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  • Articles  (165)
  • *Ecosystem  (115)
  • Models, Molecular
  • 2005-2009  (165)
  • 2005  (165)
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  • Articles  (165)
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  • 2005-2009  (165)
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  • 1
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    Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-12-17
    Description: Translesion synthesis (TLS) is the major pathway by which mammalian cells replicate across DNA lesions. Upon DNA damage, ubiquitination of proliferating cell nuclear antigen (PCNA) induces bypass of the lesion by directing the replication machinery into the TLS pathway. Yet, how this modification is recognized and interpreted in the cell remains unclear. Here we describe the identification of two ubiquitin (Ub)-binding domains (UBM and UBZ), which are evolutionarily conserved in all Y-family TLS polymerases (pols). These domains are required for binding of poleta and poliota to ubiquitin, their accumulation in replication factories, and their interaction with monoubiquitinated PCNA. Moreover, the UBZ domain of poleta is essential to efficiently restore a normal response to ultraviolet irradiation in xeroderma pigmentosum variant (XP-V) fibroblasts. Our results indicate that Ub-binding domains of Y-family polymerases play crucial regulatory roles in TLS.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bienko, Marzena -- Green, Catherine M -- Crosetto, Nicola -- Rudolf, Fabian -- Zapart, Grzegorz -- Coull, Barry -- Kannouche, Patricia -- Wider, Gerhard -- Peter, Matthias -- Lehmann, Alan R -- Hofmann, Kay -- Dikic, Ivan -- New York, N.Y. -- Science. 2005 Dec 16;310(5755):1821-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Biochemistry II, Goethe University Medical School, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16357261" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Cell Line ; Computational Biology ; DNA/*biosynthesis ; *DNA Damage ; DNA Repair ; DNA Replication ; DNA-Directed DNA Polymerase/*chemistry/genetics/*metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Point Mutation ; Proliferating Cell Nuclear Antigen/metabolism ; Protein Binding ; Protein Conformation ; Protein Interaction Mapping ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Transfection ; Ubiquitin/*metabolism ; Xeroderma Pigmentosum/genetics ; Zinc Fingers
    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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    Drought, snails, and large-scale die-off of southern U.S. salt marshes (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-12-17
    Description: Salt marshes in the southeastern United States have recently experienced massive die-off, one of many examples of widespread degradation in marine and coastal ecosystems. Although intense drought is thought to be the primary cause of this die-off, we found snail grazing to be a major contributing factor. Survey of marsh die-off areas in three states revealed high-density fronts of snails on die-off edges at 11 of 12 sites. Exclusion experiments demonstrated that snails actively converted marshes to exposed mudflats. Salt addition and comparative field studies suggest that drought-induced stress and grazers acted synergistically and to varying degrees to cause initial plant death. After these disturbances, snail fronts formed on die-off edges and subsequently propagated through healthy marsh, leading to cascading vegetation loss. These results, combined with model analyses, reveal strong interactions between increasing climatic stress and grazer pressure, both potentially related to human environmental impacts, which amplify the likelihood and intensity of runaway collapse in these coastal systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Silliman, Brian R -- van de Koppel, Johan -- Bertness, Mark D -- Stanton, Lee E -- Mendelssohn, Irving A -- New York, N.Y. -- Science. 2005 Dec 16;310(5755):1803-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, University of Florida, Gainesville, FL 32611, USA. brs@ufl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16357258" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biomass ; Climate ; *Disasters ; *Ecosystem ; Environment ; Food Chain ; Georgia ; Louisiana ; Mathematics ; Models, Biological ; Poaceae/*growth & development ; Population Density ; Snails/*physiology ; *Sodium Chloride ; *Soil ; Water
    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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    Ecology. Population evolution and island biogeography (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-12-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thorpe, Roger S -- New York, N.Y. -- Science. 2005 Dec 16;310(5755):1778-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of Wales, Bangor, Gwynedd LL57 2UW, UK. r.s.thorpe@bangor.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16357251" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bahamas ; Biological Evolution ; *Ecosystem ; Environment ; Genetic Speciation ; *Geography ; *Lizards/genetics ; Plant Development ; *Plants/anatomy & histology ; Population Density ; Population Dynamics ; Predatory Behavior ; Selection, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Island biogeography of populations: an introduced species transforms survival patterns (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-12-17
    Description: Population phenomena, which provide much of the underlying basis for the theoretical structure of island biogeography, have received little direct study. We determined a key population trait-survival-in the Bahamian lizard Anolis sagrei on islands with an experimentally introduced predatory lizard and on neighboring unmanipulated islands. On unmanipulated islands, survival declined with several variables, most notably vegetation height: The island with the shortest vegetation had nearly the highest survival recorded for any lizard. On islands with the introduced predator, which forages mostly on the ground, A. sagrei shifted to taller vegetation; unlike on unmanipulated islands, its survival was very low on islands with the shortest vegetation but was higher on the others. Thus, species introduction radically changed a resident species' relation of survival to a key island-biogeographical variable.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schoener, Thomas W -- Losos, Jonathan B -- Spiller, David A -- New York, N.Y. -- Science. 2005 Dec 16;310(5755):1807-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Evolution and Ecology, University of California, Davis, CA 95616, USA. twschoener@ucdavis.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16357259" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bahamas ; Birds ; *Ecosystem ; Environment ; *Geography ; *Lizards ; Models, Biological ; Models, Statistical ; Plant Development ; *Plants/anatomy & histology ; Population Density ; Population Dynamics ; Predatory Behavior ; *Trees/anatomy & histology/growth & development
    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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    Scaling of connectivity in marine populations (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-12-17
    Description: Defining the scale of connectivity, or exchange, among marine populations and determining the factors driving this exchange are pivotal to our understanding of the population dynamics, genetic structure, and biogeography of many coastal species. Using a high-resolution biophysical model for the Caribbean region, we report that typical larval dispersal distances of ecologically relevant magnitudes are on the scale of only 10 to 100 kilometers for a variety of reef fish species. We also show the importance of the early onset of active larval movement mediating the dispersal potential. In addition to self-recruitment, larval import from outside the local area is required to sustain most populations, although these population subsidies are very limited in particular systems. The results reveal distinct regions of population isolation based on larval dispersal that also correspond to genetic and morphological clines observed across a range of marine organisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cowen, R K -- Paris, C B -- Srinivasan, A -- New York, N.Y. -- Science. 2006 Jan 27;311(5760):522-7. Epub 2005 Dec 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA. rcowen@rsmas.miami.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16357224" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Anthozoa/genetics ; Caribbean Region ; Computer Simulation ; *Ecosystem ; Environment ; Fishes/genetics/*physiology ; Larva/physiology ; *Models, Biological ; Population Density ; Population Dynamics ; *Seawater ; *Swimming ; Water Movements
    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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    Restoration of degraded tropical forest landscapes (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-12-13
    Description: The current scale of deforestation in tropical regions and the large areas of degraded lands now present underscore the urgent need for interventions to restore biodiversity, ecological functioning, and the supply of goods and ecological services previously used by poor rural communities. Traditional timber plantations have supplied some goods but have made only minor contributions to fulfilling most of these other objectives. New approaches to reforestation are now emerging, with potential for both overcoming forest degradation and addressing rural poverty.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lamb, David -- Erskine, Peter D -- Parrotta, John A -- New York, N.Y. -- Science. 2005 Dec 9;310(5754):1628-32.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Rainforest Cooperative Research Center and School of Integrative Biology, University of Queensland, Brisbane 4072, Australia. d.lamb@uq.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16339437" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture ; Biodiversity ; *Conservation of Natural Resources ; *Ecosystem ; *Forestry ; Rural Population ; *Trees/growth & development ; *Tropical Climate ; Wood
    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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  • 7
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    Bilateral action for right whales (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-12-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sayles, Jesse S -- Green, David M -- New York, N.Y. -- Science. 2005 Dec 9;310(5754):1616-8; author reply 1616-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16339430" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Atlantic Ocean ; Canada ; *Ecosystem ; Environment ; Fisheries ; *International Cooperation ; Mortality ; Population Dynamics ; Public Policy ; Ships ; United States ; *Whales
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-12-13
    Description: Practical components for three-dimensional molecular nanofabrication must be simple to produce, stereopure, rigid, and adaptable. We report a family of DNA tetrahedra, less than 10 nanometers on a side, that can self-assemble in seconds with near-quantitative yield of one diastereomer. They can be connected by programmable DNA linkers. Their triangulated architecture confers structural stability; by compressing a DNA tetrahedron with an atomic force microscope, we have measured the axial compressibility of DNA and observed the buckling of the double helix under high loads.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goodman, R P -- Schaap, I A T -- Tardin, C F -- Erben, C M -- Berry, R M -- Schmidt, C F -- Turberfield, A J -- New York, N.Y. -- Science. 2005 Dec 9;310(5754):1661-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16339440" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Base Sequence ; Chemistry, Physical ; DNA/*chemistry ; Dimerization ; Elasticity ; Microscopy, Atomic Force ; Models, Molecular ; Molecular Structure ; *Nanostructures ; *Nanotechnology ; Nucleic Acid Conformation ; Nucleic Acid Hybridization ; Oligodeoxyribonucleotides/chemistry ; Physicochemical Phenomena ; Stereoisomerism
    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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    Snapshot of activated G proteins at the membrane: the Galphaq-GRK2-Gbetagamma complex (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-12-13
    Description: G protein-coupled receptor kinase 2 (GRK2) plays a key role in the desensitization of G protein-coupled receptor signaling by phosphorylating activated heptahelical receptors and by sequestering heterotrimeric G proteins. We report the atomic structure of GRK2 in complex with Galphaq and Gbetagamma, in which the activated Galpha subunit of Gq is fully dissociated from Gbetagamma and dramatically reoriented from its position in the inactive Galphabetagamma heterotrimer. Galphaq forms an effector-like interaction with the GRK2 regulator of G protein signaling (RGS) homology domain that is distinct from and does not overlap with that used to bind RGS proteins such as RGS4.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tesmer, Valerie M -- Kawano, Takeharu -- Shankaranarayanan, Aruna -- Kozasa, Tohru -- Tesmer, John J G -- AG006093/AG/NIA NIH HHS/ -- GM61454/GM/NIGMS NIH HHS/ -- HL071818/HL/NHLBI NIH HHS/ -- NS41441/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2005 Dec 9;310(5754):1686-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16339447" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Cattle ; Crystallography, X-Ray ; GTP-Binding Protein alpha Subunits, Gq-G11/*chemistry/metabolism ; GTP-Binding Protein beta Subunits/*chemistry/metabolism ; GTP-Binding Protein gamma Subunits/*chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; RGS Proteins/metabolism ; Signal Transduction ; beta-Adrenergic Receptor Kinases/*chemistry/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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  • 10
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    Ecology. Winning the war against island invaders (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-12-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Krajick, Kevin -- New York, N.Y. -- Science. 2005 Dec 2;310(5753):1410-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16322433" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; *Conservation of Natural Resources ; *Ecosystem ; Geography ; Humans ; *Pest Control
    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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