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Molecular architecture of lineage allocation and tissue organization in early mouse embryo (vol 572, 528, 2019) 期刊论文
NATURE, 2020, 577 (7791) : E6-E6
作者:  Peng, Guangdun;  Suo, Shengbao;  Cui, Guizhong;  Yu, Fang;  Wang, Ran;  Chen, Jun;  Chen, Shirui;  Liu, Zhiwen;  Chen, Guoyu;  Qian, Yun;  Tam, Patrick P. L.;  Han, Jing-Dong J.;  Jing, Naihe
收藏  |  浏览/下载:13/0  |  提交时间:2020/07/03
The water lily genome and the early evolution of flowering plants 期刊论文
NATURE, 2020, 577 (7788) : 79-+
作者:  Zhang, Liangsheng;  Chen, Fei;  Zhang, Xingtan;  Li, Zhen;  Zhao, Yiyong;  Lohaus, Rolf;  Chang, Xiaojun;  Dong, Wei;  Ho, Simon Y. W.;  Liu, Xing;  Song, Aixia;  Chen, Junhao;  Guo, Wenlei;  Wang, Zhengjia;  Zhuang, Yingyu;  Wang, Haifeng;  Chen, Xuequn;  Hu, Juan;  Liu, Yanhui;  Qin, Yuan;  Wang, Kai;  Dong, Shanshan;  Liu, Yang;  Zhang, Shouzhou;  Yu, Xianxian;  Wu, Qian;  Wang, Liangsheng;  Yan, Xueqing;  Jiao, Yuannian;  Kong, Hongzhi;  Zhou, Xiaofan;  Yu, Cuiwei;  Chen, Yuchu;  Li, Fan;  Wang, Jihua;  Chen, Wei;  Chen, Xinlu;  Jia, Qidong;  Zhang, Chi;  Jiang, Yifan;  Zhang, Wanbo;  Liu, Guanhua;  Fu, Jianyu;  Chen, Feng;  Ma, Hong;  Van de Peer, Yves;  Tang, Haibao
收藏  |  浏览/下载:11/0  |  提交时间:2020/07/03

Water lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form the so-called ANA-grade of angiosperms, which are extant representatives of lineages that diverged the earliest from the lineage leading to the extant mesangiosperms(1-3). Here we report the 409-megabase genome sequence of the blue-petal water lily (Nymphaea colorata). Our phylogenomic analyses support Amborellales and Nymphaeales as successive sister lineages to all other extant angiosperms. The N. colorata genome and 19 other water lily transcriptomes reveal a Nymphaealean whole-genome duplication event, which is shared by Nymphaeaceae and possibly Cabombaceae. Among the genes retained from this whole-genome duplication are homologues of genes that regulate flowering transition and flower development. The broad expression of homologues of floral ABCE genes in N. colorata might support a similarly broadly active ancestral ABCE model of floral organ determination in early angiosperms. Water lilies have evolved attractive floral scents and colours, which are features shared with mesangiosperms, and we identified their putative biosynthetic genes in N. colorata. The chemical compounds and biosynthetic genes behind floral scents suggest that they have evolved in parallel to those in mesangiosperms. Because of its unique phylogenetic position, the N. colorata genome sheds light on the early evolution of angiosperms.


  
Recycling and metabolic flexibility dictate life in the lower oceanic crust 期刊论文
NATURE, 2020, 579 (7798) : 250-+
作者:  Zhou, Peng;  Yang, Xing-Lou;  Wang, Xian-Guang;  Hu, Ben;  Zhang, Lei;  Zhang, Wei;  Si, Hao-Rui;  Zhu, Yan;  Li, Bei;  Huang, Chao-Lin;  Chen, Hui-Dong;  Chen, Jing;  Luo, Yun;  Guo, Hua;  Jiang, Ren-Di;  Liu, Mei-Qin;  Chen, Ying;  Shen, Xu-Rui;  Wang, Xi;  Zheng, Xiao-Shuang;  Zhao, Kai;  Chen, Quan-Jiao;  Deng, Fei;  Liu, Lin-Lin;  Yan, Bing;  Zhan, Fa-Xian;  Wang, Yan-Yi;  Xiao, Geng-Fu;  Shi, Zheng-Li
收藏  |  浏览/下载:37/0  |  提交时间:2020/05/13

The lithified lower oceanic crust is one of Earth'  s last biological frontiers as it is difficult to access. It is challenging for microbiota that live in marine subsurface sediments or igneous basement to obtain sufficient carbon resources and energy to support growth(1-3) or to meet basal power requirements(4) during periods of resource scarcity. Here we show how limited and unpredictable sources of carbon and energy dictate survival strategies used by low-biomass microbial communities that live 10-750 m below the seafloor at Atlantis Bank, Indian Ocean, where Earth'  s lower crust is exposed at the seafloor. Assays of enzyme activities, lipid biomarkers, marker genes and microscopy indicate heterogeneously distributed and viable biomass with ultralow cell densities (fewer than 2,000 cells per cm(3)). Expression of genes involved in unexpected heterotrophic processes includes those with a role in the degradation of polyaromatic hydrocarbons, use of polyhydroxyalkanoates as carbon-storage molecules and recycling of amino acids to produce compounds that can participate in redox reactions and energy production. Our study provides insights into how microorganisms in the plutonic crust are able to survive within fractures or porous substrates by coupling sources of energy to organic and inorganic carbon resources that are probably delivered through the circulation of subseafloor fluids or seawater.


  
Signatures of self-organized criticality in an ultracold atomic gas (vol 577, pg 481, 2020) 期刊论文
NATURE, 2020, 579 (7800) : E13-E13
作者:  Zhou, Xiaoling;  Feng, Zongqiang;  Zhu, Linli;  Xu, Jianing;  Miyagi, Lowell;  Dong, Hongliang;  Sheng, Hongwei;  Wang, Yanju;  Li, Quan;  Ma, Yanming;  Zhang, Hengzhong;  Yan, Jinyuan;  Tamura, Nobumichi;  Kunz, Martin;  Lutker, Katie;  Huang, Tianlin;  Hughes, Darcy A.;  Huang, Xiaoxu;  Chen, Bin
收藏  |  浏览/下载:17/0  |  提交时间:2020/07/03

An amendment to this paper has been published and can be accessed via a link at the top of the paper.


  
Mechanism of adrenergic Ca(V)1.2 stimulation revealed by proximity proteomics 期刊论文
NATURE, 2020, 577 (7792) : 695-+
作者:  Peng, Guangdun;  Suo, Shengbao;  Cui, Guizhong;  Yu, Fang;  Wang, Ran;  Chen, Jun;  Chen, Shirui;  Liu, Zhiwen;  Chen, Guoyu;  Qian, Yun;  Tam, Patrick P. L.;  Han, Jing-Dong J.;  Jing, Naihe
收藏  |  浏览/下载:24/0  |  提交时间:2020/07/03

An in vivo approach to identify proteins whose enrichment near cardiac Ca(V)1.2 channels changes upon beta-adrenergic stimulation finds the G protein Rad, which is phosphorylated by protein kinase A, thereby relieving channel inhibition by Rad and causing an increased Ca2+ current.


Increased cardiac contractility during the fight-or-flight response is caused by beta-adrenergic augmentation of Ca(V)1.2 voltage-gated calcium channels(1-4). However, this augmentation persists in transgenic murine hearts expressing mutant Ca(V)1.2 alpha(1C) and beta subunits that can no longer be phosphorylated by protein kinase A-an essential downstream mediator of beta-adrenergic signalling-suggesting that non-channel factors are also required. Here we identify the mechanism by which beta-adrenergic agonists stimulate voltage-gated calcium channels. We express alpha(1C) or beta(2B) subunits conjugated to ascorbate peroxidase(5) in mouse hearts, and use multiplexed quantitative proteomics(6,7) to track hundreds of proteins in the proximity of Ca(V)1.2. We observe that the calcium-channel inhibitor Rad(8,9), a monomeric G protein, is enriched in the Ca(V)1.2 microenvironment but is depleted during beta-adrenergic stimulation. Phosphorylation by protein kinase A of specific serine residues on Rad decreases its affinity for beta subunits and relieves constitutive inhibition of Ca(V)1.2, observed as an increase in channel open probability. Expression of Rad or its homologue Rem in HEK293T cells also imparts stimulation of Ca(V)1.3 and Ca(V)2.2 by protein kinase A, revealing an evolutionarily conserved mechanism that confers adrenergic modulation upon voltage-gated calcium channels.


  
Decoding the development of the human hippocampus 期刊论文
NATURE, 2020, 577 (7791) : 531-+
作者:  Zhong, Suijuan;  Ding, Wenyu;  Sun, Le;  Lu, Yufeng;  Dong, Hao;  Fan, Xiaoying;  Liu, Zeyuan;  Chen, Ruiguo;  Zhang, Shu;  Ma, Qiang;  Tang, Fuchou;  Wu, Qian;  Wang, Xiaoqun
收藏  |  浏览/下载:13/0  |  提交时间:2020/07/03

The hippocampus is an important part of the limbic system in the human brain that has essential roles in spatial navigation and the consolidation of information from short-term memory to long-term memory(1,2). Here we use single-cell RNA sequencing and assay for transposase-accessible chromatin using sequencing (ATAC-seq) analysis to illustrate the cell types, cell linage, molecular features and transcriptional regulation of the developing human hippocampus. Using the transcriptomes of 30,416 cells from the human hippocampus at gestational weeks 16-27, we identify 47 cell subtypes and their developmental trajectories. We also identify the migrating paths and cell lineages of PAX6(+) and HOPX+ hippocampal progenitors, and regional markers of CA1, CA3 and dentate gyrus neurons. Multiomic data have uncovered transcriptional regulatory networks of the dentate gyrus marker PROX1. We also illustrate spatially specific gene expression in the developing human prefrontal cortex and hippocampus. The molecular features of the human hippocampus at gestational weeks 16-20 are similar to those of the mouse at postnatal days 0-5 and reveal gene expression differences between the two species. Transient expression of the primate-specific gene NBPF1 leads to a marked increase in PROX1(+) cells in the mouse hippocampus. These data provides a blueprint for understanding human hippocampal development and a tool for investigating related diseases.


Single-cell RNA sequencing is used to catalogue and explore the developmental trajectories of more than 30,000 cells in the developing human hippocampus.


  
B cells and tertiary lymphoid structures promote immunotherapy response 期刊论文
NATURE, 2020, 577 (7791) : 549-+
作者:  Zhang, Liangsheng;  Chen, Fei;  Zhang, Xingtan;  Li, Zhen;  Zhao, Yiyong;  Lohaus, Rolf;  Chang, Xiaojun;  Dong, Wei;  Ho, Simon Y. W.;  Liu, Xing;  Song, Aixia;  Chen, Junhao;  Guo, Wenlei;  Wang, Zhengjia;  Zhuang, Yingyu;  Wang, Haifeng;  Chen, Xuequn;  Hu, Juan;  Liu, Yanhui;  Qin, Yuan;  Wang, Kai;  Dong, Shanshan;  Liu, Yang;  Zhang, Shouzhou;  Yu, Xianxian;  Wu, Qian;  Wang, Liangsheng;  Yan, Xueqing;  Jiao, Yuannian;  Kong, Hongzhi;  Zhou, Xiaofan;  Yu, Cuiwei;  Chen, Yuchu;  Li, Fan;  Wang, Jihua;  Chen, Wei;  Chen, Xinlu;  Jia, Qidong;  Zhang, Chi;  Jiang, Yifan;  Zhang, Wanbo;  Liu, Guanhua;  Fu, Jianyu;  Chen, Feng;  Ma, Hong;  Van de Peer, Yves;  Tang, Haibao
收藏  |  浏览/下载:41/0  |  提交时间:2020/07/03

Multiomic profiling of several cohorts of patients treated with immune checkpoint blockade highlights the presence and potential role of B cells and tertiary lymphoid structures in promoting therapy response.


Treatment with immune checkpoint blockade (ICB) has revolutionized cancer therapy. Until now, predictive biomarkers(1-10) and strategies to augment clinical response have largely focused on the T cell compartment. However, other immune subsets may also contribute to anti-tumour immunity(11-15), although these have been less well-studied in ICB treatment(16). A previously conducted neoadjuvant ICB trial in patients with melanoma showed via targeted expression profiling(17) that B cell signatures were enriched in the tumours of patients who respond to treatment versus non-responding patients. To build on this, here we performed bulk RNA sequencing and found that B cell markers were the most differentially expressed genes in the tumours of responders versus non-responders. Our findings were corroborated using a computational method (MCP-counter(18)) to estimate the immune and stromal composition in this and two other ICB-treated cohorts (patients with melanoma and renal cell carcinoma). Histological evaluation highlighted the localization of B cells within tertiary lymphoid structures. We assessed the potential functional contributions of B cells via bulk and single-cell RNA sequencing, which demonstrate clonal expansion and unique functional states of B cells in responders. Mass cytometry showed that switched memory B cells were enriched in the tumours of responders. Together, these data provide insights into the potential role of B cells and tertiary lymphoid structures in the response to ICB treatment, with implications for the development of biomarkers and therapeutic targets.


  
The promise and challenge of therapeutic genome editing 期刊论文
NATURE, 2020, 578 (7794) : 229-236
作者:  Zhong, Suijuan;  Ding, Wenyu;  Sun, Le;  Lu, Yufeng;  Dong, Hao;  Fan, Xiaoying;  Liu, Zeyuan;  Chen, Ruiguo;  Zhang, Shu;  Ma, Qiang;  Tang, Fuchou;  Wu, Qian;  Wang, Xiaoqun
收藏  |  浏览/下载:37/0  |  提交时间:2020/07/03

Genome editing, which involves the precise manipulation of cellular DNA sequences to alter cell fates and organism traits, has the potential to both improve our understanding of human genetics and cure genetic disease. Here I discuss the scientific, technical and ethical aspects of using CRISPR (clustered regularly interspaced short palindromic repeats) technology for therapeutic applications in humans, focusing on specific examples that highlight both opportunities and challenges. Genome editing is-or will soon be-in the clinic for several diseases, with more applications under development. The rapid pace of the field demands active efforts to ensure that this breakthrough technology is used responsibly to treat, cure and prevent genetic disease.


  
Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours 期刊论文
NATURE, 2018, 555 (7696) : 371-+
作者:  Ma, Xiaotu;  Liu, Yu;  Liu, Yanling;  Alexandrov, Ludmil B.;  Edmonson, Michael N.;  Gawad, Charles;  Zhou, Xin;  Li, Yongjin;  Rusch, Michael C.;  Easton, John;  Huether, Robert;  Gonzalez-Pena, Veronica;  Wilkinson, Mark R.;  Hermida, Leandro C.;  Davis, Sean;  Sioson, Edgar;  Pounds, Stanley;  Cao, Xueyuan;  Ries, Rhonda E.;  Wang, Zhaoming;  Chen, Xiang;  Dong, Li;  Diskin, Sharon J.;  Smith, Malcolm A.;  Auvil, Jaime M. Guidry;  Meltzer, Paul S.;  Lau, Ching C.;  Perlman, Elizabeth J.;  Maris, John M.;  Meshinchi, Soheil;  Hunger, Stephen P.;  Gerhard, Daniela S.;  Zhang, Jinghui
收藏  |  浏览/下载:15/0  |  提交时间:2019/11/27
Architecture of an HIV-1 reverse transcriptase initiation complex 期刊论文
NATURE, 2018, 557 (7703) : 118-+
作者:  Larsen, Kevin P.;  Mathiharan, Yamuna Kalyani;  Kappel, Kalli;  Coey, Aaron T.;  Chen, Dong-Hua;  Barrero, Daniel;  Madigan, Lauren;  Puglisi, Joseph D.;  Skiniotis, Georgios;  Puglisi, Elisabetta Viani
收藏  |  浏览/下载:6/0  |  提交时间:2019/11/27