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  • 1
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    Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-01-09
    Description: Yeasts, which have been a component of the human diet for at least 7,000 years, possess an elaborate cell wall alpha-mannan. The influence of yeast mannan on the ecology of the human microbiota is unknown. Here we show that yeast alpha-mannan is a viable food source for the Gram-negative bacterium Bacteroides thetaiotaomicron, a dominant member of the microbiota. Detailed biochemical analysis and targeted gene disruption studies support a model whereby limited cleavage of alpha-mannan on the surface generates large oligosaccharides that are subsequently depolymerized to mannose by the action of periplasmic enzymes. Co-culturing studies showed that metabolism of yeast mannan by B. thetaiotaomicron presents a 'selfish' model for the catabolism of this difficult to breakdown polysaccharide. Genomic comparison with B. thetaiotaomicron in conjunction with cell culture studies show that a cohort of highly successful members of the microbiota has evolved to consume sterically-restricted yeast glycans, an adaptation that may reflect the incorporation of eukaryotic microorganisms into the human diet.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cuskin, Fiona -- Lowe, Elisabeth C -- Temple, Max J -- Zhu, Yanping -- Cameron, Elizabeth A -- Pudlo, Nicholas A -- Porter, Nathan T -- Urs, Karthik -- Thompson, Andrew J -- Cartmell, Alan -- Rogowski, Artur -- Hamilton, Brian S -- Chen, Rui -- Tolbert, Thomas J -- Piens, Kathleen -- Bracke, Debby -- Vervecken, Wouter -- Hakki, Zalihe -- Speciale, Gaetano -- Munoz-Munoz, Jose L -- Day, Andrew -- Pena, Maria J -- McLean, Richard -- Suits, Michael D -- Boraston, Alisdair B -- Atherly, Todd -- Ziemer, Cherie J -- Williams, Spencer J -- Davies, Gideon J -- Abbott, D Wade -- Martens, Eric C -- Gilbert, Harry J -- 097907/Wellcome Trust/United Kingdom -- BB/G016127/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- GM090080/GM/NIGMS NIH HHS/ -- MOP-68913/Canadian Institutes of Health Research/Canada -- WT097907AIA/Wellcome Trust/United Kingdom -- England -- Nature. 2015 Jan 8;517(7533):165-9. doi: 10.1038/nature13995.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK [2] Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, USA. ; Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK. ; Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109 USA. ; Department of Chemistry, University of York, York YO10 5DD, UK. ; School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia. ; Interdisciplinary Biochemistry Graduate Program, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, USA. ; Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, USA. ; Department of Pharmaceutical Chemistry, University of Kansas School of Pharmacy, 2095 Constant Avenue, Lawrence, Kansas 66047, USA. ; Oxyrane, 9052 Ghent, Belgium. ; Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, USA. ; Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta T1J 4B1, Canada. ; Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada. ; USDA, Agricultural Research Service, National Laboratory for Agriculture and the Environment, Ames, Iowa 50011, USA. ; 1] Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, USA [2] Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta T1J 4B1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25567280" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacteroidetes/cytology/enzymology/genetics/*metabolism ; Biological Evolution ; Carbohydrate Conformation ; Diet ; Enzymes/genetics/metabolism ; Female ; Gastrointestinal Tract/*microbiology ; Genetic Loci/genetics ; Germ-Free Life ; Glycoproteins/chemistry/metabolism ; Humans ; Male ; Mannans/chemistry/*metabolism ; Mannose/metabolism ; Mice ; *Models, Biological ; Models, Molecular ; Oligosaccharides/chemistry/metabolism ; Periplasm/enzymology ; Yeasts/*chemistry
    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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  • 2
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    The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-04-15
    Description: The mechanisms by which hepatitis C virus (HCV) induces chronic infection in the vast majority of infected individuals are unknown. Sequences within the HCV E1 and E2 envelope genes were analyzed during the acute phase of hepatitis C in 12 patients with different clinical outcomes. Acute resolving hepatitis was associated with relative evolutionary stasis of the heterogeneous viral population (quasispecies), whereas progressing hepatitis correlated with genetic evolution of HCV. Consistent with the hypothesis of selective pressure by the host immune system, the sequence changes occurred almost exclusively within the hypervariable region 1 of the E2 gene and were temporally correlated with antibody seroconversion. These data indicate that the evolutionary dynamics of the HCV quasispecies during the acute phase of hepatitis C predict whether the infection will resolve or become chronic.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Farci, P -- Shimoda, A -- Coiana, A -- Diaz, G -- Peddis, G -- Melpolder, J C -- Strazzera, A -- Chien, D Y -- Munoz, S J -- Balestrieri, A -- Purcell, R H -- Alter, H J -- New York, N.Y. -- Science. 2000 Apr 14;288(5464):339-44.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medical Sciences, University of Cagliari, Via San Giorgio 12, 09124 Cagliari, Italy. farcip@pacs.unica.it〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10764648" target="_blank"〉PubMed〈/a〉
    Keywords: Acute Disease ; Adult ; Aged ; Antibodies, Viral ; Disease Progression ; *Evolution, Molecular ; Female ; Genes, Viral ; Genetic Variation ; Hepacivirus/*genetics/immunology/physiology ; Hepatitis C/immunology/*virology ; Hepatitis C Antibodies/biosynthesis ; Hepatitis C, Chronic/immunology/*virology ; Humans ; Male ; Middle Aged ; Molecular Sequence Data ; Phylogeny ; Prospective Studies ; Selection, Genetic ; Time Factors ; Viral Envelope Proteins/*genetics/immunology ; Virus Replication
    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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    Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-01
    Description: Although common among bacteria, lateral gene transfer-the movement of genes between distantly related organisms-is thought to occur only rarely between bacteria and multicellular eukaryotes. However, the presence of endosymbionts, such as Wolbachia pipientis, within some eukaryotic germlines may facilitate bacterial gene transfers to eukaryotic host genomes. We therefore examined host genomes for evidence of gene transfer events from Wolbachia bacteria to their hosts. We found and confirmed transfers into the genomes of four insect and four nematode species that range from nearly the entire Wolbachia genome (〉1 megabase) to short (〈500 base pairs) insertions. Potential Wolbachia-to-host transfers were also detected computationally in three additional sequenced insect genomes. We also show that some of these inserted Wolbachia genes are transcribed within eukaryotic cells lacking endosymbionts. Therefore, heritable lateral gene transfer occurs into eukaryotic hosts from their prokaryote symbionts, potentially providing a mechanism for acquisition of new genes and functions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dunning Hotopp, Julie C -- Clark, Michael E -- Oliveira, Deodoro C S G -- Foster, Jeremy M -- Fischer, Peter -- Munoz Torres, Monica C -- Giebel, Jonathan D -- Kumar, Nikhil -- Ishmael, Nadeeza -- Wang, Shiliang -- Ingram, Jessica -- Nene, Rahul V -- Shepard, Jessica -- Tomkins, Jeffrey -- Richards, Stephen -- Spiro, David J -- Ghedin, Elodie -- Slatko, Barton E -- Tettelin, Herve -- Werren, John H -- New York, N.Y. -- Science. 2007 Sep 21;317(5845):1753-6. Epub 2007 Aug 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomic Research, J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850, USA. jhotopp@som.umaryland.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17761848" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chromosome Mapping ; Crosses, Genetic ; DNA, Bacterial ; Drosophila/genetics/microbiology ; Female ; *Gene Transfer, Horizontal ; Genes, Bacterial ; In Situ Hybridization, Fluorescence ; Insects/*genetics/microbiology ; Male ; Molecular Sequence Data ; Nematoda/*genetics/microbiology ; Retroelements ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Symbiosis ; Wolbachia/*genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Natural and sexual selection in a wild insect population (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-06-05
    Description: The understanding of natural and sexual selection requires both field and laboratory studies to exploit the advantages and avoid the disadvantages of each approach. However, studies have tended to be polarized among the types of organisms studied, with vertebrates studied in the field and invertebrates in the lab. We used video monitoring combined with DNA profiling of all of the members of a wild population of field crickets across two generations to capture the factors predicting the reproductive success of males and females. The factors that predict a male's success in gaining mates differ from those that predict how many offspring he has. We confirm the fundamental prediction that males vary more in their reproductive success than females, and we find that females as well as males leave more offspring when they mate with more partners.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rodriguez-Munoz, R -- Bretman, A -- Slate, J -- Walling, C A -- Tregenza, T -- New York, N.Y. -- Science. 2010 Jun 4;328(5983):1269-72. doi: 10.1126/science.1188102.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Ecology and Conservation, School of Biosciences, University of Exeter, Cornwall Campus, Penryn TR10 EZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20522773" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Behavior, Animal ; Female ; *Genetic Fitness ; Gryllidae/*genetics/*physiology ; Male ; *Mating Preference, Animal ; Microsatellite Repeats ; Oviposition ; Reproduction ; *Selection, Genetic ; *Sex Characteristics ; Sexual Behavior, Animal ; Vocalization, Animal
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Functional and evolutionary insights from the genomes of three parasitoid Nasonia species (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-01-16
    Description: We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2849982/" 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/PMC2849982/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Werren, John H -- Richards, Stephen -- Desjardins, Christopher A -- Niehuis, Oliver -- Gadau, Jurgen -- Colbourne, John K -- Nasonia Genome Working Group -- Beukeboom, Leo W -- Desplan, Claude -- Elsik, Christine G -- Grimmelikhuijzen, Cornelis J P -- Kitts, Paul -- Lynch, Jeremy A -- Murphy, Terence -- Oliveira, Deodoro C S G -- Smith, Christopher D -- van de Zande, Louis -- Worley, Kim C -- Zdobnov, Evgeny M -- Aerts, Maarten -- Albert, Stefan -- Anaya, Victor H -- Anzola, Juan M -- Barchuk, Angel R -- Behura, Susanta K -- Bera, Agata N -- Berenbaum, May R -- Bertossa, Rinaldo C -- Bitondi, Marcia M G -- Bordenstein, Seth R -- Bork, Peer -- Bornberg-Bauer, Erich -- Brunain, Marleen -- Cazzamali, Giuseppe -- Chaboub, Lesley -- Chacko, Joseph -- Chavez, Dean -- Childers, Christopher P -- Choi, Jeong-Hyeon -- Clark, Michael E -- Claudianos, Charles -- Clinton, Rochelle A -- Cree, Andrew G -- Cristino, Alexandre S -- Dang, Phat M -- Darby, Alistair C -- de Graaf, Dirk C -- Devreese, Bart -- Dinh, Huyen H -- Edwards, Rachel -- Elango, Navin -- Elhaik, Eran -- Ermolaeva, Olga -- Evans, Jay D -- Foret, Sylvain -- Fowler, Gerald R -- Gerlach, Daniel -- Gibson, Joshua D -- Gilbert, Donald G -- Graur, Dan -- Grunder, Stefan -- Hagen, Darren E -- Han, Yi -- Hauser, Frank -- Hultmark, Da -- Hunter, Henry C 4th -- Hurst, Gregory D D -- Jhangian, Shalini N -- Jiang, Huaiyang -- Johnson, Reed M -- Jones, Andrew K -- Junier, Thomas -- Kadowaki, Tatsuhiko -- Kamping, Albert -- Kapustin, Yuri -- Kechavarzi, Bobak -- Kim, Jaebum -- Kim, Jay -- Kiryutin, Boris -- Koevoets, Tosca -- Kovar, Christie L -- Kriventseva, Evgenia V -- Kucharski, Robert -- Lee, Heewook -- Lee, Sandra L -- Lees, Kristin -- Lewis, Lora R -- Loehlin, David W -- Logsdon, John M Jr -- Lopez, Jacqueline A -- Lozado, Ryan J -- Maglott, Donna -- Maleszka, Ryszard -- Mayampurath, Anoop -- Mazur, Danielle J -- McClure, Marcella A -- Moore, Andrew D -- Morgan, Margaret B -- Muller, Jean -- Munoz-Torres, Monica C -- Muzny, Donna M -- Nazareth, Lynne V -- Neupert, Susanne -- Nguyen, Ngoc B -- Nunes, Francis M F -- Oakeshott, John G -- Okwuonu, Geoffrey O -- Pannebakker, Bart A -- Pejaver, Vikas R -- Peng, Zuogang -- Pratt, Stephen C -- Predel, Reinhard -- Pu, Ling-Ling -- Ranson, Hilary -- Raychoudhury, Rhitoban -- Rechtsteiner, Andreas -- Reese, Justin T -- Reid, Jeffrey G -- Riddle, Megan -- Robertson, Hugh M -- Romero-Severson, Jeanne -- Rosenberg, Miriam -- Sackton, Timothy B -- Sattelle, David B -- Schluns, Helge -- Schmitt, Thomas -- Schneider, Martina -- Schuler, Andreas -- Schurko, Andrew M -- Shuker, David M -- Simoes, Zila L P -- Sinha, Saurabh -- Smith, Zachary -- Solovyev, Victor -- Souvorov, Alexandre -- Springauf, Andreas -- Stafflinger, Elisabeth -- Stage, Deborah E -- Stanke, Mario -- Tanaka, Yoshiaki -- Telschow, Arndt -- Trent, Carol -- Vattathil, Selina -- Verhulst, Eveline C -- Viljakainen, Lumi -- Wanner, Kevin W -- Waterhouse, Robert M -- Whitfield, James B -- Wilkes, Timothy E -- Williamson, Michael -- Willis, Judith H -- Wolschin, Florian -- Wyder, Stefan -- Yamada, Takuji -- Yi, Soojin V -- Zecher, Courtney N -- Zhang, Lan -- Gibbs, Richard A -- 5R01GM070026-04/GM/NIGMS NIH HHS/ -- 5R01HG000747-14/HG/NHGRI NIH HHS/ -- 5R24GM084917-02/GM/NIGMS NIH HHS/ -- AI028309-13A2/AI/NIAID NIH HHS/ -- R01 AI055624/AI/NIAID NIH HHS/ -- R01 GM064864/GM/NIGMS NIH HHS/ -- R01 GM064864-04/GM/NIGMS NIH HHS/ -- R01 GM064864-05A2/GM/NIGMS NIH HHS/ -- R01 GM070026/GM/NIGMS NIH HHS/ -- R01 GM070026-04S1/GM/NIGMS NIH HHS/ -- R01 GM079484/GM/NIGMS NIH HHS/ -- R01 GM085163/GM/NIGMS NIH HHS/ -- R01 GM085163-01/GM/NIGMS NIH HHS/ -- R01 GM085233/GM/NIGMS NIH HHS/ -- R01 HG000747/HG/NHGRI NIH HHS/ -- R01 HG000747-14/HG/NHGRI NIH HHS/ -- R01GM064864/GM/NIGMS NIH HHS/ -- R24 GM084917/GM/NIGMS NIH HHS/ -- R24 GM084917-01/GM/NIGMS NIH HHS/ -- R24 GM084917-02/GM/NIGMS NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- U54 HG003273-03/HG/NHGRI NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Jan 15;327(5963):343-8. doi: 10.1126/science.1178028.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075255" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arthropods/parasitology ; *Biological Evolution ; DNA Methylation ; DNA Transposable Elements ; Female ; Gene Transfer, Horizontal ; Genes, Insect ; Genetic Speciation ; Genetic Variation ; *Genome, Insect ; Host-Parasite Interactions ; Insect Proteins/genetics/metabolism ; Insect Viruses/genetics ; Insects/genetics ; Male ; Molecular Sequence Data ; Quantitative Trait Loci ; Recombination, Genetic ; Sequence Analysis, DNA ; Wasp Venoms/chemistry/toxicity ; Wasps/*genetics/physiology ; Wolbachia/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    AID stabilizes stem-cell phenotype by removing epigenetic memory of pluripotency genes (2013)
    Nature Publishing Group (NPG)
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    Publication Date: 2013-06-28
    Description: The activation-induced cytidine deaminase (AID; also known as AICDA) enzyme is required for somatic hypermutation and class switch recombination at the immunoglobulin locus. In germinal-centre B cells, AID is highly expressed, and has an inherent mutator activity that helps generate antibody diversity. However, AID may also regulate gene expression epigenetically by directly deaminating 5-methylcytosine in concert with base-excision repair to exchange cytosine. This pathway promotes gene demethylation, thereby removing epigenetic memory. For example, AID promotes active demethylation of the genome in primordial germ cells. However, different studies have suggested either a requirement or a lack of function for AID in promoting pluripotency in somatic nuclei after fusion with embryonic stem cells. Here we tested directly whether AID regulates epigenetic memory by comparing the relative ability of cells lacking AID to reprogram from a differentiated murine cell type to an induced pluripotent stem cell. We show that Aid-null cells are transiently hyper-responsive to the reprogramming process. Although they initiate expression of pluripotency genes, they fail to stabilize in the pluripotent state. The genome of Aid-null cells remains hypermethylated in reprogramming cells, and hypermethylated genes associated with pluripotency fail to be stably upregulated, including many MYC target genes. Recent studies identified a late step of reprogramming associated with methylation status, and implicated a secondary set of pluripotency network components. AID regulates this late step, removing epigenetic memory to stabilize the pluripotent state.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3762466/" 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/PMC3762466/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kumar, Ritu -- DiMenna, Lauren -- Schrode, Nadine -- Liu, Ting-Chun -- Franck, Philipp -- Munoz-Descalzo, Silvia -- Hadjantonakis, Anna-Katerina -- Zarrin, Ali A -- Chaudhuri, Jayanta -- Elemento, Olivier -- Evans, Todd -- AI072194/AI/NIAID NIH HHS/ -- HL056182/HL/NHLBI NIH HHS/ -- P30 CA008748/CA/NCI NIH HHS/ -- R01 HD052115/HD/NICHD NIH HHS/ -- R37 HL056182/HL/NHLBI NIH HHS/ -- T32 AI007621/AI/NIAID NIH HHS/ -- England -- Nature. 2013 Aug 1;500(7460):89-92. doi: 10.1038/nature12299. Epub 2013 Jun 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Surgery, Weill Cornell Medical College, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23803762" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Dedifferentiation/genetics ; Cellular Reprogramming/genetics ; Cytidine Deaminase/genetics/*metabolism ; Epigenesis, Genetic/*genetics ; Female ; Fibroblasts/cytology/metabolism ; Gene Expression Regulation ; HEK293 Cells ; Humans ; Male ; Mice ; Pluripotent Stem Cells/*cytology/enzymology/*metabolism ; Transcription Factors/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
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    Cell death by pyroptosis drives CD4 T-cell depletion in HIV-1 infection (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-12-21
    Description: The pathway causing CD4 T-cell death in HIV-infected hosts remains poorly understood although apoptosis has been proposed as a key mechanism. We now show that caspase-3-mediated apoptosis accounts for the death of only a small fraction of CD4 T cells corresponding to those that are both activated and productively infected. The remaining over 95% of quiescent lymphoid CD4 T cells die by caspase-1-mediated pyroptosis triggered by abortive viral infection. Pyroptosis corresponds to an intensely inflammatory form of programmed cell death in which cytoplasmic contents and pro-inflammatory cytokines, including IL-1beta, are released. This death pathway thus links the two signature events in HIV infection-CD4 T-cell depletion and chronic inflammation-and creates a pathogenic vicious cycle in which dying CD4 T cells release inflammatory signals that attract more cells to die. This cycle can be broken by caspase 1 inhibitors shown to be safe in humans, raising the possibility of a new class of 'anti-AIDS' therapeutics targeting the host rather than the virus.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4047036/" 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/PMC4047036/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Doitsh, Gilad -- Galloway, Nicole L K -- Geng, Xin -- Yang, Zhiyuan -- Monroe, Kathryn M -- Zepeda, Orlando -- Hunt, Peter W -- Hatano, Hiroyu -- Sowinski, Stefanie -- Munoz-Arias, Isa -- Greene, Warner C -- 1DP1036502/DP/NCCDPHP CDC HHS/ -- DP1 DA036502/DA/NIDA NIH HHS/ -- NIH P30 AI027763/AI/NIAID NIH HHS/ -- P30 AI027763/AI/NIAID NIH HHS/ -- R21 AI102782/AI/NIAID NIH HHS/ -- R21AI102782/AI/NIAID NIH HHS/ -- T32 AI060537/AI/NIAID NIH HHS/ -- U19 AI096113/AI/NIAID NIH HHS/ -- U19AI0961133/AI/NIAID NIH HHS/ -- England -- Nature. 2014 Jan 23;505(7484):509-14. doi: 10.1038/nature12940.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Gladstone Institute of Virology and Immunology, 1650 Owens Street, San Francisco, California 94158, USA [2]. ; Gladstone Institute of Virology and Immunology, 1650 Owens Street, San Francisco, California 94158, USA. ; Department of Medicine, University of California, San Francisco, 505 Parnassus Avenue, San Francisco, California 94143, USA. ; 1] Gladstone Institute of Virology and Immunology, 1650 Owens Street, San Francisco, California 94158, USA [2] Department of Medicine, University of California, San Francisco, 505 Parnassus Avenue, San Francisco, California 94143, USA [3] Department of Microbiology and Immunology, University of California, San Francisco, 505 Parnassus Avenue, San Francisco, California 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24356306" target="_blank"〉PubMed〈/a〉
    Keywords: Administration, Oral ; Adult ; Anti-HIV Agents/pharmacology ; CD4-Positive T-Lymphocytes/cytology/drug effects/*pathology/secretion ; Caspase 1/*metabolism ; Caspase 3/metabolism ; Caspase Inhibitors/administration & dosage/pharmacology ; Cell Death/drug effects ; HIV Infections/drug therapy/enzymology/*immunology/*pathology ; HIV-1/drug effects/growth & development/*pathogenicity ; Humans ; In Vitro Techniques ; Inflammasomes/immunology/metabolism ; Inflammation/complications/immunology/pathology/virology ; Interleukin-1beta/biosynthesis/secretion ; Lymph Nodes/enzymology ; Male ; Palatine Tonsil/drug effects/virology ; Protein Precursors/biosynthesis ; Spleen/drug effects/virology ; Virus Replication
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
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    Geriatric muscle stem cells switch reversible quiescence into senescence (2014)
    Nature Publishing Group (NPG)
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    Publication Date: 2014-02-14
    Description: Regeneration of skeletal muscle depends on a population of adult stem cells (satellite cells) that remain quiescent throughout life. Satellite cell regenerative functions decline with ageing. Here we report that geriatric satellite cells are incapable of maintaining their normal quiescent state in muscle homeostatic conditions, and that this irreversibly affects their intrinsic regenerative and self-renewal capacities. In geriatric mice, resting satellite cells lose reversible quiescence by switching to an irreversible pre-senescence state, caused by derepression of p16(INK4a) (also called Cdkn2a). On injury, these cells fail to activate and expand, undergoing accelerated entry into a full senescence state (geroconversion), even in a youthful environment. p16(INK4a) silencing in geriatric satellite cells restores quiescence and muscle regenerative functions. Our results demonstrate that maintenance of quiescence in adult life depends on the active repression of senescence pathways. As p16(INK4a) is dysregulated in human geriatric satellite cells, these findings provide the basis for stem-cell rejuvenation in sarcopenic muscles.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sousa-Victor, Pedro -- Gutarra, Susana -- Garcia-Prat, Laura -- Rodriguez-Ubreva, Javier -- Ortet, Laura -- Ruiz-Bonilla, Vanessa -- Jardi, Merce -- Ballestar, Esteban -- Gonzalez, Susana -- Serrano, Antonio L -- Perdiguero, Eusebio -- Munoz-Canoves, Pura -- England -- Nature. 2014 Feb 20;506(7488):316-21. doi: 10.1038/nature13013. Epub 2014 Feb 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Cell Biology Group, Department of Experimental and Health Sciences, Pompeu Fabra University, CIBER on Neurodegenerative diseases, E-08003 Barcelona, Spain [2] Buck Institute for Research on Aging, Novato, California 94945, USA. ; 1] Cell Biology Group, Department of Experimental and Health Sciences, Pompeu Fabra University, CIBER on Neurodegenerative diseases, E-08003 Barcelona, Spain [2]. ; Chromatin and Disease Group, Cancer Epigenetics and Biology Programme, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat, E-08907 Barcelona, Spain. ; Cell Biology Group, Department of Experimental and Health Sciences, Pompeu Fabra University, CIBER on Neurodegenerative diseases, E-08003 Barcelona, Spain. ; Stem Cell Aging Group, Centro Nacional de Investigaciones Cardiovasculares, E-28029 Madrid, Spain. ; 1] Cell Biology Group, Department of Experimental and Health Sciences, Pompeu Fabra University, CIBER on Neurodegenerative diseases, E-08003 Barcelona, Spain [2] Institucio Catalana de Recerca i Estudis Avancats, E-08010 Barcelona, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24522534" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Aging/*metabolism ; Animals ; Cells, Cultured ; Cyclin-Dependent Kinase Inhibitor p16/deficiency/genetics/*metabolism ; E2F1 Transcription Factor/metabolism ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Progeria/metabolism/pathology ; Regeneration ; Rejuvenation ; Retinoblastoma Protein/metabolism ; Satellite Cells, Skeletal Muscle/*cytology/*metabolism ; Young Adult
    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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    Staphylococcus delta-toxin induces allergic skin disease by activating mast cells (2013)
    Nature Publishing Group (NPG)
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    Publication Date: 2013-11-01
    Description: Atopic dermatitis is a chronic inflammatory skin disease that affects 15-30% of children and approximately 5% of adults in industrialized countries. Although the pathogenesis of atopic dermatitis is not fully understood, the disease is mediated by an abnormal immunoglobulin-E immune response in the setting of skin barrier dysfunction. Mast cells contribute to immunoglobulin-E-mediated allergic disorders including atopic dermatitis. Upon activation, mast cells release their membrane-bound cytosolic granules leading to the release of several molecules that are important in the pathogenesis of atopic dermatitis and host defence. More than 90% of patients with atopic dermatitis are colonized with Staphylococcus aureus in the lesional skin whereas most healthy individuals do not harbour the pathogen. Several staphylococcal exotoxins can act as superantigens and/or antigens in models of atopic dermatitis. However, the role of these staphylococcal exotoxins in disease pathogenesis remains unclear. Here we report that culture supernatants of S. aureus contain potent mast-cell degranulation activity. Biochemical analysis identified delta-toxin as the mast cell degranulation-inducing factor produced by S. aureus. Mast cell degranulation induced by delta-toxin depended on phosphoinositide 3-kinase and calcium (Ca(2+)) influx; however, unlike that mediated by immunoglobulin-E crosslinking, it did not require the spleen tyrosine kinase. In addition, immunoglobulin-E enhanced delta-toxin-induced mast cell degranulation in the absence of antigen. Furthermore, S. aureus isolates recovered from patients with atopic dermatitis produced large amounts of delta-toxin. Skin colonization with S. aureus, but not a mutant deficient in delta-toxin, promoted immunoglobulin-E and interleukin-4 production, as well as inflammatory skin disease. Furthermore, enhancement of immunoglobulin-E production and dermatitis by delta-toxin was abrogated in Kit(W-sh/W-sh) mast-cell-deficient mice and restored by mast cell reconstitution. These studies identify delta-toxin as a potent inducer of mast cell degranulation and suggest a mechanistic link between S. aureus colonization and allergic skin disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090780/" 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/PMC4090780/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nakamura, Yuumi -- Oscherwitz, Jon -- Cease, Kemp B -- Chan, Susana M -- Munoz-Planillo, Raul -- Hasegawa, Mizuho -- Villaruz, Amer E -- Cheung, Gordon Y C -- McGavin, Martin J -- Travers, Jeffrey B -- Otto, Michael -- Inohara, Naohiro -- Nunez, Gabriel -- R01 AR059688/AR/NIAMS NIH HHS/ -- R01AR059688/AR/NIAMS NIH HHS/ -- R01HL062996/HL/NHLBI NIH HHS/ -- Intramural NIH HHS/ -- England -- Nature. 2013 Nov 21;503(7476):397-401. doi: 10.1038/nature12655. Epub 2013 Oct 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology and Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24172897" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacterial Toxins/*metabolism/pharmacology ; Calcium Signaling/drug effects ; *Cell Degranulation/drug effects ; Culture Media, Conditioned/pharmacology ; Dermatitis, Atopic/immunology/metabolism/*microbiology/pathology ; Female ; Immunoglobulin E/biosynthesis/immunology ; Inflammation/immunology/metabolism/microbiology/pathology ; Interleukin-4/immunology ; Intracellular Signaling Peptides and Proteins/metabolism ; Male ; Mast Cells/*cytology/drug effects ; Mice ; Phosphatidylinositol 3-Kinases/metabolism ; Protein-Tyrosine Kinases/metabolism ; Proto-Oncogene Proteins c-kit/genetics/metabolism ; Staphylococcus aureus/metabolism/*pathogenicity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Inhibition of miR-25 improves cardiac contractility in the failing heart (2014)
    Nature Publishing Group (NPG)
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    Publication Date: 2014-03-29
    Description: Heart failure is characterized by a debilitating decline in cardiac function, and recent clinical trial results indicate that improving the contractility of heart muscle cells by boosting intracellular calcium handling might be an effective therapy. MicroRNAs (miRNAs) are dysregulated in heart failure but whether they control contractility or constitute therapeutic targets remains speculative. Using high-throughput functional screening of the human microRNAome, here we identify miRNAs that suppress intracellular calcium handling in heart muscle by interacting with messenger RNA encoding the sarcoplasmic reticulum calcium uptake pump SERCA2a (also known as ATP2A2). Of 875 miRNAs tested, miR-25 potently delayed calcium uptake kinetics in cardiomyocytes in vitro and was upregulated in heart failure, both in mice and humans. Whereas adeno-associated virus 9 (AAV9)-mediated overexpression of miR-25 in vivo resulted in a significant loss of contractile function, injection of an antisense oligonucleotide (antagomiR) against miR-25 markedly halted established heart failure in a mouse model, improving cardiac function and survival relative to a control antagomiR oligonucleotide. These data reveal that increased expression of endogenous miR-25 contributes to declining cardiac function during heart failure and suggest that it might be targeted therapeutically to restore function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4131725/" 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/PMC4131725/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wahlquist, Christine -- Jeong, Dongtak -- Rojas-Munoz, Agustin -- Kho, Changwon -- Lee, Ahyoung -- Mitsuyama, Shinichi -- van Mil, Alain -- Park, Woo Jin -- Sluijter, Joost P G -- Doevendans, Pieter A F -- Hajjar, Roger J -- Mercola, Mark -- HHSN268201000045C/HL/NHLBI NIH HHS/ -- HHSN26820100045C/PHS HHS/ -- P01 HL098053/HL/NHLBI NIH HHS/ -- P01HL098053/HL/NHLBI NIH HHS/ -- P20 HL100396/HL/NHLBI NIH HHS/ -- P20HL100396/HL/NHLBI NIH HHS/ -- P30 AR061303/AR/NIAMS NIH HHS/ -- P30 CA030199/CA/NCI NIH HHS/ -- P30AR061303/AR/NIAMS NIH HHS/ -- P30CA030199/CA/NCI NIH HHS/ -- P50 HL112324/HL/NHLBI NIH HHS/ -- P50HL112324/HL/NHLBI NIH HHS/ -- R01 HL088434/HL/NHLBI NIH HHS/ -- R01 HL093183/HL/NHLBI NIH HHS/ -- R01 HL108176/HL/NHLBI NIH HHS/ -- R01 HL113601/HL/NHLBI NIH HHS/ -- R01HL088434/HL/NHLBI NIH HHS/ -- R01HL093183/HL/NHLBI NIH HHS/ -- R01HL108176/HL/NHLBI NIH HHS/ -- R01HL113601/HL/NHLBI NIH HHS/ -- S10 RR021084/RR/NCRR NIH HHS/ -- England -- Nature. 2014 Apr 24;508(7497):531-5. doi: 10.1038/nature13073. Epub 2014 Mar 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Bioengineering, University of California, San Diego, and the Muscle Development and Regeneration Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA [2]. ; 1] The Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA [2]. ; Department of Bioengineering, University of California, San Diego, and the Muscle Development and Regeneration Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA. ; The Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA. ; 1] Department of Bioengineering, University of California, San Diego, and the Muscle Development and Regeneration Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA [2] Department of Cardiology, University Medical Center Utrecht and ICIN Netherlands Heart Institute, Heidelberglaan 100, room G02.523, 3584 CX Utrecht, The Netherlands. ; Global Research Laboratory, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 500-712, South Korea. ; Department of Cardiology, University Medical Center Utrecht and ICIN Netherlands Heart Institute, Heidelberglaan 100, room G02.523, 3584 CX Utrecht, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24670661" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium/metabolism ; Dependovirus/genetics ; Disease Models, Animal ; HEK293 Cells ; Heart/drug effects/physiology/physiopathology ; Heart Failure/*genetics/*therapy ; Humans ; Kinetics ; Male ; Mice ; MicroRNAs/analysis/*antagonists & inhibitors/genetics/metabolism ; Myocardial Contraction/*drug effects ; Myocardium/metabolism ; Myocytes, Cardiac/metabolism ; Oligonucleotides, Antisense/genetics/metabolism/pharmacology ; RNA, Messenger/genetics/metabolism ; Sarcoplasmic Reticulum/metabolism ; Sarcoplasmic Reticulum Calcium-Transporting ATPases/genetics/metabolism ; Survival Analysis ; Up-Regulation/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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