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  • 1
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    Woody Hastings: 65 years of fun [Retrospectives] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-10-22
    Description: John Woodland (Woody) Hastings, Paul C. Mangelsdorf Professor of Natural Sciences and Professor Emeritus, Harvard University, died at home on August 6, 2014 after a long battle with idiopathic pulmonary fibrosis. He was 87. To those who worked with Woody, he was a personality larger than life. Woody infected those...
    Keywords: Retrospectives
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-09-04
    Description: Cyanobacteria are the simplest organisms known to have a circadian clock. A circadian clock gene cluster kaiABC was cloned from the cyanobacterium Synechococcus. Nineteen clock mutations were mapped to the three kai genes. Promoter activities upstream of the kaiA and kaiB genes showed circadian rhythms of expression, and both kaiA and kaiBC messenger RNAs displayed circadian cycling. Inactivation of any single kai gene abolished these rhythms and reduced kaiBC-promoter activity. Continuous kaiC overexpression repressed the kaiBC promoter, whereas kaiA overexpression enhanced it. Temporal kaiC overexpression reset the phase of the rhythms. Thus, a negative feedback control of kaiC expression by KaiC generates a circadian oscillation in cyanobacteria, and KaiA sustains the oscillation by enhancing kaiC expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ishiura, M -- Kutsuna, S -- Aoki, S -- Iwasaki, H -- Andersson, C R -- Tanabe, A -- Golden, S S -- Johnson, C H -- Kondo, T -- MH01179/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 1998 Sep 4;281(5382):1519-23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan. ishiura@bio.nagoya-u.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9727980" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*genetics ; Biological Clocks/*genetics ; Circadian Rhythm/*genetics ; Circadian Rhythm Signaling Peptides and Proteins ; Cloning, Molecular ; Cyanobacteria/*genetics/physiology ; Feedback ; *Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Genes, Reporter ; Luminescence ; Models, Biological ; Molecular Sequence Data ; Multigene Family ; Mutation ; Promoter Regions, Genetic ; Recombinant Fusion Proteins ; Transcription, Genetic
    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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    Structural insights into a circadian oscillator (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-01
    Description: An endogenous circadian system in cyanobacteria exerts pervasive control over cellular processes, including global gene expression. Indeed, the entire chromosome undergoes daily cycles of topological changes and compaction. The biochemical machinery underlying a circadian oscillator can be reconstituted in vitro with just three cyanobacterial proteins, KaiA, KaiB, and KaiC. These proteins interact to promote conformational changes and phosphorylation events that determine the phase of the in vitro oscillation. The high-resolution structures of these proteins suggest a ratcheting mechanism by which the KaiABC oscillator ticks unidirectionally. This posttranslational oscillator may interact with transcriptional and translational feedback loops to generate the emergent circadian behavior in vivo. The conjunction of structural, biophysical, and biochemical approaches to this system reveals molecular mechanisms of biological timekeeping.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2588432/" 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/PMC2588432/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Johnson, Carl Hirschie -- Egli, Martin -- Stewart, Phoebe L -- F32 GM71276/GM/NIGMS NIH HHS/ -- GM067152/GM/NIGMS NIH HHS/ -- GM073845/GM/NIGMS NIH HHS/ -- R01 GM067152/GM/NIGMS NIH HHS/ -- R01 GM067152-06/GM/NIGMS NIH HHS/ -- R01 GM073845/GM/NIGMS NIH HHS/ -- R01 GM073845-03/GM/NIGMS NIH HHS/ -- R01 MH043836/MH/NIMH NIH HHS/ -- R01 MH043836-17/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 2008 Oct 31;322(5902):697-701. doi: 10.1126/science.1150451.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Box 35-1634, Vanderbilt University, Nashville, TN 37235-1634, USA. carl.h.johnson@vanderbilt.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18974343" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/metabolism ; *Biological Clocks ; Cell Division ; Chromosomes, Bacterial/physiology ; *Circadian Rhythm ; Circadian Rhythm Signaling Peptides and Proteins ; Dimerization ; Models, Molecular ; Phosphorylation ; Promoter Regions, Genetic ; Protein Biosynthesis ; Protein Conformation ; Synechococcus/chemistry/genetics/*physiology ; 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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  • 4
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    Chemo-enzymatic synthesis of site-specific isotopically labeled nucleotides for use in NMR resonance assignment, dynamics and structural characterizations (2016)
    Oxford University Press
    Details
    Publication Date: 2016-04-08
    Description: Stable isotope labeling is central to NMR studies of nucleic acids. Development of methods that incorporate labels at specific atomic positions within each nucleotide promises to expand the size range of RNAs that can be studied by NMR. Using recombinantly expressed enzymes and chemically synthesized ribose and nucleobase, we have developed an inexpensive, rapid chemo-enzymatic method to label ATP and GTP site specifically and in high yields of up to 90%. We incorporated these nucleotides into RNAs with sizes ranging from 27 to 59 nucleotides using in vitro transcription: A-Site (27 nt), the iron responsive elements (29 nt), a fluoride riboswitch from Bacillus anthracis (48 nt), and a frame-shifting element from a human corona virus (59 nt). Finally, we showcase the improvement in spectral quality arising from reduced crowding and narrowed linewidths, and accurate analysis of NMR relaxation dispersion (CPMG) and TROSY-based CEST experiments to measure μs-ms time scale motions, and an improved NOESY strategy for resonance assignment. Applications of this selective labeling technology promises to reduce difficulties associated with chemical shift overlap and rapid signal decay that have made it challenging to study the structure and dynamics of large RNAs beyond the 50 nt median size found in the PDB.
    Keywords: Nucleic acid modification, Nucleic acid structure
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Non-optimal codon usage is a mechanism to achieve circadian clock conditionality (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-02-19
    Description: Circadian rhythms are oscillations in biological processes that function as a key adaptation to the daily rhythms of most environments. In the model cyanobacterial circadian clock system, the core oscillator proteins are encoded by the gene cluster kaiABC. Genes with high expression and functional importance, such as the kai genes, are usually encoded by optimal codons, yet the codon-usage bias of the kaiBC genes is not optimized for translational efficiency. We discovered a relationship between codon usage and a general property of circadian rhythms called conditionality; namely, that endogenous rhythmicity is robustly expressed under some environmental conditions but not others. Despite the generality of circadian conditionality, however, its molecular basis is unknown for any system. Here we show that in the cyanobacterium Synechococcus elongate, non-optimal codon usage was selected as a post-transcriptional mechanism to switch between circadian and non-circadian regulation of gene expression as an adaptive response to environmental conditions. When the kaiBC sequence was experimentally optimized to enhance expression of the KaiB and KaiC proteins, intrinsic rhythmicity was enhanced at cool temperatures that are experienced by this organism in its natural habitat. However, fitness at those temperatures was highest in cells in which the endogenous rhythms were suppressed at cool temperatures as compared with cells exhibiting high-amplitude rhythmicity. These results indicate natural selection against circadian systems in cyanobacteria that are intrinsically robust at cool temperatures. Modulation of circadian amplitude is therefore crucial to its adaptive significance. Moreover, these results show the direct effects of codon usage on a complex phenotype and organismal fitness. Our work also challenges the long-standing view of directional selection towards optimal codons, and provides a key example of natural selection against optimal codons to achieve adaptive responses to environmental changes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3593822/" 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/PMC3593822/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Yao -- Ma, Peijun -- Shah, Premal -- Rokas, Antonis -- Liu, Yi -- Johnson, Carl Hirschie -- GM062591/GM/NIGMS NIH HHS/ -- GM068496/GM/NIGMS NIH HHS/ -- R01 GM062591/GM/NIGMS NIH HHS/ -- R01 GM067152/GM/NIGMS NIH HHS/ -- R01 GM068496/GM/NIGMS NIH HHS/ -- R01 GM084283/GM/NIGMS NIH HHS/ -- R01 GM088595/GM/NIGMS NIH HHS/ -- England -- Nature. 2013 Mar 7;495(7439):116-20. doi: 10.1038/nature11942. Epub 2013 Feb 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23417065" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/genetics/metabolism ; Circadian Clocks/*genetics/*physiology ; Circadian Rhythm/genetics/physiology ; Circadian Rhythm Signaling Peptides and Proteins/genetics/metabolism ; Codon/*genetics ; Gene Expression Regulation, Bacterial/*genetics ; Genes, Bacterial/*genetics ; Multigene Family/genetics ; Phenotype ; Selection, Genetic ; Synechococcus/*genetics/*physiology ; Temperature
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 6
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    Peroxiredoxins are conserved markers of circadian rhythms (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-05-25
    Description: Cellular life emerged approximately 3.7 billion years ago. With scant exception, terrestrial organisms have evolved under predictable daily cycles owing to the Earth's rotation. The advantage conferred on organisms that anticipate such environmental cycles has driven the evolution of endogenous circadian rhythms that tune internal physiology to external conditions. The molecular phylogeny of mechanisms driving these rhythms has been difficult to dissect because identified clock genes and proteins are not conserved across the domains of life: Bacteria, Archaea and Eukaryota. Here we show that oxidation-reduction cycles of peroxiredoxin proteins constitute a universal marker for circadian rhythms in all domains of life, by characterizing their oscillations in a variety of model organisms. Furthermore, we explore the interconnectivity between these metabolic cycles and transcription-translation feedback loops of the clockwork in each system. Our results suggest an intimate co-evolution of cellular timekeeping with redox homeostatic mechanisms after the Great Oxidation Event approximately 2.5 billion years ago.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398137/" 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/PMC3398137/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Edgar, Rachel S -- Green, Edward W -- Zhao, Yuwei -- van Ooijen, Gerben -- Olmedo, Maria -- Qin, Ximing -- Xu, Yao -- Pan, Min -- Valekunja, Utham K -- Feeney, Kevin A -- Maywood, Elizabeth S -- Hastings, Michael H -- Baliga, Nitin S -- Merrow, Martha -- Millar, Andrew J -- Johnson, Carl H -- Kyriacou, Charalambos P -- O'Neill, John S -- Reddy, Akhilesh B -- 083643/Wellcome Trust/United Kingdom -- 083643/Z/07/Z/Wellcome Trust/United Kingdom -- 093734/Wellcome Trust/United Kingdom -- 093734/Z/10/Z/Wellcome Trust/United Kingdom -- BB/C006941/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/D019621/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/D019621/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- MC_U105170643/Medical Research Council/United Kingdom -- P50 GM076547/GM/NIGMS NIH HHS/ -- P50GM076547/GM/NIGMS NIH HHS/ -- R01 GM067152/GM/NIGMS NIH HHS/ -- R01 GM088595/GM/NIGMS NIH HHS/ -- R01GM067152/GM/NIGMS NIH HHS/ -- R01GM088595/GM/NIGMS NIH HHS/ -- R21 HL102492/HL/NHLBI NIH HHS/ -- R21HL102492/HL/NHLBI NIH HHS/ -- Medical Research Council/United Kingdom -- England -- Nature. 2012 May 16;485(7399):459-64. doi: 10.1038/nature11088.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Clinical Neurosciences, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22622569" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Archaea/metabolism ; Bacteria/metabolism ; Biomarkers/metabolism ; Catalytic Domain ; Circadian Clocks/genetics/physiology ; Circadian Rhythm/genetics/*physiology ; *Conserved Sequence ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; Feedback, Physiological ; Homeostasis ; Humans ; Models, Biological ; Molecular Sequence Data ; Oxidation-Reduction ; Peroxiredoxins/chemistry/*metabolism ; Phylogeny ; Prokaryotic Cells/metabolism ; Protein Biosynthesis ; Transcription, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 7
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    Circadian clock mutants of cyanobacteria (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-11-18
    Description: A diverse set of circadian clock mutants was isolated in a cyanobacterial strain that carries a bacterial luciferase reporter gene attached to a clock-controlled promoter. Among 150,000 clones of chemically mutagenized bioluminescent cells, 12 mutants were isolated that exhibit a broad spectrum of periods (between 16 and 60 hours), and 5 mutants were found that show a variety of unusual patterns, including arrhythmia. These mutations appear to be clock-specific. Moreover, it was demonstrated that in this cyanobacterium it is possible to clone mutant genes by complementation, which provides a means to genetically dissect the circadian mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kondo, T -- Tsinoremas, N F -- Golden, S S -- Johnson, C H -- Kutsuna, S -- Ishiura, M -- GM37040/GM/NIGMS NIH HHS/ -- MH43836/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 1994 Nov 18;266(5188):1233-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Institute for Basic Biology, Okazaki, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7973706" target="_blank"〉PubMed〈/a〉
    Keywords: Circadian Rhythm/*genetics ; Cloning, Molecular ; Cyanobacteria/*genetics/growth & development/physiology ; Darkness ; *Genes, Bacterial ; Genetic Complementation Test ; Light ; Luminescent Measurements ; Mutagenesis ; Mutation ; Temperature
    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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  • 8
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    Circadian oscillations of cytosolic and chloroplastic free calcium in plants (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-09-29
    Description: Tobacco and Arabidopsis plants, expressing a transgene for the calcium-sensitive luminescent protein apoaequorin, revealed circadian oscillations in free cytosolic calcium that can be phase-shifted by light-dark signals. When apoaequorin was targeted to the chloroplast, circadian chloroplast calcium rhythms were likewise observed after transfer of the seedlings to constant darkness. Circadian oscillations in free calcium concentrations can be expected to control many calcium-dependent enzymes and processes accounting for circadian outputs. Regulation of calcium flux is therefore fundamental to the organization of circadian systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Johnson, C H -- Knight, M R -- Kondo, T -- Masson, P -- Sedbrook, J -- Haley, A -- Trewavas, A -- GM48053/GM/NIGMS NIH HHS/ -- MH01179/MH/NIMH NIH HHS/ -- MH43836/MH/NIMH NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1995 Sep 29;269(5232):1863-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Vanderbilt University, Nashville, TN 37235, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7569925" target="_blank"〉PubMed〈/a〉
    Keywords: Aequorin/genetics/metabolism ; Apoproteins/genetics/metabolism ; Arabidopsis/genetics/*metabolism ; Calcium/*metabolism ; Calcium-Binding Proteins/genetics/metabolism ; Chloroplasts/*metabolism ; *Circadian Rhythm ; Cytosol/*metabolism ; Darkness ; Light ; Luminescence ; Plants, Genetically Modified ; *Plants, Toxic ; Recombinant Proteins/genetics/metabolism ; Tobacco/genetics/*metabolism
    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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  • 9
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    Comment on "The Arabidopsis circadian clock incorporates a cADPR-based feedback loop" (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-10-10
    Description: Dodd et al. (Reports, 14 December 2007, p. 1789) reported that the Arabidopsis circadian clock incorporates the signaling molecule cyclic adenosine diphosphate ribose (cADPR). In contrast, we found that there is no rhythm of cADPR levels nor are there any significant effects on the rhythm by cADPR overexpression, thus raising questions about the conclusions of Dodd et al.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2934760/" 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/PMC2934760/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Xiaodong -- Graeff, Richard -- Xie, Qiguang -- Gamble, Karen L -- Mori, Tetsuya -- Johnson, Carl Hirschie -- GM061568/GM/NIGMS NIH HHS/ -- K99 GM086683/GM/NIGMS NIH HHS/ -- K99 GM086683-01/GM/NIGMS NIH HHS/ -- MH043836/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 2009 Oct 9;326(5950):230; author reply 230. doi: 10.1126/science.1169503.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19815758" target="_blank"〉PubMed〈/a〉
    Keywords: ADP-ribosyl Cyclase/metabolism ; Arabidopsis/drug effects/metabolism/*physiology ; Calcium/*metabolism ; *Circadian Rhythm ; Cyclic ADP-Ribose/*metabolism ; Estradiol/pharmacology ; *Feedback, Physiological ; Niacinamide/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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  • 10
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    Circadian changes in enzyme concentration account for rhythm of enzyme activity in gonyaulax (1984)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1984-03-30
    Description: A circadian rhythm in the activity of luciferase is partly responsible for rhythmic bioluminescence in the dinoflagellate alga Gonyaulax polyedra. The cyclic activity of this enzyme can be attributed to a corresponding rhythm in the concentration of immunologically reactive luciferase protein. Hence protein turnover (synthesis or degradation or both) is used by the endogenous clock to control the daily rhythm of bioluminescence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Johnson, C H -- Roeber, J F -- Hastings, J W -- New York, N.Y. -- Science. 1984 Mar 30;223(4643):1428-30.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17746055" target="_blank"〉PubMed〈/a〉
    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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