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Phylogeographic analysis of human papillomavirus 58

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science c.ina(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, c.ina 2 shanghai Bioinformation Research center, shanghai 200235, c.ina 3 {6. of life sciences, fudan university, shanghai 2.04.3, c.ina Obstetrics and Gynecology Hospital of fudan university Shanghai 200011 China shanghai Bio-information Research center Shanghai 200235 China sc.ool of life sciences Fudan University Shanghai 200433 China

Human papillomavirus 58 (HPV58) is one type of HPV with high risk of causing cervical cancer. Unusually high prevalence of HPV58 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 HPV58 high-incidence nations and regions, like c.ina's Mainland, a comprehensive analysis of the global geographical distribution of HPV58 remains blank so far. In this study, HPV58 from the human cervical cancer tissue was detected in c.ina's Mainland, and 14 new HPV58-E6.L1 gene sequences were obtained. Moreover, phylogeographic analysis has been conducted combining the HPV58 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, c.ina, as well as Japan and other southeast Asian areas. Furthermore, Western Africa is considered to be the "root" source of the HPV58 variant, while c.ina's Mainland and southeast Asia are "transit points" and the new sources of HPV58 after receiving the isolates from the "root" source; like HPV16.and HPV18, the HPV58 might also be one of the major HPV types associated with the development and spread of cervical cancer.

关键词： human papillomavirus 58 (HPV58) cervical cancer phylogeography molecular evolution

Dynamics of Primary Events in the Photocycle of Excited Bacteriorhodopsin

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Acta Biochimica et Biophysica sinica 2004年第11期36卷 724-728页

作者： Jun-Jun LU, Ming MING, Yi YANG, Jia WU, Bo LI, Jian-Dong DING, Qing-Guo LI, and shi-Xiong QIANDepartment of Physics, fudan university, shanghai 2.04.3, c.ina Department of Macromolecular science, Key Laboratory of Molecular Engineering of Polymers, fudan university, shanghai 2.04.3, c.ina Department of Physiology and Biophysics, {6. of life sciences, fudan university, shanghai 2.04.3, c.ina Department of Physics Fudan University Shanghai 200433 China

Transient dynamic behavior of the excited bacteriorhodopsin (BR), which was isolated from the strain H. salinarum, was studied at excitation wavelength from 585 to 6.9 nm. With the one-color femtosecond (fs) pump-probe technique, we revealed the primary events in BR's photocycle that took place in an ultrafast time scale. From the analysis of the decay components of the dynamical traces, it was evident that the isomerization of the retinal

关键词： bacteriorhodopsin transient dynamics primary events femtosecond laser pump-probe technique

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 2.04.3, c.ina shanghai center for Bioinformation 1 Technology, shanghai 200235, c.ina {6. of life sciences, fudan university, shanghai 2.04.3, c.ina Bioinformation center of shanghai Institutes for Biological sciences, the chinese Academy of sciences, shanghai 200031, c.ina 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

Identification and characterization of glnA Promoter and its corresponding Trans-regulatory Protein GlnR in the Rifamycin sV Producing Actinomycete,Amycolatopsis mediterranei U32

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Acta Biochimica et Biophysica sinica 2006年第12期38卷 831-843页

作者： Hao YU~(1&) Wen-Tao PENG~1 Yang LIU~1 Ting WU~2 Yu-Feng YAO~1 Ming-Xue cUI~1 Wei-Hong JIANG~1 Guo-Ping ZHAO~(1,3,4*) 1 Laboratory of Molecular Microbiology,Institute of Plant Physiology and Ecology,shanghai Institutes for Biological sciences,chinese Academy of sciences,shanghai 200032,c.ina 2 Department of Medicinal chemistry,sc.ool of Pharmacy,fudan {6.,shanghai 200032,c.ina 3 state Key Laboratory of Genetic Engineering & Department of Microbiology,sc.ool of life science,fudan {6.,shanghai 2.04.3,c.ina 4 Laboratory of Disease and Health Genomics,chinese National Human Genome center at shanghai,shanghai 201203,c.ina Laboratory of Molecular Microbiology Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200032 China Department of Medicinal chemistry School of Pharmacy Fudan University Shanghai 200032 China state Key Laboratory of Genetic Engineering & Department of Microbiology School of Life Science Fudan University Shanghai 200433 China Laboratory of Disease and Health Genomics Chinese National Human Genome Center at Shanghai Shanghai 201203 China

The genetic requirements for the transcription of glnA,encoding the major glutaminesynthetase in a rifamycin sV-producing Amycolatopsis mediterranei strain,U32,were *** experiments showed that the promoter of U32 glnA （pglnA） was likely to have two transcriptioninitiation sites:P1and P2,located 157 and 45 nucleotides （nt） upstream of the translational start codon,*** mobility shift and DNase I footprinting analyses revealed a 30 bp cis-element locatedat 45 to 75 nt downstream of P1,or 38 to 6. nt upstream of *** sequence of the cis-element displayedhigh similarity to the corresponding regions of pglnA from streptomyces coelicolor and *** as a reporter gene,the expression levels of U32 pglnA and its deletion derivatives under differentnitrogen-source conditions were analyzed by detecting the catechol dioxygenase activities in ***54,*** J508 and *** Fs10 （glnR mutant）.These in vivo studies showed that theactivation of U32 pglnA in *** required GlnR,and its binding to the U32 pglnA was furtherconfirmed by the gel mobility shift *** and heterologous expression of the U32 glnR allowed usto detect the in vitro interaction between the U32 GlnR and the corresponding pglnA *** shown by in vivo glnR inactivation and complementation indicated that GlnR is essential for theactive transcription of glnA in U32.

关键词： glnA promoter cis-element glnR Amycolatopsis mediterranei

Preparation and characterization of some surface negatively charged residue mutants of cytochrome b_5

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chinese science Bulletin 2001年第7期46卷 555-559页

作者： WANG Yunhua, WANG Wenhu, LU Junxia, REN Yi, GU shaohua, XIE Yi & HUANG Zhongxian1. chemical Biology Lab, Department of chemistry, fudan university, shanghai 2.04.3, c.ina 2. Genetic Institute, sc.ool of life, fudan university, shanghai 2.04.3, c.ina chemical Biology Lab Department of Chemistry Fudan University Shanghai China Genetic Institute School of Life Fudan University Shanghai China

site-directed mutagenesis was used to obtain seven variants of tryptic fragment of bovine liver cytochrome bs (cyt bs), in which the negatively charged residues around the heme exposed edge of cyt bs were replaced by hydropho-bic amino acid alanine. Double-site mutants, triple-site mutants and even quadruple-site mutants were obtained. DNA sequencing and molecular weight measurements of the mutant proteins both confirmed that these site-directed muta-genesises were successfully performed. spectroelectrochem-istry of these mutant proteins revealed that the apparent redox potentials of these mutant proteins caused a positive shift of 2-10 mV. The global structure of these mutant proteins did not show much difference from that of the wild type cyt bs, providing a solid base for the further study on the roles of the proteins’ surface charges.

关键词： cytochrome bs site-directed mutagenesis negative charge on the protein surface redox potential.

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

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science c.ina(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 sc.ool of life sciences,fudan university,shanghai 2.04.3,{6. 2 Bioinformatics center,Key Lab of systems Biology,shanghai Institutes for Biological sciences,chinese Academy of sciences,shanghai 200031,{6. 3 shanghai center for Bioinformation Technology,shanghai 200235,{6. 4 sc.ool of life sciences,Tongji university,shanghai 200092,{6. 1. sc.ool 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. sc.ool 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

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, c.ina 2. college of life sciences, Beijing Normal university, Beijing 100875, c.ina 3. Institute of Viral Disease control and Prevention, chinese cDc, Beijing 100052, c.ina 4. Bioinformation center, shanghai Institutes for Biological sciences, chinese Academy of sciences, shanghai 200031, c.ina 5. shanghai center for Bioinformation Technology, shanghai 200235, c.ina 6. sc.ool of life sciences, fudan university, shanghai 2.04.3, c.ina 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. sc.ool 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 42.sequences 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

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 sc.ool of the chinese Academy of sciences, shanghai 200233, c.ina 1sc.ool of Agriculture and Biology, shanghai Jiaotong university, shanghai 201101, c.ina 2sc.ool of life science and Biotechnology, shanghai Jiaotong university, shanghai 200030, c.ina shanghaiResearch center of Biotechnology Shanghai Institute for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of Sciences sc.ool 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

Identification and characterization of a Rat Novel Gene RsEP4 Expressed specifically in central Nervous system

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Acta Biochimica et Biophysica sinica 2004年第7期36卷 501-507页

作者： Xi-Dao WANG1,2, Ling-Wei KONG1, Zhi-Qin XIE1, Yu-Qiu ZHANG3, Zhi-Xin LIN2, Zhi-Qi ZHAO3,Lei YU4, and Nai-He JING1* 1 Laboratory of Molecular cell Biology, Laboratory of stem cell Biology, Institute of Biochemistry and cell Biology, shanghai Institutes for Biological sciences, chinese Academy of sciences, Graduate sc.ool of the chinese Academy of sciences, shanghai 200031, c.ina sc.ool of life science and Biotechnology, 2 shanghai Jiaotong university, shanghai 200030, c.ina Institute of Neurobiology, fudan university, shanghai 2.04.3, c.ina 3 4 Department of cell Biology, Neurobiology and Anatomy, college of Medicine, university of cincinnati, cincinnati, Ohio, UsA Laboratory of Molecular cell Biology and stem cell Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of Sciences Shanghai China

The low-abundantly expressed genes composed the majorities of the mRNAs expressed in the central nervous system (cNs), and were thought to be important for the normal brain functions. Through differential screening a low-abundance cDNA sublibrary with mRNA from neuropathic pain of chronic constriction injury (ccI) model, we have identified a novel rat gene, rat spinal-cord expression protein 4 gene (RsEP4). The total length of RsEP4 cDNA is 2006.bp, with a 501 nucleotide open reading frame (ORF) that encodes a 16. amino acid polypeptide. Northern blot revealed that RsEP4 was expressed specifically in the cNs. In situ hybridization showed that the mRNA of RsEP4 was strongly expressed in the cA1, cA2, cA3 and DG regions of hippocampus, the Purkinje cells of cerebellum, and the small sensory neurons of dorsal horn and large motor neurons of ventral horn of spinal cord. Over-expression of RsEP4-EGFP fusion protein in the human embryonic kidney 293T cells showed that RsEP4 protein was mainly localized in the cell cytoplasm. These results suggest that RsEP4 may play some roles in the cNs.

关键词： central nervous system (cNs) rat Northern blot in situ hybridization