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Global declines in coral reef calcium carbonate production under ocean acidification and warming 期刊论文
Proceedings of the National Academy of Sciences, 2021
作者:  Christopher E. Cornwall;  Steeve Comeau;  Niklas A. Kornder;  Chris T. Perry;  Ruben van Hooidonk;  Thomas M. DeCarlo;  Morgan S. Pratchett;  Kristen D. Anderson;  Nicola Browne;  Robert Carpenter;  Guillermo Diaz-Pulido;  Juan P. D’Olivo;  Steve S. Doo;  Joana Figueiredo;  Sofia A. V. Fortunato;  Emma Kennedy;  Coulson A. Lantz;  Malcolm T. McCulloch;  Manuel González-Rivero;  Verena Schoepf;  Scott G. Smithers;  Ryan J. Lowe
收藏  |  浏览/下载:12/0  |  提交时间:2021/05/21
Global declines in coral reef calcium carbonate production under ocean acidification and warming 期刊论文
Proceedings of the National Academy of Science, 2021
作者:  Christopher E. Cornwall;  Steeve Comeau;  Niklas A. Kornder;  Chris T. Perry;  Ruben van Hooidonk;  Thomas M. DeCarlo;  Morgan S. Pratchett;  Kristen D. Anderson;  Nicola Browne;  Robert Carpenter;  Guillermo Diaz-Pulido;  Juan P. D’Olivo;  Steve S. Doo;  Joana Figueiredo;  Sofia A. V. Fortunato;  Emma Kennedy;  Coulson A. Lantz;  Malcolm T. McCulloch;  Manuel González-Rivero;  Verena Schoepf;  Scott G. Smithers;  Ryan J. Lowe
收藏  |  浏览/下载:10/0  |  提交时间:2021/05/21
Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil 期刊论文
Science, 2021
作者:  Nuno R. Faria;  Thomas A. Mellan;  Charles Whittaker;  Ingra M. Claro;  Darlan da S. Candido;  Swapnil Mishra;  Myuki A. E. Crispim;  Flavia C. S. Sales;  Iwona Hawryluk;  John T. McCrone;  Ruben J. G. Hulswit;  Lucas A. M. Franco;  Mariana S. Ramundo;  Jaqueline G. de Jesus;  Pamela S. Andrade;  Thais M. Coletti;  Giulia M. Ferreira;  Camila A. M. Silva;  Erika R. Manuli;  Rafael H. M. Pereira;  Pedro S. Peixoto;  Moritz U. G. Kraemer;  Nelson Gaburo;  Cecilia da C. Camilo;  Henrique Hoeltgebaum;  William M. Souza;  Esmenia C. Rocha;  Leandro M. de Souza;  Mariana C. de Pinho;  Leonardo J. T. Araujo;  Frederico S. V. Malta;  Aline B. de Lima;  Joice do P. Silva;  Danielle A. G. Zauli;  Alessandro C. de S. Ferreira;  Ricardo P. Schnekenberg;  Daniel J. Laydon;  Patrick G. T. Walker;  Hannah M. Schlüter;  Ana L. P. dos Santos;  Maria S. Vidal;  Valentina S. Del Caro;  Rosinaldo M. F. Filho;  Helem M. dos Santos;  Renato S. Aguiar;  José L. Proença-Modena;  Bruce Nelson;  James A. Hay;  Mélodie Monod;  Xenia Miscouridou;  Helen Coupland;  Raphael Sonabend;  Michaela Vollmer;  Axel Gandy;  Carlos A. Prete;  Vitor H. Nascimento;  Marc A. Suchard;  Thomas A. Bowden;  Sergei L. K. Pond;  Chieh-Hsi Wu;  Oliver Ratmann;  Neil M. Ferguson;  Christopher Dye;  Nick J. Loman;  Philippe Lemey;  Andrew Rambaut;  Nelson A. Fraiji;  Maria do P. S. S. Carvalho;  Oliver G. Pybus;  Seth Flaxman;  Samir Bhatt;  Ester C. Sabino
收藏  |  浏览/下载:14/0  |  提交时间:2021/06/07
Species-specific pace of development is associated with differences in protein stability 期刊论文
Science, 2020
作者:  Teresa Rayon;  Despina Stamataki;  Ruben Perez-Carrasco;  Lorena Garcia-Perez;  Christopher Barrington;  Manuela Melchionda;  Katherine Exelby;  Jorge Lazaro;  Victor L. J. Tybulewicz;  Elizabeth M. C. Fisher;  James Briscoe
收藏  |  浏览/下载:8/0  |  提交时间:2020/09/22
Parasitoids indicate major climate‐induced shifts in arctic communities 期刊论文
Global Change Biology, 2020
作者:  Tuomas Kankaanpä;  ä;  Eero Vesterinen;  Bess Hardwick;  Niels M. Schmidt;  Tommi Andersson;  Paul E. Aspholm;  Isabel C. Barrio;  Niklas Beckers;  Joë;  l Bê;  ty;  Tone Birkemoe;  Melissa DeSiervo;  Katherine H. I. Drotos;  Dorothee Ehrich;  Olivier Gilg;  Vladimir Gilg;  Nils Hein;  Toke T. Hø;  ye;  Kristian M. Jakobsen;  Camille Jodouin;  Jesse Jorna;  Mikhail V. Kozlov;  Jean‐;  Claude Kresse;  Don‐;  Jean Leandri‐;  Breton;  Nicolas Lecomte;  Maarten Loonen;  Philipp Marr;  Spencer K. Monckton;  Maia Olsen;  José;  e‐;  Anne Otis;  Michelle Pyle;  Ruben E. Roos;  Katrine Raundrup;  Daria Rozhkova;  Brigitte Sabard;  Aleksandr Sokolov;  Natalia Sokolova;  Anna M. Solecki;  Christine Urbanowicz;  Catherine Villeneuve;  Evgenya Vyguzova;  Vitali Zverev;  Tomas Roslin
收藏  |  浏览/下载:39/0  |  提交时间:2020/09/14
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.


  
Video-based AI for beat-to-beat assessment of cardiac function 期刊论文
NATURE, 2020, 580 (7802) : 252-+
作者:  Pleguezuelos-Manzano, Cayetano;  Puschhof, Jens;  Huber, Axel Rosendahl;  van Hoeck, Arne;  Wood, Henry M.;  Nomburg, Jason;  Gurjao, Carino;  Manders, Freek;  Dalmasso, Guillaume;  Stege, Paul B.;  Paganelli, Fernanda L.;  Geurts, Maarten H.;  Beumer, Joep;  Mizutani, Tomohiro;  Miao, Yi;  van der Linden, Reinier;  van der Elst, Stefan;  Garcia, K. Christopher;  Top, Janetta;  Willems, Rob J. L.;  Giannakis, Marios;  Bonnet, Richard;  Quirke, Phil;  Meyerson, Matthew;  Cuppen, Edwin;  van Boxtel, Ruben;  Clevers, Hans
收藏  |  浏览/下载:117/0  |  提交时间:2020/07/03

A video-based deep learning algorithm-EchoNet-Dynamic-accurately identifies subtle changes in ejection fraction and classifies heart failure with reduced ejection fraction using information from multiple cardiac cycles.


Accurate assessment of cardiac function is crucial for the diagnosis of cardiovascular disease(1), screening for cardiotoxicity(2) and decisions regarding the clinical management of patients with a critical illness(3). However, human assessment of cardiac function focuses on a limited sampling of cardiac cycles and has considerable inter-observer variability despite years of training(4,5). Here, to overcome this challenge, we present a video-based deep learning algorithm-EchoNet-Dynamic-that surpasses the performance of human experts in the critical tasks of segmenting the left ventricle, estimating ejection fraction and assessing cardiomyopathy. Trained on echocardiogram videos, our model accurately segments the left ventricle with a Dice similarity coefficient of 0.92, predicts ejection fraction with a mean absolute error of 4.1% and reliably classifies heart failure with reduced ejection fraction (area under the curve of 0.97). In an external dataset from another healthcare system, EchoNet-Dynamic predicts the ejection fraction with a mean absolute error of 6.0% and classifies heart failure with reduced ejection fraction with an area under the curve of 0.96. Prospective evaluation with repeated human measurements confirms that the model has variance that is comparable to or less than that of human experts. By leveraging information across multiple cardiac cycles, our model can rapidly identify subtle changes in ejection fraction, is more reproducible than human evaluation and lays the foundation for precise diagnosis of cardiovascular disease in real time. As a resource to promote further innovation, we also make publicly available a large dataset of 10,030 annotated echocardiogram videos.


  
Live-animal imaging of native haematopoietic stem and progenitor cells 期刊论文
NATURE, 2020, 578 (7794) : 278-+
作者:  Gerstung, Moritz;  Jolly, Clemency;  Leshchiner, Ignaty;  Dentro, Stefan C.;  Gonzalez, Santiago;  Rosebrock, Daniel;  Mitchell, Thomas J.;  Rubanova, Yulia;  Anur, Pavana;  Yu, Kaixian;  Tarabichi, Maxime;  Deshwar, Amit;  Wintersinger, Jeff;  Kleinheinz, Kortine;  Vazquez-Garcia, Ignacio;  Haase, Kerstin;  Jerman, Lara;  Sengupta, Subhajit;  Macintyre, Geoff;  Malikic, Salem;  Donmez, Nilgun;  Livitz, Dimitri G.;  Cmero, Marek;  Demeulemeester, Jonas;  Schumacher, Steven;  Fan, Yu;  Yao, Xiaotong;  Lee, Juhee;  Schlesner, Matthias;  Boutros, Paul C.;  Bowtell, David D.;  Zhu, Hongtu;  Getz, Gad;  Imielinski, Marcin;  Beroukhim, Rameen;  Sahinalp, S. Cenk;  Ji, Yuan;  Peifer, Martin;  Markowetz, Florian;  Mustonen, Ville;  Yuan, Ke;  Wang, Wenyi;  Morris, Quaid D.;  Spellman, Paul T.;  Wedge, David C.;  Van Loo, Peter;  Deshwar, Amit G.;  Adams, David J.;  Campbell, Peter J.;  Cao, Shaolong;  Christie, Elizabeth L.;  Cun, Yupeng;  Dawson, Kevin J.;  Drews, Ruben M.;  Eils, Roland;  Fittall, Matthew;  Garsed, Dale W.;  Ha, Gavin;  Lee-Six, Henry;  Martincorena, Inigo;  Oesper, Layla;  Peto, Myron;  Raphael, Benjamin J.;  Salcedo, Adriana;  Shi, Ruian;  Shin, Seung Jun;  Spiro, Oliver;  Stein, Lincoln D.;  Vembu, Shankar;  Wheeler, David A.;  Yang, Tsun-Po
收藏  |  浏览/下载:15/0  |  提交时间:2020/07/03

The biology of haematopoietic stem cells (HSCs) has predominantly been studied under transplantation conditions(1,2). It has been particularly challenging to study dynamic HSC behaviour, given that the visualization of HSCs in the native niche in live animals has not, to our knowledge, been achieved. Here we describe a dual genetic strategy in mice that restricts reporter labelling to a subset of the most quiescent long-term HSCs (LT-HSCs) and that is compatible with current intravital imaging approaches in the calvarial bone marrow(3-5). We show that this subset of LT-HSCs resides close to both sinusoidal blood vessels and the endosteal surface. By contrast, multipotent progenitor cells (MPPs) show greater variation in distance from the endosteum and are more likely to be associated with transition zone vessels. LT-HSCs are not found in bone marrow niches with the deepest hypoxia and instead are found in hypoxic environments similar to those of MPPs. In vivo time-lapse imaging revealed that LT-HSCs at steady-state show limited motility. Activated LT-HSCs show heterogeneous responses, with some cells becoming highly motile and a fraction of HSCs expanding clonally within spatially restricted domains. These domains have defined characteristics, as HSC expansion is found almost exclusively in a subset of bone marrow cavities with bone-remodelling activity. By contrast, cavities with low bone-resorbing activity do not harbour expanding HSCs. These findings point to previously unknown heterogeneity within the bone marrow microenvironment, imposed by the stages of bone turnover. Our approach enables the direct visualization of HSC behaviours and dissection of heterogeneity in HSC niches.


A dual genetic strategy enables the labelling and in vivo imaging of native long-term haematopoietic stem cells in the mouse calvarial bone marrow.


  
Hepatic p63 regulates steatosis via IKK beta/ER stress 期刊论文
NATURE COMMUNICATIONS, 2017, 8
作者:  Porteiro, Begona;  Fondevila, Marcos F.;  Delgado, Teresa C.;  Iglesias, Cristina;  Imbernon, Monica;  Iruzubieta, Paula;  Crespo, Javier;  Zabala-Letona, Amaia;  Ferno, Johan;  Gonzalez-Teran, Barbara;  Matesanz, Nuria;  Hernandez-Cosido, Lourdes;  Marcos, Miguel;  Tovar, Sulay;  Vidal, Anxo;  Sanchez-Ceinos, Julia;  Malagon, Maria M.;  Pombo, Celia;  Zalvide, Juan;  Carracedo, Arkaitz;  Buque, Xabier;  Dieguez, Carlos;  Sabio, Guadalupe;  Lopez, Miguel;  Aspichueta, Patricia;  Martinez-Chantar, Maria L.;  Nogueiras, Ruben
收藏  |  浏览/下载:9/0  |  提交时间:2019/11/27
Human activity is altering the world's zoogeographical regions 期刊论文
ECOLOGY LETTERS, 2019, 22 (8) : 1297-1305
作者:  Bernardo-Madrid, Ruben;  Calatayud, Joaquin;  Gonzalez-Suarez, Manuela;  Rosvall, Martin;  Lucas, Pablo M.;  Rueda, Marta;  Antonelli, Alexandre;  Revilla, Eloy
收藏  |  浏览/下载:7/0  |  提交时间:2019/11/27
Conservation  human impacts  global change  extinction  invasion  threatened species  species assemblages  uncertainty  robustness  Bioregions