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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:25/0  |  提交时间:2020/12/07
Beyond ecosystem modeling: A roadmap to community cyberinfrastructure for ecological data‐model integration 期刊论文
Global Change Biology, 2020
作者:  Istem Fer;  Anthony K. Gardella;  Alexey N. Shiklomanov;  Eleanor E. Campbell;  Elizabeth M. Cowdery;  Martin G. De Kauwe;  Ankur Desai;  Matthew J. Duveneck;  Joshua B. Fisher;  Katherine D. Haynes;  Forrest M. Hoffman;  Miriam R. Johnston;  Rob Kooper;  David S. LeBauer;  Joshua Mantooth;  William J. Parton;  Benjamin Poulter;  Tristan Quaife;  Ann Raiho;  Kevin Schaefer;  Shawn P. Serbin;  James Simkins;  Kevin R. Wilcox;  Toni Viskari;  Michael C. Dietze
收藏  |  浏览/下载:13/0  |  提交时间:2020/11/09
Extensive heterogeneity in somatic mutation and selection in the human bladder 期刊论文
Science, 2020
作者:  Andrew R. J. Lawson;  Federico Abascal;  Tim H. H. Coorens;  Yvette Hooks;  Laura O’Neill;  Calli Latimer;  Keiran Raine;  Mathijs A. Sanders;  Anne Y. Warren;  Krishnaa T. A. Mahbubani;  Bethany Bareham;  Timothy M. Butler;  Luke M. R. Harvey;  Alex Cagan;  Andrew Menzies;  Luiza Moore;  Alexandra J. Colquhoun;  William Turner;  Benjamin Thomas;  Vincent Gnanapragasam;  Nicholas Williams;  Doris M. Rassl;  Harald Vöhringer;  Sonia Zumalave;  Jyoti Nangalia;  José M. C. Tubío;  Moritz Gerstung;  Kourosh Saeb-Parsy;  Michael R. Stratton;  Peter J. Campbell;  Thomas J. Mitchell;  Iñigo Martincorena
收藏  |  浏览/下载:19/0  |  提交时间:2020/10/12
Femtosecond-to-millisecond structural changes in a light-driven sodium pump 期刊论文
NATURE, 2020, 583 (7815) : 314-+
作者:  Moore, Luiza;  Leongamornlert, Daniel;  Coorens, Tim H. H.;  Sanders, Mathijs A.;  Ellis, Peter;  Dentro, Stefan C.;  Dawson, Kevin J.;  Butler, Tim;  Rahbari, Raheleh;  Mitchell, Thomas J.;  Maura, Francesco;  Nangalia, Jyoti;  Tarpey, Patrick S.;  Brunner, Simon F.;  Lee-Six, Henry;  Hooks, Yvette;  Moody, Sarah;  Mahbubani, Krishnaa T.;  Jimenez-Linan, Mercedes;  Brosens, Jan J.;  Iacobuzio-Donahue, Christine A.;  Martincorena, Inigo;  Saeb-Parsy, Kourosh;  Campbell, Peter J.;  Stratton, Michael R.
收藏  |  浏览/下载:17/0  |  提交时间:2020/07/03

Light-driven sodium pumps actively transport small cations across cellular membranes(1). These pumps are used by microorganisms to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience. Although the resting state structures of the prototypical sodium pump Krokinobacter eikastus rhodopsin 2 (KR2) have been solved(2,3), it is unclear how structural alterations overtime allow sodium to be translocated against a concentration gradient. Here, using the Swiss X-ray Free Electron Laser(4), we have collected serial crystallographic data at ten pump-probe delays from femtoseconds to milliseconds. High-resolution structural snapshots throughout the KR2 photocycle show how retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds. Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds. Structural and spectroscopic data, in combination with quantum chemical calculations, indicate that a sodium ion bind stransiently close to the retinal within one millisecond. In the last structural intermediate, at 20 milliseconds after activation, we identified a potential second sodium-binding site close to the extracellular exit. These results provide direct molecular insight into the dynamics of active cation transport across biological membranes.


  
Two conserved epigenetic regulators prevent healthy ageing 期刊论文
NATURE, 2020
作者:  Yoshida, Kenichi;  Gowers, Kate H. C.;  Lee-Six, Henry;  Chandrasekharan, Deepak P.;  Coorens, Tim;  Maughan, Elizabeth F.;  Beal, Kathryn;  Menzies, Andrew;  Millar, Fraser R.;  Anderson, Elizabeth;  Clarke, Sarah E.;  Pennycuick, Adam;  Thakrar, Ricky M.;  Butler, Colin R.;  Kakiuchi, Nobuyuki;  Hirano, Tomonori;  Hynds, Robert E.;  Stratton, Michael R.;  Martincorena, Inigo;  Janes, Sam M.;  Campbell, Peter J.
收藏  |  浏览/下载:34/0  |  提交时间:2020/07/03

It has long been assumed that lifespan and healthspan correlate strongly, yet the two can be clearly dissociated(1-6). Although there has been a global increase in human life expectancy, increasing longevity is rarely accompanied by an extended healthspan(4,7). Thus, understanding the origin of healthy behaviours in old people remains an important and challenging task. Here we report a conserved epigenetic mechanism underlying healthy ageing. Through genome-wide RNA-interference-based screening of genes that regulate behavioural deterioration in ageing Caenorhabditis elegans, we identify 59 genes as potential modulators of the rate of age-related behavioural deterioration. Among these modulators, we found that a neuronal epigenetic reader, BAZ-2, and a neuronal histone 3 lysine 9 methyltransferase, SET-6, accelerate behavioural deterioration in C. elegans by reducing mitochondrial function, repressing the expression of nuclear-encoded mitochondrial proteins. This mechanism is conserved in cultured mouse neurons and human cells. Examination of human databases(8,9) shows that expression of the human orthologues of these C. elegans regulators, BAZ2B and EHMT1, in the frontal cortex increases with age and correlates positively with the progression of Alzheimer'  s disease. Furthermore, ablation of Baz2b, the mouse orthologue of BAZ-2, attenuates age-dependent body-weight gain and prevents cognitive decline in ageing mice. Thus our genome-wide RNA-interference screen in C. elegans has unravelled conserved epigenetic negative regulators of ageing, suggesting possible ways to achieve healthy ageing.


Two epigenetic regulators-identified in an RNA interference screen in Caenhorhabditis elegans, and conserved in mammals-diminish mitochondrial function and accelerate the age-related deterioration of behaviour.


  
Embryonal precursors of Wilms tumor 期刊论文
SCIENCE, 2019, 366 (6470) : 1247-+
作者:  Coorens, Tim H. H.;  Treger, Taryn D.;  Al-Saadi, Reem;  Moore, Luiza;  Tran, Maxine G. B.;  Mitchell, Thomas J.;  Tugnait, Suzanne;  Thevanesan, Christine;  Young, Matthew D.;  Oliver, Thomas R. W.;  Oostveen, Minou;  Collord, Grace;  Tarpey, Patrick S.;  Cagan, Alex;  Hooks, Yvette;  Brougham, Mark;  Reynolds, Ben C.;  Barone, Giuseppe;  Anderson, John;  Jorgensen, Mette;  Burke, G. A. Amos;  Visser, Johannes;  Nicholson, James C.;  Smeulders, Naima;  Mushtaq, Imran;  Stewart, Grant D.;  Campbell, Peter J.;  Wedge, David C.;  Martincorena, Inigo;  Rampling, Dyanne;  Hook, Liz;  Warren, Anne Y.;  Coleman, Nicholas;  Chowdhury, Tanzina;  Sebire, Neil;  Drost, Jarno;  Saeb-Parsy, Kourosh;  Stratton, Michael R.;  Straathof, Karin;  Pritchard-Jones, Kathy;  Behjati, Sam
收藏  |  浏览/下载:10/0  |  提交时间:2020/02/17
Somatic mutant clones colonize the human esophagus with age 期刊论文
SCIENCE, 2018, 362 (6417) : 911-+
作者:  Martincorena, Inigo;  Fowler, Joanna C.;  Wabik, Agnieszka;  Lawson, Andrew R. J.;  Abascal, Federico;  Hall, Michael W. J.;  Cagan, Alex;  Murai, Kasumi;  Mahbubani, Krishnaa;  Stratton, Michael R.;  Fitzgerald, Rebecca C.;  Handford, Penny A.;  Campbell, Peter J.;  Saeb-Parsy, Kourosh;  Jones, Philip H.
收藏  |  浏览/下载:11/0  |  提交时间:2019/11/27
Range position and climate sensitivity: The structure of among-population demographic responses to climatic variation 期刊论文
GLOBAL CHANGE BIOLOGY, 2018, 24 (1) : 439-454
作者:  Amburgey, Staci M.;  Miller, David A. W.;  Grant, Evan H. Campbell;  Rittenhouse, Tracy A. G.;  Benard, Michael F.;  Richardson, Jonathan L.;  Urban, Mark C.;  Hughson, Ward;  Brand, Adrianne B.;  Davis, Christopher J.;  Hardin, Carmen R.;  Paton, Peter W. C.;  Raithel, Christopher J.;  Relyea, Rick A.;  Scott, A. Floyd;  Skelly, David K.;  Skidds, Dennis E.;  Smith, Charles K.;  Werner, Earl E.
收藏  |  浏览/下载:16/0  |  提交时间:2019/04/09
bioclimatic envelope model  climate change  Lithobates sylvaticus  range shifts  species distribution model  state-space model  wood frog  
Loci associated with skin pigmentation identified in African populations 期刊论文
SCIENCE, 2017, 358 (6365) : 887-+
作者:  Crawford, Nicholas G.;  Kelly, Derek E.;  Hansen, Matthew E. B.;  Beltrame, Marcia H.;  Fan, Shaohua;  Bowman, Shanna L.;  Jewett, Ethan;  Ranciaro, Alessia;  Thompson, Simon;  Lo, Yancy;  Pfeifer, Susanne P.;  Jensen, Jeffrey D.;  Campbell, Michael C.;  Beggs, William;  Hormozdiari, Farhad;  Mpoloka, Sununguko Wata;  Mokone, Gaonyadiwe George;  Nyambo, Thomas;  Meskel, Dawit Wolde;  Belay, Gurja;  Haut, Jake;  Rothschild, Harriet;  Zon, Leonard;  Zhou, Yi;  Kovacs, Michael A.;  Xu, Mai;  Zhang, Tongwu;  Bishop, Kevin;  Sinclair, Jason;  Rivas, Cecilia;  Elliot, Eugene;  Choi, Jiyeon;  Li, Shengchao A.;  Hicks, Belynda;  Burgess, Shawn;  Abnet, Christian;  Watkins-Chow, Dawn E.;  Oceana, Elena;  Song, Yun S.;  Eskin, Eleazar;  Brown, Kevin M.;  Marks, Michael S.;  Loftus, Stacie K.;  Pavan, William J.;  Yeager, Meredith;  Chanock, Stephen;  Tishkoff, Sarah A.
收藏  |  浏览/下载:10/0  |  提交时间:2019/11/27
Ecological regime shift drives declining growth rates of sea turtles throughout the West Atlantic 期刊论文
GLOBAL CHANGE BIOLOGY, 2017, 23 (11)
作者:  Bjorndal, Karen A.;  Bolten, Alan B.;  Chaloupka, Milani;  Saba, Vincent S.;  Bellini, Claudio;  Marcovaldi, Maria A. G.;  Santos, Armando J. B.;  Wurdig Bortolon, Luis Felipe;  Meylan, Anne B.;  Meylan, Peter A.;  Gray, Jennifer;  Hardy, Robert;  Brost, Beth;  Bresette, Michael;  Gorham, Jonathan C.;  Connett, Stephen;  Crouchley, Barbara Van Sciver;  Dawson, Mike;  Hayes, Deborah;  Diez, Carlos E.;  van Dam, Robert P.;  Willis, Sue;  Nava, Mabel;  Hart, Kristen M.;  Cherkiss, Michael S.;  Crowder, Andrew G.;  Pollock, Clayton;  Hillis-Starr, Zandy;  Munoz Teneria, Fernando A.;  Herrera-Pavon, Roberto;  Labrada-Martagon, Vanessa;  Lorences, Armando;  Negrete-Philippe, Ana;  Lamont, Margaret M.;  Foley, Allen M.;  Bailey, Rhonda;  Carthy, Raymond R.;  Scarpino, Russell;  McMichael, Erin;  Provancha, Jane A.;  Brooks, Annabelle;  Jardim, Adriana;  Lopez-Mendilaharsu, Milagros;  Gonzalez-Paredes, Daniel;  Estrades, Andres;  Fallabrino, Alejandro;  Martinez-Souza, Gustavo;  Velez-Rubio, Gabriela M.;  Boulon, Ralf H.;  Collazo, Jaime A.;  Wershoven, Robert;  Guzman Hernandez, Vicente;  Stringell, Thomas B.;  Sanghera, Amdeep;  Richardson, Peter B.;  Broderick, Annette C.;  Phillips, Quinton;  Calosso, Marta;  Claydon, John A. B.;  Metz, Tasha L.;  Gordon, Amanda L.;  Landry, Andre M.;  Shaver, Donna J.;  Blumenthal, Janice;  Collyer, Lucy;  Godley, Brendan J.;  McGowan, Andrew;  Witt, Matthew J.;  Campbell, Cathi L.;  Lagueux, Cynthia J.;  Bethel, Thomas L.;  Kenyon, Lory
收藏  |  浏览/下载:10/0  |  提交时间:2019/04/09
Caretta caretta  Chelonia mydas  ecological regime shifts  Eretmochelys imbricata  multivariate ENSO index  sea surface temperature  seagrass  somatic growth rates