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  • 1
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    The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-12-18
    Description: An understanding of ctenophore biology is critical for reconstructing events that occurred early in animal evolution. Toward this goal, we have sequenced, assembled, and annotated the genome of the ctenophore Mnemiopsis leidyi. Our phylogenomic analyses of both amino acid positions and gene content suggest that ctenophores rather than sponges are the sister lineage to all other animals. Mnemiopsis lacks many of the genes found in bilaterian mesodermal cell types, suggesting that these cell types evolved independently. The set of neural genes in Mnemiopsis is similar to that of sponges, indicating that sponges may have lost a nervous system. These results present a newly supported view of early animal evolution that accounts for major losses and/or gains of sophisticated cell types, including nerve and muscle cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3920664/" 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/PMC3920664/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ryan, Joseph F -- Pang, Kevin -- Schnitzler, Christine E -- Nguyen, Anh-Dao -- Moreland, R Travis -- Simmons, David K -- Koch, Bernard J -- Francis, Warren R -- Havlak, Paul -- NISC Comparative Sequencing Program -- Smith, Stephen A -- Putnam, Nicholas H -- Haddock, Steven H D -- Dunn, Casey W -- Wolfsberg, Tyra G -- Mullikin, James C -- Martindale, Mark Q -- Baxevanis, Andreas D -- ZIA HG000140-13/Intramural NIH HHS/ -- ZIA HG000140-14/Intramural NIH HHS/ -- ZIA HG000140-15/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2013 Dec 13;342(6164):1242592. doi: 10.1126/science.1242592.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genome Technology Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24337300" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; *Biological Evolution ; Cell Lineage/*genetics ; Ctenophora/classification/*cytology/*genetics ; *Genome ; Mesoderm/cytology ; Molecular Sequence Data ; Muscle Development/genetics ; Neurogenesis/genetics ; Phylogeny
    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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  • 2
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    Global epigenomic reconfiguration during mammalian brain development (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-07-06
    Description: DNA methylation is implicated in mammalian brain development and plasticity underlying learning and memory. We report the genome-wide composition, patterning, cell specificity, and dynamics of DNA methylation at single-base resolution in human and mouse frontal cortex throughout their lifespan. Widespread methylome reconfiguration occurs during fetal to young adult development, coincident with synaptogenesis. During this period, highly conserved non-CG methylation (mCH) accumulates in neurons, but not glia, to become the dominant form of methylation in the human neuronal genome. Moreover, we found an mCH signature that identifies genes escaping X-chromosome inactivation. Last, whole-genome single-base resolution 5-hydroxymethylcytosine (hmC) maps revealed that hmC marks fetal brain cell genomes at putative regulatory regions that are CG-demethylated and activated in the adult brain and that CG demethylation at these hmC-poised loci depends on Tet2 activity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785061/" 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/PMC3785061/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lister, Ryan -- Mukamel, Eran A -- Nery, Joseph R -- Urich, Mark -- Puddifoot, Clare A -- Johnson, Nicholas D -- Lucero, Jacinta -- Huang, Yun -- Dwork, Andrew J -- Schultz, Matthew D -- Yu, Miao -- Tonti-Filippini, Julian -- Heyn, Holger -- Hu, Shijun -- Wu, Joseph C -- Rao, Anjana -- Esteller, Manel -- He, Chuan -- Haghighi, Fatemeh G -- Sejnowski, Terrence J -- Behrens, M Margarita -- Ecker, Joseph R -- AI44432/AI/NIAID NIH HHS/ -- CA151535/CA/NCI NIH HHS/ -- HD065812/HD/NICHD NIH HHS/ -- HG006827/HG/NHGRI NIH HHS/ -- K99NS080911/NS/NINDS NIH HHS/ -- MH094670/MH/NIMH NIH HHS/ -- R01 AI044432/AI/NIAID NIH HHS/ -- R01 CA151535/CA/NCI NIH HHS/ -- R01 HD065812/HD/NICHD NIH HHS/ -- R01 HG006827/HG/NHGRI NIH HHS/ -- R01 MH094670/MH/NIMH NIH HHS/ -- R01 MH094774/MH/NIMH NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2013 Aug 9;341(6146):1237905. doi: 10.1126/science.1237905. Epub 2013 Jul 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA. ryan.lister@uwa.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23828890" target="_blank"〉PubMed〈/a〉
    Keywords: 5-Methylcytosine/metabolism ; Adult ; Animals ; Base Sequence ; Conserved Sequence ; Cytosine/*analogs & derivatives/metabolism ; *DNA Methylation ; *Epigenesis, Genetic ; Epigenomics ; Frontal Lobe/*growth & development ; *Gene Expression Regulation, Developmental ; Genome-Wide Association Study ; Humans ; Longevity ; Mice ; Mice, Inbred C57BL ; X Chromosome Inactivation/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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  • 3
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    Mechanism of eukaryotic RNA polymerase III transcription termination (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-07-03
    Description: Gene expression in organisms involves many factors and is tightly controlled. Although much is known about the initial phase of transcription by RNA polymerase III (Pol III), the enzyme that synthesizes the majority of RNA molecules in eukaryotic cells, termination is poorly understood. Here, we show that the extensive structure of Pol III-synthesized transcripts dictates the release of elongation complexes at the end of genes. The poly-T termination signal, which does not cause termination in itself, causes catalytic inactivation and backtracking of Pol III, thus committing the enzyme to termination and transporting it to the nearest RNA secondary structure, which facilitates Pol III release. Similarity between termination mechanisms of Pol III and bacterial RNA polymerase suggests that hairpin-dependent termination may date back to the common ancestor of multisubunit RNA polymerases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760304/" 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/PMC3760304/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nielsen, Soren -- Yuzenkova, Yulia -- Zenkin, Nikolay -- 202994/European Research Council/International -- BB/F013558/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/J006378/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2013 Jun 28;340(6140):1577-80. doi: 10.1126/science.1237934.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23812715" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Molecular Sequence Data ; Nucleic Acid Conformation ; Poly T/metabolism ; Poly U/metabolism ; RNA Polymerase III/*metabolism ; RNA, Ribosomal, 5S/chemistry/genetics ; RNA, Transfer, Tyr/chemistry/genetics ; Saccharomyces cerevisiae/*enzymology/genetics ; *Transcription Termination, Genetic
    Print ISSN: 0036-8075
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  • 4
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    A guanosine-centric mechanism for RNA chaperone function (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-03-09
    Description: RNA chaperones are ubiquitous, heterogeneous proteins essential for RNA structural biogenesis and function. We investigated the mechanism of chaperone-mediated RNA folding by following the time-resolved dimerization of the packaging domain of a retroviral RNA at nucleotide resolution. In the absence of the nucleocapsid (NC) chaperone, dimerization proceeded through multiple, slow-folding intermediates. In the presence of NC, dimerization occurred rapidly through a single structural intermediate. The RNA binding domain of heterogeneous nuclear ribonucleoprotein A1 protein, a structurally unrelated chaperone, also accelerated dimerization. Both chaperones interacted primarily with guanosine residues. Replacing guanosine with more weakly pairing inosine yielded an RNA that folded rapidly without a facilitating chaperone. These results show that RNA chaperones can simplify RNA folding landscapes by weakening intramolecular interactions involving guanosine and explain many RNA chaperone activities.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338410/" 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/PMC4338410/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grohman, Jacob K -- Gorelick, Robert J -- Lickwar, Colin R -- Lieb, Jason D -- Bower, Brian D -- Znosko, Brent M -- Weeks, Kevin M -- GM031819/GM/NIGMS NIH HHS/ -- GM064803/GM/NIGMS NIH HHS/ -- GM072518/GM/NIGMS NIH HHS/ -- HHSN261200800001E/PHS HHS/ -- R01 GM031819/GM/NIGMS NIH HHS/ -- R01 GM064803/GM/NIGMS NIH HHS/ -- T32 GM007092/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Apr 12;340(6129):190-5. doi: 10.1126/science.1230715. Epub 2013 Mar 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23470731" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Dimerization ; Guanosine/chemistry/*metabolism ; Heterogeneous-Nuclear Ribonucleoprotein Group A-B/chemistry/metabolism ; Inosine/chemistry/metabolism ; Kinetics ; Models, Molecular ; Molecular Chaperones/chemistry/*metabolism ; Moloney murine leukemia virus/genetics/*metabolism ; Nucleic Acid Conformation ; Nucleocapsid Proteins/chemistry/*metabolism ; Protein Binding ; RNA, Viral/*chemistry/metabolism
    Print ISSN: 0036-8075
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  • 5
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    Expanding the fluorine chemistry of living systems using engineered polyketide synthase pathways (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-09-07
    Description: Organofluorines represent a rapidly expanding proportion of molecules that are used in pharmaceuticals, diagnostics, agrochemicals, and materials. Despite the prevalence of fluorine in synthetic compounds, the known biological scope is limited to a single pathway that produces fluoroacetate. Here, we demonstrate that this pathway can be exploited as a source of fluorinated building blocks for introduction of fluorine into natural-product scaffolds. Specifically, we have constructed pathways involving two polyketide synthase systems, and we show that fluoroacetate can be used to incorporate fluorine into the polyketide backbone in vitro. We further show that fluorine can be inserted site-selectively and introduced into polyketide products in vivo. These results highlight the prospects for the production of complex fluorinated natural products using synthetic biology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4057101/" 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/PMC4057101/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Walker, Mark C -- Thuronyi, Benjamin W -- Charkoudian, Louise K -- Lowry, Brian -- Khosla, Chaitan -- Chang, Michelle C Y -- 1 DP2 OD008696/OD/NIH HHS/ -- 1 T32 GMO66698/PHS HHS/ -- 1S10RR023679-01/RR/NCRR NIH HHS/ -- F32 CA137994/CA/NCI NIH HHS/ -- R01 GM087934/GM/NIGMS NIH HHS/ -- S10 RR16634-01/RR/NCRR NIH HHS/ -- T32 GM066698/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Sep 6;341(6150):1089-94. doi: 10.1126/science.1242345.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-1460, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24009388" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/genetics/metabolism ; Base Sequence ; Biological Products/chemistry/*metabolism ; Burkholderia/enzymology ; Coenzyme A Ligases/chemistry/genetics/metabolism ; Escherichia coli ; Fluoroacetates/chemistry/*metabolism ; Metabolic Networks and Pathways ; Molecular Sequence Data ; Polyketide Synthases/chemistry/genetics/*metabolism ; Polyketides/chemistry/*metabolism ; Protein Engineering ; Protein Structure, Tertiary ; Streptomyces coelicolor/enzymology
    Print ISSN: 0036-8075
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  • 6
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    Probing allostery through DNA (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-02-16
    Description: Allostery is well documented for proteins but less recognized for DNA-protein interactions. Here, we report that specific binding of a protein on DNA is substantially stabilized or destabilized by another protein bound nearby. The ternary complex's free energy oscillates as a function of the separation between the two proteins with a periodicity of ~10 base pairs, the helical pitch of B-form DNA, and a decay length of ~15 base pairs. The binding affinity of a protein near a DNA hairpin is similarly dependent on their separation, which-together with molecular dynamics simulations-suggests that deformation of the double-helical structure is the origin of DNA allostery. The physiological relevance of this phenomenon is illustrated by its effect on gene expression in live bacteria and on a transcription factor's affinity near nucleosomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586787/" 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/PMC3586787/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Sangjin -- Brostromer, Erik -- Xing, Dong -- Jin, Jianshi -- Chong, Shasha -- Ge, Hao -- Wang, Siyuan -- Gu, Chan -- Yang, Lijiang -- Gao, Yi Qin -- Su, Xiao-dong -- Sun, Yujie -- Xie, X Sunney -- DP1 OD000277/OD/NIH HHS/ -- New York, N.Y. -- Science. 2013 Feb 15;339(6121):816-9. doi: 10.1126/science.1229223.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23413354" target="_blank"〉PubMed〈/a〉
    Keywords: *Allosteric Regulation ; Base Sequence ; Binding Sites ; DNA, B-Form/*chemistry ; DNA-Binding Proteins/*chemistry ; DNA-Directed RNA Polymerases/chemistry ; Escherichia coli/genetics/metabolism ; Gene Expression ; *Gene Expression Regulation, Bacterial ; Lac Repressors/chemistry ; Molecular Dynamics Simulation ; Nucleosomes/chemistry ; Protein Binding ; Protein Structure, Tertiary ; Receptors, Glucocorticoid/chemistry ; Transcription Factors/*chemistry ; Viral Proteins/chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Antiviral RNA interference in mammalian cells (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-10-12
    Description: In antiviral RNA interference (RNAi), the DICER enzyme processes virus-derived double-stranded RNA (dsRNA) into small interfering RNAs (siRNAs) that guide ARGONAUTE proteins to silence complementary viral RNA. As a counterdefense, viruses deploy viral suppressors of RNAi (VSRs). Well-established in plants and invertebrates, the existence of antiviral RNAi remains unknown in mammals. Here, we show that undifferentiated mouse cells infected with encephalomyocarditis virus (EMCV) or Nodamura virus (NoV) accumulate ~22-nucleotide RNAs with all the signature features of siRNAs. These derive from viral dsRNA replication intermediates, incorporate into AGO2, are eliminated in Dicer knockout cells, and decrease in abundance upon cell differentiation. Furthermore, genetically ablating a NoV-encoded VSR that antagonizes DICER during authentic infections reduces NoV accumulation, which is rescued in RNAi-deficient mouse cells. We conclude that antiviral RNAi operates in mammalian cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3853215/" 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/PMC3853215/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maillard, P V -- Ciaudo, C -- Marchais, A -- Li, Y -- Jay, F -- Ding, S W -- Voinnet, Olivier -- R01 AI052447/AI/NIAID NIH HHS/ -- R01 GM094396/GM/NIGMS NIH HHS/ -- RC1 GM091896/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Oct 11;342(6155):235-8. doi: 10.1126/science.1241930.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Swiss Federal Institute of Technology Zurich (ETH-Z), Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24115438" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Argonaute Proteins/genetics/metabolism ; Base Sequence ; Cardiovirus Infections/*immunology ; Cell Line ; DEAD-box RNA Helicases/genetics/metabolism ; Encephalomyocarditis virus/genetics/*physiology ; Gene Knockout Techniques ; Mice ; Molecular Sequence Data ; Nodaviridae/genetics/*physiology ; RNA Interference/*immunology ; RNA Virus Infections/*immunology ; RNA, Double-Stranded/genetics/*immunology/metabolism ; RNA, Small Interfering/genetics/*immunology/metabolism ; RNA, Viral/genetics/*immunology/metabolism ; Ribonuclease III/genetics/metabolism ; Virus Replication
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  • 8
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    Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-07-23
    Description: Ten years ago, the discovery of Mimivirus, a virus infecting Acanthamoeba, initiated a reappraisal of the upper limits of the viral world, both in terms of particle size (〉0.7 micrometers) and genome complexity (〉1000 genes), dimensions typical of parasitic bacteria. The diversity of these giant viruses (the Megaviridae) was assessed by sampling a variety of aquatic environments and their associated sediments worldwide. We report the isolation of two giant viruses, one off the coast of central Chile, the other from a freshwater pond near Melbourne (Australia), without morphological or genomic resemblance to any previously defined virus families. Their micrometer-sized ovoid particles contain DNA genomes of at least 2.5 and 1.9 megabases, respectively. These viruses are the first members of the proposed "Pandoravirus" genus, a term reflecting their lack of similarity with previously described microorganisms and the surprises expected from their future study.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Philippe, Nadege -- Legendre, Matthieu -- Doutre, Gabriel -- Coute, Yohann -- Poirot, Olivier -- Lescot, Magali -- Arslan, Defne -- Seltzer, Virginie -- Bertaux, Lionel -- Bruley, Christophe -- Garin, Jerome -- Claverie, Jean-Michel -- Abergel, Chantal -- New York, N.Y. -- Science. 2013 Jul 19;341(6143):281-6. doi: 10.1126/science.1239181.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural and Genomic Information Laboratory, UMR 7256 CNRS Aix-Marseille Universite, 163 Avenue de Luminy, Case 934, 13288 Marseille cedex 9, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23869018" target="_blank"〉PubMed〈/a〉
    Keywords: Amoeba/*virology ; Base Sequence ; *Evolution, Molecular ; Fresh Water/virology ; *Genome, Viral ; Mimiviridae/*classification/*genetics/isolation & purification/ultrastructure ; Molecular Sequence Data ; Phylogeny ; Proteomics ; Seawater/virology
    Print ISSN: 0036-8075
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  • 9
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    Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-10-12
    Description: The processes that shaped modern European mitochondrial DNA (mtDNA) variation remain unclear. The initial peopling by Palaeolithic hunter-gatherers ~42,000 years ago and the immigration of Neolithic farmers into Europe ~8000 years ago appear to have played important roles but do not explain present-day mtDNA diversity. We generated mtDNA profiles of 364 individuals from prehistoric cultures in Central Europe to perform a chronological study, spanning the Early Neolithic to the Early Bronze Age (5500 to 1550 calibrated years before the common era). We used this transect through time to identify four marked shifts in genetic composition during the Neolithic period, revealing a key role for Late Neolithic cultures in shaping modern Central European genetic diversity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4039305/" 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/PMC4039305/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brandt, Guido -- Haak, Wolfgang -- Adler, Christina J -- Roth, Christina -- Szecsenyi-Nagy, Anna -- Karimnia, Sarah -- Moller-Rieker, Sabine -- Meller, Harald -- Ganslmeier, Robert -- Friederich, Susanne -- Dresely, Veit -- Nicklisch, Nicole -- Pickrell, Joseph K -- Sirocko, Frank -- Reich, David -- Cooper, Alan -- Alt, Kurt W -- Genographic Consortium -- R01 GM100233/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Oct 11;342(6155):257-61. doi: 10.1126/science.1241844.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz, Germany. brandtg@uni-mainz.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24115443" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/history ; Base Sequence ; DNA, Mitochondrial/*genetics/history ; Europe ; *Genetic Drift ; *Genetic Variation ; History, Ancient ; Humans ; Molecular Sequence Data ; Population/*genetics ; Transients and Migrants
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Multiple instances of ancient balancing selection shared between humans and chimpanzees (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-02-16
    Description: Instances in which natural selection maintains genetic variation in a population over millions of years are thought to be extremely rare. We conducted a genome-wide scan for long-lived balancing selection by looking for combinations of SNPs shared between humans and chimpanzees. In addition to the major histocompatibility complex, we identified 125 regions in which the same haplotypes are segregating in the two species, all but two of which are noncoding. In six cases, there is evidence for an ancestral polymorphism that persisted to the present in humans and chimpanzees. Regions with shared haplotypes are significantly enriched for membrane glycoproteins, and a similar trend is seen among shared coding polymorphisms. These findings indicate that ancient balancing selection has shaped human variation and point to genes involved in host-pathogen interactions as common targets.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3612375/" 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/PMC3612375/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leffler, Ellen M -- Gao, Ziyue -- Pfeifer, Susanne -- Segurel, Laure -- Auton, Adam -- Venn, Oliver -- Bowden, Rory -- Bontrop, Ronald -- Wall, Jeffrey D -- Sella, Guy -- Donnelly, Peter -- McVean, Gilean -- Przeworski, Molly -- 075491/Z/04/B/Wellcome Trust/United Kingdom -- 086084/Z/08/Z/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 090532/Z/09/Z/Wellcome Trust/United Kingdom -- 095552/Wellcome Trust/United Kingdom -- 095552/Z/11/Z/Wellcome Trust/United Kingdom -- GM72861/GM/NIGMS NIH HHS/ -- HG005226/HG/NHGRI NIH HHS/ -- R01 GM072861/GM/NIGMS NIH HHS/ -- T32 GM007197/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2013 Mar 29;339(6127):1578-82. doi: 10.1126/science.1234070. Epub 2013 Feb 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA. emleffler@uchicago.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23413192" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Genetic Association Studies ; Genome, Human/*genetics ; Haplotypes ; Host-Pathogen Interactions/*genetics ; Humans ; Molecular Sequence Data ; Pan troglodytes/*genetics ; Pedigree ; Polymorphism, Single Nucleotide ; *Selection, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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