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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 2.02.5,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

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 2.02.5, china 3 School of Life Sciences, Fudan University, shanghai 200433, 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 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

Performance and mechanism study for low-temperature SCR of NO with propylene in excess oxygen over Pt/TiO_2 catalyst

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Journal of Environmental Sciences 2010年第9期22卷 1441-1446页

作者： Zhixiang Zhang,Mingxia Chen,Zhi Jiang,Wenfeng Shangguan Research center for Combustion and Environmental technology,shanghai Jiao Tong University,shanghai 200240,china. [a] Research center for Combustion Environmental technology Shanghai Jiao Tong University Shanghai 200240 China

A 0.5 wt.% Pt/TiO2 catalyst was prepared and used for the low-temperature selective catalytic reduction （SCR） of NO with C3H6 in the presence of excess oxygen. The effects of Pt loading and 02 concentration on Pt/TiO2 catalytic performance for low-temperature SCR were investigated. It was found that optimal Pt loading was 0.5 wt.% and excess 02 favored low-temperature SCR of NOx. The mechanism of low-temperature SCR of NO with C3H6 was investigated with respect to the behavior of adsorbed species over Pt/TiO2 at 150~C using in situ DRIFTS. The results indicated that surface nitrosyl species （Pt~＋-NO and Ti3＋-NO） and pt2＋-CO are main reaction intermediates during the interactions of NO, C3H6 and 02. A simplified NO decomposition mechanism for the low-temperature SCR of NO with C3H6 was proposed.

关键词： NO low-temperature SCR Pt/TiO2 in situ DRIFTS

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 2.02.5,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

Photocatalytic energy storage ability of TiO_2-WO_3 composite prepared by wet-chemical technique

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Journal of Environmental Sciences 2010年第3期22卷 454-459页

作者： Linglin Cao, Jian Yuan, Mingxia Chen, Wenfeng Shangguan Research center for Combustion and Environment technology, shanghai Jiao Tong University, shanghai 200240, china. [a] Research center for Combustion Environment technology Shanghai Jiao Tong University Shanghai 200240 China

TiO2-WO3 hybrid photocatalysts were prepared using wet-chemical technique, and their energy storage performance was characterized by electrochemical galvanostatic method. TiO2 powder was coupled with WO3 powder, which was used as electron pool and the reductive energy could be stored in. As a result, the prepared TiO2-WO3 had good energy storage ability while pure TiO2 showed no capacity and pure WO3 showed quite low performance. The energy storage ability was affected by the crystal structure of WO3 and calcination temperature. The photocatalyst had better capacity when WO3 had low degree of crystallinity, since its loose structure made it easier for electrons and cations to pass through. The photocatalytic energy storage performance was also affected by the molar ratio of TiO2 to WO3. Energy storage capacity was significantly dependent on the composition, reaching the maximum value at TiO2/WO3 1：1 （mol/mol）.

关键词： photocatalyst TiO2-WO3 energy storage

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 2.02.5,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

Biological networks to the analysis of microarray data

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Progress in Natural Science:Materials International 2006年第12期16卷 1242-1251页

作者： FANG Zhuo~1, LUO Qingming~1**, ZHANG Guoqing~1 and LI Yixue~2**(1. Hubei Bioinformatics and Molecular Imaging Key Laboratory,Huazhong University of Science and technology, Wuhan 430074, china 2. shanghai center for bioinformation and technology, shanghai 2.02.5, china) [a]Hubei Bioinformatics and Molecular Imaging Key Laboratory Huazhong University of Science and Technology Wuhan China [b]shanghai center for bioinformation and technology Shanghai China

Microarray technology, which permits rapid and large-scale screening for patterns of gene expressions, usually generates a large amount of data. How to mine the biological meanings under these data is one of the main challenges in bioinformatics. Compared to the pure mathematical techniques, those methods incorporated with some prior biological knowledge generally bring better interpretations. Recently, a new analysis, in which the knowledge of biological networks such as metabolic network and protein interaction network is introduced, is widely applied to microarray data analysis. The microarray data analysis based on biological networks contains two main research aspects: identification of active components in biological networks and assessment of gene sets significance. In this paper, we briefly review the progress of these two categories of analyses, especially some representative methods.

关键词： biological networks microarray data analysis subnetwork gene set.

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 bioinformation technology,shanghai 2.02.5,china 3 College of Life Science and technology,shanghai Jiaotong University,shanghai 200030,china 4 bioinformation center of shanghai Institutes for Biological Sciences,Chinese Academy of Sciences,shanghai 200031,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

Progress in the detection of human genome structural variations

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Science china(Life Sciences) 2009年第6期52卷 560-567页

作者： WU XueMei1,3 & XIAO HuaSheng1,2 1 center of Functional Genomics,Key Laboratory of System Biology,shanghai Institutes for Biological Sciences,Chinese Academy of Sciences,shanghai 200031,china 2 National Engineering center for Biochip at shanghai,shanghai 201203,china 3 Graduate School of the Chinese Academy of Sciences,shanghai 200031,china 1. center of Functional Genomics Key Laboratory of System Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China 3. Graduate School of the Chinese Academy of Sciences Shanghai 200031 China 2. National Engineering center for Biochip at shanghai Shanghai 201203 China

The emerging of high-throughput and high-resolution genomic technologies led to the detection of submicroscopic variants ranging from 1 kb to 3 Mb in the human *** variants include copy number variations(CNVs),inversions,insertions,deletions and other complex rearrangements of DNA *** paper briefly reviews the commonly used technologies to discover both genomic structural variants and their potential ***,we highlight the array-based,PCR-based and sequencing-based assays,including array-based comparative genomic hybridization(aCGH),representational oligonucleotide microarray analysis(ROMA),multiplex amplifiable probe hybridization(MAPH),multiplex ligation-dependent probe amplification(MLPA),paired-end mapping(PEM),and next-generation DNA sequencing ***,we discuss the limitations and challenges of current assays and give advices on how to make the database of genomic variations more reliable.

关键词： structural variation cytogenetic microarray PCR paired end mapping(PEM) next-generation sequencing