[ { "id": "https://authors.library.caltech.edu/records/y9p3r-dma37", "eprint_status": "archive", "datestamp": "2024-01-19 18:45:45", "lastmod": "2024-01-19 20:39:53", "type": "article", "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" }, "orcid": "0000-0003-0047-951X" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Combinatorial expression motifs in signaling pathways", "ispublished": "pub", "full_text_status": "public", "note": "
We would like to thank Benjamin Emert, Heidi Klumpe, Rachael Kuintzle, Matthew Langley, James Linton, Nicolas Pelaez-Restrapo, Judy Shon, and other members of the Elowitz lab for suggestions and critical feedback on this work, as well as critical feedback from Miri Adler, Yaron Antebi, Jialong Jiang, Matt Thomson, and Kai Zinn. 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 declare no competing interests.
\n\n\nIn animal cells, molecular pathways often comprise families of variant components, such as ligands or receptors. These pathway components are differentially expressed by different cell types, potentially tailoring pathway function to cell context. However, it has remained unclear how pathway expression profiles are distributed across cell types and whether similar profiles can occur in dissimilar cell types. Here, using single-cell gene expression datasets, we identified pathway expression motifs, defined as recurrent expression profiles that are broadly distributed across diverse cell types. Motifs appeared in core pathways, including TGF-β, Notch, Wnt, and the SRSF splice factors, and involved combinatorial co-expression of multiple components. Motif usage was weakly correlated between pathways in adult cell types and during dynamic developmental transitions. Together, these results suggest a mosaic view of cell type organization, in which different cell types operate many of the same pathways in distinct modes.
\n\u00a9 2022 The Authors. Published by American Chemical Society. This publication is licensed under CC-BY 4.0.
\n\nThis work is supported by the Defense Advanced Research Projects Agency under contract no. HR0011-17-2-0008, by the National Institutes of Health grant RO1 HD075605A, and by National Science Foundation grant EF-2021552 under subaward UWSC10142. M.B.E. is a Howard Hughes Medical Institute Investigator.
\n\nY.M.: conceptualization, formal analysis, investigation, and writing; J.Z.: formal analysis and investigation; M.W.B.: conceptualization, supervision, and funding; M.B.E: conceptualization, supervision, writing, and funding.
\n\nThe authors declare the following competing financial interest(s): M.W.B. is a founder and employee of Primordium Labs.
\n\nPlasmids and their maps available for requests at Addgene (addgene.org/browse/article/28233817/). The key cell lines are available upon request. EM-Seq raw and processed data is deposited at Gene Expression Omnibus (GSE224403). Data and codes for analysis and generating figures are available at data.caltech (doi: 10.22002/ct5kt-cv878).
", "abstract": "Methylation of cytosines in CG dinucleotides (CpGs) within promoters has been shown to lead to gene silencing in mammals in natural contexts. Recently, engineered recruitment of methyltransferases (DNMTs) at specific loci was shown to be sufficient to silence synthetic and endogenous gene expression through this mechanism. A critical parameter for DNA methylation-based silencing is the distribution of CpGs within the target promoter. However, how the number or density of CpGs in the target promoter affects the dynamics of silencing by DNMT recruitment has remained unclear. Here, we constructed a library of promoters with systematically varying CpG content, and analyzed the rate of silencing in response to recruitment of DNMT. We observed a tight correlation between silencing rate and CpG content. Further, methylation-specific analysis revealed a constant accumulation rate of methylation at the promoter after DNMT recruitment. We identified a single CpG site between TATA box and transcription start site (TSS) that accounted for a substantial part of the difference in silencing rates between promoters with differing CpG content, indicating that certain residues play disproportionate roles in controlling silencing. Together, these results provide a library of promoters for synthetic epigenetic and gene regulation applications, as well as insights into the regulatory link between CpG content and silencing rate.
", "date": "2023-09-15", "date_type": "published", "publication": "ACS Synthetic Biology", "volume": "12", "number": "9", "publisher": "American Chemical Society", "pagerange": "2536-2545", "issn": "2161-5063", "official_url": "https://authors.library.caltech.edu/records/42eqy-fkv91", "funders": { "items": [ { "agency": "Defense Advanced Research Projects Agency", "grant_number": "HR0011-17-2-0008" }, { "agency": "National Institutes of Health", "grant_number": "RO1 HD075605A" }, { "agency": "National Science Foundation", "grant_number": "EF-2021552" }, { "agency": "National Science Foundation", "grant_number": "UWSC10142" }, {} ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1021/acssynbio.3c00078", "pmcid": "PMC10510725", "primary_object": { "basename": "acssynbio.3c00078.pdf", "url": "https://authors.library.caltech.edu/records/42eqy-fkv91/files/acssynbio.3c00078.pdf" }, "related_objects": [ { "basename": "sb3c00078_si_001.pdf", "url": "https://authors.library.caltech.edu/records/42eqy-fkv91/files/sb3c00078_si_001.pdf" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Ma, Yitong; Budde, Mark W.; et el." }, { "id": "https://authors.library.caltech.edu/records/5wh3x-cj477", "eprint_status": "archive", "datestamp": "2023-10-02 21:51:45", "lastmod": "2024-01-09 22:19:46", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Horns-Felix", "name": { "family": "Horns", "given": "Felix" }, "orcid": "0000-0001-5872-5061" }, { "id": "Martniez-Joe-A", "name": { "family": "Martinez", "given": "Joe A." } }, { "id": "Fan-Chengcheng", "name": { "family": "Fan", "given": "Chengcheng" }, "orcid": "0000-0003-4213-5758" }, { "id": "Haque-Mehernaz", "name": { "family": "Haque", "given": "Mehernaz" } }, { "id": "Linton-James-M", "name": { "family": "Linton", "given": "James M." } }, { "id": "Tobin-Victoria-R", "name": { "family": "Tobin", "given": "Victoria" }, "orcid": "0000-0002-2195-639X" }, { "id": "Santat-Leah", "name": { "family": "Santat", "given": "Leah" }, "orcid": "0000-0003-0511-9740" }, { "id": "Maggiolo-Ailiena-O", "name": { "family": "Maggiolo", "given": "Ailiena O." }, "orcid": "0000-0003-1707-5060" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "id": "Lois-Carlos", "name": { "family": "Lois", "given": "Carlos" }, "orcid": "0000-0002-7305-2317" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Engineering RNA export for measurement and manipulation of living cells", "ispublished": "pub", "full_text_status": "public", "keywords": "General Biochemistry, Genetics and Molecular Biology", "note": "We thank M. Blanco, M. Guttman, J. Keeffe, Y. Garcia-Flores, S. Mazmanian, and S. Chen for access to equipment; A. Hori for sharing cells; H. Larsen for mRNA production; I.M. Strazhnik for illustrations; D. Chadly, M. Tran, B. Emert, A. Askary, and R. Zhu for scientific input; and S. Xia, R. Du, D. Li, and M. Sui for critical feedback. Electron microscopy was performed in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. Sequencing was performed at the Single-Cell Profiling Center in the Beckman Institute at Caltech. The research was supported by the National Institutes of Health R01MH116508 (to M.B.E.), the Allen Discovery Center, a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation (award number UWSC10142 to M.B.E.), and the National Institute of Biomedical Imaging and Bioengineering of the National Institutes of Health R01EB030015 (to M.B.E.). M.B.E. is a Howard Hughes Medical Institute investigator. F.H. is a Howard Hughes Medical Institute Fellow of the Helen Hay Whitney Foundation.
\n\nF.H. conceived of RNA export and its use for reporting. F.H. and M.B.E. conceived of cell-based RNA delivery. F.H., J.A.M., V.T., C.L., and M.B.E. designed experiments. F.H., J.A.M., C.F., M.H., J.M.L., V.T., L.S., and C.L. performed experiments. F.H., J.A.M., A.O.M., and M.B.E. analyzed data. P.J.B. provided instrumentation and support. F.H. and M.B.E. wrote the manuscript, with input from all authors.
\n\nPatent applications have been filed by the California Institute of Technology related to this work (US application numbers 17/820,232 and 17/820,235). M.B.E. is a scientific advisory board member or consultant at TeraCyte, Primordium, and Spatial Genomics
\n\n\u00a9 2023 The Authors. Published by Elsevier Under a Creative Commons license - Attribution 4.0 International (CC BY 4.0)
", "abstract": "A system for programmable export of RNA molecules from living cells would enable both non-destructive monitoring of cell dynamics and engineering of cells capable of delivering executable RNA programs to other cells. We developed genetically encoded cellular RNA exporters, inspired by viruses, that efficiently and selectively package and secrete target RNA molecules from mammalian cells within protective nanoparticles. Exporting and sequencing RNA barcodes enabled non-destructive monitoring of cell population dynamics with clonal resolution. Further, by incorporating fusogens into the nanoparticles, we demonstrated delivery, expression, and functional activity of exported mRNA in recipient cells. We term these systems COURIER (Controlled Output and Uptake of RNA for Interrogation, Expression, and Regulation). COURIER enables measurement of cell dynamics and establishes a foundation for hybrid cell and gene therapies based on cell-to-cell delivery of RNA.
", "date": "2023-08-17", "date_type": "published", "publication": "Cell", "volume": "186", "number": "17", "publisher": "Cell Press", "pagerange": "3642-3658.e32", "issn": "0092-8674", "official_url": "https://authors.library.caltech.edu/records/5wh3x-cj477", "funders": { "items": [ { "agency": "National Institutes of Health", "grant_number": "R01MH116508" }, { "agency": "Allen Discovery Center", "grant_number": "UWSC10142" }, { "agency": "National Institute of Biomedical Imaging and Bioengineering", "grant_number": "R01EB030015" }, {}, {} ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.cell.2023.06.013", "pmcid": "PMC10528933", "primary_object": { "basename": "1-s2.0-S009286742300689X-main.pdf", "url": "https://authors.library.caltech.edu/records/5wh3x-cj477/files/1-s2.0-S009286742300689X-main.pdf" }, "resource_type": "article", "pub_year": "2023", "author_list": "Horns, Felix; Martinez, Joe A.; et el." }, { "id": "https://authors.library.caltech.edu/records/hj8zd-08q75", "eprint_status": "archive", "datestamp": "2023-10-20 15:52:18", "lastmod": "2024-01-09 22:19:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhu-Ronghui", "name": { "family": "Zhu", "given": "Ronghui" }, "orcid": "0000-0001-8171-482X" }, { "id": "Santat-Leah-A", "name": { "family": "Santat", "given": "Leah A." }, "orcid": "0000-0003-0511-9740" }, { "id": "Markson-Joseph-S", "name": { "family": "Markson", "given": "Joseph S." }, "orcid": "0000-0002-3167-3887" }, { "id": "Nandagopal-Nagarajan", "name": { "family": "Nandagopal", "given": "Nagarajan" }, "orcid": "0000-0002-0469-6549" }, { "id": "Gregrowicz-Jan", "name": { "family": "Gregrowicz", "given": "Jan" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Reconstitution of morphogen shuttling circuits", "ispublished": "pub", "full_text_status": "public", "keywords": "Multidisciplinary", "note": "\u00a9 2023 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\nWe thank P. Li and S. Wang for sharing sequential plating protocol and codes for analyzing gradients, as well as for many suggestions on the project; H. Klumpe for sharing the BMP receiver cell line; F. Ding, E. Hui and A. Curtis for scientific inputs on the projects; N. Barkai, U. Alon, A. Eldar, J. Briscoe, B. Shilo, D. Sprinzak, A. McMahon, and M. Wilson for insights and discussions; J. Bois for teaching and sharing Caltech BE150 course materials for mathematical modeling; Z. Chen, J. M. Linton., Y. Takei, D. Li, B. Gu., and D. M. Chadly for critical feedback on the manuscript; and other members of the Elowitz laboratory for scientific input and support. J.S.M. was affiliated with California Institute of Technology at the time of this study and is currently affiliated with Novo Ventures. N.N. was affiliated with California Institute of Technology at the time of this study and is currently affiliated with the Department of Systems Biology, Harvard Medical School. R.Z. was affiliated with California Institute of Technology at the time of this study and is currently affiliated with Gladstone-UCSF Institute of Genomic Immunology and Department of Genetics, Stanford University. M.B.E. is a Howard Hughes Medical Institute investigator.
\n\nThis work was supported by the NSF (EFRI 1137269) 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. This work was also supported by the National Institute of Arthritis and Musculoskeletal and Skin Diseases of the NIH under award number F32AR067103 (to J.S.M.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH; N.N. was a Howard Hughes Medical Institute International Student Research fellow; J.G. was supported by the Boehringer Ingelheim Fonds PhD fellowship. This article is subject to HHMI's Open Access to Publication policy. HHMI laboratory 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\nR.Z., J.S.M., N.N., and M.B.E. conceived the project. R.Z., L.A.S., J.S.M., N.N., J.G., and M.B.E. designed the experiments. R.Z., L.A.S., J.S.M., N.N., and J.G. performed the experiments. R.Z., L.A.S., J.S.M., N.N., J.G., and M.B.E. analyzed data. R.Z., J.S.M., and M.B.E. did mathematical modeling. R.Z., L.A.S., and M.B.E. wrote the manuscript with input from all authors.
\n\nAll DNA constructs (table S2) and cell lines (table S3) are available from M.B.E. or through the Addgene repository under a material transfer agreement with California Institute of Technology. All data generated and all the computational and data analysis and modeling codes used in the current study are available at data.caltech.edu/records/0sdrn-73r13. All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials.
\n\nThe authors declare that they have no competing interests.
", "abstract": "Developing tissues form spatial patterns by establishing concentration gradients of diffusible signaling proteins called morphogens. The bone morphogenetic protein (BMP) morphogen pathway uses a family of extracellular modulators to reshape signaling gradients by actively \"shuttling\" ligands to different locations. It has remained unclear what circuits are sufficient to enable shuttling, what other patterns they can generate, and whether shuttling is evolutionarily conserved. Here, using a synthetic, bottom-up approach, we compared the spatiotemporal dynamics of different extracellular circuits. Three proteins\u2014Chordin, Twsg, and the BMP-1 protease\u2014successfully displaced gradients by shuttling ligands away from the site of production. A mathematical model explained the different spatial dynamics of this and other circuits. Last, combining mammalian and\n Drosophila\n components in the same system suggests that shuttling is a conserved capability. Together, these results reveal principles through which extracellular circuits control the spatiotemporal dynamics of morphogen signaling.", "date": "2023-07-14", "date_type": "published", "publication": "Science Advances", "volume": "9", "number": "28", "publisher": "American Association for the Advancement of Science", "pagerange": "eadf9336", "issn": "2375-2548", "official_url": "https://authors.library.caltech.edu/records/hj8zd-08q75", "funders": { "items": [ { "grant_number": "EFMA-1137269" }, { "grant_number": "W911NF-09-0001" }, { "grant_number": "F32AR067103" }, {}, {} ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1126/sciadv.adf9336", "pmcid": "PMC10337948", "primary_object": { "basename": "sciadv.adf9336.pdf", "url": "https://authors.library.caltech.edu/records/hj8zd-08q75/files/sciadv.adf9336.pdf" }, "related_objects": [ { "basename": "sciadv.adf9336_movies_s1_to_s8.zip", "url": "https://authors.library.caltech.edu/records/hj8zd-08q75/files/sciadv.adf9336_movies_s1_to_s8.zip" }, { "basename": "sciadv.adf9336_sm.pdf", "url": "https://authors.library.caltech.edu/records/hj8zd-08q75/files/sciadv.adf9336_sm.pdf" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Zhu, Ronghui; Santat, Leah A.; et el." }, { "id": "https://authors.library.caltech.edu/records/1nbj8-kzc90", "eprint_id": 121787, "eprint_status": "archive", "datestamp": "2023-08-22 20:46:04", "lastmod": "2023-12-22 23:20:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kong-Qing", "name": { "family": "Kong", "given": "Qing" }, "orcid": "0000-0002-3902-243X" }, { "id": "Xia-Shiyu", "name": { "family": "Xia", "given": "Shiyu" }, "orcid": "0000-0001-9024-0689" }, { "id": "Pan-Xingxin", "name": { "family": "Pan", "given": "Xingxin" }, "orcid": "0000-0002-4429-4878" }, { "id": "Ye-Kaixiong", "name": { "family": "Ye", "given": "Kaixiong" }, "orcid": "0000-0003-4658-7292" }, { "id": "Li-Zhouyihan", "name": { "family": "Li", "given": "Zhouyihan" }, "orcid": "0000-0002-9307-0096" }, { "id": "Li-Haoyan", "name": { "family": "Li", "given": "Haoyan" }, "orcid": "0000-0002-6786-0705" }, { "id": "Tang-Xiaoqiang", "name": { "family": "Tang", "given": "Xiaoqiang" }, "orcid": "0000-0002-3434-267X" }, { "id": "Sahni-Nidhi", "name": { "family": "Sahni", "given": "Nidhi" }, "orcid": "0000-0002-9155-5882" }, { "id": "Yi-S-Stephen", "name": { "family": "Yi", "given": "S. Stephen" }, "orcid": "0000-0003-0047-8103" }, { "id": "Liu-Xing", "name": { "family": "Liu", "given": "Xing" }, "orcid": "0000-0002-6277-3856" }, { "id": "Wu-Hao", "name": { "family": "Wu", "given": "Hao" }, "orcid": "0000-0002-7281-8579" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Lieberman-Judy", "name": { "family": "Lieberman", "given": "Judy" }, "orcid": "0000-0002-6200-4715" }, { "id": "Zhang-Zhibin", "name": { "family": "Zhang", "given": "Zhibin" }, "orcid": "0000-0003-1349-2713" } ] }, "title": "Alternative splicing of GSDMB modulates killer lymphocyte-triggered pyroptosis", "ispublished": "pub", "full_text_status": "public", "keywords": "General Medicine; Immunology", "note": "\u00a9 2023 The Authors, some rights reserved; exclusive licensee\nAmerican Association for the Advancement of Science. No claim to original U.S. Government Works. \n\nWe thank MD Anderson Sequencing and Microarray Facility (SMF) for Sanger sequencing. We thank X. Ma at Boston Children's Hospital, S. Gu at MD Anderson Cancer Center, and J. Ruan at University of Connecticut Health Center for helpful discussion. \n\nThis study was supported by the University of Texas Rising STARs Award and Elsa U. Pardee Research Grant to Z.Z.; National Institutes of Health grant R01CA240955 to J.L.; Howard Hughes Medical Institute funding, National Institutes of Health grant R01EB030015, and Rothenberg Innovation Initiative (RI2) at Caltech grant 25570017 to M.B.E.; National Institutes of Health grant R01AI139914 to H.W.; Ovarian Cancer Research Alliance Early Career Investigator Grant 649968 and Department of Defense grant W81XWH-18-PRCRP-CDA CA181455 to N.S.; National Institutes of Health grant R35GM133658, Komen Foundation grant CCR19609287, and the 2022\u20132023 program in Oncological Data and Computational Sciences sponsored by the Joint Center for Computational Oncology between the Oden Institute, MD Anderson, and TACC to S.S.Y.; postdoctoral fellowship from Jane Coffin Childs Memorial Fund for Medical Research to S.X.; and National Institutes of Health grant P30CA016672 to MD Anderson SMF. \n\nAuthor contributions: Q.K. and Z.Z. conceived the study. Z.Z., Q.K., and S.X. designed experiments and analyzed data. Q.K. performed most of the experiments with the assistance of Z.L., H.L., and X.T. S.X. performed structure analysis and modeling. X.P., N.S., and S.S.Y. performed bioinformatics analysis on tumor patient samples. K.Y. performed SNP genome-wide association studies analysis. J.L., X.L., S.X., M.B.E., and H.W. provided valuable editing and comments. Z.Z., Q.K., J.L., and S.X. wrote the manuscript. \n\nThe authors declare that they have no competing interests. \n\nData and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper or the Supplementary Materials.\n\nAccepted Version - nihms-1914945.pdf
Supplemental Material - sciimmunol.adg3196_data_file_s1.zip
Supplemental Material - sciimmunol.adg3196_mdar_reproducibility_checklist.pdf
Supplemental Material - sciimmunol.adg3196_sm.pdf
", "abstract": "Granzyme A from killer lymphocytes cleaves gasdermin B (GSDMB) and triggers pyroptosis in targeted human tumor cells, eliciting antitumor immunity. However, GSDMB has a controversial role in pyroptosis and has been linked to both anti- and protumor functions. Here, we found that GSDMB splicing variants are functionally distinct. Cleaved N-terminal (NT) fragments of GSDMB isoforms 3 and 4 caused pyroptosis, but isoforms 1, 2, and 5 did not. The nonfunctional isoforms have a deleted or modified exon 6 and therefore lack a stable belt motif. The belt likely contributes to the insertion of oligomeric GSDMB-NTs into the membrane. Consistently, noncytotoxic GSDMB-NTs blocked pyroptosis caused by cytotoxic GSDMB-NTs in a dominant-negative manner. Upon natural killer (NK) cell attack, GSDMB3-expressing cells died by pyroptosis, whereas GSDMB4-expressing cells died by mixed pyroptosis and apoptosis, and GSDMB1/2-expressing cells died only by apoptosis. GSDMB4 partially resisted NK cell-triggered cleavage, suggesting that only GSDMB3 is fully functional. GSDMB1-3 were the most abundant isoforms in the tested tumor cell lines and were similarly induced by interferon-\u03b3 and the chemotherapy drug methotrexate. Expression of cytotoxic GSDMB3/4 isoforms, but not GSDMB1/2 isoforms that are frequently up-regulated in tumors, was associated with better outcomes in bladder and cervical cancers, suggesting that GSDMB3/4-mediated pyroptosis was protective in those tumors. Our study indicates that tumors may block and evade killer cell-triggered pyroptosis by generating noncytotoxic GSDMB isoforms. Therefore, therapeutics that favor the production of cytotoxic GSDMB isoforms by alternative splicing may improve antitumor immunity.", "date": "2023-04-28", "date_type": "published", "publication": "Science Immunology", "volume": "8", "number": "82", "publisher": "American Association for the Advancement of Science", "pagerange": "Art. No. eadg3196", "id_number": "CaltechAUTHORS:20230613-730735700.10", "issn": "2470-9468", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230613-730735700.10", "funders": { "items": [ { "agency": "University of Texas" }, { "agency": "NIH", "grant_number": "R01CA240955" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "R01EB030015" }, { "agency": "Rothenberg Innovation Initiative (RI2)", "grant_number": "25570017" }, { "agency": "NIH", "grant_number": "R01AI139914" }, { "agency": "Ovarian Cancer Research Alliance", "grant_number": "649968" }, { "agency": "Department of Defense", "grant_number": "W81XWH-18-PRCRP-CDA CA181455" }, { "agency": "NIH", "grant_number": "R35GM133658" }, { "agency": "Komen Foundation", "grant_number": "CCR19609287" }, { "agency": "Joint Center for Computational Oncology" }, { "agency": "Jane Coffin Childs Memorial Fund for Medical Research" }, { "agency": "NIH", "grant_number": "P30CA016672" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1126/sciimmunol.adg3196", "pmcid": "PMC10338320", "primary_object": { "basename": "nihms-1914945.pdf", "url": "https://authors.library.caltech.edu/records/1nbj8-kzc90/files/nihms-1914945.pdf" }, "related_objects": [ { "basename": "sciimmunol.adg3196_data_file_s1.zip", "url": "https://authors.library.caltech.edu/records/1nbj8-kzc90/files/sciimmunol.adg3196_data_file_s1.zip" }, { "basename": "sciimmunol.adg3196_mdar_reproducibility_checklist.pdf", "url": "https://authors.library.caltech.edu/records/1nbj8-kzc90/files/sciimmunol.adg3196_mdar_reproducibility_checklist.pdf" }, { "basename": "sciimmunol.adg3196_sm.pdf", "url": "https://authors.library.caltech.edu/records/1nbj8-kzc90/files/sciimmunol.adg3196_sm.pdf" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Kong, Qing; Xia, Shiyu; et el." }, { "id": "https://authors.library.caltech.edu/records/cm1xz-hrt65", "eprint_id": 119035, "eprint_status": "archive", "datestamp": "2023-08-22 18:31:16", "lastmod": "2023-12-13 16:49:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cabrera-Alan", "name": { "family": "Cabrera", "given": "Alan" }, "orcid": "0000-0002-2546-0260" }, { "name": { "family": "Edelstein", "given": "Hailey I." }, "orcid": "0000-0002-8077-5492" }, { "name": { "family": "Glykofrydis", "given": "Fokion" }, "orcid": "0000-0002-0865-4573" }, { "name": { "family": "Love", "given": "Kasey S." }, "orcid": "0000-0001-7544-0340" }, { "name": { "family": "Palacios", "given": "Sebastian" } }, { "name": { "family": "Tycko", "given": "Josh" }, "orcid": "0000-0002-4108-0575" }, { "name": { "family": "Zhang", "given": "Meng" }, "orcid": "0000-0002-4076-6276" }, { "name": { "family": "Lensch", "given": "Sarah" }, "orcid": "0000-0003-1450-3242" }, { "name": { "family": "Shields", "given": "Cara E." }, "orcid": "0000-0002-3791-8259" }, { "name": { "family": "Livingston", "given": "Mark" } }, { "name": { "family": "Weiss", "given": "Ron" } }, { "name": { "family": "Zhao", "given": "Huimin" } }, { "name": { "family": "Haynes", "given": "Karmella A." }, "orcid": "0000-0002-5975-577X" }, { "name": { "family": "Morsut", "given": "Leonardo" }, "orcid": "0000-0001-7049-3478" }, { "name": { "family": "Chen", "given": "Yvonne Y." }, "orcid": "0000-0002-5583-119X" }, { "name": { "family": "Khalil", "given": "Ahmad S." }, "orcid": "0000-0002-8214-0546" }, { "name": { "family": "Wong", "given": "Wilson W." }, "orcid": "0000-0001-8394-889X" }, { "name": { "family": "Collins", "given": "James J." } }, { "name": { "family": "Rosser", "given": "Susan J." }, "orcid": "0000-0002-2560-6485" }, { "name": { "family": "Polizzi", "given": "Karen" }, "orcid": "0000-0001-5435-2667" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "name": { "family": "Fussenegger", "given": "Martin" }, "orcid": "0000-0001-8545-667X" }, { "name": { "family": "Hilton", "given": "Isaac B." }, "orcid": "0000-0002-3064-8532" }, { "name": { "family": "Leonard", "given": "Joshua N." }, "orcid": "0000-0003-4359-6126" }, { "name": { "family": "Bintu", "given": "Lacramioara" }, "orcid": "0000-0001-5443-6633" }, { "name": { "family": "Galloway", "given": "Kate E." }, "orcid": "0000-0001-7416-3193" }, { "name": { "family": "Deans", "given": "Tara L." }, "orcid": "0000-0002-2361-2195" } ] }, "title": "The sound of silence: Transgene silencing in mammalian cell engineering", "ispublished": "pub", "full_text_status": "public", "keywords": "Cell Biology; Histology; Pathology and Forensic Medicine", "note": "Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) \n\nFunding for this work was supported in part by the National Institutes of Health grants 1DP2CA250006-01 (T.L.D.), 1R01GM129011 (W.W.W.), R01EB029483 (W.W.W.), 1R01EB026510 (J.N.L.), R21EB030772 (I.B.H.), R35GM143532 (I.B.H.), R35GM143033 (K.E.G.), R35GM138256 (L.M.), 4K00DK126120-03 (J.T.), R01EB029483 (A.S.K.), R35GM128947 (L.B.), R01EB030946 (R.W.), R01EB025256 (R.W.), 1UM1HG009402 (H.Z.), U54DK107965 (H.Z.), R21CA232244 (K.A.H.), 1RC2DK120535-01A1 (J.J.C.), and 1U01 DK 127420-01 (M.B.E.), the National Science Foundation grants CBET-2034495 (L.M.), CBET-2145528 (L.M.), 2141064 (K.S.L.), EF-1921677 (A.S.K.), and EF-2021552 under subaward UWSC10142 (M.B.E.). Further support was also provided by the Biotechnology and Biological Sciences Research Council (BBSRC) BB/S006206/1 (K.P.) and BB/M018040/1 (S.J.R.), ElectroGene 785800 (M.F.), the SNF (M.F.), the Paul Allen Foundation (W.W.W.), AOFSR FA9550-22-1-0316 (K.E.G.), the Wellcome Sanger Institute LEAP 21-275 (L.M.), the Parker Institute for Cancer Immunotherapy (Y.Y.C.), the W.H. Coulter Department of Biomedical Engineering at Emory University (C.E.S.), and the DoD Vannevar Bush Faculty Fellowship N00014-20-1-2825 (A.S.K.). M.B.E. is a Howard Hughes Medical Institute investigator. The authors listed with equal contribution are listed in the author list in alphabetical order.", "abstract": "To elucidate principles operating in native biological systems and to develop novel biotechnologies, synthetic biology aims to build and integrate synthetic gene circuits within native transcriptional networks. The utility of synthetic gene circuits for cell engineering relies on the ability to control the expression of all constituent transgene components. Transgene silencing, defined as the loss of expression over time, persists as an obstacle for engineering primary cells and stem cells with transgenic cargos. In this review, we highlight the challenge that transgene silencing poses to the robust engineering of mammalian cells, outline potential molecular mechanisms of silencing, and present approaches for preventing transgene silencing. We conclude with a perspective identifying future research directions for improving the performance of synthetic gene circuits.", "date": "2022-12-21", "date_type": "published", "publisher": "Cell Press", "id_number": "CaltechAUTHORS:20230203-893712500.43", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230203-893712500.43", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.cels.2022.11.005", "pmcid": "PMC9880859", "resource_type": "article", "pub_year": "2022", "author_list": "Cabrera, Alan; Edelstein, Hailey I.; et el." }, { "id": "https://authors.library.caltech.edu/records/cfa4m-40a78", "eprint_id": 119035, "eprint_status": "archive", "datestamp": "2023-12-21 18:29:45", "lastmod": "2024-01-09 22:21:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cabrera-Alan", "name": { "family": "Cabrera", "given": "Alan" }, "orcid": "0000-0002-2546-0260" }, { "name": { "family": "Edelstein", "given": "Hailey I." }, "orcid": "0000-0002-8077-5492" }, { "name": { "family": "Glykofrydis", "given": "Fokion" }, "orcid": "0000-0002-0865-4573" }, { "name": { "family": "Love", "given": "Kasey S." }, "orcid": "0000-0001-7544-0340" }, { "name": { "family": "Palacios", "given": "Sebastian" } }, { "name": { "family": "Tycko", "given": "Josh" }, "orcid": "0000-0002-4108-0575" }, { "name": { "family": "Zhang", "given": "Meng" }, "orcid": "0000-0002-4076-6276" }, { "name": { "family": "Lensch", "given": "Sarah" }, "orcid": "0000-0003-1450-3242" }, { "name": { "family": "Shields", "given": "Cara E." }, "orcid": "0000-0002-3791-8259" }, { "name": { "family": "Livingston", "given": "Mark" } }, { "name": { "family": "Weiss", "given": "Ron" } }, { "name": { "family": "Zhao", "given": "Huimin" } }, { "name": { "family": "Haynes", "given": "Karmella A." }, "orcid": "0000-0002-5975-577X" }, { "name": { "family": "Morsut", "given": "Leonardo" }, "orcid": "0000-0001-7049-3478" }, { "name": { "family": "Chen", "given": "Yvonne Y." }, "orcid": "0000-0002-5583-119X" }, { "name": { "family": "Khalil", "given": "Ahmad S." }, "orcid": "0000-0002-8214-0546" }, { "name": { "family": "Wong", "given": "Wilson W." }, "orcid": "0000-0001-8394-889X" }, { "name": { "family": "Collins", "given": "James J." } }, { "id": "Rosser-Susan-J", "name": { "family": "Rosser", "given": "Susan J." }, "orcid": "0000-0002-2560-6485" }, { "id": "Polizzi-Karen", "name": { "family": "Polizzi", "given": "Karen" }, "orcid": "0000-0001-5435-2667" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Fussenegger-Martin", "name": { "family": "Fussenegger", "given": "Martin" }, "orcid": "0000-0001-8545-667X" }, { "id": "Hilton-Isaac-B", "name": { "family": "Hilton", "given": "Isaac B." }, "orcid": "0000-0002-3064-8532" }, { "id": "Leonard-Joshua-N", "name": { "family": "Leonard", "given": "Joshua N." }, "orcid": "0000-0003-4359-6126" }, { "id": "Bintu-Lacramioara", "name": { "family": "Bintu", "given": "Lacramioara" }, "orcid": "0000-0001-5443-6633" }, { "id": "Galloway-Kate-E", "name": { "family": "Galloway", "given": "Kate E." }, "orcid": "0000-0001-7416-3193" }, { "id": "Deans-Tara-L", "name": { "family": "Deans", "given": "Tara L." }, "orcid": "0000-0002-2361-2195" } ] }, "title": "The sound of silence: Transgene silencing in mammalian cell engineering", "ispublished": "pub", "full_text_status": "public", "keywords": "Cell Biology; Histology; Pathology and Forensic Medicine", "note": "Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) \n\nFunding for this work was supported in part by the National Institutes of Health grants 1DP2CA250006-01 (T.L.D.), 1R01GM129011 (W.W.W.), R01EB029483 (W.W.W.), 1R01EB026510 (J.N.L.), R21EB030772 (I.B.H.), R35GM143532 (I.B.H.), R35GM143033 (K.E.G.), R35GM138256 (L.M.), 4K00DK126120-03 (J.T.), R01EB029483 (A.S.K.), R35GM128947 (L.B.), R01EB030946 (R.W.), R01EB025256 (R.W.), 1UM1HG009402 (H.Z.), U54DK107965 (H.Z.), R21CA232244 (K.A.H.), 1RC2DK120535-01A1 (J.J.C.), and 1U01 DK 127420-01 (M.B.E.), the National Science Foundation grants CBET-2034495 (L.M.), CBET-2145528 (L.M.), 2141064 (K.S.L.), EF-1921677 (A.S.K.), and EF-2021552 under subaward UWSC10142 (M.B.E.). Further support was also provided by the Biotechnology and Biological Sciences Research Council (BBSRC) BB/S006206/1 (K.P.) and BB/M018040/1 (S.J.R.), ElectroGene 785800 (M.F.), the SNF (M.F.), the Paul Allen Foundation (W.W.W.), AOFSR FA9550-22-1-0316 (K.E.G.), the Wellcome Sanger Institute LEAP 21-275 (L.M.), the Parker Institute for Cancer Immunotherapy (Y.Y.C.), the W.H. Coulter Department of Biomedical Engineering at Emory University (C.E.S.), and the DoD Vannevar Bush Faculty Fellowship N00014-20-1-2825 (A.S.K.). M.B.E. is a Howard Hughes Medical Institute investigator. The authors listed with equal contribution are listed in the author list in alphabetical order.\n\nJ.T. and L.B. acknowledge outside interest in Stylus Medicine.
", "abstract": "To elucidate principles operating in native biological systems and to develop novel biotechnologies, synthetic biology aims to build and integrate synthetic gene circuits within native transcriptional networks. The utility of synthetic gene circuits for cell engineering relies on the ability to control the expression of all constituent transgene components. Transgene silencing, defined as the loss of expression over time, persists as an obstacle for engineering primary cells and stem cells with transgenic cargos. In this review, we highlight the challenge that transgene silencing poses to the robust engineering of mammalian cells, outline potential molecular mechanisms of silencing, and present approaches for preventing transgene silencing. We conclude with a perspective identifying future research directions for improving the performance of synthetic gene circuits.", "date": "2022-12-21", "date_type": "published", "publication": "Cell Systems", "volume": "13", "number": "12", "publisher": "Cell Press", "pagerange": "950-973", "id_number": "CaltechAUTHORS:20230203-893712500.43", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230203-893712500.43", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "grant_number": "1DP2CA250006-01" }, { "grant_number": "1R01GM129011" }, { "grant_number": "R01EB029483" }, { "grant_number": "1R01EB026510" }, { "grant_number": "R21EB030772" }, { "grant_number": "R35GM143532" }, { "grant_number": "R35GM143033" }, { "grant_number": "R35GM138256" }, { "grant_number": "4K00DK126120-03" }, { "grant_number": "R01EB029483" }, { "grant_number": "R35GM128947" }, { "grant_number": "R01EB030946" }, { "grant_number": "R01EB025256" }, { "grant_number": "1UM1HG009402" }, { "grant_number": "U54DK107965" }, { "grant_number": "R21CA232244" }, { "grant_number": "1RC2DK120535-01A1" }, { "grant_number": "1U01 DK 127420-01" }, { "grant_number": "CBET-2034495" }, { "grant_number": "CBET-2145528" }, { "grant_number": "DGE-2141064" }, { "grant_number": "EF-1921677" }, { "grant_number": "EF-2021552" }, { "grant_number": "BB/S006206/1" }, { "grant_number": "BB/M018040/1" }, {}, {}, { "grant_number": "FA9550-22-1-0316" }, { "grant_number": "LEAP 21-275" }, {}, {}, { "grant_number": "Vannevar Bush Faculty Fellowship" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.cels.2022.11.005", "pmcid": "PMC9880859", "primary_object": { "basename": "1-s2.0-S2405471222004641-main.pdf", "url": "https://authors.library.caltech.edu/records/cfa4m-40a78/files/1-s2.0-S2405471222004641-main.pdf" }, "resource_type": "article", "pub_year": "2022", "author_list": "Cabrera, Alan; Edelstein, Hailey I.; et el." }, { "id": "https://authors.library.caltech.edu/records/0hqa5-02a70", "eprint_id": 119357, "eprint_status": "archive", "datestamp": "2023-08-22 18:21:17", "lastmod": "2023-12-22 23:20:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Sheng", "name": { "family": "Wang", "given": "Sheng" } }, { "id": "Garcia-Ojalvo-Jordi", "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": "pub", "full_text_status": "public", "keywords": "Cell Biology; Histology; Pathology and Forensic Medicine", "note": "\u00a9 2022 The Authors. Published by Elsevier. Attribution 4.0 International (CC BY 4.0) \n\nM.B.E. 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 advised program of the Paul G. Allen Family Foundation. J.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 R&D (grant CEX2018-000792-M), and by the Generalitat de Catalunya. We acknowledge insightful feedback from Elowitz lab members. \n\nWe previously granted a CC BY 4.0 license to the public and a sublicensable license to HHMI in our research articles pursuant to which we have the right to make the author-accepted manuscript of our article immediately available upon publication, and any rights we grant in our research articles are subject to the public and HHMI licenses. \n\nAuthor contributions. Conceptualization and investigation, S.W., J.G.-O., and M.B.E.; formal analysis, software, and visualization, S.W.; writing: S.W., J.G.-O., and M.B.E. \n\nData and code availability: \n\n\u2022 All data have been deposited at the CaltechDATA research data repository (https://doi.org/10.22002/4y293-6eg49) and are publicly available as of the date of publication. The DOI is listed in the key resources table. \n\n\u2022 All original code has been deposited at the CaltechDATA research data repository (https://doi.org/10.22002/4y293-6eg49) and is publicly available as of the date of publication. The DOI is listed in the key resources table. \n\n\u2022 Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.\n\nThe authors declare no competing interests.\n\nPublished - 1-s2.0-S2405471222004367-main.pdf
Supplemental Material - 1-s2.0-S2405471222004367-mmc1.pdf
", "abstract": "During multicellular development, periodic spatial patterning systems generate repetitive structures, such as digits, vertebrae, and teeth. Turing patterning provides a foundational paradigm for understanding such systems. The simplest Turing systems are believed to require at least two morphogens to generate periodic patterns. Here, using mathematical modeling, we show that a simpler circuit, including only a single diffusible morphogen, is sufficient to generate long-range, spatially periodic patterns that propagate outward from transient initiating perturbations and remain stable after the perturbation is removed. Furthermore, an additional bistable intracellular feedback or operation on a growing cell lattice can make patterning robust to noise. 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": "2022-12", "date_type": "published", "publication": "Cell Systems", "volume": "13", "number": "12", "publisher": "Cell Press", "pagerange": "1033-1047.e7", "id_number": "CaltechAUTHORS:20230221-18374200.6", "issn": "2405-4712", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230221-18374200.6", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Allen Discovery Center", "grant_number": "UWSC10142" }, { "agency": "Paul G. Allen Family Foundation" }, { "agency": "Ministerio de Ciencia e Innovaci\u00f3n (MICINN)" }, { "agency": "European Regional Development Fund", "grant_number": "CEX2018-000792-M" }, { "agency": "European Regional Development Fund", "grant_number": "PGC2018-101251-B-I00" }, { "agency": "Generalitat de Catalunya" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.cels.2022.11.001", "primary_object": { "basename": "1-s2.0-S2405471222004367-main.pdf", "url": "https://authors.library.caltech.edu/records/0hqa5-02a70/files/1-s2.0-S2405471222004367-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S2405471222004367-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/0hqa5-02a70/files/1-s2.0-S2405471222004367-mmc1.pdf" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Wang, Sheng; Garcia-Ojalvo, Jordi; et el." }, { "id": "https://authors.library.caltech.edu/records/ny5rx-x3886", "eprint_id": 117309, "eprint_status": "archive", "datestamp": "2023-08-22 17:54:55", "lastmod": "2023-12-22 23:08:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Amadei-Gianluca", "name": { "family": "Amadei", "given": "Gianluca" }, "orcid": "0000-0001-5405-968X" }, { "id": "Handford-Charlotte-E", "name": { "family": "Handford", "given": "Charlotte E." }, "orcid": "0000-0002-5245-8027" }, { "id": "Qiu-Chengxiang", "name": { "family": "Qiu", "given": "Chengxiang" }, "orcid": "0000-0002-6346-8669" }, { "id": "De-Jonghe-Joachim", "name": { "family": "De Jonghe", "given": "Joachim" }, "orcid": "0000-0003-0584-8265" }, { "id": "Greenfeld-Hannah", "name": { "family": "Greenfeld", "given": "Hannah" } }, { "id": "Tran-Martin", "name": { "family": "Tran", "given": "Martin" } }, { "id": "Martin-Beth-K", "name": { "family": "Martin", "given": "Beth K." }, "orcid": "0000-0002-9661-014X" }, { "id": "Chen-Dong-Yuan", "name": { "family": "Chen", "given": "Dong-Yuan" }, "orcid": "0000-0003-2179-2847" }, { "id": "Aguilera-Castrejon-Alejandro", "name": { "family": "Aguilera-Castrejon", "given": "Alejandro" }, "orcid": "0000-0002-1339-7778" }, { "id": "Hanna-Jacob-H", "name": { "family": "Hanna", "given": "Jacob H." }, "orcid": "0000-0003-2042-9974" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Hollfelder-Florian", "name": { "family": "Hollfelder", "given": "Florian" }, "orcid": "0000-0002-1367-6312" }, { "id": "Shendure-Jay", "name": { "family": "Shendure", "given": "Jay" }, "orcid": "0000-0002-1516-1865" }, { "id": "Glover-D-M", "name": { "family": "Glover", "given": "David M." }, "orcid": "0000-0003-0956-0103" }, { "id": "Zernicka-Goetz-M", "name": { "family": "Zernicka-Goetz", "given": "Magdalena" }, "orcid": "0000-0002-7004-2471" } ] }, "title": "Embryo\u00a0model completes gastrulation to neurulation and organogenesis", "ispublished": "pub", "full_text_status": "public", "keywords": "Multidisciplinary", "note": "We thank all members of the M.Z.-G. laboratory for their suggestions throughout this project, and M. Shahbazi and R. Hadas for help and discussions. This project has been made possible through the following grants to M.Z.-G.: NIH Pioneer Award (DP1 HD104575-01), European Research Council (669198), the Wellcome Trust (207415/Z/17/Z), Open Philanthropy/Silicon Valley Community Foundation and Weston Havens Foundation and the Centre for Trophoblast Research. F.H. was supported by the ERC (69566) and the Wellcome Trust (WT108438/C/15/Z). J.D.J. was supported by the Biotechnology and Biological Sciences Research Council. C.E.H. was supported by the Centre for Trophoblast Research, and the Leventis Foundation. A grant from the Paul G. Allen Frontiers Group (Allen Discovery Centre for Cell Lineage Tracing) supported M.Z.-G., M.B.E. and J.S. J.S. is also supported by the National Human Genome Research Institute (1UM1HG011586 to J.S.; R01HG010632 to J.S.) and is an Investigator of the Howard Hughes Medical Institute. M.B.E. is also an Investigator of the Howard Hughes Medical Institute and is supported by an NIH grant (R01 MH116508). H.G. is supported by a Biology and Biological Engineering postdoctoral fellowship from Caltech. D.-Y.C. is supported by a NIH-NRSA postdoctoral fellowship (5F32HD105442). \n\nThese authors contributed equally: Gianluca Amadei, Charlotte E. Handford. \n\nContributions. G.A. and C.E.H. designed and carried out the experiments and data analysis. C.Q. performed the tiny-sci-RNA-seq bioinformatic analysis. J.D.J. performed the library preparation for the inDrop scRNA-seq and bioinformatics analysis. H.G. and M.T. performed and analysed the sequential smFISH. B.K.M. performed the library preparation for tiny-sci-RNA-seq. D.-Y.C. collected rat serum. A.A.-C. and J.H.H. provided the gas mixer and pressurising chamber for the last day of ETiX embryoid culture. M.E. supervised the sequential smFISH performed by H.G. and M.T. F.H. supervised the scRNA-seq analysis performed by J.D.J. J.S. supervised the tiny-sci-RNA-seq analysis performed by B.K.M. and C.Q. M.Z.-G., G.A., C.E.H. and D.M.G. wrote the manuscript. M.Z.-G. conceived, planned and supervised the study. \n\nData availability. All unique and stable reagents generated in this study are available from the corresponding author with a completed Materials Transfer Agreement. Raw single-cell sequencing data generated by this work have been deposited in the NCBI Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/geo/) and are accessible through the following accession numbers: the inDrops scRNA-seq dataset is available at GSE189425; the tiny-sci-RNA-seq dataset is available at GSE209792. Source data are provided with this paper. \n\nCode availability. The code used to analyse the inDrops scRNA-seq data is available at https://github.com/fhlab/scRNAseq_inducedETX The code used to analyse the tiny-sci-RNA-seq data is available at https://github.com/ChengxiangQiu/ETiX_Amadei. \n\nCompeting interests. J.H.H. is a founder and chief scientific advisor to RenewalBio Ltd. M.Z.-G., G.A. and C.E.H. are applicants and inventors on a patent filed jointly on 5 May 2022 by Caltech and the University of Cambridge pertaining to and covering 'Generation of Synthetic Embryos from Multiple Stem Cell Types' under CIT file no.: CIT-8826-P and serial number: 63/344,251. The other authors declare no competing interests. \n\nPeer review information. Nature thanks Segiu Pasca, Manu Setty and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.\n\nPublished - 41586_2022_Article_5246.pdf
", "abstract": "Embryonic stem (ES) cells can undergo many aspects of mammalian embryogenesis in vitro, but their developmental potential is substantially extended by interactions with extraembryonic stem cells, including trophoblast stem (TS) cells, extraembryonic endoderm stem (XEN) cells and inducible XEN (iXEN) cells. Here we assembled stem cell-derived embryos in vitro from mouse ES cells, TS cells and iXEN cells and showed that they recapitulate the development of whole natural mouse embryo in utero up to day 8.5 post-fertilization. Our embryo model displays headfolds with defined forebrain and midbrain regions and develops a beating heart-like structure, a trunk comprising a neural tube and somites, a tail bud containing neuromesodermal progenitors, a gut tube, and primordial germ cells. This complete embryo model develops within an extraembryonic yolk sac that initiates blood island development. Notably, we demonstrate that the neurulating embryo model assembled from Pax6-knockout ES cells aggregated with wild-type TS cells and iXEN cells recapitulates the ventral domain expansion of the neural tube that occurs in natural, ubiquitous Pax6-knockout embryos. Thus, these complete embryoids are a powerful in vitro model for dissecting the roles of diverse cell lineages and genes in development. Our results demonstrate the self-organization ability of ES cells and two types of extraembryonic stem cells to reconstitute mammalian development through and beyond gastrulation to neurulation and early organogenesis.", "date": "2022-10-06", "date_type": "published", "publication": "Nature", "volume": "610", "number": "7930", "publisher": "Nature Publishing Group", "pagerange": "143-153", "id_number": "CaltechAUTHORS:20221010-454096500.25", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221010-454096500.25", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "DP1 HD104575-01" }, { "agency": "European Research Council (ERC)", "grant_number": "669198" }, { "agency": "Wellcome Trust", "grant_number": "207415/Z/17/Z" }, { "agency": "Open Philanthropy" }, { "agency": "Silicon Valley Community Foundation" }, { "agency": "Weston Havens Foundation" }, { "agency": "Centre for Trophoblast Research" }, { "agency": "European Research Council (ERC)", "grant_number": "695669" }, { "agency": "Wellcome Trust", "grant_number": "WT108438/C/15/Z" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)" }, { "agency": "Leventis Foundation" }, { "agency": "Paul G. Allen Frontiers Group" }, { "agency": "NIH", "grant_number": "1UM1HG011586" }, { "agency": "NIH", "grant_number": "R01HG010632" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "R01 MH116508" }, { "agency": "Caltech Division of Biology and Biological Engineering" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "5F32HD105442" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41586-022-05246-3", "pmcid": "PMC9534772", "primary_object": { "basename": "41586_2022_Article_5246.pdf", "url": "https://authors.library.caltech.edu/records/ny5rx-x3886/files/41586_2022_Article_5246.pdf" }, "resource_type": "article", "pub_year": "2022", "author_list": "Amadei, Gianluca; Handford, Charlotte E.; et el." }, { "id": "https://authors.library.caltech.edu/records/9nx6n-5ne43", "eprint_id": 104579, "eprint_status": "archive", "datestamp": "2023-08-22 16:21:55", "lastmod": "2023-12-22 23:20:08", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ding-Fangyuan", "name": { "family": "Ding", "given": "Fangyuan" }, "orcid": "0000-0003-0118-5441" }, { "id": "Su-Christina-J", "name": { "family": "Su", "given": "Christina J." }, "orcid": "0000-0002-9223-9777" }, { "id": "Edmonds-KeHuan-Kuo", "name": { "family": "Edmonds", "given": "KeHuan Kuo" } }, { "id": "Liang-Guohao", "name": { "family": "Liang", "given": "Guohao" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Dynamics and functional roles of splicing factor autoregulation", "ispublished": "pub", "full_text_status": "public", "keywords": "negative autoregulatory splicing; feedback dynamics; biological noise; label-free single-cell movie tracking; feedback adaptation; mathematical model", "note": "\u00a9 2022 The Author(s). This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). \n\nReceived 19 July 2021, Revised 1 February 2022, Accepted 31 May 2022, Available online 21 June 2022, Version of Record 21 June 2022. \n\nWe thank F. Tan for providing the western blot protocol, N. Nandagopal and Y. Antebi for technical assistance, and Life Sciences Editors (Sabbi Lall) for critical feedback on the manuscript. We also thank S. Sun, A.R. Krainer, D. Sprinzak, D. Baltimore, J.G. Ojalvo, and N. Wingreen for discussion and feedback on the project. F.D. was supported by a fellowship from the Schlumberger Foundation. C.J.S. is supported by NIH National Institute of General Medical Sciences training grant no. GM008042, and by a David Geffen Medical Scholarship. The work was funded by the Gordon and Betty Moore Foundation through grant no. GBMF2809 to the Caltech Programmable Molecular Technology Initiative and the Institute for Collaborative Biotechnologies through grant no. W911NF-09-0001 from the US Army Research Office, AWS Machine Learning Research Awards, and the Intel Corporation. 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. 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: F.D. and M.B.E. designed the experiments. F.D., K.E., and G.L. performed experiments. F.D. analyzed data. C.S. and F.D. performed the mathematical modeling. F.D., C.J.S., and M.B.E. wrote the manuscript. \n\nThe authors declare no competing interests. \n\nData and code availability: Data generated in this study are available from the lead contact upon request. All data reported in this paper will be shared by the lead contact upon request. Original codes are deposited and publicly accessible. DOI is listed in the Key resources table. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.\n\nPublished - 1-s2.0-S2211124722007719-main.pdf
Submitted - 2020.07.22.216887v1.full.pdf
Supplemental Material - 1-s2.0-S2211124722007719-mmc1.pdf
", "abstract": "Non-core spliceosome components are essential, conserved regulators of alternative splicing. They provide concentration-dependent control of diverse pre-mRNAs. Many splicing factors direct unproductive splicing of their own pre-mRNAs through negative autoregulation. However, the impact of such feedback loops on splicing dynamics at the single-cell level remains unclear. Here, we developed a system to quantitatively analyze negative autoregulatory splicing dynamics by splicing factor SRSF1 in response to perturbations in single HEK293 cells. We show that negative autoregulatory splicing provides critical functions for gene regulation, establishing a ceiling of SRSF1 protein concentration, reducing cell-cell heterogeneity in SRSF1 levels, and buffering variation in transcription. Most important, it adapts SRSF1 splicing activity to variations in demand from other pre-mRNA substrates. A minimal mathematical model of autoregulatory splicing explains these experimentally observed features and provides values for effective biochemical parameters. These results reveal the unique functional roles that splicing negative autoregulation plays in homeostatically regulating transcriptional programs.", "date": "2022-06-21", "date_type": "published", "publication": "Cell Reports", "volume": "39", "number": "12", "publisher": "Cell Press", "pagerange": "Art. No. 110985", "id_number": "CaltechAUTHORS:20200727-084029052", "issn": "2211-1247", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200727-084029052", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Schlumberger Foundation" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "GM008042" }, { "agency": "David Geffen Medical Scholarship" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-09-0001" }, { "agency": "Amazon Web Services" }, { "agency": "Intel" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.celrep.2022.110985", "pmcid": "PMC9262138", "primary_object": { "basename": "1-s2.0-S2211124722007719-main.pdf", "url": "https://authors.library.caltech.edu/records/9nx6n-5ne43/files/1-s2.0-S2211124722007719-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S2211124722007719-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/9nx6n-5ne43/files/1-s2.0-S2211124722007719-mmc1.pdf" }, { "basename": "2020.07.22.216887v1.full.pdf", "url": "https://authors.library.caltech.edu/records/9nx6n-5ne43/files/2020.07.22.216887v1.full.pdf" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Ding, Fangyuan; Su, Christina J.; et el." }, { "id": "https://authors.library.caltech.edu/records/4a7y9-nzb92", "eprint_id": 107015, "eprint_status": "archive", "datestamp": "2023-08-22 15:39:13", "lastmod": "2024-02-06 19:45:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Su-Christina-J", "name": { "family": "Su", "given": "Christina J." }, "orcid": "0000-0002-9223-9777" }, { "id": "Murugan-Arvind", "name": { "family": "Murugan", "given": "Arvind" }, "orcid": "0000-0001-5464-917X" }, { "id": "Linton-James-M", "name": { "family": "Linton", "given": "James M." } }, { "id": "Yeluri-Akshay", "name": { "family": "Yeluri", "given": "Akshay" }, "orcid": "0000-0001-8654-1673" }, { "id": "Bois-J-S", "name": { "family": "Bois", "given": "Justin S." }, "orcid": "0000-0001-7137-8746" }, { "id": "Klumpe-Heidi-E", "name": { "family": "Klumpe", "given": "Heidi" }, "orcid": "0000-0001-8938-2006" }, { "id": "Langley-Matthew-A", "name": { "family": "Langley", "given": "Matthew A." }, "orcid": "0000-0003-2890-5584" }, { "id": "Antebi-Yaron-E", "name": { "family": "Antebi", "given": "Yaron E." }, "orcid": "0000-0002-5771-6814" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Ligand-receptor promiscuity enables cellular addressing", "ispublished": "pub", "full_text_status": "public", "keywords": "bone morphogenetic protein; BMP; signaling pathways; promiscuity; combinatorial signaling; ligand-receptor interactions; communication systems; signal processing; information theory; cell-type specificity", "note": "\u00a9 2022 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). \n\nReceived 29 December 2020, Revised 8 November 2021, Accepted 16 March 2022, Available online 13 April 2022. \n\nWe thank Ke-Huan Chow, Alejandro Granados, Bo Gu, Rachael Kuintzle, Yitong Ma, Nagarajan Nandagopal, Leah Santat, Martin Tran, and other members of the Elowitz lab for scientific input and feedback. We thank Samantha Butler, Sarah Denny, Jordi Garcia-Ojalvo, Lea Goentoro, Elliot Hui, Jay Lieberman, Roy Kishony, Alan Moses, Xiling Shen, Matt Thomson, Ned Wingreen, and Vincent Zaballa for helpful discussions. This work was supported by the Allen Discovery Center Program (award UWSC10142), a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation; the Defense Advanced Research Projects Agency (contract HR0011-16-0138); the Gordon and Betty Moore Foundation (grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative); the Human Frontiers Science Program (grant RGP0020); the Institute for Collaborative Biotechnologies (grant W911NF-09-0001 from the U.S. Army Research Office); and the National Institutes of Health (NIH) (grants R01 HD075335A and R01 MH116508). This work does not necessarily reflect the position or policy of the U.S. Government, and no official endorsement should be inferred. C.J.S. was supported by the NIH National Institute of General Medical Sciences (grant T32 GM008042) and a David Geffen Medical Scholarship. H.K. was supported by a National Science Foundation graduate research fellowship (grant DGE-1144469). Y.E.A. was supported by the Israel Science Foundation (grant 1105/20) and is the incumbent Sygnet Career Development Chair for Bioinformatics. M.B.E. is a Howard Hughes Medical Institute investigator. \n\nAuthor contributions: C.J.S., A.M., Y.E.A., and M.B.E. conceived and designed the research. J.M.L., H.K., M.A.L., and Y.E.A. performed experiments. C.J.S., A.M., A.Y., J.B., and Y.E.A. developed mathematical models and performed computational analysis. C.J.S., A.M., Y.E.A., and M.B.E. wrote the manuscript. \n\nDeclaration of interests: C.J.S. is presently at the University of Illinois College of Medicine. H.K. is currently at the Department of Biomedical Engineering at Boston University. The authors have a patent related to this work (U.S. patent number 10,527,631). \n\nData and code availability: All data have been deposited at the CaltechDATA research data repository (https://doi.org/10.22002/D1.1692) and are publicly available as of the date of publication. The DOI is listed in the key resources table. \n\nAll original code has been deposited at GitHub (https://github.com/christinasu/PromiSys) as well as the CaltechDATA research data repository (https://doi.org/10.22002/D1.20047) and is publicly available as of the date of publication. The DOI is listed in the key resources table. \n\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.\n\nPublished - 1-s2.0-S2405471222001284-main.pdf
Submitted - 2020.12.08.412643v1.full.pdf
Supplemental Material - 1-s2.0-S2405471222001284-mmc1.pdf
", "abstract": "In multicellular organisms, secreted ligands selectively activate, or \"address,\" specific target cell populations to control cell fate decision-making and other processes. Key cell-cell communication pathways use multiple promiscuously interacting ligands and receptors, provoking the question of how addressing specificity can emerge from molecular promiscuity. To investigate this issue, we developed a general mathematical modeling framework based on the bone morphogenetic protein (BMP) pathway architecture. We find that promiscuously interacting ligand-receptor systems allow a small number of ligands, acting in combinations, to address a larger number of individual cell types, defined by their receptor expression profiles. Promiscuous systems outperform seemingly more specific one-to-one signaling architectures in addressing capability. Combinatorial addressing extends to groups of cell types, is robust to receptor expression noise, grows more powerful with increases in the number of receptor variants, and is maximized by specific biochemical parameter relationships. Together, these results identify design principles governing cellular addressing by ligand combinations.", "date": "2022-05-18", "date_type": "published", "publication": "Cell Systems", "volume": "13", "number": "5", "publisher": "Cell Press", "pagerange": "408-425", "id_number": "CaltechAUTHORS:20201210-134335099", "issn": "2405-4712", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201210-134335099", "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": "Defense Advanced Research Projects Agency (DARPA)", "grant_number": "HR0011-16-0138" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "Caltech Programmable Molecular Technology Initiative" }, { "agency": "Human Frontier Science Program", "grant_number": "RGP0020" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-09-0001" }, { "agency": "NIH", "grant_number": "R01 HD075335A" }, { "agency": "NIH", "grant_number": "R01 MH116508" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 GM008042" }, { "agency": "David Geffen Medical Scholarship" }, { "agency": "NSF Graduate Research Fellowship", "grant_number": "DGE-1144469" }, { "agency": "Israel Science Foundation", "grant_number": "1105/20" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.cels.2022.03.001", "primary_object": { "basename": "1-s2.0-S2405471222001284-main.pdf", "url": "https://authors.library.caltech.edu/records/4a7y9-nzb92/files/1-s2.0-S2405471222001284-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S2405471222001284-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/4a7y9-nzb92/files/1-s2.0-S2405471222001284-mmc1.pdf" }, { "basename": "2020.12.08.412643v1.full.pdf", "url": "https://authors.library.caltech.edu/records/4a7y9-nzb92/files/2020.12.08.412643v1.full.pdf" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Su, Christina J.; Murugan, Arvind; et el." }, { "id": "https://authors.library.caltech.edu/records/4jqdv-nrv37", "eprint_id": 107007, "eprint_status": "archive", "datestamp": "2023-08-22 15:39:05", "lastmod": "2023-12-22 23:20:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Klumpe-Heidi-E", "name": { "family": "Klumpe", "given": "Heidi E." }, "orcid": "0000-0001-8938-2006" }, { "id": "Langley-Matthew-A", "name": { "family": "Langley", "given": "Matthew A." }, "orcid": "0000-0003-2890-5584" }, { "id": "Linton-James-M", "name": { "family": "Linton", "given": "James M." } }, { "id": "Su-Christina-J", "name": { "family": "Su", "given": "Christina J." }, "orcid": "0000-0002-9223-9777" }, { "id": "Antebi-Yaron-E", "name": { "family": "Antebi", "given": "Yaron E." }, "orcid": "0000-0002-5771-6814" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "The context-dependent, combinatorial logic of BMP signaling", "ispublished": "pub", "full_text_status": "public", "keywords": "bone morphogenetic protein; BMP; signaling pathways; cell context; combinatorial signaling; promiscuous ligand-receptor interactions; pairwise interaction analysis", "note": "\u00a9 2022 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). \n\nReceived 5 December 2020, Revised 23 March 2021, Accepted 18 March 2022, Available online 13 April 2022. \n\nThis work was supported by the Defense Advanced Research Projects Agency (contract HR0011-16-0138), the Gordon and Betty Moore Foundation (grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative), the Human Frontiers Science Program (grant RGP0020), the Institute for Collaborative Biotechnologies (grant W911NF-09-0001 from the U.S. Army Research Office), the National Institutes of Health (NIH) (grants R01 HD075335A and R01 MH116508), and the Paul G. Allen Frontiers Group and Prime Awarding Agency (award UWSC10142). This work does not necessarily reflect the position or policy of the U.S. Government, and no official endorsement should be inferred. H.E.K. is supported by a National Science Foundation graduate research fellowship (grant DGE-1144469). C.J.S. is supported by the NIH National Institute of General Medical Sciences (grant T32 GM008042) and a David Geffen Medical Scholarship. M.A.L. is supported by the National Sciences and Engineering Research Council of Canada Postgraduate Doctoral Scholarship. Y.E.A is supported by the Israel Science Foundation (grant 1105/20) and is the incumbent Sygnet Career Development Chair for Bioinformatics. M.B.E. is a Howard Hughes Medical Institute investigator. \n\nAuthor contributions: H.E.K., Y.E.A., and M.B.E. conceived and designed the experiments. H.E.K., M.A.L., and J.M.L. performed the experiments. H.E.K. and M.A.L. analyzed the experimental data. H.E.K., Y.E.A., and C.J.S. developed and fit the model. H.E.K., Y.E.A., and M.B.E. wrote the paper. \n\nDeclaration of interests: The authors have one patent related to this work, US patent number 10,527,631. H.E.K. is currently a postdoctoral researcher at the Department of Biomedical Engineering at Boston University. C.J.S. is currently a medical student at the University of Illinois, Chicago. \n\nData and code availability: Source data statement: Flow cytometry and qPCR data have been deposited at Caltech DATA and are publicly available as of the date of publication. DOIs are listed in the key resources table. This paper also analyzes existing, publicly available data. The accession numbers for these datasets are also listed in the key resources table. \n\nCode statement: All original code has been deposited at Caltech DATA and is publicly available as of the date of publication. DOIs are listed in the key resources table. \n\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.\n\nPublished - 1-s2.0-S2405471222001296-main.pdf
Submitted - 2020.12.08.416503v1.full.pdf
Supplemental Material - 1-s2.0-S2405471222001296-mmc1.pdf
Supplemental Material - 1-s2.0-S2405471222001296-mmc2.xlsx
", "abstract": "Cell-cell communication systems typically comprise families of ligand and receptor variants that function together in combinations. Pathway activation depends on the complex way in which ligands are presented extracellularly and receptors are expressed by the signal-receiving cell. To understand the combinatorial logic of such a system, we systematically measured pairwise bone morphogenetic protein (BMP) ligand interactions in cells with varying receptor expression. Ligands could be classified into equivalence groups based on their profile of positive and negative synergies with other ligands. These groups varied with receptor expression, explaining how ligands can functionally replace each other in one context but not another. Context-dependent combinatorial interactions could be explained by a biochemical model based on the competitive formation of alternative signaling complexes with distinct activities. Together, these results provide insights into the roles of BMP combinations in developmental and therapeutic contexts and establish a framework for analyzing other combinatorial, context-dependent signaling systems.", "date": "2022-05-18", "date_type": "published", "publication": "Cell Systems", "volume": "13", "number": "5", "publisher": "Cell Press", "pagerange": "388-407", "id_number": "CaltechAUTHORS:20201210-094756085", "issn": "2405-4712", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201210-094756085", "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": "HR0011-16-0138" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "Human Frontier Science Program", "grant_number": "RGP0020" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-09-0001" }, { "agency": "NIH", "grant_number": "R01 HD075335A" }, { "agency": "NIH", "grant_number": "R01 MH116508" }, { "agency": "Paul G. Allen Frontiers Group", "grant_number": "UWSC10142" }, { "agency": "NSF Graduate Research Fellowship", "grant_number": "DGE-1144469" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 GM008042" }, { "agency": "David Geffen Medical Scholarship" }, { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)" }, { "agency": "Israel Science Foundation", "grant_number": "1105/20" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.cels.2022.03.002", "pmcid": "PMC9127470", "primary_object": { "basename": "1-s2.0-S2405471222001296-main.pdf", "url": "https://authors.library.caltech.edu/records/4jqdv-nrv37/files/1-s2.0-S2405471222001296-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S2405471222001296-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/4jqdv-nrv37/files/1-s2.0-S2405471222001296-mmc1.pdf" }, { "basename": "1-s2.0-S2405471222001296-mmc2.xlsx", "url": "https://authors.library.caltech.edu/records/4jqdv-nrv37/files/1-s2.0-S2405471222001296-mmc2.xlsx" }, { "basename": "2020.12.08.416503v1.full.pdf", "url": "https://authors.library.caltech.edu/records/4jqdv-nrv37/files/2020.12.08.416503v1.full.pdf" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Klumpe, Heidi E.; Langley, Matthew A.; et el." }, { "id": "https://authors.library.caltech.edu/records/yc4sr-fb679", "eprint_id": 105302, "eprint_status": "archive", "datestamp": "2023-08-22 14:37:41", "lastmod": "2023-12-22 23:34:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ma-Yitong", "name": { "family": "Ma", "given": "Yitong" }, "orcid": "0000-0003-4446-7326" }, { "id": "Budde-Mark-W", "name": { "family": "Budde", "given": "Mark W." }, "orcid": "0000-0002-4359-1424" }, { "id": "Mayalu-Micha\u00eblle-N", "name": { "family": "Mayalu", "given": "Micha\u00eblle N." }, "orcid": "0000-0002-9678-0157" }, { "id": "Zhu-Junqin", "name": { "family": "Zhu", "given": "Junqin" }, "orcid": "0000-0002-8159-6402" }, { "id": "Lu-Andrew-C", "name": { "family": "Lu", "given": "Andrew C." }, "orcid": "0000-0002-7594-6445" }, { "id": "Murray-R-M", "name": { "family": "Murray", "given": "Richard M." }, "orcid": "0000-0002-5785-7481" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Synthetic mammalian signaling circuits for robust cell population control", "ispublished": "pub", "full_text_status": "public", "keywords": "mammalian synthetic biology; quorum sensing; synthetic circuits; cell population control; auxin; paradoxical control; synthetic signaling", "note": "\u00a9 2022 Elsevier Inc. \n\nReceived 3 September 2020, Revised 18 November 2021, Accepted 28 January 2022, Available online 1 March 2022. \n\nWe thank Igor Antoshechkin, Vijaya Kumar, and Jeff Park for technical assistance and advice; Xinying Ren and Leopold Green from Murray lab for discussion; Haley Larsen, Ke-Kuan Chow, Felix Horns, Duncan Chadly, Christina Su, Ronghui Zhu, Lucy Chong, and other members of the Elowitz lab for critical feedback on the manuscript; and Uri Alon, Omer Karin, Siyu Chen, and Matt Thomson for scientific input and advice. This work is based on work supported by the Defense Advanced Research Projects Agency under contract no. HR0011-17-2-0008, by the National Institute of Health grant R01 MH116508, 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 Millard and Muriel Jacobs Genetics and Genomics Laboratory at California Institute of Technology. M.B.E. is a Howard Hughes Medical Institute investigator. A.C.L. is supported by a fellowship from the Taiwanese Ministry of Education. The content of the information does not necessarily reflect the position or the policy of the U.S. government, and no official endorsement should be inferred. \n\nAuthor contributions: Project direction, supervision, and funding: M.W.B., M.B.E., and R.M.M.; design of research: Y.M., M.W.B., and M.B.E.; experimental investigation: Y.M., M.W.B., J.Z., and A.C.L.; data analysis: Y.M., M.W.B., M.N.M., and M.B.E.; mathematical modeling: Y.M., M.N.M., and M.B.E.; paper writing: Y.M., M.W.B., M.W.M., and M.B.E. \n\nDeclaration of interests: A patent application has been filed based on the work described here. M.W.B. is a founder and employee of Primordium Labs. \n\nData and code availability: The targeted DNA sequencing data have been deposited at NCBI Sequence Read Archive and are publicly available as of the date of publication. Accession numbers are listed in the key resources table. \n\nThe bulk RNA sequencing data have been deposited at GEO and are publicly available as of the date of publication. Accession numbers are listed in the key resources table. \n\nThe plasmid GenBank files, raw data, and processing/plotting scripts for generating the figures shown in this paper are available at data.caltech.edu. The DOI is listed in the key resources table. \n\nAll original codes used for processing the images and the movies, and codes for mathematical modeling section (Figures 4 and S3) is available at github and is publicly available as of the date of publication. DOIs and links are listed in the key resources table.\n\nAccepted Version - nihms-1784285.pdf
Submitted - 2020.09.02.278564v2.full.pdf
Supplemental Material - 1-s2.0-S0092867422001374-mmc1.pdf
Supplemental Material - 1-s2.0-S0092867422001374-mmc5.mp4
", "abstract": "In multicellular organisms, cells actively sense and control their own population density. Synthetic mammalian quorum-sensing circuits could provide insight into principles of population control and extend cell therapies. However, a key challenge is reducing their inherent sensitivity to \"cheater\" mutations that evade control. Here, we repurposed the plant hormone auxin to enable orthogonal mammalian cell-cell communication and quorum sensing. We designed a paradoxical population control circuit, termed \"Paradaux,\" in which auxin stimulates and inhibits net cell growth at different concentrations. This circuit limited population size over extended timescales of up to 42 days of continuous culture. By contrast, when operating in a non-paradoxical regime, population control became more susceptible to mutational escape. These results establish auxin as a versatile \"private\" communication system and demonstrate that paradoxical circuit architectures can provide robust population control.", "date": "2022-03-17", "date_type": "published", "publication": "Cell", "volume": "185", "number": "6", "publisher": "Cell Press", "pagerange": "967-979", "id_number": "CaltechAUTHORS:20200909-145940519", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200909-145940519", "funders": { "items": [ { "agency": "Defense Advanced Research Projects Agency (DARPA)", "grant_number": "HR0011-17-2-0008" }, { "agency": "NIH", "grant_number": "R01 MH116508" }, { "agency": "Paul G. Allen Frontiers Group", "grant_number": "UWSC10142" }, { "agency": "Paul G. Allen Family Foundation" }, { "agency": "Millard and Muriel Jacobs Genetics and Genomics Laboratory" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ministry of Education (Taipei)" } ] }, "local_group": { "items": [ { "id": "Millard-and-Muriel-Jacobs-Genetics-and-Genomics-Laboratory" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.cell.2022.01.026", "pmcid": "PMC8995209", "primary_object": { "basename": "nihms-1784285.pdf", "url": "https://authors.library.caltech.edu/records/yc4sr-fb679/files/nihms-1784285.pdf" }, "related_objects": [ { "basename": "1-s2.0-S0092867422001374-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/yc4sr-fb679/files/1-s2.0-S0092867422001374-mmc1.pdf" }, { "basename": "1-s2.0-S0092867422001374-mmc5.mp4", "url": "https://authors.library.caltech.edu/records/yc4sr-fb679/files/1-s2.0-S0092867422001374-mmc5.mp4" }, { "basename": "2020.09.02.278564v2.full.pdf", "url": "https://authors.library.caltech.edu/records/yc4sr-fb679/files/2020.09.02.278564v2.full.pdf" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Ma, Yitong; Budde, Mark W.; et el." }, { "id": "https://authors.library.caltech.edu/records/7d2gz-agv16", "eprint_id": 111639, "eprint_status": "archive", "datestamp": "2023-08-20 07:02:24", "lastmod": "2023-12-22 23:20:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Vlahos-Alexander-E", "name": { "family": "Vlahos", "given": "Alexander E." }, "orcid": "0000-0002-2154-8791" }, { "id": "Kang-Jeewoo", "name": { "family": "Kang", "given": "Jeewoo" }, "orcid": "0000-0002-1439-2602" }, { "id": "Aldrete-Carlos-A", "name": { "family": "Aldrete", "given": "Carlos A." }, "orcid": "0000-0003-3795-4572" }, { "id": "Zhu-Ronghui", "name": { "family": "Zhu", "given": "Ronghui" }, "orcid": "0000-0001-8171-482X" }, { "id": "Chong-Lucy-S", "name": { "family": "Chong", "given": "Lucy S." }, "orcid": "0000-0002-5858-9984" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Gao-Xiaojing-J", "name": { "family": "Gao", "given": "Xiaojing J." }, "orcid": "0000-0002-3094-1456" } ] }, "title": "Protease-controlled secretion and display of intercellular signals", "ispublished": "pub", "full_text_status": "public", "keywords": "Intercellular communication, synthetic biology, proteases, protein secretion, KRAS, protease-based signalling", "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 07 October 2021; Accepted 03 February 2022; Published 17 February 2022. \n\nWe would like to thank Dr. Lin, and Dr. Leonard for kindly sharing some of their plasmids that were used in this work. We would also like to thank Leo Scheller for providing the protocol for the SEAP assays. This work was funded by NIH (4R00EB027723-02, X.J.G), Stanford Cancer Institute (Cancer Innovation Award #216174, X.J.G.), Stanford SystemX Alliance (Seed Grant, X.J.G.), NSERC (PDF-557516-2021, A.E.V.), the International Human Frontier Science Program Organization (LT000221/2021-L, A.E.V.), and the Stanford Graduate Fellowship (J.K. and C.A.). \n\nData availability: New plasmids used in this study will be made available for distribution from Addgene (https://www.addgene.org/Xiaojing_Gao/). Annotated plasmid sequences used in this study are provided in the Source Data as GeneBank files. Raw.fcs files are available from the corresponding authors upon reasonable request. Raw experimental data and p-values for each figure are provided as Source Data. Source data are provided with this paper. \n\nCode availability: EasyFlow MATLAB code used for flow cytometry analysis is available from the GitHub repository at https://github.com/AntebiLab/easyflow.git. \n\nAuthor Contributions: A.E.V. and X.J.G. conceived and directed the study. A.E.V, J.K, and C.A. performed most of the experiments. X.J.G. created the HRAS-sensing protease, and L.S.C and R.Z. created the protease-activated protease under M.B.E.'s supervision. A.E.V, and J.K. analyzed the data for the manuscript. A.E.V., J.K. and X.J.G. wrote the manuscript. All authors provided feedback on the manuscript. \n\nCompeting interests: The board of trustees of the Leland Stanford Junior University have filed a patent on behalf of the inventors (A.E.V., J.K., and X.J.G.) of the RELEASE platform described (US provisional Application No. 63/282689). The remaining authors declare no competing interests. \n\nPeer review information: Nature Communications thanks Yingxiao Wang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.\n\nPublished - s41467-022-28623-y.pdf
Submitted - 2021.10.18.464444v1.full.pdf
Supplemental Material - 41467_2022_28623_MOESM1_ESM.docx
Supplemental Material - 41467_2022_28623_MOESM2_ESM.pdf
Supplemental Material - 41467_2022_28623_MOESM3_ESM.pdf
Supplemental Material - 41467_2022_28623_MOESM4_ESM.pdf
Supplemental Material - 41467_2022_28623_MOESM5_ESM.xlsx
Supplemental Material - 41467_2022_28623_MOESM6_ESM.xlsx
Supplemental Material - 41467_2022_28623_MOESM7_ESM.zip
", "abstract": "To program intercellular communication for biomedicine, it is crucial to regulate the secretion and surface display of signaling proteins. If such regulations are at the protein level, there are additional advantages, including compact delivery and direct interactions with endogenous signaling pathways. Here we create a modular, generalizable design called Retained Endoplasmic Cleavable Secretion (RELEASE), with engineered proteins retained in the endoplasmic reticulum and displayed/secreted in response to specific proteases. The design allows functional regulation of multiple synthetic and natural proteins by synthetic protease circuits to realize diverse signal processing capabilities, including logic operation and threshold tuning. By linking RELEASE to additional sensing and processing circuits, we can achieve elevated protein secretion in response to \"undruggable\" oncogene KRAS mutants. RELEASE should enable the local, programmable delivery of intercellular cues for a broad variety of fields such as neurobiology, cancer immunotherapy and cell transplantation.", "date": "2022-02-17", "date_type": "published", "publication": "Nature Communications", "volume": "13", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 912", "id_number": "CaltechAUTHORS:20211026-141150169", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211026-141150169", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "4R00EB027723-02" }, { "agency": "Stanford Cancer Institute", "grant_number": "216174" }, { "agency": "Stanford SystemX Alliance" }, { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)", "grant_number": "PDF-557516-2021" }, { "agency": "Human Frontier Science Program", "grant_number": "LT000221/2021-L" }, { "agency": "Stanford University" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41467-022-28623-y", "pmcid": "PMC8854555", "primary_object": { "basename": "41467_2022_28623_MOESM1_ESM.docx", "url": "https://authors.library.caltech.edu/records/7d2gz-agv16/files/41467_2022_28623_MOESM1_ESM.docx" }, "related_objects": [ { "basename": "41467_2022_28623_MOESM3_ESM.pdf", "url": "https://authors.library.caltech.edu/records/7d2gz-agv16/files/41467_2022_28623_MOESM3_ESM.pdf" }, { "basename": "41467_2022_28623_MOESM5_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/7d2gz-agv16/files/41467_2022_28623_MOESM5_ESM.xlsx" }, { "basename": "2021.10.18.464444v1.full.pdf", "url": "https://authors.library.caltech.edu/records/7d2gz-agv16/files/2021.10.18.464444v1.full.pdf" }, { "basename": "41467_2022_28623_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/7d2gz-agv16/files/41467_2022_28623_MOESM2_ESM.pdf" }, { "basename": "41467_2022_28623_MOESM4_ESM.pdf", "url": "https://authors.library.caltech.edu/records/7d2gz-agv16/files/41467_2022_28623_MOESM4_ESM.pdf" }, { "basename": "41467_2022_28623_MOESM6_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/7d2gz-agv16/files/41467_2022_28623_MOESM6_ESM.xlsx" }, { "basename": "41467_2022_28623_MOESM7_ESM.zip", "url": "https://authors.library.caltech.edu/records/7d2gz-agv16/files/41467_2022_28623_MOESM7_ESM.zip" }, { "basename": "s41467-022-28623-y.pdf", "url": "https://authors.library.caltech.edu/records/7d2gz-agv16/files/s41467-022-28623-y.pdf" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Vlahos, Alexander E.; Kang, Jeewoo; et el." }, { "id": "https://authors.library.caltech.edu/records/dcas8-y4s76", "eprint_id": 108036, "eprint_status": "archive", "datestamp": "2023-08-20 06:49:42", "lastmod": "2023-12-22 23:20:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhu-Ronghui", "name": { "family": "Zhu", "given": "Ronghui" }, "orcid": "0000-0001-8171-482X" }, { "id": "del-Rio-Salgado-Jesus-Maria", "name": { "family": "del Rio-Salgado", "given": "Jesus M." } }, { "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": "Synthetic multistability in mammalian cells", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2022 American Association for the Advancement of Science. \n\nReceived 10 February 2021; accepted 29 November 2021. \n\nWe thank M. Budde for suggestions on MultiFate circuit design; J. Tijerina at Caltech Flow Cytometry Facility for help with cell sorting; X. Wang and F. Horns for timely help with experiments during COVID and lab move; S. Xie for help with MultiFate-2 monoclone screening; S. Xie and S. Satia for advice on coding; J. Bois for teaching and sharing Caltech BE150 course materials for mathematical modeling; A. Khalil for suggestions on the choice of zinc fingers; R. Kuintzle, F. Horns, L. Chong, Z. Chen, M. Flynn, H. Klumpe, M. Budde, B. Gu, J. Gregrowicz, and E. Mun for critical feedback; and other members of the Elowitz lab for scientific input and support. \n\nSupported by DARPA (HR0011-17-2-0008, M.B.E.); the Allen Discovery Center program, a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation (UWSC10142, M.B.E.); the Spanish Ministry of Science and Innovation and FEDER (PGC2018-101251-B-I00, J.G.-O.); \"Maria de Maeztu\" Programme for Units of Excellence in R&D (CEX2018-000792-M, J.G.-O.); and the Generalitat de Catalunya (ICREA Academia program, J.G.-O.). M.B.E. is a Howard Hughes Medical Institute investigator. \n\nAuthor contributions: R.Z. and M.B.E. conceived of the project. R.Z. and M.B.E. designed experiments. R.Z. performed experiments. R.Z. and M.B.E. analyzed data. R.Z., J.M.d.R.-S., J.G.-O., and M.B.E. did mathematical modeling. R.Z. and M.B.E. wrote the manuscript with input from all authors. \n\nCompeting interests: R.Z. and M.B.E. are inventors on a US provisional patent application related to this work. \n\nData and materials availability: All DNA constructs (table S2) and cell lines (table S3) are available from M.B.E. or through the Addgene repository under a material agreement with California Institute of Technology. All data generated and all the computational and data analysis and modeling code used in the current study are available at data.caltech.edu/records/1882.\n\nSubmitted - 2021.02.10.430659v1.full.pdf
Supplemental Material - science.abg9765_mdar_reproducibility_checklist.pdf
Supplemental Material - science.abg9765_movies_s1_to_s6.zip
Supplemental Material - science.abg9765_sm.pdf
", "abstract": "In multicellular organisms, gene regulatory circuits generate thousands of molecularly distinct, mitotically heritable states through the property of multistability. Designing synthetic multistable circuits would provide insight into natural cell fate control circuit architectures and would allow engineering of multicellular programs that require interactions among distinct cell types. We created MultiFate, a naturally inspired, synthetic circuit that supports long-term, controllable, and expandable multistability in mammalian cells. MultiFate uses engineered zinc finger transcription factors that transcriptionally self-activate as homodimers and mutually inhibit one another through heterodimerization. Using a model-based design, we engineered MultiFate circuits that generate as many as seven states, each stable for at least 18 days. MultiFate permits controlled state switching and modulation of state stability through external inputs and can be expanded with additional transcription factors. These results provide a foundation for engineering multicellular behaviors in mammalian cells.", "date": "2022-01-21", "date_type": "published", "publication": "Science", "volume": "375", "number": "6578", "publisher": "American Association for the Advancement of Science", "pagerange": "Art. No. eabg9765", "id_number": "CaltechAUTHORS:20210212-105104460", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210212-105104460", "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": "Allen Discovery Center" }, { "agency": "Paul G. Allen Frontiers Group", "grant_number": "UWSC10142" }, { "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" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1126/science.abg9765", "primary_object": { "basename": "science.abg9765_sm.pdf", "url": "https://authors.library.caltech.edu/records/dcas8-y4s76/files/science.abg9765_sm.pdf" }, "related_objects": [ { "basename": "2021.02.10.430659v1.full.pdf", "url": "https://authors.library.caltech.edu/records/dcas8-y4s76/files/2021.02.10.430659v1.full.pdf" }, { "basename": "science.abg9765_mdar_reproducibility_checklist.pdf", "url": "https://authors.library.caltech.edu/records/dcas8-y4s76/files/science.abg9765_mdar_reproducibility_checklist.pdf" }, { "basename": "science.abg9765_movies_s1_to_s6.zip", "url": "https://authors.library.caltech.edu/records/dcas8-y4s76/files/science.abg9765_movies_s1_to_s6.zip" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Zhu, Ronghui; del Rio-Salgado, Jesus M.; et el." }, { "id": "https://authors.library.caltech.edu/records/wp4n2-mww55", "eprint_id": 111294, "eprint_status": "archive", "datestamp": "2023-08-22 12:27:39", "lastmod": "2023-12-22 23:08:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cable-Jennifer", "name": { "family": "Cable", "given": "Jennifer" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "name": { "family": "Domingos", "given": "Ana I." } }, { "name": { "family": "Habib", "given": "Naomi" }, "orcid": "0000-0002-6049-2487" }, { "name": { "family": "Itzkovitz", "given": "Shalev" }, "orcid": "0000-0003-0685-2522" }, { "name": { "family": "Hamidzada", "given": "Homaira" } }, { "name": { "family": "Balzer", "given": "Michael S." }, "orcid": "0000-0003-0508-1260" }, { "name": { "family": "Yanai", "given": "Itai" }, "orcid": "0000-0002-8438-2741" }, { "name": { "family": "Liberali", "given": "Prisca" }, "orcid": "0000-0003-0695-6081" }, { "name": { "family": "Whited", "given": "Jessica" }, "orcid": "0000-0002-3709-6515" }, { "name": { "family": "Streets", "given": "Aaron" }, "orcid": "0000-0002-3909-8389" }, { "id": "Cai-Long", "name": { "family": "Cai", "given": "Long" }, "orcid": "0000-0002-7154-5361" }, { "name": { "family": "Stergachis", "given": "Andrew B." }, "orcid": "0000-0002-1299-3674" }, { "name": { "family": "Hong", "given": "Clarice Kit Yee" }, "orcid": "0000-0002-9485-1425" }, { "name": { "family": "Keren", "given": "Leeat" }, "orcid": "0000-0002-6799-6303" }, { "name": { "family": "Guilliams", "given": "Martin" }, "orcid": "0000-0003-3525-7570" }, { "name": { "family": "Alon", "given": "Uri" } }, { "name": { "family": "Shalek", "given": "Alex K." }, "orcid": "0000-0001-5670-8778" }, { "name": { "family": "Hamel", "given": "Regan" }, "orcid": "0000-0003-0013-6226" }, { "name": { "family": "Pfau", "given": "Sarah J." }, "orcid": "0000-0001-7528-0666" }, { "name": { "family": "Raj", "given": "Arjun" } }, { "name": { "family": "Quake", "given": "Stephen R." }, "orcid": "0000-0002-1613-0809" }, { "name": { "family": "Zhang", "given": "Nancy R." } }, { "name": { "family": "Fan", "given": "Jean" }, "orcid": "0000-0002-0212-5451" }, { "name": { "family": "Trapnell", "given": "Cole" }, "orcid": "0000-0002-8105-4347" }, { "name": { "family": "Wang", "given": "Bo" } }, { "name": { "family": "Greenwald", "given": "Noah F." }, "orcid": "0000-0002-7836-4379" }, { "name": { "family": "Vento-Tormo", "given": "Roser" } }, { "name": { "family": "Santos", "given": "Silvia D. M." }, "orcid": "0000-0002-2906-7888" }, { "name": { "family": "Spencer", "given": "Sabrina L." }, "orcid": "0000-0002-5798-3007" }, { "name": { "family": "Garcia", "given": "Hernan G." } }, { "name": { "family": "Arekatla", "given": "Geethika" } }, { "name": { "family": "Gaiti", "given": "Federico" }, "orcid": "0000-0001-5111-8816" }, { "name": { "family": "Arbel-Goren", "given": "Rinat" }, "orcid": "0000-0002-7253-2036" }, { "name": { "family": "Rulands", "given": "Steffen" }, "orcid": "0000-0001-6398-1553" }, { "name": { "family": "Junker", "given": "Jan Philipp" }, "orcid": "0000-0002-2826-8290" }, { "name": { "family": "Klein", "given": "Allon M." }, "orcid": "0000-0001-8913-7879" }, { "name": { "family": "Morris", "given": "Samantha A." } }, { "name": { "family": "Murray", "given": "John I." } }, { "name": { "family": "Galloway", "given": "Kate E." }, "orcid": "0000-0001-7416-3193" }, { "name": { "family": "Ratz", "given": "Michael" }, "orcid": "0000-0002-9795-8033" }, { "name": { "family": "Romeike", "given": "Merrit" }, "orcid": "0000-0002-5890-2213" } ] }, "title": "Single cell biology\u2014a Keystone Symposia report", "ispublished": "pub", "full_text_status": "restricted", "keywords": "development; differentiation; lineage tracing; reprogramming; single cell sequencing; spatial transcriptomics", "note": "\u00a9 2021 New York Academy of Sciences. \n\nIssue Online: 20 December 2021; Version of Record online: 03 October 2021; Manuscript accepted: 24 August 2021; Manuscript received: 24 August 2021. \n\nM.S. Balzer is supported by German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) Grant BA 6205/2-1. M. Ratz is supported by a DFG Research Fellowship, Grant RA 2889/1-1. J. Fan is supported by the National Science Foundation, Grant No. 2047611. \n\nThe authors declare no competing interests.", "abstract": "Single cell biology has the potential to elucidate many critical biological processes and diseases, from development and regeneration to cancer. Single cell analyses are uncovering the molecular diversity of cells, revealing a clearer picture of the variation among and between different cell types. New techniques are beginning to unravel how differences in cell state\u2014transcriptional, epigenetic, and other characteristics\u2014can lead to different cell fates among genetically identical cells, which underlies complex processes such as embryonic development, drug resistance, response to injury, and cellular reprogramming. Single cell technologies also pose significant challenges relating to processing and analyzing vast amounts of data collected. To realize the potential of single cell technologies, new computational approaches are needed. On March 17\u201319, 2021, experts in single cell biology met virtually for the Keystone eSymposium \"Single Cell Biology\" to discuss advances both in single cell applications and technologies.", "date": "2021-12", "date_type": "published", "publication": "Annals of the New York Academy of Sciences", "volume": "1506", "publisher": "New York Academy of Sciences", "pagerange": "74-97", "id_number": "CaltechAUTHORS:20211008-183538677", "issn": "0077-8923", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211008-183538677", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "BA 6205/2-1" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "RA 2889/1-1" }, { "agency": "NSF", "grant_number": "DBI-2047611" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1111/nyas.14692", "resource_type": "article", "pub_year": "2021", "author_list": "Cable, Jennifer; Elowitz, Michael B.; et el." }, { "id": "https://authors.library.caltech.edu/records/fq0yw-pnf65", "eprint_id": 109625, "eprint_status": "archive", "datestamp": "2023-08-22 10:53:23", "lastmod": "2023-12-22 23:19:55", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gong-Wuming", "name": { "family": "Gong", "given": "Wuming" } }, { "id": "Granados-Alejandro-A", "name": { "family": "Granados", "given": "Alejandro A." }, "orcid": "0000-0002-6275-9800" }, { "name": { "family": "Hu", "given": "Jingyuan" } }, { "name": { "family": "Jones", "given": "Matthew G." } }, { "name": { "family": "Raz", "given": "Ofir" } }, { "name": { "family": "Salvador-Mart\u00ednez", "given": "Irepan" } }, { "name": { "family": "Zhang", "given": "Hanrui" } }, { "id": "Chow-Ke-Huan-K", "name": { "family": "Chow", "given": "Ke-Huan K." }, "orcid": "0000-0002-7317-2669" }, { "name": { "family": "Kwak", "given": "Il-Youp" } }, { "name": { "family": "Retkute", "given": "Renata" } }, { "name": { "family": "Prusokas", "given": "Alidivinas" } }, { "name": { "family": "Prusokas", "given": "Augustinas" } }, { "name": { "family": "Khodaverdian", "given": "Alex" } }, { "name": { "family": "Zhang", "given": "Richard" } }, { "name": { "family": "Rao", "given": "Suhas" } }, { "name": { "family": "Wang", "given": "Robert" } }, { "name": { "family": "Rennert", "given": "Phil" } }, { "name": { "family": "Saipradeep", "given": "Vangala G." } }, { "name": { "family": "Sivadasan", "given": "Naveen" } }, { "name": { "family": "Rao", "given": "Aditya" } }, { "name": { "family": "Joseph", "given": "Thomas" } }, { "name": { "family": "Srinivasan", "given": "Rajgopal" } }, { "name": { "family": "Peng", "given": "Jiajie" } }, { "name": { "family": "Han", "given": "Lu" } }, { "name": { "family": "Shang", "given": "Xuequn" } }, { "name": { "family": "Garry", "given": "Daniel J." } }, { "name": { "family": "Yu", "given": "Thomas" } }, { "name": { "family": "Chung", "given": "Verena" } }, { "name": { "family": "Mason", "given": "Michael" } }, { "name": { "family": "Liu", "given": "Zhandong" } }, { "name": { "family": "Guan", "given": "Yuanfang" } }, { "name": { "family": "Yosef", "given": "Nir" } }, { "name": { "family": "Shendure", "given": "Jay" } }, { "name": { "family": "Telford", "given": "Maximilian J." } }, { "name": { "family": "Shapiro", "given": "Ehud" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "name": { "family": "Meyer", "given": "Pablo" } } ] }, "title": "Benchmarked approaches for reconstruction of in\u00a0vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees", "ispublished": "pub", "full_text_status": "public", "keywords": "cell lineage tracing; intmemoir; CRISPR; C.\u00a0elegans; crowdsourcing; benchmarking; machine learning; simulation; lineage reconstruction; M. musculus", "note": "\u00a9 2021 The Author(s). Published by Elsevier. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). \n\nReceived 21 August 2020, Revised 1 February 2021, Accepted 11 May 2021, Available online 18 June 2021. \n\nFunding: the research was funded by the Paul G. Allen Frontiers Group Prime Awarding Agency and HFSP (RGP0002/2016) to I.S.-M. and M.J.T. \n\nAuthor contributions. A.A.G., I.S.-M., O.R., Y.G., Z.L., N.Y., J.S., M.J.T., E.S., M.B.E., and P.M. designed research; A.A.G., O.R., I.S.-M., W.G., J.H., H.Z., R.R., M.G.J., and P.M. analyzed data; K.-H.K.C., I.-Y.K., Al.P., Au.P., A.K., R.Z., S.R., R.W., P.R., V.G.S., N.S., A.R., T.J., R.S., J.P., L.H., and X.S. analyzed data; A.A.G., O.R., I.S., W.G., J.H., H.Z., R.R., M.G.J., and P.M., wrote the manuscript. \n\nData and software availability. We compiled all the challenge related methods in a wiki: https://github.com/Lineage-Reconstruction-DREAM-Challenge/hub/wiki. \n\nData availability. All challenge datasets and participants submissions are available at: https://www.synapse.org/#!Synapse:syn20821809. \n\nThe authors declare no competing interests.\n\nPublished - 1-s2.0-S2405471221001940-main.pdf
Supplemental Material - 1-s2.0-S2405471221001940-mmc1.pdf
Supplemental Material - 1-s2.0-S2405471221001940-mmc2.txt
Supplemental Material - 1-s2.0-S2405471221001940-mmc3.rtf
Supplemental Material - 1-s2.0-S2405471221001940-mmc4.rtf
Supplemental Material - 1-s2.0-S2405471221001940-mmc5.pdf
", "abstract": "The recent advent of CRISPR and other molecular tools enabled the reconstruction of cell lineages based on induced DNA mutations and promises to solve the ones of more complex organisms. To date, no lineage reconstruction algorithms have been rigorously examined for their performance and robustness across dataset types and number of cells. To benchmark such methods, we decided to organize a DREAM challenge using in vitro experimental intMEMOIR recordings and in silico data for a C. elegans lineage tree of about 1,000 cells and a Mus musculus tree of 10,000 cells. Some of the 22 approaches submitted had excellent performance, but structural features of the trees prevented optimal reconstructions. Using smaller sub-trees as training sets proved to be a good approach for tuning algorithms to reconstruct larger trees. The simulation and reconstruction methods here generated delineate a potential way forward for solving larger cell lineage trees such as in mouse.", "date": "2021-08-18", "date_type": "published", "publication": "Cell Systems", "volume": "12", "number": "8", "publisher": "Cell Press", "pagerange": "810-826", "id_number": "CaltechAUTHORS:20210628-191053293", "issn": "2405-4712", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210628-191053293", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Paul G. Allen Frontiers Group" }, { "agency": "Human Frontier Science Program", "grant_number": "RGP0002/2016" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.cels.2021.05.008", "primary_object": { "basename": "1-s2.0-S2405471221001940-mmc3.rtf", "url": "https://authors.library.caltech.edu/records/fq0yw-pnf65/files/1-s2.0-S2405471221001940-mmc3.rtf" }, "related_objects": [ { "basename": "1-s2.0-S2405471221001940-mmc4.rtf", "url": "https://authors.library.caltech.edu/records/fq0yw-pnf65/files/1-s2.0-S2405471221001940-mmc4.rtf" }, { "basename": "1-s2.0-S2405471221001940-mmc5.pdf", "url": "https://authors.library.caltech.edu/records/fq0yw-pnf65/files/1-s2.0-S2405471221001940-mmc5.pdf" }, { "basename": "1-s2.0-S2405471221001940-main.pdf", "url": "https://authors.library.caltech.edu/records/fq0yw-pnf65/files/1-s2.0-S2405471221001940-main.pdf" }, { "basename": "1-s2.0-S2405471221001940-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/fq0yw-pnf65/files/1-s2.0-S2405471221001940-mmc1.pdf" }, { "basename": "1-s2.0-S2405471221001940-mmc2.txt", "url": "https://authors.library.caltech.edu/records/fq0yw-pnf65/files/1-s2.0-S2405471221001940-mmc2.txt" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Gong, Wuming; Granados, Alejandro A.; et el." }, { "id": "https://authors.library.caltech.edu/records/jg2yt-f4n17", "eprint_id": 108706, "eprint_status": "archive", "datestamp": "2023-08-20 02:51:07", "lastmod": "2023-12-22 23:19:57", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chen-Zibo", "name": { "family": "Chen", "given": "Zibo" }, "orcid": "0000-0003-2990-2895" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Programmable protein circuit design", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 Elsevier Inc. \n\nAvailable online 12 April 2021. \n\nWe thank E. Winfree, J. Gregrowicz, F. Horns, L. Chong, S. Boyken, A. Askary, and M. Budde for helpful discussions. This work was supported by National Institutes of Health grant R01 MH116508, the Allen Discovery Center program under award number UWSC10142, a Paul G. Allen Frontiers Group-advised program of the Paul G. Allen Family Foundation, and by the National Institute of Biomedical Imaging and Bioengineering of the National Institutes of Health under award number R01EB030015. Z.C. was 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. 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 National Institutes of Health. \n\nDeclaration of interests: Z.C. and M.B.E. are inventors on patents and patent applications related to protein circuit design.\n\nAccepted Version - nihms-1690930.pdf
", "abstract": "A fundamental challenge in synthetic biology is to create molecular circuits that can program complex cellular functions. Because proteins can bind, cleave, and chemically modify one another and interface directly and rapidly with endogenous pathways, they could extend the capabilities of synthetic circuits beyond what is possible with gene regulation alone. However, the very diversity that makes proteins so powerful also complicates efforts to harness them as well-controlled synthetic circuit components. Recent work has begun to address this challenge, focusing on principles such as orthogonality and composability that permit construction of diverse circuit-level functions from a limited set of engineered protein components. These approaches are now enabling the engineering of circuits that can sense, transmit, and process information; dynamically control cellular behaviors; and enable new therapeutic strategies, establishing a powerful paradigm for programming biology.", "date": "2021-04-29", "date_type": "published", "publication": "Cell", "volume": "184", "number": "9", "publisher": "Cell Press", "pagerange": "2284-2301", "id_number": "CaltechAUTHORS:20210413-072526147", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210413-072526147", "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": "Paul G. Allen Family Foundation" }, { "agency": "NIH", "grant_number": "R01EB030015" }, { "agency": "Damon Runyon Cancer Research Foundation", "grant_number": "DRG-2388-20" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.cell.2021.03.007", "pmcid": "PMC8087657", "primary_object": { "basename": "nihms-1690930.pdf", "url": "https://authors.library.caltech.edu/records/jg2yt-f4n17/files/nihms-1690930.pdf" }, "resource_type": "article", "pub_year": "2021", "author_list": "Chen, Zibo and Elowitz, Michael B." }, { "id": "https://authors.library.caltech.edu/records/zjfrp-a9k69", "eprint_id": 101552, "eprint_status": "archive", "datestamp": "2023-08-20 02:41:40", "lastmod": "2023-12-22 23:08:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chow-Ke-Huan-K", "name": { "family": "Chow", "given": "Ke-Huan K." }, "orcid": "0000-0002-7317-2669" }, { "id": "Budde-Mark-W", "name": { "family": "Budde", "given": "Mark W." }, "orcid": "0000-0002-4359-1424" }, { "id": "Granados-Alejandro-A", "name": { "family": "Granados", "given": "Alejandro A." }, "orcid": "0000-0002-6275-9800" }, { "id": "Cabrera-Maria", "name": { "family": "Cabrera", "given": "Maria" }, "orcid": "0000-0001-7026-1132" }, { "id": "Yoon-Shinae", "name": { "family": "Yoon", "given": "Shinae" } }, { "id": "Cho-Soomin", "name": { "family": "Cho", "given": "Soomin" }, "orcid": "0000-0003-2971-9337" }, { "id": "Huang-Ting-Hao", "name": { "family": "Huang", "given": "Ting-hao" }, "orcid": "0000-0002-2546-3525" }, { "id": "Koulena-Noushin", "name": { "family": "Koulena", "given": "Noushin" }, "orcid": "0000-0002-9419-5712" }, { "id": "Frieda-Kirsten-L", "name": { "family": "Frieda", "given": "Kirsten L." } }, { "id": "Cai-Long", "name": { "family": "Cai", "given": "Long" }, "orcid": "0000-0002-7154-5361" }, { "id": "Lois-C", "name": { "family": "Lois", "given": "Carlos" }, "orcid": "0000-0002-7305-2317" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Imaging cell lineage with a synthetic digital recording system", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 American Association for the Advancement of Science.\nThis is an article distributed under the terms of the Science Journals Default License.\n\nReceived 20 February 2020; accepted 25 February 2021.\n\nWe thank L. Sanchez-Guardado, H. Choi, C. Calvert, G. Shin, C. Tischbirek, Y. Takei, S. Shah, and N. Pierson for technical assistance and advice; A. Askary, X. Gao, F. Horns, D. Chadly, C. Su, and other members of the Elowitz lab for critical feedback on the manuscript; and A. Shur, P. Meyer, R. Lu, and J. Linton for scientific input and advice. \n\nFunding: This research was supported by the Allen Discovery Center program, a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation (grant UWSC10142 to M.B.E., C.L., and L.C.), the National Institutes of Health (NIH) (grant R01 MH116508 to M.B.E., C.L., and L.C.), and Burroughs Wellcome Fund CASI (K.L.F.), and M.B.E. is a Howard Hughes Medical Institute investigator. M.B.E. acknowledges Fritz Thyssen Stiftung for support for a visiting fellowship to Berlin. \n\nAuthors contributions: K.K.C., M.W.B., A.A.G., K.L.F., L.C., C.L., and M.B.E. designed research. K.K.C., M.W.B., M.C., S.Y., S.C., and N.K. performed experiments. A.A.G., M.W.B., K.K.C., T.H., C.L., and M.B.E. analyzed data. K.K.C., M.W.B., A.A.G., C.L., and M.B.E. wrote the manuscript. \n\nCompeting interests: K.L.F., K.K.C., L.C., and M.B.E. are inventors on a patent application for recording technologies. \n\nData and materials availability: Plasmids to implement intMEMOIR in mES cells and Drosophila melanogaster are available from the Addgene repository (ID: 158387, 158389, 158390, and 158391), Drosophila melanogaster lines are available from the Bloomington repository (RRID: BDSC_90853 and BDSC_90854), and the intMEM1 cell line will be made available from C.L. and M.B.E. under the terms of the Uniform Biological Material Transfer Agreement (UBMTA). The data, code, and analysis to generate the results in the manuscript and the sequence information of relevant constructs are freely available on (63).\n\nSubmitted - 2020.02.21.958678v2.full.pdf
Supplemental Material - abb3099_Chow_SM.pdf
Supplemental Material - abb3099_Reproducibility_Checklist.pdf
Supplemental Material - abb3099_table_S1.xlsx
Supplemental Material - abb3099_table_S2.xlsx
Supplemental Material - abb3099_table_S3.xlsx
Supplemental Material - abb3099_table_S4.xlsx
Supplemental Material - abb3099s1.mp4
Supplemental Material - abb3099s2.mp4
Supplemental Material - abb3099s3.mp4
", "abstract": "Cell lineage plays a pivotal role in cell fate determination. Chow et al. demonstrate the use of an integrase-based synthetic barcode system called intMEMOIR, which uses the serine integrase Bxb1 to perform irreversible nucleotide edits. Inducible editing either deletes or inverts its target region, thus encoding information in three-state memory elements, or trits, and avoiding undesired recombination events. Using intMEMOIR combined with single-molecule fluorescence in situ hybridization, the authors were able to identify clonal structures as well as gene expression patterns in the fly brain, enabling both clonal analysis and expression profiling with intact spatial information. The ability to visualize cell lineage relationships directly within their native tissue context provides insights into development and disease.", "date": "2021-04-09", "date_type": "published", "publication": "Science", "volume": "372", "number": "6538", "publisher": "American Association for the Advancement of Science", "pagerange": "Art. No. eabb3099", "id_number": "CaltechAUTHORS:20200225-135944187", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200225-135944187", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Paul G. Allen Family Foundation", "grant_number": "UWSC10142" }, { "agency": "NIH", "grant_number": "R01 MH116508" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Fritz Thyssen Stiftung" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1126/science.abb3099", "primary_object": { "basename": "abb3099_table_S2.xlsx", "url": "https://authors.library.caltech.edu/records/zjfrp-a9k69/files/abb3099_table_S2.xlsx" }, "related_objects": [ { "basename": "abb3099_table_S3.xlsx", "url": "https://authors.library.caltech.edu/records/zjfrp-a9k69/files/abb3099_table_S3.xlsx" }, { "basename": "abb3099_table_S4.xlsx", "url": "https://authors.library.caltech.edu/records/zjfrp-a9k69/files/abb3099_table_S4.xlsx" }, { "basename": "abb3099s2.mp4", "url": "https://authors.library.caltech.edu/records/zjfrp-a9k69/files/abb3099s2.mp4" }, { "basename": "abb3099_Reproducibility_Checklist.pdf", "url": "https://authors.library.caltech.edu/records/zjfrp-a9k69/files/abb3099_Reproducibility_Checklist.pdf" }, { "basename": "abb3099_Chow_SM.pdf", "url": "https://authors.library.caltech.edu/records/zjfrp-a9k69/files/abb3099_Chow_SM.pdf" }, { "basename": "abb3099_table_S1.xlsx", "url": "https://authors.library.caltech.edu/records/zjfrp-a9k69/files/abb3099_table_S1.xlsx" }, { "basename": "abb3099s1.mp4", "url": "https://authors.library.caltech.edu/records/zjfrp-a9k69/files/abb3099s1.mp4" }, { "basename": "abb3099s3.mp4", "url": "https://authors.library.caltech.edu/records/zjfrp-a9k69/files/abb3099s3.mp4" }, { "basename": "2020.02.21.958678v2.full.pdf", "url": "https://authors.library.caltech.edu/records/zjfrp-a9k69/files/2020.02.21.958678v2.full.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Chow, Ke-Huan K.; Budde, Mark W.; et el." }, { "id": "https://authors.library.caltech.edu/records/x8ffe-pb390", "eprint_id": 98783, "eprint_status": "archive", "datestamp": "2023-08-19 19:20:43", "lastmod": "2023-10-20 22:10:26", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Askary-Amjad", "name": { "family": "Askary", "given": "Amjad" }, "orcid": "0000-0002-2913-8498" }, { "id": "S\u00e1nchez-Guardado-Luis", "name": { "family": "S\u00e1nchez-Guardado", "given": "Luis" }, "orcid": "0000-0001-5598-8608" }, { "id": "Linton-James-M", "name": { "family": "Linton", "given": "James M." } }, { "id": "Chadly-Duncan-M", "name": { "family": "Chadly", "given": "Duncan M." }, "orcid": "0000-0002-8417-1522" }, { "id": "Budde-Mark-W", "name": { "family": "Budde", "given": "Mark W." }, "orcid": "0000-0002-4359-1424" }, { "id": "Cai-Long", "name": { "family": "Cai", "given": "Long" }, "orcid": "0000-0002-7154-5361" }, { "id": "Lois-C", "name": { "family": "Lois", "given": "Carlos" }, "orcid": "0000-0002-7305-2317" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 Springer Nature Limited. \n\nReceive 18 December 2018; Revised 23 September 2019; Accepted 28 September 2019; Published 18 November 2019. \n\nData availability: Data that are not included in the paper are available at https://data.caltech.edu/records/1303 (https://doi.org/10.22002/D1.1303) or from the corresponding author. \n\nCode availability: Scripts for all analyses presented in this paper are available at https://data.caltech.edu/records/1303 (https://doi.org/10.22002/D1.1303) or from the corresponding author. \n\nWe are grateful to M. Schwartzkopf, H. Choi and N. Pierce for advice with HCR; K. Chow for help with cell culture; S. Shah for insightful discussions; and F. Ding for advice on image analysis. We also thank all the members of Elowitz, Cai and Lois laboratories for helpful discussions and critical feedback. Some of the imaging for this paper was performed in the Biological Imaging Facility with the support of the Caltech Beckman Institute and the Arnold and Mabel Beckman Foundation. The research was funded by the National Institutes of Health (NIH) (grant R01 MH116508 to M.B.E., C.L. and L.C.), the Paul G. Allen Frontiers Group and Prime Awarding Agency (grant UWSC10142 to M.B.E., C.L. and L.C.), the Jane Coffin Childs Memorial Fund for Medical Research (grant 61-1650 to A.A.) and an NIH\u2013NRSA training grant (T32 GM07616 to D.M.C.). M.B.E. is a Howard Hughes Medical Institute investigator. \n\nAuthor Contributions: A.A., L.S.-G., L.C., C.L. and M.B.E. designed research. A.A., L.S.-G., J.M.L. and M.W.B. performed experiments. A.A., D.M.C. and M.B.E. analyzed data. A.A. and M.B.E. wrote the manuscript. \n\nCompeting interests: Authors have submitted a provisional patent application that is based on the technology described in this manuscript.\n\nIn the version of this article initially published, the y-axis label in Fig. 1g read \"Proportion of cells with active site(s) (%).\" The correct label is \"Proportion of cells with no active site(s) (%).\" And, near the bottom of Fig. 4a, the probe for original variant (orange) was shown with a C nucleotide and the probe for edited base variants (red) was shown with T; these nucleotides were switched with each other. The errors have been corrected in the HTML and PDF versions of the article.\n\nAccepted Version - nihms-1540812.pdf
Supplemental Material - 41587_2019_299_MOESM1_ESM.pdf
Supplemental Material - 41587_2019_299_MOESM2_ESM.pdf
Supplemental Material - 41587_2019_299_MOESM3_ESM.xlsx
", "abstract": "Molecular barcoding technologies that uniquely identify single cells are hampered by limitations in barcode measurement. Readout by sequencing does not preserve the spatial organization of cells in tissues, whereas imaging methods preserve spatial structure but are less sensitive to barcode sequence. Here we introduce a system for image-based readout of short (20-base-pair) DNA barcodes. In this system, called Zombie, phage RNA polymerases transcribe engineered barcodes in fixed cells. The resulting RNA is subsequently detected by fluorescent in situ hybridization. Using competing match and mismatch probes, Zombie can accurately discriminate single-nucleotide differences in the barcodes. This method allows in situ readout of dense combinatorial barcode libraries and single-base mutations produced by CRISPR base editors without requiring barcode expression in live cells. Zombie functions across diverse contexts, including cell culture, chick embryos and adult mouse brain tissue. The ability to sensitively read out compact and diverse DNA barcodes by imaging will facilitate a broad range of barcoding and genomic recording strategies.", "date": "2020-01", "date_type": "published", "publication": "Nature Biotechnology", "volume": "38", "number": "1", "publisher": "Nature Publishing Group", "pagerange": "66-75", "id_number": "CaltechAUTHORS:20190920-163128957", "issn": "1087-0156", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190920-163128957", "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": "NIH", "grant_number": "R01 MH116508" }, { "agency": "Paul G. Allen Frontiers Group", "grant_number": "UWSC10142" }, { "agency": "Jane Coffin Childs Memorial Fund for Medical Research", "grant_number": "61-1650" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 GM07616" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1038/s41587-019-0299-4", "pmcid": "PMC6954335", "primary_object": { "basename": "41587_2019_299_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/x8ffe-pb390/files/41587_2019_299_MOESM1_ESM.pdf" }, "related_objects": [ { "basename": "41587_2019_299_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/x8ffe-pb390/files/41587_2019_299_MOESM2_ESM.pdf" }, { "basename": "41587_2019_299_MOESM3_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/x8ffe-pb390/files/41587_2019_299_MOESM3_ESM.xlsx" }, { "basename": "nihms-1540812.pdf", "url": "https://authors.library.caltech.edu/records/x8ffe-pb390/files/nihms-1540812.pdf" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Askary, Amjad; S\u00e1nchez-Guardado, Luis; et el." }, { "id": "https://authors.library.caltech.edu/records/xj81z-bfr11", "eprint_id": 97231, "eprint_status": "archive", "datestamp": "2023-08-19 16:05:31", "lastmod": "2023-10-20 22:04:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Li-Pulin", "name": { "family": "Li", "given": "Pulin" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Communication codes in developmental signaling pathways", "ispublished": "pub", "full_text_status": "public", "keywords": "Communication codes, Signal processing, Pathway\narchitecture", "note": "\u00a9 2019 Published by The Company of Biologists Ltd. \n\nWe thank L. Goentoro, J. Briscoe, A. Kicheva, S. Megason, A. Aulehla and E. Siggia for hepful discussion. We also thank C. L. Frick, N. Nandagopal, J. M. Linton, H. Klumpe, R. Kuintzle, L. Santat, R. Zhu and other members of the Elowitz lab for critical reading of the manuscript. \n\nThe authors declare no competing or financial interests. \n\nThe authors are supported by the Howard Hughes Medical Institute (M.B.E.) and the Eunice Kennedy Shriver National Institute of Child Health and Human Development Pathway to Independence Career Award (R00HD087532 to P.L.). Deposited in PMC for release after 12 months.\n\nPublished - dev170977.full.pdf
", "abstract": "A handful of core intercellular signaling pathways play pivotal roles in a broad variety of developmental processes. It has remained puzzling how so few pathways can provide the precision and specificity of cell-cell communication required for multicellular development. Solving this requires us to quantitatively understand how developmentally relevant signaling information is actively sensed, transformed and spatially distributed by signaling pathways. Recently, single cell analysis and cell-based reconstitution, among other approaches, have begun to reveal the 'communication codes' through which information is represented in the identities, concentrations, combinations and dynamics of extracellular ligands. They have also revealed how signaling pathways decipher these features and control the spatial distribution of signaling in multicellular contexts. Here, we review recent work reporting the discovery and analysis of communication codes and discuss their implications for diverse developmental processes.", "date": "2019-06", "date_type": "published", "publication": "Development", "volume": "146", "number": "12", "publisher": "Company of Biologists", "pagerange": "Art. No. dev170977", "id_number": "CaltechAUTHORS:20190718-110919202", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190718-110919202", "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": "R00HD087532" } ] }, "doi": "10.1242/dev.170977", "pmcid": "PMC6602343", "primary_object": { "basename": "dev170977.full.pdf", "url": "https://authors.library.caltech.edu/records/xj81z-bfr11/files/dev170977.full.pdf" }, "resource_type": "article", "pub_year": "2019", "author_list": "Li, Pulin and Elowitz, Michael B." }, { "id": "https://authors.library.caltech.edu/records/6gyk0-6zr59", "eprint_id": 90703, "eprint_status": "archive", "datestamp": "2023-08-22 01:40:15", "lastmod": "2023-10-23 16:10:44", "type": "article", "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": "Constitutive splicing and economies of scale in gene expression", "ispublished": "pub", "full_text_status": "public", "keywords": "Cellular imaging; Fluorescence in situ hybridization; RNA splicing", "note": "\u00a9 2019 Nature Publishing Group. \n\nReceived 27 November 2018; Accepted 11 April 2019; Published 27 May 2019. \n\nData availability: Source data for Figs. 2, 3d,e, 4 and 5d are available online. All other original data, Matlab code, DNA constructs and cell lines are available upon request. \n\nWe thank T. Cooper for DNA constructs of minigene RG6, P. Li for providing Gli1 inducible protocol, Z. Singer and Y. Antebi for technical assistance, M. Guttman, C. Su, H. Klumpe, M. Budde and L. Bintu for critical feedbacks on the manuscript. We also thank M. Guttman, G. Seelig, D. Black, D. Baltimore, M. Moore, J.G. Ojalvo and N. Wingreen for discussion and feedback on the project. The 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\nAuthor Contributions: F.D. conceived of the project. F.D. and M.B.E. designed experiments. F.D. performed experiments, analyzed data and did mathematical modeling. F.D. and M.B.E. wrote the manuscript. \n\nThe authors declare no competing interests.\n\nAccepted Version - nihms-1033862.pdf
Submitted - 457432.full.pdf
Supplemental Material - 41594_2019_226_MOESM1_ESM.pdf
Supplemental Material - 41594_2019_226_MOESM2_ESM.pdf
Supplemental Material - 41594_2019_226_MOESM3_ESM.zip
Supplemental Material - 41594_2019_226_MOESM4_ESM.zip
Supplemental Material - 41594_2019_226_MOESM5_ESM.zip
Supplemental Material - 41594_2019_226_MOESM6_ESM.zip
", "abstract": "In eukaryotic cells, many introns are constitutively, rather than alternatively, spliced and therefore do not contribute to isoform diversification. It has remained unclear what functional roles such constitutive splicing provides. To explore this issue, we asked how splicing affects the efficiency with which individual pre-messenger RNA transcripts are productively processed across different gene expression levels. We developed a quantitative single-molecule fluorescence in situ hybridization-based method to quantify splicing efficiency at transcription active sites in single cells. We found that both natural and synthetic genes in mouse and human cells exhibited an unexpected 'economy of scale' behavior in which splicing efficiency increased with transcription rate. Correlations between splicing efficiency and spatial proximity to nuclear speckles could explain this counterintuitive behavior. Functionally, economy of scale splicing represents a non-linear filter that amplifies the expression of genes when they are more strongly transcribed. These results indicate that constitutive splicing plays an active functional role in modulating gene expression.", "date": "2019-06", "date_type": "published", "publication": "Nature Structural & Molecular Biology", "volume": "26", "number": "6", "publisher": "Nature Publishing Group", "pagerange": "424-432", "id_number": "CaltechAUTHORS:20181107-102333115", "issn": "1545-9985", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181107-102333115", "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)" } ] }, "doi": "10.1038/s41594-019-0226-x", "pmcid": "PMC6663491", "primary_object": { "basename": "457432.full.pdf", "url": "https://authors.library.caltech.edu/records/6gyk0-6zr59/files/457432.full.pdf" }, "related_objects": [ { "basename": "nihms-1033862.pdf", "url": "https://authors.library.caltech.edu/records/6gyk0-6zr59/files/nihms-1033862.pdf" }, { "basename": "41594_2019_226_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/6gyk0-6zr59/files/41594_2019_226_MOESM1_ESM.pdf" }, { "basename": "41594_2019_226_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/6gyk0-6zr59/files/41594_2019_226_MOESM2_ESM.pdf" }, { "basename": "41594_2019_226_MOESM3_ESM.zip", "url": "https://authors.library.caltech.edu/records/6gyk0-6zr59/files/41594_2019_226_MOESM3_ESM.zip" }, { "basename": "41594_2019_226_MOESM4_ESM.zip", "url": "https://authors.library.caltech.edu/records/6gyk0-6zr59/files/41594_2019_226_MOESM4_ESM.zip" }, { "basename": "41594_2019_226_MOESM5_ESM.zip", "url": "https://authors.library.caltech.edu/records/6gyk0-6zr59/files/41594_2019_226_MOESM5_ESM.zip" }, { "basename": "41594_2019_226_MOESM6_ESM.zip", "url": "https://authors.library.caltech.edu/records/6gyk0-6zr59/files/41594_2019_226_MOESM6_ESM.zip" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Ding, Fangyuan and Elowitz, Michael B." }, { "id": "https://authors.library.caltech.edu/records/t7nsk-pqz47", "eprint_id": 90525, "eprint_status": "archive", "datestamp": "2023-08-19 13:50:29", "lastmod": "2023-10-20 22:08:08", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nandagopal-N", "name": { "family": "Nandagopal", "given": "Nagarajan" } }, { "id": "Santat-L-A", "name": { "family": "Santat", "given": "Leah A." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Cis-activation in the Notch signaling pathway", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019, Nandagopal et al. This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited. \n\nReceived: 26 April 2018; Accepted: 09 January 2019; Published: 10 January 2019. \n\nThis work was supported by Howard Hughes Medical Institute (M.B.E.), and the Defense Advanced Research Projects Agency under Contract No. HR0011-16-0138, by the National Institutes of Health grant R01 HD075335 and the NSF under grant EFRI 1137269. N.N. was a Howard Hughes Medical Institute International Student Research fellow. We thank Pulin Li, Mark Budde, Heidi Klumpe, Ronghui Zhu, Rachael Kuintzle, Laurent Potvin-Trottier and James Linton for critical feedback on the manuscript. Harry Choi and Colby Calvert, Caltech Flow Cytometry Facility, Caltech Biological Imaging Facility, and the Millard and Muriel Jacobs Genetics and Genomics Laboratory at Caltech provided essential technical assistance. \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:\nNagarajan Nandagopal, Leah A Santat, Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Writing\u2014original draft, Writing\u2014review and editing; Michael B Elowitz, Conceptualization, Resources, Supervision, Funding acquisition, Investigation, Methodology, Writing\u2014original draft, Project administration, Writing\u2014review and editing. \n\nThe authors declare that no competing interests exist. \n\nData availability: RNA sequencing data have been deposited in GEO under accession codes GSE113937. Source data files have been provided for Figure 5.\n\nPublished - elife-37880-v2.pdf
Submitted - 313171.full.pdf
Supplemental Material - elife-37880-supp-v1.zip
", "abstract": "The Notch signaling pathway consists of transmembrane ligands and receptors that can interact both within the same cell (cis) and across cell boundaries (trans). Previous work has shown that cis-interactions act to inhibit productive signaling. Here, by analyzing Notch activation in single cells while controlling cell density and ligand expression level, we show that cis-ligands can also activate Notch receptors. This cis-activation process resembles trans-activation in its ligand level dependence, susceptibility to cis-inhibition, and sensitivity to Fringe modification. Cis-activation occurred for multiple ligand-receptor pairs, in diverse cell types, and affected survival in neural stem cells. Finally, mathematical modeling shows how cis-activation could potentially expand the capabilities of Notch signaling, for example enabling 'negative' (repressive) signaling. These results establish cis-activation as an additional mode of signaling in the Notch pathway, and should contribute to a more complete understanding of how Notch signaling functions in developmental, physiological, and biomedical contexts.", "date": "2019-01-10", "date_type": "published", "publication": "eLife", "volume": "8", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e37880", "id_number": "CaltechAUTHORS:20181030-150639915", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181030-150639915", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)", "grant_number": "HR0011-16-0138" }, { "agency": "NIH", "grant_number": "R01 HD075335" }, { "agency": "NSF", "grant_number": "EFRI-1137269" } ] }, "doi": "10.7554/eLife.37880", "pmcid": "PMC6345567", "primary_object": { "basename": "313171.full.pdf", "url": "https://authors.library.caltech.edu/records/t7nsk-pqz47/files/313171.full.pdf" }, "related_objects": [ { "basename": "elife-37880-supp-v1.zip", "url": "https://authors.library.caltech.edu/records/t7nsk-pqz47/files/elife-37880-supp-v1.zip" }, { "basename": "elife-37880-v2.pdf", "url": "https://authors.library.caltech.edu/records/t7nsk-pqz47/files/elife-37880-v2.pdf" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Nandagopal, Nagarajan; Santat, Leah A.; et el." }, { "id": "https://authors.library.caltech.edu/records/71hzb-qgg05", "eprint_id": 90521, "eprint_status": "archive", "datestamp": "2023-08-19 12:46:19", "lastmod": "2023-10-23 15:45:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ng-Kenneth-K-N", "name": { "family": "Ng", "given": "Kenneth K. N." } }, { "id": "Yui-Mary-A", "name": { "family": "Yui", "given": "Mary A." }, "orcid": "0000-0002-3136-2181" }, { "id": "Mehta-Arnav", "name": { "family": "Mehta", "given": "Arnav" } }, { "id": "Siu-Sharmayne", "name": { "family": "Siu", "given": "Sharmayne" } }, { "id": "Irwin-B", "name": { "family": "Irwin", "given": "Blythe" } }, { "id": "Pease-Shirley-S", "name": { "family": "Pease", "given": "Shirley" } }, { "id": "Hirose-Satoshi", "name": { "family": "Hirose", "given": "Satoshi" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Rothenberg-E-V", "name": { "family": "Rothenberg", "given": "Ellen V." }, "orcid": "0000-0002-3901-347X" }, { "id": "Kueh-Hao-Yuan", "name": { "family": "Kueh", "given": "Hao Yuan" }, "orcid": "0000-0001-6272-6673" } ] }, "title": "A stochastic epigenetic switch controls the dynamics of T-cell lineage commitment", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2018 Ng 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: 26 April 2018; Accepted: 11 October 2018; Published: 20 November 2018. \n\nData availability: Imaging data, along with MATLAB image processing scripts have been deposited in github: https://github.com/KuehLabUW/ictrack/ (copy archived at https://github.com/elifesciences-publications/ictrack). Source data for Figs. 2,3,4,5, Figure 3-figure supplements 1,2 and 3 have also been included. \n\nWe thank M Lerica Gutierrez Quiloan for mouse genotyping and maintenance; N Verduzco and I Soto for animal husbandry; RA Diamond, K Beadle, and D Perez for cell sorting. We also thank members of Kueh, Rothenberg and Elowitz labs for feedback, and T Mitchison for valuable discussions. We also thank Sandy Nandagopal, Pulin Li, Zeba Wunderlich and Nick Pease for comments. This work was funded by an NIH K99/R00 Award (5R00HL119638), a Tietze Foundation Stem Cell Scientist Award, and a CRI/Irvington Postdoctoral Fellowship (to HYK); NIH grants R01AI095943, R01AI083514, and R01HL119102 (to EVR), California Institute for Regenerative Medicine Bridges to Stem Cell Research (to KKHN); and the Louis A Garfinkle Memorial Laboratory Fund, the Al Sherman Foundation, and the Albert Billings Ruddock Professorship (to EVR). \n\nThe funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. \n\nEthics: Animal experimentation: This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. Animals were bred and maintained in either the Laboratory Animal Facility of the California Institute of Technology, or that of the University of Washington. Animal protocols were reviewed and approved by the Institute Animal Care and Use Committees (IACUC) of the California Institute of Technology (Protocols #1445 and #1409) and the University of Washington Protocol #4397-01. \n\nAuthor contributions: Kenneth KH Ng, Data curation, Formal analysis, Investigation, Writing\u2014original draft, Writing\u2014\nreview and editing; Mary A Yui, Data curation, Formal analysis, Investigation; Arnav Mehta, Satoshi Hirose, Investigation; Sharmayne Siu, Blythe Irwin, Formal analysis, Investigation; Shirley Pease, Resources; Michael B Elowitz, Ellen V Rothenberg, Conceptualization, Supervision, Funding acquisition, Methodology, Writing\u2014original draft, Writing\u2014review and editing; Hao Yuan Kueh, Conceptualization, Data curation, Formal analysis, Supervision, Funding acquisition, Investigation, Methodology, Writing\u2014original draft, Writing\u2014review and editing.\n\nPublished - elife-37851-v1.pdf
Submitted - 318675.full.pdf
Supplemental Material - elife-37851-supp1-v1.docx
Supplemental Material - elife-37851-transrepform-v1.docx
", "abstract": "Cell fate decisions occur through the switch-like, irreversible activation of fate-specifying genes. These activation events are often assumed to be tightly coupled to changes in upstream transcription factors, but could also be constrained by cis-epigenetic mechanisms at individual gene loci. Here, we studied the activation of Bcl11b, which controls T-cell fate commitment. To disentangle cis and trans effects, we generated mice where two Bcl11b copies are tagged with distinguishable fluorescent proteins. Quantitative live microscopy of progenitors from these mice revealed that Bcl11b turned on after a stochastic delay averaging multiple days, which varied not only between cells but also between Bcl11b alleles within the same cell. Genetic perturbations, together with mathematical modeling, showed that a distal enhancer controls the rate of epigenetic activation, while a parallel Notch-dependent trans-acting step stimulates expression from activated loci. These results show that developmental fate transitions can be controlled by stochastic cis-acting events on individual loci.", "date": "2018-11-20", "date_type": "published", "publication": "eLife", "volume": "7", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e37851", "id_number": "CaltechAUTHORS:20181030-143317624", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181030-143317624", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "5R00HL119638" }, { "agency": "Cancer Research Institute" }, { "agency": "NIH", "grant_number": "R01AI095943" }, { "agency": "NIH", "grant_number": "R01AI083514" }, { "agency": "NIH", "grant_number": "R01HL119102" }, { "agency": "California Institute for Regenerative Medicine (CIRM)" }, { "agency": "Louis A. Garfinkle Memorial Laboratory Fund" }, { "agency": "Al Sherman Foundation" }, { "agency": "Albert Billings Ruddock Professorship" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "John H. Tietze Foundation Trust" } ] }, "doi": "10.7554/eLife.37851", "pmcid": "PMC6245732", "primary_object": { "basename": "elife-37851-transrepform-v1.docx", "url": "https://authors.library.caltech.edu/records/71hzb-qgg05/files/elife-37851-transrepform-v1.docx" }, "related_objects": [ { "basename": "elife-37851-v1.pdf", "url": "https://authors.library.caltech.edu/records/71hzb-qgg05/files/elife-37851-v1.pdf" }, { "basename": "318675.full.pdf", "url": "https://authors.library.caltech.edu/records/71hzb-qgg05/files/318675.full.pdf" }, { "basename": "elife-37851-supp1-v1.docx", "url": "https://authors.library.caltech.edu/records/71hzb-qgg05/files/elife-37851-supp1-v1.docx" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Ng, Kenneth K. N.; Yui, Mary A.; et el." }, { "id": "https://authors.library.caltech.edu/records/sacbt-zcq12", "eprint_id": 90229, "eprint_status": "archive", "datestamp": "2023-09-22 22:50:13", "lastmod": "2023-10-23 23:29:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Martinez-Corral-R", "name": { "family": "Martinez-Corral", "given": "Rosa" } }, { "id": "Raimundez-E", "name": { "family": "Raimundez", "given": "Elba" } }, { "id": "Lin-Yihan", "name": { "family": "Lin", "given": "Yihan" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Garcia-Ojalvo-J", "name": { "family": "Garcia-Ojalvo", "given": "Jordi" } } ] }, "title": "Self-Amplifying Pulsatile Protein Dynamics without Positive Feedback", "ispublished": "pub", "full_text_status": "public", "keywords": "cell signaling dynamics; protein activation; feedback; biological noise; protein activity pulses; cellular oscillations; ultrasensitivity", "note": "\u00a9 2018 Elsevier Inc. \n\nReceived 27 April 2018, Revised 27 July 2018, Accepted 23 August 2018, Available online 10 October 2018. \n\nThis work was supported by the Spanish Ministry of Economy and Competitiveness and FEDER (project FIS2015-66503-C3-1-P) and by the Generalitat de Catalunya (project 2017SGR1054). R.M.C. acknowledges financial support from La Caixa Foundation. J.G.O. acknowledges support from the ICREA Academia programme and from the \"Mar\u00eda de Maeztu\" Programme for Units of Excellence in R&D (Spanish Ministry of Economy and Competitiveness, MDM-2014-0370). Y.L. acknowledges the support from the National Natural Science Foundation of China (Grant No. 31771425) and the Thousand Young Talents Program of China. M.B.E. is a Howard Hughes Medical Institute Investigator. This work was supported by the National Science Foundation grant #1547056. \n\nAuthor Contributions: Conceptualization, R.M.C., M.B.E., and J.G.O.; Methodology, R.M.C. and J.G.O.; Investigation, R.M.C. and E.R.; Formal Analysis, R.M.C. and E.R.; Resources, Y.L. and M.B.E.; Data Curation, R.M.C. and Y.L.; Writing Original Draft, R.M.C. and J.G.O.; Writing Review & Editing, all authors; Supervision, Y.L., M.B.E., and J.G.O.; Funding Acquisition, J.G.O. \n\nThe authors declare no competing interests.\n\nSupplemental Material - 1-s2.0-S2405471218303594-mmc1.pdf
", "abstract": "Many proteins exhibit dynamic activation patterns in the form of irregular pulses. Such behavior is typically attributed to a combination of positive and negative feedback loops in the underlying regulatory network. However, the presence of positive feedbacks is difficult to demonstrate unequivocally, raising the question of whether stochastic pulses can arise from negative feedback only. Here, we use the protein kinase A (PKA) system, a key regulator of the yeast pulsatile transcription factor Msn2, as a case example to show that irregular pulses of protein activity can arise from a negative feedback loop alone. Simplification to two variables reveals that a combination of zero-order ultrasensitivity, timescale separation between the activator and the repressor, and an effective delay in the feedback are sufficient to amplify a perturbation into a pulse. The same circuit topology can account for both activation and inactivation pulses, pointing toward a general mechanism of stochastic pulse generation.", "date": "2018-10-24", "date_type": "published", "publication": "Cell Systems", "volume": "7", "number": "4", "publisher": "Elsevier", "pagerange": "453-462", "id_number": "CaltechAUTHORS:20181010-111625116", "issn": "2405-4712", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181010-111625116", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Ministerio de Econom\u00eda, Industria y Competitividad (MINECO)", "grant_number": "FIS2015-66503-C3-1-P" }, { "agency": "Generalitat de Catalunya", "grant_number": "2017SGR1054" }, { "agency": "La Caixa Foundation" }, { "agency": "ICREA Academia Programme" }, { "agency": "Ministerio de Econom\u00eda, Industria y Competitividad (MINECO)", "grant_number": "MDM-2014-0370" }, { "agency": "National Natural Science Foundation of China", "grant_number": "31771425" }, { "agency": "Thousand Young Talents Program of China" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NSF", "grant_number": "MCB-1547056" } ] }, "doi": "10.1016/j.cels.2018.08.012", "primary_object": { "basename": "1-s2.0-S2405471218303594-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/sacbt-zcq12/files/1-s2.0-S2405471218303594-mmc1.pdf" }, "resource_type": "article", "pub_year": "2018", "author_list": "Martinez-Corral, Rosa; Raimundez, Elba; et el." }, { "id": "https://authors.library.caltech.edu/records/m9nh0-t8p73", "eprint_id": 90393, "eprint_status": "archive", "datestamp": "2023-08-19 11:44:09", "lastmod": "2023-10-18 23:25:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Siddique-H", "name": { "family": "Siddique", "given": "Hifzur" } }, { "id": "Zheng-Mengmei", "name": { "family": "Zheng", "given": "Mengmei" } }, { "id": "Kou-Yi", "name": { "family": "Kou", "given": "Yi" } }, { "id": "Chen-Chia-Lin-Chen", "name": { "family": "Chen", "given": "Chia-Lin Chen" } }, { "id": "Kumar-D-B-U", "name": { "family": "Kumar", "given": "Dinesh Babu Uthaya" } }, { "id": "Winer-P", "name": { "family": "Winer", "given": "Peleg" } }, { "id": "Rokan-A", "name": { "family": "Rokan", "given": "Ahmed" } }, { "id": "Punj-V", "name": { "family": "Punj", "given": "Vasu" } }, { "id": "Sher-L-S", "name": { "family": "Sher", "given": "Linda S." } }, { "id": "Tahara-S-M", "name": { "family": "Tahara", "given": "Stanley M." } }, { "id": "Ray-R", "name": { "family": "Ray", "given": "Ratna" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael" }, "orcid": "0000-0002-1221-0967" }, { "id": "Liang-Chengyu", "name": { "family": "Liang", "given": "Chengyu" } }, { "id": "Chen-Lin", "name": { "family": "Chen", "given": "Lin" } }, { "id": "Tsukamoto-Hidekazu", "name": { "family": "Tsukamoto", "given": "Hidekazu" } }, { "id": "Machida-Keigo", "name": { "family": "Machida", "given": "Keigo" } } ] }, "title": "Novel NOTCH-Binding Protein Directs Self-Renewal of Tumor-Initiating Stem-like Cells and HCC Development through Cell Fate Reprogramming", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2018 by the American Association for the Study of Liver Diseases. \n\nIssue Online: 01 October 2018. \n\nThis project was supported by NIH grants 1R01AA018857-01, pilot project funding (5P30DK048522-13), P50AA011999 (Animal Core, Morphology Core, and Pilot Project Program), P30CA014089 and R24AA012885 (Integrative Liver Cell Core). This research is also supported by a Research Scholar Grant, RSG-12-177-01-MPC and pilot funding (IRG-58-007-48) from the American Cancer Society. \n\nDisclosures: Hidekazu Tsukamoto \u2013 Gilead Sciences Inc.: Grant/Research Support; EA Pharma Co. Ltd: Consulting; Otsuka Pharmaceutical: Grant/Research Support. \n\nThe following people have nothing to disclose: Ahmed Rokan, Vasu Punj, Linda S. Sher. \n\nDisclosure information not available at the time of publication: Hifzur Siddique, Mengmei Zheng, Yi Kou, Chia-Lin Chen Chen, Dinesh Babu Uthaya Kumar, Peleg Winer, Stanley M Tahara, Ratna Ray, Michael Elowitz, Chengyu Liang, Lin Chen, Keigo Machida", "abstract": "Liver tumor-initiating stem-like cells (TICs)\nwhich are defective in asymmetric cell division and responsible for liver tumor recurrence (PNAS 106, 1548-1553; Cell Metab 23, 206-219), have been isolated from 4 different animal models of HCC and patient HCC (J Clin Invest 2013;123:2832-49). We identified a novel NUMB binding protein, TBC1D15 in TICs, which is upregulated and destabilizes p53 via NUMB phosphorylation (p-NUMB) (Hepatology 62, 1466-1479). However, TBC1D15 still transforms p53-deficient hepatoblasts, suggesting other undisclosed mechanisms facilitated by this oncoprotein.", "date": "2018-10", "date_type": "published", "publication": "Hepatology", "volume": "68", "number": "S1", "publisher": "Wiley", "pagerange": "Art. No. 1365", "id_number": "CaltechAUTHORS:20181024-102930532", "issn": "0270-9139", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181024-102930532", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "1R01AA018857-01" }, { "agency": "NIH", "grant_number": "5P30DK048522-13" }, { "agency": "NIH", "grant_number": "P50AA011999" }, { "agency": "NIH", "grant_number": "P30CA014089" }, { "agency": "NIH", "grant_number": "R24AA012885" }, { "agency": "American Cancer Society", "grant_number": "RSG-12-177-01-MPC" }, { "agency": "American Cancer Society", "grant_number": "IRG-58-007-48" } ] }, "doi": "10.1002/hep.30257", "resource_type": "article", "pub_year": "2018", "author_list": "Siddique, Hifzur; Zheng, Mengmei; et el." }, { "id": "https://authors.library.caltech.edu/records/keqy2-b6k25", "eprint_id": 89789, "eprint_status": "archive", "datestamp": "2023-08-19 11:33:13", "lastmod": "2023-10-18 22:59:46", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gao-Xiaojing-J", "name": { "family": "Gao", "given": "Xiaojing J." } }, { "id": "Chong-Lucy-S", "name": { "family": "Chong", "given": "Lucy S." } }, { "id": "Kim-Matthew-S", "name": { "family": "Kim", "given": "Matthew S." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Programmable protein circuits in living cells", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2018 American Association for the Advancement of Science. This is an article distributed under the terms of the Science Journals Default License. \n\nReceived 5 March 2018; accepted 14 August 2018. \n\nWe thank J. Markson, Y. Antebi, N. Nandagopal, and J. Ruan for technical assistance; A. Varshavsky, R. Deshaies, and P. Coffino for scientific input and advice; and R. Kishony, G. Seelig, J.G. Ojalvo, J. Markson, L. Potvin-Trottier, K. Frieda, R. Zhu, and A. Granados 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.), 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. 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., and M.S.K. performed experiments. X.J.G., L.S.C., M.S.K., and M.B.E. analyzed data and did mathematical modeling. X.J.G., L.S.C., and M.B.E. wrote the manuscript, with input from all authors. \n\nCompeting interests: All authors are inventors on U.S. patent application 62/619,001 (\"A System for Programming Protein-level Circuits in Living Cells\") submitted by Caltech. \n\nData and materials availability: All DNA constructs are available from Addgene (www.addgene.org/depositing/75869/), and cell lines 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 upon request from the corresponding author.\n\nAccepted Version - nihms-1574655.pdf
Supplemental Material - aat5062_Gao_SM.pdf
Supplemental Material - aat5062_Gao_Table_S1.xlsx
Supplemental Material - aat5062s1.mov
", "abstract": "Synthetic protein-level circuits could enable engineering of powerful new cellular behaviors. Rational protein circuit design would be facilitated by a composable protein-protein regulation system in which individual protein components can regulate one another to create a variety of different circuit architectures. In this study, we show that engineered viral proteases can function as composable protein components, which can together implement a broad variety of circuit-level functions in mammalian cells. In this system, termed CHOMP (circuits of hacked orthogonal modular proteases), input proteases dock with and cleave target proteases to inhibit their function. These components can be connected to generate regulatory cascades, binary logic gates, and dynamic analog signal-processing functions. To demonstrate the utility of this system, we rationally designed a circuit that induces cell death in response to upstream activators of the Ras oncogene. Because CHOMP circuits can perform complex functions yet be encoded as single transcripts and delivered without genomic integration, they offer a scalable platform to facilitate protein circuit engineering for biotechnological applications.", "date": "2018-09-21", "date_type": "published", "publication": "Science", "volume": "361", "number": "6408", "publisher": "American Association for the Advancement of Science", "pagerange": "1252-1258", "id_number": "CaltechAUTHORS:20180920-125150716", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180920-125150716", "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": "Helen Hay Whitney Foundation", "grant_number": "F1047" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1126/science.aat5062", "pmcid": "PMC7176481", "primary_object": { "basename": "aat5062_Gao_SM.pdf", "url": "https://authors.library.caltech.edu/records/keqy2-b6k25/files/aat5062_Gao_SM.pdf" }, "related_objects": [ { "basename": "aat5062_Gao_Table_S1.xlsx", "url": "https://authors.library.caltech.edu/records/keqy2-b6k25/files/aat5062_Gao_Table_S1.xlsx" }, { "basename": "aat5062s1.mov", "url": "https://authors.library.caltech.edu/records/keqy2-b6k25/files/aat5062s1.mov" }, { "basename": "nihms-1574655.pdf", "url": "https://authors.library.caltech.edu/records/keqy2-b6k25/files/nihms-1574655.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Gao, Xiaojing J.; Chong, Lucy S.; et el." }, { "id": "https://authors.library.caltech.edu/records/ctvjd-n4009", "eprint_id": 90198, "eprint_status": "archive", "datestamp": "2023-08-19 10:47:22", "lastmod": "2023-10-18 23:16:26", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Siddique-H-R", "name": { "family": "Siddique", "given": "H. R." } }, { "id": "Zheng-M", "name": { "family": "Zheng", "given": "M." } }, { "id": "Kou-Y", "name": { "family": "Kou", "given": "Y." } }, { "id": "Chen-C-L", "name": { "family": "Chen", "given": "C.-L." } }, { "id": "Uthaya-Kumar-D-B", "name": { "family": "Uthaya Kumar", "given": "D. B." } }, { "id": "Punj-V", "name": { "family": "Punj", "given": "V." } }, { "id": "Winer-P", "name": { "family": "Winer", "given": "P." } }, { "id": "Pita-A", "name": { "family": "Pita", "given": "A." } }, { "id": "Sher-L", "name": { "family": "Sher", "given": "L." } }, { "id": "Tahara-S-M", "name": { "family": "Tahara", "given": "S. M." } }, { "id": "Giacca-M", "name": { "family": "Giacca", "given": "M." } }, { "id": "Ray-R-B", "name": { "family": "Ray", "given": "R. B." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "M." }, "orcid": "0000-0002-1221-0967" }, { "id": "Liang-C", "name": { "family": "Liang", "given": "C." } }, { "id": "Chen-L", "name": { "family": "Chen", "given": "L." } }, { "id": "Tsukamoto-H", "name": { "family": "Tsukamoto", "given": "H." } }, { "id": "Machida-K", "name": { "family": "Machida", "given": "K." } } ] }, "title": "Cell fate and metabolic reprogramming of tumor-initiating stem-like cells", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2018 John Wiley & Sons, Inc. \n\nFirst published: 30 August 2018.", "abstract": "Background & Aims: Tumor-initiating stem-like cells (TICs) are defective in maintaining asymmetric cell division and responsible for tumor recurrence. Stem cell markers such as Nanog have been implicated in various cancer, but whether they are functionally contributing to cancer pathogenesis has remained unclear. Novel NOTCH/NUMB-interacting protein, TBC1D15, is overexpressed and contributes to p53 degradation in TICs. Aims are to identify NANOG- or TBC1D15-mediated oncogenic mechanisms and to test tumorigenic roles. \n\nMethods: We determined novel targets of NANOG in tumor-initiating cells (TICs) from patient and mouse-models of hepatocellular carcinoma (HCC) using genome-wide NANOG-binding site analysis (ChIP-seq) and how Nanog is regulated at the transcriptional to promote oncogenesis and self-renewal in TICs. TBC1D15 interacting proteins were searched by large-scale immunoaffinity purification and LC-MS analysis. We examined HCC development in alcohol Western diet (AWD)-fed HCV NS5A Tg mice with hepatocyte-specific TBC1D15 deficiency or hepatocyte-specific expression of non-phosphorylatable NUMB mutations (non-p-NUMB). \n\nResults: Silencing NANOG inhibits tumor development in HCC mouse-models and genesis of TICs. NANOG binds genes of oxidative phosphorylation and b-oxidation in mitochondria. Silencing\nNANOG promotes oxidative phosphorylation and b-oxidation, indicating that NANOG is a suppressor of mitochondria-mediated energy production. We identified NuMA1, RANGAP1 and NOTCH1-4 as TBC1D15-interacting proteins. TBC1D15-NuMA1 association impaired NuMA1-LAN interaction which is essential for an asymmetric division machinery, thereby promoting TIC self-renewal. TBC1D15-NOTCH1 interaction activated and stabilized NOTCH1 and NOTCH1 Intracellular Domain (N1ICD) which in turn upregulated transcription of Nanog essential for TICs. \n\nConclusions: These results suggest that NANOG-mediated metabolic reprogramming through suppression of mitochondria function in both experimental and clinical HCC downstream of TLR4/\nNANOG generates TICs and drives liver tumorigenesis. TBC1D15 and p-NUMB are required for liver tumor development in vivo.", "date": "2018-08", "date_type": "published", "publication": "Alcoholism: Clinical and Experimental Research", "volume": "42", "number": "S2", "publisher": "Wiley", "pagerange": "Art. No. 427", "id_number": "CaltechAUTHORS:20181009-132205192", "issn": "0145-6008", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181009-132205192", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1111/acer.13834", "resource_type": "article", "pub_year": "2018", "author_list": "Siddique, H. R.; Zheng, M.; et el." }, { "id": "https://authors.library.caltech.edu/records/4jkqx-t4e23", "eprint_id": 86771, "eprint_status": "archive", "datestamp": "2023-08-19 09:23:00", "lastmod": "2023-10-20 21:51:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Rosenthal-Adam-Z", "name": { "family": "Rosenthal", "given": "Adam Z." }, "orcid": "0000-0002-6936-3665" }, { "id": "Qi-Yutao", "name": { "family": "Qi", "given": "Yutao" } }, { "id": "Hormoz-Sahand", "name": { "family": "Hormoz", "given": "Sahand" } }, { "id": "Park-Jin", "name": { "family": "Park", "given": "Jin" } }, { "id": "Hsin-Jung Li-S", "name": { "family": "Hsin-Jung Li", "given": "Sophia" }, "orcid": "0000-0001-8972-6921" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael" }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Metabolic interactions between dynamic bacterial subpopulations", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2018 Rosenthal et al. This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited. \n\nReceived: 25 October 2017; Accepted: 21 May 2018; Published: 29 May 2018. \n\nWe thank Jared Leadbetter, Ned Wingreen, Xinning Zhang, Avigdor Eldar, Joe Levine, Eric Matson, Mark Budde, Joe Markson, and members of the Elowitz lab for discussions and comments. This research was supported by the by Defense Advanced Research Projects Agency Biochronicity Grant DARPA-BAA-11\u201366, NIH R01GM079771, National Science Foundation grant 1547056, and a Caltech CEMI (Center for Environmental Microbial Interactions at Caltech Interactions) grant (AZR). \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: Adam Z Rosenthal, Michael B Elowitz, Conceptualization, Formal analysis, Writing\u2014original draft, Writing\u2014review and editing; Yutao Qi, Sahand Hormoz, Sophia Hsin-Jung Li, Formal analysis; Jin Park, Methodology. \n\nData availability: Data are included in supplementary files.\n\nPublished - elife-33099-v2.pdf
Submitted - 208686.full.pdf
Supplemental Material - elife-33099-supp-v1.zip
", "abstract": "Individual microbial species are known to occupy distinct metabolic niches within multi-species communities. However, it has remained largely unclear whether metabolic specialization can similarly occur within a clonal bacterial population. More specifically, it is not clear what functions such specialization could provide and how specialization could be coordinated dynamically. Here, we show that exponentially growing Bacillus subtilis cultures divide into distinct interacting metabolic subpopulations, including one population that produces acetate, and another population that differentially expresses metabolic genes for the production of acetoin, a pH-neutral storage molecule. These subpopulations exhibit distinct growth rates and dynamic interconversion between states. Furthermore, acetate concentration influences the relative sizes of the different subpopulations. These results show that clonal populations can use metabolic specialization to control the environment through a process of dynamic, environmentally-sensitive state-switching.", "date": "2018-05-29", "date_type": "published", "publication": "eLife", "volume": "7", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e33099", "id_number": "CaltechAUTHORS:20180604-074815229", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180604-074815229", "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": "DARPA-BAA-11-66" }, { "agency": "NIH", "grant_number": "R01GM079771" }, { "agency": "NSF", "grant_number": "MCB-1547056" }, { "agency": "Caltech Center for Environmental Microbial Interactions (CEMI)" } ] }, "local_group": { "items": [ { "id": "Caltech-Center-for-Environmental-Microbial-Interactions-(CEMI)" } ] }, "doi": "10.7554/eLife.33099", "pmcid": "PMC6025961", "primary_object": { "basename": "208686.full.pdf", "url": "https://authors.library.caltech.edu/records/4jkqx-t4e23/files/208686.full.pdf" }, "related_objects": [ { "basename": "elife-33099-supp-v1.zip", "url": "https://authors.library.caltech.edu/records/4jkqx-t4e23/files/elife-33099-supp-v1.zip" }, { "basename": "elife-33099-v2.pdf", "url": "https://authors.library.caltech.edu/records/4jkqx-t4e23/files/elife-33099-v2.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Rosenthal, Adam Z.; Qi, Yutao; et el." }, { "id": "https://authors.library.caltech.edu/records/97cxn-p6c90", "eprint_id": 82731, "eprint_status": "archive", "datestamp": "2023-08-19 09:08:16", "lastmod": "2023-10-17 22:38:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Li-Pulin", "name": { "family": "Li", "given": "Pulin" } }, { "id": "Markson-Joseph-S", "name": { "family": "Markson", "given": "Joseph S." } }, { "id": "Wang-Sheng", "name": { "family": "Wang", "given": "Sheng" } }, { "id": "Chen-Siheng", "name": { "family": "Chen", "given": "Siheng" } }, { "id": "Vachharajani-Vipul", "name": { "family": "Vachharajani", "given": "Vipul" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Morphogen gradient reconstitution reveals Hedgehog pathway design principles", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2018 American Association for the Advancement of Science. \n\nReceived 14 June 2017; accepted 22 March 2018;\nPublished online 5 April 2018.\n\nWe thank J. Briscoe and A. McMahon for DNA constructs and helpful discussion, Y. Antebi for data analysis programs and discussion of modeling, J. Bois for advice on model simulation, Z. Singer for cloning ERT2-GAL4, F. Tan for suggesting the rocker experiment, and the Elowitz laboratory for discussion. We also thank U. Alon, N. Barkai, P. Beachy, A. Eldar, J. Garcia-Ojalvo, L. Goentoro, E. Hui, P. Jordan, B. Shilo, B. Shraiman, and D. Sprinzak for discussion and feedback. Funding: The work was funded by the Howard Hughes Medical Institute (M.B.E.), American Cancer Society Postdoc Fellowship 127270-PF-15-032-01-DDC (P.L.), NICHD (Eunice Kennedy Shriver National Institute of Child Health and Human Development) Pathway to Independence Career Award K99HD087532 (P.L.), NIH Ruth Kirschstein National Research Service Award F32 AR067103 (J.S.M.), Institute for Collaborative Biotechnologies contract W911NF-09-D-0001 through the U.S. Army Research Office, and BBSRC (UK Biotechnology and Biological Sciences Research Council)\u2013NSF award 1546197. The RNA-sequencing work was supported by the Millard and Muriel Jacobs Genetics and Genomics Laboratory at the California Institute of Technology. Author contributions: P.L. and M.B.E. conceived the project and designed the experiments. P.L., S.W., and V.V. performed the experiments. P.L., J.S.M., and S.W. analyzed the experimental data. J.S.M., P.L., and S.C. developed the mathematical models. P.L., J.S.M., and M.B.E. wrote the paper. Competing interests: The authors declare no competing interests. Data and materials availability: Original data, Matlab code, DNA constructs, and cell lines are available upon request.\n\nAccepted Version - nihms-1016389.pdf
Supplemental Material - aao0645_Li_SM.pdf
Supplemental Material - aao0645s1.mp4
Supplemental Material - aao0645s2.mp4
Supplemental Material - aao0645s3.mp4
Supplemental Material - aao0645s4.mp4
Supplemental Material - aao0645s5.mp4
Supplemental Material - aao0645s6.mp4
", "abstract": "In developing tissues, cells estimate their spatial position by sensing graded concentrations of diffusible signaling proteins called morphogens. Morphogen-sensing pathways exhibit diverse molecular architectures, whose roles in controlling patterning dynamics and precision have been unclear. In this work, combining cell-based in vitro gradient reconstitution, genetic rewiring, and mathematical modeling, we systematically analyzed the distinctive architectural features of the Sonic Hedgehog pathway. We found that the combination of double-negative regulatory logic and negative feedback through the PTCH receptor accelerates gradient formation and improves robustness to variation in the morphogen production rate compared with alternative designs. The ability to isolate morphogen patterning from concurrent developmental processes and to compare the patterning behaviors of alternative, rewired pathway architectures offers a powerful way to understand and engineer multicellular patterning.", "date": "2018-05-04", "date_type": "published", "publication": "Science", "volume": "360", "number": "6388", "publisher": "American Association for the Advancement of Science", "pagerange": "543-548", "id_number": "CaltechAUTHORS:20171027-105758623", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171027-105758623", "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": "127270-PF-15-032-01-DDC" }, { "agency": "NIH", "grant_number": "K99HD087532" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "F32 AR067103" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-09-D-0001" }, { "agency": "NSF", "grant_number": "MCB-1546197" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)" }, { "agency": "Millard and Muriel Jacobs Genetics and Genomics Laboratory" } ] }, "doi": "10.1126/science.aao0645", "pmcid": "PMC6516753", "primary_object": { "basename": "aao0645s1.mp4", "url": "https://authors.library.caltech.edu/records/97cxn-p6c90/files/aao0645s1.mp4" }, "related_objects": [ { "basename": "aao0645s2.mp4", "url": "https://authors.library.caltech.edu/records/97cxn-p6c90/files/aao0645s2.mp4" }, { "basename": "aao0645s3.mp4", "url": "https://authors.library.caltech.edu/records/97cxn-p6c90/files/aao0645s3.mp4" }, { "basename": "aao0645s4.mp4", "url": "https://authors.library.caltech.edu/records/97cxn-p6c90/files/aao0645s4.mp4" }, { "basename": "aao0645s5.mp4", "url": "https://authors.library.caltech.edu/records/97cxn-p6c90/files/aao0645s5.mp4" }, { "basename": "aao0645s6.mp4", "url": "https://authors.library.caltech.edu/records/97cxn-p6c90/files/aao0645s6.mp4" }, { "basename": "nihms-1016389.pdf", "url": "https://authors.library.caltech.edu/records/97cxn-p6c90/files/nihms-1016389.pdf" }, { "basename": "aao0645_Li_SM.pdf", "url": "https://authors.library.caltech.edu/records/97cxn-p6c90/files/aao0645_Li_SM.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Li, Pulin; Markson, Joseph S.; et el." }, { "id": "https://authors.library.caltech.edu/records/2pkmc-vvm92", "eprint_id": 84831, "eprint_status": "archive", "datestamp": "2023-08-21 22:49:16", "lastmod": "2023-10-18 16:44:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Park-Jin", "name": { "family": "Park", "given": "Jin" } }, { "id": "Dies-Marta", "name": { "family": "Dies", "given": "Marta" } }, { "id": "Lin-Yihan", "name": { "family": "Lin", "given": "Yihan" } }, { "id": "Hormoz-Sahand", "name": { "family": "Hormoz", "given": "Sahand" } }, { "id": "Smith-Unna-Stephanie-E", "name": { "family": "Smith-Unna", "given": "Stephanie E." } }, { "id": "Quinodoz-Sofia-A", "name": { "family": "Quinodoz", "given": "Sofia A." }, "orcid": "0000-0003-1862-5204" }, { "id": "Hern\u00e1ndez-Jim\u00e9nez-Mar\u00eda-Jes\u00fas", "name": { "family": "Hern\u00e1ndez-Jim\u00e9nez", "given": "Mar\u00eda Jes\u00fas" } }, { "id": "Garcia-Ojalvo-Jordi", "name": { "family": "Garcia-Ojalvo", "given": "Jordi" } }, { "id": "Locke-James-C-W", "name": { "family": "Locke", "given": "James C. W." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Molecular Time Sharing through Dynamic Pulsing in Single Cells", "ispublished": "pub", "full_text_status": "public", "keywords": "sharing; time sharing; pulsing; partitioning; shared resources; microfluidics", "note": "\u00a9 2018 The Authors. Published by Elsevier Inc. Open Access funded by National Institutes of Health. Under a Creative Commons license, Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) \n\nReceived 7 March 2017, Revised 4 September 2017, Accepted 10 January 2018, Available online 14 February 2018. Published: February 14, 2018. \n\nData and Software Availability: All data and software used in this manuscript are available upon request, for contact information see section 'Contact for Reagent and Resource Sharing'. \n\nAdditional Resources: All relevant information, software, and data are provided in previous sections. \n\nAuthor Contributions: Conceptualization, J.P., M.D., J.G.-O., J.C.W.L., and M.B.E.; Methodology, J.P., M.D., J.G.-O., J.C.W.L., and M.B.E.; Software, J.P., M.D., Y.L., S.H., S.E.S.-U., S.Q., J.G.-O., J.C.W.L., and M.B.E.; Validation, J.P., M.D., M.J.H.-J, J.G.-O., J.C.W.L., and M.B.E.; Formal Analysis, J.P., M.D., Y.L., J.G.-O., J.C.W.L., and M.B.E.; Investigation, all authors; Writing, J.P., M.D., S.H., J.G.-O., J.C.W.L., and M.B.E.; Visualization, J.P., M.D., Y.L., S.H., J.G.-O., J.C.W.L., and M.B.E.; Funding Acquisition, J.P., M.D., J.G.-O., J.C.W.L., and M.B.E. \n\nThe authors declare no competing interests. \n\nWe would like to thank Matt Cabeen, Richard Losick, Nathan Lord, Johan Paulsson, and Suckjoon Jun for discussions and experimental training on the mother machine. We also thank members of the Elowitz lab for comments and feedback on the manuscript. This work was supported by NIH grants R01 GM079771B and R01 HD075605A (to M.B.E.), T32 GM07616 (to J.P.), and NIHGMS K99BM118910 (to S.H.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. It was also supported by National Science Foundation grant 1547056 and the Institute for Collaborative Biotechnologies through grant W911NF-09-0001 (KK9150) 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. J.G.-O. and M.D. were supported by the Spanish Ministry of Economy and Competitiveness (MINECO) and FEDER (project FIS2015-66503-C3-1-P), the ICREA Academia program, and the Maria de Maeztu Program for Units of Excellence in R&D (MINECO, project MDM-2014-0370). Work in the Locke laboratory was supported by the European Research Council under the European Union's Seventh Framework Program (FP/2007-2013)/ERC Grant Agreement 338060, a fellowship from the Gatsby Foundation (GAT3272/GLC), and an award from the Human Frontier Science Program (CDA00068/2012).\n\nPublished - 1-s2.0-S2405471218300115-main.pdf
Supplemental Material - mmc1.pdf
Supplemental Material - mmc2.mp4
Supplemental Material - mmc3.mp4
Supplemental Material - mmc4.mp4
", "abstract": "In cells, specific regulators often compete for limited amounts of a core enzymatic resource. It is typically assumed that competition leads to partitioning of core enzyme molecules among regulators at constant levels. Alternatively, however, different regulatory species could time share, or take turns utilizing, the core resource. Using quantitative time-lapse microscopy, we analyzed sigma factor activity dynamics, and their competition for RNA polymerase, in individual Bacillus subtilis cells under energy stress. Multiple alternative sigma factors were activated in \u223c1-hr pulses in stochastic and repetitive fashion. Pairwise analysis revealed that two sigma factors rarely pulse simultaneously and that some pairs are anti-correlated, indicating that RNAP utilization alternates among different sigma factors. Mathematical modeling revealed how stochastic time-sharing dynamics can emerge from pulse-generating sigma factor regulatory circuits actively competing for RNAP. Time sharing provides a mechanism for cells to dynamically control the distribution of cell states within a population. Since core molecular components are limiting in many other systems, time sharing may represent a general mode of regulation.", "date": "2018-02-28", "date_type": "published", "publication": "Cell Systems", "volume": "6", "number": "2", "publisher": "Cell Press", "pagerange": "216-229", "id_number": "CaltechAUTHORS:20180214-131202804", "issn": "2405-4712", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180214-131202804", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 GM079771B" }, { "agency": "NIH", "grant_number": "R01 HD075605A" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 GM07616" }, { "agency": "NIH", "grant_number": "K99BM118910" }, { "agency": "NSF", "grant_number": "MCB-1547056" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-09-0001" }, { "agency": "Fondo Europeo de Desarrollo Regional (FEDER)", "grant_number": "FIS2015-66503-C3-1-P" }, { "agency": "ICREA Academia program" }, { "agency": "Ministerio de Econom\u00eda, Industria y Competitividad (MINECO)", "grant_number": "MDM-2014-0370" }, { "agency": "European Research Council (ERC)", "grant_number": "338060" }, { "agency": "Gatsby Foundation", "grant_number": "GAT3272/GLC" }, { "agency": "Human Frontier Science Program", "grant_number": "CDA00068/2012" } ] }, "doi": "10.1016/j.cels.2018.01.011", "pmcid": "PMC6070344", "primary_object": { "basename": "1-s2.0-S2405471218300115-main.pdf", "url": "https://authors.library.caltech.edu/records/2pkmc-vvm92/files/1-s2.0-S2405471218300115-main.pdf" }, "related_objects": [ { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/2pkmc-vvm92/files/mmc1.pdf" }, { "basename": "mmc2.mp4", "url": "https://authors.library.caltech.edu/records/2pkmc-vvm92/files/mmc2.mp4" }, { "basename": "mmc3.mp4", "url": "https://authors.library.caltech.edu/records/2pkmc-vvm92/files/mmc3.mp4" }, { "basename": "mmc4.mp4", "url": "https://authors.library.caltech.edu/records/2pkmc-vvm92/files/mmc4.mp4" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Park, Jin; Dies, Marta; et el." }, { "id": "https://authors.library.caltech.edu/records/rt20n-mff72", "eprint_id": 84637, "eprint_status": "archive", "datestamp": "2023-08-21 22:45:23", "lastmod": "2023-10-18 16:25:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nandagopal-Nagarajan", "name": { "family": "Nandagopal", "given": "Nagarajan" } }, { "id": "Santat-Leah-A", "name": { "family": "Santat", "given": "Leah A." } }, { "id": "LeBon-Lauren", "name": { "family": "LeBon", "given": "Lauren" } }, { "id": "Sprinzak-David", "name": { "family": "Sprinzak", "given": "David" } }, { "id": "Bronner-M-E", "name": { "family": "Bronner", "given": "Marianne E." }, "orcid": "0000-0003-4274-1862" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Dynamic Ligand Discrimination in the Notch Signaling Pathway", "ispublished": "pub", "full_text_status": "public", "keywords": "systems biology; Notch pathway; intercellular signaling; ligand multiplicity; single cell dynamics; signaling dynamics; signal encoding; signal decoding; myogenesis", "note": "\u00a9 2018 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). \n\nOpen Access funded by the US Department of Defense (DoD) or performed by an employee of DoD. \n\nAvailable online 1 February 2018. \n\nAuthor Contributions: Conceptualization, N.N. and M.B.E.; Methodology, N.N. and M.B.E.; Investigation, N.N. and L.A.S.; Resources, L.L.B. and M.E.B.; Writing \u2013 Original Draft, N.N. and M.B.E.; Writing \u2013 Review & Editing, N.N., L.A.S., D.S., M.E.B., and M.B.E.; Visualization, N.N., D.S., an d M.B.E.; Supervision and Funding Acquisition, M.B.E. \n\nWe thank Mark Budde, Joe Markson, Pulin Li, Yihan Lin, James Linton, Emily Capra, Jordi Garcia-Ojalvo, and Xiaojing Gao for critical feedback on the manuscript, and Young-Wook Jun, Roy Kishony, Irv Bernstein, Stephen Blacklow, and Elizabeth Jensen for helpful discussions. Harry Choi and Colby Calvert, Caltech Flow Cytometry Facility, Caltech Biological Imaging Facility, and the Millard and Muriel Jacobs Genetics and Genomics Laboratory at Caltech provided essential technical assistance. This work was supported by the Defense Advanced Research Projects Agency (HR0011-16-0138), by the NIH (R01 HD075335), and the NSF (EFRI 1137269). N.N. was a Howard Hughes Medical Institute International Student Research fellow. \n\nThe authors declare no competing interests.\n\nPublished - 1-s2.0-S0092867418300023-main.pdf
Accepted Version - nihms-999667.pdf
Supplemental Material - mmc1.pdf
Supplemental Material - mmc2.mp4
Supplemental Material - mmc3.mp4
Supplemental Material - mmc4.mp4
Supplemental Material - mmc5.mp4
Supplemental Material - mmc6.mp4
", "abstract": "The Notch signaling pathway comprises multiple ligands that are used in distinct biological contexts. In principle, different ligands could activate distinct target programs in signal-receiving cells, but it is unclear how such ligand discrimination could occur. Here, we show that cells use dynamics to discriminate signaling by the ligands Dll1 and Dll4 through the Notch1 receptor. Quantitative single-cell imaging revealed that Dll1 activates Notch1 in discrete, frequency-modulated pulses that specifically upregulate the Notch target gene Hes1. By contrast, Dll4 activates Notch1 in a sustained, amplitude-modulated manner that predominantly upregulates Hey1 and HeyL. Ectopic expression of Dll1 or Dll4 in chick neural crest produced opposite effects on myogenic differentiation, showing that ligand discrimination can occur in vivo. Finally, analysis of chimeric ligands suggests that ligand-receptor clustering underlies dynamic encoding of ligand identity. The ability of the pathway to utilize ligands as distinct communication channels has implications for diverse Notch-dependent processes.", "date": "2018-02-08", "date_type": "published", "publication": "Cell", "volume": "172", "number": "4", "publisher": "Cell Press", "pagerange": "869-880", "id_number": "CaltechAUTHORS:20180201-152120268", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180201-152120268", "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": "HR0011-16-0138" }, { "agency": "NIH", "grant_number": "R01 HD075335" }, { "agency": "NSF", "grant_number": "EFMA-1137269" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1016/j.cell.2018.01.002", "pmcid": "PMC6414217", "primary_object": { "basename": "mmc4.mp4", "url": "https://authors.library.caltech.edu/records/rt20n-mff72/files/mmc4.mp4" }, "related_objects": [ { "basename": "mmc5.mp4", "url": "https://authors.library.caltech.edu/records/rt20n-mff72/files/mmc5.mp4" }, { "basename": "mmc6.mp4", "url": "https://authors.library.caltech.edu/records/rt20n-mff72/files/mmc6.mp4" }, { "basename": "nihms-999667.pdf", "url": "https://authors.library.caltech.edu/records/rt20n-mff72/files/nihms-999667.pdf" }, { "basename": "1-s2.0-S0092867418300023-main.pdf", "url": "https://authors.library.caltech.edu/records/rt20n-mff72/files/1-s2.0-S0092867418300023-main.pdf" }, { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/rt20n-mff72/files/mmc1.pdf" }, { "basename": "mmc2.mp4", "url": "https://authors.library.caltech.edu/records/rt20n-mff72/files/mmc2.mp4" }, { "basename": "mmc3.mp4", "url": "https://authors.library.caltech.edu/records/rt20n-mff72/files/mmc3.mp4" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Nandagopal, Nagarajan; Santat, Leah A.; et el." }, { "id": "https://authors.library.caltech.edu/records/34eds-bhx22", "eprint_id": 83200, "eprint_status": "archive", "datestamp": "2023-08-19 06:17:51", "lastmod": "2023-10-17 22:58:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tycko-J", "name": { "family": "Tycko", "given": "Josh" } }, { "id": "Van-M-V", "name": { "family": "Van", "given": "Mike V." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Bintu-L", "name": { "family": "Bintu", "given": "Lacramioara" } } ] }, "title": "Advancing towards a global mammalian gene regulation model through single-cell analysis and synthetic biology", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 Published by Elsevier Inc. \n\nReceived 25 July 2017, Revised 4 October 2017, Accepted 26 October 2017, Available online 10 November 2017.", "abstract": "Engineering complex genetic functions in mammalian cells will require predictive models of gene regulation. Since gene expression is stochastic, leading to cell-to-cell heterogeneity, these models depend on single-cell measurements. Here, we summarize recent microscopy and sequencing-based single-cell measurements of transcription and its chromatin-based regulation. Then, we describe synthetic biology methods for manipulating chromatin, and highlight how they could be coupled to single-cell measurements. We discuss theoretical models that connect some chromatin inputs to transcriptional outputs. Finally, we point out the connections between the models that would allow us to integrate them into one global input-output gene regulatory function.", "date": "2017-12", "date_type": "published", "publication": "Current Opinion in Biomedical Engineering", "volume": "4", "publisher": "Elsevier", "pagerange": "174-193", "id_number": "CaltechAUTHORS:20171114-145510367", "issn": "2468-4511", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171114-145510367", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.cobme.2017.10.011", "resource_type": "article", "pub_year": "2017", "author_list": "Tycko, Josh; Van, Mike V.; et el." }, { "id": "https://authors.library.caltech.edu/records/m8axx-x2s82", "eprint_id": 81266, "eprint_status": "archive", "datestamp": "2023-08-21 21:44:10", "lastmod": "2023-10-17 19:42:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Antebi-Yaron-E", "name": { "family": "Antebi", "given": "Yaron E." }, "orcid": "0000-0002-5771-6814" }, { "id": "Linton-James-M", "name": { "family": "Linton", "given": "James M." } }, { "id": "Klumpe-Heidi-E", "name": { "family": "Klumpe", "given": "Heidi" }, "orcid": "0000-0001-8938-2006" }, { "id": "Bintu-Bogdan", "name": { "family": "Bintu", "given": "Bogdan" }, "orcid": "0000-0001-9096-5858" }, { "id": "Gong-Mengsha", "name": { "family": "Gong", "given": "Mengsha" } }, { "id": "Su-Christina-J", "name": { "family": "Su", "given": "Christina" }, "orcid": "0000-0002-9223-9777" }, { "id": "McCardell-Reed", "name": { "family": "McCardell", "given": "Reed" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Combinatorial Signal Perception in the BMP Pathway", "ispublished": "pub", "full_text_status": "public", "keywords": "bone morphogenetic protein; BMP; signaling pathways; multiplicity; promiscuity receptor-ligand interactions; signal perception; SMAD; signal processing", "note": "\u00a9 2017 Elsevier Inc. \n\nReceived 4 October 2016, Revised 26 April 2017, Accepted 8 August 2017, Available online 7 September 2017. \n\nWe thank Uri Alon, James Briscoe, Marcelo Ehrlich, Jordi Garcia-Ojalvo, Lea Goentoro, Roy Kishony, Vicki Rosen, Boris Shraiman, Ned Wingreen, and members of the Elowitz lab for helpful discussions and feedback. We thank the Caltech Flow Cytometry Facility and the Millard and Muriel Jacobs Genetics and Genomics Laboratory at Caltech for technical assistance. This work was supported by the Gordon and Betty Moore Foundation (grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative), the Human Frontiers Science Program (grant RGP0020), the NIH (grant R01 HD75335A), the Defense Advanced Research Projects Agency (contract HR0011-16-0138), and the Institute for Collaborative Biotechnologies (grant W911NF-09-0001 from the US Army Research Office). This work does not necessarily reflect the position or policy of the US Government, and no official endorsement should be inferred. H.K. is supported by a National Science Foundation graduate research fellowship (grant DGE-1144469). C.S. is supported by the NIH (National Institute of General Medical Sciences training grant T32 GM008042) and by a David Geffen Medical Scholarship. Y.E.A., J.M.L., and M.B.E. filed a provisional patent application relating to this work.\n\nAccepted Version - nihms900407.pdf
Supplemental Material - mmc1.pdf
", "abstract": "The bone morphogenetic protein (BMP) signaling pathway comprises multiple ligands and receptors that interact promiscuously with one another and typically appear in combinations. This feature is often explained in terms of redundancy and regulatory flexibility, but it has remained unclear what signal-processing capabilities it provides. Here, we show that the BMP pathway processes multi-ligand inputs using a specific repertoire of computations, including ratiometric sensing, balance detection, and imbalance detection. These computations operate on the relative levels of different ligands and can arise directly from competitive receptor-ligand interactions. Furthermore, cells can select different computations to perform on the same ligand combination through expression of alternative sets of receptor variants. These results provide a direct signal-processing role for promiscuous receptor-ligand interactions and establish operational principles for quantitatively controlling cells with BMP ligands. Similar principles could apply to other promiscuous signaling pathways.", "date": "2017-09-07", "date_type": "published", "publication": "Cell", "volume": "170", "number": "6", "publisher": "Cell Press", "pagerange": "1184-1196", "id_number": "CaltechAUTHORS:20170908-115917940", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170908-115917940", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "Human Frontier Science Program", "grant_number": "RGP0020" }, { "agency": "NIH", "grant_number": "R01 HD75335A" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)", "grant_number": "HR0011-16-0138" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-09-0001" }, { "agency": "NSF Graduate Research Fellowship", "grant_number": "DGE-1144469" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 GM008042" }, { "agency": "David Geffen Medical Scholarship" } ] }, "doi": "10.1016/j.cell.2017.08.015", "pmcid": "PMC5612783", "primary_object": { "basename": "nihms900407.pdf", "url": "https://authors.library.caltech.edu/records/m8axx-x2s82/files/nihms900407.pdf" }, "related_objects": [ { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/m8axx-x2s82/files/mmc1.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Antebi, Yaron E.; Linton, James M.; et el." }, { "id": "https://authors.library.caltech.edu/records/he21r-5z560", "eprint_id": 77447, "eprint_status": "archive", "datestamp": "2023-08-19 03:05:23", "lastmod": "2023-10-23 15:09:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yuan-Guo-Cheng", "name": { "family": "Yuan", "given": "Guo-Cheng" }, "orcid": "0000-0002-2283-4714" }, { "id": "Cai-Long", "name": { "family": "Cai", "given": "Long" }, "orcid": "0000-0002-7154-5361" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael" }, "orcid": "0000-0002-1221-0967" }, { "id": "Enver-Tariq", "name": { "family": "Enver", "given": "Tariq" } }, { "id": "Fan-Guoping", "name": { "family": "Fan", "given": "Guoping" } }, { "id": "Guo-Guoji", "name": { "family": "Guo", "given": "Guoji" } }, { "id": "Irizarry-Rafael", "name": { "family": "Irizarry", "given": "Rafael" } }, { "id": "Kharchenko-Peter", "name": { "family": "Kharchenko", "given": "Peter" } }, { "id": "Kim-Junhyong", "name": { "family": "Kim", "given": "Junhyong" } }, { "id": "Orkin-Stuart", "name": { "family": "Orkin", "given": "Stuart" } }, { "id": "Quackenbush-Assieh", "name": { "family": "Quackenbush", "given": "Assieh" } }, { "id": "Saadatpour-Assieh", "name": { "family": "Saadatpour", "given": "Assieh" } }, { "id": "Schroeder-Timm", "name": { "family": "Schroeder", "given": "Timm" } }, { "id": "Shivdasani-Ramesh", "name": { "family": "Shivdasani", "given": "Ramesh" } }, { "id": "Tirosh-Itay", "name": { "family": "Tirosh", "given": "Itay" } } ] }, "title": "Challenges and emerging directions in single-cell analysis", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 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: 18 December 2016; Accepted: 21 April 2017; Published online: 08 May 2017. \n\nThis article is a result of the discussions at the Radcliffe Institute Exploratory Seminar on \"Theoretical Challenges in Single-Cell Analysis\" in June 2016. We are grateful for the Radcliffe Institute's generous financial and logistical support. \n\nThe work was supported by a Radcliffe Institute Exploratory Seminar Award and by the NIH grants R13-CA124365 and R01-DK081113S1. \n\nAvailability of data and materials: Not applicable. \n\nAuthors' contributions: GCY conceived the study. All authors participated in the discussions and writing of the manuscript. All authors read and approved the final manuscript. \n\nThe authors declare that they have no competing interests. \n\nEthics approval and consent to participate: Not applicable.\n\nPublished - art_3A10.1186_2Fs13059-017-1218-y.pdf
Submitted - 127761.full.pdf
", "abstract": "Single-cell analysis is a rapidly evolving approach to characterize genome-scale molecular information at the individual cell level. Development of single-cell technologies and computational methods has enabled systematic investigation of cellular heterogeneity in a wide range of tissues and cell populations, yielding fresh insights into the composition, dynamics, and regulatory mechanisms of cell states in development and disease. Despite substantial advances, significant challenges remain in the analysis, integration, and interpretation of single-cell omics data. Here, we discuss the state of the field and recent advances and look to future opportunities.", "date": "2017-05-08", "date_type": "published", "publication": "Genome Biology", "volume": "18", "number": "1", "publisher": "BioMed Central", "pagerange": "Art. No. 84", "id_number": "CaltechAUTHORS:20170515-103755842", "issn": "1474-760X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170515-103755842", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Radcliffe Institute" }, { "agency": "NIH", "grant_number": "R13-CA124365" }, { "agency": "NIH", "grant_number": "R01-DK081113S1" } ] }, "doi": "10.1186/s13059-017-1218-y", "pmcid": "PMC5421338", "primary_object": { "basename": "art_3A10.1186_2Fs13059-017-1218-y.pdf", "url": "https://authors.library.caltech.edu/records/he21r-5z560/files/art_3A10.1186_2Fs13059-017-1218-y.pdf" }, "related_objects": [ { "basename": "127761.full.pdf", "url": "https://authors.library.caltech.edu/records/he21r-5z560/files/127761.full.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Yuan, Guo-Cheng; Cai, Long; et el." }, { "id": "https://authors.library.caltech.edu/records/v8xvr-3ca95", "eprint_id": 77206, "eprint_status": "archive", "datestamp": "2023-08-19 02:09:17", "lastmod": "2023-10-25 21:58:36", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Clevers-H", "name": { "family": "Clevers", "given": "Hans" } }, { "id": "Rafelski-S", "name": { "family": "Rafelski", "given": "Susanne" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael" }, "orcid": "0000-0002-1221-0967" }, { "id": "Klein-A", "name": { "family": "Klein", "given": "Allon" } }, { "id": "Shendure-J", "name": { "family": "Shendure", "given": "Jay" } }, { "id": "Trapnell-C", "name": { "family": "Trapnell", "given": "Cole" } }, { "id": "Lein-E-S", "name": { "family": "Lein", "given": "Ed" } }, { "id": "Lundberg-E", "name": { "family": "Lundberg", "given": "Emma" } }, { "id": "Uhlen-M", "name": { "family": "Uhlen", "given": "Matthias" } }, { "id": "Martinez-Arias-A", "name": { "family": "Martinez-Arias", "given": "Alfonso" } }, { "id": "Sanes-J-R", "name": { "family": "Sanes", "given": "Joshua R." } }, { "id": "Blainey-P", "name": { "family": "Blainey", "given": "Paul" } }, { "id": "Eberwine-J", "name": { "family": "Eberwine", "given": "James" } }, { "id": "Kim-Junhyong", "name": { "family": "Kim", "given": "Junhyong" } }, { "id": "Love-J-C", "name": { "family": "Love", "given": "J. Christopher" } } ] }, "title": "What Is Your Conceptual Definition of \"Cell Type\" in the Context of a Mature Organism?", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2017 Elsevier Inc. \n\nAvailable online 22 March 2017.", "abstract": "[no abstract]", "date": "2017-03-22", "date_type": "published", "publication": "Cell Systems", "volume": "4", "number": "3", "publisher": "Elsevier", "pagerange": "255-259", "id_number": "CaltechAUTHORS:20170505-081744915", "issn": "2405-4712", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170505-081744915", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.cels.2017.03.006", "resource_type": "article", "pub_year": "2017", "author_list": "Clevers, Hans; Rafelski, Susanne; et el." }, { "id": "https://authors.library.caltech.edu/records/r69md-x7w88", "eprint_id": 78847, "eprint_status": "archive", "datestamp": "2023-08-19 01:19:34", "lastmod": "2023-10-26 14:23:40", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Antebi-Yaron-E", "name": { "family": "Antebi", "given": "Yaron E." }, "orcid": "0000-0002-5771-6814" }, { "id": "Nandagopal-Nagarajan", "name": { "family": "Nandagopal", "given": "Nagarajan" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "An operational view of intercellular signaling pathways", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 The Authors. Published by Elsevier Ltd. Under a Creative Commons license Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) \n\nAvailable online 24 February 2017. \n\nThis work was supported by the Gordon and Betty Moore Foundation through Grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative, by the Human Frontiers Science Program (EFRI-11137269), by NIHR01 HD075335, by grant W911NF-11-2-0055 from the U.S. Army Research Office and by the Institute for Collaborative Biotechnologies through grant W911NF-09-0001 from the U.S. Army Research Office. This work does not necessarily reflect the position or policy of the Government and no official endorsement should be inferred. N.N was supported by HHMI as an International Student Research fellow.\n\nPublished - 1-s2.0-S2452310016300233-main.pdf
Accepted Version - nihms855396.pdf
", "abstract": "Animal cells use a conserved repertoire of intercellular signaling pathways to communicate with one another. These pathways are well-studied from a molecular point of view. However, we often lack an \"operational\" understanding that would allow us to use these pathways to rationally control cellular behaviors. This requires knowing what dynamic input features each pathway perceives and how it processes those inputs to control downstream processes. To address these questions, researchers have begun to reconstitute signaling pathways in living cells, analyzing their dynamic responses to stimuli, and developing new functional representations of their behavior. Here we review important insights obtained through these new approaches, and discuss challenges and opportunities in understanding signaling pathways from an operational point of view.", "date": "2017-02", "date_type": "published", "publication": "Current Opinion in Systems Biology", "volume": "1", "publisher": "Elsevier", "pagerange": "16-24", "id_number": "CaltechAUTHORS:20170707-101505335", "issn": "2452-3100", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170707-101505335", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "Human Frontier Science Program", "grant_number": "EFRI-11137269" }, { "agency": "NIH", "grant_number": "R01 HD075335" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-11-2-0055" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-09-0001" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1016/j.coisb.2016.12.003", "pmcid": "PMC5665397", "primary_object": { "basename": "1-s2.0-S2452310016300233-main.pdf", "url": "https://authors.library.caltech.edu/records/r69md-x7w88/files/1-s2.0-S2452310016300233-main.pdf" }, "related_objects": [ { "basename": "nihms855396.pdf", "url": "https://authors.library.caltech.edu/records/r69md-x7w88/files/nihms855396.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Antebi, Yaron E.; Nandagopal, Nagarajan; et el." }, { "id": "https://authors.library.caltech.edu/records/h1tvx-s6y87", "eprint_id": 71682, "eprint_status": "archive", "datestamp": "2023-08-19 00:59:48", "lastmod": "2023-10-23 16:01:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Frieda-Kirsten-L", "name": { "family": "Frieda", "given": "Kirsten L." } }, { "id": "Linton-James-M", "name": { "family": "Linton", "given": "James M." } }, { "id": "Hormoz-Sahand", "name": { "family": "Hormoz", "given": "Sahand" } }, { "id": "Choi-Joonhyuk", "name": { "family": "Choi", "given": "Joonhyuk" } }, { "id": "Chow-Ke-Huan-K", "name": { "family": "Chow", "given": "Ke-Huan K." }, "orcid": "0000-0002-7317-2669" }, { "id": "Singer-Zachary-S", "name": { "family": "Singer", "given": "Zachary S." } }, { "id": "Budde-Mark-W", "name": { "family": "Budde", "given": "Mark W." }, "orcid": "0000-0002-4359-1424" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Cai-Long", "name": { "family": "Cai", "given": "Long" }, "orcid": "0000-0002-7154-5361" } ] }, "title": "Synthetic recording and in situ readout of lineage information in single cells", "ispublished": "pub", "full_text_status": "public", "keywords": "Genetic engineering, Cell proliferation", "note": "\u00a9 2016 Macmillan Publishers Limited, part of Springer Nature. \n\nReceived 30 June 2016; Accepted 11 November 2016; Published online 21 November 2016. \n\nWe thank Martin Budd and Hanqing Li for helpful suggestions. We thank Roy Kishony, and members of the Elowitz and Cai labs \nfor discussions and comments on the manuscript. This research was supported by the Allen Distinguished Investigator Program, through The Paul G. Allen Frontiers Group, NIH R01HD075605 and K99GM118910 (to S.H.), the Gordon and Betty Moore Foundation Grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative, and the Beckman Institute pilot program. \n\nAuthor Contributions: K.L.F. and J.M.L. performed the experiments with assistance from S.H., J.C., K.K.C., Z.S.S.; K.L.F. and S.H. analyzed the data; S.H. performed the simulations; M.B.E. and L.C. supervised the project. All authors wrote the manuscript.\n\nAccepted Version - nihms-1016385.pdf
Supplemental Material - nature20777-s1.pdf
Supplemental Material - nature20777-s2.xlsx
Supplemental Material - nature20777-s3.xlsx
", "abstract": "Reconstructing the lineage relationships and dynamic event histories of individual cells within their native spatial context is a long-standing challenge in biology. Many biological processes of interest occur in optically opaque or physically inaccessible contexts, necessitating approaches other than direct imaging. Here, we describe a new synthetic system that enables cells to record lineage information and event histories in the genome in a format that can be subsequently read out in single cells in situ. This system, termed Memory by Engineered Mutagenesis with Optical In situ Readout (MEMOIR), is based on a set of barcoded recording elements termed scratchpads. The state of a given scratchpad can be irreversibly altered by Cas9-based targeted mutagenesis, and read out in single cells through multiplexed single-molecule RNA fluorescence hybridization (smFISH). To demonstrate a proof of principle of MEMOIR, we engineered mouse embryonic stem (ES) cells to contain multiple scratchpads and other recording components. In these cells, scratchpads were altered in a progressive and stochastic fashion as cells proliferated. Analysis of the final states of scratchpads in single cells in situ enabled reconstruction of the lineage trees of cell colonies. Combining analysis of endogenous gene expression with lineage reconstruction in the same cells further allowed inference of the dynamic rates at which ES cells switch between two gene expression states. Finally, using simulations, we showed how parallel MEMOIR systems operating in the same cell can enable recording and readout of dynamic cellular event histories. MEMOIR thus provides a versatile platform for information recording and in situ, single cell readout across diverse biological systems.", "date": "2017-01-05", "date_type": "published", "publication": "Nature", "volume": "541", "number": "7635", "publisher": "Nature Publishing Group", "pagerange": "107-111", "id_number": "CaltechAUTHORS:20161102-141950462", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161102-141950462", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Paul G. Allen Frontiers Group" }, { "agency": "NIH", "grant_number": "R01HD075605" }, { "agency": "NIH", "grant_number": "K99GM118910" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "Caltech Beckman Institute" } ] }, "doi": "10.1038/nature20777", "pmcid": "PMC6487260", "primary_object": { "basename": "nature20777-s1.pdf", "url": "https://authors.library.caltech.edu/records/h1tvx-s6y87/files/nature20777-s1.pdf" }, "related_objects": [ { "basename": "nature20777-s2.xlsx", "url": "https://authors.library.caltech.edu/records/h1tvx-s6y87/files/nature20777-s2.xlsx" }, { "basename": "nature20777-s3.xlsx", "url": "https://authors.library.caltech.edu/records/h1tvx-s6y87/files/nature20777-s3.xlsx" }, { "basename": "nihms-1016385.pdf", "url": "https://authors.library.caltech.edu/records/h1tvx-s6y87/files/nihms-1016385.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Frieda, Kirsten L.; Linton, James M.; et el." }, { "id": "https://authors.library.caltech.edu/records/9kv8f-88h40", "eprint_id": 72313, "eprint_status": "archive", "datestamp": "2023-08-22 19:09:43", "lastmod": "2023-10-23 21:37:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hormoz-Sahand", "name": { "family": "Hormoz", "given": "Sahand" } }, { "id": "Singer-Zakary-S", "name": { "family": "Singer", "given": "Zakary S." } }, { "id": "Linton-James-M", "name": { "family": "Linton", "given": "James M." } }, { "id": "Antebi-Yaron-E", "name": { "family": "Antebi", "given": "Yaron E." }, "orcid": "0000-0002-5771-6814" }, { "id": "Shraiman-Boris-I", "name": { "family": "Shraiman", "given": "Boris I." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements", "ispublished": "pub", "full_text_status": "public", "keywords": "Lineage; Cell State Transition; Inference; Dynamics; Single Cell; Heterogeneity; Stochasticity; Stem Cells; Time-lapse Microscopy; Single-molecule FISH", "note": "\u00a9 2016 Elsevier. \n\nReceived 24 November 2015; revised 1 June 2016; accepted 18 October 2016; published 23 November 2016. \n\nWe thank Jordi Garcia-Ojalvo and David Sprinzak for helpful comments on the manuscript. We thank Fred Tan for construction of the Zscan4 reporter, and members of the M.B.E. Lab for fruitful discussions. This work was supported by the NIH grants R01HD075605A, R01GM086793A, and P50GM068763, Human Frontiers Science Program, grant RGP0020/2012, and in part by the National Science Foundation under grant NSF PHY-1125915. S.H. also acknowledges support from NIH grant K99GM118910. This work is funded by the Gordon and Betty Moore Foundation through grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative. \n\nAuthor Contributions: S.H., Z.S.S., and M.B.E. designed experiments. S.H. and Z.S.S. performed experiments and analyzed data. J.M.L. and Z.S.S. constructed cell lines with help from S.H. Y.E.A. developed the movie tracking system. B.I.S. and M.B.E. supervised research. S.H., Z.S.S., and M.B.E. wrote the manuscript with substantial input from all authors. \n\nData and Software Availability: All the analysis software, including those used for movie tracking, FISH dot detection/counting, and KCA analysis is available upon request (see CONTACT FOR REAGENT AND RESOURCE SHARING). The data visualization package is also hosted on the Elowitz lab website: http://www.elowitz.caltech.edu/. \n\nThe accession number for the data reported in this paper is NCBI's GEO: GSE86417. \n\nAdditional Resources: The complete end-point FISH data and the associated lineage relationships is available on the Elowitz lab website (http://www.elowitz.caltech.edu/) for interactive viewing using a novel visualization tool, CellLines, developed by the Elowitz Lab in collaboration with the Caltech Data Visualization Program.\n\nAccepted Version - nihms824919.pdf
Supplemental Material - mmc1.pdf
Supplemental Material - mmc2.xlsx
Supplemental Material - mmc3.xlsx
Supplemental Material - mmc4.xlsx
Supplemental Material - mmc5.mp4
", "abstract": "As they proliferate, living cells undergo transitions between specific molecularly and developmentally distinct states. Despite the functional centrality of these transitions in multicellular organisms, it has remained challenging to determine which transitions occur and at what rates without perturbations and cell engineering. Here, we introduce kin correlation analysis (KCA) and show that quantitative cell-state transition dynamics can be inferred, without direct observation, from the clustering of cell states on pedigrees (lineage trees). Combining KCA with pedigrees obtained from time-lapse imaging and endpoint single-molecule RNA-fluorescence in situ hybridization (RNA-FISH) measurements of gene expression, we determined the cell-state transition network of mouse embryonic stem (ES) cells. This analysis revealed that mouse ES cells exhibit stochastic and reversible transitions along a linear chain of states ranging from 2C-like to epiblast-like. Our approach is broadly applicable and may be applied to systems with irreversible transitions and non-stationary dynamics, such as in cancer and development.", "date": "2016-11-23", "date_type": "published", "publication": "Cell Systems", "volume": "3", "number": "5", "publisher": "Cell Press", "pagerange": "419-433", "id_number": "CaltechAUTHORS:20161128-114511280", "issn": "2405-4712", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161128-114511280", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01HD075605A" }, { "agency": "NIH", "grant_number": "R01GM086793A" }, { "agency": "NIH", "grant_number": "P50GM068763" }, { "agency": "Human Frontier Science Program", "grant_number": "RGP0020/2012" }, { "agency": "NSF", "grant_number": "PHY-1125915" }, { "agency": "NIH", "grant_number": "K99GM118910" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1016/j.cels.2016.10.015", "pmcid": "PMC5142829", "primary_object": { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/9kv8f-88h40/files/mmc1.pdf" }, "related_objects": [ { "basename": "mmc2.xlsx", "url": "https://authors.library.caltech.edu/records/9kv8f-88h40/files/mmc2.xlsx" }, { "basename": "mmc3.xlsx", "url": "https://authors.library.caltech.edu/records/9kv8f-88h40/files/mmc3.xlsx" }, { "basename": "mmc4.xlsx", "url": "https://authors.library.caltech.edu/records/9kv8f-88h40/files/mmc4.xlsx" }, { "basename": "mmc5.mp4", "url": "https://authors.library.caltech.edu/records/9kv8f-88h40/files/mmc5.mp4" }, { "basename": "nihms824919.pdf", "url": "https://authors.library.caltech.edu/records/9kv8f-88h40/files/nihms824919.pdf" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Hormoz, Sahand; Singer, Zakary S.; et el." }, { "id": "https://authors.library.caltech.edu/records/x1d9t-d8954", "eprint_id": 71151, "eprint_status": "archive", "datestamp": "2023-08-20 14:16:56", "lastmod": "2023-10-23 15:22:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gao-Xiaojing-J", "name": { "family": "Gao", "given": "Xiaojing J." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Synthetic biology: Precision timing in a cell", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2016 Macmillan Publishers Limited, part of Springer Nature. \n\nPublished online 12 October 2016.", "abstract": "A 16-year-old synthetic genetic circuit that produces gene-expression oscillations in bacterial cells has been given an upgrade, making it an exceptionally precise biological clock.", "date": "2016-10-27", "date_type": "published", "publication": "Nature", "volume": "538", "number": "7626", "publisher": "Nature Publishing Group", "pagerange": "462-463", "id_number": "CaltechAUTHORS:20161017-101223005", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161017-101223005", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1038/nature19478", "resource_type": "article", "pub_year": "2016", "author_list": "Gao, Xiaojing J. and Elowitz, Michael B." }, { "id": "https://authors.library.caltech.edu/records/n0xgs-vjw12", "eprint_id": 67892, "eprint_status": "archive", "datestamp": "2023-08-20 13:04:30", "lastmod": "2023-10-19 22:03:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kueh-Hao-Yuan", "name": { "family": "Kueh", "given": "Hao Yuan" }, "orcid": "0000-0001-6272-6673" }, { "id": "Yui-Mary-A", "name": { "family": "Yui", "given": "Mary A." }, "orcid": "0000-0002-3136-2181" }, { "id": "Ng-Kenneth-K-H", "name": { "family": "Ng", "given": "Kenneth K. H." } }, { "id": "Pease-Shirley-S", "name": { "family": "Pease", "given": "Shirley S." } }, { "id": "Zhang-Jingli-A", "name": { "family": "Zhang", "given": "Jingli A." } }, { "id": "Damle-Sagar-S", "name": { "family": "Damle", "given": "Sagar S." } }, { "id": "Freedman-George", "name": { "family": "Freedman", "given": "George" } }, { "id": "Siu-Sharmayne", "name": { "family": "Siu", "given": "Sharmayne" } }, { "id": "Bernstein-Irwin-D", "name": { "family": "Bernstein", "given": "Irwin D." }, "orcid": "0000-0003-0795-3392" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Rothenberg-E-V", "name": { "family": "Rothenberg", "given": "Ellen V." }, "orcid": "0000-0002-3901-347X" } ] }, "title": "Asynchronous combinatorial action of four regulatory factors activates Bcl11b for T cell commitment", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 Macmillan Publishers Limited. \n\nReceived 26 January 2016; Accepted 14 June 2016; Published online 04 July 2016. \n\nWe thank M. Lerica Gutierrez Quiloan for assistance with mouse genotyping and maintenance; N. Verduzco and I. Soto for animal husbandry; J. Longmate for help with statistical analysis of alternate-lineage-potential experiments; R.A. Diamond, K. Beadle, J. Grimm, D. Perez and J. Verceles for cell sorting; N. Feng for initial flow cytometric analysis; J. Hahn for advice on BAC recombineering; S. Qin for assistance with qPCR experiments; X.Wang for performing pilot studies with microwell arrays; and J. Ungerb\u00e4ck for assistance with visualizing genome track data. We also thank A. Bhandoola, L. Xu and W. Pear (University of Pennsylvania); J. Telfer (University of Massachusetts) and N. Masuyama (University of Tokyo) for constructs. This work was funded by a CRI/Irvington Postdoctoral Fellowship and a US National Institutes of Health (NIH) K99/R00 Award (K99HL119638A) to H.Y.K.; a California Institute for Regenerative Medicine Bridges to Stem-Cell Research award to K.K.H.N. (TB1-01176); NIH grants to E.V.R. (R01 AI083514, R01 AI095943, RC2 CA148278, R33 HL089123, R01 CA90233 and R01 HL119102) and M.A.Y. (R01 AI064590); NIH/HHS grant U01HL100395 (I.D.B.); the Albert Billings Ruddock Professorship to E.V.R.; and the Al Sherman Foundation and the Louis A. Garfinkle Memorial Laboratory Fund to E.V.R.'s lab. \n\nAuthor Contributions: H.Y.K. designed research, performed experiments, analyzed data and wrote the paper. M.A.Y. designed research, performed experiments, analyzed data and wrote the paper. K.K.H.N., and S.S.P. performed experiments. S.S.D., G.F. and I.D.B. provided reagents. J.A.Z. performed experiments and analyzed data. S.S. analyzed data. M.B.E. designed research. E.V.R. designed research, analyzed data and wrote the paper. \n\nCode availability: Image analysis code is available upon request to H.Y.K. \n\nThe authors declare no competing financial interests.\n\nAccepted Version - nihms795848.pdf
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", "abstract": "During T cell development, multipotent progenitors relinquish competence for other fates and commit to the T cell lineage by turning on Bcl11b, which encodes a transcription factor. To clarify lineage commitment mechanisms, we followed developing T cells at the single-cell level using Bcl11b knock-in fluorescent reporter mice. Notch signaling and Notch-activated transcription factors collaborate to activate Bcl11b expression irrespectively of Notch-dependent proliferation. These inputs work via three distinct, asynchronous mechanisms: an early locus 'poising' function dependent on TCF-1 and GATA-3, a stochastic-permissivity function dependent on Notch signaling, and a separate amplitude-control function dependent on Runx1, a factor already present in multipotent progenitors. Despite their necessity for Bcl11b expression, these inputs act in a stage-specific manner, providing a multitiered mechanism for developmental gene regulation.", "date": "2016-08", "date_type": "published", "publication": "Nature Immunology", "volume": "17", "number": "8", "publisher": "Nature Publishing Group", "pagerange": "956-965", "id_number": "CaltechAUTHORS:20160613-162442836", "issn": "1529-2908", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160613-162442836", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "CRI/Irvington Postdoctoral Fellowship" }, { "agency": "NIH", "grant_number": "K99HL119638A" }, { "agency": "California Institute for Regenerative Medicine (CIRM)", "grant_number": "TB1-01176" }, { "agency": "NIH", "grant_number": "R01 AI083514" }, { "agency": "NIH", "grant_number": "R01 AI095943" }, { "agency": "NIH", "grant_number": "RC2 CA148278" }, { "agency": "NIH", "grant_number": "R33 HL089123" }, { "agency": "NIH", "grant_number": "R01 CA90233" }, { "agency": "NIH", "grant_number": "R01 HL119102" }, { "agency": "NIH", "grant_number": "R01 AI064590" }, { "agency": "NIH", "grant_number": "U01HL100395" }, { "agency": "Albert Billings Ruddock Professorship" }, { "agency": "Al Sherman Foundation" }, { "agency": "Louis A. Garfinkle Memorial Laboratory Fund" } ] }, "doi": "10.1038/ni.3514", "pmcid": "PMC4955789", "primary_object": { "basename": "ni.3514-S1.pdf", "url": "https://authors.library.caltech.edu/records/n0xgs-vjw12/files/ni.3514-S1.pdf" }, "related_objects": [ { "basename": "ni_3514-SF3.jpg", "url": "https://authors.library.caltech.edu/records/n0xgs-vjw12/files/ni_3514-SF3.jpg" }, { "basename": "ni_3514-SF6.jpg", "url": "https://authors.library.caltech.edu/records/n0xgs-vjw12/files/ni_3514-SF6.jpg" }, { "basename": "ni_3514-SF7.jpg", "url": "https://authors.library.caltech.edu/records/n0xgs-vjw12/files/ni_3514-SF7.jpg" }, { "basename": "ni_3514-SF8.jpg", "url": "https://authors.library.caltech.edu/records/n0xgs-vjw12/files/ni_3514-SF8.jpg" }, { "basename": "nihms795848.pdf", "url": "https://authors.library.caltech.edu/records/n0xgs-vjw12/files/nihms795848.pdf" }, { "basename": "ni.3514-S2.xlsx", "url": "https://authors.library.caltech.edu/records/n0xgs-vjw12/files/ni.3514-S2.xlsx" }, { "basename": "ni.3514-S3.xlsx", "url": "https://authors.library.caltech.edu/records/n0xgs-vjw12/files/ni.3514-S3.xlsx" }, { "basename": "ni_3514-SF1.jpg", "url": "https://authors.library.caltech.edu/records/n0xgs-vjw12/files/ni_3514-SF1.jpg" }, { "basename": "ni_3514-SF2.jpg", "url": "https://authors.library.caltech.edu/records/n0xgs-vjw12/files/ni_3514-SF2.jpg" }, { "basename": "ni_3514-SF4.jpg", "url": "https://authors.library.caltech.edu/records/n0xgs-vjw12/files/ni_3514-SF4.jpg" }, { "basename": "ni_3514-SF5.jpg", "url": "https://authors.library.caltech.edu/records/n0xgs-vjw12/files/ni_3514-SF5.jpg" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Kueh, Hao Yuan; Yui, Mary A.; et el." }, { "id": "https://authors.library.caltech.edu/records/xv89r-d8958", "eprint_id": 71347, "eprint_status": "archive", "datestamp": "2023-08-20 13:10:14", "lastmod": "2023-10-23 15:39:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Rothenberg-E-V", "name": { "family": "Rothenberg", "given": "E." }, "orcid": "0000-0002-3901-347X" }, { "id": "Kueh-Hao-Yuan", "name": { "family": "Kueh", "given": "H. Y." }, "orcid": "0000-0001-6272-6673" }, { "id": "Hosokawa-Hiroyuki", "name": { "family": "Hosokawa", "given": "H." }, "orcid": "0000-0002-9592-2889" }, { "id": "Ng-K-K-H", "name": { "family": "Ng", "given": "K. K. H." } }, { "id": "Mehta-Arnav", "name": { "family": "Mehta", "given": "A." } }, { "id": "Pease-Shirley-S", "name": { "family": "Pease", "given": "S. S." } }, { "id": "Romero-Wolf-M", "name": { "family": "Romero-Wolf", "given": "M." }, "orcid": "0000-0002-8024-7198" }, { "id": "Ungerb\u00e4ck-J", "name": { "family": "Ungerb\u00e4ck", "given": "J." } }, { "id": "Wang-X", "name": { "family": "Wang", "given": "X." } }, { "id": "Yui-Mary-A", "name": { "family": "Yui", "given": "M. A." }, "orcid": "0000-0002-3136-2181" }, { "id": "Zeng-W-B", "name": { "family": "Zeng", "given": "W. B." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "M. B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Mortazavi-A", "name": { "family": "Mortazavi", "given": "A." }, "orcid": "0000-0002-4259-6362" } ] }, "title": "Dissecting the transcriptional regulatory network for early T-cell commitment", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2016 The Authors. European Journal of Immunology \u00a9 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. \n\nFirst published: 19 August 2016.", "abstract": "Multipotent precursors proliferating in the thymus become committed to a T-cell fate when their access\nto alternative cell fates is intrinsically and unconditionally closed. This process involves very dynamic\nchanges in transcription factor expression and activity: PU.1 and other factors expressed in\nmultipotent progenitors are downregulated and are usually permanently silenced, while T-cell\ntranscription factors, especially Bcl11b, are sharply activated. The abrupt activation of Bcl11b from a\nsilent state is not only a landmark in T-cell differentiation, marking commitment, but also a functional\ncontributor to commitment. Key target genes affected by Bcl11b function at this particular stage will be\ndescribed: many of them appear to be under the control of Bcl11b as a repressor. Recent proteomic\ncharacterization of Bcl11b-containing protein complexes indicates the corepressor and coactivator\npartners that it uses to mediate different types of regulatory activity at different genomic sites. Since\nBcl11b is such a powerful factor, a central question is how the onset of expression of Bcl11b itself is\ncontrolled. The talk will describe the combination of trans-acting factors that are needed to open the\nBcl11b locus and activate it, and show that these factors each play slightly different temporal and\nfunctional roles in the activation process. Interestingly, evidence will also be shown for an epigenetic\ncomponent of Bcl11b regulation that further slows its activation but helps to make it irreversible.", "date": "2016-08", "date_type": "published", "publication": "European Journal of Immunology", "volume": "46", "number": "S1", "publisher": "Wiley", "pagerange": "797", "id_number": "CaltechAUTHORS:20161021-124515838", "issn": "0014-2980", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161021-124515838", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1002/eji.201670200", "resource_type": "article", "pub_year": "2016", "author_list": "Rothenberg, E.; Kueh, H. Y.; et el." }, { "id": "https://authors.library.caltech.edu/records/6gg68-bse49", "eprint_id": 65531, "eprint_status": "archive", "datestamp": "2023-08-20 10:56:12", "lastmod": "2023-10-18 16:06:14", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lin-Yihan", "name": { "family": "Lin", "given": "Yihan" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Central Dogma Goes Digital", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2016 Elsevier Inc.\n\nAvailable online 17 March 2016.", "abstract": "In this issue of Molecular Cell, Tay and colleagues ( Albayrak et al., 2016) describe a new technique to digitally quantify the numbers of protein and mRNA in the same mammalian cell, providing a new way to look at the central dogma of molecular biology.", "date": "2016-03-17", "date_type": "published", "publication": "Molecular Cell", "volume": "61", "number": "6", "publisher": "Elsevier", "pagerange": "791-792", "id_number": "CaltechAUTHORS:20160321-104414916", "issn": "1097-2765", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160321-104414916", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.molcel.2016.03.005", "resource_type": "article", "pub_year": "2016", "author_list": "Lin, Yihan and Elowitz, Michael B." }, { "id": "https://authors.library.caltech.edu/records/e686y-qa817", "eprint_id": 64495, "eprint_status": "archive", "datestamp": "2023-08-20 10:17:38", "lastmod": "2023-10-17 21:27:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bintu-Lacramioara", "name": { "family": "Bintu", "given": "Lacramioara" }, "orcid": "0000-0001-5443-6633" }, { "id": "Yong-John", "name": { "family": "Yong", "given": "John" } }, { "id": "Antebi-Yaron-E", "name": { "family": "Antebi", "given": "Yaron E." }, "orcid": "0000-0002-5771-6814" }, { "id": "McCue-Kayla", "name": { "family": "McCue", "given": "Kayla" } }, { "id": "Kazuki-Yasuhiro", "name": { "family": "Kazuki", "given": "Yasuhiro" }, "orcid": "0000-0003-4818-4710" }, { "id": "Uno-Narumi", "name": { "family": "Uno", "given": "Narumi" } }, { "id": "Oshimura-Mitsuo", "name": { "family": "Oshimura", "given": "Mitsuo" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Dynamics of epigenetic regulation at the single-cell level", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 American Association for the Advancement of Science. \n\nReceived 7 April 2015; accepted 1 December 2015. \n\nWe thank G. M. Abadi, J. Cao, L. Santat, and the Caltech Flow Cytometry Facility for technical assistance and U. Alon, L. Cai, J. Garcia-Ojalvo, A. I. Geraschenko, M. Guttman, B. A. Hay, R. Kishony, A. Moses, R. Phillips, K. Plath, E. Rothenberg, M.-H. Sung, and members of the Elowitz lab for discussions and feedback. This work was supported by the NIH (grants R01 HD075335A and R01 HD075605A to M.B.E.), the Defense Advanced Research Projects Agency (grant W911NF-11-2-0055 to M.B.E.), the Human Frontier Science Program (grant RGP0020/2012 to M.B.E. and Y.E.A.), the Jane Coffin Childs Memorial Fund for Medical Research (postdoctoral fellowship to L.B.), the Beckman Institute at California Institute of Technology (equipment grant to L.B.), the Burroughs Wellcome Fund (Career at the Scientific Interface Award to L.B.), the Gordon and Betty Moore Foundation (through grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative), and HHMI (M.B.E.). M.B.E., L.B., J.Y., and California Institute of Technology filed a provisional patent application (CIT-7162-P) that relates to fractional control devices based on CRs.\n\nAccepted Version - nihms825209.pdf
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", "abstract": "Chromatin regulators play a major role in establishing and maintaining gene expression states. Yet how they control gene expression in single cells, quantitatively and over time, remains unclear. We used time-lapse microscopy to analyze the dynamic effects of four silencers associated with diverse modifications: DNA methylation, histone deacetylation, and histone methylation. For all regulators, silencing and reactivation occurred in all-or-none events, enabling the regulators to modulate the fraction of cells silenced rather than the amount of gene expression. These dynamics could be described by a three-state model involving stochastic transitions between active, reversibly silent, and irreversibly silent states. Through their individual transition rates, these regulators operate over different time scales and generate distinct types of epigenetic memory. Our results provide a framework for understanding and engineering mammalian chromatin regulation and epigenetic memory.", "date": "2016-02-12", "date_type": "published", "publication": "Science", "volume": "351", "number": "6274", "publisher": "American Association for the Advancement of Science", "pagerange": "720-724", "id_number": "CaltechAUTHORS:20160216-093925349", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160216-093925349", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 HD075335A" }, { "agency": "NIH", "grant_number": "R01 HD075605A" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)", "grant_number": "W911NF-11-2-0055" }, { "agency": "Human Frontier Science Program", "grant_number": "RGP0020/2012" }, { "agency": "Jane Coffin Childs Memorial Fund" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1126/science.aab2956", "pmcid": "PMC5108652", "primary_object": { "basename": "aab2956s1.mp4", "url": "https://authors.library.caltech.edu/records/e686y-qa817/files/aab2956s1.mp4" }, "related_objects": [ { "basename": "aab2956s10.mp4", "url": "https://authors.library.caltech.edu/records/e686y-qa817/files/aab2956s10.mp4" }, { "basename": "aab2956s11.mp4", "url": "https://authors.library.caltech.edu/records/e686y-qa817/files/aab2956s11.mp4" }, { "basename": "aab2956s9.mp4", "url": "https://authors.library.caltech.edu/records/e686y-qa817/files/aab2956s9.mp4" }, { "basename": "aab2956s12.mp4", "url": "https://authors.library.caltech.edu/records/e686y-qa817/files/aab2956s12.mp4" }, { "basename": "aab2956s16.avi", "url": "https://authors.library.caltech.edu/records/e686y-qa817/files/aab2956s16.avi" }, { "basename": "aab2956s4.mp4", "url": "https://authors.library.caltech.edu/records/e686y-qa817/files/aab2956s4.mp4" }, { "basename": "aab2956s7.avi", "url": "https://authors.library.caltech.edu/records/e686y-qa817/files/aab2956s7.avi" }, { "basename": "aab2956s8.avi", "url": "https://authors.library.caltech.edu/records/e686y-qa817/files/aab2956s8.avi" }, { "basename": "nihms825209.pdf", "url": "https://authors.library.caltech.edu/records/e686y-qa817/files/nihms825209.pdf" }, { "basename": "Bintu.SM.pdf", "url": "https://authors.library.caltech.edu/records/e686y-qa817/files/Bintu.SM.pdf" }, { "basename": "aab2956s13.avi", "url": "https://authors.library.caltech.edu/records/e686y-qa817/files/aab2956s13.avi" }, { "basename": "aab2956s14.avi", "url": "https://authors.library.caltech.edu/records/e686y-qa817/files/aab2956s14.avi" }, { "basename": "aab2956s15.avi", "url": "https://authors.library.caltech.edu/records/e686y-qa817/files/aab2956s15.avi" }, { "basename": "aab2956s5.avi", "url": "https://authors.library.caltech.edu/records/e686y-qa817/files/aab2956s5.avi" }, { "basename": "aab2956s2.mp4", "url": "https://authors.library.caltech.edu/records/e686y-qa817/files/aab2956s2.mp4" }, { "basename": "aab2956s3.mp4", "url": "https://authors.library.caltech.edu/records/e686y-qa817/files/aab2956s3.mp4" }, { "basename": "aab2956s6.avi", "url": "https://authors.library.caltech.edu/records/e686y-qa817/files/aab2956s6.avi" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Bintu, Lacramioara; Yong, John; et el." }, { "id": "https://authors.library.caltech.edu/records/72nva-kvd34", "eprint_id": 59247, "eprint_status": "archive", "datestamp": "2023-08-20 09:02:16", "lastmod": "2023-10-23 20:14:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lin-Yihan", "name": { "family": "Lin", "given": "Yihan" }, "orcid": "0000-0002-2763-5538" }, { "id": "Sohn-Chang-Ho", "name": { "family": "Sohn", "given": "Chang Ho" }, "orcid": "0000-0002-7585-1841" }, { "id": "Dalal-Chiraj-K", "name": { "family": "Dalal", "given": "Chiraj K." }, "orcid": "0000-0002-3624-8409" }, { "id": "Cai-Long", "name": { "family": "Cai", "given": "Long" }, "orcid": "0000-0002-7154-5361" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Combinatorial gene regulation by modulation of relative pulse timing", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2015 Macmillan Publishers Limited. \n\nReceived 02 January 2015; Accepted 04 September 2015; Published online 14 October 2015. \n\nWe thank U. Alon, R. Corral, R. Deshaies, A. Eldar, J. Garcia-Ojalvo, R. Kishony, A. Moses, G. Seelig, P. Swain, and members of the Elowitz laboratory for comments and feedback on themanuscript. We also thank the core sequencing facility at Caltech for help on RNA-Seq. This work was supported by the NIH (R01 GM079771B, R01 GM086793A), the NSF (Award no. 1547056), DARPA (HR0011-05-1-0057), and by the Gordon and Betty Moore Foundation through Grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative. L.C. acknowledges the Ellison foundation for support. \n\nAuthor Contributions: Y.L. and M.B.E. designed experiments. Y.L. performed experiments and analysed data with input from all authors. C.K.D. and L.C. initially observed the correlation between Msn2 and Mig1 dynamics and C.H.S. conducted preliminary analysis of target gene expression. M.B.E. supervised research. Y.L. and M.B.E. wrote the manuscript with input from all authors. \n\nThe authors declare no competing financial interests. \n\nRNA-Seq data have been deposited at Gene Expression Omnibus (GEO) under the accession code GSE71712.\n\nAccepted Version - nihms722821.pdf
Supplemental Material - nature15710-s1.pdf
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", "abstract": "Studies of individual living cells have revealed that many transcription factors activate in dynamic, and often stochastic, pulses within the same cell. However, it has remained unclear whether cells might exploit the dynamic interaction of these pulses to control gene expression. Here, using quantitative single-cell time-lapse imaging of Saccharomyces cerevisiae, we show that the pulsatile transcription factors Msn2 and Mig1 combinatorially regulate their target genes through modulation of their relative pulse timing. The activator Msn2 and repressor Mig1 showed pulsed activation in either a temporally overlapping or non-overlapping manner during their transient response to different inputs, with only the non-overlapping dynamics efficiently activating target gene expression. Similarly, under constant environmental conditions, where Msn2 and Mig1 exhibit sporadic pulsing, glucose concentration modulated the temporal overlap between pulses of the two factors. Together, these results reveal a time-based mode of combinatorial gene regulation. Regulation through relative signal timing is common in engineering and neurobiology, and these results suggest that it could also function broadly within the signalling and regulatory systems of the cell.", "date": "2015-11-05", "date_type": "published", "publication": "Nature", "volume": "527", "number": "7576", "publisher": "Nature Publishing Group", "pagerange": "54-58", "id_number": "CaltechAUTHORS:20150805-144646254", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150805-144646254", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 GM079771B" }, { "agency": "NIH", "grant_number": "R01 GM086793A" }, { "agency": "NSF", "grant_number": "MCB-1547056" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)", "grant_number": "HR0011-05-1-0057" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "Ellison Medical Foundation" } ] }, "doi": "10.1038/nature15710", "pmcid": "PMC4870307", "primary_object": { "basename": "nature15710-sf7.jpg", "url": "https://authors.library.caltech.edu/records/72nva-kvd34/files/nature15710-sf7.jpg" }, "related_objects": [ { "basename": "nature15710-sf8.jpg", "url": "https://authors.library.caltech.edu/records/72nva-kvd34/files/nature15710-sf8.jpg" }, { "basename": "nature15710-sf9.jpg", "url": "https://authors.library.caltech.edu/records/72nva-kvd34/files/nature15710-sf9.jpg" }, { "basename": "nature15710-sv2.mov", "url": "https://authors.library.caltech.edu/records/72nva-kvd34/files/nature15710-sv2.mov" }, { "basename": "nature15710-sf1.jpg", "url": "https://authors.library.caltech.edu/records/72nva-kvd34/files/nature15710-sf1.jpg" }, { "basename": "nature15710-sf10.jpg", "url": "https://authors.library.caltech.edu/records/72nva-kvd34/files/nature15710-sf10.jpg" }, { "basename": "nature15710-sf2.jpg", "url": "https://authors.library.caltech.edu/records/72nva-kvd34/files/nature15710-sf2.jpg" }, { "basename": "nature15710-sf5.jpg", "url": "https://authors.library.caltech.edu/records/72nva-kvd34/files/nature15710-sf5.jpg" }, { "basename": "nature15710-sf3.jpg", "url": "https://authors.library.caltech.edu/records/72nva-kvd34/files/nature15710-sf3.jpg" }, { "basename": "nature15710-sf4.jpg", "url": "https://authors.library.caltech.edu/records/72nva-kvd34/files/nature15710-sf4.jpg" }, { "basename": "nature15710-sv1.mov", "url": "https://authors.library.caltech.edu/records/72nva-kvd34/files/nature15710-sv1.mov" }, { "basename": "nature15710-s1.pdf", "url": "https://authors.library.caltech.edu/records/72nva-kvd34/files/nature15710-s1.pdf" }, { "basename": "nature15710-sv4.mov", "url": "https://authors.library.caltech.edu/records/72nva-kvd34/files/nature15710-sv4.mov" }, { "basename": "nihms722821.pdf", "url": "https://authors.library.caltech.edu/records/72nva-kvd34/files/nihms722821.pdf" }, { "basename": "nature15710-sf6.jpg", "url": "https://authors.library.caltech.edu/records/72nva-kvd34/files/nature15710-sf6.jpg" }, { "basename": "nature15710-sv3.mov", "url": "https://authors.library.caltech.edu/records/72nva-kvd34/files/nature15710-sv3.mov" }, { "basename": "nature15710-sv5.mov", "url": "https://authors.library.caltech.edu/records/72nva-kvd34/files/nature15710-sv5.mov" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Lin, Yihan; Sohn, Chang Ho; et el." }, { "id": "https://authors.library.caltech.edu/records/1peqg-qfe69", "eprint_id": 53548, "eprint_status": "archive", "datestamp": "2023-08-20 04:33:47", "lastmod": "2023-10-19 21:51:16", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kim-Daniel-H", "name": { "family": "Kim", "given": "Daniel H." } }, { "id": "Marinov-G-K", "name": { "family": "Marinov", "given": "Georgi K." }, "orcid": "0000-0003-1822-7273" }, { "id": "Pepke-S", "name": { "family": "Pepke", "given": "Shirley" } }, { "id": "Singer-Z-S", "name": { "family": "Singer", "given": "Zakary S." } }, { "id": "He-Peng", "name": { "family": "He", "given": "Peng" } }, { "id": "Williams-B", "name": { "family": "Williams", "given": "Brian" } }, { "id": "Schroth-G-P", "name": { "family": "Schroth", "given": "Gary P." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Wold-B-J", "name": { "family": "Wold", "given": "Barbara J." }, "orcid": "0000-0003-3235-8130" } ] }, "title": "Single-Cell Transcriptome Analysis Reveals Dynamic Changes in lncRNA Expression during Reprogramming", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2015 Elsevier Inc. Received: February 7, 2014. Revised: October 21, 2014. Accepted: November 10, 2014. Published: January 8, 2015.\n\nWe thank Ellen Rothenberg, Paul Sternberg, and Chuck Murry for helpful discussions; Jorge Mata and Scott Wang for tail tip excision; Josh Verceles, Diana Perez, and Rochelle Diamond for cell sorting; Igor Antoshechkin for sequencing; Henry Amrhein and Diane Trout for data curation; Shujun Luo\nfor single-cell protocol development; and Maria Moon and Hank Huang for illustration and graphic design. D.H.K. was supported by a Fellowship Award from the Damon Runyon Cancer Research Foundation and the Beckman Fellows Program at the California Institute of Technology. G.P.S. is an employee and shareholder of Illumina. M.B.E. is an Investigator of the Howard Hughes Medical Institute. This work was supported by NIH R01HD075605A and HFSP.RGP0200 funding to M.B.E.; Gordon and Betty Moore Foundation Grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative; and the Bren Chair, Caltech Beckman Institute, and NIH NHGRI funding to B.J.W.\n\nSequencing data have been deposited in the National Center for Biotechnology Information Gene Expression Omnibus under accession number GSE55291.\n\nAccepted Version - nihms-642325.pdf
Supplemental Material - mmc1.pdf
Supplemental Material - mmc2.xlsx
", "abstract": "Cellular reprogramming highlights the epigenetic plasticity of the somatic cell state. Long noncoding RNAs (lncRNAs) have emerging roles in epigenetic regulation, but their potential functions in reprogramming cell fate have been largely unexplored. We used single-cell RNA sequencing to characterize the expression patterns of over 16,000 genes, including 437 lncRNAs, during defined stages of reprogramming to pluripotency. Self-organizing maps (SOMs) were used as an intuitive way to structure and interrogate transcriptome data at the single-cell level. Early molecular events during reprogramming involved the activation of Ras signaling pathways, along with hundreds of lncRNAs. Loss-of-function studies showed that activated lncRNAs can repress lineage-specific genes, while lncRNAs activated in multiple reprogramming cell types can regulate metabolic gene expression. Our findings demonstrate that reprogramming cells activate defined sets of functionally relevant lncRNAs and provide a resource to further investigate how dynamic changes in the transcriptome reprogram cell state.", "date": "2015-01-08", "date_type": "published", "publication": "Cell Stem Cell", "volume": "16", "number": "1", "publisher": "Elsevier", "pagerange": "88-101", "id_number": "CaltechAUTHORS:20150112-083957342", "issn": "1934-5909", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150112-083957342", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Damon Runyon Cancer Research Foundation" }, { "agency": "Caltech Beckman Institute" }, { "agency": "NIH", "grant_number": "R01HD075605A" }, { "agency": "Human Frontier Science Program", "grant_number": "HFSP.RGP0200" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "Bren Chair" }, { "agency": "Caltech Beckman Institute" } ] }, "doi": "10.1016/j.stem.2014.11.005", "pmcid": "PMC4291542", "primary_object": { "basename": "mmc2.xlsx", "url": "https://authors.library.caltech.edu/records/1peqg-qfe69/files/mmc2.xlsx" }, "related_objects": [ { "basename": "nihms-642325.pdf", "url": "https://authors.library.caltech.edu/records/1peqg-qfe69/files/nihms-642325.pdf" }, { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/1peqg-qfe69/files/mmc1.pdf" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Kim, Daniel H.; Marinov, Georgi K.; et el." }, { "id": "https://authors.library.caltech.edu/records/70dpj-v1f57", "eprint_id": 54242, "eprint_status": "archive", "datestamp": "2023-08-20 04:04:41", "lastmod": "2023-10-20 15:43:25", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Markson-J-S", "name": { "family": "Markson", "given": "Joseph S." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Synthetic Biology of Multicellular Systems: New Platforms and Applications for Animal Cells and Organisms", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 American Chemical Society.\n\nReceived: December 3, 2014; published: December 19, 2014.\n\nAccepted Version - nihms699891.pdf
", "abstract": "Like life itself, synthetic biology began with unicellular\norganisms. Early synthetic biologists built genetic circuits\nin model prokaryotes and yeast because of their relative\nbiological simplicity and ease of genetic manipulation. With\nsuperior genetic tools, faster generation times, and betterunderstood endogenous gene expression machinery, prokaryotes and yeast were (and remain) appealing hosts for the engineering of synthetic systems. Now in its second decade, synthetic biology in unicellular organisms has produced myriad synthetic genetic circuits, a number of industrial applications, and fundamental new biological insights unlikely to have emerged from nonsynthetic approaches.", "date": "2014-12-19", "date_type": "published", "publication": "ACS Synthetic Biology", "volume": "3", "number": "12", "publisher": "American Chemical Society", "pagerange": "875-876", "id_number": "CaltechAUTHORS:20150130-091522471", "issn": "2161-5063", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150130-091522471", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1021/sb500358y", "pmcid": "PMC4476972", "primary_object": { "basename": "nihms699891.pdf", "url": "https://authors.library.caltech.edu/records/70dpj-v1f57/files/nihms699891.pdf" }, "resource_type": "article", "pub_year": "2014", "author_list": "Markson, Joseph S. and Elowitz, Michael B." }, { "id": "https://authors.library.caltech.edu/records/xgkj2-bqj78", "eprint_id": 56030, "eprint_status": "archive", "datestamp": "2023-08-20 03:59:14", "lastmod": "2023-10-20 23:34:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sanghez-V", "name": { "family": "Sanghez", "given": "Valentina" }, "orcid": "0000-0002-4131-7480" }, { "id": "Kee-Dustin", "name": { "family": "Kee", "given": "Dustin" } }, { "id": "Beuder-S", "name": { "family": "Beuder", "given": "Steven" } }, { "id": "Rux-D", "name": { "family": "Rux", "given": "Danielle" } }, { "id": "Osawa-Mitsujiro", "name": { "family": "Osawa", "given": "Mitsujiro" } }, { "id": "Markson-J-S", "name": { "family": "Markson", "given": "Joe" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael" }, "orcid": "0000-0002-1221-0967" }, { "id": "Kyba-M", "name": { "family": "Kyba", "given": "Michael" } }, { "id": "Iacobino-M", "name": { "family": "Iacobino", "given": "Michelina" } } ] }, "title": "HoxA3 Controls Notch Pathway to Repress Blood Development", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2014 by The American Society of Hematology.", "abstract": "Hematopoietic stem cells (HSC) are generated from a specialized subset of endothelial cells, hemogenic endothelium. Previous studies performed by our group showed that HoxA3 restrains the cell at the hemogenic endothelium stage, inhibiting further differentiation toward blood by direct repression of Runx1. Building on our previous work, we show here that overexpression of HoxA3 affects the Notch pathway. Upon HoxA3 upregulation in endothelial cells, Jag1 is induced, Mfng (Manic) and Lfng (Lunatic) fringes are downregulated, and there is a trend towards Notch target gene repression. These data suggest that in the presence of HoxA3, endothelial cells are blocked from receiving Notch signal through ligand cis-inhibition with resulting blood inhibition. In order to test this hypothesis, we evaluated the effect of activation or inhibition of the Notch pathway during blood development. We show here that the number of blood progenitors originating from the hemogenic endothelium is decreased when the Notch pathway is inhibited. Conversely, induction of the pathway by upregulation of NICD (Notch1 Intra Cellular Domain) promotes an increase in the number of blood progenitors originating from hemogenic endothelium. Furthermore, inhibition of the pathway when HoxA3 is upregulated has little or no effect in blood while induction of the pathway in HoxA3 presence in part promotes blood development. Taken together, these results demonstrate that Notch pathway is both sufficient and essential for blood development. Specifically HoxA3 inhibits Notch signal reception in two ways: 1) HoxA3 increases Jag1 ligand expression that acts in cis-inhibition; 2) represses Manic and Lunatic fringes both necessary to increase the affinity of Notch receptors for the Delta ligands. When this blockage is bypassed by NICD upregulation, blood is formed, demonstrating that HoxA3-dependent Notch inhibition results in blood suppression.", "date": "2014-12-06", "date_type": "published", "publication": "Blood", "volume": "124", "number": "21", "publisher": "American Society of Hematology", "id_number": "CaltechAUTHORS:20150324-122948946", "issn": "0006-4971", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150324-122948946", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "resource_type": "article", "pub_year": "2014", "author_list": "Sanghez, Valentina; Kee, Dustin; et el." }, { "id": "https://authors.library.caltech.edu/records/e72gb-kqs62", "eprint_id": 52195, "eprint_status": "archive", "datestamp": "2023-08-20 03:22:59", "lastmod": "2023-10-18 19:39:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Levine-J-H", "name": { "family": "Levine", "given": "Joe H." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Polyphasic feedback enables tunable cellular timers", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 Elsevier B.V.\n\nAccepted Version - nihms-689285.pdf
Supplemental Material - mmc1.pdf
", "abstract": "Cellular 'timers' provide an important function in living cells [1]. Timers help cells defer their responses to stimuli, often for time intervals extending over multiple cell cycles (Figure 1A, left). For example, mammalian oligodendrocyte precursors typically proliferate for \u223c7 divisions before differentiating during neural development [2]. The bacterium Bacillus subtilis can respond to sudden nutrient limitation by transforming into a dormant spore after \u223c5 cell cycles [3]. Timers can balance proliferation with differentiation to control the sizes of various cell populations. Some timers appear to operate in a largely cell-autonomous fashion, but the underlying genetic circuit mechanisms that enable this remain poorly understood. Protein dilution poses stringent challenges to timer circuits by continually diluting out timer components in proliferating cells ( Figure 1A, right). Recent work suggests that pulsatile or oscillatory dynamics can facilitate timer functions 3 and 4. Here, we show how polyphasic positive feedback \u2014 a pulsed architecture that breaks a feedback signal into temporally distinct phases \u2014 counteracts protein dilution to facilitate timer behavior.", "date": "2014-10-20", "date_type": "published", "publication": "Current Biology", "volume": "24", "number": "20", "publisher": "Cell Press", "pagerange": "R994-R995", "id_number": "CaltechAUTHORS:20141201-083856186", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141201-083856186", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.cub.2014.08.030", "pmcid": "PMC4451454", "primary_object": { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/e72gb-kqs62/files/mmc1.pdf" }, "related_objects": [ { "basename": "nihms-689285.pdf", "url": "https://authors.library.caltech.edu/records/e72gb-kqs62/files/nihms-689285.pdf" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Levine, Joe H. and Elowitz, Michael B." }, { "id": "https://authors.library.caltech.edu/records/3435n-2mq05", "eprint_id": 50222, "eprint_status": "archive", "datestamp": "2023-08-20 03:01:53", "lastmod": "2023-10-17 22:51:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "LeBon-L", "name": { "family": "LeBon", "given": "Lauren" } }, { "id": "Lee-Tom-V", "name": { "family": "Lee", "given": "Tom V." } }, { "id": "Jafar-Nejad-H", "name": { "family": "Jafar-Nejad", "given": "Hamed" } }, { "id": "Sprinzak-D", "name": { "family": "Sprinzak", "given": "David" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Fringe proteins modulate Notch-ligand cis and trans interactions to specify signaling states", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 LeBon et al. This\narticle is distributed under the\nterms of the Creative Commons\nAttribution License, which\npermits unrestricted use and\nredistribution provided that the\noriginal author and source are\ncredited.\n\nReceived: 06 April 2014; Accepted: 31 August 2014; Published: 25 September 2014.\n\nThis work was supported by the Gordon and Betty Moore Foundation through Grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative; the National Science Foundation under Grant No. EFRI 1137269 and The NIH under grant R01 HD705335. We also acknowledge support from\nthe NIH/NIGMS (R01GM084135 to HJN) and the March of Dimes Foundation (#1-FY10-501 to HJN). We thank Pulin Li, Joseph Markson, Sandy Nandagopal, Amit Lakhanpal, Emily Capra, Fangyuan Ding, and Leah Santat for technical assistance, as well as discussions and comments, Gerry Weinmaster for\nhelpful comments on the manuscript, Yi-Dong Li and Jessica Leonardi for assistance with the generation of transgenic flies, and Robert Fleming, Shinya Yamamoto, and The Bloomington Drosophila Stock Center for fly strains.\n\nThe funders had no role in study design, data collection and\ninterpretation, or the decision to submit the work for publication.\n\nAuthor contributions:\nLL, TVL, DS, Conception and design, Acquisition of data, Analysis and interpretation of data,\nDrafting or revising the article; HJ-N, MBE, Conception and design, Analysis and interpretation\nof data, Drafting or revising the article.\n\nCorrection:\nHamed Jafar-Nejad and David Sprinzak were incorrectly listed as third and fourth authors respectively. The correct author order is: Lauren LeBon, Tom V Lee, David Sprinzak, Hamed Jafar-Nejad and Michael B Elowitz.\n\nPublished - Fringe_proteins_modulate_Notch-ligand_cis_and_trans_interactions_to_specify_signaling_states.pdf
Supplemental Material - supplementary-file-1.media-3.docx
", "abstract": "The Notch signaling pathway consists of multiple types of receptors and ligands, whose interactions can be tuned by Fringe glycosyltransferases. A major challenge is to determine how these components control the specificity and directionality of Notch signaling in developmental contexts. Here, we analyzed same-cell (cis) Notch-ligand interactions for Notch1, Dll1, and Jag1, and their dependence on Fringe protein expression in mammalian cells. We found that Dll1 and Jag1 can cis-inhibit Notch1, and Fringe proteins modulate these interactions in a way that parallels their effects on trans interactions. Fringe similarly modulated Notch-ligand cis interactions during Drosophila development. Based on these and previously identified interactions, we show how the design of the Notch signaling pathway leads to a restricted repertoire of signaling states that promote heterotypic signaling between distinct cell types, providing insight into the design principles of the Notch signaling system, and the specific developmental process of Drosophila dorsal-ventral boundary formation.", "date": "2014-09-25", "date_type": "published", "publication": "eLife", "volume": "3", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e02950", "id_number": "CaltechAUTHORS:20141007-094944386", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141007-094944386", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "NSF", "grant_number": "EFRI-1137269" }, { "agency": "NIH", "grant_number": "R01 HD705335" }, { "agency": "NIH", "grant_number": "R01GM084135" }, { "agency": "March of Dimes Foundation", "grant_number": "1-FY10-501" } ] }, "doi": "10.7554/eLife.02950", "pmcid": "PMC4174579", "primary_object": { "basename": "Fringe_proteins_modulate_Notch-ligand_cis_and_trans_interactions_to_specify_signaling_states.pdf", "url": "https://authors.library.caltech.edu/records/3435n-2mq05/files/Fringe_proteins_modulate_Notch-ligand_cis_and_trans_interactions_to_specify_signaling_states.pdf" }, "related_objects": [ { "basename": "supplementary-file-1.media-3.docx", "url": "https://authors.library.caltech.edu/records/3435n-2mq05/files/supplementary-file-1.media-3.docx" } ], "resource_type": "article", "pub_year": "2014", "author_list": "LeBon, Lauren; Lee, Tom V.; et el." }, { "id": "https://authors.library.caltech.edu/records/ey2f8-hnp09", "eprint_id": 49514, "eprint_status": "archive", "datestamp": "2023-08-20 02:59:47", "lastmod": "2023-10-17 21:30:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dalal-C-K", "name": { "family": "Dalal", "given": "Chiraj K." }, "orcid": "0000-0002-3624-8409" }, { "id": "Cai-Long", "name": { "family": "Cai", "given": "Long" }, "orcid": "0000-0002-7154-5361" }, { "id": "Lin-Yihan", "name": { "family": "Lin", "given": "Yihan" } }, { "id": "Rahbar-K", "name": { "family": "Rahbar", "given": "Kasra" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Pulsatile Dynamics in the Yeast Proteome", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 Elsevier Ltd. \n\nReceived: April 19, 2014; Revised: July 23, 2014; Accepted: July 28, 2014; Published: September 11, 2014. \n\nWe thank T.F. Chou for initial assistance in obtaining and culturing the yeast GFP library collection. We thank A. Moses, J.G. Oj\u00e1lvo, and P. Swain for comments on the manuscript and acknowledge NIH grants P50 GM068763 and R01 GM079771B for funding. \n\nAuthor Contributions: C.K.D., L.C., and M.B.E. conceived and designed the screen. C.K.D, L.C., and K.R conducted and analyzed the screen. Y.L. conducted and analyzed the two-color experiments. C.K.D., L.C., and M.B.E. wrote the manuscript with help from Y.L and K.R.\n\nAccepted Version - nihms627456.pdf
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", "abstract": "The activation of transcription factors in response to environmental conditions is fundamental to cellular regulation. Recent work has revealed that some transcription factors are activated in stochastic pulses of nuclear localization, rather than at a constant level, even in a constant environment. In such cases, signals control the mean activity of the transcription factor by modulating the frequency, duration, or amplitude of these pulses. Although specific pulsatile transcription factors have been identified in diverse cell types, it has remained unclear how prevalent pulsing is within the cell, how variable pulsing behaviors are between genes, and whether pulsing is specific to transcriptional regulators or is employed more broadly. To address these issues, we performed a proteome-wide movie-based screen to systematically identify localization-based pulsing behaviors in Saccharomyces cerevisiae. The screen examined all genes in a previously developed fluorescent protein fusion library of 4,159 strains in multiple media conditions. This approach revealed stochastic pulsing in ten proteins, all transcription factors. In each case, pulse dynamics were heterogeneous and unsynchronized among cells in clonal populations. Pulsing is the only dynamic localization behavior that we observed, and it tends to occur in pairs of paralogous and redundant proteins. Taken together, these results suggest that pulsatile dynamics play a pervasive role in yeast and may be similarly prevalent in other eukaryotic species.", "date": "2014-09-22", "date_type": "published", "publication": "Current Biology", "volume": "24", "number": "18", "publisher": "Cell Press", "pagerange": "2189-2194", "id_number": "CaltechAUTHORS:20140909-172029209", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140909-172029209", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P50 GM068763" }, { "agency": "NIH", "grant_number": "R01 GM079771B" } ] }, "doi": "10.1016/j.cub.2014.07.076", "pmcid": "PMC4203654", "primary_object": { "basename": "mmc3.xlsx", "url": "https://authors.library.caltech.edu/records/ey2f8-hnp09/files/mmc3.xlsx" }, "related_objects": [ { "basename": "mmc4.xls", "url": "https://authors.library.caltech.edu/records/ey2f8-hnp09/files/mmc4.xls" }, { "basename": "mmc5.mp4", "url": "https://authors.library.caltech.edu/records/ey2f8-hnp09/files/mmc5.mp4" }, { "basename": "nihms627456.pdf", "url": "https://authors.library.caltech.edu/records/ey2f8-hnp09/files/nihms627456.pdf" }, { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/ey2f8-hnp09/files/mmc1.pdf" }, { "basename": "mmc2.xlsx", "url": "https://authors.library.caltech.edu/records/ey2f8-hnp09/files/mmc2.xlsx" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Dalal, Chiraj K.; Cai, Long; et el." }, { "id": "https://authors.library.caltech.edu/records/11ye6-9qx23", "eprint_id": 49618, "eprint_status": "archive", "datestamp": "2023-08-20 02:17:18", "lastmod": "2023-10-17 21:35:16", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kueh-Hao-Yuan", "name": { "family": "Kueh", "given": "Hao Yuan" }, "orcid": "0000-0001-6272-6673" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Rothenberg-E-V", "name": { "family": "Rothenberg", "given": "Ellen V." }, "orcid": "0000-0002-3901-347X" } ] }, "title": "Macrophage and T-cell fate control: Insights from tracking transcription factor dynamics in single cells", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2014 Elsevier Inc. \n\nAvailable online 1 August 2014.", "abstract": "Hematopoietic stem and progenitor cells employ circuits of regulatory genes to integrate developmental signals and stabilize fate choices. These progenitors show considerable cell-to-cell heterogeneity in their fate choices; thus, to better understand how regulatory genes control fate decisions, we tracked their levels in single progenitors over time using timelapse live-cell imaging. We examined two hematopoietic fate transitions: 1) macrophage differentiation, driven by the up-regulation of the myeloid transcription factor PU.1; and 2) T-cell fate commitment, controlled by the activation of the T-cell specific transcription factor Bcl11b. In our study of macrophage differentiation, we found that cell cycle length acts as critical mediator in the positive feedback circuit controlling differentiation (Kueh et al. 2013). By following PU.1 regulation in single cells containing a knock-in PU.1-GFP reporter, we found that developing macrophages lengthen their cell cycles to promote stable PU.1 accumulation, and that PU.1 itself promotes cell cycle lengthening, completing a positive feedback loop that stabilizes its own expression. Mathematical modeling furthered showed that this cell cycle feedback circuit robustly stabilizes a slow-dividing differentiated state. In our studies on T-cell fate commitment, we found that Notch signaling \u2013 the primary driver of development \u2013 enhances the frequency of all-or-none Bcl11b gene activation to promote commitment. By analyzing progenitors from mice containing a knock-in Bcl11b-YFP reporter, we found that uncommitted (Bcl11b-DN2A) progenitors can activate Bcl11b transcription and undergo fate commitment in the absence of Notch signaling, and that Notch signaling does not modulate the level of Bcl11b transcription, but instead increases the rate at which progenitors switch Bcl11b to an actively expressing state. These results reveal insights into how signaling pathways activate regulatory gene expression to instruct cell fate.", "date": "2014-08", "date_type": "published", "publication": "Experimental Hematology", "volume": "42", "number": "8", "publisher": "Elsevier", "pagerange": "S16", "id_number": "CaltechAUTHORS:20140911-141135837", "issn": "0301-472X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140911-141135837", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.exphem.2014.07.054", "resource_type": "article", "pub_year": "2014", "author_list": "Kueh, Hao Yuan; Elowitz, Michael B.; et el." }, { "id": "https://authors.library.caltech.edu/records/77t57-k8q45", "eprint_id": 47542, "eprint_status": "archive", "datestamp": "2023-08-20 01:53:04", "lastmod": "2023-10-26 20:41:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Singer-Z-S", "name": { "family": "Singer", "given": "Zakary S." } }, { "id": "Yong-John", "name": { "family": "Yong", "given": "John" } }, { "id": "Tischler-J", "name": { "family": "Tischler", "given": "Julia" } }, { "id": "Hackett-J-A", "name": { "family": "Hackett", "given": "Jamie A." } }, { "id": "Altinok-A", "name": { "family": "Altinok", "given": "Alphan" } }, { "id": "Surani-M-A", "name": { "family": "Surani", "given": "M. Azim" } }, { "id": "Cai-Long", "name": { "family": "Cai", "given": "Long" }, "orcid": "0000-0002-7154-5361" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 Elsevier Inc. Copyright \u00a9 2014 The Authors. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/). \n\nReceived 18 October 2013, Revised 4 April 2014, Accepted 18 June 2014, Available online 18 July 2014. \n\nWe thank Jordi Garcia-Ojalvo, Xiling Shen, Georg Seelig, Arjun Raj, and David Sprinzak for helpful comments on the manuscript; the Kathrin Plath Lab, the Austin Smith Lab, and RIKEN for kindly providing reporter and knockout cell lines; and the Caltech FACS Facility for assistance with cell sorting. This work was supported by the National Institutes of Health grants R01HD075605A, R01GM086793A, and P50GM068763; the Weston Havens Foundation; Human Frontiers Science Program; the Packard Foundation; a Wellcome Trust Investigators Grant to M.A.S.; and a KAUST, APART, and\nCIRM Fellowship to J.T. This work is funded by the Gordon and Betty Moore Foundation through Grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative. Open Access funded by Wellcome Trust. \n\nSequencing data have been deposted in NCBI's GEO under accession number GSE58396.\n\nAuthor Contributions: Z.S.S. and J.Y. contributed equally and are listed alphabetically. Z.S.S., J.Y.,\nJ.T., L.C., M.A.S., and M.B.E. conceived experiments. Z.S.S., J.Y., J.T., and\nJ.A.H. performed experiments and analyzed data, with Z.S.S. leading smFISH\nand methylation experiments and J.Y. leading the movie experiments and\nmodeling. A.A. contributed computational algorithms. M.A.S. and M.B.E. supervised\nresearch. Z.S.S., J.T., J.Y., and M.B.E. wrote the manuscript with\nsubstantial input from all authors.\n\nPublished - 1-s2.0-S1097276514005632-main.pdf
Supplemental Material - mmc1.pdf
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Supplemental Material - mmc6.mp4
", "abstract": "Cell populations can be strikingly heterogeneous, composed of multiple cellular states, each exhibiting stochastic noise in its gene expression. A major challenge is to disentangle these two types of variability and to understand the dynamic processes and mechanisms that control them. Embryonic stem cells (ESCs) provide an ideal model system to address this issue because they exhibit heterogeneous and dynamic expression of functionally important regulatory factors. We analyzed gene expression in individual ESCs using single-molecule RNA-FISH and quantitative time-lapse movies. These data discriminated stochastic switching between two coherent (correlated) gene expression states and burst-like transcriptional noise. We further showed that the \"2i\" signaling pathway inhibitors modulate both types of variation. Finally, we found that DNA methylation plays a key role in maintaining these metastable states. Together, these results show how ESC gene expression states and dynamics arise from a combination of intrinsic noise, coherent cellular states, and epigenetic regulation.", "date": "2014-07-17", "date_type": "published", "publication": "Molecular Cell", "volume": "55", "number": "2", "publisher": "Elsevier", "pagerange": "319-331", "id_number": "CaltechAUTHORS:20140729-074318148", "issn": "1097-2765", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140729-074318148", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01HD075605A" }, { "agency": "NIH", "grant_number": "R01GM086793A" }, { "agency": "NIH", "grant_number": "P50GM068763" }, { "agency": "Weston Havens Foundation" }, { "agency": "Human Frontiers Science Program" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Wellcome Trust" }, { "agency": "King Abdullah University of Science and Technology (KAUST)" }, { "agency": "APART Fellowship" }, { "agency": "California Institute for Regenerative Medicine (CIRM)" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" } ] }, "doi": "10.1016/j.molcel.2014.06.029", "pmcid": "PMC4104113", "primary_object": { "basename": "1-s2.0-S1097276514005632-main.pdf", "url": "https://authors.library.caltech.edu/records/77t57-k8q45/files/1-s2.0-S1097276514005632-main.pdf" }, "related_objects": [ { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/77t57-k8q45/files/mmc1.pdf" }, { "basename": "mmc2.xlsx", "url": "https://authors.library.caltech.edu/records/77t57-k8q45/files/mmc2.xlsx" }, { "basename": "mmc3.mp4", "url": "https://authors.library.caltech.edu/records/77t57-k8q45/files/mmc3.mp4" }, { "basename": "mmc4.mp4", "url": "https://authors.library.caltech.edu/records/77t57-k8q45/files/mmc4.mp4" }, { "basename": "mmc5.mp4", "url": "https://authors.library.caltech.edu/records/77t57-k8q45/files/mmc5.mp4" }, { "basename": "mmc6.mp4", "url": "https://authors.library.caltech.edu/records/77t57-k8q45/files/mmc6.mp4" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Singer, Zakary S.; Yong, John; et el." }, { "id": "https://authors.library.caltech.edu/records/1hq9f-xtb58", "eprint_id": 45072, "eprint_status": "archive", "datestamp": "2023-08-22 12:32:07", "lastmod": "2023-10-26 17:32:36", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tan-Frederick-E", "name": { "family": "Tan", "given": "Frederick E." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Brf1 posttranscriptionally regulates pluripotency and differentiation responses downstream of Erk MAP kinase", "ispublished": "pub", "full_text_status": "public", "keywords": "stem cell biology; AU-rich element RNA-binding proteins; developmental mechanisms; developmental signaling pathways; gene regulation dynamics", "note": "\u00a9 2014 National Academy of Sciences. \n\nEdited by Gideon Dreyfuss, University of Pennsylvania, Philadelphia, PA, and approved March 25, 2014 (received for review November 6, 2013). Published ahead of print April 14, 2014. \n\nWe thank Dr. Kathrin Plath (University of California, Los Angeles) and Dr. Angie Rizzino (University of Nebraska Medical Center) for the kind donation of cell culture reagents; Dr. Azim Surani (University of Cambridge) for fruitful discussions; Rochelle Diamond, Diana Perez, and Josh Verceles from the Caltech Flow Cytometry Facility; Igor Antoshechkin and Vijaya Kumar from the Millard and Muriel Jacobs Genetics and Genomics Laboratory at Caltech; Leah Santat, Yaron Antebi, Joe Markson, James Linton, Pierre Neveu, John Yong, Zakary Singer, Julia Tischler, Joe Levine, and Sandy Nandagopal for fruitful discussions. This work was supported by a Human Frontiers Science Program Grant (RGP0020/2012), the Weston Havens Foundation, and the David and Lucille Packard Foundation. F.E.T. was supported by the National Defense Science and Engineering Graduate Research Fellowship. \n\nAuthor contributions: F.E.T. and M.B.E. designed research; F.E.T. performed research; F.E.T. contributed new reagents/analytic tools; F.E.T. and M.B.E. analyzed data; and F.E.T. and M.B.E. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nThis article is a PNAS Direct Submission. \n\nData deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE40104). \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1320873111/-/DCSupplemental.\n\nPublished - PNAS-2014-Tan-E1740-8.pdf
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Supplemental Material - sd03.xlsx
Supplemental Material - sd04.xlsx
", "abstract": "AU-rich element mRNA-binding proteins (AUBPs) are key regulators of development, but how they are controlled and what functional roles they play depends on cellular context. Here, we show that Brf1 (zfp36l1), an AUBP from the Zfp36 protein family, operates downstream of FGF/Erk MAP kinase signaling to regulate pluripotency and cell fate decision making in mouse embryonic stem cells (mESCs). FGF/Erk MAP kinase signaling up-regulates Brf1, which disrupts the expression of core pluripotency-associated genes and attenuates mESC self-renewal without inducing differentiation. These regulatory effects are mediated by rapid and direct destabilization of Brf1 targets, such as Nanog mRNA. Enhancing Brf1 expression does not compromise mESC pluripotency but does preferentially regulate mesendoderm commitment during differentiation, accelerating the expression of primitive streak markers. Together, these studies demonstrate that FGF signals use targeted mRNA degradation by Brf1 to enable rapid posttranscriptional control of gene expression in mESCs.", "date": "2014-04-29", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "111", "number": "17", "publisher": "National Academy of Sciences", "pagerange": "E1740-E1748", "id_number": "CaltechAUTHORS:20140421-105002893", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140421-105002893", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Human Frontier Science Program", "grant_number": "RGP0020/2012" }, { "agency": "Weston Havens Foundation" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "National Defense Science and Engineering Graduate (NDSEG) Fellowship" } ] }, "doi": "10.1073/pnas.1320873111", "pmcid": "PMC4035916", "primary_object": { "basename": "PNAS-2014-Tan-E1740-8.pdf", "url": "https://authors.library.caltech.edu/records/1hq9f-xtb58/files/PNAS-2014-Tan-E1740-8.pdf" }, "related_objects": [ { "basename": "pnas.201320873SI.pdf", "url": "https://authors.library.caltech.edu/records/1hq9f-xtb58/files/pnas.201320873SI.pdf" }, { "basename": "sd01.xlsx", "url": "https://authors.library.caltech.edu/records/1hq9f-xtb58/files/sd01.xlsx" }, { "basename": "sd02.xlsx", "url": "https://authors.library.caltech.edu/records/1hq9f-xtb58/files/sd02.xlsx" }, { "basename": "sd03.xlsx", "url": "https://authors.library.caltech.edu/records/1hq9f-xtb58/files/sd03.xlsx" }, { "basename": "sd04.xlsx", "url": "https://authors.library.caltech.edu/records/1hq9f-xtb58/files/sd04.xlsx" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Tan, Frederick E. and Elowitz, Michael B." }, { "id": "https://authors.library.caltech.edu/records/d8p8t-j2w69", "eprint_id": 43981, "eprint_status": "archive", "datestamp": "2023-08-20 00:05:35", "lastmod": "2023-11-16 16:44:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Church-George-M", "name": { "family": "Church", "given": "George M." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Smolke-C-D", "name": { "family": "Smolke", "given": "Christina D." }, "orcid": "0000-0002-5449-8495" }, { "id": "Voigt-Christopher-A", "name": { "family": "Voigt", "given": "Christopher A." } }, { "id": "Weiss-Ron", "name": { "family": "Weiss", "given": "Ron" } } ] }, "title": "Realizing the potential of synthetic biology", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 Macmillan Publishers Limited.\nPublished online 12 March 2014.\n\nG.M.C. is supported by grants from the US Department of\nEnergy (DOE), US Defense Advanced Research Projects\nAgency (DARPA), US National Human Genome Research\nInstitute (NHGRI), US National Science Foundation (NSF) and\nPersonal Genome Project (PGP). C.D.S. is supported by funds\nfrom the US National Institutes of Health (NIH), NSF, DARPA,\nHuman Frontiers Science Program (HFSP), and Bill and\nMelinda Gates Foundation.\n\nAccepted Version - nihms-1840027.pdf
", "abstract": "Synthetic biology, despite still being in its infancy, is increasingly\nproviding valuable information for applications in the clinic, the biotechnology\nindustry and in basic molecular research. Both its unique potential and the\nchallenges it presents have brought together the expertise of an eclectic group of\nscientists, from cell biologists to engineers. In this Viewpoint article, five experts\ndiscuss their views on the future of synthetic biology, on its main achievements in\nbasic and applied science, and on the bioethical issues that are associated with the\ndesign of new biological systems.", "date": "2014-04", "date_type": "published", "publication": "Nature Reviews. Molecular Cell Biology", "volume": "15", "number": "4", "publisher": "Nature Publishing Group", "pagerange": "289-294", "id_number": "CaltechAUTHORS:20140225-111459679", "issn": "1471-0072", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140225-111459679", "funders": { "items": [ { "agency": "Department of Energy (DOE)" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "NSF" }, { "agency": "Personal Genome Project (PGP)" }, { "agency": "NIH" }, { "agency": "Human Frontier Science Program" }, { "agency": "Bill and Melinda Gates Foundation" } ] }, "doi": "10.1038/nrm3767", "pmcid": "PMC9645560", "primary_object": { "basename": "nihms-1840027.pdf", "url": "https://authors.library.caltech.edu/records/d8p8t-j2w69/files/nihms-1840027.pdf" }, "resource_type": "article", "pub_year": "2014", "author_list": "Church, George M.; Elowitz, Michael B.; et el." }, { "id": "https://authors.library.caltech.edu/records/4e2pt-2vf07", "eprint_id": 43213, "eprint_status": "archive", "datestamp": "2023-08-19 22:31:19", "lastmod": "2023-10-25 23:22:14", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Levine-J-H", "name": { "family": "Levine", "given": "Joe H." } }, { "id": "Lin-Yihan", "name": { "family": "Lin", "given": "Yihan" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Functional Roles of Pulsing in Genetic Circuits", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 American Association for the Advancement of Science. \n\nWe thank M. Dunlop, J. Dworkin,\nN. Friedman, J. Garcia-Ojalvo, R. Kishony, G. Lahav,\nJ. McKinney, R. Murray, R. Phillips, G. Suel, S. Tay,\nN. Wingreen, and members of the Elowitz lab including\nM. Budde, F. Ding, P. Li, J. Markson, and A. Rosenthal\nfor critical comments and feedback. This work was\nsupported by NIH grants R01 GM079771-06, R01\nGM086793A, and P50GM068763; Defense Advanced\nResearch Projects Agency Biochronicity program grant\nD12AP00025; and the Packard Foundation.\n\nAccepted Version - nihms596211.pdf
", "abstract": "A fundamental problem in biology is to understand how genetic circuits implement core cellular functions. Time-lapse microscopy techniques are beginning to provide a direct view of circuit dynamics in individual living cells. Unexpectedly, we are discovering that key transcription and regulatory factors pulse on and off repeatedly, and often stochastically, even when cells are maintained in constant conditions. This type of spontaneous dynamic behavior is pervasive, appearing in diverse cell types from microbes to mammalian cells. Here, we review recent work showing how pulsing is generated and controlled by underlying regulatory circuits and how it provides critical capabilities to cells in stress response, signaling, and development. A major theme is the ability of pulsing to enable time-based regulation analogous to strategies used in engineered systems. Thus, pulsatile dynamics is emerging as a central, and still largely unexplored, layer of temporal organization in the cell.", "date": "2013-12-06", "date_type": "published", "publication": "Science", "volume": "342", "number": "6163", "publisher": "American Association for the Advancement of Science", "pagerange": "1193-1200", "id_number": "CaltechAUTHORS:20140106-085309612", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140106-085309612", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 GM079771-06" }, { "agency": "NIH", "grant_number": "R01 GM086793A" }, { "agency": "NIH", "grant_number": "P50GM068763" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)", "grant_number": "D12AP00025" }, { "agency": "David and Lucile Packard Foundation" } ] }, "doi": "10.1126/science.1239999", "pmcid": "PMC4100686", "primary_object": { "basename": "nihms596211.pdf", "url": "https://authors.library.caltech.edu/records/4e2pt-2vf07/files/nihms596211.pdf" }, "resource_type": "article", "pub_year": "2013", "author_list": "Levine, Joe H.; Lin, Yihan; et el." }, { "id": "https://authors.library.caltech.edu/records/dxstp-01v95", "eprint_id": 41115, "eprint_status": "archive", "datestamp": "2023-08-19 21:03:29", "lastmod": "2023-10-24 23:28:16", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kueh-Hao-Yuan", "name": { "family": "Kueh", "given": "Hao Yuan" }, "orcid": "0000-0001-6272-6673" }, { "id": "Champhekhar-A", "name": { "family": "Champhekhar", "given": "Ameya" } }, { "id": "Nutt-S-L", "name": { "family": "Nutt", "given": "Stephen L." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Rothenberg-E-V", "name": { "family": "Rothenberg", "given": "Ellen V." }, "orcid": "0000-0002-3901-347X" } ] }, "title": "Positive Feedback Between PU.1 and the Cell Cycle Controls Myeloid Differentiation", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 American Association for the Advancement of Science.\n\nReceived 21 May 2013; accepted 5 July 2013\nPublished online 18 July 2013.\n\nWe thank R. Butler and S. Washburn for\nmouse care and J. Verceles, J. Grimm, and D. Perez of the\nCaltech Flow Cytometry Facility for cell sorting. We also\nthank members of the Rothenberg and Elowitz labs and\nL. Goentoro for insightful discussions. The data presented in\nthis manuscript are tabulated in the main paper and the\nsupplementary materials. This work was supported by a Cancer\nResearch Institute/Irvington Postdoctoral Fellowship to H.Y.K.;\nan Australian Research Council Future Fellowship and the\nVictorian State Government Operational Infrastructure Support,\nNational Health and Medical Research Council of Australia\nIndependent Research Institute Infrastructure Scheme to S.L.N.;\nNIH grants to E.V.R. (RC2 CA148278, R33 HL089123, R01\nAI083514, and R01 CA90233); the Albert Billings Ruddock\nProfessorship; the Al Sherman Foundation; and the Louis\nA. Garfinkle Memorial Laboratory Fund.\n\nAccepted Version - nihms548960.pdf
Supplemental Material - Kueh.SM.pdf
", "abstract": "Regulatory gene circuits with positive-feedback loops control stem cell differentiation, but several mechanisms can contribute to positive feedback. Here, we dissect feedback mechanisms through which the transcription factor PU.1 controls lymphoid and myeloid differentiation. Quantitative live-cell imaging revealed that developing B cells decrease PU.1 levels by reducing PU.1 transcription, whereas developing macrophages increase PU.1 levels by lengthening their cell cycles, which causes stable PU.1 accumulation. Exogenous PU.1 expression in progenitors increases endogenous PU.1 levels by inducing cell cycle lengthening, implying positive feedback between a regulatory factor and the cell cycle. Mathematical modeling showed that this cell cycle\u2013coupled feedback architecture effectively stabilizes a slow-dividing differentiated state. These results show that cell cycle duration functions as an integral part of a positive autoregulatory circuit to control cell fate.", "date": "2013-08-09", "date_type": "published", "publication": "Science", "volume": "341", "number": "6146", "publisher": "American Association for the Advancement of Science", "pagerange": "670-673", "id_number": "CaltechAUTHORS:20130905-110028915", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130905-110028915", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Cancer Research Institute/Irvington Postdoctoral Fellowship" }, { "agency": "Australian Research Council" }, { "agency": "Victorian State Government" }, { "agency": "National Health and Medical Research Council (NHMRC)" }, { "agency": "NIH", "grant_number": "RC2 CA148278" }, { "agency": "NIH", "grant_number": "R33 HL089123" }, { "agency": "NIH", "grant_number": "R01 AI083514" }, { "agency": "NIH", "grant_number": "R01 CA90233" }, { "agency": "Albert Billings Ruddock Professorship" }, { "agency": "Al Sherman Foundation" }, { "agency": "Louis A. Garfinkle Memorial Laboratory Fund" } ] }, "doi": "10.1126/science.1240831", "pmcid": "PMC3913367", "primary_object": { "basename": "Kueh.SM.pdf", "url": "https://authors.library.caltech.edu/records/dxstp-01v95/files/Kueh.SM.pdf" }, "related_objects": [ { "basename": "nihms548960.pdf", "url": "https://authors.library.caltech.edu/records/dxstp-01v95/files/nihms548960.pdf" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Kueh, Hao Yuan; Champhekhar, Ameya; et el." }, { "id": "https://authors.library.caltech.edu/records/bhxja-vc626", "eprint_id": 38076, "eprint_status": "archive", "datestamp": "2023-08-22 08:53:20", "lastmod": "2023-10-23 19:44:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Young-J-W", "name": { "family": "Young", "given": "Jonathan W." } }, { "id": "Locke-J-C-W", "name": { "family": "Locke", "given": "James C. W." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Rate of environmental change determines stress response specificity", "ispublished": "pub", "full_text_status": "public", "keywords": "systems biology; single-cell dynamics; computational biology", "note": "\u00a9 2013 National Academy of Sciences.\nFreely available online through the PNAS open access option.\nEdited by Bonnie L. Bassler, Howard Hughes Medical Institute and Princeton University, Princeton, NJ, and approved January 2, 2013 (received for review August 2, 2012).\nPublished online before print February 13, 2013.\nWe thank C. Price and D. Rudner for providing strains.\nWe thank A. Eldar, R. Kishony, C. Price, N. Wingreen, J. Levine, and other members of M.B.E.'s laboratory for helpful discussions. Work in M.B.E.'s laboratory was supported by NIH Grants R01GM079771 and R01GM086793, US\nNational Science Foundation CAREER Award 0644463, and the Packard Foundation. J.C.W.L. was supported by the International Human Frontier Science Program Organization and the European Molecular Biology Organization.\n\nAuthor contributions: J.W.Y., J.C.W.L., and M.B.E. designed research; J.W.Y. and J.C.W.L. performed research; J.W.Y., J.C.W.L., and M.B.E. analyzed data; and J.W.Y., J.C.W.L., and M.B.E. wrote the paper.\n\nPublished - PNAS-2013-Young-4140-5.pdf
Supplemental Material - pnas.201213060SI.pdf
Supplemental Material - sm01.mov
", "abstract": "Cells use general stress response pathways to activate diverse target genes in response to a variety of stresses. However, general stress responses coexist with more specific pathways that are activated by individual stresses, provoking the fundamental question of whether and how cells control the generality or specificity of their response to a particular stress. Here we address this issue using quantitative time-lapse microscopy of the Bacillus subtilis environmental stress response, mediated by \u03c3^B. We analyzed \u03c3^B activation in response to stresses such as salt and ethanol imposed at varying rates of increase. Dynamically, \u03c3^B responded to these stresses with a single adaptive activity pulse, whose amplitude depended on the rate at which the stress increased. This rate-responsive behavior can be understood from mathematical modeling of a key negative feedback loop in the underlying regulatory circuit. Using RNAseq we analyzed the effects of both rapid and gradual increases of ethanol and salt stress across the genome. Because of the rate responsiveness of \u03c3^B activation, salt and ethanol regulons overlap under rapid, but not gradual, increases in stress. Thus, the cell responds specifically to individual stresses that appear gradually, while using \u03c3^B to broaden the cellular response under more rapidly deteriorating conditions. Such dynamic control of specificity could be a critical function of other general stress response pathways.", "date": "2013-03-05", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "110", "number": "10", "publisher": "National Academy of Sciences", "pagerange": "4140-4145", "id_number": "CaltechAUTHORS:20130423-105410788", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130423-105410788", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01GM079771" }, { "agency": "NIH", "grant_number": "R01GM086793" }, { "agency": "NSF", "grant_number": "MCB-0644463" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Human Frontier Science Program" }, { "agency": "European Molecular Biology Organization (EMBO)" } ] }, "doi": "10.1073/pnas.1213060110", "pmcid": "PMC3593889", "primary_object": { "basename": "pnas.201213060SI.pdf", "url": "https://authors.library.caltech.edu/records/bhxja-vc626/files/pnas.201213060SI.pdf" }, "related_objects": [ { "basename": "sm01.mov", "url": "https://authors.library.caltech.edu/records/bhxja-vc626/files/sm01.mov" }, { "basename": "PNAS-2013-Young-4140-5.pdf", "url": "https://authors.library.caltech.edu/records/bhxja-vc626/files/PNAS-2013-Young-4140-5.pdf" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Young, Jonathan W.; Locke, James C. W.; et el." }, { "id": "https://authors.library.caltech.edu/records/wgetd-z1b37", "eprint_id": 29121, "eprint_status": "archive", "datestamp": "2023-08-19 09:20:43", "lastmod": "2023-10-24 18:22:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Rosenthal-Adam-Z", "name": { "family": "Rosenthal", "given": "Adam Z." }, "orcid": "0000-0002-6936-3665" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Following evolution of bacterial antibiotic resistance in real time", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2012 Nature Publishing Group, a division of Macmillan Publishers Limited.\n\nPublished online 27 December 2011. \n\nThe authors declare no competing financial interests.", "abstract": "A new study reports the development of the 'morbidostat', a device that allows for continuous culture of bacteria under a constant drug selection pressure using computer feedback control of antibiotic concentration. This device, together with bacterial whole-genome sequencing, allowed the authors to follow the evolution of resistance-conferring mutations in Escherichia coli populations in real time, providing support for deterministic evolution of resistance in some situations.", "date": "2012-01", "date_type": "published", "publication": "Nature Genetics", "volume": "44", "number": "1", "publisher": "Nature Publishing Group", "pagerange": "11-13", "id_number": "CaltechAUTHORS:20120203-102759226", "issn": "1061-4036", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120203-102759226", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1038/ng.1048", "resource_type": "article", "pub_year": "2012", "author_list": "Rosenthal, Adam Z. and Elowitz, Michael B." }, { "id": "https://authors.library.caltech.edu/records/6a8zh-ta653", "eprint_id": 29362, "eprint_status": "archive", "datestamp": "2023-08-19 09:22:25", "lastmod": "2023-10-24 22:08:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Young-J-W", "name": { "family": "Young", "given": "Jonathan W." } }, { "id": "Locke-J-C-W", "name": { "family": "Locke", "given": "James C. W." } }, { "id": "Altinok-A", "name": { "family": "Altinok", "given": "Alphan" } }, { "id": "Rosenfeld-N", "name": { "family": "Rosenfeld", "given": "Nitzan" } }, { "id": "Bacarian-T", "name": { "family": "Bacarian", "given": "Tigran" } }, { "id": "Swain-P-S", "name": { "family": "Swain", "given": "Peter S." } }, { "id": "Mjolsness-E-D", "name": { "family": "Mjolsness", "given": "Eric" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Nature America, Inc. \n\nPublished online 15 December 2011. \n\nWe thank J. Park and additional Elowitz Lab members (former and present) for helpful comments regarding the manuscript. The authors declare no competing financial interests. This research was supported by US National Institutes of Health grant R01GM07977, the National Science Foundation CAREER Award 0644463 and the Packard Foundation.\nAuthor Contributions: J.W.Y., J.C.W.L. and M.B.E. wrote and developed the protocol. A.A. helped with developing a website and modifying the Schnitzcells software package for public release. N.R., P.S.S. and M.B.E. were major original developers of Schnitzcells, and T.B. and E.M. optimized the tracking algorithm.\n\nAccepted Version - nihms605711.pdf
", "abstract": "Quantitative single-cell time-lapse microscopy is a powerful method for analyzing gene circuit dynamics and heterogeneous cell behavior. We describe the application of this method to imaging bacteria by using an automated microscopy system. This protocol has been used to analyze sporulation and competence differentiation in Bacillus subtilis, and to quantify gene regulation and its fluctuations in individual Escherichia coli cells. The protocol involves seeding and growing bacteria on small agarose pads and imaging the resulting microcolonies. Images are then reviewed and analyzed using our laboratory's custom MATLAB analysis code, which segments and tracks cells in a frame-to-frame method. This process yields quantitative expression data on cell lineages, which can illustrate dynamic expression profiles and facilitate mathematical models of gene circuits. With fast-growing bacteria, such as E. coli or B. subtilis, image acquisition can be completed in 1 d, with an additional 1\u20132 d for progressing through the analysis procedure.", "date": "2012-01", "date_type": "published", "publication": "Nature Protocols", "volume": "7", "number": "1", "publisher": "Nature Publishing Group", "pagerange": "80-88", "id_number": "CaltechAUTHORS:20120217-105727788", "issn": "1754-2189", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120217-105727788", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01GM07977" }, { "agency": "NSF", "grant_number": "MCB-0644463" }, { "agency": "David and Lucile Packard Foundation" } ] }, "doi": "10.1038/nprot.2011.432", "pmcid": "PMC4161363", "primary_object": { "basename": "nihms605711.pdf", "url": "https://authors.library.caltech.edu/records/6a8zh-ta653/files/nihms605711.pdf" }, "resource_type": "article", "pub_year": "2012", "author_list": "Young, Jonathan W.; Locke, James C. W.; et el." }, { "id": "https://authors.library.caltech.edu/records/5xnk2-fwk63", "eprint_id": 29704, "eprint_status": "archive", "datestamp": "2023-08-19 09:23:49", "lastmod": "2023-10-24 22:23:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Levine-J-H", "name": { "family": "Levine", "given": "Joe H." } }, { "id": "Fontes-M-E", "name": { "family": "Fontes", "given": "Michael E." } }, { "id": "Dworkin-J", "name": { "family": "Dworkin", "given": "Jonathan" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Pulsed Feedback Defers Cellular Differentiation", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Levine 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 July 8, 2011; Accepted December 19, 2011; Published January 31, 2012.\n\nThis work was supported by US NIH grant R01GM079771, NSF grant 0644463, and the Packard Foundation. JL was supported in part by a Rosen Fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\nWe thank Shaunak Sen, Avigdor Eldar, Jon Young, James Locke, and Jordi Garcia-Ojalvo for help and critical feedback during the course of this work, and members of the Elowitz Lab for general discussions. We also thank the Burkholder, Fujita, Grossman, Hoch, Lazazzera, Losick, and\nRudner labs for the generous gift of B. subtilis strains.\nAuthor Contributions:\nThe author(s) have made the following declarations about their contributions: Conceived and designed the experiments: JHL MBE JD. Performed the experiments: JHL MEF. Analyzed the data: JHL MBE. Contributed reagents/materials/analysis tools: JHL MEF MBE. Wrote the paper: JHL MBE.\n\nPublished - Levine2012p17380Plos_Biol.pdf
Supplemental Material - journal.pbio.1001252.s001.pdf
Supplemental Material - journal.pbio.1001252.s002.pdf
Supplemental Material - journal.pbio.1001252.s003.pdf
Supplemental Material - journal.pbio.1001252.s004.pdf
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Supplemental Material - journal.pbio.1001252.s010.pdf
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Supplemental Material - journal.pbio.1001252.s012.pdf
Supplemental Material - journal.pbio.1001252.s013.pdf
Supplemental Material - journal.pbio.1001252.s014.doc
", "abstract": "Environmental signals induce diverse cellular differentiation programs. In certain systems, cells defer differentiation for extended time periods after the signal appears, proliferating through multiple rounds of cell division before committing to a new fate. How can cells set a deferral time much longer than the cell cycle? Here we study Bacillus subtilis cells that respond to sudden nutrient limitation with multiple rounds of growth and division before differentiating into spores. A well-characterized genetic circuit controls the concentration and phosphorylation of the master regulator Spo0A, which rises to a critical concentration to initiate sporulation. However, it remains unclear how this circuit enables cells to defer sporulation for multiple cell cycles. Using quantitative time-lapse fluorescence microscopy of Spo0A dynamics in individual cells, we observed pulses of Spo0A phosphorylation at a characteristic cell cycle phase. Pulse amplitudes grew systematically and cell-autonomously over multiple cell cycles leading up to sporulation. This pulse growth required a key positive feedback loop involving the sporulation kinases, without which the deferral of sporulation became ultrasensitive to kinase expression. Thus, deferral is controlled by a pulsed positive feedback loop in which kinase expression is activated by pulses of Spo0A phosphorylation. This pulsed positive feedback architecture provides a more robust mechanism for setting deferral times than constitutive kinase expression. Finally, using mathematical modeling, we show how pulsing and time delays together enable \"polyphasic\" positive feedback, in which different parts of a feedback loop are active at different times. Polyphasic feedback can enable more accurate tuning of long deferral times. Together, these results suggest that Bacillus subtilis uses a pulsed positive feedback loop to implement a \"timer\" that operates over timescales much longer than a cell cycle.", "date": "2012-01", "date_type": "published", "publication": "PLoS Biology", "volume": "10", "number": "1", "publisher": "Public Library of Science", "pagerange": "e1001252", "id_number": "CaltechAUTHORS:20120313-120007998", "issn": "1544-9173", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120313-120007998", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01GM079771" }, { "agency": "NSF", "grant_number": "MCB-0644463" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Donna and Benjamin M. Rosen Bioengineering Center" } ] }, "doi": "10.1371/journal.pbio.1001252", "pmcid": "PMC3269414", "primary_object": { "basename": "journal.pbio.1001252.s002.pdf", "url": "https://authors.library.caltech.edu/records/5xnk2-fwk63/files/journal.pbio.1001252.s002.pdf" }, "related_objects": [ { "basename": "journal.pbio.1001252.s006.pdf", "url": "https://authors.library.caltech.edu/records/5xnk2-fwk63/files/journal.pbio.1001252.s006.pdf" }, { "basename": "journal.pbio.1001252.s008.pdf", "url": "https://authors.library.caltech.edu/records/5xnk2-fwk63/files/journal.pbio.1001252.s008.pdf" }, { "basename": "journal.pbio.1001252.s009.pdf", "url": "https://authors.library.caltech.edu/records/5xnk2-fwk63/files/journal.pbio.1001252.s009.pdf" }, { "basename": "journal.pbio.1001252.s013.pdf", "url": "https://authors.library.caltech.edu/records/5xnk2-fwk63/files/journal.pbio.1001252.s013.pdf" }, { "basename": "journal.pbio.1001252.s014.doc", "url": "https://authors.library.caltech.edu/records/5xnk2-fwk63/files/journal.pbio.1001252.s014.doc" }, { "basename": "Levine2012p17380Plos_Biol.pdf", "url": "https://authors.library.caltech.edu/records/5xnk2-fwk63/files/Levine2012p17380Plos_Biol.pdf" }, { "basename": "journal.pbio.1001252.s010.pdf", "url": "https://authors.library.caltech.edu/records/5xnk2-fwk63/files/journal.pbio.1001252.s010.pdf" }, { "basename": "journal.pbio.1001252.s001.pdf", "url": "https://authors.library.caltech.edu/records/5xnk2-fwk63/files/journal.pbio.1001252.s001.pdf" }, { "basename": "journal.pbio.1001252.s003.pdf", "url": "https://authors.library.caltech.edu/records/5xnk2-fwk63/files/journal.pbio.1001252.s003.pdf" }, { "basename": "journal.pbio.1001252.s011.pdf", "url": "https://authors.library.caltech.edu/records/5xnk2-fwk63/files/journal.pbio.1001252.s011.pdf" }, { "basename": "journal.pbio.1001252.s012.pdf", "url": "https://authors.library.caltech.edu/records/5xnk2-fwk63/files/journal.pbio.1001252.s012.pdf" }, { "basename": "journal.pbio.1001252.s004.pdf", "url": "https://authors.library.caltech.edu/records/5xnk2-fwk63/files/journal.pbio.1001252.s004.pdf" }, { "basename": "journal.pbio.1001252.s005.pdf", "url": "https://authors.library.caltech.edu/records/5xnk2-fwk63/files/journal.pbio.1001252.s005.pdf" }, { "basename": "journal.pbio.1001252.s007.pdf", "url": "https://authors.library.caltech.edu/records/5xnk2-fwk63/files/journal.pbio.1001252.s007.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Levine, Joe H.; Fontes, Michael E.; et el." }, { "id": "https://authors.library.caltech.edu/records/sgw2z-4a022", "eprint_id": 27795, "eprint_status": "archive", "datestamp": "2023-08-19 08:25:46", "lastmod": "2023-10-24 17:25:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Locke-J-C-W", "name": { "family": "Locke", "given": "James C. W." } }, { "id": "Young-J-W", "name": { "family": "Young", "given": "Jonathan W." } }, { "id": "Fontes-M", "name": { "family": "Fontes", "given": "Michelle" } }, { "id": "Hern\u00e1ndez-Jim\u00e9nez-M-J", "name": { "family": "Hern\u00e1ndez Jim\u00e9nez", "given": "Mar\u00eda Jes\u03cds" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Stochastic Pulse Regulation in Bacterial Stress Response", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 American Association for the Advancement of Science. \n\nReceived for publication 10 May 2011. Accepted for publication 1 September 2011. \n\nWe thank C. Price and D. Rudner for providing strains. We thank A. Eldar, R. Kishony, C. Price, N. Wingreen, J. Levine, and other members of M.B.E's\nlaboratory for helpful discussions. Work in M.B.E's\nlaboratory was supported by NIH grants R01GM079771\nand P50 GM068763, U.S. National Science Foundation\nCAREER Award 0644463, and the Packard Foundation.\nJ.C.W.L was supported by the International Human\nFrontier Science Program Organization and the European\nMolecular Biology Organization.\n\nAccepted Version - nihms605703.pdf
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", "abstract": "Gene regulatory circuits can use dynamic, and even stochastic, strategies to respond to environmental conditions. We examined activation of the general stress response mediated by the alternative sigma factor, \u03c3^B, in individual Bacillus subtilis cells. We observed that energy stress activates \u03c3^B in discrete stochastic pulses, with increasing levels of stress leading to higher pulse frequencies. By perturbing and rewiring the endogenous system, we found that this behavior results from three key features of the \u03c3^B circuit: an ultrasensitive phosphorylation switch; stochasticity (\"noise\"), which activates that switch; and a mixed (positive and negative) transcriptional feedback, which can both amplify a pulse and switch it off. Together, these results show how prokaryotes encode signals using stochastic pulse frequency modulation through a compact regulatory architecture.", "date": "2011-10-21", "date_type": "published", "publication": "Science", "volume": "334", "number": "6054", "publisher": "American Association for the Advancement of Science", "pagerange": "366-369", "id_number": "CaltechAUTHORS:20111116-082912789", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111116-082912789", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01GM079771" }, { "agency": "NIH", "grant_number": "P50 GM068763" }, { "agency": "NSF", "grant_number": "MCB-0644463" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Human Frontier Science Program" }, { "agency": "European Molecular Biology Organization (EMBO)" } ] }, "doi": "10.1126/science.1208144", "pmcid": "PMC4100694", "primary_object": { "basename": "1208144s1.mov", "url": "https://authors.library.caltech.edu/records/sgw2z-4a022/files/1208144s1.mov" }, "related_objects": [ { "basename": "1208144s2.mov", "url": "https://authors.library.caltech.edu/records/sgw2z-4a022/files/1208144s2.mov" }, { "basename": "LockeSOM.pdf", "url": "https://authors.library.caltech.edu/records/sgw2z-4a022/files/LockeSOM.pdf" }, { "basename": "nihms605703.pdf", "url": "https://authors.library.caltech.edu/records/sgw2z-4a022/files/nihms605703.pdf" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Locke, James C. W.; Young, Jonathan W.; et el." }, { "id": "https://authors.library.caltech.edu/records/p5kjq-wec04", "eprint_id": 27685, "eprint_status": "archive", "datestamp": "2023-08-22 03:56:17", "lastmod": "2023-10-24 17:20:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zheng-Guoan", "name": { "family": "Zheng", "given": "Guoan" } }, { "id": "Lee-Seung-Ah", "name": { "family": "Lee", "given": "Seung Ah" } }, { "id": "Antebi-Y", "name": { "family": "Antebi", "given": "Yaron" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Yang-Changhuei", "name": { "family": "Yang", "given": "Changhuei" }, "orcid": "0000-0001-8791-0354" } ] }, "title": "The ePetri dish, an on-chip cell imaging platform based on subpixel perspective sweeping microscopy (SPSM)", "ispublished": "pub", "full_text_status": "public", "keywords": "lensless imaging; time-lapse microscopy; on-chip cellular imaging; stem cell differentiation tracking; superresolution algorithm", "note": "\u00a9 2011 National Academy of Sciences. Freely available online through the PNAS open access option. \n\nEdited by David A. Weitz, Harvard University, Cambridge, MA, and approved August 23, 2011 (received for review July 5, 2011). Published online before print October 3, 2011. \n\nWe thank Dr. Benjamin Judkewitz for HeLa cell tracking and Mr. Samuel Yang for analyzing some of the data. We acknowledge funding support from the Coulter Foundation. \n\nAuthor contributions: G.Z. and C.Y. designed research; G.Z., S.A.L., and Y.A. performed research; G.Z. analyzed data; and G.Z., S.A.L., Y.A., M.B.E., and C.Y. wrote the paper.\n\nPublished - Zheng2011p16157P_Natl_Acad_Sci_Usa.pdf
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", "abstract": "We report a chip-scale lensless wide-field-of-view microscopy imaging technique, subpixel perspective sweeping microscopy, which can render microscopy images of growing or confluent cell cultures autonomously. We demonstrate that this technology can be used to build smart Petri dish platforms, termed ePetri, for cell culture experiments. This technique leverages the recent broad and cheap availability of high performance image sensor chips to provide a low-cost and automated microscopy solution. Unlike the two major classes of lensless microscopy methods, optofluidic microscopy and digital in-line holography microscopy, this new approach is fully capable of working with cell cultures or any samples in which cells may be contiguously connected. With our prototype, we demonstrate the ability to image samples of area 6 mm \u00d7 4 mm at 660-nm resolution. As a further demonstration, we showed that the method can be applied to image color stained cell culture sample and to image and track cell culture growth directly within an incubator. Finally, we showed that this method can track embryonic stem cell differentiations over the entire sensor surface. Smart Petri dish based on this technology can significantly streamline and improve cell culture experiments by cutting down on human labor and contamination risks.", "date": "2011-10-11", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "108", "number": "41", "publisher": "National Academy of Sciences", "pagerange": "16889-16894", "id_number": "CaltechAUTHORS:20111108-160027564", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111108-160027564", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Wallace H. Coulter Foundation" } ] }, "doi": "10.1073/pnas.1110681108", "pmcid": "PMC3193234", "primary_object": { "basename": "Zheng2011p16157P_Natl_Acad_Sci_Usa.pdf", "url": "https://authors.library.caltech.edu/records/p5kjq-wec04/files/Zheng2011p16157P_Natl_Acad_Sci_Usa.pdf" }, "related_objects": [ { "basename": "pnas.1110681108_SI.pdf", "url": "https://authors.library.caltech.edu/records/p5kjq-wec04/files/pnas.1110681108_SI.pdf" }, { "basename": "SM01.mov", "url": "https://authors.library.caltech.edu/records/p5kjq-wec04/files/SM01.mov" }, { "basename": "SM02.mov", "url": "https://authors.library.caltech.edu/records/p5kjq-wec04/files/SM02.mov" }, { "basename": "SM03.mov", "url": "https://authors.library.caltech.edu/records/p5kjq-wec04/files/SM03.mov" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Zheng, Guoan; Lee, Seung Ah; et el." }, { "id": "https://authors.library.caltech.edu/records/acvew-kqv48", "eprint_id": 28385, "eprint_status": "archive", "datestamp": "2023-08-19 08:10:42", "lastmod": "2023-10-24 17:51:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sen-Shaunak", "name": { "family": "Sen", "given": "Shaunak" }, "orcid": "0000-0002-1412-8633" }, { "id": "Garcia-Ojalvo-J", "name": { "family": "Garcia-Ojalvo", "given": "Jordi" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Dynamical Consequences of Bandpass Feedback Loops in a Bacterial Phosphorelay", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Sen 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. Received March 4, 2011; Accepted August 26, 2011; Published September 29, 2011. Editor: Vladimir Brezina, Mount Sinai School of Medicine, United States of America. Funding: S.S. acknowledges financial support from the Betty and Gordon Moore Foundation, Caltech through the Poincare Fellowship. Funding for J.G.-O. is provided by the Ministerio de Ciencia e Innovacion (Spain, project FIS2009-13360), Instituto de Salud Carlos III (Spain, REEM network), and by the ICREA Academia Programme. Funding for M.B.E. is provided by NIH grant R01GM079771 and US National Science Foundation CAREER Award 0644463. The funders had no role in\nstudy design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank C. Dalal, J. Locke, J. Levine, J. Young, R. Murray, and members\nof the Elowitz laboratory for comments. Author Contributions: Conceived and designed the experiments: SS JGO MBE. Performed the experiments: SS. Analyzed the data: SS JGO MBE. Wrote the paper: SS JGO MBE.\n\nPublished - Sen2011p16434PLoS_ONE.pdf
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", "abstract": "Under conditions of nutrient limitation, Bacillus subtilis cells terminally differentiate into a dormant spore state. Progression to sporulation is controlled by a genetic circuit consisting of a phosphorelay embedded in multiple transcriptional feedback loops, which is used to activate the master regulator Spo0A by phosphorylation. These transcriptional regulatory interactions are \"bandpass\"-like, in the sense that activation occurs within a limited band of Spo0A~P concentrations. Additionally, recent results show that the phosphorelay activation occurs in pulses, in a cell-cycle dependent fashion. However, the impact of these pulsed bandpass interactions on the circuit dynamics preceding sporulation remains unclear. In order to address this question, we measured key features of the bandpass interactions at the single-cell level and analyzed them in the context of a simple mathematical model. The model predicted the emergence of a delayed phase shift between the pulsing activity of the different sporulation genes, as well as the existence of a stable state, with elevated Spo0A activity but no sporulation, embedded within the dynamical structure of the system. To test the model, we used time-lapse fluorescence microscopy to measure dynamics of single cells initiating sporulation. We observed the delayed phase shift emerging during the progression to sporulation, while a re-engineering of the sporulation circuit revealed behavior resembling the predicted additional state. These results show that periodically-driven bandpass feedback loops can give rise to complex dynamics in the progression towards sporulation.", "date": "2011-09-29", "date_type": "published", "publication": "PLoS ONE", "volume": "6", "number": "9", "publisher": "Public Library of Science", "pagerange": "Art. No. e25102", "id_number": "CaltechAUTHORS:20111209-090440032", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111209-090440032", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Betty and Gordon Moore Foundation" }, { "agency": "Ministerio de Ciencia e Innovaci\u00f3n (MCINN)", "grant_number": "FIS2009-13360" }, { "agency": "Instituto de Salud Carlos III" }, { "agency": "ICREA Academia Programme" }, { "agency": "NIH", "grant_number": "R01GM079771" }, { "agency": "NSF", "grant_number": "MCB-0644463" }, { "agency": "Caltech" } ] }, "doi": "10.1371/journal.pone.0025102", "pmcid": "PMC3182994", "primary_object": { "basename": "FigureS5.pdf", "url": "https://authors.library.caltech.edu/records/acvew-kqv48/files/FigureS5.pdf" }, "related_objects": [ { "basename": "Sen2011p16434PLoS_ONE.pdf", "url": "https://authors.library.caltech.edu/records/acvew-kqv48/files/Sen2011p16434PLoS_ONE.pdf" }, { "basename": "TextS1.pdf", "url": "https://authors.library.caltech.edu/records/acvew-kqv48/files/TextS1.pdf" }, { "basename": "FigureS1.pdf", "url": "https://authors.library.caltech.edu/records/acvew-kqv48/files/FigureS1.pdf" }, { "basename": "FigureS2.pdf", "url": "https://authors.library.caltech.edu/records/acvew-kqv48/files/FigureS2.pdf" }, { "basename": "FigureS3.pdf", "url": "https://authors.library.caltech.edu/records/acvew-kqv48/files/FigureS3.pdf" }, { "basename": "FigureS4.pdf", "url": "https://authors.library.caltech.edu/records/acvew-kqv48/files/FigureS4.pdf" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Sen, Shaunak; Garcia-Ojalvo, Jordi; et el." }, { "id": "https://authors.library.caltech.edu/records/mdr3y-z7k86", "eprint_id": 25385, "eprint_status": "archive", "datestamp": "2023-08-19 08:00:05", "lastmod": "2023-10-24 15:50:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nandagopal-N", "name": { "family": "Nandagopal", "given": "Nagarajan" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Synthetic Biology: Integrated Gene Circuits", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 American Association for the Advancement of Science. \n\nThe authors thank D. Sprinzak, J. Locke,\nJ. Levine, P. Neveu, J. Young, and other members of the\nElowitz lab for helpful discussions and critical reading of the\nmanuscript. This work was supported by NIH grants\n5R01GM086793, 5R01GM079771, and P50GM068763;\nNSF Career Award 0644463; and a Packard Fellowship.\n\nAccepted Version - nihms605862.pdf
", "abstract": "A major goal of synthetic biology is to develop a deeper understanding of biological design principles from the bottom up, by building circuits and studying their behavior in cells. Investigators initially sought to design circuits \"from scratch\" that functioned as independently as possible from the underlying cellular system. More recently, researchers have begun to develop a new generation of synthetic circuits that integrate more closely with endogenous cellular processes. These approaches are providing fundamental insights into the regulatory architecture, dynamics, and evolution of genetic circuits and enabling new levels of control across diverse biological systems.", "date": "2011-09-02", "date_type": "published", "publication": "Science", "volume": "333", "number": "6047", "publisher": "American Association for the Advancement of Science", "pagerange": "1244-1248", "id_number": "CaltechAUTHORS:20110921-101054272", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110921-101054272", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "5R01GM086793" }, { "agency": "NIH", "grant_number": "5R01GM079771" }, { "agency": "NIH", "grant_number": "P50GM068763" }, { "agency": "NSF", "grant_number": "MCB-0644463" }, { "agency": "David and Lucile Packard Foundation" } ] }, "doi": "10.1126/science.1207084", "pmcid": "PMC4117316", "primary_object": { "basename": "nihms605862.pdf", "url": "https://authors.library.caltech.edu/records/mdr3y-z7k86/files/nihms605862.pdf" }, "resource_type": "article", "pub_year": "2011", "author_list": "Nandagopal, Nagarajan and Elowitz, Michael B." }, { "id": "https://authors.library.caltech.edu/records/za8bf-a2q74", "eprint_id": 24432, "eprint_status": "archive", "datestamp": "2023-08-19 06:55:40", "lastmod": "2023-10-23 22:42:30", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sprinzak-D", "name": { "family": "Sprinzak", "given": "David" } }, { "id": "Lakhanpal-A", "name": { "family": "Lakhanpal", "given": "Amit" } }, { "id": "LeBon-L", "name": { "family": "LeBon", "given": "Lauren" } }, { "id": "Garcia-Ojalvo-J", "name": { "family": "Garcia-Ojalvo", "given": "Jordi" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Mutual Inactivation of Notch Receptors and Ligands Facilitates Developmental Patterning", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Sprinzak 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.\nReceived November 12, 2010; Accepted April 12, 2011; Published June 9, 2011.\nEditor: Denis Thieffry, Ecole Normale Sup\u00e9rieure, France.\nFunding: This work was supported by US National Institutes of Health Fellowship F32GM77014 (DS, www.nih.gov), Fannie and John Hertz Foundation (AL, www.\nhertzfoundation.org), UCLA/Caltech Medical Scientist Training Program, NIH GM08042 (AL, mstp.healthsciences.ucla.edu), Ministerio de Ciencia e Innovacion\nproject FIS2009-13360 (JGO, web.micinn.es), Instituto de Salud Carlos III (JGO, www.isciii.es), ICREA Academia program (JGO, www.icrea.cat), Caltech Center for\nBiological Circuit Design (www.cbcd.caltech.edu), and The Packard Foundation (www.packard.org). The funders had no role in study design, data collection and\nanalysis, decision to publish, or preparation of the manuscript.\n\nAuthor Contributions:\nConceived and designed the experiments: DS AL JGO MBE. Performed\nthe experiments: DS AL LL JGO. Wrote the paper: DS AL JGO MBE.\n\nPublished - Sprinzak2011p14797Plos_Comput_Biol.pdf
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Supplemental Material - Table_S1.pdf
Supplemental Material - Text_S1.pdf
", "abstract": "Developmental patterning requires juxtacrine signaling in order to tightly coordinate the fates of neighboring cells. Recent work has shown that Notch and Delta, the canonical metazoan juxtacrine signaling receptor and ligand, mutually inactivate each other in the same cell. This cis-interaction generates mutually exclusive sending and receiving states in individual cells. It generally remains unclear, however, how this mutual inactivation and the resulting switching behavior can impact developmental patterning circuits. Here we address this question using mathematical modeling in the context of two canonical pattern formation processes: boundary formation and lateral inhibition. For boundary formation, in a model motivated by Drosophila wing vein patterning, we find that mutual inactivation allows sharp boundary formation across a broader range of parameters than models lacking mutual inactivation. This model with mutual inactivation also exhibits robustness to correlated gene expression perturbations. For lateral inhibition, we find that mutual inactivation speeds up patterning dynamics, relieves the need for cooperative regulatory interactions, and expands the range of parameter values that permit pattern formation, compared to canonical models. Furthermore, mutual inactivation enables a simple lateral inhibition circuit architecture which requires only a single downstream regulatory step. Both model systems show how mutual inactivation can facilitate robust fine-grained patterning processes that would be difficult to implement without it, by encoding a difference-promoting feedback within the signaling system itself. Together, these results provide a framework for analysis of more complex Notch-dependent developmental systems.", "date": "2011-06", "date_type": "published", "publication": "PLoS Computational Biology", "volume": "7", "number": "6", "publisher": "Public Library of Science", "pagerange": "Art. No. e1002069", "id_number": "CaltechAUTHORS:20110715-110958369", "issn": "1553-734X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110715-110958369", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "F32GM77014" }, { "agency": "Fannie and John Hertz Foundation" }, { "agency": "UCLA/Caltech Medical Scientist Training Program" }, { "agency": "NIH", "grant_number": "GM08042" }, { "agency": "Ministerio de Ciencia e Innovaci\u00f3n (MCINN)", "grant_number": "FIS2009-13360" }, { "agency": "Instituto de Salud Carlos III" }, { "agency": "ICREA" }, { "agency": "Caltech Center for Biological Circuit Design" }, { "agency": "David and Lucile Packard Foundation" } ] }, "doi": "10.1371/journal.pcbi.1002069", "pmcid": "PMC3111533", "primary_object": { "basename": "Figure_S1.tif", "url": "https://authors.library.caltech.edu/records/za8bf-a2q74/files/Figure_S1.tif" }, "related_objects": [ { "basename": "Figure_S2.tif", "url": "https://authors.library.caltech.edu/records/za8bf-a2q74/files/Figure_S2.tif" }, { "basename": "Figure_S3.tif", "url": "https://authors.library.caltech.edu/records/za8bf-a2q74/files/Figure_S3.tif" }, { "basename": "Figure_S4.tif", "url": "https://authors.library.caltech.edu/records/za8bf-a2q74/files/Figure_S4.tif" }, { "basename": "Sprinzak2011p14797Plos_Comput_Biol.pdf", "url": "https://authors.library.caltech.edu/records/za8bf-a2q74/files/Sprinzak2011p14797Plos_Comput_Biol.pdf" }, { "basename": "Table_S1.pdf", "url": "https://authors.library.caltech.edu/records/za8bf-a2q74/files/Table_S1.pdf" }, { "basename": "Text_S1.pdf", "url": "https://authors.library.caltech.edu/records/za8bf-a2q74/files/Text_S1.pdf" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Sprinzak, David; Lakhanpal, Amit; et el." }, { "id": "https://authors.library.caltech.edu/records/xz74s-dk032", "eprint_id": 24181, "eprint_status": "archive", "datestamp": "2023-08-19 06:50:08", "lastmod": "2023-10-23 20:22:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Young-J-W", "name": { "family": "Young", "given": "Jonathan W." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Mixed Messages: How Bacteria Resolve Conflicting Signals", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Elsevier Inc. \n\nAvailable online 19 May 2011.\n\nAccepted Version - nihms605709.pdf
Supplemental Material - mmc1.pdf
", "abstract": "An elegant new study by Bollenbach and Kishony (2011) in this issue of Molecular Cell shows how bacteria resolve the apparent conflicts created when they face two signals with opposite effects on gene expression.", "date": "2011-05-20", "date_type": "published", "publication": "Molecular Cell", "volume": "42", "number": "4", "publisher": "Elsevier", "pagerange": "405-406", "id_number": "CaltechAUTHORS:20110623-101742295", "issn": "1097-2765", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110623-101742295", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.molcel.2011.05.005", "pmcid": "PMC4117311", "primary_object": { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/xz74s-dk032/files/mmc1.pdf" }, "related_objects": [ { "basename": "nihms605709.pdf", "url": "https://authors.library.caltech.edu/records/xz74s-dk032/files/nihms605709.pdf" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Young, Jonathan W. and Elowitz, Michael B." }, { "id": "https://authors.library.caltech.edu/records/mdqrq-dqj28", "eprint_id": 21431, "eprint_status": "archive", "datestamp": "2023-08-22 01:35:00", "lastmod": "2023-10-21 00:01:57", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Lim-Wendell-A", "name": { "family": "Lim", "given": "Wendell A." } } ] }, "title": "Build life to understand it", "ispublished": "pub", "full_text_status": "public", "keywords": "Developmental biology; Cell biology", "note": "\u00a9 2010 Macmillan Publishers Limited. \n\nPublished online 15 December 2010.\n\nAccepted Version - nihms279886.pdf
", "abstract": "Biologists and engineers should work together: synthetic biology reveals how organisms develop and function, argue Michael Elowitz and Wendell A. Lim.", "date": "2010-12-16", "date_type": "published", "publication": "Nature", "volume": "468", "publisher": "Nature Publishing Group", "pagerange": "889-890", "id_number": "CaltechAUTHORS:20101220-102123623", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101220-102123623", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1038/468889a", "pmcid": "PMC3068207", "primary_object": { "basename": "nihms279886.pdf", "url": "https://authors.library.caltech.edu/records/mdqrq-dqj28/files/nihms279886.pdf" }, "resource_type": "article", "pub_year": "2010", "author_list": "Elowitz, Michael B. and Lim, Wendell A." }, { "id": "https://authors.library.caltech.edu/records/f3ka4-5m529", "eprint_id": 20384, "eprint_status": "archive", "datestamp": "2023-08-19 03:53:12", "lastmod": "2023-10-20 22:29:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Acar-M", "name": { "family": "Acar", "given": "Murat" } }, { "id": "Pando-B-F", "name": { "family": "Pando", "given": "Bernardo F." } }, { "id": "Arnold-F-H", "name": { "family": "Arnold", "given": "Frances H." }, "orcid": "0000-0002-4027-364X" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "van-Oudenaarden-A", "name": { "family": "van Oudenaarden", "given": "Alexander" } } ] }, "title": "A General Mechanism for Network-Dosage Compensation in Gene Circuits", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2010 American Association for the Advancement of Science.\n\nReceived 6 April 2010; accepted 9 August 2010.\n\n\nThe authors would like to thank J. J. Collins, M. Thattai,\nand H. Youk for helpful discussions and/or comments on\nthe manuscript. M.A. was supported by a fellowship grant\nfrom the Center for Biological Circuit Design at Caltech.\nB.F.P. and A.v.O were supported by grants from NIH and\nNSF. Work in the Elowitz laboratory was supported by the\nPackard Foundation, NSF, and NIH. Work in the Arnold\nlaboratory was supported by NIH.\n\nAccepted Version - nihms303988.pdf
Supplemental Material - 1.pdf
", "abstract": "Coping with variations in network dosage is crucial for maintaining optimal function in gene networks.\nWe explored how network structure facilitates network-level dosage compensation. By using the yeast\ngalactose network as a model, we combinatorially deleted one of the two copies of its four regulatory\ngenes and found that network activity was robust to the change in network dosage. A mathematical\nanalysis revealed that a two-component genetic circuit with elements of opposite regulatory activity\n(activator and inhibitor) constitutes a minimal requirement for network-dosage invariance. Specific\ninteraction topologies and a one-to-one interaction stoichiometry between the activating and inhibiting\nagents were additional essential elements facilitating dosage invariance. This mechanism of network-dosage\ninvariance could represent a general design for gene network structure in cells.", "date": "2010-09-24", "date_type": "published", "publication": "Science", "volume": "329", "number": "5999", "publisher": "American Association for the Advancement of Science", "pagerange": "1656-1660", "id_number": "CaltechAUTHORS:20101011-132711462", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101011-132711462", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech Center for Biological Circuit Design" }, { "agency": "NIH" }, { "agency": "NSF" }, { "agency": "David and Lucile Packard Foundation" } ] }, "doi": "10.1126/science.1190544", "pmcid": "PMC3138731", "primary_object": { "basename": "1.pdf", "url": "https://authors.library.caltech.edu/records/f3ka4-5m529/files/1.pdf" }, "related_objects": [ { "basename": "nihms303988.pdf", "url": "https://authors.library.caltech.edu/records/f3ka4-5m529/files/nihms303988.pdf" } ], "resource_type": "article", "pub_year": "2010", "author_list": "Acar, Murat; Pando, Bernardo F.; et el." }, { "id": "https://authors.library.caltech.edu/records/wt55j-38628", "eprint_id": 20036, "eprint_status": "archive", "datestamp": "2023-08-22 00:49:53", "lastmod": "2023-10-20 22:09:44", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Eldar-A", "name": { "family": "Eldar", "given": "Avigdor" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Functional roles for noise in genetic circuits", "ispublished": "pub", "full_text_status": "public", "keywords": "Molecular biology; Biophysics; Stem cells; Evolution", "note": "\u00a9 2010 Nature Publishing Group.\n\nWe thank G. Su\u00a8el, A. Raj, F. Tan and J. Rossant for providing images. We thank N. Wingreen, D. J. Anderson, R. Kishony, J.-G. Ojalvo, G. Su\u00a8el, H. Y. Kueh and members of the Elowitz laboratory for discussions. Work in M.B.E.'s\nlaboratory was supported by NIH grants R01GM079771, P50 GM068763, NSF CAREER Award 0644463 and the Packard Foundation. A.E. was supported by EMBO, the International Human Frontier Science Organization and a Baxter fellowship.\n\nAccepted Version - nihms-611255.pdf
", "abstract": "The genetic circuits that regulate cellular functions are subject to stochastic fluctuations, or 'noise', in the levels of their components. Noise, far from just a nuisance, has begun to be appreciated for its essential role in key cellular activities. Noise functions in both microbial and eukaryotic cells, in multicellular development, and in evolution. It enables coordination of gene expression across large regulons, as well as probabilistic differentiation strategies that function across cell populations. At the longest timescales, noise may facilitate evolutionary transitions. Here we review examples and emerging principles that connect noise, the architecture of the gene circuits in which it is present, and the biological functions it enables. We further indicate some of the important challenges and opportunities going forward.", "date": "2010-09-09", "date_type": "published", "publication": "Nature", "volume": "467", "number": "7312", "publisher": "Nature Publishing Group", "pagerange": "167-173", "id_number": "CaltechAUTHORS:20100920-101630573", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100920-101630573", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01GM079771" }, { "agency": "NIH", "grant_number": "P50 GM068763" }, { "agency": "NSF", "grant_number": "MCB-0644463" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "European Molecular Biology Organization (EMBO)" }, { "agency": "Human Frontier Science Program" }, { "agency": "Baxter fellowship" } ] }, "doi": "10.1038/nature09326", "pmcid": "PMC4100692", "primary_object": { "basename": "nihms-611255.pdf", "url": "https://authors.library.caltech.edu/records/wt55j-38628/files/nihms-611255.pdf" }, "resource_type": "article", "pub_year": "2010", "author_list": "Eldar, Avigdor and Elowitz, Michael B." }, { "id": "https://authors.library.caltech.edu/records/zgtj4-3tq26", "eprint_id": 42311, "eprint_status": "archive", "datestamp": "2023-08-19 03:16:29", "lastmod": "2023-10-25 15:49:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cox-R-S-III", "name": { "family": "Cox", "given": "Robert Sidney, III" } }, { "id": "Dunlop-M-J", "name": { "family": "Dunlop", "given": "Mary J." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "A synthetic three-color scaffold for monitoring genetic regulation and noise", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2010 Cox et al; licensee BioMed Central Ltd. This 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. \n\nReceived: 20 January 2010; Accepted: 21 July 2010; Published: 21 July 2010. \n\nWe thank R. Phillips, M. Fontes, J. Young, C. Dalal, H. Garcia, F. Tan, L. Cai, G.\nSuel, J. Huang, R. Murray, J. Garcia-Ojalvo, U. Alon, R. Kishony, N. Rosenfeld,\nD. Morris, B. Wold, P. Sternberg, C. Smolke, E. Winfree, J. Leadbetter, and B.\nShraiman for helpful discussions. M. Surette helped with the DNA design, G.\nSeelig assisted with the control experiments in Table 1, A. Eldar invented the\ndata representation shown in Figure 2. This research was supported by US\nNational Institutes of Health grants R01GM079771, P50GM068763, National\nScience Foundation CAREER Award 0644463 and the Packard Foundation.\nRSC was supported by the Caltech Center for Biological Circuit Design. MJD\nwas supported by the Institute for Collaborative Biotechnologies through\ngrant DAAD19-03-D-0004 from the US Army Research Office. \n\nAuthors' contributions:\nRSC designed the DNA sequences, performed the experiments and drafted\nthe manuscript. MJD carried out the time-lapse data analysis and\nmathematical modeling, and helped write the manuscript. MBE conceived of\nthe study, and participated in its design and coordination. All authors read\nand approved the final manuscript.\nCompeting interests:\nThe authors declare that they have no competing interests.\n\nPublished - 1754-1611-4-10.pdf
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Supplemental Material - 1754-1611-4-10-s4.avi
", "abstract": "Background: Current methods for analyzing the dynamics of natural regulatory networks, and quantifying\nsynthetic circuit function, are limited by the lack of well-characterized genetic measurement tools. Fluorescent\nreporters have been used to measure dynamic gene expression, but recent attempts to monitor multiple genes\nsimultaneously in single cells have not focused on independent, isolated measurements. Multiple reporters can be\nused to observe interactions between natural genes, or to facilitate the 'debugging' of biologically engineered\ngenetic networks. Using three distinguishable reporter genes in a single cell can reveal information not obtainable\nfrom only one or two reporters. One application of multiple reporters is the use of genetic noise to reveal\nregulatory connections between genes. Experiments in both natural and synthetic systems would benefit from a\nwell-characterized platform for expressing multiple reporter genes and synthetic network components.\nResults: We describe such a plasmid-based platform for the design and optimization of synthetic gene networks,\nand for analysis of endogenous gene networks. This network scaffold consists of three distinguishable fluorescent\nreporter genes controlled by inducible promoters, with conveniently placed restriction sites to make modifications\nstraightforward. We quantitatively characterize the scaffold in Escherichia coli with single-cell fluorescence imaging\nand time-lapse microscopy. The three spectrally distinct reporters allow independent monitoring of genetic\nregulation and analysis of genetic noise. As a novel application of this tool we show that the presence of genetic\nnoise can reveal transcriptional co-regulation due to a hidden factor, and can distinguish constitutive from\nregulated gene expression.\nConclusion: We have constructed a general chassis where three promoters from natural genes or components of\nsynthetic networks can be easily inserted and independently monitored on a single construct using optimized\nfluorescent protein reporters. We have quantitatively characterized the baseline behavior of the chassis so that it\ncan be used to measure dynamic gene regulation and noise. Overall, the system will be useful both for analyzing\nnatural genetic networks and assembling synthetic ones.", "date": "2010-07-21", "date_type": "published", "publication": "Journal of Biological Engineering", "volume": "4", "publisher": "BioMed Central", "pagerange": "Art. No. 10", "id_number": "CaltechAUTHORS:20131107-140415442", "issn": "1754-1611", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131107-140415442", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01GM079771" }, { "agency": "NIH", "grant_number": "P50GM068763" }, { "agency": "NSF", "grant_number": "MCB-0644463" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Caltech Center for Biological Circuit Design" }, { "agency": "Army Research Office (ARO)", "grant_number": "DAAD19-03-D-0004" } ] }, "doi": "10.1186/1754-1611-4-10", "pmcid": "PMC2918530", "primary_object": { "basename": "1754-1611-4-10-s3.avi", "url": "https://authors.library.caltech.edu/records/zgtj4-3tq26/files/1754-1611-4-10-s3.avi" }, "related_objects": [ { "basename": "1754-1611-4-10-s4.avi", "url": "https://authors.library.caltech.edu/records/zgtj4-3tq26/files/1754-1611-4-10-s4.avi" }, { "basename": "1754-1611-4-10.pdf", "url": "https://authors.library.caltech.edu/records/zgtj4-3tq26/files/1754-1611-4-10.pdf" }, { "basename": "1754-1611-4-10-s1.gb", "url": "https://authors.library.caltech.edu/records/zgtj4-3tq26/files/1754-1611-4-10-s1.gb" }, { "basename": "1754-1611-4-10-s2.pdf", "url": "https://authors.library.caltech.edu/records/zgtj4-3tq26/files/1754-1611-4-10-s2.pdf" } ], "resource_type": "article", "pub_year": "2010", "author_list": "Cox, Robert Sidney, III; Dunlop, Mary J.; et el." }, { "id": "https://authors.library.caltech.edu/records/pgs47-kh709", "eprint_id": 18466, "eprint_status": "archive", "datestamp": "2023-08-19 02:30:41", "lastmod": "2023-10-20 16:24:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sprinzak-D", "name": { "family": "Sprinzak", "given": "David" } }, { "id": "Lakhanpal-A", "name": { "family": "Lakhanpal", "given": "Amit" } }, { "id": "LeBon-L", "name": { "family": "LeBon", "given": "Lauren" } }, { "id": "Santat-L-A", "name": { "family": "Santat", "given": "Leah A." } }, { "id": "Fontes-M-E", "name": { "family": "Fontes", "given": "Michelle E." } }, { "id": "Anderson-G-A", "name": { "family": "Anderson", "given": "Graham A." } }, { "id": "Garcia-Ojalvo-J", "name": { "family": "Garcia-Ojalvo", "given": "Jordi" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Cis-interactions between Notch and Delta generate mutually exclusive signalling states", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2010 Macmillan Publishers Limited. \n\nReceived 27 April 2009; accepted 26 February 2010. Published online 25 April 2010. \n\nWe would like to thank I. Bernstein for the IgG-Deltaext,\nU. Lendahl for the 12xCSL reporter construct, J. Aster for human NOTCH1 and other\nconstructs, and G. Weinmaster for the rat DLL1 construct and advice. We also\nthank R. Tsien and K. Thorn for mCherry, S. Megason and S. Fraser for H2B\u2013citrine\nand other constructs, R. Diamond and D. Perez for assistance with FACS, and F. Tan\nand J. Yong for help with cloning some of the constructs. We thank A. Eldar,\nJ. Locke, G. Seelig, R. Kishony, B. Shraiman, A. C. Oates and members of the Elowitz\nlaboratory for discussions and advice. This work was supported by the US National Institutes of Health Fellowship F32GM77014 (D.S.), the Caltech Center for\nBiological Circuit Design and the Packard Foundation. A.L. acknowledges support\nfrom the Fannie and John Hertz Foundation and the UCLA/Caltech Medical\nScientist Training Program (NIH GM08042). J.G.O. acknowledges support from\nthe Ministerio de Ciencia e Innovacion (Spain, project FIS2009-13360 and the I3\nprogramme).\nAuthor Contributions: D.S. and M.B.E. designed the research. D.S., L.A.S., M.E.F.\nand G.A.A. built cell lines and performed experiments. D.S., A.L., L.L., J.G.-O. and\nM.B.E. performed data analysis and mathematical modelling. D.S. and M.B.E. wrote\nthe manuscript with substantial input from the other authors.\n\nAccepted Version - nihms183310.pdf
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", "abstract": "The Notch\u2013Delta signalling pathway allows communication between neighbouring cells during development^1. It has a critical role in the formation of 'fine-grained' patterns, generating distinct cell fates among groups of initially equivalent neighbouring cells and sharply delineating neighbouring regions in developing tissues. The Delta ligand has been shown to have two activities: it transactivates Notch in neighbouring cells and cis-inhibits Notch in its own cell. However, it remains unclear how Notch integrates these two activities and how the resulting system facilitates pattern formation. Here we report the development of a quantitative time-lapse microscopy platform for analysing Notch\u2013Delta signalling dynamics in individual mammalian cells, with the aim of addressing these issues. By controlling both cis- and trans-Delta concentrations, and monitoring the dynamics of a Notch reporter, we measured the combined cis\u2013trans input\u2013output relationship in the Notch\u2013Delta system. The data revealed a striking difference between the responses of Notch to trans- and cis-Delta: whereas the response to trans-Delta is graded, the response to cis-Delta is sharp and occurs at a fixed threshold, independent of trans-Delta. We developed a simple mathematical model that shows how these behaviours emerge from the mutual inactivation of Notch and Delta proteins in the same cell. This interaction generates an ultrasensitive switch between mutually exclusive sending (high Delta/low Notch) and receiving (high Notch/low Delta) signalling states. At the multicellular level, this switch can amplify small differences between neighbouring cells even without transcription-mediated feedback. This Notch\u2013Delta signalling switch facilitates the formation of sharp boundaries and lateral-inhibition patterns in models of development, and provides insight into previously unexplained mutant behaviours.", "date": "2010-05-06", "date_type": "published", "publication": "Nature", "volume": "465", "number": "7294", "publisher": "Nature Publishing Group", "pagerange": "86-91", "id_number": "CaltechAUTHORS:20100526-144631743", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100526-144631743", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "F32GM77014" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "GM08042" }, { "agency": "Caltech Center for Biological Circuit Design" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Fannie and John Hertz Foundation" }, { "agency": "Ministerio de Ciencia e Innovaci\u00f3n (MCINN)", "grant_number": "FIS2009-13360" } ] }, "doi": "10.1038/nature08959", "pmcid": "PMC2886601", "primary_object": { "basename": "nature08959-s2.avi", "url": "https://authors.library.caltech.edu/records/pgs47-kh709/files/nature08959-s2.avi" }, "related_objects": [ { "basename": "nature08959-s3.avi", "url": "https://authors.library.caltech.edu/records/pgs47-kh709/files/nature08959-s3.avi" }, { "basename": "nature08959-s4.avi", "url": "https://authors.library.caltech.edu/records/pgs47-kh709/files/nature08959-s4.avi" }, { "basename": "nihms183310.pdf", "url": "https://authors.library.caltech.edu/records/pgs47-kh709/files/nihms183310.pdf" }, { "basename": "nature08959-s1.pdf", "url": "https://authors.library.caltech.edu/records/pgs47-kh709/files/nature08959-s1.pdf" } ], "resource_type": "article", "pub_year": "2010", "author_list": "Sprinzak, David; Lakhanpal, Amit; et el." }, { "id": "https://authors.library.caltech.edu/records/36tpr-v6j20", "eprint_id": 16809, "eprint_status": "archive", "datestamp": "2023-08-21 22:33:18", "lastmod": "2023-10-19 22:34:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "\u00c7a\u011fatay-T", "name": { "family": "\u00c7a\u011fatay", "given": "Tolga" } }, { "id": "Turcotte-M", "name": { "family": "Turcotte", "given": "Marc" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Garcia-Ojalvo-J", "name": { "family": "Garcia-Ojalvo", "given": "Jordi" } }, { "id": "S\u00fcel-G-M", "name": { "family": "S\u00fcel", "given": "G\u00fcrol M." } } ] }, "title": "Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits", "ispublished": "pub", "full_text_status": "public", "keywords": "microbio; signaling; sysbio", "note": "\u00a9 2009 Elsevier Inc. \n\nReceived 1 April 2009; revised 6 June 2009; accepted 21 July 2009. Published online: October 22, 2009. Available online 22 October 2009. \n\nSupplemental Data include Supplemental Experimental Procedures, 17 figures, and seven tables and can be found with this article online at http://www.cell.com/supplemental/S0092-8674(09)01033-2. \n\nWe thank Steve Altschuler, Robin Hiesinger, Rama Ranganathan, Michael Rosen, Elliott Ross, Katherine Suel, and Lani Wu for critical reading of this manuscript and helpful discussions. We also thank Alma Alvarado of the Suel laboratory for technical assistance. The authors acknowledge the Texas Advanced Computing Center at University of Texas, Austin, for providing computing resources. M.T. is supported by National Institutes of Health grant K25 GM071957. J.G.-O. acknowledges financial support from Ministerio de Ciencia e Innovacion (Spain, project ORDEN and I3 program) and from the\nEuropean Commission (project GABA). This work was supported by research grants to G.M.S. by the Welch Foundation (I-1674) and the James S. McDonnell Foundation (220020141). G.M.S. is a W.W. Caruth Jr. Scholar of Biomedical Research. This work is dedicated to the memory of Merdol and Nursxat Suel.\n\nSupplemental Material - Cagatay2009p6362Cell_supp.pdf
", "abstract": "Gene regulatory circuits with different architectures (patterns of regulatory interactions) can generate similar dynamics. This raises the question of why a particular circuit architecture is selected to implement a given cellular process. To investigate this problem, we compared the Bacillus subtilis circuit that regulates differentiation into the competence state to an engineered circuit with an alternative architecture (SynEx) in silico and in vivo. Time-lapse microscopy measurements showed that SynEx cells generated competence dynamics similar to native cells and reconstituted the physiology of differentiation. However, architectural differences between the circuits altered the dynamic distribution of stochastic fluctuations (noise) during circuit operation. This distinction in noise causes functional differences between the circuits by selectively controlling the timing of competence episodes and response of the system to various DNA concentrations. These results reveal a tradeoff between temporal precision and physiological response range that is controlled by distinct noise characteristics of alternative circuit architectures.", "date": "2009-10-30", "date_type": "published", "publication": "Cell", "volume": "139", "number": "3", "publisher": "Cell Press", "pagerange": "512-522", "id_number": "CaltechAUTHORS:20091125-110115141", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20091125-110115141", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "K25 GM071957" }, { "agency": "Ministerio de Ciencia e Innovaci\u00f3n (MCINN)" }, { "agency": "European Commission" }, { "agency": "Robert A. Welch Foundation", "grant_number": "I-1674" }, { "agency": "James S. McDonnell Foundation", "grant_number": "220020141" } ] }, "doi": "10.1016/j.cell.2009.07.046", "primary_object": { "basename": "Cagatay2009p6362Cell_supp.pdf", "url": "https://authors.library.caltech.edu/records/36tpr-v6j20/files/Cagatay2009p6362Cell_supp.pdf" }, "resource_type": "article", "pub_year": "2009", "author_list": "\u00c7a\u011fatay, Tolga; Turcotte, Marc; et el." }, { "id": "https://authors.library.caltech.edu/records/qx9qd-03y84", "eprint_id": 15171, "eprint_status": "archive", "datestamp": "2023-08-20 02:20:29", "lastmod": "2023-10-18 21:02:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Eldar-A", "name": { "family": "Eldar", "given": "Avigdor" } }, { "id": "Chary-V-K", "name": { "family": "Chary", "given": "Vasant K." } }, { "id": "Xenopoulos-P", "name": { "family": "Xenopoulos", "given": "Panagiotis" } }, { "id": "Fontres-M-E", "name": { "family": "Fontes", "given": "Michelle E." } }, { "id": "Los\u00f3n-O-C", "name": { "family": "Los\u00f3n", "given": "Oliver C." } }, { "id": "Dworkin-J", "name": { "family": "Dworkin", "given": "Jonathan" } }, { "id": "Piggot-P-J", "name": { "family": "Piggot", "given": "Patrick J." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Partial penetrance facilitates developmental evolution in bacteria", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2009 Nature Publishing Group. \n\nReceived 6 December 2008; Accepted 15 May 2009; Published online 5 July 2009; Corrected 23 July 2009. \n\nWe thank J. Leadbetter and E. Matson for their help with the\nanaerobic species. We thank R. Losick, A. Grossman, M. Fujita and A. Arkin for\nstrains and advice.Wethank R. Kishony, D. Jones, Wolfgang Schwarz, G. Suel, J.-G.\nOjalvo, B. Shraiman, J. Levine, J. C. W. Locke, D. Sprinzak, L. Cai and other members\nof M.B.E. and P.J.P. labs for helpful discussions. Work in the P.J.P.'s lab was\nsupported by Public Health Service Grant GM43577 from the US National\nInstitutes of Health (NIH). Work in M.B.E.'s lab was supported by NIH grants\nR01GM079771 and P50 GM068763, US National Science Foundation CAREER\nAward 0644463 and the Packard Foundation. A.E. was supported by the\nInternational Human Frontier Science Organization and the European Molecular\nBiology Organization.\nAuthor Contributions A.E., V.K.C., J.D., P.J.P. and M.B.E. designed the research; A.E., V.K.C., P.X., M.E.F. and O.C.L. performed the experiments; A.E. and V.K.C. analysed the results; and A.E. and M.B.E. wrote the paper. \n\nSupplementary Information is linked to the online version of the paper at www.nature.com/nature.\n\nAccepted Version - nihms118072.pdf
Supplemental Material - nature08150-s1.pdf
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", "abstract": "Development normally occurs similarly in all individuals within an isogenic population, but mutations often affect the fates of individual organisms differently. This phenomenon, known as partial penetrance, has been observed in diverse developmental systems. However, it remains unclear how the underlying genetic network specifies the set of possible alternative fates and how the relative frequencies of these fates evolve. Here we identify a stochastic cell fate determination process that operates in Bacillus subtilis sporulation mutants and show how it allows genetic control of the penetrance of multiple fates. Mutations in an intercompartmental signalling process generate a set of discrete alternative fates not observed in wild-type cells, including rare formation of two viable 'twin' spores, rather than one within a single cell. By genetically modulating chromosome replication and septation, we can systematically tune the penetrance of each mutant fate. Furthermore, signalling and replication perturbations synergize to significantly increase the penetrance of twin sporulation. These results suggest a potential pathway for developmental evolution between monosporulation and twin sporulation through states of intermediate twin penetrance. Furthermore, time-lapse microscopy of twin sporulation in wild-type Clostridium oceanicum shows a strong resemblance to twin sporulation in these B. subtilis mutants. Together the results suggest that noise can facilitate developmental evolution by enabling the initial expression of discrete morphological traits at low penetrance, and allowing their stabilization by gradual adjustment of genetic parameters.", "date": "2009-07-23", "date_type": "published", "publication": "Nature", "volume": "460", "number": "7254", "publisher": "Nature Publishing Group", "pagerange": "510-514", "id_number": "CaltechAUTHORS:20090819-114359740", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090819-114359740", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM43577" }, { "agency": "NIH", "grant_number": "R01GM079771" }, { "agency": "NIH", "grant_number": "P50 GM068763" }, { "agency": "NSF", "grant_number": "MCB-0644463" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Human Frontier Science Program" }, { "agency": "European Molecular Biology Organization (EMBO)" } ] }, "doi": "10.1038/nature08150", "pmcid": "PMC2716064", "primary_object": { "basename": "nature08150-s1.pdf", "url": "https://authors.library.caltech.edu/records/qx9qd-03y84/files/nature08150-s1.pdf" }, "related_objects": [ { "basename": "nature08150-s2.mov", "url": "https://authors.library.caltech.edu/records/qx9qd-03y84/files/nature08150-s2.mov" }, { "basename": "nature08150-s3.mov", "url": "https://authors.library.caltech.edu/records/qx9qd-03y84/files/nature08150-s3.mov" }, { "basename": "nihms118072.pdf", "url": "https://authors.library.caltech.edu/records/qx9qd-03y84/files/nihms118072.pdf" } ], "resource_type": "article", "pub_year": "2009", "author_list": "Eldar, Avigdor; Chary, Vasant K.; et el." }, { "id": "https://authors.library.caltech.edu/records/1596c-hmj61", "eprint_id": 102842, "eprint_status": "archive", "datestamp": "2023-08-20 01:38:12", "lastmod": "2023-10-20 00:32:58", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Locke-J-C-W", "name": { "family": "Locke", "given": "James C. W." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Using movies to analyse gene circuit dynamics in single cells", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2009 Nature Publishing Group. \n\nWe thank A. Eldar, J. Young, L. Cai, C. Dalal and all members of the Elowitz groups for their feedback and suggestions. J.L. was supported by a Human Frontiers Fellowship. This work was supported by US National Institutes of Health grants R01GM079771 and P50 GM068763, National Science Foundation CAREER Award 0644463 and the Packard Foundation.\n\nAccepted Version - nihms174923.pdf
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", "abstract": "Many bacterial systems rely on dynamic genetic circuits to control crucial biological processes. A major goal of systems biology is to understand these behaviours in terms of individual genes and their interactions. However, traditional techniques based on population averages 'wash out' crucial dynamics that are either unsynchronized between cells or are driven by fluctuations, or 'noise', in cellular components. Recently, the combination of time-lapse microscopy, quantitative image analysis and fluorescent protein reporters has enabled direct observation of multiple cellular components over time in individual cells. In conjunction with mathematical modelling, these techniques are now providing powerful insights into genetic circuit behaviour in diverse microbial systems.", "date": "2009-05", "date_type": "published", "publication": "Nature Reviews Microbiology", "volume": "7", "number": "5", "publisher": "Nature Publishing Group", "pagerange": "383-392", "id_number": "CaltechAUTHORS:20200428-095144359", "issn": "1740-1526", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200428-095144359", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01GM079771" }, { "agency": "NIH", "grant_number": "P50 GM068763" }, { "agency": "NSF", "grant_number": "MCB-0644463" }, { "agency": "David and Lucile Packard Foundation" } ] }, "doi": "10.1038/nrmicro2056", "pmcid": "PMC2853934", "primary_object": { "basename": "41579_2009_BFnrmicro2056_MOESM1_ESM.mov", "url": "https://authors.library.caltech.edu/records/1596c-hmj61/files/41579_2009_BFnrmicro2056_MOESM1_ESM.mov" }, "related_objects": [ { "basename": "41579_2009_BFnrmicro2056_MOESM2_ESM.mov", "url": "https://authors.library.caltech.edu/records/1596c-hmj61/files/41579_2009_BFnrmicro2056_MOESM2_ESM.mov" }, { "basename": "nihms174923.pdf", "url": "https://authors.library.caltech.edu/records/1596c-hmj61/files/nihms174923.pdf" } ], "resource_type": "article", "pub_year": "2009", "author_list": "Locke, James C. W. and Elowitz, Michael B." }, { "id": "https://authors.library.caltech.edu/records/xe98t-9dg72", "eprint_id": 13444, "eprint_status": "archive", "datestamp": "2023-08-22 13:43:31", "lastmod": "2023-10-17 23:54:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dunlop-M-J", "name": { "family": "Dunlop", "given": "Mary J." } }, { "id": "Cox-R-S-III", "name": { "family": "Cox", "given": "Robert Sidney, III" } }, { "id": "Levine-J-H", "name": { "family": "Levine", "given": "Joseph H." } }, { "id": "Murray-R-M", "name": { "family": "Murray", "given": "Richard M." }, "orcid": "0000-0002-5785-7481" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Regulatory activity revealed by dynamic correlations in gene expression noise", "ispublished": "pub", "full_text_status": "public", "keywords": "incoherent feedforward loop; Escherichia-coli; Bacillius-subtilis; consequences; construction; networks; pathway; system; time; cell", "note": "\u00a9 2008 Nature Publishing Group. \n\nReceived 9 June; accepted 23 September; published online 23 November 2008. \n\nWe thank M. Fontes, F. Tan, L. Cai, E. Franco, and all members of the Elowitz\nand Murray groups for their feedback and suggestions. H. Garcia provided advice on the chromosomal integration and gene knockout experiments. We thank J. Garcia-Ojalvo, U. Alon, R. Kishony, N. Rosenfeld and B. Shraiman for discussions. M.J.D. and R.M.M. are supported by the Institute for Collaborative Biotechnologies through grant DAAD19-03-D-0004 from the US Army Research Office. M.J.D. was additionally supported by a Department of Energy\nComputational Science Graduate Fellowship. This research was supported by US National Institutes of Health grants R01GM079771, P50 GM068763, National Science Foundation CAREER Award 0644463 and the Packard Foundation.\n\nAccepted Version - nihms166225.pdf
Supplemental Material - DUNng08supp.pdf
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", "abstract": "Gene regulatory interactions are context dependent, active in some cellular states but not in others. Stochastic fluctuations, or 'noise', in gene expression propagate through active, but not inactive, regulatory links^(1,2). Thus, correlations in gene expression noise could provide a noninvasive means to probe the activity states of regulatory links. However, global, 'extrinsic', noise sources generate correlations even without direct regulatory links. Here we show that single-cell time-lapse microscopy, by revealing time lags due to regulation, can discriminate between active regulatory connections and extrinsic noise. We demonstrate this principle mathematically, using stochastic modeling, and experimentally, using simple synthetic gene circuits. We then use this approach to analyze dynamic noise correlations in the galactose metabolism genes of Escherichia coli. We find that the CRP-GalS-GalE feed-forward loop is inactive in standard conditions but can become active in a GalR mutant. These results show how noise can help analyze the context dependence of regulatory interactions in endogenous gene circuits.", "date": "2008-12", "date_type": "published", "publication": "Nature Genetics", "volume": "40", "number": "12", "publisher": "Nature Publishing Group", "pagerange": "1493-1498", "id_number": "CaltechAUTHORS:DUNng08", "issn": "1061-4036", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:DUNng08", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Army Research Office (ARO)", "grant_number": "DAAD19-03-D-0004" }, { "agency": "Department of Energy (DOE)" }, { "agency": "NIH", "grant_number": "R01GM079771" }, { "agency": "NIH", "grant_number": "P50 GM068763" }, { "agency": "NSF", "grant_number": "MCB-0644463" }, { "agency": "David and Lucile Packard Foundation" } ] }, "doi": "10.1038/ng.281", "pmcid": "PMC2829635", "primary_object": { "basename": "DUNng08movie1.avi", "url": "https://authors.library.caltech.edu/records/xe98t-9dg72/files/DUNng08movie1.avi" }, "related_objects": [ { "basename": "DUNng08movie2.avi", "url": "https://authors.library.caltech.edu/records/xe98t-9dg72/files/DUNng08movie2.avi" }, { "basename": "DUNng08supp.pdf", "url": "https://authors.library.caltech.edu/records/xe98t-9dg72/files/DUNng08supp.pdf" }, { "basename": "nihms166225.pdf", "url": "https://authors.library.caltech.edu/records/xe98t-9dg72/files/nihms166225.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Dunlop, Mary J.; Cox, Robert Sidney, III; et el." }, { "id": "https://authors.library.caltech.edu/records/5b636-xfq63", "eprint_id": 13259, "eprint_status": "archive", "datestamp": "2023-08-22 13:08:29", "lastmod": "2023-10-17 23:21:46", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cai-Long", "name": { "family": "Cai", "given": "Long" }, "orcid": "0000-0002-7154-5361" }, { "id": "Dalal-C-K", "name": { "family": "Dalal", "given": "Chiraj K." }, "orcid": "0000-0002-3624-8409" }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Frequency-modulated nuclear localization bursts coordinate gene regulation", "ispublished": "pub", "full_text_status": "public", "keywords": "SACCHAROMYCES-CEREVISIAE; TRANSCRIPTION FACTOR; PROTEIN EXPRESSION; BUDDING YEAST; SINGLE-CELL; GLOBAL ANALYSIS; DOCKING SITE; CALCINEURIN; NOISE; OSCILLATIONS", "note": "\u00a9 2008 Nature Publishing Group. \n\nReceived 15 May 2008; Accepted 18 July 2008. \n\nWe thank M. Cyert for the CDRE and Crz1 mutant plasmids, K. Cunningham for the Crz1 overexpression plasmid pLE66, J. Stadler for the pGW845 FRET plasmid, S. Ramanathan for image analysis code, and K. Thorn, C.-L. Guo and L. LeBon for technical assistance. We thank U. Alon, M. Carlson, M. Cyert, H. Garcia, R. Kishony, G. Lahav, J.-G. Ojalvo, I. Riedel-Kruse, B. Shraiman, G. S\u00fcel, members of the laboratory, and especially N. Friedman for discussions. L.C. is supported by the Beckman Fellows Program at Caltech. This work was supported by National Institutes of Health grants R01GM079771 and P50 GM068763 for National Centers of Systems Biology, and the Packard Foundation.\n\nAccepted Version - nihms70624.pdf
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", "abstract": "In yeast, the transcription factor Crz1 is dephosphorylated and translocates into the nucleus in response to extracellular calcium. Here we show, using time-lapse microscopy, that Crz1 exhibits short bursts of nuclear localization (typically lasting 2 min) that occur stochastically in individual cells and propagate to the expression of downstream genes. Strikingly, calcium concentration controls the frequency, but not the duration, of localization bursts. Using an analytic model, we also show that this frequency modulation of bursts ensures proportional expression of multiple target genes across a wide dynamic range of expression levels, independent of promoter characteristics. We experimentally confirm this theory with natural and synthetic Crz1 target promoters. Another stress-response transcription factor, Msn2, exhibits similar, but largely uncorrelated, localization bursts under calcium stress suggesting that frequency-modulation regulation of localization bursts may be a general control strategy used by the cell to coordinate multi-gene responses to external signals.", "date": "2008-09-25", "date_type": "published", "publication": "Nature", "volume": "455", "number": "7212", "publisher": "Nature Publishing Group", "pagerange": "485-491", "id_number": "CaltechAUTHORS:CAInat08", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:CAInat08", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01GM079771" }, { "agency": "NIH", "grant_number": "P50 GM068763" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Caltech Beckman Institute" } ] }, "doi": "10.1038/nature07292", "pmcid": "PMC2695983", "primary_object": { "basename": "CAInat08.mov", "url": "https://authors.library.caltech.edu/records/5b636-xfq63/files/CAInat08.mov" }, "related_objects": [ { "basename": "CAInat08supp.pdf", "url": "https://authors.library.caltech.edu/records/5b636-xfq63/files/CAInat08supp.pdf" }, { "basename": "nihms70624.pdf", "url": "https://authors.library.caltech.edu/records/5b636-xfq63/files/nihms70624.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Cai, Long; Dalal, Chiraj K.; et el." }, { "id": "https://authors.library.caltech.edu/records/pjtw4-8ps83", "eprint_id": 12177, "eprint_status": "archive", "datestamp": "2023-08-22 11:01:50", "lastmod": "2023-10-17 16:34:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Presser-A", "name": { "family": "Presser", "given": "Aviva" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Kellis-M", "name": { "family": "Kellis", "given": "Manolis" } }, { "id": "Kishony-R", "name": { "family": "Kishony", "given": "Roy" } } ] }, "title": "The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication", "ispublished": "pub", "full_text_status": "public", "keywords": "gene duplication; network motifs; self-interacting proteins; whole-genome duplication", "note": "\u00a9 2008 by the National Academy of Sciences.\n\nEdited by Leonid Kruglyak, Princeton University, Princeton, NJ, and accepted by the Editorial Board November 20, 2007 (received for review August 2, 2007). Published online before print January 16, 2008, doi: 10.1073/pnas.0707293105. This article is a PNAS Direct Submission. L.K. is a guest editor invited by the Editorial Board. \n\nWe acknowledge N. Barkai, M. Brenner, A. DeLuna, E. Lieberman, I. Nachman, I. Wapinski, and K. Wolfe for their advice and helpful discussions and E. Lieberman and R. Milo for critical readings of the manuscript. This work was supported in part by National Institutes of Health Grants GM068763 (to M.B.E.) and R01GM081617 (to R.K.). A.P. was supported by a National Science Foundation Graduate Fellowship and a National Defense Science and Engineering Graduate Fellowship. \n\nAuthor contributions: A.P., M.B.E., and R.K. designed research; A.P. performed research; A.P., M.K., and R.K. analyzed data; and A.P., M.B.E., M.K., and R.K. 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/0707293105/DC1.\n\nPublished - PREpnas08.pdf
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", "abstract": "Gene duplication is an important mechanism in the evolution of protein interaction networks. Duplications are followed by the gain and loss of interactions, rewiring the network at some unknown rate. Because rewiring is likely to change the distribution of network motifs within the duplicated interaction set, it should be possible to study network rewiring by tracking the evolution of these motifs. We have developed a mathematical framework that, together with duplication data from comparative genomic and proteomic studies, allows us to infer the connectivity of the preduplication network and the changes in connectivity over time. We focused on the whole-genome duplication (WGD) event in Saccharomyces cerevisiae. The model allowed us to predict the frequency of intergene interaction before WGD and the post duplication probabilities of interaction gain and loss. We find that the predicted frequency of self-interactions in the preduplication network is significantly higher than that observed in today's network. This could suggest a structural difference between the modern and ancestral networks, preferential addition or retention of interactions between ohnologs, or selective pressure to preserve duplicates of self-interacting proteins.", "date": "2008-01-22", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "105", "number": "3", "publisher": "National Academy of Sciences", "pagerange": "950-954", "id_number": "CaltechAUTHORS:PREpnas08", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:PREpnas08", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM068763" }, { "agency": "NIH", "grant_number": "R01GM081617" }, { "agency": "National Defense Science and Engineering Graduate (NDSEG) Fellowship" } ] }, "doi": "10.1073/pnas.0707293105", "pmcid": "PMC2242688", "primary_object": { "basename": "07293SuppText.pdf", "url": "https://authors.library.caltech.edu/records/pjtw4-8ps83/files/07293SuppText.pdf" }, "related_objects": [ { "basename": "07293Table3.pdf", "url": "https://authors.library.caltech.edu/records/pjtw4-8ps83/files/07293Table3.pdf" }, { "basename": "07293Table4.pdf", "url": "https://authors.library.caltech.edu/records/pjtw4-8ps83/files/07293Table4.pdf" }, { "basename": "PREpnas08.pdf", "url": "https://authors.library.caltech.edu/records/pjtw4-8ps83/files/PREpnas08.pdf" }, { "basename": "07293Fig4.pdf", "url": "https://authors.library.caltech.edu/records/pjtw4-8ps83/files/07293Fig4.pdf" }, { "basename": "07293Fig5.pdf", "url": "https://authors.library.caltech.edu/records/pjtw4-8ps83/files/07293Fig5.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Presser, Aviva; Elowitz, Michael B.; et el." }, { "id": "https://authors.library.caltech.edu/records/jms47-b5592", "eprint_id": 102843, "eprint_status": "archive", "datestamp": "2023-08-22 10:26:53", "lastmod": "2023-10-20 00:33:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Rosenfeld-N", "name": { "family": "Rosenfeld", "given": "Nitzan" } }, { "id": "Young-J-W", "name": { "family": "Young", "given": "Jonathan W." } }, { "id": "Alon-U", "name": { "family": "Alon", "given": "Uri" } }, { "id": "Swain-P-S", "name": { "family": "Swain", "given": "Peter S." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Accurate prediction of gene feedback circuit behavior from component properties", "ispublished": "pub", "full_text_status": "public", "keywords": "auto-regulation; feedback; GRF; quantification; regulatory elements", "note": "\u00a9 2007 EMBO and Nature Publishing Group. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits distribution, and reproduction in any medium, provided the original author and source are credited. This license does not permit commercial exploitation or the creation of derivative works without specific permission. \n\nReceived 11.6.07; accepted 12.9.07. \n\nThis work was supported by grants from HFSP (to MBE and UA), NIH (R01 GM079771 and GM068763 to the Center for Modular Biology) and NSF. PSS was supported by the National Science and Engineering Research Council and by a Tier II Canada Research Chair.\n\nPublished - msb4100185.pdf
Supplemental Material - downloadSupplement_doi=10.1038_2Fmsb4100185_file=msb4100185-sup-0001.jpg
Supplemental Material - downloadSupplement_doi=10.1038_2Fmsb4100185_file=msb4100185-sup-0002.jpg
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", "abstract": "A basic assumption underlying synthetic biology is that analysis of genetic circuit elements, such as regulatory proteins and promoters, can be used to understand and predict the behavior of circuits containing those elements. To test this assumption, we used time\u2010lapse fluorescence microscopy to quantitatively analyze two autoregulatory negative feedback circuits. By measuring the gene regulation functions of the corresponding repressor\u2013promoter interactions, we accurately predicted the expression level of the autoregulatory feedback loops, in molecular units. This demonstration that quantitative characterization of regulatory elements can predict the behavior of genetic circuits supports a fundamental requirement of synthetic biology.", "date": "2007-11-13", "date_type": "published", "publication": "Molecular Systems Biology", "volume": "3", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 143", "id_number": "CaltechAUTHORS:20200428-095144474", "issn": "1744-4292", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200428-095144474", "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": "R01 GM079771" }, { "agency": "NIH", "grant_number": "GM068763" }, { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)" }, { "agency": "Canada Research Chairs Program" } ] }, "doi": "10.1038/msb4100185", "pmcid": "PMC2132446", "primary_object": { "basename": "msb4100185.pdf", "url": "https://authors.library.caltech.edu/records/jms47-b5592/files/msb4100185.pdf" }, "resource_type": "article", "pub_year": "2007", "author_list": "Rosenfeld, Nitzan; Young, Jonathan W.; et el." }, { "id": "https://authors.library.caltech.edu/records/q2ge4-8h313", "eprint_id": 102841, "eprint_status": "archive", "datestamp": "2023-08-22 10:26:47", "lastmod": "2023-10-20 00:32:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cox-R-S-III", "name": { "family": "Cox", "given": "Robert Sidney, III" } }, { "id": "Surette-M-G", "name": { "family": "Surette", "given": "Michael G." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Programming gene expression with combinatorial promoters", "ispublished": "pub", "full_text_status": "public", "keywords": "combinatorial promoter; logic gate; signal integration; synthetic biology; transcription regulation", "note": "\u00a9 2007 EMBO and Nature Publishing Group This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits distribution, and reproduction in any medium, provided the original author and source are credited. This license does not permit commercial exploitation or the creation of derivative works without specific permission. \n\nReceived 19.6.07; accepted 21.9.07. \n\nWe thank Aaron White for help with library design and construction, Mercedes Paulino for help preparing figures, and Carla Davidson for plasmid pCD136. Avidgor Eldar contributed to the logic\u2010symmetry space formalism. T Irie, D Morris, P Sternberg, E Winfree, G Anderson, J Locke, H Garcia, R Kishony, U Alon, and C Dalal provided helpful discussions. We thank W Kim, C Vizcarra, G Seelig, and J Kim for technical assistance. RSC was partially supported by the National Physical Science Consortium and Sandia National Laboratory. MGS is supported as an Alberta Heritage Foundation for Medical Research (AHFMR) Scientist and Canada Research Chair in Microbial Gene Expression. This work was supported by NIH (grants R01GM079771 to MBE and 5P50 GM068763 to the Center for Modular Biology), HFSP, the Packard Foundation, and the Caltech Center for Biological Circuit Design.\n\nPublished - msb4100187.pdf
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Supplemental Material - downloadSupplement_doi=10.1038_2Fmsb4100187_file=msb4100187-sup-0009.pdf
", "abstract": "Promoters control the expression of genes in response to one or more transcription factors (TFs). The architecture of a promoter is the arrangement and type of binding sites within it. To understand natural genetic circuits and to design promoters for synthetic biology, it is essential to understand the relationship between promoter function and architecture. We constructed a combinatorial library of random promoter architectures. We characterized 288 promoters in Escherichia coli, each containing up to three inputs from four different TFs. The library design allowed for multiple \u221210 and \u221235 boxes, and we observed varied promoter strength over five decades. To further analyze the functional repertoire, we defined a representation of promoter function in terms of regulatory range, logic type, and symmetry. Using these results, we identified heuristic rules for programming gene expression with combinatorial promoters.", "date": "2007-11-13", "date_type": "published", "publication": "Molecular Systems Biology", "volume": "3", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 145", "id_number": "CaltechAUTHORS:20200428-095144189", "issn": "1744-4292", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200428-095144189", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Physical Science Consortium" }, { "agency": "Sandia National Laboratories" }, { "agency": "Alberta Heritage Foundation for Medical Research" }, { "agency": "Canada Research Chairs Program" }, { "agency": "NIH", "grant_number": "R01GM079771" }, { "agency": "NIH", "grant_number": "5P50 GM068763" }, { "agency": "Human Frontier Science Program" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Caltech Center for Biological Circuit Design" } ] }, "doi": "10.1038/msb4100187", "pmcid": "PMC2132448", "primary_object": { "basename": "msb4100187.pdf", "url": "https://authors.library.caltech.edu/records/q2ge4-8h313/files/msb4100187.pdf" }, "resource_type": "article", "pub_year": "2007", "author_list": "Cox, Robert Sidney, III; Surette, Michael G.; et el." }, { "id": "https://authors.library.caltech.edu/records/t1g1s-xgm65", "eprint_id": 51738, "eprint_status": "archive", "datestamp": "2023-08-19 19:52:38", "lastmod": "2023-10-18 17:06:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "S\u00fcel-G-M", "name": { "family": "S\u00fcel", "given": "G\u00fcrol M." } }, { "id": "Kulkarni-R-P", "name": { "family": "Kulkarni", "given": "Rajan P." } }, { "id": "Dworkin-J", "name": { "family": "Dworkin", "given": "Jonathan" } }, { "id": "Garcia-Ojalvo-J", "name": { "family": "Garcia-Ojalvo", "given": "Jordi" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Tunability and Noise Dependence in Differentiation Dynamics", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2007 American Association for the Advancement of Science.\n\nReceived 13 November 2006; accepted 26 February 2007.\n\nWe thank R. Kishony, B. Shraiman, U. Alon, R. Ranganathan,\nS. Altschuler, L. Wu, and K. S\u00fcel, together with members of the\nElowitz laboratory, for thoughtful comments and discussions.\nThis work was supported by grants from NIH (R01 GM079771\nto M.B.E. and GM068763 to the Center for Modular Biology),\nthe Searle Scholars Program, the Human Frontiers Science\nProgram, and the Packard Foundation. G.M.S. is supported by\nCalifornia Institute of Technology Center for Biological Circuit\nDesign and the University of Texas Southwestern's Endowed\nScholars Program. J.G.O. acknowledges financial support from the Ministerio de Educacion y Ciencia (Spain, project FIS2006-11452) and from the Generalitat de Catalunya.\n\nSupplemental Material - Suel_SOM.pdf
", "abstract": "The dynamic process of differentiation depends on the architecture, quantitative parameters, and noise of underlying genetic circuits. However, it remains unclear how these elements combine to control cellular behavior. We analyzed the probabilistic and transient differentiation of Bacillus subtilis cells into the state of competence. A few key parameters independently tuned the frequency of initiation and the duration of competence episodes and allowed the circuit to access different dynamic regimes, including oscillation. Altering circuit architecture showed that the duration of competence events can be made more precise. We used an experimental method to reduce global cellular noise and showed that noise levels are correlated with frequency of differentiation events. Together, the data reveal a noise-dependent circuit that is remarkably resilient and tunable in terms of its dynamic behavior.", "date": "2007-03-23", "date_type": "published", "publication": "Science", "volume": "315", "number": "5819", "publisher": "American Association for the Advancement of Science", "pagerange": "1716-1719", "id_number": "CaltechAUTHORS:20141114-080404724", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141114-080404724", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 GM079771" }, { "agency": "NIH", "grant_number": "GM068763" }, { "agency": "Searle Scholars Program" }, { "agency": "Human Frontier Science Program" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Caltech Center for Biological Circuit Design" }, { "agency": "University of Texas Southwestern" }, { "agency": "Ministerio de Educacion y Ciencia (MEC)", "grant_number": "FIS2006-11452" }, { "agency": "Generalitat de Catalunya" } ] }, "doi": "10.1126/science.1137455", "primary_object": { "basename": "Suel_SOM.pdf", "url": "https://authors.library.caltech.edu/records/t1g1s-xgm65/files/Suel_SOM.pdf" }, "resource_type": "article", "pub_year": "2007", "author_list": "S\u00fcel, G\u00fcrol M.; Kulkarni, Rajan P.; et el." }, { "id": "https://authors.library.caltech.edu/records/wps75-94303", "eprint_id": 102877, "eprint_status": "archive", "datestamp": "2023-08-19 18:17:32", "lastmod": "2023-10-20 00:35:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Rosenfeld-N", "name": { "family": "Rosenfeld", "given": "Nitzan" } }, { "id": "Perkins-T-J", "name": { "family": "Perkins", "given": "Theodore J." } }, { "id": "Alon-U", "name": { "family": "Alon", "given": "Uri" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Swain-P-S", "name": { "family": "Swain", "given": "Peter S." } } ] }, "title": "A Fluctuation Method to Quantify In Vivo Fluorescence Data", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2006 The Biophysical Society. Published by Elsevier Inc. \n\nReceived 22 August 2005, Accepted 19 April 2006, Available online 6 January 2009. \n\nWe thank Derek Bowie, Robert Sidney Cox III, Jon Young, and the anonymous referees for useful comments. M.B.E. acknowledges a CASI award from the Burroughs Wellcome Fund and the Searle Scholars Program. U.A. and M.B.E. are supported by the Human Frontiers Science Program. P.S.S. is supported by the National Sciences and Engineering Research Council (Canada) and by a Tier II Canada Research Chair.", "abstract": "Quantitative in vivo measurements are essential for developing a predictive understanding of cellular behavior. Here we present a technique that converts observed fluorescence intensities into numbers of molecules. By transiently expressing a fluorescently tagged protein and then following its dilution during growth and division, we observe asymmetric partitioning of fluorescence between daughter cells at each division. Such partition asymmetries are set by the actual numbers of proteins present, and thus provide a means to quantify fluorescence levels. We present a Bayesian algorithm that infers from such data both the fluorescence conversion factor and an estimate of the measurement error. Our algorithm works for arbitrarily sized data sets and handles consistently any missing measurements. We verify the algorithm with extensive simulation and demonstrate its application to experimental data from Escherichia coli. Our technique should provide a quantitative internal calibration to systems biology studies of both synthetic and endogenous cellular networks.", "date": "2006-07-15", "date_type": "published", "publication": "Biophysical Journal", "volume": "91", "number": "2", "publisher": "Biophysical Society", "pagerange": "759-766", "id_number": "CaltechAUTHORS:20200428-123053062", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200428-123053062", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Burroughs Wellcome Fund" }, { "agency": "Searle Scholars Program" }, { "agency": "Human Frontier Science Program" }, { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)" }, { "agency": "Canada Research Chairs Program" } ] }, "doi": "10.1529/biophysj.105.073098", "pmcid": "PMC1483091", "resource_type": "article", "pub_year": "2006", "author_list": "Rosenfeld, Nitzan; Perkins, Theodore J.; et el." }, { "id": "https://authors.library.caltech.edu/records/gsagm-5zn04", "eprint_id": 102891, "eprint_status": "archive", "datestamp": "2023-08-19 17:33:41", "lastmod": "2023-10-20 00:36:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "S\u00fcel-G-M", "name": { "family": "S\u00fcel", "given": "G\u00fcrol M." } }, { "id": "Garcia-Ojalvo-J", "name": { "family": "Garcia-Ojalvo", "given": "Jordi" } }, { "id": "Liberman-L-M", "name": { "family": "Liberman", "given": "Louisa M." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "An excitable gene regulatory circuit induces transient cellular differentiation", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 Nature Publishing Group. \n\nReceived 15 September 2005; Accepted 18 January 2006; Issue Date 23 March 2006. \n\nWe thank U. Alon, D. Dubnau, J. Dworkin, A. Eldar, J. Ferrell, R. Kishony, B. Lazazzera, R. Losick, A. Raj, B. Shraiman, D. Sprinzak, M. Surette and members of the laboratory for comments. G.M.S. is supported by the Caltech Center for Biological Circuit Design. J.G.-O. acknowledges financial support from the Generalitat de Catalunya and the Ministerio de Educacion y Ciencia (Spain). M.B.E. acknowledges support from the Searle Scholars Program and the Burroughs Wellcome Fund CASI program. \n\nThe authors declare no competing financial interests.\n\nSupplemental Material - 41586_2006_BFnature04588_MOESM1_ESM.pdf
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", "abstract": "Certain types of cellular differentiation are probabilistic and transient. In such systems individual cells can switch to an alternative state and, after some time, switch back again. In Bacillus subtilis, competence is an example of such a transiently differentiated state associated with the capability for DNA uptake from the environment. Individual genes and proteins underlying differentiation into the competent state have been identified, but it has been unclear how these genes interact dynamically in individual cells to control both spontaneous entry into competence and return to vegetative growth. Here we show that this behaviour can be understood in terms of excitability in the underlying genetic circuit. Using quantitative fluorescence time-lapse microscopy, we directly observed the activities of multiple circuit components simultaneously in individual cells, and analysed the resulting data in terms of a mathematical model. We find that an excitable core module containing positive and negative feedback loops can explain both entry into, and exit from, the competent state. We further tested this model by analysing initiation in sister cells, and by re-engineering the gene circuit to specifically block exit. Excitable dynamics driven by noise naturally generate stochastic and transient responses, thereby providing an ideal mechanism for competence regulation.", "date": "2006-03-23", "date_type": "published", "publication": "Nature", "volume": "440", "number": "7083", "publisher": "Nature Publishing Group", "pagerange": "545-550", "id_number": "CaltechAUTHORS:20200428-150756338", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200428-150756338", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech Center for Biological Circuit Design" }, { "agency": "Generalitat de Catalunya" }, { "agency": "Ministerio de Educaci\u00f3n y Ciencia (MEC)" }, { "agency": "Searle Scholars Program" }, { "agency": "Burroughs Wellcome Fund" } ] }, "doi": "10.1038/nature04588", "primary_object": { "basename": "41586_2006_BFnature04588_MOESM4_ESM.mov", "url": "https://authors.library.caltech.edu/records/gsagm-5zn04/files/41586_2006_BFnature04588_MOESM4_ESM.mov" }, "related_objects": [ { "basename": "41586_2006_BFnature04588_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/gsagm-5zn04/files/41586_2006_BFnature04588_MOESM1_ESM.pdf" }, { "basename": "41586_2006_BFnature04588_MOESM2_ESM.mov", "url": "https://authors.library.caltech.edu/records/gsagm-5zn04/files/41586_2006_BFnature04588_MOESM2_ESM.mov" }, { "basename": "41586_2006_BFnature04588_MOESM3_ESM.mov", "url": "https://authors.library.caltech.edu/records/gsagm-5zn04/files/41586_2006_BFnature04588_MOESM3_ESM.mov" } ], "resource_type": "article", "pub_year": "2006", "author_list": "S\u00fcel, G\u00fcrol M.; Garcia-Ojalvo, Jordi; et el." }, { "id": "https://authors.library.caltech.edu/records/csxa2-bn725", "eprint_id": 56061, "eprint_status": "archive", "datestamp": "2023-08-19 16:41:23", "lastmod": "2023-10-20 23:36:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sprinzak-D", "name": { "family": "Sprinzak", "given": "David" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Reconstruction of genetic circuits", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2015 Nature Publishing Group.\n\n24 November 2005.\n\nSynthetic biology work in the laboratory is supported by a Burroughs-Wellcome CASI award, The HFSP program and the Searle Scholars program. D.S. would like to acknowledge the support of the Yad Hanadiv Foundation and the CBCD at Caltech. We would like to thank J. W. Chin, C. Guet, S. Leibler, J. Liao, W. Lim, C. Smolke and R. Weiss for contributing figures. We are grateful to R. Kishony, E. Sprinzak, C. Dalal, G. Suel and members of the laboratory for discussions and comments.", "abstract": "The complex genetic circuits found in cells are ordinarily studied by analysis of genetic and biochemical perturbations. The inherent modularity of biological components like genes and proteins enables a complementary approach: one can construct and analyse synthetic genetic circuits based on their natural counterparts. Such synthetic circuits can be used as simple in vivo models to explore the relation between the structure and function of a genetic circuit. Here we describe recent progress in this area of synthetic biology, highlighting newly developed genetic components and biological lessons learned from this approach.", "date": "2005-11-24", "date_type": "published", "publication": "Nature", "volume": "438", "number": "7067", "publisher": "Nature Publishing Group", "pagerange": "443-448", "id_number": "CaltechAUTHORS:20150325-092313161", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150325-092313161", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1038/nature04335", "resource_type": "article", "pub_year": "2005", "author_list": "Sprinzak, David and Elowitz, Michael B." }, { "id": "https://authors.library.caltech.edu/records/8sxst-5nq97", "eprint_id": 55913, "eprint_status": "archive", "datestamp": "2023-08-19 16:25:27", "lastmod": "2023-10-20 23:24:40", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Eldar-A", "name": { "family": "Eldar", "given": "Avigdor" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael" }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Systems biology: Deviations in mating", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2005 Nature Publishing Group.", "abstract": "Why do cells of the same type, grown in the same conditions, look and behave so differently? Studying fluctuations in a well-characterized genetic pathway in yeast hints at how such variation arises.", "date": "2005-09-29", "date_type": "published", "publication": "Nature", "volume": "437", "number": "7059", "publisher": "Nature Publishing Group", "pagerange": "631-632", "id_number": "CaltechAUTHORS:20150319-083605488", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150319-083605488", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1038/437631a", "resource_type": "article", "pub_year": "2005", "author_list": "Eldar, Avigdor and Elowitz, Michael" }, { "id": "https://authors.library.caltech.edu/records/nhf6g-65r79", "eprint_id": 51874, "eprint_status": "archive", "datestamp": "2023-08-19 15:33:12", "lastmod": "2023-10-18 18:04:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Rosenfeld-N", "name": { "family": "Rosenfeld", "given": "Nitzan" } }, { "id": "Young-J-W", "name": { "family": "Young", "given": "Jonathan W." } }, { "id": "Alon-U", "name": { "family": "Alon", "given": "Uri" } }, { "id": "Swain-P-S", "name": { "family": "Swain", "given": "Peter S." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Gene Regulation at the Single-Cell Level", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2005 American Association for the Advancement of Science.\n\nReceived 29 October 2004; accepted 4 February 2005.\n\nWe thank Z. Ben-Haim, R. Clifford, S. Itzkovitz, Z.\nKam, R. Kishony, A. J. Levine, A. Mayo, R. Milo, R.\nPhillips, M. Ptashne, J. Shapiro, B. Shraiman, E. Siggia,\nand M. G. Surette for helpful discussions. M.B.E. is\nsupported by a CASI award from the Burroughs\nWellcome Fund, the Searle Scholars Program, and\nthe Seaver Institute. U.A. and M.B.E. are supported\nby the Human Frontiers Science Program. P.S.S.\nacknowledges support from a Tier II Canada Research\nChair and the Natural Sciences and Engineering\nResearch Council of Canada. N.R. dedicates\nthis work to the memory of his father, Yasha (Yaakov)\nRosenfeld.\n\nSupplemental Material - 1106914s1.mov
Supplemental Material - 1106914s2.mov
Supplemental Material - 1106914s3.mov
Supplemental Material - Rosenfeld.SOM.pdf
", "abstract": "The quantitative relation between transcription factor concentrations and the rate of protein production from downstream genes is central to the function of genetic networks. Here we show that this relation, which we call the gene regulation function (GRF), fluctuates dynamically in individual living cells, thereby limiting the accuracy with which transcriptional genetic circuits can transfer signals. Using fluorescent reporter genes and fusion proteins, we characterized the bacteriophage lambda promoter P_R in Escherichia coli. A novel technique based on binomial errors in protein partitioning enabled calibration of in vivo biochemical parameters in molecular units. We found that protein production rates fluctuate over a time scale of about one cell cycle, while intrinsic noise decays rapidly. Thus, biochemical parameters, noise, and slowly varying cellular states together determine the effective single-cell GRF. These results can form a basis for quantitative modeling of natural gene circuits and for design of synthetic ones.", "date": "2005-03-25", "date_type": "published", "publication": "Science", "volume": "307", "number": "5717", "publisher": "American Association for the Advancement of Science", "pagerange": "1962-1965", "id_number": "CaltechAUTHORS:20141117-154819881", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141117-154819881", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Burroughs Wellcome Fund" }, { "agency": "Searle Scholars Program" }, { "agency": "Seaver Institute" }, { "agency": "Human Frontier Science Program" }, { "agency": "Canada Research Chairs Program" }, { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)" } ] }, "doi": "10.1126/science.1106914", "primary_object": { "basename": "1106914s1.mov", "url": "https://authors.library.caltech.edu/records/nhf6g-65r79/files/1106914s1.mov" }, "related_objects": [ { "basename": "1106914s2.mov", "url": "https://authors.library.caltech.edu/records/nhf6g-65r79/files/1106914s2.mov" }, { "basename": "1106914s3.mov", "url": "https://authors.library.caltech.edu/records/nhf6g-65r79/files/1106914s3.mov" }, { "basename": "Rosenfeld.SOM.pdf", "url": "https://authors.library.caltech.edu/records/nhf6g-65r79/files/Rosenfeld.SOM.pdf" } ], "resource_type": "article", "pub_year": "2005", "author_list": "Rosenfeld, Nitzan; Young, Jonathan W.; et el." }, { "id": "https://authors.library.caltech.edu/records/0avf9-tz931", "eprint_id": 936, "eprint_status": "archive", "datestamp": "2023-08-22 02:12:14", "lastmod": "2023-10-13 22:03:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Garcia-Ojalvo-J", "name": { "family": "Garcia-Ojalvo", "given": "Jordi" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Strogatz-S-H", "name": { "family": "Strogatz", "given": "Steven H." } } ] }, "title": "Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing", "ispublished": "pub", "full_text_status": "public", "keywords": "CIRCADIAN CLOCK, SUPRACHIASMATIC NUCLEUS, SUSTAINED OSCILLATIONS, BIOLOGICAL RHYTHMS, EMERGING COHERENCE, TEMPORAL PRECISION, NOISE, NEURONS, GENE, SYNCHRONIZATION", "note": "\u00a9 2004 by the National Academy of Sciences. \n\nEdited by Charles S. Peskin, New York University, New York, NY, and approved June 7, 2004 (received for review October 31, 2003). \n\nJ.G.-O. is partially supported by the National Science Foundation Integrative Graduate Education and Research Traineeship Program on Nonlinear Systems (Cornell University), Ministerio de Educacion, Cultura y Deportes (Spain) Grant PR2003-0253, and Ministerio de Ciencia y Tecnolog\u0131a (Spain) and Fonds Europeen de Developpement Regional (European Union) Projects BFM2002-04369 and BFM2003-07850. M.B.E. acknowledges generous support from the Burroughs\u2013Wellcome Fund and the Seaver Institute. S.H.S. thanks the National Science Foundation for financial support. \n\nThis paper was submitted directly (Track II) to the PNAS office.\n\nPublished - GARpnas04.pdf
", "abstract": "Diverse biochemical rhythms are generated by thousands of cellular oscillators that somehow manage to operate synchronously. In fields ranging from circadian biology to endocrinology, it remains an exciting challenge to understand how collective rhythms emerge in multicellular structures. Using mathematical and computational modeling, we study the effect of coupling through intercell signaling in a population of Escherichia coli cells expressing a synthetic biological clock. Our results predict that a diverse and noisy community of such genetic oscillators interacting through a quorum-sensing mechanism should self-synchronize in a robust way, leading to a substantially improved global rhythmicity in the system. As such, the particular system of coupled genetic oscillators considered here might be a good candidate to provide the first quantitative example of a synchronization transition in a population of biological oscillators.", "date": "2004-07-27", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "101", "number": "30", "publisher": "National Academy of Sciences", "pagerange": "10955-10960", "id_number": "CaltechAUTHORS:GARpnas04", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:GARpnas04", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1073/pnas.0307095101", "pmcid": "PMC503725", "primary_object": { "basename": "GARpnas04.pdf", "url": "https://authors.library.caltech.edu/records/0avf9-tz931/files/GARpnas04.pdf" }, "resource_type": "article", "pub_year": "2004", "author_list": "Garcia-Ojalvo, Jordi; Elowitz, Michael B.; et el." }, { "id": "https://authors.library.caltech.edu/records/y35w4-qpj73", "eprint_id": 56468, "eprint_status": "archive", "datestamp": "2023-08-19 13:04:06", "lastmod": "2023-10-23 15:27:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lahav-Galit", "name": { "family": "Lahav", "given": "Galit" } }, { "id": "Rosenfeld-Nitzan", "name": { "family": "Rosenfeld", "given": "Nitzan" } }, { "id": "Sigal-Alex", "name": { "family": "Sigal", "given": "Alex" }, "orcid": "0000-0001-8571-2004" }, { "id": "Geva-Zatorsky-Naama", "name": { "family": "Geva-Zatorsky", "given": "Naama" } }, { "id": "Levine-A-J", "name": { "family": "Levine", "given": "Arnold J." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Alon-Uri", "name": { "family": "Alon", "given": "Uri" } } ] }, "title": "Dynamics of the p53-Mdm2 feedback loop in individual cells", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2004 Nature Publishing Group. Received 21 September; accepted 15 December 2003. Published online: 18 January 2004.\n\nWe thank M. Oren, D. Ginsberg and Z. Kam for help, reagents and discussions; L. Ben-Artzi and A. Lahav for assistance; and B. Geiger, Y. Liron, V. Rotter, C. Walsh and all members of our laboratory for discussions. We acknowledge support from the ISF, Minerva, Abisch-Frenkel, Harry M. Ringel and Mr. and Mrs. Mordechai Segal foundations and a David Aftalion postdoctoral fellowship to G.L. This work is dedicated to the memory of Yasha (Yaakov) Rosenfeld.", "abstract": "The tumor suppressor p53, one of the most intensely investigated proteins, is usually studied by experiments that are averaged over cell populations, potentially masking the dynamic behavior in individual cells. We present a system for following, in individual living cells, the dynamics of p53 and its negative regulator Mdm2 (refs. 1,4\u22127): this system uses functional p53-CFP and Mdm2-YFP fusion proteins and time-lapse fluorescence microscopy. We found that p53 was expressed in a series of discrete pulses after DNA damage. Genetically identical cells had different numbers of pulses: zero, one, two or more. The mean height and duration of each pulse were fixed and did not depend on the amount of DNA damage. The mean number of pulses, however, increased with DNA damage. This approach can be used to study other signaling systems and suggests that the p53-Mdm2 feedback loop generates a 'digital' clock that releases well-timed quanta of p53 until damage is repaired or the cell dies.", "date": "2004-02", "date_type": "published", "publication": "Nature Genetics", "volume": "36", "number": "2", "publisher": "Nature Publishing Group", "pagerange": "147-150", "id_number": "CaltechAUTHORS:20150408-095048891", "issn": "1061-4036", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150408-095048891", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Israel Science Foundation" }, { "agency": "Minerva" }, { "agency": "Abisch-Frenkel" }, { "agency": "Harry M. Ringel Foundation" }, { "agency": "Mr. and Mrs. Mordechai Segal Foundation" }, { "agency": "David Aftalion postdoctoral fellowship" } ] }, "doi": "10.1038/ng1293", "resource_type": "article", "pub_year": "2004", "author_list": "Lahav, Galit; Rosenfeld, Nitzan; et el." }, { "id": "https://authors.library.caltech.edu/records/fcbtb-xyh19", "eprint_id": 1471, "eprint_status": "archive", "datestamp": "2023-08-22 00:57:51", "lastmod": "2023-10-13 22:50:04", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Overholtzer-M", "name": { "family": "Overholtzer", "given": "Michael" } }, { "id": "Rao-P-H", "name": { "family": "Rao", "given": "Pulivarthi H." } }, { "id": "Favis-R", "name": { "family": "Favis", "given": "Reyna" } }, { "id": "Lu-Xin-Yan", "name": { "family": "Lu", "given": "Xin-Yan" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Barany-F", "name": { "family": "Barany", "given": "Francis" } }, { "id": "Ladanyi-M", "name": { "family": "Ladanyi", "given": "Marc" } }, { "id": "Gorlick-R", "name": { "family": "Gorlick", "given": "Richard" } }, { "id": "Levine-A-J", "name": { "family": "Levine", "given": "Arnold J." } } ] }, "title": "The presence of p53 mutations in human osteosarcomas correlates with high levels of genomic instability", "ispublished": "pub", "full_text_status": "public", "keywords": "WILD-TYPE P53; POLYMERASE-CHAIN-REACTION; GENE AMPLIFICATION; TUMOR-SUPPRESSOR; HOMOLOGOUS RECOMBINATION; FRAUMENI-SYNDROME; MDM-2 ONCOGENE; BLADDER-CANCER; CELL CARCINOMA; MICE", "note": "\u00a9 2003 by the National Academy of Sciences. \n\nContributed by Arnold J. Levine, July 31, 2003. \n\nPublished online before print September 12, 2003, 10.1073/pnas.1934852100. \n\nWe thank members of the Levine Laboratory for helpful discussions, especially Drs. Kenan Onel, Archontoula Stoffel, Shengkan Jin, and Gareth Bond and Christine Walsh.\n\nPublished - OVEpnas03.pdf
", "abstract": "The p53 gene is a critical tumor suppressor that is inactivated in a majority of cancers. The central role of p53 in response to stresses such as DNA damage, hypoxia, and oncogene activation underlies this high frequency of negative selection during tumorigenic transformation. Mutations in p53 disrupt checkpoint responses to DNA damage and result in the potential for destabilization of the genome. Consistent with this, p53 mutant cells have been shown to accumulate genomic alterations in cell culture, mouse models, and some human tumors. The relationship between p53 mutation and genomic instability in human osteosarcoma is addressed in this report. Similar to some other primary human tumors, the mutation of p53 correlates significantly with the presence of high levels of genomic instability in osteosarcomas. Surprisingly, osteosarcomas harboring an amplification of the HDM2 oncogene, which inhibits the tumor-suppressive properties of p53, do not display high levels of genomic instability. These results demonstrate that the inactivation of p53 in osteosarcomas directly by mutation versus indirectly by HDM2 amplification may have different cellular consequences with respect to the stability of the genome.", "date": "2003-09-30", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "100", "number": "20", "publisher": "National Academy of Sciences", "pagerange": "11547-11552", "id_number": "CaltechAUTHORS:OVEpnas03", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:OVEpnas03", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1073/pnas.1934852100", "pmcid": "PMC208795", "primary_object": { "basename": "OVEpnas03.pdf", "url": "https://authors.library.caltech.edu/records/fcbtb-xyh19/files/OVEpnas03.pdf" }, "resource_type": "article", "pub_year": "2003", "author_list": "Overholtzer, Michael; Rao, Pulivarthi H.; et el." }, { "id": "https://authors.library.caltech.edu/records/fvem5-cka33", "eprint_id": 102878, "eprint_status": "archive", "datestamp": "2023-08-21 23:51:45", "lastmod": "2023-10-20 00:35:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Rosenfeld-N", "name": { "family": "Rosenfeld", "given": "Nitzan" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Alon-U", "name": { "family": "Alon", "given": "Uri" } } ] }, "title": "Negative Autoregulation Speeds the Response Times of Transcription Networks", "ispublished": "pub", "full_text_status": "restricted", "keywords": "autogenous control; biophysics; design principles; feedback kinetics; systems-biology", "note": "\u00a9 2002 Elsevier Science Ltd. \n\nReceived 9 May 2002, Revised 2 September 2002, Accepted 7 September 2002, Available online 29 October 2002. \n\nWe thank A. Becskei, L. Serrano, R. Lutz and H. Bujard for plasmids. We thank P. Bashkin for assistance. We thank N. Barkai for illuminating discussions and suggestions. We thank M. Surette, S. Leibler, O. Stock, A. Levine and all members of our laboratory for discussions. This work was supported by the Israel Science Foundation, the Human Frontiers Science Project and the Minerva foundation. M.E. is supported by the Seaver institute and the Burroughs-Wellcome Fund. N.R. dedicates this work to the memory of his father, Yasha Rosenfeld.", "abstract": "Cells regulate gene expression using networks of transcription interactions; it is of interest to discover the principles that govern the dynamical behavior of such networks. An important characteristic of these systems is the rise-time: the delay from the initiation of production until half maximal product concentration is reached. Here we employ synthetic gene circuits in Escherichia coli to measure the rise-times of non-self-regulated and of negatively autoregulated transcription units. Non-self-regulated units have a rise-time of one cell-cycle. We demonstrate experimentally that negative autoregulation feedback (also termed autogenous control) reduces the rise-time to about one fifth of a cell-cycle. This agrees with an analytical solution of a mathematical model for negative autoregulation. This may help in understanding the function of negative autoregulation, which appears in over 40% of known transcription factors in E. coli.", "date": "2002-11-08", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "323", "number": "5", "publisher": "Elsevier", "pagerange": "785-793", "id_number": "CaltechAUTHORS:20200428-124412749", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200428-124412749", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Israel Science Foundation" }, { "agency": "Human Frontier Science Program" }, { "agency": "Minerva Foundation" }, { "agency": "Seaver Institute" }, { "agency": "Burroughs-Wellcome Fund" } ] }, "doi": "10.1016/s0022-2836(02)00994-4", "resource_type": "article", "pub_year": "2002", "author_list": "Rosenfeld, Nitzan; Elowitz, Michael B.; et el." }, { "id": "https://authors.library.caltech.edu/records/z0ctt-h4446", "eprint_id": 1494, "eprint_status": "archive", "datestamp": "2023-08-21 23:46:20", "lastmod": "2023-10-13 22:50:46", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Swain-P-S", "name": { "family": "Swain", "given": "Peter S." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Siggia-E-D", "name": { "family": "Siggia", "given": "Eric D." } } ] }, "title": "Intrinsic and extrinsic contributions to stochasticity in gene expression", "ispublished": "pub", "full_text_status": "public", "keywords": "Escherichia-coli; noise; transcription; fluctuations; simulation; networks; model; cell", "note": "\u00a9 2002 by the National Academy of Sciences. \n\nEdited by Robert H. Austin, Princeton University, Princeton, NJ, and approved June 17, 2002 (received for review January 23, 2002). Published online before print September 17, 2002, 10.1073/pnas.162041399. \n\nWe are grateful for conversations with S. Bekiranov, A. J. Levine, J. Paulsson, N. Rajewsky, B. Shraiman, N. Socci, and M. Zapotocky. P.S.S., M.B.E., and E.D.S. acknowledge support from the National Institutes of Health (GM59018), the Seaver Institute and Burroughs-Wellcome Fund, and the National Science Foundation (DMR0129848), respectively. This paper was submitted directly (Track II) to the PNAS office.\n\nPublished - SWApnas02.pdf
", "abstract": "Gene expression is a stochastic, or \"noisy,\" process. This noise comes about in two ways. The inherent stochasticity of biochemical processes such as transcription and translation generates \"intrinsic\" noise. In addition, fluctuations in the amounts or states of other cellular components lead indirectly to variation in the expression of a particular gene and thus represent \"extrinsic\" noise. Here, we show how the total variation in the level of expression of a given gene can be decomposed into its intrinsic and extrinsic components. We demonstrate theoretically that simultaneous measurement of two identical genes per cell enables discrimination of these two types of noise. Analytic expressions for intrinsic noise are given for a model that involves all the major steps in transcription and translation. These expressions give the sensitivity to various parameters, quantify the deviation from Poisson statistics, and provide a way of fitting experiment. Transcription dominates the intrinsic noise when the average number of proteins made per mRNA transcript is greater than similar or equal to 2. Below this number, translational effects also become important. Gene replication and cell division, included in the model, cause protein numbers to tend to a limit cycle. We calculate a general form for the extrinsic noise and illustrate it with the particular case of a single fluctuating extrinsic variable-a repressor protein, which acts on the gene of interest. All results are confirmed by stochastic simulation using plausible parameters for Escherichia coli.", "date": "2002-10-01", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "99", "number": "20", "publisher": "National Academy of Sciences", "pagerange": "12795-12800", "id_number": "CaltechAUTHORS:SWApnas02", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:SWApnas02", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1073/pnas.162041399", "pmcid": "PMC130539", "primary_object": { "basename": "SWApnas02.pdf", "url": "https://authors.library.caltech.edu/records/z0ctt-h4446/files/SWApnas02.pdf" }, "resource_type": "article", "pub_year": "2002", "author_list": "Swain, Peter S.; Elowitz, Michael B.; et el." }, { "id": "https://authors.library.caltech.edu/records/wsymf-b6c81", "eprint_id": 102879, "eprint_status": "archive", "datestamp": "2023-08-19 09:56:38", "lastmod": "2023-10-20 00:35:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Levine-A-J", "name": { "family": "Levine", "given": "Arnold J." } }, { "id": "Siggia-E-D", "name": { "family": "Siggia", "given": "Eric D." }, "orcid": "0000-0001-7482-1854" }, { "id": "Swain-P-S", "name": { "family": "Swain", "given": "Peter S." } } ] }, "title": "Stochastic Gene Expression in a Single Cell", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2002 American Association for the Advancement of Science. \n\nReceived 14 February 2002; accepted 13 June 2002. \n\nWe thank U. Alon, S. Bekiranov, J. Dworkin, D. Endy, C. Guet, R. Kishony, S. Leibler, D. O'Carroll, N. Rajewsky, B. Shraiman, D. Thaler, and especially M. G. Surette for conversations and suggestions; A. Teresky and the Levine Lab for help; and J. Paulsson for his suggestion about the extrinsic noise profile. Recombination-proficient strains were provided by D. Court. Supported by the Burroughs-Wellcome Fund and the Seaver Institute (M.B.E.) and by NIH grant GM59018 (P.S.S.).\n\nSupplemental Material - ElowitzSOM.pdf
", "abstract": "Clonal populations of cells exhibit substantial phenotypic variation. Such heterogeneity can be essential for many biological processes and is conjectured to arise from stochasticity, or noise, in gene expression. We constructed strains of Escherichia coli that enable detection of noise and discrimination between the two mechanisms by which it is generated. Both stochasticity inherent in the biochemical process of gene expression (intrinsic noise) and fluctuations in other cellular components (extrinsic noise) contribute substantially to overall variation. Transcription rate, regulatory dynamics, and genetic factors control the amplitude of noise. These results establish a quantitative foundation for modeling noise in genetic networks and reveal how low intracellular copy numbers of molecules can fundamentally limit the precision of gene regulation.", "date": "2002-08-16", "date_type": "published", "publication": "Science", "volume": "297", "number": "5584", "publisher": "American Association for the Advancement of Science", "pagerange": "1183-1186", "id_number": "CaltechAUTHORS:20200428-125210088", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200428-125210088", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Burroughs Wellcome Fund" }, { "agency": "Seaver Institute" }, { "agency": "NIH", "grant_number": "GM59018" } ] }, "doi": "10.1126/science.1070919", "primary_object": { "basename": "ElowitzSOM.pdf", "url": "https://authors.library.caltech.edu/records/wsymf-b6c81/files/ElowitzSOM.pdf" }, "resource_type": "article", "pub_year": "2002", "author_list": "Elowitz, Michael B.; Levine, Arnold J.; et el." }, { "id": "https://authors.library.caltech.edu/records/cvgm2-s3h66", "eprint_id": 102880, "eprint_status": "archive", "datestamp": "2023-08-19 05:18:16", "lastmod": "2023-10-20 00:35:32", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Leibler-S", "name": { "family": "Leibler", "given": "Stanislas" } } ] }, "title": "A synthetic oscillatory network of transcriptional regulators", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2000 Nature Publishing Group. \n\nReceived 06 July 1999; Accepted 09 November 1999; Issue Date 20 January 2000. \n\nWe thank H. Bujard, S. Freundlieb, A. Hochschild, R. Lutz and C. Sternberg for plasmids and advice; U. Alon, N. Barkai, P. Cluzel, L. Frisen, C. Guet, T. Hyman, R. Kishony, A. Jaedicke, P. Lopez, F. N\u00e9d\u00e9lec, S. Pichler, R. Kishony, T. Silhavy, T. Surrey, J. Vilar, C. Wiggins and E. Winfree for discussions; M. Surette for advice and encouragement; L. Hartwell and C. Weitz for comments on the manuscript; and F. Kafatos and E. Karsenti for hospitality and support at the European Molecular Biology Laboratory (EMBL), where part of this work was done. This work was partly supported by the US National Institutes of Health and the von Humboldt Foundation.", "abstract": "Networks of interacting biomolecules carry out many essential functions in living cells, but the 'design principles' underlying the functioning of such intracellular networks remain poorly understood, despite intensive efforts including quantitative analysis of relatively simple systems. Here we present a complementary approach to this problem: the design and construction of a synthetic network to implement a particular function. We used three transcriptional repressor systems that are not part of any natural biological clock to build an oscillating network, termed the repressilator, in Escherichia coli. The network periodically induces the synthesis of green fluorescent protein as a readout of its state in individual cells. The resulting oscillations, with typical periods of hours, are slower than the cell-division cycle, so the state of the oscillator has to be transmitted from generation to generation. This artificial clock displays noisy behaviour, possibly because of stochastic fluctuations of its components. Such 'rational network design' may lead both to the engineering of new cellular behaviours and to an improved understanding of naturally occurring networks.", "date": "2000-01-20", "date_type": "published", "publication": "Nature", "volume": "403", "number": "6767", "publisher": "Nature Publishing Group", "pagerange": "335-338", "id_number": "CaltechAUTHORS:20200428-131623929", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200428-131623929", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Alexander von Humboldt Foundation" } ] }, "doi": "10.1038/35002125", "resource_type": "article", "pub_year": "2000", "author_list": "Elowitz, Michael B. and Leibler, Stanislas" }, { "id": "https://authors.library.caltech.edu/records/7qfgc-q5698", "eprint_id": 7094, "eprint_status": "archive", "datestamp": "2023-08-22 13:28:13", "lastmod": "2023-10-23 19:29:14", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Surette-M-G", "name": { "family": "Surette", "given": "Michael G." } }, { "id": "Wolf-P-E", "name": { "family": "Wolf", "given": "Pierre-Etienne" } }, { "id": "Stock-J-B", "name": { "family": "Stock", "given": "Jeffrey B." } }, { "id": "Leibler-S", "name": { "family": "Leibler", "given": "Stanislas" } } ] }, "title": "Protein Mobility in the Cytoplasm of Escherichia coli", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1999, American Society for Microbiology. \n\nReceived 7 August 1998/Accepted 21 October 1998. \n\nWe thank B. Aguera y Arcas, U. Alon, T. Holy, and A. C. Maggs for help with data analysis and software. We also thank U. Alon, P. Cluzel, L. Frisen, P. Lopez, and T. Surrey for critical reading of the manuscript. We are grateful to B. P. Cormack for providing GFP mutants.\n\nPublished - ELOjbact99.pdf
Supplemental Material - ELOjbact99fig1.jpg
Supplemental Material - ELOjbact99fig2.jpg
Supplemental Material - ELOjbact99fig3.jpg
Supplemental Material - ELOjbact99fig4.jpg
Supplemental Material - ELOjbact99fig5.jpg
", "abstract": "The rate of protein diffusion in bacterial cytoplasm may constrain a variety of cellular functions and limit the rates of many biochemical reactions in vivo. In this paper, we report noninvasive measurements of the apparent diffusion coefficient of green fluorescent protein (GFP) in the cytoplasm of Escherichia coli. These measurements were made in two ways: by photobleaching of GFP fluorescence and by photoactivation of a red-emitting fluorescent state of GFP (M. B. Elowitz, M. G. Surette, P. E. Wolf, J. Stock, and S. Leibler, Curr. Biol. 7:809-812, 1997). The apparent diffusion coefficient, Da, of GFP in E. coli DH5alpha was found to be 7.7 \u00b1 2.5 \u00b5m^2/s. A 72-kDa fusion protein composed of GFP and a cytoplasmically localized maltose binding protein domain moves more slowly, with Da of 2.5 \u00b1 0.6 \u00b5m^2/s. In addition, GFP mobility can depend strongly on at least two factors: first, Da is reduced to 3.6 \u00b1 0.7 \u00b5m^2/s at high levels of GFP expression; second, the addition to GFP of a small tag consisting of six histidine residues reduces Da to 4.0 \u00b1 2.0 \u00b5m^2/s. Thus, a single effective cytoplasmic viscosity cannot explain all values of Da reported here. These measurements have implications for the understanding of intracellular biochemical networks.", "date": "1999-01", "date_type": "published", "publication": "Journal of Bacteriology", "volume": "181", "number": "1", "publisher": "American Society for Microbiology", "pagerange": "197-203", "id_number": "CaltechAUTHORS:ELOjbact99", "issn": "0021-9193", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:ELOjbact99", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "pmcid": "PMC103549", "primary_object": { "basename": "medium.png", "url": "https://authors.library.caltech.edu/records/7qfgc-q5698/files/medium.png" }, "related_objects": [ { "basename": "small.png", "url": "https://authors.library.caltech.edu/records/7qfgc-q5698/files/small.png" }, { "basename": "ELOjbact99.pdf", "url": "https://authors.library.caltech.edu/records/7qfgc-q5698/files/ELOjbact99.pdf" }, { "basename": "ELOjbact99fig1.jpg", "url": "https://authors.library.caltech.edu/records/7qfgc-q5698/files/ELOjbact99fig1.jpg" }, { "basename": "ELOjbact99fig2.jpg", "url": "https://authors.library.caltech.edu/records/7qfgc-q5698/files/ELOjbact99fig2.jpg" }, { "basename": "ELOjbact99fig3.jpg", "url": "https://authors.library.caltech.edu/records/7qfgc-q5698/files/ELOjbact99fig3.jpg" }, { "basename": "ELOjbact99fig4.jpg", "url": "https://authors.library.caltech.edu/records/7qfgc-q5698/files/ELOjbact99fig4.jpg" }, { "basename": "ELOjbact99fig5.jpg", "url": "https://authors.library.caltech.edu/records/7qfgc-q5698/files/ELOjbact99fig5.jpg" } ], "resource_type": "article", "pub_year": "1999", "author_list": "Elowitz, Michael B.; Surette, Michael G.; et el." }, { "id": "https://authors.library.caltech.edu/records/4f4p8-92f20", "eprint_id": 1468, "eprint_status": "archive", "datestamp": "2023-08-22 12:45:44", "lastmod": "2023-10-23 17:44:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Surrey-T", "name": { "family": "Surrey", "given": "Thomas" } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Wolf-P-E", "name": { "family": "Wolf", "given": "Pierre-Etienne" } }, { "id": "Yang-Feng", "name": { "family": "Yang", "given": "Feng" } }, { "id": "N\u00e9d\u00e9lec-F", "name": { "family": "N\u00e9d\u00e9lec", "given": "Fran\u00e7ois" } }, { "id": "Shokat-K", "name": { "family": "Shokat", "given": "Kevan" } }, { "id": "Leibler-S", "name": { "family": "Leibler", "given": "Stanislas" } } ] }, "title": "Chromophore-assisted light inactivation and self-organization of microtubules and motors", "ispublished": "pub", "full_text_status": "public", "keywords": "GREEN FLUORESCENT PROTEIN; LASER INACTIVATION; GENE-EXPRESSION; GROWTH CONE; KINESIN; CHROMOSOMES", "note": "\u00a9 1998 by the National Academy of Sciences. \n\nCommunicated by Kai Simons, European Molecular Biology Laboratory, Heidelberg, Germany, December 29, 1997 (received for review December 9, 1997).\n \nWe thank Jeff Gelles for plasmid pEY4, Mark Rose for plasmid pGTEPI, Brendan Cormack for GFP mutants, and Jill Johnson for taxol. We also thank Joseph Forkey for running the pulsed laser apparatus and Jerome Zawadsky and Bob Austin for help in the cw laser experiments. We acknowledge Martha Fonseca for preparing C12A5 cell culture supernatants. The partial support of the National Institutes of Health, the National Science Foundation, and the Human Frontier Science Program Organization is gratefully acknowledged. T.S.'s research was also supported by the Deutsche Forschungsgemeinschaft. \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 - SURpnas98.pdf
", "abstract": "Chromophore assisted light inactivation (CALI) offers the only method capable of modulating specific protein activities in localized regions and at particular times. Here, we generalize CALI so that it can be applied to a wider range of tasks. Specifically, we show that CALI can work with a genetically inserted epitope tag; we investigate the effectiveness of alternative dyes, especially fluorescein, comparing them with the standard CALI dye, malachite green; and we study the relative efficiencies of pulsed and continuous-wave illumination. We then use fluorescein-labeled hemagglutinin antibody fragments, together with relatively low-power continuous-wave illumination to examine the effectiveness of CALI targeted to kinesin. We show that CALI can destroy kinesin activity in at least two ways: it can either result in the apparent loss of motor activity, or it can cause irreversible attachment of the kinesin enzyme to its microtubule substrate. Finally, we apply this implementation of CALI to an in vine system of motor proteins and microtubules that is capable of self-organized aster formation. In this system, CALI can effectively perturb local structure formation by blocking or reducing the degree of aster formation in chosen regions of the sample, without influencing structure formation elsewhere.", "date": "1998-04-14", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "95", "number": "8", "publisher": "National Academy of Sciences", "pagerange": "4293-4298", "id_number": "CaltechAUTHORS:SURpnas98", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:SURpnas98", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "NSF" }, { "agency": "Human Frontier Science Program" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)" } ] }, "pmcid": "PMC22482", "primary_object": { "basename": "SURpnas98.pdf", "url": "https://authors.library.caltech.edu/records/4f4p8-92f20/files/SURpnas98.pdf" }, "resource_type": "article", "pub_year": "1998", "author_list": "Surrey, Thomas; Elowitz, Michael B.; et el." }, { "id": "https://authors.library.caltech.edu/records/84cwa-xr056", "eprint_id": 102881, "eprint_status": "archive", "datestamp": "2023-08-19 01:53:58", "lastmod": "2023-10-20 00:35:36", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Surette-M-G", "name": { "family": "Surette", "given": "Michael G." } }, { "id": "Wolf-P-E", "name": { "family": "Wolf", "given": "Pierre-Etienne" } }, { "id": "Stock-J-B", "name": { "family": "Stock", "given": "Jeff" } }, { "id": "Leibler-S", "name": { "family": "Leibler", "given": "Stanislas" } } ] }, "title": "Photoactivation turns green fluorescent protein red", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1997 Elsevier Science Ltd. \n\nReceived 2 July 1997, Revised 25 July 1997, Accepted 8 August 1997, Available online 10 April 2004. \n\nWe are grateful to Hannah R. Morris and Patrick J. Treado for generous assistance with spectral imaging; to Lotti Frisen for help photoactivating yeast; to Andrew Beavis and Jerome Zawadski for assistance with lasers; to R. Tsien and B. Cormack for providing GFP mutants; and to Philippe Cluzel, Lotti Frisen, Andrew Murray, Kevan Shokat, Thomas Surrey, and Feng Yang for helpful discussions and encouragement. This work has been partially supported by grants from the N.I.H., the N.S.F., and the H.F.S.P. (to S.L.).", "abstract": "In the few years since its gene was first cloned, the Aequorea victoria green fluorescent protein (GFP) has become a powerful tool in cell biology, functioning as a marker for gene expression, protein localization and protein dynamics in living cells [1], [2], [3]. GFP variants with improved fluorescence intensity and altered spectral characteristics have been identified, but additional GFP variants are still desirable for multiple labeling experiments, protein interaction studies and improved visibility in some organisms [4]. In particular, long-wavelength (red) fluorescence has remained elusive. Here we describe a red-emitting, green-absorbing fluorescent state of GFP that is generated by photoactivation with blue light. GFP can be switched to its red-emitting state easily with a laser or fluorescence microscope lamp under conditions of low oxygen concentration. This previously unnoticed ability enables regional, non-invasive marking of proteins in vivo. In particular, we report here the use of GFP photoactivation to make the first direct measurements of protein diffusion in the cytoplasm of living bacteria.", "date": "1997-10", "date_type": "published", "publication": "Current Biology", "volume": "7", "number": "10", "publisher": "Cell Press", "pagerange": "809-812", "id_number": "CaltechAUTHORS:20200428-133426011", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200428-133426011", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "NSF" }, { "agency": "Human Frontier Science Program" } ] }, "collection": "CaltechAUTHORS", "doi": "10.1016/s0960-9822(06)00342-3", "resource_type": "article", "pub_year": "1997", "author_list": "Elowitz, Michael B.; Surette, Michael G.; et el." }, { "id": "https://authors.library.caltech.edu/records/19eyv-qe119", "eprint_id": 8915, "eprint_status": "archive", "datestamp": "2023-08-22 10:31:35", "lastmod": "2023-10-16 21:48:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bourdieu-L", "name": { "family": "Bourdieu", "given": "L." } }, { "id": "Duke-T", "name": { "family": "Duke", "given": "T." } }, { "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "M. B." }, "orcid": "0000-0002-1221-0967" }, { "id": "Winkelmann-D-A", "name": { "family": "Winkelmann", "given": "D. A." } }, { "id": "Leibler-S", "name": { "family": "Leibler", "given": "S." } }, { "id": "Libchaber-A", "name": { "family": "Libchaber", "given": "A." } } ] }, "title": "Spiral Defects in Motility Assays: A Measure of Motor Protein Force", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1995 The American Physical Society. \n\nReceived 30 January 1995. \n\nThis work is supported by NSF Grant No. PHY-9408905. Partial support of NIH (Grant No. GM-50712) and HSFP is also acknowledged. We thank J. Howard for discussions and for providing us with purified kinesin, T.E. Holy for his contribution to the numerical simulation, and A. Ott for this contribution to the actin myosin experimental setup.\n\nPublished - BOUprl95.pdf
", "abstract": "In a commonly used motility assay, cytoskeletal filaments are observed as they glide over a surface coated with motor proteins. Defects in the motion frequently interrupt the flow of filaments. Examination of one such defect, in which a filament adopts a spiral form and rotates about a fixed point, provides a simple measure of the force exerted by the motor proteins. We demonstrate the universality of this approach by estimating the elementary forces of both myosin and kinesin.", "date": "1995-07-03", "date_type": "published", "publication": "Physical Review Letters", "volume": "75", "number": "1", "publisher": "American Physical Society", "pagerange": "176-179", "id_number": "CaltechAUTHORS:BOUprl95", "issn": "0031-9007", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:BOUprl95", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "PHY-9408905" }, { "agency": "NIH", "grant_number": "GM-50712" }, { "agency": "Human Frontier Science Program" } ] }, "doi": "10.1103/PhysRevLett.75.176", "primary_object": { "basename": "BOUprl95.pdf", "url": "https://authors.library.caltech.edu/records/19eyv-qe119/files/BOUprl95.pdf" }, "resource_type": "article", "pub_year": "1995", "author_list": "Bourdieu, L.; Duke, T.; et el." } ]