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  • *Gene Regulatory Networks  (2)
  • American Association for the Advancement of Science (AAAS)  (2)
  • Blackwell Science Ltd
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Publisher
  • American Association for the Advancement of Science (AAAS)  (2)
  • Blackwell Science Ltd
Years
  • 1
    Publication Date: 2014-04-12
    Description: Genome-wide characterization of the in vivo cellular response to perturbation is fundamental to understanding how cells survive stress. Identifying the proteins and pathways perturbed by small molecules affects biology and medicine by revealing the mechanisms of drug action. We used a yeast chemogenomics platform that quantifies the requirement for each gene for resistance to a compound in vivo to profile 3250 small molecules in a systematic and unbiased manner. We identified 317 compounds that specifically perturb the function of 121 genes and characterized the mechanism of specific compounds. Global analysis revealed that the cellular response to small molecules is limited and described by a network of 45 major chemogenomic signatures. Our results provide a resource for the discovery of functional interactions among genes, chemicals, and biological processes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4254748/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4254748/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Anna Y -- St Onge, Robert P -- Proctor, Michael J -- Wallace, Iain M -- Nile, Aaron H -- Spagnuolo, Paul A -- Jitkova, Yulia -- Gronda, Marcela -- Wu, Yan -- Kim, Moshe K -- Cheung-Ong, Kahlin -- Torres, Nikko P -- Spear, Eric D -- Han, Mitchell K L -- Schlecht, Ulrich -- Suresh, Sundari -- Duby, Geoffrey -- Heisler, Lawrence E -- Surendra, Anuradha -- Fung, Eula -- Urbanus, Malene L -- Gebbia, Marinella -- Lissina, Elena -- Miranda, Molly -- Chiang, Jennifer H -- Aparicio, Ana Maria -- Zeghouf, Mahel -- Davis, Ronald W -- Cherfils, Jacqueline -- Boutry, Marc -- Kaiser, Chris A -- Cummins, Carolyn L -- Trimble, William S -- Brown, Grant W -- Schimmer, Aaron D -- Bankaitis, Vytas A -- Nislow, Corey -- Bader, Gary D -- Giaever, Guri -- GM103504/GM/NIGMS NIH HHS/ -- GM44530/GM/NIGMS NIH HHS/ -- MOP-700724/Canadian Institutes of Health Research/Canada -- MOP-79368/Canadian Institutes of Health Research/Canada -- MOP-81340/Canadian Institutes of Health Research/Canada -- P01 HG000205/HG/NHGRI NIH HHS/ -- P41 GM103504/GM/NIGMS NIH HHS/ -- R01 003317-07/PHS HHS/ -- R01 CA157456/CA/NCI NIH HHS/ -- R01 GM044530/GM/NIGMS NIH HHS/ -- R01 HG003317/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2014 Apr 11;344(6180):208-11. doi: 10.1126/science.1250217.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24723613" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line, Tumor ; Cells/*drug effects ; Drug Evaluation, Preclinical/*methods ; Drug Resistance/*genetics ; *Gene Regulatory Networks ; Genome-Wide Association Study/*methods ; Haploinsufficiency ; Humans ; Pharmacogenetics ; Saccharomyces cerevisiae/drug effects/genetics ; Small Molecule Libraries/*pharmacology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2015-09-01
    Description: A challenge of synthetic biology is the creation of cooperative microbial systems that exhibit population-level behaviors. Such systems use cellular signaling mechanisms to regulate gene expression across multiple cell types. We describe the construction of a synthetic microbial consortium consisting of two distinct cell types-an "activator" strain and a "repressor" strain. These strains produced two orthogonal cell-signaling molecules that regulate gene expression within a synthetic circuit spanning both strains. The two strains generated emergent, population-level oscillations only when cultured together. Certain network topologies of the two-strain circuit were better at maintaining robust oscillations than others. The ability to program population-level dynamics through the genetic engineering of multiple cooperative strains points the way toward engineering complex synthetic tissues and organs with multiple cell types.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4597888/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4597888/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Ye -- Kim, Jae Kyoung -- Hirning, Andrew J -- Josic, Kresimir -- Bennett, Matthew R -- R01 GM104974/GM/NIGMS NIH HHS/ -- R01GM104974/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 Aug 28;349(6251):986-9. doi: 10.1126/science.aaa3794.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biosciences, Rice University, Houston, TX 77005, USA. ; Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea. Mathematical Biosciences Institute, The Ohio State University, Columbus, OH 43210, USA. ; Department of Mathematics, University of Houston, Houston, TX 77204, USA. Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA. ; Department of Biosciences, Rice University, Houston, TX 77005, USA. Institute of Biosciences and Bioengineering, Rice University, Houston, TX 77005, USA. matthew.bennett@rice.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26315440" target="_blank"〉PubMed〈/a〉
    Keywords: 4-Butyrolactone/analogs & derivatives/metabolism ; Escherichia coli/*genetics/*physiology ; Escherichia coli Proteins/genetics/metabolism ; Feedback, Physiological ; *Gene Expression Regulation, Bacterial ; *Gene Regulatory Networks ; Genetic Engineering ; Lab-On-A-Chip Devices ; Microbial Consortia/*genetics/*physiology ; Microbial Interactions ; Models, Biological ; Promoter Regions, Genetic ; Quorum Sensing ; Signal Transduction ; Synthetic Biology ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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