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  • 1
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    Genome sequence diversity and clues to the evolution of variola (smallpox) virus (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Characterization of a novel coronavirus associated with severe acute respiratory syndrome (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-06
    Description: In March 2003, a novel coronavirus (SARS-CoV) was discovered in association with cases of severe acute respiratory syndrome (SARS). The sequence of the complete genome of SARS-CoV was determined, and the initial characterization of the viral genome is presented in this report. The genome of SARS-CoV is 29,727 nucleotides in length and has 11 open reading frames, and its genome organization is similar to that of other coronaviruses. Phylogenetic analyses and sequence comparisons showed that SARS-CoV is not closely related to any of the previously characterized coronaviruses.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rota, Paul A -- Oberste, M Steven -- Monroe, Stephan S -- Nix, W Allan -- Campagnoli, Ray -- Icenogle, Joseph P -- Penaranda, Silvia -- Bankamp, Bettina -- Maher, Kaija -- Chen, Min-Hsin -- Tong, Suxiong -- Tamin, Azaibi -- Lowe, Luis -- Frace, Michael -- DeRisi, Joseph L -- Chen, Qi -- Wang, David -- Erdman, Dean D -- Peret, Teresa C T -- Burns, Cara -- Ksiazek, Thomas G -- Rollin, Pierre E -- Sanchez, Anthony -- Liffick, Stephanie -- Holloway, Brian -- Limor, Josef -- McCaustland, Karen -- Olsen-Rasmussen, Melissa -- Fouchier, Ron -- Gunther, Stephan -- Osterhaus, Albert D M E -- Drosten, Christian -- Pallansch, Mark A -- Anderson, Larry J -- Bellini, William J -- New York, N.Y. -- Science. 2003 May 30;300(5624):1394-9. Epub 2003 May 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA. prota@cdc.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12730500" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Conserved Sequence ; Coronavirus/classification/genetics ; DNA, Complementary ; Endopeptidases/chemistry/genetics ; *Genome, Viral ; Humans ; Membrane Glycoproteins/chemistry/genetics ; Molecular Sequence Data ; Nucleocapsid Proteins/chemistry/genetics ; Open Reading Frames ; Phylogeny ; Polyproteins/chemistry/genetics ; RNA Replicase/chemistry/genetics ; RNA, Messenger/genetics/metabolism ; RNA, Viral/*genetics ; Regulatory Sequences, Nucleic Acid ; SARS Virus/chemistry/classification/*genetics/isolation & purification ; Sequence Analysis, DNA ; Severe Acute Respiratory Syndrome/virology ; Spike Glycoprotein, Coronavirus ; Transcription, Genetic ; Viral Envelope Proteins/chemistry/genetics ; Viral Matrix Proteins/chemistry/genetics ; Viral Proteins/chemistry/*genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Darwinian selection on a selfing locus (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-18
    Description: The shift to self-pollination is one of the most prevalent evolutionary transitions in flowering plants. In the selfing plant Arabidopsis thaliana, pseudogenes at the SCR and SRK self-incompatibility loci are believed to underlie the evolution of self-fertilization. Positive directional selection has driven the evolutionary fixation of pseudogene alleles of SCR, leading to substantially reduced nucleotide variation. Coalescent simulations indicate that this adaptive event may have occurred very recently and is possibly associated with the post-Pleistocene expansion of A. thaliana from glacial refugia. This suggests that ancillary morphological innovations associated with self-pollination can evolve rapidly after the inactivation of the self-incompatibility response.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shimizu, Kentaro K -- Cork, Jennifer M -- Caicedo, Ana L -- Mays, Charlotte A -- Moore, Richard C -- Olsen, Kenneth M -- Ruzsa, Stephanie -- Coop, Graham -- Bustamante, Carlos D -- Awadalla, Philip -- Purugganan, Michael D -- New York, N.Y. -- Science. 2004 Dec 17;306(5704):2081-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, North Carolina State University, Box 7614, Raleigh, NC 27695, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15604405" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Arabidopsis/*genetics/*physiology ; Biological Evolution ; Chromosome Mapping ; Climate ; DNA, Intergenic ; *Genes, Plant ; Genetic Variation ; Genome, Plant ; Geography ; Haplotypes ; Likelihood Functions ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Plant Proteins ; Pollen ; Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Protein Kinases/*genetics/physiology ; *Pseudogenes ; Recombination, Genetic ; *Selection, Genetic ; Time
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Transmission of equine influenza virus to dogs (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-09-28
    Description: Molecular and antigenic analyses of three influenza viruses isolated from outbreaks of severe respiratory disease in racing greyhounds revealed that they are closely related to H3N8 equine influenza virus. Phylogenetic analysis indicated that the canine influenza virus genomes form a monophyletic group, consistent with a single interspecies virus transfer. Molecular changes in the hemagglutinin suggested adaptive evolution in the new host. The etiologic role of this virus in respiratory disease was supported by the temporal association of rising antibody titers with disease and by experimental inoculation studies. The geographic expansion of the infection and its persistence for several years indicate efficient transmission of canine influenza virus among greyhounds. Evidence of infection in pet dogs suggests that this infection may also become enzootic in this population.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Crawford, P C -- Dubovi, Edward J -- Castleman, William L -- Stephenson, Iain -- Gibbs, E P J -- Chen, Limei -- Smith, Catherine -- Hill, Richard C -- Ferro, Pamela -- Pompey, Justine -- Bright, Rick A -- Medina, Marie-Jo -- Johnson, Calvin M -- Olsen, Christopher W -- Cox, Nancy J -- Klimov, Alexander I -- Katz, Jacqueline M -- Donis, Ruben O -- New York, N.Y. -- Science. 2005 Oct 21;310(5747):482-5. Epub 2005 Sep 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16186182" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Antibodies, Viral/blood ; Cell Line ; Cytopathogenic Effect, Viral ; Disease Outbreaks/*veterinary ; Dog Diseases/epidemiology/pathology/*transmission/*virology ; Dogs ; Florida/epidemiology ; Hemagglutinin Glycoproteins, Influenza Virus/chemistry/genetics ; Horse Diseases/transmission/*virology ; Horses ; *Influenza A Virus, H3N8 Subtype/classification/immunology/isolation & ; purification/pathogenicity ; Molecular Sequence Data ; Orthomyxoviridae Infections/epidemiology/transmission/*veterinary/virology ; Phylogeny ; Respiratory System/pathology ; Sequence Analysis, RNA ; Species Specificity ; United States/epidemiology ; Virus Shedding
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Genomic minimalism in the early diverging intestinal parasite Giardia lamblia (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-29
    Description: The genome of the eukaryotic protist Giardia lamblia, an important human intestinal parasite, is compact in structure and content, contains few introns or mitochondrial relics, and has simplified machinery for DNA replication, transcription, RNA processing, and most metabolic pathways. Protein kinases comprise the single largest protein class and reflect Giardia's requirement for a complex signal transduction network for coordinating differentiation. Lateral gene transfer from bacterial and archaeal donors has shaped Giardia's genome, and previously unknown gene families, for example, cysteine-rich structural proteins, have been discovered. Unexpectedly, the genome shows little evidence of heterozygosity, supporting recent speculations that this organism is sexual. This genome sequence will not only be valuable for investigating the evolution of eukaryotes, but will also be applied to the search for new therapeutics for this parasite.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Morrison, Hilary G -- McArthur, Andrew G -- Gillin, Frances D -- Aley, Stephen B -- Adam, Rodney D -- Olsen, Gary J -- Best, Aaron A -- Cande, W Zacheus -- Chen, Feng -- Cipriano, Michael J -- Davids, Barbara J -- Dawson, Scott C -- Elmendorf, Heidi G -- Hehl, Adrian B -- Holder, Michael E -- Huse, Susan M -- Kim, Ulandt U -- Lasek-Nesselquist, Erica -- Manning, Gerard -- Nigam, Anuranjini -- Nixon, Julie E J -- Palm, Daniel -- Passamaneck, Nora E -- Prabhu, Anjali -- Reich, Claudia I -- Reiner, David S -- Samuelson, John -- Svard, Staffan G -- Sogin, Mitchell L -- AI42488/AI/NIAID NIH HHS/ -- AI43273/AI/NIAID NIH HHS/ -- AI51687/AI/NIAID NIH HHS/ -- R01 AI043273/AI/NIAID NIH HHS/ -- R01 AI048082/AI/NIAID NIH HHS/ -- R01 HG004164/HG/NHGRI NIH HHS/ -- R01 HG004164-01/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 28;317(5846):1921-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Marine Biological Laboratory, Woods Hole, MA 02543-1015, USA. morrison@mbl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17901334" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Biological Evolution ; DNA Replication/genetics ; *Eukaryotic Cells ; Gene Transfer, Horizontal ; Genes, Protozoan ; *Genome, Protozoan ; Genomics ; Giardia lamblia/classification/*genetics/physiology ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Kinases/genetics/metabolism ; Protozoan Proteins/chemistry/genetics/metabolism ; RNA Processing, Post-Transcriptional ; Signal Transduction ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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