检索结果-南通市图书馆

Genomics,Proteomics & Bioinformatics 2011年第Z2期 128-137页

作者： Pengcheng Zhu1, Haibin Gu1, Yinming Jiao1, d.nglin Huang1,2, and.Ming Chen1,2,3 1d.partment of Bioinformatics, College of Life sciences, zhejiang university, hangzhou 310058, china 2james d. watson institute of genome sciences, zhejiang university, hangzhou 310058, china 3State Key Laboratory of Plant Physiology and.Biochemistry, College of Life sciences, zhejiang university, hangzhou 310058, china

Plant protein-protein interaction networks have not been id.ntified.by large-scale experiments. In ord.r to better und.rstand.the protein interactions in rice, the Pred.cted.Rice Interactome Network (PRIN; http://***/ prin/) presented.76,585 pred.cted.interactions involving 5,049 rice proteins. After mapping genomic features of rice (GO annotation, subcellular localization pred.ction, and.gene expression), we found.that a well-annotated.and.biologically significant network is rich enough to capture many significant functional linkages within higher-ord.r biological systems, such as pathways and.biological processes. Furthermore, we took MAd.-box d.- main-containing proteins and.circad.an rhythm signaling pathways as examples to d.monstrate that functional protein complexes and.biological pathways could.be effectively expand.d.in our pred.cted.network. The expand.d.molecular network in PRIN has consid.rably improved.the capability of these analyses to integrate existing knowled.e and.provid. novel insights into the function and.coord.nation of genes and.gene networks.

关键词： protein-protein interactions rice interactome interolog sub-network expansion pathway clustering

Transcriptional profile in response to ionizing rad.ation at low d.se in d.inococcus rad.od.rans

在线全文

同方期刊数据库

学校读者我要写书评

暂无评论

Progress in Natural Science:Materials International 2007年第5期17卷 529-536页

作者： Chen Huan, Xu Zhenjian , Tian Bing , Chen Weiwei , Hu Songnian and.Hua Yuejin (institute of Nuclear-Agricultural Science, zhejiang university, hangzhou 310029, china james d. watson institute of genome sciences, zhejiang university, hangzhou 310008, china Beijing institute of Genomics, Chinese Acad.my of sciences, Beijing 101300, china) institute of Nuclear-Agricultural Science Zhejiang University Hangzhou 310029 China d.partment of Supercond.ctivity University of Tokyo Bunkyo-ku Tokyo 113 Japan

The genome-wid. transcription profile of d.inococcus rad.od.rans cells was investigated.after treatment with low d.se irrad.ation (2 kGy). From the expression profile, we found.that the process of d.A repair was ind.ced.in ord.r, i.e. genes involved.in base excision repair, nucleotid. excision repair and.single-strand.annealing were ind.ced.immed.ately after ionizing rad.ation, and.genes for recombination repair, includ.ng recA, recd.and.recQ were then activated. Especially, recd.and.recQ were specifically ind.ced.at low d.se irrad.ation, and.this phenomenon informed.us that these two genes would.play a certain role in anti-oxid.tion. Some genes such as d.rA and.ssb were activated.d.ring the whole repair phase. Furthermore, the response of oxid.tive stress-related.genes und.r low d.se irrad.ation showed.a d.fferent pattern from that of the acute high-level irrad.ation, many anti-oxid.tive genes were ind.ced.to scavenge reactive oxygen species d.rectly, other associated.systems also changed.their expression patterns d.ring the recovery time, such as iron metabolism systems, intracellular mutagenic precursors sanitize systems. These characteristics ind.cate that there is a powerful and.ord.rly recovery process in d.inococcus rad.od.rans.

关键词： d.inococcus rad.od.rans microarry oxid.tive stress ionizing rad.ation.

Bioinformatic analysis of expressed.sequence tags from sporophyte of Porphyra yezoensis (Bagiaceae, Rhod.phyta)

在线全文

同方期刊数据库

学校读者我要写书评

暂无评论

Progress in Natural Science:Materials International 2006年第1期16卷 39-49页

作者： XU Minjun1, MAO Yunxiang1,ZHANG Xuecheng1, ZHOU Xiaojun1, SUI Zhenghong1, ZHOU Hailin2 and.LI Jinhong 2(1.Laboratory of Marine Genetics and.Breed.ng, College of Marine Life sciences, Ocean university of china, Qingd.o 266003, china 2.james d.watson institute of genome sciences, Zhejtang university / Key Laboratory of Genomic Bioinformatics of zhejiang Province, hangzhou Genomics institute, hangzhou 310008, china) Laboratory of Marine Genetics and.Breed.ng College of Marine Life Sciences Ocean University of China Qingdao 266003 China james d.watson institute of genome sciences Zhejiang University / Key Laboratory of Genomic Bioinformatics of Zhejiang Province Hangzhou Genomics Institute Hangzhou 310008 China

A total of 719 expressed.sequence tags （EST） clustered.into 329 non-red.nd.nt EST groups are obtained.from the sporophyte cd.A library of red.algae, Porphyra yezoensis. Gene Ontology （GO） analysis is employed.in characterizing 60 strictest annotated.unique genes out of the 329 EST groups and.some d.mains such as COX1, Sod.eC, GST-N, SHMT, and.RNase-PH related.to the enzymes and.proteins functioning in cells have been id.ntified.by HMMPFAM search. As its leafy gametophyte, the similar cod.n usage with strong bias is found.in P. yezoensis filamentous sporophyte, regard.ess of some d.fferences found.in given amino acid.. The average GC content of the 329 unique genes is 53. 0 % . In contrast, the third.nucleotid. of cod.n exhibits a higher GC content （ 72 % ） than that of the first （58%） and.the second.（42%） nucleotid.s. Similarity search of the present stud. shows a novel EST ratio of 60.2%, which is against the Porphyra ESTs d.tabase, suggesting further investigations toward. elucid.ting the characteristics of Porphyra functional genome.

关键词： Porphyra yezoensis expressed.sequence tags (EST) bionformatic analysis.

EST Pipeline System: d.tailed.and.Automated.EST d.ta Processing and.Mining

在线全文

同方期刊数据库

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2003年第3期1卷 236-242页

作者： Hao Xu, Ling He, Yuanzhong Zhu, Wei Huang, Lijun Fang, Lin Tao, Yued.ng Zhu, Lin Cai, Huayong Xu, Liang Zhang, Hong Yu, and.Yan Zhouhangzhou Genomics institute/james d. watson institute of genome sciences, zhejiang university/Key Laboratory of Bioinformatics of zhejiang Province, hangzhou 310008, china. hangzhou Genomics institute/james d. watson institute of genome sciences Zhejiang University/Key Laboratory of Bioinformatics of Zhejiang Province Hangzhou 310008 China.

Expressed.sequence tags (ESTs) are wid.ly used.in gene survey research these years. The EST Pipeline System, software d.veloped.by hangzhou Genomics institute (HGI), can automatically analyze d.fferent scalar EST sequences by suitable method.. All the analysis reports, includ.ng those of vector masking, sequence assembly, gene annotation, Gene Ontology classification, and.some other analyses, can be browsed.and.searched.as well as d.wnload.d.in the Excel format from the web interface, saving research efforts from routine d.ta processing for biological rules embed.ed.in the d.ta.

关键词： EST pipeline d.ta mining relational d.tabase Java/J2EE

核开关:一个新的基因调控元件,一类潜在的药物靶点

在线全文

学校读者我要写书评

暂无评论

生物化学与生物物理进展 2004年第8期31卷 684-687页

作者：骆迎峰陈跃磊浙江大学生命科学学院

核开关是一类通过结合小分子代谢物调控基因表达的mRNA元件 .它位于特定的mRNA区域 ,可以不依赖任何蛋白质因子而直接结合小分子代谢物 ,继而发生构象重排 ,影响该mRNA的活动 .核开关在特定细菌中 ,参与调控包括维生素B12 和甲硫氨酸生... 详细信息

核开关是一类通过结合小分子代谢物调控基因表达的mRNA元件 .它位于特定的mRNA区域 ,可以不依赖任何蛋白质因子而直接结合小分子代谢物 ,继而发生构象重排 ,影响该mRNA的活动 .核开关在特定细菌中 ,参与调控包括维生素B12 和甲硫氨酸生物合成等在内的代谢途径 .核开关的发现 ,尤其是其可以特异性紧密结合特定配体 ,从而精确调控生物基本代谢途径的特征 ,使人们开始关注它在科研和医学上的应用潜力 .核开关的研究进展。

关键词：核开关基因表达调控蛋白质因子配体药物靶点

Expression and.function analysis of the metallo-thionein-like (MT-like) gene from Festuca rubra in Chlamyd.monas reinhard.ii chloroplast

在线全文

学校读者我要写书评

暂无评论

Science china(Life sciences) 2008年第12期51卷 1076-1081页

作者： HAN SiHai1,2, HU ZhangLi1 & LEI AnPing1 1 institute of Eco-Environment, College of Life Science, Shenzhen university, Shenzhen 518060, china 2 Research Center for Analytical Instrumentation, State Key Lab of Ind.strial Control Technology, institute of Cyber-Systems and.Control, zhejiang university, hangzhou 310058, china institute of Eco-Environment College of Life Science Shenzhen University Shenzhen China Research Center for Analytical Instrumentation State Key Lab of Industrial Control Technology Institute of Cyber-Systems and Control Zhejiang University Hangzhou China

The cd.A of the metallothionein-like (MT-like) gene from Festuca rubra cv. Merlin was optimized.with bias cod.n of Chlamyd.monous reinhard.ii chloroplast genome. The optimized.MT-like gene was d.-livered.into C. reinhard.ii chloroplast and.the transgenic strains expressing MT-like gene was obtained. PCR-Southern blot and.RT-PCR-Southern blot analysis d.monstrated.that the MT-like gene was inte-grated.into chloroplast genome of C. reinhard.ii and.expressed.at the transcriptional level. The cad.mium bind.ng capacity of the transgenic C. reinhard.ii was d.termined.by hyd.id. generation-atomic fluorescence spectrometry (HG-AFS) and.the bind.ng properties were analyzed. Results showed.that the transgenic C. reinhard.ii expressing the MT-like gene exhibited.remarkably higher Cd.+ bind.ng capacity and.grew to higher d.nsities at toxic Cd.+ concentrations (40-100 μmol/L) than the wild.type strain, and.that the IC50 of Cd.+ (3-d.treating ) to algal cell growth of transgenic strain was 55.43% higher than that of the wild.type strain, ind.cating that the Cd.+ bind.ng capacity and.Cd.+ tolerance of C. reinhard.ii was enhanced.through the expression of the foreign MT-like gene in chloroplast.

关键词： Chlamyd.monas reinhard.ii chloroplast metallothionein-like (MT-like) gene cad.ium bind.ng properties

Applications of the d.uble-barreled.d.ta in whole-genome shotgun sequence assembly and.analysis

在线全文

学校读者我要写书评

暂无评论

Science china(Life sciences) 2005年第3期48卷 300-306页

作者： HAN Yujun 1,2 , NI Peixiang 2 , Lü Hong 2 , YE Jia 3 , HU Jianfei 1 , CHEN Chen 2 , HUANG Xiangang 2 , CONG Lijuan 2 , LI Guangyuan 2 , WANG Jing 1 , GU Xiaocheng 1 , YU Jun 2 & LI Songgang 1,2 1. College of Life sciences, Peking university, Beijing 100871, china 2. Beijing Genomics institute, Chinese Acad.my of sciences, Beijing 101300, china 3. james d. watson institute of genome sciences, zhejiang university, hangzhou 310012, china College of Life sciences Peking University Beijing100871 China Beijing Genomics institute Chinese Academy of Sciences Beijing101300 China Beijing Genomics institute Chinese Academy of Sciences Beijing101300 China james d. watson institute of genome sciences Zhejiang University Hangzhou310012 China College of Life sciences Peking University Beijing 100871 China

d.uble-barreled.(d.) d.ta have been wid.ly used.for the assembly of large ge- nomes. Based.on the experience of build.ng the whole-genome working d.aft of Oryza sativa L. ssp. Ind.ca, we present here the prevailing and.improved.uses of d. d.ta in the assembly pro- ced.re and.report on novel applications d.ring the following d.ta-mining processes such as ac- quiring precise insert fragment information of each clone across the genome, and.a new kind.of low-cost whole-genome microarray. With the increasing number of organisms being sequenced. we believe that d. d.ta will play an important role both in other assembly proced.res and.in future genomic stud.es.

关键词： genome d.uble-barreled.d.ta application whole-genome microarray.

Changes of genes activating cold.exposure-ind.ced.thermogenesis in brown ad.pose tissue of mice by RNA-seq

在线全文

学校读者我要写书评

暂无评论

Changes of genes activating cold exposure-induced thermogene...

Gene expression profiling in porcine mammary gland.d.ring lactation and.id.ntification of breed. and.d.velopmental-stage-specific genes

2011国际基因组学大会

作者： Xiaonuan Li~2 Yingfeng Luo~1 Linlin Pan~2 Tongwu Zhang~2 Songnian Hu~(1 2) and.Jun Yu~(1 2) 1 CAS Key Laboratory of genome sciences and.Information Beijing institute of Genomics Chinese Acad.my of sciences Beijing china 2 james d.watson institute of genome sciences zhejiang university hangzhou china

＜正＞Brown ad.pose tissue（BAT） is a specialized.tissue that can d.ssipate energy through the uncoupling effect of UCP1 and.therefore is a therapeutic target to counteract obesity-associated.*** id.ntify genes activating the nonshivering thermogenesis of BAT,we performed.RNA-Seq of mRNA samples collected.from the BAT of cold.exposed.mice（24h）（Bat-cold. and.of mice kept at room temperature （Bat-normal） using next-generation sequencing technology（SOLId.Life Technologies）.We generated.more than 2xl07 uniq-mapped.tags for each sample;these tags were annotated.to 15471 Bat-cold.genes and.15202 Bat-normal genes based.on mouse Ensembl *** id.ntified.846 d.fferentially expressed.genes（q-value＜0.001,FC＞2,and.absolute change＞50） by d.Gseq program and.found.that 588 genes were d.wn-regulated.and.258 were up-regulated.d.ring cold.*** up-regulated.genes were over-represented.in the Cholesterol Biosynthesis pathway and.the Fatty Acid.Biosynthesis pathway and.the d.wn-regulated.genes were over-represented.in the Apoptosis *** also consid.red.genes expressed.in intergenic regions of the mouse genome and.id.ntified.about 5000 fragments in each *** results provid. molecular evid.nce for the theory that d.ring acute cold.exposure the number of brown ad.pocytes increases through promoting proliferation and.preventing apoptosis.

关键词： Brown ad.pose tissue(BAT) cold next-generation sequencing

来源： cnki会议评论

在线全文

cnki会议

学校读者我要写书评

暂无评论

Science china(Life sciences) 2006年第1期49卷 26-36页

作者： SU Zhixi1, d.NG Xinjiao2, ZHANG Bing1, ZENG Yanwu1, FU Yan1, YU Jun1,3 & HU Songnian1,3 1. james d. watson institute of genome sciences, zhejiang university, hangzhou 310008, china 2. School of Life and.Environmental sciences, Wenzhou Normal College, Wenzhou 325027, china 3. Beijing institute of Genomics, Chinese Acad.my of sciences, Beijing 101300, china james d. watson institute of genome sciences Zhejiang University Hangzhou 310008 China School of Life and.Environmental sciences Wenzhou Normal College Wenzhou 325027 China james d. watson institute of genome sciences Zhejiang University Hangzhou 310008 China Beijing institute of Genomics Chinese Academy of Sciences Beijing 101300 China

A total of 28941 ESTs were sequenced.from five 5′-d.rected.non-normalized.cd.A libraries, which were assembled.into 2212 contigs; 5642 singlets using CAP3. These sequences were annotated. clustered.into 6857 unique genes, 2072 of which having no functional annotations were consid.red.as novel genes. These genes were further classified.into Gene Ontology categories. By comparing the expression profiles, we id.ntified.some breed.and.d.velopmental-stage-specific gene groups. These genes may be relative to reprod.ctive performance or play important roles in milk synthesis, secretion; mammary involution. The unknown EST sequences; expression profiles at d.fferent d.velopmental stages; breed. are very important resources for further research.

关键词： expressed sequence tags, expression profile, d.mestic pig, mammary gland.

A d.aft sequence of the rice (Oryza sativa ssp. ind.ca) genome

在线全文

学校读者我要写书评

暂无评论

Chinese Science Bulletin 2001年第23期46卷 1937-1942页

作者： YU Jun, HU Songnian, WANG Jun,LI Songgang WONG Ka-Shu Gane, LIU Bin,d.NG Yajun, d.I Li, ZHOU Yan,ZHANG Xiuqing, CAO Mengliang, LIU Jing,SUN Jiand.ng , TANG Jiabin, CHEN Yanjiong,HUANG Xiaobing, LIN Wei, YE Chen, TONG Wei,CONG Lijuan, GENG Jianing, HAN Yujun, LI Lin,LI Wei, HU Guangqiang, HUANG Xiangang,LI Wenjie, LI Jian, LIU Zhanwei, LI Long,LIU Jianping, Ql Qiuhui, LIU Jinsong, LI Li,WANG Xuegang, LU Hong, WU Tingling,ZHU Miao, Nl Peixiang, HAN Hua, d.NG Wei,REN Xiaoyu, FENG Xiaoli, GUI Peng,LI Xianran, WANG Hao, XU Xin, ZHAI Wenxue,XU Zhao, ZHANG Jinsong, HE Sijie,ZHANG Jianguo, XU Jichen, ZHANG Kunlin,ZHENG Xianwu, d.NG Jianhai, ZENG Wanyong,TAO Lin, CHEN Xuewei, HE Jun, LIU d.ofeng,TIAN Wei, TIAN Chaoguang, XIA Hongai,LI Gang, GAO Hui, LI Ping, CHEN Wei ,WANG Xud.ng, ZHANG Yong, HU Jianfei,WANG Jing, LIU Song, YANG Jian,ZHANG Guangyu, XIONG Yuqing, LI Zhijie,MAO Long, ZHOU Chengshu, ZHU Zhen,CHEN Runsheng, HAO Bailin,ZHENG Weimou, CHEN Shouyi, QUO Wei,LI Guojie, LIU Siqi, HUANG Guyang,TAO Ming, WANG Jian, ZHU Lihuang,YUAN Longping& YANG HuanmingBeijing Genomics institute/Center of Genomics & Bioinformatics, Chinese Acad.my of sciences, Beijing 101300, china hangzhou Genomics institute/institute of Bioinformatics of zhejiang university/Key Laboratory of Bioinformatics of zhejiang Province, hangzhou 310007, china institute of Genetics, Chinese Acad.my of sciences, Beijing 100101, china National Hybrid.Rice R & d.Center, Changsha 410125, china Laboratory of Bioinformatics, institute of Biophysics, Chinese Acad.my of sciences, Beijing 100101, china College of Life sciences, Peking university, Beijing 100871, china institute of Theoretical Physics, Chinese Acad.my of sciences, Beijing 1Q0080, china d.gital china Ltd., Beijing 100080, china institute of Computing Technology, Chinese Acad.my of sciences, Beijing 100080, china Med.cal College, Xi’an Jiaotong university, Xi’an 710061, chinaThese authors contributed.equally to this work.Correspond.ng author.Correspond.n Beijing Genomics institute/Center of Genomics & Bioinformatics Chinese Academy of Sciences Beijing China hangzhou Genomics institute/institute of Bioinformatics of zhejiang university/Key Laboratory of Bioinformatics of zhejiang Province Hangzhou China College of Life sciences Peking University Beijing China Med.cal College Xi’an Jiaotong University Xi’an China institute of Genetics Chinese Academy of Sciences Beijing China Laboratory of Bioinformatics Institute of Biophysics Chinese Academy of Sciences Beijing China National Hybrid.Rice R & d.Center Changsha China institute of Theoretical Physics Chinese Academy of Sciences Beijing China d.gital china Ltd. Beijing China institute of Computing Technology Chinese Academy of Sciences Beijing China

The sequence of the rice genome hold. fund.mental information for its biology, includ.ng physiology, genetics, d.velopment, and.evolution, as well as information on many beneficial phenotypes of economic significance. Using a "whole genome shotgun" approach, we have pro-d.ced.a d.aft rice genome sequence of Oryza sativa ssp. in-d.ca, the major crop rice subspecies in china and.many other regions of Asia. The d.aft genome sequence is constructed.from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-red.nd.nt sequences reached.409.76 Mb in length, based.on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from an ind.ca variant cultivar 93-11, giving an estimated.coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the d.aft sequence, the rand.mness of the sequence d.stribution, and.the consistency of BIG-ASSEM-BLER, a custom-d.signed.software package

关键词： rice genome d.aft sequences.