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Structure modeling and spatial epitope analysis for HA protein of the novel H1N1 influenza virus

Chinese Science Bulletin 2009年第13期54卷 2171-2173页

作者： WU Di XU TianLei SUN Jing DAI JianXin DING GuoHui HE YunGang ZHOU ZhengFeng XIONG Hui DONG Hui JIN WeiRong BIAN Chao JIN Li WANG HongYan WANG XiaoNing YANG Zhong ZHONG Yang WANG Hao CHE XiaoYan HUANG Zhong LAN Ke SUN Bing WU Fan YUAN ZhenAn ZHANG Xi ZHOU XiaoNong ZHOU JiaHai MA ZhiYong TONG GuangZhi GUO YaJun ZHAO GuoPing LI YiXue CAO ZhiWei School of Life Sciences and Technology Tongji University Shanghai 200092 China shanghai center for Bioinformation Technology Shanghai 200235 China School of Life Sciences Fudan University Shanghai 200433 China Cancer Institute of the Second Military Medical University Shanghai 200433 China School of Life Sciences and Technology South China University of Technology Guangzhou 510641 China National Engineering Research center for Antibody Drugs Shanghai 201203 China Zhujiang Hospital Southern Medical University Guangzhou 510282 China shanghai Municipal center for Disease Control & Prevention Shanghai 200336 China shanghai Institutes of Biological Sciences Chinese Academy of Sciences (Lab of Computational Genomics CAS-MPG Partner Institute of Computational Biology center of bioinformatics Key Lab of System Biology Lab of Synthetic Biology Institute of Plant Physiology & Ecology Institute Pasteur) Shanghai 200031 China National Engineering Research center for Biochip Technology Shanghai Biochip Co. Ltd Shanghai 201203 China National Institute for Parasitic Diseases Chinese Center for Disease Control and Prevention Shanghai 200025 China shanghai Institute of Organic Chemistry Chinese Academy of Sciences Shanghai 200032 China shanghai Veterinary Research Institute Chinese Academy of Agricultural Sciences Shanghai 200241 China

In recent months,a novel influenza virus H1N1 broke out around the *** bioinformatics technology,the 3D structure of HA protein was obtained,and the epitope residues were predicted with the method developed in our group for this novel flu virus.58 amino acids were identified as potential epitope residues,the majority of which clustered at the surface of the globular head of HA *** it is located at the similar position,the epitope of HA protein for the novel H1N1 flu virus has obvious differences in the electrostatic potential compared to that of HA proteins from previous flu viruses.

关键词：禽流感病毒抗原表位 A蛋白结构建模和空间生物信息学技术三维结构残留物

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Correction to:Metformin activates chaperone-mediated autophagy and improves disease pathologies in an Alzheimer disease mouse model

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Protein & Cell 2022年第3期13卷 227-229页

作者： Xiaoyan Xu Yaqin Sun Xufeng Cen Bing Shan Qingwei Zhao Tingxue Xie Zhe Wang Tingjun Hou Yu Xue Mengmeng Zhang Di Peng Qiming Sun Cong Yi Ayaz Najafov Hongguang Xia Department of Biochemistry&Research center of Clinical Pharmacy of The First Affiliated Hospital Zhejiang University School of MedicineHangzhou 310058China Liangzhu Laboratory Zhejiang University Medical CenterHangzhou 311121China Department of Cell Biology Harvard Medical SchoolBostonMA 02115USA Interdisciplinary Research center on Biology and Chemistry Shanghai Institute of Organic ChemistryChinese Academy of SciencesShanghai 201203China College of Pharmaceutical Sciences Hangzhou Institute of innovative MedicineZhejiang UniversityHangzhou 310058China Key Laboratory of Molecular Biophysics of Ministry of Education Hubei Bioinformatics and Molecular Imaging Key LaboratoryCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan 430074China

CORRECTION TO:PROTEIN CELL HTTPS://***/10.1007/S13238-021-00858-3 In legend of figure 1,this sentence“(C)293THK cells were treated as in a”should be corrected as“(C)293THK cells were treated as in(A)”.In legend of figure 2,“E-64D(10μmol/L)”in description of panel(B)should be *** section“Metformin activates chaperone-mediated autophagy”of RESULTS,E-64D in sentence“Metformininduced degradation of HK2 and PKM2 was blocked by lysosomal inhibitors(E-64D,Bafilomycin A1 and Leupeptin+NH4Cl)”should be removed.

关键词： Metformin Alzheimer removed

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Chinese Medicine Meets Conventional Medicine in Targeting COVID-19 Pathophysiology,Complications and Comorbidities

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Chinese Journal of Integrative Medicine 2022年第7期28卷 627-635页

作者： WANG Shan-shan ZENG Xian WANG Ya-li Zhuoma Dongzhi ZHAO Yu-fen CHEN Yu-zong Qian Xuesen Collaborative Research center of Astrochemistry and Space Life Sciences Institute of Drug Discovery TechnologyNingbo UniversityNingboZhejiang Province 315211China Department of Biological Medicines&shanghai Engineering Research center of Immunotherapeutics Fudan University School of PharmacyShanghai 201203China bioinformatics and Drug Design Group Department of PharmacyNational University of Singapore117543Singapore Medical College Tibet UniversityLhasa 850011China Department of Chemical Biology College of Chemistry and Chemical Engineeringand The Key Laboratory for Chemical Biology of Fujian ProvinceXiamen UniversityXiamenFujian Province 361005China Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology(Ministry of Education) Department of ChemistryTsinghua UniversityBeijing 102206China

Objective: To investigate how the National Health Commission of China(NHCC)-recommended Chinese medicines(CMs) modulate the major maladjustments of coronavirus disease 2019(COVID-19),particularly the clinically observed complications and comorbidities. Methods: By focusing on the potent targets in common with the conventional medicines, we investigated the mechanisms of 11 NHCC-recommended CMs in the modulation of the major COVID-19 pathophysiology(hyperinflammations, viral replication), complications(pain, headache) and comorbidities(hypertension, obesity, diabetes). The constituent herbs of these CMs and their chemical ingredients were from the Traditional Chinese Medicine Information Database. The experimentally-determined targets and the activity values of the chemical ingredients of these CMs were from the Natural Product Activity and Species Source Database. The approved and clinical trial drugs against these targets were searched from the Therapeutic Target Database and DrugBank Database. Pathways of the targets was obtained from Kyoto Encyclopedia of Genes and Genomes and additional literature search. Results: Overall,9 CMs modulated 6 targets discovered by the COVID-19 target discovery studies, 8 and 11 CMs modulated 8and 6 targets of the approved or clinical trial drugs for the treatment of the major COVID-19 complications and comorbidities, respectively. Conclusion: The coordinated actions of each NHCC-recommended CM against a few targets of the major COVID-19 pathophysiology, complications and comorbidities, partly have common mechanisms with the conventional medicines.

关键词： COVID-19 Chinese medicine target therapeutic mechanism pathophysiology comorbidity

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Bi-directional Selection in Upland Rice Leads to Its Adaptive Differentiation from Lowland Rice in Drought Resistance and Productivity

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Molecular Plant 2019年第2期12卷 170-184页

作者： Hui Xia Zhi Luo Jie Xiong Xiaosong Ma Qiaojun Lou Haibin Wei Jie Qiu Hua Yang Guolan Liu Longjiang Fan Liang Chen Lijun Luo shanghai Agrobiological Gene center Shanghai China College of Plant Sciences & Tech no logy Huazho ng Agricultural University Wuhan China lnstitute of Crop Science & Institute of bioinformatics College of Agriculture and Biotechnology Zhejiang University Hangzhou China These authors contributed equally to this article.

Drought resistance is required in rice breeding to address the challenge of frequent droughts . However, the evolutionary mechanism of rice drought resistance is not fully understood. We investigated the genetic differentiation between upland and lowland rice domesticated in agro-ecosystems with contrasting water-soil conditions using genome-wide SNPs. We estimated morphological differences among upland and lowland rice in drought resistance and productivity through common garden experiments. Upland rice had better drought resistance but poorer productivity. The negative correlations between traits of drought resistance and productivity are attributed to the underlying genetic trade-offs through tight linkages (e.g., DCA1 and OsCesA7) or pleiotropic effects (e.g., LAX1). The genetic trade-offs are comm on and greatly shape the evolutio n of drought resista nee in upland rice . In genomic regions associated with both productivity and drought resistance, signs of balancing selection were detected in upland rice, while signs of directional selection were detected in lowland rice, potentially contributing to their adaptive differentiation. Signs of balancing selection in upland rice resulted from bi-directional selection during its domestication in drought-prone upland *** genome-wide association analysis, we ide ntified several valuable quantitative trait loci associated with drought resista nee, for which highly differentiated genes should be considered candidates. Bi-directional selection breaking tight linkages by accumulating recombination events would be applicable in breeding water-saving and droughtresistance rice.

关键词： drought resistance upland rice ecological adaptation ecotype trade-off domestication

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The mutation network for the hemagglutinin gene from the novel influenza A (H1N1) virus

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Chinese Science Bulletin 2009年第13期54卷 2168-2170页

作者： HE YunGang DING GuoHui BIAN Chao HUANG Zhong LAN Ke SUN Bing WANG XueCai LI YiXue WANG HongYan WANG XiaoNing YANG Zhong ZHONG Yang JIN WeiRong XIONG Hui DAI JianXin GUO YaJun WANG Hao CHE XiaoYan WU Fan YUAN ZhenAn ZHANG Xi CAO ZhiWei ZHOU XiaoNong ZHOU JiaHai MA ZhiYong TONG GuangZhi ZHAO GuoPing JIN Li shanghai Institutes of Biological Sciences Chinese Academy of Sciences (Key Laboratory of Computational Biology CAS-MPG Partner Institute of Computational Biology center of bioinformatics Key Lab of System Biology Lab of Synthetic Biology Institute of Plant Physiology & Ecology Institute Pasteur) Shanghai 200031 China School of Life Sciences Fudan University Shanghai 200433 China shanghai-MOST Key Laboratory for Disease and Health Genomics Chinese National Human Genome Center at Shanghai Shanghai 201203 China Cancer Institute Second Military Medical University Shanghai 200433 China School of Life Sciences and Technology South China University of Technology Guangzhou 510641 China National Engineering Research center for Antibody Drugs Shanghai 201203 China Zhujiang Hospital Southern Medical University G uangzhou 510282 China shanghai Municipal center for Disease Control & Prevention Shanghai 200336 China shanghai center for Bioinformation Technology Shanghai 200235 China School of Life Sciences and Technology Tongji University Shanghai 200092 China National Institute for Parasitic Diseases Chinese Center for Disease Control and Prevention Shanghai 200025 China shanghai Institute of Organic Chemistry Chinese Academy of Sciences Shanghai 200032 China shanghai Veterinary Research Institute Chinese Academy of Agricultural Sciences Shanghai 200241 China National Engineering Research center for Biochip Technology Shanghai Biochip Co. Ltd Shanghai 201203 China

A mutation network for the hemagglutinin gene(HA) of the novel type A(H1N1) influenza virus was *** homology analysis indicated that one HA sequence type from the viruses mainly isolated from Mexico was likely the original type in this *** on the 658A and 1408T mutations in HA,the viruses evolving into this epidemic were divided into three categories,the Mexico,the transitional and the New York *** three groups of viruses presented distinctive clustering features in their geographic distributions.

关键词：流感病毒血凝素基因流行性感冒突变网络序列类型同源性分析地理分布

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The Current State and Perspectives of Systems Biology

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Science Foundation in China 2006年第1期14卷 48-53页

作者： Tielui Shi Bioinformation center Shanghai Institutes for Biological Sciences. CAS. Shanghai 200032 Bioinformation center. shanghai University Shanghai 200444 shanghai center for Bioinformation Technology Shanghai 200235

Emerging as a new field in biology recently, Systems Biology provides a branch new way to study the biological activities in organisms. In order to decode the complexity of life systematically, systems biology integrates the '-omics' and uses the high throughput methods from transcriptomics, protomics and metabonomics to detect the dynamic activities in cell; and then, it incorporates bioinfor-matics methods to integrate and analyze those data, and simulate the biological processes based on the model built from those integrated data. In this paper, the current state, the research field and the methods for the Systems Biology are introduced briefly, and then, several ideas about future development in this field are also proposed.

关键词：系统生物学生物系统建模高吞吐量基因调节网络蛋白质

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Integrative Analysis of Genome,3D Genome,and Transcriptome Alterations of Clinical Lung Cancer Samples

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Genomics, Proteomics & bioinformatics 2021年第5期19卷 741-753页

作者： Tingting Li Ruifeng Li Xuan Dong Lin Shi Miao Lin Ting Peng Pengze Wu Yuting Liu Xiaoting Li Xuheng He Xu Han Bin Kang Yinan Wang Zhiheng Liu Qing Chen Yue Shen Mingxiang Feng Xiangdong Wang Duojiao Wu Jian Wang Cheng Li center for bioinformatics School of Life SciencesCenter for Statistical SciencePeking UniversityBeijing 100871China BGI-Shenzhen Shenzhen 518083China Zhongshan Hospital Institute of Clinical Science Fudan UniversityShanghai Institute of Clinical BioinformaticsShanghai 200433China Fudan University center for Clinical bioinformatics Shanghai 200433China Department of Thoracic Surgery Zhongshan Hospital of Fudan UniversityShanghai 200032China School of Life Sciences Tsinghua UniversityBeijing 100084China BGI-Qingdao Qingdao 266426China Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics BGI-ShenzhenShenzhen 518083China iCarbonX Shenzhen 518053China Digital Life Research Institute Shenzhen 518110China State Key Laboratory of Proteomics National Center of Biomedical AnalysisInstitute of Basic Medical SciencesBeijing 100850China China National GeneBank BGI-ShenzhenShenzhen 518083China

Genomic studies of cancer cell alterations,such as mutations,copy number variations(CNVs),and translocations,greatly promote our understanding of the genesis and development of ***,the 3D genome architecture of cancers remains less studied due to the complexity of cancer genomes and technical *** explore the 3D genome structure in clinical lung cancer,we performed Hi-C experiments using paired normal and tumor cells harvested from patients with lung cancer,combining with RNA sequenceing *** demonstrated the feasibility of studying 3D genome of clinical lung cancer samples with a small number of cells(1×10^(4)),compared the genome architecture between clinical samples and cell lines of lung cancer,and identified conserved and changed spatial chromatin structures between normal and cancer *** also showed that Hi-C data can be used to infer CNVs and point mutations in *** integrating those different types of cancer alterations,we showed significant associations between CNVs,3D genome,and gene *** propose that 3D genome mediates the effects of cancer genomic alterations on gene expression through altering regulatory chromatin *** study highlights the importance of analyzing 3D genomes of clinical cancer samples in addition to cancer cell lines and provides an integrative genomic analysis pipeline for future larger-scale studies in lung cancer and other cancers.

关键词： Lung cancer 3D genome Copy number variation Clinical sample Integrative genomic analysis

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CO2 Laser Moxibustion for Knee Osteoarthritis: Study Protocol for A Multicenter, Double-Blind, Randomized Controlled Trial

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Chinese Journal of Integrative Medicine 2020年第8期26卷 568-576页

作者： GUO Meng-hu ZHAO Ling WU Fan DU Jiong DING Chen-huan GE Jing-hua TAN Ming T LAO Li-xing SHEN Xue-yong CHENG Ke School of Acupuncture-Moxibustion and Tuina Shanghai University of Traditional Chinese MedicineShanghai 201203China Shuguang Hospital Affiliated to shanghai University of Traditional Chinese Medicine Shanghai 200021China Renji Hospital Affiliated to shanghai Jiaotong University Shanghai 200127China shanghai Changning Tianshan Traditional Chinese Medicine Hospital Shanghai 200051China Department of Biostatistics Bioinformatics and BiomathematicsGeorgetown University Medical CenterWashingtonD.C.20057USA School of Chinese Medicine University of Hong KongHong Kong SARChina

Background:Knee osteoarthritis(OA)is a major cause of disability among the older *** treatments are safe and *** is commonly used in treating knee OA in Chinese medicine(CM).CO2 Laser moxibustion device is a substitute for traditional moxibustion,which mimics the effects of traditional *** data are needed to support its application in knee ***:The trial aims to assess the effect and safety of CO2 laser moxibustion in patients with knee osteoarthritis compared with a sham ***:This is a protocol for a multicenter,randomized,double-blind,placebo-controlled trial.A total of 392 participants were recruited and assigned to the CO2 laser moxibustion group and sham laser moxibustion group with a 1:1 ratio at 6 outpatient clinics in shanghai,*** in both groups received treatment at the affected knee(s)at the acupuncture point Dubi(ST 35)and an Ashi *** were 3 sessions per week for 4 weeks,and an additional 20-week *** outcomes were changes in the Western Ontario and McMaster Universities Osteoarthritis Index(WOMAC)pain scores at week *** outcomes were WOMAC function score,stiffness score and overall score,VAS pain,Short-Form heath survey(SF-36),and patients’global *** serum levels of cytokines involved in progress of knee OA were *** was assessed during the whole *** effectiveness was assessed by both participants and treatment ***:CO2 laser moxibustion device,designed as a substitute for CM moxibustion,is easy to use and control with no choking smoke and smell,and is a plausible method for double-blind *** study would provide rigorous evidence for the effect and safety of CO2 laser moxibustion in treating knee OA.

关键词： Chinese medicine laser moxibustion knee osteoarthritis pain randomized controlled trial

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Dynamic Perception of Jasmonates by the F-Box Protein C0l1

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Molecular Plant 2018年第10期11卷 1237-1247页

作者： Jianbin Yan Ruifeng Yao Li Chen Suhua Lit Min Gut Fajun Nan Daoxin Xie MOE Key Laboratory of bioinformatics Tsinghua-Peking Joint Center for Life Sciences School of Life Sciences Tsinghua University Beijing 100084 China State Key Laboratory of Drug Research the National Center for Drug Screening Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai201203 China These authors contributed equally to this article.

Jasmonates （JAs） are cyclic fatty acid-derived phytohormones that regulate diverse aspects of plant defense and development. The endogenous active JA molecule （＋）-7-iso-JA-L-Ile （JA-Ile） and its analog coronatine trigger formation of a complex with the F-box protein C011 and JAZ repressors to induce degra- dation of the JAZs through the 26S proteasome pathway in a COil-dependent manner. To reveal the forma-tion process of COI1-JA-JAZ ternary complex, we employed several biochemical approaches to examine how JA is dynamically perceived. These analyses showed that the COI1 proteins of Arabidopsis and rice bind JA with appreciable binding affinity and revealed the kinetics and thermodynamics of the COI1-JA-JAZ ternary complex. Our results suggest that COI1 is the primary receptor perceiving the active JA molecule to initially form a COI1-JA complex that subsequently recruits JAZs for further signal transduction.

关键词： phytohormone receptor jasmonate C011

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Next-generation sequencing technologies for personalized medicine:promising but challenging

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Science China(Life Sciences) 2013年第2期56卷 101-103页

作者： CHEN Geng SHI TieLiu center for bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal University

In the past several years,next-generation sequencing(NGS) technologies have greatly revolutionized our approaches to explore and depict the characteristics and functions of the genomes for various *** NGS technologies have been broadly used in diverse fields including genomics(genome sequencing and exome sequencing) [1,2],transcriptomics(RNA-Seq) [3,4] and epigenomics(ChIP-Seq,

关键词：测序技术个性化挑战性基因组测序医药基因组学物种

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