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  • Animals  (178)
  • Mutation  (26)
  • Phylogeny  (26)
  • American Association for the Advancement of Science (AAAS)  (205)
  • 2010-2014  (205)
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  • 11
    Publication Date: 2013-06-15
    Description: Leprosy was endemic in Europe until the Middle Ages. Using DNA array capture, we have obtained genome sequences of Mycobacterium leprae from skeletons of five medieval leprosy cases from the United Kingdom, Sweden, and Denmark. In one case, the DNA was so well preserved that full de novo assembly of the ancient bacterial genome could be achieved through shotgun sequencing alone. The ancient M. leprae sequences were compared with those of 11 modern strains, representing diverse genotypes and geographic origins. The comparisons revealed remarkable genomic conservation during the past 1000 years, a European origin for leprosy in the Americas, and the presence of an M. leprae genotype in medieval Europe now commonly associated with the Middle East. The exceptional preservation of M. leprae biomarkers, both DNA and mycolic acids, in ancient skeletons has major implications for palaeomicrobiology and human pathogen evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schuenemann, Verena J -- Singh, Pushpendra -- Mendum, Thomas A -- Krause-Kyora, Ben -- Jager, Gunter -- Bos, Kirsten I -- Herbig, Alexander -- Economou, Christos -- Benjak, Andrej -- Busso, Philippe -- Nebel, Almut -- Boldsen, Jesper L -- Kjellstrom, Anna -- Wu, Huihai -- Stewart, Graham R -- Taylor, G Michael -- Bauer, Peter -- Lee, Oona Y-C -- Wu, Houdini H T -- Minnikin, David E -- Besra, Gurdyal S -- Tucker, Katie -- Roffey, Simon -- Sow, Samba O -- Cole, Stewart T -- Nieselt, Kay -- Krause, Johannes -- New York, N.Y. -- Science. 2013 Jul 12;341(6142):179-83. doi: 10.1126/science.1238286. Epub 2013 Jun 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Archaeological Sciences, University of Tubingen, 72070 Tubingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23765279" target="_blank"〉PubMed〈/a〉
    Keywords: Bone and Bones/microbiology ; DNA, Bacterial/chemistry/genetics/isolation & purification ; Denmark ; Endemic Diseases/history ; *Evolution, Molecular ; Genome, Bacterial/*genetics ; Great Britain ; History, Medieval ; Humans ; Leprosy/epidemiology/history/*microbiology ; Mycobacterium leprae/*classification/*genetics/isolation & purification ; Mycolic Acids/chemistry ; Phylogeny ; Sweden ; Tooth/microbiology
    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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  • 12
    Publication Date: 2013-10-19
    Description: Genetic mutations cause primary immunodeficiencies (PIDs) that predispose to infections. Here, we describe activated PI3K-delta syndrome (APDS), a PID associated with a dominant gain-of-function mutation in which lysine replaced glutamic acid at residue 1021 (E1021K) in the p110delta protein, the catalytic subunit of phosphoinositide 3-kinase delta (PI3Kdelta), encoded by the PIK3CD gene. We found E1021K in 17 patients from seven unrelated families, but not among 3346 healthy subjects. APDS was characterized by recurrent respiratory infections, progressive airway damage, lymphopenia, increased circulating transitional B cells, increased immunoglobulin M, and reduced immunoglobulin G2 levels in serum and impaired vaccine responses. The E1021K mutation enhanced membrane association and kinase activity of p110delta. Patient-derived lymphocytes had increased levels of phosphatidylinositol 3,4,5-trisphosphate and phosphorylated AKT protein and were prone to activation-induced cell death. Selective p110delta inhibitors IC87114 and GS-1101 reduced the activity of the mutant enzyme in vitro, which suggested a therapeutic approach for patients with APDS.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930011/" 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/PMC3930011/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Angulo, Ivan -- Vadas, Oscar -- Garcon, Fabien -- Banham-Hall, Edward -- Plagnol, Vincent -- Leahy, Timothy R -- Baxendale, Helen -- Coulter, Tanya -- Curtis, James -- Wu, Changxin -- Blake-Palmer, Katherine -- Perisic, Olga -- Smyth, Deborah -- Maes, Mailis -- Fiddler, Christine -- Juss, Jatinder -- Cilliers, Deirdre -- Markelj, Gasper -- Chandra, Anita -- Farmer, George -- Kielkowska, Anna -- Clark, Jonathan -- Kracker, Sven -- Debre, Marianne -- Picard, Capucine -- Pellier, Isabelle -- Jabado, Nada -- Morris, James A -- Barcenas-Morales, Gabriela -- Fischer, Alain -- Stephens, Len -- Hawkins, Phillip -- Barrett, Jeffrey C -- Abinun, Mario -- Clatworthy, Menna -- Durandy, Anne -- Doffinger, Rainer -- Chilvers, Edwin R -- Cant, Andrew J -- Kumararatne, Dinakantha -- Okkenhaug, Klaus -- Williams, Roger L -- Condliffe, Alison -- Nejentsev, Sergey -- 095198/Wellcome Trust/United Kingdom -- 095198/Z/10/Z/Wellcome Trust/United Kingdom -- 095691/Wellcome Trust/United Kingdom -- BB/J004456/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- MC_U105184308/Medical Research Council/United Kingdom -- U105184308/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2013 Nov 15;342(6160):866-71. doi: 10.1126/science.1243292. Epub 2013 Oct 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, University of Cambridge, Cambridge, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24136356" target="_blank"〉PubMed〈/a〉
    Keywords: Class I Phosphatidylinositol 3-Kinases ; *Genetic Predisposition to Disease ; Humans ; Immunologic Deficiency Syndromes/*genetics/immunology/*pathology ; Lymphocytes/immunology ; Mutation ; Pedigree ; Phosphatidylinositol 3-Kinases/*genetics ; Phosphatidylinositol Phosphates/metabolism ; Proto-Oncogene Proteins c-akt/metabolism ; Respiratory Tract Infections/*genetics/immunology/*pathology
    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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  • 13
    Publication Date: 2010-12-24
    Description: We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor-binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142569/" 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/PMC3142569/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gerstein, Mark B -- Lu, Zhi John -- Van Nostrand, Eric L -- Cheng, Chao -- Arshinoff, Bradley I -- Liu, Tao -- Yip, Kevin Y -- Robilotto, Rebecca -- Rechtsteiner, Andreas -- Ikegami, Kohta -- Alves, Pedro -- Chateigner, Aurelien -- Perry, Marc -- Morris, Mitzi -- Auerbach, Raymond K -- Feng, Xin -- Leng, Jing -- Vielle, Anne -- Niu, Wei -- Rhrissorrakrai, Kahn -- Agarwal, Ashish -- Alexander, Roger P -- Barber, Galt -- Brdlik, Cathleen M -- Brennan, Jennifer -- Brouillet, Jeremy Jean -- Carr, Adrian -- Cheung, Ming-Sin -- Clawson, Hiram -- Contrino, Sergio -- Dannenberg, Luke O -- Dernburg, Abby F -- Desai, Arshad -- Dick, Lindsay -- Dose, Andrea C -- Du, Jiang -- Egelhofer, Thea -- Ercan, Sevinc -- Euskirchen, Ghia -- Ewing, Brent -- Feingold, Elise A -- Gassmann, Reto -- Good, Peter J -- Green, Phil -- Gullier, Francois -- Gutwein, Michelle -- Guyer, Mark S -- Habegger, Lukas -- Han, Ting -- Henikoff, Jorja G -- Henz, Stefan R -- Hinrichs, Angie -- Holster, Heather -- Hyman, Tony -- Iniguez, A Leo -- Janette, Judith -- Jensen, Morten -- Kato, Masaomi -- Kent, W James -- Kephart, Ellen -- Khivansara, Vishal -- Khurana, Ekta -- Kim, John K -- Kolasinska-Zwierz, Paulina -- Lai, Eric C -- Latorre, Isabel -- Leahey, Amber -- Lewis, Suzanna -- Lloyd, Paul -- Lochovsky, Lucas -- Lowdon, Rebecca F -- Lubling, Yaniv -- Lyne, Rachel -- MacCoss, Michael -- Mackowiak, Sebastian D -- Mangone, Marco -- McKay, Sheldon -- Mecenas, Desirea -- Merrihew, Gennifer -- Miller, David M 3rd -- Muroyama, Andrew -- Murray, John I -- Ooi, Siew-Loon -- Pham, Hoang -- Phippen, Taryn -- Preston, Elicia A -- Rajewsky, Nikolaus -- Ratsch, Gunnar -- Rosenbaum, Heidi -- Rozowsky, Joel -- Rutherford, Kim -- Ruzanov, Peter -- Sarov, Mihail -- Sasidharan, Rajkumar -- Sboner, Andrea -- Scheid, Paul -- Segal, Eran -- Shin, Hyunjin -- Shou, Chong -- Slack, Frank J -- Slightam, Cindie -- Smith, Richard -- Spencer, William C -- Stinson, E O -- Taing, Scott -- Takasaki, Teruaki -- Vafeados, Dionne -- Voronina, Ksenia -- Wang, Guilin -- Washington, Nicole L -- Whittle, Christina M -- Wu, Beijing -- Yan, Koon-Kiu -- Zeller, Georg -- Zha, Zheng -- Zhong, Mei -- Zhou, Xingliang -- modENCODE Consortium -- Ahringer, Julie -- Strome, Susan -- Gunsalus, Kristin C -- Micklem, Gos -- Liu, X Shirley -- Reinke, Valerie -- Kim, Stuart K -- Hillier, LaDeana W -- Henikoff, Steven -- Piano, Fabio -- Snyder, Michael -- Stein, Lincoln -- Lieb, Jason D -- Waterston, Robert H -- 054523/Wellcome Trust/United Kingdom -- R01 GM088565/GM/NIGMS NIH HHS/ -- R01 GM088565-03/GM/NIGMS NIH HHS/ -- R01GM088565/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2010 Dec 24;330(6012):1775-87. doi: 10.1126/science.1196914. Epub 2010 Dec 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA. modencode.worm.pi@gersteinlab.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21177976" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Caenorhabditis elegans/*genetics/growth & development/metabolism ; Caenorhabditis elegans Proteins/genetics/metabolism ; Chromatin/genetics/metabolism/ultrastructure ; *Chromosomes/genetics/metabolism/ultrastructure ; Computational Biology/methods ; Conserved Sequence ; Evolution, Molecular ; *Gene Expression Profiling ; *Gene Expression Regulation ; Gene Regulatory Networks ; Genes, Helminth ; *Genome, Helminth ; Genomics/methods ; Histones/metabolism ; Models, Genetic ; *Molecular Sequence Annotation ; RNA, Helminth/genetics/metabolism ; RNA, Untranslated/genetics/metabolism ; Regulatory Sequences, Nucleic Acid ; Transcription Factors/genetics/metabolism
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  • 14
    Publication Date: 2010-10-28
    Description: Using data for 25,780 species categorized on the International Union for Conservation of Nature Red List, we present an assessment of the status of the world's vertebrates. One-fifth of species are classified as Threatened, and we show that this figure is increasing: On average, 52 species of mammals, birds, and amphibians move one category closer to extinction each year. However, this overall pattern conceals the impact of conservation successes, and we show that the rate of deterioration would have been at least one-fifth again as much in the absence of these. Nonetheless, current conservation efforts remain insufficient to offset the main drivers of biodiversity loss in these groups: agricultural expansion, logging, overexploitation, and invasive alien species.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hoffmann, Michael -- Hilton-Taylor, Craig -- Angulo, Ariadne -- Bohm, Monika -- Brooks, Thomas M -- Butchart, Stuart H M -- Carpenter, Kent E -- Chanson, Janice -- Collen, Ben -- Cox, Neil A -- Darwall, William R T -- Dulvy, Nicholas K -- Harrison, Lucy R -- Katariya, Vineet -- Pollock, Caroline M -- Quader, Suhel -- Richman, Nadia I -- Rodrigues, Ana S L -- Tognelli, Marcelo F -- Vie, Jean-Christophe -- Aguiar, John M -- Allen, David J -- Allen, Gerald R -- Amori, Giovanni -- Ananjeva, Natalia B -- Andreone, Franco -- Andrew, Paul -- Aquino Ortiz, Aida Luz -- Baillie, Jonathan E M -- Baldi, Ricardo -- Bell, Ben D -- Biju, S D -- Bird, Jeremy P -- Black-Decima, Patricia -- Blanc, J Julian -- Bolanos, Federico -- Bolivar-G, Wilmar -- Burfield, Ian J -- Burton, James A -- Capper, David R -- Castro, Fernando -- Catullo, Gianluca -- Cavanagh, Rachel D -- Channing, Alan -- Chao, Ning Labbish -- Chenery, Anna M -- Chiozza, Federica -- Clausnitzer, Viola -- Collar, Nigel J -- Collett, Leah C -- Collette, Bruce B -- Cortez Fernandez, Claudia F -- Craig, Matthew T -- Crosby, Michael J -- Cumberlidge, Neil -- Cuttelod, Annabelle -- Derocher, Andrew E -- Diesmos, Arvin C -- Donaldson, John S -- Duckworth, J W -- Dutson, Guy -- Dutta, S K -- Emslie, Richard H -- Farjon, Aljos -- Fowler, Sarah -- Freyhof, Jorg -- Garshelis, David L -- Gerlach, Justin -- Gower, David J -- Grant, Tandora D -- Hammerson, Geoffrey A -- Harris, Richard B -- Heaney, Lawrence R -- Hedges, S Blair -- Hero, Jean-Marc -- Hughes, Baz -- Hussain, Syed Ainul -- Icochea M, Javier -- Inger, Robert F -- Ishii, Nobuo -- Iskandar, Djoko T -- Jenkins, Richard K B -- Kaneko, Yoshio -- Kottelat, Maurice -- Kovacs, Kit M -- Kuzmin, Sergius L -- La Marca, Enrique -- Lamoreux, John F -- Lau, Michael W N -- Lavilla, Esteban O -- Leus, Kristin -- Lewison, Rebecca L -- Lichtenstein, Gabriela -- Livingstone, Suzanne R -- Lukoschek, Vimoksalehi -- Mallon, David P -- McGowan, Philip J K -- McIvor, Anna -- Moehlman, Patricia D -- Molur, Sanjay -- Munoz Alonso, Antonio -- Musick, John A -- Nowell, Kristin -- Nussbaum, Ronald A -- Olech, Wanda -- Orlov, Nikolay L -- Papenfuss, Theodore J -- Parra-Olea, Gabriela -- Perrin, William F -- Polidoro, Beth A -- Pourkazemi, Mohammad -- Racey, Paul A -- Ragle, James S -- Ram, Mala -- Rathbun, Galen -- Reynolds, Robert P -- Rhodin, Anders G J -- Richards, Stephen J -- Rodriguez, Lily O -- Ron, Santiago R -- Rondinini, Carlo -- Rylands, Anthony B -- Sadovy de Mitcheson, Yvonne -- Sanciangco, Jonnell C -- Sanders, Kate L -- Santos-Barrera, Georgina -- Schipper, Jan -- Self-Sullivan, Caryn -- Shi, Yichuan -- Shoemaker, Alan -- Short, Frederick T -- Sillero-Zubiri, Claudio -- Silvano, Debora L -- Smith, Kevin G -- Smith, Andrew T -- Snoeks, Jos -- Stattersfield, Alison J -- Symes, Andrew J -- Taber, Andrew B -- Talukdar, Bibhab K -- Temple, Helen J -- Timmins, Rob -- Tobias, Joseph A -- Tsytsulina, Katerina -- Tweddle, Denis -- Ubeda, Carmen -- Valenti, Sarah V -- van Dijk, Peter Paul -- Veiga, Liza M -- Veloso, Alberto -- Wege, David C -- Wilkinson, Mark -- Williamson, Elizabeth A -- Xie, Feng -- Young, Bruce E -- Akcakaya, H Resit -- Bennun, Leon -- Blackburn, Tim M -- Boitani, Luigi -- Dublin, Holly T -- da Fonseca, Gustavo A B -- Gascon, Claude -- Lacher, Thomas E Jr -- Mace, Georgina M -- Mainka, Susan A -- McNeely, Jeffery A -- Mittermeier, Russell A -- Reid, Gordon McGregor -- Rodriguez, Jon Paul -- Rosenberg, Andrew A -- Samways, Michael J -- Smart, Jane -- Stein, Bruce A -- Stuart, Simon N -- New York, N.Y. -- Science. 2010 Dec 10;330(6010):1503-9. doi: 10.1126/science.1194442. Epub 2010 Oct 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉IUCN SSC Species Survival Commission, c/o United Nations Environment Programme World Conservation Monitoring Centre, 219 Huntingdon Road, Cambridge CB3 0DL, UK. mike.hoffmann@iucn.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20978281" target="_blank"〉PubMed〈/a〉
    Keywords: Amphibians ; Animals ; *Biodiversity ; Birds ; *Conservation of Natural Resources ; *Ecosystem ; Endangered Species/statistics & numerical data/trends ; Extinction, Biological ; Introduced Species ; Mammals ; Population Dynamics ; *Vertebrates
    Print ISSN: 0036-8075
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  • 15
    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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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 16
    Publication Date: 2011-07-19
    Description: Brown rot decay removes cellulose and hemicellulose from wood--residual lignin contributing up to 30% of forest soil carbon--and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the "dry rot" fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eastwood, Daniel C -- Floudas, Dimitrios -- Binder, Manfred -- Majcherczyk, Andrzej -- Schneider, Patrick -- Aerts, Andrea -- Asiegbu, Fred O -- Baker, Scott E -- Barry, Kerrie -- Bendiksby, Mika -- Blumentritt, Melanie -- Coutinho, Pedro M -- Cullen, Dan -- de Vries, Ronald P -- Gathman, Allen -- Goodell, Barry -- Henrissat, Bernard -- Ihrmark, Katarina -- Kauserud, Havard -- Kohler, Annegret -- LaButti, Kurt -- Lapidus, Alla -- Lavin, Jose L -- Lee, Yong-Hwan -- Lindquist, Erika -- Lilly, Walt -- Lucas, Susan -- Morin, Emmanuelle -- Murat, Claude -- Oguiza, Jose A -- Park, Jongsun -- Pisabarro, Antonio G -- Riley, Robert -- Rosling, Anna -- Salamov, Asaf -- Schmidt, Olaf -- Schmutz, Jeremy -- Skrede, Inger -- Stenlid, Jan -- Wiebenga, Ad -- Xie, Xinfeng -- Kues, Ursula -- Hibbett, David S -- Hoffmeister, Dirk -- Hogberg, Nils -- Martin, Francis -- Grigoriev, Igor V -- Watkinson, Sarah C -- New York, N.Y. -- Science. 2011 Aug 5;333(6043):762-5. doi: 10.1126/science.1205411. Epub 2011 Jul 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉College of Science, University of Swansea, Singleton Park, Swansea SA2 8PP, UK. d.c.eastwood@swansea.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21764756" target="_blank"〉PubMed〈/a〉
    Keywords: Angiosperms/microbiology ; Basidiomycota/classification/enzymology/*genetics/physiology ; *Biodiversity ; Biological Evolution ; Biota ; Cell Wall/*metabolism ; Coniferophyta/microbiology ; Coriolaceae/enzymology/genetics/physiology ; Gene Expression Profiling ; Genes, Fungal ; Genomics ; Lignin/metabolism ; Mycorrhizae/enzymology/*genetics/physiology ; Oxidoreductases/genetics/metabolism ; Peroxidases/genetics/metabolism ; Phylogeny ; Proteome ; Symbiosis ; Trees/*microbiology ; Wood/metabolism/*microbiology
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  • 17
    Publication Date: 2011-01-15
    Description: Circadian regulation of plant-animal endosymbioses is complicated by a diversity of internal and external cues. Here, we show that stress-related genes in corals are coupled to the circadian clock, anticipating major changes in the intracellular milieu. In this regard, numerous chaperones are "hard-wired" to the clock, effectively preparing the coral for the consequences of oxidative protein damage imposed by symbiont photosynthesis (when O(2) 〉 250% saturation), including synexpression of antioxidant genes being light-gated. Conversely, central metabolism appears to be regulated by the hypoxia-inducible factor system in coral. These results reveal the complexity of endosymbiosis as well as the plasticity regulation downstream of the circadian clock.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Levy, O -- Kaniewska, P -- Alon, S -- Eisenberg, E -- Karako-Lampert, S -- Bay, L K -- Reef, R -- Rodriguez-Lanetty, M -- Miller, D J -- Hoegh-Guldberg, O -- New York, N.Y. -- Science. 2011 Jan 14;331(6014):175. doi: 10.1126/science.1196419.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21233378" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anthozoa/*genetics/physiology ; Biosynthetic Pathways/genetics ; *Circadian Clocks ; Circadian Rhythm ; Dinoflagellida/*physiology ; *Gene Expression Regulation ; Glycolysis/genetics ; Hypoxia-Inducible Factor 1, alpha Subunit/genetics/metabolism ; Molecular Chaperones/genetics ; Oligonucleotide Array Sequence Analysis ; Oxidation-Reduction ; Stress, Physiological ; *Symbiosis
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  • 18
    Publication Date: 2011-07-09
    Description: There is limited regeneration of lost tissue after central nervous system injury, and the lesion is sealed with a scar. The role of the scar, which often is referred to as the glial scar because of its abundance of astrocytes, is complex and has been discussed for more than a century. Here we show that a specific pericyte subtype gives rise to scar-forming stromal cells, which outnumber astrocytes, in the injured spinal cord. Blocking the generation of progeny by this pericyte subtype results in failure to seal the injured tissue. The formation of connective tissue is common to many injuries and pathologies, and here we demonstrate a cellular origin of fibrosis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goritz, Christian -- Dias, David O -- Tomilin, Nikolay -- Barbacid, Mariano -- Shupliakov, Oleg -- Frisen, Jonas -- 250297/European Research Council/International -- New York, N.Y. -- Science. 2011 Jul 8;333(6039):238-42. doi: 10.1126/science.1203165.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21737741" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Astrocytes/pathology/physiology ; Blood Vessels/pathology ; Cell Count ; Cell Proliferation ; Cicatrix/*pathology ; Fibrosis ; Mice ; Mice, Transgenic ; Pericytes/*pathology/physiology ; Spinal Cord/blood supply/*pathology ; Spinal Cord Injuries/*pathology ; Stromal Cells/pathology
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  • 19
    Publication Date: 2012-06-16
    Description: Excessive nutrient loading is a major threat to aquatic ecosystems worldwide that leads to profound changes in aquatic biodiversity and biogeochemical processes. Systematic quantitative assessment of functional ecosystem measures for river networks is, however, lacking, especially at continental scales. Here, we narrow this gap by means of a pan-European field experiment on a fundamental ecosystem process--leaf-litter breakdown--in 100 streams across a greater than 1000-fold nutrient gradient. Dramatically slowed breakdown at both extremes of the gradient indicated strong nutrient limitation in unaffected systems, potential for strong stimulation in moderately altered systems, and inhibition in highly polluted streams. This large-scale response pattern emphasizes the need to complement established structural approaches (such as water chemistry, hydrogeomorphology, and biological diversity metrics) with functional measures (such as litter-breakdown rate, whole-system metabolism, and nutrient spiraling) for assessing ecosystem health.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Woodward, Guy -- Gessner, Mark O -- Giller, Paul S -- Gulis, Vladislav -- Hladyz, Sally -- Lecerf, Antoine -- Malmqvist, Bjorn -- McKie, Brendan G -- Tiegs, Scott D -- Cariss, Helen -- Dobson, Mike -- Elosegi, Arturo -- Ferreira, Veronica -- Graca, Manuel A S -- Fleituch, Tadeusz -- Lacoursiere, Jean O -- Nistorescu, Marius -- Pozo, Jesus -- Risnoveanu, Geta -- Schindler, Markus -- Vadineanu, Angheluta -- Vought, Lena B-M -- Chauvet, Eric -- New York, N.Y. -- Science. 2012 Jun 15;336(6087):1438-40. doi: 10.1126/science.1219534.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, Ecology and Plant Science, University College Cork, National University of Ireland, Cork, Enterprise Centre, Distillery Fields, Cork, Ireland. g.woodward@qmul.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22700929" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; Biomass ; *Ecosystem ; Europe ; Eutrophication ; Ilex ; Invertebrates/*metabolism ; *Plant Leaves ; Quercus ; *Rivers/microbiology ; *Water Pollution, Chemical
    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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  • 20
    Publication Date: 2013-01-26
    Description: We report genomic analysis of 300 meningiomas, the most common primary brain tumors, leading to the discovery of mutations in TRAF7, a proapoptotic E3 ubiquitin ligase, in nearly one-fourth of all meningiomas. Mutations in TRAF7 commonly occurred with a recurrent mutation (K409Q) in KLF4, a transcription factor known for its role in inducing pluripotency, or with AKT1(E17K), a mutation known to activate the PI3K pathway. SMO mutations, which activate Hedgehog signaling, were identified in ~5% of non-NF2 mutant meningiomas. These non-NF2 meningiomas were clinically distinctive-nearly always benign, with chromosomal stability, and originating from the medial skull base. In contrast, meningiomas with mutant NF2 and/or chromosome 22 loss were more likely to be atypical, showing genomic instability, and localizing to the cerebral and cerebellar hemispheres. Collectively, these findings identify distinct meningioma subtypes, suggesting avenues for targeted therapeutics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clark, Victoria E -- Erson-Omay, E Zeynep -- Serin, Akdes -- Yin, Jun -- Cotney, Justin -- Ozduman, Koray -- Avsar, Timucin -- Li, Jie -- Murray, Phillip B -- Henegariu, Octavian -- Yilmaz, Saliha -- Gunel, Jennifer Moliterno -- Carrion-Grant, Geneive -- Yilmaz, Baran -- Grady, Conor -- Tanrikulu, Bahattin -- Bakircioglu, Mehmet -- Kaymakcalan, Hande -- Caglayan, Ahmet Okay -- Sencar, Leman -- Ceyhun, Emre -- Atik, A Fatih -- Bayri, Yasar -- Bai, Hanwen -- Kolb, Luis E -- Hebert, Ryan M -- Omay, S Bulent -- Mishra-Gorur, Ketu -- Choi, Murim -- Overton, John D -- Holland, Eric C -- Mane, Shrikant -- State, Matthew W -- Bilguvar, Kaya -- Baehring, Joachim M -- Gutin, Philip H -- Piepmeier, Joseph M -- Vortmeyer, Alexander -- Brennan, Cameron W -- Pamir, M Necmettin -- Kilic, Turker -- Lifton, Richard P -- Noonan, James P -- Yasuno, Katsuhito -- Gunel, Murat -- T32 GM007205/GM/NIGMS NIH HHS/ -- T32GM07205/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2013 Mar 1;339(6123):1077-80. doi: 10.1126/science.1233009. Epub 2013 Jan 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT 06510, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23348505" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Aged ; Aged, 80 and over ; Brain Neoplasms/classification/*genetics/pathology ; Chromosomes, Human, Pair 22/genetics ; DNA Mutational Analysis ; Female ; Genes, Neurofibromatosis 2 ; Genomic Instability ; Genomics ; Humans ; Kruppel-Like Transcription Factors/*genetics ; Male ; Meningeal Neoplasms/classification/*genetics/pathology ; Meningioma/classification/*genetics/pathology ; Middle Aged ; Mutation ; Neoplasm Grading ; Proto-Oncogene Proteins c-akt/*genetics ; Receptors, G-Protein-Coupled/*genetics ; Tumor Necrosis Factor Receptor-Associated Peptides and 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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