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Accurate prediction of protein structures and interactions using a three-track neural network 期刊论文
Science, 2021
作者:  Minkyung Baek;  Frank DiMaio;  Ivan Anishchenko;  Justas Dauparas;  Sergey Ovchinnikov;  Gyu Rie Lee;  Jue Wang;  Qian Cong;  Lisa N. Kinch;  R. Dustin Schaeffer;  Claudia Millán;  Hahnbeom Park;  Carson Adams;  Caleb R. Glassman;  Andy DeGiovanni;  Jose H. Pereira;  Andria V. Rodrigues;  Alberdina A. van Dijk;  Ana C. Ebrecht;  Diederik J. Opperman;  Theo Sagmeister;  Christoph Buhlheller;  Tea Pavkov-Keller;  Manoj K. Rathinaswamy;  Udit Dalwadi;  Calvin K. Yip;  John E. Burke;  K. Christopher Garcia;  Nick V. Grishin;  Paul D. Adams;  Randy J. Read;  David Baker
收藏  |  浏览/下载:18/0  |  提交时间:2021/08/25
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.


  
Drought supersedes warming in determining volatile and tissue defenses of pinon pine (Pinus edulis) 期刊论文
ENVIRONMENTAL RESEARCH LETTERS, 2019, 14 (6)
作者:  Trowbridge, Amy M.;  Stoy, Paul C.;  Adams, Henry D.;  Law, Darin J.;  Breshears, David D.;  Helmig, Detlev;  Monson, Russell K.
收藏  |  浏览/下载:8/0  |  提交时间:2019/11/26
drought  heat stress  monoterpenes  Pinus edulis  plant defense  secondary metabolites  volatile organic compounds  
ALPK1 hotspot mutation as a driver of human spiradenoma and spiradenocarcinoma 期刊论文
NATURE COMMUNICATIONS, 2019, 10
作者:  Rashid, Mamunur;  van der Horst, Michiel;  Mentzel, Thomas;  Butera, Francesca;  Ferreira, Ingrid;  Pance, Alena;  Rutten, Arno;  Luzar, Bostjan;  Marusic, Zlatko;  Aubain, Nicolas de Saint;  Ko, Jennifer S.;  Billings, Steven D.;  Chen, Sofia;  Daoud, Marie Abi;  Hewinson, James;  Louzada, Sandra;  Harms, Paul W.;  Cerretelli, Guia;  Robles-Espinoza, Carla Daniela;  Patel, Rajiv M.;  van der Weyden, Louise;  Bakal, Chris;  Hornick, Jason L.;  Arends, Mark J.;  Brenn, Thomas;  Adams, David J.
收藏  |  浏览/下载:9/0  |  提交时间:2019/11/27
Crystal structure of TcpK in complex with oriT DNA of the antibiotic resistance plasmid pCW3 期刊论文
NATURE COMMUNICATIONS, 2018, 9
作者:  Traore, Daouda A. K.;  Wisniewski, Jessica A.;  Flanigan, Sarena F.;  Conroy, Paul J.;  Panjikar, Santosh;  Mok, Yee-Foong;  Lao, Carmen;  Griffin, Michael D. W.;  Adams, Vicki;  Rood, Julian I.;  Whisstock, James C.
收藏  |  浏览/下载:13/0  |  提交时间:2019/11/27
Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution 期刊论文
NATURE, 2017, 545 (7655) : 446-+
作者:  Abbosh, Christopher;  Birkbak, Nicolai J.;  Wilson, Gareth A.;  Jamal-Hanjani, Mariam;  Constantin, Tudor;  Salari, Raheleh;  Le Quesne, John;  Moore, David A.;  Veeriah, Selvaraju;  Rosenthal, Rachel;  Marafioti, Teresa;  Kirkizlar, Eser;  Watkins, Thomas B. K.;  McGranahan, Nicholas;  Ward, Sophia;  Martinson, Luke;  Riley, Joan;  Fraioli, Francesco;  Al Bakir, Maise;  Gronroos, Eva;  Zambrana, Francisco;  Endozo, Raymondo;  Bi, Wenya Linda;  Fennessy, Fiona M.;  Sponer, Nicole;  Johnson, Diana;  Laycock, Joanne;  Shafi, Seema;  Czyzewska-Khan, Justyna;  Rowan, Andrew;  Chambers, Tim;  Matthews, Nik;  Turajlic, Samra;  Hiley, Crispin;  Lee, Siow Ming;  Forster, Martin D.;  Ahmad, Tanya;  Falzon, Mary;  Borg, Elaine;  Lawrence, David;  Hayward, Martin;  Kolvekar, Shyam;  Panagiotopoulos, Nikolaos;  Janes, Sam M.;  Thakrar, Ricky;  Ahmed, Asia;  Blackhall, Fiona;  Summers, Yvonne;  Hafez, Dina;  Naik, Ashwini;  Ganguly, Apratim;  Kareht, Stephanie;  Shah, Rajesh;  Joseph, Leena;  Quinn, Anne Marie;  Crosbie, Phil A.;  Naidu, Babu;  Middleton, Gary;  Langman, Gerald;  Trotter, Simon;  Nicolson, Marianne;  Remmen, Hardy;  Kerr, Keith;  Chetty, Mahendran;  Gomersall, Lesley;  Fennell, Dean A.;  Nakas, Apostolos;  Rathinam, Sridhar;  Anand, Girija;  Khan, Sajid;  Russell, Peter;  Ezhil, Veni;  Ismail, Babikir;  Irvin-Sellers, Melanie;  Prakash, Vineet;  Lester, Jason F.;  Kornaszewska, Malgorzata;  Attanoos, Richard;  Adams, Haydn;  Davies, Helen;  Oukrif, Dahmane;  Akarca, Ayse U.;  Hartley, John A.;  Lowe, Helen L.;  Lock, Sara;  Iles, Natasha;  Bell, Harriet;  Ngai, Yenting;  Elgar, Greg;  Szallasi, Zoltan;  Schwarz, Roland F.;  Herrero, Javier;  Stewart, Aengus;  Quezada, Sergio A.;  Peggs, Karl S.;  Van Loo, Peter;  Dive, Caroline;  Lin, C. Jimmy;  Rabinowitz, Matthew;  Aerts, Hugo J. W. L.;  Hackshaw, Allan;  Shaw, Jacqui A.;  Zimmermann, Bernhard G.;  Swanton, Charles;  Jamal-Hanjani, Mariam;  Abbosh, Christopher;  Veeriah, Selvaraju;  Shafi, Seema;  Czyzewska-Khan, Justyna;  Johnson, Diana;  Laycock, Joanne;  Bosshard-Carter, Leticia;  Goh, Gerald;  Rosenthal, Rachel;  Gorman, Pat;  Murugaesu, Nirupa;  Hynds, Robert E.;  Wilson, Gareth A.;  Birkbak, Nicolai J.;  Watkins, Thomas B. K.;  McGranahan, Nicholas;  Horswell, Stuart;  Al Bakir, Maise;  Gronroos, Eva;  Mitter, Richard;  Escudero, Mickael;  Stewart, Aengus;  Van Loo, Peter;  Rowan, Andrew;  Xu, Hang;  Turajlic, Samra;  Hiley, Crispin;  Goldman, Jacki;  Stone, Richard Kevin;  Denner, Tamara;  Matthews, Nik;  Elgar, Greg;  Ward, Sophia;  Biggs, Jennifer;  Costa, Marta;  Begum, Sharmin;  Phillimore, Ben;  Chambers, Tim;  Nye, Emma;  Graca, Sofia;  Joshi, Kroopa;  Furness, Andrew;  Ben Aissa, Assma;  Wong, Yien Ning Sophia;  Georgiou, Andy;  Quezada, Sergio A.;  Peggs, Karl S.;  Hartley, John A.;  Lowe, Helen L.;  Herrero, Javier;  Lawrence, David;  Hayward, Martin;  Panagiotopoulos, Nikolaos;  Kolvekar, Shyam;  Falzon, Mary;  Borg, Elaine;  Marafioti, Teresa;  Simeon, Celia;  Hector, Gemma;  Smith, Amy;  Aranda, Marie;  Novelli, Marco;  Oukrif, Dahmane;  Akarca, Ayse U.;  Janes, Sam M.;  Thakrar, Ricky;  Forster, Martin D.;  Ahmad, Tanya;  Lee, Siow Ming;  Papadatos-Pastos, Dionysis;  Carnell, Dawn;  Mendes, Ruheena;  George, Jeremy;  Navani, Neal;  Ahmed, Asia;  Taylor, Magali;  Choudhary, Junaid;  Summers, Yvonne;  Califano, Raffaele;  Taylor, Paul;  Shah, Rajesh;  Krysiak, Piotr;  Rammohan, Kendadai;  Fontaine, Eustace;  Booton, Richard;  Evison, Matthew;  Crosbie, Phil A.;  Moss, Stuart;  Idries, Faiza;  Joseph, Leena;  Bishop, Paul;  Chaturvedi, Anshuman;  Quinn, Anne Marie;  Doran, Helen;  Leek, Angela;  Harrison, Phil;  Moore, Katrina;  Waddington, Rachael;  Novasio, Juliette;  Blackhall, Fiona;  Rogan, Jane;  Smith, Elaine;  Dive, Caroline;  Tugwood, Jonathan;  Brady, Ged;  Rothwell, Dominic G.;  Chemi, Francesca;  Pierce, Jackie;  Gulati, Sakshi;  Naidu, Babu;  Langman, Gerald;  Trotter, Simon;  Bellamy, Mary;  Bancroft, Hollie;  Kerr, Amy;  Kadiri, Salma;  Webb, Joanne;  Middleton, Gary;  Djearaman, Madava;  Fennell, Dean A.;  Shaw, Jacqui A.;  Le Quesne, John;  Moore, David A.;  Thomas, Anne;  Walter, Harriet;  Riley, Joan;  Martinson, Luke;  Nakas, Apostolos;  Rathinam, Sridhar;  Monteiro, William;  Marshall, Hilary;  Nelson, Louise;  Bennett, Jonathan;  Primrose, Lindsay;  Anand, Girija;  Khan, Sajid;  Amadi, Anita;  Nicolson, Marianne;  Kerr, Keith;  Palmer, Shirley;  Remmen, Hardy;  Miller, Joy;  Buchan, Keith;  Chetty, Mahendran;  Gomersall, Lesley;  Lester, Jason F.;  Edwards, Alison;  Morgan, Fiona;  Adams, Haydn;  Davies, Helen;  Kornaszewska, Malgorzata;  Attanoos, Richard;  Lock, Sara;  Verjee, Azmina;  MacKenzie, Mairead;  Wilcox, Maggie;  Bell, Harriet;  Iles, Natasha;  Hackshaw, Allan;  Ngai, Yenting;  Smith, Sean;  Gower, Nicole;  Ottensmeier, Christian;  Chee, Serena;  Johnson, Benjamin;  Alzetani, Aiman;  Shaw, Emily;  Lim, Eric;  De Sousa, Paulo;  Barbosa, Monica Tavares;  Bowman, Alex;  Jordan, Simon;  Rice, Alexandra;  Raubenheimer, Hilgardt;  Proli, Chiara;  Cufari, Maria Elena;  Ronquillo, John Carlo;  Kwayie, Angela;  Bhayani, Harshil;  Hamilton, Morag;  Bakar, Yusura;  Mensah, Natalie;  Ambrose, Lyn;  Devaraj, Anand;  Buderi, Silviu;  Finch, Jonathan;  Azcarate, Leire;  Chavan, Hema;  Green, Sophie;  Mashinga, Hillaria;  Nicholson, Andrew G.;  Lau, Kelvin;  Sheaff, Michael;  Schmid, Peter;  Conibear, John;  Ezhil, Veni;  Ismail, Babikir;  Irvin-Sellers, Melanie;  Prakash, Vineet;  Russell, Peter;  Light, Teresa;  Horey, Tracey;  Danson, Sarah;  Bury, Jonathan;  Edwards, John;  Hill, Jennifer;  Matthews, Sue;  Kitsanta, Yota;  Suvarna, Kim;  Fisher, Patricia;  Keerio, Allah Dino;  Shackcloth, Michael;  Gosney, John;  Postmus, Pieter;  Feeney, Sarah;  Asante-Siaw, Julius;  Constantin, Tudor;  Salari, Raheleh;  Sponer, Nicole;  Naik, Ashwini;  Zimmermann, Bernhard G.;  Rabinowitz, Matthew;  Aerts, Hugo J. W. L.;  Dentro, Stefan;  Dessimoz, Christophe
收藏  |  浏览/下载:24/0  |  提交时间:2019/04/09