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  • Models, Biological
  • American Association for the Advancement of Science (AAAS)  (36)
  • EMBO Press
  • Essen : Verl. Glückauf
  • Krefeld : Geologischer Dienst Nordhein-Westfalen
  • Oxford University Press
  • 2005-2009  (36)
  • 1990-1994
  • 1955-1959
  • 2008  (36)
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (36)
  • EMBO Press
  • Essen : Verl. Glückauf
  • Krefeld : Geologischer Dienst Nordhein-Westfalen
  • Oxford University Press
    • +
Years
  • 2005-2009  (36)
  • 1990-1994
  • 1955-1959
Year
  • 1
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    Evolution. Dynamics of body size evolution (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-09-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roy, Kaustuv -- New York, N.Y. -- Science. 2008 Sep 12;321(5895):1451-2. doi: 10.1126/science.1163097.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Ecology, Behavior and Evolution, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. kroy@ucsd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18787156" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Body Size ; Climate ; Ecosystem ; Extinction, Biological ; Greenhouse Effect ; Models, Biological ; Population Dynamics ; Stochastic Processes ; 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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  • 2
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    Feedback loops shape cellular signals in space and time (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-18
    Description: Positive and negative feedback loops are common regulatory elements in biological signaling systems. We discuss core feedback motifs that have distinct roles in shaping signaling responses in space and time. We also discuss approaches to experimentally investigate feedback loops in signaling systems.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2680159/" 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/PMC2680159/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brandman, Onn -- Meyer, Tobias -- R01 GM030179/GM/NIGMS NIH HHS/ -- R01 GM030179-25/GM/NIGMS NIH HHS/ -- R01 GM063702/GM/NIGMS NIH HHS/ -- R01 GM063702-06/GM/NIGMS NIH HHS/ -- R01GM030179/GM/NIGMS NIH HHS/ -- R01GM063702/GM/NIGMS NIH HHS/ -- R01MH064801/MH/NIMH NIH HHS/ -- R33 CA120732/CA/NCI NIH HHS/ -- R33 CA120732-02/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2008 Oct 17;322(5900):390-5. doi: 10.1126/science.1160617.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, University of California-San Francisco and Howard Hughes Medical Institute, San Francisco, CA 94158, USA. Onn.Brandman@ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18927383" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium/metabolism ; *Calcium Signaling ; Cell Membrane/metabolism ; Chemotaxis, Leukocyte ; Computer Simulation ; Endoplasmic Reticulum/metabolism ; *Feedback, Physiological ; Models, Biological ; Neutrophils/*metabolism/physiology ; Phosphatidylinositol 3-Kinases/*metabolism ; *Signal Transduction
    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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    Experimental evidence for spatial self-organization and its emergent effects in mussel bed ecosystems (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-01
    Description: Spatial self-organization is the main theoretical explanation for the global occurrence of regular or otherwise coherent spatial patterns in ecosystems. Using mussel beds as a model ecosystem, we provide an experimental demonstration of spatial self-organization. Under homogeneous laboratory conditions, mussels developed regular patterns, similar to those in the field. An individual-based model derived from our experiments showed that interactions between individuals explained the observed patterns. Furthermore, a field study showed that pattern formation affected ecosystem-level processes in terms of improved growth and resistance to wave action. Our results imply that spatial self-organization is an important determinant of the structure and functioning of ecosystems, and it needs to be considered in their conservation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van de Koppel, Johan -- Gascoigne, Joanna C -- Theraulaz, Guy -- Rietkerk, Max -- Mooij, Wolf M -- Herman, Peter M J -- D18866/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Oct 31;322(5902):739-42. doi: 10.1126/science.1163952.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Spatial Ecology Department, the Netherlands Institute of Ecology (NIOO-KNAW), Post Office Box 140, 4400 AC Yerseke, Netherlands. J.vandeKoppel@nioo.knaw.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18974353" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biomass ; Bivalvia/*physiology ; *Ecosystem ; Models, Biological ; Movement ; Population Dynamics ; Spatial Behavior ; Wales
    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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    Robust, tunable biological oscillations from interlinked positive and negative feedback loops (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-05
    Description: A simple negative feedback loop of interacting genes or proteins has the potential to generate sustained oscillations. However, many biological oscillators also have a positive feedback loop, raising the question of what advantages the extra loop imparts. Through computational studies, we show that it is generally difficult to adjust a negative feedback oscillator's frequency without compromising its amplitude, whereas with positive-plus-negative feedback, one can achieve a widely tunable frequency and near-constant amplitude. This tunability makes the latter design suitable for biological rhythms like heartbeats and cell cycles that need to provide a constant output over a range of frequencies. Positive-plus-negative oscillators also appear to be more robust and easier to evolve, rationalizing why they are found in contexts where an adjustable frequency is unimportant.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728800/" 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/PMC2728800/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tsai, Tony Yu-Chen -- Choi, Yoon Sup -- Ma, Wenzhe -- Pomerening, Joseph R -- Tang, Chao -- Ferrell, James E Jr -- GM61726/GM/NIGMS NIH HHS/ -- GM77544/GM/NIGMS NIH HHS/ -- R01 GM061276/GM/NIGMS NIH HHS/ -- R01 GM061276-06/GM/NIGMS NIH HHS/ -- R01 GM061276-07/GM/NIGMS NIH HHS/ -- R01 GM061276-08/GM/NIGMS NIH HHS/ -- R01 GM077544/GM/NIGMS NIH HHS/ -- R01 GM077544-01/GM/NIGMS NIH HHS/ -- R01 GM077544-02/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Jul 4;321(5885):126-9. doi: 10.1126/science.1156951.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305-5174, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18599789" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Anaphase-Promoting Complex-Cyclosome ; Animals ; *Biological Clocks ; Biological Evolution ; CDC2 Protein Kinase/*metabolism ; *Cell Cycle ; Cell Division ; Circadian Rhythm ; Cyclin B/biosynthesis/metabolism ; Embryo, Nonmammalian/cytology/metabolism ; *Feedback, Physiological ; Interphase ; Models, Biological ; Monte Carlo Method ; Ubiquitin-Protein Ligase Complexes/metabolism ; Xenopus Proteins/metabolism ; Xenopus laevis
    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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  • 5
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    Molecular architecture of the "stressosome," a signal integration and transduction hub (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-04
    Description: A commonly used strategy by microorganisms to survive multiple stresses involves a signal transduction cascade that increases the expression of stress-responsive genes. Stress signals can be integrated by a multiprotein signaling hub that responds to various signals to effect a single outcome. We obtained a medium-resolution cryo-electron microscopy reconstruction of the 1.8-megadalton "stressosome" from Bacillus subtilis. Fitting known crystal structures of components into this reconstruction gave a pseudoatomic structure, which had a virus capsid-like core with sensory extensions. We suggest that the different sensory extensions respond to different signals, whereas the conserved domains in the core integrate the varied signals. The architecture of the stressosome provides the potential for cooperativity, suggesting that the response could be tuned dependent on the magnitude of chemophysical insult.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marles-Wright, Jon -- Grant, Tim -- Delumeau, Olivier -- van Duinen, Gijs -- Firbank, Susan J -- Lewis, Peter J -- Murray, James W -- Newman, Joseph A -- Quin, Maureen B -- Race, Paul R -- Rohou, Alexis -- Tichelaar, Willem -- van Heel, Marin -- Lewis, Richard J -- BB/D000521/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/F001533/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Oct 3;322(5898):92-6. doi: 10.1126/science.1159572.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18832644" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacillus subtilis/*chemistry/metabolism/ultrastructure ; Bacterial Proteins/*chemistry/metabolism/ultrastructure ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Image Processing, Computer-Assisted ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Multiprotein Complexes/*chemistry/metabolism/ultrastructure ; Phosphoproteins/*chemistry/metabolism/ultrastructure ; Phosphorylation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/*chemistry/metabolism/ultrastructure ; Sigma Factor/metabolism ; *Signal Transduction
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  • 6
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    Wnt3a-mediated formation of phosphatidylinositol 4,5-bisphosphate regulates LRP6 phosphorylation (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-09-06
    Description: The canonical Wnt-beta-catenin signaling pathway is initiated by inducing phosphorylation of one of the Wnt receptors, low-density lipoprotein receptor-related protein 6 (LRP6), at threonine residue 1479 (Thr1479) and serine residue 1490 (Ser1490). By screening a human kinase small interfering RNA library, we identified phosphatidylinositol 4-kinase type II alpha and phosphatidylinositol-4-phosphate 5-kinase type I (PIP5KI) as required for Wnt3a-induced LRP6 phosphorylation at Ser1490 in mammalian cells and confirmed that these kinases are important for Wnt signaling in Xenopus embryos. Wnt3a stimulates the formation of phosphatidylinositol 4,5-bisphosphates [PtdIns (4,5)P2] through frizzled and dishevelled, the latter of which directly interacted with and activated PIP5KI. In turn, PtdIns (4,5)P2 regulated phosphorylation of LRP6 at Thr1479 and Ser1490. Therefore, our study reveals a signaling mechanism for Wnt to regulate LRP6 phosphorylation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2532521/" 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/PMC2532521/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pan, Weijun -- Choi, Sun-Cheol -- Wang, He -- Qin, Yuanbo -- Volpicelli-Daley, Laura -- Swan, Laura -- Lucast, Louise -- Khoo, Cynthia -- Zhang, Xiaowu -- Li, Lin -- Abrams, Charles S -- Sokol, Sergei Y -- Wu, Dianqing -- AR051476/AR/NIAMS NIH HHS/ -- CA132317/CA/NCI NIH HHS/ -- DA018343/DA/NIDA NIH HHS/ -- HL080706/HL/NHLBI NIH HHS/ -- NS36251/NS/NINDS NIH HHS/ -- P30 DA018343/DA/NIDA NIH HHS/ -- R01 AR051476/AR/NIAMS NIH HHS/ -- R01 AR051476-01A1/AR/NIAMS NIH HHS/ -- R01 AR051476-02/AR/NIAMS NIH HHS/ -- R01 AR051476-03/AR/NIAMS NIH HHS/ -- R01 CA132317/CA/NCI NIH HHS/ -- R01 CA132317-01A2/CA/NCI NIH HHS/ -- R01 CA139395/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2008 Sep 5;321(5894):1350-3. doi: 10.1126/science.1160741.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18772438" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/metabolism ; Animals ; Axin Protein ; Cell Line ; Frizzled Receptors/metabolism ; Humans ; LDL-Receptor Related Proteins/*metabolism ; Low Density Lipoprotein Receptor-Related Protein-6 ; Mice ; Models, Biological ; Phosphatidylinositol 4,5-Diphosphate/*metabolism ; Phosphoproteins/metabolism ; Phosphorylation ; Phosphotransferases (Alcohol Group Acceptor)/metabolism ; RNA, Small Interfering ; Recombinant Proteins/metabolism ; Repressor Proteins/metabolism ; Serine/metabolism ; Signal Transduction ; Threonine/metabolism ; Wnt Proteins/*metabolism ; Wnt3 Protein ; Wnt3A Protein ; Xenopus/embryology ; Xenopus Proteins
    Print ISSN: 0036-8075
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  • 7
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    The serine protease TMPRSS6 is required to sense iron deficiency (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-05-03
    Description: Hepcidin, a liver-derived protein that restricts enteric iron absorption, is the key regulator of body iron content. Several proteins induce expression of the hepcidin-encoding gene Hamp in response to infection or high levels of iron. However, mechanism(s) of Hamp suppression during iron depletion are poorly understood. We describe mask: a recessive, chemically induced mutant mouse phenotype, characterized by progressive loss of body (but not facial) hair and microcytic anemia. The mask phenotype results from reduced absorption of dietary iron caused by high levels of hepcidin and is due to a splicing defect in the transmembrane serine protease 6 gene Tmprss6. Overexpression of normal TMPRSS6 protein suppresses activation of the Hamp promoter, and the TMPRSS6 cytoplasmic domain mediates Hamp suppression via proximal promoter element(s). TMPRSS6 is an essential component of a pathway that detects iron deficiency and blocks Hamp transcription, permitting enhanced dietary iron absorption.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430097/" 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/PMC2430097/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Du, Xin -- She, Ellen -- Gelbart, Terri -- Truksa, Jaroslav -- Lee, Pauline -- Xia, Yu -- Khovananth, Kevin -- Mudd, Suzanne -- Mann, Navjiwan -- Moresco, Eva Marie Y -- Beutler, Ernest -- Beutler, Bruce -- AI054523/AI/NIAID NIH HHS/ -- DK53505-09/DK/NIDDK NIH HHS/ -- R01 DK053505-09/DK/NIDDK NIH HHS/ -- U54 AI054523/AI/NIAID NIH HHS/ -- U54 AI054523-019005/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2008 May 23;320(5879):1088-92. doi: 10.1126/science.1157121. Epub 2008 May 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18451267" target="_blank"〉PubMed〈/a〉
    Keywords: Anemia, Macrocytic/genetics/metabolism ; Animals ; Antimicrobial Cationic Peptides/*genetics/metabolism ; Cell Line, Tumor ; Gene Expression Regulation ; Hepcidins ; Humans ; Iron/blood/*deficiency/metabolism ; Membrane Proteins/chemistry/genetics/*metabolism ; Mice ; Mice, Mutant Strains ; Mice, Transgenic ; Models, Biological ; Mutation ; Phenotype ; Promoter Regions, Genetic ; Protein Structure, Tertiary ; Serine Endopeptidases/chemistry/genetics/*metabolism ; Signal Transduction ; Transfection
    Print ISSN: 0036-8075
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  • 8
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    Systems biology. The scale of prediction (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-06-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baliga, Nitin S -- New York, N.Y. -- Science. 2008 Jun 6;320(5881):1297-8. doi: 10.1126/science.1159485.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Systems Biology, 1441 N. 34th Street, Seattle, WA 98103, USA. nbaliga@systemsbiology.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18535232" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; *Bacterial Physiological Phenomena ; Computer Simulation ; Directed Molecular Evolution ; *Ecosystem ; Environment ; Escherichia coli/genetics/physiology ; *Gene Regulatory Networks ; *Metabolic Networks and Pathways ; Models, Biological ; Systems Biology
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  • 9
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    Traction dynamics of filopodia on compliant substrates (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-12-17
    Description: Cells sense the environment's mechanical stiffness to control their own shape, migration, and fate. To better understand stiffness sensing, we constructed a stochastic model of the "motor-clutch" force transmission system, where molecular clutches link F-actin to the substrate and mechanically resist myosin-driven F-actin retrograde flow. The model predicts two distinct regimes: (i) "frictional slippage," with fast retrograde flow and low traction forces on stiff substrates and (ii) oscillatory "load-and-fail" dynamics, with slower retrograde flow and higher traction forces on soft substrates. We experimentally confirmed these model predictions in embryonic chick forebrain neurons by measuring the nanoscale dynamics of single-growth-cone filopodia. Furthermore, we experimentally observed a model-predicted switch in F-actin dynamics around an elastic modulus of 1 kilopascal. Thus, a motor-clutch system inherently senses and responds to the mechanical stiffness of the local environment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chan, Clarence E -- Odde, David J -- R01-GM-76177/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Dec 12;322(5908):1687-91. doi: 10.1126/science.1163595.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19074349" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/*physiology ; Actins/*physiology ; Animals ; Biomechanical Phenomena ; Cell Adhesion ; Cells, Cultured ; Chick Embryo ; Compliance ; Computer Simulation ; Elastic Modulus ; Elasticity ; Growth Cones/*physiology/ultrastructure ; Models, Biological ; Myosin Type II/physiology ; Neurons/physiology ; Pseudopodia/*physiology ; Surface Tension
    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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  • 10
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    Biophysics. Clutch dynamics (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-12-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aratyn-Schaus, Yvonne -- Gardel, Margaret L -- DP1 OD003354/OD/NIH HHS/ -- DP1 OD003354-01/OD/NIH HHS/ -- DP1 OD003354-02/OD/NIH HHS/ -- New York, N.Y. -- Science. 2008 Dec 12;322(5908):1646-7. doi: 10.1126/science.1168102.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19074337" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/*physiology ; Actins/*physiology ; Animals ; Biomechanical Phenomena ; *Cell Adhesion ; Extracellular Matrix/physiology ; Focal Adhesions/*physiology ; Growth Cones/*physiology ; Models, Biological ; Myosin Type II/physiology ; Pseudopodia/*physiology
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  • 11
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    Structural basis for specific substrate recognition by the chloroplast signal recognition particle protein cpSRP43 (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-16
    Description: Secretory and membrane proteins carry amino-terminal signal sequences that, in cotranslational targeting, are recognized by the signal recognition particle protein SRP54 without sequence specificity. The most abundant membrane proteins on Earth are the light-harvesting chlorophyll a/b binding proteins (LHCPs). They are synthesized in the cytoplasm, imported into the chloroplast, and posttranslationally targeted to the thylakoid membrane by cpSRP, a heterodimer formed by cpSRP54 and cpSRP43. We present the 1.5 angstrom crystal structure of cpSRP43 characterized by a unique arrangement of chromodomains and ankyrin repeats. The overall shape and charge distribution of cpSRP43 resembles the SRP RNA, which is absent in chloroplasts. The complex with the internal signal sequence of LHCPs reveals that cpSRP43 specifically recognizes a DPLG peptide motif. We describe how cpSPR43 adapts the universally conserved SRP system to posttranslational targeting and insertion of the LHCP family of membrane proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stengel, Katharina F -- Holdermann, Iris -- Cain, Peter -- Robinson, Colin -- Wild, Klemens -- Sinning, Irmgard -- New York, N.Y. -- Science. 2008 Jul 11;321(5886):253-6. doi: 10.1126/science.1158640.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biochemie-Zentrum der Universitat Heidelberg, INF328, D-69120 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18621669" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Ankyrin Repeat ; Arabidopsis/chemistry/*metabolism ; Arabidopsis Proteins/*chemistry/metabolism ; Calorimetry ; Chloroplast Proteins ; Crystallography, X-Ray ; Dimerization ; Hydrophobic and Hydrophilic Interactions ; Light-Harvesting Protein Complexes/chemistry/*metabolism ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits ; RNA, Plant/chemistry/metabolism ; Signal Recognition Particle/*chemistry/*metabolism ; Thylakoids/metabolism
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  • 12
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    Auxin gradients are associated with polarity changes in trees (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-06-21
    Description: Models of plant growth and development propose that changes in cell polarity are mediated by gradients of the plant hormone auxin. With use of gas chromatography-mass spectrometry, we measured the redistribution of endogenous auxin in stems of quaking aspen trees (Populus tremuloides) after wounding. Persistent (lasting at least 24 hours) auxin gradients were observed in the region of the cambium where cell polarity was changing. A computer model of the auxin redistribution shows agreement with measured concentrations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kramer, Eric M -- Lewandowski, Michael -- Beri, Satvik -- Bernard, Jessica -- Borkowski, Matthew -- Borkowski, Michael H -- Burchfield, Laura Ann -- Mathisen, Brenda -- Normanly, Jennifer -- New York, N.Y. -- Science. 2008 Jun 20;320(5883):1610. doi: 10.1126/science.1156130.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Physics Department, Bard College at Simon'sRock, Great Barrington, MA 01230, USA and Centre for Plant Integrative Biology at the University of Nottingham, UK. ekramer@simons-rock.edu [corrected]〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18566279" target="_blank"〉PubMed〈/a〉
    Keywords: *Cell Polarity ; Computer Simulation ; Indoleacetic Acids/*metabolism ; Meristem/cytology/*metabolism ; Models, Biological ; Populus/*cytology/growth & development/*metabolism ; Wood/*cytology
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  • 13
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    Regulation of microtubule dynamics by reaction cascades around chromosomes (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-10-25
    Description: During spindle assembly, chromosomes generate gradients of microtubule stabilization through a reaction-diffusion process, but how this is achieved is not well understood. We measured the spatial distribution of microtubule aster asymmetry around chromosomes by incubating centrosomes and micropatterned chromatin patches in frog egg extracts. We then screened for microtubule stabilization gradient shapes that would generate such spatial distributions with the use of computer simulations. Only a long-range, sharply decaying microtubule stabilization gradient could generate aster asymmetries fitting the experimental data. We propose a reaction-diffusion model that combines the chromosome generated Ran-guanosine triphosphate-Importin reaction network to a secondary phosphorylation network as a potential mechanism for the generation of such gradients.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Athale, Chaitanya A -- Dinarina, Ana -- Mora-Coral, Maria -- Pugieux, Celine -- Nedelec, Francois -- Karsenti, Eric -- New York, N.Y. -- Science. 2008 Nov 21;322(5905):1243-7. doi: 10.1126/science.1161820. Epub 2008 Oct 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18948504" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Cycle Proteins/physiology ; Centrosome/physiology ; Chromatin/physiology ; Chromosomes, Human/physiology ; Computer Simulation ; Diffusion ; Humans ; Microtubule-Associated Proteins/physiology ; Microtubules/*physiology ; Models, Biological ; Nuclear Proteins/physiology ; Ovum/cytology ; Phosphoproteins/physiology ; Spindle Apparatus/*physiology ; Xenopus ; Xenopus Proteins/physiology ; ran GTP-Binding Protein/metabolism
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  • 14
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    Physiology. Burn fat, live longer (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-11-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xie, Ting -- New York, N.Y. -- Science. 2008 Nov 7;322(5903):865-6. doi: 10.1126/science.1166150.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA. tgx@stowersinstitute.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18988829" target="_blank"〉PubMed〈/a〉
    Keywords: Aging ; Animals ; Caenorhabditis elegans/genetics/*physiology ; Caenorhabditis elegans Proteins/metabolism ; Cell Proliferation ; Forkhead Transcription Factors ; Genes, Helminth ; Germ Cells/cytology/*metabolism ; Intestines/cytology/metabolism ; Intracellular Signaling Peptides and Proteins/metabolism ; Lipase/genetics/metabolism ; *Lipid Metabolism ; *Longevity ; Models, Animal ; Models, Biological ; Reproduction ; Signal Transduction ; Stem Cells/cytology/*metabolism ; Transcription Factors/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 15
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    The evolution and distribution of species body size (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-07-19
    Description: The distribution of species body size within taxonomic groups exhibits a heavy right tail extending over many orders of magnitude, where most species are much larger than the smallest species. We provide a simple model of cladogenetic diffusion over evolutionary time that omits explicit mechanisms for interspecific competition and other microevolutionary processes, yet fully explains the shape of this distribution. We estimate the model's parameters from fossil data and find that it robustly reproduces the distribution of 4002 mammal species from the late Quaternary. The observed fit suggests that the asymmetric distribution arises from a fundamental trade-off between the short-term selective advantages (Cope's rule) and long-term selective risks of increased species body size in the presence of a taxon-specific lower limit on body size.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clauset, Aaron -- Erwin, Douglas H -- New York, N.Y. -- Science. 2008 Jul 18;321(5887):399-401. doi: 10.1126/science.1157534.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA. aaronc@santafe.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18635801" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Body Size ; Computer Simulation ; Extinction, Biological ; Fossils ; Genetic Speciation ; Mammals/*anatomy & histology/classification/physiology ; Models, Biological ; Selection, Genetic
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  • 16
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    Resource partitioning and sympatric differentiation among closely related bacterioplankton (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-05-24
    Description: Identifying ecologically differentiated populations within complex microbial communities remains challenging, yet is critical for interpreting the evolution and ecology of microbes in the wild. Here we describe spatial and temporal resource partitioning among Vibrionaceae strains coexisting in coastal bacterioplankton. A quantitative model (AdaptML) establishes the evolutionary history of ecological differentiation, thus revealing populations specific for seasons and life-styles (combinations of free-living, particle, or zooplankton associations). These ecological population boundaries frequently occur at deep phylogenetic levels (consistent with named species); however, recent and perhaps ongoing adaptive radiation is evident in Vibrio splendidus, which comprises numerous ecologically distinct populations at different levels of phylogenetic differentiation. Thus, environmental specialization may be an important correlate or even trigger of speciation among sympatric microbes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hunt, Dana E -- David, Lawrence A -- Gevers, Dirk -- Preheim, Sarah P -- Alm, Eric J -- Polz, Martin F -- New York, N.Y. -- Science. 2008 May 23;320(5879):1081-5. doi: 10.1126/science.1157890.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497299" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Animals ; Atlantic Ocean ; Biological Evolution ; *Ecosystem ; *Genetic Speciation ; Markov Chains ; Models, Biological ; Molecular Sequence Data ; Phylogeny ; Plankton/*physiology ; Seasons ; Seawater/*microbiology ; Vibrio/classification/genetics/physiology ; Vibrionaceae/classification/genetics/*physiology ; Zooplankton/physiology
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    Myosin I can act as a molecular force sensor (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-07-05
    Description: The ability to sense molecular tension is crucial for a wide array of cellular processes, including the detection of auditory stimuli, control of cell shape, and internalization and transport of membranes. We show that myosin I, a motor protein that has been implicated in powering key steps in these processes, dramatically alters its motile properties in response to tension. We measured the displacement generated by single myosin I molecules, and we determined the actin-attachment kinetics with varying tensions using an optical trap. The rate of myosin I detachment from actin decreases 〉75-fold under tension of 2 piconewtons or less, resulting in myosin I transitioning from a low (〈0.2) to a high (〉0.9) duty-ratio motor. This impressive tension sensitivity supports a role for myosin I as a molecular force sensor.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2493443/" 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/PMC2493443/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Laakso, Joseph M -- Lewis, John H -- Shuman, Henry -- Ostap, E Michael -- AR051174/AR/NIAMS NIH HHS/ -- GM057247/GM/NIGMS NIH HHS/ -- P01 AR051174/AR/NIAMS NIH HHS/ -- P01 AR051174-050003/AR/NIAMS NIH HHS/ -- R01 GM057247-10/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Jul 4;321(5885):133-6. doi: 10.1126/science.1159419.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Pennsylvania Muscle Institute and Department of Physiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18599791" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/*metabolism ; Actomyosin/physiology ; Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Animals ; Biophysical Phenomena ; Biophysics ; Kinetics ; Likelihood Functions ; Models, Biological ; Molecular Motor Proteins/metabolism/*physiology ; Monte Carlo Method ; Myosin Type I/chemistry/metabolism/*physiology ; Optical Tweezers ; Protein Structure, Tertiary ; Rabbits ; Stress, Mechanical
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    Morphogenetic cell movements: diversity from modular mechanical properties (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-12-06
    Description: Animal tissue and organ development requires the orchestration of cell movements, including those of interconnected cell groups, termed collective cell movements. Such movements are incredibly diverse. Recent work suggests that two core cellular properties, cell-cell adhesion and contractility, can largely determine geometry, packing, sorting, and rearrangement of epithelial cell layers. Two additional force-generating properties, the ability to generate cell protrusions and cell adhesion to the extracellular matrix, contribute to active motility. These mechanical properties can be regulated independently in cells, suggesting that they can be employed in a combinatorial manner. A small number of properties used in combination could, in principle, generate a diverse array of cell shapes and arrangements and thus orchestrate the varied morphogenetic events observed during metazoan organ development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Montell, Denise J -- R01GM73164/GM/NIGMS NIH HHS/ -- U54 GM064346/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Dec 5;322(5907):1502-5. doi: 10.1126/science.1164073.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry, Center for Cell Dynamics, Rangos Building, Suite 450, 855 North Wolfe Street, Baltimore, MD 21205, USA. dmontell@jhmi.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19056976" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Adhesion ; *Cell Movement ; Cell Physiological Processes ; Cell Polarity ; Cell Shape ; Cell Surface Extensions/physiology/ultrastructure ; *Embryonic Development ; Extracellular Matrix/physiology ; Models, Biological ; *Morphogenesis ; Organogenesis
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  • 19
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    Midbody targeting of the ESCRT machinery by a noncanonical coiled coil in CEP55 (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-10-25
    Description: The ESCRT (endosomal sorting complex required for transport) machinery is required for the scission of membrane necks in processes including the budding of HIV-1 and cytokinesis. An essential step in cytokinesis is recruitment of the ESCRT-I complex and the ESCRT-associated protein ALIX to the midbody (the structure that tethers two daughter cells) by the protein CEP55. Biochemical experiments show that peptides from ALIX and the ESCRT-I subunit TSG101 compete for binding to the ESCRT and ALIX-binding region (EABR) of CEP55. We solved the crystal structure of EABR bound to an ALIX peptide at a resolution of 2.0 angstroms. The structure shows that EABR forms an aberrant dimeric parallel coiled coil. Bulky and charged residues at the interface of the two central heptad repeats create asymmetry and a single binding site for an ALIX or TSG101 peptide. Both ALIX and ESCRT-I are required for cytokinesis, which suggests that multiple CEP55 dimers are required for function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720046/" 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/PMC2720046/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Hyung Ho -- Elia, Natalie -- Ghirlando, Rodolfo -- Lippincott-Schwartz, Jennifer -- Hurley, James H -- Z01 DK036125-01/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2008 Oct 24;322(5901):576-80. doi: 10.1126/science.1162042.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18948538" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Calcium-Binding Proteins/*chemistry/*metabolism ; Cell Cycle Proteins/*chemistry/*metabolism ; Cellular Structures/metabolism ; Crystallography, X-Ray ; *Cytokinesis ; DNA-Binding Proteins/chemistry/metabolism ; Dimerization ; Endosomal Sorting Complexes Required for Transport ; Endosomes/metabolism ; HeLa Cells ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Biological ; Models, Molecular ; Nuclear Proteins/*chemistry/*metabolism ; Peptide Fragments/chemistry/metabolism ; Protein Binding ; Protein Conformation ; Transcription Factors/chemistry/metabolism ; Transfection
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  • 20
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    Developmental biology. On growth and force (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-12-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mulder, Bela -- New York, N.Y. -- Science. 2008 Dec 12;322(5908):1643-4. doi: 10.1126/science.1168512.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomolecular Systems, FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, Netherlands. mulder@amolf.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19074335" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arabidopsis/anatomy & histology/*cytology/*growth & development ; Cell Physiological Phenomena ; Cell Shape ; Cell Wall/physiology/ultrastructure ; Cellulose ; Dinitrobenzenes/pharmacology ; Meristem/cytology/growth & development ; Microfibrils/physiology ; Microtubules/*physiology ; Models, Biological ; Morphogenesis ; Plant Cells ; Plant Development ; Plant Shoots/anatomy & histology/cytology/*growth & development ; Stress, Mechanical ; Sulfanilamides/pharmacology ; Tubulin Modulators/pharmacology
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  • 21
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    From signals to patterns: space, time, and mathematics in developmental biology (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-10-18
    Description: We now have a wealth of information about the molecular signals that act on cells in embryos, but how do the control systems based on these signals generate pattern and govern the timing of developmental events? Here, I discuss four examples to show how mathematical modeling and quantitative experimentation can give some useful answers. The examples concern the Bicoid gradient in the early Drosophila embryo, the dorsoventral patterning of a frog embryo by bone morphogenetic protein signals, the auxin-mediated patterning of plant meristems, and the Notch-dependent somite segmentation clock.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lewis, Julian -- Cancer Research UK/United Kingdom -- New York, N.Y. -- Science. 2008 Oct 17;322(5900):399-403. doi: 10.1126/science.1166154.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vertebrate Development Laboratory, Cancer Research UK London Research Institute, London WC2A 3PX, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18927385" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Body Patterning ; Bone Morphogenetic Proteins/metabolism ; Drosophila/embryology/metabolism ; Embryo, Nonmammalian/*metabolism ; *Embryonic Development ; Feedback, Physiological ; Homeodomain Proteins/metabolism ; Indoleacetic Acids/metabolism ; Mathematics ; Meristem/*growth & development/metabolism ; Models, Biological ; Receptors, Notch/metabolism ; *Signal Transduction ; Somites/embryology ; Trans-Activators/metabolism ; Xenopus/embryology/metabolism ; Zebrafish/embryology/metabolism
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  • 22
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    Reconstitution of pilus assembly reveals a bacterial outer membrane catalyst (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-03-29
    Description: Type 1 pili from uropathogenic Escherichia coli are a prototype of adhesive surface organelles assembled and secreted by the conserved chaperone/usher pathway. We reconstituted type 1 pilus biogenesis from purified pilus proteins. The usher FimD acted as a catalyst to accelerate the ordered assembly of protein subunits independently of cellular energy. Its activity was highly dependent on the adhesin subunit FimH, which triggered the conversion of FimD into a high-efficiency assembly catalyst. Furthermore, a simple kinetic model adequately rationalized usher-catalyzed pilus assembly in vivo. Our results contribute to a mechanistic understanding of protein-catalyzed biogenesis of supramolecular protein complexes at the bacterial outer cell membrane.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nishiyama, Mireille -- Ishikawa, Takashi -- Rechsteiner, Helene -- Glockshuber, Rudi -- New York, N.Y. -- Science. 2008 Apr 18;320(5874):376-9. doi: 10.1126/science.1154994. Epub 2008 Mar 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, Eidgenossische Technische Hochschule (ETH) Zurich, 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18369105" target="_blank"〉PubMed〈/a〉
    Keywords: Adhesins, Escherichia coli/metabolism ; Bacterial Outer Membrane Proteins/*metabolism ; Catalysis ; Escherichia coli/*metabolism/ultrastructure ; Escherichia coli Proteins/genetics/*metabolism ; Fimbriae Proteins/genetics/*metabolism ; Fimbriae, Bacterial/*metabolism/ultrastructure ; Kinetics ; Models, Biological ; Temperature
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    Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-11
    Description: A long-standing goal of biology is to map the behavior of all cells during vertebrate embryogenesis. We developed digital scanned laser light sheet fluorescence microscopy and recorded nuclei localization and movement in entire wild-type and mutant zebrafish embryos over the first 24 hours of development. Multiview in vivo imaging at 1.5 billion voxels per minute provides "digital embryos," that is, comprehensive databases of cell positions, divisions, and migratory tracks. Our analysis of global cell division patterns reveals a maternally defined initial morphodynamic symmetry break, which identifies the embryonic body axis. We further derive a model of germ layer formation and show that the mesendoderm forms from one-third of the embryo's cells in a single event. Our digital embryos, with 55 million nucleus entries, are provided as a resource.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Keller, Philipp J -- Schmidt, Annette D -- Wittbrodt, Joachim -- Stelzer, Ernst H K -- New York, N.Y. -- Science. 2008 Nov 14;322(5904):1065-9. doi: 10.1126/science.1162493. Epub 2008 Oct 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany. keller@embl.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18845710" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Animals ; Body Patterning ; *Cell Division ; Cell Nucleus/physiology ; Databases, Factual ; Embryo, Nonmammalian/*cytology ; *Embryonic Development ; Endoderm/embryology ; Germ Layers/cytology/*embryology/physiology ; Image Processing, Computer-Assisted ; Mesoderm/embryology ; Microscopy, Fluorescence/methods ; Models, Biological ; Motion Pictures as Topic ; Mutation ; Software ; Zebrafish/*embryology/genetics ; beta Catenin/analysis
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    Spatial regulators for bacterial cell division self-organize into surface waves in vitro (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-05-10
    Description: In the bacterium Escherichia coli, the Min proteins oscillate between the cell poles to select the cell center as division site. This dynamic pattern has been proposed to arise by self-organization of these proteins, and several models have suggested a reaction-diffusion type mechanism. Here, we found that the Min proteins spontaneously formed planar surface waves on a flat membrane in vitro. The formation and maintenance of these patterns, which extended for hundreds of micrometers, required adenosine 5'-triphosphate (ATP), and they persisted for hours. We present a reaction-diffusion model of the MinD and MinE dynamics that accounts for our experimental observations and also captures the in vivo oscillations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Loose, Martin -- Fischer-Friedrich, Elisabeth -- Ries, Jonas -- Kruse, Karsten -- Schwille, Petra -- New York, N.Y. -- Science. 2008 May 9;320(5877):789-92. doi: 10.1126/science.1154413.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biotechnologisches Zentrum der Technischen Universitat Dresden, Tatzberg 47-51, 01307 Dresden, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18467587" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*physiology ; Adenosine Triphosphate/physiology ; Bacterial Proteins ; Cell Cycle Proteins/*physiology ; Cell Division/*physiology ; Cell-Free System ; Cytoskeletal Proteins ; Diffusion ; Escherichia coli/*physiology ; Escherichia coli Proteins/*physiology ; Models, Biological ; Oscillometry
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    An oncogene-induced DNA damage model for cancer development (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-03-08
    Description: Of all types of DNA damage, DNA double-strand breaks (DSBs) pose the greatest challenge to cells. One might have, therefore, anticipated that a sizable number of DNA DSBs would be incompatible with cell proliferation. Yet recent experimental findings suggest that, in both precancerous lesions and cancers, activated oncogenes induce stalling and collapse of DNA replication forks, which in turn leads to formation of DNA DSBs. This continuous formation of DNA DSBs may contribute to the genomic instability that characterizes the vast majority of human cancers. In addition, in precancerous lesions, these DNA DSBs activate p53, which, by inducing apoptosis or senescence, raises a barrier to tumor progression. Breach of this barrier by various mechanisms, most notably by p53 mutations, that impair the DNA damage response pathway allows cancers to develop. Thus, oncogene-induced DNA damage may explain two key features of cancer: genomic instability and the high frequency of p53 mutations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Halazonetis, Thanos D -- Gorgoulis, Vassilis G -- Bartek, Jiri -- New York, N.Y. -- Science. 2008 Mar 7;319(5868):1352-5. doi: 10.1126/science.1140735.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Department of Biochemistry, University of Geneva, CH-1205 Geneva, Switzerland. Thanos.Halazonetis@molbio.unige.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18323444" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Proliferation ; DNA Breaks, Double-Stranded ; *DNA Damage ; DNA Replication ; Disease Progression ; Genes, p53 ; Genomic Instability ; Humans ; Models, Biological ; Mutation ; Neoplasms/*genetics/pathology/physiopathology ; *Oncogenes ; Precancerous Conditions/*genetics/pathology/physiopathology ; Tumor Suppressor Protein p53/metabolism
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    Developmental patterning by mechanical signals in Arabidopsis (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-12-17
    Description: A central question in developmental biology is whether and how mechanical forces serve as cues for cellular behavior and thereby regulate morphogenesis. We found that morphogenesis at the Arabidopsis shoot apex depends on the microtubule cytoskeleton, which in turn is regulated by mechanical stress. A combination of experiments and modeling shows that a feedback loop encompassing tissue morphology, stress patterns, and microtubule-mediated cellular properties is sufficient to account for the coordinated patterns of microtubule arrays observed in epidermal cells, as well as for patterns of apical morphogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hamant, Olivier -- Heisler, Marcus G -- Jonsson, Henrik -- Krupinski, Pawel -- Uyttewaal, Magalie -- Bokov, Plamen -- Corson, Francis -- Sahlin, Patrik -- Boudaoud, Arezki -- Meyerowitz, Elliot M -- Couder, Yves -- Traas, Jan -- New York, N.Y. -- Science. 2008 Dec 12;322(5908):1650-5. doi: 10.1126/science.1165594.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉INRA, Laboratoire de Reproduction et Developpement des Plantes, 46 Allee d'Italie, 69364 Lyon Cedex 07, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19074340" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/anatomy & histology/cytology/*growth & development ; Cell Shape ; Cell Wall/physiology/ultrastructure ; Cellulose ; Dinitrobenzenes/pharmacology ; Meristem/cytology/*growth & development ; Microfibrils/physiology ; Microtubules/*physiology/ultrastructure ; Models, Biological ; Morphogenesis ; Plant Epidermis/physiology ; Plant Shoots/anatomy & histology/cytology/*growth & development ; Plant Stems/cytology/growth & development ; Pressure ; Stress, Mechanical ; Sulfanilamides/pharmacology ; Tubulin Modulators/pharmacology
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  • 27
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    Detection of GTP-tubulin conformation in vivo reveals a role for GTP remnants in microtubule rescues (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-10-18
    Description: Microtubules display dynamic instability, with alternating phases of growth and shrinkage separated by catastrophe and rescue events. The guanosine triphosphate (GTP) cap at the growing end of microtubules, whose presence is essential to prevent microtubule catastrophes in vitro, has been difficult to observe in vivo. We selected a recombinant antibody that specifically recognizes GTP-bound tubulin in microtubules and found that GTP-tubulin was indeed present at the plus end of growing microtubules. Unexpectedly, GTP-tubulin remnants were also present in older parts of microtubules, which suggests that GTP hydrolysis is sometimes incomplete during polymerization. Observations in living cells suggested that these GTP remnants may be responsible for the rescue events in which microtubules recover from catastrophe.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dimitrov, Ariane -- Quesnoit, Melanie -- Moutel, Sandrine -- Cantaloube, Isabelle -- Pous, Christian -- Perez, Franck -- New York, N.Y. -- Science. 2008 Nov 28;322(5906):1353-6. doi: 10.1126/science.1165401. Epub 2008 Oct 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CNRS UMR144, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18927356" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies/immunology ; Cell Line ; Computer Simulation ; Dimerization ; Fluorescent Antibody Technique ; Guanosine Triphosphate/*analysis/metabolism ; HeLa Cells ; Humans ; Microtubules/*chemistry/metabolism/ultrastructure ; Models, Biological ; Monte Carlo Method ; Protein Conformation ; Recombinant Fusion Proteins/metabolism ; Tubulin/analysis/*chemistry/immunology/metabolism
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    Molecular biology. The paradox of silent heterochromatin (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-05-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Djupedal, Ingela -- Ekwall, Karl -- New York, N.Y. -- Science. 2008 May 2;320(5876):624-5. doi: 10.1126/science.1158923.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biosciences and Medical Nutrition, Karolinska Institutet, Sweden/School of Life Sciences, University College Sodertorn, NOVUM, 141 57 Huddinge, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18451292" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Cycle/genetics ; Heterochromatin/*physiology ; Models, Biological ; RNA Interference ; RNA Polymerase II/metabolism ; RNA, Fungal/physiology ; Schizosaccharomyces/genetics/physiology ; Transcription, Genetic
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    Cancer. Aneuploidy advantages? (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-11-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hernando, Eva -- New York, N.Y. -- Science. 2008 Oct 31;322(5902):692-3. doi: 10.1126/science.1166151.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, New York University School of Medicine, New York, NY 10016, USA. eva.hernando@med.nyu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18974340" target="_blank"〉PubMed〈/a〉
    Keywords: *Aneuploidy ; Animals ; Cell Line ; Cell Movement ; Cell Proliferation ; Cell Survival ; *Cell Transformation, Neoplastic ; Cells, Cultured ; Gene Amplification ; Genomic Instability ; Humans ; Mice ; Models, Biological ; Mutation ; Neoplasms/*genetics ; *Trisomy
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    A competitive inhibitor traps LeuT in an open-to-out conformation (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-12-17
    Description: Secondary transporters are workhorses of cellular membranes, catalyzing the movement of small molecules and ions across the bilayer and coupling substrate passage to ion gradients. However, the conformational changes that accompany substrate transport, the mechanism by which a substrate moves through the transporter, and principles of competitive inhibition remain unclear. We used crystallographic and functional studies on the leucine transporter (LeuT), a model for neurotransmitter sodium symporters, to show that various amino acid substrates induce the same occluded conformational state and that a competitive inhibitor, tryptophan (Trp), traps LeuT in an open-to-out conformation. In the Trp complex, the extracellular gate residues arginine 30 and aspartic acid 404 define a second weak binding site for substrates or inhibitors as they permeate from the extracellular solution to the primary substrate site, which demonstrates how residues that participate in gating also mediate permeation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832577/" 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/PMC2832577/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Singh, Satinder K -- Piscitelli, Chayne L -- Yamashita, Atsuko -- Gouaux, Eric -- K99 MH083050-02/MH/NIMH NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 MH070039/MH/NIMH NIH HHS/ -- R01 MH070039-05/MH/NIMH NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Dec 12;322(5908):1655-61. doi: 10.1126/science.1166777.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vollum Institute, Oregon Health and Science University, 3181 Southwest Sam Jackson Park Road, Portland, OR 97239, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19074341" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Transport Systems/antagonists & inhibitors/*chemistry/*metabolism ; Amino Acids/metabolism/pharmacology ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Binding, Competitive ; Biological Transport ; Crystallization ; Crystallography, X-Ray ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Leucine/*metabolism ; Ligands ; Models, Biological ; Models, Molecular ; Protein Conformation ; Protein Structure, Tertiary ; Sodium/metabolism ; Symporters/antagonists & inhibitors/*chemistry/*metabolism ; Tryptophan/metabolism/*pharmacology
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    Origin of stem cells in organogenesis (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-12-06
    Description: The development of individual organs in animal embryos involves the formation of tissue-specific stem cells that sustain cell renewal of their own tissue for the lifetime of the organism. Although details of their origin are not always known, tissue-specific stem cells usually share the expression of key transcription factors with cells of the embryonic rudiment from which they arise, and are probably in a similar developmental state. On the other hand, the isolation of pluripotent stem cells from the postnatal organism has encouraged the formulation of models of embryonic and postnatal development that are at variance with the conventional ones. Possible explanations for the existence of such cells, and the issue of whether they also exist in vivo, are discussed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Slack, J M W -- G0300415/Medical Research Council/United Kingdom -- G0500220/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Dec 5;322(5907):1498-501. doi: 10.1126/science.1162782.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Stem Cell Institute, University of Minnesota, McGuire Translational Research Facility, 2001 6th Street SE, Minneapolis, MN 55455, USA. slack017@umn.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19056975" target="_blank"〉PubMed〈/a〉
    Keywords: Adult Stem Cells/cytology/physiology ; Animals ; Cell Differentiation ; Cell Lineage ; Cell Separation ; Cell Transdifferentiation ; Cells, Cultured ; Embryonic Stem Cells/cytology/physiology ; Humans ; Models, Biological ; Neural Crest/cytology ; *Organogenesis ; Pluripotent Stem Cells/cytology/physiology ; Stem Cell Niche ; Stem Cells/cytology/*physiology ; Transcription Factors/metabolism
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    Energy uptake and allocation during ontogeny (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-11-01
    Description: All organisms face the problem of how to fuel ontogenetic growth. We present a model, empirically grounded in data from birds and mammals, that correctly predicts how growing animals allocate food energy between synthesis of new biomass and maintenance of existing biomass. Previous energy budget models have typically had their bases in rates of either food consumption or metabolic energy expenditure. Our model provides a framework that reconciles these two approaches and highlights the fundamental principles that determine rates of food assimilation and rates of energy allocation to maintenance, biosynthesis, activity, and storage. The model predicts that growth and assimilation rates for all animals should cluster closely around two universal curves. Data for mammals and birds of diverse body sizes and taxa support these predictions.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2891030/" 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/PMC2891030/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hou, Chen -- Zuo, Wenyun -- Moses, Melanie E -- Woodruff, William H -- Brown, James H -- West, Geoffrey B -- DK36263/DK/NIDDK NIH HHS/ -- P20 RR-018754/RR/NCRR NIH HHS/ -- P20 RR018754/RR/NCRR NIH HHS/ -- P20 RR018754-06A1/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2008 Oct 31;322(5902):736-9. doi: 10.1126/science.1162302.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA. houc@santafe.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18974352" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Basal Metabolism ; Biomass ; Birds/embryology/growth & development/*metabolism ; Body Size ; *Energy Intake ; *Energy Metabolism ; Female ; Food ; *Growth ; Male ; Mammals/embryology/growth & development/*metabolism ; Mathematics ; Models, Biological
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    Membrane proteins of the endoplasmic reticulum induce high-curvature tubules (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-03-01
    Description: The tubular structure of the endoplasmic reticulum (ER) appears to be generated by integral membrane proteins, the reticulons and a protein family consisting of DP1 in mammals and Yop1p in yeast. Here, individual members of these families were found to be sufficient to generate membrane tubules. When we purified yeast Yop1p and incorporated it into proteoliposomes, narrow tubules (approximately 15 to 17 nanometers in diameter) were generated. Tubule formation occurred with different lipids; required essentially only the central portion of the protein, including its two long hydrophobic segments; and was prevented by mutations that affected tubule formation in vivo. Tubules were also formed by reconstituted purified yeast Rtn1p. Tubules made in vitro were narrower than normal ER tubules, due to a higher concentration of tubule-inducing proteins. The shape and oligomerization of the "morphogenic" proteins could explain the formation of the tubular ER.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hu, Junjie -- Shibata, Yoko -- Voss, Christiane -- Shemesh, Tom -- Li, Zongli -- Coughlin, Margaret -- Kozlov, Michael M -- Rapoport, Tom A -- Prinz, William A -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2008 Feb 29;319(5867):1247-50. doi: 10.1126/science.1153634.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18309084" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Biopolymers/chemistry/metabolism ; COS Cells ; Cercopithecus aethiops ; Endoplasmic Reticulum/*chemistry/metabolism/*ultrastructure ; Hydrophobic and Hydrophilic Interactions ; Intracellular Membranes/chemistry/ultrastructure ; Lipid Bilayers ; Membrane Lipids/chemistry ; Membrane Proteins/*chemistry/*metabolism ; Membrane Transport Proteins/*chemistry/*metabolism ; Microscopy, Electron ; Models, Biological ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Proteolipids/chemistry ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism
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    The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-01-26
    Description: The propagation of information through signaling cascades spans a wide range of time scales, including the rapid ligand-receptor interaction and the much slower response of downstream gene expression. To determine which dynamic range dominates a response, we used periodic stimuli to measure the frequency dependence of signal transduction in the osmo-adaptation pathway of Saccharomyces cerevisiae. We applied system identification methods to infer a concise predictive model. We found that the dynamics of the osmo-adaptation response are dominated by a fast-acting negative feedback through the kinase Hog1 that does not require protein synthesis. After large osmotic shocks, an additional, much slower, negative feedback through gene expression allows cells to respond faster to future stimuli.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2916730/" 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/PMC2916730/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mettetal, Jerome T -- Muzzey, Dale -- Gomez-Uribe, Carlos -- van Oudenaarden, Alexander -- 5 R90 DK071511-01/DK/NIDDK NIH HHS/ -- R01 GM068957/GM/NIGMS NIH HHS/ -- R01 GM068957-05/GM/NIGMS NIH HHS/ -- R01 GM068957-06/GM/NIGMS NIH HHS/ -- R01-GM068957/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Jan 25;319(5862):482-4. doi: 10.1126/science.1151582.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18218902" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; Cell Nucleus/metabolism ; *Feedback, Physiological ; Gene Expression Regulation, Fungal ; Gene Regulatory Networks ; Glycerol/*metabolism ; Mitogen-Activated Protein Kinases/*metabolism ; Models, Biological ; Osmolar Concentration ; Osmotic Pressure ; Phosphorylation ; Saccharomyces cerevisiae/genetics/metabolism/*physiology ; Saccharomyces cerevisiae Proteins/*metabolism ; Signal Transduction ; Systems Biology
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    Cell signaling. Getting your loops straight. Introduction (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ray, L Bryan -- New York, N.Y. -- Science. 2008 Oct 17;322(5900):389. doi: 10.1126/science.322.5900.389.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18927382" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Feedback, Physiological ; Models, Biological ; *Signal Transduction ; Yeasts/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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  • 36
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    Predictive behavior within microbial genetic networks (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-05-10
    Description: The homeostatic framework has dominated our understanding of cellular physiology. We question whether homeostasis alone adequately explains microbial responses to environmental stimuli, and explore the capacity of intracellular networks for predictive behavior in a fashion similar to metazoan nervous systems. We show that in silico biochemical networks, evolving randomly under precisely defined complex habitats, capture the dynamical, multidimensional structure of diverse environments by forming internal representations that allow prediction of environmental change. We provide evidence for such anticipatory behavior by revealing striking correlations of Escherichia coli transcriptional responses to temperature and oxygen perturbations-precisely mirroring the covariation of these parameters upon transitions between the outside world and the mammalian gastrointestinal tract. We further show that these internal correlations reflect a true associative learning paradigm, because they show rapid decoupling upon exposure to novel environments.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2931280/" 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/PMC2931280/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tagkopoulos, Ilias -- Liu, Yir-Chung -- Tavazoie, Saeed -- DP1 OD003787/OD/NIH HHS/ -- P50 GM071508/GM/NIGMS NIH HHS/ -- P50 GM071508-01/GM/NIGMS NIH HHS/ -- P50 GM071508-06/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Jun 6;320(5881):1313-7. doi: 10.1126/science.1154456. Epub 2008 May 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Electrical Engineering, Princeton University, Princeton, NJ 08544, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18467556" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; Aerobiosis ; Anaerobiosis ; Computer Simulation ; Directed Molecular Evolution ; Ecosystem ; Escherichia coli/*genetics/growth & development/*physiology ; *Gene Regulatory Networks ; Homeostasis ; Kinetics ; *Metabolic Networks and Pathways ; Models, Biological ; Models, Statistical ; Mutation ; Oligonucleotide Array Sequence Analysis ; Oxygen/analysis ; Temperature ; *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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