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  • Nature Publishing Group (NPG)  (6)
  • 2010-2014  (6)
  • 1
    Publication Date: 2011-08-19
    Description: Latency and ongoing replication have both been proposed to explain the drug-insensitive human immunodeficiency virus (HIV) reservoir maintained during antiretroviral therapy. Here we explore a novel mechanism for ongoing HIV replication in the face of antiretroviral drugs. We propose a model whereby multiple infections per cell lead to reduced sensitivity to drugs without requiring drug-resistant mutations, and experimentally validate the model using multiple infections per cell by cell-free HIV in the presence of the drug tenofovir. We then examine the drug sensitivity of cell-to-cell spread of HIV, a mode of HIV transmission that can lead to multiple infection events per target cell. Infections originating from cell-free virus decrease strongly in the presence of antiretrovirals tenofovir and efavirenz whereas infections involving cell-to-cell spread are markedly less sensitive to the drugs. The reduction in sensitivity is sufficient to keep multiple rounds of infection from terminating in the presence of drugs. We examine replication from cell-to-cell spread in the presence of clinical drug concentrations using a stochastic infection model and find that replication is intermittent, without substantial accumulation of mutations. If cell-to-cell spread has the same properties in vivo, it may have adverse consequences for the immune system, lead to therapy failure in individuals with risk factors, and potentially contribute to viral persistence and hence be a barrier to curing HIV infection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sigal, Alex -- Kim, Jocelyn T -- Balazs, Alejandro B -- Dekel, Erez -- Mayo, Avi -- Milo, Ron -- Baltimore, David -- HHSN266200500035C/PHS HHS/ -- T32 AI089398/AI/NIAID NIH HHS/ -- England -- Nature. 2011 Aug 17;477(7362):95-8. doi: 10.1038/nature10347.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21849975" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/analogs & derivatives/pharmacology ; Anti-Retroviral Agents/*pharmacology ; Cell Line ; Drug Resistance, Viral/physiology ; HEK293 Cells ; HIV Infections/transmission/*virology ; HIV-1/drug effects/*physiology ; Humans ; Models, Biological ; Organophosphonates/pharmacology ; Tenofovir ; Virus Replication/drug effects/*physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2014-04-18
    Description: The geochemistry of Martian meteorites provides a wealth of information about the solid planet and the surface and atmospheric processes that occurred on Mars. The degree to which Martian magmas may have assimilated crustal material, thus altering the geochemical signatures acquired from their mantle sources, is unclear. This issue features prominently in efforts to understand whether the source of light rare-earth elements in enriched shergottites lies in crustal material incorporated into melts or in mixing between enriched and depleted mantle reservoirs. Sulphur isotope systematics offer insight into some aspects of crustal assimilation. The presence of igneous sulphides in Martian meteorites with sulphur isotope signatures indicative of mass-independent fractionation suggests the assimilation of sulphur both during passage of magmas through the crust of Mars and at sites of emplacement. Here we report isotopic analyses of 40 Martian meteorites that represent more than half of the distinct known Martian meteorites, including 30 shergottites (28 plus 2 pairs, where pairs are separate fragments of a single meteorite), 8 nakhlites (5 plus 3 pairs), Allan Hills 84001 and Chassigny. Our data provide strong evidence that assimilation of sulphur into Martian magmas was a common occurrence throughout much of the planet's history. The signature of mass-independent fractionation observed also indicates that the atmospheric imprint of photochemical processing preserved in Martian meteoritic sulphide and sulphate is distinct from that observed in terrestrial analogues, suggesting fundamental differences between the dominant sulphur chemistry in the atmosphere of Mars and that in the atmosphere of Earth.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Franz, Heather B -- Kim, Sang-Tae -- Farquhar, James -- Day, James M D -- Economos, Rita C -- McKeegan, Kevin D -- Schmitt, Axel K -- Irving, Anthony J -- Hoek, Joost -- Dottin, James 3rd -- England -- Nature. 2014 Apr 17;508(7496):364-8. doi: 10.1038/nature13175.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Center for Research and Exploration in Space Science and Technology, NASA Goddard Space Flight Center, Greenbelt, Maryland 20771, USA [2] Department of Geology and Earth System Science Interdisciplinary Center, University of Maryland, College Park, Maryland 20742, USA. ; School of Geography and Earth Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada. ; Department of Geology and Earth System Science Interdisciplinary Center, University of Maryland, College Park, Maryland 20742, USA. ; Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, USA. ; Department of Earth and Space Sciences, University of California, Los Angeles, California 90095, USA. ; Department of Earth and Space Sciences, University of Washington, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24740066" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2014-11-20
    Description: Oxidative stress promotes genomic instability and human diseases. A common oxidized nucleoside is 8-oxo-7,8-dihydro-2'-deoxyguanosine, which is found both in DNA (8-oxo-G) and as a free nucleotide (8-oxo-dGTP). Nucleotide pools are especially vulnerable to oxidative damage. Therefore cells encode an enzyme (MutT/MTH1) that removes free oxidized nucleotides. This cleansing function is required for cancer cell survival and to modulate Escherichia coli antibiotic sensitivity in a DNA polymerase (pol)-dependent manner. How polymerases discriminate between damaged and non-damaged nucleotides is not well understood. This analysis is essential given the role of oxidized nucleotides in mutagenesis, cancer therapeutics, and bacterial antibiotics. Even with cellular sanitizing activities, nucleotide pools contain enough 8-oxo-dGTP to promote mutagenesis. This arises from the dual coding potential where 8-oxo-dGTP(anti) base pairs with cytosine and 8-oxo-dGTP(syn) uses its Hoogsteen edge to base pair with adenine. Here we use time-lapse crystallography to follow 8-oxo-dGTP insertion opposite adenine or cytosine with human pol beta, to reveal that insertion is accommodated in either the syn- or anti-conformation, respectively. For 8-oxo-dGTP(anti) insertion, a novel divalent metal relieves repulsive interactions between the adducted guanine base and the triphosphate of the oxidized nucleotide. With either templating base, hydrogen-bonding interactions between the bases are lost as the enzyme reopens after catalysis, leading to a cytotoxic nicked DNA repair intermediate. Combining structural snapshots with kinetic and computational analysis reveals how 8-oxo-dGTP uses charge modulation during insertion that can lead to a blocked DNA repair intermediate.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4312183/" 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/PMC4312183/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Freudenthal, Bret D -- Beard, William A -- Perera, Lalith -- Shock, David D -- Kim, Taejin -- Schlick, Tamar -- Wilson, Samuel H -- 1U19CA105010/CA/NCI NIH HHS/ -- U19 CA177547/CA/NCI NIH HHS/ -- Z01-ES050158/ES/NIEHS NIH HHS/ -- Z01-ES050161/ES/NIEHS NIH HHS/ -- ZIA ES050158-18/Intramural NIH HHS/ -- ZIA ES050159-18/Intramural NIH HHS/ -- ZIC-ES043010/ES/NIEHS NIH HHS/ -- England -- Nature. 2015 Jan 29;517(7536):635-9. doi: 10.1038/nature13886. Epub 2014 Nov 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, PO Box 12233, Research Triangle Park, North Carolina 27709-2233, USA. ; 1] Department of Chemistry, New York University, and NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 10th Floor Silver Center, 100 Washington Square East, New York, New York 10003, USA [2] Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, New York 10012, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25409153" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/chemistry/metabolism ; Base Pairing ; Catalytic Domain ; Crystallography, X-Ray ; Cytosine/chemistry/metabolism ; Cytotoxins/chemistry/*metabolism/toxicity ; DNA/biosynthesis/chemistry ; *DNA Damage ; DNA Polymerase beta/*chemistry/*metabolism ; DNA Repair ; DNA Replication ; Deoxyguanine Nucleotides/chemistry/*metabolism/*toxicity ; Guanine/analogs & derivatives/chemistry/metabolism ; Humans ; Hydrogen Bonding ; Kinetics ; Models, Molecular ; Molecular Conformation ; *Mutagenesis ; Neoplasms/enzymology/genetics ; Oxidation-Reduction ; Oxidative Stress ; Static Electricity ; Substrate Specificity ; Time Factors
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  • 4
    Publication Date: 2012-10-05
    Description: Grain boundaries in graphene are formed by the joining of islands during the initial growth stage, and these boundaries govern transport properties and related device performance. Although information on the atomic rearrangement at graphene grain boundaries can be obtained using transmission electron microscopy and scanning tunnelling microscopy, large-scale information regarding the distribution of graphene grain boundaries is not easily accessible. Here we use optical microscopy to observe the grain boundaries of large-area graphene (grown on copper foil) directly, without transfer of the graphene. This imaging technique was realized by selectively oxidizing the underlying copper foil through graphene grain boundaries functionalized with O and OH radicals generated by ultraviolet irradiation under moisture-rich ambient conditions: selective diffusion of oxygen radicals through OH-functionalized defect sites was demonstrated by density functional calculations. The sheet resistance of large-area graphene decreased as the graphene grain sizes increased, but no strong correlation with the grain size of the copper was revealed, in contrast to a previous report. Furthermore, the influence of graphene grain boundaries on crack propagation (initialized by bending) and termination was clearly visualized using our technique. Our approach can be used as a simple protocol for evaluating the grain boundaries of other two-dimensional layered structures, such as boron nitride and exfoliated clays.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Duong, Dinh Loc -- Han, Gang Hee -- Lee, Seung Mi -- Gunes, Fethullah -- Kim, Eun Sung -- Kim, Sung Tae -- Kim, Heetae -- Ta, Quang Huy -- So, Kang Pyo -- Yoon, Seok Jun -- Chae, Seung Jin -- Jo, Young Woo -- Park, Min Ho -- Chae, Sang Hoon -- Lim, Seong Chu -- Choi, Jae Young -- Lee, Young Hee -- England -- Nature. 2012 Oct 11;490(7419):235-9. doi: 10.1038/nature11562. Epub 2012 Oct 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon 440-746, South Korea.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23034653" target="_blank"〉PubMed〈/a〉
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  • 5
    Publication Date: 2011-11-19
    Description: As silicon-based electronics approach the limit of improvements to performance and capacity through dimensional scaling, attention in the semiconductor field has turned to graphene, a single layer of carbon atoms arranged in a honeycomb lattice. Its high mobility of charge carriers (electrons and holes) could lead to its use in the next generation of high-performance devices. Graphene is unlikely to replace silicon completely, however, because of the poor on/off current ratio resulting from its zero bandgap. But it could be used to improve silicon-based devices, in particular in high-speed electronics and optical modulators.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Kinam -- Choi, Jae-Young -- Kim, Taek -- Cho, Seong-Ho -- Chung, Hyun-Jong -- England -- Nature. 2011 Nov 16;479(7373):338-44. doi: 10.1038/nature10680.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Samsung Advanced Institute of Technology (SAIT), Samsung Electronics, Yongin-Si, Gyeonggi-Do 446-712, South Korea. kn_kim@samsung.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22094694" target="_blank"〉PubMed〈/a〉
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  • 6
    Publication Date: 2013-02-01
    Description: Logic devices based on magnetism show promise for increasing computational efficiency while decreasing consumed power. They offer zero quiescent power and yet combine novel functions such as programmable logic operation and non-volatile built-in memory. However, practical efforts to adapt a magnetic device to logic suffer from a low signal-to-noise ratio and other performance attributes that are not adequate for logic gates. Rather than exploiting magnetoresistive effects that result from spin-dependent transport of carriers, we have approached the development of a magnetic logic device in a different way: we use the phenomenon of large magnetoresistance found in non-magnetic semiconductors in high electric fields. Here we report a device showing a strong diode characteristic that is highly sensitive to both the sign and the magnitude of an external magnetic field, offering a reversible change between two different characteristic states by the application of a magnetic field. This feature results from magnetic control of carrier generation and recombination in an InSb p-n bilayer channel. Simple circuits combining such elementary devices are fabricated and tested, and Boolean logic functions including AND, OR, NAND and NOR are performed. They are programmed dynamically by external electric or magnetic signals, demonstrating magnetic-field-controlled semiconductor reconfigurable logic at room temperature. This magnetic technology permits a new kind of spintronic device, characterized as a current switch rather than a voltage switch, and provides a simple and compact platform for non-volatile reconfigurable logic devices.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Joo, Sungjung -- Kim, Taeyueb -- Shin, Sang Hoon -- Lim, Ju Young -- Hong, Jinki -- Song, Jin Dong -- Chang, Joonyeon -- Lee, Hyun-Woo -- Rhie, Kungwon -- Han, Suk Hee -- Shin, Kyung-Ho -- Johnson, Mark -- England -- Nature. 2013 Feb 7;494(7435):72-6. doi: 10.1038/nature11817. Epub 2013 Jan 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Spin Convergence Research Center, KIST, Seoul 130-650, South Korea.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23364687" target="_blank"〉PubMed〈/a〉
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