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Functional analysis of schistosomes EF-hand domain-containing tegument proteins

chinese science Bulletin 2007年第15期52卷 2100-2107页

作者： YU FuDong1,2,3,KANG Bin1,3,LI YuanYuan3,4.& LI YiXue1,3 1 Bioinformatics center,Key Laboratory of systems Biology,shanghai Institutes for biological sciences,{4. academy of sci-ences,shanghai 2.0031,China 2 Graduate University of chinese academy of sciences,shanghai 2.0031,China 3 shanghai center for bioinformation Technology,shanghai 200235,China 4.Key Laboratory of systems Biology,shanghai Institutes for biological sciences,{4. academy of sciences,shanghai 2.0031,China Bioinformatics center Key Laboratory of Systems Biology Shanghai Institutesfor Biological Sciences Chinese Academy of Sciences Shanghai 200031 China

schistosomes cause schistosomiasis disease which severely threatens human health. Little is known about the functions of EF-hand domain containing schistosomes tegument proteins other than as an-tigens. More possible functions of these tegument proteins were investigated with in silico analyses including protein-protein functional interaction,site-specific variation and glycosylation modification. The analysis results suggested that schistosomes could actively modulate host immune responses for its own favor through functional interactions with host proteins with immunomodulatory function,and passively regulate host immune responses through sequence variation under positive selection and glycosylating the recognition sites of host immune attack. In addition,the analysis of the C-terminal domain of these tegument proteins indicated that they could assist schistosomes in escaping host immune attacks through inhibiting chemotaxis and non-complement fixing antibody (IgG4. responses. In summary,our results suggested that these tegument antigen proteins could assist schistosomes in escaping and modulating host immune responses for self-protection during the process of host-para-site interaction.

关键词：寄生虫血吸虫皮蛋白质健康

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The contribution of cis-regulatory elements to head-to-head gene pairs' co-expression pattern

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science China(Life sciences) 2009年第1期52卷 74-79页

作者： HAO Pei1,2,YU Yao2,3,ZHANG XiaoYan4.TU Kang2,FAN HaiWei2 & ZHONG Yang1 1 school of Life sciences,Fudan University,shanghai 2004.3,China 2 Bioinformatics center,Key Lab of systems Biology,shanghai Institutes for{4. sciences,chinese academy of sciences,shanghai 2.0031,China 3 shanghai center for bioinformation Technology,shanghai 200235,China 4.school of Life sciences,Tongji University,shanghai 200092,China 1. school of Life sciences Fudan University Shanghai 200433 China 2. Bioinformatics center Key Lab of Systems Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China 3. shanghai center for bioinformation Technology Shanghai 200235 China 4. school of Life sciences Tongji University Shanghai 200092 China

Transcription regulation is one of the most critical pipelines in biological process,in which cis-elements play the role as gene expression *** attempt to deduce the principles underlying the co-expression of "head-to-head" gene pairs by analyzing activities or behaviors of the shared cis-elements.A network component analysis was performed to estimate the impact of cis-elements on gene promoters and their activities under different *** discoveries reveal how biological system uses those regulatory elements to control the expression pattern of "head-to-head" gene pairs and the whole transcription regulation system.

关键词： transcription regulation cis-elements "head-to-head" gene pairs

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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,{4. Institutes for biological sciences, chinese academy of sciences, shanghai 2.0031, China 5.{4. center for bioinformation Technology,{4. 200235, China 6. school of Life sciences, Fudan University,{4. 2004.3, China 1. Laboratory of systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences 100093 Beijing China 2. College of Life sciences Beijing Normal University 100875 Beijing China 3. Institute of Viral Disease Control and Prevention Chinese CDC 100052 Beijing China 4. bioinformation center Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 200031 Shanghai China 5. shanghai center for bioinformation Technology 200235 Shanghai China 6. school of Life sciences Fudan University 200433 Shanghai China

The genome oiganization and expression strategy of severe acute respiratory syndrome coronavirus (sARs-CoV) have been described extensively. 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. Previous studies suggested that amino acid replacements in the spike protein coulddramatically alter the pathogenesis and virulence of some coronaviruses. 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, might make this pathogen adapt to a new host, In this study, we investigated a total of 108 complete sequences of the sARs-CoV s gene from Gen-Bank (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 4.0}equences was obtained using the program Clustal-X. Then, we reconstructed the most recent common ancestor (MRCA) sequences of thesARs-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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semantic search among Heterogeneous biological Databases Based on Gene Ontology

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Acta Biochimica et Biophysica sinica 2004年第5期36卷 365-370页

作者： shun-Liang CAO, Lei QIN1, Wei-Zhong HE1, Yang ZHONG2, Yang-Yong ZHU, and Yi-Xue LI1,3* Department of Computing and Information Technology, Fudan University, shanghai 2004.3, China shanghai center for bioinformation 1 Technology, shanghai 200235, China school of Life sciences, Fudan University, shanghai 2004.3, China bioinformation center of shanghai Institutes for biological sciences, the chinese academy of sciences, shanghai 2.0031, China Department of Computing and Information Technology Fudan University Shanghai China

semantic search is a key issue in integration of heterogeneous biological databases. In this paper, we present a methodology for implementing semantic search in BioDW, an integrated biological data warehouse. Two tables are presented: the DB2GO table to correlate Gene Ontology (GO) annotated entries from BioDW data sources with GO, and the semantic similarity table to record similarity scores derived from any pair of GO terms. Based on the two tables, multifarious ways for semantic search are provided and the corresponding entries in heterogeneous biological databases in semantic terms can be expediently searched.

关键词： Gene Ontology semantic search BioDW

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A meta-analysis of oxidative stress markers in schizophrenia

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中国科学：生命科学英文版 2010年第1期53卷 112-124页

作者： ZHANG Ming1,2,ZHAO ZhongMing3,HE Lin1,2,4.& WAN ChunLing1,2 1 Bio-X center,Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders(Ministry of Education),shanghai Jiao Tong University,shanghai 200030,China 2 Institutes for Nutritional sciences,shanghai Institute of biological sciences,chinese academy of sciences,shanghai 2.0031,China 3 Departments of Biomedical Informatics,Psychiatry,and Cancer Biology,Vanderbilt University Medical center,Nashville,TN 37232,UsA 4.Institutes of Biomedical sciences,Fudan University,shanghai 200032,China 1. Bio-X center Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) Shanghai Jiao Tong University Shanghai 200030 China2. Institutes for Nutritional Sciences Shanghai Institute of Biological Sciences Chinese Academy of Sciences Shanghai 200031 China3. Departments of Biomedical Informatics Psychiatry and Cancer Biology Vanderbilt University Medical Center Nashville TN 37232 USA4. Institutes of Biomedical Sciences Fudan University Shanghai 200032 China

Oxidative stress has been identified as a possible element in the neuropathological processes of schizophrenia(sCZ).Alteration of oxidative stress markers has been reported in sCZ studies,but with inconsistent *** evaluate the risk of oxidative stress to schizophrenia,a meta-analysis was conducted,including five markers of oxidative stress [thiobarbituric reactive substances(TBARs),nitric oxide(NO),catalase(CAT),glutathione peroxidase(GP) and superoxide dismutase(sOD)] in sCZ patients versus healthy *** study showed that TBARs and NO significantly increased in sCZ,while sOD activity significantly decreased in the disorganized type of sCZ *** significant effect size was found for the activities of GP and CAT in sCZ patients(P>0.05).Egger’s regression test observed no significant publication bias across the oxidative stress markers,but found high heterogeneities in all the 5 *** subgroup analysis suggested that the ethnicity,sample size of patients and sample sources may contribute to the heterogeneity of the results for TBARs,NO and *** result further demonstrated the involvement of oxidative stress in the pathophysiology of schizophrenia.

关键词： schizophrenia oxidative stress meta-analysis lipid peroxidation nitric oxide antioxidant enzymes

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Association between Alcohol, smoking and HLA-DQA1*0201 Genotype in Psoriasis

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Acta Biochimica et Biophysica sinica 2004年第9期36卷 597-602页

作者： Guang-Yong ZHENG1,2#, sheng-Cai WEI3#, Tie-Liu sHI1, and Yi-Xue LI1* 1Bioinformatics center, shanghai Institutes for biological sciences,{4., Graduate school of the{4., shanghai 2.0031, China Research center for Proteome Analysis, Institute of Biochemistry and Cell Biology, shanghai Institutes for biological sciences, {4., Graduate school of the{4., shanghai 2.0031, China 3Guangzhou Institute of Dermatology, Guangzhou 510095, China Bioinformatics center Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of Sciences

Psoriasis is a chronic skin disease triggered by genetic, environment or other risk factors such as infection, drugs, stress, moisture, alcohol, and smoking. A major psoriasis susceptibility locus at 6p21.3 has been identified. Further studies found that HLA-DQA1*0201 allele was associated with psoriasis. However, there were few data exploring an association between the environmental factors and susceptibility genes. In this study, the samples of 189 patients with psoriasis and 333 healthy controls were collected with their consent and were carried on analysis through polymerase chain reaction sequence-specific primer (PCR- ssP) method. The proportion of male psoriasis patients engaging in the smoking and alcohol was much higher than that of the control group (P201 allele was present at significantly higher frequency in the patients with psoriasis (OR=4.25, Pssociation was found between smoking, alcohol and HLA-DQA1*0201 in male patients with psoriasis (OR>6.91, P4..

关键词： psoriasis HLA-DQA1*0201 allele smoking alcohol association

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six specific Lysihe Residues are Crucial in Maintaining the structure and Function of soluble Manganese stabilizing Protein

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Acta Biochimica et Biophysica sinica 2006年第9期 611-619页

作者： Jin-Peng GAO~(1,2#) Feng ZHANG~(1,3#) Li ZHANG~4.Yin-Long GUO~4.Kang-Cheng RUAN~5 De-An JIANG~3* Chun-He XU~1 1 Institute of Plant Physiology and Ecology,shanghai Institutes for biological sciences,chinese{4. of sciences,shanghai 200032,China 2 Graduate school of the chinese academy of sciences,shanghai 200032,China 3 College of Life sciences,Zhejiang University,Hangzhou 310029,China 4.shanghai Mass spectrometry center,shanghai Institute of Organic Chemistry,chinese{4. of sciences,shanghai 2.0031,China 5 Laboratory of Proteomics,Institute of Biochemistry and Cell Biology,shanghai Institutes for biological sciences,chinese{4. of sciences,shanghai 2.0031,China

When manganese stabilizing protein （MsP） was treated with 0.5mM N-succinimidyl propionate（NsP）,the rebinding ability and oxygen-releasing capabilities of the modified MsP were not altered,in spiteof changes of MsP surface Lys ***,far-ultraviolet circular dichroism and intrinsicfluorescence spectra analysis revealed that 0.5 mM NsP-modified MsP retained most of its native secondaryand tertiary *** of the sites of NsP modification by staphylococcus V8protease digestion ofthe modified protein,as well as analysis by matrix-assisted laser desorption ionization-time of flight massspectrometry,indicated that seven Lys residues were *** results suggested that these residues arenot absolutely essential to the structure and function of ***,when the NsP concentration wasincreased to 4.M,the modified MsP was unable to bind photosystem Ⅱ and completely lost its *** far-ultraviolet circular dichroism and intrinsic fluorescence spectra analysis revealed a clearconformational change in MsP after 4.mM NsP treatment,suggesting that some Lys residues are involved inmaintaining the structure and function of *** by matrix-assisted laser desorption ionization-timeof flight mass spectrometry indicated that another six Lys residues,namely Lys20,Lys101,Lys196,Lys207,Lys130 （or Lys137） and Lys66 （or Lys76）,were modified by 4.mM ***,these six Lys residuesare crucial in maintaining the structure and function of soluble MsP.

关键词： chemical modification fluorescence spectrum circular dichroism spectrum manganese stabilizing protein Lys residue

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Display of aggregation-prone ligand binding domain of human PPAR gamma on surface of bacteriophage lambda

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Acta Pharmacologica sinica 2006年第1期27卷 91-99页

作者： Bo KONG~(2,4. Wei-jun MA~(2,3,5)2 Institute of Health sciences.shanghai Institutes for biological sciences,{4. academy of sciences and Medical school of shanghai Jiao Tong University.shanghai 200025.China 3 shaughai Research center of Biotechnology,shanghai Institutes for biological sciences,Chiese academy og sciences,shanghai 200233.China 4.Graduate school of the chinese academy of sciences InstituteofHealthsciences ShanghaiInstitutesforBiologicalSciencesChineseAcademyofSciencesandMedicalSchoolofShanghaiJiaoTongUniversityShanghai200025China

Aim:To display the aggregation-prone ligand binding domain (LBD) of the hu-man peroxisome proliferator-activated receptor gamma (PPARγ) on the surface ofbacteriophages to establish an easy screening assay for the identification of PPARγ***:Plasmids were constructed for the expression of the PPARγLBD as a fusion to the N-terminus of the g3p protein of filamentous phage or theC-terminus of the capsid protein D (pD) of phage *** fusion proteinswere expressed in E coli and solubility characteristics were *** against the LBD as well as the pD protein were prepared for Westernblot analysis and phage capture ***:The pD-LBD fusion protein waspartially soluble,whereas the LBD-g3p fusion protein was detected only in theinsoluble *** pD-LBD fusion protein was efficiently incorporated inphage ***,the LBD was shown to be displayed on the surfaceof bacteriophage *** average,the pD-LBD fusion protein accounted for28% of the total pD protein in the lambda head ***:The hydro-phobic PPARγ LBD was expressed as a soluble form of fusion protein in E coli anddisplayed on the surface of bacteriophage lambda when it was fused to the lambdapD *** lambda pD fusion system could be used for improving the solu-bility of proteins that tend to form inclusion bodies when expressed in E *** phage particles displaying the LBD of PPARy may be of great value for theidentification of novel PPARγ ligands.

关键词： protein expression lambda phage surface display nuclear receptor peroxisome proliferator-activated receptors ligand binding domain

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EMMA:An Efficient Massive Mapping Algorithm Using Improved Approximate Mapping Filtering

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Acta Biochimica et Biophysica sinica 2006年第12期38卷 857-864页

作者： Xin ZHANG~1 Zhi-Wei CAO~2 Zhi-Xin LIN~3 Qing-Kang WANG~1* Yi-Xue LI~4. 1 Institute of Micro/Nano science and Technology,shanghai Jiaotong University,shanghai 200030,China 2 shanghai center for{4. Technology,shanghai 200235,China 3 College of Life science and Technology,shanghai Jiaotong University,shanghai 200030,China 4.4. center of shanghai Institutes for biological sciences,chinese {14. of sciences,shanghai 2.0031,China shanghai center for bioinformation Technology Shanghai 200235China Institute of Micro/Nano science and Technology Shanghai Jiaotong UniversityShanghai 200030China

Efficient massive mapping algorithm (EMMA),an algorithm on efficiently mapping massivecDNAs onto genomic sequences,has recently been *** process of mapping massive cDNAsonto genomic sequences has been improved using more approximate mapping filtering based on an enhancedsuffix array coupled with a pruned fast hash table,algorithms of block alignment extensions,and *** compared with the classical BLAT software in this field,the computing of EMMA ranges fromtwo to forty-one times faster under similar prediction precisions.

关键词： cDNA mapping maximal exact match enhanced suffix array pruned fast hash table extension algorithm

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Learn to fight from the war

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chinese science Bulletin 2009年第13期54卷 2157-2158页

作者： ZHAO GuoPing shanghai-MOsT Key Laboratory for Disease and Health Genomics,chinese National Human Genome center at shanghai,shanghai 201203,China Lab of synthetic Biology,shanghai Institutes of biological sciences,chinese academy of sciences,shanghai 2.0031,China National Engineering Research center for Biochip Technology,shanghai Biochip Co.Ltd.,shanghai 201203,China school of Life sciences,Fudan University,shanghai 2004.3,China ZHONG Yang school of Life sciences,Fudan University,shanghai 2004.3,China shanghai center for bioinformation Technology,shanghai 200235,China shanghai-MOsT Key Laboratory for Disease and Health Genomics Chinese National Human Genome Center at Shanghai Shanghai 201203 China Lab of synthetic Biology Shanghai Institutes of Biological Sciences Chinese Academy of Sciences Shanghai 200031 China National Engineering Research center for Biochip Technology Shanghai Biochip Co. Ltd. Shanghai 201203 China school of Life sciences Fudan University Shanghai 200433 China shanghai center for bioinformation Technology Shanghai 200235 China

In March 2009,a novel type A (H1N1) influenza broke out in North America and rapidly spread all over the world.

关键词：世界卫生组织战争军备竞赛 WHO 流感

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