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Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms 期刊论文
Science, 2020
作者:  David E. Gordon;  Joseph Hiatt;  Mehdi Bouhaddou;  Veronica V. Rezelj;  Svenja Ulferts;  Hannes Braberg;  Alexander S. Jureka;  Kirsten Obernier;  Jeffrey Z. Guo;  Jyoti Batra;  Robyn M. Kaake;  Andrew R. Weckstein;  Tristan W. Owens;  Meghna Gupta;  Sergei Pourmal;  Erron W. Titus;  Merve Cakir;  Margaret Soucheray;  Michael McGregor;  Zeynep Cakir;  Gwendolyn Jang;  Matthew J. O’Meara;  Tia A. Tummino;  Ziyang Zhang;  Helene Foussard;  Ajda Rojc;  Yuan Zhou;  Dmitry Kuchenov;  Ruth Hüttenhain;  Jiewei Xu;  Manon Eckhardt;  Danielle L. Swaney;  Jacqueline M. Fabius;  Manisha Ummadi;  Beril Tutuncuoglu;  Ujjwal Rathore;  Maya Modak;  Paige Haas;  Kelsey M. Haas;  Zun Zar Chi Naing;  Ernst H. Pulido;  Ying Shi;  Inigo Barrio-Hernandez;  Danish Memon;  Eirini Petsalaki;  Alistair Dunham;  Miguel Correa Marrero;  David Burke;  Cassandra Koh;  Thomas Vallet;  Jesus A. Silvas;  Caleigh M. Azumaya;  Christian Billesbølle;  Axel F. Brilot;  Melody G. Campbell;  Amy Diallo;  Miles Sasha Dickinson;  Devan Diwanji;  Nadia Herrera;  Nick Hoppe;  Huong T. Kratochvil;  Yanxin Liu;  Gregory E. Merz;  Michelle Moritz;  Henry C. Nguyen;  Carlos Nowotny;  Cristina Puchades;  Alexandrea N. Rizo;  Ursula Schulze-Gahmen;  Amber M. Smith;  Ming Sun;  Iris D. Young;  Jianhua Zhao;  Daniel Asarnow;  Justin Biel;  Alisa Bowen;  Julian R. Braxton;  Jen Chen;  Cynthia M. Chio;  Un Seng Chio;  Ishan Deshpande;  Loan Doan;  Bryan Faust;  Sebastian Flores;  Mingliang Jin;  Kate Kim;  Victor L. Lam;  Fei Li;  Junrui Li;  Yen-Li Li;  Yang Li;  Xi Liu;  Megan Lo;  Kyle E. Lopez;  Arthur A. Melo;  Frank R. Moss;  Phuong Nguyen;  Joana Paulino;  Komal Ishwar Pawar;  Jessica K. Peters;  Thomas H. Pospiech;  Maliheh Safari;  Smriti Sangwan;  Kaitlin Schaefer;  Paul V. Thomas;  Aye C. Thwin;  Raphael Trenker;  Eric Tse;  Tsz Kin Martin Tsui;  Feng Wang;  Natalie Whitis;  Zanlin Yu;  Kaihua Zhang;  Yang Zhang;  Fengbo Zhou;  Daniel Saltzberg;  QCRG Structural Biology Consortium12†;  Anthony J. Hodder;  Amber S. Shun-Shion;  Daniel M. Williams;  Kris M. White;  Romel Rosales;  Thomas Kehrer;  Lisa Miorin;  Elena Moreno;  Arvind H. Patel;  Suzannah Rihn;  Mir M. Khalid;  Albert Vallejo-Gracia;  Parinaz Fozouni;  Camille R. Simoneau;  Theodore L. Roth;  David Wu;  Mohd Anisul Karim;  Maya Ghoussaini;  Ian Dunham;  Francesco Berardi;  Sebastian Weigang;  Maxime Chazal;  Jisoo Park;  James Logue;  Marisa McGrath;  Stuart Weston;  Robert Haupt;  C. James Hastie;  Matthew Elliott;  Fiona Brown;  Kerry A. Burness;  Elaine Reid;  Mark Dorward;  Clare Johnson;  Stuart G. Wilkinson;  Anna Geyer;  Daniel M. Giesel;  Carla Baillie;  Samantha Raggett;  Hannah Leech;  Rachel Toth;  Nicola Goodman;  Kathleen C. Keough;  Abigail L. Lind;  Zoonomia Consortium‡;  Reyna J. Klesh;  Kafi R. Hemphill;  Jared Carlson-Stevermer;  Jennifer Oki;  Kevin Holden;  Travis Maures;  Katherine S. Pollard;  Andrej Sali;  David A. Agard;  Yifan Cheng;  James S. Fraser;  Adam Frost;  Natalia Jura;  Tanja Kortemme;  Aashish Manglik;  Daniel R. Southworth;  Robert M. Stroud;  Dario R. Alessi;  Paul Davies;  Matthew B. Frieman;  Trey Ideker;  Carmen Abate;  Nolwenn Jouvenet;  Georg Kochs;  Brian Shoichet;  Melanie Ott;  Massimo Palmarini;  Kevan M. Shokat;  Adolfo García-Sastre;  Jeremy A. Rassen;  Robert Grosse;  Oren S. Rosenberg;  Kliment A. Verba;  Christopher F. Basler;  Marco Vignuzzi;  Andrew A. Peden;  Pedro Beltrao;  Nevan J. Krogan
收藏  |  浏览/下载:27/0  |  提交时间:2020/12/07
Coherently forming a single molecule in an optical trap 期刊论文
Science, 2020
作者:  Xiaodong He;  Kunpeng Wang;  Jun Zhuang;  Peng Xu;  Xiang Gao;  Ruijun Guo;  Cheng Sheng;  Min Liu;  Jin Wang;  Jiaming Li;  G. V. Shlyapnikov;  Mingsheng Zhan
收藏  |  浏览/下载:20/0  |  提交时间:2020/10/20
Nitrogen‐induced acidification, not N‐nutrient, dominates suppressive N effects on arbuscular mycorrhizal fungi 期刊论文
Global Change Biology, 2020
作者:  Shang Pan;  Yang Wang;  Yunpeng Qiu;  Dima Chen;  Lin Zhang;  Chenglong Ye;  Hui Guo;  Weixing Zhu;  Aiqun Chen;  Guohua Xu;  Yi Zhang;  Yongfei Bai;  Shuijin Hu
收藏  |  浏览/下载:9/0  |  提交时间:2020/09/30
An orally available non-nucleotide STING agonist with antitumor activity 期刊论文
Science, 2020
作者:  Bo-Sheng Pan;  Samanthi A. Perera;  Jennifer A. Piesvaux;  Jeremy P. Presland;  Gottfried K. Schroeder;  Jared N. Cumming;  B. Wesley Trotter;  Michael D. Altman;  Alexei V. Buevich;  Brandon Cash;  Saso Cemerski;  Wonsuk Chang;  Yiping Chen;  Peter J. Dandliker;  Guo Feng;  Andrew Haidle;  Timothy Henderson;  James Jewell;  Ilona Kariv;  Ian Knemeyer;  Johnny Kopinja;  Brian M. Lacey;  Jason Laskey;  Charles A. Lesburg;  Rui Liang;  Brian J. Long;  Min Lu;  Yanhong Ma;  Ellen C. Minnihan;  Greg O’Donnell;  Ryan Otte;  Laura Price;  Larissa Rakhilina;  Berengere Sauvagnat;  Sharad Sharma;  Sriram Tyagarajan;  Hyun Woo;  Daniel F. Wyss;  Serena Xu;  David Jonathan Bennett;  George H. Addona
收藏  |  浏览/下载:17/0  |  提交时间:2020/08/25
Horizontal gene transfer of Fhb7 from fungus underlies Fusarium head blight resistance in wheat 期刊论文
Science, 2020
作者:  Hongwei Wang;  Silong Sun;  Wenyang Ge;  Lanfei Zhao;  Bingqian Hou;  Kai Wang;  Zhongfan Lyu;  Liyang Chen;  Shoushen Xu;  Jun Guo;  Min Li;  Peisen Su;  Xuefeng Li;  Guiping Wang;  Cunyao Bo;  Xiaojian Fang;  Wenwen Zhuang;  Xinxin Cheng;  Jianwen Wu;  Luhao Dong;  Wuying Chen;  Wen Li;  Guilian Xiao;  Jinxiao Zhao;  Yongchao Hao;  Ying Xu;  Yu Gao;  Wenjing Liu;  Yanhe Liu;  Huayan Yin;  Jiazhu Li;  Xiang Li;  Yan Zhao;  Xiaoqian Wang;  Fei Ni;  Xin Ma;  Anfei Li;  Steven S. Xu;  Guihua Bai;  Eviatar Nevo;  Caixia Gao;  Herbert Ohm;  Lingrang Kong
收藏  |  浏览/下载:17/0  |  提交时间:2020/05/25
Global conservation of species' niches 期刊论文
NATURE, 2020, 580 (7802) : 232-+
作者:  Guo, Xiaoyan;  Aviles, Giovanni;  Liu, Yi;  Tian, Ruilin;  Unger, Bret A.;  Lin, Yu-Hsiu T.;  Wiita, Arun P.;  Xu, Ke;  Correia, M. Almira;  Kampmann, Martin
收藏  |  浏览/下载:30/0  |  提交时间:2020/07/03

Environmental change is rapidly accelerating, and many species will need to adapt to survive(1). Ensuring that protected areas cover populations across a broad range of environmental conditions could safeguard the processes that lead to such adaptations(1-3). However, international conservation policies have largely neglected these considerations when setting targets for the expansion of protected areas(4). Here we show that-of 19,937 vertebrate species globally(5-8)-the representation of environmental conditions across their habitats in protected areas (hereafter, niche representation) is inadequate for 4,836 (93.1%) amphibian, 8,653 (89.5%) bird and 4,608 (90.9%) terrestrial mammal species. Expanding existing protected areas to cover these gaps would encompass 33.8% of the total land surface-exceeding the current target of 17% that has been adopted by governments. Priority locations for expanding the system of protected areas to improve niche representation occur in global biodiversity hotspots(9), including Colombia, Papua New Guinea, South Africa and southwest China, as well as across most of the major land masses of the Earth. Conversely, we also show that planning for the expansion of protected areas without explicitly considering environmental conditions would marginally reduce the land area required to 30.7%, but that this would lead to inadequate niche representation for 7,798 (39.1%) species. As the governments of the world prepare to renegotiate global conservation targets, policymakers have the opportunity to help to maintain the adaptive potential of species by considering niche representation within protected areas(1,2).


Protected areas would need to expand to 33.8% of the total land surface to adequately represent environmental conditions across the habitats of amphibians, birds and terrestrial mammals, far exceeding the current 17% target.


  
Centrosome anchoring regulates progenitor properties and cortical formation 期刊论文
NATURE, 2020
作者:  Guo, Xiaoyan;  Aviles, Giovanni;  Liu, Yi;  Tian, Ruilin;  Unger, Bret A.;  Lin, Yu-Hsiu T.;  Wiita, Arun P.;  Xu, Ke;  Correia, M. Almira;  Kampmann, Martin
收藏  |  浏览/下载:15/0  |  提交时间:2020/07/03

CEP83-mediated anchoring of the centrosome to the apical membrane in radial glial progenitor cells regulates their mechanical properties and thereby influences the size and configuration of the mammalian cortex.


Radial glial progenitor cells (RGPs) are the major neural progenitor cells that generate neurons and glia in the developing mammalian cerebral cortex(1-4). In RGPs, the centrosome is positioned away from the nucleus at the apical surface of the ventricular zone of the cerebral cortex(5-8). However, the molecular basis and precise function of this distinctive subcellular organization of the centrosome are largely unknown. Here we show in mice that anchoring of the centrosome to the apical membrane controls the mechanical properties of cortical RGPs, and consequently their mitotic behaviour and the size and formation of the cortex. The mother centriole in RGPs develops distal appendages that anchor it to the apical membrane. Selective removal of centrosomal protein 83 (CEP83) eliminates these distal appendages and disrupts the anchorage of the centrosome to the apical membrane, resulting in the disorganization of microtubules and stretching and stiffening of the apical membrane. The elimination of CEP83 also activates the mechanically sensitive yes-associated protein (YAP) and promotes the excessive proliferation of RGPs, together with a subsequent overproduction of intermediate progenitor cells, which leads to the formation of an enlarged cortex with abnormal folding. Simultaneous elimination of YAP suppresses the cortical enlargement and folding that is induced by the removal of CEP83. Together, these results indicate a previously unknown role of the centrosome in regulating the mechanical features of neural progenitor cells and the size and configuration of the mammalian cerebral cortex.


  
Mutational signature in colorectal cancer caused by genotoxic pks(+)E. coli 期刊论文
NATURE, 2020, 580 (7802) : 269-+
作者:  Lin, Xi;  Li, Mingyue;  Wang, Niandong;  Wu, Yiran;  Luo, Zhipu;  Guo, Shimeng;  Han, Gye-Won;  Li, Shaobai;  Yue, Yang;  Wei, Xiaohu;  Xie, Xin;  Chen, Yong;  Zhao, Suwen;  Wu, Jian;  Lei, Ming;  Xu, Fei
收藏  |  浏览/下载:24/0  |  提交时间:2020/07/03

Various species of the intestinal microbiota have been associated with the development of colorectal cancer(1,2), but it has not been demonstrated that bacteria have a direct role in the occurrence of oncogenic mutations. Escherichia coli can carry the pathogenicity island pks, which encodes a set of enzymes that synthesize colibactin(3). This compound is believed to alkylate DNA on adenine residues(4,5) and induces double-strand breaks in cultured cells(3). Here we expose human intestinal organoids to genotoxic pks(+)E. coli by repeated luminal injection over five months. Whole-genome sequencing of clonal organoids before and after this exposure revealed a distinct mutational signature that was absent from organoids injected with isogenic pks-mutant bacteria. The same mutational signature was detected in a subset of 5,876 human cancer genomes from two independent cohorts, predominantly in colorectal cancer. Our study describes a distinct mutational signature in colorectal cancer and implies that the underlying mutational process results directly from past exposure to bacteria carrying the colibactin-producing pks pathogenicity island.


Organoids derived from human intestinal cells that are co-cultured with bacteria carrying the genotoxic pks(+) island develop a distinct mutational signature associated with colorectal cancer.


  
Improved protein structure prediction using potentials from deep learning 期刊论文
NATURE, 2020, 577 (7792) : 706-+
作者:  Ma, Runze;  Cao, Duanyun;  Zhu, Chongqin;  Tian, Ye;  Peng, Jinbo;  Guo, Jing;  Chen, Ji;  Li, Xin-Zheng;  Francisco, Joseph S.;  Zeng, Xiao Cheng;  Xu, Li-Mei;  Wang, En-Ge;  Jiang, Ying
收藏  |  浏览/下载:143/0  |  提交时间:2020/07/03

Protein structure prediction can be used to determine the three-dimensional shape of a protein from its amino acid sequence(1). This problem is of fundamental importance as the structure of a protein largely determines its function(2)  however, protein structures can be difficult to determine experimentally. Considerable progress has recently been made by leveraging genetic information. It is possible to infer which amino acid residues are in contact by analysing covariation in homologous sequences, which aids in the prediction of protein structures(3). Here we show that we can train a neural network to make accurate predictions of the distances between pairs of residues, which convey more information about the structure than contact predictions. Using this information, we construct a potential of mean force(4) that can accurately describe the shape of a protein. We find that the resulting potential can be optimized by a simple gradient descent algorithm to generate structures without complex sampling procedures. The resulting system, named AlphaFold, achieves high accuracy, even for sequences with fewer homologous sequences. In the recent Critical Assessment of Protein Structure Prediction(5) (CASP13)-a blind assessment of the state of the field-AlphaFold created high-accuracy structures (with template modelling (TM) scores(6) of 0.7 or higher) for 24 out of 43 free modelling domains, whereas the next best method, which used sampling and contact information, achieved such accuracy for only 14 out of 43 domains. AlphaFold represents a considerable advance in protein-structure prediction. We expect this increased accuracy to enable insights into the function and malfunction of proteins, especially in cases for which no structures for homologous proteins have been experimentally determined(7).