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  • United States  (22)
  • *Evolution, Molecular  (13)
  • Binding Sites
  • American Association for the Advancement of Science (AAAS)  (42)
  • 2010-2014  (42)
  • 1995-1999
  • 1980-1984
  • 1970-1974
  • 2012  (42)
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  • 2010-2014  (42)
  • 1995-1999
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  • 1
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    The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-06-30
    Description: Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non-lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Floudas, Dimitrios -- Binder, Manfred -- Riley, Robert -- Barry, Kerrie -- Blanchette, Robert A -- Henrissat, Bernard -- Martinez, Angel T -- Otillar, Robert -- Spatafora, Joseph W -- Yadav, Jagjit S -- Aerts, Andrea -- Benoit, Isabelle -- Boyd, Alex -- Carlson, Alexis -- Copeland, Alex -- Coutinho, Pedro M -- de Vries, Ronald P -- Ferreira, Patricia -- Findley, Keisha -- Foster, Brian -- Gaskell, Jill -- Glotzer, Dylan -- Gorecki, Pawel -- Heitman, Joseph -- Hesse, Cedar -- Hori, Chiaki -- Igarashi, Kiyohiko -- Jurgens, Joel A -- Kallen, Nathan -- Kersten, Phil -- Kohler, Annegret -- Kues, Ursula -- Kumar, T K Arun -- Kuo, Alan -- LaButti, Kurt -- Larrondo, Luis F -- Lindquist, Erika -- Ling, Albee -- Lombard, Vincent -- Lucas, Susan -- Lundell, Taina -- Martin, Rachael -- McLaughlin, David J -- Morgenstern, Ingo -- Morin, Emanuelle -- Murat, Claude -- Nagy, Laszlo G -- Nolan, Matt -- Ohm, Robin A -- Patyshakuliyeva, Aleksandrina -- Rokas, Antonis -- Ruiz-Duenas, Francisco J -- Sabat, Grzegorz -- Salamov, Asaf -- Samejima, Masahiro -- Schmutz, Jeremy -- Slot, Jason C -- St John, Franz -- Stenlid, Jan -- Sun, Hui -- Sun, Sheng -- Syed, Khajamohiddin -- Tsang, Adrian -- Wiebenga, Ad -- Young, Darcy -- Pisabarro, Antonio -- Eastwood, Daniel C -- Martin, Francis -- Cullen, Dan -- Grigoriev, Igor V -- Hibbett, David S -- New York, N.Y. -- Science. 2012 Jun 29;336(6089):1715-9. doi: 10.1126/science.1221748.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biology Department, Clark University, Worcester, MA 01610, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22745431" target="_blank"〉PubMed〈/a〉
    Keywords: Basidiomycota/classification/*enzymology/*genetics ; Bayes Theorem ; *Evolution, Molecular ; *Genome, Fungal ; Indoles ; Lignin/*metabolism ; Peroxidases/*genetics/metabolism ; Wood/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Evolution and functional impact of rare coding variation from deep sequencing of human exomes (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-05-19
    Description: As a first step toward understanding how rare variants contribute to risk for complex diseases, we sequenced 15,585 human protein-coding genes to an average median depth of 111x in 2440 individuals of European (n = 1351) and African (n = 1088) ancestry. We identified over 500,000 single-nucleotide variants (SNVs), the majority of which were rare (86% with a minor allele frequency less than 0.5%), previously unknown (82%), and population-specific (82%). On average, 2.3% of the 13,595 SNVs each person carried were predicted to affect protein function of ~313 genes per genome, and ~95.7% of SNVs predicted to be functionally important were rare. This excess of rare functional variants is due to the combined effects of explosive, recent accelerated population growth and weak purifying selection. Furthermore, we show that large sample sizes will be required to associate rare variants with complex traits.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708544/" 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/PMC3708544/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tennessen, Jacob A -- Bigham, Abigail W -- O'Connor, Timothy D -- Fu, Wenqing -- Kenny, Eimear E -- Gravel, Simon -- McGee, Sean -- Do, Ron -- Liu, Xiaoming -- Jun, Goo -- Kang, Hyun Min -- Jordan, Daniel -- Leal, Suzanne M -- Gabriel, Stacey -- Rieder, Mark J -- Abecasis, Goncalo -- Altshuler, David -- Nickerson, Deborah A -- Boerwinkle, Eric -- Sunyaev, Shamil -- Bustamante, Carlos D -- Bamshad, Michael J -- Akey, Joshua M -- Broad GO -- Seattle GO -- NHLBI Exome Sequencing Project -- R01 HG003229/HG/NHGRI NIH HHS/ -- RC2 HL-102923/HL/NHLBI NIH HHS/ -- RC2 HL-102924/HL/NHLBI NIH HHS/ -- RC2 HL-102925/HL/NHLBI NIH HHS/ -- RC2 HL-102926/HL/NHLBI NIH HHS/ -- RC2 HL-103010/HL/NHLBI NIH HHS/ -- RC2 HL102926/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2012 Jul 6;337(6090):64-9. doi: 10.1126/science.1219240. Epub 2012 May 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22604720" target="_blank"〉PubMed〈/a〉
    Keywords: African Americans/*genetics ; Disease/genetics ; European Continental Ancestry Group/*genetics ; *Evolution, Molecular ; *Exome ; Female ; Gene Frequency ; Genetic Association Studies ; Genetic Predisposition to Disease ; *Genetic Variation ; *Genome, Human ; *High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Polymorphism, Single Nucleotide ; Population Growth ; Selection, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    The ancient drug salicylate directly activates AMP-activated protein kinase (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-04-21
    Description: Salicylate, a plant product, has been in medicinal use since ancient times. More recently, it has been replaced by synthetic derivatives such as aspirin and salsalate, both of which are rapidly broken down to salicylate in vivo. At concentrations reached in plasma after administration of salsalate or of aspirin at high doses, salicylate activates adenosine monophosphate-activated protein kinase (AMPK), a central regulator of cell growth and metabolism. Salicylate binds at the same site as the synthetic activator A-769662 to cause allosteric activation and inhibition of dephosphorylation of the activating phosphorylation site, threonine-172. In AMPK knockout mice, effects of salicylate to increase fat utilization and to lower plasma fatty acids in vivo were lost. Our results suggest that AMPK activation could explain some beneficial effects of salsalate and aspirin in humans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3399766/" 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/PMC3399766/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hawley, Simon A -- Fullerton, Morgan D -- Ross, Fiona A -- Schertzer, Jonathan D -- Chevtzoff, Cyrille -- Walker, Katherine J -- Peggie, Mark W -- Zibrova, Darya -- Green, Kevin A -- Mustard, Kirsty J -- Kemp, Bruce E -- Sakamoto, Kei -- Steinberg, Gregory R -- Hardie, D Grahame -- 080982/Wellcome Trust/United Kingdom -- 097726/Wellcome Trust/United Kingdom -- MC_U127088492/Medical Research Council/United Kingdom -- Canadian Institutes of Health Research/Canada -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2012 May 18;336(6083):918-22. doi: 10.1126/science.1215327. Epub 2012 Apr 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Cell Signalling and Immunology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22517326" target="_blank"〉PubMed〈/a〉
    Keywords: AMP-Activated Protein Kinases/genetics/*metabolism ; Amino Acid Substitution ; Animals ; Aspirin/pharmacology ; Binding Sites ; Carbohydrate Metabolism/drug effects ; Cell Line ; Enzyme Activation ; Enzyme Activators/pharmacology ; HEK293 Cells ; Humans ; Lipid Metabolism/drug effects ; Liver/drug effects/metabolism ; Mice ; Mice, Knockout ; Mutation ; Oxygen Consumption/drug effects ; Phosphorylation ; Pyrones/pharmacology ; Rats ; Salicylates/blood/*metabolism/*pharmacology ; Thiophenes/pharmacology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    The potential for respiratory droplet-transmissible A/H5N1 influenza virus to evolve in a mammalian host (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-06-23
    Description: Avian A/H5N1 influenza viruses pose a pandemic threat. As few as five amino acid substitutions, or four with reassortment, might be sufficient for mammal-to-mammal transmission through respiratory droplets. From surveillance data, we found that two of these substitutions are common in A/H5N1 viruses, and thus, some viruses might require only three additional substitutions to become transmissible via respiratory droplets between mammals. We used a mathematical model of within-host virus evolution to study factors that could increase and decrease the probability of the remaining substitutions evolving after the virus has infected a mammalian host. These factors, combined with the presence of some of these substitutions in circulating strains, make a virus evolving in nature a potentially serious threat. These results highlight critical areas in which more data are needed for assessing, and potentially averting, this threat.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426314/" 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/PMC3426314/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Russell, Colin A -- Fonville, Judith M -- Brown, Andre E X -- Burke, David F -- Smith, David L -- James, Sarah L -- Herfst, Sander -- van Boheemen, Sander -- Linster, Martin -- Schrauwen, Eefje J -- Katzelnick, Leah -- Mosterin, Ana -- Kuiken, Thijs -- Maher, Eileen -- Neumann, Gabriele -- Osterhaus, Albert D M E -- Kawaoka, Yoshihiro -- Fouchier, Ron A M -- Smith, Derek J -- DP1 OD000490/OD/NIH HHS/ -- DP1-OD000490-01/OD/NIH HHS/ -- HHSN266200700010C/AI/NIAID NIH HHS/ -- HHSN266200700010C/PHS HHS/ -- R01 AI 069274/AI/NIAID NIH HHS/ -- R56 AI069274/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2012 Jun 22;336(6088):1541-7. doi: 10.1126/science.1222526.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, University of Cambridge, Cambridge, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22723414" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Air Microbiology ; Amino Acid Substitution ; Animals ; Birds ; *Evolution, Molecular ; Genetic Fitness ; Glycosylation ; Hemagglutinin Glycoproteins, Influenza Virus/*genetics/metabolism ; High-Throughput Nucleotide Sequencing ; Humans ; Influenza A Virus, H5N1 Subtype/*genetics/*pathogenicity ; Influenza in Birds/virology ; Influenza, Human/immunology/transmission/*virology ; Mammals ; Models, Biological ; Mutation ; Orthomyxoviridae Infections/transmission/*virology ; Probability ; RNA Replicase/*genetics ; Receptors, Virus/metabolism ; Respiratory System/*virology ; Selection, Genetic ; Sialic Acids/metabolism ; Viral Proteins/*genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-02-22
    Description: The primary endosymbiotic origin of the plastid in eukaryotes more than 1 billion years ago led to the evolution of algae and plants. We analyzed draft genome and transcriptome data from the basally diverging alga Cyanophora paradoxa and provide evidence for a single origin of the primary plastid in the eukaryote supergroup Plantae. C. paradoxa retains ancestral features of starch biosynthesis, fermentation, and plastid protein translocation common to plants and algae but lacks typical eukaryotic light-harvesting complex proteins. Traces of an ancient link to parasites such as Chlamydiae were found in the genomes of C. paradoxa and other Plantae. Apparently, Chlamydia-like bacteria donated genes that allow export of photosynthate from the plastid and its polymerization into storage polysaccharide in the cytosol.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Price, Dana C -- Chan, Cheong Xin -- Yoon, Hwan Su -- Yang, Eun Chan -- Qiu, Huan -- Weber, Andreas P M -- Schwacke, Rainer -- Gross, Jeferson -- Blouin, Nicolas A -- Lane, Chris -- Reyes-Prieto, Adrian -- Durnford, Dion G -- Neilson, Jonathan A D -- Lang, B Franz -- Burger, Gertraud -- Steiner, Jurgen M -- Loffelhardt, Wolfgang -- Meuser, Jonathan E -- Posewitz, Matthew C -- Ball, Steven -- Arias, Maria Cecilia -- Henrissat, Bernard -- Coutinho, Pedro M -- Rensing, Stefan A -- Symeonidi, Aikaterini -- Doddapaneni, Harshavardhan -- Green, Beverley R -- Rajah, Veeran D -- Boore, Jeffrey -- Bhattacharya, Debashish -- MSP-14226/Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2012 Feb 17;335(6070):843-7. doi: 10.1126/science.1213561.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22344442" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Evolution ; Cyanobacteria/genetics ; Cyanophora/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Plant ; Molecular Sequence Data ; Photosynthesis/*genetics ; Phylogeny ; Symbiosis
    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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  • 6
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    Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-03
    Description: Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional conditions that the organism might encounter in nature. We comprehensively mapped transcription units (TUs) and grouped 2935 promoters into regulons controlled by various RNA polymerase sigma factors, accounting for ~66% of the observed variance in transcriptional activity. This global classification of promoters and detailed description of TUs revealed that a large proportion of the detected antisense RNAs arose from potentially spurious transcription initiation by alternative sigma factors and from imperfect control of transcription termination.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nicolas, Pierre -- Mader, Ulrike -- Dervyn, Etienne -- Rochat, Tatiana -- Leduc, Aurelie -- Pigeonneau, Nathalie -- Bidnenko, Elena -- Marchadier, Elodie -- Hoebeke, Mark -- Aymerich, Stephane -- Becher, Dorte -- Bisicchia, Paola -- Botella, Eric -- Delumeau, Olivier -- Doherty, Geoff -- Denham, Emma L -- Fogg, Mark J -- Fromion, Vincent -- Goelzer, Anne -- Hansen, Annette -- Hartig, Elisabeth -- Harwood, Colin R -- Homuth, Georg -- Jarmer, Hanne -- Jules, Matthieu -- Klipp, Edda -- Le Chat, Ludovic -- Lecointe, Francois -- Lewis, Peter -- Liebermeister, Wolfram -- March, Anika -- Mars, Ruben A T -- Nannapaneni, Priyanka -- Noone, David -- Pohl, Susanne -- Rinn, Bernd -- Rugheimer, Frank -- Sappa, Praveen K -- Samson, Franck -- Schaffer, Marc -- Schwikowski, Benno -- Steil, Leif -- Stulke, Jorg -- Wiegert, Thomas -- Devine, Kevin M -- Wilkinson, Anthony J -- van Dijl, Jan Maarten -- Hecker, Michael -- Volker, Uwe -- Bessieres, Philippe -- Noirot, Philippe -- New York, N.Y. -- Science. 2012 Mar 2;335(6072):1103-6. doi: 10.1126/science.1206848.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉INRA, UR1077, Mathematique Informatique et Genome, Jouy-en-Josas, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22383849" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Algorithms ; Bacillus subtilis/*genetics/*physiology ; Binding Sites ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Gene Regulatory Networks ; Oligonucleotide Array Sequence Analysis ; *Promoter Regions, Genetic ; RNA, Antisense/genetics/metabolism ; RNA, Bacterial/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Regulon ; Sigma Factor/metabolism ; Terminator Regions, Genetic ; *Transcription, Genetic ; *Transcriptome
    Print ISSN: 0036-8075
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  • 7
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    Public health and biosecurity. Adaptations of avian flu virus are a cause for concern (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-02-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berns, Kenneth I -- Casadevall, Arturo -- Cohen, Murray L -- Ehrlich, Susan A -- Enquist, Lynn W -- Fitch, J Patrick -- Franz, David R -- Fraser-Liggett, Claire M -- Grant, Christine M -- Imperiale, Michael J -- Kanabrocki, Joseph -- Keim, Paul S -- Lemon, Stanley M -- Levy, Stuart B -- Lumpkin, John R -- Miller, Jeffery F -- Murch, Randall -- Nance, Mark E -- Osterholm, Michael T -- Relman, David A -- Roth, James A -- Vidaver, Anne K -- New York, N.Y. -- Science. 2012 Feb 10;335(6069):660-1. doi: 10.1126/science.1217994. Epub 2012 Jan 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genetics Institute, University of Florida, Gainesville, FL 32611, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22294736" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Advisory Committees ; Animals ; Biological Warfare Agents ; Containment of Biohazards ; Humans ; Influenza A Virus, H5N1 Subtype/*pathogenicity ; Influenza, Human/epidemiology/transmission/*virology ; National Institutes of Health (U.S.) ; Orthomyxoviridae Infections/transmission/*virology ; *Public Health ; *Publishing ; Risk Assessment ; Security Measures ; United States
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Network context and selection in the evolution to enzyme specificity (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-09-01
    Description: Enzymes are thought to have evolved highly specific catalytic activities from promiscuous ancestral proteins. By analyzing a genome-scale model of Escherichia coli metabolism, we found that 37% of its enzymes act on a variety of substrates and catalyze 65% of the known metabolic reactions. However, it is not apparent why these generalist enzymes remain. Here, we show that there are marked differences between generalist enzymes and specialist enzymes, known to catalyze a single chemical reaction on one particular substrate in vivo. Specialist enzymes (i) are frequently essential, (ii) maintain higher metabolic flux, and (iii) require more regulation of enzyme activity to control metabolic flux in dynamic environments than do generalist enzymes. Furthermore, these properties are conserved in Archaea and Eukarya. Thus, the metabolic network context and environmental conditions influence enzyme evolution toward high specificity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3536066/" 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/PMC3536066/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nam, Hojung -- Lewis, Nathan E -- Lerman, Joshua A -- Lee, Dae-Hee -- Chang, Roger L -- Kim, Donghyuk -- Palsson, Bernhard O -- 2R01GM057089-13/GM/NIGMS NIH HHS/ -- R01 GM057089/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Aug 31;337(6098):1101-4. doi: 10.1126/science.1216861.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bioengineering, University of California San Diego, La Jolla, CA 92093-0412, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22936779" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; Computational Biology ; Enzymes/*genetics/*metabolism ; Escherichia coli/*enzymology/genetics ; *Evolution, Molecular ; *Metabolic Networks and Pathways ; *Selection, Genetic ; Substrate Specificity
    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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  • 9
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    Conspecific negative density dependence and forest diversity (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-05-19
    Description: Conspecific negative density-dependent establishment, in which local abundance negatively affects establishment of conspecific seedlings through host-specific enemies, can influence species diversity of plant communities, but the generality of this process is not well understood. We tested the strength of density dependence using the United States Forest Service's Forest Inventory and Analysis database containing 151 species from more than 200,000 forest plots spanning 4,000,000 square kilometers. We found that most species experienced conspecific negative density dependence (CNDD), but there was little effect of heterospecific density. Additionally, abundant species exhibited weaker CNDD than rarer species, and species-rich regions exhibited stronger CNDD than species-poor regions. Collectively, our results provide evidence that CNDD is a pervasive mechanism driving diversity across a gradient from boreal to subtropical forests.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Johnson, Daniel J -- Beaulieu, Wesley T -- Bever, James D -- Clay, Keith -- New York, N.Y. -- Science. 2012 May 18;336(6083):904-7. doi: 10.1126/science.1220269.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Indiana University, Bloomington, IN 47405, USA. dj4@indiana.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22605774" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodiversity ; Databases, Factual ; *Ecosystem ; Seedlings/growth & development ; Species Specificity ; *Trees/growth & development ; United States
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    The evolutionary landscape of alternative splicing in vertebrate species (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-12-22
    Description: How species with similar repertoires of protein-coding genes differ so markedly at the phenotypic level is poorly understood. By comparing organ transcriptomes from vertebrate species spanning ~350 million years of evolution, we observed significant differences in alternative splicing complexity between vertebrate lineages, with the highest complexity in primates. Within 6 million years, the splicing profiles of physiologically equivalent organs diverged such that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species-specific splicing patterns are cis-directed. However, a subset of pronounced splicing changes are predicted to remodel protein interactions involving trans-acting regulators. These events likely further contributed to the diversification of splicing and other transcriptomic changes that underlie phenotypic differences among vertebrate species.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barbosa-Morais, Nuno L -- Irimia, Manuel -- Pan, Qun -- Xiong, Hui Y -- Gueroussov, Serge -- Lee, Leo J -- Slobodeniuc, Valentina -- Kutter, Claudia -- Watt, Stephen -- Colak, Recep -- Kim, TaeHyung -- Misquitta-Ali, Christine M -- Wilson, Michael D -- Kim, Philip M -- Odom, Duncan T -- Frey, Brendan J -- Blencowe, Benjamin J -- 15603/Cancer Research UK/United Kingdom -- A15603/Cancer Research UK/United Kingdom -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2012 Dec 21;338(6114):1587-93. doi: 10.1126/science.1230612.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23258890" target="_blank"〉PubMed〈/a〉
    Keywords: *Alternative Splicing ; Animals ; Biological Evolution ; Chickens/genetics ; *Evolution, Molecular ; Exons ; Introns ; Lizards/genetics ; Mice/genetics ; Mice, Inbred C57BL/genetics ; Opossums/genetics ; Phenotype ; Platypus/genetics ; Primates/genetics ; RNA Splice Sites ; Regulatory Sequences, Ribonucleic Acid ; Species Specificity ; *Transcriptome ; Vertebrates/*genetics ; Xenopus/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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