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  • 1
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    Synthetic microRNAs can control infection [Microbiology] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-03-26
    Description: Systematic genetic perturbation screening in human cells remains technically challenging. Typically, large libraries of chemically synthesized siRNA oligonucleotides are used, each designed to degrade a specific cellular mRNA via the RNA interference (RNAi) mechanism. Here, we report on data from three genome-wide siRNA screens, conducted to uncover host factors required...
    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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    Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-10-05
    Description: Comparison of the genomes and proteomes of the two diptera Anopheles gambiae and Drosophila melanogaster, which diverged about 250 million years ago, reveals considerable similarities. However, numerous differences are also observed; some of these must reflect the selection and subsequent adaptation associated with different ecologies and life strategies. Almost half of the genes in both genomes are interpreted as orthologs and show an average sequence identity of about 56%, which is slightly lower than that observed between the orthologs of the pufferfish and human (diverged about 450 million years ago). This indicates that these two insects diverged considerably faster than vertebrates. Aligned sequences reveal that orthologous genes have retained only half of their intron/exon structure, indicating that intron gains or losses have occurred at a rate of about one per gene per 125 million years. Chromosomal arms exhibit significant remnants of homology between the two species, although only 34% of the genes colocalize in small "microsyntenic" clusters, and major interarm transfers as well as intra-arm shuffling of gene order are detected.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zdobnov, Evgeny M -- von Mering, Christian -- Letunic, Ivica -- Torrents, David -- Suyama, Mikita -- Copley, Richard R -- Christophides, George K -- Thomasova, Dana -- Holt, Robert A -- Subramanian, G Mani -- Mueller, Hans-Michael -- Dimopoulos, George -- Law, John H -- Wells, Michael A -- Birney, Ewan -- Charlab, Rosane -- Halpern, Aaron L -- Kokoza, Elena -- Kraft, Cheryl L -- Lai, Zhongwu -- Lewis, Suzanna -- Louis, Christos -- Barillas-Mury, Carolina -- Nusskern, Deborah -- Rubin, Gerald M -- Salzberg, Steven L -- Sutton, Granger G -- Topalis, Pantelis -- Wides, Ron -- Wincker, Patrick -- Yandell, Mark -- Collins, Frank H -- Ribeiro, Jose -- Gelbart, William M -- Kafatos, Fotis C -- Bork, Peer -- New York, N.Y. -- Science. 2002 Oct 4;298(5591):149-59.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12364792" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anopheles/chemistry/*genetics/physiology ; Biological Evolution ; Chromosome Inversion ; Chromosomes/genetics ; Cluster Analysis ; Dosage Compensation, Genetic ; Drosophila Proteins/chemistry/genetics/physiology ; Drosophila melanogaster/chemistry/*genetics/physiology ; Exons ; Gene Order ; Genes, Insect ; *Genome ; Insect Proteins/chemistry/genetics/physiology ; Introns ; Physical Chromosome Mapping ; Protein Structure, Tertiary ; *Proteome ; Pseudogenes ; Sequence Homology, Nucleic Acid ; Species Specificity ; Synteny
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Toward automatic reconstruction of a highly resolved tree of life (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-03-04
    Description: We have developed an automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains. The tree has its basis in a concatenation of 31 orthologs occurring in 191 species with sequenced genomes. It revealed interdomain discrepancies in taxonomic classification. Systematic detection and subsequent exclusion of products of horizontal gene transfer increased phylogenetic resolution, allowing us to confirm accepted relationships and resolve disputed and preliminary classifications. For example, we place the phylum Acidobacteria as a sister group of delta-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ciccarelli, Francesca D -- Doerks, Tobias -- von Mering, Christian -- Creevey, Christopher J -- Snel, Berend -- Bork, Peer -- New York, N.Y. -- Science. 2006 Mar 3;311(5765):1283-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16513982" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acyl-tRNA Synthetases/genetics ; Animals ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Biological Evolution ; Computational Biology ; Eukaryotic Cells ; Gene Transfer, Horizontal ; *Genome ; Invertebrates/*classification/genetics ; *Phylogeny ; Plants/*classification/genetics ; Protein Biosynthesis ; Ribosomal Proteins/genetics ; Vertebrates/*classification/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Quantitative phylogenetic assessment of microbial communities in diverse environments (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-03
    Description: The taxonomic composition of environmental communities is an important indicator of their ecology and function. We used a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative, and accurate picture of community composition than that provided by traditional ribosomal RNA-based approaches depending on the polymerase chain reaction. Mapping marker genes from four diverse environmental data sets onto a reference species phylogeny shows that certain communities evolve faster than others. The method also enables determination of preferred habitats for entire microbial clades and provides evidence that such habitat preferences are often remarkably stable over time.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉von Mering, C -- Hugenholtz, P -- Raes, J -- Tringe, S G -- Doerks, T -- Jensen, L J -- Ward, N -- Bork, P -- New York, N.Y. -- Science. 2007 Feb 23;315(5815):1126-30. Epub 2007 Feb 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17272687" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacteria/*classification/genetics ; Biological Evolution ; Bone and Bones/microbiology ; *Ecosystem ; *Environmental Microbiology ; Genes, Bacterial ; Genes, rRNA ; Genetic Markers ; *Genomics ; Likelihood Functions ; Mining ; *Phylogeny ; Seawater/microbiology ; Soil Microbiology ; Water Microbiology ; Whales/microbiology
    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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    Comparative metagenomics of microbial communities (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-04-23
    Description: The species complexity of microbial communities and challenges in culturing representative isolates make it difficult to obtain assembled genomes. Here we characterize and compare the metabolic capabilities of terrestrial and marine microbial communities using largely unassembled sequence data obtained by shotgun sequencing DNA isolated from the various environments. Quantitative gene content analysis reveals habitat-specific fingerprints that reflect known characteristics of the sampled environments. The identification of environment-specific genes through a gene-centric comparative analysis presents new opportunities for interpreting and diagnosing environments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tringe, Susannah Green -- von Mering, Christian -- Kobayashi, Arthur -- Salamov, Asaf A -- Chen, Kevin -- Chang, Hwai W -- Podar, Mircea -- Short, Jay M -- Mathur, Eric J -- Detter, John C -- Bork, Peer -- Hugenholtz, Philip -- Rubin, Edward M -- New York, N.Y. -- Science. 2005 Apr 22;308(5721):554-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15845853" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Archaea/classification/genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Biofilms ; Bone and Bones/microbiology ; Computational Biology ; *Ecosystem ; Energy Metabolism ; Eukaryotic Cells/metabolism ; Gene Library ; Genes ; Genes, Bacterial ; *Genome ; Genome, Bacterial ; *Genomics ; Molecular Sequence Data ; Operon ; Phylogeny ; Polymerase Chain Reaction ; Proteins/genetics/metabolism ; Proteome ; Seawater/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; Whales/*microbiology
    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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    Immunity-related genes and gene families in Anopheles gambiae (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-10-05
    Description: We have identified 242 Anopheles gambiae genes from 18 gene families implicated in innate immunity and have detected marked diversification relative to Drosophila melanogaster. Immune-related gene families involved in recognition, signal modulation, and effector systems show a marked deficit of orthologs and excessive gene expansions, possibly reflecting selection pressures from different pathogens encountered in these insects' very different life-styles. In contrast, the multifunctional Toll signal transduction pathway is substantially conserved, presumably because of counterselection for developmental stability. Representative expression profiles confirm that sequence diversification is accompanied by specific responses to different immune challenges. Alternative RNA splicing may also contribute to expansion of the immune repertoire.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Christophides, George K -- Zdobnov, Evgeny -- Barillas-Mury, Carolina -- Birney, Ewan -- Blandin, Stephanie -- Blass, Claudia -- Brey, Paul T -- Collins, Frank H -- Danielli, Alberto -- Dimopoulos, George -- Hetru, Charles -- Hoa, Ngo T -- Hoffmann, Jules A -- Kanzok, Stefan M -- Letunic, Ivica -- Levashina, Elena A -- Loukeris, Thanasis G -- Lycett, Gareth -- Meister, Stephan -- Michel, Kristin -- Moita, Luis F -- Muller, Hans-Michael -- Osta, Mike A -- Paskewitz, Susan M -- Reichhart, Jean-Marc -- Rzhetsky, Andrey -- Troxler, Laurent -- Vernick, Kenneth D -- Vlachou, Dina -- Volz, Jennifer -- von Mering, Christian -- Xu, Jiannong -- Zheng, Liangbiao -- Bork, Peer -- Kafatos, Fotis C -- New York, N.Y. -- Science. 2002 Oct 4;298(5591):159-65.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12364793" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Animals ; Anopheles/*genetics/*immunology/metabolism/microbiology/parasitology ; Apoptosis ; Bacteria/immunology ; Catechol Oxidase/metabolism ; Computational Biology ; Drosophila Proteins/chemistry/genetics/metabolism ; Drosophila melanogaster/genetics/immunology/metabolism ; Enzyme Precursors/metabolism ; Gene Expression Regulation ; *Genes, Insect ; Genome ; Immunity, Innate ; Insect Proteins/chemistry/genetics/metabolism ; Multigene Family ; Peptides/metabolism ; Phylogeny ; Plasmodium/immunology/physiology ; Protein Structure, Tertiary ; Selection, Genetic ; Serine Endopeptidases/metabolism ; Serpins/metabolism ; Signal Transduction
    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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  • 7
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    Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-03-10
    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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  • 8
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    Genome evolution reveals biochemical networks and functional modules (2003)
    National Academy of Sciences
    Details
    Publication Date: 2003-12-12
    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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  • 9
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    eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-07
    Description: eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations. Developments since the latest public release include changes to the algorithm for creating OGs across taxonomic levels, making nested groups hierarchically consistent. This allows for a better propagation of functional terms across nested OGs and led to the novel annotation of 95 890 previously uncharacterized OGs, increasing overall annotation coverage from 67% to 72%. The functional annotations of OGs have been expanded to also provide Gene Ontology terms, KEGG pathways and SMART/Pfam domains for each group. Moreover, eggNOG now provides pairwise orthology relationships within OGs based on analysis of phylogenetic trees. We have also incorporated a framework for quickly mapping novel sequences to OGs based on precomputed HMM profiles. Finally, eggNOG version 4.5 incorporates a novel data set spanning 2605 viral OGs, covering 5228 proteins from 352 viral proteomes. All data are accessible for bulk downloading, as a web-service, and through a completely redesigned web interface. The new access points provide faster searches and a number of new browsing and visualization capabilities, facilitating the needs of both experts and less experienced users. eggNOG v4.5 is available at http://eggnog.embl.de .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data (2016)
    Oxford University Press
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    Publication Date: 2016-01-07
    Description: Interactions between proteins and small molecules are an integral part of biological processes in living organisms. Information on these interactions is dispersed over many databases, texts and prediction methods, which makes it difficult to get a comprehensive overview of the available evidence. To address this, we have developed STITCH (‘Search Tool for Interacting Chemicals’) that integrates these disparate data sources for 430 000 chemicals into a single, easy-to-use resource. In addition to the increased scope of the database, we have implemented a new network view that gives the user the ability to view binding affinities of chemicals in the interaction network. This enables the user to get a quick overview of the potential effects of the chemical on its interaction partners. For each organism, STITCH provides a global network; however, not all proteins have the same pattern of spatial expression. Therefore, only a certain subset of interactions can occur simultaneously. In the new, fifth release of STITCH, we have implemented functionality to filter out the proteins and chemicals not associated with a given tissue. The STITCH database can be downloaded in full, accessed programmatically via an extensive API, or searched via a redesigned web interface at http://stitch.embl.de .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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