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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:13/0  |  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.


  
Olfactory receptor and circuit evolution promote host specialization 期刊论文
NATURE, 2020
作者:  Chen, Tse-An;  Chuu, Chih-Piao;  Tseng, Chien-Chih;  Wen, Chao-Kai;  Wong, H. -S. Philip;  Pan, Shuangyuan;  Li, Rongtan;  Chao, Tzu-Ang;  Chueh, Wei-Chen;  Zhang, Yanfeng;  Fu, Qiang;  Yakobson, Boris I.;  Chang, Wen-Hao;  Li, Lain-Jong
收藏  |  浏览/下载:8/0  |  提交时间:2020/07/03

The evolution of animal behaviour is poorly understood(1,2). Despite numerous correlations between interspecific divergence in behaviour and nervous system structure and function, demonstrations of the genetic basis of these behavioural differences remain rare(3-5). Here we develop a neurogenetic model, Drosophila sechellia, a species that displays marked differences in behaviour compared to its close cousin Drosophila melanogaster(6,7), which are linked to its extreme specialization on noni fruit (Morinda citrifolia)(8-16). Using calcium imaging, we identify olfactory pathways in D. sechellia that detect volatiles emitted by the noni host. Our mutational analysis indicates roles for different olfactory receptors in long- and short-range attraction to noni, and our cross-species allele-transfer experiments demonstrate that the tuning of one of these receptors is important for species-specific host-seeking. We identify the molecular determinants of this functional change, and characterize their evolutionary origin and behavioural importance. We perform circuit tracing in the D. sechellia brain, and find that receptor adaptations are accompanied by increased sensory pooling onto interneurons as well as species-specific central projection patterns. This work reveals an accumulation of molecular, physiological and anatomical traits that are linked to behavioural divergence between species, and defines a model for investigating speciation and the evolution of the nervous system.


A neurogenetic model, Drosophila sechellia-a relative of Drosophila melanogaster that has developed an extreme specialization for a single host plant-sheds light on the evolution of interspecific differences in behaviour.


  
Spontaneous gyrotropic electronic order in a transition-metal dichalcogenide 期刊论文
NATURE, 2020, 578 (7796) : 545-+
作者:  Kum, Hyun S.;  Lee, Hyungwoo;  Kim, Sungkyu;  Lindemann, Shane;  Kong, Wei;  Qiao, Kuan;  Chen, Peng;  Irwin, Julian;  Lee, June Hyuk;  Xie, Saien;  Subramanian, Shruti;  Shim, Jaewoo;  Bae, Sang-Hoon;  Choi, Chanyeol;  Ranno, Luigi;  Seo, Seungju;  Lee, Sangho;  Bauer, Jackson;  Li, Huashan;  Lee, Kyusang;  Robinson, Joshua A.;  Ross, Caroline A.;  Schlom, Darrell G.;  Rzchowski, Mark S.;  Eom, Chang-Beom;  Kim, Jeehwan
收藏  |  浏览/下载:10/0  |  提交时间:2020/07/03

Chirality is ubiquitous in nature, and populations of opposite chiralities are surprisingly asymmetric at fundamental levels(1,2). Examples range from parity violation in the subatomic weak force to homochirality in biomolecules. The ability to achieve chirality-selective synthesis (chiral induction) is of great importance in stereochemistry, molecular biology and pharmacology(2). In condensed matter physics, a crystalline electronic system is geometrically chiral when it lacks mirror planes, space-inversion centres or rotoinversion axes(1). Typically, geometrical chirality is predefined by the chiral lattice structure of a material, which is fixed on formation of the crystal. By contrast, in materials with gyrotropic order(3-6), electrons spontaneously organize themselves to exhibit macroscopic chirality in an originally achiral lattice. Although such order-which has been proposed as the quantum analogue of cholesteric liquid crystals-has attracted considerable interest(3-15), no clear observation or manipulation of gyrotropic order has been achieved so far. Here we report the realization of optical chiral induction and the observation of a gyrotropically ordered phase in the transition-metal dichalcogenide semimetal 1T-TiSe2. We show that shining mid-infrared circularly polarized light on 1T-TiSe2 while cooling it below the critical temperature leads to the preferential formation of one chiral domain. The chirality of this state is confirmed by the measurement of an out-of-plane circular photogalvanic current, the direction of which depends on the optical induction. Although the role of domain walls requires further investigation with local probes, the methodology demonstrated here can be applied to realize and control chiral electronic phases in other quantum materials(4,16).


Optical chiral induction and spontaneous gyrotropic electronic order are realized in the transition-metal chalcogenide 1T-TiSe2 by using illumination with mid-infrared circularly polarized light and simultaneous cooling below the critical temperature.


  
Structural basis of energy transfer in Porphyridium purpureum phycobilisome 期刊论文
NATURE, 2020
作者:  Long, Haizhen;  Zhang, Liwei;  Lv, Mengjie;  Wen, Zengqi;  Zhang, Wenhao;  Chen, Xiulan;  Zhang, Peitao;  Li, Tongqing;  Chang, Luyuan;  Jin, Caiwei;  Wu, Guozhao;  Wang, Xi;  Yang, Fuquan;  Pei, Jianfeng;  Chen, Ping;  Margueron, Raphael;  Deng, Haiteng;  Zhu, Mingzhao;  Li, Guohong
收藏  |  浏览/下载:26/0  |  提交时间:2020/07/03

The cryo-electron microscopy structure of a phycobilisome from the red alga Porphyridium purpureum reveals how aromatic interactions between the linker proteins and the chromophores drive a unidirectional transfer of energy.


Photosynthetic organisms have developed various light-harvesting systems to adapt to their environments(1). Phycobilisomes are large light-harvesting protein complexes found in cyanobacteria and red algae(2-4), although how the energies of the chromophores within these complexes are modulated by their environment is unclear. Here we report the cryo-electron microscopy structure of a 14.7-megadalton phycobilisome with a hemiellipsoidal shape from the red alga Porphyridium purpureum. Within this complex we determine the structures of 706 protein subunits, including 528 phycoerythrin, 72 phycocyanin, 46 allophycocyanin and 60 linker proteins. In addition, 1,598 chromophores are resolved comprising 1,430 phycoerythrobilin, 48 phycourobilin and 120 phycocyanobilin molecules. The markedly improved resolution of our structure compared with that of the phycobilisome of Griffithsia pacifica(5) enabled us to build an accurate atomic model of the P. purpureum phycobilisome system. The model reveals how the linker proteins affect the microenvironment of the chromophores, and suggests that interactions of the aromatic amino acids of the linker proteins with the chromophores may be a key factor in fine-tuning the energy states of the chromophores to ensure the efficient unidirectional transfer of energy.


  
Gram-scale bottom-up flash graphene synthesis 期刊论文
NATURE, 2020, 577 (7792) : 647-651
作者:  Long, Haizhen;  Zhang, Liwei;  Lv, Mengjie;  Wen, Zengqi;  Zhang, Wenhao;  Chen, Xiulan;  Zhang, Peitao;  Li, Tongqing;  Chang, Luyuan;  Jin, Caiwei;  Wu, Guozhao;  Wang, Xi;  Yang, Fuquan;  Pei, Jianfeng;  Chen, Ping;  Margueron, Raphael;  Deng, Haiteng;  Zhu, Mingzhao;  Li, Guohong
收藏  |  浏览/下载:13/0  |  提交时间:2020/07/03

Most bulk-scale graphene is produced by a top-down approach, exfoliating graphite, which often requires large amounts of solvent with high-energy mixing, shearing, sonication or electrochemical treatment(1-3). Although chemical oxidation of graphite to graphene oxide promotes exfoliation, it requires harsh oxidants and leaves the graphene with a defective perforated structure after the subsequent reduction step(3,4). Bottom-up synthesis of high-quality graphene is often restricted to ultrasmall amounts if performed by chemical vapour deposition or advanced synthetic organic methods, or it provides a defect-ridden structure if carried out in bulk solution(4-6). Here we show that flash Joule heating of inexpensive carbon sources-such as coal, petroleum coke, biochar, carbon black, discarded food, rubber tyres and mixed plastic waste-can afford gram-scale quantities of graphene in less than one second. The product, named flash graphene (FG) after the process used to produce it, shows turbostratic arrangement (that is, little order) between the stacked graphene layers. FG synthesis uses no furnace and no solvents or reactive gases. Yields depend on the carbon content of the source  when using a high-carbon source, such as carbon black, anthracitic coal or calcined coke, yields can range from 80 to 90 per cent with carbon purity greater than 99 per cent. No purification steps are necessary. Raman spectroscopy analysis shows a low-intensity or absent D band for FG, indicating that FG has among the lowest defect concentrations reported so far for graphene, and confirms the turbostratic stacking of FG, which is clearly distinguished from turbostratic graphite. The disordered orientation of FG layers facilitates its rapid exfoliation upon mixing during composite formation. The electric energy cost for FG synthesis is only about 7.2 kilojoules per gram, which could render FG suitable for use in bulk composites of plastic, metals, plywood, concrete and other building materials.


Flash Joule heating of inexpensive carbon sources is used to produce gram-scale quantities of high-quality graphene in under a second, without the need for a furnace, solvents or reactive gases.


  
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:42/0  |  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.


  
An Argonaute phosphorylation cycle promotes microRNA-mediated silencing 期刊论文
NATURE, 2017, 542 (7640) : 197-202
作者:  Golden, Ryan J.;  Chen, Beibei;  Li, Tuo;  Braun, Juliane;  Manjunath, Hema;  Chen, Xiang;  Wu, Jiaxi;  Schmid, Vanessa;  Chang, Tsung-Cheng;  Kopp, Florian;  Ramirez-Martinez, Andres;  Tagliabracci, Vincent S.;  Chen, Zhijian J.;  Xie, Yang;  Mendell, Joshua T.
收藏  |  浏览/下载:8/0  |  提交时间:2019/04/09