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Phylogeographic analysis of human papillomavirus 5.

Science China(Life Sciences) 2009年第12期52卷 1164-1172页

作者： LI YanYun1, LI ZuoFeng2, HE YiFeng1, KANG Yu1, ZHANG XiaoYan1, CHENG MingJun1, ZHONG Yang2, 3· & XU CongJian1· 1 Obstetrics and Gynecology Hospital of Fudan University, shanghai 200011, China 2 shanghai bioinformation Research center,{4., China 3 School of Life Sciences, Fudan University, shanghai 2004.3, China Obstetrics and Gynecology Hospital of Fudan University Shanghai 200011 China shanghai Bio-information Research center Shanghai 200235 China School of Life Sciences Fudan University Shanghai 200433 China

Human papillomavirus 5. (HPV5.) is one type of HPV with high risk of causing cervical cancer. Unusually high prevalence of HPV5. has been reported in Asia, Africa and some other areas. However, due to the scattered distribution of global data, in addition to the lack of data of some HPV5. high-incidence nations and regions, like China's Mainland, a comprehensive analysis of the global geographical distribution of HPV5. remains blank so far. In this study, HPV5. from the human cervical cancer tissue was detected in China's Mainland, and 14.new HPV5.-E6/L1 gene sequences were obtained. Moreover, phylogeographic analysis has been conducted combining the HPV5. sequences that have been deposited in GenBank since 1985. The study result shows that the sequences detected from the shanghai, Jiangsu and Sichuan areas are homologous with those found in the past from Hong Kong and Xi'an, China, as well as Japan and other Southeast Asian areas. Furthermore, Western Africa is considered to be the "root" source of the HPV5. variant, while China's Mainland and Southeast Asia are "transit points" and the new sources of HPV5. after receiving the isolates from the "root" source; like HPV16 and HPV18, the HPV5. might also be one of the major HPV types associated with the development and spread of cervical cancer.

关键词： human papillomavirus 5. (HPV5.) cervical cancer phylogeography molecular evolution

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A measure of semantic similarity between gene ontology terms based on semantic pathway covering

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Progress in Natural Science:Materials International 2006年第07期16卷 721-726页

作者： LI Rong, CAO Shunliang, LI Yuanyuan, TAN Hao, ZHU Yangyong, ZHONG Yang and LI Yixue ( Department of Computing and Information technology, Fudan University, shanghai 2004.3, China shanghai center for Bioin-formation technology,{5., China School of Life Sciences, Fudan University, shanghai 2004.3, China Bioinfor-rnation center of shanghai Institute for Biological Sciences, Chinese Academy of Sciences, shanghai 200031, China) [a]Department of Computing an Information technology Fudan University Shanghai China [b]shanghai center for bioinformation technology Shanghai China [c]School of Life Sciences Fundan University Shanghai China [d]bioinformation center of shanghai Institute for Biological Sciences Chinese Academy of Sciences Shanghai China

Semantic similarity between Gene Ontology (GO) terms is critical in resolving semantic heterogeneousness when integrating heterogeneous biological databases. Traditionally, distance based and information content based measures are two major methods. In this paper, a new method based on semantic pathway covering is proposed and an algorithm, COMBINE algorithm, is presented, which considers information contents of two given nodes and those of all nodes included in the two nodes' pathways. Experiments show that COMBINE algorithm obtains the highest correlation index compared with those distance based and information content based algorithms.

关键词： Gene Ontology semantic similarity measure information content.

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Recognition of Gene Acceptor Site Based on Multi-objective Optimization

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Acta Biochimica et Biophysica Sinica 2005年第7期37卷 435-439页

作者： Jing ZHAO~(1,3,4. Yue-Min ZHU~2 Pei-Ming SONG~1 Qing FANG~1 Jian-Hua LUO~(1,3) 1 School of Life Science & technology,shanghai Jiaotong University,shanghai 20024.,China 2 CREATIS,CNRS UMR 5.15.INSA Lyon,69621 Villeurbanne Cedex,France 3 shanghai {4. for {5. and technology,shanghai 2.02.5,China 4.Logistical Engineering University,Chongqing 4.0016,China SchoolofLifeScience&technology ShanghaiJiaotongUniversityShanghai200240China

A new method for predicting the gene acceptor site based on multi-objective optimization isintroduced in this *** models for the acceptor,branch and distance between acceptor site andbranch site were constructed according to the characteristics of the sequences from the exon-intron databaseand using common biological *** acceptor function,branch function and distance functionwere defined respectively,and the multi-objective optimization model was constructed to recognize thesplice *** test results show that the algorithm used in this study performs better than the SplicePredictor,which is one of the leading acceptor site detectors.

关键词： multi-objective optimization acceptor site recognition

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Identification and Analysis of Genes Present in Leptospira interrogans serovar lai but Absent in L. biflexa serovar monvalerio

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Acta Biochimica et Biophysica Sinica 2004年第12期36卷 832-839页

作者： Ping HE, Xiang-Yan ZHANG, Xiao-Kui GUO*, Bao-Yu HU, Xiao-Tian HUANG, Yang YANG, and Guo-Ping ZHAO1,2* Department of Microbiology and Parasitology, shanghai Second Medical University, shanghai 200025. China 1 Research center of Bio{4., Institutes for Biological Sciences, Chinese Academy of Sciences, shanghai 200031, China 2Chinese National Human Genome center at shanghai, Zhangjiang High Tech Park, shanghai 201203, China Department of Microbiology and Parasitology Shanghai Second Medical UniversityShanghai 200025 China Research center of Biotechnology Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200031 China Chinese National Human Genome center at shanghaiZhangjiang High Tech Park Shanghai 201203 China

Genes present in virulent bacterial strains but absent in avirulent close relatives can be of great biologic and clinical interest. This project aimed to identify strain specific DNA sequences of Leptospira interrogans serovar lai, which is absent in the saprophytic L. biflexa serovar monvalerio, via suppression subtractive hybridization with the former as the tester while the latter as the driver. The mixture of PCR amplified DNA fragments from two subtractive hybridization experiments were cloned into pMD18-T vector and the positive clones were identified by dot blotting against the chromosome DNA of the two strains individually. After DNA sequencing and analysis, the distribution of these genomic fragment sequences in a panel of pathogenic and nonpathogenic leptospires was investigated employing dot blot analysis. Among the 188 positive clones randomly chosen, 24.contained the tester strain specific genomic regions, of which, 5. were non-coding fragments while the others contained 23 distinct protein coding sequences. Besides 9 genes encoding functional proteins, 12 genes encode unknown proteins and the rest two genes encode proteins with recognizable domain structures, one for a putative leucine-rich repeats (LRR) family protein while the other as an outer-membrane protein. Our experiment results indicated that suppression subtractive hybridiza- tion is effective for screening specific DNA sequences between two leptospiral strains, and some of these sequences might be responsible for virulence determination. Further analysis of these DNA sequences will provide important information on the pathogenesis of Leptospira.

关键词： Leptospira interrogans serovar lai suppression subtractive hybridization (SSH) specific genes

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Identification and Characterization of hmr19 Gene Encoding a Multidrug Resistance Efflux Protein from Streptomyces hygroscopicus *** Strain 10-22

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Acta Biochimica et Biophysica Sinica 2004年第8期36卷 519-528页

作者： Lei QIN , Heng-An WANG1 , Zhong-Qin WU, Xiao-Feng ZHANG, Mei-Lei JIN,Zi-Xin DENG2, and Guo-Ping ZHAOshanghaiResearch center of Biotechnology, shanghai Institute for Biological Sciences, Chinese Academy of Sciences,Graduate School of the Chinese Academy of Sciences, shanghai 200233, China 1School of Agriculture and Biology, shanghai Jiaotong University, shanghai 201101, China 2School of Life Science and Biotechnology, shanghai Jiaotong University, shanghai 200030, China shanghaiResearch center of Biotechnology Shanghai Institute for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of Sciences School of Agriculture and Biology Shanghai Jiaotong University

The hmr19 gene was cloned from Streptomyces hygroscopicus subsp. yingchengensis strain 10- 22, a bacterium strain producing agricultural antibiotics. Sequence similarity comparison indicates that hmr19 gene may encode a predicted protein with 14.putative transmembrane α-helical spanners, belonging to the drug:H+ antiporter-2 family of the major facilitator superfamily. The expression of hmr19 in the mycelium of strain 10-22 was detected by Western blotting analysis. Gene replacement technology was employed to construct an hmr19 disruption mutant. The growth inhibition test against different antibiotics indicated that the mutant strain was 5.20 fold more susceptible to tetracycline, vancomycin and mitomycin C than the parental wild type strain. The mutant took up tetracycline much faster and accumulated more antibiotics than the wild type strain 10-22. While with the addition of an energy uncoupler, carbonyl cyanide m- chlorophenylhydrazone, the characteristics of the accumulation of [3H]tetracycline in these two strains were almost the same. It was thus concluded that hmr19 encoded a multidrug resistance efflux protein.

关键词： multidrug resistance (MDR) gene replacement (knockout) Streptomyces Streptomyces hygroscopicus subsp. yingchengensis strain 10-22

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Hydrothermal Preparation and Photocatalytic Water Splitting Properties of ZrW_2O_8

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Journal of Wuhan University of technology(Materials Science) 2010年第6期25卷 919-923页

作者：蒋丽上官文峰 Research center for Combustion and Environment technology Shanghai Jiao Tong University

ZrW2O8 was prepared by adjusting Zr：W mole ratio and HCl concentration in hydrothermal reaction *** obtained sample was crystallized in α-ZrW2O8 phase （cubic,P213）,with band gap energy of 4.0 *** properties of photocatalytic water splitting were examined under UV light *** average rate of H2 evolution over 0.3wt% Pt/ZrW2O8 in the presence of CH3 OH as electron donor （ED） was 23.4.μmol/h,while the average rate of O2 evolution over ZrW2O8 in the presence of AgNO3 as electron scavenger （ES） was 9.8 μmol/***,H2 was evolved over 0.3wt% Pt/ZrW2O8 from pure water splitting at a rate of 5.2 μmol/*** study indicated that the band structure of ZrW2O8 was suitable for reducing H ＋ to H2 and oxidizing H2O to *** band structure and photocatalytic water splitting properties of ZrW2O8,different from either ZrO2 （5.0 eV） or WO3 （2.7 eV）,were attributed to the hybridization of W5. and Zr4. in conduction band （CB） as well as the change in crystal structure.

关键词： photocatalyst hydrogen zirconium tungsten oxide hydrothermal preparation

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Comparative Analysis of Two-component Signal Transduction System in Two Streptomycete Genomes

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Acta Biochimica et Biophysica Sinica 2007年第5期39卷 317-325页

作者： WU WEI~(1,3#), Weihua WANG~(2#), Zhiwei CAO~(3#), Hong YU~3, Xiaojing WANG~1, Jing ZHAO~3, Hao TAN~3, Hao XU~3, Weihong JIANG~(2*), and Yixue LI~(1,3*) 1 bioinformation center, Key Lab of Systems Biology, shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, shanghai 200031, China 2 Laboratory of Molecular Microbiology, Institute of Plant Physiology and Ecology, shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, shanghai 200032, China 3 shanghai center for bioinformation technology, shanghai 2.02.5, China bioinformationcenter KeyLabofSystemsBiologyShanghaiInstitutesforBiologicalSciencesChineseAcademyofSciencesGraduateSchooloftheChineseAcademyofSciencesShanghai200031China

Species of the genus Streptomyces are major bacteria responsible for producing most natural antibiotics. Streptomyces coelicolor A3(2) and Streptomyces avermitilis were sequenced in 2002 and 2003, respectively. Two-component signal transduction systems (TCSs), consisting of a histidine sensor kinase (SK) and a cognate response regulator (RR), form the most common mechanism of transmembrane signal transduction in prokaryotes. TCSs in S. coelicolor A3(2) have been analyzed in detail. Here, we identify and classify the SK and RR of S. avermitilis and compare the TCSs with those of S. coelicolor A3(2) by computational approaches. Phylogenetic analysis of the cognate SK-RR pairs of the two species indicated that the cognate SK-RR pairs fall into four classes according to the distribution of their orthologs in other organisms. In addition to the cognate SK-RR pairs, some potential partners of non-cognate SK-RR were found, including those of unpaired SK and orphan RR and the cross-talk between different components in either strain. Our study provides new clues for further exploration of the molecular regulation mechanism of streptomycetes with industrial importance.

关键词： Streptomyces two-component system cross-talk phylogenetic analysis

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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 200031,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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Study on Residual Oil HDS Process with Mechanism Model and ANN Model

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China Petroleum Processing & Petrochemical technology 2009年第1期11卷 39-43页

作者： Ma Chengguo Weng Huixin (Research center of Petroleum Processing, ECUST, shanghai 200237) Research center of Petroleum Processing ECUST Shanghai 200237 China

Based on the Residual Oil Hydrodesulfurization Treatment Unit (S-RHT), the n-order reaction kinetic model for residual oil HDS reactions and artificial neural network (ANN) model were developed to determine the sulfur content of hydrogenated residual oil. The established ANN model covered 4.input variables, 1 output variable and 1 hidden layer with 15.neurons. The comparison between the results of two models was listed. The results showed that the predicted mean relative errors of the two models with three different sample data were less than 5. and both the two models had good predictive precision and extrapolative feature for the HDS process. The mean relative error of 5.sets of testing data of the ANN model was 1.62%—3.23%, all of which were smaller than that of the common mechanism model (3.4.%— 4.13%). It showed that the ANN model was better than the mechanism model both in terms of fitting results and fitting difficulty. The models could be easily applied in practice and could also provide a reference for the further research of residual oil HDS process.

关键词： residual oil hydrodesulfurization (HDS) mechanism model artificial neural network (ANN) model

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Mechanisms of antiprostate cancer by gum mastic:NF-κB signal as target

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Acta Pharmacologica Sinica 2007年第3期28卷 446-452页

作者： Mei-lan HE~(2,4. Ang LI~2 Chun-su XU~2 Shun-li WANG~3 Meng-jie ZHANG~2 Hua GU~2 Yao-qin YANG~3 Hui-hong TAO~3 ~2Institute of Cancer Research,Life Science and technology School,Tongji University,shanghai 200092,China ~3Cellular Morphology center,Medical School,Tongji University,shanghai 200092,China Institute of Cancer Research Life Science and Technology School Tongji University Shanghai 200092 China Cellular Morphology center Medical School Tongji University Shanghai 200092 China

Aim:To study the effect of gum mastic,a natural resin,on the proliferation ofandrogen-independent prostate cancer PC-3 cells,and further investigate themechanisms involved in this regulatory system,taking nuclear factor κB(NF-κB)signal as the ***:3-(4.5.dimethylthiazol-2-yl)-2,5.diphenyltetrazoliumbromide(MTT)assay and a flow cytometer were used to detect the effect of gummastic on the proliferation of PC-3 ***,reporter gene assay,RT-PCR,andWestern blotting were carried out to study the effects of gum mastic on the NF-κBprotein level and the NF-κB signal *** expression of genes involved inthe NF-κB signal pathway,including cyclin D1,inhibitors of κBs(IκBα),andphosphorylated Akt(p-AKT),were *** addition,transient transfectionassays with the 5.NF-κB consensus sequence promoter was also used to test theeffects of gum ***:Gum mastic inhibited PC-3 cell growth and blockedthe PC-3 cell cycle in the G1 *** mastic also suppressed NF-κB activity inthe PC-3 *** expression of cyclin D1,a crucial cell cycle regulator and anNF-κB downstream target gene,was reduced as ***,gum masticdecreased the p-AKT protein level and increased the IκBα protein ***:Gum mastic inhibited the proliferation and blocked the cell cycleprogression in PC-3 cells by suppressing NF-κB activity and the NF-κB signalpathway.

关键词： gum mastic prostate cancer NF-κB signal

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