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Applications of the double-barreled data in whole-genome shotgun sequence assembly and analysis

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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 academy of sciences, beijing 101300, china 3. James D. Watson institute of Genome sciences, Zhejiang University, Hangzhou 310012, china College of Life sciences Peking University Beijing China beijing genomics institute Chinese Academy of Sciences Beijing China James D. Watson institute of Genome sciences Zhejiang University Hangzhou China

Double-barreled (DB) data have been widely used for the assembly of large ge- nomes. Based on the experience of building the whole-genome working draft of Oryza sativa L. ssp. Indica, we present here the prevailing and improved uses of DB data in the assembly pro- cedure and report on novel applications during the following data-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 DB data will play an important role both in other assembly procedures and in future genomic studies.

关键词： genome double-barreled data application whole-genome microarray.

Identification of human dopamine receptors agonists from chinese herbs

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Acta Pharmacologica Sinica 2007年第1期28卷 132-139页

作者： Yi-lin ZHANG~(1,2,3,4) Hai-qing ZHANG~(1,2,3,4) Xiao-yu LIU~3 Shi-neng HUA~3 Lu-bing ZHOU~3 Jun YU~2 Xue-hai TAN~(3,5)1 Graduate School of the chinese academy of sciences,beijing 100039,china 2 beijing genomics institute,chinese academy of sciences beijing 101300,china 3 HD Biosciences Co Ltd,Shanghai 201203,china Graduate School of the chinese academy of sciences Beijing China beijing genomics institute Chinese Academy of Sciences Beijing China HD Biosciences Co Ltd Shanghai China

Aim:To find human dopamine receptors,especially Dl-like receptor specific ago-nists from chinese herbs as potential antihypertension drug ***:TwoD l-like receptor cell lines carrying a μ-lactamase reporter gene,and a D2 receptorcell line coexpressing a promiscuous G protein G15 were constructed using HEK293cells.A natural compound library made from fractionated samples of herbal ex-tracts was used for high-throughput screening（HTS）against one of the cell lines,HEK/D5R/*** interested hits were evaluated for their activities againstvarious dopamine ***:Fourteen hits were identified from primaryscreening,of which 2 of the better hit samples,HD0522 and HD0059,were selectedfor further material and activity analysis,and to obtain 2 compounds that ap-peared as 2 single peaks in HPLC,HD0522H01 and ***0059H01could activate D 1,D2,and D5 receptors,with EC50values of 2.28 μg/mL,0.85 μg/mL,and 1.41 μg/mL,***0522H01 could only activate DlR and D5Rwith EC50values of 2.95 μg/mL and 8.38 μg/***:We established cell-based assays for 3 different human dopamine receptors and identified specificagonists HD0522H01 and HD0059H01 through *** specific agonist to D1-like receptors,HD0522H01,may become a new natural product-based drug leadfor antihypertension treatment.

关键词： dopamine receptors natural products high throughput screening hypertension

水稻叶绿体蛋白质在生长发育过程中的表达研究

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生物化学与生物物理进展 2010年第9期37卷 988-995页

作者：白辉王宪云曹英豪李晓明李莉云陈浩刘丽娟朱健辉刘国振中国科学院北京基因组研究所北京101300 河北农业大学生命科学学院保定071001

在植物中,叶绿体是负责光合作用的细胞器,对叶绿体内的各种生物过程人们已经积累了很多知识,但对叶绿体蛋白质的表达还所知甚少.为了解水稻叶绿体蛋白质在正常生长发育过程中的表达情况,尝试基于抗体的水稻蛋白质组学策略.选取了10个水... 详细信息

在植物中,叶绿体是负责光合作用的细胞器,对叶绿体内的各种生物过程人们已经积累了很多知识,但对叶绿体蛋白质的表达还所知甚少.为了解水稻叶绿体蛋白质在正常生长发育过程中的表达情况,尝试基于抗体的水稻蛋白质组学策略.选取了10个水稻叶绿体基因,利用表达的蛋白质或合成的抗原决定簇片段制备了抗体,用Westernblotting检测了相应蛋白质在5个发育时期的根、茎、叶及穗组织中的表达.发现10个蛋白质均在叶片中表达,在根中不表达.与原初反应相关的叶绿素A/B结合蛋白1和2(CAB1和CAB2)、与电子传递相关的放氧增强蛋白1(OEE1)及与活性氧清除相关的过氧还蛋白过氧化物酶(2-CysP)和硫氧还蛋白(Trx)在茎中表达.而在卡尔文循环中发挥作用的Rubisco活化酶(RCA)、甘油醛-3-磷酸脱氢酶(GAPDH)、果糖二磷酸醛缩酶(FBPA)和景天庚酮糖-1,7-二磷酸酶(SBPase)蛋白质在茎中不表达.在穗中,这些蛋白质的表达时序不同,CAB2和2-CysP在穗发育的全程表达,CAB1和OEE1在中后期表达,而卡尔文循环中的蛋白质只在中期表达.有意思的是,卡尔文循环中的蛋白质表达模式相似,这一结果从蛋白质表达水平支持它们之间的相互衔接关系.此外,实验还揭示了可能的蛋白质修饰、二聚体及不同的转录本现象.将目标基因的表达谱与转录谱进行比较,发现二者间有一定的平行性,但也有明显的区别.以水稻叶绿体蛋白质为对象,直观并相对定量地揭示了它们的表达模式,为阐释其功能提供了信息,也为基于抗体的水稻蛋白质组学策略提供了一个初步数据.

关键词：水稻叶绿体光合作用蛋白质表达谱基于抗体的蛋白质组学

More active glycolytic pathway in esophageal squamous cell carcinoma

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More active glycolytic pathway in esophageal squamous cell c...

Being the Pioneer of Life sciences in china——Introduction to beijing genomics institute

全国肿瘤流行病学和肿瘤病因学学术会议

作者： Zhao Xiaohang~1,Liu Fei~1,Wang Lishun~2,Liu Siqi~2,Wang Rong~3, Xu Ningzhi~1,Xu Yang~1,Sun Yulin~1 1 State Key Laboratory of Molecular Oncology,Cancer institute & Hospital,chinese academy of Medical sciences & Peking Union Medical College,beijing 100021,china 2 beijing institute of genomics,chinese academy of sciences,beijing,101300,china. 3 Department of Genetic and Genomic Science,Department of Structural and Chemical Biology, Mount Sinai,School of Medicine,New York City,NY,USA

Cancer cells are resistant to apoptosis and show a shift in energy production from mitochondrial oxidative phosphorylation to cytosolic *** observe the metabolic reprogramming of esophageal cancer,8 pairs of tissue specimens of esophageal squamous cell carcinoma(ESCC) were separated and identified via 2-DE-MALDI-TOF-MS strategy.A total of 37 differentially expressed proteins were recognized as an exclusive profile that could distinguish ESCC from normal esophagus tissues,including 23 up-regulated and 14 down-regulated proteins. In which,five key proteins of glycolytic pathway were identified overexpressed in ESCC with lymph node *** glucose metabolism and lactate production of ESCC cells were found more active than that of the normal epithelia *** migration of esophageal cancer cells KYSE410 was found more effective than that of KYSE30 ***,it was also found KYSE410 with higher aerobic glycolysis and invasion capability than that of KYSE30 ***,the oligomycin,a respiration suppressor through suppressing the ATPase-F1 subunit, was enhanced glycolysis of KYSE30 cells,whereas it was no effect on KYSE410 *** may be energy supportment of KYSE30 partially depended on oxygen respiration and KYSE410 was more depending on *** data suggested that the Warburg effect may also exist in esophageal cancer and cancer cell movement was correlated with aerobic glycolysis.

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genomics, Proteomics & Bioinformatics 2004年第1期2卷 59-63页

作者： Xin Zhang beijing genomics institute, beijing 101300, china. beijing genomics institute Beijing 101300 China

The beijing genomics institute (BGI) of chinese academy of sciences (CAS) wasofficially founded in December 2003. Its predecessor, beijing Huada genomics Research Center, haspresented significant contributions to the development of life sciences in china by its excellentscientific innovations and achievements in the last five years. From the participation ofInternational Human Genome Project (HGP) to the independent completion of the whole-genome draft andfine maps of chinese super hybrid rice genome, from the porcine genome research cooperated withDenmark to the international chicken genome research, and from the silkworm genome projectaccomplished together with The Southwest Agriculture University of china to the great contributionsto the national campaign against SARS, all these facts illustrate that BGI not only has afirst-class scientific research power in the world but also is full of devotion to the flourish ofscience and nation. During these years, we have upheld the strategy of ''Advance through projects,strive for innovation, grow through cooperation'', in the aim of making BGI as one of the pioneers ofCAS climbing the peak of life sciences in the world.

关键词： chinese academy of sciences beijing genomics institute innovation life sciences

Discovery of immune related factors in Fenneropenaeus chinensis by annotation of ESTs

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Progress in Natural Science:Materials International 2004年第1期14卷 48-55页

作者： SHEN Yaoqing 1,2 , XIANG Jianhai 1*, WANG Bing 1,2 , LI Fuhua 1 and TONG Wei 3(1. Experimental Marine Biology Laboratory, institute of Oceanology, chinese academy of sciences, Qingdao 266071,china 2. Graduate School of the chinese academy of sciences, beijing 100039, china 3. genomics & Bioinformatics institute, chinese academy of sciences, beijing 101300, china) chinese Acad Sci Inst Oceanol Expt Marine Biol Lab Qingdao 266071 Peoples R China chinese Acad Sci Grad Sch Beijing 100039 Peoples R China chinese Acad Sci Geonom & Bioinformat Inst Beijing 101300 Peoples R China

A total of 10446 expressed sequence tags (ESTs) are obtained by a large scale sequencing of a cDNA library from cephalothorax of adult Fenneropenaeus chinensis . An EST analysis platform was built up based on local computers and bioinformatic techniques were used to annotate these ESTs in order to promptly find possible functional genes, especially for immune related factors. About 4% of the ESTs show similarity to the coding sequences of such factors, including lectin, serine protease, serpin, lysozyme, etc. These ESTs provide a partial profile of the immune system in F. chinensis and useful information for further study on these genes.

关键词： Fenneropenaeus chinensis bioinformatics ESTs immune factors

Overview of HBV whole genome data in public repositories and the chinese HBV reference sequences

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Progress in Natural Science:Materials International 2008年第1期18卷 13-20页

作者： Guanghua Wu a,b, Huiguo Ding c, Changqing Zeng b,* a Graduate School of chinese academy of sciences, beijing 100049, china b beijing institute of genomics, chinese academy of sciences, beijing 101300, china c beijing Youan Hospital, Capital Medical University, beijing 100069, china Graduate School of chinese academy of sciences Beijing 100049 China beijing institute of genomics Chinese Academy of Sciences Beijing 101300 China beijing Youan Hospital Capital Medical University Beijing 100069 China

The number of Hepatitis B virus (HBV) whole genomic sequences in public nucleotide databases (GenBank, EMBL, and DDBJ) had reached 866 by January 1, 2007. Coming from 46 countries and regions, these sequences were categorized as eight genotypes (A–H). With the statistical and phylogenetic analysis on all available complete genomic data of HBV, we here present an overview of HBV sequences in public databases. From all registered 229 HBV genomes in chinese regions as well as 59 sequencing data from our research group, we report the establishment of reference sequences of HBV strains prevailing in china. These analyses provide clues for the effects of HBV genotypes in host clinical progressions, geographic distribution of the infection, and the viral evolutionary history. Moreover, the viral sequence reference would be helpful in the identiffcation of various HBV mutations. Based on the analysis of various public databases, we suggest that the chinese HBV database with the clinical information should be constructed.

关键词： Public databases HBV genomic sequences Genotype Subtype chinese reference sequences

MODELLING AND NUMERICAL SOLUTIONS OF A GAUGE PERIODIC TIME DEPENDENT GINZBURG-LANDAU MODEL FOR TYPE-Ⅱ SUPERCONDUCTORS

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Journal of Computational Mathematics 1997年第4期15卷 365-384页

作者： Zhi-ming Chen (institute of Mathematics, chinese academy of sciences, beijing, china) 中科院数学所北京

In this paper we seek the solutions of the time dependent Ginzburg-Landau model for type-Ⅱ superconductors such that the associated physical observables are spatially periodic with respect to some lattice whose basic lattice cell is not necessarily rectangular. After appropriately foring the gange, the model can be formulated as a system of nonlinear parabolic partial differential equations with quasi-periodic boundary conditions. We first give some results concerning the existence, uniqueness and regularity of solutions and then we propose a semiimplicit finite element scheme solving the system of nonlinear partial dmerential equations and show the optimal error estimates both in the L2 and energy *** also report on some numerical results at the end of the paper.

关键词： Math QT MODELLING AND NUMERICAL SOLUTIONS OF A GAUGE PERIODIC TIME DEPENDENT GINZBURG-LANDAU MODEL FOR TYPE SUPERCONDUCTORS

Finding Signals for Plant Promoters

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genomics, Proteomics & Bioinformatics 2003年第1期1卷 68-73页

作者： Weimou Zhenginstitute of Theoretical Physics, chinese academy of sciences, beijing 100080, china beijing genomicsinstitute, chinese academy of sciences, beijing 101300, china institute of Theoretical Physics Chinese Academy of Sciences Beijing 100080 China beijing genomics institute Chinese Academy of Sciences Beijing 101300 China

The strongest signal of plant promoter is searched with the model of single motif with two types. It turns out that the dominant type is the TATA-box. The other type may be called TATA-less signal, and may be used in gene finders for promoter recognition. While the TATA signals are very close for the monocot and the dicot, their TATA-less signals are significantly different. A general and flexible multi-motif model is also proposed for promoter analysis based on dynamic programming. By extending the Gibbs sampler to the dynamic programming and introducing temperature, an efficient algorithm is developed for searching signals in plant promoters.

关键词： for on is as et Pro Finding Signals for Plant Promoters been of into