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  • Models, Biological  (178)
  • Engineering
  • American Association for the Advancement of Science (AAAS)  (182)
  • Goleta, CA
  • 2010-2014  (182)
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  • 1
    Publication Date: 2011-06-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Merali, Zeeya -- New York, N.Y. -- Science. 2011 Jun 17;332(6036):1376-7. doi: 10.1126/science.332.6036.1376.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21680824" target="_blank"〉PubMed〈/a〉
    Keywords: Biomedical Engineering ; China ; Engineering ; *Equipment Design ; History, 20th Century ; History, 21st Century ; Housing ; Spacecraft ; *Stents
    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: 2012-05-26
    Description: Plants use day-length information to coordinate flowering time with the appropriate season to maximize reproduction. In Arabidopsis, the long day-specific expression of CONSTANS (CO) protein is crucial for flowering induction. Although light signaling regulates CO protein stability, the mechanism by which CO is stabilized in the long-day afternoon has remained elusive. Here, we demonstrate that FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) protein stabilizes CO protein in the afternoon in long days. FKF1 interacts with CO through its LOV domain, and blue light enhances this interaction. In addition, FKF1 simultaneously removes CYCLING DOF FACTOR 1 (CDF1), which represses CO and FLOWERING LOCUS T (FT) transcription. Together with CO transcriptional regulation, FKF1 protein controls robust FT mRNA induction through multiple feedforward mechanisms that accurately control flowering timing.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737243/" 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/PMC3737243/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Song, Young Hun -- Smith, Robert W -- To, Benjamin J -- Millar, Andrew J -- Imaizumi, Takato -- BB/F005237/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/F59011/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G019621/Biotechnology and Biological Sciences Research Council/United Kingdom -- GM079712/GM/NIGMS NIH HHS/ -- R01 GM079712/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 May 25;336(6084):1045-9. doi: 10.1126/science.1219644.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22628657" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics/growth & development/metabolism/*physiology ; Arabidopsis Proteins/chemistry/*genetics/*metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Flowers/*growth & development ; Gene Expression Regulation, Plant ; Light ; Models, Biological ; Mutation ; *Photoperiod ; Plants, Genetically Modified ; Promoter Regions, Genetic ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Stability ; RNA, Messenger/genetics/metabolism ; RNA, Plant/genetics/metabolism ; Repressor Proteins/metabolism ; Transcription Factors/genetics/*metabolism ; 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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  • 3
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-09-08
    Description: Cells have developed ways to sense and control the size of their organelles. Size-sensing mechanisms range from direct measurements provided by dedicated reporters to indirect functional readouts, and they are used to modify organelle size under both normal and stress conditions. Organelle size can also be controlled in the absence of an identifiable size sensor. Studies on flagella have dissected principles of size sensing and control, and it will be exciting to see how these principles apply to other organelles.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3625396/" 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/PMC3625396/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chan, Yee-Hung M -- Marshall, Wallace F -- 1F32GM090442-01A1/GM/NIGMS NIH HHS/ -- P50 GM081879/GM/NIGMS NIH HHS/ -- P50GM081879/GM/NIGMS NIH HHS/ -- R01 GM097017/GM/NIGMS NIH HHS/ -- R01GM097017/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Sep 7;337(6099):1186-9. doi: 10.1126/science.1223539.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, UCSF Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA. yhmchan@ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22955827" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Transport ; *Cell Physiological Phenomena ; Flagella/metabolism/physiology/ultrastructure ; Humans ; Models, Biological ; *Organelle Size ; *Organelles/chemistry/metabolism/ultrastructure
    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
    Publication Date: 2010-05-08
    Description: Proper protein localization is essential for all cells. However, the precise mechanism by which high fidelity is achieved is not well understood for any protein-targeting pathway. To address this fundamental question, we investigated the signal recognition particle (SRP) pathway in Escherichia coli, which delivers proteins to the bacterial inner membrane through recognition of signal sequences on cargo proteins. Fidelity was thought to arise from the inability of SRP to bind strongly to incorrect cargos. Using biophysical assays, we found that incorrect cargos were also rejected through a series of checkpoints during subsequent steps of targeting. Thus, high fidelity of substrate selection is achieved through the cumulative effect of multiple checkpoints; this principle may be generally applicable to other pathways involving selective signal recognition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760334/" 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/PMC3760334/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Xin -- Rashid, Rumana -- Wang, Kai -- Shan, Shu-ou -- GM078024/GM/NIGMS NIH HHS/ -- R01 GM078024/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 May 7;328(5979):757-60. doi: 10.1126/science.1186743.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20448185" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/metabolism ; Escherichia coli/*metabolism ; Escherichia coli Proteins/chemistry/*metabolism ; Fluorescence Resonance Energy Transfer ; Guanosine Triphosphate/metabolism ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Models, Biological ; Protein Binding ; Protein Biosynthesis ; *Protein Sorting Signals ; *Protein Transport ; Ribosomes/metabolism ; Signal Recognition Particle/*metabolism ; Thermodynamics
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2014-05-17
    Description: Nuclear magnetic resonance (NMR) spectroscopy is useful to determine molecular structure in tissues grown in vitro only if their fidelity, relative to native tissue, can be established. Here, we use multidimensional NMR spectra of animal and in vitro model tissues as fingerprints of their respective molecular structures, allowing us to compare the intact tissues at atomic length scales. To obtain spectra from animal tissues, we developed a heavy mouse enriched by about 20% in the NMR-active isotopes carbon-13 and nitrogen-15. The resulting spectra allowed us to refine an in vitro model of developing bone and to probe its detailed structure. The identification of an unexpected molecule, poly(adenosine diphosphate ribose), that may be implicated in calcification of the bone matrix, illustrates the analytical power of this approach.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chow, W Ying -- Rajan, Rakesh -- Muller, Karin H -- Reid, David G -- Skepper, Jeremy N -- Wong, Wai Ching -- Brooks, Roger A -- Green, Maggie -- Bihan, Dominique -- Farndale, Richard W -- Slatter, David A -- Shanahan, Catherine M -- Duer, Melinda J -- BB/G021392/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- G0500707/Medical Research Council/United Kingdom -- PG/08/011/24416/British Heart Foundation/United Kingdom -- PG/10/43/28390/British Heart Foundation/United Kingdom -- RG/09/003/27122/British Heart Foundation/United Kingdom -- RG/11/14/29056/British Heart Foundation/United Kingdom -- New York, N.Y. -- Science. 2014 May 16;344(6185):742-6. doi: 10.1126/science.1248167.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. ; Orthopaedic Research Unit, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK. ; Department of Physiology, Development, and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3DY, UK. ; Central Biomedical Resources, University of Cambridge, School of Clinical Medicine, West Forvie Building, Forvie Site, Robinson Way, Cambridge CB2 0SZ, UK. ; Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK. ; British Heart Foundation Centre of Research Excellence, Cardiovascular Division, James Black Centre, King's College London, 125 Coldharbour Lane, London SE5 9NU, UK. ; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. mjd13@cam.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24833391" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Bone Development ; *Calcification, Physiologic ; Carbon Isotopes ; Extracellular Matrix/chemistry ; Growth Plate/growth & development ; Mice ; Models, Biological ; Nitrogen Isotopes ; Nuclear Magnetic Resonance, Biomolecular/*methods ; Poly Adenosine Diphosphate Ribose/*analysis ; Sheep
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2011-09-24
    Description: Nonhexameric helicases use adenosine triphosphate (ATP) to unzip base pairs in double-stranded nucleic acids (dsNAs). Studies have suggested that these helicases unzip dsNAs in single-base pair increments, consuming one ATP molecule per base pair, but direct evidence for this mechanism is lacking. We used optical tweezers to follow the unwinding of double-stranded RNA by the hepatitis C virus NS3 helicase. Single-base pair steps by NS3 were observed, along with nascent nucleotide release that was asynchronous with base pair opening. Asynchronous release of nascent nucleotides rationalizes various observations of its dsNA unwinding and may be used to coordinate the translocation speed of NS3 along the RNA during viral replication.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172460/" 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/PMC4172460/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cheng, Wei -- Arunajadai, Srikesh G -- Moffitt, Jeffrey R -- Tinoco, Ignacio Jr -- Bustamante, Carlos -- 5R01GM010840/GM/NIGMS NIH HHS/ -- 5R01GM032543/GM/NIGMS NIH HHS/ -- R01 GM010840/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Sep 23;333(6050):1746-9. doi: 10.1126/science.1206023.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA. chengwe@umich.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21940894" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Algorithms ; Base Pairing ; Hepacivirus/*enzymology ; Kinetics ; Models, Biological ; Nucleic Acid Conformation ; Optical Tweezers ; RNA Helicases/*metabolism ; RNA, Double-Stranded/chemistry/*metabolism ; RNA, Viral/chemistry/*metabolism ; Viral Nonstructural Proteins/*metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2013-08-03
    Description: Insects often undergo regular outbreaks in population density but identifying the causal mechanism for such outbreaks in any particular species has proven difficult. Here, we show that outbreak cycles in the tea tortrix Adoxophyes honmai can be explained by temperature-driven changes in system stability. Wavelet analysis of a 51-year time series spanning more than 200 outbreaks reveals a threshold in outbreak amplitude each spring when temperature exceeds 15 degrees C and a secession of outbreaks each fall as temperature decreases. This is in close agreement with our independently parameterized mathematical model that predicts the system crosses a Hopf bifurcation from stability to sustained cycles as temperature increases. These results suggest that temperature can alter system stability and provide an explanation for generation cycles in multivoltine insects.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nelson, William A -- Bjornstad, Ottar N -- Yamanaka, Takehiko -- New York, N.Y. -- Science. 2013 Aug 16;341(6147):796-9. doi: 10.1126/science.1238477. Epub 2013 Aug 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Queen's University, Kingston, Ontario, Canada. nelsonw@queensu.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23907532" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Life Cycle Stages ; Models, Biological ; Moths/growth & development/*physiology ; Population Density ; Population Dynamics ; *Seasons ; *Temperature ; Wavelet Analysis
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2012-04-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vinson, Valda -- Purnell, Beverly A -- Zahn, Laura M -- Travis, John -- New York, N.Y. -- Science. 2012 Apr 13;336(6078):171. doi: 10.1126/science.336.6078.171.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22499935" target="_blank"〉PubMed〈/a〉
    Keywords: *Computational Biology ; Computer Simulation ; Genomics ; Models, Biological ; Morphogenesis
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-02-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hilser, Vincent J -- GM63747/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Feb 5;327(5966):653-4. doi: 10.1126/science.1186121.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA. vjhilser@utmb.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20133562" target="_blank"〉PubMed〈/a〉
    Keywords: *Allosteric Regulation ; Allosteric Site ; Ligands ; Models, Biological ; Models, Molecular ; Molecular Motor Proteins/chemistry/metabolism ; Protein Conformation ; Protein Subunits/*chemistry/*metabolism ; Proteins/*chemistry/*metabolism ; *Signal Transduction
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2010-05-22
    Description: Cell surface receptors convert extracellular cues into receptor activation, thereby triggering intracellular signaling networks and controlling cellular decisions. A major unresolved issue is the identification of receptor properties that critically determine processing of ligand-encoded information. We show by mathematical modeling of quantitative data and experimental validation that rapid ligand depletion and replenishment of the cell surface receptor are characteristic features of the erythropoietin (Epo) receptor (EpoR). The amount of Epo-EpoR complexes and EpoR activation integrated over time corresponds linearly to ligand input; this process is carried out over a broad range of ligand concentrations. This relation depends solely on EpoR turnover independent of ligand binding, which suggests an essential role of large intracellular receptor pools. These receptor properties enable the system to cope with basal and acute demand in the hematopoietic system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Becker, Verena -- Schilling, Marcel -- Bachmann, Julie -- Baumann, Ute -- Raue, Andreas -- Maiwald, Thomas -- Timmer, Jens -- Klingmuller, Ursula -- New York, N.Y. -- Science. 2010 Jun 11;328(5984):1404-8. doi: 10.1126/science.1184913. Epub 2010 May 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division Systems Biology of Signal Transduction, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20488988" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Cell Membrane/*metabolism ; Computer Simulation ; Endocytosis ; Epoetin Alfa ; Erythropoietin/metabolism/pharmacology ; Kinetics ; Ligands ; Mice ; Models, Biological ; Protein Binding ; Receptors, Erythropoietin/*metabolism ; Recombinant Proteins ; Signal Transduction
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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