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  • 1
    Publication Date: 2011-07-23
    Description: 5-methylcytosine (5mC) in DNA plays an important role in gene expression, genomic imprinting, and suppression of transposable elements. 5mC can be converted to 5-hydroxymethylcytosine (5hmC) by the Tet (ten eleven translocation) proteins. Here, we show that, in addition to 5hmC, the Tet proteins can generate 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) from 5mC in an enzymatic activity-dependent manner. Furthermore, we reveal the presence of 5fC and 5caC in genomic DNA of mouse embryonic stem cells and mouse organs. The genomic content of 5hmC, 5fC, and 5caC can be increased or reduced through overexpression or depletion of Tet proteins. Thus, we identify two previously unknown cytosine derivatives in genomic DNA as the products of Tet proteins. Our study raises the possibility that DNA demethylation may occur through Tet-catalyzed oxidation followed by decarboxylation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495246/" 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/PMC3495246/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ito, Shinsuke -- Shen, Li -- Dai, Qing -- Wu, Susan C -- Collins, Leonard B -- Swenberg, James A -- He, Chuan -- Zhang, Yi -- GM071440/GM/NIGMS NIH HHS/ -- GM68804/GM/NIGMS NIH HHS/ -- P30 ES010126/ES/NIEHS NIH HHS/ -- P30 ES010126-11/ES/NIEHS NIH HHS/ -- P30ES10126/ES/NIEHS NIH HHS/ -- P42 ES005948/ES/NIEHS NIH HHS/ -- P42 ES005948-17/ES/NIEHS NIH HHS/ -- P42ES5948/ES/NIEHS NIH HHS/ -- R01 GM068804/GM/NIGMS NIH HHS/ -- U01 DK089565/DK/NIDDK NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Sep 2;333(6047):1300-3. doi: 10.1126/science.1210597. Epub 2011 Jul 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7295, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21778364" target="_blank"〉PubMed〈/a〉
    Keywords: 5-Methylcytosine/*metabolism ; Animals ; Cell Line ; Cytosine/*analogs & derivatives/metabolism ; DNA/*metabolism ; DNA Methylation ; DNA-Binding Proteins/genetics/*metabolism ; Embryonic Stem Cells/metabolism ; Humans ; Mice ; Oxidation-Reduction ; Proto-Oncogene Proteins/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism
    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
    Publication Date: 2008-05-10
    Description: The identification of human artifacts at the early archaeological site of Monte Verde in southern Chile has raised questions of when and how people reached the tip of South America without leaving much other evidence in the New World. Remains of nine species of marine algae were recovered from hearths and other features at Monte Verde II, an upper occupational layer, and were directly dated between 14,220 and 13,980 calendar years before the present ( approximately 12,310 and 12,290 carbon-14 years ago). These findings support the archaeological interpretation of the site and indicate that the site's inhabitants used seaweed from distant beaches and estuarine environments for food and medicine. These data are consistent with the ideas that an early settlement of South America was along the Pacific coast and that seaweeds were important to the diet and health of early humans in the Americas.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dillehay, Tom D -- Ramirez, C -- Pino, M -- Collins, M B -- Rossen, J -- Pino-Navarro, J D -- New York, N.Y. -- Science. 2008 May 9;320(5877):784-6. doi: 10.1126/science.1156533.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Anthropology, Vanderbilt University, Nashville, TN 37265, USA. tom.d.dillehay@vanderbilt.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18467586" target="_blank"〉PubMed〈/a〉
    Keywords: Chile ; Diet ; *Emigration and Immigration ; *Eukaryota ; Food Supply ; History, Ancient ; Humans ; North America ; Oceans and Seas ; *Seaweed ; South America
    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
    Publication Date: 2011-03-26
    Description: Compelling archaeological evidence of an occupation older than Clovis (~12.8 to 13.1 thousand years ago) in North America is present at only a few sites, and the stone tool assemblages from these sites are small and varied. The Debra L. Friedkin site, Texas, contains an assemblage of 15,528 artifacts that define the Buttermilk Creek Complex, which stratigraphically underlies a Clovis assemblage and dates between ~13.2 and 15.5 thousand years ago. The Buttermilk Creek Complex confirms the emerging view that people occupied the Americas before Clovis and provides a large artifact assemblage to explore Clovis origins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Waters, Michael R -- Forman, Steven L -- Jennings, Thomas A -- Nordt, Lee C -- Driese, Steven G -- Feinberg, Joshua M -- Keene, Joshua L -- Halligan, Jessi -- Lindquist, Anna -- Pierson, James -- Hallmark, Charles T -- Collins, Michael B -- Wiederhold, James E -- New York, N.Y. -- Science. 2011 Mar 25;331(6024):1599-603. doi: 10.1126/science.1201855.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for the Study of the First Americans, Departments of Anthropology and Geography, Texas A&M University, College Station, TX 77843-4352, USA. mwaters@tamu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21436451" target="_blank"〉PubMed〈/a〉
    Keywords: Anthropology, Cultural/*history ; Archaeology ; Geologic Sediments ; History, Ancient ; Humans ; Texas
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2015-12-18
    Description: The Gorkha earthquake (magnitude 7.8) on 25 April 2015 and later aftershocks struck South Asia, killing ~9000 people and damaging a large region. Supported by a large campaign of responsive satellite data acquisitions over the earthquake disaster zone, our team undertook a satellite image survey of the earthquakes' induced geohazards in Nepal and China and an assessment of the geomorphic, tectonic, and lithologic controls on quake-induced landslides. Timely analysis and communication aided response and recovery and informed decision-makers. We mapped 4312 coseismic and postseismic landslides. We also surveyed 491 glacier lakes for earthquake damage but found only nine landslide-impacted lakes and no visible satellite evidence of outbursts. Landslide densities correlate with slope, peak ground acceleration, surface downdrop, and specific metamorphic lithologies and large plutonic intrusions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kargel, J S -- Leonard, G J -- Shugar, D H -- Haritashya, U K -- Bevington, A -- Fielding, E J -- Fujita, K -- Geertsema, M -- Miles, E S -- Steiner, J -- Anderson, E -- Bajracharya, S -- Bawden, G W -- Breashears, D F -- Byers, A -- Collins, B -- Dhital, M R -- Donnellan, A -- Evans, T L -- Geai, M L -- Glasscoe, M T -- Green, D -- Gurung, D R -- Heijenk, R -- Hilborn, A -- Hudnut, K -- Huyck, C -- Immerzeel, W W -- Liming, Jiang -- Jibson, R -- Kaab, A -- Khanal, N R -- Kirschbaum, D -- Kraaijenbrink, P D A -- Lamsal, D -- Shiyin, Liu -- Mingyang, Lv -- McKinney, D -- Nahirnick, N K -- Zhuotong, Nan -- Ojha, S -- Olsenholler, J -- Painter, T H -- Pleasants, M -- Pratima, K C -- Yuan, Q I -- Raup, B H -- Regmi, D -- Rounce, D R -- Sakai, A -- Donghui, Shangguan -- Shea, J M -- Shrestha, A B -- Shukla, A -- Stumm, D -- van der Kooij, M -- Voss, K -- Xin, Wang -- Weihs, B -- Wolfe, D -- Lizong, Wu -- Xiaojun, Yao -- Yoder, M R -- Young, N -- New York, N.Y. -- Science. 2016 Jan 8;351(6269):aac8353. doi: 10.1126/science.aac8353. Epub 2015 Dec 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Hydrology and Water Resources, University of Arizona, Tucson, AZ, USA. kargel@hwr.arizona.edu dshugar@uw.edu uharitashya1@udayton.edu. ; Department of Hydrology and Water Resources, University of Arizona, Tucson, AZ, USA. ; School of Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, WA, USA. kargel@hwr.arizona.edu dshugar@uw.edu uharitashya1@udayton.edu. ; Department of Geology, University of Dayton, Dayton, OH, USA. kargel@hwr.arizona.edu dshugar@uw.edu uharitashya1@udayton.edu. ; Ministry of Forests, Lands and Natural Resource Operations, Prince George, BC, Canada. ; Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA. ; Graduate School of Environmental Studies, Nagoya University, Nagoya, Japan. ; Scott Polar Research Institute, University of Cambridge, Cambridge, UK. ; Institute of Environmental Engineering, Federal Institute of Technology-ETH, Zurich, Switzerland. ; NASA Marshall Space Flight Center, Huntsville, AL, USA. ; International Centre for Integrated Mountain Development, Kathmandu, Nepal. ; NASA Headquarters, Washington, DC, USA. ; GlacierWorks, Marblehead, MA, USA. ; The Mountain Institute, Elkins, WV, USA. ; U.S. Geological Survey, Menlo Park, CA, USA. ; Central Department of Geology, Tribhuvan University, Kirtipur, Kathmandu, Nepal. ; Department of Geography, University of Victoria, Victoria, BC, Canada. ; CVA Engineering, Suresnes, France. ; Earthquake Science Center, U.S. Geological Survey, Pasadena, CA, USA. ; ImageCat, Long Beach, CA, USA. ; Faculty of Geosciences, Utrecht University, Utrecht, Netherlands. ; State Key Laboratory of Geodesy and Earth's Dynamics, Institute of Geodesy and Geophysics, Chinese Academy of Sciences, Wuhan, Hubei Province, China. ; U.S. Geological Survey, Golden, CO, USA. ; Department of Geosciences, University of Oslo, Blindern, Oslo, Norway. ; Hydrological Sciences Laboratory, NASA Goddard Space Flight Center, Greenbelt, MD, USA. ; Cold and Arid Regions of Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, China. ; School of Earth Sciences and Engineering, Nanjing University, Nanjing, China. ; Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX, USA. ; School of Geography Science, Nanjing Normal University, Nanjing, China. ; Department of Geography, Texas A&M University, College Station, TX, USA. ; Department of Geology, University of Dayton, Dayton, OH, USA. ; Arizona Remote Sensing Center, School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA. ; National Snow and Ice Data Center, University of Colorado, Boulder, CO, USA. ; Himalayan Research Center, Kathmandu, Nepal. ; Environmental and Water Resources Engineering, University of Texas at Austin, Austin, TX, USA. ; Wadia Institute of Himalayan Geology, Dehradun, India. ; MacDonald Dettwiler and Associates-GSI, Ottawa, Ontario, Canada. ; Department of Geography, University of California, Santa Barbara, Santa Barbara, CA, USA. ; College of Architecture and Urban Planning, Hunan University of Science and Technology, Xiangtan, China. ; Geography Department, Kansas State University, Manhattan, KS, USA. ; Global Land Ice Measurements from Space (GLIMS) Steward, Alaska Region, Anchorage, AK, USA. ; College of Geographical Science and Environment, Northwest Normal University, China. ; Department of Physics, University of California, Davis, Davis, CA, USA. ; Antarctic Climate and Ecosystems Cooperative Research Centre, University of Tasmania, Hobart, TAS, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26676355" target="_blank"〉PubMed〈/a〉
    Keywords: Disasters/*prevention & control ; Earthquakes/*mortality ; Environmental Monitoring/*methods ; Floods ; Humans ; Lakes ; Landslides/*mortality ; Nepal ; Safety Management/*methods ; Satellite Imagery
    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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