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  • *Biological Evolution  (49)
  • Binding Sites
  • American Association for the Advancement of Science (AAAS)  (87)
  • American Institute of Physics (AIP)
  • Oxford University Press
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  • American Association for the Advancement of Science (AAAS)  (87)
  • American Institute of Physics (AIP)
  • Oxford University Press
  • Nature Publishing Group (NPG)  (66)
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  • 2010-2014  (87)
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  • 1
    Publication Date: 2010-01-02
    Description: Meiotic recombination events cluster into narrow segments of the genome, defined as hotspots. Here, we demonstrate that a major player for hotspot specification is the Prdm9 gene. First, two mouse strains that differ in hotspot usage are polymorphic for the zinc finger DNA binding array of PRDM9. Second, the human consensus PRDM9 allele is predicted to recognize the 13-mer motif enriched at human hotspots; this DNA binding specificity is verified by in vitro studies. Third, allelic variants of PRDM9 zinc fingers are significantly associated with variability in genome-wide hotspot usage among humans. Our results provide a molecular basis for the distribution of meiotic recombination in mammals, in which the binding of PRDM9 to specific DNA sequences targets the initiation of recombination at specific locations in the genome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4295902/" 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/PMC4295902/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baudat, F -- Buard, J -- Grey, C -- Fledel-Alon, A -- Ober, C -- Przeworski, M -- Coop, G -- de Massy, B -- 03S1/PHS HHS/ -- GM83098/GM/NIGMS NIH HHS/ -- HD21244/HD/NICHD NIH HHS/ -- HL085197/HL/NHLBI NIH HHS/ -- R01 GM083098/GM/NIGMS NIH HHS/ -- R01 HD021244/HD/NICHD NIH HHS/ -- R01 HL085197/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Feb 12;327(5967):836-40. doi: 10.1126/science.1183439. Epub 2009 Dec 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Genetique Humaine, UPR1142, CNRS, Montpellier, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20044539" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; DNA/chemistry/metabolism ; DNA Breaks, Double-Stranded ; DNA-Binding Proteins/chemistry/genetics/metabolism ; Genome ; Genome, Human ; Genotype ; Histone-Lysine N-Methyltransferase/chemistry/*genetics/*metabolism ; Humans ; Meiosis/*genetics ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; Phenotype ; *Recombination, Genetic ; Zinc Fingers/genetics
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  • 2
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-05-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Balter, Michael -- New York, N.Y. -- Science. 2010 May 21;328(5981):969-71. doi: 10.1126/science.328.5981.969.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20489002" target="_blank"〉PubMed〈/a〉
    Keywords: *Animal Communication ; Animals ; *Biological Evolution ; Brain/anatomy & histology/physiology ; Child, Preschool ; Dominance, Cerebral ; *Gestures ; Hominidae/anatomy & histology/physiology ; Humans ; Infant ; *Language ; Language Development ; Sign Language ; Songbirds/anatomy & histology/physiology ; *Speech ; Vocalization, Animal
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  • 3
    Publication Date: 2010-10-23
    Description: CD4(+)Foxp3(+) regulatory T (T(reg)) cells are important for maintaining immune tolerance. Understanding the molecular mechanism that regulates T(reg) differentiation will facilitate the development of effective therapeutic strategies against autoimmune diseases. We report here that the SUMO E3 ligase PIAS1 restricts the differentiation of natural T(reg) cells by maintaining a repressive chromatin state of the Foxp3 promoter. PIAS1 acts by binding to the Foxp3 promoter to recruit DNA methyltransferases and heterochromatin protein 1 for epigenetic modifications. Pias1 deletion caused promoter demethylation, reduced histone H3 methylation at Lys(9), and enhanced promoter accessibility. Consistently, Pias1(-/-) mice displayed an increased natural T(reg) cell population and were resistant to the development of experimental autoimmune encephalomyelitis. Our studies have identified an epigenetic mechanism that negatively regulates the differentiation of natural T(reg) cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3043201/" 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/PMC3043201/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Bin -- Tahk, Samuel -- Yee, Kathleen M -- Fan, Guoping -- Shuai, Ke -- K01 AR52717-01/AR/NIAMS NIH HHS/ -- R01 AI063286/AI/NIAID NIH HHS/ -- R01 AI063286-05/AI/NIAID NIH HHS/ -- R01 GM085797/GM/NIGMS NIH HHS/ -- R01 GM085797-03/GM/NIGMS NIH HHS/ -- R01AI063286/AI/NIAID NIH HHS/ -- R01GM085797/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Oct 22;330(6003):521-5. doi: 10.1126/science.1193787.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Hematology-Oncology, Department of Medicine, 11-934 Factor Building, 10833 Le Conte Avenue, University of California, Los Angeles, Los Angeles, CA 90095, USA. bliu@ucla.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20966256" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; CD4-Positive T-Lymphocytes/cytology ; Chromatin/metabolism ; DNA (Cytosine-5-)-Methyltransferase/metabolism ; DNA Methylation ; Encephalomyelitis, Autoimmune, Experimental/immunology ; *Epigenesis, Genetic ; Female ; Forkhead Transcription Factors/genetics ; Histones/metabolism ; Lymphopoiesis/*genetics ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Inbred Strains ; Promoter Regions, Genetic ; Protein Inhibitors of Activated STAT/*physiology ; Repressor Proteins/*physiology ; T-Lymphocytes, Regulatory/*cytology/immunology ; Ubiquitin-Protein Ligases/*physiology
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  • 4
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-04-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Narbonne, Guy M -- New York, N.Y. -- Science. 2010 Apr 2;328(5974):53-4. doi: 10.1126/science.1188688.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geological Sciences and Geological Engineering, Queen's University, Kingston, ON K7L 3N6, Canada. narbonne@geol.queensu.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360098" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Carbon/analysis ; China ; Evolution, Chemical ; *Fossils ; Geologic Sediments/*chemistry ; Hydrogen Sulfide/analysis ; Iron/analysis ; Oceans and Seas ; Oxidation-Reduction ; Oxygen/analysis ; Seawater/*chemistry
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  • 5
    Publication Date: 2010-10-12
    Description: Penguin feathers are highly modified in form and function, but there have been no fossils to inform their evolution. A giant penguin with feathers was recovered from the late Eocene (~36 million years ago) of Peru. The fossil reveals that key feathering features, including undifferentiated primary wing feathers and broad body contour feather shafts, evolved early in the penguin lineage. Analyses of fossilized color-imparting melanosomes reveal that their dimensions were similar to those of non-penguin avian taxa and that the feathering may have been predominantly gray and reddish-brown. In contrast, the dark black-brown color of extant penguin feathers is generated by large, ellipsoidal melanosomes previously unknown for birds. The nanostructure of penguin feathers was thus modified after earlier macrostructural modifications of feather shape linked to aquatic flight.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clarke, Julia A -- Ksepka, Daniel T -- Salas-Gismondi, Rodolfo -- Altamirano, Ali J -- Shawkey, Matthew D -- D'Alba, Liliana -- Vinther, Jakob -- DeVries, Thomas J -- Baby, Patrice -- New York, N.Y. -- Science. 2010 Nov 12;330(6006):954-7. doi: 10.1126/science.1193604. Epub 2010 Sep 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geological Sciences, University of Texas at Austin, Austin, TX 78712, USA. julia_clarke@jsg.utexas.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20929737" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Bone and Bones/anatomy & histology ; Feathers/*anatomy & histology/ultrastructure ; *Fossils ; Melanosomes/ultrastructure ; Microscopy, Electron, Scanning ; Peru ; Phylogeny ; *Pigmentation ; Spheniscidae/*anatomy & histology/classification ; Wings, Animal/anatomy & histology
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  • 6
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-05-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Levy, Emmanuel D -- Landry, Christian R -- Michnick, Stephen W -- New York, N.Y. -- Science. 2010 May 21;328(5981):983-4. doi: 10.1126/science.1190993.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departement de Biochimie, Universite de Montreal, Montreal, Quebec, Canada H3T 1J4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20489011" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Mass Spectrometry ; Metabolic Networks and Pathways ; Models, Biological ; Phosphoprotein Phosphatases/*metabolism ; Phosphorylation ; Protein Interaction Mapping ; Protein Kinases/*metabolism ; Saccharomyces cerevisiae/enzymology/*metabolism ; Saccharomyces cerevisiae Proteins/*metabolism ; *Signal Transduction
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  • 7
    Publication Date: 2010-12-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thanukos, Anastasia -- Scotchmoor, Judith G -- Caldwell, Roy -- Lindberg, David R -- 51003439/Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Dec 24;330(6012):1764-5. doi: 10.1126/science.1186994. Epub 2010 Dec 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of California Museum of Paleontology, University of California, Berkeley, Berkeley, CA 94720-4780, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21127217" target="_blank"〉PubMed〈/a〉
    Keywords: Awards and Prizes ; *Biological Evolution ; Biology/*education ; *Internet ; Science/*education ; Teaching ; *Teaching Materials
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  • 8
    Publication Date: 2010-02-13
    Description: The Ediacaran Period (635 to 542 million years ago) was a time of fundamental environmental and evolutionary change, culminating in the first appearance of macroscopic animals. Here, we present a detailed spatial and temporal record of Ediacaran ocean chemistry for the Doushantuo Formation in the Nanhua Basin, South China. We find evidence for a metastable zone of euxinic (anoxic and sulfidic) waters impinging on the continental shelf and sandwiched within ferruginous [Fe(II)-enriched] deep waters. A stratified ocean with coeval oxic, sulfidic, and ferruginous zones, favored by overall low oceanic sulfate concentrations, was maintained dynamically throughout the Ediacaran Period. Our model reconciles seemingly conflicting geochemical redox conditions proposed previously for Ediacaran deep oceans and helps to explain the patchy temporal record of early metazoan fossils.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Chao -- Love, Gordon D -- Lyons, Timothy W -- Fike, David A -- Sessions, Alex L -- Chu, Xuelei -- New York, N.Y. -- Science. 2010 Apr 2;328(5974):80-3. doi: 10.1126/science.1182369. Epub 2010 Feb 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Sciences, University of California, Riverside, CA 92521, USA. chaoli@ucr.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20150442" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Carbonates/analysis ; China ; Ferrous Compounds/analysis ; *Fossils ; Geologic Sediments/*chemistry ; Hydrogen Sulfide ; Iron ; Oceans and Seas ; Oxidation-Reduction ; Oxygen/*analysis ; Seawater/*chemistry ; Sulfates/analysis
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  • 9
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-04-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cohen, Jon -- New York, N.Y. -- Science. 2010 Apr 2;328(5974):43. doi: 10.1126/science.328.5974.43.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360089" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Bone and Bones/*anatomy & histology/radiography ; California ; Databases as Topic ; Humans ; Pan troglodytes/*anatomy & histology ; Skull/anatomy & histology ; Tomography, X-Ray Computed ; Universities
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  • 10
    Publication Date: 2010-08-07
    Description: The class Ib ribonucleotide reductase of Escherichia coli can initiate reduction of nucleotides to deoxynucleotides with either a Mn(III)2-tyrosyl radical (Y*) or a Fe(III)2-Y* cofactor in the NrdF subunit. Whereas Fe(III)2-Y* can self-assemble from Fe(II)2-NrdF and O2, activation of Mn(II)2-NrdF requires a reduced flavoprotein, NrdI, proposed to form the oxidant for cofactor assembly by reduction of O2. The crystal structures reported here of E. coli Mn(II)2-NrdF and Fe(II)2-NrdF reveal different coordination environments, suggesting distinct initial binding sites for the oxidants during cofactor activation. In the structures of Mn(II)2-NrdF in complex with reduced and oxidized NrdI, a continuous channel connects the NrdI flavin cofactor to the NrdF Mn(II)2 active site. Crystallographic detection of a putative peroxide in this channel supports the proposed mechanism of Mn(III)2-Y* cofactor assembly.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3020666/" 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/PMC3020666/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boal, Amie K -- Cotruvo, Joseph A Jr -- Stubbe, JoAnne -- Rosenzweig, Amy C -- GM58518/GM/NIGMS NIH HHS/ -- GM81393/GM/NIGMS NIH HHS/ -- R01 GM058518/GM/NIGMS NIH HHS/ -- R01 GM058518-13/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Sep 17;329(5998):1526-30. doi: 10.1126/science.1190187. Epub 2010 Aug 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL 60208, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20688982" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalytic Domain ; Coenzymes/chemistry/metabolism ; Crystallography, X-Ray ; Enzyme Activation ; Escherichia coli/*enzymology ; Escherichia coli Proteins/*chemistry/*metabolism ; Ferrous Compounds/chemistry/metabolism ; Flavin Mononucleotide/chemistry/metabolism ; Flavodoxin/*chemistry/metabolism ; Hydrogen Bonding ; Ligands ; Manganese/*chemistry/metabolism ; Models, Molecular ; Oxidants/chemistry/metabolism ; Oxidation-Reduction ; Oxygen/chemistry/metabolism ; Peroxides/chemistry/metabolism ; Protein Folding ; Protein Multimerization ; Protein Subunits/chemistry/metabolism ; Ribonucleotide Reductases/*chemistry/*metabolism
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  • 11
    Publication Date: 2010-05-29
    Description: White and colleagues (Research Articles, 2 October 2009, pp. 64-106 and www.sciencemag.org/ardipithecus) reported Ardipithecus ramidus as an exclusive member of the human lineage post-African ape divergence. However, their analysis of shared-derived characters provides insufficient evidence of an ancestor-descendant relationship and exclusivity to the hominid lineage. Molecular and anatomical studies rather suggest that Ar. ramidus predates the human/African ape divergence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sarmiento, Esteban E -- New York, N.Y. -- Science. 2010 May 28;328(5982):1105; author reply 1105. doi: 10.1126/science.1184148.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Human Evolution Foundation, East Brunswick, NJ 08816, USA. este444@yahoo.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20508113" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Bone and Bones/anatomy & histology ; *Fossils ; Hominidae/*anatomy & histology/*classification/physiology ; Humans ; Locomotion ; Paleodontology ; Time
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  • 12
    Publication Date: 2010-02-27
    Description: Transcriptional positive-feedback loops are widely associated with bistability, characterized by two stable expression states that allow cells to respond to analog signals in a digital manner. Using a synthetic system in budding yeast, we show that positive feedback involving a promoter with multiple transcription factor (TF) binding sites can induce a steady-state bimodal response without cooperative binding of the TF. Deterministic models of this system do not predict bistability. Rather, the bimodal response requires a short-lived TF and stochastic fluctuations in the TF's expression. Multiple binding sites provide these fluctuations. Because many promoters possess multiple binding sites and many TFs are unstable, positive-feedback loops in gene regulatory networks may exhibit bimodal responses, but not necessarily because of deterministic bistability, as is commonly thought.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉To, Tsz-Leung -- Maheshri, Narendra -- New York, N.Y. -- Science. 2010 Feb 26;327(5969):1142-5. doi: 10.1126/science.1178962.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20185727" target="_blank"〉PubMed〈/a〉
    Keywords: Active Transport, Cell Nucleus ; Binding Sites ; Cell Nucleus/metabolism ; Doxycycline/metabolism ; Feedback, Physiological ; *Gene Expression Regulation, Fungal ; *Gene Regulatory Networks ; Models, Genetic ; Models, Statistical ; Promoter Regions, Genetic ; Protein Stability ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism ; Stochastic Processes ; Transcription Factors/chemistry/genetics/*metabolism ; *Transcription, Genetic
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  • 13
    Publication Date: 2010-03-20
    Description: Differences in gene expression may play a major role in speciation and phenotypic diversity. We examined genome-wide differences in transcription factor (TF) binding in several humans and a single chimpanzee by using chromatin immunoprecipitation followed by sequencing. The binding sites of RNA polymerase II (PolII) and a key regulator of immune responses, nuclear factor kappaB (p65), were mapped in 10 lymphoblastoid cell lines, and 25 and 7.5% of the respective binding regions were found to differ between individuals. Binding differences were frequently associated with single-nucleotide polymorphisms and genomic structural variants, and these differences were often correlated with differences in gene expression, suggesting functional consequences of binding variation. Furthermore, comparing PolII binding between humans and chimpanzee suggests extensive divergence in TF binding. Our results indicate that many differences in individuals and species occur at the level of TF binding, and they provide insight into the genetic events responsible for these differences.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2938768/" 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/PMC2938768/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kasowski, Maya -- Grubert, Fabian -- Heffelfinger, Christopher -- Hariharan, Manoj -- Asabere, Akwasi -- Waszak, Sebastian M -- Habegger, Lukas -- Rozowsky, Joel -- Shi, Minyi -- Urban, Alexander E -- Hong, Mi-Young -- Karczewski, Konrad J -- Huber, Wolfgang -- Weissman, Sherman M -- Gerstein, Mark B -- Korbel, Jan O -- Snyder, Michael -- R01 CA077808/CA/NCI NIH HHS/ -- R01 CA077808-09/CA/NCI NIH HHS/ -- T32 GM007205/GM/NIGMS NIH HHS/ -- T32 GM007205-34/GM/NIGMS NIH HHS/ -- T32GM07205/GM/NIGMS NIH HHS/ -- U54 HG004558/HG/NHGRI NIH HHS/ -- U54 HG004558-04/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Apr 9;328(5975):232-5. doi: 10.1126/science.1183621. Epub 2010 Mar 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20299548" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Line ; Chromatin Immunoprecipitation ; DNA Copy Number Variations ; DNA, Intergenic ; Female ; *Gene Expression Regulation ; Humans ; Male ; Pan troglodytes/genetics ; *Polymorphism, Single Nucleotide ; Protein Binding ; RNA Polymerase II/genetics/*metabolism ; Sequence Analysis, DNA ; Species Specificity ; Transcription Factor RelA/genetics/*metabolism ; Transcription Initiation Site
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  • 14
    Publication Date: 2010-01-16
    Description: Integrins mediate cell adhesion to the extracellular matrix and transmit signals within the cell that stimulate cell spreading, retraction, migration, and proliferation. The mechanism of integrin outside-in signaling has been unclear. We found that the heterotrimeric guanine nucleotide-binding protein (G protein) Galpha13 directly bound to the integrin beta3 cytoplasmic domain and that Galpha13-integrin interaction was promoted by ligand binding to the integrin alphaIIbbeta3 and by guanosine triphosphate (GTP) loading of Galpha13. Interference of Galpha13 expression or a myristoylated fragment of Galpha13 that inhibited interaction of alphaIIbbeta3 with Galpha13 diminished activation of protein kinase c-Src and stimulated the small guanosine triphosphatase RhoA, consequently inhibiting cell spreading and accelerating cell retraction. We conclude that integrins are noncanonical Galpha13-coupled receptors that provide a mechanism for dynamic regulation of RhoA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842917/" 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/PMC2842917/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gong, Haixia -- Shen, Bo -- Flevaris, Panagiotis -- Chow, Christina -- Lam, Stephen C-T -- Voyno-Yasenetskaya, Tatyana A -- Kozasa, Tohru -- Du, Xiaoping -- GM061454/GM/NIGMS NIH HHS/ -- GM074001/GM/NIGMS NIH HHS/ -- HL062350/HL/NHLBI NIH HHS/ -- HL068819/HL/NHLBI NIH HHS/ -- HL080264/HL/NHLBI NIH HHS/ -- R01 GM061454/GM/NIGMS NIH HHS/ -- R01 GM061454-09/GM/NIGMS NIH HHS/ -- R01 GM074001/GM/NIGMS NIH HHS/ -- R01 GM074001-02/GM/NIGMS NIH HHS/ -- R01 HL062350/HL/NHLBI NIH HHS/ -- R01 HL062350-09/HL/NHLBI NIH HHS/ -- R01 HL068819/HL/NHLBI NIH HHS/ -- R01 HL068819-08/HL/NHLBI NIH HHS/ -- R01 HL080264/HL/NHLBI NIH HHS/ -- R01 HL080264-04/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2010 Jan 15;327(5963):340-3. doi: 10.1126/science.1174779.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of Illinois at Chicago, 835 South Wolcott Avenue, Room E403, Chicago, IL 60612, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075254" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Blood Platelets/*physiology ; Clot Retraction ; Fibrinogen/metabolism ; GTP-Binding Protein alpha Subunits, G12-G13/genetics/*metabolism ; Humans ; Integrin beta3/*metabolism ; Ligands ; Mice ; Mice, Inbred C57BL ; Phosphorylation ; Platelet Adhesiveness ; Platelet Glycoprotein GPIIb-IIIa Complex/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; Proto-Oncogene Proteins pp60(c-src)/metabolism ; RNA, Small Interfering ; Recombinant Fusion Proteins/metabolism ; *Signal Transduction ; rhoA GTP-Binding Protein/antagonists & inhibitors/metabolism
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  • 15
    Publication Date: 2010-10-12
    Description: Efficient enzymatic conversion of crystalline polysaccharides is crucial for an economically and environmentally sustainable bioeconomy but remains unfavorably inefficient. We describe an enzyme that acts on the surface of crystalline chitin, where it introduces chain breaks and generates oxidized chain ends, thus promoting further degradation by chitinases. This enzymatic activity was discovered and further characterized by using mass spectrometry and chromatographic separation methods to detect oxidized products generated in the absence or presence of H(2)(18)O or (18)O(2). There are strong indications that similar enzymes exist that work on cellulose. Our findings not only demonstrate the existence of a hitherto unknown enzyme activity but also provide new avenues toward more efficient enzymatic conversion of biomass.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vaaje-Kolstad, Gustav -- Westereng, Bjorge -- Horn, Svein J -- Liu, Zhanliang -- Zhai, Hong -- Sorlie, Morten -- Eijsink, Vincent G H -- New York, N.Y. -- Science. 2010 Oct 8;330(6001):219-22. doi: 10.1126/science.1192231.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Post Office Box 5003, 1432 As, Norway.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20929773" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/antagonists & inhibitors/chemistry/genetics/*metabolism ; Binding Sites ; Biocatalysis ; Biomass ; Carrier Proteins/antagonists & inhibitors/chemistry/genetics/*metabolism ; Cations, Divalent/metabolism/pharmacology ; Chitin/*metabolism ; Chitinase/*metabolism ; Chromatography, High Pressure Liquid ; Edetic Acid/pharmacology ; Enzyme Inhibitors/pharmacology ; Hydrolysis ; Isotope Labeling ; Oligosaccharides/metabolism ; Oxidation-Reduction ; Oxygen Isotopes/metabolism ; Serratia marcescens/*enzymology ; Solubility ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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  • 16
    Publication Date: 2010-09-18
    Description: Hybrids between species are often sterile or inviable because the long-diverged genomes of their parents cause developmental problems when they come together in a single individual. According to the Dobzhansky-Muller (DM) model, the number of genes involved in these "intrinsic postzygotic incompatibilities" should increase faster than linearly with the divergence time between species. This straightforward prediction of the DM model has remained contentious owing to a lack of explicit tests. Examining two pairs of Drosophila species, we show that the number of genes involved in postzygotic isolation increases at least as fast as the square of the number of substitutions (an index of divergence time) between species. This observation verifies a key prediction of the DM model.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Matute, Daniel R -- Butler, Ian A -- Turissini, David A -- Coyne, Jerry A -- R01GM058260/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Sep 17;329(5998):1518-21. doi: 10.1126/science.1193440.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA. dmatute@uchicago.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20847270" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Crosses, Genetic ; Drosophila/*genetics/physiology ; Drosophila melanogaster/genetics/physiology ; Epistasis, Genetic ; Female ; *Genes, Insect ; *Genetic Speciation ; *Hybridization, Genetic ; Infertility ; Male ; Models, Genetic ; Reproduction ; Species Specificity
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  • 17
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-01-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boomsma, Jacobus J -- Pamilo, Pekka -- New York, N.Y. -- Science. 2010 Jan 1;327(5961):45. doi: 10.1126/science.1185061.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark. jjboomsma@bio.ku.dk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20044566" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Australia ; Behavior, Animal ; *Biological Evolution ; History, 20th Century ; History, 21st Century ; *Insects/genetics/physiology ; Social Behavior
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  • 18
    Publication Date: 2010-01-09
    Description: Large-scale biodiversity gradients among environments and habitats are usually attributed to a complex array of ecological and evolutionary factors. We tested the evolutionary component of such gradients by compiling the environments of the geologically oldest occurrences of marine genera and using sampling standardization to assess if originations tended to be clustered in particular environments. Shallow, tropical environments and carbonate substrates all tend to have harbored high origination rates. Diversity within these environments tended to be preferentially generated in reefs, probably because of their habitat complexity. Reefs were also prolific at exporting diversity to other environments, which might be a consequence of low-diversity habitats being more susceptible to invasions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kiessling, Wolfgang -- Simpson, Carl -- Foote, Michael -- New York, N.Y. -- Science. 2010 Jan 8;327(5962):196-8. doi: 10.1126/science.1182241.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Museum fur Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity at the Humboldt University Berlin, 10115 Berlin, Germany. wolfgang.kiessling@mfn-berlin.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20056888" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Anthozoa ; *Biodiversity ; *Biological Evolution ; Calcium Carbonate ; *Ecosystem ; Environment ; Fishes ; *Fossils ; Geography ; *Invertebrates/classification
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  • 19
    Publication Date: 2010-11-27
    Description: The extinction of dinosaurs at the Cretaceous/Paleogene (K/Pg) boundary was the seminal event that opened the door for the subsequent diversification of terrestrial mammals. Our compilation of maximum body size at the ordinal level by sub-epoch shows a near-exponential increase after the K/Pg. On each continent, the maximum size of mammals leveled off after 40 million years ago and thereafter remained approximately constant. There was remarkable congruence in the rate, trajectory, and upper limit across continents, orders, and trophic guilds, despite differences in geological and climatic history, turnover of lineages, and ecological variation. Our analysis suggests that although the primary driver for the evolution of giant mammals was diversification to fill ecological niches, environmental temperature and land area may have ultimately constrained the maximum size achieved.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, Felisa A -- Boyer, Alison G -- Brown, James H -- Costa, Daniel P -- Dayan, Tamar -- Ernest, S K Morgan -- Evans, Alistair R -- Fortelius, Mikael -- Gittleman, John L -- Hamilton, Marcus J -- Harding, Larisa E -- Lintulaakso, Kari -- Lyons, S Kathleen -- McCain, Christy -- Okie, Jordan G -- Saarinen, Juha J -- Sibly, Richard M -- Stephens, Patrick R -- Theodor, Jessica -- Uhen, Mark D -- New York, N.Y. -- Science. 2010 Nov 26;330(6008):1216-9. doi: 10.1126/science.1194830.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, MSC03 2020, University of New Mexico, Albuquerque, NM 87131, USA. fasmith@unm.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21109666" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Atmosphere ; *Biological Evolution ; *Body Size ; Ecosystem ; Environment ; Extinction, Biological ; Fossils ; Geography ; Mammals/*anatomy & histology/classification/growth & development ; Models, Biological ; Oxygen ; Phylogeny ; Temperature
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  • 20
    Publication Date: 2010-01-16
    Description: We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2849982/" 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/PMC2849982/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Werren, John H -- Richards, Stephen -- Desjardins, Christopher A -- Niehuis, Oliver -- Gadau, Jurgen -- Colbourne, John K -- Nasonia Genome Working Group -- Beukeboom, Leo W -- Desplan, Claude -- Elsik, Christine G -- Grimmelikhuijzen, Cornelis J P -- Kitts, Paul -- Lynch, Jeremy A -- Murphy, Terence -- Oliveira, Deodoro C S G -- Smith, Christopher D -- van de Zande, Louis -- Worley, Kim C -- Zdobnov, Evgeny M -- Aerts, Maarten -- Albert, Stefan -- Anaya, Victor H -- Anzola, Juan M -- Barchuk, Angel R -- Behura, Susanta K -- Bera, Agata N -- Berenbaum, May R -- Bertossa, Rinaldo C -- Bitondi, Marcia M G -- Bordenstein, Seth R -- Bork, Peer -- Bornberg-Bauer, Erich -- Brunain, Marleen -- Cazzamali, Giuseppe -- Chaboub, Lesley -- Chacko, Joseph -- Chavez, Dean -- Childers, Christopher P -- Choi, Jeong-Hyeon -- Clark, Michael E -- Claudianos, Charles -- Clinton, Rochelle A -- Cree, Andrew G -- Cristino, Alexandre S -- Dang, Phat M -- Darby, Alistair C -- de Graaf, Dirk C -- Devreese, Bart -- Dinh, Huyen H -- Edwards, Rachel -- Elango, Navin -- Elhaik, Eran -- Ermolaeva, Olga -- Evans, Jay D -- Foret, Sylvain -- Fowler, Gerald R -- Gerlach, Daniel -- Gibson, Joshua D -- Gilbert, Donald G -- Graur, Dan -- Grunder, Stefan -- Hagen, Darren E -- Han, Yi -- Hauser, Frank -- Hultmark, Da -- Hunter, Henry C 4th -- Hurst, Gregory D D -- Jhangian, Shalini N -- Jiang, Huaiyang -- Johnson, Reed M -- Jones, Andrew K -- Junier, Thomas -- Kadowaki, Tatsuhiko -- Kamping, Albert -- Kapustin, Yuri -- Kechavarzi, Bobak -- Kim, Jaebum -- Kim, Jay -- Kiryutin, Boris -- Koevoets, Tosca -- Kovar, Christie L -- Kriventseva, Evgenia V -- Kucharski, Robert -- Lee, Heewook -- Lee, Sandra L -- Lees, Kristin -- Lewis, Lora R -- Loehlin, David W -- Logsdon, John M Jr -- Lopez, Jacqueline A -- Lozado, Ryan J -- Maglott, Donna -- Maleszka, Ryszard -- Mayampurath, Anoop -- Mazur, Danielle J -- McClure, Marcella A -- Moore, Andrew D -- Morgan, Margaret B -- Muller, Jean -- Munoz-Torres, Monica C -- Muzny, Donna M -- Nazareth, Lynne V -- Neupert, Susanne -- Nguyen, Ngoc B -- Nunes, Francis M F -- Oakeshott, John G -- Okwuonu, Geoffrey O -- Pannebakker, Bart A -- Pejaver, Vikas R -- Peng, Zuogang -- Pratt, Stephen C -- Predel, Reinhard -- Pu, Ling-Ling -- Ranson, Hilary -- Raychoudhury, Rhitoban -- Rechtsteiner, Andreas -- Reese, Justin T -- Reid, Jeffrey G -- Riddle, Megan -- Robertson, Hugh M -- Romero-Severson, Jeanne -- Rosenberg, Miriam -- Sackton, Timothy B -- Sattelle, David B -- Schluns, Helge -- Schmitt, Thomas -- Schneider, Martina -- Schuler, Andreas -- Schurko, Andrew M -- Shuker, David M -- Simoes, Zila L P -- Sinha, Saurabh -- Smith, Zachary -- Solovyev, Victor -- Souvorov, Alexandre -- Springauf, Andreas -- Stafflinger, Elisabeth -- Stage, Deborah E -- Stanke, Mario -- Tanaka, Yoshiaki -- Telschow, Arndt -- Trent, Carol -- Vattathil, Selina -- Verhulst, Eveline C -- Viljakainen, Lumi -- Wanner, Kevin W -- Waterhouse, Robert M -- Whitfield, James B -- Wilkes, Timothy E -- Williamson, Michael -- Willis, Judith H -- Wolschin, Florian -- Wyder, Stefan -- Yamada, Takuji -- Yi, Soojin V -- Zecher, Courtney N -- Zhang, Lan -- Gibbs, Richard A -- 5R01GM070026-04/GM/NIGMS NIH HHS/ -- 5R01HG000747-14/HG/NHGRI NIH HHS/ -- 5R24GM084917-02/GM/NIGMS NIH HHS/ -- AI028309-13A2/AI/NIAID NIH HHS/ -- R01 AI055624/AI/NIAID NIH HHS/ -- R01 GM064864/GM/NIGMS NIH HHS/ -- R01 GM064864-04/GM/NIGMS NIH HHS/ -- R01 GM064864-05A2/GM/NIGMS NIH HHS/ -- R01 GM070026/GM/NIGMS NIH HHS/ -- R01 GM070026-04S1/GM/NIGMS NIH HHS/ -- R01 GM079484/GM/NIGMS NIH HHS/ -- R01 GM085163/GM/NIGMS NIH HHS/ -- R01 GM085163-01/GM/NIGMS NIH HHS/ -- R01 GM085233/GM/NIGMS NIH HHS/ -- R01 HG000747/HG/NHGRI NIH HHS/ -- R01 HG000747-14/HG/NHGRI NIH HHS/ -- R01GM064864/GM/NIGMS NIH HHS/ -- R24 GM084917/GM/NIGMS NIH HHS/ -- R24 GM084917-01/GM/NIGMS NIH HHS/ -- R24 GM084917-02/GM/NIGMS NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- U54 HG003273-03/HG/NHGRI NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Jan 15;327(5963):343-8. doi: 10.1126/science.1178028.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075255" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arthropods/parasitology ; *Biological Evolution ; DNA Methylation ; DNA Transposable Elements ; Female ; Gene Transfer, Horizontal ; Genes, Insect ; Genetic Speciation ; Genetic Variation ; *Genome, Insect ; Host-Parasite Interactions ; Insect Proteins/genetics/metabolism ; Insect Viruses/genetics ; Insects/genetics ; Male ; Molecular Sequence Data ; Quantitative Trait Loci ; Recombination, Genetic ; Sequence Analysis, DNA ; Wasp Venoms/chemistry/toxicity ; Wasps/*genetics/physiology ; Wolbachia/genetics
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  • 21
    Publication Date: 2010-02-13
    Description: Microorganisms can switch from a planktonic, free-swimming life-style to a sessile, colonial state, called a biofilm, which confers resistance to environmental stress. Conversion between the motile and biofilm life-styles has been attributed to increased levels of the prokaryotic second messenger cyclic di-guanosine monophosphate (c-di-GMP), yet the signaling mechanisms mediating such a global switch are poorly understood. Here we show that the transcriptional regulator VpsT from Vibrio cholerae directly senses c-di-GMP to inversely control extracellular matrix production and motility, which identifies VpsT as a master regulator for biofilm formation. Rather than being regulated by phosphorylation, VpsT undergoes a change in oligomerization on c-di-GMP binding.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828054/" 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/PMC2828054/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Krasteva, Petya V -- Fong, Jiunn C N -- Shikuma, Nicholas J -- Beyhan, Sinem -- Navarro, Marcos V A S -- Yildiz, Fitnat H -- Sondermann, Holger -- 1R01GM081373/GM/NIGMS NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 AI055987/AI/NIAID NIH HHS/ -- R01 AI055987-06A1/AI/NIAID NIH HHS/ -- R01 GM081373/GM/NIGMS NIH HHS/ -- R01 GM081373-03/GM/NIGMS NIH HHS/ -- R01AI055987/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2010 Feb 12;327(5967):866-8. doi: 10.1126/science.1181185.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20150502" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Bacterial Proteins/chemistry/genetics/*metabolism ; Binding Sites ; Biofilms/*growth & development ; Crystallography, X-Ray ; Cyclic GMP/*analogs & derivatives/metabolism ; DNA, Bacterial/metabolism ; Dimerization ; Extracellular Matrix/*metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Models, Molecular ; Movement ; Point Mutation ; Polysaccharides, Bacterial/genetics/metabolism ; Protein Folding ; Protein Multimerization ; Protein Structure, Tertiary ; Signal Transduction ; Transcription Factors/chemistry/genetics/*metabolism ; Transcription, Genetic ; Vibrio cholerae O1/cytology/genetics/*physiology
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  • 22
    Publication Date: 2010-04-24
    Description: The structure of the sodium-benzylhydantoin transport protein Mhp1 from Microbacterium liquefaciens comprises a five-helix inverted repeat, which is widespread among secondary transporters. Here, we report the crystal structure of an inward-facing conformation of Mhp1 at 3.8 angstroms resolution, complementing its previously described structures in outward-facing and occluded states. From analyses of the three structures and molecular dynamics simulations, we propose a mechanism for the transport cycle in Mhp1. Switching from the outward- to the inward-facing state, to effect the inward release of sodium and benzylhydantoin, is primarily achieved by a rigid body movement of transmembrane helices 3, 4, 8, and 9 relative to the rest of the protein. This forms the basis of an alternating access mechanism applicable to many transporters of this emerging superfamily.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885435/" 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/PMC2885435/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shimamura, Tatsuro -- Weyand, Simone -- Beckstein, Oliver -- Rutherford, Nicholas G -- Hadden, Jonathan M -- Sharples, David -- Sansom, Mark S P -- Iwata, So -- Henderson, Peter J F -- Cameron, Alexander D -- 062164/Z/00/Z/Wellcome Trust/United Kingdom -- 079209/Wellcome Trust/United Kingdom -- BB/C51725/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G020043/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G023425/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBS/B/14418/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2010 Apr 23;328(5977):470-3. doi: 10.1126/science.1186303.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20413494" target="_blank"〉PubMed〈/a〉
    Keywords: Actinomycetales/*chemistry/metabolism ; Amino Acid Motifs ; Bacterial Proteins/chemistry/metabolism ; Binding Sites ; Biological Transport ; Crystallography, X-Ray ; Hydantoins/chemistry/*metabolism ; Ion Transport ; Membrane Transport Proteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Dynamics Simulation ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Sodium/*metabolism
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  • 23
    Publication Date: 2010-01-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Whiten, Andrew -- McGrew, William C -- Aiello, Leslie C -- Boesch, Christophe -- Boyd, Robert -- Byrne, Richard W -- Dunbar, Robin I M -- Matsuzawa, Tetsuro -- Silk, Joan B -- Tomasello, Michael -- van Schaik, Carel P -- Wrangham, Richard -- New York, N.Y. -- Science. 2010 Jan 22;327(5964):410; author reply 410-1. doi: 10.1126/science.327.5964.410-a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20093456" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Behavior ; Behavior, Animal ; *Biological Evolution ; Cognition ; Female ; *Hominidae/classification ; Humans ; Male ; *Pan troglodytes/classification
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  • 24
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-01-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2010 Jan 29;327(5965):519. doi: 10.1126/science.327.5965.519.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20110481" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Anthozoa/classification/genetics ; Biodiversity ; *Biological Evolution ; Cnidaria/classification/genetics ; *Ecosystem ; Genes ; Genetic Speciation ; Geologic Sediments ; Phylogeny ; *Seawater
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 25
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-02-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2010 Feb 5;327(5966):633. doi: 10.1126/science.327.5966.633-a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20133547" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Animals ; *Biological Evolution ; *Bufonidae/anatomy & histology/classification/physiology ; Genetic Speciation ; Population Dynamics ; South America
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  • 26
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-01-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harrison, Terry -- New York, N.Y. -- Science. 2010 Jan 29;327(5965):532-4. doi: 10.1126/science.1184703.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for the Study of Human Origins, Department of Anthropology, New York University, New York, NY 10003, USA. terry.harrison@nyu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20110491" target="_blank"〉PubMed〈/a〉
    Keywords: Africa ; Animals ; Asia ; *Biological Evolution ; Cercopithecidae/classification ; Climate ; Europe ; Extinction, Biological ; Fossils ; *Hominidae/classification ; Humans ; Paleontology ; Pan troglodytes ; Phylogeny ; Seasons ; Time
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  • 27
    Publication Date: 2010-11-26
    Description: Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760481/" 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/PMC3760481/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Denoeud, France -- Henriet, Simon -- Mungpakdee, Sutada -- Aury, Jean-Marc -- Da Silva, Corinne -- Brinkmann, Henner -- Mikhaleva, Jana -- Olsen, Lisbeth Charlotte -- Jubin, Claire -- Canestro, Cristian -- Bouquet, Jean-Marie -- Danks, Gemma -- Poulain, Julie -- Campsteijn, Coen -- Adamski, Marcin -- Cross, Ismael -- Yadetie, Fekadu -- Muffato, Matthieu -- Louis, Alexandra -- Butcher, Stephen -- Tsagkogeorga, Georgia -- Konrad, Anke -- Singh, Sarabdeep -- Jensen, Marit Flo -- Huynh Cong, Evelyne -- Eikeseth-Otteraa, Helen -- Noel, Benjamin -- Anthouard, Veronique -- Porcel, Betina M -- Kachouri-Lafond, Rym -- Nishino, Atsuo -- Ugolini, Matteo -- Chourrout, Pascal -- Nishida, Hiroki -- Aasland, Rein -- Huzurbazar, Snehalata -- Westhof, Eric -- Delsuc, Frederic -- Lehrach, Hans -- Reinhardt, Richard -- Weissenbach, Jean -- Roy, Scott W -- Artiguenave, Francois -- Postlethwait, John H -- Manak, J Robert -- Thompson, Eric M -- Jaillon, Olivier -- Du Pasquier, Louis -- Boudinot, Pierre -- Liberles, David A -- Volff, Jean-Nicolas -- Philippe, Herve -- Lenhard, Boris -- Roest Crollius, Hugues -- Wincker, Patrick -- Chourrout, Daniel -- Z01 LM000073-12/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Dec 3;330(6009):1381-5. doi: 10.1126/science.1194167. Epub 2010 Nov 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Commissariat a l'Energie Atomique, Institut de Genomique, Genoscope, Evry, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21097902" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; DNA Transposable Elements ; DNA, Intergenic ; Exons ; Gene Order ; Genes, Duplicate ; Genes, Homeobox ; *Genome ; Introns ; Invertebrates/classification/genetics ; Molecular Sequence Data ; Recombination, Genetic ; Spliceosomes/metabolism ; Synteny ; Urochordata/anatomy & histology/classification/*genetics/immunology ; Vertebrates/classification/genetics
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  • 28
    Publication Date: 2010-06-19
    Description: T cells transformed by Herpesvirus saimiri express seven viral U-rich noncoding RNAs of unknown function called HSURs. We noted that conserved sequences in HSURs 1 and 2 constitute potential binding sites for three host-cell microRNAs (miRNAs). Coimmunoprecipitation experiments confirmed that HSURs 1 and 2 interact with the predicted miRNAs in virally transformed T cells. The abundance of one of these miRNAs, miR-27, is dramatically lowered in transformed cells, with consequent effects on the expression of miR-27 target genes. Transient knockdown and ectopic expression of HSUR 1 demonstrate that it directs degradation of mature miR-27 in a sequence-specific and binding-dependent manner. This viral strategy illustrates use of a ncRNA to manipulate host-cell gene expression via the miRNA pathway.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3075239/" 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/PMC3075239/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cazalla, Demian -- Yario, Therese -- Steitz, Joan A -- CA16038/CA/NCI NIH HHS/ -- P01 CA016038/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Jun 18;328(5985):1563-6. doi: 10.1126/science.1187197.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, Boyer Center for Molecular Medicine, 295 Congress Avenue, New Haven, CT 06536, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20558719" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Pairing ; Binding Sites ; Callithrix ; Cell Line, Transformed ; Cell Transformation, Viral ; Conserved Sequence ; *Down-Regulation ; Herpesvirus 2, Saimiriine/*genetics/metabolism ; Humans ; Jurkat Cells ; MicroRNAs/chemistry/genetics/*metabolism ; *RNA Stability ; RNA, Untranslated/chemistry/*metabolism ; RNA, Viral/chemistry/*metabolism ; T-Lymphocytes
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  • 29
    Publication Date: 2010-07-03
    Description: Proton-pumping respiratory complex I is one of the largest and most complicated membrane protein complexes. Its function is critical for efficient energy supply in aerobic cells, and malfunctions are implicated in many neurodegenerative disorders. Here, we report an x-ray crystallographic analysis of mitochondrial complex I. The positions of all iron-sulfur clusters relative to the membrane arm were determined in the complete enzyme complex. The ubiquinone reduction site resides close to 30 angstroms above the membrane domain. The arrangement of functional modules suggests conformational coupling of redox chemistry with proton pumping and essentially excludes direct mechanisms. We suggest that a approximately 60-angstrom-long helical transmission element is critical for transducing conformational energy to proton-pumping elements in the distal module of the membrane arm.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hunte, Carola -- Zickermann, Volker -- Brandt, Ulrich -- New York, N.Y. -- Science. 2010 Jul 23;329(5990):448-51. doi: 10.1126/science.1191046. Epub 2010 Jul 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Biochemistry and Molecular Biology, Centre for Biological Signalling Studies (BIOSS), University of Freiburg, D-79104 Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20595580" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Electron Transport Complex I/*chemistry/*metabolism ; Fungal Proteins/chemistry/metabolism ; Iron/chemistry ; Mitochondria/enzymology ; Mitochondrial Proteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Protons ; Sulfur/chemistry ; Ubiquinone/chemistry/metabolism ; Yarrowia/*enzymology
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  • 30
    Publication Date: 2010-10-12
    Description: Marx and Uhen (Reports, 19 February 2010, p. 993) suggested that correlated diversity changes in the fossil record of whales and diatoms reflects secular evolutionary signals of underlying ecological drivers. We question the meaning of this association and outline avenues for more complete testing of correlations between productivity and marine consumers through geologic time.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pyenson, Nicholas D -- Irmis, Randall B -- Lipps, Jere H -- New York, N.Y. -- Science. 2010 Oct 8;330(6001):178; author reply 178. doi: 10.1126/science.1189866.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, 6270 University Boulevard, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. pyensonn@si.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20929760" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; *Biological Evolution ; Climate ; *Diatoms ; *Ecosystem ; Food Chain ; *Fossils ; Geologic Sediments ; Oceans and Seas ; *Whales
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  • 31
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-02-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alcock, Felicity -- Clements, Abigail -- Webb, Chaille -- Lithgow, Trevor -- New York, N.Y. -- Science. 2010 Feb 5;327(5966):649-50. doi: 10.1126/science.1182129.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne 3800, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20133559" target="_blank"〉PubMed〈/a〉
    Keywords: Alphaproteobacteria/genetics/*metabolism ; Amino Acid Transport Systems/chemistry/metabolism ; Bacterial Proteins/chemistry/metabolism ; *Biological Evolution ; *Eukaryotic Cells/metabolism/ultrastructure ; Evolution, Molecular ; *Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins/chemistry/*metabolism ; *Protein Transport ; *Symbiosis
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  • 32
    Publication Date: 2010-07-24
    Description: DNA methylation at proximal promoters facilitates lineage restriction by silencing cell type-specific genes. However, euchromatic DNA methylation frequently occurs in regions outside promoters. The functions of such nonproximal promoter DNA methylation are unclear. Here we show that the de novo DNA methyltransferase Dnmt3a is expressed in postnatal neural stem cells (NSCs) and is required for neurogenesis. Genome-wide analysis of postnatal NSCs indicates that Dnmt3a occupies and methylates intergenic regions and gene bodies flanking proximal promoters of a large cohort of transcriptionally permissive genes, many of which encode regulators of neurogenesis. Surprisingly, Dnmt3a-dependent nonproximal promoter methylation promotes expression of these neurogenic genes by functionally antagonizing Polycomb repression. Thus, nonpromoter DNA methylation by Dnmt3a may be used for maintaining active chromatin states of genes critical for development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3539760/" 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/PMC3539760/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Hao -- Coskun, Volkan -- Tao, Jifang -- Xie, Wei -- Ge, Weihong -- Yoshikawa, Kazuaki -- Li, En -- Zhang, Yi -- Sun, Yi Eve -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Jul 23;329(5990):444-8. doi: 10.1126/science.1190485.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA. haowu7@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20651149" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Brain/cytology/growth & development/*metabolism ; Chromatin Immunoprecipitation ; DNA (Cytosine-5-)-Methyltransferase/*metabolism ; *DNA Methylation ; DNA, Intergenic ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; Genome ; Histones/genetics/metabolism ; Mice ; Mice, Knockout ; Nervous System/growth & development ; Neurogenesis/*genetics ; Neuroglia/cytology ; Neurons/*cytology/metabolism ; Polycomb-Group Proteins ; Promoter Regions, Genetic ; Repressor Proteins/metabolism ; Stem Cells/*metabolism ; *Transcription, Genetic
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  • 33
    Publication Date: 2010-03-27
    Description: Phosphoinositide 3-kinases (PI3Ks) are lipid kinases with diverse roles in health and disease. The primordial PI3K, Vps34, is present in all eukaryotes and has essential roles in autophagy, membrane trafficking, and cell signaling. We solved the crystal structure of Vps34 at 2.9 angstrom resolution, which revealed a constricted adenine-binding pocket, suggesting the reason that specific inhibitors of this class of PI3K have proven elusive. Both the phosphoinositide-binding loop and the carboxyl-terminal helix of Vps34 mediate catalysis on membranes and suppress futile adenosine triphosphatase cycles. Vps34 appears to alternate between a closed cytosolic form and an open form on the membrane. Structures of Vps34 complexes with a series of inhibitors reveal the reason that an autophagy inhibitor preferentially inhibits Vps34 and underpin the development of new potent and specific Vps34 inhibitors.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860105/" 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/PMC2860105/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miller, Simon -- Tavshanjian, Brandon -- Oleksy, Arkadiusz -- Perisic, Olga -- Houseman, Benjamin T -- Shokat, Kevan M -- Williams, Roger L -- MC_U105184308/Medical Research Council/United Kingdom -- U.1051.03.014(78824)/Medical Research Council/United Kingdom -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Mar 26;327(5973):1638-42. doi: 10.1126/science.1184429.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20339072" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/*analogs & derivatives/metabolism/pharmacology ; Adenosine Triphosphatases/metabolism ; Animals ; Autophagy/*drug effects ; Binding Sites ; Catalysis ; Catalytic Domain ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Drosophila Proteins/*antagonists & inhibitors/*chemistry/genetics/metabolism ; Drosophila melanogaster ; Enzyme Inhibitors/chemical synthesis/chemistry/*metabolism/pharmacology ; Furans/chemistry/metabolism/pharmacology ; Humans ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Phosphatidylinositol 3-Kinases/*antagonists & ; inhibitors/*chemistry/genetics/metabolism ; Phosphatidylinositols/metabolism ; Point Mutation ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyridines/chemistry/metabolism/pharmacology ; Pyrimidines/chemistry/metabolism/pharmacology
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  • 34
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-10-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mindell, Joseph A -- New York, N.Y. -- Science. 2010 Oct 29;330(6004):601-2. doi: 10.1126/science.1198306.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Membrane Transport Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA. mindellj@ninds.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21030639" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/*chemistry/metabolism ; Antiporters/*chemistry/metabolism ; Binding Sites ; Chloride Channels/*chemistry/metabolism ; Chlorides/*metabolism ; Crystallization ; Crystallography, X-Ray ; Cytoplasm/chemistry ; Eukaryota/*chemistry ; Glutamic Acid/metabolism ; Ion Channel Gating ; Ion Transport ; Models, Molecular ; Protein Structure, Tertiary ; Protons
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  • 35
    Publication Date: 2010-02-06
    Description: The bacterial flagellar switch that controls the direction of flagellar rotation during chemotaxis has a highly cooperative response. This has previously been understood in terms of the classic two-state, concerted model of allosteric regulation. Here, we used high-resolution optical microscopy to observe switching of single motors and uncover the stochastic multistate nature of the switch. Our observations are in detailed quantitative agreement with a recent general model of allosteric cooperativity that exhibits conformational spread--the stochastic growth and shrinkage of domains of adjacent subunits sharing a particular conformational state. We expect that conformational spread will be important in explaining cooperativity in other large signaling complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bai, Fan -- Branch, Richard W -- Nicolau, Dan V Jr -- Pilizota, Teuta -- Steel, Bradley C -- Maini, Philip K -- Berry, Richard M -- BB/E00458X/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/H01991X/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2010 Feb 5;327(5966):685-9. doi: 10.1126/science.1182105.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20133571" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Bacterial Proteins/chemistry/metabolism ; Binding Sites ; Escherichia coli/metabolism ; Escherichia coli Proteins/*chemistry/*metabolism ; Flagella/*chemistry ; Membrane Proteins/chemistry/metabolism ; Models, Biological ; Models, Molecular ; Molecular Motor Proteins/*chemistry/*metabolism ; Monte Carlo Method ; Protein Binding ; Protein Conformation ; Protein Subunits/*chemistry/*metabolism ; Signal Transduction ; Thermodynamics
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  • 36
    Publication Date: 2010-05-29
    Description: High-conductance voltage- and Ca2+-activated K+ (BK) channels encode negative feedback regulation of membrane voltage and Ca2+ signaling, playing a central role in numerous physiological processes. We determined the x-ray structure of the human BK Ca2+ gating apparatus at a resolution of 3.0 angstroms and deduced its tetrameric assembly by solving a 6 angstrom resolution structure of a Na+-activated homolog. Two tandem C-terminal regulator of K+ conductance (RCK) domains from each of four channel subunits form a 350-kilodalton gating ring at the intracellular membrane surface. A sequence of aspartic amino acids that is known as the Ca2+ bowl, and is located within the second of the tandem RCK domains, creates four Ca2+ binding sites on the outer perimeter of the gating ring at the "assembly interface" between RCK domains. Functionally important mutations cluster near the Ca2+ bowl, near the "flexible interface" between RCK domains, and on the surface of the gating ring that faces the voltage sensors. The structure suggests that the Ca2+ gating ring, in addition to regulating the pore directly, may also modulate the voltage sensor.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022345/" 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/PMC3022345/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yuan, Peng -- Leonetti, Manuel D -- Pico, Alexander R -- Hsiung, Yichun -- MacKinnon, Roderick -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 GM043949/GM/NIGMS NIH HHS/ -- R01 GM043949-20/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Jul 9;329(5988):182-6. doi: 10.1126/science.1190414. Epub 2010 May 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20508092" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Calcium/*metabolism ; Crystallography, X-Ray ; Humans ; *Ion Channel Gating ; Large-Conductance Calcium-Activated Potassium Channel alpha ; Subunits/*chemistry/genetics/*metabolism ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Patch-Clamp Techniques ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Sodium/metabolism
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  • 37
    Publication Date: 2010-10-12
    Description: CLC proteins transport chloride (Cl(-)) ions across cell membranes to control the electrical potential of muscle cells, transfer electrolytes across epithelia, and control the pH and electrolyte composition of intracellular organelles. Some members of this protein family are Cl(-) ion channels, whereas others are secondary active transporters that exchange Cl(-) ions and protons (H(+)) with a 2:1 stoichiometry. We have determined the structure of a eukaryotic CLC transporter at 3.5 angstrom resolution. Cytoplasmic cystathionine beta-synthase (CBS) domains are strategically positioned to regulate the ion-transport pathway, and many disease-causing mutations in human CLCs reside on the CBS-transmembrane interface. Comparison with prokaryotic CLC shows that a gating glutamate residue changes conformation and suggests a basis for 2:1 Cl(-)/H(+) exchange and a simple mechanistic connection between CLC channels and transporters.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3079386/" 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/PMC3079386/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feng, Liang -- Campbell, Ernest B -- Hsiung, Yichun -- MacKinnon, Roderick -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 GM043949/GM/NIGMS NIH HHS/ -- R01 GM043949-20/GM/NIGMS NIH HHS/ -- R01 GM043949-21/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Oct 29;330(6004):635-41. doi: 10.1126/science.1195230. Epub 2010 Sep 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20929736" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/chemistry/metabolism ; Animals ; Antiporters/*chemistry/metabolism ; Binding Sites ; Cell Line ; Cell Membrane/chemistry ; Chloride Channels/*chemistry/metabolism ; Chlorides/*metabolism ; Crystallization ; Crystallography, X-Ray ; Cystathionine beta-Synthase/chemistry ; Cytoplasm/chemistry ; Glutamic Acid/metabolism ; Ion Channel Gating ; Ion Transport ; Models, Biological ; Models, Molecular ; Protein Conformation ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Protons ; Rhodophyta/*chemistry/metabolism
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  • 38
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-12-18
    Description: Carbon and water flow between plants and the atmosphere is regulated by the opening and closing of minute stomatal pores in surfaces of leaves. By changing the aperture of stomata, plants regulate water loss and photosynthetic carbon gain in response to many environmental stimuli, but stomatal movements cannot yet be reliably predicted. We found that the complexity that characterizes stomatal control in seed plants is absent in early-diverging vascular plant lineages. Lycophyte and fern stomata are shown to lack key responses to abscisic acid and epidermal cell turgor, making their behavior highly predictable. These results indicate that a fundamental transition from passive to active metabolic control of plant water balance occurred after the divergence of ferns about 360 million years ago.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brodribb, Tim J -- McAdam, Scott A M -- New York, N.Y. -- Science. 2011 Feb 4;331(6017):582-5. doi: 10.1126/science.1197985. Epub 2010 Dec 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Plant Science, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia. timothyb@utas.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21163966" target="_blank"〉PubMed〈/a〉
    Keywords: Abscisic Acid/metabolism/pharmacology ; Angiosperms/metabolism/*physiology ; *Biological Evolution ; Ferns/metabolism/*physiology ; Gymnosperms/metabolism/*physiology ; Light ; Lycopodiaceae/metabolism/*physiology ; Plant Epidermis/metabolism ; Plant Leaves/*metabolism ; Plant Stomata/cytology/*physiology ; Plant Transpiration ; Vapor Pressure ; Water/metabolism
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  • 39
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-11-26
    Description: The last common ancestor of plants and animals may have lived 1 billion years ago. Plants and animals have occasionally exchanged genes but, for the most part, have countered selective pressures independently. Microbes (bacteria, eukaryotes, and viruses) were omnipresent threats, influencing the direction of multicellular evolution. Receptors that detect molecular signatures of infectious organisms mediate awareness of nonself and are integral to host defense in plants and animals alike. The discoveries leading to elucidation of these receptors and their ligands followed a similar logical and methodological pathway in both plant and animal research.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ronald, Pamela C -- Beutler, Bruce -- New York, N.Y. -- Science. 2010 Nov 19;330(6007):1061-4. doi: 10.1126/science.1189468.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Pathology, University of California, Davis, CA 95616, USA. pcronald@ucdavis.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21097929" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Humans ; *Immunity/genetics ; Immunity, Innate ; Plant Proteins/genetics/immunology ; Plants/genetics/*immunology/microbiology ; *Receptors, Immunologic/physiology
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  • 40
    Publication Date: 2010-04-03
    Description: Voltage sensors regulate the conformations of voltage-dependent ion channels and enzymes. Their nearly switchlike response as a function of membrane voltage comes from the movement of positively charged amino acids, arginine or lysine, across the membrane field. We used mutations with natural and unnatural amino acids, electrophysiological recordings, and x-ray crystallography to identify a charge transfer center in voltage sensors that facilitates this movement. This center consists of a rigid cyclic "cap" and two negatively charged amino acids to interact with a positive charge. Specific mutations induce a preference for lysine relative to arginine. By placing lysine at specific locations, the voltage sensor can be stabilized in different conformations, which enables a dissection of voltage sensor movements and their relation to ion channel opening.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2869078/" 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/PMC2869078/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tao, Xiao -- Lee, Alice -- Limapichat, Walrati -- Dougherty, Dennis A -- MacKinnon, Roderick -- GM43949/GM/NIGMS NIH HHS/ -- NS 34407/NS/NINDS NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 GM043949/GM/NIGMS NIH HHS/ -- R01 GM043949-20/GM/NIGMS NIH HHS/ -- R37 NS034407/NS/NINDS NIH HHS/ -- R37 NS034407-15/NS/NINDS NIH HHS/ -- R37 NS034407-15S1/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Apr 2;328(5974):67-73. doi: 10.1126/science.1185954.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360102" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Arginine/chemistry ; Binding Sites ; Crystallography, X-Ray ; Electric Capacitance ; *Ion Channel Gating ; Kv1.2 Potassium Channel/*chemistry/*metabolism ; Lysine/chemistry ; Models, Molecular ; Molecular Sequence Data ; Patch-Clamp Techniques ; Phenylalanine/chemistry ; Protein Conformation ; Rats ; Recombinant Fusion Proteins/chemistry/metabolism ; Shab Potassium Channels/*chemistry/*metabolism ; Shaker Superfamily of Potassium Channels/chemistry/metabolism ; Tryptophan/chemistry ; Xenopus laevis
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  • 41
    Publication Date: 2010-12-24
    Description: To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495/" 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/PMC3192495/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉modENCODE Consortium -- Roy, Sushmita -- Ernst, Jason -- Kharchenko, Peter V -- Kheradpour, Pouya -- Negre, Nicolas -- Eaton, Matthew L -- Landolin, Jane M -- Bristow, Christopher A -- Ma, Lijia -- Lin, Michael F -- Washietl, Stefan -- Arshinoff, Bradley I -- Ay, Ferhat -- Meyer, Patrick E -- Robine, Nicolas -- Washington, Nicole L -- Di Stefano, Luisa -- Berezikov, Eugene -- Brown, Christopher D -- Candeias, Rogerio -- Carlson, Joseph W -- Carr, Adrian -- Jungreis, Irwin -- Marbach, Daniel -- Sealfon, Rachel -- Tolstorukov, Michael Y -- Will, Sebastian -- Alekseyenko, Artyom A -- Artieri, Carlo -- Booth, Benjamin W -- Brooks, Angela N -- Dai, Qi -- Davis, Carrie A -- Duff, Michael O -- Feng, Xin -- Gorchakov, Andrey A -- Gu, Tingting -- Henikoff, Jorja G -- Kapranov, Philipp -- Li, Renhua -- MacAlpine, Heather K -- Malone, John -- Minoda, Aki -- Nordman, Jared -- Okamura, Katsutomo -- Perry, Marc -- Powell, Sara K -- Riddle, Nicole C -- Sakai, Akiko -- Samsonova, Anastasia -- Sandler, Jeremy E -- Schwartz, Yuri B -- Sher, Noa -- Spokony, Rebecca -- Sturgill, David -- van Baren, Marijke -- Wan, Kenneth H -- Yang, Li -- Yu, Charles -- Feingold, Elise -- Good, Peter -- Guyer, Mark -- Lowdon, Rebecca -- Ahmad, Kami -- Andrews, Justen -- Berger, Bonnie -- Brenner, Steven E -- Brent, Michael R -- Cherbas, Lucy -- Elgin, Sarah C R -- Gingeras, Thomas R -- Grossman, Robert -- Hoskins, Roger A -- Kaufman, Thomas C -- Kent, William -- Kuroda, Mitzi I -- Orr-Weaver, Terry -- Perrimon, Norbert -- Pirrotta, Vincenzo -- Posakony, James W -- Ren, Bing -- Russell, Steven -- Cherbas, Peter -- Graveley, Brenton R -- Lewis, Suzanna -- Micklem, Gos -- Oliver, Brian -- Park, Peter J -- Celniker, Susan E -- Henikoff, Steven -- Karpen, Gary H -- Lai, Eric C -- MacAlpine, David M -- Stein, Lincoln D -- White, Kevin P -- Kellis, Manolis -- R01 HG004037/HG/NHGRI NIH HHS/ -- R01HG004037/HG/NHGRI NIH HHS/ -- RC2HG005639/HG/NHGRI NIH HHS/ -- U01 HG004258/HG/NHGRI NIH HHS/ -- U01 HG004271/HG/NHGRI NIH HHS/ -- U01 HG004279/HG/NHGRI NIH HHS/ -- U01HG004258/HG/NHGRI NIH HHS/ -- U01HG004261/HG/NHGRI NIH HHS/ -- U01HG004264/HG/NHGRI NIH HHS/ -- U01HG004271/HG/NHGRI NIH HHS/ -- U01HG004274/HG/NHGRI NIH HHS/ -- U01HG004279/HG/NHGRI NIH HHS/ -- U41HG004269/HG/NHGRI NIH HHS/ -- ZIA DK015600-14/Intramural NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Dec 24;330(6012):1787-97. doi: 10.1126/science.1198374. Epub 2010 Dec 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21177974" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; *Chromatin/genetics/metabolism ; Computational Biology/methods ; Drosophila Proteins/genetics/metabolism ; Drosophila melanogaster/*genetics/growth & development/metabolism ; Epigenesis, Genetic ; Gene Expression Regulation ; *Gene Regulatory Networks ; Genes, Insect ; *Genome, Insect ; Genomics/methods ; Histones/metabolism ; *Molecular Sequence Annotation ; Nucleosomes/genetics/metabolism ; Promoter Regions, Genetic ; RNA, Small Untranslated/genetics/metabolism ; Transcription Factors/metabolism ; Transcription, Genetic
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  • 42
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-04-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Balter, Michael -- New York, N.Y. -- Science. 2010 Apr 9;328(5975):162. doi: 10.1126/science.328.5975.162.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20378789" target="_blank"〉PubMed〈/a〉
    Keywords: *Behavior ; *Biological Evolution ; Brain/physiology ; Humans ; *Memory, Short-Term ; *Models, Psychological
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  • 43
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-04-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Balter, Michael -- New York, N.Y. -- Science. 2010 Apr 9;328(5975):160-3. doi: 10.1126/science.328.5975.160.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20378788" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Art ; *Biological Evolution ; *Cognition ; Creativity ; Cultural Evolution ; Executive Function ; Hominidae ; Humans ; *Memory, Short-Term ; Models, Psychological ; Symbolism
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  • 44
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-02-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Levens, David -- Gupta, Ashutosh -- New York, N.Y. -- Science. 2010 Feb 26;327(5969):1088-9. doi: 10.1126/science.1187268.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA. levensd@mail.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20185714" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Feedback, Physiological ; *Gene Expression Regulation ; *Gene Regulatory Networks ; Promoter Regions, Genetic ; Recombinant Proteins/metabolism ; Stochastic Processes ; Transcription Factors/*genetics/*metabolism ; *Transcription, Genetic
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  • 45
    Publication Date: 2010-03-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Balter, Michael -- New York, N.Y. -- Science. 2010 Mar 26;327(5973):1566-7. doi: 10.1126/science.327.5973.1566-b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20339040" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; DNA, Mitochondrial/chemistry/*genetics ; Finger Phalanges ; Genome, Mitochondrial ; Hominidae/*classification/genetics ; Humans ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Siberia ; Time
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  • 46
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-10-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stuessy, Tod -- New York, N.Y. -- Science. 2010 Sep 24;329(5999):1605-6. doi: 10.1126/science.1195336.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Systematic and Evolutionary Botany, Biodiversity Center, University of Vienna, Rennweg 14, A-1030 Vienna, Austria. tod.stuessy@univie.ac.at〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20929832" target="_blank"〉PubMed〈/a〉
    Keywords: *Asteraceae/anatomy & histology/classification ; *Biological Evolution ; Flowers/anatomy & histology ; *Fossils ; *Helianthus/anatomy & histology/classification/genetics ; Phylogeny ; South America
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  • 47
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-10-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cohen, Jon -- New York, N.Y. -- Science. 2010 Sep 24;329(5999):1586-7. doi: 10.1126/science.329.5999.1586.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20929818" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Ape Diseases/parasitology ; *Biological Evolution ; DNA, Protozoan/analysis/genetics ; Feces/*parasitology ; Gorilla gorilla/*parasitology ; Humans ; Malaria/parasitology/veterinary ; Malaria, Falciparum/parasitology ; Pan paniscus/parasitology ; Pan troglodytes/*parasitology ; Plasmodium/classification/*genetics/isolation & purification ; Plasmodium falciparum/*genetics
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  • 48
    Publication Date: 2010-10-12
    Description: Fossil capitula and pollen grains of Asteraceae from the Eocene of Patagonia, southern Argentina, exhibit morphological features recognized today in taxa, such as Mutisioideae and Carduoideae, that are phylogenetically close to the root of the asteracean tree. This fossil supports the hypothesis of a South American origin of Asteraceae and an Eocene age of divergence and suggests that an ancestral stock of Asteraceae may have formed part of a geoflora developed in southern Gondwana before the establishment of effective dispersal barriers within this landmass.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barreda, V D -- Palazzesi, L -- Telleria, M C -- Katinas, L -- Crisci, J V -- Bremer, K -- Passalia, M G -- Corsolini, R -- Rodriguez Brizuela, R -- Bechis, F -- New York, N.Y. -- Science. 2010 Sep 24;329(5999):1621. doi: 10.1126/science.1193108.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Seccion Paleopalinologia, Division Paleobotanica, Museo Argentino de Ciencias Naturales Bernardino Rivadavia, Avenida Angel Gallardo 470, C1405DJR Buenos Aires, Argentina. vbarreda@macn.gov.ar〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20929840" target="_blank"〉PubMed〈/a〉
    Keywords: Argentina ; *Asteraceae/anatomy & histology/classification/genetics ; *Biological Evolution ; Climate ; Flowers/*anatomy & histology ; *Fossils ; Phylogeny ; Pollen ; South America
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  • 49
    Publication Date: 2010-06-05
    Description: Three-prime untranslated regions (3'UTRs) of metazoan messenger RNAs (mRNAs) contain numerous regulatory elements, yet remain largely uncharacterized. Using polyA capture, 3' rapid amplification of complementary DNA (cDNA) ends, full-length cDNAs, and RNA-seq, we defined approximately 26,000 distinct 3'UTRs in Caenorhabditis elegans for approximately 85% of the 18,328 experimentally supported protein-coding genes and revised approximately 40% of gene models. Alternative 3'UTR isoforms are frequent, often differentially expressed during development. Average 3'UTR length decreases with animal age. Surprisingly, no polyadenylation signal (PAS) was detected for 13% of polyadenylation sites, predominantly among shorter alternative isoforms. Trans-spliced (versus non-trans-spliced) mRNAs possess longer 3'UTRs and frequently contain no PAS or variant PAS. We identified conserved 3'UTR motifs, isoform-specific predicted microRNA target sites, and polyadenylation of most histone genes. Our data reveal a rich complexity of 3'UTRs, both genome-wide and throughout development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142571/" 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/PMC3142571/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mangone, Marco -- Manoharan, Arun Prasad -- Thierry-Mieg, Danielle -- Thierry-Mieg, Jean -- Han, Ting -- Mackowiak, Sebastian D -- Mis, Emily -- Zegar, Charles -- Gutwein, Michelle R -- Khivansara, Vishal -- Attie, Oliver -- Chen, Kevin -- Salehi-Ashtiani, Kourosh -- Vidal, Marc -- Harkins, Timothy T -- Bouffard, Pascal -- Suzuki, Yutaka -- Sugano, Sumio -- Kohara, Yuji -- Rajewsky, Nikolaus -- Piano, Fabio -- Gunsalus, Kristin C -- Kim, John K -- R00HG004515/HG/NHGRI NIH HHS/ -- R01 GM088565/GM/NIGMS NIH HHS/ -- R01 GM088565-03/GM/NIGMS NIH HHS/ -- R01GM088565/GM/NIGMS NIH HHS/ -- U01-HG004276/HG/NHGRI NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Jul 23;329(5990):432-5. doi: 10.1126/science.1191244. Epub 2010 Jun 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, New York, NY 10003, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20522740" target="_blank"〉PubMed〈/a〉
    Keywords: *3' Untranslated Regions ; Animals ; Binding Sites ; Caenorhabditis elegans/embryology/*genetics/growth & development ; Computational Biology ; Conserved Sequence ; Disorders of Sex Development ; Gene Expression Regulation, Developmental ; Gene Library ; *Genes, Helminth ; Helminth Proteins/genetics ; Histones/genetics ; Male ; MicroRNAs/metabolism ; Operon ; Poly A/metabolism ; Polyadenylation ; RNA, Helminth/*genetics ; RNA, Messenger/genetics ; Trans-Splicing
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  • 50
    Publication Date: 2010-11-06
    Description: The brain's visual cortex processes information concerning form, pattern, and motion within functional maps that reflect the layout of neuronal circuits. We analyzed functional maps of orientation preference in the ferret, tree shrew, and galago--three species separated since the basal radiation of placental mammals more than 65 million years ago--and found a common organizing principle. A symmetry-based class of models for the self-organization of cortical networks predicts all essential features of the layout of these neuronal circuits, but only if suppressive long-range interactions dominate development. We show mathematically that orientation-selective long-range connectivity can mediate the required interactions. Our results suggest that self-organization has canalized the evolution of the neuronal circuitry underlying orientation preference maps into a single common design.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3138194/" 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/PMC3138194/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kaschube, Matthias -- Schnabel, Michael -- Lowel, Siegrid -- Coppola, David M -- White, Leonard E -- Wolf, Fred -- EY06821/EY/NEI NIH HHS/ -- EY11488/EY/NEI NIH HHS/ -- P50 GM071508/GM/NIGMS NIH HHS/ -- P50 GM071508-08/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Nov 19;330(6007):1113-6. doi: 10.1126/science.1194869. Epub 2010 Nov 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institute for Dynamics and Self-Organization, Bernstein Center for Computational Neuroscience, Faculty of Physics, Gottingen University, D-37073 Gottingen, Germany. kaschube@princeton.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21051599" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Ferrets/anatomy & histology ; Galago/anatomy & histology ; Neurons/*cytology ; Tupaiidae/anatomy & histology ; Visual Cortex/*anatomy & histology/cytology
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  • 51
    Publication Date: 2010-04-03
    Description: The MADS-domain transcription factor APETALA1 (AP1) is a key regulator of Arabidopsis flower development. To understand the molecular mechanisms underlying AP1 function, we identified its target genes during floral initiation using a combination of gene expression profiling and genome-wide binding studies. Many of its targets encode transcriptional regulators, including known floral repressors. The latter genes are down-regulated by AP1, suggesting that it initiates floral development by abrogating the inhibitory effects of these genes. Although AP1 acts predominantly as a transcriptional repressor during the earliest stages of flower development, at more advanced stages it also activates regulatory genes required for floral organ formation, indicating a dynamic mode of action. Our results further imply that AP1 orchestrates floral initiation by integrating growth, patterning, and hormonal pathways.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kaufmann, Kerstin -- Wellmer, Frank -- Muino, Jose M -- Ferrier, Thilia -- Wuest, Samuel E -- Kumar, Vijaya -- Serrano-Mislata, Antonio -- Madueno, Francisco -- Krajewski, Pawel -- Meyerowitz, Elliot M -- Angenent, Gerco C -- Riechmann, Jose Luis -- New York, N.Y. -- Science. 2010 Apr 2;328(5974):85-9. doi: 10.1126/science.1185244.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Business Unit Bioscience, Plant Research International, Wageningen 6700 AA, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360106" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/*genetics/*growth & development/metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Binding Sites ; Chromatin Immunoprecipitation ; Down-Regulation ; Flowers/*growth & development ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Genes, Plant ; Genome, Plant ; Homeodomain Proteins/genetics/metabolism ; MADS Domain Proteins/genetics/*metabolism ; Oligonucleotide Array Sequence Analysis ; Transcription Factors/genetics/*metabolism ; Transcription Initiation Site ; *Transcription, Genetic ; Transcriptional Activation
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  • 52
    Publication Date: 2010-09-04
    Description: Coxsackie and adenovirus receptor (CAR) is the primary cellular receptor for group B coxsackieviruses and most adenovirus serotypes and plays a crucial role in adenoviral gene therapy. Recent discovery of the interaction between junctional adhesion molecule-like protein (JAML) and CAR uncovered important functional roles in immunity, inflammation, and tissue homeostasis. Crystal structures of JAML ectodomain (2.2 angstroms) and its complex with CAR (2.8 angstroms) reveal an unusual immunoglobulin-domain assembly for JAML and a charged interface that confers high specificity. Biochemical and mutagenesis studies illustrate how CAR-mediated clustering of JAML recruits phosphoinositide 3-kinase (P13K) to a JAML intracellular sequence motif as delineated for the alphabeta T cell costimulatory receptor CD28. Thus, CAR and JAML are cell signaling receptors of the immune system with implications for asthma, cancer, and chronic nonhealing wounds.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951132/" 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/PMC2951132/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Verdino, Petra -- Witherden, Deborah A -- Havran, Wendy L -- Wilson, Ian A -- AI064811/AI/NIAID NIH HHS/ -- AI42266/AI/NIAID NIH HHS/ -- AI52257/AI/NIAID NIH HHS/ -- CA58896/CA/NCI NIH HHS/ -- R01 AI036964/AI/NIAID NIH HHS/ -- R01 AI052257/AI/NIAID NIH HHS/ -- R01 AI052257-05/AI/NIAID NIH HHS/ -- R01 AI064811/AI/NIAID NIH HHS/ -- R01 AI064811-01A1/AI/NIAID NIH HHS/ -- R01 CA058896/CA/NCI NIH HHS/ -- R01 CA058896-16A1/CA/NCI NIH HHS/ -- R01 GM080301/GM/NIGMS NIH HHS/ -- R37 AI042266/AI/NIAID NIH HHS/ -- R37 AI042266-13/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2010 Sep 3;329(5996):1210-4. doi: 10.1126/science.1187996.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20813955" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD28/metabolism ; Binding Sites ; CHO Cells ; Cell Adhesion Molecules/*chemistry/*metabolism ; Coxsackie and Adenovirus Receptor-Like Membrane Protein ; Cricetinae ; Cricetulus ; Crystallization ; Crystallography, X-Ray ; Epithelium/immunology ; Glycosylation ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Mice ; Phosphatidylinositol 3-Kinases/*metabolism ; Physicochemical Processes ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Tertiary ; Receptors, Antigen, T-Cell, gamma-delta/immunology/metabolism ; Receptors, Virus/*chemistry/*metabolism ; *Signal Transduction ; T-Lymphocyte Subsets/immunology/metabolism
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  • 53
    Publication Date: 2010-04-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhattacharjee, Yudhijit -- New York, N.Y. -- Science. 2010 Apr 9;328(5975):150-1. doi: 10.1126/science.328.5975.150.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20378779" target="_blank"〉PubMed〈/a〉
    Keywords: Astronomical Phenomena ; *Biological Evolution ; Data Collection ; *Educational Status ; Humans ; Public Opinion ; Religion and Science ; *Science ; United States ; *United States Government Agencies
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  • 54
    Publication Date: 2010-11-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gray, Michael W -- Lukes, Julius -- Archibald, John M -- Keeling, Patrick J -- Doolittle, W Ford -- New York, N.Y. -- Science. 2010 Nov 12;330(6006):920-1. doi: 10.1126/science.1198594.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21071654" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Cell Physiological Processes ; Genome, Mitochondrial ; Introns ; Mitochondria/genetics/physiology ; Models, Biological ; Mutation ; RNA Editing ; RNA Splicing ; Ribosomes/physiology ; Selection, Genetic ; Spliceosomes/genetics/physiology
    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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  • 55
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-08-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gibbons, Ann -- New York, N.Y. -- Science. 2010 Aug 13;329(5993):740-2. doi: 10.1126/science.329.5993.740.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20705825" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics ; *Biological Evolution ; Gene Frequency ; Genetic Techniques ; Genetics, Population/*methods ; *Genome, Human ; Haplotypes ; Humans ; Models, Genetic ; Multifactorial Inheritance ; Mutation ; *Polymorphism, Single Nucleotide ; *Selection, Genetic
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  • 56
    Publication Date: 2010-07-10
    Description: Long intergenic noncoding RNAs (lincRNAs) regulate chromatin states and epigenetic inheritance. Here, we show that the lincRNA HOTAIR serves as a scaffold for at least two distinct histone modification complexes. A 5' domain of HOTAIR binds polycomb repressive complex 2 (PRC2), whereas a 3' domain of HOTAIR binds the LSD1/CoREST/REST complex. The ability to tether two distinct complexes enables RNA-mediated assembly of PRC2 and LSD1 and coordinates targeting of PRC2 and LSD1 to chromatin for coupled histone H3 lysine 27 methylation and lysine 4 demethylation. Our results suggest that lincRNAs may serve as scaffolds by providing binding surfaces to assemble select histone modification enzymes, thereby specifying the pattern of histone modifications on target genes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2967777/" 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/PMC2967777/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tsai, Miao-Chih -- Manor, Ohad -- Wan, Yue -- Mosammaparast, Nima -- Wang, Jordon K -- Lan, Fei -- Shi, Yang -- Segal, Eran -- Chang, Howard Y -- R01 CA118750/CA/NCI NIH HHS/ -- R01 CA119176/CA/NCI NIH HHS/ -- R01 CA119176-05/CA/NCI NIH HHS/ -- R01-CA118487/CA/NCI NIH HHS/ -- R01-HG004361/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Aug 6;329(5992):689-93. doi: 10.1126/science.1192002. Epub 2010 Jul 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Program in Epithelial 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/20616235" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carrier Proteins/metabolism ; Cell Line ; Cells, Cultured ; Chromatin/*metabolism ; Chromatin Immunoprecipitation ; Co-Repressor Proteins ; DNA-Binding Proteins/*metabolism ; HeLa Cells ; Histone Demethylases/*metabolism ; Histones/*metabolism ; Humans ; Methylation ; Mutation ; Nerve Tissue Proteins/metabolism ; Nuclear Proteins/metabolism ; Nucleic Acid Conformation ; Polycomb Repressive Complex 2 ; Polycomb-Group Proteins ; Promoter Regions, Genetic ; Protein Binding ; RNA Interference ; RNA, Untranslated/chemistry/*metabolism ; Repressor Proteins/*metabolism ; Transcription Factors/*metabolism ; Transcription, Genetic
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  • 57
    Publication Date: 2010-02-20
    Description: Modern cetaceans, a poster child of evolution, play an important role in the ocean ecosystem as apex predators and nutrient distributors, as well as evolutionary "stepping stones" for the deep sea biota. Recent discussions on the impact of climate change and marine exploitation on current cetacean populations may benefit from insights into what factors have influenced cetacean diversity in the past. Previous studies suggested that the rise of diatoms as dominant marine primary producers and global temperature change were key factors in the evolution of modern whales. Based on a comprehensive diversity data set, we show that much of observed cetacean paleodiversity can indeed be explained by diatom diversity in conjunction with variations in climate as indicated by oxygen stable isotope records (delta18O).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, Felix G -- Uhen, Mark D -- New York, N.Y. -- Science. 2010 Feb 19;327(5968):993-6. doi: 10.1126/science.1185581.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geology, University of Otago, 360 Leith Walk, Post Office Box 56, Dunedin, Otago 9016, New Zealand. f.g.marx@bristol.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20167785" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; *Biological Evolution ; *Cetacea/classification/physiology ; *Climate Change ; *Diatoms ; *Ecosystem ; Feeding Behavior ; Food Chain ; *Fossils ; Geologic Sediments ; Oceans and Seas ; Seawater ; Temperature ; *Whales/classification/physiology
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  • 58
    Publication Date: 2010-04-10
    Description: Transcription factors (TFs) direct gene expression by binding to DNA regulatory regions. To explore the evolution of gene regulation, we used chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) to determine experimentally the genome-wide occupancy of two TFs, CCAAT/enhancer-binding protein alpha and hepatocyte nuclear factor 4 alpha, in the livers of five vertebrates. Although each TF displays highly conserved DNA binding preferences, most binding is species-specific, and aligned binding events present in all five species are rare. Regions near genes with expression levels that are dependent on a TF are often bound by the TF in multiple species yet show no enhanced DNA sequence constraint. Binding divergence between species can be largely explained by sequence changes to the bound motifs. Among the binding events lost in one lineage, only half are recovered by another binding event within 10 kilobases. Our results reveal large interspecies differences in transcriptional regulation and provide insight into regulatory evolution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008766/" 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/PMC3008766/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schmidt, Dominic -- Wilson, Michael D -- Ballester, Benoit -- Schwalie, Petra C -- Brown, Gordon D -- Marshall, Aileen -- Kutter, Claudia -- Watt, Stephen -- Martinez-Jimenez, Celia P -- Mackay, Sarah -- Talianidis, Iannis -- Flicek, Paul -- Odom, Duncan T -- 062023/Wellcome Trust/United Kingdom -- 079643/Wellcome Trust/United Kingdom -- 15603/Cancer Research UK/United Kingdom -- 202218/European Research Council/International -- A15603/Cancer Research UK/United Kingdom -- WT062023/Wellcome Trust/United Kingdom -- WT079643/Wellcome Trust/United Kingdom -- Cancer Research UK/United Kingdom -- New York, N.Y. -- Science. 2010 May 21;328(5981):1036-40. doi: 10.1126/science.1186176. Epub 2010 Apr 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20378774" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Animals ; Base Sequence ; Binding Sites ; Biological Evolution ; CCAAT-Enhancer-Binding Protein-alpha/*metabolism ; Chickens/genetics ; Chromatin Immunoprecipitation ; DNA/genetics/metabolism ; Dogs ; *Evolution, Molecular ; *Gene Expression Regulation ; *Genome ; Genome, Human ; Hepatocyte Nuclear Factor 4/*metabolism ; Humans ; Liver/*metabolism ; Mice ; Opossums/genetics ; Protein Binding ; Regulatory Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Species Specificity ; Vertebrates/*genetics/metabolism
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  • 59
    Publication Date: 2010-05-29
    Description: Host defense peptides such as defensins are components of innate immunity and have retained antibiotic activity throughout evolution. Their activity is thought to be due to amphipathic structures, which enable binding and disruption of microbial cytoplasmic membranes. Contrary to this, we show that plectasin, a fungal defensin, acts by directly binding the bacterial cell-wall precursor Lipid II. A wide range of genetic and biochemical approaches identify cell-wall biosynthesis as the pathway targeted by plectasin. In vitro assays for cell-wall synthesis identified Lipid II as the specific cellular target. Consistently, binding studies confirmed the formation of an equimolar stoichiometric complex between Lipid II and plectasin. Furthermore, key residues in plectasin involved in complex formation were identified using nuclear magnetic resonance spectroscopy and computational modeling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schneider, Tanja -- Kruse, Thomas -- Wimmer, Reinhard -- Wiedemann, Imke -- Sass, Vera -- Pag, Ulrike -- Jansen, Andrea -- Nielsen, Allan K -- Mygind, Per H -- Raventos, Dorotea S -- Neve, Soren -- Ravn, Birthe -- Bonvin, Alexandre M J J -- De Maria, Leonardo -- Andersen, Anders S -- Gammelgaard, Lora K -- Sahl, Hans-Georg -- Kristensen, Hans-Henrik -- New York, N.Y. -- Science. 2010 May 28;328(5982):1168-72. doi: 10.1126/science.1185723.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Pharmaceutical Microbiology Section, Institute for Medical Microbiology, Immunology, and Parasitology, University of Bonn, D-53115 Bonn, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20508130" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/pharmacology ; Ascomycota/chemistry ; Bacillus subtilis/drug effects/growth & development/*metabolism/ultrastructure ; Binding Sites ; Cell Membrane/metabolism ; Cell Wall/*metabolism ; Computer Simulation ; Defensins/*metabolism/pharmacology ; Fungal Proteins/*metabolism/pharmacology ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Oligonucleotide Array Sequence Analysis ; Peptides/*metabolism/pharmacology ; Protein Conformation ; Staphylococcus/drug effects/growth & development/*metabolism/ultrastructure ; Uridine Diphosphate N-Acetylmuramic Acid/*analogs & derivatives/metabolism ; Vancomycin/pharmacology
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  • 60
    Publication Date: 2010-04-17
    Description: Cbln1, secreted from cerebellar granule cells, and the orphan glutamate receptor delta2 (GluD2), expressed by Purkinje cells, are essential for synapse integrity between these neurons in adult mice. Nevertheless, no endogenous binding partners for these molecules have been identified. We found that Cbln1 binds directly to the N-terminal domain of GluD2. GluD2 expression by postsynaptic cells, combined with exogenously applied Cbln1, was necessary and sufficient to induce new synapses in vitro and in the adult cerebellum in vivo. Further, beads coated with recombinant Cbln1 directly induced presynaptic differentiation and indirectly caused clustering of postsynaptic molecules via GluD2. These results indicate that the Cbln1-GluD2 complex is a unique synapse organizer that acts bidirectionally on both pre- and postsynaptic components.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Matsuda, Keiko -- Miura, Eriko -- Miyazaki, Taisuke -- Kakegawa, Wataru -- Emi, Kyoichi -- Narumi, Sakae -- Fukazawa, Yugo -- Ito-Ishida, Aya -- Kondo, Tetsuro -- Shigemoto, Ryuichi -- Watanabe, Masahiko -- Yuzaki, Michisuke -- New York, N.Y. -- Science. 2010 Apr 16;328(5976):363-8. doi: 10.1126/science.1185152.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, School of Medicine, Keio University, Tokyo 160-8582, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20395510" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Line ; Cells, Cultured ; Cerebellum/cytology/*physiology ; Coculture Techniques ; Excitatory Postsynaptic Potentials ; Humans ; Ligands ; Mice ; Nerve Tissue Proteins/*metabolism ; Presynaptic Terminals/physiology ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Precursors/*metabolism ; Purkinje Cells/metabolism/*physiology ; Rats ; Receptors, Glutamate/chemistry/*metabolism ; Recombinant Fusion Proteins/metabolism ; Synapses/*physiology ; Synaptic Membranes/metabolism
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  • 61
    Publication Date: 2010-02-06
    Description: Recent studies have identified range expansion as a potential driver of speciation. Yet it remains poorly understood how, under identical extrinsic settings, differential tendencies for geographic movement of taxa originate and subsequently affect diversification. We identified multiple traits that predict large distributional ranges in extant species of toads (Bufonidae) and used statistical methods to define and phylogenetically reconstruct an optimal range-expansion phenotype. Our results indicate that lineage-specific range-shifting abilities increased through an accumulation of adaptive traits that culminated in such a phenotype. This initiated the episode of global colonization and triggered the major radiation of toads. Evolution toward a range-expansion phenotype might be crucial to understanding both ancient widespread radiations and the evolutionary background of contemporary invasive species such as the cane toad.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Van Bocxlaer, Ines -- Loader, Simon P -- Roelants, Kim -- Biju, S D -- Menegon, Michele -- Bossuyt, Franky -- New York, N.Y. -- Science. 2010 Feb 5;327(5966):679-82. doi: 10.1126/science.1181707.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biology Department, Amphibian Evolution Lab, Unit of Ecology and Systematics, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20133569" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Biological ; Africa ; Animals ; Asia ; Australia ; Bayes Theorem ; *Biological Evolution ; *Bufonidae/anatomy & histology/classification/genetics/physiology ; Genetic Speciation ; Geography ; Likelihood Functions ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Population Dynamics ; Reproduction ; South America ; Species Specificity
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  • 62
    Publication Date: 2010-02-13
    Description: Synaptic vesicle fusion in brain synapses occurs in phases that are either tightly coupled to action potentials (synchronous), immediately following action potentials (asynchronous), or as stochastic events in the absence of action potentials (spontaneous). Synaptotagmin-1, -2, and -9 are vesicle-associated Ca2+ sensors for synchronous release. Here we found that double C2 domain (Doc2) proteins act as Ca2+ sensors to trigger spontaneous release. Although Doc2 proteins are cytosolic, they function analogously to synaptotagmin-1 but with a higher Ca2+ sensitivity. Doc2 proteins bound to N-ethylmaleimide-sensitive factor attachment receptor (SNARE) complexes in competition with synaptotagmin-1. Thus, different classes of multiple C2 domain-containing molecules trigger synchronous versus spontaneous fusion, which suggests a general mechanism for synaptic vesicle fusion triggered by the combined actions of SNAREs and multiple C2 domain-containing proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846320/" 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/PMC2846320/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Groffen, Alexander J -- Martens, Sascha -- Diez Arazola, Rocio -- Cornelisse, L Niels -- Lozovaya, Natalia -- de Jong, Arthur P H -- Goriounova, Natalia A -- Habets, Ron L P -- Takai, Yoshimi -- Borst, J Gerard -- Brose, Nils -- McMahon, Harvey T -- Verhage, Matthijs -- MC_U105178795/Medical Research Council/United Kingdom -- U.1051.02.007(78795)/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2010 Mar 26;327(5973):1614-8. doi: 10.1126/science.1183765. Epub 2010 Feb 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Functional Genomics, CNCR, Neuroscience Campus Amsterdam, VU University and VU Medical Center, Amsterdam, 1081 HV, Netherlands. sander.groffen@cncr.vu.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20150444" target="_blank"〉PubMed〈/a〉
    Keywords: Action Potentials ; Animals ; Binding Sites ; Calcium/*metabolism ; Calcium-Binding Proteins/chemistry/genetics/*metabolism ; Cells, Cultured ; Excitatory Postsynaptic Potentials ; Hippocampus/cytology ; Inhibitory Postsynaptic Potentials ; Membrane Fusion ; Mice ; Mice, Knockout ; Mutant Proteins/genetics/metabolism ; Nerve Tissue Proteins/chemistry/genetics/*metabolism ; Neurons/physiology ; Neurotransmitter Agents/*metabolism ; Patch-Clamp Techniques ; Protein Structure, Tertiary ; Purkinje Cells/physiology ; Rats ; SNARE Proteins/metabolism ; *Synaptic Transmission ; Synaptic Vesicles/*physiology ; Synaptotagmin I/metabolism
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  • 63
    Publication Date: 2010-04-24
    Description: Bacterial NusG is a highly conserved transcription factor that is required for most Rho activity in vivo. We show by nuclear magnetic resonance spectroscopy that Escherichia coli NusG carboxyl-terminal domain forms a complex alternatively with Rho or with transcription factor NusE, a protein identical to 30S ribosomal protein S10. Because NusG amino-terminal domain contacts RNA polymerase and the NusG carboxy-terminal domain interaction site of NusE is accessible in the ribosomal 30S subunit, NusG may act as a link between transcription and translation. Uncoupling of transcription and translation at the ends of bacterial operons enables transcription termination by Rho factor, and competition between ribosomal NusE and Rho for NusG helps to explain why Rho cannot terminate translated transcripts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burmann, Bjorn M -- Schweimer, Kristian -- Luo, Xiao -- Wahl, Markus C -- Stitt, Barbara L -- Gottesman, Max E -- Rosch, Paul -- GM037219/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Apr 23;328(5977):501-4. doi: 10.1126/science.1184953.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Lehrstuhl Biopolymere und Forschungszentrum fur Bio-Makromolekule, Universitat Bayreuth, Universitatsstrasse 30, 95447 Bayreuth, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20413501" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Binding, Competitive ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/biosynthesis/chemistry/*genetics/metabolism ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Operon ; Peptide Elongation Factors/chemistry/*metabolism ; Protein Binding ; *Protein Biosynthesis ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Ribosomal Proteins/chemistry/*metabolism ; Ribosome Subunits, Small, Bacterial/metabolism ; Transcription Factors/chemistry/*metabolism ; *Transcription, Genetic
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  • 64
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-08-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2010 Aug 6;329(5992):623-5. doi: 10.1126/science.329.5992.623.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20688995" target="_blank"〉PubMed〈/a〉
    Keywords: Angiosperms/classification/*genetics ; *Biological Evolution ; Genes, Plant ; Genome, Chloroplast ; History, 20th Century ; History, 21st Century ; Phylogeny ; Polyploidy ; Tragopogon/classification/*genetics ; United States
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  • 65
    Publication Date: 2010-03-20
    Description: The extent to which variation in chromatin structure and transcription factor binding may influence gene expression, and thus underlie or contribute to variation in phenotype, is unknown. To address this question, we cataloged both individual-to-individual variation and differences between homologous chromosomes within the same individual (allele-specific variation) in chromatin structure and transcription factor binding in lymphoblastoid cells derived from individuals of geographically diverse ancestry. Ten percent of active chromatin sites were individual-specific; a similar proportion were allele-specific. Both individual-specific and allele-specific sites were commonly transmitted from parent to child, which suggests that they are heritable features of the human genome. Our study shows that heritable chromatin status and transcription factor binding differ as a result of genetic variation and may underlie phenotypic variation in humans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929018/" 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/PMC2929018/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McDaniell, Ryan -- Lee, Bum-Kyu -- Song, Lingyun -- Liu, Zheng -- Boyle, Alan P -- Erdos, Michael R -- Scott, Laura J -- Morken, Mario A -- Kucera, Katerina S -- Battenhouse, Anna -- Keefe, Damian -- Collins, Francis S -- Willard, Huntington F -- Lieb, Jason D -- Furey, Terrence S -- Crawford, Gregory E -- Iyer, Vishwanath R -- Birney, Ewan -- U54 HG004563/HG/NHGRI NIH HHS/ -- U54 HG004563-03/HG/NHGRI NIH HHS/ -- Z01 HG000024/HG/NHGRI NIH HHS/ -- Z01 HG000024-13/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Apr 9;328(5975):235-9. doi: 10.1126/science.1184655. Epub 2010 Mar 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20299549" target="_blank"〉PubMed〈/a〉
    Keywords: African Continental Ancestry Group ; *Alleles ; Binding Sites ; Cell Line ; Chromatin/chemistry/*genetics/*metabolism ; Chromatin Immunoprecipitation ; Chromosomes, Human/genetics/metabolism ; Chromosomes, Human, X/genetics/metabolism ; Deoxyribonuclease I/metabolism ; European Continental Ancestry Group ; Female ; *Gene Expression Regulation ; *Genetic Variation ; Humans ; Male ; Nuclear Family ; Polymorphism, Single Nucleotide ; Protein Binding ; Regulatory Elements, Transcriptional ; Repressor Proteins/*metabolism ; Sequence Analysis, DNA ; Transcription Factors/*metabolism ; X Chromosome Inactivation
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  • 66
    Publication Date: 2010-05-22
    Description: The interactions of protein kinases and phosphatases with their regulatory subunits and substrates underpin cellular regulation. We identified a kinase and phosphatase interaction (KPI) network of 1844 interactions in budding yeast by mass spectrometric analysis of protein complexes. The KPI network contained many dense local regions of interactions that suggested new functions. Notably, the cell cycle phosphatase Cdc14 associated with multiple kinases that revealed roles for Cdc14 in mitogen-activated protein kinase signaling, the DNA damage response, and metabolism, whereas interactions of the target of rapamycin complex 1 (TORC1) uncovered new effector kinases in nitrogen and carbon metabolism. An extensive backbone of kinase-kinase interactions cross-connects the proteome and may serve to coordinate diverse cellular responses.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983991/" 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/PMC3983991/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Breitkreutz, Ashton -- Choi, Hyungwon -- Sharom, Jeffrey R -- Boucher, Lorrie -- Neduva, Victor -- Larsen, Brett -- Lin, Zhen-Yuan -- Breitkreutz, Bobby-Joe -- Stark, Chris -- Liu, Guomin -- Ahn, Jessica -- Dewar-Darch, Danielle -- Reguly, Teresa -- Tang, Xiaojing -- Almeida, Ricardo -- Qin, Zhaohui Steve -- Pawson, Tony -- Gingras, Anne-Claude -- Nesvizhskii, Alexey I -- Tyers, Mike -- CA-126239/CA/NCI NIH HHS/ -- MOP-12246/Canadian Institutes of Health Research/Canada -- MOP-57793/Canadian Institutes of Health Research/Canada -- MOP-84314/Canadian Institutes of Health Research/Canada -- R01 CA126239/CA/NCI NIH HHS/ -- R01 GM094231/GM/NIGMS NIH HHS/ -- R01 OD010929/OD/NIH HHS/ -- R01 RR024031/RR/NCRR NIH HHS/ -- R01 RR024031-05/RR/NCRR NIH HHS/ -- R01RR024031/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2010 May 21;328(5981):1043-6. doi: 10.1126/science.1176495.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1X5, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20489023" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carbon/metabolism ; Cell Cycle Proteins/metabolism ; DNA Damage ; MAP Kinase Signaling System ; Mass Spectrometry ; Metabolic Networks and Pathways ; Models, Biological ; Nitrogen/metabolism ; Phosphoprotein Phosphatases/*metabolism ; Phosphorylation ; Protein Interaction Mapping ; Protein Kinases/*metabolism ; Protein Subunits/metabolism ; Protein Tyrosine Phosphatases/metabolism ; Protein-Serine-Threonine Kinases/metabolism ; Proteome ; Saccharomyces cerevisiae/*enzymology/metabolism ; Saccharomyces cerevisiae Proteins/*metabolism ; Signal Transduction
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  • 67
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-10-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dawkins, Richard -- New York, N.Y. -- Science. 2010 Oct 1;330(6000):49. doi: 10.1126/science.1197701.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20929802" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; History, 21st Century ; Humans ; Reproduction ; Selection, Genetic ; United States
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  • 68
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-06-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McInerney, Joseph D -- Dougherty, Michael J -- New York, N.Y. -- Science. 2010 Jun 4;328(5983):1228. doi: 10.1126/science.328.5983.1228-b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20522758" target="_blank"〉PubMed〈/a〉
    Keywords: *Astronomical Phenomena ; *Biological Evolution ; *Culture ; Data Collection ; Humans ; *Public Opinion ; United States ; United States Government Agencies
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  • 69
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-07-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weyand, Simone -- Iwata, So -- New York, N.Y. -- Science. 2010 Jul 9;329(5988):151-2. doi: 10.1126/science.1192680.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20616256" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Calcium/*metabolism ; Humans ; *Ion Channel Gating ; Large-Conductance Calcium-Activated Potassium Channels/*chemistry/*metabolism ; Models, Molecular ; Protein Conformation ; Protein Structure, Tertiary
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  • 70
    Publication Date: 2010-08-21
    Description: The marine bacterium Vibrio parahaemolyticus causes gastroenteritis in humans and encodes the type III effector protein VPA0450, which contributes to host cell death caused by autophagy, cell rounding, and cell lysis. We found that VPA0450 is an inositol polyphosphate 5-phosphatase that hydrolyzed the D5 phosphate from the plasma membrane phospholipid phosphatidylinositol 4,5-bisphosphate. VPA0450 disrupted cytoskeletal binding sites on the inner surface of membranes of human cells and caused plasma membrane blebbing, which compromised membrane integrity and probably contributed to cell death by facilitating lysis. Thus, bacterial pathogens can disrupt adaptor protein-binding sites required for proper membrane and cytoskeleton dynamics by altering the homeostasis of membrane-bound inositol-signaling molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Broberg, Christopher A -- Zhang, Lingling -- Gonzalez, Herman -- Laskowski-Arce, Michelle A -- Orth, Kim -- 5T32GM008203/GM/NIGMS NIH HHS/ -- R01-AI056404/AI/NIAID NIH HHS/ -- R01-AI087808/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2010 Sep 24;329(5999):1660-2. doi: 10.1126/science.1192850. Epub 2010 Aug 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20724587" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/metabolism ; Amino Acid Sequence ; Autophagy ; Bacterial Proteins/chemistry/genetics/*metabolism ; Binding Sites ; Cell Membrane/*physiology/ultrastructure ; Cell Shape ; Computational Biology ; Cytoskeleton/physiology/ultrastructure ; HeLa Cells ; Homeostasis ; Humans ; Molecular Sequence Data ; Phosphatidylinositol 4,5-Diphosphate/metabolism ; Phosphatidylinositols/*metabolism ; Phosphoric Monoester Hydrolases/chemistry/genetics/*metabolism ; Protein Interaction Domains and Motifs ; Signal Transduction ; Transfection ; Vibrio parahaemolyticus/*enzymology/*pathogenicity
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  • 71
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-03-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hamback, Peter A -- New York, N.Y. -- Science. 2010 Mar 26;327(5973):1583-4. doi: 10.1126/science.1187724.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Botany, Stockholm University, SE-106 91 Stockholm, Sweden. peter.hamback@botan.su.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20339053" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Aphids/*physiology ; Asclepias/growth & development/*physiology ; Beetles/*physiology ; *Biological Evolution ; Biomass ; Cues ; *Ecosystem ; *Food Chain ; *Plant Physiological Phenomena ; Predatory Behavior ; Sesquiterpenes/metabolism
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  • 72
    Publication Date: 2010-10-12
    Description: Atmospheric reactions and slow geological processes controlled Earth's earliest nitrogen cycle, and by ~2.7 billion years ago, a linked suite of microbial processes evolved to form the modern nitrogen cycle with robust natural feedbacks and controls. Over the past century, however, the development of new agricultural practices to satisfy a growing global demand for food has drastically disrupted the nitrogen cycle. This has led to extensive eutrophication of fresh waters and coastal zones as well as increased inventories of the potent greenhouse gas nitrous oxide (N(2)O). Microbial processes will ultimately restore balance to the nitrogen cycle, but the damage done by humans to the nitrogen economy of the planet will persist for decades, possibly centuries, if active intervention and careful management strategies are not initiated.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Canfield, Donald E -- Glazer, Alexander N -- Falkowski, Paul G -- New York, N.Y. -- Science. 2010 Oct 8;330(6001):192-6. doi: 10.1126/science.1186120.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biology and Nordic Center for Earth Evolution, University of Southern Denmark, Campusvej 55, Odense M, Denmark. dec@biology.sdu.dk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20929768" target="_blank"〉PubMed〈/a〉
    Keywords: Archaea/genetics/*metabolism ; Atmosphere ; Bacteria/genetics/*metabolism ; *Biological Evolution ; Crops, Agricultural/growth & development/metabolism ; Ecological and Environmental Processes ; Eukaryota/genetics/*metabolism ; Evolution, Planetary ; Forecasting ; Humans ; Nitrogen/*chemistry/*metabolism ; Nitrogen Compounds/chemistry/metabolism ; Oxidation-Reduction ; Physicochemical Processes
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  • 73
    Publication Date: 2010-09-18
    Description: Tyrannosaurs, the group of dinosaurian carnivores that includes Tyrannosaurus rex and its closest relatives, are icons of prehistory. They are also the most intensively studied extinct dinosaurs, and thanks to large sample sizes and an influx of new discoveries, have become ancient exemplar organisms used to study many themes in vertebrate paleontology. A phylogeny that includes recently described species shows that tyrannosaurs originated by the Middle Jurassic but remained mostly small and ecologically marginal until the latest Cretaceous. Anatomical, biomechanical, and histological studies of T. rex and other derived tyrannosaurs show that large tyrannosaurs could not run rapidly, were capable of crushing bite forces, had accelerated growth rates and keen senses, and underwent pronounced changes during ontogeny. The biology and evolutionary history of tyrannosaurs provide a foundation for comparison with other dinosaurs and living organisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brusatte, Stephen L -- Norell, Mark A -- Carr, Thomas D -- Erickson, Gregory M -- Hutchinson, John R -- Balanoff, Amy M -- Bever, Gabe S -- Choiniere, Jonah N -- Makovicky, Peter J -- Xu, Xing -- New York, N.Y. -- Science. 2010 Sep 17;329(5998):1481-5. doi: 10.1126/science.1193304.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA. sbrusatte@amnh.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20847260" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Behavior, Animal ; *Biological Evolution ; *Dinosaurs/anatomy & histology/growth & development/physiology ; Ecosystem ; *Fossils ; Phylogeny ; Population Dynamics
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  • 74
    Publication Date: 2010-05-08
    Description: From bacteria to fish, a remarkable variety of marine life depends on bioluminescence (the chemical generation of light) for finding food, attracting mates, and evading predators. Disparate biochemical systems and diverse phylogenetic distribution patterns of light-emitting organisms highlight the ecological benefits of bioluminescence, with biochemical and genetic analyses providing new insights into the mechanisms of its evolution. The origins and functions of some bioluminescent systems, however, remain obscure. Here, I review recent advances in understanding bioluminescence in the ocean and highlight future research efforts that will unite molecular details with ecological and evolutionary relationships.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Widder, E A -- New York, N.Y. -- Science. 2010 May 7;328(5979):704-8. doi: 10.1126/science.1174269.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ocean Research and Conservation Association, Fort Pierce, FL 34949, USA. ewidder@teamorca.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20448176" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; *Biological Evolution ; *Ecosystem ; Fishes/*physiology ; Gram-Negative Bacteria/classification/genetics/*physiology ; Invertebrates/*physiology ; Luciferases/metabolism ; *Luminescence ; Luminescent Measurements ; Luminescent Proteins ; Oceans and Seas ; *Seawater/microbiology ; Selection, Genetic ; Species Specificity ; Symbiosis
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  • 75
    Publication Date: 2010-06-19
    Description: Conservation priorities are calculated on the basis of species richness, endemism, and threats. However, areas ranked highly for these factors may not represent regions of maximal evolutionary potential. The relationship between geography and evolutionary innovation was analyzed in a dominant complex of Caribbean reef corals, in which morphological and genetic data concur on species differences. Based on geometric morphometrics of Pleistocene corals and genetically characterized modern colonies, we found that morphological disparity varies from the center to the edge of the Caribbean, and we show that lineages are static at well-connected central locations but split or fuse in edge zones where gene flow is limited. Thus, conservation efforts in corals should focus not only on the centers of diversity but also on peripheral areas of species ranges and population connectivity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Budd, Ann F -- Pandolfi, John M -- New York, N.Y. -- Science. 2010 Jun 18;328(5985):1558-61. doi: 10.1126/science.1188947.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geoscience, University of Iowa, Iowa City, IA 52242, USA. ann-budd@uiowa.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20558718" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Animals ; Anthozoa/*anatomy & histology/classification/*genetics ; Barbados ; *Biodiversity ; *Biological Evolution ; Caribbean Region ; Extinction, Biological ; *Fossils ; Gene Flow ; Genetic Speciation ; Geography ; Hybridization, Genetic
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-11-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Devos, Damien P -- Reynaud, Emmanuel G -- New York, N.Y. -- Science. 2010 Nov 26;330(6008):1187-8. doi: 10.1126/science.1196720.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany. devos@embl.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21109658" target="_blank"〉PubMed〈/a〉
    Keywords: *Archaea/physiology/ultrastructure ; Bacterial Proteins/biosynthesis/genetics ; *Biological Evolution ; Cell Membrane/ultrastructure ; Cytoskeletal Proteins/biosynthesis/genetics ; Endocytosis ; *Eukaryota/physiology/ultrastructure ; Gram-Negative Bacteria/*classification/*genetics/physiology ; Intracellular Membranes/physiology/ultrastructure ; Peptidoglycan/biosynthesis ; Periplasm/physiology/ultrastructure ; Phenotype ; Phylogeny ; Symbiosis ; Tubulin/biosynthesis/genetics
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  • 77
    Publication Date: 2010-05-01
    Description: The evolution of grasses using C4 photosynthesis and their sudden rise to ecological dominance 3 to 8 million years ago is among the most dramatic examples of biome assembly in the geological record. A growing body of work suggests that the patterns and drivers of C4 grassland expansion were considerably more complex than originally assumed. Previous research has benefited substantially from dialog between geologists and ecologists, but current research must now integrate fully with phylogenetics. A synthesis of grass evolutionary biology with grassland ecosystem science will further our knowledge of the evolution of traits that promote dominance in grassland systems and will provide a new context in which to evaluate the relative importance of C4 photosynthesis in transforming ecosystems across large regions of Earth.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Edwards, Erika J -- Osborne, Colin P -- Stromberg, Caroline A E -- Smith, Stephen A -- C4 Grasses Consortium -- Bond, William J -- Christin, Pascal-Antoine -- Cousins, Asaph B -- Duvall, Melvin R -- Fox, David L -- Freckleton, Robert P -- Ghannoum, Oula -- Hartwell, James -- Huang, Yongsong -- Janis, Christine M -- Keeley, Jon E -- Kellogg, Elizabeth A -- Knapp, Alan K -- Leakey, Andrew D B -- Nelson, David M -- Saarela, Jeffery M -- Sage, Rowan F -- Sala, Osvaldo E -- Salamin, Nicolas -- Still, Christopher J -- Tipple, Brett -- New York, N.Y. -- Science. 2010 Apr 30;328(5978):587-91. doi: 10.1126/science.1177216.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA. erika_edwards@brown.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20431008" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Carbon Dioxide/metabolism ; Climate ; *Ecosystem ; Fossils ; Genetic Speciation ; Geography ; *Photosynthesis ; Phylogeny ; *Poaceae/classification/genetics/growth & development/metabolism ; Temperature ; Trees
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  • 78
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-10-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wright, Stephen I -- Barrett, Spencer C H -- New York, N.Y. -- Science. 2010 Oct 22;330(6003):459-60. doi: 10.1126/science.1198063.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada. stephen.wright@utoronto.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20966240" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Extinction, Biological ; Fertilization/*physiology ; Genetic Speciation ; Inbreeding ; *Selection, Genetic ; Solanaceae/*physiology
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  • 79
    Publication Date: 2010-03-27
    Description: Predators determine herbivore and plant biomass via so-called trophic cascades, and the strength of such effects is influenced by ecosystem productivity. To determine whether evolutionary trade-offs among plant traits influence patterns of trophic control, we manipulated predators and soil fertility and measured impacts of a major herbivore (the aphid Aphis nerii) on 16 milkweed species (Asclepias spp.) in a phylogenetic field experiment. Herbivore density was determined by variation in predation and trade-offs between herbivore resistance and plant growth strategy. Neither herbivore density nor predator effects on herbivores predicted the cascading effects of predators on plant biomass. Instead, cascade strength was strongly and positively associated with milkweed response to soil fertility. Accordingly, contemporary patterns of trophic control are driven by evolutionary convergent trade-offs faced by plants.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mooney, Kailen A -- Halitschke, Rayko -- Kessler, Andre -- Agrawal, Anurag A -- New York, N.Y. -- Science. 2010 Mar 26;327(5973):1642-4. doi: 10.1126/science.1184814.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697-2525 USA. mooneyk@uci.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20339073" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Aphids/*physiology ; Asclepias/growth & development/*physiology ; *Biological Evolution ; Biomass ; Cues ; *Ecosystem ; *Food Chain ; Population Density ; Predatory Behavior ; Sesquiterpenes/metabolism ; Soil ; Species Specificity
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 80
    Publication Date: 2010-11-26
    Description: Dopamine modulates movement, cognition, and emotion through activation of dopamine G protein-coupled receptors in the brain. The crystal structure of the human dopamine D3 receptor (D3R) in complex with the small molecule D2R/D3R-specific antagonist eticlopride reveals important features of the ligand binding pocket and extracellular loops. On the intracellular side of the receptor, a locked conformation of the ionic lock and two distinctly different conformations of intracellular loop 2 are observed. Docking of R-22, a D3R-selective antagonist, reveals an extracellular extension of the eticlopride binding site that comprises a second binding pocket for the aryl amide of R-22, which differs between the highly homologous D2R and D3R. This difference provides direction to the design of D3R-selective agents for treating drug abuse and other neuropsychiatric indications.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058422/" 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/PMC3058422/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chien, Ellen Y T -- Liu, Wei -- Zhao, Qiang -- Katritch, Vsevolod -- Han, Gye Won -- Hanson, Michael A -- Shi, Lei -- Newman, Amy Hauck -- Javitch, Jonathan A -- Cherezov, Vadim -- Stevens, Raymond C -- DA022413/DA/NIDA NIH HHS/ -- DA023694/DA/NIDA NIH HHS/ -- GM075915/GM/NIGMS NIH HHS/ -- K05 DA022413/DA/NIDA NIH HHS/ -- K05 DA022413-05/DA/NIDA NIH HHS/ -- MH54137/MH/NIMH NIH HHS/ -- P50 GM073197/GM/NIGMS NIH HHS/ -- P50 GM073197-07/GM/NIGMS NIH HHS/ -- R00 DA023694/DA/NIDA NIH HHS/ -- R00 DA023694-04/DA/NIDA NIH HHS/ -- R01 GM089857/GM/NIGMS NIH HHS/ -- R01 MH054137/MH/NIMH NIH HHS/ -- R01 MH054137-16/MH/NIMH NIH HHS/ -- R21 RR025336/RR/NCRR NIH HHS/ -- R21 RR025336-01A1/RR/NCRR NIH HHS/ -- U54 GM074961/GM/NIGMS NIH HHS/ -- U54 GM074961-050001/GM/NIGMS NIH HHS/ -- U54 GM094618/GM/NIGMS NIH HHS/ -- U54 GM094618-01/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Nov 19;330(6007):1091-5. doi: 10.1126/science.1197410.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21097933" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arginine/chemistry ; Binding Sites ; Cell Line ; Crystallography, X-Ray ; Dopamine Antagonists/*chemistry ; Dopamine D2 Receptor Antagonists ; Humans ; Models, Molecular ; Protein Conformation ; Receptors, Dopamine D3/antagonists & inhibitors/*chemistry ; Recombinant Proteins/chemistry ; Salicylamides/*chemistry ; Spodoptera
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  • 81
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-09-18
    Description: Among the reproductive barriers that can isolate species, hybrid sterility is frequently due to dysfunctional interactions between loci that accumulate between differentiating lineages. Theory describing the evolution of these incompatibilities has generated the prediction, still empirically untested, that loci underlying hybrid incompatibility should accumulate faster than linearly with time--the "snowball effect." We evaluated the accumulation of quantitative trait loci (QTL) between species in the plant group Solanum and found evidence for a faster-than-linear accumulation of hybrid seed sterility QTL, thus empirically evaluating and confirming this theoretical prediction. In comparison, loci underlying traits unrelated to hybrid sterility show no evidence for an accelerating rate of accumulation between species.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moyle, Leonie C -- Nakazato, Takuya -- New York, N.Y. -- Science. 2010 Sep 17;329(5998):1521-3. doi: 10.1126/science.1193063.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Indiana University, Bloomington, IN 47405, USA. lmoyle@indiana.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20847271" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Chromosome Mapping ; Epistasis, Genetic ; *Genes, Plant ; *Genetic Speciation ; *Hybridization, Genetic ; Linear Models ; Lycopersicon esculentum/*genetics/physiology ; Models, Genetic ; Plant Infertility/*genetics ; Pollen/genetics/physiology ; *Quantitative Trait Loci ; Reproduction/genetics ; Seeds/genetics/physiology ; Solanum/*genetics/physiology ; Species Specificity
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 82
    Publication Date: 2010-10-16
    Description: Crystallization of L-cystine is a critical step in the pathogenesis of cystine kidney stones. Treatments for this disease are somewhat effective but often lead to adverse side effects. Real-time in situ atomic force microscopy (AFM) reveals that L-cystine dimethylester (L-CDME) and L-cystine methylester (L-CME) dramatically reduce the growth velocity of the six symmetry-equivalent {100} steps because of specific binding at the crystal surface, which frustrates the attachment of L-cystine molecules. L-CDME and L-CME produce l-cystine crystals with different habits that reveal distinct binding modes at the crystal surfaces. The AFM observations are mirrored by reduced crystal yield and crystal size in the presence of L-CDME and L-CME, collectively suggesting a new pathway to the prevention of L-cystine stones by rational design of crystal growth inhibitors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rimer, Jeffrey D -- An, Zhihua -- Zhu, Zina -- Lee, Michael H -- Goldfarb, David S -- Wesson, Jeffrey A -- Ward, Michael D -- 1U54DK083908-01/DK/NIDDK NIH HHS/ -- R01 DK068551/DK/NIDDK NIH HHS/ -- R01-DK068551/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2010 Oct 15;330(6002):337-41. doi: 10.1126/science.1191968.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and the Molecular Design Institute, New York University (NYU), 100 Washington Square East, New York, NY 10003-6688, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20947757" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Cystine/*analogs & derivatives/*chemistry/metabolism/pharmacology ; Cystinuria/complications/*drug therapy ; Drug Design ; Humans ; Hydrogen Bonding ; Kidney Calculi/chemistry/etiology/*prevention & control ; Microscopy, Atomic Force ; Models, Molecular ; Molecular Mimicry ; Molecular Structure ; Physicochemical Processes ; Solubility
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  • 83
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-01-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stone, Richard -- New York, N.Y. -- Science. 2010 Jan 29;327(5965):508. doi: 10.1126/science.327.5965.508.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20110471" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Birds/anatomy & histology/classification/physiology ; Bone and Bones/anatomy & histology ; China ; *Dinosaurs/anatomy & histology/classification/physiology ; *Feathers/anatomy & histology/physiology ; Flight, Animal ; *Fossils ; Melanins/analysis ; Melanosomes/chemistry ; Pigmentation
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  • 84
    Publication Date: 2010-04-17
    Description: Eukaryotic cytosine methylation represses transcription but also occurs in the bodies of active genes, and the extent of methylation biology conservation is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons is not. We show that methylation of plant transposons in the CHG context extends to green algae and that exclusion of histone H2A.Z from methylated DNA is conserved between plants and animals, and we present evidence for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zemach, Assaf -- McDaniel, Ivy E -- Silva, Pedro -- Zilberman, Daniel -- New York, N.Y. -- Science. 2010 May 14;328(5980):916-9. doi: 10.1126/science.1186366. Epub 2010 Apr 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant and Microbial Biology, 211 Koshland Hall, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20395474" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Chlorophyta/genetics ; CpG Islands ; DNA (Cytosine-5-)-Methyltransferase/metabolism ; *DNA Methylation ; DNA Transposable Elements ; Eukaryota/*genetics/metabolism ; Fungi/genetics/metabolism ; Gene Expression Regulation ; *Genome ; *Genome, Fungal ; *Genome, Plant ; Histones/metabolism ; Phylogeny ; Plants/genetics/metabolism ; Promoter Regions, Genetic ; Selection, Genetic ; Transcription, Genetic
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  • 85
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-04-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roberts, Jeffrey W -- New York, N.Y. -- Science. 2010 Apr 23;328(5977):436-7. doi: 10.1126/science.1189971.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA. jwr7@cornell.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20413480" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/metabolism ; Binding Sites ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/metabolism ; Models, Genetic ; Peptide Elongation Factors/metabolism ; *Protein Biosynthesis ; RNA, Bacterial/biosynthesis/*metabolism ; RNA, Messenger/biosynthesis/*metabolism ; RNA, Ribosomal/biosynthesis ; RNA-Binding Proteins/metabolism ; Ribosomal Proteins/metabolism ; Ribosomes/*metabolism ; Transcription Factors/metabolism ; *Transcription, Genetic
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  • 86
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-07-03
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390060/" 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/PMC4390060/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Storz, Jay F -- R01 HL087216/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2010 Jul 2;329(5987):40-1. doi: 10.1126/science.1192481.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA. jstorz2@unl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20595602" target="_blank"〉PubMed〈/a〉
    Keywords: *Acclimatization ; *Altitude ; Asian Continental Ancestry Group/genetics ; Basic Helix-Loop-Helix Transcription Factors/genetics ; *Biological Evolution ; Erythropoiesis ; Ethnic Groups/genetics ; Genetic Association Studies ; Genomics ; Hemoglobins/analysis ; Humans ; Hypoxia-Inducible Factor-Proline Dioxygenases ; *Oxygen/blood ; PPAR alpha/genetics ; Procollagen-Proline Dioxygenase/genetics ; *Selection, Genetic ; Signal Transduction ; *Stress, Physiological ; Tibet
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  • 87
    Publication Date: 2010-06-19
    Description: The control of RNA alternative splicing is critical for generating biological diversity. Despite emerging genome-wide technologies to study RNA complexity, reliable and comprehensive RNA-regulatory networks have not been defined. Here, we used Bayesian networks to probabilistically model diverse data sets and predict the target networks of specific regulators. We applied this strategy to identify approximately 700 alternative splicing events directly regulated by the neuron-specific factor Nova in the mouse brain, integrating RNA-binding data, splicing microarray data, Nova-binding motifs, and evolutionary signatures. The resulting integrative network revealed combinatorial regulation by Nova and the neuronal splicing factor Fox, interplay between phosphorylation and splicing, and potential links to neurologic disease. Thus, we have developed a general approach to understanding mammalian RNA regulation at the systems level.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3412410/" 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/PMC3412410/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Chaolin -- Frias, Maria A -- Mele, Aldo -- Ruggiu, Matteo -- Eom, Taesun -- Marney, Christina B -- Wang, Huidong -- Licatalosi, Donny D -- Fak, John J -- Darnell, Robert B -- K99 GM095713/GM/NIGMS NIH HHS/ -- NS34389/NS/NINDS NIH HHS/ -- UL1 RR024143/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Jul 23;329(5990):439-43. doi: 10.1126/science.1191150. Epub 2010 Jun 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA. czhang@rockefeller.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20558669" target="_blank"〉PubMed〈/a〉
    Keywords: *Alternative Splicing ; Animals ; Antigens, Neoplasm/*metabolism ; Artificial Intelligence ; Bayes Theorem ; Binding Sites ; Brain/*metabolism ; Cell Line ; Computational Biology ; Evolution, Molecular ; Exons ; *Gene Regulatory Networks ; Humans ; Introns ; Mice ; Models, Genetic ; Models, Statistical ; Nerve Tissue Proteins/*metabolism ; Nervous System Diseases/genetics ; Oligonucleotide Array Sequence Analysis ; Phosphorylation ; Protein Binding ; Proteins/genetics/metabolism ; RNA/metabolism ; RNA-Binding Proteins/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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