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  • Animals  (24)
  • Quantum optics, physics of lasers, nonlinear optics, classical optics
  • ddc:330
  • Nature Publishing Group (NPG)  (24)
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  • 11
    Publication Date: 2013-10-04
    Description: The recognition of autophagy related 16-like 1 (ATG16L1) as a genetic risk factor has exposed the critical role of autophagy in Crohn's disease. Homozygosity for the highly prevalent ATG16L1 risk allele, or murine hypomorphic (HM) activity, causes Paneth cell dysfunction. As Atg16l1(HM) mice do not develop spontaneous intestinal inflammation, the mechanism(s) by which ATG16L1 contributes to disease remains obscure. Deletion of the unfolded protein response (UPR) transcription factor X-box binding protein-1 (Xbp1) in intestinal epithelial cells, the human orthologue of which harbours rare inflammatory bowel disease risk variants, results in endoplasmic reticulum (ER) stress, Paneth cell impairment and spontaneous enteritis. Unresolved ER stress is a common feature of inflammatory bowel disease epithelium, and several genetic risk factors of Crohn's disease affect Paneth cells. Here we show that impairment in either UPR (Xbp1(DeltaIEC)) or autophagy function (Atg16l1(DeltaIEC) or Atg7(DeltaIEC)) in intestinal epithelial cells results in each other's compensatory engagement, and severe spontaneous Crohn's-disease-like transmural ileitis if both mechanisms are compromised. Xbp1(DeltaIEC) mice show autophagosome formation in hypomorphic Paneth cells, which is linked to ER stress via protein kinase RNA-like endoplasmic reticulum kinase (PERK), elongation initiation factor 2alpha (eIF2alpha) and activating transcription factor 4 (ATF4). Ileitis is dependent on commensal microbiota and derives from increased intestinal epithelial cell death, inositol requiring enzyme 1alpha (IRE1alpha)-regulated NF-kappaB activation and tumour-necrosis factor signalling, which are synergistically increased when autophagy is deficient. ATG16L1 restrains IRE1alpha activity, and augmentation of autophagy in intestinal epithelial cells ameliorates ER stress-induced intestinal inflammation and eases NF-kappaB overactivation and intestinal epithelial cell death. ER stress, autophagy induction and spontaneous ileitis emerge from Paneth-cell-specific deletion of Xbp1. Genetically and environmentally controlled UPR function within Paneth cells may therefore set the threshold for the development of intestinal inflammation upon hypomorphic ATG16L1 function and implicate ileal Crohn's disease as a specific disorder of Paneth cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3862182/" 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/PMC3862182/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Adolph, Timon E -- Tomczak, Michal F -- Niederreiter, Lukas -- Ko, Hyun-Jeong -- Bock, Janne -- Martinez-Naves, Eduardo -- Glickman, Jonathan N -- Tschurtschenthaler, Markus -- Hartwig, John -- Hosomi, Shuhei -- Flak, Magdalena B -- Cusick, Jennifer L -- Kohno, Kenji -- Iwawaki, Takao -- Billmann-Born, Susanne -- Raine, Tim -- Bharti, Richa -- Lucius, Ralph -- Kweon, Mi-Na -- Marciniak, Stefan J -- Choi, Augustine -- Hagen, Susan J -- Schreiber, Stefan -- Rosenstiel, Philip -- Kaser, Arthur -- Blumberg, Richard S -- 100140/Wellcome Trust/United Kingdom -- 260961/European Research Council/International -- DK0034854/DK/NIDDK NIH HHS/ -- DK044319/DK/NIDDK NIH HHS/ -- DK051362/DK/NIDDK NIH HHS/ -- DK053056/DK/NIDDK NIH HHS/ -- DK088199/DK/NIDDK NIH HHS/ -- G1002610/Medical Research Council/United Kingdom -- R01 DK044319/DK/NIDDK NIH HHS/ -- R01 DK051362/DK/NIDDK NIH HHS/ -- R01 DK053056/DK/NIDDK NIH HHS/ -- R01 DK088199/DK/NIDDK NIH HHS/ -- England -- Nature. 2013 Nov 14;503(7475):272-6. doi: 10.1038/nature12599. Epub 2013 Oct 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Division of Gastroenterology and Hepatology, Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, UK [2].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24089213" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Autophagy/genetics ; Carrier Proteins/genetics/metabolism ; Cell Line ; DNA-Binding Proteins/genetics/metabolism ; Endoplasmic Reticulum Stress/genetics ; Inflammation ; Intestinal Diseases/genetics/*physiopathology ; Intestinal Mucosa/cytology/*pathology ; Mice ; Paneth Cells/*pathology ; Signal Transduction ; Transcription Factors/genetics/metabolism ; Unfolded Protein Response/physiology ; eIF-2 Kinase/metabolism
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  • 12
    Publication Date: 2013-07-03
    Description: DNA methylation is a heritable epigenetic modification involved in gene silencing, imprinting, and the suppression of retrotransposons. Global DNA demethylation occurs in the early embryo and the germ line, and may be mediated by Tet (ten eleven translocation) enzymes, which convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Tet enzymes have been studied extensively in mouse embryonic stem (ES) cells, which are generally cultured in the absence of vitamin C, a potential cofactor for Fe(II) 2-oxoglutarate dioxygenase enzymes such as Tet enzymes. Here we report that addition of vitamin C to mouse ES cells promotes Tet activity, leading to a rapid and global increase in 5hmC. This is followed by DNA demethylation of many gene promoters and upregulation of demethylated germline genes. Tet1 binding is enriched near the transcription start site of genes affected by vitamin C treatment. Importantly, vitamin C, but not other antioxidants, enhances the activity of recombinant Tet1 in a biochemical assay, and the vitamin-C-induced changes in 5hmC and 5mC are entirely suppressed in Tet1 and Tet2 double knockout ES cells. Vitamin C has a stronger effect on regions that gain methylation in cultured ES cells compared to blastocysts, and in vivo are methylated only after implantation. In contrast, imprinted regions and intracisternal A particle retroelements, which are resistant to demethylation in the early embryo, are resistant to vitamin-C-induced DNA demethylation. Collectively, the results of this study establish vitamin C as a direct regulator of Tet activity and DNA methylation fidelity in ES cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893718/" 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/PMC3893718/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Blaschke, Kathryn -- Ebata, Kevin T -- Karimi, Mohammad M -- Zepeda-Martinez, Jorge A -- Goyal, Preeti -- Mahapatra, Sahasransu -- Tam, Angela -- Laird, Diana J -- Hirst, Martin -- Rao, Anjana -- Lorincz, Matthew C -- Ramalho-Santos, Miguel -- 92093/Canadian Institutes of Health Research/Canada -- CA151535/CA/NCI NIH HHS/ -- DP2 OD007420/OD/NIH HHS/ -- DP2OD004698/OD/NIH HHS/ -- HD065812/HD/NICHD NIH HHS/ -- P30 DK063720/DK/NIDDK NIH HHS/ -- R01 AI044432/AI/NIAID NIH HHS/ -- R01 CA151535/CA/NCI NIH HHS/ -- R01 HD065812/HD/NICHD NIH HHS/ -- R01 OD012204/OD/NIH HHS/ -- England -- Nature. 2013 Aug 8;500(7461):222-6. doi: 10.1038/nature12362. Epub 2013 Jun 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Obstetrics and Gynecology and Center for Reproductive Sciences, University of California San Francisco, San Francisco, California 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23812591" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antioxidants/pharmacology ; Ascorbic Acid/*pharmacology ; Blastocyst/metabolism ; Cell Line ; Culture Media/chemistry ; Cytosine/analogs & derivatives/metabolism ; DNA Methylation/*drug effects ; DNA-Binding Proteins/genetics/*metabolism ; Embryonic Stem Cells/*drug effects/metabolism ; Gene Expression Regulation, Developmental/drug effects ; Gene Knockout Techniques ; Mice ; Protein Binding/drug effects ; Proto-Oncogene Proteins/genetics/*metabolism ; Recombinant Proteins/genetics/metabolism
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  • 13
    Publication Date: 2013-12-07
    Description: Excavations of a complex of caves in the Sierra de Atapuerca in northern Spain have unearthed hominin fossils that range in age from the early Pleistocene to the Holocene. One of these sites, the 'Sima de los Huesos' ('pit of bones'), has yielded the world's largest assemblage of Middle Pleistocene hominin fossils, consisting of at least 28 individuals dated to over 300,000 years ago. The skeletal remains share a number of morphological features with fossils classified as Homo heidelbergensis and also display distinct Neanderthal-derived traits. Here we determine an almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos and show that it is closely related to the lineage leading to mitochondrial genomes of Denisovans, an eastern Eurasian sister group to Neanderthals. Our results pave the way for DNA research on hominins from the Middle Pleistocene.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meyer, Matthias -- Fu, Qiaomei -- Aximu-Petri, Ayinuer -- Glocke, Isabelle -- Nickel, Birgit -- Arsuaga, Juan-Luis -- Martinez, Ignacio -- Gracia, Ana -- de Castro, Jose Maria Bermudez -- Carbonell, Eudald -- Paabo, Svante -- England -- Nature. 2014 Jan 16;505(7483):403-6. doi: 10.1038/nature12788. Epub 2013 Dec 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. ; 1] Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany [2] Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. ; 1] Centro de Investigacion Sobre la Evolucion y Comportamiento Humanos, Universidad Complutense de Madrid-Instituto de Salud Carlos III, 28029 Madrid, Spain [2] Departamento de Paleontologia, Facultad de Ciencias Geologicas, Universidad Complutense de Madrid, 28040 Madrid, Spain. ; 1] Centro de Investigacion Sobre la Evolucion y Comportamiento Humanos, Universidad Complutense de Madrid-Instituto de Salud Carlos III, 28029 Madrid, Spain [2] Area de Paleontologia, Depto. de Geografia y Geologia, Universidad de Alcala, Alcala de Henares, 28871 Madrid, Spain. ; Centro Nacional de Investigacion sobre la Evolucion Humana, Paseo Sierra de Atapuerca, 09002 Burgos, Spain. ; 1] Institut Catala de Paleoecologia Humana i Evolucio Social, C/Marcel.li Domingo s/n (Edifici W3), Campus Sescelades, 43007 Tarragona, Spain [2] Area de Prehistoria, Dept. d'Historia i Historia de l'Art, Univ. Rovira i Virgili, Fac. de Lletres, Av. Catalunya, 35, 43002 Tarragona, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24305051" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bayes Theorem ; Consensus Sequence/genetics ; Cytosine/metabolism ; DNA, Mitochondrial/genetics ; Deamination ; Femur/anatomy & histology/metabolism ; *Fossils ; Genome, Mitochondrial/*genetics ; Hominidae/anatomy & histology/*classification/*genetics ; Molecular Sequence Data ; Neanderthals/genetics ; *Phylogeny ; Spain
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  • 14
    Publication Date: 2014-08-01
    Description: Self-renewal is the hallmark feature both of normal stem cells and cancer stem cells. Since the regenerative capacity of normal haematopoietic stem cells is limited by the accumulation of reactive oxygen species and DNA double-strand breaks, we speculated that DNA damage might also constrain leukaemic self-renewal and malignant haematopoiesis. Here we show that the histone methyl-transferase MLL4, a suppressor of B-cell lymphoma, is required for stem-cell activity and an aggressive form of acute myeloid leukaemia harbouring the MLL-AF9 oncogene. Deletion of MLL4 enhances myelopoiesis and myeloid differentiation of leukaemic blasts, which protects mice from death related to acute myeloid leukaemia. MLL4 exerts its function by regulating transcriptional programs associated with the antioxidant response. Addition of reactive oxygen species scavengers or ectopic expression of FOXO3 protects MLL4(-/-) MLL-AF9 cells from DNA damage and inhibits myeloid maturation. Similar to MLL4 deficiency, loss of ATM or BRCA1 sensitizes transformed cells to differentiation, suggesting that myeloid differentiation is promoted by loss of genome integrity. Indeed, we show that restriction-enzyme-induced double-strand breaks are sufficient to induce differentiation of MLL-AF9 blasts, which requires cyclin-dependent kinase inhibitor p21(Cip1) (Cdkn1a) activity. In summary, we have uncovered an unexpected tumour-promoting role of genome guardians in enforcing the oncogene-induced differentiation blockade in acute myeloid leukaemia.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410707/" 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/PMC4410707/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Santos, Margarida A -- Faryabi, Robert B -- Ergen, Aysegul V -- Day, Amanda M -- Malhowski, Amy -- Canela, Andres -- Onozawa, Masahiro -- Lee, Ji-Eun -- Callen, Elsa -- Gutierrez-Martinez, Paula -- Chen, Hua-Tang -- Wong, Nancy -- Finkel, Nadia -- Deshpande, Aniruddha -- Sharrow, Susan -- Rossi, Derrick J -- Ito, Keisuke -- Ge, Kai -- Aplan, Peter D -- Armstrong, Scott A -- Nussenzweig, Andre -- CA140575/CA/NCI NIH HHS/ -- CA66996/CA/NCI NIH HHS/ -- P30 CA008748/CA/NCI NIH HHS/ -- R00 CA139009/CA/NCI NIH HHS/ -- R01 DK098263/DK/NIDDK NIH HHS/ -- R01 DK100689/DK/NIDDK NIH HHS/ -- Intramural NIH HHS/ -- England -- Nature. 2014 Oct 2;514(7520):107-11. doi: 10.1038/nature13483. Epub 2014 Jul 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA. ; 1] Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA [2]. ; The Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA. ; Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA. ; 1] Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA [2] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA. ; Human Oncology and Pathogenesis Program and Department of Pediatrics, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA. ; Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA. ; Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Departments of Cell Biology and Medicine, Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25079327" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Ataxia Telangiectasia Mutated Proteins/metabolism ; BRCA1 Protein/genetics/metabolism ; Cell Transformation, Neoplastic ; Cyclin-Dependent Kinase Inhibitor p21/metabolism ; DNA Breaks, Double-Stranded ; *DNA Damage ; DNA Repair ; Female ; Gene Expression Regulation, Neoplastic ; Genes, BRCA1 ; Hematopoietic Stem Cells/cytology/metabolism/pathology ; Histone-Lysine N-Methyltransferase/deficiency/genetics/metabolism ; Leukemia, Myeloid, Acute/*enzymology/*pathology ; Male ; Mice ; *Myelopoiesis ; Oncogene Proteins, Fusion/genetics/metabolism ; Reactive Oxygen Species/metabolism
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  • 15
    Publication Date: 2011-11-25
    Description: The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and an extreme record of pesticide resistance. Here we present the completely sequenced and annotated spider mite genome, representing the first complete chelicerate genome. At 90 megabases T. urticae has the smallest sequenced arthropod genome. Compared with other arthropods, the spider mite genome shows unique changes in the hormonal environment and organization of the Hox complex, and also reveals evolutionary innovation of silk production. We find strong signatures of polyphagy and detoxification in gene families associated with feeding on different hosts and in new gene families acquired by lateral gene transfer. Deep transcriptome analysis of mites feeding on different plants shows how this pest responds to a changing host environment. The T. urticae genome thus offers new insights into arthropod evolution and plant-herbivore interactions, and provides unique opportunities for developing novel plant protection strategies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grbic, Miodrag -- Van Leeuwen, Thomas -- Clark, Richard M -- Rombauts, Stephane -- Rouze, Pierre -- Grbic, Vojislava -- Osborne, Edward J -- Dermauw, Wannes -- Ngoc, Phuong Cao Thi -- Ortego, Felix -- Hernandez-Crespo, Pedro -- Diaz, Isabel -- Martinez, Manuel -- Navajas, Maria -- Sucena, Elio -- Magalhaes, Sara -- Nagy, Lisa -- Pace, Ryan M -- Djuranovic, Sergej -- Smagghe, Guy -- Iga, Masatoshi -- Christiaens, Olivier -- Veenstra, Jan A -- Ewer, John -- Villalobos, Rodrigo Mancilla -- Hutter, Jeffrey L -- Hudson, Stephen D -- Velez, Marisela -- Yi, Soojin V -- Zeng, Jia -- Pires-daSilva, Andre -- Roch, Fernando -- Cazaux, Marc -- Navarro, Marie -- Zhurov, Vladimir -- Acevedo, Gustavo -- Bjelica, Anica -- Fawcett, Jeffrey A -- Bonnet, Eric -- Martens, Cindy -- Baele, Guy -- Wissler, Lothar -- Sanchez-Rodriguez, Aminael -- Tirry, Luc -- Blais, Catherine -- Demeestere, Kristof -- Henz, Stefan R -- Gregory, T Ryan -- Mathieu, Johannes -- Verdon, Lou -- Farinelli, Laurent -- Schmutz, Jeremy -- Lindquist, Erika -- Feyereisen, Rene -- Van de Peer, Yves -- England -- Nature. 2011 Nov 23;479(7374):487-92. doi: 10.1038/nature10640.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, The University of Western Ontario, London N6A 5B7, Canada. mgrbic@uwo.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22113690" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics/physiology ; Animals ; Ecdysterone/analogs & derivatives/genetics ; Evolution, Molecular ; Fibroins/genetics ; Gene Expression Regulation ; Gene Transfer, Horizontal/genetics ; Genes, Homeobox/genetics ; Genome/*genetics ; Genomics ; Herbivory/*genetics/physiology ; Molecular Sequence Data ; Molting/genetics ; Multigene Family/genetics ; Nanostructures/chemistry ; Plants/parasitology ; Silk/biosynthesis/chemistry ; Tetranychidae/*genetics/*physiology ; Transcriptome/genetics
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  • 16
    Publication Date: 2012-03-09
    Description: Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303130/" 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/PMC3303130/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scally, Aylwyn -- Dutheil, Julien Y -- Hillier, LaDeana W -- Jordan, Gregory E -- Goodhead, Ian -- Herrero, Javier -- Hobolth, Asger -- Lappalainen, Tuuli -- Mailund, Thomas -- Marques-Bonet, Tomas -- McCarthy, Shane -- Montgomery, Stephen H -- Schwalie, Petra C -- Tang, Y Amy -- Ward, Michelle C -- Xue, Yali -- Yngvadottir, Bryndis -- Alkan, Can -- Andersen, Lars N -- Ayub, Qasim -- Ball, Edward V -- Beal, Kathryn -- Bradley, Brenda J -- Chen, Yuan -- Clee, Chris M -- Fitzgerald, Stephen -- Graves, Tina A -- Gu, Yong -- Heath, Paul -- Heger, Andreas -- Karakoc, Emre -- Kolb-Kokocinski, Anja -- Laird, Gavin K -- Lunter, Gerton -- Meader, Stephen -- Mort, Matthew -- Mullikin, James C -- Munch, Kasper -- O'Connor, Timothy D -- Phillips, Andrew D -- Prado-Martinez, Javier -- Rogers, Anthony S -- Sajjadian, Saba -- Schmidt, Dominic -- Shaw, Katy -- Simpson, Jared T -- Stenson, Peter D -- Turner, Daniel J -- Vigilant, Linda -- Vilella, Albert J -- Whitener, Weldon -- Zhu, Baoli -- Cooper, David N -- de Jong, Pieter -- Dermitzakis, Emmanouil T -- Eichler, Evan E -- Flicek, Paul -- Goldman, Nick -- Mundy, Nicholas I -- Ning, Zemin -- Odom, Duncan T -- Ponting, Chris P -- Quail, Michael A -- Ryder, Oliver A -- Searle, Stephen M -- Warren, Wesley C -- Wilson, Richard K -- Schierup, Mikkel H -- Rogers, Jane -- Tyler-Smith, Chris -- Durbin, Richard -- 062023/Wellcome Trust/United Kingdom -- 075491/Z/04/Wellcome Trust/United Kingdom -- 077009/Wellcome Trust/United Kingdom -- 077192/Wellcome Trust/United Kingdom -- 077198/Wellcome Trust/United Kingdom -- 089066/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 095908/Wellcome Trust/United Kingdom -- 15603/Cancer Research UK/United Kingdom -- 202218/European Research Council/International -- A15603/Cancer Research UK/United Kingdom -- G0501331/Medical Research Council/United Kingdom -- G0701805/Medical Research Council/United Kingdom -- HG002385/HG/NHGRI NIH HHS/ -- U54 HG003079/HG/NHGRI NIH HHS/ -- WT062023/Wellcome Trust/United Kingdom -- WT077009/Wellcome Trust/United Kingdom -- WT077192/Wellcome Trust/United Kingdom -- WT077198/Wellcome Trust/United Kingdom -- WT089066/Wellcome Trust/United Kingdom -- Medical Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- England -- Nature. 2012 Mar 7;483(7388):169-75. doi: 10.1038/nature10842.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22398555" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Evolution, Molecular ; Female ; Gene Expression Regulation ; *Genetic Speciation ; Genetic Variation/genetics ; Genome/*genetics ; Genomics ; Gorilla gorilla/*genetics ; Humans ; Macaca mulatta/genetics ; Molecular Sequence Data ; Pan troglodytes/genetics ; Phylogeny ; Pongo/genetics ; Proteins/genetics ; Sequence Alignment ; Species Specificity ; Transcription, Genetic
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  • 17
    Publication Date: 2013-07-05
    Description: Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3822165/" 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/PMC3822165/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prado-Martinez, Javier -- Sudmant, Peter H -- Kidd, Jeffrey M -- Li, Heng -- Kelley, Joanna L -- Lorente-Galdos, Belen -- Veeramah, Krishna R -- Woerner, August E -- O'Connor, Timothy D -- Santpere, Gabriel -- Cagan, Alexander -- Theunert, Christoph -- Casals, Ferran -- Laayouni, Hafid -- Munch, Kasper -- Hobolth, Asger -- Halager, Anders E -- Malig, Maika -- Hernandez-Rodriguez, Jessica -- Hernando-Herraez, Irene -- Prufer, Kay -- Pybus, Marc -- Johnstone, Laurel -- Lachmann, Michael -- Alkan, Can -- Twigg, Dorina -- Petit, Natalia -- Baker, Carl -- Hormozdiari, Fereydoun -- Fernandez-Callejo, Marcos -- Dabad, Marc -- Wilson, Michael L -- Stevison, Laurie -- Camprubi, Cristina -- Carvalho, Tiago -- Ruiz-Herrera, Aurora -- Vives, Laura -- Mele, Marta -- Abello, Teresa -- Kondova, Ivanela -- Bontrop, Ronald E -- Pusey, Anne -- Lankester, Felix -- Kiyang, John A -- Bergl, Richard A -- Lonsdorf, Elizabeth -- Myers, Simon -- Ventura, Mario -- Gagneux, Pascal -- Comas, David -- Siegismund, Hans -- Blanc, Julie -- Agueda-Calpena, Lidia -- Gut, Marta -- Fulton, Lucinda -- Tishkoff, Sarah A -- Mullikin, James C -- Wilson, Richard K -- Gut, Ivo G -- Gonder, Mary Katherine -- Ryder, Oliver A -- Hahn, Beatrice H -- Navarro, Arcadi -- Akey, Joshua M -- Bertranpetit, Jaume -- Reich, David -- Mailund, Thomas -- Schierup, Mikkel H -- Hvilsom, Christina -- Andres, Aida M -- Wall, Jeffrey D -- Bustamante, Carlos D -- Hammer, Michael F -- Eichler, Evan E -- Marques-Bonet, Tomas -- 090532/Wellcome Trust/United Kingdom -- 260372/European Research Council/International -- DP1 ES022577/ES/NIEHS NIH HHS/ -- DP1ES022577-04/DP/NCCDPHP CDC HHS/ -- GM100233/GM/NIGMS NIH HHS/ -- HG002385/HG/NHGRI NIH HHS/ -- R01 GM095882/GM/NIGMS NIH HHS/ -- R01 GM100233/GM/NIGMS NIH HHS/ -- R01 HG002385/HG/NHGRI NIH HHS/ -- R01_HG005226/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2013 Jul 25;499(7459):471-5. doi: 10.1038/nature12228. Epub 2013 Jul 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23823723" target="_blank"〉PubMed〈/a〉
    Keywords: Africa ; Animals ; Animals, Wild/genetics ; Animals, Zoo/genetics ; Asia, Southeastern ; Evolution, Molecular ; Gene Flow/genetics ; *Genetic Variation ; Genetics, Population ; Genome/genetics ; Gorilla gorilla/classification/genetics ; Hominidae/classification/*genetics ; Humans ; Inbreeding ; Pan paniscus/classification/genetics ; Pan troglodytes/classification/genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Population Density
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    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 18
    Publication Date: 2015-06-19
    Description: There is an urgent need for new drugs to treat malaria, with broad therapeutic potential and novel modes of action, to widen the scope of treatment and to overcome emerging drug resistance. Here we describe the discovery of DDD107498, a compound with a potent and novel spectrum of antimalarial activity against multiple life-cycle stages of the Plasmodium parasite, with good pharmacokinetic properties and an acceptable safety profile. DDD107498 demonstrates potential to address a variety of clinical needs, including single-dose treatment, transmission blocking and chemoprotection. DDD107498 was developed from a screening programme against blood-stage malaria parasites; its molecular target has been identified as translation elongation factor 2 (eEF2), which is responsible for the GTP-dependent translocation of the ribosome along messenger RNA, and is essential for protein synthesis. This discovery of eEF2 as a viable antimalarial drug target opens up new possibilities for drug discovery.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700930/" 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/PMC4700930/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baragana, Beatriz -- Hallyburton, Irene -- Lee, Marcus C S -- Norcross, Neil R -- Grimaldi, Raffaella -- Otto, Thomas D -- Proto, William R -- Blagborough, Andrew M -- Meister, Stephan -- Wirjanata, Grennady -- Ruecker, Andrea -- Upton, Leanna M -- Abraham, Tara S -- Almeida, Mariana J -- Pradhan, Anupam -- Porzelle, Achim -- Martinez, Maria Santos -- Bolscher, Judith M -- Woodland, Andrew -- Norval, Suzanne -- Zuccotto, Fabio -- Thomas, John -- Simeons, Frederick -- Stojanovski, Laste -- Osuna-Cabello, Maria -- Brock, Paddy M -- Churcher, Tom S -- Sala, Katarzyna A -- Zakutansky, Sara E -- Jimenez-Diaz, Maria Belen -- Sanz, Laura Maria -- Riley, Jennifer -- Basak, Rajshekhar -- Campbell, Michael -- Avery, Vicky M -- Sauerwein, Robert W -- Dechering, Koen J -- Noviyanti, Rintis -- Campo, Brice -- Frearson, Julie A -- Angulo-Barturen, Inigo -- Ferrer-Bazaga, Santiago -- Gamo, Francisco Javier -- Wyatt, Paul G -- Leroy, Didier -- Siegl, Peter -- Delves, Michael J -- Kyle, Dennis E -- Wittlin, Sergio -- Marfurt, Jutta -- Price, Ric N -- Sinden, Robert E -- Winzeler, Elizabeth A -- Charman, Susan A -- Bebrevska, Lidiya -- Gray, David W -- Campbell, Simon -- Fairlamb, Alan H -- Willis, Paul A -- Rayner, Julian C -- Fidock, David A -- Read, Kevin D -- Gilbert, Ian H -- 079838/Wellcome Trust/United Kingdom -- 091625/Wellcome Trust/United Kingdom -- 098051/Wellcome Trust/United Kingdom -- 100476/Wellcome Trust/United Kingdom -- R01 AI090141/AI/NIAID NIH HHS/ -- R01 AI103058/AI/NIAID NIH HHS/ -- England -- Nature. 2015 Jun 18;522(7556):315-20. doi: 10.1038/nature14451.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK. ; Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA. ; Malaria Programme, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK. ; Department of Life Sciences, Imperial College, London SW7 2AZ, UK. ; University of California, San Diego, School of Medicine, 9500 Gilman Drive 0760, La Jolla, California 92093, USA. ; Global Health and Tropical Medicine Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, Northern Territory 0811, Australia. ; Department of Global Health, College of Public Health University of South Florida, 3720 Spectrum Boulevard, Suite 304, Tampa, Florida 33612, USA. ; GlaxoSmithKline, Tres Cantos Medicines Development Campus-Diseases of the Developing World, Severo Ochoa 2, Tres Cantos 28760, Madrid, Spain. ; TropIQ Health Sciences, Geert Grooteplein 28, Huispost 268, 6525 GA Nijmegen, The Netherlands. ; Centre for Drug Candidate Optimisation, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia. ; Eskitis Institute, Brisbane Innovation Park, Nathan Campus, Griffith University, Queensland 4111, Australia. ; Malaria Pathogenesis Laboratory, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, 10430 Jakarta, Indonesia. ; Medicines for Malaria Venture, PO Box 1826, 20 route de Pre-Bois, 1215 Geneva 15, Switzerland. ; Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland. ; 1] Global Health and Tropical Medicine Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, Northern Territory 0811, Australia [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK. ; 1] Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA [2] Division of Infectious Diseases, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26085270" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antimalarials/administration & dosage/adverse ; effects/pharmacokinetics/*pharmacology ; Drug Discovery ; Female ; Gene Expression Regulation/*drug effects ; Life Cycle Stages/drug effects ; Liver/drug effects/parasitology ; Malaria/drug therapy/*parasitology ; Male ; Models, Molecular ; Peptide Elongation Factor 2/antagonists & inhibitors/metabolism ; Plasmodium/*drug effects/genetics/growth & development/*metabolism ; Plasmodium berghei/drug effects/physiology ; Plasmodium falciparum/drug effects/metabolism ; Plasmodium vivax/drug effects/metabolism ; Protein Biosynthesis/*drug effects ; Quinolines/administration & dosage/chemistry/pharmacokinetics/*pharmacology
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  • 19
    Publication Date: 2015-02-18
    Description: Darwin's finches, inhabiting the Galapagos archipelago and Cocos Island, constitute an iconic model for studies of speciation and adaptive evolution. Here we report the results of whole-genome re-sequencing of 120 individuals representing all of the Darwin's finch species and two close relatives. Phylogenetic analysis reveals important discrepancies with the phenotype-based taxonomy. We find extensive evidence for interspecific gene flow throughout the radiation. Hybridization has given rise to species of mixed ancestry. A 240 kilobase haplotype encompassing the ALX1 gene that encodes a transcription factor affecting craniofacial development is strongly associated with beak shape diversity across Darwin's finch species as well as within the medium ground finch (Geospiza fortis), a species that has undergone rapid evolution of beak shape in response to environmental changes. The ALX1 haplotype has contributed to diversification of beak shapes among the Darwin's finches and, thereby, to an expanded utilization of food resources.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lamichhaney, Sangeet -- Berglund, Jonas -- Almen, Markus Sallman -- Maqbool, Khurram -- Grabherr, Manfred -- Martinez-Barrio, Alvaro -- Promerova, Marta -- Rubin, Carl-Johan -- Wang, Chao -- Zamani, Neda -- Grant, B Rosemary -- Grant, Peter R -- Webster, Matthew T -- Andersson, Leif -- England -- Nature. 2015 Feb 19;518(7539):371-5. doi: 10.1038/nature14181. Epub 2015 Feb 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden. ; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden. ; 1] Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden [2] Department of Plant Physiology, Umea University, SE-901 87 Umea, Sweden. ; Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA. ; 1] Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden [2] Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden [3] Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25686609" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Avian Proteins/genetics/metabolism ; Beak/*anatomy & histology ; Ecuador ; *Evolution, Molecular ; Female ; Finches/*anatomy & histology/classification/embryology/*genetics ; Gene Flow ; Genome/genetics ; Haplotypes/genetics ; Hybridization, Genetic ; Indian Ocean Islands ; Male ; Molecular Sequence Data ; Phylogeny ; Transcription Factors/genetics/metabolism
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    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 20
    Publication Date: 2016-03-16
    Description: A unique assemblage of 28 hominin individuals, found in Sima de los Huesos in the Sierra de Atapuerca in Spain, has recently been dated to approximately 430,000 years ago. An interesting question is how these Middle Pleistocene hominins were related to those who lived in the Late Pleistocene epoch, in particular to Neanderthals in western Eurasia and to Denisovans, a sister group of Neanderthals so far known only from southern Siberia. While the Sima de los Huesos hominins share some derived morphological features with Neanderthals, the mitochondrial genome retrieved from one individual from Sima de los Huesos is more closely related to the mitochondrial DNA of Denisovans than to that of Neanderthals. However, since the mitochondrial DNA does not reveal the full picture of relationships among populations, we have investigated DNA preservation in several individuals found at Sima de los Huesos. Here we recover nuclear DNA sequences from two specimens, which show that the Sima de los Huesos hominins were related to Neanderthals rather than to Denisovans, indicating that the population divergence between Neanderthals and Denisovans predates 430,000 years ago. A mitochondrial DNA recovered from one of the specimens shares the previously described relationship to Denisovan mitochondrial DNAs, suggesting, among other possibilities, that the mitochondrial DNA gene pool of Neanderthals turned over later in their history.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meyer, Matthias -- Arsuaga, Juan-Luis -- de Filippo, Cesare -- Nagel, Sarah -- Aximu-Petri, Ayinuer -- Nickel, Birgit -- Martinez, Ignacio -- Gracia, Ana -- Bermudez de Castro, Jose Maria -- Carbonell, Eudald -- Viola, Bence -- Kelso, Janet -- Prufer, Kay -- Paabo, Svante -- England -- Nature. 2016 Mar 24;531(7595):504-7. doi: 10.1038/nature17405. Epub 2016 Mar 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. ; Centro de Investigacion Sobre la Evolucion y Comportamiento Humanos, Universidad Complutense de Madrid-Instituto de Salud Carlos III, 28029 Madrid, Spain. ; Departamento de Paleontologia, Facultad de Ciencias Geologicas, Universidad Complutense de Madrid, 28040 Madrid, Spain. ; Area de Paleontologia, Departamento de Geografia y Geologia, Universidad de Alcala, Alcala de Henares, 28871 Madrid, Spain. ; Centro Nacional de Investigacion sobre la Evolucion Humana, Paseo Sierra de Atapuerca, 09002 Burgos, Spain. ; Institut Catala de Paleoecologia Humana i Evolucio Social, C/Marcel.li Domingo s/n (Edifici W3), Campus Sescelades, 43007 Tarragona, Spain. ; Area de Prehistoria, Departament d'Historia i Historia de l'Art, Universitat Rovira i Virgili, Facultat de Lletres, Avinguda de Catalunya, 35, 43002 Tarragona, Spain. ; Department of Anthropology, University of Toronto, 19 Russell Street, Toronto, Ontario M5S 2S2, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26976447" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; DNA, Mitochondrial/genetics ; Fossils ; Genome, Mitochondrial/genetics ; Hominidae/classification/*genetics ; Male ; Neanderthals/classification/genetics ; *Phylogeny ; Sequence Alignment ; Spain
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