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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.


  
Microbial evolutionary strategies in a dynamic ocean 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2020, 117 (11) : 5943-5948
作者:  Walworth, Nathan G.;  Zakem, Emily J.;  Dunne, John P.;  Collins, Sinead;  Levine, Naomi M.
收藏  |  浏览/下载:10/0  |  提交时间:2020/05/13
evolution  marine microbes  fluctuating environment  adaptation timescales  advection  
A plant genetic network for preventing dysbiosis in the phyllosphere 期刊论文
NATURE, 2020, 580 (7805) : 653-+
作者:  van den Brink, Susanne C.;  Alemany, Anna;  van Batenburg, Vincent;  Moris, Naomi;  Blotenburg, Marloes;  Vivie, Judith;  Baillie-Johnson, Peter;  Nichols, Jennifer;  Sonnen, Katharina F.;  Martinez Arias, Alfonso;  van Oudenaarden, Alexander
收藏  |  浏览/下载:59/0  |  提交时间:2020/07/03

Mutations in genes involved in immune signalling and vesicle trafficking cause defects in the leaf microbiome of Arabidopsis thaliana that result in damage to leaf tissues, suggesting mechanisms by which terrestrial plants control the level and diversity of endophytic phyllosphere microbiota.


The aboveground parts of terrestrial plants, collectively called the phyllosphere, have a key role in the global balance of atmospheric carbon dioxide and oxygen. The phyllosphere represents one of the most abundant habitats for microbiota colonization. Whether and how plants control phyllosphere microbiota to ensure plant health is not well understood. Here we show that the Arabidopsis quadruple mutant (min7 fls2 efr cerk1  hereafter, mfec)(1), simultaneously defective in pattern-triggered immunity and the MIN7 vesicle-trafficking pathway, or a constitutively activated cell death1 (cad1) mutant, carrying a S205F mutation in a membrane-attack-complex/perforin (MACPF)-domain protein, harbour altered endophytic phyllosphere microbiota and display leaf-tissue damage associated with dysbiosis. The Shannon diversity index and the relative abundance of Firmicutes were markedly reduced, whereas Proteobacteria were enriched in the mfec and cad1(S205F) mutants, bearing cross-kingdom resemblance to some aspects of the dysbiosis that occurs in human inflammatory bowel disease. Bacterial community transplantation experiments demonstrated a causal role of a properly assembled leaf bacterial community in phyllosphere health. Pattern-triggered immune signalling, MIN7 and CAD1 are found in major land plant lineages and are probably key components of a genetic network through which terrestrial plants control the level and nurture the diversity of endophytic phyllosphere microbiota for survival and health in a microorganism-rich environment.


  
Performance-limiting nanoscale trap clusters at grain junctions in halide perovskites 期刊论文
NATURE, 2020, 580 (7803) : 360-+
作者:  van den Brink, Susanne C.;  Alemany, Anna;  van Batenburg, Vincent;  Moris, Naomi;  Blotenburg, Marloes;  Vivie, Judith;  Baillie-Johnson, Peter;  Nichols, Jennifer;  Sonnen, Katharina F.;  Arias, Alfonso;  van Oudenaarden, Alexander
收藏  |  浏览/下载:27/0  |  提交时间:2020/07/03

Halide perovskite materials have promising performance characteristics for low-cost optoelectronic applications. Photovoltaic devices fabricated from perovskite absorbers have reached power conversion efficiencies above 25 per cent in single-junction devices and 28 per cent in tandem devices(1,2). This strong performance (albeit below the practical limits of about 30 per cent and 35 per cent, respectively(3)) is surprising in thin films processed from solution at low-temperature, a method that generally produces abundant crystalline defects(4). Although point defects often induce only shallow electronic states in the perovskite bandgap that do not affect performance(5), perovskite devices still have many states deep within the bandgap that trap charge carriers and cause them to recombine non-radiatively. These deep trap states thus induce local variations in photoluminescence and limit the device performance(6). The origin and distribution of these trap states are unknown, but they have been associated with light-induced halide segregation in mixed-halide perovskite compositions(7) and with local strain(8), both of which make devices less stable(9). Here we use photoemission electron microscopy to image the trap distribution in state-of-the-art halide perovskite films. Instead of a relatively uniform distribution within regions of poor photoluminescence efficiency, we observe discrete, nanoscale trap clusters. By correlating microscopy measurements with scanning electron analytical techniques, we find that these trap clusters appear at the interfaces between crystallographically and compositionally distinct entities. Finally, by generating time-resolved photoemission sequences of the photo-excited carrier trapping process(10,11), we reveal a hole-trapping character with the kinetics limited by diffusion of holes to the local trap clusters. Our approach shows that managing structure and composition on the nanoscale will be essential for optimal performance of halide perovskite devices.


  
gamma delta T cells and adipocyte IL-17RC control fat innervation and thermogenesis 期刊论文
NATURE, 2020, 578 (7796) : 610-+
作者:  Staus, Dean P.;  Hu, Hongli;  Robertson, Michael J.;  Kleinhenz, Alissa L. W.;  Wingler, Laura M.;  Capel, William D.;  Latorraca, Naomi R.;  Lefkowitz, Robert J.;  Skiniotis, Georgios
收藏  |  浏览/下载:42/0  |  提交时间:2020/07/03

V gamma 6(+) V delta 1(+) gamma delta T cells control tolerance to cold by activating adipocyte IL-17RC and promoting sympathetic innervation of thermogenic adipose tissue in mice.


The sympathetic nervous system innervates peripheral organs to regulate their function and maintain homeostasis, whereas target cells also produce neurotrophic factors to promote sympathetic innervation(1,2). The molecular basis of this bi-directional communication remains to be fully determined. Here we use thermogenic adipose tissue from mice as a model system to show that T cells, specifically gamma delta T cells, have a crucial role in promoting sympathetic innervation, at least in part by driving the expression of TGF beta 1 in parenchymal cells via the IL-17 receptor C (IL-17RC). Ablation of IL-17RC specifically in adipose tissue reduces expression of TGF beta 1 in adipocytes, impairs local sympathetic innervation and causes obesity and other metabolic phenotypes that are consistent with defective thermogenesis  innervation can be fully rescued by restoring TGF beta 1 expression. Ablating gamma delta tau cells and the IL-17RC signalling pathway also impairs sympathetic innervation in other tissues such as salivary glands. These findings demonstrate coordination between T cells and parenchymal cells to regulate sympathetic innervation.


  
The atmosphere of Mars as observed by InSight 期刊论文
NATURE GEOSCIENCE, 2020, 13 (3) : 190-+
作者:  Banfield, Don;  Spiga, Aymeric;  Newman, Claire;  Forget, Francois;  Lemmon, Mark;  Lorenz, Ralph;  Murdoch, Naomi;  Viudez-Moreiras, Daniel;  Pla-Garcia, Jorge;  Garcia, Raphael F.;  Lognonne, Philippe;  Karatekin, Ozgur;  Perrin, Clement;  Martire, Leo;  Teanby, Nicholas;  Hove, Bart Van;  Maki, Justin N.;  Kenda, Balthasar;  Mueller, Nils T.;  Rodriguez, Sebastien;  Kawamura, Taichi;  McClean, John B.;  Stott, Alexander E.;  Charalambous, Constantinos;  Millour, Ehouarn;  Johnson, Catherine L.;  Mittelholz, Anna;  Maattanen, Anni;  Lewis, Stephen R.;  Clinton, John;  Staehler, Simon C.;  Ceylan, Savas;  Giardini, Domenico;  Warren, Tristram;  Pike, William T.;  Daubar, Ingrid;  Golombek, Matthew;  Rolland, Lucie;  Widmer-Schnidrig, Rudolf;  Mimoun, David;  Beucler, Eric;  Jacob, Alice;  Lucas, Antoine;  Baker, Mariah;  Ansan, Veronique;  Hurst, Kenneth;  Mora-Sotomayor, Luis;  Navarro, Sara;  Torres, Josefina;  Lepinette, Alain;  Molina, Antonio;  Marin-Jimenez, Mercedes;  Gomez-Elvira, Javier;  Peinado, Veronica;  Rodriguez-Manfredi, Jose-Antonio;  Carcich, Brian T.;  Sackett, Stephen;  Russell, Christopher T.;  Spohn, Tilman;  Smrekar, Suzanne E.;  Banerdt, W. Bruce
收藏  |  浏览/下载:14/0  |  提交时间:2020/05/13
Initial results from the InSight mission on Mars 期刊论文
NATURE GEOSCIENCE, 2020, 13 (3) : 183-+
作者:  Banerdt, W. Bruce;  Smrekar, Suzanne E.;  Banfield, Don;  Giardini, Domenico;  Golombek, Matthew;  Johnson, Catherine L.;  Lognonne, Philippe;  Spiga, Aymeric;  Spohn, Tilman;  Perrin, Clement;  Staehler, Simon C.;  Antonangeli, Daniele;  Asmar, Sami;  Beghein, Caroline;  Bowles, Neil;  Bozdag, Ebru;  Chi, Peter;  Christensen, Ulrich;  Clinton, John;  Collins, Gareth S.;  Daubar, Ingrid;  Dehant, Veronique;  Drilleau, Melanie;  Fillingim, Matthew;  Folkner, William;  Garcia, Raphael F.;  Garvin, Jim;  Grant, John;  Grott, Matthias;  Grygorczuk, Jerzy;  Hudson, Troy;  Irving, Jessica C. E.;  Kargl, Guenter;  Kawamura, Taichi;  Kedar, Sharon;  King, Scott;  Knapmeyer-Endrun, Brigitte;  Knapmeyer, Martin;  Lemmon, Mark;  Lorenz, Ralph;  Maki, Justin N.;  Margerin, Ludovic;  McLennan, Scott M.;  Michaut, Chloe;  Mimoun, David;  Mittelholz, Anna;  Mocquet, Antoine;  Morgan, Paul;  Mueller, Nils T.;  Murdoch, Naomi;  Nagihara, Seiichi;  Newman, Claire;  Nimmo, Francis;  Panning, Mark;  Pike, W. Thomas;  Plesa, Ana-Catalina;  Rodriguez, Sebastien;  Rodriguez-Manfredi, Jose Antonio;  Russell, Christopher T.;  Schmerr, Nicholas;  Siegler, Matt;  Stanley, Sabine;  Stutzmann, Eleanore;  Teanby, Nicholas;  Tromp, Jeroen;  Van Driel, Martin;  Warner, Nicholas;  Weber, Renee;  Wieczorek, Mark
收藏  |  浏览/下载:24/0  |  提交时间:2020/05/13
Automated radial synthesis of organic molecules 期刊论文
NATURE, 2020, 579 (7799) : 379-+
作者:  van den Brink, Susanne C.;  Alemany, Anna;  van Batenburg, Vincent;  Moris, Naomi;  Blotenburg, Marloes;  Vivie, Judith;  Baillie-Johnson, Peter;  Nichols, Jennifer;  Sonnen, Katharina F.;  Martinez Arias, Alfonso;  van Oudenaarden, Alexander
收藏  |  浏览/下载:16/0  |  提交时间:2020/07/03

An automated synthesis instrument comprising a series of continuous flow modules that are radially arranged around a central switching station can achieve both linear and convergent syntheses.


Automated synthesis platforms accelerate and simplify the preparation of molecules by removing the physical barriers to organic synthesis. This provides unrestricted access to biopolymers and small molecules via reproducible and directly comparable chemical processes. Current automated multistep syntheses rely on either iterative(1-4) or linear processes(5-9), and require compromises in terms of versatility and the use of equipment. Here we report an approach towards the automated synthesis of small molecules, based on a series of continuous flow modules that are radially arranged around a central switching station. Using this approach, concise volumes can be exposed to any reaction conditions required for a desired transformation. Sequential, non-simultaneous reactions can be combined to perform multistep processes, enabling the use of variable flow rates, reuse of reactors under different conditions, and the storage of intermediates. This fully automated instrument is capable of both linear and convergent syntheses and does not require manual reconfiguration between different processes. The capabilities of this approach are demonstrated by performing optimizations and multistep syntheses of targets, varying concentrations via inline dilutions, exploring several strategies for the multistep synthesis of the anticonvulsant drug rufinamide(10), synthesizing eighteen compounds of two derivative libraries that are prepared using different reaction pathways and chemistries, and using the same reagents to perform metallaphotoredox carbon-nitrogen cross-couplings(11) in a photochemical module-all without instrument reconfiguration.


  
Electrically pumped topological laser with valley edge modes 期刊论文
NATURE, 2020, 578 (7794) : 246-+
作者:  Erickson, Peter;  van Asselt, Harro;  Koplow, Doug;  Lazarus, Michael;  Newell, Peter;  Oreskes, Naomi;  Supran, Geoffrey
收藏  |  浏览/下载:46/0  |  提交时间:2020/07/03

Quantum cascade lasers are compact, electrically pumped light sources in the technologically important mid-infrared and terahertz region of the electromagnetic spectrum(1,2). Recently, the concept of topology(3) has been expanded from condensed matter physics into photonics(4), giving rise to a new type of lasing(5-8) using topologically protected photonic modes that can efficiently bypass corners and defects(4). Previous demonstrations of topological lasers have required an external laser source for optical pumping and have operated in the conventional optical frequency regime(5-8). Here we demonstrate an electrically pumped terahertz quantum cascade laser based on topologically protected valley edge states(9-11). Unlike topological lasers that rely on large-scale features to impart topological protection, our compact design makes use of the valley degree of freedom in photonic crystals(10,11), analogous to two-dimensional gapped valleytronic materials(12). Lasing with regularly spaced emission peaks occurs in a sharp-cornered triangular cavity, even if perturbations are introduced into the underlying structure, owing to the existence of topologically protected valley edge states that circulate around the cavity without experiencing localization. We probe the properties of the topological lasing modes by adding different outcouplers to the topological cavity. The laser based on valley edge states may open routes to the practical use of topological protection in electrically driven laser sources.


  
Quantifying secondary transport at single-molecule resolution (vol 71, pg 124, 2020) 期刊论文
NATURE, 2020
作者:  Staus, Dean P.;  Hu, Hongli;  Robertson, Michael J.;  Kleinhenz, Alissa L. W.;  Wingler, Laura M.;  Capel, William D.;  Latorraca, Naomi R.;  Lefkowitz, Robert J.;  Skiniotis, Georgios
收藏  |  浏览/下载:16/0  |  提交时间:2020/07/03

An Amendment to this paper has been published and can be accessed via a link at the top of the paper.