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  • Base Sequence  (1,231)
  • Cloning, Molecular  (654)
  • American Association for the Advancement of Science (AAAS)  (1,699)
  • American Institute of Physics (AIP)
  • Oxford University Press
  • 2000-2004  (281)
  • 1995-1999  (582)
  • 1990-1994  (836)
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (1,699)
  • American Institute of Physics (AIP)
  • Oxford University Press
Years
Year
  • 1
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    Ultraconserved elements in the human genome (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-05-08
    Description: There are 481 segments longer than 200 base pairs (bp) that are absolutely conserved (100% identity with no insertions or deletions) between orthologous regions of the human, rat, and mouse genomes. Nearly all of these segments are also conserved in the chicken and dog genomes, with an average of 95 and 99% identity, respectively. Many are also significantly conserved in fish. These ultraconserved elements of the human genome are most often located either overlapping exons in genes involved in RNA processing or in introns or nearby genes involved in the regulation of transcription and development. Along with more than 5000 sequences of over 100 bp that are absolutely conserved among the three sequenced mammals, these represent a class of genetic elements whose functions and evolutionary origins are yet to be determined, but which are more highly conserved between these species than are proteins and appear to be essential for the ontogeny of mammals and other vertebrates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bejerano, Gill -- Pheasant, Michael -- Makunin, Igor -- Stephen, Stuart -- Kent, W James -- Mattick, John S -- Haussler, David -- 1P41HG02371/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2004 May 28;304(5675):1321-5. Epub 2004 May 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA. jill@soe.ucsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15131266" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Animals ; Base Sequence ; Chickens/genetics ; Computational Biology ; *Conserved Sequence ; DNA, Intergenic ; Dogs/genetics ; Evolution, Molecular ; Exons ; Gene Expression Regulation ; Genes ; Genome ; *Genome, Human ; Humans ; Introns ; Mice/genetics ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; RNA/chemistry/genetics/metabolism ; Rats/genetics ; Takifugu/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Coordination of meiotic recombination, pairing, and synapsis by PHS1 (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-06
    Description: Pairing, synapsis, and recombination are prerequisites for accurate chromosome segregation in meiosis. The phs1 gene in maize is required for pairing to occur between homologous chromosomes. In the phs1 mutant, homologous chromosome synapsis is completely replaced by synapsis between nonhomologous partners. The phs1 gene is also required for installation of the meiotic recombination machinery on chromosomes, as the mutant almost completely lacks chromosomal foci of the recombination protein RAD51. Thus, in the phs1 mutant, synapsis is uncoupled from recombination and pairing. The protein encoded by the phs1 gene likely acts in a multistep process to coordinate pairing, recombination, and synapsis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pawlowski, Wojciech P -- Golubovskaya, Inna N -- Timofejeva, Ljudmilla -- Meeley, Robert B -- Sheridan, William F -- Cande, W Zacheus -- New York, N.Y. -- Science. 2004 Jan 2;303(5654):89-92.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA. wpawlows@nature.berkeley.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14704428" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cell Nucleus/metabolism ; *Chromosome Pairing ; Chromosomes, Plant/*physiology ; Cloning, Molecular ; Conserved Sequence ; DNA, Plant/metabolism ; DNA-Binding Proteins ; Genes, Plant ; In Situ Hybridization, Fluorescence ; In Situ Nick-End Labeling/methods ; *Meiosis ; Molecular Sequence Data ; Mutation ; Phenotype ; Plant Proteins/chemistry/genetics/*physiology ; RNA, Ribosomal, 5S/genetics ; Rad51 Recombinase ; *Recombination, Genetic ; Sequence Alignment ; Synaptonemal Complex/metabolism/ultrastructure ; Telomere/physiology ; Zea mays/*genetics/physiology
    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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  • 3
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    The Biology of Genomes meeting. The case of the disappearing DNA hotspots (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-06-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2004 Jun 11;304(5677):1590.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15192195" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Biological Evolution ; *Genome ; *Genome, Human ; Humans ; Pan troglodytes/*genetics ; *Polymorphism, Single Nucleotide ; *Recombination, Genetic
    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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  • 4
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    Uridine addition after microRNA-directed cleavage (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-11-06
    Description: One of the important roles of microRNA (miRNA) is to direct the cleavage of messenger RNA (mRNA). However, the mechanisms of decay of the cleaved mRNA products is not well understood. We show that miRNA-directed cleavage products in organisms as diverse as Arabidopsis, mouse, and Epstein-Barr virus have at their 3' ends a stretch (1 to 24 nucleotides) of oligouridine posttranscriptionally added downstream of the cleavage site. This 3' uridine addition, as shown for Arabidopsis, is correlated with decapping and 5' shortening of the cleaved products, suggesting a mechanistic step in the miRNA-directed mRNA decay mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shen, Binzhang -- Goodman, Howard M -- New York, N.Y. -- Science. 2004 Nov 5;306(5698):997.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, and Department of Molecular Biology, Massachusetts General Hospital, 50 Blossom Street, Boston, MA 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15528436" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arabidopsis ; Cells, Cultured ; Cloning, Molecular ; Herpesvirus 4, Human/metabolism ; Humans ; Mice ; MicroRNAs/*metabolism ; Poly U/metabolism ; RNA, Messenger/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Uridine/*metabolism
    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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  • 5
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    Recruitment and spreading of the C. elegans dosage compensation complex along X chromosomes (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-21
    Description: To achieve X-chromosome dosage compensation, organisms must distinguish X chromosomes from autosomes. We identified multiple, cis-acting regions that recruit the Caenorhabditis elegans dosage compensation complex (DCC) through a search for regions of X that bind the complex when detached from X. The DCC normally assembles along the entire X chromosome, but not all detached regions recruit the complex, despite having genes known to be dosage compensated on the native X. Thus, the DCC binds first to recruitment sites, then spreads to neighboring X regions to accomplish chromosome-wide gene repression. From a large chromosomal domain, we defined a 793-base pair fragment that functions in vivo as an X-recognition element to recruit the DCC.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Csankovszki, Gyorgyi -- McDonel, Patrick -- Meyer, Barbara J -- F32-GM065007/GM/NIGMS NIH HHS/ -- R37-GM30702/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 20;303(5661):1182-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3204, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14976312" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Genetically Modified ; Base Sequence ; Binding Sites ; Caenorhabditis elegans/*genetics/metabolism ; Caenorhabditis elegans Proteins/*metabolism ; Carrier Proteins/metabolism ; Chromosomes/metabolism ; Cosmids ; DNA-Binding Proteins/metabolism ; Disorders of Sex Development ; *Dosage Compensation, Genetic ; Female ; In Situ Hybridization, Fluorescence ; Male ; Models, Genetic ; Molecular Sequence Data ; Nuclear Proteins/metabolism ; Repetitive Sequences, Nucleic Acid ; X Chromosome/*metabolism
    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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  • 6
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    Evolution of a protochordate allorecognition locus (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉De Tomaso, Anthony W -- Weissman, Irving L -- AI10332/AI/NIAID NIH HHS/ -- AI41588/AI/NIAID NIH HHS/ -- R01 AI041588/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 13;303(5660):977.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA. tdet@stanford.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14963321" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; *Biological Evolution ; Cloning, Molecular ; Crosses, Genetic ; Heterozygote ; Homozygote ; Immunogenetics ; *Polymorphism, Genetic ; Urochordata/*genetics/growth & development/immunology
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Mouse brain organization revealed through direct genome-scale TF expression analysis (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-25
    Description: In the developing brain, transcription factors (TFs) direct the formation of a diverse array of neurons and glia. We identifed 1445 putative TFs in the mouse genome. We used in situ hybridization to map the expression of over 1000 of these TFs and TF-coregulator genes in the brains of developing mice. We found that 349 of these genes showed restricted expression patterns that were adequate to describe the anatomical organization of the brain. We provide a comprehensive inventory of murine TFs and their expression patterns in a searchable brain atlas database.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gray, Paul A -- Fu, Hui -- Luo, Ping -- Zhao, Qing -- Yu, Jing -- Ferrari, Annette -- Tenzen, Toyoaki -- Yuk, Dong-In -- Tsung, Eric F -- Cai, Zhaohui -- Alberta, John A -- Cheng, Le-Ping -- Liu, Yang -- Stenman, Jan M -- Valerius, M Todd -- Billings, Nathan -- Kim, Haesun A -- Greenberg, Michael E -- McMahon, Andrew P -- Rowitch, David H -- Stiles, Charles D -- Ma, Qiufu -- New York, N.Y. -- Science. 2004 Dec 24;306(5705):2255-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15618518" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Newborn ; Brain/anatomy & histology/embryology/*growth & development/*metabolism ; Cloning, Molecular ; Corpus Striatum/anatomy & histology/embryology/growth & development/metabolism ; DNA Primers ; Databases, Factual ; *Gene Expression Profiling ; *Genome ; Hypothalamus/anatomy & histology/embryology/growth & development/metabolism ; In Situ Hybridization ; Mesencephalon/anatomy & histology/embryology/growth & development/metabolism ; Mice ; Neocortex/anatomy & histology/embryology/growth & development/metabolism ; Polymerase Chain Reaction ; Rhombencephalon/anatomy & histology/embryology/growth & development/metabolism ; Spinal Cord/anatomy & histology/embryology/growth & development/metabolism ; Thalamus/anatomy & histology/embryology/growth & development/metabolism ; Transcription Factors/*genetics/*metabolism
    Print ISSN: 0036-8075
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  • 8
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    Multiple Ebola virus transmission events and rapid decline of central African wildlife (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-17
    Description: Several human and animal Ebola outbreaks have occurred over the past 4 years in Gabon and the Republic of Congo. The human outbreaks consisted of multiple simultaneous epidemics caused by different viral strains, and each epidemic resulted from the handling of a distinct gorilla, chimpanzee, or duiker carcass. These animal populations declined markedly during human Ebola outbreaks, apparently as a result of Ebola infection. Recovered carcasses were infected by a variety of Ebola strains, suggesting that Ebola outbreaks in great apes result from multiple virus introductions from the natural host. Surveillance of animal mortality may help to predict and prevent human Ebola outbreaks.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leroy, Eric M -- Rouquet, Pierre -- Formenty, Pierre -- Souquiere, Sandrine -- Kilbourne, Annelisa -- Froment, Jean-Marc -- Bermejo, Magdalena -- Smit, Sheilag -- Karesh, William -- Swanepoel, Robert -- Zaki, Sherif R -- Rollin, Pierre E -- New York, N.Y. -- Science. 2004 Jan 16;303(5656):387-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Recherche pour le Developpement, UR034, Centre International de Recherches Medicales de Franceville, BP 769 Franceville, Gabon. Eric.Leroy@ird.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14726594" target="_blank"〉PubMed〈/a〉
    Keywords: Africa, Central/epidemiology ; Animals ; Animals, Wild/*virology ; Ape Diseases/*epidemiology/virology ; Base Sequence ; *Disease Outbreaks/veterinary ; Disease Reservoirs ; Ebolavirus/classification/*genetics/isolation & purification ; Gabon/epidemiology ; Genes, Viral ; Gorilla gorilla/virology ; Hemorrhagic Fever, Ebola/*epidemiology/transmission/*veterinary/virology ; Humans ; Molecular Sequence Data ; Pan troglodytes/virology ; Population Density ; Population Surveillance ; Ruminants/virology ; Viral Envelope Proteins/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    The complete genome sequence of Propionibacterium acnes, a commensal of human skin (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-08-03
    Description: Propionibacterium acnes is a major inhabitant of adult human skin, where it resides within sebaceous follicles, usually as a harmless commensal although it has been implicated in acne vulgaris formation. The entire genome sequence of this Gram-positive bacterium encodes 2333 putative genes and revealed numerous gene products involved in degrading host molecules, including sialidases, neuraminidases, endoglycoceramidases, lipases, and pore-forming factors. Surface-associated and other immunogenic factors have been identified, which might be involved in triggering acne inflammation and other P. acnes-associated diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bruggemann, Holger -- Henne, Anke -- Hoster, Frank -- Liesegang, Heiko -- Wiezer, Arnim -- Strittmatter, Axel -- Hujer, Sandra -- Durre, Peter -- Gottschalk, Gerhard -- New York, N.Y. -- Science. 2004 Jul 30;305(5684):671-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Gottingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Gottingen, Grisebachstrasse 8, 37077 Gottingen, Germany. hbruegg@pasteur.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15286373" target="_blank"〉PubMed〈/a〉
    Keywords: Acne Vulgaris/immunology/microbiology ; Amino Acid Motifs ; Amino Acid Sequence ; Antigens, Bacterial/chemistry/genetics ; Bacterial Proteins/chemistry/genetics/immunology ; Base Sequence ; Chromosomes, Bacterial/genetics ; Computational Biology ; Energy Metabolism ; Esterases/genetics/metabolism ; Genes, Bacterial ; *Genome, Bacterial ; Heat-Shock Proteins/chemistry/genetics ; Humans ; Hydrolases/genetics/metabolism ; Lipase/genetics/metabolism ; Molecular Sequence Data ; Oxidative Phosphorylation ; Propionibacterium acnes/*genetics/immunology/physiology ; *Sequence Analysis, DNA ; Skin/*microbiology
    Print ISSN: 0036-8075
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  • 10
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    Structure of the uncleaved human H1 hemagglutinin from the extinct 1918 influenza virus (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-07
    Description: The 1918 "Spanish" influenza pandemic represents the largest recorded outbreak of any infectious disease. The crystal structure of the uncleaved precursor of the major surface antigen of the extinct 1918 virus was determined at 3.0 angstrom resolution after reassembly of the hemagglutinin gene from viral RNA fragments preserved in 1918 formalin-fixed lung tissues. A narrow avian-like receptor-binding site, two previously unobserved histidine patches, and a less exposed surface loop at the cleavage site that activates viral membrane fusion reveal structural features primarily found in avian viruses, which may have contributed to the extraordinarily high infectivity and mortality rates observed during 1918.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stevens, James -- Corper, Adam L -- Basler, Christopher F -- Taubenberger, Jeffery K -- Palese, Peter -- Wilson, Ian A -- AI058113/AI/NIAID NIH HHS/ -- AI42266/AI/NIAID NIH HHS/ -- AI50619/AI/NIAID NIH HHS/ -- CA55896/CA/NCI NIH HHS/ -- P50-GM 62411/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1866-70. Epub 2004 Feb 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, The 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/14764887" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Carbohydrate Conformation ; Cloning, Molecular ; Crystallography, X-Ray ; Glycosylation ; Hemagglutinin Glycoproteins, Influenza Virus/*chemistry/metabolism ; Histidine/chemistry/metabolism ; History, 20th Century ; Humans ; Hydrogen Bonding ; Influenza A virus/classification/*immunology/pathogenicity ; Influenza, Human/epidemiology/history/virology ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Virus/metabolism ; Sialic Acids/metabolism
    Print ISSN: 0036-8075
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  • 11
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    RNA-mediated metal-metal bond formation in the synthesis of hexagonal palladium nanoparticles (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-04-17
    Description: RNA sequences have been discovered that mediate the growth of hexagonal palladium nanoparticles. In vitro selection techniques were used to evolve an initial library of approximately 10(14) unique RNA sequences through eight cycles of selection to yield several active sequence families. Of the five families, all representative members could form crystalline hexagonal palladium platelets. The palladium particle growth occurred in aqueous solution at ambient temperature, without any endogenous reducing agent, and at low concentrations of metal precursor (100 micromolar). Relative to metal precursor, the RNA concentration was significantly lower (1 micromolar), yet micrometer-size crystalline hexagonal palladium particles were formed rapidly (7.5 to 1 minutes).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gugliotti, Lina A -- Feldheim, Daniel L -- Eaton, Bruce E -- New York, N.Y. -- Science. 2004 May 7;304(5672):850-2. Epub 2004 Apr 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15087507" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Chemistry, Physical ; Crystallization ; DNA, Complementary ; DNA-Directed RNA Polymerases/metabolism ; *Nanotubes ; Palladium/*chemistry ; Particle Size ; Physicochemical Phenomena ; Polymerase Chain Reaction ; RNA/*chemistry ; Temperature ; Transcription, Genetic ; Viral Proteins
    Print ISSN: 0036-8075
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  • 12
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    Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-31
    Description: Sixty-one SARS coronavirus genomic sequences derived from the early, middle, and late phases of the severe acute respiratory syndrome (SARS) epidemic were analyzed together with two viral sequences from palm civets. Genotypes characteristic of each phase were discovered, and the earliest genotypes were similar to the animal SARS-like coronaviruses. Major deletions were observed in the Orf8 region of the genome, both at the start and the end of the epidemic. The neutral mutation rate of the viral genome was constant but the amino acid substitution rate of the coding sequences slowed during the course of the epidemic. The spike protein showed the strongest initial responses to positive selection pressures, followed by subsequent purifying selection and eventual stabilization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chinese SARS Molecular Epidemiology Consortium -- New York, N.Y. -- Science. 2004 Mar 12;303(5664):1666-9. Epub 2004 Jan 29.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14752165" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Amino Acid Substitution ; Animals ; Base Sequence ; Carnivora/virology ; China/epidemiology ; Cluster Analysis ; Coronavirus/genetics/isolation & purification ; *Disease Outbreaks ; *Evolution, Molecular ; *Genome, Viral ; Genotype ; Humans ; Membrane Glycoproteins/genetics ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Open Reading Frames ; Phylogeny ; Point Mutation ; RNA, Viral/genetics ; SARS Virus/*genetics/isolation & purification/physiology ; Selection, Genetic ; Sequence Deletion ; Severe Acute Respiratory Syndrome/*epidemiology/*virology ; Spike Glycoprotein, Coronavirus ; Viral Envelope Proteins/genetics ; Viral Matrix Proteins/chemistry/genetics
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  • 13
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    The ubiquitin ligase SCFFbw7 antagonizes apoptotic JNK signaling (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-24
    Description: Jun N-terminal kinases (JNKs) are essential for neuronal microtubule assembly and apoptosis. Phosphorylation of the activating protein 1 (AP1) transcription factor c-Jun, at multiple sites within its transactivation domain, is required for JNK-induced neurotoxicity. We report that in neurons the stability of c-Jun is regulated by the E3 ligase SCF(Fbw7), which ubiquitinates phosphorylated c-Jun and facilitates c-Jun degradation. Fbw7 depletion resulted in accumulation of phosphorylated c-Jun, stimulation of AP1 activity, and neuronal apoptosis. SCF(Fbw7) therefore antagonizes the apoptotic c-Jun-dependent effector arm of JNK signaling, allowing neurons to tolerate potentially neurotoxic JNK activity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nateri, Abdolrahman S -- Riera-Sans, Lluis -- Da Costa, Clive -- Behrens, Axel -- New York, N.Y. -- Science. 2004 Feb 27;303(5662):1374-8. Epub 2004 Jan 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Mammalian Genetics Laboratory, Cancer Research UK, London Research Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3PX, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14739463" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Apoptosis ; Base Sequence ; Cell Cycle Proteins/genetics/*metabolism ; Cell Line ; F-Box Proteins/genetics/*metabolism ; Humans ; JNK Mitogen-Activated Protein Kinases ; MAP Kinase Signaling System ; Mice ; Mitogen-Activated Protein Kinases/*metabolism ; Molecular Sequence Data ; Neurons/*physiology ; PC12 Cells ; Phosphorylation ; Proto-Oncogene Proteins c-jun/*metabolism ; RNA, Small Interfering/metabolism ; Rats ; Transcription Factor AP-1/metabolism ; Transfection ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligases/genetics/*metabolism
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  • 14
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    Lacticin 481: in vitro reconstitution of lantibiotic synthetase activity (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-31
    Description: The lantibiotic lacticin 481 is synthesized on ribosomes as a prepeptide (LctA) and posttranslationally modified to its mature form. These modifications include dehydration of serines and threonines, followed by intramolecular addition of cysteines to the unsaturated amino acids, which generates cyclic thioethers. This process breaks eight chemical bonds and forms six newbonds and is catalyzed by one enzyme, LctM. We have characterized the in vitro activity of LctM, which completely processed a series of LctA mutants, displaying a permissive substrate specificity that holds promise for antibiotic engineering.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xie, Lili -- Miller, Leah M -- Chatterjee, Champak -- Averin, Olga -- Kelleher, Neil L -- van der Donk, Wilfred A -- GM 067725/GM/NIGMS NIH HHS/ -- GM58822/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jan 30;303(5658):679-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14752162" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*biosynthesis/genetics ; *Bacteriocins ; Cloning, Molecular ; Cysteine/metabolism ; Enzymes/chemistry/genetics/isolation & purification/*metabolism ; Escherichia coli/genetics ; Lactococcus lactis/enzymology/genetics/*metabolism ; Molecular Sequence Data ; Mutation ; Protein Precursors/chemistry/metabolism ; Protein Processing, Post-Translational ; Serine/metabolism ; Spectrometry, Mass, Electrospray Ionization ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Substrate Specificity ; Threonine/metabolism
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  • 15
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    A previously unknown maltose transporter essential for starch degradation in leaves (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-06
    Description: A previously unknown maltose transporter is essential for the conversion of starch to sucrose in Arabidopsis leaves at night. The transporter was identified by isolating two allelic mutants with high starch levels and very high maltose, an intermediate of starch breakdown. The mutations affect a gene of previously unknown function, MEX1. We show that MEX1is a maltose transporter that is unrelated to other sugar transporters. The severe mex1 phenotype demonstrates that MEX1is the predominant route of carbohydrate export from chloroplasts at night. Homologous genes in plants including rice and potato indicate that maltose export is of widespread significance.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Niittyla, Totte -- Messerli, Gaelle -- Trevisan, Martine -- Chen, Jychian -- Smith, Alison M -- Zeeman, Samuel C -- New York, N.Y. -- Science. 2004 Jan 2;303(5654):87-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14704427" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Biological Transport ; Chloroplasts/metabolism ; Cloning, Molecular ; Crosses, Genetic ; DNA, Complementary ; Genes, Plant ; Glucose/metabolism ; Maltose/*metabolism ; Molecular Sequence Data ; Monosaccharide Transport Proteins/chemistry/genetics/*metabolism ; Mutation ; Phenotype ; Plant Leaves/*metabolism ; Recombinant Fusion Proteins/metabolism ; Sequence Alignment ; Starch/*metabolism
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  • 16
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    Femtomolar sensitivity of a NO sensor from Clostridium botulinum (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-09
    Description: Nitric oxide (NO) is extremely toxic to Clostridium botulinum, but its molecular targets are unknown. Here, we identify a heme protein sensor (SONO) that displays femtomolar affinity for NO. The crystal structure of the SONO heme domain reveals a previously undescribed fold and a strategically placed tyrosine residue that modulates heme-nitrosyl coordination. Furthermore, the domain architecture of a SONO ortholog cloned from Chlamydomonas reinhardtii indicates that NO signaling through cyclic guanosine monophosphate arose before the origin of multicellular eukaryotes. Our findings have broad implications for understanding bacterial responses to NO, as well as for the activation of mammalian NO-sensitive guanylyl cyclase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nioche, Pierre -- Berka, Vladimir -- Vipond, Julia -- Minton, Nigel -- Tsai, Ah-Lim -- Raman, C S -- AY343540/PHS HHS/ -- R01 AI054444/AI/NIAID NIH HHS/ -- R01 AI054444-05/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2004 Nov 26;306(5701):1550-3. Epub 2004 Oct 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Research Center and Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15472039" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Bacterial Proteins/chemistry/metabolism ; Biological Evolution ; Carrier Proteins/*chemistry/genetics/*metabolism ; Chemotaxis ; Chlamydomonas reinhardtii/chemistry/genetics/metabolism ; Cloning, Molecular ; Clostridium botulinum/*chemistry/genetics/*metabolism ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Escherichia coli/genetics/growth & development ; Guanylate Cyclase ; Heme/chemistry/metabolism ; Hemeproteins/*chemistry/genetics/*metabolism ; Humans ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Nitric Oxide/*metabolism ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protoporphyrins/analysis/metabolism ; Receptors, Cytoplasmic and Nuclear/chemistry/metabolism ; Sequence Alignment ; Signal Transduction ; Static Electricity ; Thermoanaerobacter/chemistry
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  • 17
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    MicroRNA-directed cleavage of HOXB8 mRNA (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-04-24
    Description: MicroRNAs (miRNAs) are endogenous approximately 22-nucleotide RNAs, some of which are known to play important regulatory roles in animals by targeting the messages of protein-coding genes for translational repression. We find that miR-196, a miRNA encoded at three paralogous locations in the A, B, and C mammalian HOX clusters, has extensive, evolutionarily conserved complementarity to messages of HOXB8, HOXC8, and HOXD8. RNA fragments diagnostic of miR-196-directed cleavage of HOXB8 were detected in mouse embryos. Cell culture experiments demonstrated down-regulation of HOXB8, HOXC8, HOXD8, and HOXA7 and supported the cleavage mechanism for miR-196-directed repression of HOXB8. These results point to a miRNA-mediated mechanism for the posttranscriptional restriction of HOX gene expression during vertebrate development and demonstrate that metazoan miRNAs can repress expression of their natural targets through mRNA cleavage in addition to inhibiting productive translation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yekta, Soraya -- Shih, I-Hung -- Bartel, David P -- New York, N.Y. -- Science. 2004 Apr 23;304(5670):594-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15105502" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions ; Animals ; Base Sequence ; Down-Regulation ; *Genes, Homeobox ; Genes, Reporter ; HeLa Cells ; Homeodomain Proteins/*genetics ; Humans ; Mice ; MicroRNAs/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Neoplasm Proteins/genetics ; RNA, Messenger/chemistry/*genetics/*metabolism ; Sequence Alignment ; Transcription Factors/genetics ; Transfection
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  • 18
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    Species-specific recognition of single-stranded RNA via toll-like receptor 7 and 8 (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-21
    Description: Double-stranded ribonucleic acid (dsRNA) serves as a danger signal associated with viral infection and leads to stimulation of innate immune cells. In contrast, the immunostimulatory potential of single-stranded RNA (ssRNA) is poorly understood and innate immune receptors for ssRNA are unknown. We report that guanosine (G)- and uridine (U)-rich ssRNA oligonucleotides derived from human immunodeficiency virus-1 (HIV-1) stimulate dendritic cells (DC) and macrophages to secrete interferon-alpha and proinflammatory, as well as regulatory, cytokines. By using Toll-like receptor (TLR)-deficient mice and genetic complementation, we show that murine TLR7 and human TLR8 mediate species-specific recognition of GU-rich ssRNA. These data suggest that ssRNA represents a physiological ligand for TLR7 and TLR8.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Heil, Florian -- Hemmi, Hiroaki -- Hochrein, Hubertus -- Ampenberger, Franziska -- Kirschning, Carsten -- Akira, Shizuo -- Lipford, Grayson -- Wagner, Hermann -- Bauer, Stefan -- New York, N.Y. -- Science. 2004 Mar 5;303(5663):1526-9. Epub 2004 Feb 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Medical Microbiology, Immunology and Hygiene, Technische Universitat Munchen, Trogerstr. 9, D - 81675 Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14976262" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing ; Animals ; Antigens, Differentiation/metabolism ; Base Sequence ; Cytokines/biosynthesis ; Dendritic Cells/*immunology ; Fatty Acids, Monounsaturated ; Genetic Complementation Test ; Guanosine/analysis ; HIV-1/genetics/*immunology ; Humans ; Interferon-alpha/biosynthesis ; Leukocytes, Mononuclear/immunology ; Macrophages/*immunology ; Membrane Glycoproteins/genetics/*metabolism ; Mice ; Mice, Inbred C57BL ; Myeloid Differentiation Factor 88 ; Oligoribonucleotides/chemistry/*immunology ; Quaternary Ammonium Compounds ; RNA, Viral/chemistry/*immunology/metabolism ; Receptors, Cell Surface/genetics/*metabolism ; Receptors, Immunologic/metabolism ; Species Specificity ; Thionucleotides/chemistry/immunology ; Toll-Like Receptor 7 ; Toll-Like Receptor 8 ; Toll-Like Receptors ; Transfection ; Uridine/analysis
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    Infectious diseases. WHO ramps up bird flu vaccine efforts (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Normile, Dennis -- New York, N.Y. -- Science. 2004 Jan 30;303(5658):609.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14752135" target="_blank"〉PubMed〈/a〉
    Keywords: Cloning, Molecular ; Hemagglutinins, Viral/genetics/immunology ; Humans ; Influenza A virus/genetics/*immunology ; *Influenza Vaccines ; Influenza, Human/*prevention & control/transmission/virology ; Neuraminidase/genetics/immunology ; Patents as Topic ; Vaccines, Synthetic ; *World Health Organization
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  • 20
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    A glycine-dependent riboswitch that uses cooperative binding to control gene expression (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-10-09
    Description: We identified a previously unknown riboswitch class in bacteria that is selectively triggered by glycine. A representative of these glycine-sensing RNAs from Bacillus subtilis operates as a rare genetic on switch for the gcvT operon, which codes for proteins that form the glycine cleavage system. Most glycine riboswitches integrate two ligand-binding domains that function cooperatively to more closely approximate a two-state genetic switch. This advanced form of riboswitch may have evolved to ensure that excess glycine is efficiently used to provide carbon flux through the citric acid cycle and maintain adequate amounts of the amino acid for protein synthesis. Thus, riboswitches perform key regulatory roles and exhibit complex performance characteristics that previously had been observed only with protein factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mandal, Maumita -- Lee, Mark -- Barrick, Jeffrey E -- Weinberg, Zasha -- Emilsson, Gail Mitchell -- Ruzzo, Walter L -- Breaker, Ronald R -- New York, N.Y. -- Science. 2004 Oct 8;306(5694):275-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular, and Developmental Biology, Yale University, Post Office 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/15472076" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Untranslated Regions/chemistry/*metabolism ; Allosteric Regulation ; Allosteric Site ; Bacillus subtilis/*genetics/metabolism ; Base Pairing ; Base Sequence ; Binding Sites ; *Gene Expression Regulation, Bacterial ; Glycine/*metabolism ; Ligands ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Operon ; RNA, Bacterial/chemistry/*metabolism ; RNA, Messenger/chemistry/*metabolism ; Transcription, Genetic ; Vibrio cholerae/*genetics/metabolism
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  • 21
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    Basis for structural diversity in homologous RNAs (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-10-02
    Description: Large RNA molecules, such as ribozymes, fold with well-defined tertiary structures that are important for their activity. There are many instances of ribozymes with identical function but differences in their secondary structures, suggesting alternative tertiary folds. Here, we report a crystal structure of the 161-nucleotide specificity domain of an A-type ribonuclease P that differs in secondary and tertiary structure from the specificity domain of a B-type molecule. Despite the differences, the cores of the domains have similar three-dimensional structure. Remarkably, the similar geometry of the cores is stabilized by a different set of interactions involving distinct auxiliary elements.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Krasilnikov, Andrey S -- Xiao, Yinghua -- Pan, Tao -- Mondragon, Alfonso -- New York, N.Y. -- Science. 2004 Oct 1;306(5693):104-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, IL 60208, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15459389" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Catalytic Domain ; Conserved Sequence ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA Precursors/chemistry/metabolism ; RNA, Bacterial/*chemistry/metabolism ; RNA, Transfer/chemistry/metabolism ; Ribonuclease P/*chemistry/metabolism ; Ribonucleotides/chemistry/metabolism ; Thermus thermophilus/*chemistry/enzymology
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    Global identification of human transcribed sequences with genome tiling arrays (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-11-13
    Description: Elucidating the transcribed regions of the genome constitutes a fundamental aspect of human biology, yet this remains an outstanding problem. To comprehensively identify coding sequences, we constructed a series of high-density oligonucleotide tiling arrays representing sense and antisense strands of the entire nonrepetitive sequence of the human genome. Transcribed sequences were located across the genome via hybridization to complementary DNA samples, reverse-transcribed from polyadenylated RNA obtained from human liver tissue. In addition to identifying many known and predicted genes, we found 10,595 transcribed sequences not detected by other methods. A large fraction of these are located in intergenic regions distal from previously annotated genes and exhibit significant homology to other mammalian proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bertone, Paul -- Stolc, Viktor -- Royce, Thomas E -- Rozowsky, Joel S -- Urban, Alexander E -- Zhu, Xiaowei -- Rinn, John L -- Tongprasit, Waraporn -- Samanta, Manoj -- Weissman, Sherman -- Gerstein, Mark -- Snyder, Michael -- P50 HG02357/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2004 Dec 24;306(5705):2242-6. Epub 2004 Nov 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15539566" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Computational Biology ; Conserved Sequence ; CpG Islands ; DNA, Complementary ; DNA, Intergenic ; Databases, Genetic ; Exons ; *Genome, Human ; Humans ; Introns ; Mice ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis/*methods ; Oligonucleotide Probes ; Proteins/chemistry/genetics ; RNA, Messenger/genetics ; Reproducibility of Results ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; *Transcription, Genetic
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  • 23
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    The genetic basis of singlet oxygen-induced stress responses of Arabidopsis thaliana (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-11-13
    Description: Plants under oxidative stress suffer from damages that have been interpreted as unavoidable consequences of injuries inflicted upon plants by toxic levels of reactive oxygen species (ROS). However, this paradigm needs to be modified. Inactivation of a single gene, EXECUTER1, is sufficient to abrogate stress responses of Arabidopsis thaliana caused by the release of singlet oxygen: External conditions under which these stress responses are observed and the amounts of ROS that accumulate in plants exposed to these environmental conditions do not directly cause damages. Instead, seedling lethality and growth inhibition of mature plants result from genetic programs that are activated after the release of singlet oxygen has been perceived by the plant.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wagner, Daniela -- Przybyla, Dominika -- Op den Camp, Roel -- Kim, Chanhong -- Landgraf, Frank -- Lee, Keun Pyo -- Wursch, Marco -- Laloi, Christophe -- Nater, Mena -- Hideg, Eva -- Apel, Klaus -- New York, N.Y. -- Science. 2004 Nov 12;306(5699):1183-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Plant Sciences, Plant Genetics, Swiss Federal Institute of Technology (ETH), CH-8092 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15539603" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/cytology/*genetics/growth & development/*physiology ; Arabidopsis Proteins/chemistry/*genetics/*physiology ; Cell Death/drug effects ; Chromosome Mapping ; Cloning, Molecular ; Cosmids ; Darkness ; Diuron/pharmacology ; Gene Expression Regulation, Plant ; Genes, Plant ; Genetic Complementation Test ; Light ; Molecular Sequence Data ; Mutation ; Open Reading Frames ; *Oxidative Stress ; Photosystem II Protein Complex/metabolism ; Plant Leaves/cytology/drug effects/metabolism ; Reactive Oxygen Species/metabolism ; Singlet Oxygen/*metabolism ; Transformation, Genetic
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  • 24
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    Plant cuticular lipid export requires an ABC transporter (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-23
    Description: A waxy protective cuticle coats all primary aerial plant tissues. Its synthesis requires extensive export of lipids from epidermal cells to the plant surface. Arabidopsis cer5 mutants had reduced stem cuticular wax loads and accumulated sheetlike inclusions in the cytoplasm of wax-secreting cells. These inclusions represented abnormal deposits of cuticular wax and resembled inclusions found in a human disorder caused by a defective peroxisomal adenosine triphosphate binding cassette (ABC) transporter. We found that the CER5 gene encodes an ABC transporter localized in the plasma membrane of epidermal cells and conclude that it is required for wax export to the cuticle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pighin, Jamie A -- Zheng, Huanquan -- Balakshin, Laura J -- Goodman, Ian P -- Western, Tamara L -- Jetter, Reinhard -- Kunst, Ljerka -- Samuels, A Lacey -- New York, N.Y. -- Science. 2004 Oct 22;306(5696):702-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Botany, University of British Columbia (UBC), 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15499022" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/chemistry/genetics/*metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Arabidopsis/cytology/genetics/*metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Biological Transport, Active ; Cell Membrane/metabolism ; Cloning, Molecular ; Dimerization ; Genes, Plant ; Inclusion Bodies/ultrastructure ; *Lipid Metabolism ; Microscopy, Electron ; Molecular Sequence Data ; Mutagenesis, Insertional ; Mutation ; Plant Epidermis/cytology/*metabolism/ultrastructure ; Plant Stems/cytology/metabolism/ultrastructure ; Plants, Genetically Modified ; Recombinant Fusion Proteins/metabolism ; Vacuoles/ultrastructure ; Waxes/*metabolism
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  • 25
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    A putative Ca2+ and calmodulin-dependent protein kinase required for bacterial and fungal symbioses (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-14
    Description: Legumes can enter into symbiotic relationships with both nitrogen-fixing bacteria (rhizobia) and mycorrhizal fungi. Nodulation by rhizobia results from a signal transduction pathway induced in legume roots by rhizobial Nod factors. DMI3, a Medicago truncatula gene that acts immediately downstream of calcium spiking in this signaling pathway and is required for both nodulation and mycorrhizal infection, has high sequence similarity to genes encoding calcium and calmodulin-dependent protein kinases (CCaMKs). This indicates that calcium spiking is likely an essential component of the signaling cascade leading to nodule development and mycorrhizal infection, and sheds light on the biological role of plant CCaMKs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Levy, Julien -- Bres, Cecile -- Geurts, Rene -- Chalhoub, Boulos -- Kulikova, Olga -- Duc, Gerard -- Journet, Etienne-Pascal -- Ane, Jean-Michel -- Lauber, Emmanuelle -- Bisseling, Ton -- Denarie, Jean -- Rosenberg, Charles -- Debelle, Frederic -- New York, N.Y. -- Science. 2004 Feb 27;303(5662):1361-4. Epub 2004 Feb 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire des Interactions Plantes-Microorganismes INRA-CNRS, BP27, 31326 Castanet-Tolosan Cedex, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14963335" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Calcium/metabolism ; Calcium Signaling ; Calcium-Calmodulin-Dependent Protein Kinases/chemistry/genetics/*metabolism ; Calmodulin/metabolism ; Chromosomes, Artificial, Bacterial ; Cloning, Molecular ; EF Hand Motifs ; Expressed Sequence Tags ; Gene Expression Regulation, Plant ; Genes, Plant ; Lipopolysaccharides/metabolism ; Medicago/*enzymology/genetics/microbiology ; Molecular Sequence Data ; Mutation ; Mycorrhizae/*physiology ; Peas/*enzymology/genetics/microbiology ; Plant Roots/enzymology/microbiology ; Protein Structure, Tertiary ; Rhizobium/genetics ; Sinorhizobium meliloti/*physiology ; *Symbiosis ; Transformation, Genetic
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    Cofolding organizes alfalfa mosaic virus RNA and coat protein for replication (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-18
    Description: Alfalfa mosaic virus genomic RNAs are infectious only when the viral coat protein binds to the RNA 3' termini. The crystal structure of an alfalfa mosaic virus RNA-peptide complex reveals that conserved AUGC repeats and Pro-Thr-x-Arg-Ser-x-x-Tyr coat protein amino acids cofold upon interacting. Alternating AUGC residues have opposite orientation, and they base pair in different adjacent duplexes. Localized RNA backbone reversals stabilized by arginine-guanine interactions place the adenosines and guanines in reverse order in the duplex. The results suggest that a uniform, organized 3' conformation, similar to that found on viral RNAs with transfer RNA-like ends, may be essential for replication.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1500904/" 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/PMC1500904/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guogas, Laura M -- Filman, David J -- Hogle, James M -- Gehrke, Lee -- AI20566/AI/NIAID NIH HHS/ -- GM42504/GM/NIGMS NIH HHS/ -- R01 AI020566/AI/NIAID NIH HHS/ -- R01 GM042504/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Dec 17;306(5704):2108-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15604410" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions ; Alfalfa mosaic virus/*chemistry/*physiology ; Amino Acid Sequence ; Base Pairing ; Base Sequence ; Binding Sites ; Capsid Proteins/*chemistry/metabolism ; Crystallization ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Folding ; Protein Structure, Secondary ; RNA, Viral/*chemistry/metabolism ; Repetitive Sequences, Nucleic Acid ; *Virus Replication
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    Translation of DNA signals into polymer assembly instructions (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-18
    Description: We developed a DNA nanomechanical device that enables the positional synthesis of products whose sequences are determined by the state of the device. This machine emulates the translational capabilities of the ribosome. The device has been prototyped to make specific DNA sequences. The state of the device is established by the addition of DNA set strands. There is no transcriptional relationship between the set strands and the product strands. The device has potential applications that include designer polymer synthesis, encryption of information, and use as a variable-input device for DNA-based computation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3470904/" 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/PMC3470904/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liao, Shiping -- Seeman, Nadrian C -- R37 GM029554/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Dec 17;306(5704):2072-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, New York University, New York, NY 10003, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15604403" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Chemistry, Physical ; DNA/*chemistry ; *Nanostructures ; Nanotechnology ; Nucleic Acid Conformation ; Physicochemical Phenomena ; Polymers/*chemistry ; Protein Biosynthesis ; RNA, Transfer/metabolism ; Ribosomes/metabolism
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    A membrane-anchored protein kinase involved in Brassica self-incompatibility signaling (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-06
    Description: Self-incompatibility (SI) response in Brassica is initiated by haplotype-specific interactions between the pollen-borne ligand S locus protein 11/SCR and its stigmatic S receptor kinase, SRK. This binding induces autophosphorylation of SRK, which is then thought to trigger a signaling cascade that leads to self-pollen rejection. A recessive mutation of the modifier (m) gene eliminates the SI response in stigma. Positional cloning of M has revealed that it encodes a membrane-anchored cytoplasmic serine/threonine protein kinase, designated M locus protein kinase (MLPK). Transient expression of MLPK restores the ability of mm papilla cells to reject self-pollen, suggesting that MLPK is a positive mediator of Brassica SI signaling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murase, Kohji -- Shiba, Hiroshi -- Iwano, Megumi -- Che, Fang-Sik -- Watanabe, Masao -- Isogai, Akira -- Takayama, Seiji -- New York, N.Y. -- Science. 2004 Mar 5;303(5663):1516-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0101, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15001779" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Brassica rapa/enzymology/genetics/*physiology ; Cell Membrane/*enzymology ; Cloning, Molecular ; Cytoplasm/enzymology ; Flowers/enzymology/*physiology ; Genes, Plant ; Haplotypes ; Membrane Proteins/chemistry/genetics/*metabolism ; Mutation ; Open Reading Frames ; Phosphorylation ; Physical Chromosome Mapping ; Plant Proteins ; Pollen/physiology ; Protein Kinases/*metabolism ; Protein-Serine-Threonine Kinases/chemistry/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; *Signal Transduction
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    The wheat VRN2 gene is a flowering repressor down-regulated by vernalization (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-16
    Description: Plants with a winter growth habit flower earlier when exposed for several weeks to cold temperatures, a process called vernalization. We report here the positional cloning of the wheat vernalization gene VRN2, a dominant repressor of flowering that is down-regulated by vernalization. Loss of function of VRN2, whether by natural mutations or deletions, resulted in spring lines, which do not require vernalization to flower. Reduction of the RNA level of VRN2 by RNA interference accelerated the flowering time of transgenic winter-wheat plants by more than a month.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4737501/" 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/PMC4737501/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yan, Liuling -- Loukoianov, Artem -- Blechl, Ann -- Tranquilli, Gabriela -- Ramakrishna, Wusirika -- SanMiguel, Phillip -- Bennetzen, Jeffrey L -- Echenique, Viviana -- Dubcovsky, Jorge -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2004 Mar 12;303(5664):1640-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Agronomy and Range Science, University of California, Davis, CA 95616, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15016992" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Arabidopsis/genetics/growth & development ; Base Sequence ; Chromosome Mapping ; Cloning, Molecular ; *Cold Temperature ; Down-Regulation ; Epistasis, Genetic ; Evolution, Molecular ; Flowers/*growth & development ; Gene Deletion ; *Gene Expression Regulation, Plant ; Genes, Plant ; Genetic Variation ; Hordeum/genetics ; Molecular Sequence Data ; Mutation ; Plant Proteins/chemistry/genetics/physiology ; Plants, Genetically Modified ; Promoter Regions, Genetic ; Protein Structure, Tertiary ; RNA Interference ; RNA, Messenger/genetics/metabolism ; RNA, Plant/genetics/metabolism ; Seasons ; Transcription, Genetic ; Triticum/*genetics/*growth & development
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    RNA branching and debranching in the yeast retrovirus-like element Ty1 (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-13
    Description: Ty elements of Saccharomyces cerevisiae are long terminal repeat (LTR) retroelements related to retroviruses. Normal levels of Ty1 transposition require Dbr1p, a cellular enzyme that cleaves 2'-5' RNA bonds. We show that Ty1 RNAs lacking identifiable 5' ends accumulate in virus-like particles (VLPs) in dbr1 mutants. Debranching this RNA in vitro with Dbr1p creates an uncapped version of the normal Ty1 RNA 5' end. We show that the 5' nucleotide (nt) of Ty1 RNA forms a 2'-5' bond with a nt near the 3' end of the same RNA, creating a lariat. The properties of the lariat suggest it forms by a novel mechanism and that branching and debranching may play roles in Ty1 reverse transcription at the minus-strand transfer step.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cheng, Zhi -- Menees, Thomas M -- New York, N.Y. -- Science. 2004 Jan 9;303(5655):240-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14716018" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Base Sequence ; Blotting, Northern ; DNA, Complementary/metabolism ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; RNA Caps ; RNA Nucleotidyltransferases/genetics/metabolism ; RNA, Fungal/*chemistry/genetics/*metabolism ; RNA, Messenger/chemistry/genetics/metabolism ; RNA-Directed DNA Polymerase/metabolism ; Retroelements/genetics/*physiology ; Reverse Transcriptase Polymerase Chain Reaction ; Ribonuclease H/metabolism ; Saccharomyces cerevisiae/*genetics ; Terminal Repeat Sequences ; Transcription, Genetic
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    Diversification of Ig superfamily genes in an invertebrate (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-07-13
    Description: The freshwater snail Biomphalaria glabrata possesses a diverse family of fibrinogen-related proteins (FREPs), hemolymph polypeptides that consist of one or two amino-terminal immunoglobulin superfamily (IgSF) domains and a carboxyl-terminal fibrinogen domain. Here, we show that the IgSF1 domain of the FREP3 subfamily is diversified at the genomic level at higher rates than those recorded for control genes. All sequence variants are derived from a small set of nine source sequences by point mutation and recombinatorial processes. Diverse FREP3 transcripts are also produced. We hypothesize a mechanism present in snails that is capable of diversifying molecules involved in internal defense.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Si-Ming -- Adema, Coen M -- Kepler, Thomas B -- Loker, Eric S -- R01AI24340/AI/NIAID NIH HHS/ -- R01AI52363/AI/NIAID NIH HHS/ -- RR-1P20RR18754/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2004 Jul 9;305(5681):251-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15247481" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Base Sequence ; Biomphalaria/embryology/*genetics/immunology ; Blotting, Southern ; Computational Biology ; DNA, Complementary ; Disorders of Sex Development ; Genes, Immunoglobulin ; *Genetic Variation ; Hemocytes ; Immunoglobulins/chemistry/*genetics ; Molecular Sequence Data ; Point Mutation ; Polymerase Chain Reaction ; Protein Structure, Tertiary ; Recombination, Genetic
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    Functional adaptation of BabA, the H. pylori ABO blood group antigen binding adhesin (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-07-27
    Description: Adherence by Helicobacter pylori increases the risk of gastric disease. Here, we report that more than 95% of strains that bind fucosylated blood group antigen bind A, B, and O antigens (generalists), whereas 60% of adherent South American Amerindian strains bind blood group O antigens best (specialists). This specialization coincides with the unique predominance of blood group O in these Amerindians. Strains differed about 1500-fold in binding affinities, and diversifying selection was evident in babA sequences. We propose that cycles of selection for increased and decreased bacterial adherence contribute to babA diversity and that these cycles have led to gradual replacement of generalist binding by specialist binding in blood group O-dominant human populations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aspholm-Hurtig, Marina -- Dailide, Giedrius -- Lahmann, Martina -- Kalia, Awdhesh -- Ilver, Dag -- Roche, Niamh -- Vikstrom, Susanne -- Sjostrom, Rolf -- Linden, Sara -- Backstrom, Anna -- Lundberg, Carina -- Arnqvist, Anna -- Mahdavi, Jafar -- Nilsson, Ulf J -- Velapatino, Billie -- Gilman, Robert H -- Gerhard, Markus -- Alarcon, Teresa -- Lopez-Brea, Manuel -- Nakazawa, Teruko -- Fox, James G -- Correa, Pelayo -- Dominguez-Bello, Maria Gloria -- Perez-Perez, Guillermo I -- Blaser, Martin J -- Normark, Staffan -- Carlstedt, Ingemar -- Oscarson, Stefan -- Teneberg, Susann -- Berg, Douglas E -- Boren, Thomas -- P30 DK52574/DK/NIDDK NIH HHS/ -- R01 AI38166/AI/NIAID NIH HHS/ -- R01 DK53727/DK/NIDDK NIH HHS/ -- R01 DK63041/DK/NIDDK NIH HHS/ -- R03 AI49161/AI/NIAID NIH HHS/ -- R0IGM62370/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jul 23;305(5683):519-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Odontology, section of Oral Microbiology, Umea University, SE-901 87 Umea, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15273394" target="_blank"〉PubMed〈/a〉
    Keywords: ABO Blood-Group System/*metabolism ; Adaptation, Biological ; Adhesins, Bacterial/chemistry/*genetics/immunology/*metabolism ; Alleles ; *Bacterial Adhesion ; Base Sequence ; Binding Sites ; Evolution, Molecular ; Fucose/metabolism ; Gastric Mucosa/microbiology ; Helicobacter Infections/microbiology ; Helicobacter pylori/genetics/immunology/*physiology ; Humans ; Indians, South American ; Lewis Blood-Group System/metabolism ; Molecular Sequence Data ; Mutation ; Peru ; Phenotype ; Phylogeny ; Protein Binding ; Selection, Genetic ; Transformation, Bacterial
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    The PIDDosome, a protein complex implicated in activation of caspase-2 in response to genotoxic stress (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-04-10
    Description: Apoptosis is triggered by activation of initiator caspases upon complex-mediated clustering of the inactive zymogen, as occurs in the caspase-9-activating apoptosome complex. Likewise, caspase-2, which is involved in stress-induced apoptosis, is recruited into a large protein complex, the molecular composition of which remains elusive. We show that activation of caspase-2 occurs in a complex that contains the death domain-containing protein PIDD, whose expression is induced by p53, and the adaptor protein RAIDD. Increased PIDD expression resulted in spontaneous activation of caspase-2 and sensitization to apoptosis by genotoxic stimuli. Because PIDD functions in p53-mediated apoptosis, the complex assembled by PIDD and caspase-2 is likely to regulate apoptosis induced by genotoxins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tinel, Antoine -- Tschopp, Jurg -- New York, N.Y. -- Science. 2004 May 7;304(5672):843-6. Epub 2004 Apr 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Lausanne, Chemin des Boveresses 155, CH-1066 Epalinges, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15073321" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptor Proteins, Signal Transducing ; *Apoptosis ; CRADD Signaling Adaptor Protein ; Carrier Proteins/chemistry/*metabolism ; Caspase 2 ; Caspases/*metabolism ; Cell Line ; Cell Line, Tumor ; Cloning, Molecular ; *DNA Damage ; Death Domain Receptor Signaling Adaptor Proteins ; Doxorubicin/pharmacology ; Enzyme Activation ; Etoposide/pharmacology ; Humans ; Protein Structure, Tertiary ; Proteins/chemistry/metabolism ; RNA, Small Interfering ; Signal Transduction ; Transfection ; Tumor Suppressor Protein p53/metabolism
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    Building programmable jigsaw puzzles with RNA (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-12-18
    Description: One challenge in supramolecular chemistry is the design of versatile, self-assembling building blocks to attain total control of arrangement of matter at a molecular level. We have achieved reliable prediction and design of the three-dimensional structure of artificial RNA building blocks to generate molecular jigsaw puzzle units called tectosquares. They can be programmed with control over their geometry, topology, directionality, and addressability to algorithmically self-assemble into a variety of complex nanoscopic fabrics with predefined periodic and aperiodic patterns and finite dimensions. This work emphasizes the modular and hierarchical characteristics of RNA by showing that small RNA structural motifs can code the precise topology of large molecular architectures. It demonstrates that fully addressable materials based on RNA can be synthesized and provides insights into self-assembly processes involving large populations of RNA molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chworos, Arkadiusz -- Severcan, Isil -- Koyfman, Alexey Y -- Weinkam, Patrick -- Oroudjev, Emin -- Hansma, Helen G -- Jaeger, Luc -- New York, N.Y. -- Science. 2004 Dec 17;306(5704):2068-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15604402" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Base Sequence ; Chemistry, Physical ; Dimerization ; Magnesium ; Microscopy, Atomic Force ; *Nanostructures ; Nucleic Acid Conformation ; Oligoribonucleotides/chemistry ; Physicochemical Phenomena ; RNA/*chemistry ; RNA, Ribosomal/chemistry ; Temperature ; Thermodynamics
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    The structure of a mycobacterial outer-membrane channel (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-02-21
    Description: Mycobacteria have low-permeability outer membranes that render them resistant to most antibiotics. Hydrophilic nutrients can enter by way of transmembrane-channel proteins called porins. An x-ray analysis of the main porin from Mycobacterium smegmatis, MspA, revealed a homooctameric goblet-like conformation with a single central channel. This is the first structure of a mycobacterial outer-membrane protein. No structure-related protein was found in the Protein Data Bank. MspA contains two consecutive beta barrels with nonpolar outer surfaces that form a ribbon around the porin, which is too narrow to fit the thickness of the mycobacterial outer membrane in contemporary models.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Faller, Michael -- Niederweis, Michael -- Schulz, Georg E -- New York, N.Y. -- Science. 2004 Feb 20;303(5661):1189-92.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14976314" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arginine/chemistry ; Cell Membrane Permeability ; Cloning, Molecular ; Crystallization ; Crystallography, X-Ray ; Electric Conductivity ; Escherichia coli/genetics ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Mycobacterium smegmatis/*chemistry/metabolism ; Porins/*chemistry/genetics/metabolism ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry
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    Positional signaling mediated by a receptor-like kinase in Arabidopsis (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-25
    Description: The position-dependent specification of root epidermal cells in Arabidopsis provides an elegant paradigm for cell patterning during development. Here, we describe a new gene, SCRAMBLED (SCM), required for cells to appropriately interpret their location within the developing root epidermis. SCM encodes a receptor-like kinase protein with a predicted extracellular domain of six leucine-rich repeats and an intracellular serine-threonine kinase domain. SCM regulates the expression of the GLABRA2, CAPRICE, WEREWOLF, and ENHANCER OF GLABRA3 transcription factor genes that define the cell fates. Further, the SCM gene is expressed throughout the developing root. Therefore, SCM likely enables developing epidermal cells to detect positional cues and establish an appropriate cell-type pattern.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kwak, Su-Hwan -- Shen, Ronglai -- Schiefelbein, John -- New York, N.Y. -- Science. 2005 Feb 18;307(5712):1111-3. Epub 2004 Dec 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15618487" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/cytology/*enzymology/*genetics/growth & development ; Arabidopsis Proteins/chemistry/*genetics/*metabolism ; Cell Division ; Cloning, Molecular ; Gene Expression Regulation, Plant ; Genes, Plant ; Genes, Reporter ; Hydrophobic and Hydrophilic Interactions ; In Situ Hybridization ; Molecular Sequence Data ; Mutation ; Plant Epidermis/cytology/enzymology/growth & development ; Plant Roots/cytology/enzymology/growth & development ; Plants, Genetically Modified ; Protein Sorting Signals ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/chemistry/*genetics/*metabolism ; RNA, Messenger/genetics/metabolism ; RNA, Plant/genetics/metabolism ; Receptor Protein-Tyrosine Kinases/chemistry/*genetics/*metabolism ; *Signal Transduction ; Transcription Factors/genetics/metabolism
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    Plant biology. Remembrance of winter past (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, Jean -- New York, N.Y. -- Science. 2004 Mar 12;303(5664):1607.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15016978" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/*genetics/growth & development ; Arabidopsis Proteins/genetics/physiology ; Carrier Proteins/genetics/physiology ; Cloning, Molecular ; *Cold Temperature ; DNA-Binding Proteins/genetics/physiology ; Flowers/*growth & development ; *Gene Expression Regulation, Plant ; Genes, Plant ; Genome, Plant ; MADS Domain Proteins/genetics/physiology ; Nuclear Proteins/genetics/physiology ; Plant Proteins/physiology ; Repressor Proteins/genetics/physiology ; Triticum/*genetics/*growth & development
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    Identification of virus-encoded microRNAs (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-05-01
    Description: RNA silencing processes are guided by small RNAs that are derived from double-stranded RNA. To probe for function of RNA silencing during infection of human cells by a DNA virus, we recorded the small RNA profile of cells infected by Epstein-Barr virus (EBV). We show that EBV expresses several microRNA (miRNA) genes. Given that miRNAs function in RNA silencing pathways either by targeting messenger RNAs for degradation or by repressing translation, we identified viral regulators of host and/or viral gene expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pfeffer, Sebastien -- Zavolan, Mihaela -- Grasser, Friedrich A -- Chien, Minchen -- Russo, James J -- Ju, Jingyue -- John, Bino -- Enright, Anton J -- Marks, Debora -- Sander, Chris -- Tuschl, Thomas -- R01-GM068476-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Apr 30;304(5671):734-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15118162" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Callithrix ; Cell Line ; Cell Line, Tumor ; Cloning, Molecular ; Computational Biology ; DNA-Binding Proteins/genetics/metabolism ; DNA-Directed DNA Polymerase/genetics/metabolism ; Gene Expression ; Herpesvirus 4, Human/*genetics/physiology ; Humans ; MicroRNAs/*genetics/metabolism ; Proteins/genetics/metabolism ; *RNA Interference ; RNA, Double-Stranded/genetics ; RNA, Messenger/genetics/metabolism ; RNA, Viral/*genetics/metabolism ; Untranslated Regions ; Viral Proteins/genetics/metabolism ; Virus Latency
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    Human De-etiolated-1 regulates c-Jun by assembling a CUL4A ubiquitin ligase (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-24
    Description: Arabidopsis thaliana De-etiolated-1 (AtDET1) is a highly conserved protein, with orthologs in vertebrate and invertebrate organisms. AtDET1 negatively regulates photomorphogenesis, but its biochemical mechanism and function in other species are unknown. We report that human DET1 (hDET1) promotes ubiquitination and degradation of the proto-oncogenic transcription factor c-Jun by assembling a multisubunit ubiquitin ligase containing DNA Damage Binding Protein-1 (DDB1), cullin 4A (CUL4A), Regulator of Cullins-1 (ROC1), and constitutively photomorphogenic-1. Ablation of any subunit by RNA interference stabilized c-Jun and increased c-Jun-activated transcription. These findings characterize a c-Jun ubiquitin ligase and define a specific function for hDET1 in mammalian cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wertz, Ingrid E -- O'Rourke, Karen M -- Zhang, Zemin -- Dornan, David -- Arnott, David -- Deshaies, Raymond J -- Dixit, Vishva M -- GM065997/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 27;303(5662):1371-4. Epub 2004 Jan 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Oncology, Genentech, Inc., South San Francisco, CA 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14739464" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Carrier Proteins/chemistry/genetics/*metabolism ; Cell Line ; Cloning, Molecular ; Cullin Proteins/genetics/*metabolism ; DNA-Binding Proteins/metabolism ; Genes, jun ; Humans ; Molecular Sequence Data ; Nuclear Proteins/chemistry/genetics/metabolism ; Protein Binding ; Proteomics ; Proto-Oncogene Proteins c-jun/*metabolism ; RNA, Messenger/genetics/metabolism ; RNA, Small Interfering/metabolism ; Transfection ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligases/chemistry/*metabolism
    Print ISSN: 0036-8075
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    Reverse methanogenesis: testing the hypothesis with environmental genomics (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-09-09
    Description: Microbial methane consumption in anoxic sediments significantly impacts the global environment by reducing the flux of greenhouse gases from ocean to atmosphere. Despite its significance, the biological mechanisms controlling anaerobic methane oxidation are not well characterized. One current model suggests that relatives of methane-producing Archaea developed the capacity to reverse methanogenesis and thereby to consume methane to produce cellular carbon and energy. We report here a test of the "reverse-methanogenesis" hypothesis by genomic analyses of methane-oxidizing Archaea from deep-sea sediments. Our results show that nearly all genes typically associated with methane production are present in one specific group of archaeal methanotrophs. These genome-based observations support previous hypotheses and provide an informed foundation for metabolic modeling of anaerobic methane oxidation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hallam, Steven J -- Putnam, Nik -- Preston, Christina M -- Detter, John C -- Rokhsar, Daniel -- Richardson, Paul M -- DeLong, Edward F -- New York, N.Y. -- Science. 2004 Sep 3;305(5689):1457-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Monterey Bay Aquarium Research Institute, Moss Landing, CA 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15353801" target="_blank"〉PubMed〈/a〉
    Keywords: Anaerobiosis ; Archaea/classification/genetics/*metabolism ; Carbon Dioxide/metabolism ; Cloning, Molecular ; Gene Library ; Genes, Archaeal ; Genes, rRNA ; *Genome, Archaeal ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Phylogeny ; Pterins/metabolism ; RNA, Archaeal/genetics ; RNA, Ribosomal/genetics ; Seawater/microbiology ; Sulfates/metabolism
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    Materials science. Nucleic acid nanotechnology (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yan, Hao -- New York, N.Y. -- Science. 2004 Dec 17;306(5704):2048-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biodesign Institute and the Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA. hao.yan@asu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15604395" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Base Sequence ; Chemistry, Physical ; DNA/*chemistry ; *Nanostructures ; Nanotechnology ; Nucleic Acid Conformation ; Physicochemical Phenomena ; Polymers/*chemistry ; RNA/*chemistry ; Ribosomes
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    Dendrite development regulated by CREST, a calcium-regulated transcriptional activator (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-13
    Description: The lasting effects of neuronal activity on brain development involve calcium-dependent gene expression. Using a strategy called transactivator trap, we cloned a calcium-responsive transactivator called CREST (for calcium-responsive transactivator). CREST is a SYT-related nuclear protein that interacts with adenosine 3',5'-monophosphate (cAMP) response element-binding protein (CREB)-binding protein (CBP) and is expressed in the developing brain. Mice that have a targeted disruption of the crest gene are viable but display defects in cortical and hippocampal dendrite development. Cortical neurons from crest mutant mice are compromised in calcium-dependent dendritic growth. Thus, calcium activation of CREST-mediated transcription helps regulate neuronal morphogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aizawa, Hiroyuki -- Hu, Shu-Ching -- Bobb, Kathryn -- Balakrishnan, Karthik -- Ince, Gulayse -- Gurevich, Inga -- Cowan, Mitra -- Ghosh, Anirvan -- MH60598/MH/NIMH NIH HHS/ -- NS39993/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jan 9;303(5655):197-202.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14716005" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Blotting, Northern ; Brain/cytology/embryology/growth & development/metabolism ; CREB-Binding Protein ; Calcium/*metabolism ; Calcium Channels/metabolism ; Cell Line ; Cells, Cultured ; Cerebral Cortex/cytology/embryology/metabolism ; Cloning, Molecular ; Dendrites/*physiology/ultrastructure ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Library ; Gene Targeting ; Humans ; In Situ Hybridization ; Mice ; Mice, Knockout ; Molecular Sequence Data ; Mutation ; Nervous System/embryology/growth & development/metabolism ; Neurons/*physiology/ultrastructure ; Nuclear Proteins/metabolism ; Protein Structure, Tertiary ; Rats ; Recombinant Fusion Proteins/metabolism ; Trans-Activators/chemistry/genetics/*metabolism ; *Transcription, Genetic ; *Transcriptional Activation ; Transfection
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    Host-parasite coevolutionary conflict between Arabidopsis and downy mildew (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-14
    Description: Plants are constantly exposed to attack by an array of diverse pathogens but lack a somatically adaptive immune system. In spite of this, natural plant populations do not often suffer destructive disease epidemics. Elucidating how allelic diversity within plant genes that function to detect pathogens (resistance genes) counteracts changing structures of pathogen genes required for host invasion (pathogenicity effectors) is critical to our understanding of the dynamics of natural plant populations. The RPP13 resistance gene is the most polymorphic gene analyzed to date in the model plant Arabidopsis thaliana. Here we report the cloning of the avirulence gene, ATR13, that triggers RPP13-mediated resistance, and we show that it too exhibits extreme levels of amino acid polymorphism. Evidence of diversifying selection visible in both components suggests that the host and pathogen may be locked in a coevolutionary conflict at these loci, where attempts to evade host resistance by the pathogen are matched by the development of new detection capabilities by the host.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Allen, Rebecca L -- Bittner-Eddy, Peter D -- Grenville-Briggs, Laura J -- Meitz, Julia C -- Rehmany, Anne P -- Rose, Laura E -- Beynon, Jim L -- New York, N.Y. -- Science. 2004 Dec 10;306(5703):1957-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Warwick, HRI University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15591208" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/genetics/metabolism/*microbiology ; Arabidopsis Proteins/*genetics/metabolism ; Biolistics ; *Biological Evolution ; Cloning, Molecular ; Fungal Proteins/chemistry/*genetics/physiology ; *Genes, Fungal ; *Genes, Plant ; Molecular Sequence Data ; Oomycetes/*genetics/pathogenicity/physiology ; Plant Diseases/microbiology ; Polymorphism, Genetic ; Protein Sorting Signals ; Selection, Genetic
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    Ciliary photoreceptors with a vertebrate-type opsin in an invertebrate brain (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-30
    Description: For vision, insect and vertebrate eyes use rhabdomeric and ciliary photoreceptor cells, respectively. These cells show distinct architecture and transduce the light signal by different phototransductory cascades. In the marine rag-worm Platynereis, we find both cell types: rhabdomeric photoreceptor cells in the eyes and ciliary photoreceptor cells in the brain. The latter use a photopigment closely related to vertebrate rod and cone opsins. Comparative analysis indicates that both types of photoreceptors, with distinct opsins, coexisted in Urbilateria, the last common ancestor of insects and vertebrates, and sheds new light on vertebrate eye evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Arendt, Detlev -- Tessmar-Raible, Kristin -- Snyman, Heidi -- Dorresteijn, Adriaan W -- Wittbrodt, Joachim -- New York, N.Y. -- Science. 2004 Oct 29;306(5697):869-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Developmental Biology Department, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany. detlev.arendt@embl.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15514158" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Biological Evolution ; Brain/cytology ; Cilia/ultrastructure ; Circadian Rhythm ; Cloning, Molecular ; Conserved Sequence ; Eye/cytology ; Gene Duplication ; Genes, Homeobox ; Molecular Sequence Data ; Photoreceptor Cells, Invertebrate/*chemistry/cytology ; Photoreceptor Cells, Vertebrate/chemistry/cytology ; Phylogeny ; Polychaeta/chemistry/*cytology/*genetics ; Retinal Ganglion Cells/cytology ; Rod Opsins/analysis/*chemistry/*genetics
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    A toll-like receptor that prevents infection by uropathogenic bacteria (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-06
    Description: Toll-like receptors (TLRs) recognize molecular patterns displayed by microorganisms, and their subsequent activation leads to the transcription of appropriate host-defense genes. Here we report the cloning and characterization of a member of the mammalian TLR family, TLR11, that displays a distinct pattern of expression in macrophages and liver, kidney, and bladder epithelial cells. Cells expressing TLR11 fail to respond to known TLR ligands but instead respond specifically to uropathogenic bacteria. Mice lacking TLR11 are highly susceptible to infection of the kidneys by uropathogenic bacteria, indicating a potentially important role for TLR11 in preventing infection of internal organs of the urogenital system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Dekai -- Zhang, Guolong -- Hayden, Matthew S -- Greenblatt, Matthew B -- Bussey, Crystal -- Flavell, Richard A -- Ghosh, Sankar -- GM07205/GM/NIGMS NIH HHS/ -- R01-AI59440/AI/NIAID NIH HHS/ -- R37-AI33443/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2004 Mar 5;303(5663):1522-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Immunobiology and Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15001781" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cell Line ; Cloning, Molecular ; Codon, Terminator ; Colony Count, Microbial ; Disease Susceptibility ; Epithelial Cells/metabolism ; Escherichia coli/growth & development/immunology/*pathogenicity ; Escherichia coli Infections/*immunology/microbiology ; Gene Expression Profiling ; Humans ; Immunity, Innate ; Kidney/immunology/*metabolism/microbiology ; Ligands ; Liver/metabolism ; Macrophages/metabolism ; Mice ; Mice, Knockout ; Molecular Sequence Data ; NF-kappa B/metabolism ; Polymorphism, Genetic ; Receptors, Cell Surface/chemistry/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Signal Transduction ; Toll-Like Receptors ; Transfection ; Tumor Necrosis Factor-alpha/metabolism ; Urinary Bladder/immunology/*metabolism/microbiology ; Urinary Tract Infections/*immunology/microbiology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Medicago truncatula DMI1 required for bacterial and fungal symbioses in legumes (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-14
    Description: Legumes form symbiotic associations with both mycorrhizal fungi and nitrogen-fixing soil bacteria called rhizobia. Several of the plant genes required for transduction of rhizobial signals, the Nod factors, are also necessary for mycorrhizal symbiosis. Here, we describe the cloning and characterization of one such gene from the legume Medicago truncatula. The DMI1 (does not make infections) gene encodes a novel protein with low global similarity to a ligand-gated cation channel domain of archaea. The protein is highly conserved in angiosperms and ancestral to land plants. We suggest that DMI1 represents an ancient plant-specific innovation, potentially enabling mycorrhizal associations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ane, Jean-Michel -- Kiss, Gyorgy B -- Riely, Brendan K -- Penmetsa, R Varma -- Oldroyd, Giles E D -- Ayax, Celine -- Levy, Julien -- Debelle, Frederic -- Baek, Jong-Min -- Kalo, Peter -- Rosenberg, Charles -- Roe, Bruce A -- Long, Sharon R -- Denarie, Jean -- Cook, Douglas R -- New York, N.Y. -- Science. 2004 Feb 27;303(5662):1364-7. Epub 2004 Feb 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14963334" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Arabidopsis/genetics ; Chromosomes, Artificial, Bacterial ; Cloning, Molecular ; Fabaceae/genetics/metabolism/microbiology ; Gene Expression Regulation, Plant ; *Genes, Plant ; Lipopolysaccharides/metabolism ; Medicago/*genetics/metabolism/*microbiology ; Molecular Sequence Data ; Mycorrhizae/*physiology ; Nitrogen Fixation ; Phylogeny ; Plant Proteins/chemistry/genetics/*physiology ; Plant Roots/metabolism ; Protein Structure, Tertiary ; Recombination, Genetic ; Rhizobiaceae/*physiology ; Sequence Homology, Amino Acid ; Signal Transduction ; *Symbiosis ; Transgenes
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    Retrograde viral delivery of IGF-1 prolongs survival in a mouse ALS model (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-09
    Description: Amyotrophic lateral sclerosis (ALS) is a progressive, lethal neuromuscular disease that is associated with the degeneration of spinal and brainstem motor neurons, leading to atrophy of limb, axial, and respiratory muscles. The cause of ALS is unknown, and there is no effective therapy. Neurotrophic factors are candidates for therapeutic evaluation in ALS. Although chronic delivery of molecules to the central nervous system has proven difficult, we recently discovered that adeno-associated virus can be retrogradely transported efficiently from muscle to motor neurons of the spinal cord. We report that insulin-like growth factor 1 prolongs life and delays disease progression, even when delivered at the time of overt disease symptoms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kaspar, Brian K -- Llado, Jeronia -- Sherkat, Nushin -- Rothstein, Jeffrey D -- Gage, Fred H -- AG12992/AG/NIA NIH HHS/ -- AG21876/AG/NIA NIH HHS/ -- NS33958/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2003 Aug 8;301(5634):839-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Genetics, 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/12907804" target="_blank"〉PubMed〈/a〉
    Keywords: Amyotrophic Lateral Sclerosis/pathology/physiopathology/*therapy ; Animals ; Apoptosis ; Base Sequence ; Caspase 9 ; Caspases/metabolism ; Cell Count ; Dependovirus/*genetics ; Disease Models, Animal ; Disease Progression ; Gene Transfer Techniques ; *Genetic Therapy ; *Genetic Vectors/administration & dosage ; Glial Cell Line-Derived Neurotrophic Factor ; Green Fluorescent Proteins ; Insulin-Like Growth Factor I/*genetics ; Luminescent Proteins/genetics ; Male ; Mice ; Mice, Transgenic ; Molecular Sequence Data ; Motor Neurons/pathology/virology ; Muscle, Skeletal/virology ; Nerve Growth Factors/genetics ; *Protein-Serine-Threonine Kinases ; Proto-Oncogene Proteins/metabolism ; Proto-Oncogene Proteins c-akt ; Random Allocation ; Spinal Cord/chemistry/pathology/virology ; Superoxide Dismutase/genetics/metabolism ; Ubiquitin/analysis
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    Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs) (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-10-04
    Description: Analysis of the human and mouse genomes identified an abundance of conserved non-genic sequences (CNGs). The significance and evolutionary depth of their conservation remain unanswered. We have quantified levels and patterns of conservation of 191 CNGs of human chromosome 21 in 14 mammalian species. We found that CNGs are significantly more conserved than protein-coding genes and noncoding RNAS (ncRNAs) within the mammalian class from primates to monotremes to marsupials. The pattern of substitutions in CNGs differed from that seen in protein-coding and ncRNA genes and resembled that of protein-binding regions. About 0.3% to 1% of the human genome corresponds to a previously unknown class of extremely constrained CNGs shared among mammals.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dermitzakis, Emmanouil T -- Reymond, Alexandre -- Scamuffa, Nathalie -- Ucla, Catherine -- Kirkness, Ewen -- Rossier, Colette -- Antonarakis, Stylianos E -- New York, N.Y. -- Science. 2003 Nov 7;302(5647):1033-5. Epub 2003 Oct 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Medical Genetics and National Center of Competence in Research (NCCR) Frontiers in Genetics, University of Geneva Medical School and University Hospitals, 1211 Geneva, Switzerland. Emmanouil.Dermitzakis@medecine.unige.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14526086" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Chromosomes, Human, Pair 21/*genetics ; Chromosomes, Mammalian/*genetics ; *Conserved Sequence ; DNA, Intergenic/*genetics ; Discriminant Analysis ; *Evolution, Molecular ; Female ; Genetic Code ; Genome ; Humans ; Male ; Mammals/*genetics ; Molecular Sequence Data ; Polymerase Chain Reaction ; Proteins/genetics ; RNA, Untranslated/genetics ; Selection, Genetic ; Sequence Alignment ; Species Specificity ; Time ; Transcription, Genetic
    Print ISSN: 0036-8075
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    Enrichment of gene-coding sequences in maize by genome filtration (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-20
    Description: Approximately 80% of the maize genome comprises highly repetitive sequences interspersed with single-copy, gene-rich sequences, and standard genome sequencing strategies are not readily adaptable to this type of genome. Methodologies that enrich for genic sequences might more rapidly generate useful results from complex genomes. Equivalent numbers of clones from maize selected by techniques called methylation filtering and High C0t selection were sequenced to generate approximately 200,000 reads (approximately 132 megabases), which were assembled into contigs. Combination of the two techniques resulted in a sixfold reduction in the effective genome size and a fourfold increase in the gene identification rate in comparison to a nonenriched library.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Whitelaw, C A -- Barbazuk, W B -- Pertea, G -- Chan, A P -- Cheung, F -- Lee, Y -- Zheng, L -- van Heeringen, S -- Karamycheva, S -- Bennetzen, J L -- SanMiguel, P -- Lakey, N -- Bedell, J -- Yuan, Y -- Budiman, M A -- Resnick, A -- Van Aken, S -- Utterback, T -- Riedmuller, S -- Williams, M -- Feldblyum, T -- Schubert, K -- Beachy, R -- Fraser, C M -- Quackenbush, J -- New York, N.Y. -- Science. 2003 Dec 19;302(5653):2118-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Institute for Genomic Research (TIGR), 9712 Medical Center Drive, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14684821" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosomes, Plant/genetics ; Cloning, Molecular ; Computational Biology ; Contig Mapping ; DNA Methylation ; DNA, Plant/genetics ; Databases, Nucleic Acid ; Expressed Sequence Tags ; Gene Dosage ; Gene Library ; *Genes, Plant ; *Genome, Plant ; Molecular Sequence Data ; Repetitive Sequences, Nucleic Acid ; Retroelements ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; Transcription, Genetic ; Zea mays/*genetics
    Print ISSN: 0036-8075
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    Whales before whaling in the North Atlantic (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-07-26
    Description: It is well known that hunting dramatically reduced all baleen whale populations, yet reliable estimates of former whale abundances are elusive. Based on coalescent models for mitochondrial DNA sequence variation, the genetic diversity of North Atlantic whales suggests population sizes of approximately 240,000 humpback, 360,000 fin, and 265,000 minke whales. Estimates for fin and humpback whales are far greater than those previously calculated for prewhaling populations and 6 to 20 times higher than present-day population estimates. Such discrepancies suggest the need for a quantitative reevaluation of historical whale populations and a fundamental revision in our conception of the natural state of the oceans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roman, Joe -- Palumbi, Stephen R -- New York, N.Y. -- Science. 2003 Jul 25;301(5632):508-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12881568" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Atlantic Ocean ; Base Sequence ; Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; *Ecosystem ; Female ; Genetic Variation ; Genetics, Population ; Male ; Molecular Sequence Data ; Population Density ; Population Dynamics ; Time Factors ; *Whales/classification/genetics
    Print ISSN: 0036-8075
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    Genetic control of surface curvature (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-01
    Description: Although curvature of biological surfaces has been considered from mathematical and biophysical perspectives, its molecular and developmental basis is unclear. We have studied the cin mutant of Antirrhinum, which has crinkly rather than flat leaves. Leaves of cin display excess growth in marginal regions, resulting in a gradual introduction of negative curvature during development. This reflects a change in the shape and the progression of a cell-cycle arrest front moving from the leaf tip toward the base. CIN encodes a TCP protein and is expressed downstream of the arrest front. We propose that CIN promotes zero curvature (flatness) by making cells more sensitive to an arrest signal, particularly in marginal regions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nath, Utpal -- Crawford, Brian C W -- Carpenter, Rosemary -- Coen, Enrico -- New York, N.Y. -- Science. 2003 Feb 28;299(5611):1404-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12610308" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antirrhinum/cytology/*genetics/*growth & development/metabolism ; Base Sequence ; Cell Cycle ; Cell Differentiation ; Cell Division ; Cell Size ; Cyclin D3 ; Cyclins/genetics/metabolism ; Gene Deletion ; *Gene Expression Regulation, Plant ; *Genes, Plant ; Histones/genetics/metabolism ; Molecular Sequence Data ; Mutagenesis, Insertional ; Mutation ; Plant Leaves/anatomy & histology/cytology/*growth & development/metabolism ; Plant Proteins/chemistry/genetics/metabolism ; Surface Properties ; Transcription Factors/chemistry/genetics/*metabolism
    Print ISSN: 0036-8075
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    Consensus and ancestral state HIV vaccines (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nickle, David C -- Jensen, Mark A -- Gottlieb, Geoffrey S -- Shriner, Daniel -- Learn, Gerald H -- Rodrigo, Allen G -- Mullins, James I -- New York, N.Y. -- Science. 2003 Mar 7;299(5612):1515-8; author reply 1515-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12624248" target="_blank"〉PubMed〈/a〉
    Keywords: *AIDS Vaccines/immunology ; Base Sequence ; Consensus Sequence ; Evolution, Molecular ; Genes, env ; Genes, gag ; Genetic Variation ; HIV Antigens/genetics/immunology ; HIV-1/classification/*genetics/*immunology ; Humans ; *Phylogeny
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    Scanning human gene deserts for long-range enhancers (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-10-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nobrega, Marcelo A -- Ovcharenko, Ivan -- Afzal, Veena -- Rubin, Edward M -- HL66728/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2003 Oct 17;302(5644):413.〈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/14563999" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anura/genetics ; Base Sequence ; Conserved Sequence ; *DNA, Intergenic ; *Drosophila Proteins ; *Enhancer Elements, Genetic ; Evolution, Molecular ; Gene Expression Regulation ; Genes, Reporter ; Humans ; Introns ; Mice ; Mice, Transgenic ; Nuclear Proteins/*genetics ; Synteny ; Takifugu/genetics ; Tetraodontiformes/genetics ; Xenopus/genetics ; Zebrafish/genetics
    Print ISSN: 0036-8075
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    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-07-19
    Description: We collected and completely sequenced 28,469 full-length complementary DNA clones from Oryza sativa L. ssp. japonica cv. Nipponbare. Through homology searches of publicly available sequence data, we assigned tentative protein functions to 21,596 clones (75.86%). Mapping of the cDNA clones to genomic DNA revealed that there are 19,000 to 20,500 transcription units in the rice genome. Protein informatics analysis against the InterPro database revealed the existence of proteins presented in rice but not in Arabidopsis. Sixty-four percent of our cDNAs are homologous to Arabidopsis proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rice Full-Length cDNA Consortium -- National Institute of Agrobiological Sciences Rice Full-Length cDNA Project Team -- Kikuchi, Shoshi -- Satoh, Kouji -- Nagata, Toshifumi -- Kawagashira, Nobuyuki -- Doi, Koji -- Kishimoto, Naoki -- Yazaki, Junshi -- Ishikawa, Masahiro -- Yamada, Hitomi -- Ooka, Hisako -- Hotta, Isamu -- Kojima, Keiichi -- Namiki, Takahiro -- Ohneda, Eisuke -- Yahagi, Wataru -- Suzuki, Kohji -- Li, Chao Jie -- Ohtsuki, Kenji -- Shishiki, Toru -- Foundation of Advancement of International Science Genome Sequencing & Analysis Group -- Otomo, Yasuhiro -- Murakami, Kazuo -- Iida, Yoshiharu -- Sugano, Sumio -- Fujimura, Tatsuto -- Suzuki, Yutaka -- Tsunoda, Yuki -- Kurosaki, Takashi -- Kodama, Takeko -- Masuda, Hiromi -- Kobayashi, Michie -- Xie, Quihong -- Lu, Min -- Narikawa, Ryuya -- Sugiyama, Akio -- Mizuno, Kouichi -- Yokomizo, Satoko -- Niikura, Junko -- Ikeda, Rieko -- Ishibiki, Junya -- Kawamata, Midori -- Yoshimura, Akemi -- Miura, Junichirou -- Kusumegi, Takahiro -- Oka, Mitsuru -- Ryu, Risa -- Ueda, Mariko -- Matsubara, Kenichi -- RIKEN -- Kawai, Jun -- Carninci, Piero -- Adachi, Jun -- Aizawa, Katsunori -- Arakawa, Takahiro -- Fukuda, Shiro -- Hara, Ayako -- Hashizume, Wataru -- Hayatsu, Norihito -- Imotani, Koichi -- Ishii, Yoshiyuki -- Itoh, Masayoshi -- Kagawa, Ikuko -- Kondo, Shinji -- Konno, Hideaki -- Miyazaki, Ai -- Osato, Naoki -- Ota, Yoshimi -- Saito, Rintaro -- Sasaki, Daisuke -- Sato, Kenjiro -- Shibata, Kazuhiro -- Shinagawa, Akira -- Shiraki, Toshiyuki -- Yoshino, Masayasu -- Hayashizaki, Yoshihide -- Yasunishi, Ayako -- New York, N.Y. -- Science. 2003 Jul 18;301(5631):376-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, National Institute of Agrobiological Sciences, 2-1-2 Kannon-dai, Tsukuba, Ibaraki 305-8602, Japan. skikuchi@nias.affrc.go.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12869764" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Amino Acid Sequence ; Cloning, Molecular ; Computational Biology ; DNA, Complementary ; Databases, Nucleic Acid ; Databases, Protein ; Genes, Plant ; *Genome, Plant ; Molecular Sequence Data ; Open Reading Frames ; Oryza/*genetics ; Plant Proteins/chemistry/genetics/physiology ; Protein Structure, Tertiary ; RNA, Antisense/genetics ; *Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Transcription Factors/chemistry/genetics ; Transcription, Genetic
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    Derepression of BDNF transcription involves calcium-dependent phosphorylation of MeCP2 (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-11-01
    Description: Mutations in MeCP2, which encodes a protein that has been proposed to function as a global transcriptional repressor, are the cause of Rett syndrome (RT T), an X-linked progressive neurological disorder. Although the selective inactivation of MeCP2 in neurons is sufficient to confer a Rett-like phenotype in mice, the specific functions of MeCP2 in postmitotic neurons are not known. We find that MeCP2 binds selectively to BDNF promoter III and functions to repress expression of the BDNF gene. Membrane depolarization triggers the calcium-dependent phosphorylation and release of MeCP2 from BDNF promoter III, thereby facilitating transcription. These studies indicate that MeCP2 plays a key role in the control of neuronal activity-dependent gene regulation and suggest that the deregulation of this process may underlie the pathology of RT T.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Wen G -- Chang, Qiang -- Lin, Yingxi -- Meissner, Alexander -- West, Anne E -- Griffith, Eric C -- Jaenisch, Rudolf -- Greenberg, Michael E -- HD 18655/HD/NICHD NIH HHS/ -- NS28829/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2003 Oct 31;302(5646):885-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Neuroscience, Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14593183" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Brain-Derived Neurotrophic Factor/*genetics ; Calcium/*metabolism ; Cell Membrane/physiology ; Cells, Cultured ; *Chromosomal Proteins, Non-Histone ; Cloning, Molecular ; CpG Islands ; DNA Methylation ; DNA-Binding Proteins/*metabolism ; Electrophoretic Mobility Shift Assay ; *Gene Expression Regulation ; Gene Silencing ; Histones/metabolism ; Methyl-CpG-Binding Protein 2 ; Methylation ; Mice ; Mice, Knockout ; Neurons/metabolism/physiology ; Phosphorylation ; Potassium Chloride/pharmacology ; Precipitin Tests ; Promoter Regions, Genetic ; Rats ; *Repressor Proteins ; Rett Syndrome/genetics ; *Transcription, Genetic
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    ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-01-11
    Description: Proteins of the ARGONAUTE family are important in diverse posttranscriptional RNA-mediated gene-silencing systems as well as in transcriptional gene silencing in Drosophila and fission yeast and in programmed DNA elimination in Tetrahymena. We cloned ARGONAUTE4 (AGO4) from a screen for mutants that suppress silencing of the Arabidopsis SUPERMAN (SUP) gene. The ago4-1 mutant reactivated silent SUP alleles and decreased CpNpG and asymmetric DNA methylation as well as histone H3 lysine-9 methylation. In addition, ago4-1 blocked histone and DNA methylation and the accumulation of 25-nucleotide small interfering RNAs (siRNAs) that correspond to the retroelement AtSN1. These results suggest that AGO4 and long siRNAs direct chromatin modifications, including histone methylation and non-CpG DNA methylation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zilberman, Daniel -- Cao, Xiaofeng -- Jacobsen, Steven E -- GM07185/GM/NIGMS NIH HHS/ -- GM60398/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):716-9. Epub 2003 Jan 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cell, and Developmental Biology, Molecular Biology Institute, University of California, Los Angeles, CA 90095-1606.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12522258" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/chemistry/*genetics/*metabolism ; Argonaute Proteins ; Cloning, Molecular ; *DNA Methylation ; DNA, Plant/metabolism ; DNA-Cytosine Methylases/genetics/metabolism ; Dinucleoside Phosphates/metabolism ; Gene Silencing ; Genes, Plant ; Genes, Suppressor ; Histone-Lysine N-Methyltransferase ; Histones/*metabolism ; Methylation ; Methyltransferases/genetics/metabolism ; Mutation ; RNA, Plant/metabolism ; RNA, Small Interfering/*metabolism ; Retroelements ; Suppression, Genetic ; Transcription Factors/genetics/metabolism
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    Intellectual property. Judge turns Rochester's golden patent into lead (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Malakoff, David -- New York, N.Y. -- Science. 2003 Mar 14;299(5613):1638-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12637705" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Inflammatory Agents, Non-Steroidal ; Celecoxib ; Cloning, Molecular ; Cyclooxygenase 2 ; Cyclooxygenase 2 Inhibitors ; *Cyclooxygenase Inhibitors ; Drug Industry/*legislation & jurisprudence ; Isoenzymes/*antagonists & inhibitors/*genetics ; New York ; Patents as Topic/*legislation & jurisprudence ; Prostaglandin-Endoperoxide Synthases/*genetics ; Pyrazoles ; Sulfonamides ; United States ; Universities/*legislation & jurisprudence
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    Botany. Relieving DELLA restraint (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harberd, Nicholas P -- New York, N.Y. -- Science. 2003 Mar 21;299(5614):1853-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉John Innes Centre, Norwich, Norfolk NR4 7UH, UK. nicholas.harberd@bbsrc.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12649470" target="_blank"〉PubMed〈/a〉
    Keywords: Cloning, Molecular ; Genes, Plant ; Gibberellins/*metabolism/pharmacology ; Indoleacetic Acids/metabolism ; Ligases/metabolism ; Models, Biological ; Mutation ; Oryza/genetics/*growth & development/metabolism ; Peptide Hydrolases/metabolism ; Phosphorylation ; Plant Proteins/*genetics/*metabolism ; *Proteasome Endopeptidase Complex ; Signal Transduction ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligases
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    Genomics. Defining genes in the genomics era (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-04-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Snyder, Michael -- Gerstein, Mark -- New York, N.Y. -- Science. 2003 Apr 11;300(5617):258-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12690176" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Base Sequence ; Conserved Sequence ; Gene Silencing ; *Genes ; Genome, Fungal ; Genome, Human ; *Genomics ; Humans ; Open Reading Frames ; Pseudogenes ; Saccharomyces cerevisiae/genetics ; Transcription, Genetic
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    LysM domain receptor kinases regulating rhizobial Nod factor-induced infection (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-30
    Description: The rhizobial infection of legumes has the most stringent demand toward Nod factor structure of all host responses, and therefore a specific Nod factor entry receptor has been proposed. The SYM2 gene identified in certain ecotypes of pea (Pisum sativum) is a good candidate for such an entry receptor. We exploited the close phylogenetic relationship of pea and the model legume Medicago truncatula to identify genes specifically involved in rhizobial infection. The SYM2 orthologous region of M. truncatula contains 15 putative receptor-like genes, of which 7 are LysM domain-containing receptor-like kinases (LYKs). Using reverse genetics in M. truncatula, we show that two LYK genes are specifically involved in infection thread formation. This, as well as the properties of the LysM domains, strongly suggests that they are Nod factor entry receptors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Limpens, Erik -- Franken, Carolien -- Smit, Patrick -- Willemse, Joost -- Bisseling, Ton -- Geurts, Rene -- New York, N.Y. -- Science. 2003 Oct 24;302(5645):630-3. Epub 2003 Aug 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, Dreijenlaan 3, 6703HA, Wageningen, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12947035" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Gene Expression ; *Genes, Plant ; Ligands ; Lipopolysaccharides/*metabolism ; Medicago/genetics/microbiology/*physiology ; Models, Biological ; Molecular Sequence Data ; Mutation ; Nitrogen Fixation ; Peas ; Phenotype ; Plant Roots/*microbiology/physiology ; Protein Kinases/chemistry/*genetics/*metabolism ; Protein Structure, Tertiary ; RNA Interference ; Signal Transduction ; Sinorhizobium meliloti/chemistry/genetics/growth & development/*physiology ; *Symbiosis
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    Empirical analysis of transcriptional activity in the Arabidopsis genome (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-11-01
    Description: Functional analysis of a genome requires accurate gene structure information and a complete gene inventory. A dual experimental strategy was used to verify and correct the initial genome sequence annotation of the reference plant Arabidopsis. Sequencing full-length cDNAs and hybridizations using RNA populations from various tissues to a set of high-density oligonucleotide arrays spanning the entire genome allowed the accurate annotation of thousands of gene structures. We identified 5817 novel transcription units, including a substantial amount of antisense gene transcription, and 40 genes within the genetically defined centromeres. This approach resulted in completion of approximately 30% of the Arabidopsis ORFeome as a resource for global functional experimentation of the plant proteome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yamada, Kayoko -- Lim, Jun -- Dale, Joseph M -- Chen, Huaming -- Shinn, Paul -- Palm, Curtis J -- Southwick, Audrey M -- Wu, Hank C -- Kim, Christopher -- Nguyen, Michelle -- Pham, Paul -- Cheuk, Rosa -- Karlin-Newmann, George -- Liu, Shirley X -- Lam, Bao -- Sakano, Hitomi -- Wu, Troy -- Yu, Guixia -- Miranda, Molly -- Quach, Hong L -- Tripp, Matthew -- Chang, Charlie H -- Lee, Jeong M -- Toriumi, Mitsue -- Chan, Marie M H -- Tang, Carolyn C -- Onodera, Courtney S -- Deng, Justine M -- Akiyama, Kenji -- Ansari, Yasser -- Arakawa, Takahiro -- Banh, Jenny -- Banno, Fumika -- Bowser, Leah -- Brooks, Shelise -- Carninci, Piero -- Chao, Qimin -- Choy, Nathan -- Enju, Akiko -- Goldsmith, Andrew D -- Gurjal, Mani -- Hansen, Nancy F -- Hayashizaki, Yoshihide -- Johnson-Hopson, Chanda -- Hsuan, Vickie W -- Iida, Kei -- Karnes, Meagan -- Khan, Shehnaz -- Koesema, Eric -- Ishida, Junko -- Jiang, Paul X -- Jones, Ted -- Kawai, Jun -- Kamiya, Asako -- Meyers, Cristina -- Nakajima, Maiko -- Narusaka, Mari -- Seki, Motoaki -- Sakurai, Tetsuya -- Satou, Masakazu -- Tamse, Racquel -- Vaysberg, Maria -- Wallender, Erika K -- Wong, Cecilia -- Yamamura, Yuki -- Yuan, Shiaulou -- Shinozaki, Kazuo -- Davis, Ronald W -- Theologis, Athanasios -- Ecker, Joseph R -- New York, N.Y. -- Science. 2003 Oct 31;302(5646):842-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Gene Expression Center, Albany, CA 94710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14593172" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/*genetics ; Chromosome Mapping ; Chromosomes, Plant/genetics ; Cloning, Molecular ; Computational Biology ; DNA, Complementary/genetics ; DNA, Intergenic ; Expressed Sequence Tags ; Gene Expression Profiling ; Genes, Plant ; *Genome, Plant ; Genomics ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis ; Open Reading Frames ; RNA, Messenger/*genetics ; RNA, Plant/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; *Transcription, Genetic
    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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    Virology. The SARS coronavirus: a postgenomic era (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holmes, Kathryn V -- Enjuanes, Luis -- New York, N.Y. -- Science. 2003 May 30;300(5624):1377-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, University of Colorado Health Sciences Center, Denver, CO 80262, USA. kathryn.holmes@UCHSC.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12775826" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antigens, Viral/immunology ; Antiviral Agents ; Base Sequence ; Coronavirus/classification/genetics ; Drug Design ; Evolution, Molecular ; *Genome, Viral ; Humans ; Open Reading Frames ; Phylogeny ; RNA, Messenger/genetics ; RNA, Viral/*genetics ; Regulatory Sequences, Nucleic Acid ; SARS Virus/classification/*genetics/physiology ; Sequence Analysis, DNA ; Severe Acute Respiratory Syndrome/drug therapy/prevention & control/virology ; Transcription, Genetic ; Viral Proteins/chemistry/genetics/physiology ; Viral Vaccines
    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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    Nervous system targets of RNA editing identified by comparative genomics (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-09
    Description: An unknown number of precursor messenger RNAs undergo genetic recoding by modification of adenosine to inosine, a reaction catalyzed by the adenosine deaminases acting on RNA (ADARs). Discovery of these edited transcripts has always been serendipitous. Using comparative genomics, we identified a phylogenetic signature of RNA editing. We report the identification and experimental verification of 16 previously unknown ADAR target genes in the fruit fly Drosophila and one in humans-more than the sum total previously reported. All of these genes are involved in rapid electrical and chemical neurotransmission, and many of the edited sites recode conserved and functionally important amino acids. These results point to a pivotal role for RNA editing in nervous system function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hoopengardner, Barry -- Bhalla, Tarun -- Staber, Cynthia -- Reenan, Robert -- R01 GM062291/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Aug 8;301(5634):832-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics and Developmental Biology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12907802" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine/metabolism ; Adenosine Deaminase/*metabolism ; Animals ; Base Sequence ; Drosophila/*genetics ; Drosophila melanogaster/genetics ; *Genes, Insect ; Genomics ; Humans ; Inosine/metabolism ; Ion Channel Gating ; Ion Channels/*genetics/metabolism ; Molecular Sequence Data ; Nervous System/metabolism ; Phylogeny ; Potassium Channels/genetics/metabolism ; *RNA Editing ; RNA-Binding Proteins ; Reverse Transcriptase Polymerase Chain Reaction ; Synapses ; *Synaptic Transmission
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Diverse plant and animal genetic records from Holocene and Pleistocene sediments (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-04-19
    Description: Genetic analyses of permafrost and temperate sediments reveal that plant and animal DNA may be preserved for long periods, even in the absence of obvious macrofossils. In Siberia, five permafrost cores ranging from 400,000 to 10,000 years old contained at least 19 different plant taxa, including the oldest authenticated ancient DNA sequences known, and megafaunal sequences including mammoth, bison, and horse. The genetic data record a number of dramatic changes in the taxonomic diversity and composition of Beringian vegetation and fauna. Temperate cave sediments in New Zealand also yielded DNA sequences of extinct biota, including two species of ratite moa, and 29 plant taxa characteristic of the prehuman environment. Therefore, many sedimentary deposits may contain unique, and widespread, genetic records of paleoenvironments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Willerslev, Eske -- Hansen, Anders J -- Binladen, Jonas -- Brand, Tina B -- Gilbert, M Thomas P -- Shapiro, Beth -- Bunce, Michael -- Wiuf, Carsten -- Gilichinsky, David A -- Cooper, Alan -- New York, N.Y. -- Science. 2003 May 2;300(5620):791-5. Epub 2003 Apr 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Evolutionary Biology, Zoological Institute, University of Copenhagen, Universitetsparken 15, Denmark DK-2100 O.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12702808" target="_blank"〉PubMed〈/a〉
    Keywords: Angiosperms/classification/genetics ; Animals ; Base Sequence ; Bryopsida/classification/genetics ; Cloning, Molecular ; DNA/*analysis/genetics ; DNA, Chloroplast/analysis ; DNA, Mitochondrial/analysis/genetics ; DNA, Plant/*analysis/genetics ; Ecosystem ; Fossils ; *Geologic Sediments ; Gymnosperms/classification/genetics ; History, Ancient ; Mammals/classification/genetics ; New Zealand ; Phylogeny ; *Plants/classification ; Polymerase Chain Reaction ; Siberia ; *Soil ; *Vertebrates/classification/genetics
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Genetics. Modifying the message (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nadeau, Joseph H -- New York, N.Y. -- Science. 2003 Aug 15;301(5635):927-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Case Western Reserve University, Cleveland, OH 44106, USA. jhn4@cwru.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12920288" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carrier Proteins/*genetics/physiology ; Cloning, Molecular ; Codon, Terminator ; Exons ; Gene Expression Regulation ; Humans ; Ion Transport ; Mice ; Mice, Inbred C57BL ; Mice, Neurologic Mutants ; Mutation ; NAV1.6 Voltage-Gated Sodium Channel ; *Nerve Tissue Proteins ; Nervous System Diseases/*genetics/metabolism ; Phenotype ; RNA Precursors/genetics/metabolism ; *RNA Splicing ; RNA, Messenger/genetics/metabolism ; Sodium/metabolism ; Sodium Channels/*genetics/metabolism ; Transcription, Genetic ; Zinc Fingers
    Print ISSN: 0036-8075
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    Modulating sphingolipid biosynthetic pathway rescues photoreceptor degeneration (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-15
    Description: Mutations in proteins of the Drosophila phototransduction cascade, a prototypic guanine nucleotide-binding protein-coupled receptor signaling system, lead to retinal degeneration and have been used as models to understand human degenerative disorders. Here, modulating the sphingolipid biosynthetic pathway rescued retinal degeneration in Drosophila mutants. Targeted expression of Drosophila neutral ceramidase rescued retinal degeneration in arrestin and phospholipase C mutants. Decreasing flux through the de novo sphingolipid biosynthetic pathway also suppressed degeneration in these mutants. Both genetic backgrounds modulated the endocytic machinery because they suppressed defects in a dynamin mutant. Suppression of degeneration in arrestin mutant flies expressing ceramidase correlated with a decrease in ceramide levels. Thus, enzymes of sphingolipid metabolism may be suitable targets in the therapeutic management of retinal degeneration.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Acharya, Usha -- Patel, Shetal -- Koundakjian, Edmund -- Nagashima, Kunio -- Han, Xianlin -- Acharya, Jairaj K -- New York, N.Y. -- Science. 2003 Mar 14;299(5613):1740-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Regulation of Cell Growth Laboratory, National Cancer Institute-Frederick, Frederick, MD 21702, USA. acharyau@mail.ncifcrf.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12637747" target="_blank"〉PubMed〈/a〉
    Keywords: Acyltransferases/genetics/metabolism ; Amidohydrolases/genetics/*metabolism ; Animals ; Animals, Genetically Modified ; Apoptosis ; Arrestins/genetics/metabolism ; Ceramidases ; Ceramides/biosynthesis/*metabolism ; Clathrin/physiology ; Cloning, Molecular ; Crosses, Genetic ; Drosophila/genetics/*physiology ; Dynamins/genetics/physiology ; Electroretinography ; *Endocytosis ; Genes, Insect ; Light ; Mutation ; Necrosis ; Neutral Ceramidase ; Phosphatidylinositol Diacylglycerol-Lyase ; Phosphoproteins/genetics/metabolism ; Photoreceptor Cells, Invertebrate/cytology/*physiology/ultrastructure ; Receptors, Cell Surface/metabolism ; Retinal Degeneration/genetics ; Rhodopsin/metabolism ; Serine C-Palmitoyltransferase ; Spectrometry, Mass, Electrospray Ionization ; Sphingosine/metabolism ; Type C Phospholipases/genetics/metabolism ; *Vision, Ocular
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Positional cloning of the human quantitative trait locus underlying taste sensitivity to phenylthiocarbamide (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-22
    Description: The ability to taste the substance phenylthiocarbamide (PTC) has been widely used for genetic and anthropological studies, but genetic studies have produced conflicting results and demonstrated complex inheritance for this trait. We have identified a small region on chromosome 7q that shows strong linkage disequilibrium between single-nucleotide polymorphism (SNP) markers and PTC taste sensitivity in unrelated subjects. This region contains a single gene that encodes a member of the TAS2R bitter taste receptor family. We identified three coding SNPs giving rise to five haplotypes in this gene worldwide. These haplotypes completely explain the bimodal distribution of PTC taste sensitivity, thus accounting for the inheritance of the classically defined taste insensitivity and for 55 to 85% of the variance in PTC sensitivity. Distinct phenotypes were associated with specific haplotypes, which demonstrates that this gene has a direct influence on PTC taste sensitivity and that sequence variants at different sites interact with each other within the encoded gene product.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Un-kyung -- Jorgenson, Eric -- Coon, Hilary -- Leppert, Mark -- Risch, Neil -- Drayna, Dennis -- M01-RR00064/RR/NCRR NIH HHS/ -- T32 HG00044/HG/NHGRI NIH HHS/ -- Z01-000046-04/PHS HHS/ -- New York, N.Y. -- Science. 2003 Feb 21;299(5610):1221-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Institute on Deafness and Other Communication Disorders, National Institutes of Health, 5 Research Court, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12595690" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Substitution ; Animals ; Cebidae/genetics ; Chromosomes, Human, Pair 7/genetics ; Cloning, Molecular ; Computational Biology ; Continental Population Groups/genetics ; Evolution, Molecular ; Female ; Genetic Linkage ; Haplotypes ; Heterozygote ; Hominidae/genetics ; Homozygote ; Humans ; Linkage Disequilibrium ; Macaca fascicularis/genetics ; Male ; *Phenylthiourea ; *Polymorphism, Single Nucleotide ; *Quantitative Trait Loci ; Receptors, Cell Surface/chemistry/*genetics/physiology ; Receptors, G-Protein-Coupled ; Sequence Analysis, DNA ; Taste/*genetics ; Taste Threshold
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    Infectious diseases. Hungry for details, scientists zoom in on SARS genomes (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Enserink, Martin -- Vogel, Gretchen -- New York, N.Y. -- Science. 2003 May 2;300(5620):715-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12730563" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Coronavirus/classification/genetics ; Databases, Nucleic Acid ; *Genetic Variation ; *Genome, Viral ; Humans ; Internet ; Mutation ; Publishing ; SARS Virus/classification/*genetics/isolation & purification ; Severe Acute Respiratory Syndrome/*virology
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Characterization of mammalian selenoproteomes (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-31
    Description: In the genetic code, UGA serves as a stop signal and a selenocysteine codon, but no computational methods for identifying its coding function are available. Consequently, most selenoprotein genes are misannotated. We identified selenoprotein genes in sequenced mammalian genomes by methods that rely on identification of selenocysteine insertion RNA structures, the coding potential of UGA codons, and the presence of cysteine-containing homologs. The human selenoproteome consists of 25 selenoproteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kryukov, Gregory V -- Castellano, Sergi -- Novoselov, Sergey V -- Lobanov, Alexey V -- Zehtab, Omid -- Guigo, Roderic -- Gladyshev, Vadim N -- GM61603/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 May 30;300(5624):1439-43.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Nebraska, Lincoln, NE 68588-0664, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12775843" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Codon ; Codon, Terminator ; Computational Biology ; DNA Transposable Elements ; Gene Expression Profiling ; Genome, Human ; Humans ; Mice ; Molecular Sequence Data ; Open Reading Frames ; Proteins/*chemistry/*genetics ; *Proteome ; Rats ; *Selenium ; Selenocysteine/chemistry/*genetics ; Selenoproteins ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Software
    Print ISSN: 0036-8075
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    The Genome sequence of the SARS-associated coronavirus (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-06
    Description: We sequenced the 29,751-base genome of the severe acute respiratory syndrome (SARS)-associated coronavirus known as the Tor2 isolate. The genome sequence reveals that this coronavirus is only moderately related to other known coronaviruses, including two human coronaviruses, HCoV-OC43 and HCoV-229E. Phylogenetic analysis of the predicted viral proteins indicates that the virus does not closely resemble any of the three previously known groups of coronaviruses. The genome sequence will aid in the diagnosis of SARS virus infection in humans and potential animal hosts (using polymerase chain reaction and immunological tests), in the development of antivirals (including neutralizing antibodies), and in the identification of putative epitopes for vaccine development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marra, Marco A -- Jones, Steven J M -- Astell, Caroline R -- Holt, Robert A -- Brooks-Wilson, Angela -- Butterfield, Yaron S N -- Khattra, Jaswinder -- Asano, Jennifer K -- Barber, Sarah A -- Chan, Susanna Y -- Cloutier, Alison -- Coughlin, Shaun M -- Freeman, Doug -- Girn, Noreen -- Griffith, Obi L -- Leach, Stephen R -- Mayo, Michael -- McDonald, Helen -- Montgomery, Stephen B -- Pandoh, Pawan K -- Petrescu, Anca S -- Robertson, A Gordon -- Schein, Jacqueline E -- Siddiqui, Asim -- Smailus, Duane E -- Stott, Jeff M -- Yang, George S -- Plummer, Francis -- Andonov, Anton -- Artsob, Harvey -- Bastien, Nathalie -- Bernard, Kathy -- Booth, Timothy F -- Bowness, Donnie -- Czub, Martin -- Drebot, Michael -- Fernando, Lisa -- Flick, Ramon -- Garbutt, Michael -- Gray, Michael -- Grolla, Allen -- Jones, Steven -- Feldmann, Heinz -- Meyers, Adrienne -- Kabani, Amin -- Li, Yan -- Normand, Susan -- Stroher, Ute -- Tipples, Graham A -- Tyler, Shaun -- Vogrig, Robert -- Ward, Diane -- Watson, Brynn -- Brunham, Robert C -- Krajden, Mel -- Petric, Martin -- Skowronski, Danuta M -- Upton, Chris -- Roper, Rachel L -- New York, N.Y. -- Science. 2003 May 30;300(5624):1399-404. Epub 2003 May 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉British Columbia Cancer Agency (BCCA) Genome Sciences Centre, 600 West 10th Avenue, Vancouver, British Columbia V5Z 4E6, Canada. mmarra@bccgsc.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12730501" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions ; 5' Untranslated Regions ; Animals ; Base Sequence ; Conserved Sequence ; Coronavirus/classification/genetics ; DNA, Complementary ; Frameshifting, Ribosomal ; *Genome, Viral ; Humans ; Membrane Glycoproteins/chemistry/genetics ; Nucleocapsid Proteins/chemistry/genetics ; Open Reading Frames ; Phylogeny ; RNA Replicase/chemistry/genetics ; RNA, Viral/*genetics/isolation & purification ; Regulatory Sequences, Nucleic Acid ; SARS Virus/classification/*genetics/isolation & purification ; Sequence Analysis, DNA ; Severe Acute Respiratory Syndrome/virology ; Spike Glycoprotein, Coronavirus ; Viral Envelope Proteins/chemistry/genetics ; Viral Matrix Proteins/chemistry/genetics ; Viral Proteins/chemistry/*genetics
    Print ISSN: 0036-8075
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    Conserved role of nanos proteins in germ cell development (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-30
    Description: In Drosophila, maternally supplied Nanos functions in the migration of primordial germ cells (PGCs) into the gonad; in mice, zygotic genes are involved instead. We report the cloning and the functional analyses of nanos2 and nanos3 in mice. These genes are differentially expressed in mouse PGCs. nanos2 is predominantly expressed in male germ cells, and the elimination of this gene results in a complete loss of spermatogonia. However, nanos3 is found in migrating PGCs, and the elimination of this factor results in the complete loss of germ cells in both sexes. Hence, although mice and flies differ in their mechanisms for germ cell specification, there seems to be conserved function for nanos proteins among invertebrates and vertebrates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tsuda, Masayuki -- Sasaoka, Yumiko -- Kiso, Makoto -- Abe, Kuniya -- Haraguchi, Seiki -- Kobayashi, Satoru -- Saga, Yumiko -- New York, N.Y. -- Science. 2003 Aug 29;301(5637):1239-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Mammalian Development, National Institute of Genetics, SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12947200" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Apoptosis ; Carrier Proteins/chemistry/genetics/*physiology ; Cell Count ; Cell Division ; Cell Movement ; Cloning, Molecular ; Female ; Gene Expression Profiling ; Gene Targeting ; Germ Cells/*growth & development/*metabolism ; Gonads/embryology/growth & development/*metabolism ; In Situ Nick-End Labeling ; Male ; Mice ; Mice, Knockout ; Molecular Sequence Data ; Organ Size ; Ovary/anatomy & histology/metabolism ; Ovum/physiology ; Phenotype ; *RNA-Binding Proteins ; Spermatogenesis ; Spermatozoa/physiology ; Testis/anatomy & histology/embryology/growth & development/metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Control of effector CD8+ T cell function by the transcription factor Eomesodermin (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-11-08
    Description: Activated CD8+ T cells play a critical role in host defense against viruses, intracellular microbes, and tumors. It is not clear if a key regulatory transcription factor unites the effector functions of CD8+ T cells. We now show that Eomesodermin (Eomes), a paralogue of T-bet, is induced in effector CD8+ T cells in vitro and in vivo. Ectopic expression of Eomes was sufficient to invoke attributes of effector CD8+ T cells, including interferon-gamma (IFN-gamma), perforin, and granzyme B. Loss-of-function analysis suggests Eomes may also be necessary for full effector differentiation of CD8+ T cells. We suggest that Eomesodermin is likely to complement the actions of T-bet and act as a key regulatory gene in the development of cell-mediated immunity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pearce, Erika L -- Mullen, Alan C -- Martins, Gislaine A -- Krawczyk, Connie M -- Hutchins, Anne S -- Zediak, Valerie P -- Banica, Monica -- DiCioccio, Catherine B -- Gross, Darrick A -- Mao, Chai-An -- Shen, Hao -- Cereb, Nezih -- Yang, Soo Y -- Lindsten, Tullia -- Rossant, Janet -- Hunter, Christopher A -- Reiner, Steven L -- AI-042370/AI/NIAID NIH HHS/ -- GM-07229/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Nov 7;302(5647):1041-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Abramson Family Cancer Research Institute, and Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14605368" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Arenaviridae Infections/immunology ; Base Sequence ; CD8-Positive T-Lymphocytes/*immunology/physiology ; Cell Differentiation ; Cytotoxicity, Immunologic ; Gene Expression Regulation ; Granzymes ; Interferon-gamma/biosynthesis ; Lymphocyte Activation ; Lymphocytic choriomeningitis virus/immunology ; Membrane Glycoproteins/biosynthesis/genetics ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Molecular Sequence Data ; Perforin ; Pore Forming Cytotoxic Proteins ; RNA, Messenger/genetics/metabolism ; Serine Endopeptidases/biosynthesis/genetics ; T-Box Domain Proteins/chemistry/genetics/*physiology ; Th2 Cells/immunology/physiology ; Transcription Factors/chemistry/genetics/physiology
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    Plant biology. Seeing red (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-01-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bartel, Bonnie -- Matsuda, Seiichi P T -- New York, N.Y. -- Science. 2003 Jan 17;299(5605):352-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12532002" target="_blank"〉PubMed〈/a〉
    Keywords: Anthocyanins/*biosynthesis/chemistry/*metabolism ; Arabidopsis/enzymology/genetics/*metabolism ; *Arabidopsis Proteins ; Cloning, Molecular ; Genes, Plant ; Medicago/*enzymology/genetics/metabolism ; Molecular Conformation ; NADH, NADPH Oxidoreductases/genetics/*metabolism ; Oxidation-Reduction ; Oxygenases/genetics/metabolism ; *Proanthocyanidins ; Recombinant Proteins/metabolism ; Stereoisomerism ; Tannins/*biosynthesis/chemistry ; Tobacco/genetics
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    Illuminating the circadian clock in monarch butterfly migration (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-24
    Description: Migratory monarch butterflies use a time-compensated Sun compass to navigate to their overwintering grounds in Mexico. Here, we report that constant light, which disrupts circadian clock function at both the behavioral and molecular levels in monarchs, also disrupts the time-compensated component of flight navigation. We further show that ultraviolet light is important for flight navigation but is not required for photic entrainment of circadian rhythms. Tracing these distinct light-input pathways into the brain should aid our understanding of the clock-compass mechanisms necessary for successful migration.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Froy, Oren -- Gotter, Anthony L -- Casselman, Amy L -- Reppert, Steven M -- New York, N.Y. -- Science. 2003 May 23;300(5623):1303-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, University of Massachusetts Medical School, LRB-728, 364 Plantation Street, Worcester, MA 01605, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12764200" target="_blank"〉PubMed〈/a〉
    Keywords: *Animal Migration ; Animals ; Biological Clocks/*physiology ; Butterflies/genetics/*physiology ; Circadian Rhythm/*physiology ; Cloning, Molecular ; Darkness ; Flight, Animal ; Light ; Nuclear Proteins/genetics/physiology ; Period Circadian Proteins ; Solar System ; Ultraviolet Rays
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    Hypermutation of HIV-1 DNA in the absence of the Vif protein (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lecossier, Denise -- Bouchonnet, Francine -- Clavel, Francois -- Hance, Allan J -- New York, N.Y. -- Science. 2003 May 16;300(5622):1112.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉INSERM U552, Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12750511" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Cell Line ; Cytidine Deaminase ; DNA Mutational Analysis ; DNA, Viral/biosynthesis/*genetics ; Gene Products, vif/*physiology ; HIV-1/genetics/*physiology ; HeLa Cells ; Humans ; Molecular Sequence Data ; *Mutation ; Nucleoside Deaminases ; Proteins/physiology ; Repressor Proteins ; Virion/genetics/physiology ; Virus Replication ; vif Gene Products, Human Immunodeficiency Virus
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    Synthesis of serotonin by a second tryptophan hydroxylase isoform (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-01-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Walther, Diego J -- Peter, Jens-Uwe -- Bashammakh, Saleh -- Hortnagl, Heide -- Voits, Mechthild -- Fink, Heidrun -- Bader, Michael -- New York, N.Y. -- Science. 2003 Jan 3;299(5603):76.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Delbruck Center for Molecular Medicine (MDC), Robert-Rossle-Strasse 10, D-13092 Berlin-Buch, Germany. dwalther@mdc-berlin.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12511643" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Brain/*enzymology/metabolism ; COS Cells ; Cloning, Molecular ; Conserved Sequence ; DNA, Complementary ; Duodenum/enzymology/metabolism ; Humans ; Hydroxylation ; Isoenzymes/chemistry/genetics/metabolism ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; RNA, Messenger/genetics/metabolism ; Rats ; Serotonin/*biosynthesis ; Transfection ; Tryptophan Hydroxylase/chemistry/genetics/*metabolism
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    Selective trafficking of non-cell-autonomous proteins mediated by NtNCAPP1 (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-01-18
    Description: In plants, cell-to-cell communication is mediated by plasmodesmata and involves the trafficking of non-cell-autonomous proteins (NCAPs). A component in this pathway, Nicotiana tabacum NON-CELL-AUTONOMOUS PATHWAY PROTEIN1 (NtNCAPP1), was affinity purified and cloned. Protein overlay assays and in vivo studies showed that NtNCAPP1 is located on the endoplasmic reticulum at the cell periphery and displays specificity in its interaction with NCAPs. Deletion of the NtNCAPP1 amino-terminal transmembrane domain produced a dominant-negative mutant that blocked the trafficking of specific NCAPs. Transgenic tobacco plants expressing this mutant form of NtNCAPP1 and plants in which the NtNCAPP1 gene was silenced were compromised in their ability to regulate leaf and floral development. These results support a model in which NCAP delivery to plasmodesmata is both selective and regulated.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Jung-Youn -- Yoo, Byung-Chun -- Rojas, Maria R -- Gomez-Ospina, Natalia -- Staehelin, L Andrew -- Lucas, William J -- GM18639/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Jan 17;299(5605):392-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Plant Biology, Division of Biological Sciences, University of California, 1 Shields Avenue, Davis, CA 95616, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12532017" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cell Communication ; Cell Line ; Cloning, Molecular ; Cytoplasm/metabolism ; Endoplasmic Reticulum/metabolism ; Flowers/growth & development ; Gene Silencing ; Green Fluorescent Proteins ; Immunohistochemistry ; Luminescent Proteins/metabolism ; Molecular Sequence Data ; Mutation ; Phenotype ; Plant Leaves/growth & development ; Plant Proteins/chemistry/genetics/*isolation & purification/*metabolism ; Plants, Genetically Modified ; Plasmodesmata/*metabolism ; Protein Transport ; Recombinant Fusion Proteins/metabolism ; Tobacco/genetics/growth & development/*metabolism ; Tobacco Mosaic Virus ; Viral Proteins/metabolism
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    Mutation of MEF2A in an inherited disorder with features of coronary artery disease (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-03
    Description: The early genetic pathway(s) triggering the pathogenesis of coronary artery disease (CAD) and myocardial infarction (MI) remain largely unknown. Here, we describe an autosomal dominant form of CAD/MI (adCAD1) that is caused by the deletion of seven amino acids in transcription factor MEF2A. The deletion disrupts nuclear localization of MEF2A, reduces MEF2A-mediated transcription activation, and abolishes synergistic activation by MEF2A and by the transcription factor GATA-1 through a dominant-negative mechanism. The MEF2A protein demonstrates strong expression in the endothelium of coronary arteries. These results identify a pathogenic gene for a familial vascular disease with features of CAD and implicate the MEF2A signaling pathway in the pathogenesis of CAD/MI.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1618876/" 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/PMC1618876/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Lejin -- Fan, Chun -- Topol, Sarah E -- Topol, Eric J -- Wang, Qing -- R01 HL065630/HL/NHLBI NIH HHS/ -- R01 HL066251/HL/NHLBI NIH HHS/ -- R01 HL65630/HL/NHLBI NIH HHS/ -- R01 HL66251/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2003 Nov 28;302(5650):1578-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Cardiovascular Genetics, Department of Cardiovascular Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14645853" target="_blank"〉PubMed〈/a〉
    Keywords: Aged ; Amino Acid Sequence ; Animals ; Arteries/metabolism ; Base Sequence ; Cell Nucleus/metabolism ; Chromosomes, Human, Pair 15/genetics ; Coronary Artery Disease/*genetics/metabolism ; Coronary Vessels/metabolism ; DNA-Binding Proteins/chemistry/*genetics/metabolism ; Dimerization ; Endothelium, Vascular/metabolism ; Erythroid-Specific DNA-Binding Factors ; Female ; Fluorescent Antibody Technique ; GATA1 Transcription Factor ; Gene Expression ; Genes, Dominant ; Genetic Linkage ; Genetic Markers ; Genetic Predisposition to Disease ; Humans ; MADS Domain Proteins ; MEF2 Transcription Factors ; Male ; Middle Aged ; Molecular Sequence Data ; Muscle, Smooth/cytology/metabolism ; Myocardial Infarction/*genetics/metabolism ; Myogenic Regulatory Factors ; Pedigree ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Protein Transport ; Rats ; Risk Factors ; *Sequence Deletion ; Signal Transduction ; Transcription Factors/chemistry/*genetics/metabolism ; Transcriptional Activation
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    The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-24
    Description: Alu repetitive elements can be inserted into mature messenger RNAs via a splicing-mediated process termed exonization. To understand the molecular basis and the regulation of the process of turning intronic Alus into new exons, we compiled and analyzed a data set of human exonized Alus. We revealed a mechanism that governs 3' splice-site selection in these exons during alternative splicing. On the basis of these findings, we identified mutations that activated the exonization of a silent intronic Alu.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lev-Maor, Galit -- Sorek, Rotem -- Shomron, Noam -- Ast, Gil -- New York, N.Y. -- Science. 2003 May 23;300(5623):1288-91.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12764196" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Deaminase/genetics ; *Alternative Splicing ; Alu Elements/*genetics ; Cell Line ; Cloning, Molecular ; DNA, Antisense ; Dinucleoside Phosphates/genetics ; *Exons ; Genome, Human ; Glucosyltransferases/genetics ; Humans ; Introns ; Mutagenesis, Site-Directed ; Point Mutation ; Polymerase Chain Reaction ; RNA-Binding Proteins ; Ribonucleoproteins, Small Nuclear/genetics/physiology ; Spliceosomes/metabolism ; Transfection ; Tumor Cells, Cultured
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    Constitutive display of cryptic translation products by MHC class I molecules (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-09-06
    Description: Major histocompatibility complex (MHC) class I molecules display tens of thousands of peptides on the cell surface, derived from virtually all endogenous proteins, for inspection by cytotoxic T cells (CTLs). We show that, in normal mouse cells, MHC I molecules present a peptide encoded in the 3' "untranslated" region. Despite its rarity, the peptide elicits CTL responses and induces self-tolerance, establishing that immune surveillance extends well beyond conventional polypeptides. Furthermore, translation of this cryptic peptide occurs by a previously unknown mechanism that decodes the CUG initiation codon as leucine rather than the canonical methionine.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schwab, Susan R -- Li, Katy C -- Kang, Chulho -- Shastri, Nilabh -- New York, N.Y. -- Science. 2003 Sep 5;301(5638):1367-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Immunology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3200, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12958358" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions ; Amino Acid Sequence ; Animals ; *Antigen Presentation ; B-Lymphocytes/metabolism ; Base Sequence ; Codon, Initiator ; Codon, Terminator ; Dendritic Cells/immunology/metabolism ; Female ; Fibroblasts/metabolism ; H-2 Antigens/*immunology ; Hybridomas ; Leucine/genetics/metabolism ; Male ; Mice ; Mice, Transgenic ; Minor Histocompatibility Antigens/genetics ; Molecular Sequence Data ; Peptides/*genetics/*immunology ; *Protein Biosynthesis ; Proteins/genetics ; Self Tolerance ; Spleen/cytology/immunology ; T-Lymphocytes, Cytotoxic/immunology ; Transfection ; Transgenes
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    Finding functional features in Saccharomyces genomes by phylogenetic footprinting (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-31
    Description: The sifting and winnowing of DNA sequence that occur during evolution cause nonfunctional sequences to diverge, leaving phylogenetic footprints of functional sequence elements in comparisons of genome sequences. We searched for such footprints among the genome sequences of six Saccharomyces species and identified potentially functional sequences. Comparison of these sequences allowed us to revise the catalog of yeast genes and identify sequence motifs that may be targets of transcriptional regulatory proteins. Some of these conserved sequence motifs reside upstream of genes with similar functional annotations or similar expression patterns or those bound by the same transcription factor and are thus good candidates for functional regulatory sequences.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cliften, Paul -- Sudarsanam, Priya -- Desikan, Ashwin -- Fulton, Lucinda -- Fulton, Bob -- Majors, John -- Waterston, Robert -- Cohen, Barak A -- Johnston, Mark -- R01 GM63803/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Jul 4;301(5629):71-6. Epub 2003 May 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12775844" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Base Sequence ; Binding Sites ; Computational Biology ; *Conserved Sequence ; *DNA, Intergenic ; Gene Expression Profiling ; Genes, Fungal ; *Genome, Fungal ; Molecular Sequence Data ; *Phylogeny ; *Regulatory Sequences, Nucleic Acid ; Saccharomyces/classification/*genetics/physiology ; Saccharomyces cerevisiae/genetics/physiology ; Sequence Alignment ; Sequence Analysis, DNA ; Transcription Factors/metabolism
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    GUN4, a regulator of chlorophyll synthesis and intracellular signaling (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-08
    Description: Nuclear genes control plastid differentiation in response to developmental signals, environmental signals, and retrograde signals from plastids themselves. In return, plastids emit signals that are essential for proper expression of many nuclear photosynthetic genes. Accumulation of magnesium-protoporphyrin IX (Mg-Proto), an intermediate in chlorophyll biosynthesis, is a plastid signal that represses nuclear transcription through a signaling pathway that, in Arabidopsis, requires the GUN4 gene. GUN4 binds the product and substrate of Mg- chelatase, an enzyme that produces Mg-Proto, and activates Mg-chelatase. Thus, GUN4 participates in plastid-to-nucleus signaling by regulating Mg-Proto synthesis or trafficking.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Larkin, Robert M -- Alonso, Jose M -- Ecker, Joseph R -- Chory, Joanne -- New York, N.Y. -- Science. 2003 Feb 7;299(5608):902-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 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/12574634" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Arabidopsis/*genetics/growth & development/metabolism ; Arabidopsis Proteins/chemistry/*genetics/isolation & purification/*metabolism ; Carrier Proteins/chemistry/*genetics/isolation & purification/*metabolism ; Cell Nucleus/metabolism ; Chlorophyll/*biosynthesis ; Chloroplasts/*metabolism ; Chromosome Mapping ; Chromosomes, Plant ; Cloning, Molecular ; Cyanobacteria/enzymology/genetics/metabolism ; Deuteroporphyrins/metabolism ; Enzyme Activation ; *Genes, Plant ; Genes, Reporter ; *Intracellular Signaling Peptides and Proteins ; Lyases/chemistry/isolation & purification/metabolism ; Magnesium/metabolism ; Molecular Sequence Data ; Mutation ; Mutation, Missense ; Protein Binding ; Protein Subunits/metabolism ; Protein Transport ; Protoporphyrins/*metabolism ; Recombinant Proteins/metabolism ; *Signal Transduction ; Thylakoids/chemistry/enzymology
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    Evolution. Heirlooms in the attic (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-11-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Johnston, Mark -- Stormo, Gary D -- New York, N.Y. -- Science. 2003 Nov 7;302(5647):997-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA. mj@wustl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14605357" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Chickens/genetics ; Chromosomes/genetics ; Chromosomes, Human, Pair 21/genetics ; Chromosomes, Human, Pair 7/genetics ; Chromosomes, Mammalian/genetics ; *Conserved Sequence ; DNA, Intergenic/*genetics ; *Evolution, Molecular ; Fishes/genetics ; Genome ; Genome, Human ; Humans ; Mammals/genetics ; Polymerase Chain Reaction ; Species Specificity
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    Essential role of Fkbp6 in male fertility and homologous chromosome pairing in meiosis (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-24
    Description: Meiosis is a critical stage of gametogenesis in which alignment and synapsis of chromosomal pairs occur, allowing for the recombination of maternal and paternal genomes. Here we show that FK506 binding protein (Fkbp6) localizes to meiotic chromosome cores and regions of homologous chromosome synapsis. Targeted inactivation of Fkbp6 in mice results in aspermic males and the absence of normal pachytene spermatocytes. Moreover, we identified the deletion of Fkbp6 exon 8 as the causative mutation in spontaneously male sterile as/as mutant rats. Loss of Fkbp6 results in abnormal pairing and misalignments between homologous chromosomes, nonhomologous partner switches, and autosynapsis of X chromosome cores in meiotic spermatocytes. Fertility and meiosis are normal in Fkbp6 mutant females. Thus, Fkbp6 is a component of the synaptonemal complex essential for sex-specific fertility and for the fidelity of homologous chromosome pairing in meiosis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2882960/" 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/PMC2882960/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Crackower, Michael A -- Kolas, Nadine K -- Noguchi, Junko -- Sarao, Renu -- Kikuchi, Kazuhiro -- Kaneko, Hiroyuki -- Kobayashi, Eiji -- Kawai, Yasuhiro -- Kozieradzki, Ivona -- Landers, Rushin -- Mo, Rong -- Hui, Chi-Chung -- Nieves, Edward -- Cohen, Paula E -- Osborne, Lucy R -- Wada, Teiji -- Kunieda, Tetsuo -- Moens, Peter B -- Penninger, Josef M -- 38103/Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2003 May 23;300(5623):1291-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), c/o Dr. Bohrgasse 7, 1030, Vienna, Austria.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12764197" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Apoptosis ; Chromosome Pairing/*physiology ; Cloning, Molecular ; Exons ; Female ; Fertility/*physiology ; Gene Targeting ; Humans ; Infertility, Male/genetics/*physiopathology ; Male ; *Meiosis ; Mice ; Molecular Sequence Data ; Mutation ; Nuclear Proteins/genetics/metabolism ; Oogenesis ; Ovary/physiology ; Prophase ; Rats ; Sequence Deletion ; Spermatids/physiology ; Spermatocytes/physiology/ultrastructure ; Spermatogenesis ; Synaptonemal Complex/*physiology ; Tacrolimus Binding Proteins/chemistry/*genetics/*physiology ; Testis/physiology ; X Chromosome/physiology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Hong Kong SARS sequence (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-07-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leung, Frederick C -- New York, N.Y. -- Science. 2003 Jul 18;301(5631):309-10.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12869741" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Untranslated Regions ; Base Sequence ; DNA Primers ; Gene Library ; *Genome, Viral ; Internet ; RNA, Viral/*genetics ; SARS Virus/*genetics ; Sequence Analysis, RNA
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  • 86
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    Evolution of the protein repertoire (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-06-14
    Description: Most proteins have been formed by gene duplication, recombination, and divergence. Proteins of known structure can be matched to about 50% of genome sequences, and these data provide a quantitative description and can suggest hypotheses about the origins of these processes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chothia, Cyrus -- Gough, Julian -- Vogel, Christine -- Teichmann, Sarah A -- New York, N.Y. -- Science. 2003 Jun 13;300(5626):1701-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Studies Division, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12805536" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; Catalysis ; Computational Biology ; Enzymes/*chemistry/*genetics/metabolism ; *Evolution, Molecular ; Gene Duplication ; Genome ; Humans ; Metabolism ; Mutation ; Protein Structure, Tertiary ; Proteins/*chemistry/*genetics/metabolism ; Recombination, Genetic ; Substrate Specificity
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-30
    Description: We used a multiplexed approach based on flow-stretched DNA to monitor the enzymatic digestion of lambda-phage DNA by individual bacteriophage lambda exonuclease molecules. Statistical analyses of multiple single-molecule trajectories observed simultaneously reveal that the catalytic rate is dependent on the local base content of the substrate DNA. By relating single-molecule kinetics to the free energies of hydrogen bonding and base stacking, we establish that the melting of a base from the DNA is the rate-limiting step in the catalytic cycle. The catalytic rate also exhibits large fluctuations independent of the sequence, which we attribute to conformational changes of the enzyme-DNA complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van Oijen, Antoine M -- Blainey, Paul C -- Crampton, Donald J -- Richardson, Charles C -- Ellenberger, Tom -- Xie, X Sunney -- 5R01GM61577-03/GM/NIGMS NIH HHS/ -- R01GM55390-07/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Aug 29;301(5637):1235-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12947199" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage lambda/*enzymology ; Base Composition ; Base Sequence ; Binding Sites ; Catalysis ; DNA, Single-Stranded/chemistry/*metabolism ; DNA, Viral/chemistry/*metabolism ; Exodeoxyribonucleases/chemistry/*metabolism ; Hydrogen Bonding ; Hydrolysis ; Kinetics ; Nucleic Acid Conformation ; Protein Conformation ; Thermodynamics ; Viral Proteins
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Molecular biology. A self-help guide for a trim genome (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-06-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Selker, Eric U -- New York, N.Y. -- Science. 2003 Jun 6;300(5625):1517-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12791973" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Cell Nucleus/metabolism ; DNA Transposable Elements ; DNA, Protozoan/genetics/*metabolism ; Genes, Protozoan ; *Genome, Protozoan ; Methylation ; Models, Genetic ; Protozoan Proteins/genetics/metabolism ; RNA Interference ; RNA, Double-Stranded/*metabolism ; RNA, Protozoan/*metabolism ; Repetitive Sequences, Nucleic Acid ; *Sequence Deletion ; Tetrahymena thermophila/*genetics/growth & development/metabolism ; Transgenes
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 89
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    Spatiotemporal rescue of memory dysfunction in Drosophila (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-06
    Description: We have developed a method for temporal and regional gene expression targeting (TARGET) in Drosophila and show the simultaneous spatial and temporal rescue of a memory defect. The transient expression of the rutabaga-encoded adenylyl cyclase in the mushroom bodies of the adult brain was necessary and sufficient to rescue the rutabaga memory deficit, which rules out a developmental brain defect in the etiology of this deficit and demonstrates an acute role for rutabaga in memory formation in these neurons. The TARGET system offers general utility in simultaneously addressing issues of when and where gene products are required.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McGuire, Sean E -- Le, Phuong T -- Osborn, Alexander J -- Matsumoto, Kunihiro -- Davis, Ronald L -- GM63929/GM/NIGMS NIH HHS/ -- NS19904/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2003 Dec 5;302(5651):1765-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14657498" target="_blank"〉PubMed〈/a〉
    Keywords: Adenylyl Cyclases/*genetics/*metabolism ; Animals ; Animals, Genetically Modified ; Cloning, Molecular ; DNA-Binding Proteins ; Drosophila/genetics/growth & development/*physiology ; Drosophila Proteins/*genetics/*metabolism ; *Gene Expression ; Genotype ; Green Fluorescent Proteins ; Luminescent Proteins/genetics/metabolism ; Memory/*physiology ; Mushroom Bodies/*physiology ; Neuronal Plasticity ; Phenotype ; Repressor Proteins/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Temperature ; Transcription Factors/genetics/metabolism ; Transgenes
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 90
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    Dating the tree of life (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-06-14
    Description: The relative merits of molecular and paleontological dates of major branching points in the tree of life are currently debated. In some cases, molecular date estimates are up to twice as old as paleontological dates. However, although it is true that paleontological dates are often too young (missing fossils), molecular dates are often too old (statistical bias). Intense study of the dating of major splits in the tree of mammals has shown rapprochement as fossil dates become older and molecular dates become younger.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Benton, Michael J -- Ayala, Francisco J -- New York, N.Y. -- Science. 2003 Jun 13;300(5626):1698-700.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK. Mike.Benton@bris.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12805535" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; Birds/classification ; Classification/*methods ; DNA/analysis ; Evolution, Molecular ; *Fossils ; Invertebrates/classification ; Mammals/classification ; *Paleontology ; *Phylogeny ; Plants/classification ; Polymorphism, Genetic ; Proteins/analysis ; RNA/analysis ; Time ; Vertebrates/classification
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    A protein interaction map of Drosophila melanogaster (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-11-08
    Description: Drosophila melanogaster is a proven model system for many aspects of human biology. Here we present a two-hybrid-based protein-interaction map of the fly proteome. A total of 10,623 predicted transcripts were isolated and screened against standard and normalized complementary DNA libraries to produce a draft map of 7048 proteins and 20,405 interactions. A computational method of rating two-hybrid interaction confidence was developed to refine this draft map to a higher confidence map of 4679 proteins and 4780 interactions. Statistical modeling of the network showed two levels of organization: a short-range organization, presumably corresponding to multiprotein complexes, and a more global organization, presumably corresponding to intercomplex connections. The network recapitulated known pathways, extended pathways, and uncovered previously unknown pathway components. This map serves as a starting point for a systems biology modeling of multicellular organisms, including humans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Giot, L -- Bader, J S -- Brouwer, C -- Chaudhuri, A -- Kuang, B -- Li, Y -- Hao, Y L -- Ooi, C E -- Godwin, B -- Vitols, E -- Vijayadamodar, G -- Pochart, P -- Machineni, H -- Welsh, M -- Kong, Y -- Zerhusen, B -- Malcolm, R -- Varrone, Z -- Collis, A -- Minto, M -- Burgess, S -- McDaniel, L -- Stimpson, E -- Spriggs, F -- Williams, J -- Neurath, K -- Ioime, N -- Agee, M -- Voss, E -- Furtak, K -- Renzulli, R -- Aanensen, N -- Carrolla, S -- Bickelhaupt, E -- Lazovatsky, Y -- DaSilva, A -- Zhong, J -- Stanyon, C A -- Finley, R L Jr -- White, K P -- Braverman, M -- Jarvie, T -- Gold, S -- Leach, M -- Knight, J -- Shimkets, R A -- McKenna, M P -- Chant, J -- Rothberg, J M -- HG01536/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2003 Dec 5;302(5651):1727-36. Epub 2003 Nov 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CuraGen Corporation, 555 Long Wharf Drive, New Haven, CT 06511, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14605208" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium/metabolism ; Cell Cycle ; Cell Differentiation ; Cloning, Molecular ; Computational Biology ; DNA, Complementary ; Drosophila Proteins/*metabolism ; Drosophila melanogaster/*genetics/*metabolism/physiology ; Genes, Insect ; Immunity, Innate ; Mathematics ; Models, Statistical ; Photoreceptor Cells, Invertebrate/cytology ; Protein Binding ; *Protein Interaction Mapping ; *Proteome ; RNA Splicing ; RNA, Messenger/genetics/metabolism ; Receptor, Epidermal Growth Factor/metabolism ; Signal Transduction ; Transcription, Genetic ; Two-Hybrid System Techniques
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    Redox regulation of germline and vulval development in Caenorhabditis elegans (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-06
    Description: In vitro studies have indicated that reactive oxygen species (ROS) and the oxidation of signaling molecules are important mediators of signal transduction. We have identified two pathways by which the altered redox chemistry of the clk-1 mutants of Caenorhabditis elegans acts in vivo on germline development. One pathway depends on the oxidation of an analog of vertebrate low density lipoprotein (LDL) and acts on the germline through the Ack-related tyrosine kinase (ARK-1) kinase and inositol trisphosphate (IP3) signaling. The other pathway is the oncogenic ras signaling pathway, whose action on germline as well as vulval development appears to be modulated by cytoplasmic ROS.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shibata, Yukimasa -- Branicky, Robyn -- Landaverde, Irene Oviedo -- Hekimi, Siegfried -- New York, N.Y. -- Science. 2003 Dec 5;302(5651):1779-82.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, McGill University, 1205 Avenue Docteur Penfield, Montreal, Quebec, Canada, H3A 1B1.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14657502" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Apolipoproteins B/genetics/metabolism ; Base Sequence ; Caenorhabditis elegans/genetics/*growth & development/*metabolism ; Caenorhabditis elegans Proteins/chemistry/genetics/metabolism ; Cholesterol/metabolism ; Cloning, Molecular ; Disorders of Sex Development ; Female ; Inositol Phosphates/metabolism ; Lipoproteins, LDL/*metabolism ; Molecular Sequence Data ; Mutation ; Oxidation-Reduction ; Phenotype ; Protein-Tyrosine Kinases/metabolism ; RNA Interference ; Reactive Oxygen Species/*metabolism ; Transcription Factors/genetics/metabolism ; Vulva/growth & development ; ras Proteins/genetics/metabolism
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    Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-09-23
    Description: Receptors for sex and adrenal steroid hormones are absent from fully sequenced invertebrate genomes and have not been recovered from other invertebrates. Here we report the isolation of an estrogen receptor ortholog from the mollusk Aplysia californica and the reconstruction, synthesis, and experimental characterization of functional domains of the ancestral protein from which all extant steroid receptors (SRs) evolved. Our findings indicate that SRs are extremely ancient and widespread, having diversified from a primordial gene before the origin of bilaterally symmetric animals, and that this ancient receptor had estrogen receptor-like functionality. This gene was lost in the lineage leading to arthropods and nematodes and became independent of hormone regulation in the Aplysia lineage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thornton, Joseph W -- Need, Eleanor -- Crews, David -- 41770/PHS HHS/ -- New York, N.Y. -- Science. 2003 Sep 19;301(5640):1714-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR 97403, USA. joet@uoregon.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14500980" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Aplysia/chemistry/genetics/*metabolism ; Biological Evolution ; CHO Cells ; Cloning, Molecular ; Cricetinae ; DNA/metabolism ; Estrogens/*metabolism/pharmacology ; *Evolution, Molecular ; Gene Duplication ; Humans ; Ligands ; Likelihood Functions ; Molecular Sequence Data ; Mutation ; *Phylogeny ; Polymerase Chain Reaction ; Protein Structure, Tertiary ; Receptors, Estrogen/chemistry/genetics/isolation & purification/*metabolism ; Receptors, Steroid/chemistry/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Signal Transduction ; Steroids/metabolism/pharmacology ; Transcription, Genetic ; Transfection
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    Signal transduction. Fishing at the cell surface (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-04-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maller, James L -- New York, N.Y. -- Science. 2003 Apr 25;300(5619):594-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Pharmacology, University of Colorado School of Medicine, Denver, CO 80262, USA. jim.maller@uchsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12714732" target="_blank"〉PubMed〈/a〉
    Keywords: Adenylyl Cyclase Inhibitors ; Adenylyl Cyclases/metabolism ; Animals ; Cell Membrane/*metabolism ; Cloning, Molecular ; Cyclic AMP/metabolism ; Female ; Fishes/genetics/metabolism ; GTP-Binding Proteins/metabolism ; *MAP Kinase Signaling System ; Mitogen-Activated Protein Kinases/metabolism ; Oocytes/metabolism/physiology ; Ovary/metabolism ; Phylogeny ; Progestins/metabolism ; Receptor Cross-Talk ; Receptors, Cell Surface/chemistry/genetics/*metabolism ; Receptors, Progesterone/chemistry/genetics/*metabolism ; Recombinant Proteins/metabolism ; Signal Transduction
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    Maize genome sequencing by methylation filtration (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-20
    Description: Gene enrichment strategies offer an alternative to sequencing large and repetitive genomes such as that of maize. We report the generation and analysis of nearly 100,000 undermethylated (or methylation filtration) maize sequences. Comparison with the rice genome reveals that methylation filtration results in a more comprehensive representation of maize genes than those that result from expressed sequence tags or transposon insertion sites sequences. About 7% of the repetitive DNA is unmethylated and thus selected in our libraries, but potentially active transposons and unmethylated organelle genomes can be identified. Reverse transcription polymerase chain reaction can be used to finish the maize transcriptome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Palmer, Lance E -- Rabinowicz, Pablo D -- O'Shaughnessy, Andrew L -- Balija, Vivekanand S -- Nascimento, Lidia U -- Dike, Sujit -- de la Bastide, Melissa -- Martienssen, Robert A -- McCombie, W Richard -- 2 T32-CA09311-25/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2003 Dec 19;302(5653):2115-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14684820" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Chromosomes, Artificial, Bacterial ; Cloning, Molecular ; Computational Biology ; Conserved Sequence ; Contig Mapping ; CpG Islands ; *DNA Methylation ; DNA Transposable Elements ; DNA, Chloroplast/genetics ; DNA, Complementary ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Databases, Nucleic Acid ; Escherichia coli/genetics ; Exons ; Expressed Sequence Tags ; Genes, Plant ; *Genome, Plant ; Genomic Library ; Oryza/genetics ; Repetitive Sequences, Nucleic Acid ; Retroelements ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; Zea mays/*genetics
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    Identification of a testicular odorant receptor mediating human sperm chemotaxis (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-29
    Description: Although it has been known for some time that olfactory receptors (ORs) reside in spermatozoa, the function of these ORs is unknown. Here, we identified, cloned, and functionally expressed a previously undescribed human testicular OR, hOR17-4. With the use of ratiofluorometric imaging, Ca2+ signals were induced by a small subset of applied chemical stimuli, establishing the molecular receptive fields for the recombinantly expressed receptor in human embryonic kidney (HEK) 293 cells and the native receptor in human spermatozoa. Bourgeonal was a powerful agonist for both recombinant and native receptor types, as well as a strong chemoattractant in subsequent behavioral bioassays. In contrast, undecanal was a potent OR antagonist to bourgeonal and related compounds. Taken together, these results indicate that hOR17-4 functions in human sperm chemotaxis and may be a critical component of the fertilization process.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Spehr, Marc -- Gisselmann, Gunter -- Poplawski, Alexandra -- Riffell, Jeffrey A -- Wetzel, Christian H -- Zimmer, Richard K -- Hatt, Hanns -- New York, N.Y. -- Science. 2003 Mar 28;299(5615):2054-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Physiology, Ruhr University Bochum, 150 University Street, D-44780 Bochum, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12663925" target="_blank"〉PubMed〈/a〉
    Keywords: Adenylyl Cyclases/metabolism ; Aldehydes/chemistry/metabolism/pharmacology ; Binding Sites ; Calcium/metabolism ; Calcium Signaling ; Cell Line ; Chemotactic Factors/chemistry/metabolism/*pharmacology ; *Chemotaxis ; Cloning, Molecular ; Dose-Response Relationship, Drug ; Fertilization ; Gene Expression Profiling ; Humans ; Ligands ; Male ; Molecular Structure ; Odors ; Receptors, Odorant/chemistry/genetics/*physiology ; Recombinant Fusion Proteins/metabolism ; Seminal Plasma Proteins/genetics/*physiology ; *Sperm Motility/drug effects ; Spermatozoa/drug effects/*physiology ; Testis/*metabolism ; Type C Phospholipases/metabolism
    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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  • 97
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    A four-base paired genetic helix with expanded size (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-11-01
    Description: We describe a new molecular class of genetic-pairing system that has a native DNA backbone but has all four base pairs replaced by new, larger pairs. The base pairs include size-expanded analogs of thymine and of adenine, both extended by the width of a benzene ring (2.4 A). The expanded-diameter double helices are more thermodynamically stable than the Watson-Crick helix, likely because of enhanced base stacking. Structural data confirm a right-handed, double-stranded, and base-paired helical form. Because of the larger base size, all the pairs of this helical system are fluorescent, which suggests practical applications in detection of natural DNA and RNA. Our findings establish that there is no apparent structural or thermodynamic prohibition against genetic systems having sizes different from the natural one.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Haibo -- Gao, Jianmin -- Lynch, Stephen R -- Saito, Y David -- Maynard, Lystranne -- Kool, Eric T -- GM52956/GM/NIGMS NIH HHS/ -- GM63587/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Oct 31;302(5646):868-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14593180" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/*analogs & derivatives/chemistry ; *Base Pairing ; Base Sequence ; Benzene/chemistry ; Circular Dichroism ; Hydrogen Bonding ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; *Nucleic Acid Conformation ; Nucleic Acid Denaturation ; Nucleic Acid Hybridization ; Oligodeoxyribonucleotides/*chemistry ; Temperature ; Thermodynamics ; Thymine/*analogs & derivatives/chemistry
    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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  • 98
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    Roles of NPM2 in chromatin and nucleolar organization in oocytes and embryos (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-04-26
    Description: Upon fertilization, remodeling of condensed maternal and paternal gamete DNA occurs to form the diploid genome. In Xenopus laevis, nucleoplasmin 2 (NPM2) decondenses sperm DNA in vitro. To study chromatin remodeling in vivo, we isolated mammalian NPM2 orthologs. Mouse NPM2 accumulates in oocyte nuclei and persists in preimplantation embryos. Npm2 knockout females have fertility defects owing to failed preimplantation embryo development. Although sperm DNA decondensation proceeds without NPM2, abnormalities are evident in oocyte and early embryonic nuclei. These defects include an absence of coalesced nucleolar structures and loss of heterochromatin and deacetylated histone H3 that normally circumscribe nucleoli in oocytes and early embryos, respectively. Thus, Npm2 is a maternal effect gene critical for nuclear and nucleolar organization and embryonic development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burns, Kathleen H -- Viveiros, Maria M -- Ren, Yongsheng -- Wang, Pei -- DeMayo, Francesco J -- Frail, Donald E -- Eppig, John J -- Matzuk, Martin M -- HD07495/HD/NICHD NIH HHS/ -- HD21970/HD/NICHD NIH HHS/ -- HD33438/HD/NICHD NIH HHS/ -- HD42500/HD/NICHD NIH HHS/ -- T32GM07330/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Apr 25;300(5619):633-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12714744" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Amino Acid Sequence ; Animals ; Base Sequence ; Cell Nucleolus/*physiology/ultrastructure ; Cell Nucleus/metabolism ; Chorionic Gonadotropin/pharmacology ; Chromatin/physiology/ultrastructure ; Crosses, Genetic ; Cytoplasm/metabolism ; Embryo, Mammalian/*physiology ; *Embryonic and Fetal Development ; Female ; Fertilization ; Heterochromatin/*physiology/ultrastructure ; Histones/metabolism ; Humans ; Male ; Meiosis ; Mice ; Mice, Knockout ; Mitosis ; Molecular Sequence Data ; Nuclear Proteins/chemistry/genetics/*physiology ; Nucleoplasmins ; Oocytes/*physiology ; Oogenesis ; Protein Biosynthesis ; Rats ; Spindle Apparatus/physiology/ultrastructure ; Transcription, Genetic ; Zygote/physiology
    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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  • 99
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    Biosynthesis of the food and cosmetic plant pigment bixin (annatto) (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-06-28
    Description: Bixin, also known as annatto, is a seed-specific pigment widely used in foods and cosmetics since pre-Columbian times. We show that three genes from Bixa orellana, native to tropical America, govern bixin biosynthesis. These genes code for lycopene cleavage dioxygenase, bixin aldehyde dehydrogenase, and norbixin carboxyl methyltransferase, which catalyze the sequential conversion of lycopene into bixin. Introduction of these three genes in Escherichia coli engineered to produce lycopene induced bixin synthesis, thus expanding the supply of this economically important plant product.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bouvier, Florence -- Dogbo, Odette -- Camara, Bilal -- New York, N.Y. -- Science. 2003 Jun 27;300(5628):2089-91.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Biologie Moleculaire des Plantes, CNRS, Universite Louis Pasteur, 67084 Strasbourg, Cedex, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12829782" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Dehydrogenase/chemistry/genetics/metabolism ; Amino Acid Sequence ; Bixaceae/*genetics/*metabolism ; Carotenoids/*biosynthesis/metabolism ; Catalysis ; Cloning, Molecular ; DNA, Complementary ; Escherichia coli/genetics/metabolism ; Gene Library ; Genes, Plant ; Methyltransferases/chemistry/genetics/metabolism ; Molecular Sequence Data ; Oxygenases/genetics/metabolism ; Recombinant Proteins/metabolism ; Seeds/genetics ; Transformation, Bacterial
    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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  • 100
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    Loss of an MDR transporter in compact stalks of maize br2 and sorghum dw3 mutants (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-10-04
    Description: Agriculturally advantageous reduction in plant height is usually achieved by blocking the action or production of gibberellins. Here, we describe a different dwarfing mechanism found in maize brachytic2 (br2) mutants characterized by compact lower stalk internodes. The height reduction in these plants results from the loss of a P-glycoprotein that modulates polar auxin transport in the maize stalk. The sorghum ortholog of br2 is dwarf3 (dw3), an unstable mutant of long-standing commercial interest and concern. A direct duplication within the dw3 gene is responsible for its mutant nature and also for its instability, because it facilitates unequal crossing-over at the locus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Multani, Dilbag S -- Briggs, Steven P -- Chamberlin, Mark A -- Blakeslee, Joshua J -- Murphy, Angus S -- Johal, Gurmukh S -- New York, N.Y. -- Science. 2003 Oct 3;302(5642):81-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Pioneer Hi-Bred International, 7250 Northwest 62nd Avenue, Johnston, IA 50131, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14526073" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Base Sequence ; Biological Transport ; Cloning, Molecular ; Crossing Over, Genetic ; Gene Duplication ; *Genes, Plant ; Genes, Recessive ; Indoleacetic Acids/*metabolism ; Light ; Molecular Sequence Data ; Mutation ; P-Glycoproteins/chemistry/*genetics/metabolism ; Plant Proteins/chemistry/genetics/metabolism ; Plant Stems/cytology/metabolism ; Poaceae/cytology/genetics/growth & development/*metabolism ; Recombination, Genetic ; Zea mays/cytology/genetics/growth & development/*metabolism
    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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