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Ultrapotent antibodies against diverse and highly transmissible SARS-CoV-2 variants 期刊论文
Science, 2021
作者:  Lingshu Wang;  Tongqing Zhou;  Yi Zhang;  Eun Sung Yang;  Chaim A. Schramm;  Wei Shi;  Amarendra Pegu;  Olamide K. Oloniniyi;  Amy R. Henry;  Samuel Darko;  Sandeep R. Narpala;  Christian Hatcher;  David R. Martinez;  Yaroslav Tsybovsky;  Emily Phung;  Olubukola M. Abiona;  Avan Antia;  Evan M. Cale;  Lauren A. Chang;  Misook Choe;  Kizzmekia S. Corbett;  Rachel L. Davis;  Anthony T. DiPiazza;  Ingelise J. Gordon;  Sabrina Helmold Hait;  Tandile Hermanus;  Prudence Kgagudi;  Farida Laboune;  Kwanyee Leung;  Tracy Liu;  Rosemarie D. Mason;  Alexandra F. Nazzari;  Laura Novik;  Sarah O’Connell;  Sijy O’Dell;  Adam S. Olia;  Stephen D. Schmidt;  Tyler Stephens;  Christopher D. Stringham;  Chloe Adrienna Talana;  I-Ting Teng;  Danielle A. Wagner;  Alicia T. Widge;  Baoshan Zhang;  Mario Roederer;  Julie E. Ledgerwood;  Tracy J. Ruckwardt;  Martin R. Gaudinski;  Penny L. Moore;  Nicole A. Doria-Rose;  Ralph S. Baric;  Barney S. Graham;  Adrian B. McDermott;  Daniel C. Douek;  Peter D. Kwong;  John R. Mascola;  Nancy J. Sullivan;  John Misasi
收藏  |  浏览/下载:50/0  |  提交时间:2021/08/17
Tobacco smoking and somatic mutations in human bronchial epithelium 期刊论文
NATURE, 2020, 578 (7794) : 266-+
作者:  Sharma, Nikhil;  Flaherty, Kali;  Lezgiyeva, Karina;  Wagner, Daniel E.;  Klein, Allon M.;  Ginty, David D.
收藏  |  浏览/下载:43/0  |  提交时间:2020/07/03

Whole-genome sequencing of normal bronchial epithelium from 16 individuals shows that tobacco smoking increases genomic heterogeneity, mutational burden and driver mutations, whereas stopping smoking promotes replenishment of the epithelium with near-normal cells.


Tobacco smoking causes lung cancer(1-3), a process that is driven by more than 60 carcinogens in cigarette smoke that directly damage and mutate DNA(4,5). The profound effects of tobacco on the genome of lung cancer cells are well-documented(6-10), but equivalent data for normal bronchial cells are lacking. Here we sequenced whole genomes of 632 colonies derived from single bronchial epithelial cells across 16 subjects. Tobacco smoking was the major influence on mutational burden, typically adding from 1,000 to 10,000 mutations per cell  massively increasing the variance both within and between subjects  and generating several distinct mutational signatures of substitutions and of insertions and deletions. A population of cells in individuals with a history of smoking had mutational burdens that were equivalent to those expected for people who had never smoked: these cells had less damage from tobacco-specific mutational processes, were fourfold more frequent in ex-smokers than current smokers and had considerably longer telomeres than their more-mutated counterparts. Driver mutations increased in frequency with age, affecting 4-14% of cells in middle-aged subjects who had never smoked. In current smokers, at least 25% of cells carried driver mutations and 0-6% of cells had two or even three drivers. Thus, tobacco smoking increases mutational burden, cell-to-cell heterogeneity and driver mutations, but quitting promotes replenishment of the bronchial epithelium from mitotically quiescent cells that have avoided tobacco mutagenesis.


  
The emergence of transcriptional identity in somatosensory neurons 期刊论文
NATURE, 2020, 577 (7790) : 392-+
作者:  Sharma, Nikhil;  Flaherty, Kali;  Lezgiyeva, Karina;  Wagner, Daniel E.;  Klein, Allon M.;  Ginty, David D.
收藏  |  浏览/下载:21/0  |  提交时间:2020/07/03

More than twelve morphologically and physiologically distinct subtypes of primary somatosensory neuron report salient features of our internal and external environments(1-4). It is unclear how specialized gene expression programs emerge during development to endow these subtypes with their unique properties. To assess the developmental progression of transcriptional maturation of each subtype of principal somatosensory neuron, we generated a transcriptomic atlas of cells traversing the primary somatosensory neuron lineage in mice. Here we show that somatosensory neurogenesis gives rise to neurons in a transcriptionally unspecialized state, characterized by co-expression of transcription factors that become restricted to select subtypes as development proceeds. Single-cell transcriptomic analyses of sensory neurons from mutant mice lacking transcription factors suggest that these broad-to-restricted transcription factors coordinate subtype-specific gene expression programs in subtypes in which their expression is maintained. We also show that neuronal targets are involved in this process  disruption of the prototypic target-derived neurotrophic factor NGF leads to aberrant subtype-restricted patterns of transcription factor expression. Our findings support a model in which cues that emanate from intermediate and final target fields promote neuronal diversification in part by transitioning cells from a transcriptionally unspecialized state to transcriptionally distinct subtypes by modulating the selection of subtype-restricted transcription factors.


  
Robust and persistent reactivation of SIV and HIV by N-803 and depletion of CD8(+) cells 期刊论文
NATURE, 2020, 578 (7793) : 154-+
作者:  Diaz-Cuadros, Margarete;  Wagner, Daniel E.;  Budjan, Christoph;  Hubaud, Alexis;  Tarazona, Oscar A.;  Donelly, Sophia;  Michaut, Arthur;  Al Tanoury, Ziad;  Yoshioka-Kobayashi, Kumiko;  Niino, Yusuke;  Kageyama, Ryoichiro;  Miyawaki, Atsushi;  Touboul, Jonathan;  Pourquie, Olivier
收藏  |  浏览/下载:46/0  |  提交时间:2020/07/03

Human immunodeficiency virus (HIV) persists indefinitely in individuals with HIV who receive antiretroviral therapy (ART) owing to a reservoir of latently infected cells that contain replication-competent virus(1-4). Here, to better understand the mechanisms responsible for latency persistence and reversal, we used the interleukin-15 superagonist N-803 in conjunction with the depletion of CD8(+) lymphocytes in ART-treated macaques infected with simian immunodeficiency virus (SIV). Although N-803 alone did not reactivate virus production, its administration after the depletion of CD8(+) lymphocytes in conjunction with ART treatment induced robust and persistent reactivation of the virus in vivo. We found viraemia of more than 60 copies per ml in all macaques (n = 14  100%) and in 41 out of a total of 56 samples (73.2%) that were collected each week after N-803 administration. Notably, concordant results were obtained in ART-treated HIV-infected humanized mice. In addition, we observed that co-culture with CD8(+) T cells blocked the in vitro latency-reversing effect of N-803 on primary human CD4(+) T cells that were latently infected with HIV. These results advance our understanding of the mechanisms responsible for latency reversal and lentivirus reactivation during ART-suppressed infection.


The interleukin-15 superagonist N-803, combined with the depletion of CD8(+) lymphocytes, induced a robust and persistent reactivation of the virus in vivo in both antiretroviral-therapy-treated SIV-infected macaques and HIV-infected humanized mice.


  
Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo 期刊论文
SCIENCE, 2018, 360 (6392) : 981-+
作者:  Wagner, Daniel E.;  Weinreb, Caleb;  Collins, Zach M.;  Briggs, James A.;  Megason, Sean G.;  Klein, Allon M.
收藏  |  浏览/下载:17/0  |  提交时间:2019/11/27
The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution 期刊论文
SCIENCE, 2018, 360 (6392) : 980-+
作者:  Briggs, James A.;  Weinreb, Caleb;  Wagner, Daniel E.;  Megason, Sean;  Peshkin, Leonid;  Kirschner, Marc W.;  Klein, Allon M.
收藏  |  浏览/下载:19/0  |  提交时间:2019/11/27
Relative importance of black carbon, brown carbon, and absorption enhancement from clear coatings in biomass burning emissions 期刊论文
ATMOSPHERIC CHEMISTRY AND PHYSICS, 2017, 17 (8)
作者:  Pokhrel, Rudra P.;  Beamesderfer, Eric R.;  Wagner, Nick L.;  Langridge, Justin M.;  Lack, Daniel A.;  Jayarathne, Thilina;  Stone, Elizabeth A.;  Stockwell, Chelsea E.;  Yokelson, Robert J.;  Murphy, Shane M.
收藏  |  浏览/下载:18/0  |  提交时间:2019/04/09