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Reconstruction of the most recent common ancestor sequences of SARS-Cov S gene and detection of adaptive evolution in the spike protein

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chinese Science Bulletin 2004年第12期49卷 1311-1313页

作者： ZHANG Yuan1, ZHENG Nan2,3, HAO Pei4,5 & ZHONG Yang6 1. laboratory of Systematic and Evolutionary Botany, Institute of Bot- any, chinese Academy of Sciences, Beijing 100093, china 2. College of Life Sciences, Beijing Normal University, Beijing 100875, china 3. Institute of Viral disease Control and Prevention, chinese CDC, Beijing 100052, china 4. Bioinformation center, shanghai Institutes for Biological Sciences, chinese Academy of Sciences, shanghai 200031, china 5. shanghai center for Bioinformation Technology, shanghai 200235, china 6. School of Life Sciences, Fudan University, shanghai 200433, china 1laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences 100093 Beijing China. 2College of Life Sciences Beijing Normal University 100875 Beijing China. 3Institute of Viral disease Control and Prevention Chinese CDC 100052 Beijing China. 4Bioinformation center Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 200031 Shanghai China. 5shanghai center for Bioinformation Technology 200235 Shanghai China. 6School of Life Sciences Fudan University 200433 Shanghai China.

The genome organization and expression strategy of severe acute respiratory syndrome coronavirus (SARSCoV) have been described extensivelyl1- 10]. As a structural glycoprotein on the virion surface, the spike protein is responsible for binding to host cellular receptors and for the fusion between the viral envelope and the cellular membrane. It also induces neutralizing antibodies in the host and mediates cellular immunity[11]. Previous studies suggested that amino acid replacements in the spike protein could dramatically alter the pathogenesis and virulence of some coronaviruses[11]. It is therefore reasonable to test the hypothesis that radical amino acid replacements in the spike protein, favored by environmental selective pressure during the process of SARS-CoV interspecific transmission[10], might make this pathogen adapt to a new host. In this study, we investigated a total of 108complete sequences of the SARS-CoV S gene from GenBank (until March 23, 2004). After omission of those records containing frame-shift mutations or low quality sequences, e.g. ZJ01, and selection of one sequence for identical records, an alignment of 42 sequences was obtained using the program Clustal-X[13]. Then, we reconstructed the most recent common ancestor (MRCA) sequences of the SARS-CoV S gene and detected the adaptive evolution in the spike protein.

关键词： SARS冠状病毒自适应进化基因表达糖蛋白分子免疫学波峰病毒

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Interaction between Mnk2 and CBC^(VHL) ubiquitin ligase E3 complex

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Science china(Life Sciences) 2006年第3期49卷 265-273页

作者： WANG Pingzhang, WANG Xin, WANG Feng, CAI Tianjing & LUO Ying chinese national human genome center, Beijing 100176, china Institute of Basic Medical Sciences, chinese Acadamy of Medical Sciences, Beijing 100005, china shanghai genomics Inc., shanghai 201203, china chinese national human genome center Beijing 100176 China Institute of Basic Medical Sciences Chinese Acadamy of Medical Sciences Beijing 100005 China chinese national human genome center Beijing 100176 China shanghai genomics Inc. Shanghai 201203 China

MAP kinase-interacting kinase-2 (Mnk2) is one of the downstream kinasesactivated by MAP kinases. It phosphorylates the eukaryotic initiation factor 4E (elF4E), althoughthe role of elF4E phosphorylation and the role of Mnk2 in the process of proteintranslation are notwell understood. Except for elF4E, other physiological substrates of Mnk2 are still unidentified. Tolook for these unidentified substrates and to reveal the physiological function of Mnk2, weperformed a yeast two-hybrid screening with Mnk2 as the bait. The results demonstrated Mnk2 couldinteract with VHL (von Hippel-Lindau tumor suppressor), Rbx1 (ring-box1) and Cul2 (Cullin2) proteinsin yeast cells. Furthermore, we validated the interaction between Mnk2 and VHL proteins inmammalian cells by co-immunoprecipitation analysis. Because the three proteins VHL, Rbx1 and Cul2are all components of the CBC^(VHL) ubiquitin ligase E3 complex, it has been shown that Mnk2 caninteract with CBC^(VHL) complex, and is probably one of the newsubstrates of the CBC^(VHL) ***, during the interaction of Mnk2 with von Hippel-Lindau (VHL) tumor suppressor- bindingprotein 1 (VBP1), it appears that Mnk2 also joins to modulate cell shape as VBP1 plays an importantrole in the process of the maturation of the cytoskeleton and in the process of morphogenesis.

关键词： Mnk2, yeast two-hybrid, CBCVHL ubiquitin ligase E3 complex, VBP1.

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Understanding SARS with Wolfram Approach

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Acta Biochimica et Biophysica Sinica 2004年第1期36卷 1-10页

作者： Da-Wei LI, Yu-Xi PAN, Yun DUAN, Zhen-De HUNG, Ming-Qing XU, and Lin HE ( Bio-X Life Science Research center, shanghai Jiao Tong University, shanghai 200030, china Institute for Nutritional science, the chinese Academy of Sciences, shanghai 200031, china ) Bio-X Life Science Research center Shanghai Jiao Tong University Shanghai 200030 China.

Stepping acquired immunodeficiency syndrome (AIDS), severe acute respiratory syndrome (SARS) as another type of disease has been threatening mankind since late last year. Many scientists worldwide are making great efforts to study the etiology of this disease with different approaches. 13 species of SARS virus have been sequenced. However, most people still largely rely on the traditional methods with some disadvantages. In this work, we used Wolfram approach to study the relationship among SARS viruses and between SARS viruses and other types of viruses, the effect of variations on the whole genome and the advantages in the analysis of SARS based on this novel approach. As a result, the similarities between SARS viruses and other coronavirusxes are not really higher than those between SARS viruses and non-coronaviruses.

关键词： genome sequence SARS visualization Wolfram approach

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胰岛素、胰高血糖素和地塞米松调节PEPCK启动子活性的体外研究

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复旦学报（医学版） 2003年第4期30卷 338-341页

作者：沈坤堂秦新裕张新韩泽广复旦大学附属中山医院普外科上海200032 国家人类基因组南方中心功能组上海201203

目的探讨胰岛素、胰高血糖素和地塞米松对PEPCK启动子活性的影响及其意义。方法将PEPCK启动子构建入表达载体pGL3-Basic,采用Lipofect脂质体转染法将携带PEPCK启动子的质粒pGL3-Basic-PEPCK转染至大鼠肝细胞株Hepal-6细胞,12 h后加入... 详细信息

目的探讨胰岛素、胰高血糖素和地塞米松对PEPCK启动子活性的影响及其意义。方法将PEPCK启动子构建入表达载体pGL3-Basic,采用Lipofect脂质体转染法将携带PEPCK启动子的质粒pGL3-Basic-PEPCK转染至大鼠肝细胞株Hepal-6细胞,12 h后加入不同浓度的胰岛素、胰高血糖素和地塞米松,孵育48 h后分别检测其报告基因萤虫素酶的活性。结果生理水平的胰岛素可明显抑制PEPCK启动子的活性,与胰岛素的浓度正相关;地塞米松则上调PEPCK启动子的活性,而胰高血糖素对其活性无影响。结论 PEPCK启动子在肝细胞中受胰岛素的负调控、地塞米松的正调控,若用于调控胰岛素基因的表达,将使糖尿病的基因治疗更安全更可行。

关键词：糖尿病胰岛素胰高血糖素地塞米松 PEPCK启动子基因治疗

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Characteristics of Obesity and Its Related Disorders in china

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Biomedical and Environmental Sciences 2010年第1期23卷 4-11页

作者： WEI-PING JIA ,CHEN WANG,SHAN JIANG,AND JIE-MIN PAN Department of Endocrinology and Metabolism,shanghai Jiao Tong University Affiliated Sixth People’s Hospital,shanghai Diabetes Institute,shanghai Clinical center of Diabetes,shanghai 200233,china Department of Endocrinology and Metabolism Shanghai Jiao Tong University Affiliated Sixth People's Hospital Shanghai Diabetes Institute Shanghai Clinical Center of Diabetes Shanghai 200233 China

Obesity is a medical condition with excess body fat accumulation to the extent which leads to serious health consequences. Abdominal obesity, also known as central obesity, refers to the presence of excess fat in the abdominal area. Obesity, especially abdominal obesity, contributes to many metabolic disorders including metabolic syndrome （MetS）, type 2 diabetes （T2DM） and cardiovascular diseases （CVD）. The incidence of obesity has increased dramaticaUy in recent yeats worldwide. In china, more than one-third of adults are overweight or obese and 10%-20% of all adults are affected by MetS. The pathogenesis underlying the abdominal obesity remains unclear. The ultimate health outcome of obesity and its related metabolic disorders have prompted physicians to take aggressive treatments （lifestyle changes, pharmacological interventions and surgical therapies） before a serious consequence becomes clinically apparent. In this review, we discuss the prevalence, pathogenesis and clinic features of obesity in china.

关键词： Obesity Metabolic syndrome Type 2 diabetes Cardiovascular disease

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genome size and sequence composition of moso bamboo: A comparative study

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Science china(Life Sciences) 2007年第5期50卷 700-705页

作者： GUI YiJie1, WANG Sheng1, QUAN LiYan1, ZHOU ChangPing2, LONG ShiBao2, ZHENG HuaJun3, JIN Liang1, ZHANG XianYin 1, MA NaiXun 4 & FAN LongJiang1 1 Institute of Crop Science/Institute of Bioinformatics, Zhejiang University, Hangzhou 310029, china 2 Zhejiang Anji Bamboo Exposition Garden, Anji 313300, china 3 chinese national human genome center at shanghai, shanghai 201203, china 4 The Research Institute of Subtropical Forestry, chinese Academy of Forestry, Fuyang 311400, china Institute of Crop Science/Institute of Bioinformatics Zhejiang University Hangzhou 310029 China Zhejiang Anji Bamboo Exposition Garden Anji 313300 China chinese national human genome center at shanghai Shanghai 201203 China The Research Institute of Subtropical Forestry Chinese Academy of Forestry Fuyang 311400 China

Moso bamboo (Phyllostachys pubescens) is one of the world's most important bamboo species. It has the largest area of all planted bamboo―over two-thirds of the total bamboo forest area―and the highest economic value in china. Moso bamboo is a tetraploid (4x=48) and a special member of the grasses family. Although several genomes have been sequenced or are being sequenced in the grasses family, we know little about the genome of the bambusoids (bamboos). In this study, the moso bamboo genome size was estimated to be about 2034 Mb by flow cytometry (FCM), using maize (cv. B73) and rice (cv. Nipponbare) as internal references. The rice genome has been sequenced and the maize genome is being sequenced. We found that the size of the moso bamboo genome was similar to that of maize but significantly larger than that of rice. To determine whether the bamboo genome had a high proportion of repeat elements, similar to that of the maize genome, approximately 1000 genome survey sequences (GSS) were generated. Sequence analysis showed that the proportion of repeat elements was 23.3% for the bamboo genome, which is significantly lower than that of the maize ge-nome (65.7%). The bamboo repeat elements were mainly Gypsy/DIRS1 and Ty1/Copia LTR retrotrans-posons (14.7%), with a few DNA transposons. However, more genomic sequences are needed to con-firm the above results due to several factors, such as the limitation of our GSS data. This study is the first to investigate sequence composition of the bamboo genome. Our results are valuable for future genome research of moso and other bamboos.

关键词： flow cytometry (FCM), genome size, GSS, Phyllostachys pubescens, repeat elements

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中国百日咳诊疗与预防指南(2024版)

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中华医学杂志 2024年第15期104卷 1258-1279页

作者：中华医学会感染病学分会儿科感染学组国家卫生健康委能力建设和继续教育儿科专委会感染组中国临床实践指南联盟方法学专委会国家儿童医学中心(上海) 国家传染病医学中心曾玫邵祝军张文宏夏君蔡洁皓陈明亮冯天行姚开虎不详复旦大学附属儿科医院感染传染科国家儿童医学中心(上海)上海200032 中国疾病预防控制中心传染病预防控制所北京102206 复旦大学附属华山医院感染科国家传染病医学中心上海200040 宁波诺丁汉大学GRADE中心宁波315100 复旦大学附属儿科医院感染传染科复旦大学附属闵行医院检验科上海临床研究中心儿科首都医科大学附属北京儿童医院北京市儿科研究所感染与微生物研究室国家儿童医学中心(北京)

百日咳再现是全球性的公共卫生问题,2018—2022年我国国内百日咳报告发病率接近20世纪80年代末的报告水平。实际上,我国的百日咳发病率被严重低估,主要因为国内尚未全面建立百日咳主动监测工作,不典型百日咳病例在临床上容易被漏诊,许... 详细信息

百日咳再现是全球性的公共卫生问题,2018—2022年我国国内百日咳报告发病率接近20世纪80年代末的报告水平。实际上,我国的百日咳发病率被严重低估,主要因为国内尚未全面建立百日咳主动监测工作,不典型百日咳病例在临床上容易被漏诊,许多医疗机构未开展百日咳的实验室诊断;同时,我国还面临百日咳鲍特菌对一线抗菌药物大环内酯类高度耐药的临床问题。为了更好地指导和规范我国百日咳病例的临床诊疗、监测和防控工作,由感染病学、流行病学、免疫规划及指南方法学专家组成指南制订小组,从实践角度提出有关百日咳诊断、治疗、预防,尤其是疫苗免疫策略的12个临床问题,经过研究问题构建、证据检索和综合、证据评价以及证据到推荐意见讨论,制订推荐意见和实施建议,为从事百日咳诊疗和防控的临床医师、微生物实验室专业人员、医院感染控制专业人员以及公共卫生领域从事传染病防控和免疫规划的专业人员提供参考。

关键词：百日咳诊断治疗预防疫苗接种

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Jackknife and Bootstrap Tests of the Composition Vector Trees

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genomics, Proteomics & Bioinformatics 2010年第4期8卷 262-267页

作者： Guanghong Zuo1,2, Zhao Xu1,3, Hongjie Yu1,4, and Bailin Hao1,5,6 1T-Life Research center & Department of Physics, Fudan University, shanghai 200433, china 2shanghai Institute of Applied Physics, chinese Acadamy of Sciences, shanghai 201800, china 3Applied Biosystems, Inc., Beijing 100027, china 4Fudan-VARI center for Genetic Epidemiology, Fudan University, shanghai 200433, china 5Institute of Theoretical Physics, chinese Acadamy of Sciences, Beijing 100190, china 6Santa Fe Institute, Santa Fe, NM 87505, USA. T-Life Research center & Department of Physics Fudan University Shanghai 200433 China.

Composition vector trees （CVTrees） are inferred from whole-genome data by an alignment-free and parameter-free method. The agreement of these trees with the corresponding taxonomy provides an objective justification of the inferred phylogeny. In this work, we show the stability and self-consistency of CVTrees by performing bootstrap and jackknife re-sampling tests adapted to this alignment-free approach. Our ultimate goal is to advocate the viewpoint that time-consuming statistical re-sampling tests can be avoided at all in using this alignment-free approach. Agreement with taxonomy should be taken as a major criterion to estimate prokaryotic phylogenetic trees.

关键词： composition vector phylogeny topological distance bootstrap jackknife CVTree

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Non-cytolytic antigen clearance in DNA-vaccinated mice with electroporation

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Acta Pharmacologica Sinica 2007年第7期28卷 1024-1030页

作者： Jin-liang PENG~(2,5),Yong-gang ZHAO~(2,5),Jun-hua MAI~2,Wen-ka PANG~2,Wei GUO~2,Guang-ming CHEN~4,Guo-yu MO~4,Gui-rong RAO~4,Yu-hong XU~(2,3,6)Schools of ~2 Life Sciences and Technology and ~3 Pharmacy,shanghai Jiao Tong University,shanghai 200240,china ~4 people's LiberationArmy's Liver disease Research center,458 Hospital of People's Liberation Army.Guangzhou 510400,china School of Life Sciences and Technology Shanghai Jiao Tong University Shanghai China People's Liberation Army's Liver disease Research center 458 Hospital of People's Liberation Army Guangzhou China School of Pharmacy Shanghai Jiao Tong University Shanghai China

Aim:To explore the potential of electroporation （EP）-mediated hepatitis B virus（HBV） DNA vaccination for the treatment of chronic HBV ***:BALB/c mice were vaccinated with HBV DNA vaccine encoding for the HBVpreS2-S antigen,combined with or without *** surface antigen expressionplasmid was administered into mice liver via a hydrodynamic injection to mimicHBV *** clearance of antigen in the serum and liver was detected byELISA assay and immunohistochemical *** histopathology of the livertissues was examined by HE staining and serum alanine aminotransferase ***:The immunogenicity of HBV DNA vaccine encoding for the HBV preS2-S antigen can be improved by EP-mediated vaccine *** elicited immuneresponses can indeed reduce the expression of HBV surface antigen （HBsAg） inhepatocytes of the mouse model that was transfected to express HBsAg using thehydrodynamic injection *** antigen clearance process did not causesignificant toxicity to liver tissue,suggesting a non-cytolytic ***:The EP-aided DNA vaccination may have potential in mediating viralclearance in chronic hepatitis B patients.

关键词： DNA vaccine hepatitis B virus electro poration antigen clearance

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Construction of a full bacterial artificial chromosome(BAC) library of Oryza sativa genome

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Cell Research 1994年第2期4卷 127-133页

作者： TAO QUANZHOU HAIYING ZHAO LONGFANG QIU GUOFAN HONG.(national center for Gene Researsh, Chincse Academy of Sciences, shanghai 200233, china）（shanghai Institute of Biochemistry, Chinesc Academyof Scienccs, shanghai 200031, china) national center for Gene Research Chinese Academy of Sciences Shanghai China shanghai Institute of Biochemistry Chinese Academy of Sciences Shanghai China

We have constructed a full BAC library for the superior eaxly indica variety of OryZa sativa, Guang Lu Ai4. The MAX Efficiency DHlOB with increased stabilltyof inserts was used as BAC host cells. The potent pBelo BACII with double selection markers was used as cloning vector. The cloning efficiency we have reached was as high as 98%, and the transformation efficiency was raised up to 1Oo transformants / pg of large fragment DNA. The BAC recombinant transformants were picked at random and analyzed for the size of inserts, which turned out to be of 120 kb in length on average. We have obtained more than 20,000 such BAC clones. According to conventional probabillty equation, they covered the entire rice genome of 420,000 kb in length. The entire length of inserts of the library obtained has the 5- to 6- fold coverage of the genome. To our knowledge, this is the first reported full BAC library for a complex genome.

关键词： bacterial artificial chromosome indica Oryza sativa library

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