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

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 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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Drug candidates from traditional chinese medicines

Drug candidates from traditional Chinese medicines

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药用植物化学与中药有效成分分析研讨会

作者： Jing-Fang Wang~2,Dong-Qing Wei~(1**) (1.College of Life Science and Biotechnology,shanghai Jiaotong University,shanghai 200240,china 2.bioinformatics center,key lab of systems biology,shanghai institutes for biological sciences,chinese academy of sciences,shanghai 200031,china)

Good progress has been made to modernize traditional chinese medicines by obtaining active components from natural *** the current case,some recent works on drug design using modern drug design tools have been *** some well defined targets,traditional chinese medicine databases have been screened so as to identify leading compounds whose potential as a drug candidate was not known *** these excellent works,two have been selected as examples to be discussed in ***,new anti-HIV candidates have been detected,namely leucovorin and agaritine derivatives. Subsequently,GTS-21 is proved to be a good candidate for Alzheimer’s *** these findings may provide a good way to find effective drug candidates with lower cost.

关键词： Drug candidates Traditional chinese Medicine Natural herbs Modern drug design tools

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

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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,chinese academy of Sci-ences,shanghai 200031,china 2 Graduate University of chinese academy of sciences,shanghai 200031,china 3 shanghai center for Bioinformation Technology,shanghai 200235,china 4 key laboratory of systems biology,shanghai institutes for biological sciences,chinese academy of sciences,shanghai 200031,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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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 200235, 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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ATPID:an integrative platform for plant systems biology

ATPID:an integrative platform for plant systems biology

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第二届植物代谢国际会议

作者： Peng Li Weidong Zang Tieliu Shi center for bioinformatics and Computational biology and The Institute of Biomedical sciences School of Life Science East china Normal University 500 Dong chuan Road shanghai 200241 center for bioinformatics and Computational biology and The Institute of Biomedical Sciences Schoolof Life Science East China Normal University 500 Dong chuan Road Shanghai 200241 Center for Bioinformatics and Computational Biology and The Institute of Biomedical Sciences S

＜正＞Protein interactions are involved in important cellular functions and biological processes that are the fundamentals of all life activities. With improvements in experimental techniques and progress in research,

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