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  • Molecular Sequence Data  (28)
  • American Association for the Advancement of Science (AAAS)  (28)
  • American Society of Hematology
  • 2010-2014
  • 2005-2009  (28)
  • 2006  (28)
Collection
Publisher
  • American Association for the Advancement of Science (AAAS)  (28)
  • American Society of Hematology
Years
  • 2010-2014
  • 2005-2009  (28)
Year
  • 1
    Publication Date: 2006-11-18
    Description: Our knowledge of Neanderthals is based on a limited number of remains and artifacts from which we must make inferences about their biology, behavior, and relationship to ourselves. Here, we describe the characterization of these extinct hominids from a new perspective, based on the development of a Neanderthal metagenomic library and its high-throughput sequencing and analysis. Several lines of evidence indicate that the 65,250 base pairs of hominid sequence so far identified in the library are of Neanderthal origin, the strongest being the ascertainment of sequence identities between Neanderthal and chimpanzee at sites where the human genomic sequence is different. These results enabled us to calculate the human-Neanderthal divergence time based on multiple randomly distributed autosomal loci. Our analyses suggest that on average the Neanderthal genomic sequence we obtained and the reference human genome sequence share a most recent common ancestor approximately 706,000 years ago, and that the human and Neanderthal ancestral populations split approximately 370,000 years ago, before the emergence of anatomically modern humans. Our finding that the Neanderthal and human genomes are at least 99.5% identical led us to develop and successfully implement a targeted method for recovering specific ancient DNA sequences from metagenomic libraries. This initial analysis of the Neanderthal genome advances our understanding of the evolutionary relationship of Homo sapiens and Homo neanderthalensis and signifies the dawn of Neanderthal genomics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2583069/" 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/PMC2583069/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Noonan, James P -- Coop, Graham -- Kudaravalli, Sridhar -- Smith, Doug -- Krause, Johannes -- Alessi, Joe -- Chen, Feng -- Platt, Darren -- Paabo, Svante -- Pritchard, Jonathan K -- Rubin, Edward M -- 1-F32-GM074367/GM/NIGMS NIH HHS/ -- HL066681/HL/NHLBI NIH HHS/ -- R01 HG002772/HG/NHGRI NIH HHS/ -- R01 HG002772-01/HG/NHGRI NIH HHS/ -- R01 HG002772-1/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2006 Nov 17;314(5802):1113-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17110569" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Bone and Bones ; Cell Nucleus ; DNA/*genetics/isolation & purification ; DNA, Mitochondrial ; *Fossils ; Gene Pool ; Genome ; Genome, Human ; Genomic Library ; History, Ancient ; Hominidae/*genetics ; Humans ; Male ; Molecular Sequence Data ; Pan troglodytes/genetics ; Polymerase Chain Reaction ; Sequence Alignment ; *Sequence Analysis, DNA/methods ; Time
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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  • 2
    Publication Date: 2006-03-25
    Description: Tracheal cytotoxin (TCT), a naturally occurring fragment of Gram-negative peptidoglycan, is a potent elicitor of innate immune responses in Drosophila. It induces the heterodimerization of its recognition receptors, the peptidoglycan recognition proteins (PGRPs) LCa and LCx, which activates the immune deficiency pathway. The crystal structure at 2.1 angstrom resolution of TCT in complex with the ectodomains of PGRP-LCa and PGRP-LCx shows that TCT is bound to and presented by the LCx ectodomain for recognition by the LCa ectodomain; the latter lacks a canonical peptidoglycan-docking groove conserved in other PGRPs. The interface, revealed in atomic detail, between TCT and the receptor complex highlights the importance of the anhydro-containing disaccharide in bridging the two ectodomains together and the critical role of diaminopimelic acid as the specificity determinant for PGRP interaction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, Chung-I -- Chelliah, Yogarany -- Borek, Dominika -- Mengin-Lecreulx, Dominique -- Deisenhofer, Johann -- New York, N.Y. -- Science. 2006 Mar 24;311(5768):1761-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, TX 75390-9050, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16556841" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Carrier Proteins/*chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Cytotoxins/*chemistry/metabolism ; Drosophila melanogaster ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Peptidoglycan/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 3
    Publication Date: 2006-07-22
    Description: CorA family members are ubiquitously distributed transporters of divalent metal cations and are considered to be the primary Mg2+ transporter of Bacteria and Archaea. We have determined a 2.9 angstrom resolution structure of CorA from Thermotoga maritima that reveals a pentameric cone-shaped protein. Two potential regulatory metal binding sites are found in the N-terminal domain that bind both Mg2+ and Co2+. The structure of CorA supports an efflux system involving dehydration and rehydration of divalent metal ions potentially mediated by a ring of conserved aspartate residues at the cytoplasmic entrance and a carbonyl funnel at the periplasmic side of the pore.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eshaghi, Said -- Niegowski, Damian -- Kohl, Andreas -- Martinez Molina, Daniel -- Lesley, Scott A -- Nordlund, Par -- New York, N.Y. -- Science. 2006 Jul 21;313(5785):354-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77 Stockholm, Sweden. Said.Eshaghi@ki.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16857941" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Cation Transport Proteins/*chemistry/metabolism ; Chlorides/analysis/metabolism ; Cobalt/chemistry/*metabolism ; Crystallography, X-Ray ; Hydrophobic and Hydrophilic Interactions ; Magnesium/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Alignment ; Thermotoga maritima/*chemistry ; Water/chemistry
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  • 4
    Publication Date: 2006-07-29
    Description: Comparative genomics of 45 epidemiologically varied variola virus isolates from the past 30 years of the smallpox era indicate low sequence diversity, suggesting that there is probably little difference in the isolates' functional gene content. Phylogenetic clustering inferred three clades coincident with their geographical origin and case-fatality rate; the latter implicated putative proteins that mediate viral virulence differences. Analysis of the viral linear DNA genome suggests that its evolution involved direct descent and DNA end-region recombination events. Knowing the sequences will help understand the viral proteome and improve diagnostic test precision, therapeutics, and systems for their assessment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Esposito, Joseph J -- Sammons, Scott A -- Frace, A Michael -- Osborne, John D -- Olsen-Rasmussen, Melissa -- Zhang, Ming -- Govil, Dhwani -- Damon, Inger K -- Kline, Richard -- Laker, Miriam -- Li, Yu -- Smith, Geoffrey L -- Meyer, Hermann -- Leduc, James W -- Wohlhueter, Robert M -- G0501257/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2006 Aug 11;313(5788):807-12. Epub 2006 Jul 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Preparedness, Detection, and Control of Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA. jesposito@cdc.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16873609" target="_blank"〉PubMed〈/a〉
    Keywords: DNA, Viral/*genetics ; Disease Outbreaks ; *Evolution, Molecular ; Gene Deletion ; *Genetic Variation ; *Genome, Viral ; Genomics ; Humans ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Proteome/analysis/genetics ; Recombination, Genetic ; Sequence Analysis, DNA ; Smallpox/epidemiology/mortality/*virology ; Variola virus/classification/*genetics/isolation & purification/pathogenicity ; Viral Proteins/chemistry/genetics ; Virulence/genetics
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  • 5
    Publication Date: 2006-01-21
    Description: Microbial resistance to antibiotics currently spans all known classes of natural and synthetic compounds. It has not only hindered our treatment of infections but also dramatically reshaped drug discovery, yet its origins have not been systematically studied. Soil-dwelling bacteria produce and encounter a myriad of antibiotics, evolving corresponding sensing and evading strategies. They are a reservoir of resistance determinants that can be mobilized into the microbial community. Study of this reservoir could provide an early warning system for future clinically relevant antibiotic resistance mechanisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉D'Costa, Vanessa M -- McGrann, Katherine M -- Hughes, Donald W -- Wright, Gerard D -- New York, N.Y. -- Science. 2006 Jan 20;311(5759):374-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Antimicrobial Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, Ontario, Canada, L8N 3Z5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16424339" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Anti-Bacterial Agents/metabolism/*pharmacology ; Ciprofloxacin/pharmacology ; Daptomycin/metabolism/pharmacology ; *Drug Resistance, Multiple, Bacterial/genetics ; Erythromycin/metabolism/pharmacology ; Genes, Bacterial ; Ketolides/metabolism/pharmacology ; Macrolides/pharmacology ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Mutation ; Rifampin/metabolism/pharmacology ; *Soil Microbiology ; Streptomyces/*drug effects/enzymology/genetics/isolation & purification ; Trimethoprim Resistance ; Vancomycin Resistance/genetics ; Virginiamycin/metabolism/pharmacology
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  • 6
    Publication Date: 2006-06-10
    Description: Vaccine-induced cellular immunity controls virus replication in simian immunodeficiency virus (SIV)-infected monkeys only transiently, leading to the question of whether such vaccines for AIDS will be effective. We immunized monkeys with plasmid DNA and replication-defective adenoviral vectors encoding SIV proteins and then challenged them with pathogenic SIV. Although these monkeys demonstrated a reduction in viremia restricted to the early phase of SIV infection, they showed a prolonged survival. This survival was associated with preserved central memory CD4+ T lymphocytes and could be predicted by the magnitude of the vaccine-induced cellular immune response. These immune correlates of vaccine efficacy should guide the evaluation of AIDS vaccines in humans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2365913/" 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/PMC2365913/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Letvin, Norman L -- Mascola, John R -- Sun, Yue -- Gorgone, Darci A -- Buzby, Adam P -- Xu, Ling -- Yang, Zhi-Yong -- Chakrabarti, Bimal -- Rao, Srinivas S -- Schmitz, Jorn E -- Montefiori, David C -- Barker, Brianne R -- Bookstein, Fred L -- Nabel, Gary J -- Z99 AI999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2006 Jun 9;312(5779):1530-3.〈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. nletvin@bidmc.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16763152" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; CD4-Positive T-Lymphocytes/*immunology ; Humans ; *Immunologic Memory ; Macaca mulatta ; Molecular Sequence Data ; Plasmids ; SAIDS Vaccines/*immunology ; Simian Acquired Immunodeficiency Syndrome/*immunology/prevention & control ; Simian Immunodeficiency Virus/*immunology ; Survival Analysis ; Vaccines, DNA/*immunology ; Vaccines, Synthetic/immunology ; Virus Replication
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  • 7
    Publication Date: 2006-11-25
    Description: The Dobzhansky-Muller model proposes that hybrid incompatibilities are caused by the interaction between genes that have functionally diverged in the respective hybridizing species. Here, we show that Lethal hybrid rescue (Lhr) has functionally diverged in Drosophila simulans and interacts with Hybrid male rescue (Hmr), which has functionally diverged in D. melanogaster, to cause lethality in F1 hybrid males. LHR localizes to heterochromatic regions of the genome and has diverged extensively in sequence between these species in a manner consistent with positive selection. Rapidly evolving heterochromatic DNA sequences may be driving the evolution of this incompatibility gene.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brideau, Nicholas J -- Flores, Heather A -- Wang, Jun -- Maheshwari, Shamoni -- Wang, Xu -- Barbash, Daniel A -- R01 GM074737-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Nov 24;314(5803):1292-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17124320" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Chromosomal Proteins, Non-Histone/metabolism ; Chromosome Mapping ; Crosses, Genetic ; Drosophila/*genetics/physiology ; Drosophila Proteins/chemistry/*genetics/metabolism ; Drosophila melanogaster/*genetics/physiology ; *Evolution, Molecular ; Female ; *Genes, Insect ; Genetic Speciation ; *Hybridization, Genetic ; Male ; Molecular Sequence Data ; Selection, Genetic ; Transformation, Genetic ; Transgenes
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  • 8
    Publication Date: 2006-08-12
    Description: Mutations in the human neurotrypsin gene are associated with autosomal recessive mental retardation. To further understand the pathophysiological consequences of the lack of this serine protease, we studied Tequila (Teq), the Drosophila neurotrypsin ortholog, using associative memory as a behavioral readout. We found that teq inactivation resulted in a long-term memory (LTM)-specific defect. After LTM conditioning of wild-type flies, teq expression transiently increased in the mushroom bodies. Moreover, specific inhibition of teq expression in adult mushroom bodies resulted in a reversible LTM defect. Hence, the Teq pathway is essential for information processing in Drosophila.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Didelot, Gerard -- Molinari, Florence -- Tchenio, Paul -- Comas, Daniel -- Milhiet, Elodie -- Munnich, Arnold -- Colleaux, Laurence -- Preat, Thomas -- New York, N.Y. -- Science. 2006 Aug 11;313(5788):851-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genes et Dynamique des Systemes de Memoire, UMR CNRS 7637, Ecole Superieure de Physique et de Chimie Industrielles, 10 Rue Vauquelin 75005 Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16902143" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Animals, Genetically Modified ; Conditioning, Classical ; Drosophila Proteins/chemistry/genetics/*physiology ; Drosophila melanogaster/genetics/*physiology ; Gene Expression ; Gene Expression Regulation ; Humans ; Learning ; *Memory ; Mifepristone/pharmacology ; Models, Animal ; Molecular Sequence Data ; Mushroom Bodies/anatomy & histology/physiology ; Mutation ; Odors ; RNA Interference ; RNA, Messenger/genetics/metabolism ; Serine Endopeptidases/chemistry/genetics/*physiology
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  • 9
    Publication Date: 2006-03-11
    Description: A biosynthetic approach was developed to control and probe cooperativity in multiunit biomotor assemblies by linking molecular motors to artificial protein scaffolds. This approach provides precise control over spatial and elastic coupling between motors. Cooperative interactions between monomeric kinesin-1 motors attached to protein scaffolds enhance hydrolysis activity and microtubule gliding velocity. However, these interactions are not influenced by changes in the elastic properties of the scaffold, distinguishing multimotor transport from that powered by unorganized monomeric motors. These results highlight the role of supramolecular architecture in determining mechanisms of collective transport.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Diehl, Michael R -- Zhang, Kechun -- Lee, Heun Jin -- Tirrell, David A -- New York, N.Y. -- Science. 2006 Mar 10;311(5766):1468-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA. diehl@rice.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16527982" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/chemistry ; Amino Acid Sequence ; Elasticity ; Elastin/chemistry ; Hydrolysis ; Kinesin/chemistry ; Microtubules/physiology ; Models, Biological ; Molecular Motor Proteins/*physiology ; Molecular Sequence Data ; Protein Engineering ; Protein Structure, Tertiary ; Proteins/chemistry/*physiology ; Recombinant Proteins/chemistry ; Structure-Activity Relationship
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  • 10
    Publication Date: 2006-01-28
    Description: The spread of H5N1 avian influenza viruses (AIVs) from China to Europe has raised global concern about their potential to infect humans and cause a pandemic. In spite of their substantial threat to human health, remarkably little AIV whole-genome information is available. We report here a preliminary analysis of the first large-scale sequencing of AIVs, including 2196 AIV genes and 169 complete genomes. We combine this new information with public AIV data to identify new gene alleles, persistent genotypes, compensatory mutations, and a potential virulence determinant.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Obenauer, John C -- Denson, Jackie -- Mehta, Perdeep K -- Su, Xiaoping -- Mukatira, Suraj -- Finkelstein, David B -- Xu, Xiequn -- Wang, Jinhua -- Ma, Jing -- Fan, Yiping -- Rakestraw, Karen M -- Webster, Robert G -- Hoffmann, Erich -- Krauss, Scott -- Zheng, Jie -- Zhang, Ziwei -- Naeve, Clayton W -- AI95357/AI/NIAID NIH HHS/ -- CA 21765/CA/NCI NIH HHS/ -- R01 GM061739/GM/NIGMS NIH HHS/ -- R01 GM069916/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Mar 17;311(5767):1576-80. Epub 2006 Jan 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16439620" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Birds/virology ; Computational Biology ; *Genes, Viral ; Genome, Viral ; Humans ; Influenza A Virus, H1N1 Subtype/genetics ; Influenza A Virus, H2N2 Subtype/genetics ; Influenza A Virus, H3N2 Subtype/genetics ; Influenza A Virus, H3N8 Subtype/genetics ; Influenza A Virus, H5N1 Subtype/chemistry/*genetics/pathogenicity ; Influenza A Virus, H5N2 Subtype/genetics ; Influenza A Virus, H7N7 Subtype/genetics ; Influenza A Virus, H9N2 Subtype/genetics ; Influenza A virus/chemistry/*genetics/isolation & purification/pathogenicity ; Influenza in Birds/virology ; Influenza, Human/virology ; Molecular Sequence Data ; Mutation ; Phylogeny ; RNA, Viral/genetics ; Reassortant Viruses/genetics ; Sequence Analysis, DNA ; Viral Nonstructural Proteins/*chemistry/genetics ; Viral Proteins/chemistry/genetics ; Virulence Factors/*chemistry/genetics
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