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  • *Biological Evolution  (518)
  • Models, Molecular  (507)
  • American Association for the Advancement of Science (AAAS)  (1,025)
  • MDPI Publishing
  • 2000-2004  (537)
  • 1995-1999  (444)
  • 1980-1984  (44)
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  • American Association for the Advancement of Science (AAAS)  (1,025)
  • MDPI Publishing
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  • 101
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    Crystal structures of human cytochrome P450 3A4 bound to metyrapone and progesterone (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-07-17
    Description: Cytochromes P450 (P450s) metabolize a wide range of endogenous compounds and xenobiotics, such as pollutants, environmental compounds, and drug molecules. The microsomal, membrane-associated, P450 isoforms CYP3A4, CYP2D6, CYP2C9, CYP2C19, CYP2E1, and CYP1A2 are responsible for the oxidative metabolism of more than 90% of marketed drugs. Cytochrome P450 3A4 (CYP3A4) metabolizes more drug molecules than all other isoforms combined. Here we report three crystal structures of CYP3A4: unliganded, bound to the inhibitor metyrapone, and bound to the substrate progesterone. The structures revealed a surprisingly small active site, with little conformational change associated with the binding of either compound. An unexpected peripheral binding site is identified, located above a phenylalanine cluster, which may be involved in the initial recognition of substrates or allosteric effectors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Williams, Pamela A -- Cosme, Jose -- Vinkovic, Dijana Matak -- Ward, Alison -- Angove, Hayley C -- Day, Philip J -- Vonrhein, Clemens -- Tickle, Ian J -- Jhoti, Harren -- New York, N.Y. -- Science. 2004 Jul 30;305(5684):683-6. Epub 2004 Jul 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Astex Technology, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15256616" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; Cytochrome P-450 CYP3A ; Cytochrome P-450 Enzyme System/*chemistry/*metabolism ; Heme/chemistry ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Metyrapone/*metabolism ; Models, Molecular ; Phenylalanine/chemistry/metabolism ; Progesterone/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Water/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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  • 102
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    Ecological Society of America meeting. Are invasive species born bad? (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-08-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Withgott, Jay -- New York, N.Y. -- Science. 2004 Aug 20;305(5687):1100-1.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15326330" target="_blank"〉PubMed〈/a〉
    Keywords: Asia ; *Biological Evolution ; *Ecosystem ; Europe ; *Plant Development ; Selection, Genetic ; United States
    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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  • 103
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    Paleontology. T. rex clan evolved head first (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stokstad, Erik -- New York, N.Y. -- Science. 2004 Oct 8;306(5694):211.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15472048" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Body Constitution ; China ; Dinosaurs/*anatomy & histology ; Extremities/anatomy & histology ; Feathers/anatomy & histology ; *Fossils ; Skull/anatomy & histology
    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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  • 104
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    Nucleosome arrays reveal the two-start organization of the chromatin fiber (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-11-30
    Description: Chromatin folding determines the accessibility of DNA constituting eukaryotic genomes and consequently is profoundly important in the mechanisms of nuclear processes such as gene regulation. Nucleosome arrays compact to form a 30-nanometer chromatin fiber of hitherto disputed structure. Two competing classes of models have been proposed in which nucleosomes are either arranged linearly in a one-start higher order helix or zigzag back and forth in a two-start helix. We analyzed compacted nucleosome arrays stabilized by introduction of disulfide cross-links and show that the chromatin fiber comprises two stacks of nucleosomes in accord with the two-start model.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dorigo, Benedetta -- Schalch, Thomas -- Kulangara, Alexandra -- Duda, Sylwia -- Schroeder, Rasmus R -- Richmond, Timothy J -- New York, N.Y. -- Science. 2004 Nov 26;306(5701):1571-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Eidgenossische Technische Hochschule (ETH) Zurich, Institute for Molecular Biology and Biophysics, ETH-Honggerberg, CH-8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15567867" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chromatin/*chemistry/ultrastructure ; DNA/chemistry/metabolism ; Electrophoresis, Polyacrylamide Gel ; Histones/chemistry/genetics/metabolism ; Microscopy, Electron ; Models, Biological ; Models, Molecular ; Multiprotein Complexes/chemistry ; Mutation ; Nucleosomes/*chemistry/ultrastructure ; Protein Folding ; Xenopus laevis
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 105
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    The binding mode of epothilone A on alpha,beta-tubulin by electron crystallography (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-08-07
    Description: The structure of epothilone A, bound to alpha,beta-tubulin in zinc-stabilized sheets, was determined by a combination of electron crystallography at 2.89 angstrom resolution and nuclear magnetic resonance-based conformational analysis. The complex explains both the broad-based epothilone structure-activity relationship and the known mutational resistance profile. Comparison with Taxol shows that the longstanding expectation of a common pharmacophore is not met, because each ligand exploits the tubulin-binding pocket in a unique and independent manner.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nettles, James H -- Li, Huilin -- Cornett, Ben -- Krahn, Joseph M -- Snyder, James P -- Downing, Kenneth H -- New York, N.Y. -- Science. 2004 Aug 6;305(5685):866-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular and Systems Pharmacology, Emory University, Atlanta, GA 30322, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15297674" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography ; Crystallography, X-Ray ; Epothilones/chemistry/*metabolism/pharmacology ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Models, Molecular ; Molecular Conformation ; Molecular Structure ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Paclitaxel/metabolism ; Protein Conformation ; Stereoisomerism ; Structure-Activity Relationship ; Tubulin/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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  • 106
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    The evolutionary origin of cooperators and defectors (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-30
    Description: Coexistence of cooperators and defectors is common in nature, yet the evolutionary origin of such social diversification is unclear. Many models have been studied on the basis of the assumption that benefits of cooperative acts only accrue to others. Here, we analyze the continuous snowdrift game, in which cooperative investments are costly but yield benefits to others as well as to the cooperator. Adaptive dynamics of investment levels often result in evolutionary diversification from initially uniform populations to a stable state in which cooperators making large investments coexist with defectors who invest very little. Thus, when individuals benefit from their own actions, large asymmetries in cooperative investments can evolve.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Doebeli, Michael -- Hauert, Christoph -- Killingback, Timothy -- New York, N.Y. -- Science. 2004 Oct 29;306(5697):859-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology and Department of Mathematics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada. doebeli@zoology.ubc.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15514155" target="_blank"〉PubMed〈/a〉
    Keywords: Altruism ; *Biological Evolution ; *Cooperative Behavior ; Cultural Evolution ; *Game Theory ; Humans ; Mathematics
    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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  • 107
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    Bird evolution. Surprise hummingbird fossil sets experts abuzz (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-05-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stokstad, Erik -- New York, N.Y. -- Science. 2004 May 7;304(5672):810-1.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15131278" target="_blank"〉PubMed〈/a〉
    Keywords: Americas ; Animals ; *Biological Evolution ; *Birds/anatomy & histology/classification ; Bone and Bones/anatomy & histology ; Europe ; *Fossils ; Germany
    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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  • 108
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    Protein kinase inhibitors: insights into drug design from structure (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-20
    Description: Protein kinases are targets for treatment of a number of diseases. This review focuses on kinase inhibitors that are in the clinic or in clinical trials and for which structural information is available. Structures have informed drug design and have illuminated the mechanism of inhibition. We review progress with the receptor tyrosine kinases (growth factor receptors EGFR, VEGFR, and FGFR) and nonreceptor tyrosine kinases (Bcr-Abl), where advances have been made with cancer therapeutic agents such as Herceptin and Gleevec. Among the serine-threonine kinases, p38, Rho-kinase, cyclin-dependent kinases, and Chk1 have been targeted with productive results for inflammation and cancer. Structures have provided insights into targeting the inactive or active form of the kinase, for targeting the global constellation of residues at the ATP site or less conserved additional pockets or single residues, and into targeting noncatalytic domains.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Noble, Martin E M -- Endicott, Jane A -- Johnson, Louise N -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1800-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Biophysics, Department of Biochemistry, Rex Richards Building, University of Oxford, Oxford 3X2 3QU, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15031492" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Antineoplastic Agents/chemistry/pharmacology/therapeutic use ; Binding Sites ; Catalytic Domain ; Clinical Trials as Topic ; *Drug Design ; Enzyme Inhibitors/*chemistry/metabolism/pharmacology/therapeutic use ; Humans ; Models, Molecular ; Molecular Structure ; Protein Conformation ; *Protein Kinase Inhibitors ; Protein Kinases/*chemistry/metabolism ; Protein Structure, Tertiary ; Signal Transduction/drug effects ; Structure-Activity Relationship
    Print ISSN: 0036-8075
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  • 109
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    Host-parasite coevolutionary conflict between Arabidopsis and downy mildew (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-14
    Description: Plants are constantly exposed to attack by an array of diverse pathogens but lack a somatically adaptive immune system. In spite of this, natural plant populations do not often suffer destructive disease epidemics. Elucidating how allelic diversity within plant genes that function to detect pathogens (resistance genes) counteracts changing structures of pathogen genes required for host invasion (pathogenicity effectors) is critical to our understanding of the dynamics of natural plant populations. The RPP13 resistance gene is the most polymorphic gene analyzed to date in the model plant Arabidopsis thaliana. Here we report the cloning of the avirulence gene, ATR13, that triggers RPP13-mediated resistance, and we show that it too exhibits extreme levels of amino acid polymorphism. Evidence of diversifying selection visible in both components suggests that the host and pathogen may be locked in a coevolutionary conflict at these loci, where attempts to evade host resistance by the pathogen are matched by the development of new detection capabilities by the host.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Allen, Rebecca L -- Bittner-Eddy, Peter D -- Grenville-Briggs, Laura J -- Meitz, Julia C -- Rehmany, Anne P -- Rose, Laura E -- Beynon, Jim L -- New York, N.Y. -- Science. 2004 Dec 10;306(5703):1957-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Warwick, HRI University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15591208" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/genetics/metabolism/*microbiology ; Arabidopsis Proteins/*genetics/metabolism ; Biolistics ; *Biological Evolution ; Cloning, Molecular ; Fungal Proteins/chemistry/*genetics/physiology ; *Genes, Fungal ; *Genes, Plant ; Molecular Sequence Data ; Oomycetes/*genetics/pathogenicity/physiology ; Plant Diseases/microbiology ; Polymorphism, Genetic ; Protein Sorting Signals ; 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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  • 110
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    Ciliary photoreceptors with a vertebrate-type opsin in an invertebrate brain (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-30
    Description: For vision, insect and vertebrate eyes use rhabdomeric and ciliary photoreceptor cells, respectively. These cells show distinct architecture and transduce the light signal by different phototransductory cascades. In the marine rag-worm Platynereis, we find both cell types: rhabdomeric photoreceptor cells in the eyes and ciliary photoreceptor cells in the brain. The latter use a photopigment closely related to vertebrate rod and cone opsins. Comparative analysis indicates that both types of photoreceptors, with distinct opsins, coexisted in Urbilateria, the last common ancestor of insects and vertebrates, and sheds new light on vertebrate eye evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Arendt, Detlev -- Tessmar-Raible, Kristin -- Snyman, Heidi -- Dorresteijn, Adriaan W -- Wittbrodt, Joachim -- New York, N.Y. -- Science. 2004 Oct 29;306(5697):869-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Developmental Biology Department, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany. detlev.arendt@embl.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15514158" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Biological Evolution ; Brain/cytology ; Cilia/ultrastructure ; Circadian Rhythm ; Cloning, Molecular ; Conserved Sequence ; Eye/cytology ; Gene Duplication ; Genes, Homeobox ; Molecular Sequence Data ; Photoreceptor Cells, Invertebrate/*chemistry/cytology ; Photoreceptor Cells, Vertebrate/chemistry/cytology ; Phylogeny ; Polychaeta/chemistry/*cytology/*genetics ; Retinal Ganglion Cells/cytology ; Rod Opsins/analysis/*chemistry/*genetics
    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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  • 111
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    Paleontology. China clamps down on mining to preserve Cambrian site (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-09-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Normile, Dennis -- Lei, Xiong -- New York, N.Y. -- Science. 2004 Sep 24;305(5692):1893-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15448238" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; China ; Conservation of Natural Resources/economics ; *Fossils ; Mining/economics/*legislation & jurisprudence ; Paleontology/*legislation & jurisprudence ; Phosphates
    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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  • 112
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    The normal function of a speciation gene, Odysseus, and its hybrid sterility effect (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-07-03
    Description: To understand how postmating isolation is connected to the normal process of species divergence and why hybrid male sterility is often the first sign of speciation, we analyzed the Odysseus (OdsH) gene of hybrid male sterility in Drosophila. We carried out expression analysis, transgenic study, and gene knockout. The combined evidence suggests that the sterility phenotype represents a novel manifestation of the gene function rather than the reduction or loss of the normal one. The gene knockout experiment identified the normal function of OdsH as a modest enhancement of sperm production in young males. The implication of a weak effect of OdsH on the normal phenotype but a strong influence on hybrid male sterility is discussed in light of Haldane's rule of postmating isolation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sun, Sha -- Ting, Chau-Ti -- Wu, Chung-I -- New York, N.Y. -- Science. 2004 Jul 2;305(5680):81-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15232104" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Drosophila/*genetics/*physiology ; Drosophila Proteins/*genetics/*physiology ; Drosophila melanogaster/genetics/physiology ; Female ; Fertility/genetics ; Gene Expression Profiling ; Gene Targeting ; *Genes, Homeobox ; Genes, Insect ; Homeodomain Proteins/*genetics/*physiology ; *Hybridization, Genetic ; In Situ Hybridization ; Male ; Phenotype ; Reproduction/genetics ; Spermatogenesis/genetics ; Testis/metabolism ; Transformation, Genetic ; Transgenes
    Print ISSN: 0036-8075
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  • 113
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    Evolution. Parallel evolution is in the genes (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hoekstra, Hopi E -- Price, Trevor -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1779-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA. hoekstra@ucsd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15031483" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Animals ; Arctic Regions ; *Biological Evolution ; Birds/anatomy & histology/*genetics/physiology ; Color ; *Feathers ; Female ; Geese/anatomy & histology/genetics/physiology ; Gene Frequency ; Heterozygote ; Male ; Melanins/analysis/biosynthesis ; Mutation ; Phenotype ; Phylogeny ; Pigmentation/*genetics ; *Polymorphism, Genetic ; Receptor, Melanocortin, Type 1/chemistry/*genetics ; Selection, Genetic ; Sexual Behavior, Animal
    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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  • 114
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    George C. Williams profile. Stretching the limits of evolutionary biology (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-05-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zimmer, Carl -- New York, N.Y. -- Science. 2004 May 28;304(5675):1235-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15166342" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Animals ; Behavior ; *Biological Evolution ; Cooperative Behavior ; Female ; History, 20th Century ; History, 21st Century ; Humans ; Male ; Pre-Eclampsia/etiology ; Pregnancy ; Selection, Genetic ; United States ; Vascular Endothelial Growth Factor Receptor-1/metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 115
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    Methanobactin, a copper-acquisition compound from methane-oxidizing bacteria (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-09-14
    Description: Siderophores are extracellular iron-binding compounds that mediate iron transport into many cells. We present evidence of analogous molecules for copper transport from methane-oxidizing bacteria, represented here by a small fluorescent chromopeptide (C45N12O14H62Cu, 1216 daltons) produced by Methylosinus trichosporium OB3b. The crystal structure of this compound, methanobactin, was resolved to 1.15 angstroms. It is composed of a tetrapeptide, a tripeptide, and several unusual moieties, including two 4-thionyl-5-hydroxy-imidazole chromophores that coordinate the copper, a pyrrolidine that confers a bend in the overall chain, and an amino-terminal isopropylester group. The copper coordination environment includes a dual nitrogen- and sulfur-donating system derived from the thionyl imidazolate moieties. Structural elucidation of this molecule has broad implications in terms of organo-copper chemistry, biological methane oxidation, and global carbon cycling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Hyung J -- Graham, David W -- DiSpirito, Alan A -- Alterman, Michail A -- Galeva, Nadezhda -- Larive, Cynthia K -- Asunskis, Dan -- Sherwood, Peter M A -- New York, N.Y. -- Science. 2004 Sep 10;305(5690):1612-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Civil, Environmental, and Architectural Engineering, University of Kansas, Lawrence, KS 66045, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15361623" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/analysis ; Chemistry, Physical ; Copper/analysis/chemistry/*metabolism ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Imidazoles/*chemistry/isolation & purification/metabolism ; Ligands ; Methane/metabolism ; Methylosinus trichosporium/chemistry/*metabolism ; Models, Molecular ; Molecular Structure ; Molecular Weight ; Oligopeptides/*chemistry/isolation & purification/metabolism ; Oxidation-Reduction ; Physicochemical Phenomena ; Spectrum Analysis
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Dephosphorylation of the calcium pump coupled to counterion occlusion (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-25
    Description: P-type ATPases extract energy by hydrolysis of adenosine triphosphate (ATP) in two steps, formation and breakdown of a covalent phosphoenzyme intermediate. This process drives active transport and countertransport of the cation pumps. We have determined the crystal structure of rabbit sarcoplasmic reticulum Ca2+ adenosine triphosphatase in complex with aluminum fluoride, which mimics the transition state of hydrolysis of the counterion-bound (protonated) phosphoenzyme. On the basis of structural analysis and biochemical data, we find this form to represent an occluded state of the proton counterions. Hydrolysis is catalyzed by the conserved Thr-Gly-Glu-Ser motif, and it exploits an associative nucleophilic reaction mechanism of the same type as phosphoryl transfer from ATP. On this basis, we propose a general mechanism of occluded transition states of Ca2+ transport and H+ countertransport coupled to phosphorylation and dephosphorylation, respectively.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Olesen, Claus -- Sorensen, Thomas Lykke-Moller -- Nielsen, Rikke Christina -- Moller, Jesper Vuust -- Nissen, Poul -- New York, N.Y. -- Science. 2004 Dec 24;306(5705):2251-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Structural Biology, Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15618517" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Aluminum Compounds/chemistry ; Amino Acid Motifs ; Animals ; Binding Sites ; Biological Transport, Active ; Calcium/metabolism ; Calcium-Transporting ATPases/*chemistry/*metabolism ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Cytoplasm/metabolism ; Fluorides/chemistry ; Hydrolysis ; Ion Transport ; Models, Chemical ; Models, Molecular ; Phosphorylation ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Tertiary ; *Protons ; Rabbits ; Sarcoplasmic Reticulum/enzymology ; Thapsigargin ; Thermodynamics
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    Paleontology. From fins to fingers (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-04-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clack, Jennifer A -- New York, N.Y. -- Science. 2004 Apr 2;304(5667):57-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University Museum of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. j.a.clack@zoo.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15060312" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Biomechanical Phenomena ; Extremities/*anatomy & histology/physiology ; Fishes/anatomy & histology/physiology ; *Fossils ; Humerus/*anatomy & histology ; Locomotion ; Pennsylvania ; Phylogeny ; Toes/anatomy & histology ; Vertebrates/*anatomy & histology/physiology
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    Architecture of the photosynthetic oxygen-evolving center (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-07
    Description: Photosynthesis uses light energy to drive the oxidation of water at an oxygen-evolving catalytic site within photosystem II (PSII). We report the structure of PSII of the cyanobacterium Thermosynechococcus elongatus at 3.5 angstrom resolution. We have assigned most of the amino acid residues of this 650-kilodalton dimeric multisubunit complex and refined the structure to reveal its molecular architecture. Consequently, we are able to describe details of the binding sites for cofactors and propose a structure of the oxygen-evolving center (OEC). The data strongly suggest that the OEC contains a cubane-like Mn3CaO4 cluster linked to a fourth Mn by a mono-micro-oxo bridge. The details of the surrounding coordination sphere of the metal cluster and the implications for a possible oxygen-evolving mechanism are discussed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ferreira, Kristina N -- Iverson, Tina M -- Maghlaoui, Karim -- Barber, James -- Iwata, So -- F32 GM068304/GM/NIGMS NIH HHS/ -- F32 GM068304-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1831-8. Epub 2004 Feb 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Imperial College London, London, SW7 2AZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14764885" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Calcium/analysis/chemistry/metabolism ; Carotenoids/chemistry/metabolism ; Chlorophyll/chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Cyanobacteria/*enzymology ; Dimerization ; Electron Transport ; Free Radicals ; Histidine/chemistry/metabolism ; Hydrogen Bonding ; Ligands ; Manganese/analysis/chemistry/metabolism ; Models, Chemical ; Models, Molecular ; Oxidation-Reduction ; Oxygen/*metabolism ; Photosynthetic Reaction Center Complex Proteins/chemistry/metabolism ; Photosystem II Protein Complex/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Tyrosine/*analogs & derivatives/chemistry/metabolism ; Water/*metabolism ; beta Carotene/chemistry/metabolism
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    Symmetry breaking and the evolution of development (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-30
    Description: Because of its simplicity, the binary-switch nature of left-right asymmetry permits meaningful comparisons among many different organisms. Phylogenetic analyses of asymmetry variation, inheritance, and molecular mechanisms reveal unexpected insights into how development evolves. First, directional asymmetry, an evolutionary novelty, arose from nonheritable origins almost as often as from mutations, implying that genetic assimilation ("phenotype precedes genotype") is a common mode of evolution. Second, the molecular pathway directing hearts leftward-the nodal cascade-varies considerably among vertebrates (homology of form does not require homology of development) and was possibly co-opted from a preexisting asymmetrical chordate organ system. Finally, declining frequencies of spontaneous asymmetry reversal throughout vertebrate evolution suggest that heart development has become more canalized.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Palmer, A Richard -- New York, N.Y. -- Science. 2004 Oct 29;306(5697):828-33.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Systematics and Evolution Group, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada. rich.palmer@ualberta.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15514148" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Body Patterning ; Brain/embryology/growth & development ; Functional Laterality ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; Genotype ; Heart/embryology/growth & development ; Inheritance Patterns ; Morphogenesis ; Mutation ; Phenotype
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    Y chromosome of D. pseudoobscura is not homologous to the ancestral Drosophila Y (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-11-06
    Description: We report a genome-wide search of Y-linked genes in Drosophila pseudoobscura. All six identifiable orthologs of the D. melanogaster Y-linked genes have autosomal inheritance in D. pseudoobscura. Four orthologs were investigated in detail and proved to be Y-linked in D. guanche and D. bifasciata, which shows that less than 18 million years ago the ancestral Drosophila Y chromosome was translocated to an autosome in the D. pseudoobscura lineage. We found 15 genes and pseudogenes in the current Y of D. pseudoobscura, and none are shared with the D. melanogaster Y. Hence, the Y chromosome in the D. pseudoobscura lineage appears to have arisen de novo and is not homologous to the D. melanogaster Y.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carvalho, Antonio Bernardo -- Clark, Andrew G -- GM64590/GM/NIGMS NIH HHS/ -- TW005673/TW/FIC NIH HHS/ -- New York, N.Y. -- Science. 2005 Jan 7;307(5706):108-10. Epub 2004 Nov 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departamento de Genetica, Universidade Federal do Rio de Janeiro, Caixa Postal 68011, CEP 21944-970, Rio de Janeiro, Brazil. bernardo@biologia.ufrj.br〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15528405" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Chromosomes/genetics/physiology ; DNA, Intergenic ; Drosophila/*genetics ; Drosophila melanogaster/genetics ; Female ; Genes, Insect ; Genetic Linkage ; Genome ; Introns ; Male ; Models, Genetic ; Phylogeny ; Polymerase Chain Reaction ; Pseudogenes ; Translocation, Genetic ; X Chromosome/genetics/physiology ; Y Chromosome/*genetics/*physiology
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    Evolution. Little else but parasites (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brown, J K M -- New York, N.Y. -- Science. 2003 Mar 14;299(5613):1680-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Disease and Stress Biology, John Innes Centre, Norwich, NR4 7UH, UK. james.brown@bbsrc.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12637729" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Basidiomycota/genetics/*pathogenicity/physiology ; *Biological Evolution ; Flax/genetics/*microbiology/physiology ; Genes, Fungal ; Genes, Plant ; *Genetic Variation ; Models, Genetic ; Plant Diseases/*microbiology ; Reproduction ; Spores, Fungal ; Virulence/*genetics
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    Loren Rieseberg profile. No garden-variety biologist (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brown, Kathryn -- New York, N.Y. -- Science. 2003 Nov 28;302(5650):1499.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14645825" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; *Biological Evolution ; Desert Climate ; Ecosystem ; Environment ; Genes, Plant ; Helianthus/*genetics/growth & development/physiology ; History, 20th Century ; History, 21st Century ; *Hybridization, Genetic ; Mutation ; Phenotype ; Sodium Chloride/pharmacology ; United States
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    Society of Vertebrate Paleontology meeting. Mammal menagerie (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-11-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stokstad, Erik -- New York, N.Y. -- Science. 2003 Nov 14;302(5648):1142.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14615511" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Body Constitution ; Diet ; *Dogs/anatomy & histology ; Jaw/anatomy & histology ; Paleontology ; *Predatory Behavior ; Time
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    Crystal structure of the GpIbalpha-thrombin complex essential for platelet aggregation (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-07-12
    Description: Direct interaction between platelet receptor glycoprotein Ibalpha (GpIbalpha) and thrombin is required for platelet aggregation and activation at sites of vascular injury. Abnormal GpIbalpha-thrombin binding is associated with many pathological conditions,including occlusive arterial thrombosis and bleeding disorders. The crystal structure of the GpIbalpha-thrombin complex at 2.6 angstrom resolution reveals simultaneous interactions of GpIbalpha with exosite I of one thrombin molecule,and with exosite II of a second thrombin molecule. In the crystal lattice,the periodic arrangement of GpIbalpha-thrombin complexes mirrors a scaffold that could serve as a driving force for tight platelet adhesion. The details of these interactions reconcile GpIbalpha-thrombin binding modes that are presently controversial,highlighting two distinct interfaces that are potential targets for development of novel antithrombotic drugs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dumas, John J -- Kumar, Ravindra -- Seehra, Jasbir -- Somers, William S -- Mosyak, Lidia -- New York, N.Y. -- Science. 2003 Jul 11;301(5630):222-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical and Screening Sciences, Wyeth, 200 Cambridge Park Drive, Cambridge, MA 02140, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12855811" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Blood Platelets/chemistry/physiology ; Crystallization ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Platelet Adhesiveness ; *Platelet Aggregation ; Platelet Glycoprotein GPIb-IX Complex/*chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Thrombin/*chemistry/*metabolism
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    Psychology. Evolution of the social brain (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-11-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dunbar, Robin -- New York, N.Y. -- Science. 2003 Nov 14;302(5648):1160-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK. rimd@liv.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14615522" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Wild ; *Biological Evolution ; *Cognition ; Endorphins/physiology ; Female ; Grooming ; Hierarchy, Social ; Language ; Neocortex/anatomy & histology/physiology ; Papio/physiology/*psychology ; *Reproduction ; *Social Behavior ; Social Dominance ; Social Support ; Vocalization, Animal
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    Rapid evolution of egg size in captive salmon (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-03-15
    Description: Captive breeding and release programs, widely used to supplement populations of declining species, minimize juvenile mortality to achieve rapid population growth. However, raising animals in benign environments may promote traits that are adaptive in captivity but maladaptive in nature. In chinook salmon, hatchery rearing relaxes natural selection favoring large eggs, allowing fecundity selection to drive exceptionally rapid evolution of small eggs. Trends toward small eggs are also evident in natural populations heavily supplemented by hatcheries, but not in minimally supplemented populations. Unintentional selection in captivity can lead to rapid changes in critical life-history traits that may reduce the success of supplementation or reintroduction programs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Heath, Daniel D -- Heath, John W -- Bryden, Colleen A -- Johnson, Rachel M -- Fox, Charles W -- New York, N.Y. -- Science. 2003 Mar 14;299(5613):1738-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Great Lakes Institute for Environmental Research and Department of Biological Sciences, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada. dheath@uwindsor.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12637746" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Body Constitution ; Body Weight ; *Breeding ; Conservation of Natural Resources ; Environment ; Female ; Fertility ; *Fisheries ; Ovum/*physiology ; Salmon/genetics/*physiology ; Selection, Genetic
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    Evolution. Evolutionary danger for rainforest species (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-07-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roff, Derek -- New York, N.Y. -- Science. 2003 Jul 4;301(5629):58-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of California, Riverside, CA 92521, USA. derek.roff@ucr.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12843382" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Animals ; Australia ; *Biological Evolution ; Climate ; Dehydration ; Drosophila/*genetics/*physiology ; Ecosystem ; Environment ; *Genetic Variation ; *Greenhouse Effect ; Selection, Genetic ; Trees
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    Closing of the nucleotide pocket of kinesin-family motors upon binding to microtubules (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-05-06
    Description: We have used adenosine diphosphate analogs containing electron paramagnetic resonance (EPR) spin moieties and EPR spectroscopy to show that the nucleotide-binding site of kinesin-family motors closes when the motor.diphosphate complex binds to microtubules. Structural analyses demonstrate that a domain movement in the switch 1 region at the nucleotide site, homologous to domain movements in the switch 1 region in the G proteins [heterotrimeric guanine nucleotide-binding proteins], explains the EPR data. The switch movement primes the motor both for the free energy-yielding nucleotide hydrolysis reaction and for subsequent conformational changes that are crucial for the generation of force and directed motion along the microtubule.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Naber, Nariman -- Minehardt, Todd J -- Rice, Sarah -- Chen, Xiaoru -- Grammer, Jean -- Matuska, Marija -- Vale, Ronald D -- Kollman, Peter A -- Car, Roberto -- Yount, Ralph G -- Cooke, Roger -- Pate, Edward -- AR39643/AR/NIAMS NIH HHS/ -- AR42895/AR/NIAMS NIH HHS/ -- DK05915/DK/NIDDK NIH HHS/ -- GM29072/GM/NIGMS NIH HHS/ -- RR1081/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2003 May 2;300(5620):798-801.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of California, San Francisco, CA 94143, USA. naber@itsa.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12730601" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine Nucleotides/*metabolism ; Adenosine Diphosphate/analogs & derivatives/metabolism ; Adenosine Triphosphate/analogs & derivatives/metabolism ; Animals ; Binding Sites ; Computer Simulation ; Crystallography, X-Ray ; *Drosophila Proteins ; Drosophila melanogaster ; Electron Spin Resonance Spectroscopy ; Humans ; Hydrogen Bonding ; Hydrolysis ; Kinesin/*chemistry/*metabolism ; Microtubules/*metabolism ; Models, Molecular ; Molecular Motor Proteins/*chemistry/*metabolism ; Molecular Probes/metabolism ; Protein Conformation ; Spin Labels
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    Separate evolutionary origins of teeth from evidence in fossil jawed vertebrates (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-02-22
    Description: Placoderms are extinct jawed fishes of the class Placodermi and are basal among jawed vertebrates. It is generally thought that teeth are absent in placoderms and that the phylogenetic origin of teeth occurred after the evolution of jaws. However, we now report the presence of tooth rows in more derived placoderms, the arthrodires. New teeth are composed of gnathostome-type dentine and develop at specific locations. Hence, it appears that these placoderm teeth develop and are regulated as in other jawed vertebrates. Because tooth development occurs only in derived forms of placoderms, we suggest that teeth evolved at least twice, through a mechanism of convergent evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, Moya Meredith -- Johanson, Zerina -- New York, N.Y. -- Science. 2003 Feb 21;299(5610):1235-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Craniofacial Development, Dental Institute, King's College London, Guy's Campus, London Bridge, London SE1 9RT, UK. moya.smith@kcl.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12595693" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Dentition ; Fishes/*anatomy & histology ; *Fossils ; *Paleodontology ; Phylogeny ; *Tooth ; Western Australia
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    Structural biology. Complex II is complex too (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-02-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hederstedt, Lars -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):671-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Organism Biology, Lund University, SE-22362 Lund, Sweden. lars.hederstedt@cob.lu.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12560540" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Anaerobiosis ; Binding Sites ; Crystallography, X-Ray ; Electron Transport ; Electron Transport Complex II ; Escherichia coli/*enzymology ; Flavin-Adenine Dinucleotide/metabolism ; Heme/chemistry/metabolism ; Models, Molecular ; Multienzyme Complexes/antagonists & inhibitors/*chemistry/*metabolism ; Oxidation-Reduction ; Oxidoreductases/antagonists & inhibitors/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Reactive Oxygen Species/metabolism ; Succinate Dehydrogenase/antagonists & inhibitors/*chemistry/*metabolism ; Succinic Acid/metabolism ; Ubiquinone/chemistry/metabolism
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    Structural dynamics of eukaryotic chromosome evolution (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-09
    Description: Large-scale genome sequencing is providing a comprehensive view of the complex evolutionary forces that have shaped the structure of eukaryotic chromosomes. Comparative sequence analyses reveal patterns of apparently random rearrangement interspersed with regions of extraordinarily rapid, localized genome evolution. Numerous subtle rearrangements near centromeres, telomeres, duplications, and interspersed repeats suggest hotspots for eukaryotic chromosome evolution. This localized chromosomal instability may play a role in rapidly evolving lineage-specific gene families and in fostering large-scale changes in gene order. Computational algorithms that take into account these dynamic forces along with traditional models of chromosomal rearrangement show promise for reconstructing the natural history of eukaryotic chromosomes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eichler, Evan E -- Sankoff, David -- GM58815/GM/NIGMS NIH HHS/ -- HD43569/HD/NICHD NIH HHS/ -- HG02385/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2003 Aug 8;301(5634):793-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Center for Human Genetics and Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH 44106, USA. eee@po.cwru.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12907789" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Centromere/physiology ; Chromosome Aberrations ; *Chromosomes/genetics/physiology/ultrastructure ; Computational Biology ; DNA Transposable Elements ; Eukaryotic Cells/physiology/*ultrastructure ; Gene Duplication ; Genome ; Humans ; Recombination, Genetic ; Synteny ; Telomere/physiology
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    Evolution. Climb every mountain? (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Elena, Santiago F -- Sanjuan, Rafael -- New York, N.Y. -- Science. 2003 Dec 19;302(5653):2074-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-UPV, 46022 Valencia, Spain. sfelena@ibmcp.upv.es〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14684807" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; Animals ; *Biological Evolution ; Chlamydomonas/physiology ; Darkness ; *Ecosystem ; Environment ; *Genetic Variation ; Genotype ; Light ; Mutation ; Phenotype ; Pseudomonas fluorescens/genetics/*physiology ; RNA Viruses/physiology ; Selection, Genetic
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    Structural basis of multiple drug-binding capacity of the AcrB multidrug efflux pump (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-10
    Description: Multidrug efflux pumps cause serious problems in cancer chemotherapy and treatment of bacterial infections. Yet high-resolution structures of ligand transporter complexes have previously been unavailable. We obtained x-ray crystallographic structures of the trimeric AcrB pump from Escherichia coli with four structurally diverse ligands. The structures show that three molecules of ligands bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilizing the binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Edward W -- McDermott, Gerry -- Zgurskaya, Helen I -- Nikaido, Hiroshi -- Koshland, Daniel E Jr -- AI 09644/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2003 May 9;300(5621):976-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12738864" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Infective Agents/chemistry/metabolism ; Anti-Infective Agents, Local/chemistry/metabolism ; Binding Sites ; Carrier Proteins/*chemistry/isolation & purification/*metabolism ; Cell Membrane/chemistry ; Chemistry, Physical ; Ciprofloxacin/chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Dequalinium/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/isolation & purification/*metabolism ; Ethidium/chemistry/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Membrane Proteins/*chemistry/isolation & purification/*metabolism ; Models, Molecular ; Multidrug Resistance-Associated Proteins ; Physicochemical Phenomena ; Protein Binding ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rhodamines/chemistry/metabolism ; Static Electricity
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    Low potential for climatic stress adaptation in a rainforest Drosophila species (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-07-05
    Description: The ability of sensitive rainforest species to evolve in response to climate change is largely unknown. We show that the Australian tropical rainforest fly Drosophila birchii exhibits clinal variation in desiccation resistance, but the most resistant population lacks the ability to evolve further resistance even after intense selection for over 30 generations. Parent-offspring comparisons indicate low heritable variation for this trait but high levels of genetic variation for morphology. D. birchii also exhibits abundant genetic variation at microsatellite loci. The low potential for resistance evolution highlights the importance of assessing evolutionary potential in targeted ecological traits and species from threatened habitats.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hoffmann, A A -- Hallas, R J -- Dean, J A -- Schiffer, M -- New York, N.Y. -- Science. 2003 Jul 4;301(5629):100-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Environmental Stress and Adaptation Research, La Trobe University, Bundoora, Victoria 3086, Australia. A.Hoffmann@latrobe.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12843394" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; Animals ; Australia ; *Biological Evolution ; *Climate ; Crosses, Genetic ; Dehydration ; Drosophila/*genetics/*physiology ; Ecosystem ; Environment ; Female ; *Genetic Variation ; Geography ; Inbreeding ; Male ; Microsatellite Repeats ; Selection, Genetic ; Trees
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    Ecology and evolution. Darwin's hummingbirds (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-04-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Altshuler, Douglas L -- Clark, Christopher James -- New York, N.Y. -- Science. 2003 Apr 25;300(5619):588-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bioengineering, California Institute of Technology, Pasadena, CA 91104, USA. doug@caltech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12714728" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Beak/*anatomy & histology ; *Biological Evolution ; Birds/*anatomy & histology/physiology ; Body Constitution ; Dominica ; Ecosystem ; Feeding Behavior ; Female ; Flowers/*anatomy & histology ; Heliconiaceae/*anatomy & histology ; Male ; Pigmentation ; Saint Lucia ; *Sex Characteristics
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    Infectious diseases. Darwinian vaccines (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zimmer, Carl -- New York, N.Y. -- Science. 2003 May 30;300(5624):1363.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12775815" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; *Communicable Disease Control ; Corynebacterium diphtheriae/pathogenicity ; Diphtheria/microbiology/prevention & control ; Diphtheria Toxin/biosynthesis ; Diphtheria Toxoid ; Humans ; Immunization Programs ; *Vaccines ; *Virulence
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    Infectious diseases. Taming pathogens: an elegant idea, but does it work? (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zimmer, Carl -- New York, N.Y. -- Science. 2003 May 30;300(5624):1362-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12775814" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Cholera/epidemiology/microbiology/transmission ; Communicable Disease Control ; Communicable Diseases/*microbiology/*parasitology/transmission/virology ; Humans ; Influenza, Human/epidemiology/transmission/virology ; *Models, Biological ; Myxoma virus/pathogenicity ; Sanitation ; Vibrio cholerae/pathogenicity ; *Virulence
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    Wing-assisted incline running and the evolution of flight (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-01-18
    Description: Flapping wings of galliform birds are routinely used to produce aerodynamic forces oriented toward the substrate to enhance hindlimb traction. Here, I document this behavior in natural and laboratory settings. Adult birds fully capable of aerial flight preferentially employ wing-assisted incline running (WAIR), rather than flying, to reach elevated refuges (such as cliffs, trees, and boulders). From the day of hatching and before attaining sustained aerial flight, developing ground birds use WAIR to enhance their locomotor performance through improved foot traction, ultimately permitting vertical running. WAIR provides insight from behaviors observable in living birds into the possible role of incipient wings in feathered theropod dinosaurs and offers a previously unstudied explanation for the evolution of avian flight.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dial, Kenneth P -- New York, N.Y. -- Science. 2003 Jan 17;299(5605):402-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Flight Laboratory, Avian Studies Program, Division of Biological Sciences, University of Montana (UM), Missoula, MT 59812, USA. kdial@selway.umt.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12532020" target="_blank"〉PubMed〈/a〉
    Keywords: Acceleration ; Animals ; *Biological Evolution ; Biomechanical Phenomena ; Birds/anatomy & histology/growth & development/*physiology ; Feathers/physiology ; *Flight, Animal ; Forelimb/physiology ; Hindlimb/physiology ; *Locomotion ; Movement ; Running ; Wings, Animal/*physiology
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  • 139
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    Adaptation limits diversification of experimental bacterial populations (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-12-20
    Description: Adaptation to a specific niche theoretically constrains a population's ability to subsequently diversify into other niches. We tested this theory using the bacterium Pseudomonas fluorescens, which diversifies into niche specialists when propagated in laboratory microcosms. Numerically dominant genotypes were allowed to diversify in isolation. As predicted, populations increased in fitness through time but showed a greatly decreased ability to diversify. Subsequent experiments demonstrated that niche generalists and reductions in intrinsic evolvability were not responsible for our data. These results show that niche specialization may come with a cost of reduced potential to diversify.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Buckling, Angus -- Wills, Matthew A -- Colegrave, Nick -- New York, N.Y. -- Science. 2003 Dec 19;302(5653):2107-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK. bssagjb@bath.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14684817" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; *Biological Evolution ; *Ecosystem ; Environment ; *Genetic Variation ; Genotype ; Mutation ; Phenotype ; Pseudomonas fluorescens/cytology/genetics/*physiology ; Selection, Genetic
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    Structural basis of a phototropin light switch (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-09-13
    Description: Phototropins are light-activated kinases important for plant responses to blue light. Light initiates signaling in these proteins by generating a covalent protein-flavin mononucleotide (FMN) adduct within sensory Per-ARNT-Sim (PAS) domains. We characterized the light-dependent changes of a phototropin PAS domain by solution nuclear magnetic resonance spectroscopy and found that an alpha helix located outside the canonical domain plays a key role in this activation process. Although this helix associates with the PAS core in the dark, photoinduced changes in the domain structure disrupt this interaction. We propose that this mechanism couples light-dependent bond formation to kinase activation and identifies a signaling pathway conserved among PAS domains.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harper, Shannon M -- Neil, Lori C -- Gardner, Kevin H -- CA90601/CA/NCI NIH HHS/ -- GM08297/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Sep 12;301(5639):1541-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Biochemistry and Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12970567" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Avena/*chemistry ; Cryptochromes ; Darkness ; *Drosophila Proteins ; *Eye Proteins ; Flavoproteins/*chemistry/metabolism ; *Light ; Models, Molecular ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; *Photoreceptor Cells, Invertebrate ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, G-Protein-Coupled ; Signal Transduction
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    Comment on "Buffered Tree Population Changes in a Quaternary Refugium: Evolutionary Implications" (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stewart, John R -- New York, N.Y. -- Science. 2003 Feb 7;299(5608):825; author reply 825.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Anthropology and AHRB Centre for the Evolutionary Analysis of Cultural Behaviour, University College London, Gower Street, London, WC1E 6BT, UK. ucsajrs@ucl.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12574604" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Climate ; *Ecosystem ; *Environment ; Europe ; Fossils ; Geography ; Pollen ; Time ; *Trees/genetics/growth & development
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  • 142
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    Major ecological transitions in wild sunflowers facilitated by hybridization (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-09
    Description: Hybridization is frequent in many organismal groups, but its role in adaptation is poorly understood. In sunflowers, species found in the most extreme habitats are ancient hybrids, and new gene combinations generated by hybridization are speculated to have contributed to ecological divergence. This possibility was tested through phenotypic and genomic comparisons of ancient and synthetic hybrids. Most trait differences in ancient hybrids could be recreated by complementary gene action in synthetic hybrids and were favored by selection. The same combinations of parental chromosomal segments required to generate extreme phenotypes in synthetic hybrids also occurred in ancient hybrids. Thus, hybridization facilitated ecological divergence in sunflowers.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rieseberg, Loren H -- Raymond, Olivier -- Rosenthal, David M -- Lai, Zhao -- Livingstone, Kevin -- Nakazato, Takuya -- Durphy, Jennifer L -- Schwarzbach, Andrea E -- Donovan, Lisa A -- Lexer, Christian -- R01 G59065/PHS HHS/ -- New York, N.Y. -- Science. 2003 Aug 29;301(5637):1211-6. Epub 2003 Aug 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Indiana University, Bloomington, IN 47405, USA. lriesebe@indiana.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12907807" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; *Biological Evolution ; Chromosome Mapping ; Diploidy ; *Ecosystem ; Environment ; Genes, Plant ; Genome, Plant ; Genotype ; Helianthus/*genetics/physiology ; *Hybridization, Genetic ; Microsatellite Repeats ; Mutation ; Phenotype ; Quantitative Trait Loci ; Selection, Genetic ; Species Specificity ; United States
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    Invertebrate paleontology. Gutsy fossil sets record for staying the course (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stokstad, Erik -- New York, N.Y. -- Science. 2003 Dec 5;302(5651):1645.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14657469" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Crustacea/*anatomy & histology/classification ; *Fossils ; Great Britain ; Paleontology ; Time
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    Comment on "Separate evolutionary origins of teeth from evidence in fossil jawed vertebrates" (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-06-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burrow, Carole J -- New York, N.Y. -- Science. 2003 Jun 13;300(5626):1661; author reply 1661.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology & Entomology, University of Queensland, QLD 4072 Australia. CBurrow@zen.uq.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12805521" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Dentition ; Fishes/*anatomy & histology ; Fossils ; Jaw/anatomy & histology ; Phylogeny ; *Tooth ; Vertebrates/*anatomy & histology
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    Self-assembly of proteins into designed networks (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-10-04
    Description: A C4-symmetric tetrameric aldolase was used to produce a quadratic network consisting of the enzyme as a rigid four-way connector and stiff streptavidin rods as spacers. Each aldolase subunit was furnished with a His6 tag for oriented binding to a planar surface and two tethered biotins for binding streptavidin in an oriented manner. The networks were improved by starting with composite units and also by binding to nickel-nitrilotriacetic acid-lipid monolayers. The mesh was adjustable in 5-nanometer increments. The production of a net with switchable mesh was initiated with the use of a calcium ion-containing beta-helix spacer that denatured on calcium ion depletion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ringler, Philippe -- Schulz, Georg E -- New York, N.Y. -- Science. 2003 Oct 3;302(5642):106-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat Freiburg, Albertstrasse 21, D-79104 Freiburg im Breisgau, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14526081" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde-Lyases/*chemistry/genetics/metabolism ; Binding Sites ; Biotin/chemistry/metabolism ; Calcium/metabolism ; Edetic Acid ; *Glycoside Hydrolases ; Lipids/chemistry ; Macromolecular Substances ; Metalloendopeptidases/chemistry/metabolism ; Microscopy, Electron ; Models, Molecular ; Mutation ; Nitrilotriacetic Acid ; Protein Conformation ; Protein Denaturation ; *Protein Engineering ; Protein Structure, Secondary ; Recombinant Fusion Proteins/chemistry ; Streptavidin/*chemistry ; beta-Galactosidase/*chemistry
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    Paleontology. Peering into ancient ears (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-11-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stokstad, Erik -- New York, N.Y. -- Science. 2003 Oct 31;302(5646):770-1.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14593145" target="_blank"〉PubMed〈/a〉
    Keywords: Alligators and Crocodiles/anatomy & histology/physiology ; Animals ; *Biological Evolution ; Biomechanical Phenomena ; Birds/anatomy & histology/physiology ; Dinosaurs/anatomy & histology/physiology ; Ear Ossicles/*anatomy & histology/physiology/radiography ; Ear, Inner/*anatomy & histology/physiology/radiography ; Flight, Animal ; *Fossils ; *Hearing ; Locomotion ; Mammals/anatomy & histology/physiology ; Paleontology ; Postural Balance ; Semicircular Canals/anatomy & histology/physiology/radiography ; Tomography, X-Ray Computed ; Vertebrates/anatomy & histology/physiology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Cell signaling. The BRCT domain: signaling with friends? (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-10-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Caldecott, Keith W -- New York, N.Y. -- Science. 2003 Oct 24;302(5645):579-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genome Damage and Stability Center, University of Sussex, Brighton BN1 9RR, UK. k.w.caldecott@sussex.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14576410" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; BRCA1 Protein/*chemistry/*metabolism ; Carrier Proteins/chemistry/metabolism ; *Cell Cycle Proteins ; DNA Damage ; DNA Repair ; DNA-Binding Proteins/chemistry/metabolism ; E2F Transcription Factors ; Models, Molecular ; Nuclear Proteins ; Peptide Library ; Phosphopeptides/*metabolism ; Phosphorylation ; Protein Binding ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Proteins/chemistry/*metabolism ; Proteomics ; RNA Helicases/chemistry/metabolism ; *Signal Transduction ; Transcription Factors/chemistry/metabolism
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  • 148
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    Antibody domain exchange is an immunological solution to carbohydrate cluster recognition (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-06-28
    Description: Human antibody 2G12 neutralizes a broad range of human immunodeficiency virus type 1 (HIV-1) isolates by binding an unusually dense cluster of carbohydrate moieties on the "silent" face of the gp120 envelope glycoprotein. Crystal structures of Fab 2G12 and its complexes with the disaccharide Manalpha1-2Man and with the oligosaccharide Man9GlcNAc2 revealed that two Fabs assemble into an interlocked VH domain-swapped dimer. Further biochemical, biophysical, and mutagenesis data strongly support a Fab-dimerized antibody as the prevalent form that recognizes gp120. The extraordinary configuration of this antibody provides an extended surface, with newly described binding sites, for multivalent interaction with a conserved cluster of oligomannose type sugars on the surface of gp120. The unique interdigitation of Fab domains within an antibody uncovers a previously unappreciated mechanism for high-affinity recognition of carbohydrate or other repeating epitopes on cell or microbial surfaces.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Calarese, Daniel A -- Scanlan, Christopher N -- Zwick, Michael B -- Deechongkit, Songpon -- Mimura, Yusuke -- Kunert, Renate -- Zhu, Ping -- Wormald, Mark R -- Stanfield, Robyn L -- Roux, Kenneth H -- Kelly, Jeffery W -- Rudd, Pauline M -- Dwek, Raymond A -- Katinger, Hermann -- Burton, Dennis R -- Wilson, Ian A -- AI33292/AI/NIAID NIH HHS/ -- GM46192/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Jun 27;300(5628):2065-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12829775" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Monoclonal/chemistry/immunology/metabolism ; Antibody Affinity ; Antibody Specificity ; Binding Sites, Antibody ; Cell Adhesion Molecules/metabolism ; Centrifugation, Density Gradient ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Disaccharides/chemistry/metabolism ; Epitopes ; HIV Antibodies/*chemistry/genetics/*immunology/metabolism ; HIV Envelope Protein gp120/*immunology ; HIV-1/*immunology ; Humans ; Hydrogen Bonding ; Immunoglobulin Fab Fragments/*chemistry/genetics/*immunology/metabolism ; Immunoglobulin Heavy Chains/chemistry/immunology ; Immunoglobulin Light Chains/chemistry/immunology ; Immunoglobulin Variable Region/chemistry/immunology ; Lectins/chemistry/immunology/metabolism ; Lectins, C-Type/metabolism ; Ligands ; Mannans/chemistry/metabolism ; Mannosides/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Oligosaccharides/chemistry/*immunology/metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Receptors, Cell Surface/metabolism
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  • 149
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    Crystallographic and spectroscopic characterization of a nonheme Fe(IV)-O complex (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-15
    Description: Following the heme paradigm, it is often proposed that dioxygen activation by nonheme monoiron enzymes involves an iron(IV)=oxo intermediate that is responsible for the substrate oxidation step. Such a transient species has now been obtained from a synthetic complex with a nonheme macrocyclic ligand and characterized spectroscopically. Its high-resolution crystal structure reveals an iron-oxygen bond length of 1.646(3) angstroms, demonstrating that a terminal iron(IV)=oxo unit can exist in a nonporphyrin ligand environment and lending credence to proposed mechanisms of nonheme iron catalysis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rohde, Jan-Uwe -- In, Jun-Hee -- Lim, Mi Hee -- Brennessel, William W -- Bukowski, Michael R -- Stubna, Audria -- Munck, Eckard -- Nam, Wonwoo -- Que, Lawrence Jr -- GM-22701/GM/NIGMS NIH HHS/ -- GM-33162/GM/NIGMS NIH HHS/ -- GM-38767/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Feb 14;299(5609):1037-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12586936" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Iron/*chemistry ; Ligands ; Models, Molecular ; Molecular Structure ; Oxidation-Reduction ; Oxygen/*chemistry ; Physicochemical Phenomena ; Spectrometry, Mass, Electrospray Ionization ; Spectroscopy, Mossbauer
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    Peroxiredoxin evolution and the regulation of hydrogen peroxide signaling (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-04-26
    Description: Eukaryotic 2-Cys peroxiredoxins (2-Cys Prxs) not only act as antioxidants, but also appear to regulate hydrogen peroxide-mediated signal transduction. We show that bacterial 2-Cys Prxs are much less sensitive to oxidative inactivation than are eukaryotic 2-Cys Prxs. By identifying two sequence motifs unique to the sensitive 2-Cys Prxs and comparing the crystal structure of a bacterial 2-Cys Prx at 2.2 angstrom resolution with other Prx structures, we define the structural origins of sensitivity. We suggest this adaptation allows 2-Cys Prxs to act as floodgates, keeping resting levels of hydrogen peroxide low, while permitting higher levels during signal transduction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wood, Zachary A -- Poole, Leslie B -- Karplus, P Andrew -- ES00210/ES/NIEHS NIH HHS/ -- GM50389/GM/NIGMS NIH HHS/ -- R01 GM050389/GM/NIGMS NIH HHS/ -- R01 GM050389-10/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Apr 25;300(5619):650-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97333, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12714747" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Bacteria/enzymology ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Cysteine/metabolism ; Disulfides/chemistry/metabolism ; Evolution, Molecular ; Humans ; Hydrogen Peroxide/*metabolism ; Models, Chemical ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Peroxidases/*chemistry/*metabolism ; Peroxiredoxins ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Salmonella typhimurium/*enzymology ; Sequence Alignment ; *Signal Transduction ; Sulfenic Acids/metabolism ; Sulfinic Acids/metabolism ; Yeasts/enzymology
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    A conserved domain in axonal targeting of Kv1 (Shaker) voltage-gated potassium channels (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-02
    Description: Axonal voltage-gated potassium (Kv1) channels regulate action-potential invasion and hence transmitter release. Although evolutionarily conserved, what mediates their axonal targeting is not known. We found that Kv1 axonal targeting required its T1 tetramerization domain. When fused to unpolarized CD4 or dendritic transferrin receptor, T1 promoted their axonal surface expression. Moreover, T1 mutations eliminating Kvbeta association compromised axonal targeting, but not surface expression, of CD4-T1 fusion proteins. Thus, proper association of Kvbeta with the Kv1 T1 domain is essential for axonal targeting.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gu, Chen -- Jan, Yuh Nung -- Jan, Lily Yeh -- New York, N.Y. -- Science. 2003 Aug 1;301(5633):646-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Departments of Physiology and Biochemistry, University of California, San Francisco, CA 94143-0725, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12893943" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Substitution ; Animals ; Antigens, CD4/metabolism ; Axons/*metabolism ; Biopolymers ; COS Cells ; Cell Line ; Cell Membrane/metabolism ; Cell Polarity ; Cells, Cultured ; Dendrites/metabolism ; Endocytosis ; Hippocampus/cytology ; Humans ; Kv1.2 Potassium Channel ; Models, Molecular ; Mutagenesis ; Neurons/metabolism ; Potassium Channels/*chemistry/*metabolism ; *Potassium Channels, Voltage-Gated ; *Protein Structure, Tertiary ; Receptors, Transferrin/metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; Shaker Superfamily of Potassium Channels ; Shal Potassium Channels ; Transfection
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    Microbiology and evolution. Modulating mutation rates in the wild (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rosenberg, Susan M -- Hastings, P J -- New York, N.Y. -- Science. 2003 May 30;300(5624):1382-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. smr@bcm.tmc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12775830" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Adenosine Triphosphatases/metabolism ; Air Microbiology ; Animals ; *Bacterial Proteins ; *Biological Evolution ; Computer Simulation ; DNA Repair ; *DNA-Binding Proteins ; DNA-Directed DNA Polymerase/metabolism ; Digestive System/microbiology ; Escherichia coli/*genetics/growth & development/*physiology ; Escherichia coli Proteins/metabolism ; Exodeoxyribonuclease V ; Exodeoxyribonucleases/metabolism ; Geologic Sediments/microbiology ; Humans ; Models, Biological ; MutS DNA Mismatch-Binding Protein ; *Mutagenesis ; Oxidative Stress ; Rec A Recombinases/metabolism ; SOS Response (Genetics) ; Water Microbiology
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  • 153
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    Crystal structure of the RC-LH1 core complex from Rhodopseudomonas palustris (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-13
    Description: The crystal structure at 4.8 angstrom resolution of the reaction center-light harvesting 1 (RC-LH1) core complex from Rhodopseudomonas palustris shows the reaction center surrounded by an oval LH1 complex that consists of 15 pairs of transmembrane helical alpha- and beta-apoproteins and their coordinated bacteriochlorophylls. Complete closure of the RC by the LH1 is prevented by a single transmembrane helix, out of register with the array of inner LH1 alpha-apoproteins. This break, located next to the binding site in the reaction center for the secondary electron acceptor ubiquinone (UQB), may provide a portal through which UQB can transfer electrons to cytochrome b/c1.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roszak, Aleksander W -- Howard, Tina D -- Southall, June -- Gardiner, Alastair T -- Law, Christopher J -- Isaacs, Neil W -- Cogdell, Richard J -- New York, N.Y. -- Science. 2003 Dec 12;302(5652):1969-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14671305" target="_blank"〉PubMed〈/a〉
    Keywords: Apoproteins/chemistry ; Bacterial Proteins/*chemistry ; Bacteriochlorophyll A/chemistry ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Light-Harvesting Protein Complexes/*chemistry ; Macromolecular Substances ; Models, Molecular ; Photosynthetic Reaction Center Complex Proteins/*chemistry ; Protein Conformation ; Protein Structure, Secondary ; Rhodopseudomonas/*chemistry ; Ubiquinone/chemistry
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  • 154
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    Evolution. Sex, sunflowers, and speciation (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbott, Richard J -- New York, N.Y. -- Science. 2003 Aug 29;301(5637):1189-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biology, University of St. Andrews, Fife KY16 9TH, UK. rja@st-and.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12947185" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; *Biological Evolution ; Diploidy ; *Ecosystem ; Environment ; Genes, Plant ; Genotype ; Helianthus/*genetics/physiology ; *Hybridization, Genetic ; Mutation ; Phenotype ; Quantitative Trait Loci ; Recombination, Genetic ; Selection, Genetic ; Species Specificity
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    Structure and mechanism of the lactose permease of Escherichia coli (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-02
    Description: Membrane transport proteins that transduce free energy stored in electrochemical ion gradients into a concentration gradient are a major class of membrane proteins. We report the crystal structure at 3.5 angstroms of the Escherichia coli lactose permease, an intensively studied member of the major facilitator superfamily of transporters. The molecule is composed of N- and C-terminal domains, each with six transmembrane helices, symmetrically positioned within the permease. A large internal hydrophilic cavity open to the cytoplasmic side represents the inward-facing conformation of the transporter. The structure with a bound lactose homolog, beta-D-galactopyranosyl-1-thio-beta-D-galactopyranoside, reveals the sugar-binding site in the cavity, and residues that play major roles in substrate recognition and proton translocation are identified. We propose a possible mechanism for lactose/proton symport (co-transport) consistent with both the structure and a large body of experimental data.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abramson, Jeff -- Smirnova, Irina -- Kasho, Vladimir -- Verner, Gillian -- Kaback, H Ronald -- Iwata, So -- DK51131: 08/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2003 Aug 1;301(5633):610-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Imperial College London, London SW7 2AZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12893935" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Binding Sites ; Biological Transport ; Cell Membrane/enzymology ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/*chemistry/enzymology ; Escherichia coli Proteins/chemistry/genetics/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ion Transport ; Lactose/*metabolism ; Membrane Transport Proteins/*chemistry/genetics/*metabolism ; Models, Molecular ; *Monosaccharide Transport Proteins ; Mutation ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protons ; Substrate Specificity ; *Symporters ; Thiogalactosides/metabolism
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    Architecture of succinate dehydrogenase and reactive oxygen species generation (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-01
    Description: The structure of Escherichia coli succinate dehydrogenase (SQR), analogous to the mitochondrial respiratory complex II, has been determined, revealing the electron transport pathway from the electron donor, succinate, to the terminal electron acceptor, ubiquinone. It was found that the SQR redox centers are arranged in a manner that aids the prevention of reactive oxygen species (ROS) formation at the flavin adenine dinucleotide. This is likely to be the main reason SQR is expressed during aerobic respiration rather than the related enzyme fumarate reductase, which produces high levels of ROS. Furthermore, symptoms of genetic disorders associated with mitochondrial SQR mutations may be a result of ROS formation resulting from impaired electron transport in the enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yankovskaya, Victoria -- Horsefield, Rob -- Tornroth, Susanna -- Luna-Chavez, Cesar -- Miyoshi, Hideto -- Leger, Christophe -- Byrne, Bernadette -- Cecchini, Gary -- Iwata, So -- GM61606/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):700-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biology Division, VA Medical Center, San Francisco, CA 94121, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12560550" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Anaerobiosis ; Binding Sites ; Crystallography, X-Ray ; Dinitrophenols/chemistry/pharmacology ; Electron Transport ; Electron Transport Complex II ; Escherichia coli/*enzymology ; Flavin-Adenine Dinucleotide/metabolism ; Heme/chemistry ; Models, Molecular ; Multienzyme Complexes/antagonists & inhibitors/*chemistry/genetics/*metabolism ; Mutation ; Oxidation-Reduction ; Oxidoreductases/antagonists & inhibitors/*chemistry/genetics/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Reactive Oxygen Species/*metabolism ; Succinate Dehydrogenase/antagonists & inhibitors/*chemistry/genetics/*metabolism ; Succinic Acid/metabolism ; Superoxides/metabolism ; Ubiquinone/chemistry/metabolism
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    Molecular basis of metal-ion selectivity and zeptomolar sensitivity by CueR (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-09-06
    Description: The earliest of a series of copper efflux genes in Escherichia coli are controlled by CueR, a member of the MerR family of transcriptional activators. Thermodynamic calibration of CueR reveals a zeptomolar (10(-21) molar) sensitivity to free Cu+, which is far less than one atom per cell. Atomic details of this extraordinary sensitivity and selectivity for +1transition-metal ions are revealed by comparing the crystal structures of CueR and a Zn2+-sensing homolog, ZntR. An unusual buried metal-receptor site in CueR restricts the metal to a linear, two-coordinate geometry and uses helix-dipole and hydrogen-bonding interactions to enhance metal binding. This binding mode is rare among metalloproteins but well suited for an ultrasensitive genetic switch.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Changela, Anita -- Chen, Kui -- Xue, Yi -- Holschen, Jackie -- Outten, Caryn E -- O'Halloran, Thomas V -- Mondragon, Alfonso -- F32 DK61868/DK/NIDDK NIH HHS/ -- GM08382/GM/NIGMS NIH HHS/ -- GM38784/GM/NIGMS NIH HHS/ -- GM51350/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Sep 5;301(5638):1383-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, 2205Tech Drive, Evanston, IL 60208, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12958362" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Binding Sites ; Copper/*metabolism ; Crystallization ; Crystallography, X-Ray ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Dimerization ; Escherichia coli/*chemistry/genetics/metabolism ; Escherichia coli Proteins/*chemistry/genetics/*metabolism ; Helix-Turn-Helix Motifs ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Metals/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Secondary ; Sequence Alignment ; Thermodynamics ; Transcription Factors/chemistry/genetics/metabolism ; Transcriptional Activation ; Zinc/metabolism
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    Paleontology. Life's diversity may truly have leaped since the dinosaurs (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-05-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kerr, Richard A -- New York, N.Y. -- Science. 2003 May 16;300(5622):1067-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12750488" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Dinosaurs ; *Fossils ; *Genetic Variation ; Mollusca/classification ; Time
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    An evolutionary advantage of haploidy in large yeast populations (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-01-25
    Description: Although seed plants and multicellular animals are predominantly diploid, the prominence of diploidy varies greatly among eukaryote life cycles, and no general evolutionary advantage of diploidy has been demonstrated. By doubling the copy number of each gene, diploidy may increase the rate at which adaptive mutations are produced. However, models suggest that this does not necessarily accelerate adaptation by diploid populations. We tested model predictions regarding rates of adaptation using asexual yeast populations. Adaptive mutations were on average partially recessive. As predicted, diploidy slowed adaptation by large populations but not by small populations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zeyl, Clifford -- Vanderford, Thomas -- Carter, Michele -- New York, N.Y. -- Science. 2003 Jan 24;299(5606):555-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Wake Forest University, Winston-Salem, NC 27109, USA. zeylcw@wfu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12543972" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; Analysis of Variance ; *Biological Evolution ; Diploidy ; Genes, Dominant ; Genes, Fungal ; Genes, Recessive ; *Haploidy ; Heterozygote ; Homozygote ; Models, Biological ; Mutation ; Reproduction ; Saccharomyces cerevisiae/*genetics/*physiology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Tempo and mode of evolutionary radiation in iguanian lizards (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-16
    Description: Identification of general properties of evolutionary radiations has been hindered by the lack of a general statistical and phylogenetic approach applicable across diverse taxa. We present a comparative analytical framework for examining phylogenetic patterns of diversification and morphological disparity with data from four iguanian-lizard taxa that exhibit substantially different patterns of evolution. Taxa whose diversification occurred disproportionately early in their evolutionary history partition more of their morphological disparity among, rather than within, subclades. This inverse relationship between timing of diversification and morphological disparity within subclades may be a general feature that transcends the historically contingent properties of different evolutionary radiations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harmon, Luke J -- Schulte, James A 2nd -- Larson, Allan -- Losos, Jonathan B -- New York, N.Y. -- Science. 2003 Aug 15;301(5635):961-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Campus Box 1137, Washington University, St. Louis, MO 63130-4899, USA. harmon@biology.wustl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12920297" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Animals ; *Biological Evolution ; Ecosystem ; Environment ; *Iguanas/anatomy & histology/classification/genetics/physiology ; Likelihood Functions ; Models, Statistical ; Phylogeny ; Species Specificity
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Structural biology. Breaching the barrier (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Locher, Kaspar P -- Bass, Randal B -- Rees, Douglas C -- New York, N.Y. -- Science. 2003 Aug 1;301(5633):603-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Molekularbiologie und Biophysik, Eidgenossische Technische Hochschule Zurich, Zurich CH-8093, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12893929" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Biological Transport ; Cell Membrane/enzymology ; Crystallography, X-Ray ; Escherichia coli/chemistry/enzymology ; Escherichia coli Proteins/*chemistry/metabolism ; Glycerophosphates/metabolism ; Lactose/metabolism ; Membrane Transport Proteins/*chemistry/metabolism ; Models, Molecular ; *Monosaccharide Transport Proteins ; Phosphates/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Symporters
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 162
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    Molecular phylogenies link rates of evolution and speciation (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-07-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Webster, Andrea J -- Payne, Robert J H -- Pagel, Mark -- New York, N.Y. -- Science. 2003 Jul 25;301(5632):478.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Animal and Microbial Sciences, University of Reading, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12881561" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Evolution, Molecular ; *Genes ; Likelihood Functions ; Mathematics ; Models, Statistical ; *Phylogeny
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    An ostracode crustacean with soft parts from the Lower Silurian (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-06
    Description: An exceptionally well-preserved ostracode from the Silurian of Herefordshire, United Kingdom, provides a rare view of the fossilized soft-part anatomy of this important group of living crustaceans and confirms that Ostracoda were extant in the Paleozoic. The fossil has striking similarity to the extant myodocopid family Cylindroleberididae, to which it is assigned, and demonstrates remarkable evolutionary stasis over 425 million years. The fossil is identified as a male on the basis of its copulatory organ.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Siveter, David J -- Sutton, Mark D -- Briggs, Derek E G -- Siveter, Derek J -- New York, N.Y. -- Science. 2003 Dec 5;302(5651):1749-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geology, University of Leicester, Leicester LE1 7RH, UK. djs@leicester.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14657495" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Crustacea/*anatomy & histology/classification ; *Fossils ; Great Britain ; Paleontology ; Time
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  • 164
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    Hexameric structure and assembly of the interleukin-6/IL-6 alpha-receptor/gp130 complex (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-06-28
    Description: Interleukin-6 (IL-6) is an immunoregulatory cytokine that activates a cell-surface signaling assembly composed of IL-6, the IL-6 alpha-receptor (IL-6Ralpha), and the shared signaling receptor gp130. The 3.65 angstrom-resolution structure of the extracellular signaling complex reveals a hexameric, interlocking assembly mediated by a total of 10 symmetry-related, thermodynamically coupled interfaces. Assembly of the hexameric complex occurs sequentially: IL-6 is first engaged by IL-6Ralpha and then presented to gp130in the proper geometry to facilitate a cooperative transition into the high-affinity, signaling-competent hexamer. The quaternary structures of other IL-6/IL-12 family signaling complexes are likely constructed by means of a similar topological blueprint.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boulanger, Martin J -- Chow, Dar-chone -- Brevnova, Elena E -- Garcia, K Christopher -- AI51321/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2003 Jun 27;300(5628):2101-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology and Department of Structural Biology, Stanford University School of Medicine, Fairchild D319, 299 Campus Drive, Stanford, CA 94305-5124, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12829785" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, CD/*chemistry/*metabolism ; Binding Sites ; Crystallography, X-Ray ; Cytokine Receptor gp130 ; Humans ; Interleukin-6/*chemistry/*metabolism ; Macromolecular Substances ; Membrane Glycoproteins/*chemistry/*metabolism ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Interleukin-6/*chemistry/*metabolism ; Signal Transduction ; Thermodynamics
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    DNA: one teacher's reflection (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-04-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kennedy, Donald -- New York, N.Y. -- Science. 2003 Apr 11;300(5617):213.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12690152" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosome Mapping ; DNA/chemistry/genetics/*history ; Gene Expression ; History, 20th Century ; History, 21st Century ; Models, Molecular ; Molecular Biology/education/*history ; Nucleic Acid Conformation
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    Invertebrate ecological immunology (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-07-26
    Description: Ecological immunology is a rapidly expanding field that examines the causes and consequences of variation in immune function in the context of evolution and of ecology. Millions of invertebrate species rely solely on innate immunity, compared with only 45,000 vertebrate species that rely additionally on an acquired immune system. Despite this difference in diversity, most studies of ecological immunology focus on vertebrates. Here we review recent progress derived largely from the mechanistic analysis of invertebrate innate immunity. Using this empirical base, we pose general questions in areas that are of central importance for the development of ecological immunology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rolff, J -- Siva-Jothy, M T -- New York, N.Y. -- Science. 2003 Jul 25;301(5632):472-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Animal and Plant Sciences, University of Sheffield, S10 2TN, Sheffield, UK. jor@sheffield.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12881560" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Ecology ; Genetic Variation ; Hormones/physiology ; *Immunity/genetics ; *Immunity, Innate/genetics ; Invertebrates/genetics/*immunology ; Selection, Genetic
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    Paleontology. Primitive jawed fishes had teeth of their own design (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stokstad, Erik -- New York, N.Y. -- Science. 2003 Feb 21;299(5610):1164.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12595662" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Dentition ; Fishes/*anatomy & histology ; *Fossils ; *Paleodontology ; *Tooth/anatomy & histology
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    Structure of Rab GDP-dissociation inhibitor in complex with prenylated YPT1 GTPase (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-10-25
    Description: Rab/Ypt guanosine triphosphatases (GTPases) represent a family of key membrane traffic regulators in eukaryotic cells whose function is governed by the guanosine diphosphate (GDP) dissociation inhibitor (RabGDI). Using a combination of chemical synthesis and protein engineering, we generated and crystallized the monoprenylated Ypt1:RabGDI complex. The structure of the complex was solved to 1.5 angstrom resolution and provides a structural basis for the ability of RabGDI to inhibit the release of nucleotide by Rab proteins. Isoprenoid binding requires a conformational change that opens a cavity in the hydrophobic core of its domain II. Analysis of the structure provides a molecular basis for understanding a RabGDI mutant that causes mental retardation in humans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rak, Alexey -- Pylypenko, Olena -- Durek, Thomas -- Watzke, Anja -- Kushnir, Susanna -- Brunsveld, Lucas -- Waldmann, Herbert -- Goody, Roger S -- Alexandrov, Kirill -- New York, N.Y. -- Science. 2003 Oct 24;302(5645):646-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physical Biochemistry, Max-Planck-Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14576435" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; Guanine Nucleotide Dissociation Inhibitors/*chemistry/genetics/metabolism ; Guanosine Diphosphate/chemistry/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Lipid Metabolism ; Magnesium/chemistry/metabolism ; Models, Molecular ; Mutation ; Protein Binding ; Protein Conformation ; Protein Prenylation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; rab GTP-Binding Proteins/*chemistry/metabolism
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    Salmonella SipA polymerizes actin by stapling filaments with nonglobular protein arms (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-09-27
    Description: Like many bacterial pathogens, Salmonella spp. use a type III secretion system to inject virulence proteins into host cells. The Salmonella invasion protein A (SipA) binds host actin, enhances its polymerization near adherent extracellular bacteria, and contributes to cytoskeletal rearrangements that internalize the pathogen. By combining x-ray crystallography of SipA with electron microscopy and image analysis of SipA-actin filaments, we show that SipA functions as a "molecular staple," in which a globular domain and two nonglobular "arms" mechanically stabilize the filament by tethering actin subunits in opposing strands. Deletion analysis of the tethering arms provides strong support for this model.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lilic, Mirjana -- Galkin, Vitold E -- Orlova, Albina -- VanLoock, Margaret S -- Egelman, Edward H -- Stebbins, C Erec -- New York, N.Y. -- Science. 2003 Sep 26;301(5641):1918-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Structural Microbiology, Rockefeller University, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14512630" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/metabolism ; Actins/*metabolism ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Binding Sites ; Crystallography, X-Ray ; Image Processing, Computer-Assisted ; Microfilament Proteins/*chemistry/genetics/*metabolism ; Microscopy, Electron ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; Salmonella typhimurium/chemistry/*metabolism ; Sequence Deletion ; Subtilisin/metabolism
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  • 170
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    Protein conformational dynamics probed by single-molecule electron transfer (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-10-11
    Description: Electron transfer is used as a probe for angstrom-scale structural changes in single protein molecules. In a flavin reductase, the fluorescence of flavin is quenched by a nearby tyrosine residue by means of photo-induced electron transfer. By probing the fluorescence lifetime of the single flavin on a photon-by-photon basis, we were able to observe the variation of flavin-tyrosine distance over time. We could then determine the potential of mean force between the flavin and the tyrosine, and a correlation analysis revealed conformational fluctuation at multiple time scales spanning from hundreds of microseconds to seconds. This phenomenon suggests the existence of multiple interconverting conformers related to the fluctuating catalytic reactivity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Haw -- Luo, Guobin -- Karnchanaphanurach, Pallop -- Louie, Tai-Man -- Rech, Ivan -- Cova, Sergio -- Xun, Luying -- Xie, X Sunney -- R01GM61577-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Oct 10;302(5643):262-6.〈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/14551431" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Catalysis ; Chemistry, Physical ; Computer Simulation ; Electrons ; Escherichia coli/enzymology ; FMN Reductase/*chemistry/genetics/metabolism ; Flavin Mononucleotide/*chemistry/metabolism ; Flavin-Adenine Dinucleotide/*chemistry/metabolism ; Flavins ; Fluorescence ; Hydrogen Bonding ; Likelihood Functions ; Mathematics ; Models, Molecular ; Mutagenesis, Site-Directed ; Photons ; Physicochemical Phenomena ; Protein Conformation ; Serine ; Spectrometry, Fluorescence ; Temperature ; Thermodynamics ; Tyrosine
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    Teaching evolution. Texas resolves war over biology texts (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-11-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holden, Constance -- New York, N.Y. -- Science. 2003 Nov 14;302(5648):1130.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14615501" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Biology/*education ; Humans ; Teaching ; Terminology as Topic ; Texas ; *Textbooks as Topic
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Biodiversity. New Chinese center marks a coming of age for field (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-10-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Normile, Dennis -- New York, N.Y. -- Science. 2003 Oct 24;302(5645):559.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14576399" target="_blank"〉PubMed〈/a〉
    Keywords: *Academies and Institutes ; Animals ; *Biological Evolution ; China ; *Ecosystem ; Germany ; Internationality ; United States
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    Biological networks: the tinkerer as an engineer (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-09-27
    Description: This viewpoint comments on recent advances in understanding the design principles of biological networks. It highlights the surprising discovery of "good-engineering" principles in biochemical circuitry that evolved by random tinkering.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alon, U -- New York, N.Y. -- Science. 2003 Sep 26;301(5641):1866-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel 76100. urialon@weizmann.ac.il〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14512615" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biochemical Phenomena ; Biochemistry ; *Biological Evolution ; *Biology ; DNA/metabolism ; Engineering ; *Models, Biological ; Proteins/metabolism ; Signal Transduction ; Systems Theory
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    Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-15
    Description: A novel coronavirus has been identified as the causative agent of severe acute respiratory syndrome (SARS). The viral main proteinase (Mpro, also called 3CLpro), which controls the activities of the coronavirus replication complex, is an attractive target for therapy. We determined crystal structures for human coronavirus (strain 229E) Mpro and for an inhibitor complex of porcine coronavirus [transmissible gastroenteritis virus (TGEV)] Mpro, and we constructed a homology model for SARS coronavirus (SARS-CoV) Mpro. The structures reveal a remarkable degree of conservation of the substrate-binding sites, which is further supported by recombinant SARS-CoV Mpro-mediated cleavage of a TGEV Mpro substrate. Molecular modeling suggests that available rhinovirus 3Cpro inhibitors may be modified to make them useful for treating SARS.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Anand, Kanchan -- Ziebuhr, John -- Wadhwani, Parvesh -- Mesters, Jeroen R -- Hilgenfeld, Rolf -- New York, N.Y. -- Science. 2003 Jun 13;300(5626):1763-7. Epub 2003 May 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biochemistry, University of Lubeck, D-23538 Lubeck, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12746549" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Chloromethyl Ketones/chemistry/metabolism ; Amino Acid Sequence ; *Antiviral Agents ; Binding Sites ; Catalytic Domain ; Coronavirus 229E, Human/*enzymology ; Crystallization ; Crystallography, X-Ray ; Cysteine Endopeptidases/*chemistry/metabolism ; Cysteine Proteinase Inhibitors/chemistry/metabolism ; Dimerization ; *Drug Design ; Humans ; Isoxazoles/chemistry/metabolism/pharmacology ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyrrolidinones/chemistry/metabolism/pharmacology ; Recombinant Proteins/chemistry/metabolism ; SARS Virus/*drug effects/*enzymology ; Sequence Alignment ; Sequence Homology, Amino Acid ; Severe Acute Respiratory Syndrome/drug therapy ; Transmissible gastroenteritis virus/enzymology
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    Design of a novel globular protein fold with atomic-level accuracy (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-11-25
    Description: A major challenge of computational protein design is the creation of novel proteins with arbitrarily chosen three-dimensional structures. Here, we used a general computational strategy that iterates between sequence design and structure prediction to design a 93-residue alpha/beta protein called Top7 with a novel sequence and topology. Top7 was found experimentally to be folded and extremely stable, and the x-ray crystal structure of Top7 is similar (root mean square deviation equals 1.2 angstroms) to the design model. The ability to design a new protein fold makes possible the exploration of the large regions of the protein universe not yet observed in nature.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kuhlman, Brian -- Dantas, Gautam -- Ireton, Gregory C -- Varani, Gabriele -- Stoddard, Barry L -- Baker, David -- New York, N.Y. -- Science. 2003 Nov 21;302(5649):1364-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14631033" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Sequence ; Circular Dichroism ; Computational Biology ; Computer Graphics ; Computer Simulation ; Crystallization ; Crystallography, X-Ray ; Databases, Protein ; Models, Molecular ; Molecular Sequence Data ; Monte Carlo Method ; Nuclear Magnetic Resonance, Biomolecular ; *Protein Conformation ; Protein Denaturation ; *Protein Engineering ; *Protein Folding ; Protein Structure, Secondary ; Proteins/*chemistry ; *Software ; Solubility ; Temperature ; Thermodynamics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    The deep roots of eukaryotes (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-06-14
    Description: Most cultivated and characterized eukaryotes can be confidently assigned to one of eight major groups. After a few false starts, we are beginning to resolve relationships among these major groups as well. However, recent developments are radically revising this picture again, particularly (i) the discovery of the likely antiquity and taxonomic diversity of ultrasmall eukaryotes, and (ii) a fundamental rethinking of the position of the root. Together these data suggest major gaps in our understanding simply of what eukaryotes are or, when it comes to the tree, even which end is up.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baldauf, S L -- New York, N.Y. -- Science. 2003 Jun 13;300(5626):1703-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of York, Box 373, Heslington, York YO10 5YW, UK. slb14@york.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12805537" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Classification/methods ; *Ecosystem ; Eukaryotic Cells/*classification ; *Phylogeny ; Polymerase Chain Reaction
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    The impact of the pull of the recent on the history of marine diversity (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-17
    Description: Up to 50% of the increase in marine animal biodiversity through the Cenozoic at the genus level has been attributed to a sampling bias termed "the Pull of the Recent," the extension of stratigraphic ranges of fossil taxa by the relatively complete sampling of the Recent biota. However, 906 of 958 living genera and subgenera of bivalve mollusks having a fossil record occur in the Pliocene or Pleistocene. The Pull of the Recent thus accounts for only 5% of the Cenozoic increase in bivalve diversity, a major component of the marine record, suggesting that the diversity increase is likely to be a genuine biological pattern.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jablonski, David -- Roy, Kaustuv -- Valentine, James W -- Price, Rebecca M -- Anderson, Philip S -- New York, N.Y. -- Science. 2003 May 16;300(5622):1133-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geophysical Sciences, University of Chicago, 5734South Ellis Avenue, Chicago, IL 60637, USA. d-jablonski@uchicago.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12750517" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Ecosystem ; *Fossils ; Models, Biological ; *Mollusca/classification ; Time
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    Evolution 2003 meeting. Genetic deficiency blamed on bacteria (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-07-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2003 Jul 25;301(5632):459.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12881548" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Bacterial Physiological Phenomena ; *Biological Evolution ; Digestion ; Diploidy ; Female ; Haploidy ; Insects/*genetics/*microbiology ; Male ; Ovum/microbiology ; *Ploidies ; Sex Characteristics ; *Symbiosis ; Wolbachia/physiology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Comment on "A green algal apicoplast ancestor" (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-07-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Waller, Ross F -- Keeling, Patrick J -- van Dooren, Giel G -- McFadden, Geoffrey I -- New York, N.Y. -- Science. 2003 Jul 4;301(5629):49; author reply 49.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and, Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12843377" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Apicomplexa/enzymology/*genetics/ultrastructure ; *Biological Evolution ; Chlorophyta/enzymology/*genetics ; Ciliophora/enzymology/genetics/ultrastructure ; Electron Transport Complex IV/chemistry/*genetics ; Gene Transfer, Horizontal ; Genes, Protozoan ; Hydrophobic and Hydrophilic Interactions ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; Plastids/*genetics ; Rhodophyta/enzymology/*genetics
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    Ancient tripartite coevolution in the attine ant-microbe symbiosis (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-01-18
    Description: The symbiosis between fungus-growing ants and the fungi they cultivate for food has been shaped by 50 million years of coevolution. Phylogenetic analyses indicate that this long coevolutionary history includes a third symbiont lineage: specialized microfungal parasites of the ants' fungus gardens. At ancient levels, the phylogenies of the three symbionts are perfectly congruent, revealing that the ant-microbe symbiosis is the product of tripartite coevolution between the farming ants, their cultivars, and the garden parasites. At recent phylogenetic levels, coevolution has been punctuated by occasional host-switching by the parasite, thus intensifying continuous coadaptation between symbionts in a tripartite arms race.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Currie, Cameron R -- Wong, Bess -- Stuart, Alison E -- Schultz, Ted R -- Rehner, Stephen A -- Mueller, Ulrich G -- Sung, Gi-Ho -- Spatafora, Joseph W -- Straus, Neil A -- New York, N.Y. -- Science. 2003 Jan 17;299(5605):386-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA. ccurrie@ku.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12532015" target="_blank"〉PubMed〈/a〉
    Keywords: Agaricales/growth & development/*physiology ; Animals ; Ants/microbiology/*physiology ; Ascomycota/physiology ; Bacterial Physiological Phenomena ; *Biological Evolution ; DNA, Fungal/analysis/genetics ; Hypocreales/classification/growth & development/isolation & ; purification/*physiology ; Phylogeny ; Sequence Analysis, DNA ; *Symbiosis
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    Molecular architecture of the multiprotein splicing factor SF3b (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-10
    Description: The splicing factor SF3b is a multiprotein complex essential for the accurate excision of introns from pre-messenger RNA. As an integral component of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP, SF3b is involved in the recognition of the pre-messenger RNA's branch site within the major and minor spliceosomes. We have determined the three-dimensional structure of the human SF3b complex by single-particle electron cryomicroscopy at a resolution of less than 10 angstroms, allowing identification of protein domains with known structural folds. The best fit of a modeled RNA-recognition motif indicates that the protein p14 is located in the central cavity of the complex. The 22 tandem helical repeats of the protein SF3b155 are located in the outer shell of the complex enclosing p14.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Golas, Monika M -- Sander, Bjoern -- Will, Cindy L -- Luhrmann, Reinhard -- Stark, Holger -- New York, N.Y. -- Science. 2003 May 9;300(5621):980-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12738865" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Cryoelectron Microscopy ; HeLa Cells ; Humans ; Image Processing, Computer-Assisted ; Macromolecular Substances ; Models, Molecular ; Multiprotein Complexes ; Phosphoproteins/*chemistry ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA Precursors/chemistry/metabolism ; RNA Splicing ; *RNA-Binding Proteins ; Repetitive Sequences, Amino Acid ; Ribonucleoprotein, U2 Small Nuclear/*chemistry ; Spliceosomes/chemistry/metabolism
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    A new species of yunnanozoan with implications for deuterostome evolution (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-01
    Description: Yunnanozoans are a distinctive clade of Lower Cambrian metazoans. Although widely accepted as deuterostomes, their exact placement within this superphylum is controversial. Here we describe a new species of Haikouella (H. jianshanensis) from the Chengjiang Lagerstatte (Yunnan, China) with exceptional preservation of a number of features. These include external gills, which suggest that the origin of the pharyngeal clefts was independent of the gills. The diagnostic branchial arches of chordates may, therefore, be composite structures. No evidence was found for the chordate-like structures that have been described in other yunnanozoans. We propose that yunnanozoans are stem-group deuterostomes, allied to the vetulicolians.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shu, Degan -- Morris, Simon Conway -- Zhang, Z F -- Liu, J N -- Han, Jian -- Chen, Ling -- Zhang, X L -- Yasui, K -- Li, Yong -- New York, N.Y. -- Science. 2003 Feb 28;299(5611):1380-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Early Life Institute and Department of Geology, Northwest University, Xi'an 710069, China. elidgshu@nwu.edu.cn〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12610301" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; China ; Chordata, Nonvertebrate/*anatomy & histology/*classification ; Digestive System/anatomy & histology ; *Fossils ; Gills/anatomy & histology ; Mouth/anatomy & histology ; Phylogeny
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    Evolution. Haploid superiority (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-01-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Greig, Duncan -- Travisano, Michael -- New York, N.Y. -- Science. 2003 Jan 24;299(5606):524-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12543960" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; *Biological Evolution ; Cell Division ; Diploidy ; Genes, Fungal ; *Haploidy ; *Mutation ; Reproduction ; Saccharomyces cerevisiae/*genetics/*physiology
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    Morphs, dispersal behavior, genetic similarity, and the evolution of cooperation (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-06-21
    Description: Genetic similarity owing to kin relationship is often invoked to explain the evolution of social cooperation. In this study, male color morphs of side-blotched lizards settle nonrandomly with respect to genetic similarity. Blue morphs tend to settle in close proximity to other blue morphs with high genetic similarity. Blue neighbors have three times the average fitness of blue males lacking such neighbors. Conversely, genetically similar males depress fitness of the orange morph. Moreover, orange males are hyperdispersed with respect to genetic similarity. Pedigree and dispersal data show that genetically similar blue neighbors are not kin. Instead, conditions for the evolution of dispersal and cooperation are promoted by an emergent property of the morph locus that increases genetic similarity within morphs: genome-wide correlational selection links many traits to the morph locus, including settlement behavior.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sinervo, Barry -- Clobert, Jean -- New York, N.Y. -- Science. 2003 Jun 20;300(5627):1949-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, Earth and Marine Sciences Building, A316, University of California, Santa Cruz, CA 95064, USA. sinervo@biology.ucsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12817150" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; *Behavior, Animal ; *Biological Evolution ; Breeding ; Cooperative Behavior ; Female ; Inbreeding ; Linkage Disequilibrium ; Lizards/*genetics/*physiology ; Male ; Microsatellite Repeats ; Pigmentation ; Selection, Genetic ; Sexual Behavior, Animal
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    BAR domains as sensors of membrane curvature: the amphiphysin BAR structure (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-12-03
    Description: The BAR (Bin/amphiphysin/Rvs) domain is the most conserved feature in amphiphysins from yeast to human and is also found in endophilins and nadrins. We solved the structure of the Drosophila amphiphysin BAR domain. It is a crescent-shaped dimer that binds preferentially to highly curved negatively charged membranes. With its N-terminal amphipathic helix and BAR domain (N-BAR), amphiphysin can drive membrane curvature in vitro and in vivo. The structure is similar to that of arfaptin2, which we find also binds and tubulates membranes. From this, we predict that BAR domains are in many protein families, including sorting nexins, centaurins, and oligophrenins. The universal and minimal BAR domain is a dimerization, membrane-binding, and curvature-sensing module.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Peter, Brian J -- Kent, Helen M -- Mills, Ian G -- Vallis, Yvonne -- Butler, P Jonathan G -- Evans, Philip R -- McMahon, Harvey T -- New York, N.Y. -- Science. 2004 Jan 23;303(5657):495-9. Epub 2003 Nov 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) 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/14645856" target="_blank"〉PubMed〈/a〉
    Keywords: ADP-Ribosylation Factors/chemistry/genetics/metabolism ; *Adaptor Proteins, Signal Transducing ; Amino Acid Sequence ; Animals ; COP-Coated Vesicles/metabolism ; Carrier Proteins/chemistry/genetics/metabolism ; Cell Membrane/chemistry/metabolism ; Clathrin/metabolism ; Clathrin-Coated Vesicles/metabolism ; Coated Vesicles/chemistry/*metabolism ; Crystallography, X-Ray ; *Cytoskeletal Proteins ; Dimerization ; Drosophila/chemistry ; Drosophila Proteins/*chemistry/*metabolism ; GTPase-Activating Proteins/chemistry/metabolism ; Liposomes/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nerve Tissue Proteins/*chemistry/genetics/*metabolism ; Nuclear Proteins/chemistry/metabolism ; Phosphoproteins/chemistry/metabolism ; Protein Binding ; Protein Structure, Secondary ; *Protein Structure, Tertiary
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    Kinesin walks hand-over-hand (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-12-20
    Description: Kinesin is a processive motor that takes 8.3-nm center-of-mass steps along microtubules for each adenosine triphosphate hydrolyzed. Whether kinesin moves by a "hand-over-hand" or an "inchworm" model has been controversial. We have labeled a single head of the kinesin dimer with a Cy3 fluorophore and localized the position of the dye to within 2 nm before and after a step. We observed that single kinesin heads take steps of 17.3 +/- 3.3 nm. A kinetic analysis of the dwell times between steps shows that the 17-nm steps alternate with 0-nm steps. These results strongly support a hand-over-hand mechanism, and not an inchworm mechanism. In addition, our results suggest that kinesin is bound by both heads to the microtubule while it waits for adenosine triphosphate in between steps.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yildiz, Ahmet -- Tomishige, Michio -- Vale, Ronald D -- Selvin, Paul R -- AR42895/AR/NIAMS NIH HHS/ -- AR44420/AR/NIAMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jan 30;303(5658):676-8. Epub 2003 Dec 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign, IL 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14684828" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate ; Carbocyanines ; Dimerization ; Fluorescence ; Fluorescent Dyes ; Humans ; Kinesin/chemistry/genetics/*metabolism ; Kinetics ; Microtubules/*metabolism ; *Models, Biological ; Models, Molecular ; Molecular Motor Proteins/chemistry/genetics/*metabolism ; Mutation ; Protein Conformation
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    Helical conformation of alkanes in a hydrophobic cavitand (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-30
    Description: Alkanes adopt extended conformations in solution that minimize steric interactions and maximize surface area. Folding can reduce the amount of hydrophobic surface exposed to solvent, but sterically unfavorable gauche interactions result. However, we found that the alkyl chains of two common surfactants in aqueous solution adopt helical conformations when bound within a synthetic receptor. The receptor recognizes the helical alkane better than the extended conformation, even though 2 to 3 kilocalories per mole of strain is introduced. The proper filling of space and burial of hydrophobic surface drive the molecular recognition between the receptor and the coiled alkane.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Trembleau, Laurent -- Rebek, Julius Jr -- GM 27932/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Aug 29;301(5637):1219-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Skaggs Institute for Chemical Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12947192" target="_blank"〉PubMed〈/a〉
    Keywords: Alkanes/*chemistry ; Benzimidazoles/*chemistry ; Chemistry, Physical ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Conformation ; Phosphorylcholine/*analogs & derivatives/*chemistry ; Physicochemical Phenomena ; Sodium Dodecyl Sulfate/*chemistry ; Solutions ; Surface Properties ; Surface-Active Agents/*chemistry ; Temperature ; Thermodynamics
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    Structure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavity (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-10-04
    Description: The cytochrome b6f complex provides the electronic connection between the photosystem I and photosystem II reaction centers of oxygenic photosynthesis and generates a transmembrane electrochemical proton gradient for adenosine triphosphate synthesis. A 3.0 angstrom crystal structure of the dimeric b6f complex from the thermophilic cyanobacterium Mastigocladus laminosus reveals a large quinone exchange cavity, stabilized by lipid, in which plastoquinone, a quinone-analog inhibitor, and a novel heme are bound. The core of the b6f complex is similar to the analogous respiratory cytochrome bc1 complex, but the domain arrangement outside the core and the complement of prosthetic groups are strikingly different. The motion of the Rieske iron-sulfur protein extrinsic domain, essential for electron transfer, must also be different in the b6f complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kurisu, Genji -- Zhang, Huamin -- Smith, Janet L -- Cramer, William A -- GM-38323/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Nov 7;302(5647):1009-14. Epub 2003 Oct 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, 915 West State Street, Purdue University, West Lafayette, IN 47907-2054, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14526088" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/chemistry ; Crystallization ; Crystallography, X-Ray ; Cyanobacteria/*chemistry/metabolism ; Cytochrome b6f Complex/*chemistry/metabolism ; Cytochromes f/chemistry/metabolism ; Dimerization ; Electron Transport ; Electron Transport Complex III/chemistry/metabolism ; Heme/chemistry ; Hydrophobic and Hydrophilic Interactions ; Iron-Sulfur Proteins/chemistry/metabolism ; Lipid Bilayers ; Models, Molecular ; *Photosynthesis ; Plastoquinone/chemistry/metabolism ; Polyenes/chemistry/metabolism ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Protons
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    Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-29
    Description: The complete genome sequence of Enterococcus faecalis V583, a vancomycin-resistant clinical isolate, revealed that more than a quarter of the genome consists of probable mobile or foreign DNA. One of the predicted mobile elements is a previously unknown vanB vancomycin-resistance conjugative transposon. Three plasmids were identified, including two pheromone-sensing conjugative plasmids, one encoding a previously undescribed pheromone inhibitor. The apparent propensity for the incorporation of mobile elements probably contributed to the rapid acquisition and dissemination of drug resistance in the enterococci.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Paulsen, I T -- Banerjei, L -- Myers, G S A -- Nelson, K E -- Seshadri, R -- Read, T D -- Fouts, D E -- Eisen, J A -- Gill, S R -- Heidelberg, J F -- Tettelin, H -- Dodson, R J -- Umayam, L -- Brinkac, L -- Beanan, M -- Daugherty, S -- DeBoy, R T -- Durkin, S -- Kolonay, J -- Madupu, R -- Nelson, W -- Vamathevan, J -- Tran, B -- Upton, J -- Hansen, T -- Shetty, J -- Khouri, H -- Utterback, T -- Radune, D -- Ketchum, K A -- Dougherty, B A -- Fraser, C M -- AI40963-02/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2003 Mar 28;299(5615):2071-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. ipaulsen@tigr.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12663927" target="_blank"〉PubMed〈/a〉
    Keywords: Adhesins, Bacterial/genetics ; Bacterial Adhesion ; Bacterial Proteins/genetics ; *Biological Evolution ; Carrier Proteins/genetics/metabolism ; Chromosomes, Bacterial/genetics ; Conjugation, Genetic ; Conserved Sequence ; DNA Transposable Elements ; Digestive System/microbiology ; Drug Resistance, Multiple, Bacterial ; Enterococcus faecalis/drug effects/*genetics/pathogenicity/physiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Gram-Positive Bacterial Infections/microbiology ; Humans ; *Interspersed Repetitive Sequences ; Lysogeny ; Open Reading Frames ; Oxidative Stress ; Plasmids ; *Sequence Analysis, DNA ; Synteny ; Vancomycin Resistance/*genetics ; Virulence/genetics ; Virulence Factors/genetics
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    Early allelic selection in maize as revealed by ancient DNA (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-11-15
    Description: Maize was domesticated from teosinte, a wild grass, by approximately 6300 years ago in Mexico. After initial domestication, early farmers continued to select for advantageous morphological and biochemical traits in this important crop. However, the timing and sequence of character selection are, thus far, known only for morphological features discernible in corn cobs. We have analyzed three genes involved in the control of plant architecture, storage protein synthesis, and starch production from archaeological maize samples from Mexico and the southwestern United States. The results reveal that the alleles typical of contemporary maize were present in Mexican maize by 4400 years ago. However, as recently as 2000 years ago, allelic selection at one of the genes may not yet have been complete.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jaenicke-Despres, Viviane -- Buckler, Ed S -- Smith, Bruce D -- Gilbert, M Thomas P -- Cooper, Alan -- Doebley, John -- Paabo, Svante -- New York, N.Y. -- Science. 2003 Nov 14;302(5648):1206-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14615538" target="_blank"〉PubMed〈/a〉
    Keywords: *Alleles ; Archaeology ; *Biological Evolution ; Crops, Agricultural/*genetics ; DNA, Plant/*genetics ; DNA-Binding Proteins/genetics/physiology ; Gene Frequency ; Genes, Plant ; Genetic Variation ; Mass Spectrometry ; Mexico ; Plant Proteins/genetics/physiology ; *Selection, Genetic ; Southwestern United States ; Time Factors ; Transcription Factors/genetics/physiology ; Zea mays/*genetics
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  • 191
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    Antibody multispecificity mediated by conformational diversity (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-01
    Description: A single antibody was shown to adopt different binding-site conformations and thereby bind unrelated antigens. Analysis by both x-ray crystallography and pre-steady-state kinetics revealed an equilibrium between different preexisting isomers, one of which possessed a promiscuous, low-affinity binding site for aromatic ligands, including the immunizing hapten. A subsequent induced-fit isomerization led to high-affinity complexes with a deep and narrow binding site. A protein antigen identified by repertoire selection made use of an unrelated antibody isomer with a wide, shallow binding site. Conformational diversity, whereby one sequence adopts multiple structures and multiple functions, can increase the effective size of the antibody repertoire but may also lead to autoimmunity and allergy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉James, Leo C -- Roversi, Pietro -- Tawfik, Dan S -- New York, N.Y. -- Science. 2003 Feb 28;299(5611):1362-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2HQ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12610298" target="_blank"〉PubMed〈/a〉
    Keywords: 2,4-Dinitrophenol/immunology ; Amino Acid Sequence ; Antibodies, Monoclonal/chemistry/immunology ; Antibody Diversity ; *Antibody Specificity ; Antigen-Antibody Complex ; Antigen-Antibody Reactions ; Antigens/*immunology ; Binding Sites, Antibody ; Cross Reactions ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Haptens/immunology ; Hydrogen Bonding ; Immunoglobulin E/*chemistry/*immunology ; Immunoglobulin Fragments/chemistry/immunology ; Isomerism ; Kinetics ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Peptide Library ; Protein Conformation ; Recombinant Proteins/immunology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 192
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    Evolution 2003 meeting. Garden flower evolves into weed (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-07-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2003 Jul 25;301(5632):458-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12881547" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Canada ; *Ecosystem ; Europe ; Silene/*genetics/*growth & development ; United States
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  • 193
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    Parasitology. A game of cat and mouth (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-01-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Volkman, Sarah K -- Hartl, Daniel L -- New York, N.Y. -- Science. 2003 Jan 17;299(5605):353-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12532003" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Cat Diseases/parasitology/transmission ; Cats ; Female ; Food Parasitology ; Genes, Protozoan ; Genetic Variation ; Humans ; Life Cycle Stages ; Mice ; Mouth ; Mutation ; Polymorphism, Genetic ; Pregnancy ; Pregnancy Complications, Parasitic/parasitology ; Recombination, Genetic ; Reproduction ; Toxoplasma/*genetics/pathogenicity/*physiology ; Toxoplasmosis/*parasitology/transmission ; Toxoplasmosis, Animal/*parasitology/transmission ; Toxoplasmosis, Congenital/epidemiology/parasitology ; Virulence
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 194
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    The structure of importin-beta bound to SREBP-2: nuclear import of a transcription factor (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-03
    Description: The sterol regulatory element-binding protein 2 (SREBP-2), a nuclear transcription factor that is essential for cholesterol metabolism, enters the nucleus through a direct interaction of its helix-loop-helix leucine zipper domain with importin-beta. We show the crystal structure of importin-beta complexed with the active form of SREBP-2. Importin-beta uses characteristic long helices like a pair of chopsticks to interact with an SREBP-2 dimer. Importin-beta changes its conformation to reveal a pseudo-twofold symmetry on its surface structure so that it can accommodate a symmetric dimer molecule. Importin-beta may use a similar strategy to recognize other dimeric cargoes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Soo Jae -- Sekimoto, Toshihiro -- Yamashita, Eiki -- Nagoshi, Emi -- Nakagawa, Atsushi -- Imamoto, Naoko -- Yoshimura, Masato -- Sakai, Hiroaki -- Chong, Khoon Tee -- Tsukihara, Tomitake -- Yoneda, Yoshihiro -- New York, N.Y. -- Science. 2003 Nov 28;302(5650):1571-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Protein Research, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14645851" target="_blank"〉PubMed〈/a〉
    Keywords: *Active Transport, Cell Nucleus ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Binding Sites ; Cell Nucleus/metabolism ; Crystallography, X-Ray ; DNA-Binding Proteins/*chemistry/*metabolism ; Dimerization ; Helix-Loop-Helix Motifs ; Humans ; Hydrophobic and Hydrophilic Interactions ; Mice ; Models, Molecular ; Molecular Sequence Data ; Nuclear Localization Signals ; Nuclear Pore/metabolism ; Protein Binding ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sterol Regulatory Element Binding Protein 2 ; Transcription Factors/*chemistry/*metabolism ; beta Karyopherins/*chemistry/*metabolism ; ran GTP-Binding Protein/metabolism
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  • 195
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    Evolution. Puzzling over the origin of species in the depths of the oldest lakes (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goldman, Erica -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):654-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12560533" target="_blank"〉PubMed〈/a〉
    Keywords: Africa ; Amphipoda/genetics ; Animals ; *Biological Evolution ; Conservation of Natural Resources ; DNA/genetics ; *Ecosystem ; Environment ; *Evolution, Molecular ; Fishes/genetics ; *Fresh Water ; Geologic Sediments ; Sexual Behavior, Animal ; Siberia ; Species Specificity ; Time Factors ; Turbellaria/classification
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  • 196
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    Conservation biology. Rapid evolution can foil even the best-laid plans (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zimmer, Carl -- New York, N.Y. -- Science. 2003 May 9;300(5621):895.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12738833" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Breeding ; *Conservation of Natural Resources ; Environment ; Fisheries ; *Fishes/genetics/growth & development/physiology ; Plant Development ; Reproduction ; *Selection, Genetic ; Sexual Maturation
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  • 197
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    Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-02
    Description: The major facilitator superfamily represents the largest group of secondary membrane transporters in the cell. Here we report the 3.3 angstrom resolution structure of a member of this superfamily, GlpT, which transports glycerol-3-phosphate into the cytoplasm and inorganic phosphate into the periplasm. The amino- and carboxyl-terminal halves of the protein exhibit a pseudo two-fold symmetry. Closed off to the periplasm, a centrally located substrate-translocation pore contains two arginines at its closed end, which comprise the substrate-binding site. Upon substrate binding, the protein adopts a more compact conformation. We propose that GlpT operates by a single-binding site, alternating-access mechanism through a rocker-switch type of movement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Yafei -- Lemieux, M Joanne -- Song, Jinmei -- Auer, Manfred -- Wang, Da-Neng -- New York, N.Y. -- Science. 2003 Aug 1;301(5633):616-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉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/12893936" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Biological Transport ; Cell Membrane/chemistry ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/*chemistry/enzymology ; Escherichia coli Proteins/chemistry/metabolism ; Glycerophosphates/*metabolism ; Helix-Turn-Helix Motifs ; Mass Spectrometry ; Membrane Transport Proteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Periplasm/metabolism ; Phosphates/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 198
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    Watching a protein as it functions with 150-ps time-resolved x-ray crystallography (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-06-21
    Description: We report picosecond time-resolved x-ray diffraction from the myoglobin (Mb) mutant in which Leu29 is replaced by Phe (L29Fmutant). The frame-by-frame structural evolution, resolved to 1.8 angstroms, allows one to literally "watch" the protein as it executes its function. Time-resolved mid-infrared spectroscopy of flash-photolyzed L29F MbCO revealed a short-lived CO intermediate whose 140-ps lifetime is shorter than that found in wild-type protein by a factor of 1000. The electron density maps of the protein unveil transient conformational changes far more dramatic than the structural differences between the carboxy and deoxy states and depict the correlated side-chain motion responsible for rapidly sweeping CO away from its primary docking site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schotte, Friedrich -- Lim, Manho -- Jackson, Timothy A -- Smirnov, Aleksandr V -- Soman, Jayashree -- Olson, John S -- Phillips, George N Jr -- Wulff, Michael -- Anfinrud, Philip A -- AR40252/AR/NIAMS NIH HHS/ -- GM35649/GM/NIGMS NIH HHS/ -- HL47020/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2003 Jun 20;300(5627):1944-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney 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/12817148" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Animals ; Binding Sites ; Carbon Monoxide/chemistry/metabolism ; Crystallography, X-Ray/*methods ; Fourier Analysis ; Heme/chemistry ; Ligands ; Models, Molecular ; Mutagenesis, Site-Directed ; Myoglobin/*chemistry/genetics/*metabolism ; Photolysis ; Protein Conformation ; Spectrophotometry, Infrared ; Time Factors ; Whales
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  • 199
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    Adaptation in a plant-hummingbird association (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-04-26
    Description: Sexual dimorphism in bill morphology and body size of the Caribbean purple-throated carib hummingbird is associated with a reversal in floral dimorphism of its Heliconia food plants. This hummingbird is the sole pollinator of H. caribaea and H. bihai, with flowers of the former corresponding to the short, straight bills of males, the larger sex, and flowers of the latter corresponding to the long, curved bills of females. On St. Lucia, H. bihai compensates for the rarity of H. caribaea by evolving a second color morph with flowers that match the bills of males, whereas on Dominica, H. caribaea evolves a second color morph with flowers that match the bills of females. The nectar rewards of all Heliconia morphs are consistent with each sex's choice of the morph that corresponds to its bill morphology and energy requirements, supporting the hypothesis that feeding preferences have driven their coadaptation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Temeles, Ethan J -- Kress, W John -- New York, N.Y. -- Science. 2003 Apr 25;300(5619):630-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Amherst College, Amherst, MA 01002 USA. ejtemeles@amherst.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12714743" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Biological ; Analysis of Variance ; Animals ; Beak/*anatomy & histology ; *Biological Evolution ; Birds/*anatomy & histology/physiology ; Body Constitution ; Dominica ; Ecosystem ; Energy Metabolism ; Feeding Behavior ; Female ; Flowers/anatomy & histology ; Heliconiaceae/*anatomy & histology ; Male ; Pigmentation ; Saint Lucia ; *Sex Characteristics
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    A new class of bacterial RNA polymerase inhibitor affects nucleotide addition (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-10-25
    Description: RNA polymerase (RNAP) is the central enzyme of gene expression. Despite availability of crystal structures, details of its nucleotide addition cycle remain obscure. We describe bacterial RNAP inhibitors (the CBR703 series) whose properties illuminate this mechanism. These compounds inhibit known catalytic activities of RNAP (nucleotide addition, pyrophosphorolysis, and Gre-stimulated transcript cleavage) but not translocation of RNA or DNA when translocation is uncoupled from catalysis. CBR703-resistance substitutions occur on an outside surface of RNAP opposite its internal active site. We propose that CBR703 compounds inhibit nucleotide addition allosterically by hindering movements of active site structures that are linked to the CBR703 binding site through a bridge helix.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Artsimovitch, Irina -- Chu, Clement -- Lynch, A Simon -- Landick, Robert -- GM38660/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Oct 24;302(5645):650-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14576436" target="_blank"〉PubMed〈/a〉
    Keywords: Amidines/chemistry/isolation & purification/metabolism/*pharmacology ; Binding Sites ; Catalysis ; DNA, Bacterial/metabolism ; DNA-Directed RNA Polymerases/*antagonists & ; inhibitors/chemistry/genetics/*metabolism ; Drug Resistance, Bacterial ; Enzyme Inhibitors/chemistry/isolation & purification/metabolism/pharmacology ; Escherichia coli/*drug effects/genetics ; Exodeoxyribonucleases/metabolism ; Hydroxylamines/chemistry/isolation & purification/metabolism/*pharmacology ; Models, Molecular ; Mutation ; Nucleotides/*metabolism ; Phenylurea Compounds/chemistry/isolation & purification/metabolism/pharmacology ; Piperazines/chemistry/isolation & purification/pharmacology ; Promoter Regions, Genetic/drug effects ; Protein Conformation ; Protein Structure, Secondary ; Pyrazoles/chemistry/isolation & purification/pharmacology ; RNA, Bacterial/*biosynthesis ; Templates, Genetic ; Transcription, Genetic/*drug effects
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