sets of variant receptors that are expressed in different combinations in different cell types. This architecture allows one pathway to be used in a variety of configurations, which could provide distinct functional capabilities, such as responding to different ligand variants. While individual pathways have been well-studied, we have lacked a comprehensive understanding of what receptor combinations are expressed and how they are distributed across cell types. Here, combining data from multiple single-cell gene expression atlases, we analyzed the expression profiles of core signaling pathways, including TGF-\u03b2, Notch, Wnt, and Eph-ephrin, as well as non-signaling pathways. In many pathways, a limited set of receptor expression profiles are used recurrently in many distinct cell types. While some recurrent profiles are restricted to groups of closely related cells, others, which we term pathway expression motifs, reappear in distantly related cell types spanning diverse tissues and organs. Motif usage was generally uncorrelated between pathways, remained stable in a given cell type during aging, but could change in sudden punctuated transitions during development. These results suggest a mosaic view of pathway usage, in which the same core pathways can be active in many or most cell types, but operate in one of a handful of distinct modes.", "date": "2022-08-22", "date_type": "published", "id_number": "CaltechAUTHORS:20230322-368481000.42", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230322-368481000.42", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Paul G. Allen Frontiers Group", "grant_number": "UWSC10142" }, { "agency": "NIH", "grant_number": "R01 HD075335A" }, { "agency": "Caltech Summer Undergraduate Research Fellowship (SURF)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2022.08.21.504714", "primary_object": { "basename": "2022.08.21.504714v1.full.pdf", "url": "https://authors.library.caltech.edu/records/mt2za-c6023/files/2022.08.21.504714v1.full.pdf" }, "resource_type": "monograph", "pub_year": "2022", "author_list": "Granados, Alejandro A.; Kanrar, Nivedita; et el." }, { "id": "https://authors.library.caltech.edu/records/a7vwv-mhw66", "eprint_id": 115493, "eprint_status": "archive", "datestamp": "2023-08-20 08:11:15", "lastmod": "2023-12-13 16:49:17", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chen-Zibo", "name": { "family": "Chen", "given": "Zibo" }, "orcid": "0000-0003-2990-2895" }, { "id": "Linton-James-M", "name": { "family": "Linton", "given": "James M." } }, { "id": "Zhu-Ronghui", "name": { "family": "Zhu", "given": "Ronghui" }, "orcid": "0000-0001-8171-482X" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "A synthetic protein-level neural network in mammalian cells", "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 L. Chong, X. J. Gao, and U. Alon for scientific input; J. Gregrowicz, R. Du, B. Emert, B. Gu, F. Horns, D. Li, A. Lu, K. Luo, Y. Takei, and S. Xia for critical feedback. \n\nThis research was supported by the National Institute of Health grant R01 MH116508 and the Allen Discovery Center program under Award No. UWSC10142, a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation. M.B.E. is a Howard Hughes Medical Institute Investigator. Z.C. is supported by the Damon Runyon Cancer Research Foundation DRG-2388-20 and is a fellow of the Burroughs Wellcome Fund Career Awards at the Scientific Interface. \n\nAuthor contributions: Z.C. and M.B.E. conceived and designed the study; Z.C. performed mathematical modeling with help from R.Z. and M.B.E.; Z.C. and J.M.L. performed experiments; R.Z. constructed the reporter cell line; Z.C. and M.B.E. wrote the manuscript with input from all authors. \n\nData and materials availability: Raw data and code used for simulation and data analysis can be downloaded from https://data.caltech.edu/records/20215.\n\nCompeting Interest Statement. Z.C. and M.B.E. have filed a provisional patent application based on this work. \n\nThis article is subject to HHMI's Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author-accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication.\n\nSubmitted - 2022.07.10.499405v1.full.pdf
Supplemental Material - media-1.pdf
", "abstract": "Artificial neural networks provide a powerful paradigm for information processing that has transformed diverse fields. Within living cells, genetically encoded synthetic molecular networks could, in principle, harness principles of neural computation to classify molecular signals. Here, we combine de novo designed protein heterodimers and engineered viral proteases to implement a synthetic protein circuit that performs winner-take-all neural network computation. This \"perceptein\" circuit includes modules that compute weighted sums of input protein concentrations through reversible binding interactions, and allow for self-activation and mutual inhibition of protein components using irreversible proteolytic cleavage reactions. Altogether, these interactions comprise a network of 310 chemical reactions stemming from 8 expressed protein species. The complete system achieves signal classification with tunable decision boundaries in mammalian cells. These results demonstrate how engineered protein-based networks can enable programmable signal classification in living cells.", "date": "2022-07-13", "date_type": "published", "id_number": "CaltechAUTHORS:20220712-283791000", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220712-283791000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 MH116508" }, { "agency": "Paul G. Allen Frontiers Group", "grant_number": "UWSC10142" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Damon Runyon Cancer Research Foundation", "grant_number": "DRG-2388-20" }, { "agency": "Burroughs Wellcome Fund" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2022.07.10.499405", "primary_object": { "basename": "media-1.pdf", "url": "https://authors.library.caltech.edu/records/a7vwv-mhw66/files/media-1.pdf" }, "related_objects": [ { "basename": "2022.07.10.499405v1.full.pdf", "url": "https://authors.library.caltech.edu/records/a7vwv-mhw66/files/2022.07.10.499405v1.full.pdf" } ], "resource_type": "monograph", "pub_year": "2022", "author_list": "Chen, Zibo; Linton, James M.; et el." }, { "id": "https://authors.library.caltech.edu/records/ernz6-2xp43", "eprint_id": 114102, "eprint_status": "archive", "datestamp": "2023-08-20 07:20:40", "lastmod": "2023-12-13 16:49:21", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Sheng", "name": { "family": "Wang", "given": "Sheng" } }, { "id": "Garcia-Ojalvo", "name": { "family": "Garcia-Ojalvo", "given": "Jordi" }, "orcid": "0000-0002-3716-7520" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Periodic spatial patterning with a single morphogen", "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. \n\nThis version posted March 22, 2022. \n\nMBE is a Howard Hughes Medical Institute Investigator. This research was supported by the Allen Discovery Center program under Award No. UWSC10142, a Paul G. Allen Frontiers Group\nadvised program of the Paul G. Allen Family Foundation. \n\nJ.G.O. was supported by the Spanish Ministry of Science and Innovation and FEDER, under project PGC2018-101251-B-I00, by the \"Maria de Maeztu\" Programme for Units of Excellence in\nR&D (grant CEX2018-000792-M), and by the Generalitat de Catalunya (ICREA Academia programme). \n\nWe acknowledge insightful feedback from Elowitz lab members. The authors have declared that no competing interests exist. \n\nAuthor contributions: Conceptualization and Investigation: S.W., J.G-O, M.B.E.; Formal Analysis, Software, and Visualization: S.W.; Writing: S.W., J.G-O, M.B.E. \n\nCode reporting: Simulation code and data is accessible from CaltechDATA. Wang, S., Garc\u00eda-Ojalvo, J., & Elowitz, M. B. (2022). Periodic spatial patterning with a single morphogen (Version 1.0) [Data set]. CaltechDATA. https://doi.org/10.22002/D1.20060\n\nSubmitted - 2022.03.21.484932v1.full.pdf
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", "abstract": "Multicellular development employs periodic spatial patterning to generate repetitive structures such as digits, vertebrae, and teeth. Turing patterning has long provided a key paradigm for understanding such systems. The simplest Turing systems are believed to require at least two signals, or morphogens, that diffuse and react to spontaneously generate periodic patterns. Here, using mathematical modeling, we show that a minimal circuit comprising an intracellular positive feedback loop and a single diffusible morphogen is sufficient to generate stable, long-range spatially periodic cellular patterns. The model considers cells as discrete entities as a key feature, and incorporates transient boundary conditions. Linear stability analysis reveals that this single-morphogen Turing circuit can support a broad range of spatial wavelengths, including fine-grain patterns similar to those generated by classic lateral inhibition systems. Further, signals emanating from a boundary can initiate and stabilize propagating modes with a well-defined spatial wavelength. Once formed, patterns are self-sustaining and robust to noise. Finally, while noise can disrupt patterning in pre-patterned regions, its disruptive effect can be overcome by a bistable intracellular circuit loop, or by considering patterning in the context of growing tissue. Together, these results show that a single morphogen can be sufficient for robust spatial pattern formation, and should provide a foundation for engineering pattern formation in the emerging field of synthetic developmental biology.", "date": "2022-03-28", "date_type": "published", "id_number": "CaltechAUTHORS:20220328-182609385", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220328-182609385", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Paul G. Allen Frontiers Group", "grant_number": "UWSC10142" }, { "agency": "Paul G. Allen Family Foundation" }, { "agency": "Ministerio de Ciencia e Innovaci\u00f3n (MCINN)", "grant_number": "PGC2018-101251-B-I00" }, { "agency": "Fondo Europeo de Desarrollo Regional (FEDER)" }, { "agency": "Maria de Maeztu", "grant_number": "CEX2018-000792-M" }, { "agency": "Generalitat de Catalunya" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2022.03.21.484932", "primary_object": { "basename": "2022.03.21.484932v1.full.pdf", "url": "https://authors.library.caltech.edu/records/ernz6-2xp43/files/2022.03.21.484932v1.full.pdf" }, "related_objects": [ { "basename": "media-1.gif", "url": "https://authors.library.caltech.edu/records/ernz6-2xp43/files/media-1.gif" }, { "basename": "media-2.gif", "url": "https://authors.library.caltech.edu/records/ernz6-2xp43/files/media-2.gif" }, { "basename": "media-3.docx", "url": "https://authors.library.caltech.edu/records/ernz6-2xp43/files/media-3.docx" } ], "resource_type": "monograph", "pub_year": "2022", "author_list": "Wang, Sheng; Garcia-Ojalvo, Jordi; et el." }, { "id": "https://authors.library.caltech.edu/records/qz3hc-zsb05", "eprint_id": 111086, "eprint_status": "archive", "datestamp": "2023-08-22 11:17:21", "lastmod": "2023-12-13 16:49:30", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Xu-Shuhui", "name": { "family": "Xu", "given": "Shuhui" } }, { "id": "Li-Kai", "name": { "family": "Li", "given": "Kai" } }, { "id": "Ma-Liang", "name": { "family": "Ma", "given": "Liang" } }, { "id": "Zhang-Jianhan", "name": { "family": "Zhang", "given": "Jianhan" } }, { "id": "Yoon-Shinae", "name": { "family": "Yoon", "given": "Shinae" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Lin-Yihan", "name": { "family": "Lin", "given": "Yihan" }, "orcid": "0000-0002-2763-5538" } ] }, "title": "Ratiometric RNA labeling allows dynamic multiplexed analysis of gene circuits in single cells", "ispublished": "unpub", "full_text_status": "public", "keywords": "genetic circuit; gene regulatory network; temporal dynamics; multiplexing; transcriptional reporter; live-cell imaging; synthetic biology; transcriptional bursting", "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 September 23, 2021.\n\nY.L. acknowledges the supports from National Natural Science Foundation of China (Grant #\n31771425) and National Key R&D Program of China (Grant # 2020YFA0906900,\n2018YFA0900703). M.B.E. acknowledges the supports from National Science Foundation\n(Grant # 1547056; Grant # EF-2021552 under subaward UWSC10142). MBE is a Howard\nHughes Medical Institute Investigator. We thank the flow cytometry core at the National Center\nfor Protein Sciences at Peking University and the Quantitative Imaging facility at the Center\nfor Quantitative Biology at Peking University for equipment supports.\n\nData and code availability:\nThe data and code used in this paper can be downloaded from the following link:\nhttps://github.com/IndigoMad/Multiplexed-transcriptional-reporter.\n\nAuthor Contributions:\nY.L. and M.B.E. conceived the concept of the reporter; S.X., K.L. and L.M. performed the\nresearch; J.Z. and S.Y. contributed new reagents/analytic tools; S.X. K.L. and Y.L. wrote the\n\nCompeting Interest Statement:\nA patent application based on the developed technology was submitted in China.\n\nmanuscript with inputs from M.B.E.\n\nSubmitted - 2021.09.23.461487v1.full.pdf
", "abstract": "Biological processes are highly dynamic and are regulated by genes that connect with one and another, forming regulatory circuits and networks. Understanding how gene regulatory circuits operate dynamically requires monitoring the expression of multiple genes in the same cell. However, it is limited by the relatively few distinguishable fluorescent proteins. Here, we developed a multiplexed real-time transcriptional imaging method based on two RNA stem-loop binding proteins, and employed it to analyze the temporal dynamics of synthetic gene circuits. By incorporating different ratios of MS2 and PP7 stem-loops, we were able to monitor the real-time nascent transcriptional activities of up to five genes in the same cell using only two fluorescent proteins. Applying this multiplexing capability to synthetic linear or branched gene regulatory cascades revealed that propagation of transcriptional dynamics is enhanced by non-stationary dynamics and is dictated by the slowest regulatory branch in the presence of combinatorial regulation. Mathematical modeling provided further insight into temporal multi-gene interactions and helped to understand potential challenges in regulatory inference using snapshot single-cell data. Ratiometric multiplexing should scale exponentially with additional labelling channels, providing a way to track the dynamics of larger circuits.", "date": "2021-09-29", "date_type": "published", "id_number": "CaltechAUTHORS:20210929-151425994", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210929-151425994", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Natural Science Foundation of China", "grant_number": "31771425" }, { "agency": "National Key Research and Development Program of China", "grant_number": "2020YFA0906900" }, { "agency": "National Key Research and Development Program of China", "grant_number": "2018YFA0900703" }, { "agency": "NSF", "grant_number": "MCB-1547056" }, { "agency": "NSF", "grant_number": "EF-2021552" }, { "agency": "Paul G. Allen Frontiers Group", "grant_number": "UWSC10142" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2021.09.23.461487", "primary_object": { "basename": "2021.09.23.461487v1.full.pdf", "url": "https://authors.library.caltech.edu/records/qz3hc-zsb05/files/2021.09.23.461487v1.full.pdf" }, "resource_type": "monograph", "pub_year": "2021", "author_list": "Xu, Shuhui; Li, Kai; et el." }, { "id": "https://authors.library.caltech.edu/records/2z0dm-q9917", "eprint_id": 106792, "eprint_status": "archive", "datestamp": "2023-10-03 22:33:52", "lastmod": "2023-12-22 23:42:41", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Flynn-Michael-J", "name": { "family": "Flynn", "given": "Michael J." } }, { "id": "Snitser-Olga", "name": { "family": "Snitser", "given": "Olga" } }, { "id": "Flynn-James", "name": { "family": "Flynn", "given": "James" } }, { "id": "Green-Samantha", "name": { "family": "Green", "given": "Samantha" } }, { "id": "Yelin-Idan", "name": { "family": "Yelin", "given": "Idan" }, "orcid": "0000-0003-2515-4113" }, { "id": "Szwarcwort-Cohen-Moran", "name": { "family": "Szwarcwort-Cohen", "given": "Moran" } }, { "id": "Kishony-Roy", "name": { "family": "Kishony", "given": "Roy" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "A simple direct RT-LAMP SARS-CoV-2 saliva diagnostic", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. \n\nThis version posted November 22, 2020. \n\nThis project was supported by the Caltech Merkin Institute for Translational Research and the Israel Science Foundation (grant No. 3633/19) within the KillCorona Curbing Coronavirus Research Program. James Flynn provided his own funds to conduct the study at Catholic Medical Center. \n\nData Availability: All data from this study can be obtained by emailing the first author. \n\nThe authors have declared no competing interest. \n\nAuthor Declarations: \nI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. \n\nYes. \n\nThe details of the IRB/oversight body that provided approval or exemption for the research described are given below: \n\nThe IRB of the Technion at Israel Institute of Technology gave approval for Olga Snitser to collect anonymized SARS-CoV-2 swab samples and assay them with RT-qPCR and the RT-LAMP protocol developed in this paper. The IRB of Catholic Medical Center in Manchester, New Hampshire gave approval for James Flynn to collect patient saliva samples and assay them with the RT-LAMP diagnostic developed in this paper. \n\nAll necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. \n\nYes. \n\nI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). \n\nYes. \n\nI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. \n\nYes.\n\nSubmitted - 20201119-20234948v1full.pdf
", "abstract": "Widespread, frequent testing is essential for curbing the ongoing COVID-19 pandemic. Because its simplicity makes it ideal for widely distributed, high throughput testing, RT-LAMP provides an attractive alternative to RT-qPCR. However, most RT-LAMP protocols require the purification of RNA, a complex and low-throughput bottleneck that has often been subject to reagent supply shortages. Here, we report an optimized RT-LAMP-based SARS-CoV-2 diagnostic protocol for saliva and swab samples. In the protocol we replace RNA purification with a simple sample preparation step using a widely available chelating agent, as well as optimize key protocol parameters. When tested on clinical swab and saliva samples, this assay achieves a limit of detection of 105 viral genomes per ml, with sensitivity close to 90% and specificity close to 100%, and takes 45 minutes from sample collection to result, making it well suited for a COVID-19 surveillance program.", "date": "2020-11-23", "date_type": "published", "id_number": "CaltechAUTHORS:20201123-140413855", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201123-140413855", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "Israel Science Foundation", "grant_number": "3633/19" }, { "agency": "James Flynn" } ] }, "local_group": { "items": [ { "id": "Richard-Merkin-Institute" }, { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2020.11.19.20234948", "primary_object": { "basename": "20201119-20234948v1full.pdf", "url": "https://authors.library.caltech.edu/records/2z0dm-q9917/files/20201119-20234948v1full.pdf" }, "resource_type": "monograph", "pub_year": "2020", "author_list": "Flynn, Michael J.; Snitser, Olga; et el." }, { "id": "https://authors.library.caltech.edu/records/425pg-3wb39", "eprint_id": 103580, "eprint_status": "archive", "datestamp": "2023-09-15 06:35:18", "lastmod": "2023-12-13 16:49:34", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ding-Fangyuan", "name": { "family": "Ding", "given": "Fangyuan" }, "orcid": "0000-0003-0118-5441" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Quantitative single-cell splicing analysis reveals an 'economy of scale' filter for gene expression", "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 October 30, 2018. \n\nThe work was funded by a Fellowship from the Schlumberger Foundation, by the Gordon and Betty Moore Foundation through Grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative and the Institute for Collaborative Biotechnologies through grant W911NF-09-0001 from the U.S. Army Research Office. The content of the information does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred. M.B.E. is a Howard Hughes Medical Institute Investigator.\n\nSubmitted - 457432v1.full.pdf
Supplemental Material - 457432-1.pdf
", "abstract": "In eukaryotic cells, splicing affects the fate of each pre-mRNA transcript, helping to determine whether it is ultimately processed into an mRNA, or degraded. The efficiency of splicing plays a key role in gene expression. However, because it depends on the levels of multiple isoforms at the same transcriptional active site (TAS) in the same cell, splicing efficiency has been challenging to measure. Here, we introduce a quantitative single-molecule FISH-based method that enables determination of the absolute abundances of distinct RNA isoforms at individual TASs. Using this method, we discovered that splicing efficiency behaves in an unexpected 'economy of scale' manner, increasing, rather than decreasing, with gene expression levels, opposite to a standard enzymatic process. This behavior could result from an observed correlation between splicing efficiency and spatial proximity to nuclear speckles. Economy of scale splicing represents a non-linear filter that amplifies the expression of genes when they are more strongly transcribed. This method will help to reveal the roles of splicing in the quantitative control of gene expression.", "date": "2020-06-01", "date_type": "published", "id_number": "CaltechAUTHORS:20200601-094106134", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200601-094106134", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Schlumberger Foundation" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-09-0001" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/457432", "primary_object": { "basename": "457432-1.pdf", "url": "https://authors.library.caltech.edu/records/425pg-3wb39/files/457432-1.pdf" }, "related_objects": [ { "basename": "457432v1.full.pdf", "url": "https://authors.library.caltech.edu/records/425pg-3wb39/files/457432v1.full.pdf" } ], "resource_type": "monograph", "pub_year": "2020", "author_list": "Ding, Fangyuan and Elowitz, Michael B." }, { "id": "https://authors.library.caltech.edu/records/91hvf-49c47", "eprint_id": 103534, "eprint_status": "archive", "datestamp": "2023-08-19 21:32:45", "lastmod": "2023-12-13 16:49:06", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gao-Xiaojing-J", "name": { "family": "Gao", "given": "Xiaojing J." }, "orcid": "0000-0002-3094-1456" }, { "id": "Chong-Lucy-S", "name": { "family": "Chong", "given": "Lucy S." }, "orcid": "0000-0002-5858-9984" }, { "id": "Ince-M-H", "name": { "family": "Ince", "given": "Michaela H." }, "orcid": "0000-0002-8997-3188" }, { "id": "Kim-M-S", "name": { "family": "Kim", "given": "Matthew S." }, "orcid": "0000-0002-5836-8874" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Engineering multiple levels of specificity in an RNA viral vector", "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 May 27, 2020. \n\nWe thank J. Ruan and A. Erskine for technical assistance; R. Zhu, Z. Singer, H. McBride, and L. Luo for critical feedback. \n\nThe research was funded by DARPA (HR0011-17-2-0008, M.B.E.), the Gordon and Betty Moore Foundation (GMBF2809, M.B.E.), NIH (T32 GM07616, L.S.C., 1K99EB027723-01, X.J.G.), National Science Foundation Graduate Research Fellowship Program (DGE-1745301 ,L.S.C) and the Helen Hay Whitney Foundation (F1047, X.J.G.). M.B.E is a Howard Hughes Medical Institute investigator. \n\nAuthor contributions: X.J.G. and L.S.C. conceived of the project. X.J.G., L.S.C., M.S.K., and M.B.E. designed experiments. X.J.G., L.S.C., M.H.I. and M.S.K. performed experiments. X.J.G., L.S.C. and M.B.E. analyzed data. X.J.G., L.S.C., and M.B.E. wrote the manuscript, with input\nfrom all authors. \n\nCompeting interests: X.J.G, L.S.C., M.S.K., and M.B.E. are inventors on a U.S. patent provisional application related to this work. \n\nData and materials availability: All DNA constructs will be available from Addgene, and cell lines are available from M.B.E. under a material transfer agreement with Caltech. The datasets generated and analyzed and the computer code used during the current study are available at data.caltech.edu, DOI 10.22002/D1.1438 . Flow cytometry data analysis software used for this study is available at https://antebilab.github.io/easyflow/.\n\nSubmitted - 2020.05.27.119909v1.full.pdf
Supplemental Material - media-1.xlsx
Supplemental Material - media-2.mov
Supplemental Material - media-3.mov
Supplemental Material - media-4.pdf
", "abstract": "Synthetic molecular circuits could provide powerful therapeutic capabilities, but delivering them to specific cell types and controlling them remains challenging. An ideal \"smart\" viral delivery system would enable controlled release of viral vectors from \"sender\" cells, conditional entry into target cells based on cell-surface proteins, conditional replication specifically in target cells based on their intracellular protein content, and an evolutionarily robust system that allows viral elimination with drugs. Here, combining diverse technologies and components, including pseudotyping, engineered bridge proteins, degrons, and proteases, we demonstrate each of these control modes in a model system based on the rabies virus. This work shows how viral and protein engineering can enable delivery systems with multiple levels of control to maximize therapeutic specificity.", "date": "2020-05-29", "date_type": "published", "publisher": "Caltech Library", "id_number": "CaltechAUTHORS:20200529-070622811", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200529-070622811", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Defense Advanced Research Projects Agency (DARPA)", "grant_number": "HR0011-17-2-0008" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GMBF2809" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 GM07616" }, { "agency": "NIH", "grant_number": "1K99EB027723-01" }, { "agency": "NSF Graduate Research Fellowship", "grant_number": "DGE-1745301" }, { "agency": "Helen Hay Whitney Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "primary_object": { "basename": "media-3.mov", "url": "https://authors.library.caltech.edu/records/91hvf-49c47/files/media-3.mov" }, "related_objects": [ { "basename": "media-4.pdf", "url": "https://authors.library.caltech.edu/records/91hvf-49c47/files/media-4.pdf" }, { "basename": "2020.05.27.119909v1.full.pdf", "url": "https://authors.library.caltech.edu/records/91hvf-49c47/files/2020.05.27.119909v1.full.pdf" }, { "basename": "media-1.xlsx", "url": "https://authors.library.caltech.edu/records/91hvf-49c47/files/media-1.xlsx" }, { "basename": "media-2.mov", "url": "https://authors.library.caltech.edu/records/91hvf-49c47/files/media-2.mov" } ], "resource_type": "monograph", "pub_year": "2020", "author_list": "Gao, Xiaojing J.; Chong, Lucy S.; et el." } ]