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  • American Chemical Society  (17)
  • Oxford University Press  (12)
  • American Association for the Advancement of Science (AAAS)  (4)
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  • 1
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    Recurrent Gene Duplication Diversifies Genome Defense Repertoire in Drosophila (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-22
    Description: Transposable elements (TEs) comprise large fractions of many eukaryotic genomes and imperil host genome integrity. The host genome combats these challenges by encoding proteins that silence TE activity. Both the introduction of new TEs via horizontal transfer and TE sequence evolution requires constant innovation of host-encoded TE silencing machinery to keep pace with TEs. One form of host innovation is the adaptation of existing, single-copy host genes. Indeed, host suppressors of TE replication often harbor signatures of positive selection. Such signatures are especially evident in genes encoding the p iwi- i nteracting-RNA pathway of gene silencing, for example, the female germline-restricted TE silencer, HP1D/Rhino . Host genomes can also innovate via gene duplication and divergence. However, the importance of gene family expansions, contractions, and gene turnover to host genome defense has been largely unexplored. Here, we functionally characterize Oxpecker , a young, tandem duplicate gene of HP1D/rhino . We demonstrate that Oxpecker supports female fertility in Drosophila melanogaster and silences several TE families that are incompletely silenced by HP1D/Rhino in the female germline. We further show that, like Oxpecker , at least ten additional, structurally diverse, HP1D/rhino -derived daughter and "granddaughter" genes emerged during a short 15-million year period of Drosophila evolution. These young paralogs are transcribed primarily in germline tissues, where the genetic conflict between host genomes and TEs plays out. Our findings suggest that gene family expansion is an underappreciated yet potent evolutionary mechanism of genome defense diversification.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    miRNA-21 is dysregulated in response to vein grafting in multiple models and genetic ablation in mice attenuates neointima formation (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-08
    Description: Aims The long-term failure of autologous saphenous vein bypass grafts due to neointimal thickening is a major clinical burden. Identifying novel strategies to prevent neointimal thickening is important. Thus, this study aimed to identify microRNAs (miRNAs) that are dysregulated during neointimal formation and determine their pathophysiological relevance following miRNA manipulation. Methods and results We undertook a microarray approach to identify dysregulated miRNAs following engraftment in an interpositional porcine graft model. These profiling experiments identified a number of miRNAs which were dysregulated following engraftment. miR-21 levels were substantially elevated following engraftment and these results were confirmed by quantitative real-time PCR in mouse, pig, and human models of vein graft neointimal formation. Genetic ablation of miR-21 in mice or grafted veins dramatically reduced neointimal formation in a mouse model of vein grafting. Furthermore, pharmacological knockdown of miR-21 in human veins resulted in target gene de-repression and a significant reduction in neointimal formation. Conclusion This is the first report demonstrating that miR-21 plays a pathological role in vein graft failure. Furthermore, we also provided evidence that knockdown of miR-21 has therapeutic potential for the prevention of pathological vein graft remodelling.
    Print ISSN: 0195-668X
    Electronic ISSN: 1522-9645
    Topics: Medicine
    Published by Oxford University Press
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  • 3
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    The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-06
    Description: High-throughput data production technologies, particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Self-organizing and stochastic behaviors during the regeneration of hair stem cells (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-04-30
    Description: Stem cells cycle through active and quiescent states. Large populations of stem cells in an organ may cycle randomly or in a coordinated manner. Although stem cell cycling within single hair follicles has been studied, less is known about regenerative behavior in a hair follicle population. By combining predictive mathematical modeling with in vivo studies in mice and rabbits, we show that a follicle progresses through cycling stages by continuous integration of inputs from intrinsic follicular and extrinsic environmental signals based on universal patterning principles. Signaling from the WNT/bone morphogenetic protein activator/inhibitor pair is coopted to mediate interactions among follicles in the population. This regenerative strategy is robust and versatile because relative activator/inhibitor strengths can be modulated easily, adapting the organism to different physiological and evolutionary needs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3321266/" 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/PMC3321266/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Plikus, Maksim V -- Baker, Ruth E -- Chen, Chih-Chiang -- Fare, Clyde -- de la Cruz, Damon -- Andl, Thomas -- Maini, Philip K -- Millar, Sarah E -- Widelitz, Randall -- Chuong, Cheng-Ming -- AR47364/AR/NIAMS NIH HHS/ -- AR60306/AR/NIAMS NIH HHS/ -- R01 AR042177/AR/NIAMS NIH HHS/ -- R01 AR042177-17/AR/NIAMS NIH HHS/ -- R01 AR042177-18/AR/NIAMS NIH HHS/ -- R01 AR060306/AR/NIAMS NIH HHS/ -- R01 AR060306-02/AR/NIAMS NIH HHS/ -- R01 AR060306-03/AR/NIAMS NIH HHS/ -- R01-AR42177/AR/NIAMS NIH HHS/ -- R01-AR47709/AR/NIAMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Apr 29;332(6029):586-9. doi: 10.1126/science.1201647.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, University of Southern California (USC), Los Angeles, CA 90033, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21527712" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bone Morphogenetic Proteins/*metabolism ; Computer Simulation ; Hair Follicle/*cytology/*growth & development/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Models, Biological ; Rabbits ; *Regeneration ; *Signal Transduction ; Stem Cells/*physiology ; Stochastic Processes ; Wnt Proteins/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    CLIMATE ECONOMICS. Opportunities for advances in climate change economics (2016)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2016-04-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burke, M -- Craxton, M -- Kolstad, C D -- Onda, C -- Allcott, H -- Baker, E -- Barrage, L -- Carson, R -- Gillingham, K -- Graff-Zivin, J -- Greenstone, M -- Hallegatte, S -- Hanemann, W M -- Heal, G -- Hsiang, S -- Jones, B -- Kelly, D L -- Kopp, R -- Kotchen, M -- Mendelsohn, R -- Meng, K -- Metcalf, G -- Moreno-Cruz, J -- Pindyck, R -- Rose, S -- Rudik, I -- Stock, J -- Tol, R S J -- New York, N.Y. -- Science. 2016 Apr 15;352(6283):292-3. doi: 10.1126/science.aad9634. Epub 2016 Apr 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Stanford University, Stanford, CA, USA. ; Stanford University, Stanford, CA, USA. ckolstad@stanford.edu. ; New York University, New York, NY, USA. ; University of Massachusetts, Amherst, MA, USA. ; Brown University, Providence, RI, USA. ; University of California, San Diego, CA, USA. ; Yale University, New Haven, CT, USA. ; University of Chicago, Chicago, IL, USA. ; World Bank, Washington, DC, USA. ; Arizona State University, Tempe, AZ, USA. ; Columbia University, New York, NY, USA. ; University of California, Berkeley, CA, USA. ; Northwestern University, Evanston, IL, USA. ; University of Miami, Coral Gables, FL, USA. ; Resources for the Future, Washington, DC, USA. ; University of California, Santa Barbara, CA, USA. ; Tufts University, Medford, MA, USA. ; Georgia Institute of Technology, Atlanta, GA, USA. ; Massachusetts Institute of Technology, Cambridge, MA, USA. ; Electric Power Research Institute, Palo Alto, CA, USA. ; Iowa State University, Ames, IA, USA. ; Harvard University, Cambridge, MA, USA. ; University of Sussex, Falmer, UK, and Vrije Universiteit Amsterdam, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27081055" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-07-19
    Description: Brown rot decay removes cellulose and hemicellulose from wood--residual lignin contributing up to 30% of forest soil carbon--and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the "dry rot" fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eastwood, Daniel C -- Floudas, Dimitrios -- Binder, Manfred -- Majcherczyk, Andrzej -- Schneider, Patrick -- Aerts, Andrea -- Asiegbu, Fred O -- Baker, Scott E -- Barry, Kerrie -- Bendiksby, Mika -- Blumentritt, Melanie -- Coutinho, Pedro M -- Cullen, Dan -- de Vries, Ronald P -- Gathman, Allen -- Goodell, Barry -- Henrissat, Bernard -- Ihrmark, Katarina -- Kauserud, Havard -- Kohler, Annegret -- LaButti, Kurt -- Lapidus, Alla -- Lavin, Jose L -- Lee, Yong-Hwan -- Lindquist, Erika -- Lilly, Walt -- Lucas, Susan -- Morin, Emmanuelle -- Murat, Claude -- Oguiza, Jose A -- Park, Jongsun -- Pisabarro, Antonio G -- Riley, Robert -- Rosling, Anna -- Salamov, Asaf -- Schmidt, Olaf -- Schmutz, Jeremy -- Skrede, Inger -- Stenlid, Jan -- Wiebenga, Ad -- Xie, Xinfeng -- Kues, Ursula -- Hibbett, David S -- Hoffmeister, Dirk -- Hogberg, Nils -- Martin, Francis -- Grigoriev, Igor V -- Watkinson, Sarah C -- New York, N.Y. -- Science. 2011 Aug 5;333(6043):762-5. doi: 10.1126/science.1205411. Epub 2011 Jul 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉College of Science, University of Swansea, Singleton Park, Swansea SA2 8PP, UK. d.c.eastwood@swansea.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21764756" target="_blank"〉PubMed〈/a〉
    Keywords: Angiosperms/microbiology ; Basidiomycota/classification/enzymology/*genetics/physiology ; *Biodiversity ; Biological Evolution ; Biota ; Cell Wall/*metabolism ; Coniferophyta/microbiology ; Coriolaceae/enzymology/genetics/physiology ; Gene Expression Profiling ; Genes, Fungal ; Genomics ; Lignin/metabolism ; Mycorrhizae/enzymology/*genetics/physiology ; Oxidoreductases/genetics/metabolism ; Peroxidases/genetics/metabolism ; Phylogeny ; Proteome ; Symbiosis ; Trees/*microbiology ; Wood/metabolism/*microbiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    CpG methylation differences between neurons and glia are highly conserved from mouse to human (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-09
    Description: Understanding epigenetic differences that distinguish neurons and glia is of fundamental importance to the nascent field of neuroepigenetics. A recent study used genome-wide bisulfite sequencing to survey differences in DNA methylation between these two cell types, in both humans and mice. That study minimized the importance of cell type-specific differences in CpG methylation, claiming these are restricted to localized genomic regions, and instead emphasized that widespread and highly conserved differences in non-CpG methylation distinguish neurons and glia. We reanalyzed the data from that study and came to markedly different conclusions. In particular, we found widespread cell type-specific differences in CpG methylation, with a genome-wide tendency for neuronal CpG-hypermethylation punctuated by regions of glia-specific hypermethylation. Alarmingly, our analysis indicated that the majority of genes identified by the primary study as exhibiting cell type-specific CpG methylation differences were misclassified. To verify the accuracy of our analysis, we isolated neuronal and glial DNA from mouse cortex and performed quantitative bisulfite pyrosequencing at nine loci. The pyrosequencing results corroborated our analysis, without exception. Most interestingly, we found that gene-associated neuron vs. glia CpG methylation differences are highly conserved across human and mouse, and are very likely to be functional. In addition to underscoring the importance of independent verification to confirm the conclusions of genome-wide epigenetic analyses, our data indicate that CpG methylation plays a major role in neuroepigenetics, and that the mouse is likely an excellent model in which to study the role of DNA methylation in human neurodevelopment and disease.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 8
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    Depleted Basaltic Lavas from the Proto-Iceland Plume, Central East Greenland (2012)
    Oxford University Press
    Details
    Publication Date: 2012-07-19
    Description: New geochemical and isotopic data are presented for volumetrically minor, depleted low-Ti basalts that occur in the Plateau Basalt succession of central East Greenland (CEG), formed during the initial stages of opening of the North Atlantic at 55 Ma. The basalts have mid-ocean ridge basalt (MORB)-like geochemistry (e.g. depleted light rare earth elements) and are distinct from the high-Ti lavas that dominate the sequence. Rare earth element geochemistry implies derivation from a source more depleted than the typical MORB source, and suggests polybaric melting and contributions from both spinel- and garnet-facies mantle. The low-Ti basalts have Sr–Nd–Pb–Hf isotopic characteristics that are similar to those of depleted magmas from Iceland (e.g. Theistareykir) and adjacent ridges (Kolbeinsey and Reykjanes) and distinct from global MORB (e.g. negative 207 Pb, and Hf and Nd isotope compositions that plot above the mantle reference line). Isotope and trace element data indicate the involvement of two depleted source components. One component has isotopic compositions similar to other depleted components identified in the North Atlantic and has high Rb/Zr and Ba/Nb. The second is isotopically less depleted with lower Rb/Zr and Ba/Nb. Small degrees of crustal contamination (〈 1%) by both amphibolitic and granulitic crust result in relatively large changes in isotopic composition ( c . 1% lower for 206 Pb/ 204 Pb and 0·1% higher for 87 Sr/ 86 Sr depending on the contaminant). Negative Nb suggests a MORB affinity for the low-Ti magmas; however, they are distinguished from global normal (N)-MORB on the basis of vertical deviations from the Northern Hemisphere Reference Line (negative 207 Pb and positive 208 Pb), and relative enrichments in Ba, Sr and Pb. The isotopic compositions of the low-Ti CEG basalts suggest correlation with modern depleted components beneath Iceland and adjacent ridges, considered to be derived from upper mantle sources polluted by the Iceland plume. However, small positive Pb peaks when normalized to MORB, and lower Nb distinguish the CEG low-Ti basalts from depleted Icelandic compositions. The lower Nb (〈 0) and 87 Sr/ 86 Sr, and suggestion of higher 206 Pb/ 204 Pb in crustally uncontaminated parental melts imply a closer affinity to compositions from the oceanic ridges surrounding Iceland (especially the Reykjanes Ridge), yet they are subtly distinct on the basis of available trace element data. We suggest that this depleted component was an integral part of the plume that melted primarily during the rapid lithospheric uplift and extension associated with continental break-up.
    Print ISSN: 0022-3530
    Electronic ISSN: 1460-2415
    Topics: Geosciences
    Published by Oxford University Press
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  • 9
    Electronic Resource
    Electronic Resource
    Hydrogen chemical ionization tandem mass spectrometry of metalloporphyrins (1984)
    s.l. : American Chemical Society
    Analytical chemistry 56 (1984), S. 2552-2556 
    Details
    ISSN: 1520-6882
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ac00277a063
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  • 10
    Electronic Resource
    Electronic Resource
    The reactions of ambident anions with an ambident electrophile (1968)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 90 (1968), S. 3800-3808 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja01016a037
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