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  • 1
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    Activity-enhancing mutations in an E3 ligase [Biochemistry] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-04-03
    Description: Although ubiquitination plays a critical role in virtually all cellular processes, mechanistic details of ubiquitin (Ub) transfer are still being defined. To identify the molecular determinants within E3 ligases that modulate activity, we scored each member of a library of nearly 100,000 protein variants of the murine ubiquitination factor E4B...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    Survey of Legionella Species Found in Thai Soil (2012)
    Hindawi
    Details
    Publication Date: 2012-06-21
    Description: Members of the Gram-negative genus Legionella are typically found in freshwater environments, with the exception of L. longbeachae, which is present in composts and potting mixes. When contaminated aerosols are inhaled, legionellosis may result, typically as either the more serious pneumonia Legionnaires’ disease or the less severe flu-like illness Pontiac fever. It is presumed that all species of the genus Legionella are capable of causing disease in humans. As a followup to a prior clinical study of legionellosis in rural Thailand, indigenous soil samples were collected proximal to cases’ homes and workplaces and tested for the presence of legionellae by culture. We obtained 115 isolates from 22/39 soil samples and used sequence-based methods to identify 12 known species of Legionella represented by 87 isolates.
    Print ISSN: 1687-918X
    Electronic ISSN: 1687-9198
    Topics: Biology , Medicine
    Published by Hindawi
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  • 3
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    Proteomics. Proteomics in genomeland (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fields, S -- P41 RR11823/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2001 Feb 16;291(5507):1221-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Departments of Genetics and Medicine, University of Washington, Seattle, WA 98195, USA. fields@u.washington.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11233445" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biochemistry/*methods ; Chemistry, Organic/*methods ; Databases, Factual ; Forecasting ; Genetic Techniques ; *Genomics ; Humans ; Proteins/*chemistry/genetics/isolation & purification/*physiology ; *Proteome
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-12-18
    Description: Peptide recognition modules mediate many protein-protein interactions critical for the assembly of macromolecular complexes. Complete genome sequences have revealed thousands of these domains, requiring improved methods for identifying their physiologically relevant binding partners. We have developed a strategy combining computational prediction of interactions from phage-display ligand consensus sequences with large-scale two-hybrid physical interaction tests. Application to yeast SH3 domains generated a phage-display network containing 394 interactions among 206 proteins and a two-hybrid network containing 233 interactions among 145 proteins. Graph theoretic analysis identified 59 highly likely interactions common to both networks. Las17 (Bee1), a member of the Wiskott-Aldrich Syndrome protein (WASP) family of actin-assembly proteins, showed multiple SH3 interactions, many of which were confirmed in vivo by coimmunoprecipitation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tong, Amy Hin Yan -- Drees, Becky -- Nardelli, Giuliano -- Bader, Gary D -- Brannetti, Barbara -- Castagnoli, Luisa -- Evangelista, Marie -- Ferracuti, Silvia -- Nelson, Bryce -- Paoluzi, Serena -- Quondam, Michele -- Zucconi, Adriana -- Hogue, Christopher W V -- Fields, Stanley -- Boone, Charles -- Cesareni, Gianni -- P41 RR11823/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2002 Jan 11;295(5553):321-4. Epub 2001 Dec 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Banting and Best Department of Medical Research and Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada M5G 1L6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11743162" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; *Computational Biology ; Consensus Sequence ; *Cytoskeletal Proteins ; Databases, Genetic ; Databases, Protein ; Fungal Proteins/chemistry/metabolism ; Ligands ; Molecular Sequence Data ; Peptide Library ; Peptides/chemistry/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Proteins/*chemistry/*metabolism ; *Proteome ; Saccharomyces cerevisiae/chemistry/genetics ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism ; Software ; Two-Hybrid System Techniques ; Wiskott-Aldrich Syndrome Protein ; src Homology Domains
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Genetic selection of peptide inhibitors of biological pathways (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-07-27
    Description: Genetic selections were used to find peptides that inhibit biological pathways in budding yeast. The peptides were presented inside cells as peptamers, surface loops on a highly expressed and biologically inert carrier protein, a catalytically inactive derivative of staphylococcal nuclease. Peptamers that inhibited the pheromone signaling pathway, transcriptional silencing, and the spindle checkpoint were isolated. Putative targets for the inhibitors were identified by a combination of two-hybrid analysis and genetic dissection of the target pathways. This analysis identified Ydr517w as a component of the spindle checkpoint and reinforced earlier indications that Ste50 has both positive and negative roles in pheromone signaling. Analysis of transcript arrays showed that the peptamers were highly specific in their effects, which suggests that they may be useful reagents in organisms that lack sophisticated genetics as well as for identifying components of existing biological pathways that are potential targets for drug discovery.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Norman, T C -- Smith, D L -- Sorger, P K -- Drees, B L -- O'Rourke, S M -- Hughes, T R -- Roberts, C J -- Friend, S H -- Fields, S -- Murray, A W -- P41-RR11823/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1999 Jul 23;285(5427):591-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, University of California, San Francisco, CA 94143-0444, USA. tnorman@microbia.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10417390" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Calcium-Calmodulin-Dependent Protein Kinases/metabolism ; Fungal Proteins/metabolism ; G1 Phase ; Galactose/metabolism ; Lipoproteins/metabolism ; Micrococcal Nuclease ; Mitosis ; Molecular Sequence Data ; Peptide Library ; Peptides/genetics/metabolism/*pharmacology ; Pheromones/*metabolism ; Protein Binding ; Protein-Serine-Threonine Kinases ; Protein-Tyrosine Kinases ; Saccharomyces cerevisiae/cytology/genetics/*metabolism ; *Saccharomyces cerevisiae Proteins ; *Selection, Genetic ; *Signal Transduction ; Spindle Apparatus/drug effects/*metabolism ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    A biochemical genomics approach for identifying genes by the activity of their products (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-11-05
    Description: For the identification of yeast genes specifying biochemical activities, a genomic strategy that is rapid, sensitive, and widely applicable was developed with an array of 6144 individual yeast strains, each containing a different yeast open reading frame (ORF) fused to glutathione S-transferase (GST). For the identification of ORF-associated activities, strains were grown in defined pools, and GST-ORFs were purified. Then, pools were assayed for activities, and active pools were deconvoluted to identify the source strains. Three previously unknown ORF-associated activities were identified with this strategy: a cyclic phosphodiesterase that acts on adenosine diphosphate-ribose 1"-2" cyclic phosphate (Appr〉p), an Appr-1"-p-processing activity, and a cytochrome c methyltransferase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Martzen, M R -- McCraith, S M -- Spinelli, S L -- Torres, F M -- Fields, S -- Grayhack, E J -- Phizicky, E M -- GM52347/GM/NIGMS NIH HHS/ -- P41 RR11823/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1999 Nov 5;286(5442):1153-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, NY 14642, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10550052" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate Ribose/analogs & derivatives/metabolism ; Fungal Proteins/*genetics/metabolism ; *Genes, Fungal ; *Genetic Techniques ; Glutathione Transferase/genetics ; Histone-Lysine N-Methyltransferase/genetics/isolation & purification/metabolism ; *Open Reading Frames ; Phosphoric Diester Hydrolases/genetics/isolation & purification/metabolism ; Recombinant Fusion Proteins/isolation & purification ; Saccharomyces cerevisiae/*genetics ; Sensitivity and Specificity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    A three-dimensional model of the yeast genome (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-05-04
    Description: Layered on top of information conveyed by DNA sequence and chromatin are higher order structures that encompass portions of chromosomes, entire chromosomes, and even whole genomes. Interphase chromosomes are not positioned randomly within the nucleus, but instead adopt preferred conformations. Disparate DNA elements co-localize into functionally defined aggregates or 'factories' for transcription and DNA replication. In budding yeast, Drosophila and many other eukaryotes, chromosomes adopt a Rabl configuration, with arms extending from centromeres adjacent to the spindle pole body to telomeres that abut the nuclear envelope. Nonetheless, the topologies and spatial relationships of chromosomes remain poorly understood. Here we developed a method to globally capture intra- and inter-chromosomal interactions, and applied it to generate a map at kilobase resolution of the haploid genome of Saccharomyces cerevisiae. The map recapitulates known features of genome organization, thereby validating the method, and identifies new features. Extensive regional and higher order folding of individual chromosomes is observed. Chromosome XII exhibits a striking conformation that implicates the nucleolus as a formidable barrier to interaction between DNA sequences at either end. Inter-chromosomal contacts are anchored by centromeres and include interactions among transfer RNA genes, among origins of early DNA replication and among sites where chromosomal breakpoints occur. Finally, we constructed a three-dimensional model of the yeast genome. Our findings provide a glimpse of the interface between the form and function of a eukaryotic genome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874121/" 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/PMC2874121/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Duan, Zhijun -- Andronescu, Mirela -- Schutz, Kevin -- McIlwain, Sean -- Kim, Yoo Jung -- Lee, Choli -- Shendure, Jay -- Fields, Stanley -- Blau, C Anthony -- Noble, William S -- P01 GM081619/GM/NIGMS NIH HHS/ -- P01 GM081619-01/GM/NIGMS NIH HHS/ -- P01GM081619/GM/NIGMS NIH HHS/ -- P41 RR011823-100081/RR/NCRR NIH HHS/ -- P41RR0011823/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 May 20;465(7296):363-7. doi: 10.1038/nature08973. Epub 2010 May 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington 98195-8056, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20436457" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Nucleolus/genetics/metabolism ; Cell Nucleus/genetics/metabolism ; Centromere/genetics/metabolism ; Chromosome Breakpoints ; Chromosome Positioning/*physiology ; Chromosomes, Fungal/genetics/*metabolism ; DNA Replication ; *Genome, Fungal ; Haploidy ; *Imaging, Three-Dimensional ; Intranuclear Space/*metabolism ; RNA, Transfer/genetics ; Replication Origin/genetics ; Saccharomyces cerevisiae/*cytology/*genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 8
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    Presence of a potent transcription activating sequence in the p53 protein (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-08-31
    Description: The p53 gene is frequently mutated in a wide variety of human cancers. However, the role of the wild-type p53 gene in growth control is not known. Hybrid proteins that contain the DNA binding domain of yeast GAL4 and portions of p53 have been used to show that the p53 protein contains a transcription-activating sequence that functions in both yeast and mammalian cells. The NH2-terminal 73 residues of p53 activated transcription in mammalian cells as efficiently as the herpes virus protein VP16, which contains one of the strongest known activation domains. Combined with previous data that showed p53 is localized to the nucleus and can bind to DNA, these results support the idea that one function of p53 is to activate the transcription of genes that suppress cell proliferation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fields, S -- Jang, S K -- 2R37 AI15122/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1990 Aug 31;249(4972):1046-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, School of Medicine, State University of New York, Stony Brook 11794.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2144363" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Genetic Vectors ; Models, Genetic ; Nuclear Proteins/*genetics ; Oncogene Proteins/*genetics/metabolism ; Phosphoproteins/*genetics/metabolism ; RNA, Messenger/genetics ; Saccharomyces cerevisiae/genetics ; Suppression, Genetic ; Transcription Factors/*genetics ; *Transcription, Genetic ; Tumor Suppressor Protein p53 ; beta-Galactosidase/genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    Cell biology. Whither model organism research? (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-03-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fields, Stanley -- Johnston, Mark -- New York, N.Y. -- Science. 2005 Mar 25;307(5717):1885-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA 98195, USA. fields@u.washington.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15790833" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biomedical Research/*trends ; *Cell Physiological Phenomena ; *Models, Animal ; *Models, Biological ; Molecular Probe Techniques ; *Saccharomyces cerevisiae
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Regulation of yeast replicative life span by TOR and Sch9 in response to nutrients (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-11-19
    Description: Calorie restriction increases life span in many organisms, including the budding yeast Saccharomyces cerevisiae. From a large-scale analysis of 564 single-gene-deletion strains of yeast, we identified 10 gene deletions that increase replicative life span. Six of these correspond to genes encoding components of the nutrient-responsive TOR and Sch9 pathways. Calorie restriction of tor1D or sch9D cells failed to further increase life span and, like calorie restriction, deletion of either SCH9 or TOR1 increased life span independent of the Sir2 histone deacetylase. We propose that the TOR and Sch9 kinases define a primary conduit through which excess nutrient intake limits longevity in yeast.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kaeberlein, Matt -- Powers, R Wilson 3rd -- Steffen, Kristan K -- Westman, Eric A -- Hu, Di -- Dang, Nick -- Kerr, Emily O -- Kirkland, Kathryn T -- Fields, Stanley -- Kennedy, Brian K -- P30 AG013280/AG/NIA NIH HHS/ -- New York, N.Y. -- Science. 2005 Nov 18;310(5751):1193-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA 98195, USA. kaeber@u.washington.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16293764" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Division/genetics/physiology ; Gene Deletion ; Protein Kinases/*metabolism ; Protein-Serine-Threonine Kinases ; Saccharomyces cerevisiae/genetics/metabolism/*physiology ; Saccharomyces cerevisiae Proteins/genetics/*physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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