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  • Articles  (60)
  • Base Sequence  (60)
  • American Association for the Advancement of Science (AAAS)  (60)
  • Copernicus
  • National Academy of Sciences
  • 2010-2014  (27)
  • 1980-1984  (33)
  • 1945-1949
  • 1925-1929
  • 2012  (27)
  • 1983  (33)
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  • Articles  (60)
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  • 2010-2014  (27)
  • 1980-1984  (33)
  • 1945-1949
  • 1925-1929
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  • 1
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    A high-coverage genome sequence from an archaic Denisovan individual (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-09-01
    Description: We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30x) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617501/" 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/PMC3617501/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meyer, Matthias -- Kircher, Martin -- Gansauge, Marie-Theres -- Li, Heng -- Racimo, Fernando -- Mallick, Swapan -- Schraiber, Joshua G -- Jay, Flora -- Prufer, Kay -- de Filippo, Cesare -- Sudmant, Peter H -- Alkan, Can -- Fu, Qiaomei -- Do, Ron -- Rohland, Nadin -- Tandon, Arti -- Siebauer, Michael -- Green, Richard E -- Bryc, Katarzyna -- Briggs, Adrian W -- Stenzel, Udo -- Dabney, Jesse -- Shendure, Jay -- Kitzman, Jacob -- Hammer, Michael F -- Shunkov, Michael V -- Derevianko, Anatoli P -- Patterson, Nick -- Andres, Aida M -- Eichler, Evan E -- Slatkin, Montgomery -- Reich, David -- Kelso, Janet -- Paabo, Svante -- GM100233/GM/NIGMS NIH HHS/ -- R01 GM040282/GM/NIGMS NIH HHS/ -- R01 GM100233/GM/NIGMS NIH HHS/ -- R01-GM40282/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Oct 12;338(6104):222-6. doi: 10.1126/science.1224344. Epub 2012 Aug 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. mmeyer@eva.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22936568" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Base Sequence ; Fossils ; Gene Flow ; Gene Library ; *Genetic Variation ; Genome, Human/*genetics ; *Heterozygote ; Humans ; Molecular Sequence Data ; Neanderthals/*genetics ; Sequence Analysis, DNA
    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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    MARF1 regulates essential oogenic processes in mice (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-24
    Description: Development of fertilization-competent oocytes depends on integrated processes controlling meiosis, cytoplasmic development, and maintenance of genomic integrity. We show that meiosis arrest female 1 (MARF1) is required for these processes in mammalian oocytes. Mutations of Marf1 cause female infertility characterized by up-regulation of a cohort of transcripts, increased retrotransposon expression, defective cytoplasmic maturation, and meiotic arrest. Up-regulation of protein phosphatase 2 catalytic subunit (PPP2CB) is key to the meiotic arrest phenotype. Moreover, Iap and Line1 retrotransposon messenger RNAs are also up-regulated, and, concomitantly, DNA double-strand breaks are elevated in mutant oocytes. Therefore MARF1, by suppressing levels of specific transcripts, is an essential regulator of important oogenic processes leading to female fertility and the development of healthy offspring.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3612990/" 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/PMC3612990/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Su, You-Qiang -- Sugiura, Koji -- Sun, Fengyun -- Pendola, Janice K -- Cox, Gregory A -- Handel, Mary Ann -- Schimenti, John C -- Eppig, John J -- CA34196/CA/NCI NIH HHS/ -- HD42137/HD/NICHD NIH HHS/ -- P01 HD042137/HD/NICHD NIH HHS/ -- P30 CA034196/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2012 Mar 23;335(6075):1496-9. doi: 10.1126/science.1214680.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Jackson Laboratory, Bar Harbor, ME 04609, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22442484" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Cell Cycle Proteins/chemistry/genetics/*metabolism ; DNA Breaks, Double-Stranded ; Embryonic Development ; Female ; *Fertility ; Meiosis ; Mice ; Molecular Sequence Data ; Mutation ; Oocytes/*physiology ; *Oogenesis ; Phenotype ; Protein Phosphatase 2/genetics/metabolism ; Protein Structure, Tertiary ; RNA, Messenger/genetics/metabolism ; Retroelements ; Transcription, Genetic ; Transcriptome ; Up-Regulation
    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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    Decoding in the absence of a codon by tmRNA and SmpB in the ribosome (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-17
    Description: In bacteria, ribosomes stalled at the end of truncated messages are rescued by transfer-messenger RNA (tmRNA), a bifunctional molecule that acts as both a transfer RNA (tRNA) and a messenger RNA (mRNA), and SmpB, a small protein that works in concert with tmRNA. Here, we present the crystal structure of a tmRNA fragment, SmpB and elongation factor Tu bound to the ribosome at 3.2 angstroms resolution. The structure shows how SmpB plays the role of both the anticodon loop of tRNA and portions of mRNA to facilitate decoding in the absence of an mRNA codon in the A site of the ribosome and explains why the tmRNA-SmpB system does not interfere with normal translation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3763467/" 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/PMC3763467/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Neubauer, Cajetan -- Gillet, Reynald -- Kelley, Ann C -- Ramakrishnan, V -- 082086/Wellcome Trust/United Kingdom -- 096570/Wellcome Trust/United Kingdom -- MC_U105184332/Medical Research Council/United Kingdom -- U105184332/Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2012 Mar 16;335(6074):1366-9. doi: 10.1126/science.1217039.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22422985" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon ; Bacterial Proteins/chemistry/metabolism ; Base Sequence ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Peptide Elongation Factor Tu/*chemistry/metabolism ; Protein Biosynthesis ; Protein Conformation ; RNA, Bacterial/*chemistry/*metabolism ; RNA, Messenger/chemistry/metabolism ; RNA, Transfer/chemistry/metabolism ; RNA-Binding Proteins/*chemistry/*metabolism ; Ribosome Subunits, Small, Bacterial/chemistry/metabolism/ultrastructure ; Ribosomes/*chemistry/*metabolism/ultrastructure ; Thermus thermophilus/*chemistry/genetics/metabolism/ultrastructure
    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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    An overlapping protein-coding region in influenza A virus segment 3 modulates the host response (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-06-30
    Description: Influenza A virus (IAV) infection leads to variable and imperfectly understood pathogenicity. We report that segment 3 of the virus contains a second open reading frame ("X-ORF"), accessed via ribosomal frameshifting. The frameshift product, termed PA-X, comprises the endonuclease domain of the viral PA protein with a C-terminal domain encoded by the X-ORF and functions to repress cellular gene expression. PA-X also modulates IAV virulence in a mouse infection model, acting to decrease pathogenicity. Loss of PA-X expression leads to changes in the kinetics of the global host response, which notably includes increases in inflammatory, apoptotic, and T lymphocyte-signaling pathways. Thus, we have identified a previously unknown IAV protein that modulates the host response to infection, a finding with important implications for understanding IAV pathogenesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552242/" 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/PMC3552242/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jagger, B W -- Wise, H M -- Kash, J C -- Walters, K-A -- Wills, N M -- Xiao, Y-L -- Dunfee, R L -- Schwartzman, L M -- Ozinsky, A -- Bell, G L -- Dalton, R M -- Lo, A -- Efstathiou, S -- Atkins, J F -- Firth, A E -- Taubenberger, J K -- Digard, P -- 073126/Wellcome Trust/United Kingdom -- 088789/Wellcome Trust/United Kingdom -- G0700815/Medical Research Council/United Kingdom -- G0700815(82260)/Medical Research Council/United Kingdom -- G9800943/Medical Research Council/United Kingdom -- MR/J002232/1/Medical Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2012 Jul 13;337(6091):199-204. doi: 10.1126/science.1222213. Epub 2012 Jun 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22745253" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Cell Line ; Codon ; Conserved Sequence ; Female ; *Frameshifting, Ribosomal ; Gene Expression Regulation ; Genome, Viral ; HEK293 Cells ; Humans ; Influenza A Virus, H1N1 Subtype/*genetics/growth & development/pathogenicity ; Influenza A virus/*genetics/metabolism ; Lung/pathology/virology ; Mice ; Mice, Inbred BALB C ; Molecular Sequence Data ; Mutation ; *Open Reading Frames ; Orthomyxoviridae Infections/genetics/immunology/pathology/*virology ; Protein Interaction Domains and Motifs ; Proteome ; RNA Replicase/chemistry/*genetics/*metabolism ; RNA, Messenger/genetics/metabolism ; RNA, Viral/genetics/metabolism ; Reassortant Viruses/genetics ; Repressor Proteins/chemistry/*genetics/*metabolism ; Viral Nonstructural Proteins/chemistry/*genetics/*metabolism ; Viral Proteins/biosynthesis/chemistry/*genetics/*metabolism ; Virus Replication
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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  • 5
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    The shared antibiotic resistome of soil bacteria and human pathogens (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-09-01
    Description: Soil microbiota represent one of the ancient evolutionary origins of antibiotic resistance and have been proposed as a reservoir of resistance genes available for exchange with clinical pathogens. Using a high-throughput functional metagenomic approach in conjunction with a pipeline for the de novo assembly of short-read sequence data from functional selections (termed PARFuMS), we provide evidence for recent exchange of antibiotic resistance genes between environmental bacteria and clinical pathogens. We describe multidrug-resistant soil bacteria containing resistance cassettes against five classes of antibiotics (beta-lactams, aminoglycosides, amphenicols, sulfonamides, and tetracyclines) that have perfect nucleotide identity to genes from diverse human pathogens. This identity encompasses noncoding regions as well as multiple mobilization sequences, offering not only evidence of lateral exchange but also a mechanism by which antibiotic resistance disseminates.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4070369/" 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/PMC4070369/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Forsberg, Kevin J -- Reyes, Alejandro -- Wang, Bin -- Selleck, Elizabeth M -- Sommer, Morten O A -- Dantas, Gautam -- T32 GM007067/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Aug 31;337(6098):1107-11. doi: 10.1126/science.1220761.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22936781" target="_blank"〉PubMed〈/a〉
    Keywords: Aminoglycosides/pharmacology ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics/pathogenicity ; Base Sequence ; Drug Resistance, Multiple, Bacterial/*genetics ; High-Throughput Screening Assays ; Humans ; Metagenome/*drug effects/*genetics ; Metagenomics ; Molecular Sequence Data ; *Soil Microbiology ; Sulfonamides/pharmacology ; Tetracyclines/pharmacology ; beta-Lactams/pharmacology
    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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    Assembly of an evolutionarily new pathway for alpha-pyrone biosynthesis in Arabidopsis (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-08-28
    Description: Plants possess arrays of functionally diverse specialized metabolites, many of which are distributed taxonomically. Here, we describe the evolution of a class of substituted alpha-pyrone metabolites in Arabidopsis, which we have named arabidopyrones. The biosynthesis of arabidopyrones requires a cytochrome P450 enzyme (CYP84A4) to generate the catechol-substituted substrate for an extradiol ring-cleavage dioxygenase (AtLigB). Unlike other ring-cleavage-derived plant metabolites made from tyrosine, arabidopyrones are instead derived from phenylalanine through the early steps of phenylpropanoid metabolism. Whereas CYP84A4, an Arabidopsis-specific paralog of the lignin-biosynthetic enzyme CYP84A1, has neofunctionalized relative to its ancestor, AtLigB homologs are widespread among land plants and many bacteria. This study exemplifies the rapid evolution of a biochemical pathway formed by the addition of a new biological activity into an existing metabolic infrastructure.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weng, Jing-Ke -- Li, Yi -- Mo, Huaping -- Chapple, Clint -- New York, N.Y. -- Science. 2012 Aug 24;337(6097):960-4. doi: 10.1126/science.1221614.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22923580" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/enzymology/genetics/*metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Base Sequence ; Biosynthetic Pathways ; Catalytic Domain ; Cytochrome P-450 Enzyme System/chemistry/genetics/*metabolism ; Dioxygenases/genetics/metabolism ; Evolution, Molecular ; Gene Duplication ; Genome, Plant ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Phenylalanine/metabolism ; Phylogeny ; Plant Stems/metabolism ; Plants, Genetically Modified ; Pyrones/chemistry/*metabolism
    Print ISSN: 0036-8075
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  • 7
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    Glacial survival of boreal trees in northern Scandinavia (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-03
    Description: It is commonly believed that trees were absent in Scandinavia during the last glaciation and first recolonized the Scandinavian Peninsula with the retreat of its ice sheet some 9000 years ago. Here, we show the presence of a rare mitochondrial DNA haplotype of spruce that appears unique to Scandinavia and with its highest frequency to the west-an area believed to sustain ice-free refugia during most of the last ice age. We further show the survival of DNA from this haplotype in lake sediments and pollen of Trondelag in central Norway dating back ~10,300 years and chloroplast DNA of pine and spruce in lake sediments adjacent to the ice-free Andoya refugium in northwestern Norway as early as ~22,000 and 17,700 years ago, respectively. Our findings imply that conifer trees survived in ice-free refugia of Scandinavia during the last glaciation, challenging current views on survival and spread of trees as a response to climate changes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Parducci, Laura -- Jorgensen, Tina -- Tollefsrud, Mari Mette -- Elverland, Ellen -- Alm, Torbjorn -- Fontana, Sonia L -- Bennett, K D -- Haile, James -- Matetovici, Irina -- Suyama, Yoshihisa -- Edwards, Mary E -- Andersen, Kenneth -- Rasmussen, Morten -- Boessenkool, Sanne -- Coissac, Eric -- Brochmann, Christian -- Taberlet, Pierre -- Houmark-Nielsen, Michael -- Larsen, Nicolaj Krog -- Orlando, Ludovic -- Gilbert, M Thomas P -- Kjaer, Kurt H -- Alsos, Inger Greve -- Willerslev, Eske -- New York, N.Y. -- Science. 2012 Mar 2;335(6072):1083-6. doi: 10.1126/science.1216043.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22383845" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; *Ecosystem ; Europe ; *Fossils ; Geologic Sediments ; Haplotypes ; *Ice Cover ; Molecular Sequence Data ; Mutation ; Norway ; *Picea/genetics ; *Pinus/genetics ; Scandinavian and Nordic Countries ; Time
    Print ISSN: 0036-8075
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  • 8
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    Direct observation of cotranscriptional folding in an adenine riboswitch (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-10-23
    Description: Growing RNA chains fold cotranscriptionally as they are synthesized by RNA polymerase. Riboswitches, which regulate gene expression by adopting alternative RNA folds, are sensitive to cotranscriptional events. We developed an optical-trapping assay to follow the cotranscriptional folding of a nascent RNA and used it to monitor individual transcripts of the pbuE adenine riboswitch, visualizing distinct folding transitions. We report a particular folding signature for the riboswitch aptamer whose presence directs the gene-regulatory transcription outcome, and we measured the termination frequency as a function of adenine level and tension applied to the RNA. Our results demonstrate that the outcome is kinetically controlled. These experiments furnish a means to observe conformational switching in real time and enable the precise mapping of events during cotranscriptional folding.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3496414/" 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/PMC3496414/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frieda, Kirsten L -- Block, Steven M -- R37 GM057035/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Oct 19;338(6105):397-400. doi: 10.1126/science.1225722.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Program, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23087247" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/*chemistry/metabolism ; Bacillus subtilis/genetics ; Base Sequence ; Kinetics ; Molecular Sequence Data ; *Optical Tweezers ; *RNA Folding ; Riboswitch/*genetics ; *Transcription, Genetic
    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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  • 9
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    Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-10
    Description: We have identified tens of thousands of short extrachromosomal circular DNAs (microDNA) in mouse tissues as well as mouse and human cell lines. These microDNAs are 200 to 400 base pairs long, are derived from unique nonrepetitive sequence, and are enriched in the 5'-untranslated regions of genes, exons, and CpG islands. Chromosomal loci that are enriched sources of microDNA in the adult brain are somatically mosaic for microdeletions that appear to arise from the excision of microDNAs. Germline microdeletions identified by the "Thousand Genomes" project may also arise from the excision of microDNAs in the germline lineage. We have thus identified a previously unknown DNA entity in mammalian cells and provide evidence that their generation leaves behind deletions in different genomic loci.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703515/" 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/PMC3703515/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shibata, Yoshiyuki -- Kumar, Pankaj -- Layer, Ryan -- Willcox, Smaranda -- Gagan, Jeffrey R -- Griffith, Jack D -- Dutta, Anindya -- ES013773/ES/NIEHS NIH HHS/ -- GM31819/GM/NIGMS NIH HHS/ -- GM84465/GM/NIGMS NIH HHS/ -- P30 CA016086/CA/NCI NIH HHS/ -- R01 CA060499/CA/NCI NIH HHS/ -- R01 CA060499-18/CA/NCI NIH HHS/ -- R01 CA60499/CA/NCI NIH HHS/ -- R01 ES013773/ES/NIEHS NIH HHS/ -- R01 GM031819/GM/NIGMS NIH HHS/ -- R01 GM084465/GM/NIGMS NIH HHS/ -- R01 GM084465-04/GM/NIGMS NIH HHS/ -- T32 GM008136/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Apr 6;336(6077):82-6. doi: 10.1126/science.1213307. Epub 2012 Mar 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22403181" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Untranslated Regions ; Animals ; Base Pairing ; Base Sequence ; Brain/*embryology ; Brain Chemistry ; Cell Line ; Cell Line, Tumor ; *Chromosome Deletion ; Chromosomes, Human/*genetics ; Chromosomes, Mammalian/*genetics ; CpG Islands ; DNA Replication ; *DNA, Circular/analysis/chemistry/isolation & purification/metabolism ; Exons ; Germ Cells/chemistry ; Heart/embryology ; Humans ; Liver/chemistry/embryology ; Mice ; Mice, Inbred C57BL ; Microscopy, Electron ; Molecular Sequence Data ; Polymerase Chain Reaction ; Repetitive Sequences, Nucleic Acid
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  • 10
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    The tale of the TALEs (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-12-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2012 Dec 14;338(6113):1408-11. doi: 10.1126/science.338.6113.1408.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23239709" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacterial Proteins/chemistry/genetics/*metabolism ; Base Sequence ; Capsicum/microbiology ; Deoxyribonucleases/chemistry/genetics/*metabolism ; Gene Targeting/*methods ; Genetic Engineering/*methods ; Genome ; Humans ; Malus/microbiology ; Protein Conformation ; Trans-Activators/chemistry/genetics/*metabolism ; Virulence Factors/chemistry/genetics/*metabolism ; Xanthomonas/genetics/*metabolism/pathogenicity ; *Zinc Fingers
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    Patent law. Law and science collide over human gene patents (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-11-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cook-Deegan, Robert -- P50 HG003391/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2012 Nov 9;338(6108):745-7. doi: 10.1126/science.1229854.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA. bob.cd@duke.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23139317" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; *Dna ; *Genes ; Genes, BRCA1 ; Genes, BRCA2 ; Humans ; Inventions ; Patents as Topic/*legislation & jurisprudence ; *Supreme Court Decisions ; United States
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  • 12
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    iRhom2 regulation of TACE controls TNF-mediated protection against Listeria and responses to LPS (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-01-17
    Description: Innate immune responses are vital for pathogen defense but can result in septic shock when excessive. A key mediator of septic shock is tumor necrosis factor-alpha (TNFalpha), which is shed from the plasma membrane after cleavage by the TNFalpha convertase (TACE). We report that the rhomboid family member iRhom2 interacted with TACE and regulated TNFalpha shedding. iRhom2 was critical for TACE maturation and trafficking to the cell surface in hematopoietic cells. Gene-targeted iRhom2-deficient mice showed reduced serum TNFalpha in response to lipopolysaccharide (LPS) and could survive a lethal LPS dose. Furthermore, iRhom2-deficient mice failed to control the replication of Listeria monocytogenes. Our study has identified iRhom2 as a regulator of innate immunity that may be an important target for modulating sepsis and pathogen defense.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4250273/" 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/PMC4250273/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McIlwain, David R -- Lang, Philipp A -- Maretzky, Thorsten -- Hamada, Koichi -- Ohishi, Kazuhito -- Maney, Sathish Kumar -- Berger, Thorsten -- Murthy, Aditya -- Duncan, Gordon -- Xu, Haifeng C -- Lang, Karl S -- Haussinger, Dieter -- Wakeham, Andrew -- Itie-Youten, Annick -- Khokha, Rama -- Ohashi, Pamela S -- Blobel, Carl P -- Mak, Tak W -- GM64750/GM/NIGMS NIH HHS/ -- R01 GM064750/GM/NIGMS NIH HHS/ -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2012 Jan 13;335(6065):229-32. doi: 10.1126/science.1214448.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Campell Family Institute for Breast Cancer Research, Ontario Cancer Institute, University Health Network (UHN), 620 University Avenue, Toronto, Ontario M5G 2C1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22246778" target="_blank"〉PubMed〈/a〉
    Keywords: ADAM Proteins/genetics/*metabolism ; Amino Acid Sequence ; Animals ; B-Lymphocytes/immunology/metabolism ; Base Sequence ; Carrier Proteins/chemistry/genetics/*metabolism ; Cell Line ; Cell Membrane/metabolism ; Gene Deletion ; *Immunity, Innate ; Lipopolysaccharides/*immunology ; Listeria monocytogenes/immunology/physiology ; Listeriosis/*immunology/metabolism/microbiology/pathology ; Macrophages/immunology/metabolism ; Macrophages, Peritoneal/immunology/metabolism/microbiology ; Mice ; Molecular Sequence Data ; Protein Transport ; Shock, Septic/*immunology/metabolism ; Spleen/cytology ; Tumor Necrosis Factor-alpha/blood/genetics/*metabolism
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  • 13
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    An early-branching microbialite cyanobacterium forms intracellular carbonates (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-04-28
    Description: Cyanobacteria have affected major geochemical cycles (carbon, nitrogen, and oxygen) on Earth for billions of years. In particular, they have played a major role in the formation of calcium carbonates (i.e., calcification), which has been considered to be an extracellular process. We identified a cyanobacterium in modern microbialites in Lake Alchichica (Mexico) that forms intracellular amorphous calcium-magnesium-strontium-barium carbonate inclusions about 270 nanometers in average diameter, revealing an unexplored pathway for calcification. Phylogenetic analyses place this cyanobacterium within the deeply divergent order Gloeobacterales. The chemical composition and structure of the intracellular precipitates suggest some level of cellular control on the biomineralization process. This discovery expands the diversity of organisms capable of forming amorphous calcium carbonates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Couradeau, Estelle -- Benzerara, Karim -- Gerard, Emmanuelle -- Moreira, David -- Bernard, Sylvain -- Brown, Gordon E Jr -- Lopez-Garcia, Purificacion -- New York, N.Y. -- Science. 2012 Apr 27;336(6080):459-62. doi: 10.1126/science.1216171.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Mineralogie et de Physique de la Matiere Condensee, CNRS UMR 7590, Universite Pierre et Marie Curie, Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22539718" target="_blank"〉PubMed〈/a〉
    Keywords: Barium/analysis ; Base Sequence ; *Biofilms ; Calcification, Physiologic ; Calcium/analysis ; Calcium Carbonate/*analysis ; Carbonates/*analysis/metabolism ; Chemical Precipitation ; Cyanobacteria/classification/*isolation & purification/*physiology/ultrastructure ; Genes, Bacterial ; Genes, rRNA ; Inclusion Bodies/*chemistry/*ultrastructure ; Lakes/*microbiology ; Magnesium/analysis ; Mexico ; Molecular Sequence Data ; Phylogeny ; Strontium/analysis
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  • 14
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    Nucleosomes suppress spontaneous mutations base-specifically in eukaryotes (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-03-10
    Description: It is unknown how the composition and structure of DNA within the cell affect spontaneous mutations. Theory suggests that in eukaryotic genomes, nucleosomal DNA undergoes fewer C--〉T mutations because of suppressed cytosine hydrolytic deamination relative to nucleosome-depleted DNA. Comparative genomic analyses and a mutation accumulation experiment showed that nucleosome occupancy nearly eliminated cytosine deamination, resulting in an ~50% decrease of the C--〉T mutation rate in nucleosomal DNA. Furthermore, the rates of G--〉T and A--〉T mutations were also about twofold suppressed by nucleosomes. On the basis of these results, we conclude that nucleosome-dependent mutation spectra affect eukaryotic genome structure and evolution and may have implications for understanding the origin of mutations in cancers and in induced pluripotent stem cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Xiaoshu -- Chen, Zhidong -- Chen, Han -- Su, Zhijian -- Yang, Jianfeng -- Lin, Fangqin -- Shi, Suhua -- He, Xionglei -- New York, N.Y. -- Science. 2012 Mar 9;335(6073):1235-8. doi: 10.1126/science.1217580.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory of Bio-control, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22403392" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Pairing ; Base Sequence ; Caenorhabditis elegans/*genetics ; Cytosine/chemistry/metabolism ; DNA, Fungal/chemistry/genetics ; DNA, Helminth/chemistry/genetics ; DNA, Intergenic ; Deamination ; Genome, Fungal ; Germ Cells ; Models, Genetic ; *Mutation Rate ; Nucleosomes/*chemistry/*physiology ; Oryzias/embryology/*genetics ; *Point Mutation ; Polymorphism, Single Nucleotide ; Saccharomyces/genetics ; Saccharomyces cerevisiae/*genetics ; Sequence Analysis, DNA
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  • 15
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    Cost-benefit tradeoffs in engineered lac operons (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-05-19
    Description: Cells must balance the cost and benefit of protein expression to optimize organismal fitness. The lac operon of the bacterium Escherichia coli has been a model for quantifying the physiological impact of costly protein production and for elucidating the resulting regulatory mechanisms. We report quantitative fitness measurements in 27 redesigned operons that suggested that protein production is not the primary origin of fitness costs. Instead, we discovered that the lac permease activity, which relates linearly to cost, is the major physiological burden to the cell. These findings explain control points in the lac operon that minimize the cost of lac permease activity, not protein expression. Characterizing similar relationships in other systems will be important to map the impact of cost/benefit tradeoffs on cell physiology and regulation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eames, Matt -- Kortemme, Tanja -- New York, N.Y. -- Science. 2012 May 18;336(6083):911-5. doi: 10.1126/science.1219083.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate Group in Biophysics, MC 2530, University of California, San Francisco, CA 94158-2330, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22605776" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Biocatalysis ; Biological Transport ; Escherichia coli/*genetics/growth & development/metabolism ; Escherichia coli Proteins/*genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Gene Knockout Techniques ; Genetic Engineering ; Isopropyl Thiogalactoside/metabolism ; *Lac Operon ; Lac Repressors ; Lactose/metabolism ; Models, Biological ; Molecular Sequence Data ; Monosaccharide Transport Proteins/*genetics/*metabolism ; Mutation ; Symporters/*genetics/*metabolism ; beta-Galactosidase/*genetics/*metabolism
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  • 16
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    Landscape of somatic retrotransposition in human cancers (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-06-30
    Description: Transposable elements (TEs) are abundant in the human genome, and some are capable of generating new insertions through RNA intermediates. In cancer, the disruption of cellular mechanisms that normally suppress TE activity may facilitate mutagenic retrotranspositions. We performed single-nucleotide resolution analysis of TE insertions in 43 high-coverage whole-genome sequencing data sets from five cancer types. We identified 194 high-confidence somatic TE insertions, as well as thousands of polymorphic TE insertions in matched normal genomes. Somatic insertions were present in epithelial tumors but not in blood or brain cancers. Somatic L1 insertions tend to occur in genes that are commonly mutated in cancer, disrupt the expression of the target genes, and are biased toward regions of cancer-specific DNA hypomethylation, highlighting their potential impact in tumorigenesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656569/" 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/PMC3656569/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Eunjung -- Iskow, Rebecca -- Yang, Lixing -- Gokcumen, Omer -- Haseley, Psalm -- Luquette, Lovelace J 3rd -- Lohr, Jens G -- Harris, Christopher C -- Ding, Li -- Wilson, Richard K -- Wheeler, David A -- Gibbs, Richard A -- Kucherlapati, Raju -- Lee, Charles -- Kharchenko, Peter V -- Park, Peter J -- Cancer Genome Atlas Research Network -- F32 AG039979/AG/NIA NIH HHS/ -- F32AG039979/AG/NIA NIH HHS/ -- K25 AG037596/AG/NIA NIH HHS/ -- K25AG037596/AG/NIA NIH HHS/ -- R01 GM082798/GM/NIGMS NIH HHS/ -- R01GM082798/GM/NIGMS NIH HHS/ -- RC1HG005482/HG/NHGRI NIH HHS/ -- T32 CA009172/CA/NCI NIH HHS/ -- U01 HG005725/HG/NHGRI NIH HHS/ -- U01HG005209/HG/NHGRI NIH HHS/ -- U01HG005725/HG/NHGRI NIH HHS/ -- U24 CA144025/CA/NCI NIH HHS/ -- U24CA144025/CA/NCI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2012 Aug 24;337(6097):967-71. doi: 10.1126/science.1222077. Epub 2012 Jun 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22745252" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Cell Transformation, Neoplastic ; Colorectal Neoplasms/*genetics ; DNA Methylation ; Female ; Gene Expression Regulation, Neoplastic ; Genes, Neoplasm ; Genome, Human ; Glioblastoma/*genetics ; Humans ; Long Interspersed Nucleotide Elements ; Male ; Microsatellite Instability ; Molecular Sequence Annotation ; Molecular Sequence Data ; Multiple Myeloma/*genetics ; Mutagenesis, Insertional ; Mutation ; Ovarian Neoplasms/*genetics ; Prostatic Neoplasms/*genetics ; *Retroelements ; Sequence Analysis, DNA
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    Cotranscriptional role for Arabidopsis DICER-LIKE 4 in transcription termination (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-03-31
    Description: Transcription termination is emerging as an important component of gene regulation necessary to partition the genome and minimize transcriptional interference. We have discovered a role for the Arabidopsis RNA silencing enzyme DICER-LIKE 4 (DCL4) in transcription termination of an endogenous Arabidopsis gene, FCA. DCL4 directly associates with FCA chromatin in the 3' region and promotes cleavage of the nascent transcript in a domain downstream of the canonical polyA site. In a dcl4 mutant, the resulting transcriptional read-through triggers an RNA interference-mediated gene silencing of a transgene containing the same 3' region. We conclude that DCL4 promotes transcription termination of the Arabidopsis FCA gene, reducing the amount of aberrant RNA produced from the locus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Fuquan -- Bakht, Saleha -- Dean, Caroline -- BB/D010799/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G01406X/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2012 Mar 30;335(6076):1621-3. doi: 10.1126/science.1214402.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22461611" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/*genetics/metabolism ; Arabidopsis Proteins/*genetics/metabolism ; Base Sequence ; Chromatin/genetics/metabolism ; Chromatin Immunoprecipitation ; *Gene Expression Regulation, Plant ; MADS Domain Proteins/genetics/metabolism ; Molecular Sequence Data ; Mutation ; Polyadenylation ; Protein Structure, Tertiary ; RNA Interference ; RNA, Messenger/genetics/metabolism ; RNA, Plant/*genetics/metabolism ; RNA-Binding Proteins/*genetics/metabolism ; Ribonuclease III/chemistry/genetics/*metabolism ; *Transcription, Genetic ; Transgenes
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    A fine-scale chimpanzee genetic map from population sequencing (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-03-17
    Description: To study the evolution of recombination rates in apes, we developed methodology to construct a fine-scale genetic map from high-throughput sequence data from 10 Western chimpanzees, Pan troglodytes verus. Compared to the human genetic map, broad-scale recombination rates tend to be conserved, but with exceptions, particularly in regions of chromosomal rearrangements and around the site of ancestral fusion in human chromosome 2. At fine scales, chimpanzee recombination is dominated by hotspots, which show no overlap with those of humans even though rates are similarly elevated around CpG islands and decreased within genes. The hotspot-specifying protein PRDM9 shows extensive variation among Western chimpanzees, and there is little evidence that any sequence motifs are enriched in hotspots. The contrasting locations of hotspots provide a natural experiment, which demonstrates the impact of recombination on base composition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3532813/" 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/PMC3532813/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Auton, Adam -- Fledel-Alon, Adi -- Pfeifer, Susanne -- Venn, Oliver -- Segurel, Laure -- Street, Teresa -- Leffler, Ellen M -- Bowden, Rory -- Aneas, Ivy -- Broxholme, John -- Humburg, Peter -- Iqbal, Zamin -- Lunter, Gerton -- Maller, Julian -- Hernandez, Ryan D -- Melton, Cord -- Venkat, Aarti -- Nobrega, Marcelo A -- Bontrop, Ronald -- Myers, Simon -- Donnelly, Peter -- Przeworski, Molly -- McVean, Gil -- 076113/E/04/Z/Wellcome Trust/United Kingdom -- 086084/Wellcome Trust/United Kingdom -- 086084/Z/08/Z/Wellcome Trust/United Kingdom -- 086786/Z/08/Z/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 090532/Z/09/Z/Wellcome Trust/United Kingdom -- R01 GM083098/GM/NIGMS NIH HHS/ -- R01 GM83098/GM/NIGMS NIH HHS/ -- R01 HG004428/HG/NHGRI NIH HHS/ -- T32 GM007197/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Apr 13;336(6078):193-8. doi: 10.1126/science.1216872. Epub 2012 Mar 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Centre for Human Genetics, Oxford , UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22422862" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Chromosome Mapping ; Chromosomes, Human, Pair 2/genetics ; Chromosomes, Mammalian/*genetics ; CpG Islands ; Evolution, Molecular ; Female ; Genetic Variation ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Histone-Lysine N-Methyltransferase/genetics ; Humans ; Male ; Pan troglodytes/*genetics ; Polymorphism, Single Nucleotide ; *Recombination, Genetic ; Sequence Analysis, DNA ; Species Specificity
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    Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-09-01
    Description: The classical view of DNA posits that DNA must be stiff below the persistence length [〈150 base pairs (bp)], but recent studies addressing this have yielded contradictory results. We developed a fluorescence-based, protein-free assay for studying the cyclization of single DNA molecules in real time. The assay samples the equilibrium population of a sharply bent, transient species that is entirely suppressed in single-molecule mechanical measurements and is biologically more relevant than the annealed species sampled in the traditional ligase-based assay. The looping rate has a weak length dependence between 67 and 106 bp that cannot be described by the worm-like chain model. Many biologically important protein-DNA interactions that involve looping and bending of DNA below 100 bp likely use this intrinsic bendability of DNA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565842/" 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/PMC3565842/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vafabakhsh, Reza -- Ha, Taekjip -- GM065367/GM/NIGMS NIH HHS/ -- R01 GM065367/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Aug 31;337(6098):1097-101. doi: 10.1126/science.1224139.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22936778" target="_blank"〉PubMed〈/a〉
    Keywords: Avidin/chemistry ; Base Sequence ; Biotin/chemistry ; Cyclization ; DNA, Circular/*chemistry ; Fluorescence ; Fluorescence Resonance Energy Transfer/*methods ; *Nucleic Acid Conformation ; Polyethylene Glycols/chemistry
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    A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-06-30
    Description: Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. We show here that in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand, whereas the Cas9 RuvC-like domain cleaves the noncomplementary strand. The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. Our study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jinek, Martin -- Chylinski, Krzysztof -- Fonfara, Ines -- Hauer, Michael -- Doudna, Jennifer A -- Charpentier, Emmanuelle -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Aug 17;337(6096):816-21. doi: 10.1126/science.1225829. Epub 2012 Jun 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22745249" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophages/*immunology ; Base Sequence ; *DNA Breaks, Double-Stranded ; *DNA Cleavage ; Deoxyribonucleases, Type II Site-Specific/chemistry/genetics/*metabolism ; *Inverted Repeat Sequences ; Molecular Sequence Data ; Nucleic Acid Conformation ; Plasmids/metabolism ; RNA/chemistry/*metabolism ; Streptococcus pyogenes/*enzymology/physiology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-09-08
    Description: Autism spectrum disorders are a genetically heterogeneous constellation of syndromes characterized by impairments in reciprocal social interaction. Available somatic treatments have limited efficacy. We have identified inactivating mutations in the gene BCKDK (Branched Chain Ketoacid Dehydrogenase Kinase) in consanguineous families with autism, epilepsy, and intellectual disability. The encoded protein is responsible for phosphorylation-mediated inactivation of the E1alpha subunit of branched-chain ketoacid dehydrogenase (BCKDH). Patients with homozygous BCKDK mutations display reductions in BCKDK messenger RNA and protein, E1alpha phosphorylation, and plasma branched-chain amino acids. Bckdk knockout mice show abnormal brain amino acid profiles and neurobehavioral deficits that respond to dietary supplementation. Thus, autism presenting with intellectual disability and epilepsy caused by BCKDK mutations represents a potentially treatable syndrome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3704165/" 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/PMC3704165/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Novarino, Gaia -- El-Fishawy, Paul -- Kayserili, Hulya -- Meguid, Nagwa A -- Scott, Eric M -- Schroth, Jana -- Silhavy, Jennifer L -- Kara, Majdi -- Khalil, Rehab O -- Ben-Omran, Tawfeg -- Ercan-Sencicek, A Gulhan -- Hashish, Adel F -- Sanders, Stephan J -- Gupta, Abha R -- Hashem, Hebatalla S -- Matern, Dietrich -- Gabriel, Stacey -- Sweetman, Larry -- Rahimi, Yasmeen -- Harris, Robert A -- State, Matthew W -- Gleeson, Joseph G -- K08 MH087639/MH/NIMH NIH HHS/ -- K08MH087639/MH/NIMH NIH HHS/ -- P01 HD070494/HD/NICHD NIH HHS/ -- P01HD070494/HD/NICHD NIH HHS/ -- P30 NS047101/NS/NINDS NIH HHS/ -- P30NS047101/NS/NINDS NIH HHS/ -- R01 NS041537/NS/NINDS NIH HHS/ -- R01 NS048453/NS/NINDS NIH HHS/ -- R01NS048453/NS/NINDS NIH HHS/ -- R25 MH077823/MH/NIMH NIH HHS/ -- RC2 MH089956/MH/NIMH NIH HHS/ -- RC2MH089956/MH/NIMH NIH HHS/ -- T32MH018268/MH/NIMH NIH HHS/ -- U54HG003067/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Oct 19;338(6105):394-7. doi: 10.1126/science.1224631. Epub 2012 Sep 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Neurogenetics Laboratory, Howard Hughes Medical Institute, Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA. gnovarino@ucsd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22956686" target="_blank"〉PubMed〈/a〉
    Keywords: 3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)/*administration & ; dosage/deficiency/*genetics ; Adolescent ; Amino Acids, Branched-Chain/administration & dosage/blood/deficiency ; Animals ; Arginine/genetics ; Autistic Disorder/*diet therapy/enzymology/*genetics ; Base Sequence ; Brain/metabolism ; Child ; Child, Preschool ; Diet ; Epilepsy/*diet therapy/enzymology/*genetics ; Female ; Homozygote ; Humans ; Intellectual Disability/diet therapy/enzymology/genetics ; Male ; Mice ; Mice, Knockout ; Molecular Sequence Data ; Mutation ; Pedigree ; Phosphorylation ; Protein Folding ; Protein Structure, Tertiary ; RNA, Messenger/metabolism ; Young Adult
    Print ISSN: 0036-8075
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    Function, developmental genetics, and fitness consequences of a sexually antagonistic trait (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-05-05
    Description: Sexual conflict is thought to be a potent force driving the evolution of sexually dimorphic traits. In the water strider Rheumatobates rileyi, we show that elaborated traits on male antennae function to grasp resistant females during premating struggles. Using RNA interference, we uncovered novel roles of the gene distal-less (dll) in generating these male-specific traits. Furthermore, graded reduction of the grasping traits resulted in a graded reduction of mating success in males, thus demonstrating both selection for elaboration of the traits and the role of dll in their evolution. By establishing developmental genetic tools in model systems where sexual selection and conflict are understood, we can begin to reveal how selection can exploit ancient developmental genes to enable the evolution of sexually dimorphic traits.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Khila, Abderrahman -- Abouheif, Ehab -- Rowe, Locke -- New York, N.Y. -- Science. 2012 May 4;336(6081):585-9. doi: 10.1126/science.1217258.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22556252" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arthropod Antennae/anatomy & histology/growth & development/*physiology ; Base Sequence ; Biological Evolution ; Female ; Genes, Insect ; *Genetic Fitness ; Heteroptera/anatomy & histology/*genetics/growth & development/*physiology ; Homeodomain Proteins/*genetics/metabolism ; Male ; Molecular Sequence Data ; Phenotype ; RNA Interference ; *Selection, Genetic ; Sex Characteristics ; *Sexual Behavior, Animal ; Transcription Factors/*genetics/metabolism ; Transcriptome
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    AID-driven deletion causes immunoglobulin heavy chain locus suicide recombination in B cells (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-04-28
    Description: Remodeling of immunoglobulin genes by activation-induced deaminase (AID) is required for affinity maturation and class-switch recombination in mature B lymphocytes. In the immunoglobulin heavy chain locus, these processes are predominantly controlled by the 3' cis-regulatory region. We now show that this region is transcribed and undergoes AID-mediated mutation and recombination around phylogenetically conserved switchlike DNA repeats. Such recombination, which we term locus suicide recombination, deletes the whole constant region gene cluster and thus stops expression of the immunoglobulin of the B cell surface, which is critical for B cell survival. The frequency of this event is approaching that of class switching and makes it a potential regulator of B cell homeostasis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Peron, Sophie -- Laffleur, Brice -- Denis-Lagache, Nicolas -- Cook-Moreau, Jeanne -- Tinguely, Aurelien -- Delpy, Laurent -- Denizot, Yves -- Pinaud, Eric -- Cogne, Michel -- New York, N.Y. -- Science. 2012 May 18;336(6083):931-4. doi: 10.1126/science.1218692. Epub 2012 Apr 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Limoges University, CNRS, 2 rue Marcland, 87025 Limoges Cedex, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22539552" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; B-Lymphocytes/immunology/*physiology ; Base Sequence ; Cell Line ; Cell Survival ; Cytidine Deaminase/*metabolism ; *Gene Deletion ; *Gene Rearrangement, B-Lymphocyte, Heavy Chain ; *Genes, Immunoglobulin Heavy Chain ; Homeostasis ; Humans ; Immunoglobulin Class Switching ; Lymphocyte Activation ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; *Recombination, Genetic ; Regulatory Sequences, Nucleic Acid ; Repetitive Sequences, Nucleic Acid ; Transcription, Genetic
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    Developmental progression to infectivity in Trypanosoma brucei triggered by an RNA-binding protein (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-12-12
    Description: Unraveling the intricate interactions between Trypanosoma brucei, the protozoan parasite causing African trypanosomiasis, and the tsetse (Glossina) vector remains a challenge. Metacyclic trypanosomes, which inhabit the tsetse salivary glands, transmit the disease and are produced through a complex differentiation and unknown program. By overexpressing a single RNA-binding protein, TbRBP6, in cultured noninfectious trypanosomes, we recapitulated the developmental stages that have been observed in tsetse, including the generation of infective metacyclic forms expressing the variant surface glycoprotein. Thus, events leading to acquisition of infectivity in the insect vector are now accessible to laboratory investigation, providing an opening for new intervention strategies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3664091/" 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/PMC3664091/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kolev, Nikolay G -- Ramey-Butler, Kiantra -- Cross, George A M -- Ullu, Elisabetta -- Tschudi, Christian -- AI021729/AI/NIAID NIH HHS/ -- AI028798/AI/NIAID NIH HHS/ -- AI043594/AI/NIAID NIH HHS/ -- AI076879/AI/NIAID NIH HHS/ -- R01 AI021729/AI/NIAID NIH HHS/ -- R01 AI043594/AI/NIAID NIH HHS/ -- R21 AI076879/AI/NIAID NIH HHS/ -- R37 AI028798/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2012 Dec 7;338(6112):1352-3. doi: 10.1126/science.1229641.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06536, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23224556" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Gene Expression Regulation ; Molecular Sequence Data ; Protozoan Proteins/genetics/*metabolism ; RNA-Binding Proteins/genetics/*metabolism ; Trypanosoma brucei brucei/genetics/*growth & development/*pathogenicity ; Tsetse Flies/*parasitology
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    In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-04-28
    Description: Few data are available on how quickly free-living microorganisms evolve. We analyzed biofilms collected from a well-defined acid mine drainage system over 9 years to investigate the processes and determine rates of bacterial evolution directly in the environment. Population metagenomic analyses of the dominant primary producer yielded the nucleotide substitution rate, which we used to show that proliferation of a series of recombinant bacterial strains occurred over the past few decades. The ecological success of hybrid bacterial types highlights the role of evolutionary processes in rapid adaptation within natural microbial communities.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Denef, Vincent J -- Banfield, Jillian F -- New York, N.Y. -- Science. 2012 Apr 27;336(6080):462-6. doi: 10.1126/science.1218389.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth and Planetary Science, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22539719" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Bacteria/*genetics ; Bacterial Physiological Phenomena ; Base Sequence ; *Biofilms ; *Biological Evolution ; California ; *Ecosystem ; Genome, Bacterial ; Genotype ; Hybridization, Genetic ; Hydrogen-Ion Concentration ; Metagenome ; *Mining ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Single Nucleotide ; *Recombination, Genetic ; Time Factors
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    Synchronizing nuclear import of ribosomal proteins with ribosome assembly (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-11-03
    Description: Ribosomal proteins are synthesized in the cytoplasm, before nuclear import and assembly with ribosomal RNA (rRNA). Little is known about coordination of nucleocytoplasmic transport with ribosome assembly. Here, we identify a transport adaptor, symportin 1 (Syo1), that facilitates synchronized coimport of the two 5S-rRNA binding proteins Rpl5 and Rpl11. In vitro studies revealed that Syo1 concomitantly binds Rpl5-Rpl11 and furthermore recruits the import receptor Kap104. The Syo1-Rpl5-Rpl11 import complex is released from Kap104 by RanGTP and can be directly transferred onto the 5S rRNA. Syo1 can shuttle back to the cytoplasm by interaction with phenylalanine-glycine nucleoporins. X-ray crystallography uncovered how the alpha-solenoid symportin accommodates the Rpl5 amino terminus, normally bound to 5S rRNA, in an extended groove. Symportin-mediated coimport of Rpl5-Rpl11 could ensure coordinated and stoichiometric incorporation of these proteins into pre-60S ribosomes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kressler, Dieter -- Bange, Gert -- Ogawa, Yutaka -- Stjepanovic, Goran -- Bradatsch, Bettina -- Pratte, Dagmar -- Amlacher, Stefan -- Strauss, Daniela -- Yoneda, Yoshihiro -- Katahira, Jun -- Sinning, Irmgard -- Hurt, Ed -- New York, N.Y. -- Science. 2012 Nov 2;338(6107):666-71. doi: 10.1126/science.1226960.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biochemie-Zentrum der Universitat Heidelberg, Im Neuenheimer Feld 328, Heidelberg D-69120, Germany. dieter.kressler@unifr.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23118189" target="_blank"〉PubMed〈/a〉
    Keywords: *Active Transport, Cell Nucleus ; Amino Acid Sequence ; Base Sequence ; Cell Nucleus/*metabolism ; Chaetomium/metabolism ; Crystallography, X-Ray ; Fungal Proteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Conformation ; Protein Multimerization ; Protein Structure, Tertiary ; RNA, Fungal/metabolism ; RNA, Ribosomal, 5S/metabolism ; RNA-Binding Proteins/chemistry/*metabolism ; Ribosomal Proteins/chemistry/*metabolism ; Ribosomes/*metabolism ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism ; beta Karyopherins/metabolism
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    Structural basis for sequence-specific recognition of DNA by TAL effectors (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-01-10
    Description: TAL (transcription activator-like) effectors, secreted by phytopathogenic bacteria, recognize host DNA sequences through a central domain of tandem repeats. Each repeat comprises 33 to 35 conserved amino acids and targets a specific base pair by using two hypervariable residues [known as repeat variable diresidues (RVDs)] at positions 12 and 13. Here, we report the crystal structures of an 11.5-repeat TAL effector in both DNA-free and DNA-bound states. Each TAL repeat comprises two helices connected by a short RVD-containing loop. The 11.5 repeats form a right-handed, superhelical structure that tracks along the sense strand of DNA duplex, with RVDs contacting the major groove. The 12th residue stabilizes the RVD loop, whereas the 13th residue makes a base-specific contact. Understanding DNA recognition by TAL effectors may facilitate rational design of DNA-binding proteins with biotechnological applications.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586824/" 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/PMC3586824/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Deng, Dong -- Yan, Chuangye -- Pan, Xiaojing -- Mahfouz, Magdy -- Wang, Jiawei -- Zhu, Jian-Kang -- Shi, Yigong -- Yan, Nieng -- R01 GM070795/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 10;335(6069):720-3. doi: 10.1126/science.1215670. Epub 2012 Jan 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory of Bio-Membrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22223738" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/*metabolism ; Base Sequence ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA-Binding Proteins/chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Physicochemical Processes ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Repetitive Sequences, Amino Acid ; Virulence Factors/*chemistry/*metabolism ; Xanthomonas/chemistry/pathogenicity
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    Splice junctions: association with variation in protein structure (1983)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1983-06-10
    Description: A comparison between eukaryotic gene sequences and protein sequences of homologous enzymes from bacterial and mammalian organisms shows that intron-exon junctions frequently coincide with variable surface loops of the protein structures. The altered surface structures can account for functional differences among the members of a family. Sliding of the intron-exon junctions may constitute one mechanism for generating length polymorphisms and divergent sequences found in protein families. Since intron-exon junctions map to protein surfaces, the alterations mediated by sliding of these junctions can be effected without disrupting the stability of the protein core.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Craik, C S -- Rutter, W J -- Fletterick, R -- AM21344/AM/NIADDK NIH HHS/ -- AM26081/AM/NIADDK NIH HHS/ -- GM28520/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1983 Jun 10;220(4602):1125-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6344214" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bacterial Proteins ; Base Sequence ; Biological Evolution ; DNA/genetics ; Endopeptidases/genetics ; Eukaryotic Cells/metabolism ; Genes ; Genes, Bacterial ; Protein Conformation ; Proteins/*genetics ; *Serine Endopeptidases ; Tetrahydrofolate Dehydrogenase/genetics
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    Somatic mutations of immunoglobulin variable genes are restricted to the rearranged V gene (1983)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1983-06-10
    Description: An important question concerning the mechanism of somatic mutation of immunoglobulin variable (V) genes is whether it involves all of the numerous V genes in a differentiated B cell, independent of location, or if it is restricted to a particular chromosomal site. Comparison of the sequence of two alleles of a given V gene shows that the mutations are limited to the rearranged V gene, while the same V gene on the other chromosome has not undergone mutation. This indicates that a V gene sequence alone is not sufficient for somatic mutation to take place. The mutation is therefore restricted to the rearranged V gene and consequently does not occur before rearrangement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gorski, J -- Rollini, P -- Mach, B -- New York, N.Y. -- Science. 1983 Jun 10;220(4602):1179-81.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6857243" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites, Antibody/*genetics ; Chromosomes/physiology ; DNA/genetics ; *Genes ; Immunoglobulin Constant Regions/genetics ; Immunoglobulin Variable Region/*genetics ; Immunoglobulins/genetics ; Lymphocytes/metabolism ; Mice ; *Mutation
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    Simple repeat array in Epstein-Barr virus DNA encodes part of the Epstein-Barr nuclear antigen (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-06-24
    Description: The size of the Epstein-Barr virus (EBV) nuclear antigen (EBNA) in cells infected with different EBV isolates varies directly with the size of the EBV triplet repeat array, IR3. The isolate with the largest IR3 fragment has approximately 170 more codons than the isolates with the smallest IR3 fragment; it encodes an EBNA which is approximately 17,000 daltons larger than the smallest EBNA. The EBV IR3 encodes part of a 2-kilobase exon of a latently infected cell messenger RNA which must be translated into a repetitive amino acid domain of EBNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hennessy, K -- Heller, M -- van Santen, V -- Kieff, E -- CA 17281/CA/NCI NIH HHS/ -- CA 19264/CA/NCI NIH HHS/ -- GM 07183/GM/NIGMS NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1983 Jun 24;220(4604):1396-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6304878" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, Viral/*genetics ; Base Sequence ; Cell Nucleus/immunology ; DNA, Viral/*genetics ; Epstein-Barr Virus Nuclear Antigens ; Herpesvirus 4, Human/*genetics/immunology ; Humans ; Mice ; RNA, Viral/genetics
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    A nonenzymatic RNA polymerase model (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-02-18
    Description: Polynucleotide templates containing C (cytidine) as the major component facilitate the synthesis of oligonucleotides from mixtures of the activated mononucleotide derivatives (as indicated by structure 1 in the text). A nucleotide is incorporated into oligomeric products if and only if its complement is present in the template. The reaction has a high fidelity and produces products with mean chain lengths of six to ten nucleotides. Bases other than guanosine are incorporated within oligomers or at their 3' termini, but rarely at their 5' termini.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Inoue, T -- Orgel, L E -- GM-13435/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1983 Feb 18;219(4586):859-62.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6186026" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; DNA-Directed RNA Polymerases/*metabolism ; Hydrogen Bonding ; Models, Chemical ; RNA/*chemical synthesis ; Templates, Genetic
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  • 32
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    Requirement for signal peptide cleavage of Escherichia coli prolipoprotein (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-07-01
    Description: Oligonucleotide-directed site-specific mutagenesis was applied to alter the cleavage site in the signal peptide of the major outer membrane lipoprotein of Escherichia coli. Replacing the glycine residue at the cleavage site with an alanine residue did not affect the processing of the signal peptide. However, when the same cleavage site was constructed by the deletion of the glycine residue, the signal peptide was no longer cleaved. These results indicate that stringent structural integrity at the cleavage site in the lipoprotein signal sequence is required for correct processing of prolipoprotein.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Inouye, S -- Hsu, C P -- Itakura, K -- Inouye, M -- GM19043/GM/NIGMS NIH HHS/ -- GM30395/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1983 Jul 1;221(4605):59-61.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6344218" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Bacterial Outer Membrane Proteins ; Base Sequence ; DNA, Bacterial/metabolism ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/*metabolism ; *Escherichia coli Proteins ; Lipoproteins/*biosynthesis ; Membrane Proteins/biosynthesis ; Mutation ; Protein Precursors/*biosynthesis
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    Small RNA (1983)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1983-01-07
    Description: The illustration that accompanied the review by C. C. Albritton, Jr., of W. H. Goetzmann and K. Sloan's Looking Far North (Viking, New York, 1982) in the issue of 10 December, page 1109, should have been credited to the Bancroft Library, University of California, Berkeley, as well as to the book under review.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lerman, L S -- New York, N.Y. -- Science. 1983 Jan 7;219(4580):10.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6184778" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; RNA/*physiology ; RNA, Small Nuclear
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    How mammalian RNA returns to its genome (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-03-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lewin, R -- New York, N.Y. -- Science. 1983 Mar 4;219(4588):1052-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6186029" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Cell Nucleus/physiology ; DNA/*genetics ; Humans ; Poly A/genetics ; RNA/*genetics ; Repetitive Sequences, Nucleic Acid ; Transcription, Genetic
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    Protein engineering (1983)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1983-02-11
    Description: The prospects for protein engineering, including the roles of x-ray crystallography, chemical synthesis of DNA, and computer modelling of protein structure and folding, are discussed. It is now possible to attempt to modify many different properties of proteins by combining information on crystal structure and protein chemistry with artificial gene synthesis. Such techniques offer the potential for altering protein structure and function in ways not possible by any other method.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ulmer, K M -- New York, N.Y. -- Science. 1983 Feb 11;219(4585):666-71.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6572017" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Crystallography ; Genes ; *Genetic Engineering ; Models, Molecular ; Molecular Biology/trends ; Protein Conformation ; Proteins/*genetics ; X-Ray Diffraction
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    Multiple point mutations affecting the simian virus 40 enhancer (1983)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1983-02-11
    Description: Enhancers, or activators, dramatically increase the transcriptional activity of certain eukaryotic genes. A series of multiple point mutations affecting the simian virus 40 (SV40) enhancer-activator region were generated in order to define the nucleotide sequence required for this function. Three independent assays provided information leading to the identification of nucleotides essential for enhancer function. One class leads to a decrease in gene expression, while the second completely abolishes functional activity. One critical replacement appears to be the first G (guanine) in a sequence TGGAAAG (T, thymine, A, adenine) located in the 5' region of the 72 base-pair repeat of SV40. Comparison of this sequence with nucleotide sequences in other known enhancers leads to the identification of potential related core elements.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weiher, H -- Konig, M -- Gruss, P -- New York, N.Y. -- Science. 1983 Feb 11;219(4585):626-31.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6297005" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; DNA Replication ; *Gene Expression Regulation ; Mutation ; *Operon ; Plasmids ; Repetitive Sequences, Nucleic Acid ; Simian virus 40/*genetics ; Virus Replication
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    Studying promoters and terminators by gene fusion (1983)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1983-11-18
    Description: Prokaryotic gene control signals can be isolated, compared, and characterized by precise fusion in vitro to the Escherichia coli galactokinase gene (galK), which provides both a simple assay and genetic selection. This recombinant galK fusion vector system was applied to the study of promoters and terminators recognized by the Escherichia coli RNA polymerase. Three promoters created by mutation from DNA sequences having no promoter function were characterized. Mutations that inactivate promoter function were selected, structurally defined, and functionally analyzed. Similarly, transcription termination was examined, and mutations affecting terminator function were isolated and characterized.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rosenberg, M -- Chepelinsky, A B -- McKenney, K -- New York, N.Y. -- Science. 1983 Nov 18;222(4625):734-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6356355" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; DNA, Bacterial/*genetics ; DNA, Recombinant ; DNA-Directed RNA Polymerases/genetics ; Escherichia coli/genetics ; Galactokinase/genetics ; Gene Expression Regulation ; Mutation ; Nucleic Acid Conformation ; *Operon ; *Transcription, Genetic
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  • 38
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    Structure of a mouse submaxillary messenger RNA encoding epidermal growth factor and seven related proteins (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-07-15
    Description: The structure of the messenger RNA (mRNA) encoding the precursor to mouse submaxillary epidermal growth factor (EGF) was determined from the sequence of a set of overlapping complementary DNA's (cDNA). The mRNA is unexpectedly large, about 4750 nucleotide bases, and predicts the sequence of preproEGF, a protein of 1217 amino acids (133,000 molecular weight). The EGF moiety (53 amino acids) is flanked by polypeptide segments of 976 and 188 amino acids at its amino and carboyxl termini, respectively. The amino terminal segment of the precursor contains seven peptides with sequences that are similar but not identical to EGF.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scott, J -- Urdea, M -- Quiroga, M -- Sanchez-Pescador, R -- Fong, N -- Selby, M -- Rutter, W J -- Bell, G I -- 21344/PHS HHS/ -- New York, N.Y. -- Science. 1983 Jul 15;221(4607):236-40.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6602382" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Epidermal Growth Factor/biosynthesis/*genetics ; Humans ; Male ; Mice ; RNA, Messenger/*genetics ; Submandibular Gland/metabolism
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    Recombination during gene transfer into mouse cells can restore the function of deleted genes (1983)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1983-01-14
    Description: Two plasmids containing nonoverlapping deletions of the herpes simplex virus thymidine kinase gene were introduced into thymidine kinase-deficient mouse L cells by DNA-mediated gene transfer. Thymidine kinase-producing transformants were generated by a mixture of the two plasmids at a frequency significantly greater than that generated by either plasmid alone. Southern blot analyses demonstrated that functional thymidine kinase genes were generated by homologous recombination between the two deletion mutants.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Small, J -- Scangos, G -- New York, N.Y. -- Science. 1983 Jan 14;219(4581):174-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6294829" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Cells, Cultured ; Chromosome Deletion ; *Genetic Engineering ; Mice ; Mutation ; *Plasmids ; *Recombination, Genetic ; Simplexvirus ; Thymidine Kinase/*genetics
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  • 40
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    BK viral enhancer element and a human cellular homolog (1983)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1983-11-18
    Description: Comparison of two closely related primate papovaviruses, simian virus 40 (SV40) and human BK virus (BKV), reveals that the only region of extensive divergence, the tandem sequences adjacent to the origins of DNA replication, is responsible in SV40 for enhancing early gene expression. This study demonstrates a similar enhancer function for the analogous repeated region in BKV. The dissimilarity in sequence of the BKV and SV40 enhancer elements suggests that they may have been acquired since SV40 and BKV diverged. A locus cloned from the human genome homologous to the BKV tandem repeats has been shown to function as low level enhancer element in mammalian cells. These data support the hypothesis that viral enhancer sequences may be evolutionarily related to host cell sequences.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rosenthal, N -- Kress, M -- Gruss, P -- Khoury, G -- New York, N.Y. -- Science. 1983 Nov 18;222(4625):749-55.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6314501" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; BK Virus/*genetics ; Base Sequence ; Biological Evolution ; DNA, Viral/*genetics ; Gene Expression Regulation ; *Genes, Regulator ; Humans ; Plasmids ; Polyomavirus/*genetics ; Repetitive Sequences, Nucleic Acid ; Species Specificity
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    Separation of signal transduction and adaptation functions of the aspartate receptor in bacterial sensing (1983)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1983-06-03
    Description: In order to investigate the functions of stimulus recognition, signal transduction, and adaptation, the aspartate receptor gene for bacterial chemotaxis in Salmonella typhimurium has been sequenced and modified. A carboxyl-terminal truncated receptor was shown to bind aspartate and to transmit a signal to change motility behavior. However, the truncated receptor showed greatly reduced methyl-accepting capacity, and did not allow adaptation to the sensory stimulation. The separation of receptor functions by alteration of primary structure emphasizes that the receptor is directly involved in adaptation and is not solely a device for transmitting a signal across a membrane.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Russo, A F -- Koshland, D E Jr -- New York, N.Y. -- Science. 1983 Jun 3;220(4601):1016-20.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6302843" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Amino Acid Sequence ; Aspartic Acid ; *Bacterial Physiological Phenomena ; Base Sequence ; *Chemotaxis ; Escherichia coli/physiology ; Methylation ; *Receptors, Amino Acid ; Receptors, Cell Surface/genetics/*physiology ; Salmonella typhimurium/physiology ; Serine
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    Insertion sequence duplication in transpositional recombination (1983)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1983-11-18
    Description: Insertion sequences (IS) are discrete segments of DNA that can transpose from one genomic site to another and promote genetic rearrangements. A question that is central to understanding the mechanism of transpositional recombination is whether genetic rearrangements are accompanied by duplication of the IS that promotes them. Analysis of adjacent deletions mediated by IS903 provides the strongest evidence to date than any IS-mediated transpositional recombination can occur by an efficient replicative mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weinert, T A -- Schaus, N A -- Grindley, N D -- GM28470/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1983 Nov 18;222(4625):755-65.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6314502" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Chromosome Deletion ; *DNA Transposable Elements ; DNA, Bacterial/*genetics ; Plasmids ; *Recombination, Genetic ; Repetitive Sequences, Nucleic Acid
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    An inverted repeat borders a fivefold amplification in satellite DNA (1983)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1983-08-26
    Description: One variant of a complex satellite DNA of the Bermuda land crab is significantly longer than the average repeat unit of the satellite. The extra DNA in the variant is accounted for by a fivefold tandem amplification of a 0.142-kilobase sequence. The amplified sequence is bounded by a tetranucleotide inverted repeat; the upstream arm of the inverted repeat is missing from two other variants of the satellite. The latter variants contain only one copy of a sequence that is closely related to the amplified sequence. By contrast, in several satellite DNA's of other organisms, extra DNA is inserted.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bonnewell, V -- Fowler, R F -- Skinner, D M -- New York, N.Y. -- Science. 1983 Aug 26;221(4613):862-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6879182" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Brachyura/genetics ; Chromosome Inversion ; DNA, Satellite/*genetics ; *Gene Amplification ; Nucleic Acid Conformation
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  • 44
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    Murine I-A beta chain polymorphism: nucleotide sequences of three allelic I-A beta genes (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-07-15
    Description: The polymorphism of immune response genes plays a critical role in determining the immune capabilities of a particular individual. The molecular nature of this polymorphism was studied by examining the structure of the coding portions of three alleles of the I-A beta chain gene, an immune response gene whose protein product constitutes a subunit of the I-A molecule. Comparison of the I-A beta chains encoded by these alleles revealed an amino acid sequence divergence of 5 to 8 percent. The differences were found to be a series of short alterations clustered in the amino terminal half of the polypeptide.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Choi, E -- McIntyre, K -- Germain, R N -- Seidman, J G -- AI18436/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1983 Jul 15;221(4607):283-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6407114" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Animals ; Base Sequence ; *Genes, MHC Class II ; Histocompatibility Antigens Class II/immunology ; Humans ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; *Polymorphism, Genetic
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    Somatic cell genetics and gene families (1983)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1983-05-27
    Description: The utility of somatic cell genetic analysis for the chromosomal localization of genes in mammals is well established. With the development of recombinant DNA probes and efficient blotting techniques that allow visualization of single-copy cellular genes, somatic cell genetics has been extended from the level of phenotypes expressed by whole cells to the level of the cellular genome itself. This extension has proved invaluable for the analysis of genes not readily expressed in somatic cell hybrids and for the study of multigene families, especially pseudogenes dispersed in different chromosomes throughout the genome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉D'Eustachio, P -- Ruddle, F H -- GM-09966/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1983 May 27;220(4600):919-24.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6573776" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; *Chromosome Mapping ; Chromosomes, Human ; Cricetinae ; Cricetulus ; DNA, Recombinant/metabolism ; Genes ; Genetic Markers ; Genetics ; Humans ; Hybrid Cells/metabolism ; Mice ; Polymorphism, Genetic ; RNA, Messenger/metabolism
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  • 46
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    Transcription of class III genes: formation of preinitiation complexes (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-11-18
    Description: Class III genes require multiple cellular factors for transcription by RNA polymerase III; these genes form stable transcription complexes, which in the case of Xenopus 5S genes are correlated with differential expression in vivo. The minimal number and identity of the factors required to form both stable and metastable complexes on three class III genes (encoding, respectively, 5S RNA, transfer RNA, and adenovirus VA RNA species) were determined. Stable complex formation requires one common factor, whose recognition site was analyzed, and either no additional factors (the VA gene), a second common factor (the transfer RNA gene), or a third gene-specific factor (the 5S gene). The mechanism of stable complex formation and its relevance to transcriptional regulation were examined in light of the various factors and the promoter sequences recognized by these factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lassar, A B -- Martin, P L -- Roeder, R G -- CA 24223/CA/NCI NIH HHS/ -- CA 24891/CA/NCI NIH HHS/ -- GM07200/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1983 Nov 18;222(4625):740-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6356356" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; DNA-Directed RNA Polymerases/*genetics ; Eukaryotic Cells/physiology ; Gene Expression Regulation ; Genes ; Humans ; Operon ; RNA Polymerase III/*genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; RNA, Viral/genetics ; Transcription Factors/genetics ; *Transcription, Genetic
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  • 47
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    Nucleotide sequence of a light chain gene of the mouse I-A subregion: A beta d (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-08-19
    Description: Ia (I region-associated) antigens are cell-surface glycoproteins involved in the regulation of immune responsiveness. They are composed of one heavy (alpha) and one light (beta) polypeptide chain. We have sequenced the gene encoding the A beta d chain of the BALB/c mouse. The presence of six exons is predicted by comparison with the complementary DNA sequences of human beta chains and with partial protein sequence data for the A beta d polypeptide. Sequence comparisons have been made to other proteins involved in immune responses and the consequent implications for the evolutionary relationships of these genes are discussed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Malissen, M -- Hunkapiller, T -- Hood, L -- New York, N.Y. -- Science. 1983 Aug 19;221(4612):750-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6410508" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Biological Evolution ; Codon ; Genes ; *Genes, MHC Class II ; Macromolecular Substances ; Major Histocompatibility Complex ; Mice ; beta 2-Microglobulin/genetics
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    Detection of antibodies to herpes simplex virus with a continuous cell line expressing cloned glycoprotein D (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-11-04
    Description: The gene for glycoprotein D of herpes simplex virus type 1 (HSV-1) was expressed in stable mammalian cell lines. Glycoprotein D produced in these cells has a number of antigenic determinants in common with the native glycoprotein. Cell lines expressing glycoprotein D were used in an enzyme-linked immunosorbent assay to detect human antibodies to glycoprotein D. This strategy should prove useful in determining the extent to which the immune response to HSV-1 is directed toward glycoprotein D.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berman, P W -- Dowbenko, D -- Lasky, L A -- Simonsen, C C -- New York, N.Y. -- Science. 1983 Nov 4;222(4623):524-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6312563" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Viral/*analysis ; Base Sequence ; Cell Line ; Clone Cells ; DNA Restriction Enzymes ; DNA, Viral/genetics ; Enzyme-Linked Immunosorbent Assay ; *Genes ; *Genes, Viral ; Humans ; Plasmids ; Simplexvirus/genetics/*immunology ; Tetrahydrofolate Dehydrogenase/genetics ; *Viral Envelope Proteins ; Viral Proteins/*genetics/immunology
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    Viroid origin in jumping genes? (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-11-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lewin, R -- New York, N.Y. -- Science. 1983 Nov 25;222(4626):915.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6314505" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; *DNA Transposable Elements ; Viroids/*genetics
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    Nucleotide sequence and expression of the diphtheria tox228 gene in Escherichia coli (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-08-26
    Description: The complete nucleotide sequence of the diphtheria tox228 gene encoding the nontoxic serologically related protein CRM228 has been determined. A comparison of the predicted amino acid sequence with the available amino acid sequences from the wild-type toxin made it possible to deduce essentially the entire nucleotide sequence of the wild-type tox gene. The signal peptide of pro-diphtheria toxin and the putative tox promoter have been identified, a highly symmetrical nucleotide sequence downstream of the toxin gene has been detected; this region may be the corynebacteriophage beta attachment site (attP). The cloned toxin gene was expressed at a low level in Escherichia coli.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kaczorek, M -- Delpeyroux, F -- Chenciner, N -- Streeck, R E -- Murphy, J R -- Boquet, P -- Tiollais, P -- New York, N.Y. -- Science. 1983 Aug 26;221(4613):855-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6348945" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Cloning, Molecular ; Diphtheria Toxin/*genetics ; Escherichia coli/genetics ; Gene Expression Regulation ; Genes ; Genes, Bacterial ; Nucleic Acid Conformation ; Operon
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    RNA splice site selection: evidence for a 5' leads to 3' scanning model (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-06-24
    Description: Human G gamma-globin genes containing tandem duplications of the donor (5') or acceptor (3') RNA splice sites of the second intervening sequence were constructed in order to ascertain the directionality of RNA splice site selection. These genes were introduced into cultured monkey cells, and their transcripts were analyzed. Transcripts of these duplication variants were spliced only at the proximal copy of the duplicated splice sites. These data are consistent with a 5' leads to 3' model of splice site selection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lang, K M -- Spritz, R A -- AM28598/AM/NIADDK NIH HHS/ -- New York, N.Y. -- Science. 1983 Jun 24;220(4604):1351-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6304877" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Cells, Cultured ; Globins/genetics ; Haplorhini ; Humans ; Plasmids ; *RNA Splicing ; RNA, Messenger/genetics/physiology ; Simian virus 40/genetics ; Transcription, Genetic
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    Nucleotide sequence of the Rasheed rat sarcoma virus oncogene: new mutations (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-07-08
    Description: The nucleotide sequence of the oncogene of the Rasheed strain of rat sarcoma virus was determined. The oncogene (Ra-v-ras) encodes a 29,000-dalton (p29) transforming protein. This protein is distinct from the immunologically related 21,000-dalton protein (p21) of the Harvey murine sarcoma virus in its amino terminus and in having additional mutations in its carboxyl terminus. Although the functional significance of these changes is unknown, they appear to occur only in rat sarcoma virus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rasheed, S -- Norman, G L -- Heidecker, G -- CA 27246/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1983 Jul 8;221(4606):155-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6344220" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Mice ; Neoplasm Proteins/genetics ; *Oncogenes ; Proto-Oncogene Proteins p21(ras) ; Rats ; Retroviridae/*genetics
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    Nucleotide sequence analysis of the T24 human bladder carcinoma oncogene (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-06-03
    Description: The nucleotide sequence of the T24 human bladder carcinoma oncogene was determined, and the coding and noncoding sequences of the genome were identified. The amino acid sequence of p21, the translational product of the T24 oncogene, was predicted from the nucleotide sequence of the oncogene. Comparison of this sequence with that of the normal cellular homolog showed that a single point mutation in the coding sequences of the T24 oncogene resulted in the acquisition of transforming properties. Other differences between the T24 oncogene and its normal cellular homolog were found in the 5' noncoding and 3' noncoding sequences, but these differences appear to be due to polymorphism and do not play a significant role in the transformation process.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reddy, E P -- New York, N.Y. -- Science. 1983 Jun 3;220(4601):1061-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6844927" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Carcinoma/*genetics ; Cell Transformation, Neoplastic/metabolism ; Humans ; Mice ; Neoplasm Proteins/genetics ; *Oncogenes ; Oncogenic Viruses/genetics ; Rats ; Urinary Bladder Neoplasms/*genetics
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    Ectopic pro-opiolipomelanocortin: sequence of cDNA coding for beta-melanocyte-stimulating hormone and beta-endorphin (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-05-13
    Description: A recombinant bacterial plasmid, pMS1, was constructed that contains 318 nucleotides complementary to a portion of pro-opiolipomelanocortin (proOLMC) messenger RNA from an ectopic adrenocorticotropin-producing tumor. The cloned complementary DNA insert, which contains the sequence that codes for all of the beta-melanocyte-stimulating hormone and beta-endorphin portions of proOLMC, as well as the 3' nontranslated section, is identical to the genomic sequence. Hybridization of tumor proOLMC complementary DNA to RNA subjected to electrophoresis and transferred to a nitrocellulose filter revealed two proOLMC messenger RNA species in the tumor polyadenylated RNA, but only one in pituitary polyadenylated RNA. At least one of the tumor proOLMC messenger RNA's is similar, if not identical, to human pituitary proOLMC messenger RNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DeBold, C R -- Schworer, M E -- Connor, T B -- Bird, R E -- Orth, D N -- 2-R01-GM25526/GM/NIGMS NIH HHS/ -- 5-R01-CA11685/CA/NCI NIH HHS/ -- 5-R25-CA19429/CA/NCI NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1983 May 13;220(4598):721-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6301015" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Carcinoid Tumor/physiopathology ; Cloning, Molecular ; DNA, Neoplasm/genetics ; DNA, Recombinant/*metabolism ; Endorphins/*genetics ; Hormones, Ectopic/*genetics ; Humans ; Male ; Melanocyte-Stimulating Hormones/*genetics ; Middle Aged ; Pancreatic Neoplasms/physiopathology ; Pituitary Hormones, Anterior/*genetics ; Pro-Opiomelanocortin ; Protein Precursors/*genetics ; RNA, Messenger/genetics ; beta-Endorphin
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    Translocations among antibody genes in human cancer (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-11-18
    Description: The characteristic chromosomal translocations that occur in certain human malignancies offer opportunities to understand how two gene systems can affect one another when they are accidentally juxtaposed. In the case of Burkitt lymphoma, such a translocation joins the cellular oncogene, c-myc, to a region encoding one of the immunoglobulin genes. In at least one example, the coding sequence of the rearranged c-myc gene is identical to that of the normal gene, implying that the gene must be quantitatively, rather than qualitatively, altered in its expression if it is to play a role in transformation. One might expect to find the rearranged c-myc gene in a configuration that would allow it to take advantage of one of the known immunoglobulin promoters or enhancer elements. However, the rearranged c-myc gene is often placed so that it can utilize neither of these structures. Since the level of c-myc messenger RNA is often elevated in Burkitt cells, the translocation may lead to a deregulation of the c-myc gene. Further, since the normal allele in a Burkitt cell is often transcriptionally silent in the presence of a rearranged allele, a model for c-myc regulation is suggested that involves a trans-acting negative control element that might use as its target a highly conserved portion of the c-myc gene encoding two discrete transcriptional promoters.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leder, P -- Battey, J -- Lenoir, G -- Moulding, C -- Murphy, W -- Potter, H -- Stewart, T -- Taub, R -- New York, N.Y. -- Science. 1983 Nov 18;222(4625):765-71.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6356357" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Burkitt Lymphoma/*genetics ; Cell Transformation, Neoplastic/etiology ; Chromosome Aberrations/*genetics ; Chromosome Disorders ; Chromosome Mapping ; Gene Expression Regulation ; Genes ; Humans ; Immunoglobulins/genetics ; Models, Biological ; Neoplasms/*genetics ; *Oncogenes ; *Translocation, Genetic
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    5' viral and human cellular sequences corresponding to the transforming gene of simian sarcoma virus (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-02-04
    Description: The 5' nucleotide sequences of the transforming gene of simian sarcoma virus (v-sis) and its human cellular homolog (c-sis) were compared. A short homology was found between helper virus and cellular DNA sequences at the junction of v-sis and c-sis, which may have had a role in the original recombination event leading to the generation of simian sarcoma virus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Josephs, S F -- Dalla-Favera, R -- Gelmann, E P -- Gallo, R C -- Wong-Staal, F -- New York, N.Y. -- Science. 1983 Feb 4;219(4584):503-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6297002" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; *Genes, Viral ; Helper Viruses/genetics ; Humans ; *Oncogenes ; Recombination, Genetic ; Retroviridae/*genetics ; Sarcoma Virus, Woolly Monkey/*genetics
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    The human c-ras1H oncogene: a mutation in normal and neoplastic tissue from the same patient (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-02-18
    Description: The c-ras1H oncogene can be distinguished from its normal cellular counterpart by the loss of a restriction endonuclease site. This sequence alteration is the basis of a rapid screening method for the presence of this oncogene. DNA's from 34 individuals were screened by this method, and all were homozygous for the normal allele. In contrast, DNA from a patient's bladder tumor, as well as DNA from his normal bladder and leukocytes, were heterozygous at that restriction endonuclease site. Further restriction enzyme mapping pinpointed the change in the mutant allele as being one of two nucleotides, either of which would change the 12th amino acid (glycine) in the normal c-ras1H gene product. Point mutations in the codon for this amino acid have previously been described in a bladder tumor cell line and in the viral oncogene v-rasH. These results indicate that the patient carried a c-ras1H oncogene in his germ line, raising the possibility that the c-ras1H oncogene confers a predisposition to neoplasia.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Muschel, R J -- Khoury, G -- Lebowitz, P -- Koller, R -- Dhar, R -- New York, N.Y. -- Science. 1983 Feb 18;219(4586):853-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6337398" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Cell Transformation, Neoplastic/pathology ; Humans ; Mutation ; *Oncogenes ; Urinary Bladder Neoplasms/*genetics
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    Clustered third-base substitutions among wild strains of Escherichia coli (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-07-22
    Description: Nucleotide sequences of translated regions of the trp operon in 12 wild strains of Escherichia coli reveal striking uniformity among eight strains (suggesting recent common ancestry and supporting the importance of periodic selection in natural populations) and clustered substitutions in four strains (implicating events affecting runs of nucleotides).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Milkman, R -- Crawford, I P -- New York, N.Y. -- Science. 1983 Jul 22;221(4608):378-80.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6346486" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; DNA, Bacterial/genetics ; Escherichia coli/*genetics ; Genes, Bacterial
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    Isolation of human C-reactive protein complementary DNA and localization of the gene to chromosome 1 (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-07-01
    Description: With a synthetic oligonucleotide mixture as probe, complementary DNA clones of C-reactive protein were isolated from an adult human liver complementary DNA library. The clones ranged in size from 700 to 1100 base pairs and were identified by partial DNA sequence analysis. One complementary DNA clone was used as a probe for hybridization with human-rodent DNA's isolated from somatic cell hybrids and bound to nitrocellulose filters (Southern blot analysis) to assign the human C-reactive protein gene to chromosome 1.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Whitehead, A S -- Bruns, G A -- Markham, A F -- Colten, H R -- Woods, D E -- AI15033/AI/NIAID NIH HHS/ -- HD4807/HD/NICHD NIH HHS/ -- HL22487/HL/NHLBI NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1983 Jul 1;221(4605):69-71.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6857266" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; C-Reactive Protein/*genetics ; *Chromosome Mapping ; *Chromosomes, Human, 1-3 ; Cloning, Molecular ; Cricetinae ; DNA/*genetics/isolation & purification ; Genes ; Humans ; Hybrid Cells/metabolism ; Mice
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    Directed mutagenesis of dihydrofolate reductase (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-11-18
    Description: Three mutations of the enzyme dihydrofolate reductase were constructed by oligonucleotide-directed mutagenesis of the cloned Escherichia coli gene. The mutations--at residue 27, aspartic acid replaced with asparagine; at residue 39, proline replaced with cysteine; and at residue 95, glycine replaced with alanine--were designed to answer questions about the relations between molecular structure and function that were raised by the x-ray crystal structures. Properties of the mutant proteins show that Asp-27 is important for catalysis and that perturbation of the local structure at a conserved cis peptide bond following Gly-95 abolishes activity. Substitution of cysteine for proline at residue 39 results in the appearance of new forms of the enzyme that correspond to various oxidation states of the cysteine. One of these forms probably represents a species cross-linked by an intrachain disulfide bridge between the cysteine at position 85 and the new cysteine at position 39.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Villafranca, J E -- Howell, E E -- Voet, D H -- Strobel, M S -- Ogden, R C -- Abelson, J N -- Kraut, J -- CA17374/CA/NCI NIH HHS/ -- F32 GM09375/GM/NIGMS NIH HHS/ -- GM10928/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1983 Nov 18;222(4625):782-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6356360" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Disulfides ; Escherichia coli/genetics ; Gene Expression Regulation ; Genes ; Genes, Bacterial ; *Mutation ; Structure-Activity Relationship ; Tetrahydrofolate Dehydrogenase/*genetics
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