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  • Population Dynamics  (117)
  • Models, Molecular  (95)
  • American Association for the Advancement of Science (AAAS)  (212)
  • American Society of Hematology
  • EMBO Press
  • Essen : Verl. Glückauf
  • Krefeld : Geologischer Dienst Nordhein-Westfalen
  • 2005-2009  (212)
  • 2007  (104)
  • 2006  (108)
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (212)
  • American Society of Hematology
  • EMBO Press
  • Essen : Verl. Glückauf
  • Krefeld : Geologischer Dienst Nordhein-Westfalen
Years
  • 2005-2009  (212)
Year
  • 1
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    The evolutionary demography of ecological change: linking trait variation and population growth (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-03-17
    Description: Population dynamics and evolutionary change are linked by the fundamental biological processes of birth and death. This means that population growth may correlate with the strength of selection, whereas evolutionary change can leave an ecological signature. We decompose population growth in an age-structured population into contributions from variation in a quantitative trait. We report that the distribution of body sizes within a population of Soay sheep can markedly influence population dynamics, accounting for up to one-fifth of observed population growth. Our results suggest that there is substantial opportunity for evolutionary dynamics to leave an ecological signature and visa versa.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pelletier, Fanie -- Clutton-Brock, Tim -- Pemberton, Josephine -- Tuljapurkar, Shripad -- Coulson, Tim -- P01 AG 22500/AG/NIA NIH HHS/ -- P01 AG022500/AG/NIA NIH HHS/ -- P01 AG022500-04/AG/NIA NIH HHS/ -- New York, N.Y. -- Science. 2007 Mar 16;315(5818):1571-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology and the Natural Environment Research Council (NERC) Centre for Population Biology, Imperial College London, Silwood Park, Ascot, Berkshire, SL5 7PY, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17363672" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Birth Weight ; Body Size/genetics ; Body Weight/genetics ; Ecology ; Environment ; Female ; *Genetic Variation ; Hindlimb/anatomy & histology ; Male ; Mathematics ; Population Dynamics ; Population Growth ; *Quantitative Trait, Heritable ; Scotland ; *Selection, Genetic ; *Sheep/anatomy & histology/genetics/growth & development ; Weather
    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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    Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4 (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-29
    Description: The CCR5 co-receptor binds to the HIV-1 gp120 envelope glycoprotein and facilitates HIV-1 entry into cells. Its N terminus is tyrosine-sulfated, as are many antibodies that react with the co-receptor binding site on gp120. We applied nuclear magnetic resonance and crystallographic techniques to analyze the structure of the CCR5 N terminus and that of the tyrosine-sulfated antibody 412d in complex with gp120 and CD4. The conformations of tyrosine-sulfated regions of CCR5 (alpha-helix) and 412d (extended loop) are surprisingly different. Nonetheless, a critical sulfotyrosine on CCR5 and on 412d induces similar structural rearrangements in gp120. These results now provide a framework for understanding HIV-1 interactions with the CCR5 N terminus during viral entry and define a conserved site on gp120, whose recognition of sulfotyrosine engenders posttranslational mimicry by the immune system.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2278242/" 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/PMC2278242/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Chih-Chin -- Lam, Son N -- Acharya, Priyamvada -- Tang, Min -- Xiang, Shi-Hua -- Hussan, Syed Shahzad-Ul -- Stanfield, Robyn L -- Robinson, James -- Sodroski, Joseph -- Wilson, Ian A -- Wyatt, Richard -- Bewley, Carole A -- Kwong, Peter D -- P30 AI060354/AI/NIAID NIH HHS/ -- U19 AI067854/AI/NIAID NIH HHS/ -- U19 AI067854-03/AI/NIAID NIH HHS/ -- Z99 AI999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 28;317(5846):1930-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17901336" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antigens, CD4/*chemistry/immunology ; Crystallography, X-Ray ; HIV Antibodies/*chemistry/immunology ; HIV Envelope Protein gp120/*chemistry/immunology/metabolism ; HIV-1/metabolism ; Humans ; Models, Molecular ; Molecular Mimicry ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Peptide Fragments/chemistry/metabolism ; Receptors, CCR5/*chemistry/metabolism ; Sulfates/metabolism ; Tyrosine/metabolism ; Virus Internalization
    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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    Role of intermolecular forces in defining material properties of protein nanofibrils (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-22
    Description: Protein molecules have the ability to form a rich variety of natural and artificial structures and materials. We show that amyloid fibrils, ordered supramolecular nanostructures that are self-assembled from a wide range of polypeptide molecules, have rigidities varying over four orders of magnitude, and constitute a class of high-performance biomaterials. We elucidate the molecular origin of fibril material properties and show that the major contribution to their rigidity stems from a generic interbackbone hydrogen-bonding network that is modulated by variable side-chain interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Knowles, Tuomas P -- Fitzpatrick, Anthony W -- Meehan, Sarah -- Mott, Helen R -- Vendruscolo, Michele -- Dobson, Christopher M -- Welland, Mark E -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2007 Dec 21;318(5858):1900-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Nanoscience Centre, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0FF, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18096801" target="_blank"〉PubMed〈/a〉
    Keywords: Amyloid/*chemistry ; Amyloid beta-Peptides/chemistry ; Chemistry, Physical ; Elasticity ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Insulin/chemistry ; Lactalbumin/chemistry ; Lactoglobulins/chemistry ; Microscopy, Atomic Force ; Models, Molecular ; Muramidase/chemistry ; Nanostructures/*chemistry ; Peptide Termination Factors ; Peptides/*chemistry ; Physicochemical Phenomena ; Prealbumin/chemistry ; Prions/chemistry ; Protein Conformation ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/chemistry ; Surface Tension ; alpha-Crystallin B Chain/chemistry
    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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    Ecology. Tackling ecological complexity in climate impact research (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Walther, Gian-Reto -- New York, N.Y. -- Science. 2007 Feb 2;315(5812):606-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Ecology, University of Bayreuth, 95440 Bayreuth, Germany. gian-reto.walther@uni-bayreuth.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17272708" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; California ; *Climate ; *Ecosystem ; *Invertebrates/physiology ; *Plant Development ; Poaceae/growth & development ; Population Dynamics ; Rain ; Research Design ; Seasons ; Time Factors
    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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    Structural insight into pre-B cell receptor function (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-04-14
    Description: The pre-B cell receptor (pre-BCR) serves as a checkpoint in B cell development. In the 2.7 angstrom structure of a human pre-BCR Fab-like fragment, consisting of an antibody heavy chain (HC) paired with the surrogate light chain, the "unique regions" of VpreB and lambda5 replace the complementarity-determining region 3 (CDR3) loop of an antibody light chain and appear to "probe" the HC CDR3, potentially influencing the selection of the antibody repertoire. Biochemical analysis indicates that the pre-BCR is impaired in its ability to recognize antigen, which, together with electron microscopic visualization of a pre-BCR dimer, suggests ligand-independent oligomerization as the likely signaling mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bankovich, Alexander J -- Raunser, Stefan -- Juo, Z Sean -- Walz, Thomas -- Davis, Mark M -- Garcia, K Christopher -- T32 AI007290/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2007 Apr 13;316(5822):291-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17431183" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Complementarity Determining Regions/chemistry/physiology ; Crystallography, X-Ray ; Humans ; Immunoglobulin Heavy Chains/chemistry/physiology ; Immunoglobulin Light Chains/chemistry/physiology ; Immunoglobulin Light Chains, Surrogate ; Membrane Glycoproteins/*chemistry/physiology/ultrastructure ; Mice ; Models, Molecular ; Pre-B Cell Receptors ; Protein Conformation ; Receptors, Antigen, B-Cell/*chemistry/physiology/ultrastructure ; Recombinant Proteins ; Structure-Activity Relationship
    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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  • 6
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    Asymmetry in the structure of the ABC transporter-binding protein complex BtuCD-BtuF (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-04
    Description: BtuCD is an adenosine triphosphate-binding cassette (ABC) transporter that translocates vitamin B12 from the periplasmic binding protein BtuF into the cytoplasm of Escherichia coli. The 2.6 angstrom crystal structure of a complex BtuCD-F reveals substantial conformational changes as compared with the previously reported structures of BtuCD and BtuF. The lobes of BtuF are spread apart, and B12 is displaced from the binding pocket. The transmembrane BtuC subunits reveal two distinct conformations, and the translocation pathway is closed to both sides of the membrane. Electron paramagnetic resonance spectra of spin-labeled cysteine mutants reconstituted in proteoliposomes are consistent with the conformation of BtuCD-F that was observed in the crystal structure. A comparison with BtuCD and the homologous HI1470/71 protein suggests that the structure of BtuCD-F may reflect a posttranslocation intermediate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hvorup, Rikki N -- Goetz, Birke A -- Niederer, Martina -- Hollenstein, Kaspar -- Perozo, Eduardo -- Locher, Kaspar P -- New York, N.Y. -- Science. 2007 Sep 7;317(5843):1387-90. Epub 2007 Aug 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, ETH Zurich, HPK D14.3, 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17673622" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry ; Amino Acid Sequence ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Escherichia coli ; Escherichia coli Proteins/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Periplasmic Binding Proteins/*chemistry ; Protein Binding ; Protein Conformation ; Recombinant Fusion Proteins/chemistry
    Print ISSN: 0036-8075
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  • 7
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    Redefining the age of Clovis: implications for the peopling of the Americas (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-27
    Description: The Clovis complex is considered to be the oldest unequivocal evidence of humans in the Americas, dating between 11,500 and 10,900 radiocarbon years before the present (14C yr B.P.). Adjusted 14C dates and a reevaluation of the existing Clovis date record revise the Clovis time range to 11,050 to 10,800 14C yr B.P. In as few as 200 calendar years, Clovis technology originated and spread throughout North America. The revised age range for Clovis overlaps non-Clovis sites in North and South America. This and other evidence imply that humans already lived in the Americas before Clovis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Waters, Michael R -- Stafford, Thomas W Jr -- New York, N.Y. -- Science. 2007 Feb 23;315(5815):1122-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Anthropology and Geography, Center for the Study of the First Americans, Texas A&M University, 4352 TAMU, College Station, TX 77843-4352, USA. mwaters@tamu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17322060" target="_blank"〉PubMed〈/a〉
    Keywords: *Archaeology ; *Culture ; Emigration and Immigration ; History, Ancient ; Humans ; North America ; Population Dynamics ; South America ; Time
    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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  • 8
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    Molecular evolution. Resurrected proteins reveal their surprising history (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, Robert F -- New York, N.Y. -- Science. 2007 Aug 17;317(5840):884-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17702918" target="_blank"〉PubMed〈/a〉
    Keywords: Aldosterone/metabolism ; Animals ; Computer Simulation ; Crystallography, X-Ray ; Desoxycorticosterone/metabolism ; *Evolution, Molecular ; *Fishes ; Hydrocortisone/metabolism ; Models, Molecular ; Mutation ; Protein Conformation ; Receptors, Glucocorticoid/chemistry/*genetics/metabolism ; Receptors, Mineralocorticoid/chemistry/*genetics/metabolism ; Receptors, Steroid/chemistry/*genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    Stability and diversity of ecosystems (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-07-07
    Description: Understanding the relationship between diversity and stability requires a knowledge of how species interact with each other and how each is affected by the environment. The relationship is also complex, because the concept of stability is multifaceted; different types of stability describing different properties of ecosystems lead to multiple diversity-stability relationships. A growing number of empirical studies demonstrate positive diversity-stability relationships. These studies, however, have emphasized only a few types of stability, and they rarely uncover the mechanisms responsible for stability. Because anthropogenic changes often affect stability and diversity simultaneously, diversity-stability relationships cannot be understood outside the context of the environmental drivers affecting both. This shifts attention away from diversity-stability relationships toward the multiple factors, including diversity, that dictate the stability of ecosystems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ives, Anthony R -- Carpenter, Stephen R -- New York, N.Y. -- Science. 2007 Jul 6;317(5834):58-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, University of Wisconsin, Madison, WI 53706, USA. arives@wisc.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17615333" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Ecosystem ; Environment ; Extinction, Biological ; Models, Biological ; Population Dynamics
    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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    Rise and fall of species occupancy in Cenozoic fossil mollusks (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-11-17
    Description: In the time between speciation and extinction, a species' ecological and biogeographic footprint-its occupancy-will vary in response to macroecological drivers and historical contingencies. Despite their importance for understanding macroecological processes, general patterns of long-term species occupancy remain largely unknown. We documented the occupancy histories of Cenozoic marine mollusks from New Zealand. For both genera and species, these show a distinct pattern of increase to relatively short-lived peak occupancy at mid-duration, followed by a decline toward extinction. Thus, species at greatest risk for extinction are those that have already been in decline for a substantial period of time. This pattern of protracted rise and fall stands in contrast to that of incumbency, insofar as species show no general tendency to stay near maximal occupancy once established.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Foote, Michael -- Crampton, James S -- Beu, Alan G -- Marshall, Bruce A -- Cooper, Roger A -- Maxwell, Phillip A -- Matcham, Iain -- New York, N.Y. -- Science. 2007 Nov 16;318(5853):1131-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of the Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60637 USA. mfoote@uchicago.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18006744" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; *Biological Evolution ; *Extinction, Biological ; *Fossils ; *Mollusca ; Population Dynamics ; Seawater ; Time
    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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  • 11
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    Direct observation of chaperone-induced changes in a protein folding pathway (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-01
    Description: How chaperone interactions affect protein folding pathways is a central problem in biology. With the use of optical tweezers and all-atom molecular dynamics simulations, we studied the effect of chaperone SecB on the folding and unfolding pathways of maltose binding protein (MBP) at the single-molecule level. In the absence of SecB, we find that the MBP polypeptide first collapses into a molten globulelike compacted state and then folds into a stable core structure onto which several alpha helices are finally wrapped. Interactions with SecB completely prevent stable tertiary contacts in the core structure but have no detectable effect on the folding of the external alpha helices. It appears that SecB only binds to the extended or molten globulelike structure and retains MBP in this latter state. Thus during MBP translocation, no energy is required to disrupt stable tertiary interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bechtluft, Philipp -- van Leeuwen, Ruud G H -- Tyreman, Matthew -- Tomkiewicz, Danuta -- Nouwen, Nico -- Tepper, Harald L -- Driessen, Arnold J M -- Tans, Sander J -- New York, N.Y. -- Science. 2007 Nov 30;318(5855):1458-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Microbiology, Groningen Bio-molecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, Kerklaan 30, 9751 NN Haren, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18048690" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*metabolism ; Computer Simulation ; Escherichia coli Proteins/*chemistry/metabolism ; Models, Molecular ; Optical Tweezers ; Periplasmic Binding Proteins/*chemistry/metabolism ; Protein Conformation ; *Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 12
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    Structure of fungal fatty acid synthase and implications for iterative substrate shuttling (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-04-14
    Description: We report crystal structures of the 2.6-megadalton alpha6beta6 heterododecameric fatty acid synthase from Thermomyces lanuginosus at 3.1 angstrom resolution. The alpha and beta polypeptide chains form the six catalytic domains required for fatty acid synthesis and numerous expansion segments responsible for extensive intersubunit connections. Detailed views of all active sites provide insights into substrate specificities and catalytic mechanisms and reveal their unique characteristics, which are due to the integration into the multienzyme. The mode of acyl carrier protein attachment in the reaction chamber, together with the spatial distribution of active sites, suggests that iterative substrate shuttling is achieved by a relatively restricted circular motion of the carrier domain in the multifunctional enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jenni, Simon -- Leibundgut, Marc -- Boehringer, Daniel -- Frick, Christian -- Mikolasek, Bohdan -- Ban, Nenad -- New York, N.Y. -- Science. 2007 Apr 13;316(5822):254-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, ETH Zurich, 8092 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17431175" target="_blank"〉PubMed〈/a〉
    Keywords: 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase/metabolism ; Acetyltransferases/metabolism ; Acyl Carrier Protein/chemistry/metabolism/ultrastructure ; Acyltransferases/metabolism ; Amino Acid Sequence ; Ascomycota/*enzymology ; Catalytic Domain ; Crystallography, X-Ray ; Enoyl-(Acyl-Carrier-Protein) Reductase (NADH)/metabolism ; Fatty Acid Synthases/*chemistry/metabolism ; Fungal Proteins/*chemistry/metabolism ; Hydro-Lyases/metabolism ; Models, Molecular ; Molecular Sequence Data ; NADP/chemistry ; Protein Conformation ; Protein Subunits/chemistry ; Substrate Specificity
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  • 13
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    Habitat split and the global decline of amphibians (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-15
    Description: The worldwide decline in amphibians has been attributed to several causes, especially habitat loss and disease. We identified a further factor, namely "habitat split"-defined as human-induced disconnection between habitats used by different life history stages of a species-which forces forest-associated amphibians with aquatic larvae to make risky breeding migrations between suitable aquatic and terrestrial habitats. In the Brazilian Atlantic Forest, we found that habitat split negatively affects the richness of species with aquatic larvae but not the richness of species with terrestrial development (the latter can complete their life cycle inside forest remnants). This mechanism helps to explain why species with aquatic larvae have the highest incidence of population decline. These findings reinforce the need for the conservation and restoration of riparian vegetation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Becker, Carlos Guilherme -- Fonseca, Carlos Roberto -- Haddad, Celio Fernando Baptista -- Batista, Romulo Fernandes -- Prado, Paulo Inacio -- New York, N.Y. -- Science. 2007 Dec 14;318(5857):1775-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departamento de Zoologia, Universidade Estadual de Campinas, 13083-970 Campinas SP, Brazil.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18079402" target="_blank"〉PubMed〈/a〉
    Keywords: *Amphibians/growth & development/physiology ; Animal Migration ; Animals ; *Biodiversity ; Brazil ; Conservation of Natural Resources ; *Ecosystem ; Larva/physiology ; Population Dynamics ; Trees ; Water
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 14
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    Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-04-21
    Description: We report the structures of three intermediates in the O2 activation and insertion reactions of an extradiol ring-cleaving dioxygenase. A crystal of Fe2+-containing homoprotocatechuate 2,3-dioxygenase was soaked in the slow substrate 4-nitrocatechol in a low O2 atmosphere. The x-ray crystal structure shows that three different intermediates reside in different subunits of a single homotetrameric enzyme molecule. One of these is the key substrate-alkylperoxo-Fe2+ intermediate, which has been predicted, but not structurally characterized, in an oxygenase. The intermediates define the major chemical steps of the dioxygenase mechanism and point to a general mechanistic strategy for the diverse 2-His-1-carboxylate enzyme family.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720167/" 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/PMC2720167/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kovaleva, Elena G -- Lipscomb, John D -- GM24689/GM/NIGMS NIH HHS/ -- R01 GM024689/GM/NIGMS NIH HHS/ -- R01 GM024689-27/GM/NIGMS NIH HHS/ -- R01 GM024689-28/GM/NIGMS NIH HHS/ -- R37 GM024689/GM/NIGMS NIH HHS/ -- R37 GM024689-26/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Apr 20;316(5823):453-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17446402" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Brevibacterium/*enzymology ; Catalysis ; Catechols/chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Dioxygenases/*chemistry/*metabolism ; Ferric Compounds/*chemistry/metabolism ; Ferrous Compounds/chemistry ; Ligands ; Models, Chemical ; Models, Molecular ; Oxygen/chemistry/metabolism ; Protein Conformation ; Protein Subunits/chemistry/metabolism ; Superoxides/chemistry
    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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  • 15
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    Comment on "Impacts of biodiversity loss on ocean ecosystem services" (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-02
    Description: Worm et al. (Research Articles, 3 November 2006, p. 787) reported an increasing proportion of fisheries in a "collapsed" state. We show that this may be an artifact of their definition of collapse as a fixed percentage of the maximum and that an increase in the number of managed fisheries could produce similar patterns as an increase in fisheries with catches below 10% of the maximum.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilberg, Michael J -- Miller, Thomas J -- New York, N.Y. -- Science. 2007 Jun 1;316(5829):1285; author reply 1285.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, P.O. Box 38, Solomons, MD 20688, USA. wilberg@cbl.umces.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17540885" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; Conservation of Natural Resources ; *Ecosystem ; *Fisheries ; *Fishes ; Forecasting ; Population Dynamics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 16
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    Structure of the membrane protein FhaC: a member of the Omp85-TpsB transporter superfamily (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-19
    Description: In Gram-negative bacteria and eukaryotic organelles, beta-barrel proteins of the outer membrane protein 85-two-partner secretion B (Omp85-TpsB) superfamily are essential components of protein transport machineries. The TpsB transporter FhaC mediates the secretion of Bordetella pertussis filamentous hemagglutinin (FHA). We report the 3.15 A crystal structure of FhaC. The transporter comprises a 16-stranded beta barrel that is occluded by an N-terminal alpha helix and an extracellular loop and a periplasmic module composed of two aligned polypeptide-transport-associated (POTRA) domains. Functional data reveal that FHA binds to the POTRA 1 domain via its N-terminal domain and likely translocates the adhesin-repeated motifs in an extended hairpin conformation, with folding occurring at the cell surface. General features of the mechanism obtained here are likely to apply throughout the superfamily.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clantin, Bernard -- Delattre, Anne-Sophie -- Rucktooa, Prakash -- Saint, Nathalie -- Meli, Albano C -- Locht, Camille -- Jacob-Dubuisson, Francoise -- Villeret, Vincent -- New York, N.Y. -- Science. 2007 Aug 17;317(5840):957-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉UMR8161 CNRS, Institut de Biologie de Lille, Universite de Lille 1, Universite de Lille 2, 1 rue du Prof. Calmette, F-59021 Lille cedex, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17702945" target="_blank"〉PubMed〈/a〉
    Keywords: Adhesins, Bacterial/chemistry/*metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*chemistry/genetics/*metabolism ; Bordetella pertussis/*chemistry/metabolism ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Hydrophobic and Hydrophilic Interactions ; Lipid Bilayers/chemistry/metabolism ; Membrane Transport Proteins/chemistry/metabolism ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Transport ; Virulence Factors, Bordetella/chemistry/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 17
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    Thriving Arctic bottom dwellers could get strangled by warming (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-03-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Krajick, Kevin -- New York, N.Y. -- Science. 2007 Mar 16;315(5818):1527.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17363662" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arctic Regions ; Biodiversity ; *Cold Climate ; *Ecosystem ; Food Chain ; Ice Cover ; Invertebrates ; Plankton/growth & development ; Population Dynamics ; *Seawater ; Temperature
    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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  • 18
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    Comment on "A G protein coupled receptor is a plasma membrane receptor for the plant hormone abscisic acid" (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-11-10
    Description: Liu et al. (Reports, 23 March 2007, p. 1712) reported that the Arabidopsis thaliana gene GCR2 encodes a seven-transmembrane, G protein-coupled receptor for abscisic acid. We argue that GCR2 is not likely to be a transmembrane protein nor a G protein-coupled receptor. Instead, GCR2 is most likely a plant homolog of bacterial lanthionine synthetases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Johnston, Christopher A -- Temple, Brenda R -- Chen, Jin-Gui -- Gao, Yajun -- Moriyama, Etsuko N -- Jones, Alan M -- Siderovski, David P -- Willard, Francis S -- New York, N.Y. -- Science. 2007 Nov 9;318(5852):914; author reply 914.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17991845" target="_blank"〉PubMed〈/a〉
    Keywords: Abscisic Acid/*metabolism ; Algorithms ; Amino Acid Sequence ; Arabidopsis/chemistry/*metabolism ; Arabidopsis Proteins/*chemistry/isolation & purification/*metabolism ; GTP-Binding Protein alpha Subunits/metabolism ; Hydro-Lyases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Multienzyme Complexes/*chemistry/metabolism ; Plant Growth Regulators/*metabolism ; Protein Binding ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, G-Protein-Coupled/*chemistry/isolation & purification/*metabolism ; Recombinant Proteins/chemistry/metabolism ; Sequence Alignment
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  • 19
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    Biochemistry. A missing link in membrane protein evolution (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-03-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Poolman, Bert -- Geertsma, Eric R -- Slotboom, Dirk-Jan -- New York, N.Y. -- Science. 2007 Mar 2;315(5816):1229-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands. b.poolman@rug.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17332400" target="_blank"〉PubMed〈/a〉
    Keywords: Antiporters/*chemistry/genetics/metabolism ; Cell Membrane/*chemistry ; Dimerization ; Directed Molecular Evolution ; Escherichia coli/*chemistry ; Escherichia coli Proteins/*chemistry/genetics/metabolism ; *Evolution, Molecular ; Gene Duplication ; Membrane Proteins/*chemistry/genetics/metabolism ; Membrane Transport Proteins/*chemistry/genetics ; Models, Molecular ; Protein Folding ; Protein Structure, Tertiary ; Protein Subunits/chemistry
    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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  • 20
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    Ecology: managing evolving fish stocks (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-11-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jorgensen, Christian -- Enberg, Katja -- Dunlop, Erin S -- Arlinghaus, Robert -- Boukal, David S -- Brander, Keith -- Ernande, Bruno -- Gardmark, Anna -- Johnston, Fiona -- Matsumura, Shuichi -- Pardoe, Heidi -- Raab, Kristina -- Silva, Alexandra -- Vainikka, Anssi -- Dieckmann, Ulf -- Heino, Mikko -- Rijnsdorp, Adriaan D -- New York, N.Y. -- Science. 2007 Nov 23;318(5854):1247-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Bergen, N-5020 Bergen. christian.jorgensen@bio.uib.no〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18033868" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Ecosystem ; *Fisheries/methods ; *Fishes/physiology ; Population Dynamics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 21
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    Climate change affects marine fishes through the oxygen limitation of thermal tolerance (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-01-06
    Description: A cause-and-effect understanding of climate influences on ecosystems requires evaluation of thermal limits of member species and of their ability to cope with changing temperatures. Laboratory data available for marine fish and invertebrates from various climatic regions led to the hypothesis that, as a unifying principle, a mismatch between the demand for oxygen and the capacity of oxygen supply to tissues is the first mechanism to restrict whole-animal tolerance to thermal extremes. We show in the eelpout, Zoarces viviparus, a bioindicator fish species for environmental monitoring from North and Baltic Seas (Helcom), that thermally limited oxygen delivery closely matches environmental temperatures beyond which growth performance and abundance decrease. Decrements in aerobic performance in warming seas will thus be the first process to cause extinction or relocation to cooler waters.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Portner, Hans O -- Knust, Rainer -- New York, N.Y. -- Science. 2007 Jan 5;315(5808):95-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Alfred Wegener Institute for Polar and Marine Research, Animal Ecophysiology, Postfach 12 01 61, 27515 Bremerhaven, Germany. hpoertner@awi-bremerhaven.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17204649" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization ; Aerobiosis ; Animals ; Blood Circulation ; Body Size ; *Climate ; *Ecosystem ; North Sea ; Oxygen/analysis/blood/*metabolism ; Oxygen Consumption ; Perciformes/growth & development/*physiology ; Population Dynamics ; Population Growth ; Seasons ; Seawater/chemistry ; Temperature
    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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  • 22
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    PKA type IIalpha holoenzyme reveals a combinatorial strategy for isoform diversity (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-13
    Description: The catalytic (C) subunit of cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) is inhibited by two classes of regulatory subunits, RI and RII. The RII subunits are substrates as well as inhibitors and do not require adenosine triphosphate (ATP) to form holoenzyme, which distinguishes them from RI subunits. To understand the molecular basis for isoform diversity, we solved the crystal structure of an RIIalpha holoenzyme and compared it to the RIalpha holoenzyme. Unphosphorylated RIIalpha(90-400), a deletion mutant, undergoes major conformational changes as both of the cAMP-binding domains wrap around the C subunit's large lobe. The hallmark of this conformational reorganization is the helix switch in domain A. The C subunit is in an open conformation, and its carboxyl-terminal tail is disordered. This structure demonstrates the conserved and isoform-specific features of RI and RII and the importance of ATP, and also provides a new paradigm for designing isoform-specific activators or antagonists for PKA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4036697/" 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/PMC4036697/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Jian -- Brown, Simon H J -- von Daake, Sventja -- Taylor, Susan S -- GM34921/GM/NIGMS NIH HHS/ -- R01 GM034921/GM/NIGMS NIH HHS/ -- R01 GM034921-23/GM/NIGMS NIH HHS/ -- T32-CA009524/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2007 Oct 12;318(5848):274-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17932298" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Animals ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Cyclic AMP/metabolism ; Cyclic AMP-Dependent Protein Kinase RIIalpha Subunit ; Cyclic AMP-Dependent Protein Kinase RIalpha Subunit ; Cyclic AMP-Dependent Protein Kinases/*chemistry/genetics/metabolism ; Holoenzymes/chemistry ; Hydrophobic and Hydrophilic Interactions ; Isoenzymes/chemistry ; Mice ; Models, Molecular ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 23
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    Domain architecture of pyruvate carboxylase, a biotin-dependent multifunctional enzyme (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-25
    Description: Biotin-dependent multifunctional enzymes carry out metabolically important carboxyl group transfer reactions and are potential targets for the treatment of obesity and type 2 diabetes. These enzymes use a tethered biotin cofactor to carry an activated carboxyl group between distantly spaced active sites. The mechanism of this transfer has remained poorly understood. Here we report the complete structure of pyruvate carboxylase at 2.0 angstroms resolution, which shows its domain arrangement. The structure, when combined with mutagenic analysis, shows that intermediate transfer occurs between active sites on separate polypeptide chains. In addition, domain rearrangements associated with activator binding decrease the distance between active-site pairs, providing a mechanism for allosteric activation. This description provides insight into the function of biotin-dependent enzymes and presents a new paradigm for multifunctional enzyme catalysis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉St Maurice, Martin -- Reinhardt, Laurie -- Surinya, Kathy H -- Attwood, Paul V -- Wallace, John C -- Cleland, W Wallace -- Rayment, Ivan -- AR35186/AR/NIAMS NIH HHS/ -- GM070455/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Aug 24;317(5841):1076-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17717183" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/analogs & derivatives/metabolism ; Allosteric Regulation ; Binding Sites ; Biotin/*metabolism ; Catalytic Domain ; Coenzyme A/metabolism ; Crystallography, X-Ray ; Dimerization ; Enzyme Activators/metabolism ; Models, Molecular ; Mutation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyruvate Carboxylase/*chemistry/genetics/*metabolism ; Rhizobium etli/*enzymology
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  • 24
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    Structural basis of DNA replication origin recognition by an ORC protein (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-01
    Description: DNA replication in archaea and in eukaryotes share many similarities. We report the structure of an archaeal origin recognition complex protein, ORC1, bound to an origin recognition box, a DNA sequence that is found in multiple copies at replication origins. DNA binding is mediated principally by a C-terminal winged helix domain that inserts deeply into the major and minor grooves, widening them both. However, additional DNA contacts are made with the N-terminal AAA+ domain, which inserts into the minor groove at a characteristic G-rich sequence, inducing a 35 degrees bend in the duplex and providing directionality to the binding site. Both contact regions also induce substantial unwinding of the DNA. The structure provides insight into the initial step in assembly of a replication origin and recruitment of minichromosome maintenance (MCM) helicase to that origin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gaudier, Martin -- Schuwirth, Barbara S -- Westcott, Sarah L -- Wigley, Dale B -- New York, N.Y. -- Science. 2007 Aug 31;317(5842):1213-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research UK Clare Hall Laboratories, London Research Institute, Blanche Lane, South Mimms, Potters Bar, Herts EN6 3LD, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17761880" target="_blank"〉PubMed〈/a〉
    Keywords: Aeropyrum/*chemistry/metabolism ; Archaeal Proteins/*chemistry ; Binding Sites ; Crystallography, X-Ray ; DNA, Archaeal/*chemistry/metabolism ; Dimerization ; Models, Molecular ; Nucleic Acid Conformation ; Origin Recognition Complex/*chemistry ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Replication Origin
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    Biomedical research. The endangered lab chimp (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-01-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cohen, Jon -- New York, N.Y. -- Science. 2007 Jan 26;315(5811):450-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17255486" target="_blank"〉PubMed〈/a〉
    Keywords: *Animal Experimentation/ethics ; Animal Welfare ; Animals ; *Animals, Laboratory ; Breeding ; Female ; Genome ; Housing, Animal ; Male ; *Models, Animal ; National Institutes of Health (U.S.) ; *Pan troglodytes/genetics ; Population Dynamics ; United States
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 26
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    Coupling coherence distinguishes structure sensitivity in protein electron transfer (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-03
    Description: Quantum mechanical analysis of electron tunneling in nine thermally fluctuating cytochrome b562 derivatives reveals two distinct protein-mediated coupling limits. A structure-insensitive regime arises for redox partners coupled through dynamically averaged multiple-coupling pathways (in seven of the nine derivatives) where heme-edge coupling leads to the multiple-pathway regime. A structure-dependent limit governs redox partners coupled through a dominant pathway (in two of the nine derivatives) where axial-ligand coupling generates the single-pathway limit and slower rates. This two-regime paradigm provides a unified description of electron transfer rates in 26 ruthenium-modified heme and blue-copper proteins, as well as in numerous photosynthetic proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523119/" 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/PMC3523119/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prytkova, Tatiana R -- Kurnikov, Igor V -- Beratan, David N -- R01 GM048043/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Feb 2;315(5812):622-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Chemistry and Biochemistry, Duke University, Durham, NC 27708, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17272715" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry, Physical ; Computer Simulation ; Cytochrome b Group/*chemistry/*metabolism ; Cytochromes c/chemistry ; *Electron Transport ; Histidine/chemistry ; Hydrogen Bonding ; Ligands ; Mathematics ; Models, Chemical ; Models, Molecular ; Oxidation-Reduction ; Physicochemical Phenomena ; Protein Conformation ; Protein Folding ; Ruthenium
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    Mechanism of two classes of cancer mutations in the phosphoinositide 3-kinase catalytic subunit (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-07-14
    Description: Many human cancers involve up-regulation of the phosphoinositide 3-kinase PI3Kalpha, with oncogenic mutations identified in both the p110alpha catalytic and the p85alpha regulatory subunits. We used crystallographic and biochemical approaches to gain insight into activating mutations in two noncatalytic p110alpha domains-the adaptor-binding and the helical domains. A structure of the adaptor-binding domain of p110alpha in a complex with the p85alpha inter-Src homology 2 (inter-SH2) domain shows that oncogenic mutations in the adaptor-binding domain are not at the inter-SH2 interface but in a polar surface patch that is a plausible docking site for other domains in the holo p110/p85 complex. We also examined helical domain mutations and found that the Glu545 to Lys545 (E545K) oncogenic mutant disrupts an inhibitory charge-charge interaction with the p85 N-terminal SH2 domain. These studies extend our understanding of the architecture of PI3Ks and provide insight into how two classes of mutations that cause a gain in function can lead to cancer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miled, Nabil -- Yan, Ying -- Hon, Wai-Ching -- Perisic, Olga -- Zvelebil, Marketa -- Inbar, Yuval -- Schneidman-Duhovny, Dina -- Wolfson, Haim J -- Backer, Jonathan M -- Williams, Roger L -- GM55692/GM/NIGMS NIH HHS/ -- MC_U105184308/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2007 Jul 13;317(5835):239-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17626883" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; *Catalytic Domain ; Cattle ; Cell Line ; Cell Transformation, Neoplastic ; Crystallography, X-Ray ; Dimerization ; Humans ; Models, Molecular ; Molecular Sequence Data ; *Mutation ; Neoplasms/*genetics ; Phosphatidylinositol 3-Kinases/antagonists & ; inhibitors/chemistry/*genetics/*metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; src Homology Domains
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    Structural biology. Getting DNA to unwind (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Georgescu, Roxana E -- O'Donnell, Mike -- GM38839/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Aug 31;317(5842):1181-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of DNA Replication, Howard Hughes Medical Institute, Rockefeller University, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17761872" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Aeropyrum/*chemistry/metabolism ; Archaeal Proteins/*chemistry/metabolism ; Binding Sites ; DNA, Archaeal/*chemistry/metabolism ; Dimerization ; Models, Molecular ; Nucleic Acid Conformation ; Origin Recognition Complex/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Replication Origin ; Sulfolobus solfataricus/*chemistry/metabolism
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    Entomology. The case of the empty hives (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-05-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stokstad, Erik -- New York, N.Y. -- Science. 2007 May 18;316(5827):970-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17510336" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture ; Animal Nutritional Physiological Phenomena ; Animals ; Bacteria/isolation & purification ; *Bees/microbiology/parasitology/physiology ; Climate ; Diet ; Fungi/isolation & purification ; Mites ; Pesticides ; Population Dynamics ; United States ; United States Department of Agriculture ; Viruses/isolation & purification
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    Wildlife population increases in Serengeti National Park (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-03-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Young, Julie K -- Gerber, Leah R -- D'Agrosa, Caterina -- New York, N.Y. -- Science. 2007 Mar 30;315(5820):1790-1; author reply 1790-1.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17395811" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Animals, Wild ; *Buffaloes ; *Conservation of Natural Resources ; Disasters ; *Elephants ; *Law Enforcement ; Population Dynamics ; Population Growth ; Tanzania
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    LeuT-desipramine structure reveals how antidepressants block neurotransmitter reuptake (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-11
    Description: Tricyclic antidepressants exert their pharmacological effect-inhibiting the reuptake of serotonin, norepinephrine, and dopamine-by directly blocking neurotransmitter transporters (SERT, NET, and DAT, respectively) in the presynaptic membrane. The drug-binding site and the mechanism of this inhibition are poorly understood. We determined the crystal structure at 2.9 angstroms of the bacterial leucine transporter (LeuT), a homolog of SERT, NET, and DAT, in complex with leucine and the antidepressant desipramine. Desipramine binds at the inner end of the extracellular cavity of the transporter and is held in place by a hairpin loop and by a salt bridge. This binding site is separated from the leucine-binding site by the extracellular gate of the transporter. By directly locking the gate, desipramine prevents conformational changes and blocks substrate transport. Mutagenesis experiments on human SERT and DAT indicate that both the desipramine-binding site and its inhibition mechanism are probably conserved in the human neurotransmitter transporters.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711652/" 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/PMC3711652/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Zheng -- Zhen, Juan -- Karpowich, Nathan K -- Goetz, Regina M -- Law, Christopher J -- Reith, Maarten E A -- Wang, Da-Neng -- DA013261/DA/NIDA NIH HHS/ -- DA019676/DA/NIDA NIH HHS/ -- GM075026/GM/NIGMS NIH HHS/ -- GM075936/GM/NIGMS NIH HHS/ -- R01 DA013261/DA/NIDA NIH HHS/ -- R01 DA019676/DA/NIDA NIH HHS/ -- R01 DK053973/DK/NIDDK NIH HHS/ -- R21 DK060841/DK/NIDDK NIH HHS/ -- R21 GM075936/GM/NIGMS NIH HHS/ -- U54 GM075026/GM/NIGMS NIH HHS/ -- U54 GM095315/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 7;317(5843):1390-3. Epub 2007 Aug 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17690258" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antidepressive Agents, Tricyclic/chemistry/*metabolism ; Bacterial Proteins/chemistry/*metabolism ; Binding Sites ; Caenorhabditis elegans Proteins/chemistry/metabolism ; Cell Line ; Conserved Sequence ; Crystallography, X-Ray ; Desipramine/chemistry/*metabolism ; Dopamine/chemistry/metabolism ; Dopamine Uptake Inhibitors/chemistry/metabolism ; Drosophila Proteins/chemistry/metabolism ; Humans ; Leucine/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Neurotransmitter Uptake Inhibitors/chemistry/*metabolism ; Norepinephrine/chemistry/metabolism ; Norepinephrine Plasma Membrane Transport Proteins/antagonists & ; inhibitors/chemistry/metabolism ; Plasma Membrane Neurotransmitter Transport Proteins/chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Sequence Homology, Amino Acid ; Serotonin/chemistry/metabolism ; Serotonin Uptake Inhibitors/chemistry/metabolism
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    Stabilizing isopeptide bonds revealed in gram-positive bacterial pilus structure (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-08
    Description: Many bacterial pathogens have long, slender pili through which they adhere to host cells. The crystal structure of the major pilin subunit from the Gram-positive human pathogen Streptococcus pyogenes at 2.2 angstroms resolution reveals an extended structure comprising two all-beta domains. The molecules associate in columns through the crystal, with each carboxyl terminus adjacent to a conserved lysine of the next molecule. This lysine forms the isopeptide bonds that link the subunits in native pili, validating the relevance of the crystal assembly. Each subunit contains two lysine-asparagine isopeptide bonds generated by an intramolecular reaction, and we find evidence for similar isopeptide bonds in other cell surface proteins of Gram-positive bacteria. The present structure explains the strength and stability of such Gram-positive pili and could facilitate vaccine development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kang, Hae Joo -- Coulibaly, Fasseli -- Clow, Fiona -- Proft, Thomas -- Baker, Edward N -- New York, N.Y. -- Science. 2007 Dec 7;318(5856):1625-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18063798" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Asparagine/chemistry ; Chemistry, Physical ; Crystallography, X-Ray ; Fimbriae Proteins/*chemistry ; Fimbriae, Bacterial/*chemistry/ultrastructure ; Hydrogen Bonding ; Lysine/chemistry ; Models, Molecular ; Molecular Sequence Data ; Peptides/chemistry ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Streptococcus pyogenes/*chemistry/metabolism/*ultrastructure
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    Ecology. Invasion of the whiteflies (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reitz, Stuart R -- New York, N.Y. -- Science. 2007 Dec 14;318(5857):1733-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Agricultural Research Service, U.S. Department of Agriculture, Tallahassee, FL 32308, USA. stuart.reitz@ars.usda.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18079389" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Australia ; China ; *Ecosystem ; Female ; Hemiptera/classification/genetics/*physiology ; Male ; Population Dynamics ; Reproduction ; *Sexual Behavior, Animal
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    Structural basis for substrate delivery by acyl carrier protein in the yeast fatty acid synthase (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-04-14
    Description: In the multifunctional fungal fatty acid synthase (FAS), the acyl carrier protein (ACP) domain shuttles reaction intermediates covalently attached to its prosthetic phosphopantetheine group between the different enzymatic centers of the reaction cycle. Here, we report the structure of the Saccharomyces cerevisiae FAS determined at 3.1 angstrom resolution with its ACP stalled at the active site of ketoacyl synthase. The ACP contacts the base of the reaction chamber through conserved, charge-complementary surfaces, which optimally position the ACP toward the catalytic cleft of ketoacyl synthase. The conformation of the prosthetic group suggests a switchblade mechanism for acyl chain delivery to the active site of the enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leibundgut, Marc -- Jenni, Simon -- Frick, Christian -- Ban, Nenad -- New York, N.Y. -- Science. 2007 Apr 13;316(5822):288-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, ETH Zurich, 8092 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17431182" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl Carrier Protein/*chemistry/metabolism ; Acyltransferases/metabolism ; Amino Acid Sequence ; Catalytic Domain ; Crystallography, X-Ray ; Fatty Acid Synthases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/*chemistry/metabolism
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    Structural insight into the transglycosylation step of bacterial cell-wall biosynthesis (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-03-10
    Description: Peptidoglycan glycosyltransferases (GTs) catalyze the polymerization step of cell-wall biosynthesis, are membrane-bound, and are highly conserved across all bacteria. Long considered the "holy grail" of antibiotic research, they represent an essential and easily accessible drug target for antibiotic-resistant bacteria, including methicillin-resistant Staphylococcus aureus. We have determined the 2.8 angstrom structure of a bifunctional cell-wall cross-linking enzyme, including its transpeptidase and GT domains, both unliganded and complexed with the substrate analog moenomycin. The peptidoglycan GTs adopt a fold distinct from those of other GT classes. The structures give insight into critical features of the catalytic mechanism and key interactions required for enzyme inhibition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lovering, Andrew L -- de Castro, Liza H -- Lim, Daniel -- Strynadka, Natalie C J -- New York, N.Y. -- Science. 2007 Mar 9;315(5817):1402-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, and Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17347437" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Aminoacyltransferases/*chemistry/metabolism ; Anti-Bacterial Agents/chemistry/metabolism ; Apoenzymes/chemistry ; Binding Sites ; Carbohydrate Conformation ; Carbohydrate Sequence ; Catalytic Domain ; Cell Wall/*metabolism ; Crystallography, X-Ray ; Enzyme Inhibitors/chemistry/metabolism/pharmacology ; Glycosylation ; Models, Molecular ; Molecular Sequence Data ; Multienzyme Complexes/chemistry/metabolism ; Oligosaccharides/chemistry/metabolism/pharmacology ; Penicillin-Binding Proteins/*chemistry/metabolism ; Peptidoglycan/*biosynthesis ; Peptidoglycan Glycosyltransferase/*chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Staphylococcus aureus/*enzymology/metabolism
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    Structure of the zinc transporter YiiP (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-08-25
    Description: YiiP is a membrane transporter that catalyzes Zn2+/H+ exchange across the inner membrane of Escherichia coli. Mammalian homologs of YiiP play critical roles in zinc homeostasis and cell signaling. Here, we report the x-ray structure of YiiP in complex with zinc at 3.8 angstrom resolution. YiiP is a homodimer held together in a parallel orientation through four Zn2+ ions at the interface of the cytoplasmic domains, whereas the two transmembrane domains swing out to yield a Y-shaped structure. In each protomer, the cytoplasmic domain adopts a metallochaperone-like protein fold; the transmembrane domain features a bundle of six transmembrane helices and a tetrahedral Zn2+ binding site located in a cavity that is open to both the membrane outer leaflet and the periplasm.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Min -- Fu, Dax -- R01 GM065137/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 21;317(5845):1746-8. Epub 2007 Aug 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17717154" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Escherichia coli/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/metabolism ; Membrane Transport Proteins/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Sequence Alignment ; Zinc/*chemistry/metabolism
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    Structure of C8alpha-MACPF reveals mechanism of membrane attack in complement immune defense (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-09-18
    Description: Membrane attack is important for mammalian immune defense against invading microorganisms and infected host cells. Proteins of the complement membrane attack complex (MAC) and the protein perforin share a common MACPF domain that is responsible for membrane insertion and pore formation. We determined the crystal structure of the MACPF domain of complement component C8alpha at 2.5 angstrom resolution and show that it is structurally homologous to the bacterial, pore-forming, cholesterol-dependent cytolysins. The structure displays two regions that (in the bacterial cytolysins) refold into transmembrane beta hairpins, forming the lining of a barrel pore. Local hydrophobicity explains why C8alpha is the first complement protein to insert into the membrane. The size of the MACPF domain is consistent with known C9 pore sizes. These data imply that these mammalian and bacterial cytolytic proteins share a common mechanism of membrane insertion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hadders, Michael A -- Beringer, Dennis X -- Gros, Piet -- New York, N.Y. -- Science. 2007 Sep 14;317(5844):1552-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17872444" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cell Membrane/immunology/metabolism ; Complement C8/*chemistry/immunology/*metabolism ; Complement Membrane Attack Complex/*chemistry/immunology/*metabolism ; Crystallography, X-Ray ; Cytotoxins/chemistry/metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Membrane Glycoproteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Perforin ; Pore Forming Cytotoxic Proteins/chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; *Protein Structure, Tertiary
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    International conservation policy delivers benefits for birds in Europe (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-08-11
    Description: Conservation of the planet's biodiversity will depend on international policy intervention, yet evidence-based assessment of the success of such intervention is lacking. Poor understanding of the effectiveness of international policy instruments exposes them to criticism or abandonment and reduces opportunities to improve them. Comparative analyses of population trends provide strong evidence for a positive impact of one such instrument, the European Union's Birds Directive, and we identify positive associations between the rate of provision of certain conservation measures through the directive and the response of bird populations. The results suggest that supranational conservation policy can bring measurable conservation benefits, although future assessments will require the setting of quantitative objectives and an increase in the availability of data from monitoring schemes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Donald, Paul F -- Sanderson, Fiona J -- Burfield, Ian J -- Bierman, Stijn M -- Gregory, Richard D -- Waliczky, Zoltan -- New York, N.Y. -- Science. 2007 Aug 10;317(5839):810-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Royal Society for the Protection of Birds, The Lodge, Sandy, Bedfordshire SG19 2DL, UK. paul.donald@rspb.org.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17690296" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Animals, Wild ; *Biodiversity ; *Birds ; *Conservation of Natural Resources/legislation & jurisprudence ; Ecosystem ; Europe ; European Union ; *International Cooperation ; Population Dynamics ; Public Policy
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    Crystal structures of human MD-2 and its complex with antiendotoxic lipid IVa (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-16
    Description: Endotoxic lipopolysaccharide (LPS) with potent immunostimulatory activity is recognized by the receptor complex of MD-2 and Toll-like receptor 4. Crystal structures of human MD-2 and its complex with the antiendotoxic tetra-acylated lipid A core of LPS have been determined at 2.0 and 2.2 angstrom resolutions, respectively. MD-2 shows a deep hydrophobic cavity sandwiched by two beta sheets, in which four acyl chains of the ligand are fully confined. The phosphorylated glucosamine moieties are located at the entrance to the cavity. These structures suggest that MD-2 plays a principal role in endotoxin recognition and provide a basis for antiseptic drug development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ohto, Umeharu -- Fukase, Koichi -- Miyake, Kensuke -- Satow, Yoshinori -- New York, N.Y. -- Science. 2007 Jun 15;316(5831):1632-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17569869" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Fatty Acids/chemistry ; Glycolipids/*chemistry/metabolism ; Glycosylation ; Humans ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Lipid A/*analogs & derivatives/chemistry/metabolism ; Lymphocyte Antigen 96/*chemistry/metabolism ; Models, Molecular ; Phosphorylation ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary
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    Structure of a tyrosine phosphatase adhesive interaction reveals a spacer-clamp mechanism (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-01
    Description: Cell-cell contacts are fundamental to multicellular organisms and are subject to exquisite levels of control. Human RPTPmu is a type IIB receptor protein tyrosine phosphatase that both forms an adhesive contact itself and is involved in regulating adhesion by dephosphorylating components of cadherin-catenin complexes. Here we describe a 3.1 angstrom crystal structure of the RPTPmu ectodomain that forms a homophilic trans (antiparallel) dimer with an extended and rigid architecture, matching the dimensions of adherens junctions. Cell surface expression of deletion constructs induces intercellular spacings that correlate with the ectodomain length. These data suggest that the RPTPmu ectodomain acts as a distance gauge and plays a key regulatory function, locking the phosphatase to its appropriate functional location.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aricescu, A Radu -- Siebold, Christian -- Choudhuri, Kaushik -- Chang, Veronica T -- Lu, Weixian -- Davis, Simon J -- van der Merwe, P Anton -- Jones, E Yvonne -- 081894/Wellcome Trust/United Kingdom -- G9722488/Medical Research Council/United Kingdom -- G9900061/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2007 Aug 31;317(5842):1217-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research UK Receptor Structure Research Group, University of Oxford, Henry Wellcome Building of Genomic Medicine, Division of Structural Biology, Roosevelt Drive, Oxford OX3 7BN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17761881" target="_blank"〉PubMed〈/a〉
    Keywords: Adherens Junctions/chemistry/*physiology/ultrastructure ; Amino Acid Sequence ; Cell Adhesion ; Cell Adhesion Molecules/*chemistry/metabolism ; Cell Membrane/chemistry/enzymology ; Conserved Sequence ; Dimerization ; Fibronectins/chemistry ; Humans ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Immunoglobulins/chemistry ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Protein Structure, Tertiary ; Protein Tyrosine Phosphatases/*chemistry/genetics/*metabolism ; Receptor-Like Protein Tyrosine Phosphatases, Class 2
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    Mechanism of Na+/H+ antiporting (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-11
    Description: Na+/H+ antiporters are central to cellular salt and pH homeostasis. The structure of Escherichia coli NhaA was recently determined, but its mechanisms of transport and pH regulation remain elusive. We performed molecular dynamics simulations of NhaA that, with existing experimental data, enabled us to propose an atomically detailed model of antiporter function. Three conserved aspartates are key to our proposed mechanism: Asp164 (D164) is the Na+-binding site, D163 controls the alternating accessibility of this binding site to the cytoplasm or periplasm, and D133 is crucial for pH regulation. Consistent with experimental stoichiometry, two protons are required to transport a single Na+ ion: D163 protonates to reveal the Na+-binding site to the periplasm, and subsequent protonation of D164 releases Na+. Additional mutagenesis experiments further validated the model.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Arkin, Isaiah T -- Xu, Huafeng -- Jensen, Morten O -- Arbely, Eyal -- Bennett, Estelle R -- Bowers, Kevin J -- Chow, Edmond -- Dror, Ron O -- Eastwood, Michael P -- Flitman-Tene, Ravenna -- Gregersen, Brent A -- Klepeis, John L -- Kolossvary, Istvan -- Shan, Yibing -- Shaw, David E -- New York, N.Y. -- Science. 2007 Aug 10;317(5839):799-803.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉D. E. Shaw Research, New York, NY 10036, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17690293" target="_blank"〉PubMed〈/a〉
    Keywords: Aspartic Acid/metabolism ; Binding Sites ; Computer Simulation ; Crystallization ; Cytoplasm/metabolism ; Escherichia coli/growth & development/*metabolism ; Escherichia coli Proteins/*chemistry/*metabolism ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Ion Transport ; *Models, Biological ; Models, Molecular ; Mutagenesis ; Periplasm/metabolism ; Protein Conformation ; Protein Structure, Secondary ; *Protons ; Sodium/*metabolism ; Sodium-Hydrogen Antiporter/*chemistry/*metabolism
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    Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-11-10
    Description: DNA polymerase eta (Pol eta) is a eukaryotic lesion bypass polymerase that helps organisms to survive exposure to ultraviolet (UV) radiation, and tumor cells to gain resistance against cisplatin-based chemotherapy. It allows cells to replicate across cross-link lesions such as 1,2-d(GpG) cisplatin adducts (Pt-GG) and UV-induced cis-syn thymine dimers. We present structural and biochemical analysis of how Pol eta copies Pt-GG-containing DNA. The damaged DNA is bound in an open DNA binding rim. Nucleotidyl transfer requires the DNA to rotate into an active conformation, driven by hydrogen bonding of the templating base to the dNTP. For the 3'dG of the Pt-GG, this step is accomplished by a Watson-Crick base pair to dCTP and is biochemically efficient and accurate. In contrast, bypass of the 5'dG of the Pt-GG is less efficient and promiscuous for dCTP and dATP as a result of the presence of the rigid Pt cross-link. Our analysis reveals the set of structural features that enable Pol eta to replicate across strongly distorting DNA lesions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alt, Aaron -- Lammens, Katja -- Chiocchini, Claudia -- Lammens, Alfred -- Pieck, J Carsten -- Kuch, David -- Hopfner, Karl-Peter -- Carell, Thomas -- New York, N.Y. -- Science. 2007 Nov 9;318(5852):967-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Munich Center for Integrated Protein Science (CiPS), Ludwig Maximilians University, D-81377 Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17991862" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents/metabolism/*pharmacology ; Base Pairing ; Binding Sites ; Cisplatin/analogs & derivatives/chemistry/metabolism/*pharmacology ; Crystallization ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA Adducts/chemistry/*metabolism ; *DNA Damage ; DNA Replication ; DNA-Directed DNA Polymerase/chemistry/genetics/*metabolism ; Deoxycytosine Nucleotides/chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Mutagenesis, Site-Directed ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Tertiary ; Templates, Genetic
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    Structure and function of an essential component of the outer membrane protein assembly machine (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-19
    Description: Integral beta-barrel proteins are found in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria. The machine that assembles these proteins contains an integral membrane protein, called YaeT in Escherichia coli, which has one or more polypeptide transport-associated (POTRA) domains. The crystal structure of a periplasmic fragment of YaeT reveals the POTRA domain fold and suggests a model for how POTRA domains can bind different peptide sequences, as required for a machine that handles numerous beta-barrel protein precursors. Analysis of POTRA domain deletions shows which are essential and provides a view of the spatial organization of this assembly machine.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Seokhee -- Malinverni, Juliana C -- Sliz, Piotr -- Silhavy, Thomas J -- Harrison, Stephen C -- Kahne, Daniel -- GM34821/GM/NIGMS NIH HHS/ -- GM66174/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Aug 17;317(5840):961-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17702946" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*chemistry/genetics/*metabolism ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Dimerization ; Escherichia coli/*chemistry/*metabolism ; Escherichia coli Proteins/*chemistry/genetics/*metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Lipoproteins/chemistry/metabolism ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Transport
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    Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-01
    Description: The faithful duplication of genetic material depends on essential DNA replication initiation factors. Cellular initiators form higher-order assemblies on replication origins, using adenosine triphosphate (ATP) to locally remodel duplex DNA and facilitate proper loading of synthetic replisomal components. To better understand initiator function, we determined the 3.4 angstrom-resolution structure of an archaeal Cdc6/Orc1 heterodimer bound to origin DNA. The structure demonstrates that, in addition to conventional DNA binding elements, initiators use their AAA+ ATPase domains to recognize origin DNA. Together these interactions establish the polarity of initiator assembly on the origin and induce substantial distortions into origin DNA strands. Biochemical and comparative analyses indicate that AAA+/DNA contacts observed in the structure are dynamic and evolutionarily conserved, suggesting that the complex forms a core component of the basal initiation machinery.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dueber, Erin L Cunningham -- Corn, Jacob E -- Bell, Stephen D -- Berger, James M -- GM071747/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Aug 31;317(5842):1210-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Miller Institute for Basic Research in Science, 2536 Channing Way 5190, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17761879" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/chemistry ; Amino Acid Sequence ; Archaeal Proteins/*chemistry/metabolism ; Binding Sites ; Conserved Sequence ; Crystallography, X-Ray ; DNA, Archaeal/*chemistry/metabolism ; DNA, Single-Stranded/chemistry/metabolism ; Dimerization ; Helix-Turn-Helix Motifs ; Models, Molecular ; Nucleic Acid Conformation ; Origin Recognition Complex/*chemistry/metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Replication Origin ; Sulfolobus solfataricus/*chemistry/metabolism
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    A meta-analysis of effects of Bt cotton and maize on nontarget invertebrates (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-09
    Description: Although scores of experiments have examined the ecological consequences of transgenic Bacillus thuringiensis (Bt) crops, debates continue regarding the nontarget impacts of this technology. Quantitative reviews of existing studies are crucial for better gauging risks and improving future risk assessments. To encourage evidence-based risk analyses, we constructed a searchable database for nontarget effects of Bt crops. A meta-analysis of 42 field experiments indicates that nontarget invertebrates are generally more abundant in Bt cotton and Bt maize fields than in nontransgenic fields managed with insecticides. However, in comparison with insecticide-free control fields, certain nontarget taxa are less abundant in Bt fields.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marvier, Michelle -- McCreedy, Chanel -- Regetz, James -- Kareiva, Peter -- New York, N.Y. -- Science. 2007 Jun 8;316(5830):1475-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Environmental Studies Institute, Santa Clara University, Santa Clara, CA 95053, USA. mmarvier@scu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17556584" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Arthropods ; Bacillus thuringiensis/genetics ; Bacterial Proteins/*genetics ; Bacterial Toxins/*genetics ; Crops, Agricultural/*genetics/growth & development ; Databases, Factual ; Endotoxins/*genetics ; Gossypium/*genetics/growth & development ; Hemolysin Proteins/*genetics ; Insecticides ; Insects ; Pest Control, Biological ; *Plants, Genetically Modified/growth & development ; Population Dynamics ; Zea mays/*genetics
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    Reefs in trouble. Life on the mean reefs (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pala, Christopher -- New York, N.Y. -- Science. 2007 Dec 14;318(5857):1719.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18079380" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Anthozoa ; *Ecosystem ; *Fishes/physiology ; *Food Chain ; Pacific Islands ; Population Dynamics ; Predatory Behavior
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    Crystal structures of the adenylate sensor from fission yeast AMP-activated protein kinase (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-10
    Description: The 5'-AMP (adenosine monophosphate)-activated protein kinase (AMPK) coordinates metabolic function with energy availability by responding to changes in intracellular ATP (adenosine triphosphate) and AMP concentrations. Here, we report crystal structures at 2.9 and 2.6 A resolution for ATP- and AMP-bound forms of a core alphabetagamma adenylate-binding domain from the fission yeast AMPK homolog. ATP and AMP bind competitively to a single site in the gamma subunit, with their respective phosphate groups positioned near function-impairing mutants. Unexpectedly, ATP binds without counterions, amplifying its electrostatic effects on a critical regulatory region where all three subunits converge.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Townley, Robert -- Shapiro, Lawrence -- New York, N.Y. -- Science. 2007 Mar 23;315(5819):1726-9. Epub 2007 Feb 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17289942" target="_blank"〉PubMed〈/a〉
    Keywords: AMP-Activated Protein Kinases ; Adenosine Monophosphate/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Binding Sites ; Binding, Competitive ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Multienzyme Complexes/*chemistry/metabolism ; Protein Kinases/*chemistry/metabolism ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Protein-Serine-Threonine Kinases/*chemistry/metabolism ; Schizosaccharomyces/*enzymology
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    Ecology. Thinking long term (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cheke, Robert A -- New York, N.Y. -- Science. 2007 Oct 26;318(5850):577-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Natural Resources Institute, University of Greenwich at Medway, Chatham Maritime, Kent ME4 4TB, UK. r.a.cheke@greenwich.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17962543" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; China ; *Climate ; Disasters ; *Ecology ; Europe ; *Grasshoppers/physiology ; Greenhouse Effect ; *Larix ; *Moths/physiology ; Population Density ; Population Dynamics ; Rain ; Time Factors
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    The structure of a human p110alpha/p85alpha complex elucidates the effects of oncogenic PI3Kalpha mutations (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-15
    Description: PIK3CA, one of the two most frequently mutated oncogenes in human tumors, codes for p110alpha, the catalytic subunit of a phosphatidylinositol 3-kinase, isoform alpha (PI3Kalpha, p110alpha/p85). Here, we report a 3.0 angstrom resolution structure of a complex between p110alpha and a polypeptide containing the p110alpha-binding domains of p85alpha, a protein required for its enzymatic activity. The structure shows that many of the mutations occur at residues lying at the interfaces between p110alpha and p85alpha or between the kinase domain of p110alpha and other domains within the catalytic subunit. Disruptions of these interactions are likely to affect the regulation of kinase activity by p85 or the catalytic activity of the enzyme, respectively. In addition to providing new insights about the structure of PI3Kalpha, these results suggest specific mechanisms for the effect of oncogenic mutations in p110alpha and p85alpha.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Chuan-Hsiang -- Mandelker, Diana -- Schmidt-Kittler, Oleg -- Samuels, Yardena -- Velculescu, Victor E -- Kinzler, Kenneth W -- Vogelstein, Bert -- Gabelli, Sandra B -- Amzel, L Mario -- CA 43460/CA/NCI NIH HHS/ -- GM 07184/GM/NIGMS NIH HHS/ -- GM066895/GM/NIGMS NIH HHS/ -- GM07309/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Dec 14;318(5857):1744-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18079394" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate ; Amino Acid Sequence ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Molecular Sequence Data ; *Mutation ; Neoplasms/*genetics ; Phosphatidylinositol 3-Kinases/*chemistry/genetics/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/genetics/metabolism ; src Homology Domains
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    Fishing for good news (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-04-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McCauley, Douglas J -- New York, N.Y. -- Science. 2007 Apr 13;316(5822):200-1; author reply 200-1.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17431154" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biomass ; Conservation of Natural Resources ; *Ecosystem ; Fisheries ; Pacific Ocean ; Population Dynamics ; Predatory Behavior ; *Sharks ; *Tuna
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    Ecology. The heartbreak of adapting to global warming (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-01-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Tobias -- Overgaard, Johannes -- New York, N.Y. -- Science. 2007 Jan 5;315(5808):49-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoophysiology, Aarhus University, 8000 Aarhus, Denmark. tobias.wang@biology.au.dk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17204631" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization ; Aerobiosis ; Animals ; Cardiac Output ; *Ecosystem ; *Greenhouse Effect ; Heart/*physiology ; Oceans and Seas ; Oxygen/analysis/blood/*metabolism ; Oxygen Consumption ; Perciformes/*physiology ; Population Density ; Population Dynamics ; Seasons ; Seawater/chemistry ; Temperature
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    Zoology. African penguin populations reported in a puzzling decline (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-03-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koenig, Robert -- New York, N.Y. -- Science. 2007 Mar 2;315(5816):1205.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17332382" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Climate ; Conservation of Natural Resources ; Ecosystem ; Feeding Behavior ; Fishes ; Population Density ; Population Dynamics ; South Africa ; *Spheniscidae
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    Crystal structure of inhibitor-bound human 5-lipoxygenase-activating protein (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-30
    Description: Leukotrienes are proinflammatory products of arachidonic acid oxidation by 5-lipoxygenase that have been shown to be involved in respiratory and cardiovascular diseases. The integral membrane protein FLAP is essential for leukotriene biosynthesis. We describe the x-ray crystal structures of human FLAP in complex with two leukotriene biosynthesis inhibitors at 4.0 and 4.2 angstrom resolution, respectively. The structures show that inhibitors bind in membrane-embedded pockets of FLAP, which suggests how these inhibitors prevent arachidonic acid from binding to FLAP and subsequently being transferred to 5-lipoxygenase, thereby preventing leukotriene biosynthesis. This structural information provides a platform for the development of therapeutics for respiratory and cardiovascular diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ferguson, Andrew D -- McKeever, Brian M -- Xu, Shihua -- Wisniewski, Douglas -- Miller, Douglas K -- Yamin, Ting-Ting -- Spencer, Robert H -- Chu, Lin -- Ujjainwalla, Feroze -- Cunningham, Barry R -- Evans, Jilly F -- Becker, Joseph W -- New York, N.Y. -- Science. 2007 Jul 27;317(5837):510-2. Epub 2007 Jun 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicinal Chemistry, Merck Research Laboratories, Rahway, NJ 07065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17600184" target="_blank"〉PubMed〈/a〉
    Keywords: 5-Lipoxygenase-Activating Proteins ; Arachidonate 5-Lipoxygenase/metabolism ; Arachidonic Acid/metabolism ; Binding Sites ; Carrier Proteins/antagonists & inhibitors/*chemistry/genetics/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Cytosol/chemistry ; Humans ; Hydrophobic and Hydrophilic Interactions ; Indoles/*chemistry/metabolism/pharmacology ; Membrane Proteins/antagonists & inhibitors/*chemistry/genetics/metabolism ; Models, Molecular ; Mutagenesis ; Nuclear Envelope/chemistry ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Quinolines/*chemistry/metabolism/pharmacology
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    A large-scale deforestation experiment: effects of patch area and isolation on Amazon birds (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-01-16
    Description: As compared with extensive contiguous areas, small isolated habitat patches lack many species. Some species disappear after isolation; others are rarely found in any small patch, regardless of isolation. We used a 13-year data set of bird captures from a large landscape-manipulation experiment in a Brazilian Amazon forest to model the extinction-colonization dynamics of 55 species and tested basic predictions of island biogeography and metapopulation theory. From our models, we derived two metrics of species vulnerability to changes in isolation and patch area. We found a strong effect of area and a variable effect of isolation on the predicted patch occupancy by birds.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ferraz, Goncalo -- Nichols, James D -- Hines, James E -- Stouffer, Philip C -- Bierregaard, Richard O Jr -- Lovejoy, Thomas E -- New York, N.Y. -- Science. 2007 Jan 12;315(5809):238-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biological Dynamics of Forest Fragments Project, Instituto Nacional de Pesquisas da Amazonia, 69011 Manaus AM, Brazil. gferraz@inpa.gov.br〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17218527" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Birds ; Brazil ; *Conservation of Natural Resources ; *Ecosystem ; Extinction, Biological ; Likelihood Functions ; Models, Biological ; Models, Statistical ; Population Dynamics ; *Trees/growth & development
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    Comment on "Impacts of biodiversity loss on ocean ecosystem services" (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-02
    Description: Worm et al. (Research Articles, 3 November 2006, p. 787) investigated the importance of biodiversity to marine ecosystem services across temporal and spatial scales. In projecting the extent of future fisheries collapse, we argue that the authors inappropriately extrapolated beyond their available observations and used data on marine reserves and fishery closures that are not representative of global fisheries.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holker, Franz -- Beare, Doug -- Dorner, Hendrik -- di Natale, Antonio -- Ratz, Hans-Joachim -- Temming, Axel -- Casey, John -- New York, N.Y. -- Science. 2007 Jun 1;316(5829):1285; author reply 1285.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Commission, Directorate General Joint Research Centre, Institute for the Protection and Security of the Citizen, Agriculture and Fisheries Unit, TP 051, 21020, Italy. franz.hoelker@jrc.it〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17540886" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; Conservation of Natural Resources ; *Ecosystem ; *Fisheries ; *Fishes ; Forecasting ; Oceans and Seas ; Population Dynamics
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    Structure of hexameric DnaB helicase and its complex with a domain of DnaG primase (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-20
    Description: The complex between the DnaB helicase and the DnaG primase unwinds duplex DNA at the eubacterial replication fork and synthesizes the Okazaki RNA primers. The crystal structures of hexameric DnaB and its complex with the helicase binding domain (HBD) of DnaG reveal that within the hexamer the two domains of DnaB pack with strikingly different symmetries to form a distinct two-layered ring structure. Each of three bound HBDs stabilizes the DnaB hexamer in a conformation that may increase its processivity. Three positive, conserved electrostatic patches on the N-terminal domain of DnaB may also serve as a binding site for DNA and thereby guide the DNA to a DnaG active site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bailey, Scott -- Eliason, William K -- Steitz, Thomas A -- GM57510/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Oct 19;318(5849):459-63.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17947583" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA Primase/*chemistry/metabolism ; DNA, Bacterial/chemistry/metabolism ; Dimerization ; DnaB Helicases/*chemistry/metabolism ; Endodeoxyribonucleases/chemistry/metabolism ; Escherichia coli/chemistry/enzymology/metabolism ; Escherichia coli Proteins/chemistry/metabolism ; Exodeoxyribonucleases/chemistry/metabolism ; Geobacillus stearothermophilus/*enzymology/metabolism ; Image Processing, Computer-Assisted ; Models, Molecular ; Protein Binding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary
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    High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-27
    Description: Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors constitute the largest family of eukaryotic signal transduction proteins that communicate across the membrane. We report the crystal structure of a human beta2-adrenergic receptor-T4 lysozyme fusion protein bound to the partial inverse agonist carazolol at 2.4 angstrom resolution. The structure provides a high-resolution view of a human G protein-coupled receptor bound to a diffusible ligand. Ligand-binding site accessibility is enabled by the second extracellular loop, which is held out of the binding cavity by a pair of closely spaced disulfide bridges and a short helical segment within the loop. Cholesterol, a necessary component for crystallization, mediates an intriguing parallel association of receptor molecules in the crystal lattice. Although the location of carazolol in the beta2-adrenergic receptor is very similar to that of retinal in rhodopsin, structural differences in the ligand-binding site and other regions highlight the challenges in using rhodopsin as a template model for this large receptor family.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2583103/" 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/PMC2583103/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cherezov, Vadim -- Rosenbaum, Daniel M -- Hanson, Michael A -- Rasmussen, Soren G F -- Thian, Foon Sun -- Kobilka, Tong Sun -- Choi, Hee-Jung -- Kuhn, Peter -- Weis, William I -- Kobilka, Brian K -- Stevens, Raymond C -- F32 GM082028/GM/NIGMS NIH HHS/ -- GM075915/GM/NIGMS NIH HHS/ -- NS028471/NS/NINDS NIH HHS/ -- P50 GM062411/GM/NIGMS NIH HHS/ -- P50 GM073197/GM/NIGMS NIH HHS/ -- P50 GM073197-04/GM/NIGMS NIH HHS/ -- R01 GM056169/GM/NIGMS NIH HHS/ -- R01 GM089857/GM/NIGMS NIH HHS/ -- R21 GM075811/GM/NIGMS NIH HHS/ -- U54 GM074961/GM/NIGMS NIH HHS/ -- U54 GM074961-030001/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Nov 23;318(5854):1258-65. Epub 2007 Oct 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17962520" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage T4/enzymology ; Binding Sites ; Cell Membrane/chemistry/metabolism ; Cholesterol/chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Drug Inverse Agonism ; Humans ; Ligands ; Models, Molecular ; Muramidase/chemistry/metabolism ; Propanolamines/chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Receptors, Adrenergic, beta-2/*chemistry/metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; Rhodopsin/chemistry/metabolism ; Static Electricity
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    Environmental restoration. Delta blues, California style (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-07-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, Robert F -- New York, N.Y. -- Science. 2007 Jul 27;317(5837):442-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17656696" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; California ; *Conservation of Natural Resources ; *Ecosystem ; Fishes ; *Fresh Water ; Population Dynamics ; *Rivers ; *Salmoniformes ; Water Supply
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    Conservation. Scientists say Ebola has pushed western gorillas to the brink (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vogel, Gretchen -- New York, N.Y. -- Science. 2007 Sep 14;317(5844):1484.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17872416" target="_blank"〉PubMed〈/a〉
    Keywords: Africa, Central/epidemiology ; Animals ; Ape Diseases/*epidemiology/mortality/prevention & control ; Conservation of Natural Resources ; Disease Outbreaks/prevention & control/*veterinary ; Ebola Vaccines/administration & dosage ; Extinction, Biological ; *Gorilla gorilla ; Hemorrhagic Fever, Ebola/epidemiology/mortality/prevention & control/*veterinary ; Population Dynamics
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    TARP auxiliary subunits switch AMPA receptor antagonists into partial agonists (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-11-03
    Description: Quinoxalinedione compounds such as 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX) are the most commonly used alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor antagonists. However, we find that in the presence of transmembrane AMPA receptor regulatory proteins (TARPs), which are AMPA receptor auxiliary subunits, CNQX acts as a partial agonist. CNQX induced small depolarizing currents in neurons of the central nervous system, and reconstitution of this agonist activity required coexpression of TARPs. A crystal structure of CNQX bound to the TARP-less AMPA receptor ligand-binding domain showed that, although CNQX induces partial domain closure, this movement is not transduced into linker separation, suggesting that TARPs may increase agonist efficacy by strengthening the coupling between domain closure and channel opening. Our results demonstrate that the presence of an auxiliary subunit can determine whether a compound functions as an agonist or antagonist.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Menuz, Karen -- Stroud, Robert M -- Nicoll, Roger A -- Hays, Franklin A -- GM078754/GM/NIGMS NIH HHS/ -- P50 GM73210/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Nov 2;318(5851):815-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17975069" target="_blank"〉PubMed〈/a〉
    Keywords: 6-Cyano-7-nitroquinoxaline-2,3-dione/chemistry/*pharmacology ; Animals ; Benzodiazepines/pharmacology ; Binding, Competitive ; Cell Line ; Cerebellum/cytology ; Crystallography, X-Ray ; *Drug Partial Agonism ; Hippocampus/cytology ; Humans ; In Vitro Techniques ; Interneurons/drug effects ; Mice ; Models, Molecular ; Patch-Clamp Techniques ; Protein Conformation ; Protein Subunits/*physiology ; Pyramidal Cells/drug effects/metabolism ; Quinoxalines/pharmacology ; Receptors, AMPA/*agonists/*antagonists & inhibitors ; Structure-Activity Relationship ; Synaptic Transmission/drug effects ; Trichlormethiazide/pharmacology
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    Declining wild salmon populations in relation to parasites from farm salmon (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-15
    Description: Rather than benefiting wild fish, industrial aquaculture may contribute to declines in ocean fisheries and ecosystems. Farm salmon are commonly infected with salmon lice (Lepeophtheirus salmonis), which are native ectoparasitic copepods. We show that recurrent louse infestations of wild juvenile pink salmon (Oncorhynchus gorbuscha), all associated with salmon farms, have depressed wild pink salmon populations and placed them on a trajectory toward rapid local extinction. The louse-induced mortality of pink salmon is commonly over 80% and exceeds previous fishing mortality. If outbreaks continue, then local extinction is certain, and a 99% collapse in pink salmon population abundance is expected in four salmon generations. These results suggest that salmon farms can cause parasite outbreaks that erode the capacity of a coastal ecosystem to support wild salmon populations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Krkosek, Martin -- Ford, Jennifer S -- Morton, Alexandra -- Lele, Subhash -- Myers, Ransom A -- Lewis, Mark A -- New York, N.Y. -- Science. 2007 Dec 14;318(5857):1772-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Mathematical Biology, Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, AB, Canada. mkrkosek@ualberta.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18079401" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Wild ; British Columbia/epidemiology ; *Copepoda ; Disease Outbreaks/statistics & numerical data/veterinary ; Ectoparasitic Infestations/epidemiology/mortality/*veterinary ; Extinction, Biological ; Fish Diseases/*epidemiology/mortality ; *Fisheries ; Linear Models ; Models, Statistical ; Population Dynamics ; *Salmon/parasitology
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    Comment on "Impacts of biodiversity loss on ocean ecosystem services" (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-02
    Description: Worm et al. (Research Articles, 3 November 2006, p. 787) used a power relation to predict a global collapse of fisheries by the year 2048. However, a linear regression of the data for the past 40 years yields an excellent fit, with a predicted date of collapse of 2114. Thus, long-term projections of fisheries collapse are highly dependent on the specific statistical model used.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jaenike, John -- New York, N.Y. -- Science. 2007 Jun 1;316(5829):1285; author reply 1285.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Rochester, Rochester, NY 14627-0211, USA. joja@mail.rochester.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17540884" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Ecosystem ; *Fisheries ; *Fishes ; Forecasting ; Linear Models ; Models, Statistical ; Population Dynamics ; Regression Analysis
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    Ecology. Managing farming's footprint on biodiversity (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-01-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Benton, Tim G -- New York, N.Y. -- Science. 2007 Jan 19;315(5810):341-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Integrative and Comparative Biology, University of Leeds, Leeds LS2 9JT, UK. t.g.benton@leeds.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17234937" target="_blank"〉PubMed〈/a〉
    Keywords: *Agriculture ; Animals ; *Biodiversity ; *Birds ; Conservation of Natural Resources ; Crops, Agricultural/genetics ; *Ecosystem ; *Environment ; Great Britain ; Models, Statistical ; Plants, Genetically Modified ; Population Density ; Population Dynamics ; Risk Assessment
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    Culling prey promotes predator recovery--alternative states in a whole-lake experiment (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-06-26
    Description: Many top-predator fish stocks in both freshwater and marine systems have collapsed as a result of overharvesting. Consequently, some of these communities have shifted into seemingly irreversible new states. We showed, for predators feeding on prey that exhibit food-dependent growth, that culling of fish prey may promote predator recovery. We removed old stunted individuals of a prey-fish species in a large, low-productive lake, which caused an increase in the availability of small-sized prey and allowed the predator to recover. The shift in community state has been sustained for more than 15 years after the cull ended and represents an experimental demonstration of an alternative stable state in a large-scale field system. Because most animals exhibit food-dependent growth, shifts into alternative stable states resulting from overcompensating prey growth may be common in nature and may require counterintuitive management strategies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Persson, Lennart -- Amundsen, Per-Arne -- De Roos, Andre M -- Klemetsen, Anders -- Knudsen, Rune -- Primicerio, Raul -- New York, N.Y. -- Science. 2007 Jun 22;316(5832):1743-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Environmental Science, Umea University, S-901 87 Umea, Sweden. lennart.persson@emg.umu.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17588929" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Body Size ; *Ecosystem ; Fishes/*physiology ; Food Chain ; Fresh Water ; Norway ; Population Dynamics ; *Predatory Behavior ; Salmon/physiology ; Trout/physiology
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    Endangered species. U.S. announces recovery plan for a ghost bird (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stokstad, Erik -- New York, N.Y. -- Science. 2007 Aug 31;317(5842):1158.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17761857" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Birds ; Ecosystem ; Extinction, Biological ; Population Dynamics ; United States ; United States Government Agencies
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    Society for American Archaeology meeting. Climate spurred later Indus decline (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-05-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lawler, Andrew -- New York, N.Y. -- Science. 2007 May 18;316(5827):978-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17510342" target="_blank"〉PubMed〈/a〉
    Keywords: *Archaeology ; *Civilization ; *Climate ; Crops, Agricultural ; *Ethnic Groups ; Humans ; India ; Pakistan ; Population Dynamics ; Rain
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    Computational design of peptides that target transmembrane helices (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-03-31
    Description: A variety of methods exist for the design or selection of antibodies and other proteins that recognize the water-soluble regions of proteins; however, companion methods for targeting transmembrane (TM) regions are not available. Here, we describe a method for the computational design of peptides that target TM helices in a sequence-specific manner. To illustrate the method, peptides were designed that specifically recognize the TM helices of two closely related integrins (alphaIIbbeta3 and alphavbeta3) in micelles, bacterial membranes, and mammalian cells. These data show that sequence-specific recognition of helices in TM proteins can be achieved through optimization of the geometric complementarity of the target-host complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yin, Hang -- Slusky, Joanna S -- Berger, Bryan W -- Walters, Robin S -- Vilaire, Gaston -- Litvinov, Rustem I -- Lear, James D -- Caputo, Gregory A -- Bennett, Joel S -- DeGrado, William F -- 5T32 CA101968/CA/NCI NIH HHS/ -- 5T32 GM08275/GM/NIGMS NIH HHS/ -- GM54616/GM/NIGMS NIH HHS/ -- GM60610/GM/NIGMS NIH HHS/ -- HL40387/HL/NHLBI NIH HHS/ -- HL54500/HL/NHLBI NIH HHS/ -- T32 GM008275/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Mar 30;315(5820):1817-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17395823" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Motifs ; Amino Acid Sequence ; Blood Platelets/physiology ; Cell Membrane/*chemistry ; Databases, Protein ; Dimerization ; Escherichia coli/chemistry ; Fluorescence Resonance Energy Transfer ; Humans ; Integrin alphaVbeta3/*chemistry/metabolism ; Lipid Bilayers/chemistry ; Models, Molecular ; Molecular Sequence Data ; Optical Tweezers ; Osteopontin/metabolism ; Peptides/*chemistry/metabolism ; Platelet Adhesiveness ; Platelet Aggregation ; Platelet Glycoprotein GPIIb-IIIa Complex/*chemistry/metabolism ; *Protein Engineering ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Spectrum Analysis
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    Endangered Species Act. Appointee 'reshaped' science, says report (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-04-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stokstad, Erik -- New York, N.Y. -- Science. 2007 Apr 6;316(5821):37.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17412929" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Animals, Wild ; Conservation of Natural Resources/*legislation & jurisprudence ; *Fishes ; *Government Regulation ; Politics ; Population Dynamics ; United States ; *United States Government Agencies
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    Raman-assisted crystallography reveals end-on peroxide intermediates in a nonheme iron enzyme (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-04-21
    Description: Iron-peroxide intermediates are central in the reaction cycle of many iron-containing biomolecules. We trapped iron(III)-(hydro)peroxo species in crystals of superoxide reductase (SOR), a nonheme mononuclear iron enzyme that scavenges superoxide radicals. X-ray diffraction data at 1.95 angstrom resolution and Raman spectra recorded in crystallo revealed iron-(hydro)peroxo intermediates with the (hydro)peroxo group bound end-on. The dynamic SOR active site promotes the formation of transient hydrogen bond networks, which presumably assist the cleavage of the iron-oxygen bond in order to release the reaction product, hydrogen peroxide.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Katona, Gergely -- Carpentier, Philippe -- Niviere, Vincent -- Amara, Patricia -- Adam, Virgile -- Ohana, Jeremy -- Tsanov, Nikolay -- Bourgeois, Dominique -- New York, N.Y. -- Science. 2007 Apr 20;316(5823):449-53.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Biologie Structurale (IBS) Jean-Pierre Ebel, Commissariat a l'Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Universite Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17446401" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallization ; Crystallography, X-Ray ; Deltaproteobacteria/*enzymology ; Ferric Compounds/chemistry/metabolism ; Hydrogen Bonding ; Hydrogen Peroxide/*chemistry/metabolism ; Iron/*chemistry ; Ligands ; Models, Chemical ; Models, Molecular ; Oxidation-Reduction ; Oxidoreductases/*chemistry/*metabolism ; Oxygen/chemistry ; Peroxides/*chemistry ; Protein Conformation ; Protons ; Spectrum Analysis, Raman
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    Boom and bust in a polar hot zone (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-03-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stokstad, Erik -- New York, N.Y. -- Science. 2007 Mar 16;315(5818):1522-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17363659" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antarctic Regions ; *Cold Climate ; *Ecosystem ; Food Chain ; *Ice Cover ; Nesting Behavior ; Population Dynamics ; Snow ; *Spheniscidae ; Temperature
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    Ecology. Parasites from fish farms driving wild salmon to extinction (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stokstad, Erik -- New York, N.Y. -- Science. 2007 Dec 14;318(5857):1711.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18079376" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Wild ; British Columbia/epidemiology ; *Copepoda ; Ectoparasitic Infestations/epidemiology/mortality/*veterinary ; Extinction, Biological ; Fish Diseases/*epidemiology/mortality ; *Fisheries ; Population Dynamics ; *Salmon/parasitology
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    Anthropology. The missing years for modern humans (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-01-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goebel, Ted -- New York, N.Y. -- Science. 2007 Jan 12;315(5809):194-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for the Study of the First Americans, Department of Anthropology, Texas A&M University, College Station, TX 77843, USA. goebel@tamu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17218514" target="_blank"〉PubMed〈/a〉
    Keywords: Africa ; *Archaeology ; Asia ; Australia ; DNA, Mitochondrial/genetics ; *Emigration and Immigration ; Europe ; *Fossils ; Haplotypes ; Humans ; *Paleontology ; Population Dynamics ; Time
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    Pilai Poonswad profile. Subduing poachers, ducking insurgents to save a splendid bird (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stone, Richard -- New York, N.Y. -- Science. 2007 Aug 3;317(5838):592-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17673635" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Birds ; Buddhism ; Conservation of Natural Resources ; History, 20th Century ; History, 21st Century ; Islam ; Nesting Behavior ; Population Dynamics ; Thailand ; Trees
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    Ecology. Aspens return to Yellowstone, with help from some wolves (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-07-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Morell, Virginia -- New York, N.Y. -- Science. 2007 Jul 27;317(5837):438-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17656692" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Deer ; *Ecosystem ; Population Dynamics ; Populus/*growth & development ; *Wolves ; Wyoming
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    Predation risk affects reproductive physiology and demography of elk (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-17
    Description: Elk (Cervus elaphus) in the Greater Yellowstone Ecosystem alter patterns of aggregation, habitat selection, vigilance, and foraging in the presence of wolves (Canis lupus). Antipredator behaviors like these can reduce predation risk but are also likely to carry costs. Data from five elk populations studied for 16 site years showed that progesterone concentrations (from 1489 fecal samples) declined with the ratio of elk to wolves. In turn, progesterone concentrations were a good predictor of calf recruitment in the subsequent year. Together, these data suggest that wolves indirectly affect the reproductive physiology and the demography of elk through the costs of antipredator behavior.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Creel, Scott -- Christianson, David -- Liley, Stewart -- Winnie, John A Jr -- New York, N.Y. -- Science. 2007 Feb 16;315(5814):960.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology, Montana State University, 310 Lewis Hall, Bozeman, MT 59717, USA. screel@montana.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17303746" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Deer/*physiology ; Ecosystem ; Enzyme-Linked Immunosorbent Assay ; Feces ; Female ; Male ; Population Dynamics ; *Predatory Behavior ; Progesterone/metabolism ; Reproduction/*physiology ; *Wolves
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    Economics of overexploitation revisited (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-08
    Description: About 25% of the world's fisheries are depleted such that their current biomass is lower than the level that would maximize the sustained yield (MSY). By using methods not previously applied in the fisheries conservation context, we show in four disparate fisheries (including the long-lived and slow-growing orange roughy) that the dynamic maximum economic yield (MEY), the biomass that produces the largest discounted economic profits from fishing, exceeds MSY. Thus, although it is theoretically possible that maximizing discounted economic profits may cause stock depletions, our results show there is a win-win: In many fisheries at reasonable discount rates and at current prices and costs, larger fish stocks increase economic profits. An MEY target that exceeds MSY and transfers from higher, future profits to compensate fishers for the transition costs of stock rebuilding would help overcome a key cause of fisheries overexploitation, industry opposition to lower harvests.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grafton, R Q -- Kompas, T -- Hilborn, R W -- New York, N.Y. -- Science. 2007 Dec 7;318(5856):1601.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Crawford School, Australian National University, Ellery Crescent, Canberra, ACT 0200, Australia. quentin.grafton@anu.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18063793" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biomass ; Fisheries/*economics ; *Fishes ; Population Dynamics
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    Ecology. A world without corals? (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-05-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stone, Richard -- New York, N.Y. -- Science. 2007 May 4;316(5825):678-81.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17478692" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Anthozoa/microbiology/physiology ; Atmosphere ; Biodiversity ; Conservation of Natural Resources ; *Ecosystem ; Hydrogen-Ion Concentration ; Oceans and Seas ; Population Dynamics ; Seawater/chemistry
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    Oceans. Climate drives sea change (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Greene, Charles H -- Pershing, Andrew J -- New York, N.Y. -- Science. 2007 Feb 23;315(5815):1084-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth and Atmospheric Sciences, Cornell University, Ithaca, NY 14853, USA. chg2@cornell.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17322049" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arctic Regions ; Atlantic Ocean ; *Climate ; Copepoda ; Crustacea ; *Ecosystem ; Fishes ; Food Chain ; Oceans and Seas ; Phytoplankton/*growth & development ; Population Dynamics ; Population Growth ; Seasons ; Seawater ; Zooplankton/*growth & development
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    Rapid population growth of a critically endangered carnivore (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-11
    Description: Reintroductions of endangered species are controversial because of high costs and frequent failures. However, the population of black-footed ferrets descended from animals released in Shirley Basin, Wyoming, from 1991 to 1994 has grown rapidly after a decline to a low of five animals in 1997. Beginning around 2000, the population grew rapidly to an estimated 223 (95% confidence interval is 192 to 401) individuals in 2006. Matrix population modeling shows the importance of survival and reproduction during the first year of life, reflecting an uncommon life history for an endangered mammalian carnivore. Recovery of the species may benefit from more opportunistic and widespread releases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grenier, M B -- McDonald, D B -- Buskirk, S W -- New York, N.Y. -- Science. 2007 Aug 10;317(5839):779.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology and Physiology, University of Wyoming, 1000 East University Avenue, Laramie, WY 82071, USA. martin.grenier@wgf.state.wy.us〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17690288" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Communicable Diseases/epidemiology/veterinary ; *Ferrets/genetics/physiology ; Population Dynamics ; Population Growth ; Sciuridae ; Wyoming/epidemiology
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    The structural basis of ribozyme-catalyzed RNA assembly (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-03-17
    Description: Life originated, according to the RNA World hypothesis, from self-replicating ribozymes that catalyzed ligation of RNA fragments. We have solved the 2.6 angstrom crystal structure of a ligase ribozyme that catalyzes regiospecific formation of a 5' to 3' phosphodiester bond between the 5'-triphosphate and the 3'-hydroxyl termini of two RNA fragments. Invariant residues form tertiary contacts that stabilize a flexible stem of the ribozyme at the ligation site, where an essential magnesium ion coordinates three phosphates. The structure of the active site permits us to suggest how transition-state stabilization and a general base may catalyze the ligation reaction required for prebiotic RNA assembly.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Robertson, Michael P -- Scott, William G -- New York, N.Y. -- Science. 2007 Mar 16;315(5818):1549-53.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for the Molecular Biology of RNA and Department of Chemistry and Biochemistry, Robert L. Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17363667" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Binding Sites ; Catalysis ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; Directed Molecular Evolution ; Hydrogen Bonding ; Models, Molecular ; Molecular Conformation ; Nucleic Acid Conformation ; Oligoribonucleotides/chemistry/metabolism ; RNA, Catalytic/*chemistry/metabolism ; Ribonucleotides/chemistry/metabolism ; Templates, Genetic
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    Biodiversity loss in the ocean: how bad is it? (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murawski, Steven -- Methot, Richard -- Tromble, Galen -- New York, N.Y. -- Science. 2007 Jun 1;316(5829):1281-4; author reply 1281-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17540882" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; Biomass ; *Ecosystem ; *Fisheries/legislation & jurisprudence ; *Fishes ; Forecasting ; Oceans and Seas ; Population Density ; Population Dynamics ; United States
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    Structure of the prefusion form of the vesicular stomatitis virus glycoprotein G (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-10
    Description: Glycoprotein G of the vesicular stomatitis virus triggers membrane fusion via a low pH-induced structural rearrangement. Despite the equilibrium between the pre- and postfusion states, the structure of the prefusion form, determined to 3.0 angstrom resolution, shows that the fusogenic transition entails an extensive structural reorganization of G. Comparison with the structure of the postfusion form suggests a pathway for the conformational change. In the prefusion form, G has the shape of a tripod with the fusion loops exposed, which point toward the viral membrane, and with the antigenic sites located at the distal end of the molecule. A large number of G glycoproteins, perhaps organized as in the crystals, act cooperatively to induce membrane merging.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roche, Stephane -- Rey, Felix A -- Gaudin, Yves -- Bressanelli, Stephane -- New York, N.Y. -- Science. 2007 Feb 9;315(5813):843-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CNRS, Unite Mixte de Recherche (UMR) 2472, Institut National de la Recherche Agronomique (INRA), UMR 1157, Institut Federatif de Recherche 115, Laboratoire de Virologie Moleculaire et Structurale, 91198, Gif sur Yvette, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17289996" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallization ; Crystallography, X-Ray ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Membrane Fusion ; Membrane Glycoproteins/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Vesicular stomatitis Indiana virus/*chemistry ; Viral Envelope Proteins/*chemistry ; Viral Fusion Proteins/*chemistry
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    The macroecological contribution to global change solutions (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-06-16
    Description: Anthropogenic global changes threaten species and the ecosystem services upon which society depends. Effective solutions to this multifaceted crisis need scientific responses spanning disciplines and spatial scales. Macroecology develops broad-scale predictions of species' distributions and abundances, complementing the frequently local focus of global change biology. Macroecological discoveries rely particularly on correlative methods but have still proven effective in predicting global change impacts on species. However, global changes create pseudo-experimental opportunities to build stronger, mechanistic theories in macroecology that successfully predict multiple phenomena across spatial scales. Such macroecological perspectives will help address the biotic consequences of global change.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kerr, Jeremy T -- Kharouba, Heather M -- Currie, David J -- New York, N.Y. -- Science. 2007 Jun 15;316(5831):1581-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Canadian Facility for Ecoinformatics Research (CFER), University of Ottawa, Ottawa, ON K1N 6N5 Canada. jkerr@uottawa.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17569854" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; Climate ; Ecology/*methods ; *Ecosystem ; Forecasting ; Geography ; Human Activities ; Humans ; Models, Biological ; Plants ; Population Dynamics ; Statistics as Topic
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    Global pattern formation and ethnic/cultural violence (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-18
    Description: We identify a process of global pattern formation that causes regions to differentiate by culture. Violence arises at boundaries between regions that are not sufficiently well defined. We model cultural differentiation as a separation of groups whose members prefer similar neighbors, with a characteristic group size at which violence occurs. Application of this model to the area of the former Yugoslavia and to India accurately predicts the locations of reported conflict. This model also points to imposed mixing or boundary clarification as mechanisms for promoting peace.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lim, May -- Metzler, Richard -- Bar-Yam, Yaneer -- New York, N.Y. -- Science. 2007 Sep 14;317(5844):1540-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉New England Complex Systems Institute, 24 Mt. Auburn Street, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17872443" target="_blank"〉PubMed〈/a〉
    Keywords: Bosnia and Herzegovina ; Conflict (Psychology) ; Croatia ; *Culture ; Demography ; *Ethnic Groups ; Humans ; India ; Models, Statistical ; Monte Carlo Method ; Population Dynamics ; *Violence/prevention & control/statistics & numerical data ; Yugoslavia
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Cascading effects of the loss of apex predatory sharks from a coastal ocean (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-03-31
    Description: Impacts of chronic overfishing are evident in population depletions worldwide, yet indirect ecosystem effects induced by predator removal from oceanic food webs remain unpredictable. As abundances of all 11 great sharks that consume other elasmobranchs (rays, skates, and small sharks) fell over the past 35 years, 12 of 14 of these prey species increased in coastal northwest Atlantic ecosystems. Effects of this community restructuring have cascaded downward from the cownose ray, whose enhanced predation on its bay scallop prey was sufficient to terminate a century-long scallop fishery. Analogous top-down effects may be a predictable consequence of eliminating entire functional groups of predators.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Myers, Ransom A -- Baum, Julia K -- Shepherd, Travis D -- Powers, Sean P -- Peterson, Charles H -- New York, N.Y. -- Science. 2007 Mar 30;315(5820):1846-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS B3H 4J1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17395829" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Atlantic Ocean ; Bivalvia ; Conservation of Natural Resources ; *Ecosystem ; *Elasmobranchii ; Fisheries ; *Food Chain ; Ostreidae ; Population Dynamics ; Population Growth ; Predatory Behavior ; *Sharks ; Skates (Fish)
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Spring-loaded mechanism of DNA unwinding by hepatitis C virus NS3 helicase (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-07-28
    Description: NS3, an essential helicase for replication of hepatitis C virus, is a model enzyme for investigating helicase function. Using single-molecule fluorescence analysis, we showed that NS3 unwinds DNA in discrete steps of about three base pairs (bp). Dwell time analysis indicated that about three hidden steps are required before a 3-bp step is taken. Taking into account the available structural data, we propose a spring-loaded mechanism in which several steps of one nucleotide per adenosine triphosphate molecule accumulate tension on the protein-DNA complex, which is relieved periodically via a burst of 3-bp unwinding. NS3 appears to shelter the displaced strand during unwinding, and, upon encountering a barrier or after unwinding 〉18 bp, it snaps or slips backward rapidly and repeats unwinding many times in succession. Such repetitive unwinding behavior over a short stretch of duplex may help to keep secondary structures resolved during viral genome replication.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565428/" 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/PMC3565428/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Myong, Sua -- Bruno, Michael M -- Pyle, Anna M -- Ha, Taekjip -- R01 GM060620/GM/NIGMS NIH HHS/ -- R01 GM065367/GM/NIGMS NIH HHS/ -- R01-GM060620/GM/NIGMS NIH HHS/ -- R01-GM065367/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2007 Jul 27;317(5837):513-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Physics Department, University of Illinois, 1110 West Green Street, Urbana, IL 61801, USA. smyong@uiuc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17656723" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Base Pairing ; DNA/chemistry/*metabolism ; DNA Helicases/*metabolism ; Fluorescence Resonance Energy Transfer ; Hepacivirus/*enzymology ; Models, Biological ; Models, Molecular ; Nucleic Acid Conformation ; Temperature ; Viral Nonstructural Proteins/chemistry/*metabolism
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    GNAT-like strategy for polyketide chain initiation (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-11-10
    Description: An unexpected biochemical strategy for chain initiation is described for the loading module of the polyketide synthase of curacin A, an anticancer lead derived from the marine cyanobacterium Lyngbya majuscula. A central GCN5-related N-acetyltransferase (GNAT) domain bears bifunctional decarboxylase/S-acetyltransferase activity, both unprecedented for the GNAT superfamily. A CurA loading tridomain, consisting of an adaptor domain, the GNAT domain, and an acyl carrier protein, was assessed biochemically, revealing that a domain showing homology to GNAT (GNAT(L)) catalyzes (i) decarboxylation of malonyl-coenzyme A (malonyl-CoA) to acetyl-CoA and (ii) direct S-acetyl transfer from acetyl-CoA to load an adjacent acyl carrier protein domain (ACP(L)). Moreover, the N-terminal adapter domain was shown to facilitate acetyl-group transfer. Crystal structures of GNAT(L) were solved at 1.95 angstroms (ligand-free form) and 2.75 angstroms (acyl-CoA complex), showing distinct substrate tunnels for acyl-CoA and holo-ACP(L) binding. Modeling and site-directed mutagenesis experiments demonstrated that histidine-389 and threonine-355, at the convergence of the CoA and ACP tunnels, participate in malonyl-CoA decarboxylation but not in acetyl-group transfer. Decarboxylation precedes acetyl-group transfer, leading to acetyl-ACP(L) as the key curacin A starter unit.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gu, Liangcai -- Geders, Todd W -- Wang, Bo -- Gerwick, William H -- Hakansson, Kristina -- Smith, Janet L -- Sherman, David H -- DK42303/DK/NIDDK NIH HHS/ -- GM076477/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Nov 9;318(5852):970-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17991863" target="_blank"〉PubMed〈/a〉
    Keywords: Acetyl Coenzyme A/metabolism ; Acetyltransferases/*chemistry/*metabolism ; Acyl Carrier Protein/chemistry/metabolism ; Amino Acid Sequence ; Carboxy-Lyases/chemistry/metabolism ; Crystallography, X-Ray ; Cyanobacteria/*enzymology/genetics ; Cyclopropanes/*metabolism ; Decarboxylation ; Malonyl Coenzyme A/metabolism ; Models, Molecular ; Molecular Sequence Data ; Polyketide Synthases/*chemistry/genetics/*metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Thiazoles/*metabolism
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    Biodiversity loss in the ocean: how bad is it? (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Briggs, John C -- New York, N.Y. -- Science. 2007 Jun 1;316(5829):1281-4; author reply 1281-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17546726" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; Conservation of Natural Resources ; *Ecosystem ; Extinction, Biological ; *Fishes ; Invertebrates ; Oceans and Seas ; Population Dynamics ; Terminology as Topic
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    Structure of a NHEJ polymerase-mediated DNA synaptic complex (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-10-20
    Description: Nonhomologous end joining (NHEJ) is a critical DNA double-strand break (DSB) repair pathway required to maintain genome stability. Many prokaryotes possess a minimalist NHEJ apparatus required to repair DSBs during stationary phase, composed of two conserved core proteins, Ku and ligase D (LigD). The crystal structure of Mycobacterium tuberculosis polymerase domain of LigD mediating the synapsis of two noncomplementary DNA ends revealed a variety of interactions, including microhomology base pairing, mismatched and flipped-out bases, and 3' termini forming hairpin-like ends. Biochemical and biophysical studies confirmed that polymerase-induced end synapsis also occurs in solution. We propose that this DNA synaptic structure reflects an intermediate bridging stage of the NHEJ process, before end processing and ligation, with both the polymerase and the DNA sequence playing pivotal roles in determining the sequential order of synapsis and remodeling before end joining.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brissett, Nigel C -- Pitcher, Robert S -- Juarez, Raquel -- Picher, Angel J -- Green, Andrew J -- Dafforn, Timothy R -- Fox, Gavin C -- Blanco, Luis -- Doherty, Aidan J -- BB/D522746/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- G120/738/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2007 Oct 19;318(5849):456-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17947582" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Crystallography, X-Ray ; DNA Ligases/*chemistry/genetics/metabolism ; *DNA Repair ; DNA, Bacterial/*chemistry/metabolism ; Dimerization ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Mycobacterium tuberculosis/*chemistry/enzymology/genetics/metabolism ; Protein Conformation ; Protein Structure, Tertiary
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    Species interactions reverse grassland responses to changing climate (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-02-03
    Description: Predictions of ecological response to climate change are based largely on direct climatic effects on species. We show that, in a California grassland, species interactions strongly influence responses to changing climate, overturning direct climatic effects within 5 years. We manipulated the seasonality and intensity of rainfall over large, replicate plots in accordance with projections of leading climate models and examined responses across several trophic levels. Changes in seasonal water availability had pronounced effects on individual species, but as precipitation regimes were sustained across years, feedbacks and species interactions overrode autecological responses to water and reversed community trajectories. Conditions that sharply increased production and diversity through 2 years caused simplification of the food web and deep reductions in consumer abundance after 5 years. Changes in these natural grassland communities suggest a prominent role for species interactions in ecosystem response to climate change.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Suttle, K B -- Thomsen, Meredith A -- Power, Mary E -- New York, N.Y. -- Science. 2007 Feb 2;315(5812):640-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Biology, University of California, Berkeley, CA 94720, USA. kbsuttle@socrates.berkeley.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17272720" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; Biomass ; California ; *Climate ; *Ecosystem ; Food Chain ; *Invertebrates/physiology ; Nitrogen Fixation ; *Plant Development ; Poaceae/growth & development ; Population Dynamics ; Rain ; Seasons ; Time Factors
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    GPCR engineering yields high-resolution structural insights into beta2-adrenergic receptor function (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-10-27
    Description: The beta2-adrenergic receptor (beta2AR) is a well-studied prototype for heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) that respond to diffusible hormones and neurotransmitters. To overcome the structural flexibility of the beta2AR and to facilitate its crystallization, we engineered a beta2AR fusion protein in which T4 lysozyme (T4L) replaces most of the third intracellular loop of the GPCR ("beta2AR-T4L") and showed that this protein retains near-native pharmacologic properties. Analysis of adrenergic receptor ligand-binding mutants within the context of the reported high-resolution structure of beta2AR-T4L provides insights into inverse-agonist binding and the structural changes required to accommodate catecholamine agonists. Amino acids known to regulate receptor function are linked through packing interactions and a network of hydrogen bonds, suggesting a conformational pathway from the ligand-binding pocket to regions that interact with G proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rosenbaum, Daniel M -- Cherezov, Vadim -- Hanson, Michael A -- Rasmussen, Soren G F -- Thian, Foon Sun -- Kobilka, Tong Sun -- Choi, Hee-Jung -- Yao, Xiao-Jie -- Weis, William I -- Stevens, Raymond C -- Kobilka, Brian K -- F32 GM082028/GM/NIGMS NIH HHS/ -- NS028471/NS/NINDS NIH HHS/ -- P50 GM073197/GM/NIGMS NIH HHS/ -- P50 GM62411/GM/NIGMS NIH HHS/ -- R01 GM056169/GM/NIGMS NIH HHS/ -- R21 GM075811/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Nov 23;318(5854):1266-73. Epub 2007 Oct 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17962519" target="_blank"〉PubMed〈/a〉
    Keywords: Adrenergic beta-Agonists/chemistry/metabolism ; Adrenergic beta-Antagonists/chemistry/metabolism ; Amino Acid Sequence ; Bacteriophage T4/enzymology ; Binding Sites ; Cell Line ; Cell Membrane/chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Drug Inverse Agonism ; Humans ; Immunoglobulin Fab Fragments/chemistry/metabolism ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Muramidase/chemistry/metabolism ; Propanolamines/chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Adrenergic, beta-2/*chemistry/*metabolism ; Recombinant Fusion Proteins/chemistry/metabolism
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    Binding of the human Prp31 Nop domain to a composite RNA-protein platform in U4 snRNP (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-04-07
    Description: Although highly homologous, the spliceosomal hPrp31 and the nucleolar Nop56 and Nop58 (Nop56/58) proteins recognize different ribonucleoprotein (RNP) particles. hPrp31 interacts with complexes containing the 15.5K protein and U4 or U4atac small nuclear RNA (snRNA), whereas Nop56/58 associate with 15.5K-box C/D small nucleolar RNA complexes. We present structural and biochemical analyses of hPrp31-15.5K-U4 snRNA complexes that show how the conserved Nop domain in hPrp31 maintains high RNP binding selectivity despite relaxed RNA sequence requirements. The Nop domain is a genuine RNP binding module, exhibiting RNA and protein binding surfaces. Yeast two-hybrid analyses suggest a link between retinitis pigmentosa and an aberrant hPrp31-hPrp6 interaction that blocks U4/U6-U5 tri-snRNP formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Sunbin -- Li, Ping -- Dybkov, Olexandr -- Nottrott, Stephanie -- Hartmuth, Klaus -- Luhrmann, Reinhard -- Carlomagno, Teresa -- Wahl, Markus C -- New York, N.Y. -- Science. 2007 Apr 6;316(5821):115-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Abteilung Zellulare Biochemie, Max-Planck-Institut fur Biophysikalische Chemie, Am Fassberg 11, D-37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17412961" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Amino Acid Substitution ; Carrier Proteins/chemistry/metabolism ; Eye Proteins/*chemistry/*metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Small Nuclear/*chemistry/*metabolism ; RNA-Binding Proteins ; Retinitis Pigmentosa/genetics ; Ribonucleoprotein, U4-U6 Small Nuclear/*chemistry/*metabolism ; Transcription Factors
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    Structure of Galphaq-p63RhoGEF-RhoA complex reveals a pathway for the activation of RhoA by GPCRs (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-12-22
    Description: The guanine nucleotide exchange factor p63RhoGEF is an effector of the heterotrimeric guanine nucleotide-binding protein (G protein) Galphaq and thereby links Galphaq-coupled receptors (GPCRs) to the activation of the small-molecular-weight G protein RhoA. We determined the crystal structure of the Galphaq-p63RhoGEF-RhoA complex, detailing the interactions of Galphaq with the Dbl and pleckstrin homology (DH and PH) domains of p63RhoGEF. These interactions involve the effector-binding site and the C-terminal region of Galphaq and appear to relieve autoinhibition of the catalytic DH domain by the PH domain. Trio, Duet, and p63RhoGEF are shown to constitute a family of Galphaq effectors that appear to activate RhoA both in vitro and in intact cells. We propose that this structure represents the crux of an ancient signal transduction pathway that is expected to be important in an array of physiological processes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lutz, Susanne -- Shankaranarayanan, Aruna -- Coco, Cassandra -- Ridilla, Marc -- Nance, Mark R -- Vettel, Christiane -- Baltus, Doris -- Evelyn, Chris R -- Neubig, Richard R -- Wieland, Thomas -- Tesmer, John J G -- HL071818/HL/NHLBI NIH HHS/ -- HL086865/HL/NHLBI NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Dec 21;318(5858):1923-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty Mannheim, University of Heidelberg, Maybachstrasse 14, D-68169 Mannheim, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18096806" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Cell Line ; Crystallography, X-Ray ; GTP-Binding Protein alpha Subunits, Gq-G11/*chemistry/metabolism ; Guanine Nucleotide Exchange Factors/*chemistry/metabolism ; Humans ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rho Guanine Nucleotide Exchange Factors ; Signal Transduction ; rhoA GTP-Binding Protein/*chemistry/metabolism
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    Asymmetric mating interactions drive widespread invasion and displacement in a whitefly (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-11-10
    Description: The role of behavioral mechanisms in animal invasions is poorly understood. We show that asymmetric mating interactions between closely related but previously allopatric genetic groups of the whitefly Bemisia tabaci, a haplodiploid species, have been a driving force contributing to widespread invasion and displacement by alien populations. We conducted long-term field surveys, caged population experiments, and detailed behavioral observations in Zhejiang, China, and Queensland, Australia, to investigate the invasion process and its underlying behavioral mechanisms. During invasion and displacement, we found increased frequency of copulation leading to increased production of female progeny among the invader, as well as reduced copulation and female production in the indigenous genetic groups. Such asymmetric mating interactions may be critical to determining the capacity of a haplodiploid invader and the consequences for its closely related indigenous organisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Shu-Sheng -- De Barro, P J -- Xu, Jing -- Luan, Jun-Bo -- Zang, Lian-Sheng -- Ruan, Yong-Ming -- Wan, Fang-Hao -- New York, N.Y. -- Science. 2007 Dec 14;318(5857):1769-72. Epub 2007 Nov 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Insect Sciences, Zhejiang University, Hangzhou 310029, China. shshliu@zju.edu.cn〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17991828" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; China ; Copulation ; *Ecosystem ; Female ; Hemiptera/classification/genetics/*physiology ; Male ; Population Dynamics ; Queensland ; Reproduction ; Sex Ratio ; *Sexual Behavior, Animal
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    Biochemistry. Balancing cellular energy (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-03-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hardie, D Grahame -- New York, N.Y. -- Science. 2007 Mar 23;315(5819):1671-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Molecular Physiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK. d.g.hardie@dundee.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17379794" target="_blank"〉PubMed〈/a〉
    Keywords: AMP-Activated Protein Kinases ; Adenosine Monophosphate/metabolism ; Adenosine Triphosphate/metabolism ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Multienzyme Complexes/*chemistry/*metabolism ; Phosphorylation ; Protein Kinases/chemistry ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Protein-Serine-Threonine Kinases/*chemistry/*metabolism ; Schizosaccharomyces/*enzymology
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    Farmland biodiversity and the footprint of agriculture (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-01-20
    Description: Sustainable development requires the reconciliation of demands for biodiversity conservation and increased agricultural production. Assessing the impact of novel farming practices on biodiversity and ecosystem services is fundamental to this process. Using farmland birds as a model system, we present a generic risk assessment framework that accurately predicts each species' current conservation status and population growth rate associated with past changes in agriculture. We demonstrate its value by assessing the potential impact on biodiversity of two controversial land uses, genetically modified herbicide-tolerant crops and agri-environment schemes. This framework can be used to guide policy and land management decisions and to assess progress toward sustainability targets.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, S J -- Vickery, J A -- Norris, K -- New York, N.Y. -- Science. 2007 Jan 19;315(5810):381-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Agri-Environment Research, School of Agriculture, Policy, and Development, University of Reading, Reading RG6 6AR, UK. s.j.butler@reading.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17234947" target="_blank"〉PubMed〈/a〉
    Keywords: *Agriculture ; Animals ; *Biodiversity ; *Birds ; Conservation of Natural Resources ; Crops, Agricultural/genetics ; *Ecosystem ; *Environment ; Great Britain ; Linear Models ; Models, Statistical ; Plants, Genetically Modified ; Population Density ; Population Dynamics ; Risk Assessment
    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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  • 97
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    Biodiversity loss in the ocean: how bad is it? (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hilborn, Ray W -- New York, N.Y. -- Science. 2007 Jun 1;316(5829):1281-4; author reply 1281-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17546725" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; Conservation of Natural Resources ; *Ecosystem ; *Fisheries ; *Fishes ; Forecasting ; Oceans and Seas ; Population Dynamics
    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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    Local replenishment of coral reef fish populations in a marine reserve (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-05-05
    Description: The scale of larval dispersal of marine organisms is important for the design of networks of marine protected areas. We examined the fate of coral reef fish larvae produced at a small island reserve, using a mass-marking method based on maternal transmission of stable isotopes to offspring. Approximately 60% of settled juveniles were spawned at the island, for species with both short (〈2 weeks) and long (〉1 month) pelagic larval durations. If natal homing of larvae is a common life-history strategy, the appropriate spatial scales for the management and conservation of coral reefs are likely to be much smaller than previously assumed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Almany, Glenn R -- Berumen, Michael L -- Thorrold, Simon R -- Planes, Serge -- Jones, Geoffrey P -- New York, N.Y. -- Science. 2007 May 4;316(5825):742-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Australian Research Council Centre of Excellence for Coral Reef Studies and School of Marine and Tropical Biology, James Cook University, Townsville QLD 4811, Australia. glenn.almany@jcu.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17478720" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Anthozoa ; Barium Compounds ; Chlorides ; Conservation of Natural Resources ; *Ecosystem ; Female ; Geography ; Isotopes ; Larva/physiology ; Male ; Pacific Ocean ; Papua New Guinea ; Perciformes/growth & development/*physiology ; Population Dynamics ; Reproduction
    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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  • 99
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    Crystal structure of an ancient protein: evolution by conformational epistasis (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-19
    Description: The structural mechanisms by which proteins have evolved new functions are known only indirectly. We report x-ray crystal structures of a resurrected ancestral protein-the approximately 450 million-year-old precursor of vertebrate glucocorticoid (GR) and mineralocorticoid (MR) receptors. Using structural, phylogenetic, and functional analysis, we identify the specific set of historical mutations that recapitulate the evolution of GR's hormone specificity from an MR-like ancestor. These substitutions repositioned crucial residues to create new receptor-ligand and intraprotein contacts. Strong epistatic interactions occur because one substitution changes the conformational position of another site. "Permissive" mutations-substitutions of no immediate consequence, which stabilize specific elements of the protein and allow it to tolerate subsequent function-switching changes-played a major role in determining GR's evolutionary trajectory.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2519897/" 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/PMC2519897/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ortlund, Eric A -- Bridgham, Jamie T -- Redinbo, Matthew R -- Thornton, Joseph W -- F32-GM074398/GM/NIGMS NIH HHS/ -- R01 GM081592/GM/NIGMS NIH HHS/ -- R01 GM081592-01/GM/NIGMS NIH HHS/ -- R01 GM081592-02/GM/NIGMS NIH HHS/ -- R01-DK622229/DK/NIDDK NIH HHS/ -- R01-GM081592/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 14;317(5844):1544-8. Epub 2007 Aug 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17702911" target="_blank"〉PubMed〈/a〉
    Keywords: Aldosterone/metabolism ; Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Crystallography, X-Ray ; Epistasis, Genetic ; *Evolution, Molecular ; Humans ; Hydrocortisone/metabolism ; Ligands ; Likelihood Functions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Phylogeny ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Glucocorticoid/*chemistry/*genetics/metabolism ; Receptors, Mineralocorticoid/*chemistry/*genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 100
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    Sirtuin 2 inhibitors rescue alpha-synuclein-mediated toxicity in models of Parkinson's disease (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-26
    Description: The sirtuins are members of the histone deacetylase family of proteins that participate in a variety of cellular functions and play a role in aging. We identified a potent inhibitor of sirtuin 2 (SIRT2) and found that inhibition of SIRT2 rescued alpha-synuclein toxicity and modified inclusion morphology in a cellular model of Parkinson's disease. Genetic inhibition of SIRT2 via small interfering RNA similarly rescued alpha-synuclein toxicity. Furthermore, the inhibitors protected against dopaminergic cell death both in vitro and in a Drosophila model of Parkinson's disease. The results suggest a link between neurodegeneration and aging.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Outeiro, Tiago Fleming -- Kontopoulos, Eirene -- Altmann, Stephen M -- Kufareva, Irina -- Strathearn, Katherine E -- Amore, Allison M -- Volk, Catherine B -- Maxwell, Michele M -- Rochet, Jean-Christophe -- McLean, Pamela J -- Young, Anne B -- Abagyan, Ruben -- Feany, Mel B -- Hyman, Bradley T -- Kazantsev, Aleksey G -- 5P50-NS38372A-06/NS/NINDS NIH HHS/ -- R01-NS049221/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2007 Jul 27;317(5837):516-9. Epub 2007 Jun 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Alzheimer's Research Unit, MGH, Harvard Medical School, CNY 114, 16th Street, Charlestown, MA 02129, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17588900" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Animals ; Animals, Genetically Modified ; Cell Death/drug effects ; Cell Line, Tumor ; Cells, Cultured ; Disease Models, Animal ; Dopamine/physiology ; Dose-Response Relationship, Drug ; Drosophila melanogaster ; Furans/*pharmacology ; Humans ; Models, Molecular ; Neurons/cytology/drug effects ; Parkinson Disease/*drug therapy/metabolism/pathology/*physiopathology ; Protein Conformation ; Quinolines/*pharmacology ; RNA, Small Interfering/genetics ; Rats ; Sirtuin 1 ; Sirtuin 2 ; Sirtuins/*antagonists & inhibitors/chemistry/genetics/*metabolism ; Transfection ; Tubulin/metabolism ; alpha-Synuclein/genetics/*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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