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  • 1
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    A genomic regulatory network for development (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-03-02
    Description: Development of the body plan is controlled by large networks of regulatory genes. A gene regulatory network that controls the specification of endoderm and mesoderm in the sea urchin embryo is summarized here. The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory analysis, and molecular embryology. The network contains over 40 genes at present, and each node can be directly verified at the DNA sequence level by cis-regulatory analysis. Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Davidson, Eric H -- Rast, Jonathan P -- Oliveri, Paola -- Ransick, Andrew -- Calestani, Cristina -- Yuh, Chiou-Hwa -- Minokawa, Takuya -- Amore, Gabriele -- Hinman, Veronica -- Arenas-Mena, Cesar -- Otim, Ochan -- Brown, C Titus -- Livi, Carolina B -- Lee, Pei Yun -- Revilla, Roger -- Rust, Alistair G -- Pan, Zheng jun -- Schilstra, Maria J -- Clarke, Peter J C -- Arnone, Maria I -- Rowen, Lee -- Cameron, R Andrew -- McClay, David R -- Hood, Leroy -- Bolouri, Hamid -- GM-61005/GM/NIGMS NIH HHS/ -- HD-37105/HD/NICHD NIH HHS/ -- RR-06591/RR/NCRR NIH HHS/ -- RR-15044/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2002 Mar 1;295(5560):1669-78.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA. davidson@caltech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11872831" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Lineage ; Computational Biology ; Embryonic Development ; Endoderm/cytology/*physiology ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; Genes, Regulator ; *Genome ; Mesoderm/cytology/*physiology ; Models, Biological ; Models, Genetic ; Morphogenesis ; Regulatory Sequences, Nucleic Acid ; Sea Urchins/*embryology/*genetics ; Stem Cells/physiology ; Systems Theory
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Ordered phosphorylation governs oscillation of a three-protein circadian clock (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-06
    Description: The simple circadian oscillator found in cyanobacteria can be reconstituted in vitro using three proteins-KaiA, KaiB, and KaiC. The total phosphorylation level of KaiC oscillates with a circadian period, but the mechanism underlying its sustained oscillation remains unclear. We have shown that four forms of KaiC differing in their phosphorylation state appear in an ordered pattern arising from the intrinsic autokinase and autophosphatase rates of KaiC and their modulation by KaiA. Kinetic and biochemical data indicate that one of these phosphoforms inhibits the activity of KaiA through interaction with KaiB, providing the crucial feedback that sustains oscillation. A mathematical model constrained by experimental data quantitatively reproduces the circadian period and the distinctive dynamics of the four phosphoforms.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2427396/" 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/PMC2427396/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rust, Michael J -- Markson, Joseph S -- Lane, William S -- Fisher, Daniel S -- O'Shea, Erin K -- New York, N.Y. -- Science. 2007 Nov 2;318(5851):809-12. Epub 2007 Oct 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Faculty of Arts and Sciences Center for Systems Biology, Departments of Molecular and Cellular Biology and of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17916691" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*physiology ; Biological Clocks/*physiology ; Circadian Rhythm/*physiology ; Circadian Rhythm Signaling Peptides and Proteins ; Models, Biological ; Phosphorylation ; Synechococcus/*physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Light-driven changes in energy metabolism directly entrain the cyanobacterial circadian oscillator (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-01-15
    Description: Circadian clocks are self-sustained biological oscillators that can be entrained by environmental cues. Although this phenomenon has been studied in many organisms, the molecular mechanisms of entrainment remain unclear. Three cyanobacterial proteins and adenosine triphosphate (ATP) are sufficient to generate oscillations in phosphorylation in vitro. We show that changes in illumination that induce a phase shift in cultured cyanobacteria also cause changes in the ratio of ATP to adenosine diphosphate (ADP). When these nucleotide changes are simulated in the in vitro oscillator, they cause phase shifts similar to those observed in vivo. Physiological concentrations of ADP inhibit kinase activity in the oscillator, and a mathematical model constrained by data shows that this effect is sufficient to quantitatively explain entrainment of the cyanobacterial circadian clock.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3309039/" 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/PMC3309039/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rust, Michael J -- Golden, Susan S -- O'Shea, Erin K -- GM62419/GM/NIGMS NIH HHS/ -- R01 GM062419/GM/NIGMS NIH HHS/ -- R01 GM062419-08/GM/NIGMS NIH HHS/ -- R01 GM062419-09/GM/NIGMS NIH HHS/ -- R01 GM062419-09S1/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Jan 14;331(6014):220-3. doi: 10.1126/science.1197243.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Center for Systems Biology, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21233390" target="_blank"〉PubMed〈/a〉
    Keywords: ATP Synthetase Complexes/antagonists & inhibitors/metabolism ; Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Bacterial Proteins/antagonists & inhibitors/metabolism ; *Circadian Clocks ; *Circadian Rhythm ; Circadian Rhythm Signaling Peptides and Proteins/antagonists & ; inhibitors/metabolism ; Darkness ; *Energy Metabolism ; *Light ; Models, Biological ; Phosphorylation ; Synechococcus/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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