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  • Molecular Sequence Data  (41)
  • Signal Transduction  (22)
  • Nature Publishing Group (NPG)  (61)
  • 2005-2009  (61)
  • 1940-1944
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  • 1
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    Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-09-11
    Description: Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement. To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population. Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion. Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars. Here we report the sequence of the P. infestans genome, which at approximately 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for approximately 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haas, Brian J -- Kamoun, Sophien -- Zody, Michael C -- Jiang, Rays H Y -- Handsaker, Robert E -- Cano, Liliana M -- Grabherr, Manfred -- Kodira, Chinnappa D -- Raffaele, Sylvain -- Torto-Alalibo, Trudy -- Bozkurt, Tolga O -- Ah-Fong, Audrey M V -- Alvarado, Lucia -- Anderson, Vicky L -- Armstrong, Miles R -- Avrova, Anna -- Baxter, Laura -- Beynon, Jim -- Boevink, Petra C -- Bollmann, Stephanie R -- Bos, Jorunn I B -- Bulone, Vincent -- Cai, Guohong -- Cakir, Cahid -- Carrington, James C -- Chawner, Megan -- Conti, Lucio -- Costanzo, Stefano -- Ewan, Richard -- Fahlgren, Noah -- Fischbach, Michael A -- Fugelstad, Johanna -- Gilroy, Eleanor M -- Gnerre, Sante -- Green, Pamela J -- Grenville-Briggs, Laura J -- Griffith, John -- Grunwald, Niklaus J -- Horn, Karolyn -- Horner, Neil R -- Hu, Chia-Hui -- Huitema, Edgar -- Jeong, Dong-Hoon -- Jones, Alexandra M E -- Jones, Jonathan D G -- Jones, Richard W -- Karlsson, Elinor K -- Kunjeti, Sridhara G -- Lamour, Kurt -- Liu, Zhenyu -- Ma, Lijun -- Maclean, Daniel -- Chibucos, Marcus C -- McDonald, Hayes -- McWalters, Jessica -- Meijer, Harold J G -- Morgan, William -- Morris, Paul F -- Munro, Carol A -- O'Neill, Keith -- Ospina-Giraldo, Manuel -- Pinzon, Andres -- Pritchard, Leighton -- Ramsahoye, Bernard -- Ren, Qinghu -- Restrepo, Silvia -- Roy, Sourav -- Sadanandom, Ari -- Savidor, Alon -- Schornack, Sebastian -- Schwartz, David C -- Schumann, Ulrike D -- Schwessinger, Ben -- Seyer, Lauren -- Sharpe, Ted -- Silvar, Cristina -- Song, Jing -- Studholme, David J -- Sykes, Sean -- Thines, Marco -- van de Vondervoort, Peter J I -- Phuntumart, Vipaporn -- Wawra, Stephan -- Weide, Rob -- Win, Joe -- Young, Carolyn -- Zhou, Shiguo -- Fry, William -- Meyers, Blake C -- van West, Pieter -- Ristaino, Jean -- Govers, Francine -- Birch, Paul R J -- Whisson, Stephen C -- Judelson, Howard S -- Nusbaum, Chad -- BB/E007120/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G015244/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- G0400284/Medical Research Council/United Kingdom -- England -- Nature. 2009 Sep 17;461(7262):393-8. doi: 10.1038/nature08358. Epub 2009 Sep 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19741609" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/genetics ; DNA Transposable Elements/genetics ; DNA, Intergenic/genetics ; Evolution, Molecular ; Genome/*genetics ; Host-Pathogen Interactions/genetics ; Humans ; Ireland ; Molecular Sequence Data ; Necrosis ; Phenotype ; Phytophthora infestans/*genetics/pathogenicity ; Plant Diseases/immunology/*microbiology ; Solanum tuberosum/immunology/*microbiology ; Starvation
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
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    The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-04-25
    Description: Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836516/" 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/PMC2836516/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ming, Ray -- Hou, Shaobin -- Feng, Yun -- Yu, Qingyi -- Dionne-Laporte, Alexandre -- Saw, Jimmy H -- Senin, Pavel -- Wang, Wei -- Ly, Benjamin V -- Lewis, Kanako L T -- Salzberg, Steven L -- Feng, Lu -- Jones, Meghan R -- Skelton, Rachel L -- Murray, Jan E -- Chen, Cuixia -- Qian, Wubin -- Shen, Junguo -- Du, Peng -- Eustice, Moriah -- Tong, Eric -- Tang, Haibao -- Lyons, Eric -- Paull, Robert E -- Michael, Todd P -- Wall, Kerr -- Rice, Danny W -- Albert, Henrik -- Wang, Ming-Li -- Zhu, Yun J -- Schatz, Michael -- Nagarajan, Niranjan -- Acob, Ricelle A -- Guan, Peizhu -- Blas, Andrea -- Wai, Ching Man -- Ackerman, Christine M -- Ren, Yan -- Liu, Chao -- Wang, Jianmei -- Wang, Jianping -- Na, Jong-Kuk -- Shakirov, Eugene V -- Haas, Brian -- Thimmapuram, Jyothi -- Nelson, David -- Wang, Xiyin -- Bowers, John E -- Gschwend, Andrea R -- Delcher, Arthur L -- Singh, Ratnesh -- Suzuki, Jon Y -- Tripathi, Savarni -- Neupane, Kabi -- Wei, Hairong -- Irikura, Beth -- Paidi, Maya -- Jiang, Ning -- Zhang, Wenli -- Presting, Gernot -- Windsor, Aaron -- Navajas-Perez, Rafael -- Torres, Manuel J -- Feltus, F Alex -- Porter, Brad -- Li, Yingjun -- Burroughs, A Max -- Luo, Ming-Cheng -- Liu, Lei -- Christopher, David A -- Mount, Stephen M -- Moore, Paul H -- Sugimura, Tak -- Jiang, Jiming -- Schuler, Mary A -- Friedman, Vikki -- Mitchell-Olds, Thomas -- Shippen, Dorothy E -- dePamphilis, Claude W -- Palmer, Jeffrey D -- Freeling, Michael -- Paterson, Andrew H -- Gonsalves, Dennis -- Wang, Lei -- Alam, Maqsudul -- R01 GM083873/GM/NIGMS NIH HHS/ -- R01 GM083873-05/GM/NIGMS NIH HHS/ -- R01 LM006845/LM/NLM NIH HHS/ -- R01 LM006845-08/LM/NLM NIH HHS/ -- England -- Nature. 2008 Apr 24;452(7190):991-6. doi: 10.1038/nature06856.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hawaii Agriculture Research Center, Aiea, Hawaii 96701, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18432245" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics ; Carica/*genetics ; Contig Mapping ; Databases, Genetic ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Molecular Sequence Data ; Plants, Genetically Modified/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Transcription Factors/genetics ; Tropical Climate
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
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    The Phaeodactylum genome reveals the evolutionary history of diatom genomes (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-10-17
    Description: Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes ( approximately 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bowler, Chris -- Allen, Andrew E -- Badger, Jonathan H -- Grimwood, Jane -- Jabbari, Kamel -- Kuo, Alan -- Maheswari, Uma -- Martens, Cindy -- Maumus, Florian -- Otillar, Robert P -- Rayko, Edda -- Salamov, Asaf -- Vandepoele, Klaas -- Beszteri, Bank -- Gruber, Ansgar -- Heijde, Marc -- Katinka, Michael -- Mock, Thomas -- Valentin, Klaus -- Verret, Frederic -- Berges, John A -- Brownlee, Colin -- Cadoret, Jean-Paul -- Chiovitti, Anthony -- Choi, Chang Jae -- Coesel, Sacha -- De Martino, Alessandra -- Detter, J Chris -- Durkin, Colleen -- Falciatore, Angela -- Fournet, Jerome -- Haruta, Miyoshi -- Huysman, Marie J J -- Jenkins, Bethany D -- Jiroutova, Katerina -- Jorgensen, Richard E -- Joubert, Yolaine -- Kaplan, Aaron -- Kroger, Nils -- Kroth, Peter G -- La Roche, Julie -- Lindquist, Erica -- Lommer, Markus -- Martin-Jezequel, Veronique -- Lopez, Pascal J -- Lucas, Susan -- Mangogna, Manuela -- McGinnis, Karen -- Medlin, Linda K -- Montsant, Anton -- Oudot-Le Secq, Marie-Pierre -- Napoli, Carolyn -- Obornik, Miroslav -- Parker, Micaela Schnitzler -- Petit, Jean-Louis -- Porcel, Betina M -- Poulsen, Nicole -- Robison, Matthew -- Rychlewski, Leszek -- Rynearson, Tatiana A -- Schmutz, Jeremy -- Shapiro, Harris -- Siaut, Magali -- Stanley, Michele -- Sussman, Michael R -- Taylor, Alison R -- Vardi, Assaf -- von Dassow, Peter -- Vyverman, Wim -- Willis, Anusuya -- Wyrwicz, Lucjan S -- Rokhsar, Daniel S -- Weissenbach, Jean -- Armbrust, E Virginia -- Green, Beverley R -- Van de Peer, Yves -- Grigoriev, Igor V -- England -- Nature. 2008 Nov 13;456(7219):239-44. doi: 10.1038/nature07410. Epub 2008 Oct 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CNRS UMR8186, Department of Biology, Ecole Normale Superieure, 46 rue d'Ulm, 75005 Paris, France. cbowler@biologie.ens.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18923393" target="_blank"〉PubMed〈/a〉
    Keywords: DNA, Algal/analysis ; Diatoms/*genetics ; *Evolution, Molecular ; Genes, Bacterial/genetics ; Genome/*genetics ; Molecular Sequence Data ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Signal Transduction
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
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    Secreted semaphorins control spine distribution and morphogenesis in the postnatal CNS (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-12-17
    Description: The majority of excitatory synapses in the mammalian CNS (central nervous system) are formed on dendritic spines, and spine morphology and distribution are critical for synaptic transmission, synaptic integration and plasticity. Here, we show that a secreted semaphorin, Sema3F, is a negative regulator of spine development and synaptic structure. Mice with null mutations in genes encoding Sema3F, and its holoreceptor components neuropilin-2 (Npn-2, also known as Nrp2) and plexin A3 (PlexA3, also known as Plxna3), exhibit increased dentate gyrus (DG) granule cell (GC) and cortical layer V pyramidal neuron spine number and size, and also aberrant spine distribution. Moreover, Sema3F promotes loss of spines and excitatory synapses in dissociated neurons in vitro, and in Npn-2(-/-) brain slices cortical layer V and DG GCs exhibit increased mEPSC (miniature excitatory postsynaptic current) frequency. In contrast, a distinct Sema3A-Npn-1/PlexA4 signalling cascade controls basal dendritic arborization in layer V cortical neurons, but does not influence spine morphogenesis or distribution. These disparate effects of secreted semaphorins are reflected in the restricted dendritic localization of Npn-2 to apical dendrites and of Npn-1 (also known as Nrp1) to all dendrites of cortical pyramidal neurons. Therefore, Sema3F signalling controls spine distribution along select dendritic processes, and distinct secreted semaphorin signalling events orchestrate CNS connectivity through the differential control of spine morphogenesis, synapse formation, and the elaboration of dendritic morphology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842559/" 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/PMC2842559/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tran, Tracy S -- Rubio, Maria E -- Clem, Roger L -- Johnson, Dontais -- Case, Lauren -- Tessier-Lavigne, Marc -- Huganir, Richard L -- Ginty, David D -- Kolodkin, Alex L -- F32 NS051003/NS/NINDS NIH HHS/ -- P50 MH06883/MH/NIMH NIH HHS/ -- R01 DC-006881/DC/NIDCD NIH HHS/ -- R01 MH059199/MH/NIMH NIH HHS/ -- R01 MH059199-07/MH/NIMH NIH HHS/ -- R01 MH059199-08/MH/NIMH NIH HHS/ -- R01 MH059199-09/MH/NIMH NIH HHS/ -- R01 MH059199-10/MH/NIMH NIH HHS/ -- R01 MH59199/MH/NIMH NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Dec 24;462(7276):1065-9. doi: 10.1038/nature08628. Epub 2009 Dec 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010807" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Central Nervous System/cytology/drug effects/*growth & ; development/*metabolism/ultrastructure ; Female ; Gene Expression Regulation, Developmental ; Male ; Mice ; Mice, Knockout ; Neuropilin-1/metabolism ; Neuropilin-2/metabolism ; Pyramidal Cells/*cytology/drug effects/*growth & development/ultrastructure ; Recombinant Proteins/pharmacology ; Semaphorins/genetics/*metabolism/pharmacology ; Signal Transduction ; Synapses/drug effects/*physiology/ultrastructure
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
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    Innate immunity and intestinal microbiota in the development of Type 1 diabetes (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-09-23
    Description: Type 1 diabetes (T1D) is a debilitating autoimmune disease that results from T-cell-mediated destruction of insulin-producing beta-cells. Its incidence has increased during the past several decades in developed countries, suggesting that changes in the environment (including the human microbial environment) may influence disease pathogenesis. The incidence of spontaneous T1D in non-obese diabetic (NOD) mice can be affected by the microbial environment in the animal housing facility or by exposure to microbial stimuli, such as injection with mycobacteria or various microbial products. Here we show that specific pathogen-free NOD mice lacking MyD88 protein (an adaptor for multiple innate immune receptors that recognize microbial stimuli) do not develop T1D. The effect is dependent on commensal microbes because germ-free MyD88-negative NOD mice develop robust diabetes, whereas colonization of these germ-free MyD88-negative NOD mice with a defined microbial consortium (representing bacterial phyla normally present in human gut) attenuates T1D. We also find that MyD88 deficiency changes the composition of the distal gut microbiota, and that exposure to the microbiota of specific pathogen-free MyD88-negative NOD donors attenuates T1D in germ-free NOD recipients. Together, these findings indicate that interaction of the intestinal microbes with the innate immune system is a critical epigenetic factor modifying T1D predisposition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2574766/" 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/PMC2574766/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wen, Li -- Ley, Ruth E -- Volchkov, Pavel Yu -- Stranges, Peter B -- Avanesyan, Lia -- Stonebraker, Austin C -- Hu, Changyun -- Wong, F Susan -- Szot, Gregory L -- Bluestone, Jeffrey A -- Gordon, Jeffrey I -- Chervonsky, Alexander V -- DK063452/DK/NIDDK NIH HHS/ -- DK30292/DK/NIDDK NIH HHS/ -- DK42086/DK/NIDDK NIH HHS/ -- DK45735/DK/NIDDK NIH HHS/ -- DK70977/DK/NIDDK NIH HHS/ -- P30 DK042086/DK/NIDDK NIH HHS/ -- P30 DK042086-16/DK/NIDDK NIH HHS/ -- P30 DK045735/DK/NIDDK NIH HHS/ -- P30 DK045735-10/DK/NIDDK NIH HHS/ -- P30 DK045735-119006/DK/NIDDK NIH HHS/ -- P30 DK056341/DK/NIDDK NIH HHS/ -- P30 DK056341-07/DK/NIDDK NIH HHS/ -- P30 DK056341-08/DK/NIDDK NIH HHS/ -- P30 DK063720/DK/NIDDK NIH HHS/ -- P30 DK063720-01/DK/NIDDK NIH HHS/ -- P30 DK63720/DK/NIDDK NIH HHS/ -- R01 DK030292/DK/NIDDK NIH HHS/ -- R01 DK030292-24/DK/NIDDK NIH HHS/ -- R01 DK070977/DK/NIDDK NIH HHS/ -- R01 DK070977-04/DK/NIDDK NIH HHS/ -- R21 DK063452/DK/NIDDK NIH HHS/ -- R21 DK063452-02/DK/NIDDK NIH HHS/ -- R37 AI046643/AI/NIAID NIH HHS/ -- R37 AI046643-10/AI/NIAID NIH HHS/ -- R37 AI46643/AI/NIAID NIH HHS/ -- England -- Nature. 2008 Oct 23;455(7216):1109-13. doi: 10.1038/nature07336. Epub 2008 Sep 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Endocrinology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18806780" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacteria/classification/genetics/*immunology/isolation & purification ; CD8-Positive T-Lymphocytes/immunology ; Diabetes Mellitus, Type 1/genetics/*immunology/*microbiology ; Female ; Immunity, Innate/genetics/*immunology ; Interferon-gamma/immunology ; Intestines/*microbiology ; Islets of Langerhans/pathology ; Male ; Mice ; Mice, Inbred NOD ; Mice, Knockout ; Mice, SCID ; Molecular Sequence Data ; Myeloid Differentiation Factor 88/genetics ; Phylogeny ; Specific Pathogen-Free Organisms ; Time Factors
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  • 6
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    The Trichoplax genome and the nature of placozoans (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-08-23
    Description: As arguably the simplest free-living animals, placozoans may represent a primitive metazoan form, yet their biology is poorly understood. Here we report the sequencing and analysis of the approximately 98 million base pair nuclear genome of the placozoan Trichoplax adhaerens. Whole-genome phylogenetic analysis suggests that placozoans belong to a 'eumetazoan' clade that includes cnidarians and bilaterians, with sponges as the earliest diverging animals. The compact genome shows conserved gene content, gene structure and synteny in relation to the human and other complex eumetazoan genomes. Despite the apparent cellular and organismal simplicity of Trichoplax, its genome encodes a rich array of transcription factor and signalling pathway genes that are typically associated with diverse cell types and developmental processes in eumetazoans, motivating further searches for cryptic cellular complexity and/or as yet unobserved life history stages.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Srivastava, Mansi -- Begovic, Emina -- Chapman, Jarrod -- Putnam, Nicholas H -- Hellsten, Uffe -- Kawashima, Takeshi -- Kuo, Alan -- Mitros, Therese -- Salamov, Asaf -- Carpenter, Meredith L -- Signorovitch, Ana Y -- Moreno, Maria A -- Kamm, Kai -- Grimwood, Jane -- Schmutz, Jeremy -- Shapiro, Harris -- Grigoriev, Igor V -- Buss, Leo W -- Schierwater, Bernd -- Dellaporta, Stephen L -- Rokhsar, Daniel S -- England -- Nature. 2008 Aug 21;454(7207):955-60. doi: 10.1038/nature07191.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Integrative Genomics and Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA. msrivast@berkeley.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18719581" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Adhesion ; Conserved Sequence ; Extracellular Matrix/genetics ; Gene Expression Regulation, Developmental ; Genome/*genetics ; Germ Cells ; Humans ; Invertebrates/anatomy & histology/classification/*genetics/*physiology ; Phylogeny ; Reproduction/genetics ; Sequence Analysis, DNA ; Sex ; Signal Transduction ; Synteny ; Transcription Factors/genetics
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
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    Biodiversity and biogeography of phages in modern stromatolites and thrombolites (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-03-04
    Description: Viruses, and more particularly phages (viruses that infect bacteria), represent one of the most abundant living entities in aquatic and terrestrial environments. The biogeography of phages has only recently been investigated and so far reveals a cosmopolitan distribution of phage genetic material (or genotypes). Here we address this cosmopolitan distribution through the analysis of phage communities in modern microbialites, the living representatives of one of the most ancient life forms on Earth. On the basis of a comparative metagenomic analysis of viral communities associated with marine (Highborne Cay, Bahamas) and freshwater (Pozas Azules II and Rio Mesquites, Mexico) microbialites, we show that some phage genotypes are geographically restricted. The high percentage of unknown sequences recovered from the three metagenomes (〉97%), the low percentage similarities with sequences from other environmental viral (n = 42) and microbial (n = 36) metagenomes, and the absence of viral genotypes shared among microbialites indicate that viruses are genetically unique in these environments. Identifiable sequences in the Highborne Cay metagenome were dominated by single-stranded DNA microphages that were not detected in any other samples examined, including sea water, fresh water, sediment, terrestrial, extreme, metazoan-associated and marine microbial mats. Finally, a marine signature was present in the phage community of the Pozas Azules II microbialites, even though this environment has not been in contact with the ocean for tens of millions of years. Taken together, these results prove that viruses in modern microbialites display biogeographical variability and suggest that they may be derived from an ancient community.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Desnues, Christelle -- Rodriguez-Brito, Beltran -- Rayhawk, Steve -- Kelley, Scott -- Tran, Tuong -- Haynes, Matthew -- Liu, Hong -- Furlan, Mike -- Wegley, Linda -- Chau, Betty -- Ruan, Yijun -- Hall, Dana -- Angly, Florent E -- Edwards, Robert A -- Li, Linlin -- Thurber, Rebecca Vega -- Reid, R Pamela -- Siefert, Janet -- Souza, Valeria -- Valentine, David L -- Swan, Brandon K -- Breitbart, Mya -- Rohwer, Forest -- England -- Nature. 2008 Mar 20;452(7185):340-3. doi: 10.1038/nature06735. Epub 2008 Mar 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, San Diego State University, San Diego, California 92182, USA. cdesnues@yahoo.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18311127" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophages/classification/genetics/*isolation & purification/*physiology ; Bahamas ; *Biodiversity ; Capsid/chemistry ; Computational Biology ; DNA, Viral/analysis/genetics ; *Ecosystem ; Fresh Water/microbiology/virology ; Genome, Viral/genetics ; Genomics ; *Geography ; Geologic Sediments/microbiology/virology ; Mexico ; Molecular Sequence Data ; Phylogeny ; Proteome/metabolism ; Seawater/microbiology/virology ; *Water Microbiology
    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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    The genome of the blood fluke Schistosoma mansoni (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-07-17
    Description: Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries. Here we present analysis of the 363 megabase nuclear genome of the blood fluke. It encodes at least 11,809 genes, with an unusual intron size distribution, and new families of micro-exon genes that undergo frequent alternative splicing. As the first sequenced flatworm, and a representative of the Lophotrochozoa, it offers insights into early events in the evolution of the animals, including the development of a body pattern with bilateral symmetry, and the development of tissues into organs. Our analysis has been informed by the need to find new drug targets. The deficits in lipid metabolism that make schistosomes dependent on the host are revealed, and the identification of membrane receptors, ion channels and more than 300 proteases provide new insights into the biology of the life cycle and new targets. Bioinformatics approaches have identified metabolic chokepoints, and a chemogenomic screen has pinpointed schistosome proteins for which existing drugs may be active. The information generated provides an invaluable resource for the research community to develop much needed new control tools for the treatment and eradication of this important and neglected disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756445/" 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/PMC2756445/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berriman, Matthew -- Haas, Brian J -- LoVerde, Philip T -- Wilson, R Alan -- Dillon, Gary P -- Cerqueira, Gustavo C -- Mashiyama, Susan T -- Al-Lazikani, Bissan -- Andrade, Luiza F -- Ashton, Peter D -- Aslett, Martin A -- Bartholomeu, Daniella C -- Blandin, Gaelle -- Caffrey, Conor R -- Coghlan, Avril -- Coulson, Richard -- Day, Tim A -- Delcher, Art -- DeMarco, Ricardo -- Djikeng, Appolinaire -- Eyre, Tina -- Gamble, John A -- Ghedin, Elodie -- Gu, Yong -- Hertz-Fowler, Christiane -- Hirai, Hirohisha -- Hirai, Yuriko -- Houston, Robin -- Ivens, Alasdair -- Johnston, David A -- Lacerda, Daniela -- Macedo, Camila D -- McVeigh, Paul -- Ning, Zemin -- Oliveira, Guilherme -- Overington, John P -- Parkhill, Julian -- Pertea, Mihaela -- Pierce, Raymond J -- Protasio, Anna V -- Quail, Michael A -- Rajandream, Marie-Adele -- Rogers, Jane -- Sajid, Mohammed -- Salzberg, Steven L -- Stanke, Mario -- Tivey, Adrian R -- White, Owen -- Williams, David L -- Wortman, Jennifer -- Wu, Wenjie -- Zamanian, Mostafa -- Zerlotini, Adhemar -- Fraser-Liggett, Claire M -- Barrell, Barclay G -- El-Sayed, Najib M -- 086151/Wellcome Trust/United Kingdom -- 5D43TW006580/TW/FIC NIH HHS/ -- 5D43TW007012-03/TW/FIC NIH HHS/ -- AI054711-01A2/AI/NIAID NIH HHS/ -- AI48828/AI/NIAID NIH HHS/ -- R01 GM083873/GM/NIGMS NIH HHS/ -- R01 GM083873-07/GM/NIGMS NIH HHS/ -- R01 GM083873-08/GM/NIGMS NIH HHS/ -- R01 LM006845/LM/NLM NIH HHS/ -- R01 LM006845-08/LM/NLM NIH HHS/ -- R01 LM006845-09/LM/NLM NIH HHS/ -- U01 AI048828/AI/NIAID NIH HHS/ -- U01 AI048828-01/AI/NIAID NIH HHS/ -- U01 AI048828-02/AI/NIAID NIH HHS/ -- WT085775/Z/08/Z/Wellcome Trust/United Kingdom -- England -- Nature. 2009 Jul 16;460(7253):352-8. doi: 10.1038/nature08160.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Cambridge CB10 1SD, UK. mb4@sanger.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19606141" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Evolution ; Exons/genetics ; Genes, Helminth/genetics ; Genome, Helminth/*genetics ; Host-Parasite Interactions/genetics ; Introns/genetics ; Molecular Sequence Data ; Physical Chromosome Mapping ; Schistosoma mansoni/drug effects/embryology/*genetics/physiology ; Schistosomiasis mansoni/drug therapy/parasitology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
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    Translational control of intron splicing in eukaryotes (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-01-19
    Description: Most eukaryotic genes are interrupted by non-coding introns that must be accurately removed from pre-messenger RNAs to produce translatable mRNAs. Splicing is guided locally by short conserved sequences, but genes typically contain many potential splice sites, and the mechanisms specifying the correct sites remain poorly understood. In most organisms, short introns recognized by the intron definition mechanism cannot be efficiently predicted solely on the basis of sequence motifs. In multicellular eukaryotes, long introns are recognized through exon definition and most genes produce multiple mRNA variants through alternative splicing. The nonsense-mediated mRNA decay (NMD) pathway may further shape the observed sets of variants by selectively degrading those containing premature termination codons, which are frequently produced in mammals. Here we show that the tiny introns of the ciliate Paramecium tetraurelia are under strong selective pressure to cause premature termination of mRNA translation in the event of intron retention, and that the same bias is observed among the short introns of plants, fungi and animals. By knocking down the two P. tetraurelia genes encoding UPF1, a protein that is crucial in NMD, we show that the intrinsic efficiency of splicing varies widely among introns and that NMD activity can significantly reduce the fraction of unspliced mRNAs. The results suggest that, independently of alternative splicing, species with large intron numbers universally rely on NMD to compensate for suboptimal splicing efficiency and accuracy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jaillon, Olivier -- Bouhouche, Khaled -- Gout, Jean-Francois -- Aury, Jean-Marc -- Noel, Benjamin -- Saudemont, Baptiste -- Nowacki, Mariusz -- Serrano, Vincent -- Porcel, Betina M -- Segurens, Beatrice -- Le Mouel, Anne -- Lepere, Gersende -- Schachter, Vincent -- Betermier, Mireille -- Cohen, Jean -- Wincker, Patrick -- Sperling, Linda -- Duret, Laurent -- Meyer, Eric -- England -- Nature. 2008 Jan 17;451(7176):359-62. doi: 10.1038/nature06495.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genoscope (CEA), 2 rue Gaston Cremieux CP5706, 91057 Evry, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18202663" target="_blank"〉PubMed〈/a〉
    Keywords: *Alternative Splicing ; Animals ; Base Sequence ; Codon, Terminator/genetics ; Computational Biology ; Eukaryotic Cells/*metabolism ; Expressed Sequence Tags ; Genes, Protozoan/genetics ; Introns/*genetics ; Molecular Sequence Data ; Paramecium/*genetics ; *Protein Biosynthesis ; Protozoan Proteins/genetics/metabolism ; RNA Interference ; RNA Stability ; RNA, Protozoan/genetics/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    A role for VEGF as a negative regulator of pericyte function and vessel maturation (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-11-11
    Description: Angiogenesis does not only depend on endothelial cell invasion and proliferation: it also requires pericyte coverage of vascular sprouts for vessel stabilization. These processes are coordinated by vascular endothelial growth factor (VEGF) and platelet-derived growth factor (PDGF) through their cognate receptors on endothelial cells and vascular smooth muscle cells (VSMCs), respectively. PDGF induces neovascularization by priming VSMCs/pericytes to release pro-angiogenic mediators. Although VEGF directly stimulates endothelial cell proliferation and migration, its role in pericyte biology is less clear. Here we define a role for VEGF as an inhibitor of neovascularization on the basis of its capacity to disrupt VSMC function. Specifically, under conditions of PDGF-mediated angiogenesis, VEGF ablates pericyte coverage of nascent vascular sprouts, leading to vessel destabilization. At the molecular level, VEGF-mediated activation of VEGF-R2 suppresses PDGF-Rbeta signalling in VSMCs through the assembly of a previously undescribed receptor complex consisting of PDGF-Rbeta and VEGF-R2. Inhibition of VEGF-R2 not only prevents assembly of this receptor complex but also restores angiogenesis in tissues exposed to both VEGF and PDGF. Finally, genetic deletion of tumour cell VEGF disrupts PDGF-Rbeta/VEGF-R2 complex formation and increases tumour vessel maturation. These findings underscore the importance of VSMCs/pericytes in neovascularization and reveal a dichotomous role for VEGF and VEGF-R2 signalling as both a promoter of endothelial cell function and a negative regulator of VSMCs and vessel maturation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2605188/" 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/PMC2605188/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Greenberg, Joshua I -- Shields, David J -- Barillas, Samuel G -- Acevedo, Lisette M -- Murphy, Eric -- Huang, Jianhua -- Scheppke, Lea -- Stockmann, Christian -- Johnson, Randall S -- Angle, Niren -- Cheresh, David A -- GM 68524/GM/NIGMS NIH HHS/ -- P01 CA078045/CA/NCI NIH HHS/ -- P01 CA078045-050004/CA/NCI NIH HHS/ -- P01 CA078045-100004/CA/NCI NIH HHS/ -- P01 CA078045-109001/CA/NCI NIH HHS/ -- R01 CA095262/CA/NCI NIH HHS/ -- R01 CA095262-06/CA/NCI NIH HHS/ -- R01 CA118165/CA/NCI NIH HHS/ -- R01 HL078912/HL/NHLBI NIH HHS/ -- R01 HL078912-04/HL/NHLBI NIH HHS/ -- R21 CA129660/CA/NCI NIH HHS/ -- R21 CA129660-02/CA/NCI NIH HHS/ -- R37 CA050286/CA/NCI NIH HHS/ -- R37 CA050286-19/CA/NCI NIH HHS/ -- R37 CA050286-20/CA/NCI NIH HHS/ -- R37-CA082515/CA/NCI NIH HHS/ -- R37-CA50286/CA/NCI NIH HHS/ -- England -- Nature. 2008 Dec 11;456(7223):809-13. doi: 10.1038/nature07424. Epub 2008 Nov 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Surgery, School of Medicine, Moore's UCSD Cancer Center, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18997771" target="_blank"〉PubMed〈/a〉
    Keywords: Angiogenesis Inhibitors/pharmacology ; Animals ; Blood Vessels/*metabolism ; Cell Line ; Cells, Cultured ; Fibrosarcoma/blood supply ; Humans ; Mice ; Mice, Inbred C57BL ; Mice, Nude ; Neovascularization, Physiologic/drug effects/*physiology ; Pericytes/drug effects/*metabolism ; Platelet-Derived Growth Factor/*metabolism/pharmacology ; Receptor, Platelet-Derived Growth Factor beta/metabolism ; Receptors, Vascular Endothelial Growth Factor/metabolism ; Signal Transduction ; Vascular Endothelial Growth Factor A/*metabolism
    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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