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  • Mutation  (2,852)
  • *Ecosystem  (1,597)
  • Chemical Engineering
  • American Association for the Advancement of Science (AAAS)  (4,440)
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  • 101
    Publication Date: 2014-11-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ferreira, J -- Aragao, L E O C -- Barlow, J -- Barreto, P -- Berenguer, E -- Bustamante, M -- Gardner, T A -- Lees, A C -- Lima, A -- Louzada, J -- Pardini, R -- Parry, L -- Peres, C A -- Pompeu, P S -- Tabarelli, M -- Zuanon, J -- New York, N.Y. -- Science. 2014 Nov 7;346(6210):706-7. doi: 10.1126/science.1260194.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉See the supplementary materials for author af liations. joice.ferreira@embrapa.br. ; See the supplementary materials for author af liations.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25378611" target="_blank"〉PubMed〈/a〉
    Keywords: Biodiversity ; Brazil ; Conservation of Natural Resources/*trends ; *Ecosystem ; Federal Government ; *Mining ; Risk
    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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  • 102
    Publication Date: 2014-08-30
    Description: Histone H3 lysine(27)-to-methionine (H3K27M) gain-of-function mutations occur in highly aggressive pediatric gliomas. We established a Drosophila animal model for the pathogenic histone H3K27M mutation and show that its overexpression resembles polycomb repressive complex 2 (PRC2) loss-of-function phenotypes, causing derepression of PRC2 target genes and developmental perturbations. Similarly, an H3K9M mutant depletes H3K9 methylation levels and suppresses position-effect variegation in various Drosophila tissues. The histone H3K9 demethylase KDM3B/JHDM2 associates with H3K9M-containing nucleosomes, and its misregulation in Drosophila results in changes of H3K9 methylation levels and heterochromatic silencing defects. We have established histone lysine-to-methionine mutants as robust in vivo tools for inhibiting methylation pathways that also function as biochemical reagents for capturing site-specific histone-modifying enzymes, thus providing molecular insight into chromatin signaling pathways.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4508193/" 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/PMC4508193/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Herz, Hans-Martin -- Morgan, Marc -- Gao, Xin -- Jackson, Jessica -- Rickels, Ryan -- Swanson, Selene K -- Florens, Laurence -- Washburn, Michael P -- Eissenberg, Joel C -- Shilatifard, Ali -- CA R01CA089455/CA/NCI NIH HHS/ -- R01 CA089455/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2014 Aug 29;345(6200):1065-70. doi: 10.1126/science.1255104.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA. ; Saint Louis University School of Medicine, Edward A. Doisy Department of Biochemistry and Molecular Biology, St. Louis, MO, USA. ; Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA. Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA. ; Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA. ash@northwestern.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25170156" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Animals ; Chromatin/*metabolism ; Disease Models, Animal ; Drosophila Proteins/genetics ; Drosophila melanogaster ; Gene Silencing ; Glioma/genetics/metabolism ; Heterochromatin/metabolism ; Histone-Lysine N-Methyltransferase/genetics ; Histones/*genetics/metabolism ; Jumonji Domain-Containing Histone Demethylases/metabolism ; Lysine/*genetics ; Methionine/*genetics ; Methylation ; Mutation ; Signal Transduction
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  • 103
    Publication Date: 2014-07-26
    Description: In theoretical ecology, traditional studies based on dynamical stability and numerical simulations have not found a unified answer to the effect of network architecture on community persistence. Here, we introduce a mathematical framework based on the concept of structural stability to explain such a disparity of results. We investigated the range of conditions necessary for the stable coexistence of all species in mutualistic systems. We show that the apparently contradictory conclusions reached by previous studies arise as a consequence of overseeing either the necessary conditions for persistence or its dependence on model parameterization. We show that observed network architectures maximize the range of conditions for species coexistence. We discuss the applicability of structural stability to study other types of interspecific interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rohr, Rudolf P -- Saavedra, Serguei -- Bascompte, Jordi -- New York, N.Y. -- Science. 2014 Jul 25;345(6195):1253497. doi: 10.1126/science.1253497.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Integrative Ecology Group, Estacion Biologica de Donana-Consejo Superior de Investigaciones Cientificas (EBD-CSIC), Calle Americo Vespucio s/n, E-41092 Sevilla, Spain. Unit of Ecology and Evolution, Department of Biology, University of Fribourg, Chemin du Musee 10, CH-1700 Fribourg, Switzerland. ; Integrative Ecology Group, Estacion Biologica de Donana-Consejo Superior de Investigaciones Cientificas (EBD-CSIC), Calle Americo Vespucio s/n, E-41092 Sevilla, Spain. ; Integrative Ecology Group, Estacion Biologica de Donana-Consejo Superior de Investigaciones Cientificas (EBD-CSIC), Calle Americo Vespucio s/n, E-41092 Sevilla, Spain. bascompte@ebd.csic.es.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25061214" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Computer Simulation ; *Ecosystem ; *Models, Biological ; Plants ; *Symbiosis
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  • 104
    Publication Date: 2014-10-04
    Description: Human mitochondrial ribosomes are highly divergent from all other known ribosomes and are specialized to exclusively translate membrane proteins. They are linked with hereditary mitochondrial diseases and are often the unintended targets of various clinically useful antibiotics. Using single-particle cryogenic electron microscopy, we have determined the structure of its large subunit to 3.4 angstrom resolution, revealing 48 proteins, 21 of which are specific to mitochondria. The structure unveils an adaptation of the exit tunnel for hydrophobic nascent peptides, extensive remodeling of the central protuberance, including recruitment of mitochondrial valine transfer RNA (tRNA(Val)) to play an integral structural role, and changes in the tRNA binding sites related to the unusual characteristics of mitochondrial tRNAs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4246062/" 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/PMC4246062/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brown, Alan -- Amunts, Alexey -- Bai, Xiao-chen -- Sugimoto, Yoichiro -- Edwards, Patricia C -- Murshudov, Garib -- Scheres, Sjors H W -- Ramakrishnan, V -- 096570/Wellcome Trust/United Kingdom -- MC_U105184332/Medical Research Council/United Kingdom -- MC_UP_A025_1012/Medical Research Council/United Kingdom -- MC_UP_A025_1013/Medical Research Council/United Kingdom -- WT096570/Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2014 Nov 7;346(6210):718-22. doi: 10.1126/science.1258026. Epub 2014 Oct 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. ; Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. ramak@mrc-lmb.cam.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25278503" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cryoelectron Microscopy ; Humans ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/chemistry/ultrastructure ; Mutation ; Nucleic Acid Conformation ; Protein Conformation ; RNA, Transfer, Val/analysis/*chemistry ; Ribosome Subunits/*chemistry/genetics/*ultrastructure
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  • 105
    Publication Date: 2014-05-31
    Description: Phosphatidylinositol 4-kinases (PI4Ks) and small guanosine triphosphatases (GTPases) are essential for processes that require expansion and remodeling of phosphatidylinositol 4-phosphate (PI4P)-containing membranes, including cytokinesis, intracellular development of malarial pathogens, and replication of a wide range of RNA viruses. However, the structural basis for coordination of PI4K, GTPases, and their effectors is unknown. Here, we describe structures of PI4Kbeta (PI4KIIIbeta) bound to the small GTPase Rab11a without and with the Rab11 effector protein FIP3. The Rab11-PI4KIIIbeta interface is distinct compared with known structures of Rab complexes and does not involve switch regions used by GTPase effectors. Our data provide a mechanism for how PI4KIIIbeta coordinates Rab11 and its effectors on PI4P-enriched membranes and also provide strategies for the design of specific inhibitors that could potentially target plasmodial PI4KIIIbeta to combat malaria.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4046302/" 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/PMC4046302/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burke, John E -- Inglis, Alison J -- Perisic, Olga -- Masson, Glenn R -- McLaughlin, Stephen H -- Rutaganira, Florentine -- Shokat, Kevan M -- Williams, Roger L -- MC_U105184308/Medical Research Council/United Kingdom -- PG/11/109/29247/British Heart Foundation/United Kingdom -- PG11/109/29247/British Heart Foundation/United Kingdom -- R01AI099245/AI/NIAID NIH HHS/ -- T32 GM064337/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 May 30;344(6187):1035-8. doi: 10.1126/science.1253397.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. jeburke@uvic.ca rlw@mrc-lmb.cam.ac.uk. ; Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. ; Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco (UCSF), San Francisco, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24876499" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antimalarials/chemistry/pharmacology ; Binding Sites ; Cell Line ; Crystallography, X-Ray ; Drug Design ; Humans ; I-kappa B Kinase/*chemistry ; Molecular Sequence Data ; Mutation ; Phosphotransferases (Alcohol Group Acceptor)/*chemistry/genetics ; Plasmodium/drug effects/growth & development ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; rab GTP-Binding Proteins/*chemistry
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  • 106
    Publication Date: 2014-01-25
    Description: Canine transmissible venereal tumor (CTVT) is the oldest known somatic cell lineage. It is a transmissible cancer that propagates naturally in dogs. We sequenced the genomes of two CTVT tumors and found that CTVT has acquired 1.9 million somatic substitution mutations and bears evidence of exposure to ultraviolet light. CTVT is remarkably stable and lacks subclonal heterogeneity despite thousands of rearrangements, copy-number changes, and retrotransposon insertions. More than 10,000 genes carry nonsynonymous variants, and 646 genes have been lost. CTVT first arose in a dog with low genomic heterozygosity that may have lived about 11,000 years ago. The cancer spawned by this individual dispersed across continents about 500 years ago. Our results provide a genetic identikit of an ancient dog and demonstrate the robustness of mammalian somatic cells to survive for millennia despite a massive mutation burden.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3918581/" 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/PMC3918581/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murchison, Elizabeth P -- Wedge, David C -- Alexandrov, Ludmil B -- Fu, Beiyuan -- Martincorena, Inigo -- Ning, Zemin -- Tubio, Jose M C -- Werner, Emma I -- Allen, Jan -- De Nardi, Andrigo Barboza -- Donelan, Edward M -- Marino, Gabriele -- Fassati, Ariberto -- Campbell, Peter J -- Yang, Fengtang -- Burt, Austin -- Weiss, Robin A -- Stratton, Michael R -- 088340/Wellcome Trust/United Kingdom -- 098051/Wellcome Trust/United Kingdom -- G0501446/Medical Research Council/United Kingdom -- G0900950/Medical Research Council/United Kingdom -- G9721629/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2014 Jan 24;343(6169):437-40. doi: 10.1126/science.1247167.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24458646" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Lineage/*genetics ; Dog Diseases/*genetics ; Dogs/*genetics ; Founder Effect ; Gene Dosage ; Genome ; Karyotype ; Mutation ; Retroelements ; Venereal Tumors, Veterinary/*epidemiology/*genetics
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  • 107
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-06-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cardinale, Bradley -- New York, N.Y. -- Science. 2014 Jun 6;344(6188):1098. doi: 10.1126/science.344.6188.1098-a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI 48103, USA. bradcard@umich.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24904146" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Birds ; *Ecosystem ; *Fishes ; *Invertebrates ; *Mammals ; *Plants
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  • 108
    Publication Date: 2014-02-01
    Description: Ecologists have long sought to understand the factors controlling the structure of savanna vegetation. Using data from 2154 sites in savannas across Africa, Australia, and South America, we found that increasing moisture availability drives increases in fire and tree basal area, whereas fire reduces tree basal area. However, among continents, the magnitude of these effects varied substantially, so that a single model cannot adequately represent savanna woody biomass across these regions. Historical and environmental differences drive the regional variation in the functional relationships between woody vegetation, fire, and climate. These same differences will determine the regional responses of vegetation to future climates, with implications for global carbon stocks.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lehmann, Caroline E R -- Anderson, T Michael -- Sankaran, Mahesh -- Higgins, Steven I -- Archibald, Sally -- Hoffmann, William A -- Hanan, Niall P -- Williams, Richard J -- Fensham, Roderick J -- Felfili, Jeanine -- Hutley, Lindsay B -- Ratnam, Jayashree -- San Jose, Jose -- Montes, Ruben -- Franklin, Don -- Russell-Smith, Jeremy -- Ryan, Casey M -- Durigan, Giselda -- Hiernaux, Pierre -- Haidar, Ricardo -- Bowman, David M J S -- Bond, William J -- New York, N.Y. -- Science. 2014 Jan 31;343(6170):548-52. doi: 10.1126/science.1247355.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Macquarie University, New South Wales 2109, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24482480" target="_blank"〉PubMed〈/a〉
    Keywords: Africa ; Australia ; *Climate ; *Ecosystem ; *Fires ; Humidity ; Models, Biological ; South America ; *Trees
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  • 109
    Publication Date: 2014-04-05
    Description: Adrenal Cushing's syndrome is caused by excess production of glucocorticoid from adrenocortical tumors and hyperplasias, which leads to metabolic disorders. We performed whole-exome sequencing of 49 blood-tumor pairs and RNA sequencing of 44 tumors from cortisol-producing adrenocortical adenomas (ACAs), adrenocorticotropic hormone-independent macronodular adrenocortical hyperplasias (AIMAHs), and adrenocortical oncocytomas (ADOs). We identified a hotspot in the PRKACA gene with a L205R mutation in 69.2% (27 out of 39) of ACAs and validated in 65.5% of a total of 87 ACAs. Our data revealed that the activating L205R mutation, which locates in the P+1 loop of the protein kinase A (PKA) catalytic subunit, promoted PKA substrate phosphorylation and target gene expression. Moreover, we discovered the recurrently mutated gene DOT1L in AIMAHs and CLASP2 in ADOs. Collectively, these data highlight potentially functional mutated genes in adrenal Cushing's syndrome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cao, Yanan -- He, Minghui -- Gao, Zhibo -- Peng, Ying -- Li, Yanli -- Li, Lin -- Zhou, Weiwei -- Li, Xiangchun -- Zhong, Xu -- Lei, Yiming -- Su, Tingwei -- Wang, Hang -- Jiang, Yiran -- Yang, Lin -- Wei, Wei -- Yang, Xu -- Jiang, Xiuli -- Liu, Li -- He, Juan -- Ye, Junna -- Wei, Qing -- Li, Yingrui -- Wang, Weiqing -- Wang, Jun -- Ning, Guang -- New York, N.Y. -- Science. 2014 May 23;344(6186):913-7. doi: 10.1126/science.1249480. Epub 2014 Apr 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China. ; BGI-Shanghai, BGI-Shenzhen, Shenzhen, China. ; Department of Pathology, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China. ; Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China. guangning@medmail.com.cn wangj@genomics.org.cn wqingw@hotmail.com. ; BGI-Shanghai, BGI-Shenzhen, Shenzhen, China. Department of Biology, University of Copenhagen, Copenhagen, Denmark. King Abdulaziz University, Jeddah, Saudi Arabia. Macau University of Science and Technology, Macau, China. Department of Medicine, University of Hong Kong, Hong Kong. guangning@medmail.com.cn wangj@genomics.org.cn wqingw@hotmail.com. ; Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China. Laboratory of Endocrinology and Metabolism, Institute of Health Sciences, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), and Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China. guangning@medmail.com.cn wangj@genomics.org.cn wqingw@hotmail.com.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24700472" target="_blank"〉PubMed〈/a〉
    Keywords: Adrenal Cortex Neoplasms/*genetics/*metabolism ; Adrenocortical Adenoma/*genetics/*metabolism ; Amino Acid Substitution ; Arginine/genetics ; Catalytic Domain/genetics ; Cells, Cultured ; Cushing Syndrome/*genetics ; Cyclic AMP-Dependent Protein Kinase Catalytic Subunits/chemistry/*genetics ; Glucocorticoids/metabolism ; Humans ; Hydrocortisone/*metabolism ; Leucine/genetics ; Methyltransferases/genetics ; Microtubule-Associated Proteins/genetics ; Mutation
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  • 110
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-07-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pawar, Samraat -- New York, N.Y. -- Science. 2014 Jul 25;345(6195):383. doi: 10.1126/science.1256466.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire SL5 7PY, U K. s.pawar@imperial.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25061191" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Ecosystem ; *Models, Biological ; *Symbiosis
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  • 111
    Publication Date: 2014-03-29
    Description: Rapid advances in DNA synthesis techniques have made it possible to engineer viruses, biochemical pathways and assemble bacterial genomes. Here, we report the synthesis of a functional 272,871-base pair designer eukaryotic chromosome, synIII, which is based on the 316,617-base pair native Saccharomyces cerevisiae chromosome III. Changes to synIII include TAG/TAA stop-codon replacements, deletion of subtelomeric regions, introns, transfer RNAs, transposons, and silent mating loci as well as insertion of loxPsym sites to enable genome scrambling. SynIII is functional in S. cerevisiae. Scrambling of the chromosome in a heterozygous diploid reveals a large increase in a-mater derivatives resulting from loss of the MATalpha allele on synIII. The complete design and synthesis of synIII establishes S. cerevisiae as the basis for designer eukaryotic genome biology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4033833/" 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/PMC4033833/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Annaluru, Narayana -- Muller, Heloise -- Mitchell, Leslie A -- Ramalingam, Sivaprakash -- Stracquadanio, Giovanni -- Richardson, Sarah M -- Dymond, Jessica S -- Kuang, Zheng -- Scheifele, Lisa Z -- Cooper, Eric M -- Cai, Yizhi -- Zeller, Karen -- Agmon, Neta -- Han, Jeffrey S -- Hadjithomas, Michalis -- Tullman, Jennifer -- Caravelli, Katrina -- Cirelli, Kimberly -- Guo, Zheyuan -- London, Viktoriya -- Yeluru, Apurva -- Murugan, Sindurathy -- Kandavelou, Karthikeyan -- Agier, Nicolas -- Fischer, Gilles -- Yang, Kun -- Martin, J Andrew -- Bilgel, Murat -- Bohutski, Pavlo -- Boulier, Kristin M -- Capaldo, Brian J -- Chang, Joy -- Charoen, Kristie -- Choi, Woo Jin -- Deng, Peter -- DiCarlo, James E -- Doong, Judy -- Dunn, Jessilyn -- Feinberg, Jason I -- Fernandez, Christopher -- Floria, Charlotte E -- Gladowski, David -- Hadidi, Pasha -- Ishizuka, Isabel -- Jabbari, Javaneh -- Lau, Calvin Y L -- Lee, Pablo A -- Li, Sean -- Lin, Denise -- Linder, Matthias E -- Ling, Jonathan -- Liu, Jaime -- Liu, Jonathan -- London, Mariya -- Ma, Henry -- Mao, Jessica -- McDade, Jessica E -- McMillan, Alexandra -- Moore, Aaron M -- Oh, Won Chan -- Ouyang, Yu -- Patel, Ruchi -- Paul, Marina -- Paulsen, Laura C -- Qiu, Judy -- Rhee, Alex -- Rubashkin, Matthew G -- Soh, Ina Y -- Sotuyo, Nathaniel E -- Srinivas, Venkatesh -- Suarez, Allison -- Wong, Andy -- Wong, Remus -- Xie, Wei Rose -- Xu, Yijie -- Yu, Allen T -- Koszul, Romain -- Bader, Joel S -- Boeke, Jef D -- Chandrasegaran, Srinivasan -- 092076/Wellcome Trust/United Kingdom -- GM077291/GM/NIGMS NIH HHS/ -- R01 GM077291/GM/NIGMS NIH HHS/ -- R01 GM090192/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Apr 4;344(6179):55-8. doi: 10.1126/science.1249252. Epub 2014 Mar 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Environmental Health Sciences, Johns Hopkins University (JHU) School of Public Health, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24674868" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; *Chromosomes, Fungal/genetics/metabolism ; DNA, Fungal/genetics ; Genes, Fungal ; Genetic Fitness ; Genome, Fungal ; Genomic Instability ; Introns ; Molecular Sequence Data ; Mutation ; Polymerase Chain Reaction ; RNA, Fungal/genetics ; RNA, Transfer/genetics ; Saccharomyces cerevisiae/cytology/*genetics/physiology ; Sequence Analysis, DNA ; Sequence Deletion ; Synthetic Biology/*methods ; Transformation, Genetic
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  • 112
    Publication Date: 2014-02-22
    Description: Robustness, the maintenance of a character in the presence of genetic change, can help preserve adaptive traits but also may hinder evolvability, the ability to bring forth novel adaptations. We used genotype networks to analyze the binding site repertoires of 193 transcription factors from mice and yeast, providing empirical evidence that robustness and evolvability need not be conflicting properties. Network vertices represent binding sites where two sites are connected if they differ in a single nucleotide. We show that the binding sites of larger genotype networks are not only more robust, but the sequences adjacent to such networks can also bind more transcription factors, thus demonstrating that robustness can facilitate evolvability.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Payne, Joshua L -- Wagner, Andreas -- New York, N.Y. -- Science. 2014 Feb 21;343(6173):875-7. doi: 10.1126/science.1249046.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Zurich, Institute of Evolutionary Biology and Environmental Studies, Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24558158" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites/genetics ; Gene Regulatory Networks ; Mice ; Mutation ; Saccharomyces cerevisiae Proteins/chemistry ; Transcription Factors/*chemistry ; Transcription, Genetic
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  • 113
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-05-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kaiser, Jocelyn -- New York, N.Y. -- Science. 2014 May 16;344(6185):687-9. doi: 10.1126/science.344.6185.687.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24833372" target="_blank"〉PubMed〈/a〉
    Keywords: Actinin/genetics ; Animals ; Caspase 12/genetics ; *Gene Knockout Techniques ; *Genetic Association Studies ; Humans ; Mice ; *Molecular Targeted Therapy ; Muscular Dystrophies/genetics ; Mutation ; NAV1.7 Voltage-Gated Sodium Channel/genetics ; Proprotein Convertases/genetics ; Receptors, CCR5/genetics ; Serine Endopeptidases/genetics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 114
    Publication Date: 2014-10-18
    Description: Small molecules are useful tools for probing the biological function and therapeutic potential of individual proteins, but achieving selectivity is challenging when the target protein shares structural domains with other proteins. The Bromo and Extra-Terminal (BET) proteins have attracted interest because of their roles in transcriptional regulation, epigenetics, and cancer. The BET bromodomains (protein interaction modules that bind acetyl-lysine) have been targeted by potent small-molecule inhibitors, but these inhibitors lack selectivity for individual family members. We developed an ethyl derivative of an existing small-molecule inhibitor, I-BET/JQ1, and showed that it binds leucine/alanine mutant bromodomains with nanomolar affinity and achieves up to 540-fold selectivity relative to wild-type bromodomains. Cell culture studies showed that blockade of the first bromodomain alone is sufficient to displace a specific BET protein, Brd4, from chromatin. Expansion of this approach could help identify the individual roles of single BET proteins in human physiology and disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4458378/" 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/PMC4458378/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baud, Matthias G J -- Lin-Shiao, Enrique -- Cardote, Teresa -- Tallant, Cynthia -- Pschibul, Annica -- Chan, Kwok-Ho -- Zengerle, Michael -- Garcia, Jordi R -- Kwan, Terence T-L -- Ferguson, Fleur M -- Ciulli, Alessio -- 097945/Z/11/Z/Wellcome Trust/United Kingdom -- 100476/Z/12/Z/Wellcome Trust/United Kingdom -- BB/G023123/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/J001201/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2014 Oct 31;346(6209):638-41. doi: 10.1126/science.1249830. Epub 2014 Oct 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK. Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. ; Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK. ; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. ; Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK. Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. a.ciulli@dundee.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25323695" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Azepines/chemistry/pharmacology ; Cell Line, Tumor ; Chromatin/chemistry ; Crystallography, X-Ray ; Humans ; Leucine/genetics ; Models, Molecular ; Molecular Probes/*chemistry ; Mutation ; Nuclear Proteins/antagonists & inhibitors/*chemistry/genetics ; Protein Engineering/*methods ; Protein Structure, Tertiary ; Transcription Factors/antagonists & inhibitors/*chemistry/genetics ; Triazoles/chemistry/pharmacology
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  • 115
    Publication Date: 2014-04-05
    Description: Animal migrations span the globe, involving immense numbers of individuals from a wide range of taxa. Migrants transport nutrients, energy, and other organisms as they forage and are preyed upon throughout their journeys. These highly predictable, pulsed movements across large spatial scales render migration a potentially powerful yet underappreciated dimension of biodiversity that is intimately embedded within resident communities. We review examples from across the animal kingdom to distill fundamental processes by which migratory animals influence communities and ecosystems, demonstrating that they can uniquely alter energy flow, food-web topology and stability, trophic cascades, and the structure of metacommunities. Given the potential for migration to alter ecological networks worldwide, we suggest an integrative framework through which community dynamics and ecosystem functioning may explicitly consider animal migrations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bauer, S -- Hoye, B J -- New York, N.Y. -- Science. 2014 Apr 4;344(6179):1242552. doi: 10.1126/science.1242552.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bird Migration, Swiss Ornithological Institute, 6204 Sempach, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24700862" target="_blank"〉PubMed〈/a〉
    Keywords: *Animal Migration ; Animals ; *Biodiversity ; *Ecosystem ; Food Chain ; Herbivory ; Parasites/physiology ; Predatory Behavior
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  • 116
    Publication Date: 2014-03-29
    Description: The cloning of the breast cancer susceptibility genes BRCA1 and BRCA2 nearly two decades ago helped set in motion an avalanche of research exploring how genomic information can be optimally applied to identify and clinically care for individuals with a high risk of developing cancer. Genetic testing for mutations in BRCA1, BRCA2, and other breast cancer susceptibility genes has since proved to be a valuable tool for determining eligibility for enhanced screening and prevention strategies, as well as for identifying patients most likely to benefit from a targeted therapy. Here, we discuss the landscape of inherited mutations and sequence variants in BRCA1 and BRCA2, the complexities of determining disease risk when the pathogenicity of sequence variants is uncertain, and current strategies for clinical management of women who carry BRCA1/2 mutations.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4074902/" 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/PMC4074902/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Couch, Fergus J -- Nathanson, Katherine L -- Offit, Kenneth -- 3P30CA008748-47/CA/NCI NIH HHS/ -- CA016520/CA/NCI NIH HHS/ -- CA116167/CA/NCI NIH HHS/ -- CA116201/CA/NCI NIH HHS/ -- CA128978/CA/NCI NIH HHS/ -- CA135509/CA/NCI NIH HHS/ -- P50 CA116201/CA/NCI NIH HHS/ -- R01 CA128978/CA/NCI NIH HHS/ -- R01 CA135509/CA/NCI NIH HHS/ -- U01 CA116167/CA/NCI NIH HHS/ -- U01 CA164947/CA/NCI NIH HHS/ -- U01CA164947/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2014 Mar 28;343(6178):1466-70. doi: 10.1126/science.1251827.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24675953" target="_blank"〉PubMed〈/a〉
    Keywords: BRCA1 Protein/*genetics ; BRCA2 Protein/*genetics ; Breast Neoplasms/*drug therapy/genetics/prevention & control ; Cloning, Molecular ; Female ; *Genetic Predisposition to Disease ; Humans ; Models, Genetic ; Mutation ; *Precision Medicine
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  • 117
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-12-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Couzin-Frankel, Jennifer -- New York, N.Y. -- Science. 2014 Dec 5;346(6214):1167-70. doi: 10.1126/science.346.6214.1167.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25477439" target="_blank"〉PubMed〈/a〉
    Keywords: BRCA1 Protein/genetics ; BRCA2 Protein/genetics ; Breast Neoplasms/genetics/prevention & control ; Female ; *Genes, Neoplasm ; *Genetic Counseling ; Genetic Predisposition to Disease/*genetics ; *Genetic Testing ; Humans ; Jews/*genetics ; Mutation ; Neoplasms/genetics/*prevention & control ; Ovarian Neoplasms/genetics/prevention & control ; *Uncertainty
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  • 118
    Publication Date: 2014-07-12
    Description: Circulating tumor cells (CTCs) are present at low concentrations in the peripheral blood of patients with solid tumors. It has been proposed that the isolation, ex vivo culture, and characterization of CTCs may provide an opportunity to noninvasively monitor the changing patterns of drug susceptibility in individual patients as their tumors acquire new mutations. In a proof-of-concept study, we established CTC cultures from six patients with estrogen receptor-positive breast cancer. Three of five CTC lines tested were tumorigenic in mice. Genome sequencing of the CTC lines revealed preexisting mutations in the PIK3CA gene and newly acquired mutations in the estrogen receptor gene (ESR1), PIK3CA gene, and fibroblast growth factor receptor gene (FGFR2), among others. Drug sensitivity testing of CTC lines with multiple mutations revealed potential new therapeutic targets. With optimization of CTC culture conditions, this strategy may help identify the best therapies for individual cancer patients over the course of their disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4358808/" 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/PMC4358808/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Min -- Bardia, Aditya -- Aceto, Nicola -- Bersani, Francesca -- Madden, Marissa W -- Donaldson, Maria C -- Desai, Rushil -- Zhu, Huili -- Comaills, Valentine -- Zheng, Zongli -- Wittner, Ben S -- Stojanov, Petar -- Brachtel, Elena -- Sgroi, Dennis -- Kapur, Ravi -- Shioda, Toshihiro -- Ting, David T -- Ramaswamy, Sridhar -- Getz, Gad -- Iafrate, A John -- Benes, Cyril -- Toner, Mehmet -- Maheswaran, Shyamala -- Haber, Daniel A -- CA129933/CA/NCI NIH HHS/ -- EB008047/EB/NIBIB NIH HHS/ -- P41 EB002503/EB/NIBIB NIH HHS/ -- R01 CA129933/CA/NCI NIH HHS/ -- U01 EB012493/EB/NIBIB NIH HHS/ -- Howard Hughes Medical Institute/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2014 Jul 11;345(6193):216-20. doi: 10.1126/science.1253533.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA. Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. ; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA. Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA. ; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA. ; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA. Department of Pathology, Harvard Medical School, Charlestown, MA 02129, USA. Department of Medical Epidemiology and Biostatistics, Karolinska Insitutet, Stockholm, Sweden. ; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. ; Department of Pathology, Harvard Medical School, Charlestown, MA 02129, USA. ; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA. Department of Pathology, Harvard Medical School, Charlestown, MA 02129, USA. ; Center for Bioengineering in Medicine, Harvard Medical School, Charlestown, MA 02129, USA. ; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA. Department of Pathology, Harvard Medical School, Charlestown, MA 02129, USA. Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. ; Center for Bioengineering in Medicine, Harvard Medical School, Charlestown, MA 02129, USA. Department of Surgery, Harvard Medical School, Charlestown, MA 02129, USA. ; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA. Department of Surgery, Harvard Medical School, Charlestown, MA 02129, USA. maheswaran@helix.mgh.harvard.edu haber@helix.mgh.harvard.edu. ; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA. Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA. maheswaran@helix.mgh.harvard.edu haber@helix.mgh.harvard.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25013076" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antineoplastic Agents/*pharmacology/therapeutic use ; Breast Neoplasms/*drug therapy/genetics ; Cell Culture Techniques ; Cell Separation ; Culture ; Drug Resistance, Neoplasm/*genetics ; Drug Screening Assays, Antitumor/methods ; Estrogen Receptor alpha/genetics ; Female ; Gene Frequency ; Humans ; Mice ; Microfluidics/methods ; *Molecular Targeted Therapy ; Mutation ; Neoplastic Cells, Circulating/*drug effects/metabolism ; Phosphatidylinositol 3-Kinases/genetics ; Sequence Analysis, DNA ; Tumor Cells, Cultured ; Xenograft Model Antitumor Assays
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  • 119
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-10-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Couzin-Frankel, Jennifer -- New York, N.Y. -- Science. 2014 Oct 3;346(6205):24-7. doi: 10.1126/science.346.6205.24. Epub 2014 Oct 2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25278593" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Genetic Engineering ; Humans ; *Mice ; Mice, Mutant Strains ; Mutation ; Neoplasms ; Neoplasms, Experimental/*drug therapy/genetics ; Pancreatic Neoplasms/*drug therapy/genetics ; Proto-Oncogene Proteins/genetics ; Tumor Suppressor Protein p53/genetics ; *Xenograft Model Antitumor Assays ; ras Proteins/genetics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 120
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-03-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stokstad, Erik -- New York, N.Y. -- Science. 2014 Mar 21;343(6177):1301. doi: 10.1126/science.343.6177.1301.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24653015" target="_blank"〉PubMed〈/a〉
    Keywords: Colorado ; *Ecosystem ; *Floods ; Groundwater ; Mexico ; *Rivers ; Salinity ; Trees/*growth & development ; United States
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  • 121
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-03-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McNutt, Marcia -- New York, N.Y. -- Science. 2014 Mar 21;343(6177):1289. doi: 10.1126/science.1253412.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Marcia McNutt is Editor-in-Chief of Science.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24653006" target="_blank"〉PubMed〈/a〉
    Keywords: Alaska ; *Aquatic Organisms ; *Ecosystem ; Environmental Monitoring ; Environmental Restoration and Remediation ; Gulf of Mexico ; *Petroleum Pollution
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  • 122
    Publication Date: 2014-04-20
    Description: Cytoplasmic plant immune receptors recognize specific pathogen effector proteins and initiate effector-triggered immunity. In Arabidopsis, the immune receptors RPS4 and RRS1 are both required to activate defense to three different pathogens. We show that RPS4 and RRS1 physically associate. Crystal structures of the N-terminal Toll-interleukin-1 receptor/resistance (TIR) domains of RPS4 and RRS1, individually and as a heterodimeric complex (respectively at 2.05, 1.75, and 2.65 angstrom resolution), reveal a conserved TIR/TIR interaction interface. We show that TIR domain heterodimerization is required to form a functional RRS1/RPS4 effector recognition complex. The RPS4 TIR domain activates effector-independent defense, which is inhibited by the RRS1 TIR domain through the heterodimerization interface. Thus, RPS4 and RRS1 function as a receptor complex in which the two components play distinct roles in recognition and signaling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Williams, Simon J -- Sohn, Kee Hoon -- Wan, Li -- Bernoux, Maud -- Sarris, Panagiotis F -- Segonzac, Cecile -- Ve, Thomas -- Ma, Yan -- Saucet, Simon B -- Ericsson, Daniel J -- Casey, Lachlan W -- Lonhienne, Thierry -- Winzor, Donald J -- Zhang, Xiaoxiao -- Coerdt, Anne -- Parker, Jane E -- Dodds, Peter N -- Kobe, Bostjan -- Jones, Jonathan D G -- New York, N.Y. -- Science. 2014 Apr 18;344(6181):299-303. doi: 10.1126/science.1247357.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24744375" target="_blank"〉PubMed〈/a〉
    Keywords: Agrobacterium/physiology ; Amino Acid Motifs ; Arabidopsis/chemistry/*immunology/microbiology ; Arabidopsis Proteins/*chemistry/genetics/metabolism ; Bacterial Proteins/immunology/metabolism ; Cell Death ; Crystallography, X-Ray ; Immunity, Innate ; Models, Molecular ; Mutation ; Plant Diseases/immunology/microbiology ; Plant Leaves/microbiology ; Plant Proteins/*chemistry/genetics/metabolism ; Plants, Genetically Modified ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Immunologic/*chemistry/genetics/metabolism ; Signal Transduction ; Tobacco/genetics/immunology/metabolism/microbiology
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  • 123
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-01-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Couzin-Frankel, Jennifer -- R01 CA154517/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2014 Jan 24;343(6169):356-7. doi: 10.1126/science.343.6169.356.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24458615" target="_blank"〉PubMed〈/a〉
    Keywords: DNA/*genetics ; Financing, Organized ; Genetic Research/economics/*ethics/legislation & jurisprudence ; Health Information Systems/*ethics/legislation & jurisprudence ; Humans ; Molecular Epidemiology ; Mutation ; Neoplasms/*genetics ; Patient Access to Records/*ethics/legislation & jurisprudence
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  • 124
    Publication Date: 2014-04-26
    Description: Extensive genomic diversity within coexisting members of a microbial species has been revealed through selected cultured isolates and metagenomic assemblies. Yet, the cell-by-cell genomic composition of wild uncultured populations of co-occurring cells is largely unknown. In this work, we applied large-scale single-cell genomics to study populations of the globally abundant marine cyanobacterium Prochlorococcus. We show that they are composed of hundreds of subpopulations with distinct "genomic backbones," each backbone consisting of a different set of core gene alleles linked to a small distinctive set of flexible genes. These subpopulations are estimated to have diverged at least a few million years ago, suggesting ancient, stable niche partitioning. Such a large set of coexisting subpopulations may be a general feature of free-living bacterial species with huge populations in highly mixed habitats.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kashtan, Nadav -- Roggensack, Sara E -- Rodrigue, Sebastien -- Thompson, Jessie W -- Biller, Steven J -- Coe, Allison -- Ding, Huiming -- Marttinen, Pekka -- Malmstrom, Rex R -- Stocker, Roman -- Follows, Michael J -- Stepanauskas, Ramunas -- Chisholm, Sallie W -- New York, N.Y. -- Science. 2014 Apr 25;344(6182):416-20. doi: 10.1126/science.1248575.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT), 77 Massachusetts Avenue, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24763590" target="_blank"〉PubMed〈/a〉
    Keywords: Atlantic Ocean ; Biological Evolution ; Ecosystem ; Genes, Bacterial ; *Genetic Variation ; *Genome, Bacterial ; Metagenomics ; Molecular Sequence Data ; Mutation ; Phylogeny ; Polymorphism, Single Nucleotide ; Prochlorococcus/classification/*genetics/*physiology ; Seasons ; Seawater/*microbiology ; Sequence Analysis, DNA ; Single-Cell Analysis
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  • 125
    Publication Date: 2014-11-22
    Description: Through their association with a kleisin subunit (Scc1), cohesin's Smc1 and Smc3 subunits are thought to form tripartite rings that mediate sister chromatid cohesion. Unlike the structure of Smc1/Smc3 and Smc1/Scc1 interfaces, that of Smc3/Scc1 is not known. Disconnection of this interface is thought to release cohesin from chromosomes in a process regulated by acetylation. We show here that the N-terminal domain of yeast Scc1 contains two alpha helices, forming a four-helix bundle with the coiled coil emerging from Smc3's adenosine triphosphatase head. Mutations affecting this interaction compromise cohesin's association with chromosomes. The interface is far from Smc3 residues, whose acetylation prevents cohesin's dissociation from chromosomes. Cohesin complexes holding chromatids together in vivo do indeed have the configuration of hetero-trimeric rings, and sister DNAs are entrapped within these.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300515/" 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/PMC4300515/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gligoris, Thomas G -- Scheinost, Johanna C -- Burmann, Frank -- Petela, Naomi -- Chan, Kok-Lung -- Uluocak, Pelin -- Beckouet, Frederic -- Gruber, Stephan -- Nasmyth, Kim -- Lowe, Jan -- 091859/Z/10/Z/Wellcome Trust/United Kingdom -- 095514/Wellcome Trust/United Kingdom -- 095514/Z/11/Z/Wellcome Trust/United Kingdom -- C573/A 12386/Cancer Research UK/United Kingdom -- C573/A11625/Medical Research Council/United Kingdom -- MC_U105184326/Medical Research Council/United Kingdom -- U10518432/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2014 Nov 21;346(6212):963-7. doi: 10.1126/science.1256917.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK. ; Max-Planck-Institut fur Biochemie, 82152, Martinsried, Germany. ; Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK. Medical Research Council (MRC) Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK. ; Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK. Dunn School of Pathology, University of Oxford, Oxford OX1 3RF, UK. ; Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK. kim.nasmyth@bioch.ox.ac.uk jyl@mrc-lmb.cam.ac.uk. ; MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK. kim.nasmyth@bioch.ox.ac.uk jyl@mrc-lmb.cam.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25414305" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/chemistry ; Amino Acid Sequence ; Cell Cycle Proteins/*chemistry/genetics ; Chromosomal Proteins, Non-Histone/*chemistry/genetics ; Conserved Sequence ; Cross-Linking Reagents/chemistry ; Crystallography, X-Ray ; DNA/chemistry ; Mutation ; Protein Multimerization ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/*chemistry/genetics
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  • 126
    Publication Date: 2014-11-15
    Description: Targeted cancer therapies have produced substantial clinical responses, but most tumors develop resistance to these drugs. Here, we describe a pharmacogenomic platform that facilitates rapid discovery of drug combinations that can overcome resistance. We established cell culture models derived from biopsy samples of lung cancer patients whose disease had progressed while on treatment with epidermal growth factor receptor (EGFR) or anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitors and then subjected these cells to genetic analyses and a pharmacological screen. Multiple effective drug combinations were identified. For example, the combination of ALK and MAPK kinase (MEK) inhibitors was active in an ALK-positive resistant tumor that had developed a MAP2K1 activating mutation, and the combination of EGFR and fibroblast growth factor receptor (FGFR) inhibitors was active in an EGFR mutant resistant cancer with a mutation in FGFR3. Combined ALK and SRC (pp60c-src) inhibition was effective in several ALK-driven patient-derived models, a result not predicted by genetic analysis alone. With further refinements, this strategy could help direct therapeutic choices for individual patients.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4388482/" 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/PMC4388482/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Crystal, Adam S -- Shaw, Alice T -- Sequist, Lecia V -- Friboulet, Luc -- Niederst, Matthew J -- Lockerman, Elizabeth L -- Frias, Rosa L -- Gainor, Justin F -- Amzallag, Arnaud -- Greninger, Patricia -- Lee, Dana -- Kalsy, Anuj -- Gomez-Caraballo, Maria -- Elamine, Leila -- Howe, Emily -- Hur, Wooyoung -- Lifshits, Eugene -- Robinson, Hayley E -- Katayama, Ryohei -- Faber, Anthony C -- Awad, Mark M -- Ramaswamy, Sridhar -- Mino-Kenudson, Mari -- Iafrate, A John -- Benes, Cyril H -- Engelman, Jeffrey A -- 086357/Wellcome Trust/United Kingdom -- 102696/Wellcome Trust/United Kingdom -- 1U54HG006097-01/HG/NHGRI NIH HHS/ -- P50 CA090578/CA/NCI NIH HHS/ -- P50CA090578/CA/NCI NIH HHS/ -- R01 CA137008/CA/NCI NIH HHS/ -- R01 CA164273/CA/NCI NIH HHS/ -- R01CA137008/CA/NCI NIH HHS/ -- R01CA164273/CA/NCI NIH HHS/ -- U54 HG006097/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2014 Dec 19;346(6216):1480-6. doi: 10.1126/science.1254721. Epub 2014 Nov 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA. ; Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology and Harvard Medical School, Boston, MA 02115, USA. Chemical Kinomics Research Center, Korea Institute of Science and Technology, Seoul, 136-791, South Korea. ; Massachusetts General Hospital Cancer Center, Department of Pathology and Harvard Medical School, Boston, MA 02114, USA. ; Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA. jengelman@partners.org cbenes@partners.org.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25394791" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Combined Chemotherapy Protocols/*therapeutic use ; Carcinoma, Non-Small-Cell Lung/*drug therapy/enzymology/genetics ; DNA Mutational Analysis ; Drug Resistance, Neoplasm/*genetics ; Drug Screening Assays, Antitumor ; Enzyme Activation/genetics ; Humans ; Lung Neoplasms/*drug therapy/enzymology/genetics ; MAP Kinase Kinase 1/genetics/metabolism ; Molecular Targeted Therapy/*methods ; Mutation ; *Patient-Specific Modeling ; Protein Kinase Inhibitors/*therapeutic use ; Proto-Oncogene Proteins pp60(c-src)/antagonists & inhibitors ; Pyrimidines/therapeutic use ; Receptor Protein-Tyrosine Kinases/antagonists & inhibitors ; Receptor, Epidermal Growth Factor/antagonists & inhibitors ; Receptor, Fibroblast Growth Factor, Type 3/antagonists & inhibitors/genetics ; Sulfones/therapeutic use ; Tumor Cells, Cultured
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  • 127
    Publication Date: 2014-01-18
    Description: Ribosome biogenesis drives cell growth and proliferation, but mechanisms that modulate this process within specific lineages remain poorly understood. Here, we identify a Drosophila RNA polymerase I (Pol I) regulatory complex composed of Under-developed (Udd), TAF1B, and a TAF1C-like factor. Disruption of udd or TAF1B results in reduced ovarian germline stem cell (GSC) proliferation. Female GSCs display high levels of ribosomal RNA (rRNA) transcription, and Udd becomes enriched in GSCs relative to their differentiating daughters. Increasing Pol I transcription delays differentiation, whereas reducing rRNA production induces both morphological changes that accompany multicellular cyst formation and specific decreased expression of the bone morphogenetic protein (BMP) pathway component Mad. These findings demonstrate that modulating rRNA synthesis fosters changes in the cell fate, growth, and proliferation of female Drosophila GSCs and their daughters.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4084784/" 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/PMC4084784/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Qiao -- Shalaby, Nevine A -- Buszczak, Michael -- R01 GM086647/GM/NIGMS NIH HHS/ -- R01GM045820/GM/NIGMS NIH HHS/ -- R01GM086647/GM/NIGMS NIH HHS/ -- T32 DK007745/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2014 Jan 17;343(6168):298-301. doi: 10.1126/science.1246384.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9148, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24436420" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Lineage/*genetics ; *Cell Proliferation ; Drosophila Proteins/genetics/metabolism ; Drosophila melanogaster/*cytology/genetics ; Female ; *Genes, rRNA ; Histone Acetyltransferases/genetics/metabolism ; Mutation ; Nuclear Proteins/genetics/metabolism ; Ovary/cytology/*physiology ; RNA Polymerase I/genetics/*metabolism ; Stem Cells/cytology/*physiology ; TATA-Binding Protein Associated Factors ; Transcription Factor TFIID/genetics/metabolism ; Transcription Factors/genetics/metabolism ; *Transcription, Genetic
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  • 128
    Publication Date: 2014-06-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kelly, Ryan P -- Port, Jesse A -- Yamahara, Kevan M -- Martone, Rebecca G -- Lowell, Natalie -- Thomsen, Philip Francis -- Mach, Megan E -- Bennett, Meredith -- Prahler, Erin -- Caldwell, Margaret R -- Crowder, Larry B -- New York, N.Y. -- Science. 2014 Jun 27;344(6191):1455-6. doi: 10.1126/science.1251156. Epub 2014 Jun 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Marine and Environmental Affairs, University of Washington, Seattle, WA 98103, USA. Center for Ocean Solutions, Stanford University, Stanford, CA 94305, USA. rpkelly@uw.edu. ; Center for Ocean Solutions, Stanford University, Stanford, CA 94305, USA. ; School of Marine and Environmental Affairs, University of Washington, Seattle, WA 98103, USA. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24970068" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Aquatic Organisms/genetics ; DNA/*analysis ; Ecological Parameter Monitoring/*methods ; *Ecosystem ; Environmental Monitoring/*methods ; *Environmental Policy/legislation & jurisprudence ; Introduced Species
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  • 129
    Publication Date: 2014-05-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baillie, J Kenneth -- New York, N.Y. -- Science. 2014 May 23;344(6186):807-8. doi: 10.1126/science.1255074.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, UK, and Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK. j.k.baillie@ed.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24855243" target="_blank"〉PubMed〈/a〉
    Keywords: Communicable Diseases/*drug therapy/*genetics ; Disease Resistance/drug effects/*genetics/immunology ; *Genetic Predisposition to Disease ; Genetic Variation ; Genomics/*methods ; Host-Pathogen Interactions/drug effects/*genetics/immunology ; Humans ; Immune System/*drug effects/*immunology ; Membrane Proteins/genetics ; Mutation ; RNA-Binding Proteins/genetics ; Translational Medical Research
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  • 130
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-02-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2014 Jan 31;343(6170):472-3. doi: 10.1126/science.343.6170.472.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24482456" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Ants ; Biomass ; Butterflies ; Carnivory ; *Ecosystem ; Male ; *Salts ; *Sodium Chloride ; Soil/*chemistry ; Trees
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  • 131
    Publication Date: 2014-12-20
    Description: The generation of new enzymatic activities has mainly relied on repurposing the interiors of preexisting protein folds because of the challenge in designing functional, three-dimensional protein structures from first principles. Here we report an artificial metallo-beta-lactamase, constructed via the self-assembly of a structurally and functionally unrelated, monomeric redox protein into a tetrameric assembly that possesses catalytic zinc sites in its interfaces. The designed metallo-beta-lactamase is functional in the Escherichia coli periplasm and enables the bacteria to survive treatment with ampicillin. In vivo screening of libraries has yielded a variant that displays a catalytic proficiency [(k(cat)/K(m))/k(uncat)] for ampicillin hydrolysis of 2.3 x 10(6) and features the emergence of a highly mobile loop near the active site, a key component of natural beta-lactamases to enable substrate interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Song, Woon Ju -- Tezcan, F Akif -- New York, N.Y. -- Science. 2014 Dec 19;346(6216):1525-8. doi: 10.1126/science.1259680.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0356, USA. ; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0356, USA. tezcan@ucsd.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25525249" target="_blank"〉PubMed〈/a〉
    Keywords: Ampicillin/*chemistry/pharmacology ; Catalysis ; Catalytic Domain ; Crystallography, X-Ray ; *Directed Molecular Evolution ; Escherichia coli/drug effects/enzymology ; Hydrolysis ; Metalloproteins/*chemistry/genetics ; Mutation ; Periplasm/enzymology ; *Protein Engineering ; Protein Folding ; Protein Structure, Secondary ; Substrate Specificity ; Zinc/*chemistry ; beta-Lactamases/*chemistry/genetics
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  • 132
    Publication Date: 2014-12-20
    Description: Evolution and design of protein complexes are almost always viewed through the lens of amino acid mutations at protein interfaces. We showed previously that residues not involved in the physical interaction between proteins make important contributions to oligomerization by acting indirectly or allosterically. In this work, we sought to investigate the mechanism by which allosteric mutations act, using the example of the PyrR family of pyrimidine operon attenuators. In this family, a perfectly sequence-conserved helix that forms a tetrameric interface is exposed as solvent-accessible surface in dimeric orthologs. This means that mutations must be acting from a distance to destabilize the interface. We identified 11 key mutations controlling oligomeric state, all distant from the interfaces and outside ligand-binding pockets. Finally, we show that the key mutations introduce conformational changes equivalent to the conformational shift between the free versus nucleotide-bound conformations of the proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4337988/" 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/PMC4337988/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Perica, Tina -- Kondo, Yasushi -- Tiwari, Sandhya P -- McLaughlin, Stephen H -- Kemplen, Katherine R -- Zhang, Xiuwei -- Steward, Annette -- Reuter, Nathalie -- Clarke, Jane -- Teichmann, Sarah A -- 095195/Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2014 Dec 19;346(6216):1254346. doi: 10.1126/science.1254346.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. ; Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. ; Department of Molecular Biology, University of Bergen University of Bergen, P.O. Box 7803, N-5020 Bergen, Norway. Computational Biology Unit, Department of Informatics, University of Bergen, P.O. Box 7803, N-5020 Bergen, Norway. ; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. ; European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ; European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. saraht@ebi.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25525255" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation/*genetics ; Amino Acid Sequence ; Bacillus subtilis/metabolism ; Bacterial Proteins/*chemistry/genetics ; Conserved Sequence ; *Evolution, Molecular ; Ligands ; Mutation ; Pentosyltransferases/*chemistry/genetics ; Protein Binding/genetics ; Protein Conformation ; *Protein Engineering ; Protein Multimerization/*genetics ; Repressor Proteins/*chemistry/genetics
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  • 133
    Publication Date: 2014-10-11
    Description: Spatial and temporal dissection of the genomic changes occurring during the evolution of human non-small cell lung cancer (NSCLC) may help elucidate the basis for its dismal prognosis. We sequenced 25 spatially distinct regions from seven operable NSCLCs and found evidence of branched evolution, with driver mutations arising before and after subclonal diversification. There was pronounced intratumor heterogeneity in copy number alterations, translocations, and mutations associated with APOBEC cytidine deaminase activity. Despite maintained carcinogen exposure, tumors from smokers showed a relative decrease in smoking-related mutations over time, accompanied by an increase in APOBEC-associated mutations. In tumors from former smokers, genome-doubling occurred within a smoking-signature context before subclonal diversification, which suggested that a long period of tumor latency had preceded clinical detection. The regionally separated driver mutations, coupled with the relentless and heterogeneous nature of the genome instability processes, are likely to confound treatment success in NSCLC.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636050/" 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/PMC4636050/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉de Bruin, Elza C -- McGranahan, Nicholas -- Mitter, Richard -- Salm, Max -- Wedge, David C -- Yates, Lucy -- Jamal-Hanjani, Mariam -- Shafi, Seema -- Murugaesu, Nirupa -- Rowan, Andrew J -- Gronroos, Eva -- Muhammad, Madiha A -- Horswell, Stuart -- Gerlinger, Marco -- Varela, Ignacio -- Jones, David -- Marshall, John -- Voet, Thierry -- Van Loo, Peter -- Rassl, Doris M -- Rintoul, Robert C -- Janes, Sam M -- Lee, Siow-Ming -- Forster, Martin -- Ahmad, Tanya -- Lawrence, David -- Falzon, Mary -- Capitanio, Arrigo -- Harkins, Timothy T -- Lee, Clarence C -- Tom, Warren -- Teefe, Enock -- Chen, Shann-Ching -- Begum, Sharmin -- Rabinowitz, Adam -- Phillimore, Benjamin -- Spencer-Dene, Bradley -- Stamp, Gordon -- Szallasi, Zoltan -- Matthews, Nik -- Stewart, Aengus -- Campbell, Peter -- Swanton, Charles -- 088340/Wellcome Trust/United Kingdom -- 091730/Wellcome Trust/United Kingdom -- 105104/Wellcome Trust/United Kingdom -- A11590/Cancer Research UK/United Kingdom -- A17786/Cancer Research UK/United Kingdom -- A19310/Cancer Research UK/United Kingdom -- A4688/Cancer Research UK/United Kingdom -- Cancer Research UK/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2014 Oct 10;346(6206):251-6. doi: 10.1126/science.1253462.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK. ; Cancer Research UK London Research Institute, London WC2A 3LY, UK. Centre for Mathematics and Physics in the Life Science and Experimental Biology (CoMPLEX), University College London, London WC1E 6BT, UK. ; Cancer Research UK London Research Institute, London WC2A 3LY, UK. ; Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK. ; Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK. University of Cambridge, Cambridge CB2 1TN, UK. ; Instituto de Biomedicina y Biotecnologia de Cantabria (CSIC-UC-Sodercan), Departamento de Biologia Molecular, Universidad de Cantabria, Santander, Spain. ; Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK. Department of Human Genetics, University of Leuven, 3000 Leuven, Belgium. ; Papworth Hospital NHS Foundation Trust, Cambridge CB23 3RE, UK. ; Lungs for Living Research Centre, University College London, London WC1E 6BT, UK. ; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK. University College London Hospitals, London NW1 2BU, UK. ; University College London Hospitals, London NW1 2BU, UK. ; Thermo Fisher Scientific, Carlsbad, CA 92008, USA. ; Technical University of Denmark, 2800 Kongens Lyngby, Denmark. Children's Hospital Informatics Program, Harvard Medical School, Boston, MA 02115, USA. ; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK. Cancer Research UK London Research Institute, London WC2A 3LY, UK. charles.swanton@cancer.org.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25301630" target="_blank"〉PubMed〈/a〉
    Keywords: Carcinogens/toxicity ; Carcinoma, Non-Small-Cell Lung/chemically induced/*diagnosis/*genetics ; Cytidine Deaminase/genetics ; Evolution, Molecular ; Gene Dosage ; *Genetic Heterogeneity ; *Genomic Instability ; Humans ; Lung Neoplasms/chemically induced/*diagnosis/*genetics ; Mutation ; Neoplasm Recurrence, Local/genetics ; Prognosis ; Smoking/adverse effects ; Translocation, Genetic ; Tumor Cells, Cultured
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  • 134
    Publication Date: 2014-06-28
    Description: Epistatic interactions between mutations can make evolutionary trajectories contingent on the chance occurrence of initial mutations. We used experimental evolution in Saccharomyces cerevisiae to quantify this contingency, finding differences in adaptability among 64 closely related genotypes. Despite these differences, sequencing of 104 evolved clones showed that initial genotype did not constrain future mutational trajectories. Instead, reconstructed combinations of mutations revealed a pattern of diminishing-returns epistasis: Beneficial mutations have consistently smaller effects in fitter backgrounds. Taken together, these results show that beneficial mutations affecting a variety of biological processes are globally coupled; they interact strongly, but only through their combined effect on fitness. As a consequence, fitness evolution follows a predictable trajectory even though sequence-level adaptation is stochastic.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4314286/" 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/PMC4314286/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kryazhimskiy, Sergey -- Rice, Daniel P -- Jerison, Elizabeth R -- Desai, Michael M -- GM104239/GM/NIGMS NIH HHS/ -- R01 GM104239/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Jun 27;344(6191):1519-22. doi: 10.1126/science.1250939.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. skryazhi@oeb.harvard.edu mdesai@oeb.harvard.edu. ; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. ; Department of Physics, Harvard University, Cambridge, MA 02138, USA. FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. ; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Department of Physics, Harvard University, Cambridge, MA 02138, USA. FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. skryazhi@oeb.harvard.edu mdesai@oeb.harvard.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24970088" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; Base Sequence ; Directed Molecular Evolution ; *Epistasis, Genetic ; *Evolution, Molecular ; Genes, Fungal ; *Genetic Fitness ; Genome, Fungal ; Genotype ; Models, Genetic ; Molecular Sequence Annotation ; Mutation ; Saccharomyces cerevisiae/*genetics/*physiology ; Sequence Analysis, DNA ; Stochastic Processes
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  • 135
    Publication Date: 2014-07-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pfeifer, M -- Packer, C -- Burton, A C -- Garnett, S T -- Loveridge, A J -- MacNulty, D -- Platts, P J -- New York, N.Y. -- Science. 2014 Jul 25;345(6195):389. doi: 10.1126/science.345.6195.389-a. Epub 2014 Jul 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Forest Ecology and Conservation Lab, Department of Life Sciences, Imperial College London, Ascot, SL5 7PY, UK. York Institute for Tropical Ecosystems, Environment Department, University of York, York, YO10 5DD, UK. m.pfeifer@imperial.ac.uk. ; Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA. ; Alberta Innovates Technology Futures, Victoria, BC V8Z 7X8, Canada. Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada. ; Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT 0909, Australia. ; Wildlife Conservation Research Unit, Department of Zoology, Oxford University, Oxford, OX13 5QL, UK. ; Department of Wildland Resources, Utah State University, Logan, UT 84322, USA. ; York Institute for Tropical Ecosystems, Environment Department, University of York, York, YO10 5DD, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25061194" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Animals, Wild ; *Biodiversity ; *Conservation of Natural Resources ; *Ecosystem ; Humans
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  • 136
    Publication Date: 2014-03-22
    Description: Wnt/beta-catenin signaling is critical for tissue regeneration. However, it is unclear how beta-catenin controls stem cell behaviors to coordinate organized growth. Using live imaging, we show that activation of beta-catenin specifically within mouse hair follicle stem cells generates new hair growth through oriented cell divisions and cellular displacement. beta-Catenin activation is sufficient to induce hair growth independently of mesenchymal dermal papilla niche signals normally required for hair regeneration. Wild-type cells are co-opted into new hair growths by beta-catenin mutant cells, which non-cell autonomously activate Wnt signaling within the neighboring wild-type cells via Wnt ligands. This study demonstrates a mechanism by which Wnt/beta-catenin signaling controls stem cell-dependent tissue growth non-cell autonomously and advances our understanding of the mechanisms that drive coordinated regeneration.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096864/" 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/PMC4096864/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Deschene, Elizabeth R -- Myung, Peggy -- Rompolas, Panteleimon -- Zito, Giovanni -- Sun, Thomas Yang -- Taketo, Makoto M -- Saotome, Ichiko -- Greco, Valentina -- 1R01AR063663-01/AR/NIAMS NIH HHS/ -- 2P50CA121974/CA/NCI NIH HHS/ -- 5P30 AR053495-07/AR/NIAMS NIH HHS/ -- K08 AR066790/AR/NIAMS NIH HHS/ -- P30 CA016359/CA/NCI NIH HHS/ -- P50 CA121974/CA/NCI NIH HHS/ -- R01 AR063663/AR/NIAMS NIH HHS/ -- T32 GM007223/GM/NIGMS NIH HHS/ -- TG32 GM007223/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Mar 21;343(6177):1353-6. doi: 10.1126/science.1248373.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Yale Stem Cell Center, Yale Cancer Center, Yale University 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/24653033" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Differentiation ; Cell Division ; Hair/*growth & development ; Hair Follicle/*cytology/*metabolism ; Ligands ; Mice ; Models, Biological ; Mutation ; Stem Cell Niche ; Stem Cells/cytology/*metabolism ; Tamoxifen/pharmacology ; Up-Regulation ; Wnt Proteins/genetics/metabolism ; *Wnt Signaling Pathway ; beta Catenin/genetics/*metabolism
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  • 137
    Publication Date: 2014-12-06
    Description: Developing tissues that contain mutant or compromised cells present risks to animal health. Accordingly, the appearance of a population of suboptimal cells in a tissue elicits cellular interactions that prevent their contribution to the adult. Here we report that this quality control process, cell competition, uses specific components of the evolutionarily ancient and conserved innate immune system to eliminate Drosophila cells perceived as unfit. We find that Toll-related receptors (TRRs) and the cytokine Spatzle (Spz) lead to NFkappaB-dependent apoptosis. Diverse "loser" cells require different TRRs and NFkappaB factors and activate distinct pro-death genes, implying that the particular response is stipulated by the competitive context. Our findings demonstrate a functional repurposing of components of TRRs and NFkappaB signaling modules in the surveillance of cell fitness during development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meyer, S N -- Amoyel, M -- Bergantinos, C -- de la Cova, C -- Schertel, C -- Basler, K -- Johnston, L A -- P40OD018537/OD/NIH HHS/ -- R01 GM078464/GM/NIGMS NIH HHS/ -- R01-GM084947/GM/NIGMS NIH HHS/ -- R21 HD067918/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2014 Dec 5;346(6214):1258236. doi: 10.1126/science.1258236.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland. ; Department of Genetics and Development, Columbia University, New York, NY 10032, USA. ; Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland. konrad.basler@imls.uzh.ch lj180@columbia.edu. ; Department of Genetics and Development, Columbia University, New York, NY 10032, USA. konrad.basler@imls.uzh.ch lj180@columbia.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25477468" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis/genetics/*immunology ; Cell Communication/*immunology ; Drosophila Proteins/genetics/metabolism ; Drosophila melanogaster/cytology/genetics/growth & development ; Immunity, Innate/genetics/*immunology ; Mutation ; NF-kappa B/genetics/*metabolism ; Neuropeptides/genetics ; Toll-Like Receptors/genetics/*metabolism ; Transcription Factors/metabolism ; Transcription, Genetic
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  • 138
    Publication Date: 2014-10-04
    Description: Ethanol toxicity in the yeast Saccharomyces cerevisiae limits titer and productivity in the industrial production of transportation bioethanol. We show that strengthening the opposing potassium and proton electrochemical membrane gradients is a mechanism that enhances general resistance to multiple alcohols. The elevation of extracellular potassium and pH physically bolsters these gradients, increasing tolerance to higher alcohols and ethanol fermentation in commercial and laboratory strains (including a xylose-fermenting strain) under industrial-like conditions. Production per cell remains largely unchanged, with improvements deriving from heightened population viability. Likewise, up-regulation of the potassium and proton pumps in the laboratory strain enhances performance to levels exceeding those of industrial strains. Although genetically complex, alcohol tolerance can thus be dominated by a single cellular process, one controlled by a major physicochemical component but amenable to biological augmentation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4401034/" 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/PMC4401034/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lam, Felix H -- Ghaderi, Adel -- Fink, Gerald R -- Stephanopoulos, Gregory -- R01 GM035010/GM/NIGMS NIH HHS/ -- R01-GM035010/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Oct 3;346(6205):71-5. doi: 10.1126/science.1257859. Epub 2014 Oct 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA. Whitehead Institute for Biomedical Research, Cambridge, MA, USA. ; Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA. ; Whitehead Institute for Biomedical Research, Cambridge, MA, USA. gfink@wi.mit.edu gregstep@mit.edu. ; Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA. gfink@wi.mit.edu gregstep@mit.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25278607" target="_blank"〉PubMed〈/a〉
    Keywords: *Biofuels ; Cation Transport Proteins/genetics ; Cell Culture Techniques ; Cell Membrane/metabolism ; Chemical Engineering ; *Drug Resistance, Fungal/genetics ; Ethanol/*metabolism/pharmacology ; Fermentation ; Genetic Engineering ; Glucose/metabolism ; Hydrogen-Ion Concentration ; Phosphates/*metabolism ; Potassium Compounds/*metabolism ; Proton Pumps/genetics ; Proton-Translocating ATPases/genetics ; Saccharomyces cerevisiae/drug effects/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Up-Regulation ; Xylose/metabolism
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  • 139
    Publication Date: 2014-10-04
    Description: Cancer genome characterization has revealed driver mutations in genes that govern ubiquitylation; however, the mechanisms by which these alterations promote tumorigenesis remain incompletely characterized. Here, we analyzed changes in the ubiquitin landscape induced by prostate cancer-associated mutations of SPOP, an E3 ubiquitin ligase substrate-binding protein. SPOP mutants impaired ubiquitylation of a subset of proteins in a dominant-negative fashion. Of these, DEK and TRIM24 emerged as effector substrates consistently up-regulated by SPOP mutants. We highlight DEK as a SPOP substrate that exhibited decreases in ubiquitylation and proteasomal degradation resulting from heteromeric complexes of wild-type and mutant SPOP protein. DEK stabilization promoted prostate epithelial cell invasion, which implicated DEK as an oncogenic effector. More generally, these results provide a framework to decipher tumorigenic mechanisms linked to dysregulated ubiquitylation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257137/" 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/PMC4257137/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Theurillat, Jean-Philippe P -- Udeshi, Namrata D -- Errington, Wesley J -- Svinkina, Tanya -- Baca, Sylvan C -- Pop, Marius -- Wild, Peter J -- Blattner, Mirjam -- Groner, Anna C -- Rubin, Mark A -- Moch, Holger -- Prive, Gilbert G -- Carr, Steven A -- Garraway, Levi A -- T32 GM007753/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Oct 3;346(6205):85-9. doi: 10.1126/science.1250255. Epub 2014 Oct 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Harvard Medical School, Boston, MA 02115, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA. ; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. ; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada. Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada. ; Harvard Medical School, Boston, MA 02115, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA. ; Institute of Surgical Pathology, University Hospital Zurich, ZH 8091 Zurich, Switzerland. ; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065, USA. ; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA. ; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065, USA. Institute for Precision Medicine of Weill Cornell and New York Presbyterian Hospital, New York, NY 10065, USA. ; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Harvard Medical School, Boston, MA 02115, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA. Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02115, USA. levi_garraway@dfci.harvard.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25278611" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites/genetics ; Carcinogenesis/genetics/metabolism/pathology ; Carrier Proteins/metabolism ; Cell Line, Tumor ; Chromosomal Proteins, Non-Histone/metabolism ; Humans ; Male ; Molecular Sequence Data ; Mutation ; Neoplasm Invasiveness ; Nuclear Proteins/*genetics/metabolism ; Oncogene Proteins/metabolism ; Prostatic Neoplasms/genetics/*metabolism/pathology ; Proteasome Endopeptidase Complex/metabolism ; Repressor Proteins/*genetics/metabolism ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination/*genetics
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  • 140
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-05-09
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4162091/" 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/PMC4162091/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haynes, Barton F -- Verkoczy, Laurent -- R01-AI87202/AI/NIAID NIH HHS/ -- UM1 AI100645/AI/NIAID NIH HHS/ -- UM1-AI00645/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2014 May 9;344(6184):588-9. doi: 10.1126/science.1254990.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Duke Human Vaccine Institute, Departments of Medicine, Immunology and Pathology, Duke University School of Medicine, Durham, NC 27710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24812389" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines/*immunology ; Acquired Immunodeficiency Syndrome/*immunology ; Antibodies, Neutralizing/biosynthesis/genetics/*immunology ; B-Lymphocytes/immunology ; HIV Antibodies/biosynthesis/genetics/*immunology ; HIV Envelope Protein gp120/immunology ; HIV Seropositivity/immunology ; HIV-1/*immunology ; Host-Pathogen Interactions/*immunology ; Humans ; Immune Tolerance ; Molecular Mimicry/immunology ; Mutation ; Plasma Cells/immunology ; Polysaccharides/immunology
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  • 141
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-11-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Langer, Robert S -- Gura, Trisha -- New York, N.Y. -- Science. 2014 Nov 28;346(6213):1146. doi: 10.1126/science.346.6213.1146.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Trisha Gura is a freelance writer who lives in Boston. For more on life and careers visit www.sciencecareers.org.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25430772" target="_blank"〉PubMed〈/a〉
    Keywords: Biotechnology ; *Career Choice ; Chemical Engineering ; *Entrepreneurship ; *Science
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  • 142
    Publication Date: 2014-06-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dornelas, Maria -- Gotelli, Nicholas J -- McGill, Brian -- Magurran, Anne E -- New York, N.Y. -- Science. 2014 Jun 6;344(6188):1098-9. doi: 10.1126/science.344.6188.1098-b.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. Andrews, St. Andrews, Fife, KY16 9TH, UK. maadd@st-andrews.ac.uk. ; Department of Biology, University of Vermont, Burlington, VT 05405, USA. ; School of Biology and Ecology, Sustainability Solutions Initiative, University of Maine, Orono, ME 04469, USA. ; Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. Andrews, St. Andrews, Fife, KY16 9TH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24904147" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Birds ; *Ecosystem ; *Fishes ; *Invertebrates ; *Mammals ; *Plants
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  • 143
    Publication Date: 2014-04-20
    Description: The extent to which biodiversity change in local assemblages contributes to global biodiversity loss is poorly understood. We analyzed 100 time series from biomes across Earth to ask how diversity within assemblages is changing through time. We quantified patterns of temporal alpha diversity, measured as change in local diversity, and temporal beta diversity, measured as change in community composition. Contrary to our expectations, we did not detect systematic loss of alpha diversity. However, community composition changed systematically through time, in excess of predictions from null models. Heterogeneous rates of environmental change, species range shifts associated with climate change, and biotic homogenization may explain the different patterns of temporal alpha and beta diversity. Monitoring and understanding change in species composition should be a conservation priority.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dornelas, Maria -- Gotelli, Nicholas J -- McGill, Brian -- Shimadzu, Hideyasu -- Moyes, Faye -- Sievers, Caya -- Magurran, Anne E -- New York, N.Y. -- Science. 2014 Apr 18;344(6181):296-9. doi: 10.1126/science.1248484.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. Andrews, St. Andrews, Fife KY16 9TH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24744374" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Birds ; *Ecosystem ; Extinction, Biological ; *Fishes ; Introduced Species ; *Invertebrates ; *Mammals ; *Plants ; Population Dynamics ; Time Factors
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  • 144
    Publication Date: 2014-01-11
    Description: Large carnivores face serious threats and are experiencing massive declines in their populations and geographic ranges around the world. We highlight how these threats have affected the conservation status and ecological functioning of the 31 largest mammalian carnivores on Earth. Consistent with theory, empirical studies increasingly show that large carnivores have substantial effects on the structure and function of diverse ecosystems. Significant cascading trophic interactions, mediated by their prey or sympatric mesopredators, arise when some of these carnivores are extirpated from or repatriated to ecosystems. Unexpected effects of trophic cascades on various taxa and processes include changes to bird, mammal, invertebrate, and herpetofauna abundance or richness; subsidies to scavengers; altered disease dynamics; carbon sequestration; modified stream morphology; and crop damage. Promoting tolerance and coexistence with large carnivores is a crucial societal challenge that will ultimately determine the fate of Earth's largest carnivores and all that depends upon them, including humans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ripple, William J -- Estes, James A -- Beschta, Robert L -- Wilmers, Christopher C -- Ritchie, Euan G -- Hebblewhite, Mark -- Berger, Joel -- Elmhagen, Bodil -- Letnic, Mike -- Nelson, Michael P -- Schmitz, Oswald J -- Smith, Douglas W -- Wallach, Arian D -- Wirsing, Aaron J -- New York, N.Y. -- Science. 2014 Jan 10;343(6167):1241484. doi: 10.1126/science.1241484.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Trophic Cascades Program, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24408439" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Carnivora/anatomy & histology/classification/physiology ; *Ecological and Environmental Phenomena ; *Ecosystem ; *Extinction, Biological ; Humans ; Meat Products/statistics & numerical data ; Oceans and Seas ; Plants ; Population Dynamics
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  • 145
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-07-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Law, Kara Lavender -- Thompson, Richard C -- New York, N.Y. -- Science. 2014 Jul 11;345(6193):144-5. doi: 10.1126/science.1254065. Epub 2014 Jul 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Oceanography, Sea Education Association, Woods Hole, MA 02543, USA. klavender@sea.edu. ; School of Marine Science and Engineering, Plymouth University, Plymouth PL4 8AA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25013051" target="_blank"〉PubMed〈/a〉
    Keywords: Aquatic Organisms/*drug effects ; *Ecosystem ; Oceans and Seas ; Particle Size ; Plastics/*toxicity ; *Seawater ; Water Pollutants, Chemical/*toxicity ; Water Pollution, Chemical/*prevention & control
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  • 146
    Publication Date: 2014-03-22
    Description: Under resting conditions, Pink1 knockout cells and cells derived from patients with PINK1 mutations display a loss of mitochondrial complex I reductive activity, causing a decrease in the mitochondrial membrane potential. Analyzing the phosphoproteome of complex I in liver and brain from Pink1(-/-) mice, we found specific loss of phosphorylation of serine-250 in complex I subunit NdufA10. Phosphorylation of serine-250 was needed for ubiquinone reduction by complex I. Phosphomimetic NdufA10 reversed Pink1 deficits in mouse knockout cells and rescued mitochondrial depolarization and synaptic transmission defects in pink(B9)-null mutant Drosophila. Complex I deficits and adenosine triphosphate synthesis were also rescued in cells derived from PINK1 patients. Thus, this evolutionary conserved pathway may contribute to the pathogenic cascade that eventually leads to Parkinson's disease in patients with PINK1 mutations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Morais, Vanessa A -- Haddad, Dominik -- Craessaerts, Katleen -- De Bock, Pieter-Jan -- Swerts, Jef -- Vilain, Sven -- Aerts, Liesbeth -- Overbergh, Lut -- Grunewald, Anne -- Seibler, Philip -- Klein, Christine -- Gevaert, Kris -- Verstreken, Patrik -- De Strooper, Bart -- New York, N.Y. -- Science. 2014 Apr 11;344(6180):203-7. doi: 10.1126/science.1249161. Epub 2014 Mar 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉VIB Center for the Biology of Disease, 3000 Leuven, Belgium.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24652937" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Brain/enzymology ; Drosophila Proteins/*metabolism ; Electron Transport Complex I/*metabolism ; Humans ; Liver/enzymology ; Membrane Potential, Mitochondrial/genetics ; Mice ; Mice, Knockout ; Molecular Sequence Data ; Mutation ; NADH Dehydrogenase/*metabolism ; Parkinson Disease/*enzymology/*genetics ; Phosphorylation/genetics ; Protein Kinases/*genetics ; Proteome ; Serine/chemistry/metabolism
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  • 147
    Publication Date: 2014-09-13
    Description: A key question in ecology and evolution is the relative role of natural selection and neutral evolution in producing biogeographic patterns. We quantify the role of neutral processes by simulating division, mutation, and death of 100,000 individual marine bacteria cells with full 1 million-base-pair genomes in a global surface ocean circulation model. The model is run for up to 100,000 years and output is analyzed using BLAST (Basic Local Alignment Search Tool) alignment and metagenomics fragment recruitment. Simulations show the production and maintenance of biogeographic patterns, characterized by distinct provinces subject to mixing and periodic takeovers by neighbors (coalescence), after which neutral evolution reestablishes the province and the patterns reorganize. The emergent patterns are substantial (e.g., down to 99.5% DNA identity between North and Central Pacific provinces) and suggest that microbes evolve faster than ocean currents can disperse them. This approach can also be used to explore environmental selection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hellweger, Ferdi L -- van Sebille, Erik -- Fredrick, Neil D -- New York, N.Y. -- Science. 2014 Sep 12;345(6202):1346-9. doi: 10.1126/science.1254421.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, USA. ferdi@coe.neu.edu. ; Australian Research Council (ARC) Centre of Excellence for Climate System Science and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia. ; Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25214628" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/*genetics ; Computer Simulation ; Genetic Variation ; *Models, Genetic ; Mutation ; Oceans and Seas ; Phylogeography ; Seawater/*microbiology ; *Selection, Genetic
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  • 148
    Publication Date: 2014-05-09
    Description: Limited evidence exists that humans mount a mutation-specific T cell response to epithelial cancers. We used a whole-exomic-sequencing-based approach to demonstrate that tumor-infiltrating lymphocytes (TIL) from a patient with metastatic cholangiocarcinoma contained CD4+ T helper 1 (T(H)1) cells recognizing a mutation in erbb2 interacting protein (ERBB2IP) expressed by the cancer. After adoptive transfer of TIL containing about 25% mutation-specific polyfunctional T(H)1 cells, the patient achieved a decrease in target lesions with prolonged stabilization of disease. Upon disease progression, the patient was retreated with a 〉95% pure population of mutation-reactive T(H)1 cells and again experienced tumor regression. These results provide evidence that a CD4+ T cell response against a mutated antigen can be harnessed to mediate regression of a metastatic epithelial cancer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tran, Eric -- Turcotte, Simon -- Gros, Alena -- Robbins, Paul F -- Lu, Yong-Chen -- Dudley, Mark E -- Wunderlich, John R -- Somerville, Robert P -- Hogan, Katherine -- Hinrichs, Christian S -- Parkhurst, Maria R -- Yang, James C -- Rosenberg, Steven A -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2014 May 9;344(6184):641-5. doi: 10.1126/science.1251102.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24812403" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/*genetics ; Adoptive Transfer/*methods ; Adult ; Bile Duct Neoplasms/genetics/*therapy ; *Bile Ducts, Intrahepatic ; CD4-Positive T-Lymphocytes/*immunology ; Cholangiocarcinoma/genetics/*therapy ; Clinical Trials, Phase II as Topic ; Exome ; Female ; Humans ; Lymphocytes, Tumor-Infiltrating/*transplantation ; Mutation ; Receptor, ErbB-2/metabolism ; Th1 Cells/*transplantation
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  • 149
    Publication Date: 2014-05-17
    Description: Signaling from JAK (Janus kinase) protein kinases to STAT (signal transducers and activators of transcription) transcription factors is key to many aspects of biology and medicine, yet the mechanism by which cytokine receptors initiate signaling is enigmatic. We present a complete mechanistic model for activation of receptor-bound JAK2, based on an archetypal cytokine receptor, the growth hormone receptor. For this, we used fluorescence resonance energy transfer to monitor positioning of the JAK2 binding motif in the receptor dimer, substitution of the receptor extracellular domains with Jun zippers to control the position of its transmembrane (TM) helices, atomistic modeling of TM helix movements, and docking of the crystal structures of the JAK2 kinase and its inhibitory pseudokinase domain with an opposing kinase-pseudokinase domain pair. Activation of the receptor dimer induced a separation of its JAK2 binding motifs, driven by a ligand-induced transition from a parallel TM helix pair to a left-handed crossover arrangement. This separation leads to removal of the pseudokinase domain from the kinase domain of the partner JAK2 and pairing of the two kinase domains, facilitating trans-activation. This model may well generalize to other class I cytokine receptors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brooks, Andrew J -- Dai, Wei -- O'Mara, Megan L -- Abankwa, Daniel -- Chhabra, Yash -- Pelekanos, Rebecca A -- Gardon, Olivier -- Tunny, Kathryn A -- Blucher, Kristopher M -- Morton, Craig J -- Parker, Michael W -- Sierecki, Emma -- Gambin, Yann -- Gomez, Guillermo A -- Alexandrov, Kirill -- Wilson, Ian A -- Doxastakis, Manolis -- Mark, Alan E -- Waters, Michael J -- New York, N.Y. -- Science. 2014 May 16;344(6185):1249783. doi: 10.1126/science.1249783.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia. m.waters@uq.edu.au a.brooks@uq.edu.au. ; Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77004, USA. ; The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Queensland 4072, Australia. ; The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia. ; Biota Structural Biology Laboratory and Australian Cancer Research Foundation (ACRF) Rational Drug Discovery Centre, St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia. ; Biota Structural Biology Laboratory and Australian Cancer Research Foundation (ACRF) Rational Drug Discovery Centre, St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia. Department of Biochemistry and Molecular Biology and Bio21 Institute, University of Melbourne, Parkville, Victoria 3052, Australia. ; Scripps Research Institute, La Jolla, CA 92037, USA. ; The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia. The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Queensland 4072, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24833397" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Cysteine/chemistry ; Enzyme Activation ; HEK293 Cells ; Humans ; Janus Kinase 2/antagonists & inhibitors/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Somatotropin/chemistry/genetics/*metabolism
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  • 150
    Publication Date: 2014-10-04
    Description: Ethanol production for use as a biofuel is mainly achieved through simultaneous saccharification and fermentation by yeast. Operating at 〉/=40 degrees C would be beneficial in terms of increasing efficiency of the process and reducing costs, but yeast does not grow efficiently at those temperatures. We used adaptive laboratory evolution to select yeast strains with improved growth and ethanol production at 〉/=40 degrees C. Sequencing of the whole genome, genome-wide gene expression, and metabolic-flux analyses revealed a change in sterol composition, from ergosterol to fecosterol, caused by mutations in the C-5 sterol desaturase gene, and increased expression of genes involved in sterol biosynthesis. Additionally, large chromosome III rearrangements and mutations in genes associated with DNA damage and respiration were found, but contributed less to the thermotolerant phenotype.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Caspeta, Luis -- Chen, Yun -- Ghiaci, Payam -- Feizi, Amir -- Buskov, Steen -- Hallstrom, Bjorn M -- Petranovic, Dina -- Nielsen, Jens -- New York, N.Y. -- Science. 2014 Oct 3;346(6205):75-8. doi: 10.1126/science.1258137. Epub 2014 Oct 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden. ; Department of Chemical and Biological Engineering, Chalmers Unversity of Technology, SE-41296 Gothenburg, Sweden. ; Novozymes, Analytical Science, DK-4400 Kalundborg, Denmark. ; Science for Life Laboratory, Royal Institute of Technology, SE-17121 Stockholm, Sweden. ; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden. Department of Chemical and Biological Engineering, Chalmers Unversity of Technology, SE-41296 Gothenburg, Sweden. ; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden. Department of Chemical and Biological Engineering, Chalmers Unversity of Technology, SE-41296 Gothenburg, Sweden. Novo Nordisk Foundation Center for Biosustainability, DK-2970 Horsholm, Denmark. nielsenj@chalmers.se.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25278608" target="_blank"〉PubMed〈/a〉
    Keywords: *Biofuels ; Chromosomes, Fungal/genetics ; DNA Damage/genetics ; Directed Molecular Evolution ; Ergosterol/*analogs & derivatives/biosynthesis/chemistry/genetics ; Ethanol/*metabolism ; Fermentation/*genetics ; Gene Expression Regulation, Fungal ; Genome, Fungal/genetics ; *Hot Temperature ; Mutation ; Oxidoreductases/*genetics/metabolism ; Recombination, Genetic ; Saccharomyces cerevisiae/*enzymology/genetics/growth & development ; Sequence Analysis, DNA
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  • 151
    Publication Date: 2014-01-18
    Description: Mining modern genomics for cancer therapies is predicated on weeding out "bystander" alterations (nonconsequential mutations) and identifying "driver" mutations responsible for tumorigenesis and/or metastasis. We used a direct in vivo RNA interference (RNAi) strategy to screen for genes that upon repression predispose mice to squamous cell carcinomas (SCCs). Seven of our top hits-including Myh9, which encodes nonmuscle myosin IIa-have not been linked to tumor development, yet tissue-specific Myh9 RNAi and Myh9 knockout trigger invasive SCC formation on tumor-susceptible backgrounds. In human and mouse keratinocytes, myosin IIa's function is manifested not only in conventional actin-related processes but also in regulating posttranscriptional p53 stabilization. Myosin IIa is diminished in human SCCs with poor survival, which suggests that in vivo RNAi technology might be useful for identifying potent but low-penetrance tumor suppressors.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159249/" 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/PMC4159249/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schramek, Daniel -- Sendoel, Ataman -- Segal, Jeremy P -- Beronja, Slobodan -- Heller, Evan -- Oristian, Daniel -- Reva, Boris -- Fuchs, Elaine -- R37 AR027883/AR/NIAMS NIH HHS/ -- R37-AR27883/AR/NIAMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Jan 17;343(6168):309-13. doi: 10.1126/science.1248627.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24436421" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carcinoma, Squamous Cell/*genetics/*pathology ; Genetic Testing ; Head and Neck Neoplasms/genetics/pathology ; Humans ; Lung Neoplasms/secondary ; Mice ; Mice, Knockout ; Molecular Motor Proteins/genetics/*physiology ; Mutation ; Myosin Heavy Chains/genetics/*physiology ; Nonmuscle Myosin Type IIA/genetics/*physiology ; RNA Interference ; Transcription, Genetic ; Tumor Suppressor Protein p53/genetics ; Tumor Suppressor Proteins/genetics/*physiology
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  • 152
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-11-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vogel, Gretchen -- New York, N.Y. -- Science. 2014 Nov 7;346(6210):684-5. doi: 10.1126/science.346.6210.684.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25378599" target="_blank"〉PubMed〈/a〉
    Keywords: Africa, Western/epidemiology ; Ebolavirus/*genetics ; *Genomics ; Hemorrhagic Fever, Ebola/epidemiology/transmission/*virology ; Humans ; Mutation ; RNA, Viral/genetics ; Sequence Analysis, DNA
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  • 153
    Publication Date: 2014-02-01
    Description: Although interferon (IFN) signaling induces genes that limit viral infection, many pathogenic viruses overcome this host response. As an example, 2'-O methylation of the 5' cap of viral RNA subverts mammalian antiviral responses by evading restriction of Ifit1, an IFN-stimulated gene that regulates protein synthesis. However, alphaviruses replicate efficiently in cells expressing Ifit1 even though their genomic RNA has a 5' cap lacking 2'-O methylation. We show that pathogenic alphaviruses use secondary structural motifs within the 5' untranslated region (UTR) of their RNA to alter Ifit1 binding and function. Mutations within the 5'-UTR affecting RNA structural elements enabled restriction by or antagonism of Ifit1 in vitro and in vivo. These results identify an evasion mechanism by which viruses use RNA structural motifs to avoid immune restriction.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4209899/" 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/PMC4209899/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hyde, Jennifer L -- Gardner, Christina L -- Kimura, Taishi -- White, James P -- Liu, Gai -- Trobaugh, Derek W -- Huang, Cheng -- Tonelli, Marco -- Paessler, Slobodan -- Takeda, Kiyoshi -- Klimstra, William B -- Amarasinghe, Gaya K -- Diamond, Michael S -- AI049820/AI/NIAID NIH HHS/ -- P41GM66326/GM/NIGMS NIH HHS/ -- P41RR02301/RR/NCRR NIH HHS/ -- R01 AI083383/AI/NIAID NIH HHS/ -- R01 AI104972/AI/NIAID NIH HHS/ -- U19 AI083019/AI/NIAID NIH HHS/ -- UL1 TR000071/TR/NCATS NIH HHS/ -- UL1TR000071/TR/NCATS NIH HHS/ -- New York, N.Y. -- Science. 2014 Feb 14;343(6172):783-7. doi: 10.1126/science.1248465. Epub 2014 Jan 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24482115" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Untranslated Regions/immunology ; Alphavirus/*pathogenicity/physiology ; Alphavirus Infections/*immunology/virology ; Animals ; Carrier Proteins/antagonists & inhibitors/genetics/immunology ; Host-Pathogen Interactions/*immunology ; Mice ; Mice, Inbred C57BL ; Mice, Mutant Strains ; Mutation ; Nucleic Acid Conformation ; RNA Caps/*chemistry/*immunology ; RNA, Viral/*chemistry/*immunology ; Virus Replication
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  • 154
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-12-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vogel, Gretchen -- New York, N.Y. -- Science. 2014 Dec 12;346(6215):1276-7. doi: 10.1126/science.346.6215.1276.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25504694" target="_blank"〉PubMed〈/a〉
    Keywords: Antimalarials/*pharmacology ; Artemisinins/*pharmacology ; Drug Resistance/*genetics ; Drug Therapy, Combination ; *Genes, Protozoan ; Humans ; Malaria, Falciparum/drug therapy/parasitology ; Mutation ; Plasmodium falciparum/*drug effects/*genetics/growth & development ; Protozoan Proteins/genetics/metabolism
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  • 155
    Publication Date: 2014-05-03
    Description: Microbial reduction of ferric iron [Fe(III)] is an important biogeochemical process in anoxic aquifers. Depending on groundwater pH, dissimilatory metal-reducing bacteria can also respire alternative electron acceptors to survive, including elemental sulfur (S(0)). To understand the interplay of Fe/S cycling under alkaline conditions, we combined thermodynamic geochemical modeling with bioreactor experiments using Shewanella oneidensis MR-1. Under these conditions, S. oneidensis can enzymatically reduce S(0) but not goethite (alpha-FeOOH). The HS(-) produced subsequently reduces goethite abiotically. Because of the prevalence of alkaline conditions in many aquifers, Fe(III) reduction may thus proceed via S(0)-mediated electron-shuttling pathways.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Flynn, Theodore M -- O'Loughlin, Edward J -- Mishra, Bhoopesh -- DiChristina, Thomas J -- Kemner, Kenneth M -- HHSN272200900040C/PHS HHS/ -- New York, N.Y. -- Science. 2014 May 30;344(6187):1039-42. doi: 10.1126/science.1252066. Epub 2014 May 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA. Computation Institute, University of Chicago, Chicago, IL 60637, USA. ; Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA. ; Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA. Physics Department, Illinois Institute of Technology, Chicago, IL 60616, USA. ; School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA. ; Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA. kemner@anl.gov.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24789972" target="_blank"〉PubMed〈/a〉
    Keywords: Alkalies/chemistry ; Bioreactors ; Electron Transport ; Ferric Compounds/*metabolism ; Hydrogen-Ion Concentration ; Iron/*metabolism ; Iron Compounds/metabolism ; Metabolic Networks and Pathways ; Minerals/metabolism ; Models, Biological ; Mutation ; Oxidation-Reduction ; Shewanella/*enzymology/genetics ; Sulfur/*metabolism ; Thermodynamics
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  • 156
    Publication Date: 2014-11-22
    Description: Melanoma, the deadliest form of skin cancer, is an aggressive disease that is rising in incidence. Although melanoma is a historically treatment-resistant malignancy, in recent years unprecedented breakthroughs in targeted therapies and immunotherapies have revolutionized the standard of care for patients with advanced disease. Here, we provide an overview of recent developments in our understanding of melanoma risk factors, genomics, and molecular pathogenesis and how these insights have driven advances in melanoma treatment. In addition, we review benefits and limitations of current therapies and look ahead to continued progress in melanoma prevention and therapy. Remarkable achievements in the field have already produced a paradigm shift in melanoma treatment: Metastatic melanoma, once considered incurable, can now be treated with potentially curative rather than palliative intent.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4701046/" 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/PMC4701046/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lo, Jennifer A -- Fisher, David E -- P01 CA163222/CA/NCI NIH HHS/ -- P01CA163222/CA/NCI NIH HHS/ -- R01 AR043369/AR/NIAMS NIH HHS/ -- R01 CA150226/CA/NCI NIH HHS/ -- R01AR043369/AR/NIAMS NIH HHS/ -- R01CA150226/CA/NCI NIH HHS/ -- T32 GM007753/GM/NIGMS NIH HHS/ -- T32GM007753/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Nov 21;346(6212):945-9. doi: 10.1126/science.1253735.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cutaneous Biology Research Center, Department of Dermatology and MGH Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA. ; Cutaneous Biology Research Center, Department of Dermatology and MGH Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA. dfisher3@partners.org.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25414302" target="_blank"〉PubMed〈/a〉
    Keywords: Carcinogenesis/genetics/*pathology ; Drug Approval ; Epigenesis, Genetic ; Humans ; Immunotherapy ; Melanocytes/*pathology ; Melanoma/*drug therapy/genetics/pathology ; *Molecular Targeted Therapy ; Mutation ; Neoplasms, Radiation-Induced/drug therapy/genetics/pathology ; Skin Neoplasms/*drug therapy/genetics/pathology ; Sunlight ; Ultraviolet Rays/adverse effects
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  • 157
    Publication Date: 2014-04-20
    Description: Flaviviruses are emerging human pathogens and worldwide health threats. During infection, pathogenic subgenomic flaviviral RNAs (sfRNAs) are produced by resisting degradation by the 5'--〉3' host cell exonuclease Xrn1 through an unknown RNA structure-based mechanism. Here, we present the crystal structure of a complete Xrn1-resistant flaviviral RNA, which contains interwoven pseudoknots within a compact structure that depends on highly conserved nucleotides. The RNA's three-dimensional topology creates a ringlike conformation, with the 5' end of the resistant structure passing through the ring from one side of the fold to the other. Disruption of this structure prevents formation of sfRNA during flaviviral infection. Thus, sfRNA formation results from an RNA fold that interacts directly with Xrn1, presenting the enzyme with a structure that confounds its helicase activity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4163914/" 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/PMC4163914/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chapman, Erich G -- Costantino, David A -- Rabe, Jennifer L -- Moon, Stephanie L -- Wilusz, Jeffrey -- Nix, Jay C -- Kieft, Jeffrey S -- P30 CA046934/CA/NCI NIH HHS/ -- P30CA046934/CA/NCI NIH HHS/ -- U54 AI-065357/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Apr 18;344(6181):307-10. doi: 10.1126/science.1250897.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO 80045, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24744377" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Base Sequence ; Crystallography, X-Ray ; Encephalitis Virus, Murray Valley/*genetics/pathogenicity ; Exoribonucleases/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; *Nucleic Acid Conformation ; RNA, Viral/*chemistry/genetics/metabolism
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  • 158
    Publication Date: 2014-05-03
    Description: Regulation of cell volume is critical for many cellular and organismal functions, yet the molecular identity of a key player, the volume-regulated anion channel VRAC, has remained unknown. A genome-wide small interfering RNA screen in mammalian cells identified LRRC8A as a VRAC component. LRRC8A formed heteromers with other LRRC8 multispan membrane proteins. Genomic disruption of LRRC8A ablated VRAC currents. Cells with disruption of all five LRRC8 genes required LRRC8A cotransfection with other LRRC8 isoforms to reconstitute VRAC currents. The isoform combination determined VRAC inactivation kinetics. Taurine flux and regulatory volume decrease also depended on LRRC8 proteins. Our work shows that VRAC defines a class of anion channels, suggests that VRAC is identical to the volume-sensitive organic osmolyte/anion channel VSOAC, and explains the heterogeneity of native VRAC currents.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Voss, Felizia K -- Ullrich, Florian -- Munch, Jonas -- Lazarow, Katina -- Lutter, Darius -- Mah, Nancy -- Andrade-Navarro, Miguel A -- von Kries, Jens P -- Stauber, Tobias -- Jentsch, Thomas J -- New York, N.Y. -- Science. 2014 May 9;344(6184):634-8. doi: 10.1126/science.1252826. Epub 2014 Apr 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Leibniz-Institut fur Molekulare Pharmakologie (FMP), Berlin.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24790029" target="_blank"〉PubMed〈/a〉
    Keywords: Agammaglobulinemia/genetics ; *Cell Size ; Chloride Channels/*metabolism ; Gene Knockout Techniques ; Genome-Wide Association Study ; HCT116 Cells ; HEK293 Cells ; Humans ; Membrane Proteins/genetics/*metabolism ; Mutation ; Protein Multimerization ; RNA Interference ; RNA, Small Interfering/genetics ; Taurine/metabolism ; Transfection
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 159
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-03-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chapron, Guillaume -- Lopez-Bao, Jose Vicente -- New York, N.Y. -- Science. 2014 Mar 14;343(6176):1199-200. doi: 10.1126/science.343.6176.1199-b.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Grimso Wildlife Research Station, Swedish University of Agricultural Sciences, SE-73091 Riddarhyttan, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24626913" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Carnivora ; *Ecological and Environmental Phenomena ; *Ecosystem ; *Extinction, Biological ; Humans
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  • 160
    Publication Date: 2014-02-01
    Description: Hereditary spastic paraplegias (HSPs) are neurodegenerative motor neuron diseases characterized by progressive age-dependent loss of corticospinal motor tract function. Although the genetic basis is partly understood, only a fraction of cases can receive a genetic diagnosis, and a global view of HSP is lacking. By using whole-exome sequencing in combination with network analysis, we identified 18 previously unknown putative HSP genes and validated nearly all of these genes functionally or genetically. The pathways highlighted by these mutations link HSP to cellular transport, nucleotide metabolism, and synapse and axon development. Network analysis revealed a host of further candidate genes, of which three were mutated in our cohort. Our analysis links HSP to other neurodegenerative disorders and can facilitate gene discovery and mechanistic understanding of disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157572/" 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/PMC4157572/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Novarino, Gaia -- Fenstermaker, Ali G -- Zaki, Maha S -- Hofree, Matan -- Silhavy, Jennifer L -- Heiberg, Andrew D -- Abdellateef, Mostafa -- Rosti, Basak -- Scott, Eric -- Mansour, Lobna -- Masri, Amira -- Kayserili, Hulya -- Al-Aama, Jumana Y -- Abdel-Salam, Ghada M H -- Karminejad, Ariana -- Kara, Majdi -- Kara, Bulent -- Bozorgmehri, Bita -- Ben-Omran, Tawfeg -- Mojahedi, Faezeh -- Mahmoud, Iman Gamal El Din -- Bouslam, Naima -- Bouhouche, Ahmed -- Benomar, Ali -- Hanein, Sylvain -- Raymond, Laure -- Forlani, Sylvie -- Mascaro, Massimo -- Selim, Laila -- Shehata, Nabil -- Al-Allawi, Nasir -- Bindu, P S -- Azam, Matloob -- Gunel, Murat -- Caglayan, Ahmet -- Bilguvar, Kaya -- Tolun, Aslihan -- Issa, Mahmoud Y -- Schroth, Jana -- Spencer, Emily G -- Rosti, Rasim O -- Akizu, Naiara -- Vaux, Keith K -- Johansen, Anide -- Koh, Alice A -- Megahed, Hisham -- Durr, Alexandra -- Brice, Alexis -- Stevanin, Giovanni -- Gabriel, Stacy B -- Ideker, Trey -- Gleeson, Joseph G -- HHSN268200782096C/PHS HHS/ -- HHSN268201100011/PHS HHS/ -- N01-CO-12400/CO/NCI NIH HHS/ -- P01 HD070494/HD/NICHD NIH HHS/ -- P01HD070494/HD/NICHD NIH HHS/ -- P30NS047101/NS/NINDS NIH HHS/ -- R01NS041537/NS/NINDS NIH HHS/ -- R01NS048453/NS/NINDS NIH HHS/ -- R01NS052455/NS/NINDS NIH HHS/ -- U54 HG006504/HG/NHGRI NIH HHS/ -- U54HG003067/HG/NHGRI NIH HHS/ -- U54HG006504/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Jan 31;343(6170):506-11. doi: 10.1126/science.1247363.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24482476" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Axons/physiology ; Biological Transport/genetics ; Cohort Studies ; Exome/*genetics ; Gene Regulatory Networks ; *Genetic Association Studies ; Humans ; Motor Neuron Disease/*genetics ; Mutation ; Neurons/*metabolism ; Nucleotides/genetics/metabolism ; Pyramidal Tracts/*metabolism ; Sequence Analysis, DNA ; Spastic Paraplegia, Hereditary/*genetics ; Synapses/physiology ; Transcriptome ; Zebrafish
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  • 161
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-05-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Friend, Stephen H -- Schadt, Eric E -- New York, N.Y. -- Science. 2014 May 30;344(6187):970-2. doi: 10.1126/science.1255648.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Sage Bionetworks, Seattle, WA, 98109 USA Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences and the Icahn Institute for Genomics and Multiscale Biology, New York, NY 10029, USA. friend@sagebase.org eric.schadt@exchange.mssm.edu. ; Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences and the Icahn Institute for Genomics and Multiscale Biology, New York, NY 10029, USA. friend@sagebase.org eric.schadt@exchange.mssm.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24876479" target="_blank"〉PubMed〈/a〉
    Keywords: DNA Mutational Analysis ; *Genetic Association Studies ; Genetic Diseases, Inborn/*genetics/*therapy ; Genetic Predisposition to Disease/*genetics ; Genomics ; *Health ; Humans ; Molecular Targeted Therapy/*trends ; Mutation
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  • 162
    Publication Date: 2014-01-05
    Description: Social familiarity affects mating preference among various vertebrates. Here, we show that visual contact of a potential mating partner before mating (visual familiarization) enhances female preference for the familiarized male, but not for an unfamiliarized male, in medaka fish. Terminal-nerve gonadotropin-releasing hormone 3 (TN-GnRH3) neurons, an extrahypothalamic neuromodulatory system, function as a gate for activating mating preferences based on familiarity. Basal levels of TN-GnRH3 neuronal activity suppress female receptivity for any male (default mode). Visual familiarization facilitates TN-GnRH3 neuron activity (preference mode), which correlates with female preference for the familiarized male. GnRH3 peptides, which are synthesized specifically in TN-GnRH3 neurons, are required for the mode-switching via self-facilitation. Our study demonstrates the central neural mechanisms underlying the regulation of medaka female mating preference based on visual social familiarity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Okuyama, Teruhiro -- Yokoi, Saori -- Abe, Hideki -- Isoe, Yasuko -- Suehiro, Yuji -- Imada, Haruka -- Tanaka, Minoru -- Kawasaki, Takashi -- Yuba, Shunsuke -- Taniguchi, Yoshihito -- Kamei, Yasuhiro -- Okubo, Kataaki -- Shimada, Atsuko -- Naruse, Kiyoshi -- Takeda, Hiroyuki -- Oka, Yoshitaka -- Kubo, Takeo -- Takeuchi, Hideaki -- New York, N.Y. -- Science. 2014 Jan 3;343(6166):91-4. doi: 10.1126/science.1244724.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24385628" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Female ; Gonadotropin-Releasing Hormone/*physiology ; Male ; *Mating Preference, Animal ; Mutation ; Neurons/*physiology ; Oryzias/genetics/*physiology ; Pyrrolidonecarboxylic Acid/*analogs & derivatives ; *Recognition (Psychology) ; Sex Factors ; *Visual Perception
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  • 163
    Publication Date: 2014-08-12
    Description: AMPA-sensitive glutamate receptors are crucial to the structural and dynamic properties of the brain, to the development and function of the central nervous system, and to the treatment of neurological conditions from depression to cognitive impairment. However, the molecular principles underlying AMPA receptor activation have remained elusive. We determined multiple x-ray crystal structures of the GluA2 AMPA receptor in complex with a Conus striatus cone snail toxin, a positive allosteric modulator, and orthosteric agonists, at 3.8 to 4.1 angstrom resolution. We show how the toxin acts like a straightjacket on the ligand-binding domain (LBD) "gating ring," restraining the domains via both intra- and interdimer cross-links such that agonist-induced closure of the LBD "clamshells" is transduced into an irislike expansion of the gating ring. By structural analysis of activation-enhancing mutants, we show how the expansion of the LBD gating ring results in pulling forces on the M3 helices that, in turn, are coupled to ion channel gating.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263349/" 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/PMC4263349/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Lei -- Durr, Katharina L -- Gouaux, Eric -- F32 MH100331/MH/NIMH NIH HHS/ -- F32MH100331/MH/NIMH NIH HHS/ -- R01 NS038631/NS/NINDS NIH HHS/ -- R37 NS038631/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Aug 29;345(6200):1021-6. doi: 10.1126/science.1258409. Epub 2014 Aug 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA. ; Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA. Howard Hughes Medical Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA. gouauxe@ohsu.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25103405" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Conotoxins/*chemistry ; Conus Snail ; Crystallography, X-Ray ; *Ion Channel Gating ; Ligands ; Mutation ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rats ; Receptors, AMPA/*agonists/*chemistry/genetics
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  • 164
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-02-22
    Description: Biosynthesis of ubiquinones requires the intramembrane UbiA enzyme, an archetypal member of a superfamily of prenyltransferases that generates lipophilic aromatic compounds. Mutations in eukaryotic superfamily members have been linked to cardiovascular degeneration and Parkinson's disease. To understand how quinones are produced within membranes, we report the crystal structures of an archaeal UbiA in its apo and substrate-bound states at 3.3 and 3.6 angstrom resolution, respectively. The structures reveal nine transmembrane helices and an extramembrane cap domain that surround a large central cavity containing the active site. To facilitate the catalysis inside membranes, UbiA has an unusual active site that opens laterally to the lipid bilayer. Our studies illuminate general mechanisms for substrate recognition and catalysis in the UbiA superfamily and rationalize disease-related mutations in humans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390396/" 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/PMC4390396/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cheng, Wei -- Li, Weikai -- 5R00HL097083/HL/NHLBI NIH HHS/ -- GM103403/GM/NIGMS NIH HHS/ -- K99 HL097083/HL/NHLBI NIH HHS/ -- R00 HL097083/HL/NHLBI NIH HHS/ -- R01 HL121718/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2014 Feb 21;343(6173):878-81. doi: 10.1126/science.1246774.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24558159" target="_blank"〉PubMed〈/a〉
    Keywords: Aeropyrum/enzymology ; Archaeal Proteins/*chemistry/genetics ; Cardiovascular Abnormalities/genetics ; Catalysis ; *Catalytic Domain ; Cell Membrane/*enzymology ; Dimethylallyltranstransferase/*chemistry/genetics ; Humans ; Lipid Bilayers/chemistry ; Models, Chemical ; Mutation ; Parkinson Disease ; Periplasm/chemistry ; Protein Structure, Secondary ; Substrate Specificity ; Ubiquinone/*biosynthesis
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  • 165
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-09-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Servick, Kelly -- New York, N.Y. -- Science. 2014 Sep 19;345(6203):1438-9. doi: 10.1126/science.345.6203.1438.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25237080" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Brain/abnormalities ; Brain Diseases/*genetics ; Child ; DNA/genetics ; DNA Mutational Analysis/methods ; *Genetic Testing ; Genetic Variation ; Humans ; Mental Disorders/*genetics ; *Mosaicism ; Mutation ; Zygote
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 166
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-09-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mace, Georgina M -- New York, N.Y. -- Science. 2014 Sep 26;345(6204):1558-60. doi: 10.1126/science.1254704.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK. g.mace@ucl.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25258063" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Conservation of Natural Resources ; Ecological and Environmental Processes ; *Ecosystem ; Humans
    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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  • 167
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-02-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Machovina, Brian -- Feeley, Kenneth J -- New York, N.Y. -- Science. 2014 Feb 21;343(6173):838. doi: 10.1126/science.343.6173.838-a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Florida International University, Miami, FL 33199, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24558143" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Carnivora ; *Ecological and Environmental Phenomena ; *Ecosystem ; *Extinction, Biological ; Humans
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  • 168
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-02-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Servick, Kelly -- New York, N.Y. -- Science. 2014 Feb 21;343(6173):834-7. doi: 10.1126/science.343.6173.834.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24558142" target="_blank"〉PubMed〈/a〉
    Keywords: Acoustics ; Animals ; Computer Systems ; Ecological Parameter Monitoring/*methods ; *Ecosystem ; Software ; *Sound ; *Vocalization, Animal
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  • 169
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-03-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alexander, Kathleen A -- Sanderson, Claire E -- New York, N.Y. -- Science. 2014 Mar 14;343(6176):1199. doi: 10.1126/science.343.6176.1199-a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Fisheries and Wildlife Conservation, Virginia Tech University, Blacksburg, VA 24061, USA and CARACAL, Centre for Conservation of African Resources: Animals, Communities, and Land Use, Kasane, Botswana.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24626912" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Carnivora ; *Ecological and Environmental Phenomena ; *Ecosystem ; *Extinction, Biological ; Humans
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 170
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-04-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pandolfi, John M -- Lovelock, Catherine E -- New York, N.Y. -- Science. 2014 Apr 18;344(6181):266-7. doi: 10.1126/science.1252963.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, ARC Centre of Excellence for Coral Reef Studies, University of Queensland, St. Lucia, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24744366" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Birds ; *Ecosystem ; *Fishes ; *Invertebrates ; *Mammals ; *Plants
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  • 171
    Publication Date: 2014-01-18
    Description: Extracellular adenosine 5'-triphosphate (ATP) is an essential signaling molecule that is perceived in mammals by plasma membrane P2-type purinoceptors. Similar ATP receptors do not exist in plants, although extracellular ATP has been shown to play critical roles in plant growth, development, and stress responses. Here, we identify an ATP-insensitive Arabidopsis mutant, dorn1 (Does not Respond to Nucleotides 1), defective in lectin receptor kinase I.9 (Arabidopsis Information Resource accession code At5g60300). DORN1 binds ATP with high affinity (dissociation constant of 45.7 +/- 3.1 nanomolar) and is required for ATP-induced calcium response, mitogen-activated protein kinase activation, and gene expression. Ectopic expression of DORN1 increased the plant response to physical wounding. We propose that DORN1 is essential for perception of extracellular ATP and likely plays a variety of roles in plant stress resistance.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Choi, Jeongmin -- Tanaka, Kiwamu -- Cao, Yangrong -- Qi, Yue -- Qiu, Jing -- Liang, Yan -- Lee, Sang Yeol -- Stacey, Gary -- New York, N.Y. -- Science. 2014 Jan 17;343(6168):290-4. doi: 10.1126/science.343.6168.290.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Divisions of Biochemistry and Plant Sciences, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24436418" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/*metabolism ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Enzyme Activation ; Gene Expression Regulation, Plant ; Mitogen-Activated Protein Kinases/metabolism ; Mutation ; Protein Kinases/genetics/*metabolism ; Receptors, Mitogen/genetics/*metabolism ; Receptors, Purinergic P2/genetics/*metabolism ; Stress, Physiological/genetics/*physiology ; Up-Regulation
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  • 172
    Publication Date: 2014-12-17
    Description: The emergence of artemisinin resistance in Southeast Asia imperils efforts to reduce the global malaria burden. We genetically modified the Plasmodium falciparum K13 locus using zinc-finger nucleases and measured ring-stage survival rates after drug exposure in vitro; these rates correlate with parasite clearance half-lives in artemisinin-treated patients. With isolates from Cambodia, where resistance first emerged, survival rates decreased from 13 to 49% to 0.3 to 2.4% after the removal of K13 mutations. Conversely, survival rates in wild-type parasites increased from 〈/=0.6% to 2 to 29% after the insertion of K13 mutations. These mutations conferred elevated resistance to recent Cambodian isolates compared with that of reference lines, suggesting a contemporary contribution of additional genetic factors. Our data provide a conclusive rationale for worldwide K13-propeller sequencing to identify and eliminate artemisinin-resistant parasites.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4349400/" 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/PMC4349400/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Straimer, Judith -- Gnadig, Nina F -- Witkowski, Benoit -- Amaratunga, Chanaki -- Duru, Valentine -- Ramadani, Arba Pramundita -- Dacheux, Melanie -- Khim, Nimol -- Zhang, Lei -- Lam, Stephen -- Gregory, Philip D -- Urnov, Fyodor D -- Mercereau-Puijalon, Odile -- Benoit-Vical, Francoise -- Fairhurst, Rick M -- Menard, Didier -- Fidock, David A -- R01 AI109023/AI/NIAID NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2015 Jan 23;347(6220):428-31. doi: 10.1126/science.1260867. Epub 2014 Dec 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY, USA. ; Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia. ; Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. ; Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie de Coordination UPR8241, Toulouse, France. Universite de Toulouse, UPS, Institut National Polytechnique de Toulouse, Toulouse, France. ; Sangamo BioSciences, Richmond, CA, USA. ; Institut Pasteur, Parasite Molecular Immunology Unit, Paris, France. ; Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY, USA. Division of Infectious Diseases, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA. df2260@columbia.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25502314" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antimalarials/*pharmacology ; Artemisinins/*pharmacology ; Cambodia ; Drug Resistance/*genetics ; Genetic Loci ; Humans ; Malaria, Falciparum/drug therapy/parasitology ; Molecular Sequence Data ; Mutation ; Plasmodium falciparum/*drug effects/*genetics ; Protein Structure, Tertiary ; Protozoan Proteins/chemistry/*genetics
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  • 173
    Publication Date: 2013-11-23
    Description: Oxamniquine resistance evolved in the human blood fluke (Schistosoma mansoni) in Brazil in the 1970s. We crossed parental parasites differing ~500-fold in drug response, determined drug sensitivity and marker segregation in clonally derived second-generation progeny, and identified a single quantitative trait locus (logarithm of odds = 31) on chromosome 6. A sulfotransferase was identified as the causative gene by using RNA interference knockdown and biochemical complementation assays, and we subsequently demonstrated independent origins of loss-of-function mutations in field-derived and laboratory-selected resistant parasites. These results demonstrate the utility of linkage mapping in a human helminth parasite, while crystallographic analyses of protein-drug interactions illuminate the mode of drug action and provide a framework for rational design of oxamniquine derivatives that kill both S. mansoni and S. haematobium, the two species responsible for 〉99% of schistosomiasis cases worldwide.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136436/" 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/PMC4136436/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Valentim, Claudia L L -- Cioli, Donato -- Chevalier, Frederic D -- Cao, Xiaohang -- Taylor, Alexander B -- Holloway, Stephen P -- Pica-Mattoccia, Livia -- Guidi, Alessandra -- Basso, Annalisa -- Tsai, Isheng J -- Berriman, Matthew -- Carvalho-Queiroz, Claudia -- Almeida, Marcio -- Aguilar, Hector -- Frantz, Doug E -- Hart, P John -- LoVerde, Philip T -- Anderson, Timothy J C -- 098051/Wellcome Trust/United Kingdom -- 5R21-AI072704/AI/NIAID NIH HHS/ -- 5R21-AI096277/AI/NIAID NIH HHS/ -- C06 RR013556/RR/NCRR NIH HHS/ -- HHSN272201000005I/PHS HHS/ -- R01 AI097576/AI/NIAID NIH HHS/ -- R01-AI097576/AI/NIAID NIH HHS/ -- R21 AI072704/AI/NIAID NIH HHS/ -- R21 AI096277/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2013 Dec 13;342(6164):1385-9. doi: 10.1126/science.1243106. Epub 2013 Nov 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Biochemistry and Pathology, University of Texas Health Science Center, San Antonio, TX 78229, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24263136" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Drug Resistance/*genetics ; Gene Knockdown Techniques ; Genetic Linkage ; Helminth Proteins/*genetics ; Humans ; Molecular Sequence Data ; Mutation ; Oxamniquine/*pharmacology ; Phylogeny ; Protein Conformation ; Quantitative Trait Loci ; RNA Interference ; Schistosoma mansoni/*drug effects/*genetics ; Schistosomicides/*pharmacology ; Sulfotransferases/chemistry/classification/*genetics
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  • 174
    Publication Date: 2013-02-09
    Description: HSP-100 protein machines, such as ClpB, play an essential role in reactivating protein aggregates that can otherwise be lethal to cells. Although the players involved are known, including the DnaK/DnaJ/GrpE chaperone system in bacteria, details of the molecular interactions are not well understood. Using methyl-transverse relaxation-optimized nuclear magnetic resonance spectroscopy, we present an atomic-resolution model for the ClpB-DnaK complex, which we verified by mutagenesis and functional assays. ClpB and GrpE compete for binding to the DnaK nucleotide binding domain, with GrpE binding inhibiting disaggregation. DnaK, in turn, plays a dual role in both disaggregation and subsequent refolding of polypeptide chains as they emerge from the aggregate. On the basis of a combined structural-biochemical analysis, we propose a model for the mechanism of protein aggregate reactivation by ClpB.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rosenzweig, Rina -- Moradi, Shoeib -- Zarrine-Afsar, Arash -- Glover, John R -- Kay, Lewis E -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2013 Mar 1;339(6123):1080-3. doi: 10.1126/science.1233066. Epub 2013 Feb 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada. rina.rosenzweig@utoronto.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23393091" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*chemistry/genetics ; Adenosine Triphosphate/chemistry/metabolism ; Bacterial Proteins/chemistry ; Heat-Shock Proteins/*chemistry/genetics ; Hydrolysis ; *Models, Chemical ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Protein Interaction Domains and Motifs ; Protein Interaction Maps ; Protein Multimerization ; *Protein Refolding ; Protein Structure, Tertiary ; Protein Transport ; Thermus thermophilus
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  • 175
    Publication Date: 2013-03-23
    Description: Glycosylated alpha-dystroglycan (alpha-DG) serves as cellular entry receptor for multiple pathogens, and defects in its glycosylation cause hereditary Walker-Warburg syndrome (WWS). At least eight proteins are critical to glycosylate alpha-DG, but many genes mutated in WWS remain unknown. To identify modifiers of alpha-DG, we performed a haploid screen for Lassa virus entry, a hemorrhagic fever virus causing thousands of deaths annually that hijacks glycosylated alpha-DG to enter cells. In complementary screens, we profiled cells for absence of alpha-DG carbohydrate chains or biochemically related glycans. This revealed virus host factors and a suite of glycosylation units, including all known Walker-Warburg genes and five additional factors critical for the modification of alpha-DG. Our findings accentuate the complexity of this posttranslational feature and point out genes defective in dystroglycanopathies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919138/" 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/PMC3919138/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jae, Lucas T -- Raaben, Matthijs -- Riemersma, Moniek -- van Beusekom, Ellen -- Blomen, Vincent A -- Velds, Arno -- Kerkhoven, Ron M -- Carette, Jan E -- Topaloglu, Haluk -- Meinecke, Peter -- Wessels, Marja W -- Lefeber, Dirk J -- Whelan, Sean P -- van Bokhoven, Hans -- Brummelkamp, Thijn R -- AI057159/AI/NIAID NIH HHS/ -- AI081842/AI/NIAID NIH HHS/ -- R01 AI081842/AI/NIAID NIH HHS/ -- U54 AI057159/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2013 Apr 26;340(6131):479-83. doi: 10.1126/science.1233675. Epub 2013 Mar 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23519211" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cell Line ; Dystroglycans/*metabolism ; Female ; Glycosylation ; Haploidy ; Host-Pathogen Interactions/*genetics ; Humans ; Infant ; Lassa Fever/*genetics/virology ; Lassa virus/*physiology ; Male ; Membrane Proteins/*genetics ; Molecular Sequence Data ; Mutation ; Pedigree ; Proteome/*metabolism ; *Virus Internalization ; Walker-Warburg Syndrome/*genetics
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  • 176
    Publication Date: 2013-05-21
    Description: Evidence for transcriptional feedback in circadian timekeeping is abundant, yet little is known about the mechanisms underlying translational control. We found that ATAXIN-2 (ATX2), an RNA-associated protein involved in neurodegenerative disease, is a translational activator of the rate-limiting clock component PERIOD (PER) in Drosophila. ATX2 specifically interacted with TWENTY-FOUR (TYF), an activator of PER translation. RNA interference-mediated depletion of Atx2 or the expression of a mutant ATX2 protein that does not associate with polyadenylate-binding protein (PABP) suppressed behavioral rhythms and decreased abundance of PER. Although ATX2 can repress translation, depletion of Atx2 from Drosophila S2 cells inhibited translational activation by RNA-tethered TYF and disrupted the association between TYF and PABP. Thus, ATX2 coordinates an active translation complex important for PER expression and circadian rhythms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lim, Chunghun -- Allada, Ravi -- R01NS059042/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2013 May 17;340(6134):875-9. doi: 10.1126/science.1234785.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23687047" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Ataxins ; Cell Line ; *Circadian Rhythm ; Drosophila Proteins/*biosynthesis/genetics/metabolism ; Drosophila melanogaster/metabolism/*physiology ; Mutation ; Nerve Tissue Proteins/genetics/*metabolism ; Period Circadian Proteins/*biosynthesis ; Poly(A)-Binding Proteins/metabolism ; Protein Biosynthesis ; RNA Interference
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  • 177
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-07-03
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4361224/" 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/PMC4361224/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fidock, David A -- R01 AI050234/AI/NIAID NIH HHS/ -- R01 AI079709/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2013 Jun 28;340(6140):1531-3. doi: 10.1126/science.1240539.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology and Division of Infectious Diseases, Columbia University Medical Center, New York, NY 10032, USA. df2260@columbia.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23812705" target="_blank"〉PubMed〈/a〉
    Keywords: Antimalarials/*administration & dosage ; Artemisinins/*administration & dosage ; Child ; DNA Mismatch Repair/*genetics ; Disease Eradication/*methods ; Drug Resistance/*genetics ; Humans ; Malaria, Falciparum/parasitology/*prevention & control ; Mutation ; Plasmodium falciparum/drug effects/*genetics
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  • 178
    Publication Date: 2013-06-15
    Description: Epistatic interactions between mutant sites in the same protein can exert a strong influence on pathways of molecular evolution. We performed protein engineering experiments that revealed pervasive epistasis among segregating amino acid variants that contribute to adaptive functional variation in deer mouse hemoglobin (Hb). Amino acid mutations increased or decreased Hb-O2 affinity depending on the allelic state of other sites. Structural analysis revealed that epistasis for Hb-O2 affinity and allosteric regulatory control is attributable to indirect interactions between structurally remote sites. The prevalence of sign epistasis for fitness-related biochemical phenotypes has important implications for the evolutionary dynamics of protein polymorphism in natural populations.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4409680/" 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/PMC4409680/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Natarajan, Chandrasekhar -- Inoguchi, Noriko -- Weber, Roy E -- Fago, Angela -- Moriyama, Hideaki -- Storz, Jay F -- HL087216-S1/HL/NHLBI NIH HHS/ -- R01 HL087216/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2013 Jun 14;340(6138):1324-7. doi: 10.1126/science.1236862.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23766324" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological/*genetics ; Alleles ; Animals ; *Epistasis, Genetic ; *Evolution, Molecular ; Exons ; Genetic Variation ; Hemoglobins/*chemistry/*genetics ; Hydrogen Bonding ; Mutation ; Oxygen/chemistry ; Peromyscus/genetics/*physiology ; Polymorphism, Genetic ; Protein Structure, Secondary ; alpha-Globins/chemistry/genetics ; beta-Globins/genetics
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  • 179
    Publication Date: 2013-11-23
    Description: Cancer is a disease in which cells accumulate genetic aberrations that are believed to confer a clonal advantage over cells in the surrounding tissue. However, the quantitative benefit of frequently occurring mutations during tumor development remains unknown. We quantified the competitive advantage of Apc loss, Kras activation, and P53 mutations in the mouse intestine. Our findings indicate that the fate conferred by these mutations is not deterministic, and many mutated stem cells are replaced by wild-type stem cells after biased, but still stochastic events. Furthermore, P53 mutations display a condition-dependent advantage, and especially in colitis-affected intestines, clones harboring mutations in this gene are favored. Our work confirms the previously theoretical notion that the tissue architecture of the intestine suppresses the accumulation of mutated lineages.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vermeulen, Louis -- Morrissey, Edward -- van der Heijden, Maartje -- Nicholson, Anna M -- Sottoriva, Andrea -- Buczacki, Simon -- Kemp, Richard -- Tavare, Simon -- Winton, Douglas J -- Cancer Research UK/United Kingdom -- New York, N.Y. -- Science. 2013 Nov 22;342(6161):995-8. doi: 10.1126/science.1243148.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research UK, Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24264992" target="_blank"〉PubMed〈/a〉
    Keywords: Adenomatous Polyposis Coli Protein/genetics ; Animals ; Cell Transformation, Neoplastic/*genetics/*pathology ; *Gene Expression Regulation, Neoplastic ; Intestinal Neoplasms/*genetics/*pathology ; Mice ; Mice, Mutant Strains ; Models, Biological ; Mutation ; Neoplastic Stem Cells/metabolism/*pathology ; Proto-Oncogene Proteins p21(ras)/genetics ; Transcriptional Activation ; Tumor Suppressor Protein p53/genetics
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  • 180
    Publication Date: 2013-10-05
    Description: Dominant mutations in sarcomere proteins such as the myosin heavy chains (MHC) are the leading genetic causes of human hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy. We found that expression of the HCM-causing cardiac MHC gene (Myh6) R403Q mutation in mice can be selectively silenced by an RNA interference (RNAi) cassette delivered by an adeno-associated virus vector. RNAi-transduced MHC(403/+) mice developed neither hypertrophy nor myocardial fibrosis, the pathologic manifestations of HCM, for at least 6 months. Because inhibition of HCM was achieved by only a 25% reduction in the levels of the mutant transcripts, we suggest that the variable clinical phenotype in HCM patients reflects allele-specific expression and that partial silencing of mutant transcripts may have therapeutic benefit.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4100553/" 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/PMC4100553/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jiang, Jianming -- Wakimoto, Hiroko -- Seidman, J G -- Seidman, Christine E -- R01 HL084553/HL/NHLBI NIH HHS/ -- R01HL084553/HL/NHLBI NIH HHS/ -- U01 HL066582/HL/NHLBI NIH HHS/ -- U01 HL098166/HL/NHLBI NIH HHS/ -- U01HL098166/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2013 Oct 4;342(6154):111-4. doi: 10.1126/science.1236921.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24092743" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Cardiomyopathy, Hypertrophic/*diagnosis/genetics/pathology ; Dependovirus ; Fibrosis ; Gene Silencing ; *Genetic Therapy ; HEK293 Cells ; Humans ; Mice ; Mutation ; Myosin Heavy Chains/*genetics ; *RNA Interference
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 181
    Publication Date: 2013-03-16
    Description: The identification of precise mutations is required for a complete understanding of the underlying molecular and evolutionary mechanisms driving adaptive phenotypic change. Using plasticine models in the field, we show that the light coat color of deer mice that recently colonized the light-colored soil of the Nebraska Sand Hills provides a strong selective advantage against visually hunting predators. Color variation in an admixed population suggests that this light Sand Hills phenotype is composed of multiple traits. We identified distinct regions within the Agouti locus associated with each color trait and found that only haplotypes associated with light trait values have evidence of selection. Thus, local adaptation is the result of independent selection on many mutations within a single locus, each with a specific effect on an adaptive phenotype, thereby minimizing pleiotropic consequences.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836219/" 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/PMC3836219/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Linnen, Catherine R -- Poh, Yu-Ping -- Peterson, Brant K -- Barrett, Rowan D H -- Larson, Joanna G -- Jensen, Jeffrey D -- Hoekstra, Hopi E -- 308796/European Research Council/International -- New York, N.Y. -- Science. 2013 Mar 15;339(6125):1312-6. doi: 10.1126/science.1233213.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Kentucky, Lexington, KY 40506, USA. catherine.linnen@uky.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23493712" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics ; Agouti Signaling Protein/genetics ; Animals ; *Biological Evolution ; Color ; Food Chain ; *Multifactorial Inheritance ; Mutation ; Organic Chemicals ; Peromyscus/genetics/*physiology ; Pigmentation/*genetics ; Selection, Genetic
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  • 182
    Publication Date: 2013-07-03
    Description: Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a devastating disease that can cause severe yield losses. A previously uncharacterized Pgt race, designated Ug99, has overcome most of the widely used resistance genes and is threatening major wheat production areas. Here, we demonstrate that the Sr35 gene from Triticum monococcum is a coiled-coil, nucleotide-binding, leucine-rich repeat gene that confers near immunity to Ug99 and related races. This gene is absent in the A-genome diploid donor and in polyploid wheat but is effective when transferred from T. monococcum to polyploid wheat. The cloning of Sr35 opens the door to the use of biotechnological approaches to control this devastating disease and to analyses of the molecular interactions that define the wheat-rust pathosystem.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748951/" 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/PMC4748951/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Saintenac, Cyrille -- Zhang, Wenjun -- Salcedo, Andres -- Rouse, Matthew N -- Trick, Harold N -- Akhunov, Eduard -- Dubcovsky, Jorge -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2013 Aug 16;341(6147):783-6. doi: 10.1126/science.1239022. Epub 2013 Jun 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23811222" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Amino Acid Sequence ; *Basidiomycota/pathogenicity ; Cloning, Molecular ; Disease Resistance/genetics ; *Genes, Plant ; Haplotypes ; Molecular Sequence Annotation ; Molecular Sequence Data ; Mutation ; Phylogeny ; Plant Diseases/genetics/*immunology/microbiology ; Plant Proteins/chemistry/genetics ; Plant Stems/microbiology ; Plants, Genetically Modified ; Polymorphism, Single Nucleotide ; Polyploidy ; Sequence Analysis, DNA ; Triticum/*genetics/immunology/microbiology
    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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  • 183
    Publication Date: 2013-04-06
    Description: A variant upstream of human leukocyte antigen C (HLA-C) shows the most significant genome-wide effect on HIV control in European Americans and is also associated with the level of HLA-C expression. We characterized the differential cell surface expression levels of all common HLA-C allotypes and tested directly for effects of HLA-C expression on outcomes of HIV infection in 5243 individuals. Increasing HLA-C expression was associated with protection against multiple outcomes independently of individual HLA allelic effects in both African and European Americans, regardless of their distinct HLA-C frequencies and linkage relationships with HLA-B and HLA-A. Higher HLA-C expression was correlated with increased likelihood of cytotoxic T lymphocyte responses and frequency of viral escape mutation. In contrast, high HLA-C expression had a deleterious effect in Crohn's disease, suggesting a broader influence of HLA expression levels in human disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784322/" 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/PMC3784322/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Apps, Richard -- Qi, Ying -- Carlson, Jonathan M -- Chen, Haoyan -- Gao, Xiaojiang -- Thomas, Rasmi -- Yuki, Yuko -- Del Prete, Greg Q -- Goulder, Philip -- Brumme, Zabrina L -- Brumme, Chanson J -- John, Mina -- Mallal, Simon -- Nelson, George -- Bosch, Ronald -- Heckerman, David -- Stein, Judy L -- Soderberg, Kelly A -- Moody, M Anthony -- Denny, Thomas N -- Zeng, Xue -- Fang, Jingyuan -- Moffett, Ashley -- Lifson, Jeffrey D -- Goedert, James J -- Buchbinder, Susan -- Kirk, Gregory D -- Fellay, Jacques -- McLaren, Paul -- Deeks, Steven G -- Pereyra, Florencia -- Walker, Bruce -- Michael, Nelson L -- Weintrob, Amy -- Wolinsky, Steven -- Liao, Wilson -- Carrington, Mary -- 5-M01-RR-00722/RR/NCRR NIH HHS/ -- HHSN261200800001E/CA/NCI NIH HHS/ -- HHSN261200800001E/PHS HHS/ -- K08 AR057763/AR/NIAMS NIH HHS/ -- K08AR057763/AR/NIAMS NIH HHS/ -- K24 AI069994/AI/NIAID NIH HHS/ -- K24AI069994/AI/NIAID NIH HHS/ -- N02-CP-55504/CP/NCI NIH HHS/ -- P30 AI027763/AI/NIAID NIH HHS/ -- P30 AI027767/AI/NIAID NIH HHS/ -- P30 AI027767-24/AI/NIAID NIH HHS/ -- P30 MH62246/MH/NIMH NIH HHS/ -- PG/09/077/27964/British Heart Foundation/United Kingdom -- R01 AI046995/AI/NIAID NIH HHS/ -- R01 AI060460/AI/NIAID NIH HHS/ -- R01 AI087145/AI/NIAID NIH HHS/ -- R01 AR065174/AR/NIAMS NIH HHS/ -- R01-AI046995/AI/NIAID NIH HHS/ -- R01-AI060460/AI/NIAID NIH HHS/ -- R01-DA-04334/DA/NIDA NIH HHS/ -- R01-DA-12568/DA/NIDA NIH HHS/ -- R01-DA04334/DA/NIDA NIH HHS/ -- R01-DA12568/DA/NIDA NIH HHS/ -- R24 AI067039/AI/NIAID NIH HHS/ -- U01-AI-067854/AI/NIAID NIH HHS/ -- U01-AI-35039/AI/NIAID NIH HHS/ -- U01-AI-35040/AI/NIAID NIH HHS/ -- U01-AI-35041/AI/NIAID NIH HHS/ -- U01-AI-35042/AI/NIAID NIH HHS/ -- U01-AI-35043/AI/NIAID NIH HHS/ -- U01-AI-37613/AI/NIAID NIH HHS/ -- U01-AI-37984/AI/NIAID NIH HHS/ -- UL1 RR024131/RR/NCRR NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2013 Apr 5;340(6128):87-91. doi: 10.1126/science.1232685.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer and Inflammation Program, Laboratory of Experimental Immunology, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23559252" target="_blank"〉PubMed〈/a〉
    Keywords: African Americans/genetics ; Alleles ; Amino Acid Sequence ; Anti-Retroviral Agents/therapeutic use ; Crohn Disease/genetics/immunology ; *Gene Expression Regulation ; HIV/genetics/*immunology ; HIV Infections/drug therapy/*genetics/*immunology ; HLA-C Antigens/*genetics ; Humans ; Immunodominant Epitopes/genetics ; Molecular Sequence Data ; Mutation ; Peptide Fragments/immunology ; Polymorphism, Single Nucleotide ; T-Lymphocytes, Cytotoxic/*immunology ; Viral Load/genetics
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  • 184
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-11-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nijman, Sebastian M B -- Friend, Stephen H -- New York, N.Y. -- Science. 2013 Nov 15;342(6160):809-11. doi: 10.1126/science.1244669.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24233712" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Drosophila melanogaster/genetics ; Gene Targeting ; *Genes, Lethal ; *Genes, Modifier ; Genetic Therapy/*methods ; Humans ; Immunotherapy ; Molecular Targeted Therapy ; Mutation ; Neoplasms/*genetics/*therapy ; Saccharomyces cerevisiae/genetics ; Tumor Suppressor Proteins/genetics
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  • 185
    Publication Date: 2013-08-10
    Description: Numerous volatile organic compounds (VOCs) exist in Earth's atmosphere, most of which originate from biogenic emissions. Despite VOCs' critical role in tropospheric chemistry, studies for evaluating their atmosphere-ecosystem exchange (emission and deposition) have been limited to a few dominant compounds owing to a lack of appropriate measurement techniques. Using a high-mass resolution proton transfer reaction-time of flight-mass spectrometer and an absolute value eddy-covariance method, we directly measured 186 organic ions with net deposition, and 494 that have bidirectional flux. This observation of active atmosphere-ecosystem exchange of the vast majority of detected VOCs poses a challenge to current emission, air quality, and global climate models, which do not account for this extremely large range of compounds. This observation also provides new insight for understanding the atmospheric VOC budget.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, J-H -- Goldstein, A H -- Timkovsky, J -- Fares, S -- Weber, R -- Karlik, J -- Holzinger, R -- New York, N.Y. -- Science. 2013 Aug 9;341(6146):643-7. doi: 10.1126/science.1235053.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23929979" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/*chemistry ; *Ecosystem ; Mass Spectrometry ; Ozone/analysis/chemistry ; Plants/chemistry ; Volatile Organic Compounds/analysis/*chemistry
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  • 186
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-10-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aspinall, Richard -- Gregory, Peter -- New York, N.Y. -- Science. 2013 Oct 25;342(6157):421. doi: 10.1126/science.342.6157.421-a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉James Hutton Institute, Craigiebuckler, Aberdeen, AB15 8QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24159029" target="_blank"〉PubMed〈/a〉
    Keywords: *Agriculture ; Animals ; *Climate Change ; *Conservation of Natural Resources ; *Decision Support Techniques ; *Ecosystem ; *Models, Economic
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  • 187
    Publication Date: 2013-10-05
    Description: Botrytis cinerea, the causative agent of gray mold disease, is an aggressive fungal pathogen that infects more than 200 plant species. Here, we show that some B. cinerea small RNAs (Bc-sRNAs) can silence Arabidopsis and tomato genes involved in immunity. These Bc-sRNAs hijack the host RNA interference (RNAi) machinery by binding to Arabidopsis Argonaute 1 (AGO1) and selectively silencing host immunity genes. The Arabidopsis ago1 mutant exhibits reduced susceptibility to B. cinerea, and the B. cinerea dcl1 dcl2 double mutant that can no longer produce these Bc-sRNAs displays reduced pathogenicity on Arabidopsis and tomato. Thus, this fungal pathogen transfers "virulent" sRNA effectors into host plant cells to suppress host immunity and achieve infection, which demonstrates a naturally occurring cross-kingdom RNAi as an advanced virulence mechanism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096153/" 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/PMC4096153/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weiberg, Arne -- Wang, Ming -- Lin, Feng-Mao -- Zhao, Hongwei -- Zhang, Zhihong -- Kaloshian, Isgouhi -- Huang, Hsien-Da -- Jin, Hailing -- R01 GM093008/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Oct 4;342(6154):118-23. doi: 10.1126/science.1239705.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24092744" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics/*immunology/microbiology ; Arabidopsis Proteins/genetics ; Argonaute Proteins/genetics ; Botrytis/genetics/*pathogenicity ; Gene Expression Regulation, Plant ; Host-Pathogen Interactions/genetics/*immunology ; Lycopersicon esculentum/genetics/immunology/microbiology ; Mutation ; Plant Diseases/genetics/immunology/*microbiology ; *RNA Interference ; RNA, Fungal/*genetics ; RNA, Small Interfering/*genetics ; Virulence/genetics
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  • 188
    Publication Date: 2013-07-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pedaste, Margus -- de Jong, Ton -- Sarapuu, Tago -- Piksoot, Jaanika -- van Joolingen, Wouter R -- Giemza, Adam -- New York, N.Y. -- Science. 2013 Jun 28;340(6140):1537-8. doi: 10.1126/science.1229908.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Tartu, 50103 Tartu, Estonia. margus.pedaste@ut.ee〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23812708" target="_blank"〉PubMed〈/a〉
    Keywords: Ecology/*education ; *Ecosystem ; Estonia ; Germany ; Netherlands ; Problem-Based Learning/*methods ; Research Design ; *Software
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  • 189
    Publication Date: 2013-04-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Austin, A T -- Bustamante, M M C -- Nardoto, G B -- Mitre, S K -- Perez, T -- Ometto, J P H B -- Ascarrunz, N L -- Forti, M C -- Longo, K -- Gavito, M E -- Enrich-Prast, A -- Martinelli, L A -- New York, N.Y. -- Science. 2013 Apr 12;340(6129):149. doi: 10.1126/science.1231679.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Universidad de Buenos Aires, IFEVA-CONICET, Buenos Aires, Argentina.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23580515" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture ; Biomass ; *Conservation of Natural Resources ; *Ecosystem ; *Environment ; Human Activities ; Humans ; Latin America ; Nitrogen ; *Nitrogen Cycle ; Politics ; Public Health ; Public Policy
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  • 190
    Publication Date: 2013-08-03
    Description: The future impacts of anthropogenic global change on marine ecosystems are highly uncertain, but insights can be gained from past intervals of high atmospheric carbon dioxide partial pressure. The long-term geological record reveals an early Cenozoic warm climate that supported smaller polar ecosystems, few coral-algal reefs, expanded shallow-water platforms, longer food chains with less energy for top predators, and a less oxygenated ocean than today. The closest analogs for our likely future are climate transients, 10,000 to 200,000 years in duration, that occurred during the long early Cenozoic interval of elevated warmth. Although the future ocean will begin to resemble the past greenhouse world, it will retain elements of the present "icehouse" world long into the future. Changing temperatures and ocean acidification, together with rising sea level and shifts in ocean productivity, will keep marine ecosystems in a state of continuous change for 100,000 years.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Norris, R D -- Turner, S Kirtland -- Hull, P M -- Ridgwell, A -- New York, N.Y. -- Science. 2013 Aug 2;341(6145):492-8. doi: 10.1126/science.1240543.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA. rnorris@ucsd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23908226" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Evolution ; *Climate Change/history ; *Ecosystem ; Greenhouse Effect ; History, Ancient ; *Oceans and Seas ; *Seawater ; Temperature ; Tidal Waves ; Vertebrates
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  • 191
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-09-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fung, Inez -- New York, N.Y. -- Science. 2013 Sep 6;341(6150):1075-6. doi: 10.1126/science.1242004.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of California, Berkeley, Berkeley, CA 94720-4767, USA. ifung@berkeley.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24009383" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/*chemistry ; *Carbon Cycle ; Carbon Dioxide/*chemistry ; *Ecosystem ; *Trees
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  • 192
    Publication Date: 2013-09-21
    Description: The Na(+), K(+)-adenosine triphosphatase (ATPase) maintains the electrochemical gradients of Na(+) and K(+) across the plasma membrane--a prerequisite for electrical excitability and secondary transport. Hitherto, structural information has been limited to K(+)-bound or ouabain-blocked forms. We present the crystal structure of a Na(+)-bound Na(+), K(+)-ATPase as determined at 4.3 A resolution. Compared with the K(+)-bound form, large conformational changes are observed in the alpha subunit whereas the beta and gamma subunit structures are maintained. The locations of the three Na(+) sites are indicated with the unique site III at the recently suggested IIIb, as further supported by electrophysiological studies on leak currents. Extracellular release of the third Na(+) from IIIb through IIIa, followed by exchange of Na(+) for K(+) at sites I and II, is suggested.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nyblom, Maria -- Poulsen, Hanne -- Gourdon, Pontus -- Reinhard, Linda -- Andersson, Magnus -- Lindahl, Erik -- Fedosova, Natalya -- Nissen, Poul -- New York, N.Y. -- Science. 2013 Oct 4;342(6154):123-7. doi: 10.1126/science.1243352. Epub 2013 Sep 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Membrane Pumps in Cells and Disease-PUMPkin, Danish National Research Foundation, DK-8000 Aarhus, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24051246" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Membrane/enzymology ; Crystallography, X-Ray ; *Models, Molecular ; Mutation ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sodium/*chemistry ; Sodium-Potassium-Exchanging ATPase/*chemistry/genetics ; Swine
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  • 193
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-10-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Obst, Carl -- Edens, Bram -- Hein, Lars -- New York, N.Y. -- Science. 2013 Oct 25;342(6157):420. doi: 10.1126/science.342.6157.420-a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Melbourne Sustainable Society Institute, University of Melbourne, Victoria, 3010 Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24159027" target="_blank"〉PubMed〈/a〉
    Keywords: *Agriculture ; Animals ; *Climate Change ; *Conservation of Natural Resources ; *Decision Support Techniques ; *Ecosystem ; *Models, Economic
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 194
    Publication Date: 2013-02-02
    Description: Chloroplasts require protein translocons at the outer and inner envelope membranes, termed TOC and TIC, respectively, to import thousands of cytoplasmically synthesized preproteins. However, the molecular identity of the TIC translocon remains controversial. Tic20 forms a 1-megadalton complex at the inner membrane and directly interacts with translocating preproteins. We purified the 1-megadalton complex from Arabidopsis, comprising Tic20 and three other essential components, one of which is encoded by the enigmatic open reading frame ycf1 in the chloroplast genome. All four components, together with well-known TOC components, were found stoichiometrically associated with different translocating preproteins. When reconstituted into planar lipid bilayers, the purified complex formed a preprotein-sensitive channel. Thus, this complex constitutes a general TIC translocon.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kikuchi, Shingo -- Bedard, Jocelyn -- Hirano, Minako -- Hirabayashi, Yoshino -- Oishi, Maya -- Imai, Midori -- Takase, Mai -- Ide, Toru -- Nakai, Masato -- New York, N.Y. -- Science. 2013 Feb 1;339(6119):571-4. doi: 10.1126/science.1229262.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Regulation of Biological Reactions, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23372012" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/*metabolism ; Arabidopsis Proteins/genetics/isolation & purification/*metabolism ; Cell Membrane/*metabolism ; Chloroplasts/*metabolism ; Evolution, Molecular ; Gene Knockout Techniques ; Lipid Bilayers/metabolism ; Membrane Transport Proteins/genetics/isolation & purification/*metabolism ; Mutation ; Open Reading Frames ; Protein Transport
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 195
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-01-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chown, S L -- New York, N.Y. -- Science. 2013 Jan 11;339(6116):141. doi: 10.1126/science.339.6116.141-a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23307721" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Conservation of Natural Resources ; *Ecosystem ; Humans
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 196
    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
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 197
    Publication Date: 2013-07-28
    Description: Gram-negative bacteria including Escherichia coli, Citrobacter rodentium, Salmonella typhimurium, and Shigella flexneri are sensed in an ill-defined manner by an intracellular inflammasome complex that activates caspase-11. We show that macrophages loaded with synthetic lipid A, E. coli lipopolysaccharide (LPS), or S. typhimurium LPS activate caspase-11 independently of the LPS receptor Toll-like receptor 4 (TLR4). Consistent with lipid A triggering the noncanonical inflammasome, LPS containing a divergent lipid A structure antagonized caspase-11 activation in response to E. coli LPS or Gram-negative bacteria. Moreover, LPS-mutant E. coli failed to activate caspase-11. Tlr4(-/-) mice primed with TLR3 agonist polyinosinic:polycytidylic acid [poly(I:C)] to induce pro-caspase-11 expression were as susceptible as wild-type mice were to sepsis induced by E. coli LPS. These data unveil a TLR4-independent mechanism for innate immune recognition of LPS.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kayagaki, Nobuhiko -- Wong, Michael T -- Stowe, Irma B -- Ramani, Sree Ranjani -- Gonzalez, Lino C -- Akashi-Takamura, Sachiko -- Miyake, Kensuke -- Zhang, Juan -- Lee, Wyne P -- Muszynski, Artur -- Forsberg, Lennart S -- Carlson, Russell W -- Dixit, Vishva M -- New York, N.Y. -- Science. 2013 Sep 13;341(6151):1246-9. doi: 10.1126/science.1240248. Epub 2013 Jul 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA. kayagaki@gene.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23887873" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Caspases/biosynthesis ; Cholera Toxin/immunology ; Disease Models, Animal ; Escherichia coli/immunology ; Escherichia coli Infections/genetics/immunology ; *Immunity, Innate ; Inflammasomes/*immunology ; Lipid A/genetics/*immunology ; Macrophages/*immunology ; Mice ; Mice, Mutant Strains ; Mutation ; Salmonella Infections/immunology ; Salmonella typhimurium/immunology ; Sepsis/immunology ; Toll-Like Receptor 4/*immunology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 198
    facet.materialart.
    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-08-24
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893057/" 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/PMC3893057/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McCann, Kathleen L -- Baserga, Susan J -- GM 52581/GM/NIGMS NIH HHS/ -- R01 GM052581/GM/NIGMS NIH HHS/ -- R29 GM052581/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Aug 23;341(6148):849-50. doi: 10.1126/science.1244156.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23970686" target="_blank"〉PubMed〈/a〉
    Keywords: Anemia, Diamond-Blackfan/genetics ; Anemia, Macrocytic/genetics ; Animals ; Chromosome Deletion ; Chromosomes, Human, Pair 5/genetics ; Genetic Diseases, Inborn/*genetics ; Humans ; Mice ; Mutation ; Organ Specificity/genetics ; Ribosomal Proteins/*genetics ; Ribosomes/*genetics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 199
    Publication Date: 2013-01-19
    Description: A paper by Wearn et al. (Reports, 13 July 2012, p. 228) yields new insights on extinction debt. However, it leaves out the area dependence of the relaxation process. We show that this is not warranted on theoretical or observational grounds and that it may lead to erroneous conservation recommendations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Halley, John M -- Iwasa, Yoh -- Vokou, Despoina -- New York, N.Y. -- Science. 2013 Jan 18;339(6117):271. doi: 10.1126/science.1231438.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece. jhalley@cc.uoi.gr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23329033" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Conservation of Natural Resources ; *Ecosystem ; *Extinction, Biological ; *Trees ; *Vertebrates
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 200
    Publication Date: 2013-07-03
    Description: Wheat stem rust, caused by the fungus Puccinia graminis f. sp. tritici, afflicts bread wheat (Triticum aestivum). New virulent races collectively referred to as "Ug99" have emerged, which threaten global wheat production. The wheat gene Sr33, introgressed from the wild relative Aegilops tauschii into bread wheat, confers resistance to diverse stem rust races, including the Ug99 race group. We cloned Sr33, which encodes a coiled-coil, nucleotide-binding, leucine-rich repeat protein. Sr33 is orthologous to the barley (Hordeum vulgare) Mla mildew resistance genes that confer resistance to Blumeria graminis f. sp. hordei. The wheat Sr33 gene functions independently of RAR1, SGT1, and HSP90 chaperones. Haplotype analysis from diverse collections of Ae. tauschii placed the origin of Sr33 resistance near the southern coast of the Caspian Sea.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Periyannan, Sambasivam -- Moore, John -- Ayliffe, Michael -- Bansal, Urmil -- Wang, Xiaojing -- Huang, Li -- Deal, Karin -- Luo, Mingcheng -- Kong, Xiuying -- Bariana, Harbans -- Mago, Rohit -- McIntosh, Robert -- Dodds, Peter -- Dvorak, Jan -- Lagudah, Evans -- New York, N.Y. -- Science. 2013 Aug 16;341(6147):786-8. doi: 10.1126/science.1239028. Epub 2013 Jun 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Commonwealth Scientific and Industrial Research Organization (CSIRO) Plant Industry, Canberra, ACT 2601, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23811228" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Basidiomycota/pathogenicity ; Cloning, Molecular ; Disease Resistance/genetics ; *Genes, Plant ; Haplotypes ; Hordeum/genetics ; Hybridization, Genetic ; Molecular Chaperones/genetics/metabolism ; Molecular Sequence Data ; Mutation ; Plant Diseases/genetics/*immunology/microbiology ; Plant Proteins/chemistry/genetics/metabolism ; Plant Stems/microbiology ; Plants, Genetically Modified ; Poaceae/*genetics ; Synteny ; Triticum/*genetics/*microbiology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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