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  • *Biological Evolution
  • Binding Sites
  • American Association for the Advancement of Science (AAAS)  (82)
  • 2005-2009  (82)
  • 2008  (82)
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  • 2005-2009  (82)
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  • 1
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    Evolution of mammals and their gut microbes (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-05-24
    Description: Mammals are metagenomic in that they are composed of not only their own gene complements but also those of all of their associated microbes. To understand the coevolution of the mammals and their indigenous microbial communities, we conducted a network-based analysis of bacterial 16S ribosomal RNA gene sequences from the fecal microbiota of humans and 59 other mammalian species living in two zoos and in the wild. The results indicate that host diet and phylogeny both influence bacterial diversity, which increases from carnivory to omnivory to herbivory; that bacterial communities codiversified with their hosts; and that the gut microbiota of humans living a modern life-style is typical of omnivorous primates.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2649005/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2649005/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ley, Ruth E -- Hamady, Micah -- Lozupone, Catherine -- Turnbaugh, Peter J -- Ramey, Rob Roy -- Bircher, J Stephen -- Schlegel, Michael L -- Tucker, Tammy A -- Schrenzel, Mark D -- Knight, Rob -- Gordon, Jeffrey I -- DK30292/DK/NIDDK NIH HHS/ -- DK70977/DK/NIDDK NIH HHS/ -- DK78669/DK/NIDDK NIH HHS/ -- P01 DK078669/DK/NIDDK NIH HHS/ -- P01 DK078669-02/DK/NIDDK NIH HHS/ -- R01 DK030292/DK/NIDDK NIH HHS/ -- R01 DK030292-24/DK/NIDDK NIH HHS/ -- R01 DK070977/DK/NIDDK NIH HHS/ -- R01 DK070977-04/DK/NIDDK NIH HHS/ -- T32 GM065103/GM/NIGMS NIH HHS/ -- T32 GM065103-07/GM/NIGMS NIH HHS/ -- T32GM065103/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Jun 20;320(5883):1647-51. doi: 10.1126/science.1155725. Epub 2008 May 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Genome Sciences, Washington University School of Medicine, St. Louis, MO 63108, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497261" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Animals ; Animals, Wild/classification/genetics/microbiology ; Animals, Zoo/classification/genetics/microbiology ; Bacteria/*classification/genetics/isolation & purification ; *Bacterial Physiological Phenomena ; *Biological Evolution ; Carnivora/classification/genetics/microbiology ; *Diet ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Genes, rRNA ; Humans ; Mammals/classification/genetics/*microbiology ; Molecular Sequence Data ; *Phylogeny ; Primates/classification/genetics/microbiology ; RNA, Ribosomal, 16S/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Evolution. Dynamics of body size evolution (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-09-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roy, Kaustuv -- New York, N.Y. -- Science. 2008 Sep 12;321(5895):1451-2. doi: 10.1126/science.1163097.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Ecology, Behavior and Evolution, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. kroy@ucsd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18787156" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Body Size ; Climate ; Ecosystem ; Extinction, Biological ; Greenhouse Effect ; Models, Biological ; Population Dynamics ; Stochastic Processes ; Temperature
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Gene regulation in evolution: a history (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-12-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grula, John W -- New York, N.Y. -- Science. 2008 Dec 12;322(5908):1633. doi: 10.1126/science.322.5908.1633.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19074329" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; DNA Transposable Elements ; *Gene Expression Regulation ; History, 20th Century
    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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  • 4
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    Crystal structure of a self-spliced group II intron (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-04-05
    Description: Group II introns are self-splicing ribozymes that catalyze their own excision from precursor transcripts and insertion into new genetic locations. Here we report the crystal structure of an intact, self-spliced group II intron from Oceanobacillus iheyensis at 3.1 angstrom resolution. An extensive network of tertiary interactions facilitates the ordered packing of intron subdomains around a ribozyme core that includes catalytic domain V. The bulge of domain V adopts an unusual helical structure that is located adjacent to a major groove triple helix (catalytic triplex). The bulge and catalytic triplex jointly coordinate two divalent metal ions in a configuration that is consistent with a two-metal ion mechanism for catalysis. Structural and functional analogies support the hypothesis that group II introns and the spliceosome share a common ancestor.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4406475/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4406475/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Toor, Navtej -- Keating, Kevin S -- Taylor, Sean D -- Pyle, Anna Marie -- GM50313/GM/NIGMS NIH HHS/ -- R01 GM050313/GM/NIGMS NIH HHS/ -- T15 LM07056/LM/NLM NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Apr 4;320(5872):77-82. doi: 10.1126/science.1153803.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, Bass Building, New Haven, CT 06511, USA. navtej.toor@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18388288" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Bacillaceae/chemistry/*genetics ; Base Pairing ; Binding Sites ; Catalysis ; Catalytic Domain ; Crystallography, X-Ray ; Evolution, Molecular ; *Introns ; Ligands ; Magnesium/chemistry ; Models, Molecular ; Nucleic Acid Conformation ; Phylogeny ; *RNA Splicing ; RNA, Bacterial/*chemistry/metabolism ; RNA, Catalytic/*chemistry/metabolism ; Spliceosomes/chemistry/metabolism
    Print ISSN: 0036-8075
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  • 5
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    Small molecule-induced allosteric activation of the Vibrio cholerae RTX cysteine protease domain (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-11
    Description: Vibrio cholerae RTX (repeats in toxin) is an actin-disrupting toxin that is autoprocessed by an internal cysteine protease domain (CPD). The RTX CPD is efficiently activated by the eukaryote-specific small molecule inositol hexakisphosphate (InsP6), and we present the 2.1 angstrom structure of the RTX CPD in complex with InsP6. InsP6 binds to a conserved basic cleft that is distant from the protease active site. Biochemical and kinetic analyses of CPD mutants indicate that InsP6 binding induces an allosteric switch that leads to the autoprocessing and intracellular release of toxin-effector domains.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272704/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272704/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lupardus, Patrick J -- Shen, Aimee -- Bogyo, Matthew -- Garcia, K Christopher -- R01 AI078947/AI/NIAID NIH HHS/ -- R01 AI078947-04/AI/NIAID NIH HHS/ -- R01 EB005011/EB/NIBIB NIH HHS/ -- R01 EB005011-06/EB/NIBIB NIH HHS/ -- R01 EB005011-07/EB/NIBIB NIH HHS/ -- U54RR020843/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Oct 10;322(5899):265-8. doi: 10.1126/science.1162403.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18845756" target="_blank"〉PubMed〈/a〉
    Keywords: Acyltransferases/*chemistry/genetics/*metabolism ; Allosteric Regulation ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Bacterial Toxins/*chemistry/genetics/*metabolism ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Cysteine Endopeptidases/*chemistry/genetics/*metabolism ; Enzyme Activation ; Guanosine 5'-O-(3-Thiotriphosphate)/*metabolism ; Hydrogen Bonding ; Models, Molecular ; Phytic Acid/*metabolism ; Point Mutation ; Protein Structure, Secondary ; Surface Plasmon Resonance ; Vibrio cholerae/*chemistry
    Print ISSN: 0036-8075
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  • 6
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    Structural basis of toll-like receptor 3 signaling with double-stranded RNA (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-04-19
    Description: Toll-like receptor 3 (TLR3) recognizes double-stranded RNA (dsRNA), a molecular signature of most viruses, and triggers inflammatory responses that prevent viral spread. TLR3 ectodomains (ECDs) dimerize on oligonucleotides of at least 40 to 50 base pairs in length, the minimal length required for signal transduction. To establish the molecular basis for ligand binding and signaling, we determined the crystal structure of a complex between two mouse TLR3-ECDs and dsRNA at 3.4 angstrom resolution. Each TLR3-ECD binds dsRNA at two sites located at opposite ends of the TLR3 horseshoe, and an intermolecular contact between the two TLR3-ECD C-terminal domains coordinates and stabilizes the dimer. This juxtaposition could mediate downstream signaling by dimerizing the cytoplasmic Toll interleukin-1 receptor (TIR) domains. The overall shape of the TLR3-ECD does not change upon binding to dsRNA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761030/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761030/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Lin -- Botos, Istvan -- Wang, Yan -- Leonard, Joshua N -- Shiloach, Joseph -- Segal, David M -- Davies, David R -- Z01 BC009254-33/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2008 Apr 18;320(5874):379-81. doi: 10.1126/science.1155406.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Biology, 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/18420935" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; Dimerization ; Humans ; Ligands ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/genetics/metabolism ; NF-kappa B/metabolism ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Double-Stranded/*chemistry/*metabolism ; *Signal Transduction ; Toll-Like Receptor 3/*chemistry/genetics/*metabolism
    Print ISSN: 0036-8075
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  • 7
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    The premetazoan ancestry of cadherins (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-02-16
    Description: Cadherin-mediated cell adhesion and signaling is essential for metazoan development and yet is absent from all other multicellular organisms. We found cadherin genes at numbers similar to those observed in complex metazoans in one of the closest single-celled relatives of metazoans, the choanoflagellate Monosiga brevicollis. Because the evolution of metazoans from a single-celled ancestor required novel cell adhesion and signaling mechanisms, the discovery of diverse cadherins in choanoflagellates suggests that cadherins may have contributed to metazoan origins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abedin, Monika -- King, Nicole -- New York, N.Y. -- Science. 2008 Feb 15;319(5865):946-8. doi: 10.1126/science.1151084.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology and Center for Integrative Genomics, University of California at Berkeley, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18276888" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Cadherins/*chemistry/*genetics/physiology ; Cell Adhesion ; Ciona intestinalis/chemistry ; Cnidaria/chemistry ; Drosophila melanogaster/chemistry ; Eukaryota/*chemistry ; Eukaryotic Cells/*chemistry/physiology ; Mice ; Molecular Sequence Data ; Protein Structure, Tertiary ; Repetitive Sequences, Amino Acid ; Signal Transduction ; Tyrosine/metabolism ; src Homology Domains
    Print ISSN: 0036-8075
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  • 8
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    Avian paternal care had dinosaur origin (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-12-20
    Description: The repeated discovery of adult dinosaurs in close association with egg clutches leads to speculation over the type and extent of care exhibited by these extinct animals for their eggs and young. To assess parental care in Cretaceous troodontid and oviraptorid dinosaurs, we examined clutch volume and the bone histology of brooding adults. In comparison to four archosaur care regressions, the relatively large clutch volumes of Troodon, Oviraptor, and Citipati scale most closely with a bird-paternal care model. Clutch-associated adults lack the maternal and reproductively associated histologic features common to extant archosaurs. Large clutch volumes and a suite of reproductive features shared only with birds favor paternal care, possibly within a polygamous mating system. Paternal care in both troodontids and oviraptorids indicates that this care system evolved before the emergence of birds and represents birds' ancestral condition. In extant birds and over most adult sizes, paternal and biparental care correspond to the largest and smallest relative clutch volumes, respectively.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Varricchio, David J -- Moore, Jason R -- Erickson, Gregory M -- Norell, Mark A -- Jackson, Frankie D -- Borkowski, John J -- New York, N.Y. -- Science. 2008 Dec 19;322(5909):1826-8. doi: 10.1126/science.1163245.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Sciences, Montana State University, Bozeman, MT 59717, USA. djv@montana.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19095938" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Behavior, Animal ; *Biological Evolution ; *Birds/physiology ; Bone and Bones/anatomy & histology ; Clutch Size ; *Dinosaurs/physiology ; Female ; *Fossils ; Male ; Maternal Behavior ; *Nesting Behavior ; Paternal Behavior ; Regression Analysis ; *Sexual Behavior, Animal
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  • 9
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    Structural evidence for common ancestry of the nuclear pore complex and vesicle coats (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-01
    Description: Nuclear pore complexes (NPCs) facilitate nucleocytoplasmic transport. These massive assemblies comprise an eightfold symmetric scaffold of architectural proteins and central-channel phenylalanine-glycine-repeat proteins forming the transport barrier. We determined the nucleoporin 85 (Nup85)*Seh1 structure, a module in the heptameric Nup84 complex, at 3.5 angstroms resolution. Structural, biochemical, and genetic analyses position the Nup84 complex in two peripheral NPC rings. We establish a conserved tripartite element, the ancestral coatomer element ACE1, that reoccurs in several nucleoporins and vesicle coat proteins, providing structural evidence of coevolution from a common ancestor. We identified interactions that define the organization of the Nup84 complex on the basis of comparison with vesicle coats and confirmed the sites by mutagenesis. We propose that the NPC scaffold, like vesicle coats, is composed of polygons with vertices and edges forming a membrane-proximal lattice that provides docking sites for additional nucleoporins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2680690/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2680690/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brohawn, Stephen G -- Leksa, Nina C -- Spear, Eric D -- Rajashankar, Kanagalaghatta R -- Schwartz, Thomas U -- GM68762/GM/NIGMS NIH HHS/ -- GM77537/GM/NIGMS NIH HHS/ -- R01 GM077537/GM/NIGMS NIH HHS/ -- R01 GM077537-02/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Nov 28;322(5906):1369-73. doi: 10.1126/science.1165886. Epub 2008 Oct 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18974315" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Coated Vesicles/*chemistry ; Crystallography, X-Ray ; Dimerization ; Evolution, Molecular ; Membrane Proteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Nuclear Pore/*chemistry ; Nuclear Pore Complex Proteins/*chemistry/genetics/metabolism ; Nuclear Proteins/chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/metabolism ; Vesicular Transport Proteins/*chemistry
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  • 10
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    Neuroscience. Vertebrate vocalizations (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-07-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Margoliash, Daniel -- Hale, Melina E -- New York, N.Y. -- Science. 2008 Jul 18;321(5887):347-8. doi: 10.1126/science.1161775.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA. dan@bigbird.uchicago.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18635781" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Batrachoidiformes/*anatomy & histology/physiology ; *Biological Evolution ; Learning ; Motor Neurons/cytology ; Nerve Net/*cytology ; Neurons/*cytology ; Rhombencephalon/cytology ; Spinal Cord/cytology ; Vertebrates/*anatomy & histology/physiology ; *Vocalization, Animal
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  • 11
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    Asymmetric tethering of flat and curved lipid membranes by a golgin (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-05-03
    Description: Golgins, long stringlike proteins, tether cisternae and transport vesicles at the Golgi apparatus. We examined the attachment of golgin GMAP-210 to lipid membranes. GMAP-210 connected highly curved liposomes to flatter ones. This asymmetric tethering relied on motifs that sensed membrane curvature both in the N terminus of GMAP-210 and in ArfGAP1, which controlled the interaction of the C terminus of GMAP-210 with the small guanine nucleotide-binding protein Arf1. Because membrane curvature constantly changes during vesicular trafficking, this mode of tethering suggests a way to maintain the Golgi architecture without compromising membrane flow.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Drin, Guillaume -- Morello, Vincent -- Casella, Jean-Francois -- Gounon, Pierre -- Antonny, Bruno -- New York, N.Y. -- Science. 2008 May 2;320(5876):670-3. doi: 10.1126/science.1155821.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Pharmacologie Moleculaire et Cellulaire, Universite de Nice Sophia Antipolis and CNRS, 660 route des lucioles, 06560 Valbonne, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18451304" target="_blank"〉PubMed〈/a〉
    Keywords: ADP-Ribosylation Factor 1/metabolism ; Binding Sites ; Cell Line ; GTPase-Activating Proteins/metabolism ; Golgi Apparatus/chemistry/metabolism ; HeLa Cells ; Humans ; Intracellular Membranes/*chemistry/metabolism ; Liposomes ; Membrane Lipids/*chemistry ; Nuclear Proteins/*chemistry/metabolism ; Recombinant Proteins/chemistry/metabolism
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  • 12
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    Structure and functional role of dynein's microtubule-binding domain (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-12-17
    Description: Dynein motors move various cargos along microtubules within the cytoplasm and power the beating of cilia and flagella. An unusual feature of dynein is that its microtubule-binding domain (MTBD) is separated from its ring-shaped AAA+ adenosine triphosphatase (ATPase) domain by a 15-nanometer coiled-coil stalk. We report the crystal structure of the mouse cytoplasmic dynein MTBD and a portion of the coiled coil, which supports a mechanism by which the ATPase domain and MTBD may communicate through a shift in the heptad registry of the coiled coil. Surprisingly, functional data suggest that the MTBD, and not the ATPase domain, is the main determinant of the direction of dynein motility.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2663340/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2663340/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carter, Andrew P -- Garbarino, Joan E -- Wilson-Kubalek, Elizabeth M -- Shipley, Wesley E -- Cho, Carol -- Milligan, Ronald A -- Vale, Ronald D -- Gibbons, I R -- GM30401-29/GM/NIGMS NIH HHS/ -- GM52468/GM/NIGMS NIH HHS/ -- P01 AR042895/AR/NIAMS NIH HHS/ -- P01 AR042895-15/AR/NIAMS NIH HHS/ -- P01-AR42895/AR/NIAMS NIH HHS/ -- P41 RR-17573/RR/NCRR NIH HHS/ -- R01 GM097312/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Dec 12;322(5908):1691-5. doi: 10.1126/science.1164424.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19074350" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Dyneins/*chemistry/*metabolism ; Hydrophobic and Hydrophilic Interactions ; Image Processing, Computer-Assisted ; Mice ; Microscopy, Electron ; Microtubules/*metabolism/ultrastructure ; Models, Molecular ; Molecular Sequence Data ; Movement ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism
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  • 13
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    Reversible compartmentalization of de novo purine biosynthetic complexes in living cells (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-04-05
    Description: Purines are synthesized de novo in 10 chemical steps that are catalyzed by six enzymes in eukaryotes. Studies in vitro have provided little evidence of anticipated protein-protein interactions that would enable substrate channeling and regulation of the metabolic flux. We applied fluorescence microscopy to HeLa cells and discovered that all six enzymes colocalize to form clusters in the cellular cytoplasm. The association and dissociation of these enzyme clusters can be regulated dynamically, by either changing the purine levels of or adding exogenous agents to the culture media. Collectively, the data provide strong evidence for the formation of a multi-enzyme complex, the "purinosome," to carry out de novo purine biosynthesis in cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉An, Songon -- Kumar, Ravindra -- Sheets, Erin D -- Benkovic, Stephen J -- R21 AG030949/AG/NIA NIH HHS/ -- R21 AG030949-01/AG/NIA NIH HHS/ -- New York, N.Y. -- Science. 2008 Apr 4;320(5872):103-6. doi: 10.1126/science.1152241.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA. sua13@psu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18388293" target="_blank"〉PubMed〈/a〉
    Keywords: Azaserine/pharmacology ; Binding Sites ; Carbon-Nitrogen Ligases/genetics/*metabolism ; Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor/genetics/*metabolism ; Cell Compartmentation ; Cell Line ; Cell Line, Tumor ; Culture Media ; Cytoplasm/*enzymology ; Fluorescent Antibody Technique ; HeLa Cells ; Humans ; Hypoxanthine/pharmacology ; Microscopy, Fluorescence ; Multienzyme Complexes/genetics/*metabolism ; Phosphoribosylglycinamide Formyltransferase/genetics/*metabolism ; Purines/*biosynthesis ; Recombinant Fusion Proteins/metabolism ; Transfection
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  • 14
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    Oceans. Elements and evolution (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-12-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Anbar, Ariel D -- New York, N.Y. -- Science. 2008 Dec 5;322(5907):1481-3. doi: 10.1126/science.1163100.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Earth and Space Exploration and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA. anbar@asu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19056967" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere ; *Biological Evolution ; Ecosystem ; *Elements ; Eukaryotic Cells/physiology ; Fossils ; Iron/analysis ; Oceans and Seas ; Oxidation-Reduction ; Prokaryotic Cells/physiology ; Seawater/*chemistry ; Selection, Genetic ; Sulfur/analysis ; Time ; Trace Elements/analysis
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 15
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    The crystal structure of a sodium galactose transporter reveals mechanistic insights into Na+/sugar symport (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-05
    Description: Membrane transporters that use energy stored in sodium gradients to drive nutrients into cells constitute a major class of proteins. We report the crystal structure of a member of the solute sodium symporters (SSS), the Vibrio parahaemolyticus sodium/galactose symporter (vSGLT). The approximately 3.0 angstrom structure contains 14 transmembrane (TM) helices in an inward-facing conformation with a core structure of inverted repeats of 5 TM helices (TM2 to TM6 and TM7 to TM11). Galactose is bound in the center of the core, occluded from the outside solutions by hydrophobic residues. Surprisingly, the architecture of the core is similar to that of the leucine transporter (LeuT) from a different gene family. Modeling the outward-facing conformation based on the LeuT structure, in conjunction with biophysical data, provides insight into structural rearrangements for active transport.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654663/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654663/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Faham, Salem -- Watanabe, Akira -- Besserer, Gabriel Mercado -- Cascio, Duilio -- Specht, Alexandre -- Hirayama, Bruce A -- Wright, Ernest M -- Abramson, Jeff -- DK19567/DK/NIDDK NIH HHS/ -- DK44602/DK/NIDDK NIH HHS/ -- GM07844/GM/NIGMS NIH HHS/ -- R01 GM078844/GM/NIGMS NIH HHS/ -- R01 GM078844-01/GM/NIGMS NIH HHS/ -- R01 GM078844-02/GM/NIGMS NIH HHS/ -- R01 GM078844-03/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Aug 8;321(5890):810-4. doi: 10.1126/science.1160406. Epub 2008 Jul 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1751, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18599740" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Biological Transport ; Crystallography, X-Ray ; Dimerization ; Galactose/chemistry/*metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Lipid Bilayers/chemistry ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Sodium/chemistry/*metabolism ; Sodium-Glucose Transport Proteins/*chemistry/metabolism ; Vibrio parahaemolyticus/*chemistry/metabolism
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  • 16
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    Biochemistry. SNO removal (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-05-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holmgren, Arne -- New York, N.Y. -- Science. 2008 May 23;320(5879):1019-20. doi: 10.1126/science.1159246.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Nobel Institute for Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden. arne.holmgren@ki.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497281" target="_blank"〉PubMed〈/a〉
    Keywords: Apoptosis ; Binding Sites ; Caspase 3/metabolism ; Caspase Inhibitors ; Cell Nucleus/metabolism ; Cytosol/metabolism ; Humans ; Macrophages/metabolism ; Mitochondria/enzymology/metabolism ; Mitochondrial Proteins/metabolism ; Nitric Oxide/*metabolism ; S-Nitrosothiols/*metabolism ; T-Lymphocytes/metabolism ; Thioredoxin-Disulfide Reductase/*metabolism ; Thioredoxins/*metabolism
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  • 17
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    Evolutionary biology. Deciphering the genetics of evolution (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-08-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2008 Aug 8;321(5890):760-3. doi: 10.1126/science.321.5890.760.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18687933" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Evolution, Molecular ; Exons ; *Gene Expression Regulation ; Genome ; Humans ; *Mutation ; Regulatory Elements, Transcriptional/*genetics ; Regulatory Sequences, Nucleic Acid/*genetics ; Selection, Genetic
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  • 18
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    Evolution. Modernizing the modern synthesis (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2008 Jul 11;321(5886):196-7. doi: 10.1126/science.321.5886.196.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18621652" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Animals ; *Biological Evolution ; Body Patterning ; DNA/chemistry/genetics ; Developmental Biology ; Environment ; Epigenesis, Genetic ; Gene Expression Regulation ; Genetics ; Genetics, Population ; Genomics ; Mutation ; Selection, Genetic
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  • 19
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    Evolution. Competitive centromeres (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-12-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Charlesworth, Deborah -- New York, N.Y. -- Science. 2008 Dec 5;322(5907):1484-5. doi: 10.1126/science.1167573.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK. deborah.charlesworth@ed.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19056969" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; *Biological Evolution ; Centromere/*physiology ; Chromosomes, Plant/*physiology ; Crosses, Genetic ; Gene Frequency ; Genetic Markers ; Heterozygote ; Hybridization, Genetic ; Meiosis ; Mimulus/*genetics/physiology ; Models, Genetic ; Mutation ; Selection, Genetic
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  • 20
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    Human-specific gain of function in a developmental enhancer (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-09-06
    Description: Changes in gene regulation are thought to have contributed to the evolution of human development. However, in vivo evidence for uniquely human developmental regulatory function has remained elusive. In transgenic mice, a conserved noncoding sequence (HACNS1) that evolved extremely rapidly in humans acted as an enhancer of gene expression that has gained a strong limb expression domain relative to the orthologous elements from chimpanzee and rhesus macaque. This gain of function was consistent across two developmental stages in the mouse and included the presumptive anterior wrist and proximal thumb. In vivo analyses with synthetic enhancers, in which human-specific substitutions were introduced into the chimpanzee enhancer sequence or reverted in the human enhancer to the ancestral state, indicated that 13 substitutions clustered in an 81-base pair module otherwise highly constrained among terrestrial vertebrates were sufficient to confer the human-specific limb expression domain.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2658639/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2658639/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prabhakar, Shyam -- Visel, Axel -- Akiyama, Jennifer A -- Shoukry, Malak -- Lewis, Keith D -- Holt, Amy -- Plajzer-Frick, Ingrid -- Morrison, Harris -- Fitzpatrick, David R -- Afzal, Veena -- Pennacchio, Len A -- Rubin, Edward M -- Noonan, James P -- 1-F32-GM074367/GM/NIGMS NIH HHS/ -- F32 GM074367/GM/NIGMS NIH HHS/ -- F32 GM074367-02/GM/NIGMS NIH HHS/ -- HG003988/HG/NHGRI NIH HHS/ -- HL066681/HL/NHLBI NIH HHS/ -- MC_U127561093/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Sep 5;321(5894):1346-50. doi: 10.1126/science.1159974.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18772437" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Body Patterning/*genetics ; Conserved Sequence ; Embryonic Development ; *Enhancer Elements, Genetic ; Evolution, Molecular ; Extremities/*embryology ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; Humans ; Limb Buds/embryology/metabolism ; Macaca mulatta/genetics ; Mice ; Mice, Transgenic ; Molecular Sequence Data ; Mutation ; PAX9 Transcription Factor/metabolism ; Pan troglodytes/genetics ; Selection, Genetic ; Transcription Factors/metabolism
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  • 21
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    Genetics. Enhancing gene regulation (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-09-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wray, Gregory A -- Babbitt, Courtney C -- New York, N.Y. -- Science. 2008 Sep 5;321(5894):1300-1. doi: 10.1126/science.1163568.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology and Institute for Genome Science and Policy, Duke University, Box 90338, Durham, NC 27708, USA. gwray@duke.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18772422" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Chromatin Immunoprecipitation ; Computational Biology ; Conserved Sequence ; Drosophila Proteins/metabolism ; *Enhancer Elements, Genetic ; Evolution, Molecular ; *Gene Expression Regulation, Developmental ; Humans ; Introns ; Mutation ; Nuclear Proteins/metabolism ; Oligonucleotide Array Sequence Analysis ; Phosphoproteins/metabolism ; *Regulatory Sequences, Nucleic Acid ; Transcription Factors/metabolism
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  • 22
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    Leiomodin is an actin filament nucleator in muscle cells (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-04-12
    Description: Initiation of actin polymerization in cells requires nucleation factors. Here we describe an actin-binding protein, leiomodin, that acted as a strong filament nucleator in muscle cells. Leiomodin shared two actin-binding sites with the filament pointed end-capping protein tropomodulin: a flexible N-terminal region and a leucine-rich repeat domain. Leiomodin also contained a C-terminal extension of 150 residues. The smallest fragment with strong nucleation activity included the leucine-rich repeat and C-terminal extension. The N-terminal region enhanced the nucleation activity threefold and recruited tropomyosin, which weakly stimulated nucleation and mediated localization of leiomodin to the middle of muscle sarcomeres. Knocking down leiomodin severely compromised sarcomere assembly in cultured muscle cells, which suggests a role for leiomodin in the nucleation of tropomyosin-decorated filaments in muscles.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845909/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845909/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chereau, David -- Boczkowska, Malgorzata -- Skwarek-Maruszewska, Aneta -- Fujiwara, Ikuko -- Hayes, David B -- Rebowski, Grzegorz -- Lappalainen, Pekka -- Pollard, Thomas D -- Dominguez, Roberto -- GM026338/GM/NIGMS NIH HHS/ -- GM073791/GM/NIGMS NIH HHS/ -- HL086655/HL/NHLBI NIH HHS/ -- P01 HL086655/HL/NHLBI NIH HHS/ -- P01 HL086655-01A10004/HL/NHLBI NIH HHS/ -- R01 GM073791/GM/NIGMS NIH HHS/ -- R01 GM073791-04/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Apr 11;320(5873):239-43. doi: 10.1126/science.1155313.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Boston Biomedical Research Institute, Watertown, MA 02472, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18403713" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/*metabolism ; Actins/metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Cells, Cultured ; Cytoskeletal Proteins/chemistry/*metabolism ; Humans ; Microfilament Proteins/chemistry/*metabolism ; Molecular Sequence Data ; Muscle Proteins/chemistry/*metabolism ; Myocytes, Cardiac/*metabolism ; Protein Structure, Tertiary ; RNA Interference ; Rabbits ; Rats ; Sarcomeres/*metabolism ; Tropomodulin/chemistry ; Tropomyosin/chemistry/metabolism
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  • 23
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    Evolution. Who's your daddy? (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-12-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prum, Richard O -- New York, N.Y. -- Science. 2008 Dec 19;322(5909):1799-800. doi: 10.1126/science.1168808.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Post Office Box 208105, Yale University, New Haven, CT 06520, USA. richard.prum@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19095929" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Behavior, Animal ; *Biological Evolution ; *Birds/physiology ; Clutch Size ; *Dinosaurs/physiology ; Female ; *Fossils ; Male ; *Nesting Behavior ; Paternal Behavior ; Sexual Behavior, Animal
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  • 24
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    NADP regulates the yeast GAL induction system (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-02-23
    Description: Transcriptional regulation of the galactose-metabolizing genes in Saccharomyces cerevisiae depends on three core proteins: Gal4p, the transcriptional activator that binds to upstream activating DNA sequences (UAS(GAL)); Gal80p, a repressor that binds to the carboxyl terminus of Gal4p and inhibits transcription; and Gal3p, a cytoplasmic transducer that, upon binding galactose and adenosine 5'-triphosphate, relieves Gal80p repression. The current model of induction relies on Gal3p sequestering Gal80p in the cytoplasm. However, the rapid induction of this system implies that there is a missing factor. Our structure of Gal80p in complex with a peptide from the carboxyl-terminal activation domain of Gal4p reveals the existence of a dinucleotide that mediates the interaction between the two. Biochemical and in vivo experiments suggests that nicotinamide adenine dinucleotide phosphate (NADP) plays a key role in the initial induction event.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2726985/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2726985/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kumar, P Rajesh -- Yu, Yao -- Sternglanz, Rolf -- Johnston, Stephen Albert -- Joshua-Tor, Leemor -- GM074075/GM/NIGMS NIH HHS/ -- GM55641/GM/NIGMS NIH HHS/ -- P30 CA045508/CA/NCI NIH HHS/ -- R01 GM074075/GM/NIGMS NIH HHS/ -- R01 GM074075-04/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Feb 22;319(5866):1090-2. doi: 10.1126/science.1151903.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY11724, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18292341" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Crystallography, X-Ray ; DNA-Binding Proteins ; Dimerization ; Galactokinase/metabolism ; Galactose/metabolism ; Gene Expression Regulation, Fungal ; Models, Molecular ; NADP/*metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Repressor Proteins/*chemistry/genetics/*metabolism ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism ; Transcription Factors/*chemistry/genetics/*metabolism ; Transcription, Genetic
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    Ancestral monogamy shows kin selection is key to the evolution of eusociality (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-05-31
    Description: Close relatedness has long been considered crucial to the evolution of eusociality. However, it has recently been suggested that close relatedness may be a consequence, rather than a cause, of eusociality. We tested this idea with a comparative analysis of female mating frequencies in 267 species of eusocial bees, wasps, and ants. We found that mating with a single male, which maximizes relatedness, is ancestral for all eight independent eusocial lineages that we investigated. Mating with multiple males is always derived. Furthermore, we found that high polyandry (〉2 effective mates) occurs only in lineages whose workers have lost reproductive totipotency. These results provide the first evidence that monogamy was critical in the evolution of eusociality, strongly supporting the prediction of inclusive fitness theory.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hughes, William O H -- Oldroyd, Benjamin P -- Beekman, Madeleine -- Ratnieks, Francis L W -- New York, N.Y. -- Science. 2008 May 30;320(5880):1213-6. doi: 10.1126/science.1156108.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Integrative and Comparative Biology, University of Leeds, Leeds, LS2 9JT, UK. w.o.h.hughes@leeds.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18511689" target="_blank"〉PubMed〈/a〉
    Keywords: Altruism ; Animals ; Ants ; Bees ; *Biological Evolution ; Female ; Male ; Phylogeny ; *Sexual Behavior, Animal ; *Social Behavior ; Sociobiology ; Wasps
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    The evolution and distribution of species body size (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-07-19
    Description: The distribution of species body size within taxonomic groups exhibits a heavy right tail extending over many orders of magnitude, where most species are much larger than the smallest species. We provide a simple model of cladogenetic diffusion over evolutionary time that omits explicit mechanisms for interspecific competition and other microevolutionary processes, yet fully explains the shape of this distribution. We estimate the model's parameters from fossil data and find that it robustly reproduces the distribution of 4002 mammal species from the late Quaternary. The observed fit suggests that the asymmetric distribution arises from a fundamental trade-off between the short-term selective advantages (Cope's rule) and long-term selective risks of increased species body size in the presence of a taxon-specific lower limit on body size.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clauset, Aaron -- Erwin, Douglas H -- New York, N.Y. -- Science. 2008 Jul 18;321(5887):399-401. doi: 10.1126/science.1157534.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA. aaronc@santafe.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18635801" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Body Size ; Computer Simulation ; Extinction, Biological ; Fossils ; Genetic Speciation ; Mammals/*anatomy & histology/classification/physiology ; Models, Biological ; Selection, Genetic
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    The role of fisheries-induced evolution (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-04-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kuparinen, Anna -- Merila, Juha -- New York, N.Y. -- Science. 2008 Apr 4;320(5872):47-50; author reply 47-50.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18396481" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Environment ; *Fisheries ; *Fishes/genetics ; Phenotype
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Science education. Misjudged talk opens creationist rift at Royal Society (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-09-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clery, Daniel -- New York, N.Y. -- Science. 2008 Sep 26;321(5897):1752-3. doi: 10.1126/science.321.5897.1752.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18818326" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Curriculum ; Great Britain ; *Religion and Science ; Science/*education ; Societies, Scientific/*organization & administration
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    Regulated protein denitrosylation by cytosolic and mitochondrial thioredoxins (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-05-24
    Description: Nitric oxide acts substantially in cellular signal transduction through stimulus-coupled S-nitrosylation of cysteine residues. The mechanisms that might subserve protein denitrosylation in cellular signaling remain uncharacterized. Our search for denitrosylase activities focused on caspase-3, an exemplar of stimulus-dependent denitrosylation, and identified thioredoxin and thioredoxin reductase in a biochemical screen. In resting human lymphocytes, thioredoxin-1 actively denitrosylated cytosolic caspase-3 and thereby maintained a low steady-state amount of S-nitrosylation. Upon stimulation of Fas, thioredoxin-2 mediated denitrosylation of mitochondria-associated caspase-3, a process required for caspase-3 activation, and promoted apoptosis. Inhibition of thioredoxin-thioredoxin reductases enabled identification of additional substrates subject to endogenous S-nitrosylation. Thus, specific enzymatic mechanisms may regulate basal and stimulus-induced denitrosylation in mammalian cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754768/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754768/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Benhar, Moran -- Forrester, Michael T -- Hess, Douglas T -- Stamler, Jonathan S -- P01 HL075443/HL/NHLBI NIH HHS/ -- P01 HL075443-050003/HL/NHLBI NIH HHS/ -- R01 HL059130/HL/NHLBI NIH HHS/ -- R01 HL059130-11/HL/NHLBI NIH HHS/ -- U19 ES012496/ES/NIEHS NIH HHS/ -- U19 ES012496-05/ES/NIEHS NIH HHS/ -- New York, N.Y. -- Science. 2008 May 23;320(5879):1050-4. doi: 10.1126/science.1158265.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497292" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD95/metabolism ; Apoptosis ; Auranofin/pharmacology ; Binding Sites ; Caspase 3/metabolism ; Caspase Inhibitors ; Cell Line ; Cytosol/*metabolism ; Dinitrochlorobenzene/pharmacology ; HeLa Cells ; Humans ; Jurkat Cells ; Macrophages/metabolism ; Mitochondria/enzymology/*metabolism ; Mitochondrial Proteins/*metabolism ; Nitric Oxide/*metabolism ; Rats ; Recombinant Proteins/metabolism ; S-Nitrosothiols/*metabolism ; T-Lymphocytes/metabolism ; Thioredoxin-Disulfide Reductase/*metabolism ; Thioredoxins/*metabolism
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    De novo computational design of retro-aldol enzymes (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-03-08
    Description: The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Using new algorithms that rely on hashing techniques to construct active sites for multistep reactions, we designed retro-aldolases that use four different catalytic motifs to catalyze the breaking of a carbon-carbon bond in a nonnatural substrate. Of the 72 designs that were experimentally characterized, 32, spanning a range of protein folds, had detectable retro-aldolase activity. Designs that used an explicit water molecule to mediate proton shuffling were significantly more successful, with rate accelerations of up to four orders of magnitude and multiple turnovers, than those involving charged side-chain networks. The atomic accuracy of the design process was confirmed by the x-ray crystal structure of active designs embedded in two protein scaffolds, both of which were nearly superimposable on the design model.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431203/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431203/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jiang, Lin -- Althoff, Eric A -- Clemente, Fernando R -- Doyle, Lindsey -- Rothlisberger, Daniela -- Zanghellini, Alexandre -- Gallaher, Jasmine L -- Betker, Jamie L -- Tanaka, Fujie -- Barbas, Carlos F 3rd -- Hilvert, Donald -- Houk, Kendall N -- Stoddard, Barry L -- Baker, David -- R01 CA097328/CA/NCI NIH HHS/ -- R01 GM049857/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Mar 7;319(5868):1387-91. doi: 10.1126/science.1152692.〈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/18323453" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde-Lyases/*chemistry/metabolism ; *Algorithms ; Binding Sites ; Catalysis ; Catalytic Domain ; Computer Simulation ; Crystallography, X-Ray ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Models, Molecular ; Protein Conformation ; Protein Engineering
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    Science education. Louisiana opens school door for opponents of evolution (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-06-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Richards, Fayana -- New York, N.Y. -- Science. 2008 Jun 20;320(5883):1572. doi: 10.1126/science.320.5883.1572a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18566252" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Education/*legislation & jurisprudence ; Louisiana ; Science/*education ; Teaching/legislation & jurisprudence ; Teaching Materials
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    Evolution in the schools. States push academic freedom bills (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-05-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhattacharjee, Yudhijit -- New York, N.Y. -- Science. 2008 May 9;320(5877):731. doi: 10.1126/science.320.5877.731a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18467563" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Biology/education/*legislation & jurisprudence ; Education/*legislation & jurisprudence ; Politics ; *Religion and Science ; Schools/legislation & jurisprudence ; United States
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    Science education. Florida standards support evolution--with a twist (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-03-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhattacharjee, Yudhijit -- New York, N.Y. -- Science. 2008 Feb 29;319(5867):1168. doi: 10.1126/science.319.5867.1168.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18309050" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Education/*standards ; Florida ; Science/*education ; Teaching ; Terminology as Topic
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    Orrorin tugenensis femoral morphology and the evolution of hominin bipedalism (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-03-22
    Description: Bipedalism is a key human adaptation and a defining feature of the hominin clade. Fossil femora discovered in Kenya and attributed to Orrorin tugenensis, at 6 million years ago, purportedly provide the earliest postcranial evidence of hominin bipedalism, but their functional and phylogenetic affinities are controversial. We show that the O. tugenensis femur differs from those of apes and Homo and most strongly resembles those of Australopithecus and Paranthropus, indicating that O. tugenensis was bipedal but is not more closely related to Homo than to Australopithecus. Femoral morphology indicates that O. tugenensis shared distinctive hip biomechanics with australopiths, suggesting that this complex evolved early in human evolution and persisted for almost 4 million years until modifications of the hip appeared in the late Pliocene in early Homo.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Richmond, Brian G -- Jungers, William L -- New York, N.Y. -- Science. 2008 Mar 21;319(5870):1662-5. doi: 10.1126/science.1154197.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for the Advanced Study of Hominid Paleobiology, Department of Anthropology, George Washington University, 2110 G Street, NW, Washington, DC 20052, USA. brich@gwu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18356526" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Biomechanical Phenomena ; Femur/*anatomy & histology ; *Fossils ; *Gait ; Gorilla gorilla/anatomy & histology ; Hip/anatomy & histology/physiology ; *Hominidae/anatomy & histology/classification/physiology ; Humans ; Kenya ; Pan paniscus/anatomy & histology ; Pan troglodytes/anatomy & histology ; Pongo pygmaeus/anatomy & histology ; Posture ; *Walking
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    The high-affinity E. coli methionine ABC transporter: structure and allosteric regulation (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-07-16
    Description: The crystal structure of the high-affinity Escherichia coli MetNI methionine uptake transporter, a member of the adenosine triphosphate (ATP)-binding cassette (ABC) family, has been solved to 3.7 angstrom resolution. The overall architecture of MetNI reveals two copies of the adenosine triphosphatase (ATPase) MetN in complex with two copies of the transmembrane domain MetI, with the transporter adopting an inward-facing conformation exhibiting widely separated nucleotide binding domains. Each MetI subunit is organized around a core of five transmembrane helices that correspond to a subset of the helices observed in the larger membrane-spanning subunits of the molybdate (ModBC) and maltose (MalFGK) ABC transporters. In addition to the conserved nucleotide binding domain of the ABC family, MetN contains a carboxyl-terminal extension with a ferredoxin-like fold previously assigned to a conserved family of regulatory ligand-binding domains. These domains separate the nucleotide binding domains and would interfere with their association required for ATP binding and hydrolysis. Methionine binds to the dimerized carboxyl-terminal domain and is shown to inhibit ATPase activity. These observations are consistent with an allosteric regulatory mechanism operating at the level of transport activity, where increased intracellular levels of the transported ligand stabilize an inward-facing, ATPase-inactive state of MetNI to inhibit further ligand translocation into the cell.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527972/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527972/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kadaba, Neena S -- Kaiser, Jens T -- Johnson, Eric -- Lee, Allen -- Rees, Douglas C -- GM45162/GM/NIGMS NIH HHS/ -- R37 GM045162/GM/NIGMS NIH HHS/ -- R37 GM045162-18/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Jul 11;321(5886):250-3. doi: 10.1126/science.1157987.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Division of Chemistry and Chemical Engineering, Mail Code 114-96, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18621668" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry/metabolism ; Adenosine Triphosphatases/*chemistry/*metabolism ; Allosteric Regulation ; Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Dimerization ; Escherichia coli Proteins/*chemistry/*metabolism ; Membrane Transport Proteins/*chemistry/*metabolism ; Methionine/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism
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    Surface sites for engineering allosteric control in proteins (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-18
    Description: Statistical analyses of protein families reveal networks of coevolving amino acids that functionally link distantly positioned functional surfaces. Such linkages suggest a concept for engineering allosteric control into proteins: The intramolecular networks of two proteins could be joined across their surface sites such that the activity of one protein might control the activity of the other. We tested this idea by creating PAS-DHFR, a designed chimeric protein that connects a light-sensing signaling domain from a plant member of the Per/Arnt/Sim (PAS) family of proteins with Escherichia coli dihydrofolate reductase (DHFR). With no optimization, PAS-DHFR exhibited light-dependent catalytic activity that depended on the site of connection and on known signaling mechanisms in both proteins. PAS-DHFR serves as a proof of concept for engineering regulatory activities into proteins through interface design at conserved allosteric sites.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071530/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071530/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Jeeyeon -- Natarajan, Madhusudan -- Nashine, Vishal C -- Socolich, Michael -- Vo, Tina -- Russ, William P -- Benkovic, Stephen J -- Ranganathan, Rama -- R01 EY018720/EY/NEI NIH HHS/ -- R01 EY018720-01/EY/NEI NIH HHS/ -- R01 EY018720-02/EY/NEI NIH HHS/ -- R01 EY018720-03/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 2008 Oct 17;322(5900):438-42. doi: 10.1126/science.1159052.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18927392" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Allosteric Site ; Binding Sites ; Catalysis ; Cryptochromes ; Escherichia coli/enzymology ; Flavoproteins/*chemistry/metabolism ; Kinetics ; Ligands ; Light ; Models, Molecular ; NADP/metabolism ; Protein Conformation ; *Protein Engineering ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/*chemistry/*metabolism ; Tetrahydrofolate Dehydrogenase/*chemistry/metabolism
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    Evolution. Vatican science conference offers an ambiguous message (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bohannon, John -- New York, N.Y. -- Science. 2008 Nov 14;322(5904):1038. doi: 10.1126/science.322.5904.1038.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19008422" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; *Catholicism ; *Religion and Science ; Vatican City
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    Dual positive and negative regulation of wingless signaling by adenomatous polyposis coli (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-01-19
    Description: The evolutionarily conserved Wnt/Wingless signal transduction pathway directs cell proliferation, cell fate, and cell death during development in metazoans and is inappropriately activated in several types of cancer. The majority of colorectal carcinomas contain truncating mutations in the adenomatous polyposis coli (APC) tumor suppressor, a negative regulator of Wnt/Wingless signaling. Here, we demonstrate that Drosophila Apc homologs also have an activating role in both physiological and ectopic Wingless signaling. The Apc amino terminus is important for its activating function, whereas the beta-catenin binding sites are dispensable. Apc likely promotes Wingless transduction through down-regulation of Axin, a negative regulator of Wingless signaling. Given the evolutionary conservation of APC in Wnt signal transduction, an activating role may also be present in vertebrates with relevance to development and cancer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Takacs, Carter M -- Baird, Jason R -- Hughes, Edward G -- Kent, Sierra S -- Benchabane, Hassina -- Paik, Raehum -- Ahmed, Yashi -- KO8CA078532/CA/NCI NIH HHS/ -- R01 CA105038/CA/NCI NIH HHS/ -- R01CA105038/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2008 Jan 18;319(5861):333-6. doi: 10.1126/science.1151232.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics and the Norris Cotton Cancer Center, Dartmouth Medical School, Hanover, NH 03755, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18202290" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/metabolism ; Animals ; Apoptosis ; Armadillo Domain Proteins/metabolism ; Axin Protein ; Binding Sites ; Cytoskeletal Proteins/chemistry/genetics/*metabolism ; Down-Regulation ; Drosophila/genetics/growth & development/*metabolism ; Drosophila Proteins/chemistry/genetics/*metabolism ; Genes, Insect ; Mutation ; Photoreceptor Cells, Invertebrate/cytology ; Proto-Oncogene Proteins/*metabolism ; *Signal Transduction ; Transcription Factors/metabolism ; Tumor Suppressor Proteins/chemistry/genetics/*metabolism ; Wings, Animal/growth & development/metabolism ; Wnt1 Protein
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    Video games. 'Spore' documentary spawns protest by scientists who starred in it (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bohannon, John -- New York, N.Y. -- Science. 2008 Oct 24;322(5901):517. doi: 10.1126/science.322.5901.517a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18948511" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Humans ; *Motion Pictures as Topic ; *Research Personnel ; *Video Games
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    AMPylation of Rho GTPases by Vibrio VopS disrupts effector binding and downstream signaling (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-29
    Description: The Vibrio parahaemolyticus type III effector VopS is implicated in cell rounding and the collapse of the actin cytoskeleton by inhibiting Rho guanosine triphosphatases (GTPases). We found that VopS could act to covalently modify a conserved threonine residue on Rho, Rac, and Cdc42 with adenosine 5'-monophosphate (AMP). The resulting AMPylation prevented the interaction of Rho GTPases with downstream effectors, thereby inhibiting actin assembly in the infected cell. Eukaryotic proteins were also directly modified with AMP, potentially expanding the repertoire of posttranslational modifications for molecular signaling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yarbrough, Melanie L -- Li, Yan -- Kinch, Lisa N -- Grishin, Nick V -- Ball, Haydn L -- Orth, Kim -- R01-AI056404/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Jan 9;323(5911):269-72. doi: 10.1126/science.1166382. Epub 2008 Nov 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, University of Texas (UT) Southwestern Medical Center, Dallas, TX 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19039103" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Monophosphate/*metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/*metabolism ; Binding Sites ; Cell Shape ; HeLa Cells ; Humans ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Phosphorylation ; Protein Processing, Post-Translational ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Signal Transduction ; Threonine/chemistry/metabolism ; Vibrio parahaemolyticus/*metabolism/pathogenicity ; cdc42 GTP-Binding Protein/antagonists & inhibitors/chemistry/*metabolism ; rac GTP-Binding Proteins/antagonists & inhibitors/chemistry/*metabolism ; rho GTP-Binding Proteins/antagonists & inhibitors/chemistry/*metabolism
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    A mosaic of chemical coevolution in a large blue butterfly (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-01-05
    Description: Mechanisms of recognition are essential to the evolution of mutualistic and parasitic interactions between species. One such example is the larval mimicry that Maculinea butterfly caterpillars use to parasitize Myrmica ant colonies. We found that the greater the match between the surface chemistry of Maculinea alcon and two of its host Myrmica species, the more easily ant colonies were exploited. The geographic patterns of surface chemistry indicate an ongoing coevolutionary arms race between the butterflies and Myrmica rubra, which has significant genetic differentiation between populations, but not between the butterflies and a second, sympatric host, Myrmica ruginodis, which has panmictic populations. Alternative hosts may therefore provide an evolutionary refuge for a parasite during periods of counteradaptation by their preferred hosts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nash, David R -- Als, Thomas D -- Maile, Roland -- Jones, Graeme R -- Boomsma, Jacobus J -- New York, N.Y. -- Science. 2008 Jan 4;319(5859):88-90. doi: 10.1126/science.1149180.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark. DRNash@bi.ku.dk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18174441" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Animals ; Ants/chemistry/*physiology ; *Biological Evolution ; Butterflies/chemistry/genetics/growth & development/*physiology ; Hydrocarbons/*chemistry ; Larva/chemistry/physiology ; Microsatellite Repeats ; Molecular Mimicry
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    Evolution. Crossing the divide (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-02-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Couzin, Jennifer -- New York, N.Y. -- Science. 2008 Feb 22;319(5866):1034-6. doi: 10.1126/science.319.5866.1034.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18292321" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Canada ; Christianity ; Fossils ; History, 20th Century ; History, 21st Century ; *Paleontology ; *Religion and Science
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    Crystal structure of the termination module of a nonribosomal peptide synthetase (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-06-28
    Description: Nonribosomal peptide synthetases (NRPSs) are modular multidomain enzymes that act as an assembly line to catalyze the biosynthesis of complex natural products. The crystal structure of the 144-kilodalton Bacillus subtilis termination module SrfA-C was solved at 2.6 angstrom resolution. The adenylation and condensation domains of SrfA-C associate closely to form a catalytic platform, with their active sites on the same side of the platform. The peptidyl carrier protein domain is flexibly tethered to this platform and thus can move with its substrate-loaded 4'-phosphopantetheine arm between the active site of the adenylation domain and the donor side of the condensation domain. The SrfA-C crystal structure has implications for the rational redesign of NRPSs as a means of producing novel bioactive peptides.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tanovic, Alan -- Samel, Stefan A -- Essen, Lars-Oliver -- Marahiel, Mohamed A -- New York, N.Y. -- Science. 2008 Aug 1;321(5889):659-63. doi: 10.1126/science.1159850. Epub 2008 Jun 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein-Strasse, D35032 Marburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18583577" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacillus subtilis/*enzymology ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Peptide Synthases/*chemistry/metabolism ; Protein Conformation ; Protein Engineering ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism
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    A conserved mutation in an ethylene biosynthesis enzyme leads to andromonoecy in melons (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-08-09
    Description: Andromonoecy is a widespread sexual system in angiosperms characterized by plants carrying both male and bisexual flowers. In melon, this sexual form is controlled by the identity of the alleles at the andromonoecious (a) locus. Cloning of the a gene reveals that andromonoecy results from a mutation in the active site of 1-aminocyclopropane-1-carboxylic acid synthase. Expression of the active enzyme inhibits the development of the male organs and is not required for carpel development. A causal single-nucleotide polymorphism associated with andromonoecy was identified, which suggests that the a allele has been under recent positive selection and may be linked to the evolution of this sexual system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boualem, Adnane -- Fergany, Mohamed -- Fernandez, Ronan -- Troadec, Christelle -- Martin, Antoine -- Morin, Halima -- Sari, Marie-Agnes -- Collin, Fabrice -- Flowers, Jonathan M -- Pitrat, Michel -- Purugganan, Michael D -- Dogimont, Catherine -- Bendahmane, Abdelhafid -- New York, N.Y. -- Science. 2008 Aug 8;321(5890):836-8. doi: 10.1126/science.1159023.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉INRA (Institut National de la Recherche Agronomique)-CNRS, UMR1165, Unite de Recherche en Genomique Vegetale, 2 rue Gaston Cremieux, F-91057 Evry, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18687965" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Binding Sites ; Biological Evolution ; Crosses, Genetic ; Cucumis melo/*enzymology/genetics/*physiology ; Flowers/genetics/growth & development/*physiology ; Genes, Plant ; Haplotypes ; Lyases/chemistry/*genetics/metabolism ; Molecular Sequence Data ; *Mutation ; Phylogeny ; *Polymorphism, Single Nucleotide ; Reverse Transcriptase Polymerase Chain Reaction ; Selection, Genetic ; Sequence Analysis, DNA
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    Concurrent fast and slow cycling of a transcriptional activator at an endogenous promoter (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-01-26
    Description: For gene regulation, some transcriptional activators bind periodically to promoters with either a fast (approximately 1 minute) or a slow (approximately 15 to 90 minutes) cycle. It is uncertain whether the fast cycle occurs on natural promoters, and the function of either cycle in transcription remains unclear. We report that fast and slow cycling can occur simultaneously on an endogenous yeast promoter and that slow cycling in this system reflects an oscillation in the fraction of accessible promoters rather than the recruitment and release of stably bound transcriptional activators. This observation, combined with single-cell measurements of messenger RNA (mRNA) production, argues that fast cycling initiates transcription and that slow cycling regulates the quantity of mRNA produced. These findings counter the prevailing view that slow cycling initiates transcription.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Karpova, Tatiana S -- Kim, Min J -- Spriet, Corentin -- Nalley, Kip -- Stasevich, Timothy J -- Kherrouche, Zoulika -- Heliot, Laurent -- McNally, James G -- New York, N.Y. -- Science. 2008 Jan 25;319(5862):466-9. doi: 10.1126/science.1150559.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Cancer Research Core Imaging Facility, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18218898" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carrier Proteins/*genetics ; Chromatin Immunoprecipitation ; Chromosomal Proteins, Non-Histone/metabolism ; Copper/metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Fluorescence Recovery After Photobleaching ; Metallothionein ; *Promoter Regions, Genetic ; Protein Binding ; RNA, Fungal/biosynthesis ; RNA, Messenger/biosynthesis ; Recombinant Fusion Proteins ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Time Factors ; Transcription Factors/genetics/*metabolism ; *Transcription, Genetic
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    Structural biology. Symmetric transporters for asymmetric transport (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-08-09
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2630483/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2630483/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Karpowich, Nathan K -- Wang, Da-Neng -- DK053973/DK/NIDDK NIH HHS/ -- GM075026/GM/NIGMS NIH HHS/ -- GM075936/GM/NIGMS NIH HHS/ -- MH083840/MH/NIMH NIH HHS/ -- R01 DK053973/DK/NIDDK NIH HHS/ -- R01 DK053973-09/DK/NIDDK NIH HHS/ -- R01 MH083840/MH/NIMH NIH HHS/ -- R01 MH083840-01/MH/NIMH NIH HHS/ -- R21 GM075936/GM/NIGMS NIH HHS/ -- R21 GM075936-02S1/GM/NIGMS NIH HHS/ -- U54 GM075026/GM/NIGMS NIH HHS/ -- U54 GM075026-040010/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Aug 8;321(5890):781-2. doi: 10.1126/science.1161495.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA. karpowic@saturn.med.nyu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18687947" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Cell Membrane/*metabolism ; Galactose/*metabolism ; Glucose/metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Intestinal Absorption ; Intestinal Mucosa/metabolism ; Kidney/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sodium/metabolism ; Sodium-Glucose Transport Proteins/*chemistry/metabolism ; Sodium-Glucose Transporter 1/metabolism ; Sodium-Glucose Transporter 2/*metabolism ; Vibrio parahaemolyticus/*chemistry/metabolism
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    Biochemistry. RT slides home (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-11-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sarafianos, Stefan G -- Arnold, Eddy -- New York, N.Y. -- Science. 2008 Nov 14;322(5904):1059-60. doi: 10.1126/science.1167454.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Christopher S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA. sarafianoss@missouri.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19008434" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; DNA, Viral/*metabolism ; Fluorescence Resonance Energy Transfer ; HIV Reverse Transcriptase/chemistry/*metabolism ; HIV-1/*enzymology ; Models, Molecular ; Nevirapine/metabolism/pharmacology ; Oligonucleotides/metabolism ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Viral/*metabolism ; Reverse Transcriptase Inhibitors/metabolism/pharmacology
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    The role of fisheries-induced evolution (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-04-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Browman, Howard I -- Law, Richard -- Marshall, C Tara -- New York, N.Y. -- Science. 2008 Apr 4;320(5872):47-50; author reply 47-50. doi: 10.1126/science.320.5872.47b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18388275" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Ecosystem ; *Fisheries ; *Fishes ; Phenotype
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    A localized negative genetic correlation constrains microevolution of coat color in wild sheep (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-01-19
    Description: The evolutionary changes that occur over a small number of generations in natural populations often run counter to what is expected on the basis of the heritability of traits and the selective forces acting upon them. In Soay sheep, dark coat color is associated with large size, which is heritable and positively correlated with fitness, yet the frequency of dark sheep has decreased. This unexpected microevolutionary trend is explained by genetic linkage between the causal mutation underlying the color polymorphism and quantitative trait loci with antagonistic effects on size and fitness. As a consequence, homozygous dark sheep are large, but have reduced fitness relative to phenotypically indistinguishable dark heterozygotes and light sheep. This result demonstrates the importance of understanding the genetic basis of fitness variation when making predictions about the microevolutionary consequences of selection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gratten, J -- Wilson, A J -- McRae, A F -- Beraldi, D -- Visscher, P M -- Pemberton, J M -- Slate, J -- New York, N.Y. -- Science. 2008 Jan 18;319(5861):318-20. doi: 10.1126/science.1151182.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18202287" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Wild/genetics/physiology ; *Biological Evolution ; Birth Weight/genetics ; Body Size/genetics ; Female ; Genetic Linkage ; Genotype ; Hair Color/*genetics ; Heterozygote ; Homozygote ; Linear Models ; Male ; Oxidoreductases/genetics ; Phenotype ; Quantitative Trait Loci ; Reproduction ; Scotland ; Selection, Genetic ; Sheep/*genetics/physiology
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    Superiority, competition, and opportunism in the evolutionary radiation of dinosaurs (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-09-13
    Description: The rise and diversification of the dinosaurs in the Late Triassic, from 230 to 200 million years ago, is a classic example of an evolutionary radiation with supposed competitive replacement. A comparison of evolutionary rates and morphological disparity of basal dinosaurs and their chief "competitors," the crurotarsan archosaurs, shows that dinosaurs exhibited lower disparity and an indistinguishable rate of character evolution. The radiation of Triassic archosaurs as a whole is characterized by declining evolutionary rates and increasing disparity, suggesting a decoupling of character evolution from body plan variety. The results strongly suggest that historical contingency, rather than prolonged competition or general "superiority," was the primary factor in the rise of dinosaurs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brusatte, Stephen L -- Benton, Michael J -- Ruta, Marcello -- Lloyd, Graeme T -- New York, N.Y. -- Science. 2008 Sep 12;321(5895):1485-8. doi: 10.1126/science.1161833.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK. brusatte@uchicago.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18787166" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Animals ; *Biological Evolution ; *Dinosaurs/anatomy & histology/classification ; Extinction, Biological ; Paleontology ; Phylogeny
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    Paleontology. Life's innovations let it diversify, at least up to a point (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kerr, Richard A -- New York, N.Y. -- Science. 2008 Jul 4;321(5885):24-5. doi: 10.1126/science.321.5885.24a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18599746" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Biological Evolution ; Databases, Factual ; *Fossils ; Geologic Sediments ; *Invertebrates ; *Paleontology/methods ; Seawater ; Selection Bias
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    Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-15
    Description: The reverse transcriptase (RT) of human immunodeficiency virus (HIV) catalyzes a series of reactions to convert single-stranded viral RNA into double-stranded DNA for host cell integration. This process requires a variety of enzymatic activities, including DNA polymerization, RNA cleavage, strand transfer, and strand displacement synthesis. We used single-molecule fluorescence resonance energy transfer to probe the interactions between RT and nucleic acid substrates in real time. RT was observed to slide on nucleic acid duplexes, rapidly shuttling between opposite termini of the duplex. Upon reaching the DNA 3' terminus, RT can spontaneously flip into a polymerization orientation. Sliding kinetics were regulated by cognate nucleotides and anti-HIV drugs, which stabilized and destabilized the polymerization mode, respectively. These long-range translocation activities facilitate multiple stages of the reverse transcription pathway, including normal DNA polymerization and strand displacement synthesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2717043/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2717043/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Shixin -- Abbondanzieri, Elio A -- Rausch, Jason W -- Le Grice, Stuart F J -- Zhuang, Xiaowei -- GM 068518/GM/NIGMS NIH HHS/ -- R01 GM068518/GM/NIGMS NIH HHS/ -- R01 GM068518-05/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2008 Nov 14;322(5904):1092-7. doi: 10.1126/science.1163108.〈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/19008444" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carbocyanines ; DNA Primers/metabolism ; DNA, Viral/biosynthesis/*metabolism ; Fluorescence Resonance Energy Transfer ; Fluorescent Dyes ; HIV Reverse Transcriptase/chemistry/*metabolism ; HIV-1/*enzymology ; Kinetics ; Models, Molecular ; Nevirapine/metabolism/pharmacology ; Nucleic Acid Hybridization ; Nucleotides/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Viral/*metabolism ; Reverse Transcriptase Inhibitors/metabolism/pharmacology ; Reverse Transcription ; Ribonuclease H/chemistry/metabolism
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    Variation in evolutionary patterns across the geographic range of a fossil bivalve (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-25
    Description: The fossil record is the only direct source of data for studying modes (patterns) and rates of morphological change over long periods of time. Determining modes and rates is important for understanding macroevolutionary processes, but just how modes and rates vary within a taxon, and why, remain largely unaddressed. We examined patterns of morphological change in the shell of the Mesozoic marine bivalve genus Buchia over its geographic and temporal range. Most modes conformed to either random walks or stasis, and both modes and rates showed variability between locations. For example, stasis was more common in deeper marine environments, whereas random walks occurred more often at the highest paleolatitudes studied. These results indicate that the environment can play an important role in shaping patterns of evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grey, Melissa -- Haggart, James W -- Smith, Paul L -- New York, N.Y. -- Science. 2008 Nov 21;322(5905):1238-41. doi: 10.1126/science.1162046. Epub 2008 Oct 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth and Ocean Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada. mgrey@eos.ubc.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18948502" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Bivalvia/anatomy & histology ; Ecosystem ; *Fossils
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    Biochemistry. An almost-complete movie (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-12-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Diallinas, George -- New York, N.Y. -- Science. 2008 Dec 12;322(5908):1644-5. doi: 10.1126/science.1168107.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Faculty of Biology, University of Athens, Panepistimioupolis 15781, Athens, Greece. diallina@biol.uoa.gr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19074336" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Transport System X-AG/chemistry/metabolism ; Amino Acid Transport Systems/chemistry/metabolism ; Bacterial Proteins/*chemistry/*metabolism ; Binding Sites ; Cation Transport Proteins/chemistry/metabolism ; Computer Simulation ; Crystallography, X-Ray ; Ion Channel Gating ; Membrane Transport Proteins/*chemistry/*metabolism ; Models, Molecular ; Protein Conformation ; Protein Structure, Tertiary ; Sodium-Glucose Transport Proteins/chemistry/metabolism ; Symporters/chemistry/metabolism
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    The crystal structure of a mammalian fatty acid synthase (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-09-06
    Description: Mammalian fatty acid synthase is a large multienzyme that catalyzes all steps of fatty acid synthesis. We have determined its crystal structure at 3.2 angstrom resolution covering five catalytic domains, whereas the flexibly tethered terminal acyl carrier protein and thioesterase domains remain unresolved. The structure reveals a complex architecture of alternating linkers and enzymatic domains. Substrate shuttling is facilitated by flexible tethering of the acyl carrier protein domain and by the limited contact between the condensing and modifying portions of the multienzyme, which are mainly connected by linkers rather than direct interaction. The structure identifies two additional nonenzymatic domains: (i) a pseudo-ketoreductase and (ii) a peripheral pseudo-methyltransferase that is probably a remnant of an ancestral methyltransferase domain maintained in some related polyketide synthases. The structural comparison of mammalian fatty acid synthase with modular polyketide synthases shows how their segmental construction allows the variation of domain composition to achieve diverse product synthesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maier, Timm -- Leibundgut, Marc -- Ban, Nenad -- New York, N.Y. -- Science. 2008 Sep 5;321(5894):1315-22. doi: 10.1126/science.1161269.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, ETH Zurich, 8092 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18772430" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl Carrier Protein/chemistry/metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Dimerization ; Evolution, Molecular ; Fatty Acid Synthase, Type I/*chemistry ; Fatty Acids/biosynthesis ; Methyltransferases/chemistry ; Models, Molecular ; Molecular Sequence Data ; NADP/chemistry/metabolism ; Polyketide Synthases/chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Swine/*metabolism
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    Science and religion. Bracing for Islamic creationism (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-12-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hameed, Salman -- New York, N.Y. -- Science. 2008 Dec 12;322(5908):1637-8. doi: 10.1126/science.1163672.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Cognitive Science and School of Natural Science, Hampshire College, Amherst, MA 01002, USA. shameed@hampshire.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19074331" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Biology/*education ; Humans ; *Islam ; *Religion and Science ; Teaching
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    Antigen recognition by variable lymphocyte receptors (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-09-27
    Description: Variable lymphocyte receptors (VLRs) rather than antibodies play the primary role in recognition of antigens in the adaptive immune system of jawless vertebrates. Combinatorial assembly of leucine-rich repeat (LRR) gene segments achieves the required repertoire for antigen recognition. We have determined a crystal structure for a VLR-antigen complex, VLR RBC36 in complex with the H-antigen trisaccharide from human blood type O erythrocytes, at 1.67 angstrom resolution. RBC36 binds the H-trisaccharide on the concave surface of the LRR modules of the solenoid structure where three key hydrophilic residues, multiple van der Waals interactions, and the highly variable insert of the carboxyl-terminal LRR module determine antigen recognition and specificity. The concave surface assembled from the most highly variable regions of the LRRs, along with diversity in the sequence and length of the highly variable insert, can account for the recognition of diverse antigens by VLRs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581502/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581502/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Han, Byung Woo -- Herrin, Brantley R -- Cooper, Max D -- Wilson, Ian A -- AI072435/AI/NIAID NIH HHS/ -- AI42266/AI/NIAID NIH HHS/ -- R37 AI042266/AI/NIAID NIH HHS/ -- R37 AI042266-11/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2008 Sep 26;321(5897):1834-7. doi: 10.1126/science.1162484.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18818359" target="_blank"〉PubMed〈/a〉
    Keywords: ABO Blood-Group System/chemistry/*immunology/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Lampreys/*immunology ; Lymphocytes/*immunology ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Antigen/*chemistry/*immunology/metabolism ; Trisaccharides/chemistry/*immunology/metabolism
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    Physiological sex predicts hybrid sterility regardless of genotype (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-01-05
    Description: Reproductive isolation between biological species is characterized by Haldane's rule, which states that the heterogametic sex (XY or ZW) suffers the most dysfunctional effects of hybridization. It has been hypothesized that, in addition to X-linked recessive genes, Haldane's rule also reflects the faster evolution of genes related to male reproduction (faster-male evolution). We used sex-reversed hybrid Xenopus to test faster-male evolution by examining the fertility of sex-reversed individuals with the genotype of the inverse phenotypic sex. Hybrid males are sterile and hybrid females are fertile irrespective of their genotypic sex. Gene expression profiles match these adult phenotypes, and our results demonstrate that faster-male evolution is the most likely mechanism producing hybrid male sterility.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Malone, John H -- Michalak, P -- New York, N.Y. -- Science. 2008 Jan 4;319(5859):59. doi: 10.1126/science.1148231.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Texas at Arlington, Box 19498, Arlington, TX 76019, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18174434" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Crosses, Genetic ; Disorders of Sex Development ; Female ; Fertility ; Fertilization ; Gene Expression ; Genotype ; *Hybridization, Genetic ; *Infertility, Male ; Male ; Oogenesis ; Phenotype ; Selection, Genetic ; Sex Characteristics ; Spermatogenesis ; Xenopus/*genetics/physiology ; Xenopus laevis/*genetics/physiology
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    An inhibitor of FtsZ with potent and selective anti-staphylococcal activity (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-09-20
    Description: FtsZ is an essential bacterial guanosine triphosphatase and homolog of mammalian beta-tubulin that polymerizes and assembles into a ring to initiate cell division. We have created a class of small synthetic antibacterials, exemplified by PC190723, which inhibits FtsZ and prevents cell division. PC190723 has potent and selective in vitro bactericidal activity against staphylococci, including methicillin- and multi-drug-resistant Staphylococcus aureus. The putative inhibitor-binding site of PC190723 was mapped to a region of FtsZ that is analogous to the Taxol-binding site of tubulin. PC190723 was efficacious in an in vivo model of infection, curing mice infected with a lethal dose of S. aureus. The data validate FtsZ as a target for antibacterial intervention and identify PC190723 as suitable for optimization into a new anti-staphylococcal therapy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haydon, David J -- Stokes, Neil R -- Ure, Rebecca -- Galbraith, Greta -- Bennett, James M -- Brown, David R -- Baker, Patrick J -- Barynin, Vladimir V -- Rice, David W -- Sedelnikova, Sveta E -- Heal, Jonathan R -- Sheridan, Joseph M -- Aiwale, Sachin T -- Chauhan, Pramod K -- Srivastava, Anil -- Taneja, Amit -- Collins, Ian -- Errington, Jeff -- Czaplewski, Lloyd G -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2008 Sep 19;321(5896):1673-5. doi: 10.1126/science.1159961.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Prolysis, Begbroke Science Park, Oxfordshire OX5 1PF, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18801997" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; Bacillus subtilis/chemistry/*drug effects/genetics ; Bacterial Proteins/*antagonists & inhibitors/chemistry/genetics/metabolism ; Binding Sites ; Cell Division/drug effects ; Crystallography, X-Ray ; Cytoskeletal Proteins/*antagonists & inhibitors/chemistry/genetics/metabolism ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial ; Ligands ; Methicillin Resistance ; Mice ; Microbial Sensitivity Tests ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Pyridines/chemistry/metabolism/*pharmacology/therapeutic use ; Staphylococcal Infections/*drug therapy ; Staphylococcus aureus/chemistry/*drug effects ; Thiazoles/chemistry/metabolism/*pharmacology/therapeutic use ; Tubulin/chemistry/metabolism
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    The Avalon explosion: evolution of Ediacara morphospace (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-01-05
    Description: Ediacara fossils [575 to 542 million years ago (Ma)] represent Earth's oldest known complex macroscopic life forms, but their morphological history is poorly understood. A comprehensive quantitative analysis of these fossils indicates that the oldest Ediacara assemblage-the Avalon assemblage (575 to 565 Ma)-already encompassed the full range of Ediacara morphospace. A comparable morphospace range was occupied by the subsequent White Sea (560 to 550 Ma) and Nama (550 to 542 Ma) assemblages, although it was populated differently. In contrast, taxonomic richness increased in the White Sea assemblage and declined in the Nama assemblage. These diversity changes, occurring while morphospace range remained relatively constant, led to inverse shifts in morphological variance. The Avalon morphospace expansion mirrors the Cambrian explosion, and both events may reflect similar underlying mechanisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shen, Bing -- Dong, Lin -- Xiao, Shuhai -- Kowalewski, Michal -- New York, N.Y. -- Science. 2008 Jan 4;319(5859):81-4. doi: 10.1126/science.1150279.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geosciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18174439" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Biological Evolution ; *Ecosystem ; *Fossils ; Seawater
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    Convergence of Campylobacter species: implications for bacterial evolution (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-04-12
    Description: The nature of species boundaries in bacteria remains controversial. In particular, the mechanisms of bacterial speciation and maintenance in the face of frequent genetic exchange are poorly understood. Here, we report patterns of genetic exchange that show two closely related zoonotic pathogenic species, Campylobacter jejuni and Campylobacter coli, are converging as a consequence of recent changes in gene flow. Population expansion into a novel ecological niche generated by human activity is the most probable explanation for the increase in genetic exchange between these species. Bacterial speciation can therefore occur by mechanisms analogous to those seen in metazoans, where genetic diversification and incipient speciation caused by ecological factors have been reported in several genera.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sheppard, Samuel K -- McCarthy, Noel D -- Falush, Daniel -- Maiden, Martin C J -- 047072/Wellcome Trust/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2008 Apr 11;320(5873):237-9. doi: 10.1126/science.1155532.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Zoology and Statistics, University of Oxford, Peter Medawar Building, South Parks Road, Oxford OX1 3SY, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18403712" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture ; Alleles ; Animals ; *Biological Evolution ; Campylobacter coli/classification/*genetics/isolation & purification ; Campylobacter jejuni/classification/*genetics/isolation & purification ; Cluster Analysis ; Gene Flow ; Genes, Bacterial ; *Genetic Speciation ; Genetic Variation ; Haplotypes ; Humans ; *Hybridization, Genetic ; Intestines/microbiology ; Recombination, Genetic
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    The crystal structure of [Fe]-hydrogenase reveals the geometry of the active site (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-07-26
    Description: Biological formation and consumption of molecular hydrogen (H2) are catalyzed by hydrogenases, of which three phylogenetically unrelated types are known: [NiFe]-hydrogenases, [FeFe]-hydrogenases, and [Fe]-hydrogenase. We present a crystal structure of [Fe]-hydrogenase at 1.75 angstrom resolution, showing a mononuclear iron coordinated by the sulfur of cysteine 176, two carbon monoxide (CO) molecules, and the sp2-hybridized nitrogen of a 2-pyridinol compound with back-bonding properties similar to those of cyanide. The three-dimensional arrangement of the ligands is similar to that of thiolate, CO, and cyanide ligated to the low-spin iron in binuclear [NiFe]- and [FeFe]-hydrogenases, although the enzymes have evolved independently and the CO and cyanide ligands are not found in any other metalloenzyme. The related iron ligation pattern of hydrogenases exemplifies convergent evolution and presumably plays an essential role in H2 activation. This finding may stimulate the ongoing synthesis of catalysts that could substitute for platinum in applications such as fuel cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shima, Seigo -- Pilak, Oliver -- Vogt, Sonja -- Schick, Michael -- Stagni, Marco S -- Meyer-Klaucke, Wolfram -- Warkentin, Eberhard -- Thauer, Rudolf K -- Ermler, Ulrich -- New York, N.Y. -- Science. 2008 Jul 25;321(5888):572-5. doi: 10.1126/science.1158978.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Terrestrische Mikrobiologie and Laboratorium fur Mikrobiologie, Fachbereich Biologie, Philipps-Universitat Marburg, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany. shima@mpi-marburg.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18653896" target="_blank"〉PubMed〈/a〉
    Keywords: Apoenzymes/chemistry ; Binding Sites ; Carbon Monoxide/chemistry ; Catalytic Domain ; Coenzymes/chemistry ; Crystallography, X-Ray ; Cyanides/chemistry/metabolism ; Dimerization ; Evolution, Molecular ; Holoenzymes/chemistry ; Hydrogen/chemistry/*metabolism ; Hydrogenase/*chemistry/isolation & purification/metabolism ; Iron/chemistry ; Ligands ; Methane/biosynthesis ; Methanococcales/*enzymology ; Models, Molecular ; Oxidation-Reduction ; Protein Structure, Secondary ; Protein Structure, Tertiary
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    Pardis Sabeti profile. Picking up evolution's beat (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-04-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Balter, Michael -- New York, N.Y. -- Science. 2008 Apr 25;320(5875):442-3. doi: 10.1126/science.320.5875.442.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18436753" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Genome, Human ; History, 21st Century ; Humans ; Iran ; Research Support as Topic ; Selection, Genetic ; United States
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    AAAS annual meeting. How human intelligence evolved--is it science or 'paleofantasy'? (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-02-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Balter, Michael -- New York, N.Y. -- Science. 2008 Feb 22;319(5866):1028. doi: 10.1126/science.319.5866.1028a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18292315" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Brain/embryology/growth & development ; Climate ; *Cognition ; Humans ; *Intelligence ; Nerve Tissue Proteins/genetics ; Selection, Genetic
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    Human evolution. Why we're different: probing the gap between apes and humans (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-01-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Balter, Michael -- New York, N.Y. -- Science. 2008 Jan 25;319(5862):404-5. doi: 10.1126/science.319.5862.404.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18218876" target="_blank"〉PubMed〈/a〉
    Keywords: Altruism ; Animals ; *Behavior, Animal ; *Biological Evolution ; Cooperative Behavior ; Cultural Evolution ; *Hominidae/psychology ; Humans ; Imitative Behavior ; *Learning ; Reward ; *Social Behavior
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Biochemistry. A natural choice for activating hydrogen (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Armstrong, Fraser A -- Fontecilla-Camps, Juan C -- New York, N.Y. -- Science. 2008 Jul 25;321(5888):498-9. doi: 10.1126/science.1161326.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QR, UK. fraser.armstrong@chem.ox.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18653870" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carbon Dioxide/metabolism ; Carbon Monoxide/chemistry/metabolism ; Crystallography, X-Ray ; Cyanides/chemistry/metabolism ; Hydrogen/*metabolism ; Hydrogenase/*chemistry/*metabolism ; Iron/chemistry ; Ligands ; Methane/*biosynthesis ; Oxidation-Reduction
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    The microbial engines that drive Earth's biogeochemical cycles (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-05-24
    Description: Virtually all nonequilibrium electron transfers on Earth are driven by a set of nanobiological machines composed largely of multimeric protein complexes associated with a small number of prosthetic groups. These machines evolved exclusively in microbes early in our planet's history yet, despite their antiquity, are highly conserved. Hence, although there is enormous genetic diversity in nature, there remains a relatively stable set of core genes coding for the major redox reactions essential for life and biogeochemical cycles. These genes created and coevolved with biogeochemical cycles and were passed from microbe to microbe primarily by horizontal gene transfer. A major challenge in the coming decades is to understand how these machines evolved, how they work, and the processes that control their activity on both molecular and planetary scales.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Falkowski, Paul G -- Fenchel, Tom -- Delong, Edward F -- New York, N.Y. -- Science. 2008 May 23;320(5879):1034-9. doi: 10.1126/science.1153213.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal Sciences and Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ 08901, USA. falko@marine.rutgers.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497287" target="_blank"〉PubMed〈/a〉
    Keywords: Archaea/genetics/*metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Atmosphere ; Bacteria/genetics/*metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; *Biological Evolution ; *Earth (Planet) ; Ecosystem ; Elements ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Genetic Variation ; Geological Phenomena ; Geology ; *Metabolic Networks and Pathways ; Oxidation-Reduction ; Photosynthesis ; Thermodynamics
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Shadow enhancers as a source of evolutionary novelty (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-09-06
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257485/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257485/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hong, Joung-Woo -- Hendrix, David A -- Levine, Michael S -- GM46638/GM/NIGMS NIH HHS/ -- R01 GM046638/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Sep 5;321(5894):1314. doi: 10.1126/science.1160631.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, Division of Genetics, Genomics, and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18772429" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Body Patterning/genetics ; Chromatin Immunoprecipitation ; Computational Biology ; Drosophila/embryology/*genetics ; Drosophila Proteins/*metabolism ; Drosophila melanogaster/embryology/*genetics ; Embryonic Development ; *Enhancer Elements, Genetic ; *Evolution, Molecular ; Gene Expression Regulation, Developmental ; Introns ; Nuclear Proteins/*metabolism ; Oligonucleotide Array Sequence Analysis ; Phosphoproteins/*metabolism ; Phylogeny ; Transcription Factors/*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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    Evolution and faith: empathy is misplaced (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-05-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stevens, Craig W -- New York, N.Y. -- Science. 2008 May 9;320(5877):745. doi: 10.1126/science.320.5877.745b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18467570" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Christianity ; *Religion and Science
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    A competitive inhibitor traps LeuT in an open-to-out conformation (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-12-17
    Description: Secondary transporters are workhorses of cellular membranes, catalyzing the movement of small molecules and ions across the bilayer and coupling substrate passage to ion gradients. However, the conformational changes that accompany substrate transport, the mechanism by which a substrate moves through the transporter, and principles of competitive inhibition remain unclear. We used crystallographic and functional studies on the leucine transporter (LeuT), a model for neurotransmitter sodium symporters, to show that various amino acid substrates induce the same occluded conformational state and that a competitive inhibitor, tryptophan (Trp), traps LeuT in an open-to-out conformation. In the Trp complex, the extracellular gate residues arginine 30 and aspartic acid 404 define a second weak binding site for substrates or inhibitors as they permeate from the extracellular solution to the primary substrate site, which demonstrates how residues that participate in gating also mediate permeation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832577/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832577/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Singh, Satinder K -- Piscitelli, Chayne L -- Yamashita, Atsuko -- Gouaux, Eric -- K99 MH083050-02/MH/NIMH NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 MH070039/MH/NIMH NIH HHS/ -- R01 MH070039-05/MH/NIMH NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Dec 12;322(5908):1655-61. doi: 10.1126/science.1166777.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vollum Institute, Oregon Health and Science University, 3181 Southwest Sam Jackson Park Road, Portland, OR 97239, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19074341" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Transport Systems/antagonists & inhibitors/*chemistry/*metabolism ; Amino Acids/metabolism/pharmacology ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Binding, Competitive ; Biological Transport ; Crystallization ; Crystallography, X-Ray ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Leucine/*metabolism ; Ligands ; Models, Biological ; Models, Molecular ; Protein Conformation ; Protein Structure, Tertiary ; Sodium/metabolism ; Symporters/antagonists & inhibitors/*chemistry/*metabolism ; Tryptophan/metabolism/*pharmacology
    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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    Solution structure of the integral human membrane protein VDAC-1 in detergent micelles (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-08-30
    Description: The voltage-dependent anion channel (VDAC) mediates trafficking of small molecules and ions across the eukaryotic outer mitochondrial membrane. VDAC also interacts with antiapoptotic proteins from the Bcl-2 family, and this interaction inhibits release of apoptogenic proteins from the mitochondrion. We present the nuclear magnetic resonance (NMR) solution structure of recombinant human VDAC-1 reconstituted in detergent micelles. It forms a 19-stranded beta barrel with the first and last strand parallel. The hydrophobic outside perimeter of the barrel is covered by detergent molecules in a beltlike fashion. In the presence of cholesterol, recombinant VDAC-1 can form voltage-gated channels in phospholipid bilayers similar to those of the native protein. NMR measurements revealed the binding sites of VDAC-1 for the Bcl-2 protein Bcl-x(L), for reduced beta-nicotinamide adenine dinucleotide, and for cholesterol. Bcl-x(L) interacts with the VDAC barrel laterally at strands 17 and 18.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2579273/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2579273/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hiller, Sebastian -- Garces, Robert G -- Malia, Thomas J -- Orekhov, Vladislav Y -- Colombini, Marco -- Wagner, Gerhard -- EB002026/EB/NIBIB NIH HHS/ -- GM066360/GM/NIGMS NIH HHS/ -- GM075879/GM/NIGMS NIH HHS/ -- GM47467/GM/NIGMS NIH HHS/ -- P01 GM047467/GM/NIGMS NIH HHS/ -- P01 GM047467-11/GM/NIGMS NIH HHS/ -- P01 GM047467-12/GM/NIGMS NIH HHS/ -- P01 GM047467-12S2/GM/NIGMS NIH HHS/ -- P01 GM047467-13/GM/NIGMS NIH HHS/ -- P01 GM047467-14/GM/NIGMS NIH HHS/ -- P01 GM047467-14S1/GM/NIGMS NIH HHS/ -- P01 GM047467-15/GM/NIGMS NIH HHS/ -- P01 GM047467-16/GM/NIGMS NIH HHS/ -- P01 GM047467-17/GM/NIGMS NIH HHS/ -- P41 EB002026/EB/NIBIB NIH HHS/ -- P41 EB002026-28/EB/NIBIB NIH HHS/ -- P41 EB002026-29/EB/NIBIB NIH HHS/ -- P41 EB002026-30/EB/NIBIB NIH HHS/ -- P41 EB002026-31/EB/NIBIB NIH HHS/ -- P41 EB002026-32/EB/NIBIB NIH HHS/ -- P41 EB002026-33/EB/NIBIB NIH HHS/ -- P41 GM066360/GM/NIGMS NIH HHS/ -- P41 GM066360-01/GM/NIGMS NIH HHS/ -- P41 GM066360-02/GM/NIGMS NIH HHS/ -- P41 GM066360-03/GM/NIGMS NIH HHS/ -- P41 GM066360-04/GM/NIGMS NIH HHS/ -- P41 GM066360-05/GM/NIGMS NIH HHS/ -- R01 GM075879/GM/NIGMS NIH HHS/ -- R01 GM075879-01/GM/NIGMS NIH HHS/ -- R01 GM075879-02/GM/NIGMS NIH HHS/ -- R01 GM075879-03/GM/NIGMS NIH HHS/ -- R01 GM075879-04/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Aug 29;321(5893):1206-10. doi: 10.1126/science.1161302.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18755977" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Cholesterol/metabolism ; Detergents ; Dimethylamines ; Humans ; Hydrophobic and Hydrophilic Interactions ; Ion Channel Gating ; Lipid Bilayers ; Micelles ; Molecular Sequence Data ; NAD/metabolism ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Recombinant Proteins/chemistry/metabolism ; Static Electricity ; Voltage-Dependent Anion Channel 1/*chemistry/*metabolism ; bcl-X Protein/metabolism
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    Selfish genetic elements promote polyandry in a fly (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-22
    Description: It is unknown why females mate with multiple males when mating is frequently costly and a single copulation often provides enough sperm to fertilize all a female's eggs. One possibility is that remating increases the fitness of offspring, because fertilization success is biased toward the sperm of high-fitness males. We show that female Drosophila pseudoobscura evolved increased remating rates when exposed to the risk of mating with males carrying a deleterious sex ratio-distorting gene that also reduces sperm competitive ability. Because selfish genetic elements that reduce sperm competitive ability are generally associated with low genetic fitness, they may represent a common driver of the evolution of polyandry.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Price, T A R -- Hodgson, D J -- Lewis, Z -- Hurst, G D D -- Wedell, N -- New York, N.Y. -- Science. 2008 Nov 21;322(5905):1241-3. doi: 10.1126/science.1163766.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biosciences, University of Exeter, Cornwall Campus, Penryn TR10 9EZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19023079" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Drosophila ; Female ; Male ; *Repetitive Sequences, Nucleic Acid ; *Sexual Behavior, Animal ; Sperm Count
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    Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-03-15
    Description: Scaffold proteins link signaling molecules into linear pathways by physically assembling them into complexes. Scaffolds may also have a higher-order role as signal-processing hubs, serving as the target of feedback loops that optimize signaling amplitude and timing. We demonstrate that the Ste5 scaffold protein can be used as a platform to systematically reshape output of the yeast mating MAP kinase pathway. We constructed synthetic positive- and negative-feedback loops by dynamically regulating recruitment of pathway modulators to an artificial binding site on Ste5. These engineered circuits yielded diverse behaviors: ultrasensitive dose response, accelerated or delayed response times, and tunable adaptation. Protein scaffolds provide a flexible platform for reprogramming cellular responses and could be exploited to engineer cells with novel therapeutic and biotechnological functions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bashor, Caleb J -- Helman, Noah C -- Yan, Shude -- Lim, Wendell A -- New York, N.Y. -- Science. 2008 Mar 14;319(5869):1539-43. doi: 10.1126/science.1151153.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, University of California at San Francisco, 600 16th Street, San Francisco, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18339942" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Adaptor Proteins, Signal Transducing/chemistry/*metabolism ; Binding Sites ; *Feedback, Physiological ; Intracellular Signaling Peptides and Proteins/*metabolism ; Leucine Zippers ; MAP Kinase Kinase Kinases/metabolism ; *MAP Kinase Signaling System ; Mitogen-Activated Protein Kinases/metabolism ; Promoter Regions, Genetic ; Protein Precursors/metabolism/pharmacology ; Protein Tyrosine Phosphatases/metabolism ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism/pharmacology ; Systems Biology/methods
    Print ISSN: 0036-8075
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    Evolutionary origins for social vocalization in a vertebrate hindbrain-spinal compartment (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-19
    Description: The macroevolutionary events leading to neural innovations for social communication, such as vocalization, are essentially unexplored. Many fish vocalize during female courtship and territorial defense, as do amphibians, birds, and mammals. Here, we map the neural circuitry for vocalization in larval fish and show that the vocal network develops in a segment-like region across the most caudal hindbrain and rostral spinal cord. Taxonomic analysis demonstrates a highly conserved pattern between fish and all major lineages of vocal tetrapods. We propose that the vocal basis for acoustic communication among vertebrates evolved from an ancestrally shared developmental compartment already present in the early fishes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2582147/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2582147/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bass, Andrew H -- Gilland, Edwin H -- Baker, Robert -- R01 DC000092/DC/NIDCD NIH HHS/ -- R01 DC000092-33/DC/NIDCD NIH HHS/ -- New York, N.Y. -- Science. 2008 Jul 18;321(5887):417-21. doi: 10.1126/science.1157632.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA. ahb3@cornell.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18635807" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Batrachoidiformes/*anatomy & histology/growth & development/physiology ; *Biological Evolution ; Cerebellum/cytology/growth & development ; Motor Neurons/*cytology ; Nerve Net/*cytology/growth & development ; Neurons/*cytology ; Rhombencephalon/*cytology/growth & development ; Spinal Cord/*cytology/growth & development ; Vagus Nerve/cytology ; Vertebrates/anatomy & histology/growth & development/physiology ; *Vocalization, Animal
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    Structure and molecular mechanism of a nucleobase-cation-symport-1 family transporter (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-18
    Description: The nucleobase-cation-symport-1 (NCS1) transporters are essential components of salvage pathways for nucleobases and related metabolites. Here, we report the 2.85-angstrom resolution structure of the NCS1 benzyl-hydantoin transporter, Mhp1, from Microbacterium liquefaciens. Mhp1 contains 12 transmembrane helices, 10 of which are arranged in two inverted repeats of five helices. The structures of the outward-facing open and substrate-bound occluded conformations were solved, showing how the outward-facing cavity closes upon binding of substrate. Comparisons with the leucine transporter LeuT(Aa) and the galactose transporter vSGLT reveal that the outward- and inward-facing cavities are symmetrically arranged on opposite sides of the membrane. The reciprocal opening and closing of these cavities is synchronized by the inverted repeat helices 3 and 8, providing the structural basis of the alternating access model for membrane transport.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885439/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885439/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weyand, Simone -- Shimamura, Tatsuro -- Yajima, Shunsuke -- Suzuki, Shun'ichi -- Mirza, Osman -- Krusong, Kuakarun -- Carpenter, Elisabeth P -- Rutherford, Nicholas G -- Hadden, Jonathan M -- O'Reilly, John -- Ma, Pikyee -- Saidijam, Massoud -- Patching, Simon G -- Hope, Ryan J -- Norbertczak, Halina T -- Roach, Peter C J -- Iwata, So -- Henderson, Peter J F -- Cameron, Alexander D -- 062164/Z/00/Z/Wellcome Trust/United Kingdom -- 079209/Wellcome Trust/United Kingdom -- B17935/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/C51725/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G020043/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Oct 31;322(5902):709-13. doi: 10.1126/science.1164440. Epub 2008 Oct 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Membrane Protein Laboratory, Diamond Light Source Limited, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18927357" target="_blank"〉PubMed〈/a〉
    Keywords: Actinomycetales/*chemistry/metabolism ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Cations/chemistry/metabolism ; Cell Membrane/chemistry/metabolism ; Crystallography, X-Ray ; Hydantoins/chemistry/metabolism ; Ion Transport ; Models, Molecular ; Molecular Sequence Data ; Nucleobase Transport Proteins/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Sodium/metabolism ; Symporters/*chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Evolution and faith: empathy is crucial (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-05-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Whipple, Andrew -- New York, N.Y. -- Science. 2008 May 9;320(5877):745-6. doi: 10.1126/science.320.5877.745c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18467571" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Christianity ; *Religion and Science
    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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    From Darwinism to evolutionary biology (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-08-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kutschera, U -- New York, N.Y. -- Science. 2008 Aug 29;321(5893):1157-8. doi: 10.1126/science.321.5893.1157.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18755957" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Biology ; Plants ; Terminology as Topic
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Enzymes without borders: mobilizing substrates, delivering products (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-16
    Description: Many cellular reactions involve both hydrophobic and hydrophilic molecules that reside within the chemically distinct environments defined by the phospholipid-based membranes and the aqueous lumens of cytoplasm and organelles. Enzymes performing this type of reaction are required to access a lipophilic substrate located in the membranes and to catalyze its reaction with a polar, water-soluble compound. Here, we explore the different binding strategies and chemical tricks that enzymes have developed to overcome this problem. These reactions can be catalyzed by integral membrane proteins that channel a hydrophilic molecule into their active site, as well as by water-soluble enzymes that are able to capture a lipophilic substrate from the phospholipid bilayer. Many chemical and biological aspects of this type of enzymology remain to be investigated and will require the integration of protein chemistry with membrane biology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Forneris, Federico -- Mattevi, Andrea -- New York, N.Y. -- Science. 2008 Jul 11;321(5886):213-6. doi: 10.1126/science.1151118.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics and Microbiology, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18621661" target="_blank"〉PubMed〈/a〉
    Keywords: Alkyl and Aryl Transferases/chemistry/metabolism ; Amidohydrolases/chemistry/metabolism ; Binding Sites ; Catalytic Domain ; Cytosol/enzymology/metabolism ; Diffusion ; Enzymes/*chemistry/*metabolism ; Hydrophobic and Hydrophilic Interactions ; Hydroxysteroid Dehydrogenases/chemistry/metabolism ; Intracellular Membranes/enzymology/*metabolism ; Lipid Bilayers/*metabolism ; Membrane Proteins/chemistry/*metabolism ; Metalloproteases/chemistry/metabolism ; Models, Chemical ; Organelles/enzymology/*metabolism ; Peptidoglycan Glycosyltransferase/chemistry/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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    The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-10-04
    Description: The adenosine class of heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) mediates the important role of extracellular adenosine in many physiological processes and is antagonized by caffeine. We have determined the crystal structure of the human A2A adenosine receptor, in complex with a high-affinity subtype-selective antagonist, ZM241385, to 2.6 angstrom resolution. Four disulfide bridges in the extracellular domain, combined with a subtle repacking of the transmembrane helices relative to the adrenergic and rhodopsin receptor structures, define a pocket distinct from that of other structurally determined GPCRs. The arrangement allows for the binding of the antagonist in an extended conformation, perpendicular to the membrane plane. The binding site highlights an integral role for the extracellular loops, together with the helical core, in ligand recognition by this class of GPCRs and suggests a role for ZM241385 in restricting the movement of a tryptophan residue important in the activation mechanism of the class A receptors.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586971/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586971/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jaakola, Veli-Pekka -- Griffith, Mark T -- Hanson, Michael A -- Cherezov, Vadim -- Chien, Ellen Y T -- Lane, J Robert -- Ijzerman, Adriaan P -- Stevens, Raymond C -- GM075915/GM/NIGMS NIH HHS/ -- P50 GM073197/GM/NIGMS NIH HHS/ -- P50 GM073197-04/GM/NIGMS NIH HHS/ -- R01 GM089857/GM/NIGMS NIH HHS/ -- U54 GM074961/GM/NIGMS NIH HHS/ -- U54 GM074961-04/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Nov 21;322(5905):1211-7. doi: 10.1126/science.1164772. Epub 2008 Oct 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037 USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18832607" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine A2 Receptor Antagonists ; Animals ; Binding Sites ; Crystallography, X-Ray ; Humans ; Ligands ; Protein Binding ; Protein Conformation ; Receptor, Adenosine A2A/*chemistry ; Structure-Activity Relationship ; Triazines/chemistry ; Triazoles/chemistry ; Tryptophan/chemistry ; Turkeys
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Structural basis of trans-inhibition in a molybdate/tungstate ABC transporter (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-05-31
    Description: Transport across cellular membranes is an essential process that is catalyzed by diverse membrane transport proteins. The turnover rates of certain transporters are inhibited by their substrates in a process termed trans-inhibition, whose structural basis is poorly understood. We present the crystal structure of a molybdate/tungstate ABC transporter (ModBC) from Methanosarcina acetivorans in a trans-inhibited state. The regulatory domains of the nucleotide-binding subunits are in close contact and provide two oxyanion binding pockets at the shared interface. By specifically binding to these pockets, molybdate or tungstate prevent adenosine triphosphatase activity and lock the transporter in an inward-facing conformation, with the catalytic motifs of the nucleotide-binding domains separated. This allosteric effect prevents the transporter from switching between the inward-facing and the outward-facing states, thus interfering with the alternating access and release mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gerber, Sabina -- Comellas-Bigler, Mireia -- Goetz, Birke A -- Locher, Kaspar P -- New York, N.Y. -- Science. 2008 Jul 11;321(5886):246-50. doi: 10.1126/science.1156213. Epub 2008 May 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, ETH Zurich, HPK D14.3, 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18511655" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*antagonists & inhibitors/*chemistry/metabolism ; Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Archaeal Proteins/antagonists & inhibitors/*chemistry/metabolism ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Methanosarcina/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Molybdenum/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Tungsten Compounds/*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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    Spore show not gaming the science system (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-12-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rosenfeld, Michael -- New York, N.Y. -- Science. 2008 Dec 5;322(5907):1463. doi: 10.1126/science.322.5907.1463a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19056953" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Humans ; *Television ; *Video Games
    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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    Anthropology. The birth of childhood (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gibbons, Ann -- New York, N.Y. -- Science. 2008 Nov 14;322(5904):1040-3. doi: 10.1126/science.322.5904.1040.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19008424" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Brain/growth & development ; Child ; *Child Development ; Female ; *Fossils ; Hominidae/*growth & development ; Humans ; Male ; Paleodontology ; Pelvis/anatomy & histology ; *Reproduction ; Weaning
    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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