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Acta Biochimica et Biophysica Sinica 2005年第4期37卷 215-220页

作者： Lu CHEN Juan YIN Yi CHEN Jiang ZHONG Department of Microbiology and Microbial Engineering,school of life sciences,fudan university,shanghai 200433,china Department of Microbiology and Microbial Engineering School of Life Sciences Fudan University Shanghai 200433 China

The latent Epstein-Barr virus (EBV) is found in the cells of many *** example,EBVis detectable in almost all cases,and in almost all tumor cells,of non-keratinizing nasopharyngeal *** the latent virus,which will result in its lytic replication and the death of tumor cells,is a potentialapproach for the treatment of EBV-associated *** this study,three recombinant adenoviruses wereconstructed to express the Zebra gene,an EBV gene responsible for switching from the latent state to ***-specific promoters were used in order to limit Zebra expression in EBV-positive cells,andreduce the potential side *** EBV promoters used were Cp,Zp and a dual promoter combining *** Zebra protein was detected in HEK293 cells as well as the EBV-positive D98-HR1cells infected with recombinant *** EBV lyric replication early antigen,EA-D,was also detected ininfected D98-HR1,implying the initiation of lytic *** the cell viability assay,Zebra-expressingadenoviruses had little effect on EBV-negative HeLa cells,while significantly reducing the cell viability andproliferation of D98-HR1 *** results indicate that EBV virus promoters can be used in adenovirusvectors to express the Zebra gene and induce EBV lytic replication in D98-HR1 cells.

关键词： Epstein-Barr virus recombinant adenovirus lytic replication cancer

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 200433, china Department of Macromolecular Science, Key Laboratory of Molecular Engineering of Polymers, fudan university, shanghai 200433, china Department of Physiology and Biophysics, school of life sciences, fudan university, shanghai 200433, china Department of Physics Fudan UniversityShanghai 200433 China Department of Macromolecular Science Key Laboratory of Molecular Engineering of Polymers Fudan UniversityShanghai 200433 China Department of Physiology and Biophysics School of Life Sciences Fudan UniversityShanghai 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 639 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 200433, china shanghai Center for Bioinformation 1 Technology, shanghai 200235, china school of life sciences, fudan university, shanghai 200433, china Bioinformation Center of shanghai Institutes for Biological sciences, the Chinese Academy of sciences, shanghai 200031, china Department of Computing and Information Technology Fudan University Shanghai 200433 China shanghai Center for Bioinformation Technology shanghai 200235 China school of life sciences Fudan University Shanghai 200433 China Bioinformation Center of shanghai Institutes for Biological sciences the Chinese Academy of Sciences Shanghai 200031 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

Regulation of swelling-activated chloride channels in embryonic chick heart cells

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Cell Research 2003年第1期13卷 21-28页

作者： HUA WEI, VAN AI MEI, JIA TING SUN, HAN QING ZHOU, ZHI HONG ZHANGDepartment of Physiology and Biophysics, Liren Laboratory, school of life sciences, fudan university, shanghai 200433, china Fishery College, shanghai Fisheries university, shanghai 200090, china Department of Physiology and Biophysics Liren Laboratory School of Life Sciences Fudan University Shanghai China Fishery College Shanghai Fisheries University Shanghai China

Swelling-activated Cl- currents, I(ci,swell), were measured during hyposmotic shock in white Leghorn embryonic chick heart cells using the whole-cell recording of patch-clamp technique. Genistein, an inhibitor of protein tyrosine kinase (PTK), suppressed I(ci,swell), Under isosmotic condition phorbol 12-myristate 13-acetate (PMA), an activator of PKC, elicited the Cl~ current similar to that in hyposmotic solution, whereas hyposmotic shock did not elicit I(ci,swell) in chelerythrine chloride(an inhibitor of PKC)-treated cells. Con-focal microscopy experiments using FITC-phalloidin as a fluorescent label of F-actin showed that the actin network was moved from cortical region of the cell to the center after hyposmotic shock as compared with the image under isosmotic condition. When the cells were treated with cytochalasin B (CB) or cytochalasin D (CD) under isosmotic condition the disruption of the F-actin integrity was observed, and I(ci,Sweii) was not elicited. With combination treatment of CB with PMA,

关键词： swelling activation myocardium chloride current F-actin phosphorylation.

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7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 200433, china shanghai Center for Bioin-formation Technology, shanghai 200235, china school of life sciences, fudan university, shanghai 200433, china Bioinfor-rnation Center of shanghai Institute for Biological sciences, Chinese Academy of sciences, shanghai 200031, china) shanghai Ctr Bioinformat Technol Shanghai 200235 Peoples R China fudan Univ Dept Comp & Informat Technol Shanghai 200433 Peoples R China fudan Univ Sch Life Sci Shanghai 200433 Peoples R China Chinese Acad Sci Shanghai Inst Biol Sci Bioinformat Ctr Shanghai 200031 Peoples R 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.

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 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 ZHONG Yang school of life sciences,fudan university,shanghai 200433,china shanghai Center for Bioinformation Technology,shanghai 200235,china 1shanghai-MOST Key Laboratory for Disease and Health Genomics Chinese National Human Genome Center at Shanghai Shanghai 201203 China. 2Lab 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. 4school of life sciences Fudan University Shanghai 200433 China. 5shanghai 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

Phylogeographic analysis of human papillomavirus 58

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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, shanghai 200235, china 3 school of life sciences, fudan university, shanghai 200433, china Obstetrics and Gynecology Hospital of fudan university Shanghai China shanghai Bio-information Research Center Shanghai China school of life sciences Fudan University Shanghai 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 china'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 china'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, china, as well as Japan and other Southeast Asian areas. Furthermore, Western Africa is considered to be the "root" source of the HPV58 variant, while china'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

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 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 school of life sciences Fudan University Shanghai China Bioinformatics Center Key Lab of Systems Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China shanghai Center for Bioinformation Technology Shanghai China school of life sciences Tongji University Shanghai 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

Enhancement of naked FIX minigene expression by chloroquine in mice

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Acta Pharmacologica Sinica 2004年第5期25卷 28-33页

作者： Hong-yan CHEN, Huan-zhang ZHU, Bin LU, Xuan XU, Ji-hua YAO, Qi SHEN, Jing-lun XUE1State Key Laboratory of Genetic Engineering, Institute of Genetics,school of life sciences, fudan university, shanghai 200433, china Institute of Genetics School of Life Sciences Fudan University State Key Laboratory of Genetic Engineering 上海 200433

AIM: To study the effect of chloroquine on the expression of human clotting factor IX (hFIX) in mice. METHODS:Hydrodynamics-based naked DNA plasmid administration was performed by tail vein injection of 10 g of pCMV-hFIX and chloroquine (0, 100, 200, and 500 mol/L) in 2.2 mL of Ringer solution within 6-7 s, the level andstability of hFIX expression, liver damage and toxicity were then examined. RESULTS: The maximum expression ofhFIX level was 4.41.8 mg/L at 8 h after injection, 9.71.6 mg/L at 24 h only existed in 200 mol/L chloroquine-treated animals, which is 3-4 fold higher than that of control (P0.05). CONCLUSION: Chloroquine can enhance and sustain exogenous geneexpression in vivo without side effect under our experimental conditions.

关键词： chloroquine factor IX naked plasmids

人类辅助生殖技术研究的里程碑——2010年诺贝尔生理学或医学奖解读

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生物化学与生物物理进展 2010年第10期37卷 1041-1046页

作者：李大可复旦大学生命科学学院生理学和生物物理学系立人实验室上海200433

试管婴儿技术是现代医学治疗不育症的人类辅助生殖技术之一.试管婴儿技术的发展,打破了人类繁衍的自然方式和过程,是生殖医学领域的一场革命,对生命医学的发展产生了重大影响.为此,在试管婴儿技术研究中做出开创性贡献的英国科学家罗伯... 详细信息

试管婴儿技术是现代医学治疗不育症的人类辅助生殖技术之一.试管婴儿技术的发展,打破了人类繁衍的自然方式和过程,是生殖医学领域的一场革命,对生命医学的发展产生了重大影响.为此,在试管婴儿技术研究中做出开创性贡献的英国科学家罗伯特·爱德华兹,荣获2010年诺贝尔生理学或医学奖.

关键词：诺贝尔奖体外受精胚胎移植试管婴儿