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  • Molecular Sequence Data  (63)
  • Physics
  • American Association for the Advancement of Science (AAAS)  (64)
  • Wiley-Blackwell
  • 2010-2014  (64)
  • 1980-1984
  • 1925-1929
  • 2010  (64)
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  • 2010-2014  (64)
  • 1980-1984
  • 1925-1929
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  • 1
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-01-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clery, Daniel -- New York, N.Y. -- Science. 2010 Jan 8;327(5962):142-3. doi: 10.1126/science.327.5962.142.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20056871" target="_blank"〉PubMed〈/a〉
    Keywords: Medical Oncology/*instrumentation ; Nuclear Reactors ; Particle Accelerators/*instrumentation ; Physics ; Protons/therapeutic use ; Thorium
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2010-01-02
    Description: Meiotic recombination events cluster into narrow segments of the genome, defined as hotspots. Here, we demonstrate that a major player for hotspot specification is the Prdm9 gene. First, two mouse strains that differ in hotspot usage are polymorphic for the zinc finger DNA binding array of PRDM9. Second, the human consensus PRDM9 allele is predicted to recognize the 13-mer motif enriched at human hotspots; this DNA binding specificity is verified by in vitro studies. Third, allelic variants of PRDM9 zinc fingers are significantly associated with variability in genome-wide hotspot usage among humans. Our results provide a molecular basis for the distribution of meiotic recombination in mammals, in which the binding of PRDM9 to specific DNA sequences targets the initiation of recombination at specific locations in the genome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4295902/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4295902/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baudat, F -- Buard, J -- Grey, C -- Fledel-Alon, A -- Ober, C -- Przeworski, M -- Coop, G -- de Massy, B -- 03S1/PHS HHS/ -- GM83098/GM/NIGMS NIH HHS/ -- HD21244/HD/NICHD NIH HHS/ -- HL085197/HL/NHLBI NIH HHS/ -- R01 GM083098/GM/NIGMS NIH HHS/ -- R01 HD021244/HD/NICHD NIH HHS/ -- R01 HL085197/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Feb 12;327(5967):836-40. doi: 10.1126/science.1183439. Epub 2009 Dec 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Genetique Humaine, UPR1142, CNRS, Montpellier, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20044539" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; DNA/chemistry/metabolism ; DNA Breaks, Double-Stranded ; DNA-Binding Proteins/chemistry/genetics/metabolism ; Genome ; Genome, Human ; Genotype ; Histone-Lysine N-Methyltransferase/chemistry/*genetics/*metabolism ; Humans ; Meiosis/*genetics ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; Phenotype ; *Recombination, Genetic ; Zinc Fingers/genetics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2010-08-07
    Description: For RNA viruses, rapid viral evolution and the biological similarity of closely related host species have been proposed as key determinants of the occurrence and long-term outcome of cross-species transmission. Using a data set of hundreds of rabies viruses sampled from 23 North American bat species, we present a general framework to quantify per capita rates of cross-species transmission and reconstruct historical patterns of viral establishment in new host species using molecular sequence data. These estimates demonstrate diminishing frequencies of both cross-species transmission and host shifts with increasing phylogenetic distance between bat species. Evolutionary constraints on viral host range indicate that host species barriers may trump the intrinsic mutability of RNA viruses in determining the fate of emerging host-virus interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Streicker, Daniel G -- Turmelle, Amy S -- Vonhof, Maarten J -- Kuzmin, Ivan V -- McCracken, Gary F -- Rupprecht, Charles E -- 0430418/PHS HHS/ -- New York, N.Y. -- Science. 2010 Aug 6;329(5992):676-9. doi: 10.1126/science.1188836.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Rabies Team, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA. dstrike@uga.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20689015" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bayes Theorem ; Chiroptera/*classification/genetics/*virology ; Communicable Diseases, Emerging/transmission/*veterinary/virology ; Evolution, Molecular ; Genes, Viral ; Host-Pathogen Interactions ; Likelihood Functions ; Molecular Sequence Data ; Monte Carlo Method ; Nucleocapsid Proteins/genetics ; *Phylogeny ; Rabies/transmission/*veterinary/virology ; Rabies virus/classification/genetics/*pathogenicity/physiology ; Species Specificity
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  • 4
    Publication Date: 2010-12-15
    Description: Many oomycete and fungal plant pathogens are obligate biotrophs, which extract nutrients only from living plant tissue and cannot grow apart from their hosts. Although these pathogens cause substantial crop losses, little is known about the molecular basis or evolution of obligate biotrophy. Here, we report the genome sequence of the oomycete Hyaloperonospora arabidopsidis (Hpa), an obligate biotroph and natural pathogen of Arabidopsis thaliana. In comparison with genomes of related, hemibiotrophic Phytophthora species, the Hpa genome exhibits dramatic reductions in genes encoding (i) RXLR effectors and other secreted pathogenicity proteins, (ii) enzymes for assimilation of inorganic nitrogen and sulfur, and (iii) proteins associated with zoospore formation and motility. These attributes comprise a genomic signature of evolution toward obligate biotrophy.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971456/" 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/PMC3971456/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baxter, Laura -- Tripathy, Sucheta -- Ishaque, Naveed -- Boot, Nico -- Cabral, Adriana -- Kemen, Eric -- Thines, Marco -- Ah-Fong, Audrey -- Anderson, Ryan -- Badejoko, Wole -- Bittner-Eddy, Peter -- Boore, Jeffrey L -- Chibucos, Marcus C -- Coates, Mary -- Dehal, Paramvir -- Delehaunty, Kim -- Dong, Suomeng -- Downton, Polly -- Dumas, Bernard -- Fabro, Georgina -- Fronick, Catrina -- Fuerstenberg, Susan I -- Fulton, Lucinda -- Gaulin, Elodie -- Govers, Francine -- Hughes, Linda -- Humphray, Sean -- Jiang, Rays H Y -- Judelson, Howard -- Kamoun, Sophien -- Kyung, Kim -- Meijer, Harold -- Minx, Patrick -- Morris, Paul -- Nelson, Joanne -- Phuntumart, Vipa -- Qutob, Dinah -- Rehmany, Anne -- Rougon-Cardoso, Alejandra -- Ryden, Peter -- Torto-Alalibo, Trudy -- Studholme, David -- Wang, Yuanchao -- Win, Joe -- Wood, Jo -- Clifton, Sandra W -- Rogers, Jane -- Van den Ackerveken, Guido -- Jones, Jonathan D G -- McDowell, John M -- Beynon, Jim -- Tyler, Brett M -- 079643/Wellcome Trust/United Kingdom -- BB/C509123/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E007120/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E024815/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E024882/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/F0161901/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G015244/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- EP/F500025/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- T12144/Biotechnology and Biological Sciences Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2010 Dec 10;330(6010):1549-51. doi: 10.1126/science.1195203.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21148394" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Amino Acid Sequence ; Arabidopsis/*parasitology ; Enzymes/genetics ; *Evolution, Molecular ; Gene Dosage ; Genes ; *Genome ; Host-Pathogen Interactions ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; Oomycetes/*genetics/*growth & development/pathogenicity/physiology ; Phytophthora/genetics ; Plant Diseases/*parasitology ; Polymorphism, Single Nucleotide ; Proteins/genetics ; Selection, Genetic ; Sequence Analysis, DNA ; Spores/physiology ; Synteny ; Virulence Factors/genetics
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  • 5
    Publication Date: 2010-07-31
    Description: Fanconi anemia (FA) is caused by mutations in 13 Fanc genes and renders cells hypersensitive to DNA interstrand cross-linking (ICL) agents. A central event in the FA pathway is mono-ubiquitylation of the FANCI-FANCD2 (ID) protein complex. Here, we characterize a previously unrecognized nuclease, Fanconi anemia-associated nuclease 1 (FAN1), that promotes ICL repair in a manner strictly dependent on its ability to accumulate at or near sites of DNA damage and that relies on mono-ubiquitylation of the ID complex. Thus, the mono-ubiquitylated ID complex recruits the downstream repair protein FAN1 and facilitates the repair of DNA interstrand cross-links.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Ting -- Ghosal, Gargi -- Yuan, Jingsong -- Chen, Junjie -- Huang, Jun -- New York, N.Y. -- Science. 2010 Aug 6;329(5992):693-6. doi: 10.1126/science.1192656. Epub 2010 Jul 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20671156" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cell Line ; Cell Nucleus/metabolism ; DNA/*metabolism ; DNA Damage ; *DNA Repair ; Exodeoxyribonucleases/chemistry/genetics/*metabolism ; Fanconi Anemia Complementation Group D2 Protein/*metabolism ; Fanconi Anemia Complementation Group Proteins/*metabolism ; Gene Knockdown Techniques ; HeLa Cells ; Humans ; Mitomycin/pharmacology ; Molecular Sequence Data ; Mutant Proteins/metabolism ; Protein Binding ; Ubiquitinated Proteins/metabolism ; Ubiquitination ; Zinc Fingers
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  • 6
    Publication Date: 2010-12-15
    Description: The genetics of sex determination remain mysterious in many organisms, including some that are otherwise well studied. Here we report the discovery and analysis of the mating-type locus of the model organism Dictyostelium discoideum. Three forms of a single genetic locus specify this species' three mating types: two versions of the locus are entirely different in sequence, and the third resembles a composite of the other two. Single, unrelated genes are sufficient to determine two of the mating types, whereas homologs of both these genes are required in the composite type. The key genes encode polypeptides that possess no recognizable similarity to established protein families. Sex determination in the social amoebae thus appears to use regulators that are unrelated to any others currently known.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3648785/" 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/PMC3648785/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bloomfield, Gareth -- Skelton, Jason -- Ivens, Alasdair -- Tanaka, Yoshimasa -- Kay, Robert R -- 06724/Wellcome Trust/United Kingdom -- 076964/Wellcome Trust/United Kingdom -- MC_U105115237/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2010 Dec 10;330(6010):1533-6. doi: 10.1126/science.1197423.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK. garethb@mrc-lmb.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21148389" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Dictyostelium/*genetics/growth & development/*physiology ; Gene Deletion ; *Genes, Protozoan ; Genetic Loci ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Open Reading Frames ; Peptides/chemistry/genetics/physiology ; Protozoan Proteins/chemistry/*genetics/*physiology ; Reproduction/genetics
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  • 7
    Publication Date: 2010-10-12
    Description: Lymphocyte survival during immune responses is controlled by the relative expression of pro- and anti-apoptotic molecules, regulating the magnitude, quality, and duration of the response. We investigated the consequences of deleting genes encoding the anti-apoptotic molecules Mcl1 and Bcl2l1 (Bcl-x(L)) from B cells using an inducible system synchronized with expression of activation-induced cytidine deaminase (Aicda) after immunization. This revealed Mcl1 and not Bcl2l1 to be indispensable for the formation and persistence of germinal centers (GCs). Limiting Mcl1 expression reduced the magnitude of the GC response with an equivalent, but not greater, effect on memory B cell formation and no effect on persistence. Our results identify Mcl1 as the main anti-apoptotic regulator of activated B cell survival and suggest distinct mechanisms controlling survival of GC and memory B cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2991396/" 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/PMC2991396/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vikstrom, Ingela -- Carotta, Sebastian -- Luthje, Katja -- Peperzak, Victor -- Jost, Philipp J -- Glaser, Stefan -- Busslinger, Meinrad -- Bouillet, Philippe -- Strasser, Andreas -- Nutt, Stephen L -- Tarlinton, David M -- CA43540/CA/NCI NIH HHS/ -- CA80188/CA/NCI NIH HHS/ -- R01 CA043540/CA/NCI NIH HHS/ -- R01 CA043540-22/CA/NCI NIH HHS/ -- R01 CA080188-08/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2010 Nov 19;330(6007):1095-9. doi: 10.1126/science.1191793. Epub 2010 Oct 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20929728" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibody Affinity ; B-Lymphocytes/*immunology ; Cell Survival ; Gene Deletion ; Germinal Center/cytology/*immunology ; *Immunologic Memory ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; Myeloid Cell Leukemia Sequence 1 Protein ; Proto-Oncogene Proteins c-bcl-2/genetics/*immunology ; bcl-X Protein/genetics/immunology
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  • 8
    Publication Date: 2010-07-31
    Description: During embryonic development, many organs form by extensive branching of epithelia through the formation of clefts and buds. In cleft formation, buds are delineated by the conversion of epithelial cell-cell adhesions to cell-matrix adhesions, but the mechanisms of cleft formation are not clear. We have identified Btbd7 as a dynamic regulator of branching morphogenesis. Btbd7 provides a mechanistic link between the extracellular matrix and cleft propagation through its highly focal expression leading to local regulation of Snail2 (Slug), E-cadherin, and epithelial cell motility. Inhibition experiments show that Btbd7 is required for branching of embryonic mammalian salivary glands and lungs. Hence, Btbd7 is a regulatory gene that promotes epithelial tissue remodeling and formation of branched organs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3412157/" 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/PMC3412157/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Onodera, Tomohiro -- Sakai, Takayoshi -- Hsu, Jeff Chi-feng -- Matsumoto, Kazue -- Chiorini, John A -- Yamada, Kenneth M -- ZIA DE000525-20/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Jul 30;329(5991):562-5. doi: 10.1126/science.1191880.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Cell and Developmental Biology, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892-4370, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20671187" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cadherins/metabolism ; Cell Adhesion ; Cell Line ; Cell Movement ; Dogs ; Epithelial Cells/*physiology ; Fibronectins/genetics/metabolism ; Genes, Regulator ; Lung/*embryology/metabolism ; Mice ; Mice, Inbred ICR ; Models, Biological ; Molecular Sequence Data ; *Morphogenesis ; Nuclear Proteins ; Organ Culture Techniques ; Proteins/chemistry/*genetics/*physiology ; RNA, Small Interfering ; Salivary Glands/*embryology/metabolism ; Submandibular Gland/embryology ; Transcription Factors/genetics/metabolism ; Transfection
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  • 9
    Publication Date: 2010-01-02
    Description: Mammalian meiotic recombination, which preferentially occurs at specialized sites called hotspots, ensures the orderly segregation of meiotic chromosomes and creates genetic variation among offspring. A locus on mouse chromosome 17, which controls activation of recombination at multiple distant hotspots, has been mapped within a 181-kilobase interval, three of whose genes can be eliminated as candidates. The remaining gene, Prdm9, codes for a zinc finger containing histone H3K4 trimethylase that is expressed in early meiosis and whose deficiency results in sterility in both sexes. Mus musculus exhibits five alleles of Prdm9; human populations exhibit two predominant alleles and multiple minor alleles. The identification of Prdm9 as a protein regulating mammalian recombination hotspots initiates molecular studies of this important biological control system.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2821451/" 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/PMC2821451/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Parvanov, Emil D -- Petkov, Petko M -- Paigen, Kenneth -- 076468/PHS HHS/ -- 078452/PHS HHS/ -- 083408/PHS HHS/ -- CA 34196/CA/NCI NIH HHS/ -- GM 078643/GM/NIGMS NIH HHS/ -- P30 CA034196-26/CA/NCI NIH HHS/ -- P50 GM076468/GM/NIGMS NIH HHS/ -- P50 GM076468-030004/GM/NIGMS NIH HHS/ -- R01 GM078452/GM/NIGMS NIH HHS/ -- R01 GM078452-02/GM/NIGMS NIH HHS/ -- R01 GM078643/GM/NIGMS NIH HHS/ -- R01 GM078643-03/GM/NIGMS NIH HHS/ -- R01 GM083408/GM/NIGMS NIH HHS/ -- R01 GM083408-02/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Feb 12;327(5967):835. doi: 10.1126/science.1181495. Epub 2009 Dec 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Jackson Laboratory, Bar Harbor, ME 04609, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20044538" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Animals ; Chromosome Mapping ; Female ; Histone-Lysine N-Methyltransferase/chemistry/*genetics/metabolism ; Humans ; Male ; Meiosis/*genetics ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; *Recombination, Genetic ; Sequence Analysis, DNA ; Testis/metabolism ; Zinc Fingers
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  • 10
    Publication Date: 2010-08-28
    Description: The organized societies of ants include short-lived worker castes displaying specialized behavior and morphology and long-lived queens dedicated to reproduction. We sequenced and compared the genomes of two socially divergent ant species: Camponotus floridanus and Harpegnathos saltator. Both genomes contained high amounts of CpG, despite the presence of DNA methylation, which in non-Hymenoptera correlates with CpG depletion. Comparison of gene expression in different castes identified up-regulation of telomerase and sirtuin deacetylases in longer-lived H. saltator reproductives, caste-specific expression of microRNAs and SMYD histone methyltransferases, and differential regulation of genes implicated in neuronal function and chemical communication. Our findings provide clues on the molecular differences between castes in these two ants and establish a new experimental model to study epigenetics in aging and behavior.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3772619/" 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/PMC3772619/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bonasio, Roberto -- Zhang, Guojie -- Ye, Chaoyang -- Mutti, Navdeep S -- Fang, Xiaodong -- Qin, Nan -- Donahue, Greg -- Yang, Pengcheng -- Li, Qiye -- Li, Cai -- Zhang, Pei -- Huang, Zhiyong -- Berger, Shelley L -- Reinberg, Danny -- Wang, Jun -- Liebig, Jurgen -- 2009005/Howard Hughes Medical Institute/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Aug 27;329(5995):1068-71. doi: 10.1126/science.1192428.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, New York University School of Medicine, 522 First Avenue, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20798317" target="_blank"〉PubMed〈/a〉
    Keywords: Aging/genetics ; Amino Acid Sequence ; Animals ; Ants/classification/*genetics/physiology ; Behavior, Animal ; DNA/chemistry/genetics ; Dinucleoside Phosphates/analysis ; *Epigenesis, Genetic ; Gene Expression Profiling ; Gene Expression Regulation ; *Genes, Insect ; *Genome ; Group III Histone Deacetylases/genetics/metabolism ; Hydrocarbons/metabolism ; Insect Proteins/chemistry/*genetics/metabolism ; MicroRNAs/genetics ; Molecular Sequence Data ; Protein Methyltransferases/genetics/metabolism ; Proteome ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Social Behavior ; Species Specificity ; Telomerase/genetics/metabolism
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  • 11
    Publication Date: 2010-08-14
    Description: A hallmark of mitosis is the appearance of high levels of histone phosphorylation, yet the roles of these modifications remain largely unknown. Here, we demonstrate that histone H3 phosphorylated at threonine 3 is directly recognized by an evolutionarily conserved binding pocket in the BIR domain of Survivin, which is a member of the chromosomal passenger complex (CPC). This binding mediates recruitment of the CPC to chromosomes and the resulting activation of its kinase subunit Aurora B. Consistently, modulation of the kinase activity of Haspin, which phosphorylates H3T3, leads to defects in the Aurora B-dependent processes of spindle assembly and inhibition of nuclear reformation. These findings establish a direct cellular role for mitotic histone H3T3 phosphorylation, which is read and translated by the CPC to ensure accurate cell division.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3177562/" 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/PMC3177562/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kelly, Alexander E -- Ghenoiu, Cristina -- Xue, John Z -- Zierhut, Christian -- Kimura, Hiroshi -- Funabiki, Hironori -- GM075249/GM/NIGMS NIH HHS/ -- R01 GM075249/GM/NIGMS NIH HHS/ -- R01 GM075249-01/GM/NIGMS NIH HHS/ -- R01 GM075249-02/GM/NIGMS NIH HHS/ -- R01 GM075249-03/GM/NIGMS NIH HHS/ -- R01 GM075249-04/GM/NIGMS NIH HHS/ -- R01 GM075249-05/GM/NIGMS NIH HHS/ -- R01 GM075249-05S1/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Oct 8;330(6001):235-9. doi: 10.1126/science.1189505. Epub 2010 Aug 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA. akelly@rockefeller.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20705815" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Aurora Kinases ; Cell Division ; Centromere/metabolism ; Chromatin/metabolism ; Chromosomal Proteins, Non-Histone/metabolism ; Chromosomes/*metabolism ; Enzyme Activation ; Histones/*metabolism ; *Mitosis ; Molecular Sequence Data ; Phosphorylation ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein-Serine-Threonine Kinases/*metabolism ; Spindle Apparatus/metabolism ; Threonine/metabolism ; Xenopus Proteins/chemistry/*metabolism ; Xenopus laevis
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  • 12
    Publication Date: 2010-03-27
    Description: Shelterin is an essential telomeric protein complex that prevents DNA damage signaling and DNA repair at mammalian chromosome ends. Here we report on the role of the TRF2-interacting factor Rap1, a conserved shelterin subunit of unknown function. We removed Rap1 from mouse telomeres either through gene deletion or by replacing TRF2 with a mutant that does not bind Rap1. Rap1 was dispensable for the essential functions of TRF2--repression of ATM kinase signaling and nonhomologous end joining (NHEJ)--and mice lacking telomeric Rap1 were viable and fertile. However, Rap1 was critical for the repression of homology-directed repair (HDR), which can alter telomere length. The data reveal that HDR at telomeres can take place in the absence of DNA damage foci and underscore the functional compartmentalization within shelterin.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2864730/" 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/PMC2864730/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sfeir, Agnel -- Kabir, Shaheen -- van Overbeek, Megan -- Celli, Giulia B -- de Lange, Titia -- AG016642/AG/NIA NIH HHS/ -- GM049046/GM/NIGMS NIH HHS/ -- R01 AG016642/AG/NIA NIH HHS/ -- R01 AG016642-01/AG/NIA NIH HHS/ -- R01 AG016642-02/AG/NIA NIH HHS/ -- R01 AG016642-03/AG/NIA NIH HHS/ -- R01 AG016642-04/AG/NIA NIH HHS/ -- R01 AG016642-05/AG/NIA NIH HHS/ -- R01 AG016642-06/AG/NIA NIH HHS/ -- R01 AG016642-07/AG/NIA NIH HHS/ -- R01 AG016642-08/AG/NIA NIH HHS/ -- R01 AG016642-09/AG/NIA NIH HHS/ -- R01 AG016642-10/AG/NIA NIH HHS/ -- R01 AG016642-11/AG/NIA NIH HHS/ -- R01 GM049046/GM/NIGMS NIH HHS/ -- R01 GM049046-07/GM/NIGMS NIH HHS/ -- R01 GM049046-08/GM/NIGMS NIH HHS/ -- R01 GM049046-09/GM/NIGMS NIH HHS/ -- R01 GM049046-10/GM/NIGMS NIH HHS/ -- R01 GM049046-11/GM/NIGMS NIH HHS/ -- R01 GM049046-12/GM/NIGMS NIH HHS/ -- R37 GM049046/GM/NIGMS NIH HHS/ -- R37 GM049046-13/GM/NIGMS NIH HHS/ -- R37 GM049046-14/GM/NIGMS NIH HHS/ -- R37 GM049046-15/GM/NIGMS NIH HHS/ -- R37 GM049046-16/GM/NIGMS NIH HHS/ -- R37 GM049046-17/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Mar 26;327(5973):1657-61. doi: 10.1126/science.1185100.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20339076" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Ataxia Telangiectasia Mutated Proteins ; Cell Cycle Proteins/metabolism ; Cell Proliferation ; Cells, Cultured ; Checkpoint Kinase 2 ; *DNA Damage ; *DNA Repair ; DNA-Binding Proteins/metabolism ; Gene Deletion ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Molecular Sequence Data ; Protein-Serine-Threonine Kinases/metabolism ; Recombination, Genetic ; Signal Transduction ; Sister Chromatid Exchange ; Telomere/*genetics/metabolism ; Telomere-Binding Proteins/chemistry/*genetics/*metabolism ; Telomeric Repeat Binding Protein 2/genetics/metabolism ; Tumor Suppressor Proteins/metabolism
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  • 13
    Publication Date: 2010-02-27
    Description: Legume plants host nitrogen-fixing endosymbiotic Rhizobium bacteria in root nodules. In Medicago truncatula, the bacteria undergo an irreversible (terminal) differentiation mediated by hitherto unidentified plant factors. We demonstrated that these factors are nodule-specific cysteine-rich (NCR) peptides that are targeted to the bacteria and enter the bacterial membrane and cytosol. Obstruction of NCR transport in the dnf1-1 signal peptidase mutant correlated with the absence of terminal bacterial differentiation. On the contrary, ectopic expression of NCRs in legumes devoid of NCRs or challenge of cultured rhizobia with peptides provoked symptoms of terminal differentiation. Because NCRs resemble antimicrobial peptides, our findings reveal a previously unknown innovation of the host plant, which adopts effectors of the innate immune system for symbiosis to manipulate the cell fate of endosymbiotic bacteria.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Van de Velde, Willem -- Zehirov, Grigor -- Szatmari, Agnes -- Debreczeny, Monika -- Ishihara, Hironobu -- Kevei, Zoltan -- Farkas, Attila -- Mikulass, Kata -- Nagy, Andrea -- Tiricz, Hilda -- Satiat-Jeunemaitre, Beatrice -- Alunni, Benoit -- Bourge, Mickael -- Kucho, Ken-ichi -- Abe, Mikiko -- Kereszt, Attila -- Maroti, Gergely -- Uchiumi, Toshiki -- Kondorosi, Eva -- Mergaert, Peter -- New York, N.Y. -- Science. 2010 Feb 26;327(5969):1122-6. doi: 10.1126/science.1184057.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut des Sciences du Vegetal, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette Cedex, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20185722" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Anti-Bacterial Agents/pharmacology ; Cell Division ; Cell Membrane/metabolism ; Cytosol/metabolism ; Genes, Plant ; Lotus/genetics/metabolism/microbiology ; Medicago truncatula/genetics/*metabolism/*microbiology ; Molecular Sequence Data ; Nitrogen Fixation ; Peptides/chemistry/genetics/*metabolism/pharmacology ; Plant Proteins/chemistry/genetics/*metabolism ; Plants, Genetically Modified ; Protein Transport ; Root Nodules, Plant/metabolism/microbiology ; Sinorhizobium meliloti/*cytology/drug effects/*physiology ; *Symbiosis
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  • 14
    Publication Date: 2010-05-01
    Description: Bacteria form communities known as biofilms, which disassemble over time. In our studies outlined here, we found that, before biofilm disassembly, Bacillus subtilis produced a factor that prevented biofilm formation and could break down existing biofilms. The factor was shown to be a mixture of D-leucine, D-methionine, D-tyrosine, and D-tryptophan that could act at nanomolar concentrations. D-amino acid treatment caused the release of amyloid fibers that linked cells in the biofilm together. Mutants able to form biofilms in the presence of D-amino acids contained alterations in a protein (YqxM) required for the formation and anchoring of the fibers to the cell. D-amino acids also prevented biofilm formation by Staphylococcus aureus and Pseudomonas aeruginosa. D-amino acids are produced by many bacteria and, thus, may be a widespread signal for biofilm disassembly.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2921573/" 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/PMC2921573/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kolodkin-Gal, Ilana -- Romero, Diego -- Cao, Shugeng -- Clardy, Jon -- Kolter, Roberto -- Losick, Richard -- CA24487/CA/NCI NIH HHS/ -- GM086258/GM/NIGMS NIH HHS/ -- GM18546/GM/NIGMS NIH HHS/ -- GM58213/GM/NIGMS NIH HHS/ -- R01 GM018568/GM/NIGMS NIH HHS/ -- R01 GM018568-39/GM/NIGMS NIH HHS/ -- R01 GM058213/GM/NIGMS NIH HHS/ -- R01 GM086258/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Apr 30;328(5978):627-9. doi: 10.1126/science.1188628.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20431016" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acids/*metabolism/pharmacology ; Bacillus subtilis/*physiology ; Bacterial Proteins/chemistry/metabolism ; *Biofilms/growth & development ; Cell Wall ; Culture Media, Conditioned ; Genes, Bacterial ; Leucine/metabolism/pharmacology ; Methionine/metabolism/pharmacology ; Molecular Sequence Data ; Mutation ; Pseudomonas aeruginosa/physiology ; Staphylococcus aureus/physiology ; Stereoisomerism ; Tryptophan/metabolism/pharmacology ; Tyrosine/metabolism/pharmacology
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  • 15
    Publication Date: 2010-06-26
    Description: The heme-copper oxidases (HCOs) accomplish the key event of aerobic respiration; they couple O2 reduction and transmembrane proton pumping. To gain new insights into the still enigmatic process, we structurally characterized a C-family HCO--essential for the pathogenicity of many bacteria--that differs from the two other HCO families, A and B, that have been structurally analyzed. The x-ray structure of the C-family cbb3 oxidase from Pseudomonas stutzeri at 3.2 angstrom resolution shows an electron supply system different from families A and B. Like family-B HCOs, C HCOs have only one pathway, which conducts protons via an alternative tyrosine-histidine cross-link. Structural differences around hemes b and b3 suggest a different redox-driven proton-pumping mechanism and provide clues to explain the higher activity of family-C HCOs at low oxygen concentrations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Buschmann, Sabine -- Warkentin, Eberhard -- Xie, Hao -- Langer, Julian D -- Ermler, Ulrich -- Michel, Hartmut -- New York, N.Y. -- Science. 2010 Jul 16;329(5989):327-30. doi: 10.1126/science.1187303. Epub 2010 Jun 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Biophysik, Max-von-Laue-Strasse 3, D-60438 Frankfurt/Main, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20576851" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Catalytic Domain ; Crystallography, X-Ray ; Cytoplasm/metabolism ; Electron Transport ; Electron Transport Complex IV/*chemistry/*metabolism ; Heme/chemistry ; Histidine/chemistry ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Oxygen/metabolism ; Periplasm/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proton Pumps/*chemistry/*metabolism ; *Protons ; Pseudomonas stutzeri/*enzymology ; Tyrosine/chemistry
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  • 16
    Publication Date: 2010-02-27
    Description: CKAMP44, identified here by a proteomic approach, is a brain-specific type I transmembrane protein that associates with AMPA receptors in synaptic spines. CKAMP44 expressed in Xenopus oocytes reduced GluA1- and A2-mediated steady-state currents, but did not affect kainate- or N-methyl-D-aspartate (NMDA) receptor-mediated currents. Mouse hippocampal CA1 pyramidal neurons expressed CKAMP44 at low abundance, and overexpression of CKAMP44 led to stronger and faster AMPA receptor desensitization, slower recovery from desensitization, and a reduction in the paired-pulse ratio of AMPA currents. By contrast, dentate gyrus granule cells exhibited strong CKAMP44 expression, and CKAMP44 knockout increased the paired-pulse ratio of AMPA currents in lateral and medial perforant path-granule cell synapses. CKAMP44 thus modulates short-term plasticity at specific excitatory synapses.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉von Engelhardt, Jakob -- Mack, Volker -- Sprengel, Rolf -- Kavenstock, Netta -- Li, Ka Wan -- Stern-Bach, Yael -- Smit, August B -- Seeburg, Peter H -- Monyer, Hannah -- New York, N.Y. -- Science. 2010 Mar 19;327(5972):1518-22. doi: 10.1126/science.1184178. Epub 2010 Feb 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Clinical Neurobiology, University of Heidelberg, 6910 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20185686" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; CA1 Region, Hippocampal/metabolism ; Calcium Channels/metabolism ; Dendritic Spines/metabolism ; Dentate Gyrus/cytology/*metabolism ; Excitatory Postsynaptic Potentials ; Glutamic Acid/metabolism ; Guanylate Kinase ; Intracellular Signaling Peptides and Proteins/metabolism ; Membrane Proteins/metabolism ; Mice ; Mice, Knockout ; Miniature Postsynaptic Potentials ; Molecular Sequence Data ; Nerve Tissue Proteins/chemistry/genetics/*metabolism ; Neural Inhibition ; *Neuronal Plasticity ; Neurons/*metabolism ; Oocytes/metabolism ; Patch-Clamp Techniques ; Perforant Pathway ; Protein Interaction Domains and Motifs ; Protein Isoforms/genetics/metabolism ; Proteomics ; Pyramidal Cells/metabolism ; Receptors, AMPA/chemistry/*metabolism ; Recombinant Fusion Proteins/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Synapses/*physiology ; *Synaptic Transmission ; Xenopus laevis
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  • 17
    Publication Date: 2010-01-16
    Description: We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2849982/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2849982/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Werren, John H -- Richards, Stephen -- Desjardins, Christopher A -- Niehuis, Oliver -- Gadau, Jurgen -- Colbourne, John K -- Nasonia Genome Working Group -- Beukeboom, Leo W -- Desplan, Claude -- Elsik, Christine G -- Grimmelikhuijzen, Cornelis J P -- Kitts, Paul -- Lynch, Jeremy A -- Murphy, Terence -- Oliveira, Deodoro C S G -- Smith, Christopher D -- van de Zande, Louis -- Worley, Kim C -- Zdobnov, Evgeny M -- Aerts, Maarten -- Albert, Stefan -- Anaya, Victor H -- Anzola, Juan M -- Barchuk, Angel R -- Behura, Susanta K -- Bera, Agata N -- Berenbaum, May R -- Bertossa, Rinaldo C -- Bitondi, Marcia M G -- Bordenstein, Seth R -- Bork, Peer -- Bornberg-Bauer, Erich -- Brunain, Marleen -- Cazzamali, Giuseppe -- Chaboub, Lesley -- Chacko, Joseph -- Chavez, Dean -- Childers, Christopher P -- Choi, Jeong-Hyeon -- Clark, Michael E -- Claudianos, Charles -- Clinton, Rochelle A -- Cree, Andrew G -- Cristino, Alexandre S -- Dang, Phat M -- Darby, Alistair C -- de Graaf, Dirk C -- Devreese, Bart -- Dinh, Huyen H -- Edwards, Rachel -- Elango, Navin -- Elhaik, Eran -- Ermolaeva, Olga -- Evans, Jay D -- Foret, Sylvain -- Fowler, Gerald R -- Gerlach, Daniel -- Gibson, Joshua D -- Gilbert, Donald G -- Graur, Dan -- Grunder, Stefan -- Hagen, Darren E -- Han, Yi -- Hauser, Frank -- Hultmark, Da -- Hunter, Henry C 4th -- Hurst, Gregory D D -- Jhangian, Shalini N -- Jiang, Huaiyang -- Johnson, Reed M -- Jones, Andrew K -- Junier, Thomas -- Kadowaki, Tatsuhiko -- Kamping, Albert -- Kapustin, Yuri -- Kechavarzi, Bobak -- Kim, Jaebum -- Kim, Jay -- Kiryutin, Boris -- Koevoets, Tosca -- Kovar, Christie L -- Kriventseva, Evgenia V -- Kucharski, Robert -- Lee, Heewook -- Lee, Sandra L -- Lees, Kristin -- Lewis, Lora R -- Loehlin, David W -- Logsdon, John M Jr -- Lopez, Jacqueline A -- Lozado, Ryan J -- Maglott, Donna -- Maleszka, Ryszard -- Mayampurath, Anoop -- Mazur, Danielle J -- McClure, Marcella A -- Moore, Andrew D -- Morgan, Margaret B -- Muller, Jean -- Munoz-Torres, Monica C -- Muzny, Donna M -- Nazareth, Lynne V -- Neupert, Susanne -- Nguyen, Ngoc B -- Nunes, Francis M F -- Oakeshott, John G -- Okwuonu, Geoffrey O -- Pannebakker, Bart A -- Pejaver, Vikas R -- Peng, Zuogang -- Pratt, Stephen C -- Predel, Reinhard -- Pu, Ling-Ling -- Ranson, Hilary -- Raychoudhury, Rhitoban -- Rechtsteiner, Andreas -- Reese, Justin T -- Reid, Jeffrey G -- Riddle, Megan -- Robertson, Hugh M -- Romero-Severson, Jeanne -- Rosenberg, Miriam -- Sackton, Timothy B -- Sattelle, David B -- Schluns, Helge -- Schmitt, Thomas -- Schneider, Martina -- Schuler, Andreas -- Schurko, Andrew M -- Shuker, David M -- Simoes, Zila L P -- Sinha, Saurabh -- Smith, Zachary -- Solovyev, Victor -- Souvorov, Alexandre -- Springauf, Andreas -- Stafflinger, Elisabeth -- Stage, Deborah E -- Stanke, Mario -- Tanaka, Yoshiaki -- Telschow, Arndt -- Trent, Carol -- Vattathil, Selina -- Verhulst, Eveline C -- Viljakainen, Lumi -- Wanner, Kevin W -- Waterhouse, Robert M -- Whitfield, James B -- Wilkes, Timothy E -- Williamson, Michael -- Willis, Judith H -- Wolschin, Florian -- Wyder, Stefan -- Yamada, Takuji -- Yi, Soojin V -- Zecher, Courtney N -- Zhang, Lan -- Gibbs, Richard A -- 5R01GM070026-04/GM/NIGMS NIH HHS/ -- 5R01HG000747-14/HG/NHGRI NIH HHS/ -- 5R24GM084917-02/GM/NIGMS NIH HHS/ -- AI028309-13A2/AI/NIAID NIH HHS/ -- R01 AI055624/AI/NIAID NIH HHS/ -- R01 GM064864/GM/NIGMS NIH HHS/ -- R01 GM064864-04/GM/NIGMS NIH HHS/ -- R01 GM064864-05A2/GM/NIGMS NIH HHS/ -- R01 GM070026/GM/NIGMS NIH HHS/ -- R01 GM070026-04S1/GM/NIGMS NIH HHS/ -- R01 GM079484/GM/NIGMS NIH HHS/ -- R01 GM085163/GM/NIGMS NIH HHS/ -- R01 GM085163-01/GM/NIGMS NIH HHS/ -- R01 GM085233/GM/NIGMS NIH HHS/ -- R01 HG000747/HG/NHGRI NIH HHS/ -- R01 HG000747-14/HG/NHGRI NIH HHS/ -- R01GM064864/GM/NIGMS NIH HHS/ -- R24 GM084917/GM/NIGMS NIH HHS/ -- R24 GM084917-01/GM/NIGMS NIH HHS/ -- R24 GM084917-02/GM/NIGMS NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- U54 HG003273-03/HG/NHGRI NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Jan 15;327(5963):343-8. doi: 10.1126/science.1178028.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075255" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arthropods/parasitology ; *Biological Evolution ; DNA Methylation ; DNA Transposable Elements ; Female ; Gene Transfer, Horizontal ; Genes, Insect ; Genetic Speciation ; Genetic Variation ; *Genome, Insect ; Host-Parasite Interactions ; Insect Proteins/genetics/metabolism ; Insect Viruses/genetics ; Insects/genetics ; Male ; Molecular Sequence Data ; Quantitative Trait Loci ; Recombination, Genetic ; Sequence Analysis, DNA ; Wasp Venoms/chemistry/toxicity ; Wasps/*genetics/physiology ; Wolbachia/genetics
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  • 18
    Publication Date: 2010-11-06
    Description: Self-incompatibility in flowering plants prevents inbreeding and promotes outcrossing to generate genetic diversity. In Solanaceae, a multiallelic gene, S-locus F-box (SLF), was previously shown to encode the pollen determinant in self-incompatibility. It was postulated that an SLF allelic product specifically detoxifies its non-self S-ribonucleases (S-RNases), allelic products of the pistil determinant, inside pollen tubes via the ubiquitin-26S-proteasome system, thereby allowing compatible pollinations. However, it remained puzzling how SLF, with much lower allelic sequence diversity than S-RNase, might have the capacity to recognize a large repertoire of non-self S-RNases. We used in vivo functional assays and protein interaction assays to show that in Petunia, at least three types of divergent SLF proteins function as the pollen determinant, each recognizing a subset of non-self S-RNases. Our findings reveal a collaborative non-self recognition system in plants.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kubo, Ken-ichi -- Entani, Tetsuyuki -- Takara, Akie -- Wang, Ning -- Fields, Allison M -- Hua, Zhihua -- Toyoda, Mamiko -- Kawashima, Shin-ichi -- Ando, Toshio -- Isogai, Akira -- Kao, Teh-hui -- Takayama, Seiji -- New York, N.Y. -- Science. 2010 Nov 5;330(6005):796-9. doi: 10.1126/science.1195243.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21051632" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Crosses, Genetic ; F-Box Proteins/chemistry/genetics/*physiology ; Flowers/genetics/physiology ; Gene Expression Profiling ; Genes, Plant ; Genetic Variation ; Haplotypes ; Models, Genetic ; Molecular Sequence Data ; Petunia/*genetics/*physiology ; Plant Proteins/chemistry/genetics/*physiology ; Plants, Genetically Modified ; Pollen/*genetics/*physiology ; Pollen Tube/physiology ; Pollination ; Protein Interaction Mapping ; Ribonucleases/genetics/*metabolism ; Self-Fertilization ; Transgenes
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  • 19
    Publication Date: 2010-01-23
    Description: Current methods for differentiating isolates of predominant lineages of pathogenic bacteria often do not provide sufficient resolution to define precise relationships. Here, we describe a high-throughput genomics approach that provides a high-resolution view of the epidemiology and microevolution of a dominant strain of methicillin-resistant Staphylococcus aureus (MRSA). This approach reveals the global geographic structure within the lineage, its intercontinental transmission through four decades, and the potential to trace person-to-person transmission within a hospital environment. The ability to interrogate and resolve bacterial populations is applicable to a range of infectious diseases, as well as microbial ecology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2821690/" 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/PMC2821690/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harris, Simon R -- Feil, Edward J -- Holden, Matthew T G -- Quail, Michael A -- Nickerson, Emma K -- Chantratita, Narisara -- Gardete, Susana -- Tavares, Ana -- Day, Nick -- Lindsay, Jodi A -- Edgeworth, Jonathan D -- de Lencastre, Herminia -- Parkhill, Julian -- Peacock, Sharon J -- Bentley, Stephen D -- 076964/Wellcome Trust/United Kingdom -- Department of Health/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2010 Jan 22;327(5964):469-74. doi: 10.1126/science.1182395.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 15A, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20093474" target="_blank"〉PubMed〈/a〉
    Keywords: Asia/epidemiology ; Bacterial Typing Techniques ; Cross Infection/epidemiology/*microbiology/transmission ; Europe/epidemiology ; Evolution, Molecular ; *Genome, Bacterial ; Genomics/methods ; Humans ; Likelihood Functions ; Methicillin-Resistant Staphylococcus aureus/*classification/*genetics/isolation & ; purification ; Molecular Epidemiology ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; South America/epidemiology ; Staphylococcal Infections/epidemiology/*microbiology/transmission ; Time Factors ; United States/epidemiology
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  • 20
    Publication Date: 2010-11-26
    Description: Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760481/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760481/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Denoeud, France -- Henriet, Simon -- Mungpakdee, Sutada -- Aury, Jean-Marc -- Da Silva, Corinne -- Brinkmann, Henner -- Mikhaleva, Jana -- Olsen, Lisbeth Charlotte -- Jubin, Claire -- Canestro, Cristian -- Bouquet, Jean-Marie -- Danks, Gemma -- Poulain, Julie -- Campsteijn, Coen -- Adamski, Marcin -- Cross, Ismael -- Yadetie, Fekadu -- Muffato, Matthieu -- Louis, Alexandra -- Butcher, Stephen -- Tsagkogeorga, Georgia -- Konrad, Anke -- Singh, Sarabdeep -- Jensen, Marit Flo -- Huynh Cong, Evelyne -- Eikeseth-Otteraa, Helen -- Noel, Benjamin -- Anthouard, Veronique -- Porcel, Betina M -- Kachouri-Lafond, Rym -- Nishino, Atsuo -- Ugolini, Matteo -- Chourrout, Pascal -- Nishida, Hiroki -- Aasland, Rein -- Huzurbazar, Snehalata -- Westhof, Eric -- Delsuc, Frederic -- Lehrach, Hans -- Reinhardt, Richard -- Weissenbach, Jean -- Roy, Scott W -- Artiguenave, Francois -- Postlethwait, John H -- Manak, J Robert -- Thompson, Eric M -- Jaillon, Olivier -- Du Pasquier, Louis -- Boudinot, Pierre -- Liberles, David A -- Volff, Jean-Nicolas -- Philippe, Herve -- Lenhard, Boris -- Roest Crollius, Hugues -- Wincker, Patrick -- Chourrout, Daniel -- Z01 LM000073-12/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Dec 3;330(6009):1381-5. doi: 10.1126/science.1194167. Epub 2010 Nov 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Commissariat a l'Energie Atomique, Institut de Genomique, Genoscope, Evry, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21097902" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; DNA Transposable Elements ; DNA, Intergenic ; Exons ; Gene Order ; Genes, Duplicate ; Genes, Homeobox ; *Genome ; Introns ; Invertebrates/classification/genetics ; Molecular Sequence Data ; Recombination, Genetic ; Spliceosomes/metabolism ; Synteny ; Urochordata/anatomy & histology/classification/*genetics/immunology ; Vertebrates/classification/genetics
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  • 21
    Publication Date: 2010-08-26
    Description: The biological effects and expected fate of the vast amount of oil in the Gulf of Mexico from the Deepwater Horizon blowout are unknown owing to the depth and magnitude of this event. Here, we report that the dispersed hydrocarbon plume stimulated deep-sea indigenous gamma-Proteobacteria that are closely related to known petroleum degraders. Hydrocarbon-degrading genes coincided with the concentration of various oil contaminants. Changes in hydrocarbon composition with distance from the source and incubation experiments with environmental isolates demonstrated faster-than-expected hydrocarbon biodegradation rates at 5 degrees C. Based on these results, the potential exists for intrinsic bioremediation of the oil plume in the deep-water column without substantial oxygen drawdown.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hazen, Terry C -- Dubinsky, Eric A -- DeSantis, Todd Z -- Andersen, Gary L -- Piceno, Yvette M -- Singh, Navjeet -- Jansson, Janet K -- Probst, Alexander -- Borglin, Sharon E -- Fortney, Julian L -- Stringfellow, William T -- Bill, Markus -- Conrad, Mark E -- Tom, Lauren M -- Chavarria, Krystle L -- Alusi, Thana R -- Lamendella, Regina -- Joyner, Dominique C -- Spier, Chelsea -- Baelum, Jacob -- Auer, Manfred -- Zemla, Marcin L -- Chakraborty, Romy -- Sonnenthal, Eric L -- D'haeseleer, Patrik -- Holman, Hoi-Ying N -- Osman, Shariff -- Lu, Zhenmei -- Van Nostrand, Joy D -- Deng, Ye -- Zhou, Jizhong -- Mason, Olivia U -- New York, N.Y. -- Science. 2010 Oct 8;330(6001):204-8. doi: 10.1126/science.1195979. Epub 2010 Aug 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MS 70A-3317, One Cyclotron Road, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. tchazen@lbl.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20736401" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodegradation, Environmental ; Biomass ; Colony Count, Microbial ; *Environmental Pollution ; Fatty Acids/analysis ; Gammaproteobacteria/classification/growth & development/isolation & ; purification/*metabolism ; Genes, Bacterial ; Genes, rRNA ; Hydrocarbons/*metabolism ; Molecular Sequence Data ; Oceanospirillaceae/classification/genetics/isolation & purification/*metabolism ; Petroleum/*metabolism ; Phospholipids/analysis ; Phylogeny ; Seawater/*microbiology
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  • 22
    Publication Date: 2010-07-03
    Description: Proton-pumping respiratory complex I is one of the largest and most complicated membrane protein complexes. Its function is critical for efficient energy supply in aerobic cells, and malfunctions are implicated in many neurodegenerative disorders. Here, we report an x-ray crystallographic analysis of mitochondrial complex I. The positions of all iron-sulfur clusters relative to the membrane arm were determined in the complete enzyme complex. The ubiquinone reduction site resides close to 30 angstroms above the membrane domain. The arrangement of functional modules suggests conformational coupling of redox chemistry with proton pumping and essentially excludes direct mechanisms. We suggest that a approximately 60-angstrom-long helical transmission element is critical for transducing conformational energy to proton-pumping elements in the distal module of the membrane arm.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hunte, Carola -- Zickermann, Volker -- Brandt, Ulrich -- New York, N.Y. -- Science. 2010 Jul 23;329(5990):448-51. doi: 10.1126/science.1191046. Epub 2010 Jul 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Biochemistry and Molecular Biology, Centre for Biological Signalling Studies (BIOSS), University of Freiburg, D-79104 Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20595580" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Electron Transport Complex I/*chemistry/*metabolism ; Fungal Proteins/chemistry/metabolism ; Iron/chemistry ; Mitochondria/enzymology ; Mitochondrial Proteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Protons ; Sulfur/chemistry ; Ubiquinone/chemistry/metabolism ; Yarrowia/*enzymology
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  • 23
    Publication Date: 2010-04-03
    Description: Semiconservative DNA replication ensures the faithful duplication of genetic information during cell divisions. However, how epigenetic information carried by histone modifications propagates through mitotic divisions remains elusive. To address this question, the DNA replication-dependent nucleosome partition pattern must be clarified. Here, we report significant amounts of H3.3-H4 tetramers split in vivo, whereas most H3.1-H4 tetramers remained intact. Inhibiting DNA replication-dependent deposition greatly reduced the level of splitting events, which suggests that (i) the replication-independent H3.3 deposition pathway proceeds largely by cooperatively incorporating two new H3.3-H4 dimers and (ii) the majority of splitting events occurred during replication-dependent deposition. Our results support the idea that "silent" histone modifications within large heterochromatic regions are maintained by copying modifications from neighboring preexisting histones without the need for H3-H4 splitting events.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Mo -- Long, Chengzu -- Chen, Xiuzhen -- Huang, Chang -- Chen, She -- Zhu, Bing -- New York, N.Y. -- Science. 2010 Apr 2;328(5974):94-8. doi: 10.1126/science.1178994.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate Program, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360108" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Aphidicolin/pharmacology ; Cell Cycle ; Chromatin/metabolism ; *Chromatin Assembly and Disassembly ; *DNA Replication ; Epigenesis, Genetic ; HeLa Cells ; Heterochromatin/metabolism ; Histones/*chemistry/*metabolism ; Humans ; Hydroxyurea/pharmacology ; Mass Spectrometry ; Molecular Sequence Data ; Nucleosomes/*metabolism ; Protein Multimerization ; S Phase ; Transfection
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  • 24
    Publication Date: 2010-03-27
    Description: The 2009 H1N1 swine flu is the first influenza pandemic in decades. The crystal structure of the hemagglutinin from the A/California/04/2009 H1N1 virus shows that its antigenic structure, particularly within the Sa antigenic site, is extremely similar to those of human H1N1 viruses circulating early in the 20th century. The cocrystal structure of the 1918 hemagglutinin with 2D1, an antibody from a survivor of the 1918 Spanish flu that neutralizes both 1918 and 2009 H1N1 viruses, reveals an epitope that is conserved in both pandemic viruses. Thus, antigenic similarity between the 2009 and 1918-like viruses provides an explanation for the age-related immunity to the current influenza pandemic.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2897825/" 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/PMC2897825/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Rui -- Ekiert, Damian C -- Krause, Jens C -- Hai, Rong -- Crowe, James E Jr -- Wilson, Ian A -- AI057157/AI/NIAID NIH HHS/ -- AI058113/AI/NIAID NIH HHS/ -- GM080209/GM/NIGMS NIH HHS/ -- P01 AI058113/AI/NIAID NIH HHS/ -- P01 AI058113-050002/AI/NIAID NIH HHS/ -- T32 GM080209/GM/NIGMS NIH HHS/ -- T32 GM080209-01A2/GM/NIGMS NIH HHS/ -- U54 AI057157/AI/NIAID NIH HHS/ -- U54 AI057157-06/AI/NIAID NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Apr 16;328(5976):357-60. doi: 10.1126/science.1186430. Epub 2010 Mar 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20339031" target="_blank"〉PubMed〈/a〉
    Keywords: Age Factors ; Amino Acid Sequence ; Antibodies, Neutralizing/chemistry/immunology ; Antibodies, Viral/chemistry/immunology ; Antigenic Variation ; Cross Reactions ; Crystallography, X-Ray ; Disease Outbreaks ; Epitopes ; Glycosylation ; Hemagglutinin Glycoproteins, Influenza Virus/*chemistry/*immunology ; Hemagglutinins, Viral/*chemistry/*immunology ; Humans ; Immunoglobulin Fab Fragments/chemistry/immunology ; Influenza A Virus, H1N1 Subtype/*immunology ; Influenza Vaccines/immunology ; Influenza, Human/epidemiology/*immunology/virology ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation
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  • 25
    Publication Date: 2010-02-06
    Description: The cell surface receptor CED-1 mediates apoptotic cell recognition by phagocytic cells, enabling cell corpse clearance in Caenorhabditis elegans. Here, we found that the C. elegans intracellular protein sorting complex, retromer, was required for cell corpse clearance by mediating the recycling of CED-1. Retromer was recruited to the surfaces of phagosomes containing cell corpses, and its loss of function caused defective cell corpse removal. The retromer probably acted through direct interaction with CED-1 in the cell corpse recognition pathway. In the absence of retromer function, CED-1 associated with lysosomes and failed to recycle from phagosomes and cytosol to the plasma membrane. Thus, retromer is an essential mediator of apoptotic cell clearance by regulating phagocytic receptor(s) during cell corpse engulfment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Didi -- Xiao, Hui -- Zhang, Kai -- Wang, Bin -- Gao, Zhiyang -- Jian, Youli -- Qi, Xiaying -- Sun, Jianwei -- Miao, Long -- Yang, Chonglin -- New York, N.Y. -- Science. 2010 Mar 5;327(5970):1261-4. doi: 10.1126/science.1184840. Epub 2010 Feb 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing 100101, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20133524" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Apoptosis ; Caenorhabditis elegans/cytology/genetics/*physiology ; Caenorhabditis elegans Proteins/genetics/*metabolism ; Cell Membrane/metabolism ; Lysosomes/metabolism ; Membrane Proteins/*metabolism ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; *Phagocytosis ; Phagosomes/*metabolism ; *Protein Transport ; RNA Interference ; Recombinant Fusion Proteins/metabolism ; Sorting Nexins ; Vesicular Transport Proteins/genetics/*metabolism
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  • 26
    Publication Date: 2010-08-21
    Description: Chlorophylls are essential for light-harvesting and energy transduction in photosynthesis. Four chemically distinct varieties have been known for the past 60 years. Here we report isolation of a fifth, which we designate chlorophyll f. Its in vitro absorption (706 nanometers) and fluorescence (722 nanometers) maxima are red-shifted compared to all other chlorophylls from oxygenic phototrophs. On the basis of the optical, mass, and nuclear magnetic resonance spectra, we propose that chlorophyll f is [2-formyl]-chlorophyll a (C55H70O6N4Mg). This finding suggests that oxygenic photosynthesis can be extended further into the infrared region and may open associated bioenergy applications.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Min -- Schliep, Martin -- Willows, Robert D -- Cai, Zheng-Li -- Neilan, Brett A -- Scheer, Hugo -- New York, N.Y. -- Science. 2010 Sep 10;329(5997):1318-9. doi: 10.1126/science.1191127. Epub 2010 Aug 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of Sydney, NSW 2006, Australia. min.chen@sydney.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20724585" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriochlorophylls/*chemistry/*isolation & purification ; Cyanobacteria/*chemistry/classification/genetics/isolation & purification ; Genes, Bacterial ; Genes, rRNA ; Mass Spectrometry ; Molecular Sequence Data ; Molecular Structure ; Nuclear Magnetic Resonance, Biomolecular ; Photosynthesis ; Pigments, Biological/*chemistry/*isolation & purification ; RNA, Ribosomal, 16S/genetics ; Spectrometry, Fluorescence ; Western Australia
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  • 27
    Publication Date: 2010-12-15
    Description: Many plant pathogens, including those in the lineage of the Irish potato famine organism Phytophthora infestans, evolve by host jumps followed by specialization. However, how host jumps affect genome evolution remains largely unknown. To determine the patterns of sequence variation in the P. infestans lineage, we resequenced six genomes of four sister species. This revealed uneven evolutionary rates across genomes with genes in repeat-rich regions showing higher rates of structural polymorphisms and positive selection. These loci are enriched in genes induced in planta, implicating host adaptation in genome evolution. Unexpectedly, genes involved in epigenetic processes formed another class of rapidly evolving residents of the gene-sparse regions. These results demonstrate that dynamic repeat-rich genome compartments underpin accelerated gene evolution following host jumps in this pathogen lineage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Raffaele, Sylvain -- Farrer, Rhys A -- Cano, Liliana M -- Studholme, David J -- MacLean, Daniel -- Thines, Marco -- Jiang, Rays H Y -- Zody, Michael C -- Kunjeti, Sridhara G -- Donofrio, Nicole M -- Meyers, Blake C -- Nusbaum, Chad -- Kamoun, Sophien -- New York, N.Y. -- Science. 2010 Dec 10;330(6010):1540-3. doi: 10.1126/science.1193070.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21148391" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/genetics ; Amino Acid Sequence ; Computational Biology ; DNA Copy Number Variations ; Epistasis, Genetic ; *Evolution, Molecular ; Genes ; *Genome ; Host Specificity/*genetics ; Host-Parasite Interactions ; Lycopersicon esculentum/parasitology ; Molecular Sequence Data ; Phytophthora/classification/*genetics/pathogenicity/physiology ; Phytophthora infestans/classification/*genetics/*pathogenicity/physiology ; Plant Diseases/*parasitology ; Polymorphism, Single Nucleotide ; Proteins/chemistry/genetics/metabolism ; Selection, Genetic ; Sequence Analysis, DNA ; Solanum tuberosum/parasitology
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  • 28
    Publication Date: 2010-05-29
    Description: Horizontal gene transfer has been postulated to occur between crops to co-occurring parasitic plants, but empirical evidence has been lacking. We present evidence that an HGT event moved a nuclear monocot gene into the genome of the eudicot parasite witchweed (Striga hermonthica), which infects many grass species in Africa. Analysis of expressed sequence tags revealed that the genome of S. hermonthica contains a nuclear gene that is widely conserved among grass species but is not found in other eudicots. Phylogenetically, this gene clusters with sorghum genes, the monocot host of the parasitic weed, suggesting that nuclear genes can be captured by parasitic weeds in nature.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yoshida, Satoko -- Maruyama, Shinichiro -- Nozaki, Hisayoshi -- Shirasu, Ken -- New York, N.Y. -- Science. 2010 May 28;328(5982):1128. doi: 10.1126/science.1187145.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉RIKEN Plant Science Center, Tsurumi, Yokohama 230-0045, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20508124" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Blotting, Southern ; Cell Nucleus/genetics ; Conserved Sequence ; Crops, Agricultural/genetics ; Expressed Sequence Tags ; *Gene Transfer, Horizontal ; Genome, Plant ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics ; Poaceae/*genetics ; Sorghum/*genetics ; Striga/*genetics
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  • 29
    Publication Date: 2010-07-10
    Description: Cross-reactive neutralizing antibodies (NAbs) are found in the sera of many HIV-1-infected individuals, but the virologic basis of their neutralization remains poorly understood. We used knowledge of HIV-1 envelope structure to develop antigenically resurfaced glycoproteins specific for the structurally conserved site of initial CD4 receptor binding. These probes were used to identify sera with NAbs to the CD4-binding site (CD4bs) and to isolate individual B cells from such an HIV-1-infected donor. By expressing immunoglobulin genes from individual cells, we identified three monoclonal antibodies, including a pair of somatic variants that neutralized over 90% of circulating HIV-1 isolates. Exceptionally broad HIV-1 neutralization can be achieved with individual antibodies targeted to the functionally conserved CD4bs of glycoprotein 120, an important insight for future HIV-1 vaccine design.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965066/" 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/PMC2965066/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Xueling -- Yang, Zhi-Yong -- Li, Yuxing -- Hogerkorp, Carl-Magnus -- Schief, William R -- Seaman, Michael S -- Zhou, Tongqing -- Schmidt, Stephen D -- Wu, Lan -- Xu, Ling -- Longo, Nancy S -- McKee, Krisha -- O'Dell, Sijy -- Louder, Mark K -- Wycuff, Diane L -- Feng, Yu -- Nason, Martha -- Doria-Rose, Nicole -- Connors, Mark -- Kwong, Peter D -- Roederer, Mario -- Wyatt, Richard T -- Nabel, Gary J -- Mascola, John R -- Z99 AI999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Aug 13;329(5993):856-61. doi: 10.1126/science.1187659. Epub 2010 Jul 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20616233" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines ; Antibodies, Monoclonal/*immunology/isolation & purification ; Antibodies, Neutralizing/*immunology/isolation & purification ; Antibody Specificity ; Antigens, CD4/immunology/metabolism ; B-Lymphocytes/immunology ; Binding Sites, Antibody ; Cross Reactions ; Drug Design ; Enzyme-Linked Immunosorbent Assay ; Epitopes/immunology ; Genes, Immunoglobulin Heavy Chain ; Genes, Immunoglobulin Light Chain ; HIV Antibodies/*immunology/isolation & purification ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV Infections/immunology/virology ; HIV-1/genetics/*immunology ; Humans ; Molecular Sequence Data ; Neutralization Tests ; Protein Engineering ; Recombinant Proteins/chemistry/immunology/metabolism
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  • 30
    Publication Date: 2010-06-05
    Description: Staphylococcus aureus is a major human pathogen that is resistant to numerous antibiotics in clinical use. We found two nonribosomal peptide secondary metabolites--the aureusimines, made by S. aureus--that are not antibiotics, but function as regulators of virulence factor expression and are necessary for productive infections. In vivo mouse models of bacteremia showed that strains of S. aureus unable to produce aureusimines were attenuated and/or cleared from major organs, including the spleen, liver, and heart. Targeting aureusimine synthesis may offer novel leads for anti-infective drugs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wyatt, Morgan A -- Wang, Wenliang -- Roux, Christelle M -- Beasley, Federico C -- Heinrichs, David E -- Dunman, Paul M -- Magarvey, Nathan A -- MOP-38002/Canadian Institutes of Health Research/Canada -- RA107380/RA/ARRA NIH HHS/ -- New York, N.Y. -- Science. 2010 Jul 16;329(5989):294-6. doi: 10.1126/science.1188888. Epub 2010 Jun 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biomedical Sciences, M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20522739" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bacteremia/microbiology ; Dipeptides/chemistry/isolation & purification ; Heart/microbiology ; Hemolysis ; Liver/microbiology ; Mice ; Mice, Inbred BALB C ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Peptide Biosynthesis, Nucleic Acid-Independent ; Peptide Synthases/chemistry/genetics/metabolism ; Pyrazines/chemistry/*metabolism ; Spleen/microbiology ; Staphylococcal Infections/*microbiology ; Staphylococcus aureus/genetics/isolation & ; purification/*metabolism/*pathogenicity ; Virulence Factors/*metabolism
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  • 31
    Publication Date: 2010-05-01
    Description: Carotenoids are colored compounds produced by plants, fungi, and microorganisms and are required in the diet of most animals for oxidation control or light detection. Pea aphids display a red-green color polymorphism, which influences their susceptibility to natural enemies, and the carotenoid torulene occurs only in red individuals. Unexpectedly, we found that the aphid genome itself encodes multiple enzymes for carotenoid biosynthesis. Phylogenetic analyses show that these aphid genes are derived from fungal genes, which have been integrated into the genome and duplicated. Red individuals have a 30-kilobase region, encoding a single carotenoid desaturase that is absent from green individuals. A mutation causing an amino acid replacement in this desaturase results in loss of torulene and of red body color. Thus, aphids are animals that make their own carotenoids.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moran, Nancy A -- Jarvik, Tyler -- New York, N.Y. -- Science. 2010 Apr 30;328(5978):624-7. doi: 10.1126/science.1187113.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, 1041 East Lowell Street, University of Arizona, Tucson, AZ 85721, USA. nancy.moran@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20431015" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Aphids/*genetics/*metabolism/microbiology ; Carotenoids/analysis/*biosynthesis/genetics ; Crosses, Genetic ; Fungi/genetics ; Gene Duplication ; *Gene Transfer, Horizontal ; *Genes, Fungal ; *Genes, Insect ; Genome, Insect ; Heterozygote ; Molecular Sequence Data ; Mutation ; Oxidoreductases/genetics ; Phylogeny ; Pigmentation/genetics ; Pigments, Biological/chemistry ; Polymorphism, Genetic ; Sequence Analysis, DNA
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  • 32
    Publication Date: 2010-08-28
    Description: Somatic loss of wild-type alleles can produce disease traits such as neoplasia. Conversely, somatic loss of disease-causing mutations can revert phenotypes; however, these events are infrequently observed. Here we show that ichthyosis with confetti, a severe, sporadic skin disease in humans, is associated with thousands of revertant clones of normal skin that arise from loss of heterozygosity on chromosome 17q via mitotic recombination. This allowed us to map and identify disease-causing mutations in the gene encoding keratin 10 (KRT10); all result in frameshifts into the same alternative reading frame, producing an arginine-rich C-terminal peptide that redirects keratin 10 from the cytokeratin filament network to the nucleolus. The high frequency of somatic reversion in ichthyosis with confetti suggests that revertant stem cell clones are under strong positive selection and/or that the rate of mitotic recombination is elevated in individuals with this disorder.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3085938/" 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/PMC3085938/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Choate, Keith A -- Lu, Yin -- Zhou, Jing -- Choi, Murim -- Elias, Peter M -- Farhi, Anita -- Nelson-Williams, Carol -- Crumrine, Debra -- Williams, Mary L -- Nopper, Amy J -- Bree, Alanna -- Milstone, Leonard M -- Lifton, Richard P -- K08 AR056305/AR/NIAMS NIH HHS/ -- K08 AR056305-01/AR/NIAMS NIH HHS/ -- K08 AR056305-02/AR/NIAMS NIH HHS/ -- K08 AR056305-03/AR/NIAMS NIH HHS/ -- K08 AR056305-04/AR/NIAMS NIH HHS/ -- T32 AR007016/AR/NIAMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Oct 1;330(6000):94-7. doi: 10.1126/science.1192280. Epub 2010 Aug 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Dermatology, 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/20798280" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cell Nucleolus/metabolism ; Chromosome Mapping ; Chromosomes, Human, Pair 17/*genetics ; Female ; *Frameshift Mutation ; Humans ; Ichthyosiform Erythroderma, Congenital/*genetics/pathology ; Intermediate Filaments/metabolism/ultrastructure ; Keratin-10/chemistry/*genetics/metabolism ; Keratins/metabolism ; Loss of Heterozygosity ; Male ; *Mitosis ; Molecular Sequence Data ; Mosaicism ; Mutant Proteins/chemistry/genetics/metabolism ; *Recombination, Genetic ; Selection, Genetic ; Skin/pathology
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  • 33
    Publication Date: 2010-07-10
    Description: Recent studies have shown that some plants and animals harbor microbial symbionts that protect them against natural enemies. Here we demonstrate that a maternally transmitted bacterium, Spiroplasma, protects Drosophila neotestacea against the sterilizing effects of a parasitic nematode, both in the laboratory and the field. This nematode parasitizes D. neotestacea at high frequencies in natural populations, and, until recently, almost all infections resulted in complete sterility. Several lines of evidence suggest that Spiroplasma is spreading in North American populations of D. neotestacea and that a major adaptive change to a symbiont-based mode of defense is under way. These findings demonstrate the profound and potentially rapid effects of defensive symbionts, which are increasingly recognized as major players in the ecology of species interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jaenike, John -- Unckless, Robert -- Cockburn, Sarah N -- Boelio, Lisa M -- Perlman, Steve J -- New York, N.Y. -- Science. 2010 Jul 9;329(5988):212-5. doi: 10.1126/science.1188235.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Rochester, Rochester, NY 14627, USA. john.jaenike@rochester.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20616278" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; Animals ; DNA, Mitochondrial/genetics ; Drosophila/genetics/microbiology/parasitology/*physiology ; Female ; Fertility ; Haplotypes ; Host-Parasite Interactions ; Molecular Sequence Data ; Polymerase Chain Reaction ; Spiroplasma/isolation & purification/*physiology ; *Symbiosis ; Tylenchida/anatomy & histology/*physiology ; Wolbachia/isolation & purification/physiology
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  • 34
    Publication Date: 2010-05-29
    Description: High-conductance voltage- and Ca2+-activated K+ (BK) channels encode negative feedback regulation of membrane voltage and Ca2+ signaling, playing a central role in numerous physiological processes. We determined the x-ray structure of the human BK Ca2+ gating apparatus at a resolution of 3.0 angstroms and deduced its tetrameric assembly by solving a 6 angstrom resolution structure of a Na+-activated homolog. Two tandem C-terminal regulator of K+ conductance (RCK) domains from each of four channel subunits form a 350-kilodalton gating ring at the intracellular membrane surface. A sequence of aspartic amino acids that is known as the Ca2+ bowl, and is located within the second of the tandem RCK domains, creates four Ca2+ binding sites on the outer perimeter of the gating ring at the "assembly interface" between RCK domains. Functionally important mutations cluster near the Ca2+ bowl, near the "flexible interface" between RCK domains, and on the surface of the gating ring that faces the voltage sensors. The structure suggests that the Ca2+ gating ring, in addition to regulating the pore directly, may also modulate the voltage sensor.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022345/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022345/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yuan, Peng -- Leonetti, Manuel D -- Pico, Alexander R -- Hsiung, Yichun -- MacKinnon, Roderick -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 GM043949/GM/NIGMS NIH HHS/ -- R01 GM043949-20/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Jul 9;329(5988):182-6. doi: 10.1126/science.1190414. Epub 2010 May 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20508092" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Calcium/*metabolism ; Crystallography, X-Ray ; Humans ; *Ion Channel Gating ; Large-Conductance Calcium-Activated Potassium Channel alpha ; Subunits/*chemistry/genetics/*metabolism ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Patch-Clamp Techniques ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Sodium/metabolism
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  • 35
    Publication Date: 2010-12-04
    Description: Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. Although these six elements make up nucleic acids, proteins, and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here, we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, California, that is able to substitute arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical importance.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wolfe-Simon, Felisa -- Switzer Blum, Jodi -- Kulp, Thomas R -- Gordon, Gwyneth W -- Hoeft, Shelley E -- Pett-Ridge, Jennifer -- Stolz, John F -- Webb, Samuel M -- Weber, Peter K -- Davies, Paul C W -- Anbar, Ariel D -- Oremland, Ronald S -- New York, N.Y. -- Science. 2011 Jun 3;332(6034):1163-6. doi: 10.1126/science.1197258. Epub 2010 Dec 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉NASA Astrobiology Institute, USA. felisawolfesimon@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21127214" target="_blank"〉PubMed〈/a〉
    Keywords: Arsenates/analysis/*metabolism ; Arsenic/analysis/chemistry/*metabolism ; Bacterial Proteins/analysis/metabolism ; California ; Culture Media ; DNA, Bacterial/*chemistry/metabolism ; Geologic Sediments/microbiology ; Halomonadaceae/cytology/*growth & development/isolation & ; purification/*metabolism ; Molecular Sequence Data ; Phosphates/analysis/*metabolism ; Phosphorus/analysis/chemistry/*metabolism ; Spectrometry, Mass, Secondary Ion ; Vacuoles/ultrastructure ; Water Microbiology
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  • 36
    Publication Date: 2010-01-02
    Description: Many bacterial cells contain proteinaceous microcompartments that act as simple organelles by sequestering specific metabolic processes involving volatile or toxic metabolites. Here we report the three-dimensional (3D) crystal structures, with resolutions between 1.65 and 2.5 angstroms, of the four homologous proteins (EutS, EutL, EutK, and EutM) that are thought to be the major shell constituents of a functionally complex ethanolamine utilization (Eut) microcompartment. The Eut microcompartment is used to sequester the metabolism of ethanolamine in bacteria such as Escherichia coli and Salmonella enterica. The four Eut shell proteins share an overall similar 3D fold, but they have distinguishing structural features that help explain the specific roles they play in the microcompartment. For example, EutL undergoes a conformational change that is probably involved in gating molecular transport through shell protein pores, whereas structural evidence suggests that EutK might bind a nucleic acid component. Together these structures give mechanistic insight into bacterial microcompartments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tanaka, Shiho -- Sawaya, Michael R -- Yeates, Todd O -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Jan 1;327(5961):81-4. doi: 10.1126/science.1179513.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20044574" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Cell Compartmentation ; Crystallography, X-Ray ; Escherichia coli K12/*chemistry/*metabolism/ultrastructure ; Escherichia coli Proteins/*chemistry/metabolism ; Ethanolamine/*metabolism ; Metabolic Networks and Pathways ; Models, Molecular ; Molecular Sequence Data ; Polyproteins/*chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism
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  • 37
    Publication Date: 2010-04-03
    Description: Voltage sensors regulate the conformations of voltage-dependent ion channels and enzymes. Their nearly switchlike response as a function of membrane voltage comes from the movement of positively charged amino acids, arginine or lysine, across the membrane field. We used mutations with natural and unnatural amino acids, electrophysiological recordings, and x-ray crystallography to identify a charge transfer center in voltage sensors that facilitates this movement. This center consists of a rigid cyclic "cap" and two negatively charged amino acids to interact with a positive charge. Specific mutations induce a preference for lysine relative to arginine. By placing lysine at specific locations, the voltage sensor can be stabilized in different conformations, which enables a dissection of voltage sensor movements and their relation to ion channel opening.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2869078/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2869078/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tao, Xiao -- Lee, Alice -- Limapichat, Walrati -- Dougherty, Dennis A -- MacKinnon, Roderick -- GM43949/GM/NIGMS NIH HHS/ -- NS 34407/NS/NINDS NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 GM043949/GM/NIGMS NIH HHS/ -- R01 GM043949-20/GM/NIGMS NIH HHS/ -- R37 NS034407/NS/NINDS NIH HHS/ -- R37 NS034407-15/NS/NINDS NIH HHS/ -- R37 NS034407-15S1/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Apr 2;328(5974):67-73. doi: 10.1126/science.1185954.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360102" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Arginine/chemistry ; Binding Sites ; Crystallography, X-Ray ; Electric Capacitance ; *Ion Channel Gating ; Kv1.2 Potassium Channel/*chemistry/*metabolism ; Lysine/chemistry ; Models, Molecular ; Molecular Sequence Data ; Patch-Clamp Techniques ; Phenylalanine/chemistry ; Protein Conformation ; Rats ; Recombinant Fusion Proteins/chemistry/metabolism ; Shab Potassium Channels/*chemistry/*metabolism ; Shaker Superfamily of Potassium Channels/chemistry/metabolism ; Tryptophan/chemistry ; Xenopus laevis
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  • 38
    Publication Date: 2010-07-10
    Description: During HIV-1 infection, antibodies are generated against the region of the viral gp120 envelope glycoprotein that binds CD4, the primary receptor for HIV-1. Among these antibodies, VRC01 achieves broad neutralization of diverse viral strains. We determined the crystal structure of VRC01 in complex with a human immunodeficiency virus HIV-1 gp120 core. VRC01 partially mimics CD4 interaction with gp120. A shift from the CD4-defined orientation, however, focuses VRC01 onto the vulnerable site of initial CD4 attachment, allowing it to overcome the glycan and conformational masking that diminishes the neutralization potency of most CD4-binding-site antibodies. To achieve this recognition, VRC01 contacts gp120 mainly through immunoglobulin V-gene regions substantially altered from their genomic precursors. Partial receptor mimicry and extensive affinity maturation thus facilitate neutralization of HIV-1 by natural human antibodies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981354/" 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/PMC2981354/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Tongqing -- Georgiev, Ivelin -- Wu, Xueling -- Yang, Zhi-Yong -- Dai, Kaifan -- Finzi, Andres -- Kwon, Young Do -- Scheid, Johannes F -- Shi, Wei -- Xu, Ling -- Yang, Yongping -- Zhu, Jiang -- Nussenzweig, Michel C -- Sodroski, Joseph -- Shapiro, Lawrence -- Nabel, Gary J -- Mascola, John R -- Kwong, Peter D -- P30 AI060354/AI/NIAID NIH HHS/ -- Z99 AI999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Aug 13;329(5993):811-7. doi: 10.1126/science.1192819. Epub 2010 Jul 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20616231" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines ; Amino Acid Sequence ; Antibodies, Neutralizing/*chemistry/*immunology ; Antibody Affinity ; Antigenic Variation ; Antigens, CD4/chemistry/immunology/metabolism ; Base Sequence ; Binding Sites, Antibody ; Crystallography, X-Ray ; Epitopes/immunology ; HIV Antibodies/*chemistry/*immunology ; HIV Envelope Protein gp120/chemistry/genetics/*immunology ; HIV-1/*immunology ; Humans ; Immunoglobulin Fab Fragments/chemistry/immunology/metabolism ; Models, Molecular ; Molecular Mimicry ; Molecular Sequence Data ; Neutralization Tests ; Protein Conformation ; Protein Structure, Tertiary
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  • 39
    Publication Date: 2010-09-04
    Description: Mechanical stimuli drive many physiological processes, including touch and pain sensation, hearing, and blood pressure regulation. Mechanically activated (MA) cation channel activities have been recorded in many cells, but the responsible molecules have not been identified. We characterized a rapidly adapting MA current in a mouse neuroblastoma cell line. Expression profiling and RNA interference knockdown of candidate genes identified Piezo1 (Fam38A) to be required for MA currents in these cells. Piezo1 and related Piezo2 (Fam38B) are vertebrate multipass transmembrane proteins with homologs in invertebrates, plants, and protozoa. Overexpression of mouse Piezo1 or Piezo2 induced two kinetically distinct MA currents. Piezos are expressed in several tissues, and knockdown of Piezo2 in dorsal root ganglia neurons specifically reduced rapidly adapting MA currents. We propose that Piezos are components of MA cation channels.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062430/" 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/PMC3062430/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Coste, Bertrand -- Mathur, Jayanti -- Schmidt, Manuela -- Earley, Taryn J -- Ranade, Sanjeev -- Petrus, Matt J -- Dubin, Adrienne E -- Patapoutian, Ardem -- DE016927/DE/NIDCR NIH HHS/ -- NS046303/NS/NINDS NIH HHS/ -- R01 NS046303/NS/NINDS NIH HHS/ -- R01 NS046303-08/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2010 Oct 1;330(6000):55-60. doi: 10.1126/science.1193270. Epub 2010 Sep 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, The Scripps Research Institute (TSRI), La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20813920" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cations/*metabolism ; Cell Line, Tumor ; Cell Membrane/chemistry ; Cloning, Molecular ; Ganglia, Spinal/cytology ; Ion Channels/analysis/chemistry/genetics/*metabolism ; *Mechanotransduction, Cellular ; Membrane Potentials ; Mice ; Molecular Sequence Data ; Neurons/*metabolism ; Patch-Clamp Techniques ; Pressure ; Protein Structure, Tertiary ; RNA Interference ; RNA, Small Interfering/genetics ; Transfection
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  • 40
    Publication Date: 2010-12-18
    Description: Initiation and maintenance of mitosis require the activation of protein kinase cyclin B-Cdc2 and the inhibition of protein phosphatase 2A (PP2A), which, respectively, phosphorylate and dephosphorylate mitotic substrates. The protein kinase Greatwall (Gwl) is required to maintain mitosis through PP2A inhibition. We describe how Gwl activation results in PP2A inhibition. We identified cyclic adenosine monophosphate-regulated phosphoprotein 19 (Arpp19) and alpha-Endosulfine as two substrates of Gwl that, when phosphorylated by this kinase, associate with and inhibit PP2A, thus promoting mitotic entry. Conversely, in the absence of Gwl activity, Arpp19 and alpha-Endosulfine are dephosphorylated and lose their capacity to bind and inhibit PP2A. Although both proteins can inhibit PP2A, endogenous Arpp19, but not alpha-Endosulfine, is responsible for PP2A inhibition at mitotic entry in Xenopus egg extracts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gharbi-Ayachi, Aicha -- Labbe, Jean-Claude -- Burgess, Andrew -- Vigneron, Suzanne -- Strub, Jean-Marc -- Brioudes, Estelle -- Van-Dorsselaer, Alain -- Castro, Anna -- Lorca, Thierry -- New York, N.Y. -- Science. 2010 Dec 17;330(6011):1673-7. doi: 10.1126/science.1197048.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Universites Montpellier 2 et 1, Centre de Recherche de Biochimie Macromoleculaire, CNRS UMR 5237, IFR 122, 1919 Route de Mende, 34293 Montpellier cedex 5, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21164014" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; HeLa Cells ; Humans ; Interphase ; *Mitosis ; Molecular Sequence Data ; Oocytes ; Peptides/chemistry/*metabolism ; Phosphoproteins/chemistry/*metabolism ; Phosphorylation ; Protein Binding ; Protein Phosphatase 2/*antagonists & inhibitors/metabolism ; Protein-Serine-Threonine Kinases/*metabolism ; Proto-Oncogene Proteins c-mos/metabolism ; Recombinant Fusion Proteins/metabolism ; Xenopus Proteins/antagonists & inhibitors/*metabolism ; Xenopus laevis
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  • 41
    Publication Date: 2010-06-19
    Description: The emergence of pandemic H1N1/2009 influenza demonstrated that pandemic viruses could be generated in swine. Subsequent reintroduction of H1N1/2009 to swine has occurred in multiple countries. Through systematic surveillance of influenza viruses in swine from a Hong Kong abattoir, we characterize a reassortant progeny of H1N1/2009 with swine viruses. Swine experimentally infected with this reassortant developed mild illness and transmitted infection to contact animals. Continued reassortment of H1N1/2009 with swine influenza viruses could produce variants with transmissibility and altered virulence for humans. Global systematic surveillance of influenza viruses in swine is warranted.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3569847/" 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/PMC3569847/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vijaykrishna, D -- Poon, L L M -- Zhu, H C -- Ma, S K -- Li, O T W -- Cheung, C L -- Smith, G J D -- Peiris, J S M -- Guan, Y -- HHSN266200700005C/AI/NIAID NIH HHS/ -- HHSN266200700005C/PHS HHS/ -- New York, N.Y. -- Science. 2010 Jun 18;328(5985):1529. doi: 10.1126/science.1189132.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory of Emerging Infectious Diseases and Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20558710" target="_blank"〉PubMed〈/a〉
    Keywords: Abattoirs ; Animals ; Disease Outbreaks ; Genes, Viral ; Genotype ; Hemagglutinin Glycoproteins, Influenza Virus/genetics ; Hong Kong ; Humans ; Influenza A Virus, H1N1 Subtype/classification/*genetics/isolation & ; purification/pathogenicity ; Influenza A Virus, H1N2 Subtype/classification/genetics/isolation & purification ; Influenza, Human/epidemiology/virology ; Molecular Sequence Data ; Neuraminidase/genetics ; Orthomyxoviridae Infections/epidemiology/transmission/*veterinary/virology ; Phylogeny ; Population Surveillance ; Reassortant Viruses/classification/*genetics/isolation & purification ; Swine/*virology ; Swine Diseases/epidemiology/transmission/*virology
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  • 42
    Publication Date: 2010-12-15
    Description: Biotrophic pathogens, such as the related maize pathogenic fungi Ustilago maydis and Sporisorium reilianum, establish an intimate relationship with their hosts by secreting protein effectors. Because secreted effectors interacting with plant proteins should rapidly evolve, we identified variable genomic regions by sequencing the genome of S. reilianum and comparing it with the U. maydis genome. We detected 43 regions of low sequence conservation in otherwise well-conserved syntenic genomes. These regions primarily encode secreted effectors and include previously identified virulence clusters. By deletion analysis in U. maydis, we demonstrate a role in virulence for four previously unknown diversity regions. This highlights the power of comparative genomics of closely related species for identification of virulence determinants.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schirawski, Jan -- Mannhaupt, Gertrud -- Munch, Karin -- Brefort, Thomas -- Schipper, Kerstin -- Doehlemann, Gunther -- Di Stasio, Maurizio -- Rossel, Nicole -- Mendoza-Mendoza, Artemio -- Pester, Doris -- Muller, Olaf -- Winterberg, Britta -- Meyer, Elmar -- Ghareeb, Hassan -- Wollenberg, Theresa -- Munsterkotter, Martin -- Wong, Philip -- Walter, Mathias -- Stukenbrock, Eva -- Guldener, Ulrich -- Kahmann, Regine -- New York, N.Y. -- Science. 2010 Dec 10;330(6010):1546-8. doi: 10.1126/science.1195330.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043 Marburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21148393" target="_blank"〉PubMed〈/a〉
    Keywords: Conserved Sequence ; *Evolution, Molecular ; Fungal Proteins/genetics/metabolism ; Gene Deletion ; *Genome, Fungal ; Host-Pathogen Interactions/*genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; Multigene Family ; Plant Diseases/*microbiology ; RNA Interference ; Sequence Analysis, DNA ; Synteny ; Ustilaginales/genetics/*pathogenicity ; Ustilago/genetics/pathogenicity ; Virulence/genetics ; Virulence Factors/*genetics ; Zea mays/*microbiology
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  • 43
    Publication Date: 2010-05-22
    Description: We report the design, synthesis, and assembly of the 1.08-mega-base pair Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a M. capricolum recipient cell to create new M. mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including "watermark" sequences and other designed gene deletions and polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and are capable of continuous self-replication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gibson, Daniel G -- Glass, John I -- Lartigue, Carole -- Noskov, Vladimir N -- Chuang, Ray-Yuan -- Algire, Mikkel A -- Benders, Gwynedd A -- Montague, Michael G -- Ma, Li -- Moodie, Monzia M -- Merryman, Chuck -- Vashee, Sanjay -- Krishnakumar, Radha -- Assad-Garcia, Nacyra -- Andrews-Pfannkoch, Cynthia -- Denisova, Evgeniya A -- Young, Lei -- Qi, Zhi-Qing -- Segall-Shapiro, Thomas H -- Calvey, Christopher H -- Parmar, Prashanth P -- Hutchison, Clyde A 3rd -- Smith, Hamilton O -- Venter, J Craig -- New York, N.Y. -- Science. 2010 Jul 2;329(5987):52-6. doi: 10.1126/science.1190719. Epub 2010 May 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20488990" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/analysis ; Base Sequence ; *Bioengineering ; Cloning, Molecular ; DNA, Bacterial/chemical synthesis/genetics ; Escherichia coli/genetics ; Gene Deletion ; Genes, Bacterial ; *Genetic Engineering ; *Genome, Bacterial ; Molecular Sequence Data ; Mycoplasma capricolum/*genetics ; Mycoplasma mycoides/*genetics/growth & development/physiology/ultrastructure ; Phenotype ; Plasmids ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Saccharomyces cerevisiae/genetics ; Transformation, Bacterial
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  • 44
    Publication Date: 2010-09-18
    Description: The Deepwater Horizon event resulted in suspension of oil in the Gulf of Mexico water column because the leakage occurred at great depth. The distribution and fate of other abundant hydrocarbon constituents, such as natural gases, are also important in determining the impact of the leakage but are not yet well understood. From 11 to 21 June 2010, we investigated dissolved hydrocarbon gases at depth using chemical and isotopic surveys and on-site biodegradation studies. Propane and ethane were the primary drivers of microbial respiration, accounting for up to 70% of the observed oxygen depletion in fresh plumes. Propane and ethane trapped in the deep water may therefore promote rapid hydrocarbon respiration by low-diversity bacterial blooms, priming bacterial populations for degradation of other hydrocarbons in the aging plume.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Valentine, David L -- Kessler, John D -- Redmond, Molly C -- Mendes, Stephanie D -- Heintz, Monica B -- Farwell, Christopher -- Hu, Lei -- Kinnaman, Franklin S -- Yvon-Lewis, Shari -- Du, Mengran -- Chan, Eric W -- Garcia Tigreros, Fenix -- Villanueva, Christie J -- New York, N.Y. -- Science. 2010 Oct 8;330(6001):208-11. doi: 10.1126/science.1196830. Epub 2010 Sep 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA. valentine@geol.ucsb.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20847236" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodegradation, Environmental ; *Environmental Pollution ; Ethane/metabolism ; Gammaproteobacteria/*metabolism ; Hydrocarbons/*metabolism ; Methane/metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Oxygen/analysis ; Oxygen Consumption ; Petroleum/*metabolism ; Propane/*metabolism ; Seawater/*microbiology ; Water Pollutants, Chemical/metabolism
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  • 45
    Publication Date: 2010-02-06
    Description: Recent studies have identified range expansion as a potential driver of speciation. Yet it remains poorly understood how, under identical extrinsic settings, differential tendencies for geographic movement of taxa originate and subsequently affect diversification. We identified multiple traits that predict large distributional ranges in extant species of toads (Bufonidae) and used statistical methods to define and phylogenetically reconstruct an optimal range-expansion phenotype. Our results indicate that lineage-specific range-shifting abilities increased through an accumulation of adaptive traits that culminated in such a phenotype. This initiated the episode of global colonization and triggered the major radiation of toads. Evolution toward a range-expansion phenotype might be crucial to understanding both ancient widespread radiations and the evolutionary background of contemporary invasive species such as the cane toad.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Van Bocxlaer, Ines -- Loader, Simon P -- Roelants, Kim -- Biju, S D -- Menegon, Michele -- Bossuyt, Franky -- New York, N.Y. -- Science. 2010 Feb 5;327(5966):679-82. doi: 10.1126/science.1181707.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biology Department, Amphibian Evolution Lab, Unit of Ecology and Systematics, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20133569" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Biological ; Africa ; Animals ; Asia ; Australia ; Bayes Theorem ; *Biological Evolution ; *Bufonidae/anatomy & histology/classification/genetics/physiology ; Genetic Speciation ; Geography ; Likelihood Functions ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Population Dynamics ; Reproduction ; South America ; Species Specificity
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  • 46
    Publication Date: 2010-04-24
    Description: Bacterial NusG is a highly conserved transcription factor that is required for most Rho activity in vivo. We show by nuclear magnetic resonance spectroscopy that Escherichia coli NusG carboxyl-terminal domain forms a complex alternatively with Rho or with transcription factor NusE, a protein identical to 30S ribosomal protein S10. Because NusG amino-terminal domain contacts RNA polymerase and the NusG carboxy-terminal domain interaction site of NusE is accessible in the ribosomal 30S subunit, NusG may act as a link between transcription and translation. Uncoupling of transcription and translation at the ends of bacterial operons enables transcription termination by Rho factor, and competition between ribosomal NusE and Rho for NusG helps to explain why Rho cannot terminate translated transcripts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burmann, Bjorn M -- Schweimer, Kristian -- Luo, Xiao -- Wahl, Markus C -- Stitt, Barbara L -- Gottesman, Max E -- Rosch, Paul -- GM037219/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Apr 23;328(5977):501-4. doi: 10.1126/science.1184953.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Lehrstuhl Biopolymere und Forschungszentrum fur Bio-Makromolekule, Universitat Bayreuth, Universitatsstrasse 30, 95447 Bayreuth, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20413501" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Binding, Competitive ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/biosynthesis/chemistry/*genetics/metabolism ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Operon ; Peptide Elongation Factors/chemistry/*metabolism ; Protein Binding ; *Protein Biosynthesis ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Ribosomal Proteins/chemistry/*metabolism ; Ribosome Subunits, Small, Bacterial/metabolism ; Transcription Factors/chemistry/*metabolism ; *Transcription, Genetic
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  • 47
    Publication Date: 2010-12-04
    Description: Cultivated beets (Beta vulgaris ssp. vulgaris) are unable to form reproductive shoots during the first year of their life cycle. Flowering only occurs if plants get vernalized, that is, pass through the winter, and are subsequently exposed to an increasing day length (photoperiod) in spring. Here, we show that the regulation of flowering time in beets is controlled by the interplay of two paralogs of the FLOWERING LOCUS T (FT) gene in Arabidopsis that have evolved antagonistic functions. BvFT2 is functionally conserved with FT and essential for flowering. In contrast, BvFT1 represses flowering and its down-regulation is crucial for the vernalization response in beets. These data suggest that the beet has evolved a different strategy relative to Arabidopsis and cereals to regulate vernalization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pin, Pierre A -- Benlloch, Reyes -- Bonnet, Dominique -- Wremerth-Weich, Elisabeth -- Kraft, Thomas -- Gielen, Jan J L -- Nilsson, Ove -- New York, N.Y. -- Science. 2010 Dec 3;330(6009):1397-400. doi: 10.1126/science.1197004.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901-83 Umea, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21127254" target="_blank"〉PubMed〈/a〉
    Keywords: Amaranthaceae/genetics/growth & development ; Arabidopsis Proteins/genetics/metabolism ; Beta vulgaris/*genetics/*growth & development ; Cold Temperature ; Flowers/*growth & development ; Gene Expression Regulation, Plant ; *Genes, Plant ; Models, Biological ; Molecular Sequence Data ; Phenotype ; Plant Proteins/chemistry/*metabolism ; Plants, Genetically Modified ; RNA Interference ; Seasons
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  • 48
    Publication Date: 2010-08-21
    Description: The marine bacterium Vibrio parahaemolyticus causes gastroenteritis in humans and encodes the type III effector protein VPA0450, which contributes to host cell death caused by autophagy, cell rounding, and cell lysis. We found that VPA0450 is an inositol polyphosphate 5-phosphatase that hydrolyzed the D5 phosphate from the plasma membrane phospholipid phosphatidylinositol 4,5-bisphosphate. VPA0450 disrupted cytoskeletal binding sites on the inner surface of membranes of human cells and caused plasma membrane blebbing, which compromised membrane integrity and probably contributed to cell death by facilitating lysis. Thus, bacterial pathogens can disrupt adaptor protein-binding sites required for proper membrane and cytoskeleton dynamics by altering the homeostasis of membrane-bound inositol-signaling molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Broberg, Christopher A -- Zhang, Lingling -- Gonzalez, Herman -- Laskowski-Arce, Michelle A -- Orth, Kim -- 5T32GM008203/GM/NIGMS NIH HHS/ -- R01-AI056404/AI/NIAID NIH HHS/ -- R01-AI087808/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2010 Sep 24;329(5999):1660-2. doi: 10.1126/science.1192850. Epub 2010 Aug 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20724587" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/metabolism ; Amino Acid Sequence ; Autophagy ; Bacterial Proteins/chemistry/genetics/*metabolism ; Binding Sites ; Cell Membrane/*physiology/ultrastructure ; Cell Shape ; Computational Biology ; Cytoskeleton/physiology/ultrastructure ; HeLa Cells ; Homeostasis ; Humans ; Molecular Sequence Data ; Phosphatidylinositol 4,5-Diphosphate/metabolism ; Phosphatidylinositols/*metabolism ; Phosphoric Monoester Hydrolases/chemistry/genetics/*metabolism ; Protein Interaction Domains and Motifs ; Signal Transduction ; Transfection ; Vibrio parahaemolyticus/*enzymology/*pathogenicity
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  • 49
    Publication Date: 2010-10-23
    Description: Transmembrane signals initiated by a broad range of extracellular stimuli converge on nodes that regulate phospholipase C (PLC)-dependent inositol lipid hydrolysis for signal propagation. We describe how heterotrimeric guanine nucleotide-binding proteins (G proteins) activate PLC-betas and in turn are deactivated by these downstream effectors. The 2.7-angstrom structure of PLC-beta3 bound to activated Galpha(q) reveals a conserved module found within PLC-betas and other effectors optimized for rapid engagement of activated G proteins. The active site of PLC-beta3 in the complex is occluded by an intramolecular plug that is likely removed upon G protein-dependent anchoring and orientation of the lipase at membrane surfaces. A second domain of PLC-beta3 subsequently accelerates guanosine triphosphate hydrolysis by Galpha(q), causing the complex to dissociate and terminate signal propagation. Mutations within this domain dramatically delay signal termination in vitro and in vivo. Consequently, this work suggests a dynamic catch-and-release mechanism used to sharpen spatiotemporal signals mediated by diverse sensory inputs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3046049/" 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/PMC3046049/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Waldo, Gary L -- Ricks, Tiffany K -- Hicks, Stephanie N -- Cheever, Matthew L -- Kawano, Takeharu -- Tsuboi, Kazuhito -- Wang, Xiaoyue -- Montell, Craig -- Kozasa, Tohru -- Sondek, John -- Harden, T Kendall -- EY010852/EY/NEI NIH HHS/ -- GM074001/GM/NIGMS NIH HHS/ -- GM38213/GM/NIGMS NIH HHS/ -- GM57391/GM/NIGMS NIH HHS/ -- GM61454/GM/NIGMS NIH HHS/ -- R01 GM057391/GM/NIGMS NIH HHS/ -- R01 GM057391-13/GM/NIGMS NIH HHS/ -- R01 GM062299/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Nov 12;330(6006):974-80. doi: 10.1126/science.1193438. Epub 2010 Oct 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20966218" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Activation ; GTP-Binding Protein alpha Subunits, Gq-G11/*chemistry/*metabolism ; Guanosine Triphosphate/metabolism ; Humans ; Hydrogen Bonding ; Hydrolysis ; Isoenzymes/chemistry/metabolism ; Kinetics ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Phospholipase C beta/*chemistry/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Signal Transduction
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  • 50
    Publication Date: 2010-07-03
    Description: To examine the fidelity of DNA synthesis during double-strand break (DSB) repair in Saccharomyces cerevisiae we studied gene conversion in which both strands of DNA are newly synthesized. The mutation rate increases up to 1400 times over spontaneous events, with a significantly different mutation signature. Especially prominent are microhomology-mediated template switches. Recombination-induced mutations are largely independent of mismatch repair, by DNA polymerases Polzeta, Poleta, and Pol32, but result from errors made by Poldelta and Polepsilon. These observations suggest that increased DSB frequencies in oncogene-activated mammalian cells may also increase the probability of acquiring mutations required for transition to a cancerous state.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4254764/" 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/PMC4254764/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hicks, Wade M -- Kim, Minlee -- Haber, James E -- GM007122/GM/NIGMS NIH HHS/ -- GM20056/GM/NIGMS NIH HHS/ -- R01 GM020056/GM/NIGMS NIH HHS/ -- R37 GM020056/GM/NIGMS NIH HHS/ -- T32 GM007122/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Jul 2;329(5987):82-5. doi: 10.1126/science.1191125.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology and Rosenstiel Center, Brandeis University, Waltham, MA 02454-9110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20595613" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; *DNA Breaks, Double-Stranded ; DNA Mismatch Repair ; DNA Polymerase II/metabolism ; DNA Polymerase III/metabolism ; *DNA Repair ; DNA, Fungal/biosynthesis ; DNA-Directed DNA Polymerase/metabolism ; *Gene Conversion ; Genes, Fungal ; *Mitosis ; Molecular Sequence Data ; *Mutagenesis ; *Mutation ; Oncogenes ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism
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  • 51
    Publication Date: 2010-07-22
    Description: Annelids and arthropods share a similar segmented organization of the body whose evolutionary origin remains unclear. The Hedgehog signaling pathway, prominent in arthropod embryonic segment patterning, has not been shown to have a similar function outside arthropods. We show that the ligand Hedgehog, the receptor Patched, and the transcription factor Gli are all expressed in striped patterns before the morphological appearance of segments in the annelid Platynereis dumerilii. Treatments with small molecules antagonistic to Hedgehog signaling disrupt segment formation. Platynereis Hedgehog is not necessary to establish early segment patterns but is required to maintain them. The molecular similarity of segment patterning functions of the Hedgehog pathway in an annelid and in arthropods supports a common origin of segmentation in protostomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3182550/" 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/PMC3182550/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dray, Nicolas -- Tessmar-Raible, Kristin -- Le Gouar, Martine -- Vibert, Laura -- Christodoulou, Foteini -- Schipany, Katharina -- Guillou, Aurelien -- Zantke, Juliane -- Snyman, Heidi -- Behague, Julien -- Vervoort, Michel -- Arendt, Detlev -- Balavoine, Guillaume -- Y 413/Austrian Science Fund FWF/Austria -- New York, N.Y. -- Science. 2010 Jul 16;329(5989):339-42. doi: 10.1126/science.1188913.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre de Genetique Moleculaire du CNRS, FRE 3144, Avenue de la Terrasse, 91189 Gif-sur-Yvette, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20647470" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Arthropods/embryology/genetics/growth & development/metabolism ; Biological Evolution ; Body Patterning/drug effects ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Hedgehog Proteins/chemistry/genetics/*metabolism ; Larva/genetics/growth & development/metabolism ; Metamorphosis, Biological ; Molecular Sequence Data ; Phylogeny ; Piperazines/pharmacology ; Polychaeta/anatomy & histology/genetics/*growth & development/*metabolism ; Pyrazoles/pharmacology ; Receptors, Cell Surface/chemistry/genetics/*metabolism ; *Signal Transduction/drug effects ; Transcription Factors/chemistry/genetics/*metabolism ; Veratrum Alkaloids/pharmacology
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  • 52
    Publication Date: 2010-11-27
    Description: Nitric oxide reductase (NOR) is an iron-containing enzyme that catalyzes the reduction of nitric oxide (NO) to generate a major greenhouse gas, nitrous oxide (N(2)O). Here, we report the crystal structure of NOR from Pseudomonas aeruginosa at 2.7 angstrom resolution. The structure reveals details of the catalytic binuclear center. The non-heme iron (Fe(B)) is coordinated by three His and one Glu ligands, but a His-Tyr covalent linkage common in cytochrome oxidases (COX) is absent. This structural characteristic is crucial for NOR reaction. Although the overall structure of NOR is closely related to COX, neither the D- nor K-proton pathway, which connect the COX active center to the intracellular space, was observed. Protons required for the NOR reaction are probably provided from the extracellular side.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hino, Tomoya -- Matsumoto, Yushi -- Nagano, Shingo -- Sugimoto, Hiroshi -- Fukumori, Yoshihiro -- Murata, Takeshi -- Iwata, So -- Shiro, Yoshitsugu -- New York, N.Y. -- Science. 2010 Dec 17;330(6011):1666-70. doi: 10.1126/science.1195591. Epub 2010 Nov 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21109633" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/chemistry/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Cytochromes c/chemistry ; Electron Transport ; Electron Transport Complex IV/chemistry/metabolism ; Heme/chemistry ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Iron/chemistry ; Membrane Proteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nitric Oxide/*metabolism ; Nitrous Oxide/*metabolism ; Oxidation-Reduction ; Oxidoreductases/*chemistry/*metabolism ; Protein Conformation ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Protons ; Pseudomonas aeruginosa/*enzymology/metabolism
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  • 53
    Publication Date: 2010-04-10
    Description: Mice that are transgenic for rearranged antigen-specific T cell receptors (TCRs) are essential tools to study T cell development and function. Such TCRs are usually isolated from the relevant T cells after long-term culture, often after repeated antigen stimulation, which unavoidably skews the T cell population used. Random genomic integration of the TCR alpha and beta chain and expression from nonendogenous promoters represent additional drawbacks of transgenics. Using epigenetic reprogramming via somatic cell nuclear transfer, we demonstrated that T cells with predefined specificities against Toxoplasma gondii can be used to generate mouse models that express the TCR from their endogenous loci, without experimentally introduced genetic modification. The relative ease and speed with which such transnuclear models can be obtained holds promise for the construction of other disease models.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940321/" 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/PMC2940321/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kirak, Oktay -- Frickel, Eva-Maria -- Grotenbreg, Gijsbert M -- Suh, Heikyung -- Jaenisch, Rudolf -- Ploegh, Hidde L -- R01 GM062502/GM/NIGMS NIH HHS/ -- R01 GM062502-08/GM/NIGMS NIH HHS/ -- R01-HD045022/HD/NICHD NIH HHS/ -- R37 AI033456/AI/NIAID NIH HHS/ -- R37 AI033456-17/AI/NIAID NIH HHS/ -- R37-CA084198/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2010 Apr 9;328(5975):243-8. doi: 10.1126/science.1178590.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA. kirak@wi.mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20378817" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, Protozoan/*immunology ; CD8-Positive T-Lymphocytes/immunology ; Embryonic Stem Cells ; Epitopes, T-Lymphocyte ; Female ; Genes, T-Cell Receptor alpha ; Genes, T-Cell Receptor beta ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; *Mice, Transgenic ; Molecular Sequence Data ; *Nuclear Transfer Techniques ; Protozoan Proteins/genetics/immunology ; Receptors, Antigen, T-Cell, alpha-beta/genetics/*immunology ; Toxoplasma/*immunology ; Toxoplasmosis, Animal/*immunology
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  • 54
    Publication Date: 2010-07-10
    Description: The multicellular green alga Volvox carteri and its morphologically diverse close relatives (the volvocine algae) are well suited for the investigation of the evolution of multicellularity and development. We sequenced the 138-mega-base pair genome of V. carteri and compared its approximately 14,500 predicted proteins to those of its unicellular relative Chlamydomonas reinhardtii. Despite fundamental differences in organismal complexity and life history, the two species have similar protein-coding potentials and few species-specific protein-coding gene predictions. Volvox is enriched in volvocine-algal-specific proteins, including those associated with an expanded and highly compartmentalized extracellular matrix. Our analysis shows that increases in organismal complexity can be associated with modifications of lineage-specific proteins rather than large-scale invention of protein-coding capacity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2993248/" 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/PMC2993248/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prochnik, Simon E -- Umen, James -- Nedelcu, Aurora M -- Hallmann, Armin -- Miller, Stephen M -- Nishii, Ichiro -- Ferris, Patrick -- Kuo, Alan -- Mitros, Therese -- Fritz-Laylin, Lillian K -- Hellsten, Uffe -- Chapman, Jarrod -- Simakov, Oleg -- Rensing, Stefan A -- Terry, Astrid -- Pangilinan, Jasmyn -- Kapitonov, Vladimir -- Jurka, Jerzy -- Salamov, Asaf -- Shapiro, Harris -- Schmutz, Jeremy -- Grimwood, Jane -- Lindquist, Erika -- Lucas, Susan -- Grigoriev, Igor V -- Schmitt, Rudiger -- Kirk, David -- Rokhsar, Daniel S -- 5 P41 LM006252/LM/NLM NIH HHS/ -- R01 GM078376/GM/NIGMS NIH HHS/ -- R01 GM078376-01/GM/NIGMS NIH HHS/ -- R01 GM078376-02/GM/NIGMS NIH HHS/ -- R01 GM078376-03/GM/NIGMS NIH HHS/ -- R01 GM078376-04/GM/NIGMS NIH HHS/ -- R01 GM078376-04S1/GM/NIGMS NIH HHS/ -- R01 GM078376-05/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Jul 9;329(5988):223-6. doi: 10.1126/science.1188800.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20616280" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/*chemistry/*genetics/metabolism ; Biological Evolution ; Chlamydomonas reinhardtii/cytology/*genetics/growth & development/physiology ; DNA, Algal/genetics ; Evolution, Molecular ; Extracellular Matrix Proteins/chemistry/genetics ; Genes ; *Genome ; Molecular Sequence Data ; Protein Structure, Tertiary ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Species Specificity ; Synteny ; Volvox/cytology/*genetics/growth & development/physiology
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  • 55
    Publication Date: 2010-10-16
    Description: The enteric pathogen Salmonella enterica serovar Typhimurium causes food poisoning resulting in gastroenteritis. The S. Typhimurium effector Salmonella invasion protein A (SipA) promotes gastroenteritis by functional motifs that trigger either mechanisms of inflammation or bacterial entry. During infection of intestinal epithelial cells, SipA was found to be responsible for the early activation of caspase-3, an enzyme that is required for SipA cleavage at a specific recognition motif that divided the protein into its two functional domains and activated SipA in a manner necessary for pathogenicity. Other caspase-3 cleavage sites identified in S. Typhimurium appeared to be restricted to secreted effector proteins, which indicates that this may be a general strategy used by this pathogen for processing of its secreted effectors.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4085780/" 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/PMC4085780/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Srikanth, C V -- Wall, Daniel M -- Maldonado-Contreras, Ana -- Shi, Hai Ning -- Zhou, Daoguo -- Demma, Zachary -- Mumy, Karen L -- McCormick, Beth A -- DK33506/DK/NIDDK NIH HHS/ -- DK56754/DK/NIDDK NIH HHS/ -- P30 DK040561/DK/NIDDK NIH HHS/ -- P30 DK040561-15/DK/NIDDK NIH HHS/ -- R01 DK056754/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2010 Oct 15;330(6002):390-3. doi: 10.1126/science.1194598.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pediatric Gastroenterology and Nutrition, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02129, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20947770" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Bacterial Proteins/chemistry/genetics/*metabolism ; Caspase 3/*metabolism ; Cell Line, Tumor ; Enzyme Activation ; Gastroenteritis/metabolism/microbiology/pathology ; Humans ; Intestinal Mucosa/enzymology/*microbiology ; Intestines/enzymology/microbiology/pathology ; Mice ; Mice, Knockout ; Microfilament Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Neutrophil Infiltration ; Salmonella Infections, Animal/*microbiology/pathology ; Salmonella typhimurium/*metabolism/*pathogenicity ; Virulence Factors/metabolism
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  • 56
    Publication Date: 2010-10-12
    Description: For proper partitioning of chromosomes in mitosis, the chromosomal passenger complex (CPC) including Aurora B and survivin must be localized at the center of paired kinetochores, at the site called the inner centromere. It is largely unknown what defines the inner centromere and how the CPC is targeted to this site. Here, we show that the phosphorylation of histone H3-threonine 3 (H3-pT3) mediated by Haspin cooperates with Bub1-mediated histone 2A-serine 121 (H2A-S121) phosphorylation in targeting the CPC to the inner centromere in fission yeast and human cells. H3-pT3 promotes nucleosome binding of survivin, whereas phosphorylated H2A-S121 facilitates the binding of shugoshin, the centromeric CPC adaptor. Haspin colocalizes with cohesin by associating with Pds5, whereas Bub1 localizes at kinetochores. Thus, the inner centromere is defined by intersection of two histone kinases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yamagishi, Yuya -- Honda, Takashi -- Tanno, Yuji -- Watanabe, Yoshinori -- New York, N.Y. -- Science. 2010 Oct 8;330(6001):239-43. doi: 10.1126/science.1194498.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, University of Tokyo, Yayoi, Tokyo 113-0032, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20929775" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Aurora Kinase B ; Aurora Kinases ; Cell Cycle Proteins/metabolism ; Centromere/*metabolism ; Chromatin/metabolism ; Chromosomal Proteins, Non-Histone/metabolism ; Chromosome Segregation ; Chromosomes, Fungal/*physiology ; Chromosomes, Human/*physiology ; HeLa Cells ; Heterochromatin/metabolism ; Histones/*metabolism ; Humans ; Inhibitor of Apoptosis Proteins ; Intracellular Signaling Peptides and Proteins/chemistry/genetics/*metabolism ; Kinetochores/metabolism ; Microtubule-Associated Proteins/metabolism ; Mitosis ; Molecular Sequence Data ; Mutation ; Nucleosomes/metabolism ; Phosphorylation ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein-Serine-Threonine Kinases/chemistry/genetics/*metabolism ; Schizosaccharomyces/*genetics/metabolism ; Schizosaccharomyces pombe Proteins/genetics/*metabolism ; Serine/metabolism ; Threonine/metabolism
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  • 57
    Publication Date: 2010-09-18
    Description: Simian immunodeficiency virus (SIV) lineages have been identified that are endemic to Bioko Island. The time the island formed offers a geological time scale calibration point for dating the most recent common ancestor of SIV. The Bioko viruses cover the whole range of SIV genetic diversity, and each Bioko SIV clade is most closely related to viruses circulating in hosts of the same genus on the African mainland rather than to SIVs of other Bioko species. Our phylogeographic approach establishes that SIV is ancient and at least 32,000 years old. Our conservative calibration point and analyses of gene sequence saturation and dating bias suggest it may be much older.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Worobey, Michael -- Telfer, Paul -- Souquiere, Sandrine -- Hunter, Meredith -- Coleman, Clint A -- Metzger, Michael J -- Reed, Patricia -- Makuwa, Maria -- Hearn, Gail -- Honarvar, Shaya -- Roques, Pierre -- Apetrei, Cristian -- Kazanji, Mirdad -- Marx, Preston A -- 1R01AI27698/AI/NIAID NIH HHS/ -- 1R01AI44596/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2010 Sep 17;329(5998):1487. doi: 10.1126/science.1193550.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Arizona, Tucson, AZ 85721, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20847261" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cercopithecidae/*virology ; Cercopithecus/virology ; Colobus/virology ; Equatorial Guinea ; Evolution, Molecular ; Genes, pol ; Genetic Variation ; Geography ; Mandrillus/virology ; Molecular Sequence Data ; Phylogeny ; Simian Acquired Immunodeficiency Syndrome/*virology ; Simian Immunodeficiency Virus/*classification/*genetics/isolation & purification ; Time Factors
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  • 58
    Publication Date: 2010-10-12
    Description: Culex quinquefasciatus (the southern house mosquito) is an important mosquito vector of viruses such as West Nile virus and St. Louis encephalitis virus, as well as of nematodes that cause lymphatic filariasis. C. quinquefasciatus is one species within the Culex pipiens species complex and can be found throughout tropical and temperate climates of the world. The ability of C. quinquefasciatus to take blood meals from birds, livestock, and humans contributes to its ability to vector pathogens between species. Here, we describe the genomic sequence of C. quinquefasciatus: Its repertoire of 18,883 protein-coding genes is 22% larger than that of Aedes aegypti and 52% larger than that of Anopheles gambiae with multiple gene-family expansions, including olfactory and gustatory receptors, salivary gland genes, and genes associated with xenobiotic detoxification.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740384/" 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/PMC3740384/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Arensburger, Peter -- Megy, Karine -- Waterhouse, Robert M -- Abrudan, Jenica -- Amedeo, Paolo -- Antelo, Beatriz -- Bartholomay, Lyric -- Bidwell, Shelby -- Caler, Elisabet -- Camara, Francisco -- Campbell, Corey L -- Campbell, Kathryn S -- Casola, Claudio -- Castro, Marta T -- Chandramouliswaran, Ishwar -- Chapman, Sinead B -- Christley, Scott -- Costas, Javier -- Eisenstadt, Eric -- Feschotte, Cedric -- Fraser-Liggett, Claire -- Guigo, Roderic -- Haas, Brian -- Hammond, Martin -- Hansson, Bill S -- Hemingway, Janet -- Hill, Sharon R -- Howarth, Clint -- Ignell, Rickard -- Kennedy, Ryan C -- Kodira, Chinnappa D -- Lobo, Neil F -- Mao, Chunhong -- Mayhew, George -- Michel, Kristin -- Mori, Akio -- Liu, Nannan -- Naveira, Horacio -- Nene, Vishvanath -- Nguyen, Nam -- Pearson, Matthew D -- Pritham, Ellen J -- Puiu, Daniela -- Qi, Yumin -- Ranson, Hilary -- Ribeiro, Jose M C -- Roberston, Hugh M -- Severson, David W -- Shumway, Martin -- Stanke, Mario -- Strausberg, Robert L -- Sun, Cheng -- Sutton, Granger -- Tu, Zhijian Jake -- Tubio, Jose Manuel C -- Unger, Maria F -- Vanlandingham, Dana L -- Vilella, Albert J -- White, Owen -- White, Jared R -- Wondji, Charles S -- Wortman, Jennifer -- Zdobnov, Evgeny M -- Birren, Bruce -- Christensen, Bruce M -- Collins, Frank H -- Cornel, Anthony -- Dimopoulos, George -- Hannick, Linda I -- Higgs, Stephen -- Lanzaro, Gregory C -- Lawson, Daniel -- Lee, Norman H -- Muskavitch, Marc A T -- Raikhel, Alexander S -- Atkinson, Peter W -- HHSN266200400001C/PHS HHS/ -- HHSN266200400039C/AI/NIAID NIH HHS/ -- HHSN266200400039C/PHS HHS/ -- N01-AI-30071/AI/NIAID NIH HHS/ -- N01AI30071/AI/NIAID NIH HHS/ -- ZIA AI000810-13/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Oct 1;330(6000):86-8. doi: 10.1126/science.1191864.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Disease Vector Research, University of California Riverside, Riverside, CA 92521, USA. arensburger@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20929810" target="_blank"〉PubMed〈/a〉
    Keywords: Aedes/genetics ; Animals ; Anopheles gambiae/genetics ; Chromosome Mapping ; Chromosomes/*genetics ; Culex/classification/*genetics/physiology ; DNA Transposable Elements ; *Genes, Insect ; *Genome ; Insect Proteins/genetics/physiology ; Insect Vectors/genetics ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Receptors, Odorant/genetics ; Retroelements ; *Sequence Analysis, DNA
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  • 59
    Publication Date: 2010-08-14
    Description: Group I self-splicing ribozymes commonly function as components of selfish mobile genetic elements. We identified an allosteric group I ribozyme, wherein self-splicing is regulated by a distinct riboswitch class that senses the bacterial second messenger c-di-GMP. The tandem RNA sensory system resides in the 5' untranslated region of the messenger RNA for a putative virulence gene in the pathogenic bacterium Clostridium difficile. c-di-GMP binding by the riboswitch induces folding changes at atypical splice site junctions to modulate alternative RNA processing. Our findings indicate that some self-splicing ribozymes are not selfish elements but are harnessed by cells as metabolite sensors and genetic regulators.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538695/" 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/PMC4538695/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Elaine R -- Baker, Jenny L -- Weinberg, Zasha -- Sudarsan, Narasimhan -- Breaker, Ronald R -- P01 GM022778/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Aug 13;329(5993):845-8. doi: 10.1126/science.1190713.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular, and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520-8103, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20705859" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Untranslated Regions ; Aptamers, Nucleotide/chemistry ; Base Pairing ; Base Sequence ; Clostridium difficile/*genetics/metabolism/pathogenicity ; Codon, Initiator ; Cyclic GMP/*analogs & derivatives/metabolism ; Exons ; Genes, Bacterial ; Guanosine Triphosphate/metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; *RNA Splicing ; RNA, Bacterial/chemistry/*genetics/metabolism ; RNA, Catalytic/chemistry/genetics/*metabolism ; RNA, Messenger/chemistry/genetics/metabolism ; *Regulatory Sequences, Ribonucleic Acid ; *Second Messenger Systems
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  • 60
    Publication Date: 2010-03-06
    Description: Sestrins are conserved proteins that accumulate in cells exposed to stress, potentiate adenosine monophosphate-activated protein kinase (AMPK), and inhibit activation of target of rapamycin (TOR). We show that the abundance of Drosophila sestrin (dSesn) is increased upon chronic TOR activation through accumulation of reactive oxygen species that cause activation of c-Jun amino-terminal kinase and transcription factor Forkhead box O (FoxO). Loss of dSesn resulted in age-associated pathologies including triglyceride accumulation, mitochondrial dysfunction, muscle degeneration, and cardiac malfunction, which were prevented by pharmacological activation of AMPK or inhibition of TOR. Hence, dSesn appears to be a negative feedback regulator of TOR that integrates metabolic and stress inputs and prevents pathologies caused by chronic TOR activation that may result from diminished autophagic clearance of damaged mitochondria, protein aggregates, or lipids.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866632/" 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/PMC2866632/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Jun Hee -- Budanov, Andrei V -- Park, Eek Joong -- Birse, Ryan -- Kim, Teddy E -- Perkins, Guy A -- Ocorr, Karen -- Ellisman, Mark H -- Bodmer, Rolf -- Bier, Ethan -- Karin, Michael -- AI070654/AI/NIAID NIH HHS/ -- CA118165/CA/NCI NIH HHS/ -- DK082080/DK/NIDDK NIH HHS/ -- ES006376/ES/NIEHS NIH HHS/ -- NS29870/NS/NINDS NIH HHS/ -- P30 CA023100/CA/NCI NIH HHS/ -- P30-CA23100/CA/NCI NIH HHS/ -- P41-RR004050/RR/NCRR NIH HHS/ -- P42 ES010337/ES/NIEHS NIH HHS/ -- P42 ES010337-10S20010/ES/NIEHS NIH HHS/ -- P42-ES010337/ES/NIEHS NIH HHS/ -- R01 CA118165/CA/NCI NIH HHS/ -- R01 CA118165-04/CA/NCI NIH HHS/ -- R01 ES006376/ES/NIEHS NIH HHS/ -- R01 ES006376-17/ES/NIEHS NIH HHS/ -- New York, N.Y. -- Science. 2010 Mar 5;327(5970):1223-8. doi: 10.1126/science.1182228.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego (UCSD), La Jolla, CA 92093-0723, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20203043" target="_blank"〉PubMed〈/a〉
    Keywords: AMP-Activated Protein Kinases/metabolism ; *Aging ; Amino Acid Sequence ; Animals ; Autophagy ; Cell Size ; Drosophila Proteins/antagonists & ; inhibitors/chemistry/genetics/metabolism/*physiology ; Drosophila melanogaster/cytology/growth & development/metabolism/*physiology ; Fat Body/metabolism ; Feedback, Physiological ; Forkhead Transcription Factors/metabolism ; Gene Expression Regulation ; Heart/physiology ; Heat-Shock Proteins/chemistry/genetics/*physiology ; JNK Mitogen-Activated Protein Kinases/metabolism ; Mitochondria, Muscle/physiology/ultrastructure ; Models, Animal ; Molecular Sequence Data ; Muscles/physiology ; Oxidative Stress ; Protein Kinases/*metabolism ; Reactive Oxygen Species/metabolism ; Signal Transduction ; TOR Serine-Threonine Kinases ; Transcription, Genetic ; Triglycerides/metabolism ; Wings, Animal/cytology/growth & development/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 61
    Publication Date: 2010-08-21
    Description: Facioscapulohumeral muscular dystrophy (FSHD) is a common form of muscular dystrophy in adults that is foremost characterized by progressive wasting of muscles in the upper body. FSHD is associated with contraction of D4Z4 macrosatellite repeats on chromosome 4q35, but this contraction is pathogenic only in certain "permissive" chromosomal backgrounds. Here, we show that FSHD patients carry specific single-nucleotide polymorphisms in the chromosomal region distal to the last D4Z4 repeat. This FSHD-predisposing configuration creates a canonical polyadenylation signal for transcripts derived from DUX4, a double homeobox gene of unknown function that straddles the last repeat unit and the adjacent sequence. Transfection studies revealed that DUX4 transcripts are efficiently polyadenylated and are more stable when expressed from permissive chromosomes. These findings suggest that FSHD arises through a toxic gain of function attributable to the stabilized distal DUX4 transcript.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4677822/" 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/PMC4677822/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lemmers, Richard J L F -- van der Vliet, Patrick J -- Klooster, Rinse -- Sacconi, Sabrina -- Camano, Pilar -- Dauwerse, Johannes G -- Snider, Lauren -- Straasheijm, Kirsten R -- van Ommen, Gert Jan -- Padberg, George W -- Miller, Daniel G -- Tapscott, Stephen J -- Tawil, Rabi -- Frants, Rune R -- van der Maarel, Silvere M -- P01 NS069539/NS/NINDS NIH HHS/ -- P01NS069539/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2010 Sep 24;329(5999):1650-3. doi: 10.1126/science.1189044. Epub 2010 Aug 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20724583" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Adult ; Aged ; Base Sequence ; Child, Preschool ; Chromosomes, Human, Pair 10/genetics ; Chromosomes, Human, Pair 4/*genetics ; Female ; Genetic Predisposition to Disease ; Haplotypes ; Homeodomain Proteins/*genetics/physiology ; Humans ; Male ; Middle Aged ; Models, Genetic ; Molecular Sequence Data ; Muscular Dystrophy, Facioscapulohumeral/*genetics ; Polyadenylation ; Polymorphism, Single Nucleotide ; RNA Stability ; RNA, Messenger/genetics/metabolism ; *Repetitive Sequences, Nucleic Acid ; Transcription, Genetic ; Transfection ; Young Adult
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 62
    Publication Date: 2010-04-17
    Description: Although dimorphic sexes have evolved repeatedly in multicellular eukaryotes, their origins are unknown. The mating locus (MT) of the sexually dimorphic multicellular green alga Volvox carteri specifies the production of eggs and sperm and has undergone a remarkable expansion and divergence relative to MT from Chlamydomonas reinhardtii, which is a closely related unicellular species that has equal-sized gametes. Transcriptome analysis revealed a rewired gametic expression program for Volvox MT genes relative to Chlamydomonas and identified multiple gender-specific and sex-regulated transcripts. The retinoblastoma tumor suppressor homolog MAT3 is a Volvox MT gene that displays sexually regulated alternative splicing and evidence of gender-specific selection, both of which are indicative of cooption into the sexual cycle. Thus, sex-determining loci affect the evolution of both sex-related and non-sex-related genes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880461/" 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/PMC2880461/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ferris, Patrick -- Olson, Bradley J S C -- De Hoff, Peter L -- Douglass, Stephen -- Casero, David -- Prochnik, Simon -- Geng, Sa -- Rai, Rhitu -- Grimwood, Jane -- Schmutz, Jeremy -- Nishii, Ichiro -- Hamaji, Takashi -- Nozaki, Hisayoshi -- Pellegrini, Matteo -- Umen, James G -- F32 GM086037/GM/NIGMS NIH HHS/ -- R01 GM078376/GM/NIGMS NIH HHS/ -- R01 GM078376-01/GM/NIGMS NIH HHS/ -- R01 GM078376-02/GM/NIGMS NIH HHS/ -- R01 GM078376-03/GM/NIGMS NIH HHS/ -- R01 GM078376-04/GM/NIGMS NIH HHS/ -- R01 GM078376-04S1/GM/NIGMS NIH HHS/ -- T32-HG002536/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2010 Apr 16;328(5976):351-4. doi: 10.1126/science.1186222.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20395508" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/*genetics/metabolism ; Alternative Splicing ; Cell Division ; Chlamydomonas/genetics/physiology ; *Evolution, Molecular ; Gene Expression Profiling ; Gene Expression Regulation ; *Genes ; Genes, Retinoblastoma ; *Genetic Loci ; Introns ; Molecular Sequence Data ; Protozoan Proteins/genetics/metabolism ; Recombination, Genetic ; Reproduction ; Retinoblastoma Protein/genetics/metabolism ; Sequence Analysis, DNA ; Volvox/*genetics/*physiology
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  • 63
    Publication Date: 2010-03-13
    Description: MauG is a diheme enzyme responsible for the posttranslational modification of two tryptophan residues to form the tryptophan tryptophylquinone (TTQ) cofactor of methylamine dehydrogenase (MADH). MauG converts preMADH, containing monohydroxylated betaTrp57, to fully functional MADH by catalyzing the insertion of a second oxygen atom into the indole ring and covalently linking betaTrp57 to betaTrp108. We have solved the x-ray crystal structure of MauG complexed with preMADH to 2.1 angstroms. The c-type heme irons and the nascent TTQ site are separated by long distances over which electron transfer must occur to achieve catalysis. In addition, one of the hemes has an atypical His-Tyr axial ligation. The crystalline protein complex is catalytically competent; upon addition of hydrogen peroxide, MauG-dependent TTQ synthesis occurs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878131/" 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/PMC2878131/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jensen, Lyndal M R -- Sanishvili, Ruslan -- Davidson, Victor L -- Wilmot, Carrie M -- GM41574/GM/NIGMS NIH HHS/ -- GM66569/GM/NIGMS NIH HHS/ -- R01 GM041574/GM/NIGMS NIH HHS/ -- R01 GM041574-20/GM/NIGMS NIH HHS/ -- R01 GM066569/GM/NIGMS NIH HHS/ -- R01 GM066569-08/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Mar 12;327(5971):1392-4. doi: 10.1126/science.1182492.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20223990" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Biocatalysis ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Precursors/*chemistry/metabolism ; Hemeproteins/*chemistry/metabolism ; Hydrogen Peroxide/metabolism ; Indolequinones/*chemistry/metabolism ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Oxidoreductases Acting on CH-NH Group Donors/*chemistry/metabolism ; Paracoccus denitrificans/chemistry/enzymology/*metabolism ; Protein Conformation ; *Protein Processing, Post-Translational ; Tryptophan/*analogs & derivatives/chemistry/metabolism
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  • 64
    Publication Date: 2010-12-18
    Description: Maintenance of genomic methylation patterns is mediated primarily by DNA methyltransferase-1 (DNMT1). We have solved structures of mouse and human DNMT1 composed of CXXC, tandem bromo-adjacent homology (BAH1/2), and methyltransferase domains bound to DNA-containing unmethylated CpG sites. The CXXC specifically binds to unmethylated CpG dinucleotide and positions the CXXC-BAH1 linker between the DNA and the active site of DNMT1, preventing de novo methylation. In addition, a loop projecting from BAH2 interacts with the target recognition domain (TRD) of the methyltransferase, stabilizing the TRD in a retracted position and preventing it from inserting into the DNA major groove. Our studies identify an autoinhibitory mechanism, in which unmethylated CpG dinucleotides are occluded from the active site to ensure that only hemimethylated CpG dinucleotides undergo methylation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4689315/" 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/PMC4689315/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Song, Jikui -- Rechkoblit, Olga -- Bestor, Timothy H -- Patel, Dinshaw J -- P30 CA008748/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2011 Feb 25;331(6020):1036-40. doi: 10.1126/science.1195380. Epub 2010 Dec 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21163962" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Catalytic Domain ; Crystallography, X-Ray ; Cysteine ; DNA/*chemistry/*metabolism ; DNA (Cytosine-5-)-Methyltransferase/*chemistry/*metabolism ; *DNA Methylation ; DNA-Cytosine Methylases/chemistry/metabolism ; Dinucleoside Phosphates/chemistry/metabolism ; Humans ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Nucleic Acid Conformation ; Protein Binding ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Substrate Specificity
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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