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Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform 期刊论文
NATURE, 2020
作者:  Touat, Mehdi;  Li, Yvonne Y.;  Boynton, Adam N.;  Spurr, Liam F.;  Iorgulescu, J. Bryan;  Bohrson, Craig L.;  Cortes-Ciriano, Isidro;  Birzu, Cristina;  Geduldig, Jack E.;  Pelton, Kristine;  Lim-Fat, Mary Jane;  Pal, Sangita;  Ferrer-Luna, Ruben;  Ramkissoon, Shakti H.;  Dubois, Frank;  Bellamy, Charlotte;  Currimjee, Naomi;  Bonardi, Juliana;  Qian Kenin;  Ho, Patricia;  Malinowski, Seth;  Taquet, Leon;  Jones, Robert E.;  Shetty, Aniket;  Chow, Kin-Hoe;  Sharaf, Radwa;  Pavlick, Dean;  Albacker, Lee A.;  Younan, Nadia;  Baldini, Capucine;  Verreault, Maite;  Giry, Marine;  Guillerm, Erell;  Ammari, Samy;  Beuvon, Frederic;  Mokhtari, Karima;  Alentorn, Agusti;  Dehais, Caroline;  Houillier, Caroline;  Laigle-Donadey, Florence;  Psimaras, Dimitri;  Lee, Eudocia Q.;  Nayak, Lakshmi;  McFaline-Figueroa, J. Ricardo;  Carpentier, Alexandre;  Cornu, Philippe;  Capelle, Laurent;  Mathon, Bertrand;  Barnholtz-Sloan, Jill S.;  Chakravarti, Arnab;  Bi, Wenya Linda;  Chiocca, E. Antonio;  Fehnel, Katie Pricola;  Alexandrescu, Sanda;  Chi, Susan N.;  Haas-Kogan, Daphne;  Batchelor, Tracy T.;  Frampton, Garrett M.;  Alexander, Brian M.;  Huang, Raymond Y.;  Ligon, Azra H.;  Coulet, Florence;  Delattre, Jean-Yves;  Hoang-Xuan, Khe;  Meredith, David M.;  Santagata, Sandro;  Duval, Alex;  Sanson, Marc;  Cherniack, Andrew D.;  Wen, Patrick Y.;  Reardon, David A.;  Marabelle, Aurelien;  Park, Peter J.;  Idbaih, Ahmed;  Beroukhim, Rameen;  Bandopadhayay, Pratiti;  Bielle, Franck;  Ligon, Keith L.
收藏  |  浏览/下载:11/0  |  提交时间:2020/07/03

Reverse genetics has been an indispensable tool to gain insights into viral pathogenesis and vaccine development. The genomes of large RNA viruses, such as those from coronaviruses, are cumbersome to clone and manipulate inEscherichia coliowing to the size and occasional instability of the genome(1-3). Therefore, an alternative rapid and robust reverse-genetics platform for RNA viruses would benefit the research community. Here we show the full functionality of a yeast-based synthetic genomics platform to genetically reconstruct diverse RNA viruses, including members of theCoronaviridae,FlaviviridaeandPneumoviridaefamilies. Viral subgenomic fragments were generated using viral isolates, cloned viral DNA, clinical samples or synthetic DNA, and these fragments were then reassembled in one step inSaccharomyces cerevisiaeusing transformation-associated recombination cloning to maintain the genome as a yeast artificial chromosome. T7 RNA polymerase was then used to generate infectious RNA to rescue viable virus. Using this platform, we were able to engineer and generate chemically synthesized clones of the virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)(4), which has caused the recent pandemic of coronavirus disease (COVID-19), in only a week after receipt of the synthetic DNA fragments. The technical advance that we describe here facilitates rapid responses to emerging viruses as it enables the real-time generation and functional characterization of evolving RNA virus variants during an outbreak.


A yeast-based synthetic genomics platform is used to reconstruct and characterize large RNA viruses from synthetic DNA fragments  this technique will facilitate the rapid analysis of RNA viruses, such as SARS-CoV-2, during an outbreak.


  
A global assessment of Indigenous community engagement in climate research 期刊论文
ENVIRONMENTAL RESEARCH LETTERS, 2018, 13 (12)
作者:  David-Chavez, Dominique M.;  Gavin, Michael C.
收藏  |  浏览/下载:6/0  |  提交时间:2019/04/09
indigenous knowledge systems  climate research  community-based participatory research  indigenous research methods  research ethics  traditional ecological knowledge  transdisciplinary research  
Vision, voice, and the community landscape: The Missouri Place Stories pilot project 期刊论文
LANDSCAPE AND URBAN PLANNING, 2018, 173: 1-8
作者:  Gillette, Maris Boyd;  Hurley, Andrew
收藏  |  浏览/下载:6/0  |  提交时间:2019/04/09
Landscape  Urban planning  Neighborhood management  Community based research  Communalism  Urban greening  
Radiochemically-Supported Microbial Communities: A Potential Mechanism for Biocolloid Production of Importance to Actinide Transport 科技报告
来源:US Department of Energy (DOE). 出版年: 2014
作者:  Moser, Duane P;  Hamilton-Brehm, Scott D;  Fisher, Jenny C;  Bruckner, James C;  Kruger, Brittany;  Sackett, Joshua;  Russell, Charles E;  Onstott, Tullis C;  Czerwinski, Ken
收藏  |  浏览/下载:21/0  |  提交时间:2019/04/05
Due to the legacy of Cold War nuclear weapons testing  the Nevada National Security Site (NNSS  formerly known as the Nevada Test Site (NTS)) contains millions of Curies of radioactive contamination. Presented here is a summary of the results of the first comprehensive study of subsurface microbial communities of radioactive and nonradioactive aquifers at this site. To achieve the objectives of this project  cooperative actions between the Desert Research Institute (DRI)  the Nevada Field Office of the National Nuclear Security Administration (NNSA)  the Underground Test Area Activity (UGTA)  and contractors such as Navarro-Interra (NI)  were required. Ultimately  fluids from 17 boreholes and two water-filled tunnels were sampled (sometimes on multiple occasions and from multiple depths) from the NNSS  the adjacent Nevada Test and Training Range (NTTR)  and a reference hole in the Amargosa Valley near Death Valley. The sites sampled ranged from highly-radioactive nuclear device test cavities to uncontaminated perched and regional aquifers. Specific areas sampled included recharge  intermediate  and discharge zones of a 100  000-km2 internally-draining province  known as the Death Valley Regional Flow System (DVRFS)  which encompasses the entirety of the NNSS/NTTR and surrounding areas. Specific geological features sampled included: West Pahute and Ranier Mesas (recharge zone)  Yucca and Frenchman Flats (transitional zone)  and the Western edge of the Amargosa Valley near Death Valley (discharge zone). The original overarching question underlying the proposal supporting this work was stated as: Can radiochemically-produced substrates support indigenous microbial communities and subsequently stimulate biocolloid formation that can affect radionuclides in NNSS subsurface nuclear test/detonation sites? Radioactive and non-radioactive groundwater samples were thus characterized for physical parameters  aqueous geochemistry  and microbial communities using both DNA- and cultivation-based tools in an effort to understand the drivers of microbial community structure (including radioactivity) and microbial interactions with select radionuclides and other factors across the range of habitats surveyed.