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genome size and sequence composition of moso bamboo: A comparative study

Science china(Life Sciences) 2007年第5期50卷 700-705页

作者： GUI YiJie1, WANG Sheng1, QUAN LiYan1, ZHOU ChangPing2, LONG ShiBao2, ZHENG HuaJun3, JIN Liang1, ZHANG XianYin 1, MA NaiXun 4 & FAN LongJiang1 1 Institute of Crop Science/Institute of Bioinformatics, Zhejiang University, Hangzhou 310029, china 2 Zhejiang Anji Bamboo Exposition Garden, Anji 313300, china 3 chinese national human genome center at shanghai, shanghai 201203, china 4 The Research Institute of Subtropical Forestry, chinese Academy of Forestry, Fuyang 311400, china Institute of Crop Science/Institute of Bioinformatics Zhejiang University Hangzhou 310029 China Zhejiang Anji Bamboo Exposition Garden Anji 313300 China chinese national human genome center at shanghai Shanghai 201203 China The Research Institute of Subtropical Forestry Chinese Academy of Forestry Fuyang 311400 China

Moso bamboo (Phyllostachys pubescens) is one of the world's most important bamboo species. It has the largest area of all planted bamboo―over two-thirds of the total bamboo forest area―and the highest economic value in china. Moso bamboo is a tetraploid (4x=48) and a special member of the grasses family. Although several genomes have been sequenced or are being sequenced in the grasses family, we know little about the genome of the bambusoids (bamboos). In this study, the moso bamboo genome size was estimated to be about 2034 Mb by flow cytometry (FCM), using maize (cv. B73) and rice (cv. Nipponbare) as internal references. The rice genome has been sequenced and the maize genome is being sequenced. We found that the size of the moso bamboo genome was similar to that of maize but significantly larger than that of rice. To determine whether the bamboo genome had a high proportion of repeat elements, similar to that of the maize genome, approximately 1000 genome survey sequences (GSS) were generated. Sequence analysis showed that the proportion of repeat elements was 23.3% for the bamboo genome, which is significantly lower than that of the maize ge-nome (65.7%). The bamboo repeat elements were mainly Gypsy/DIRS1 and Ty1/Copia LTR retrotrans-posons (14.7%), with a few DNA transposons. However, more genomic sequences are needed to con-firm the above results due to several factors, such as the limitation of our GSS data. This study is the first to investigate sequence composition of the bamboo genome. Our results are valuable for future genome research of moso and other bamboos.

关键词： flow cytometry (FCM), genome size, GSS, Phyllostachys pubescens, repeat elements

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Recent progress in 8igenomic research of liver cancer

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Science china(Life Sciences) 2009年第1期52卷 24-30页

作者： HAN ZeGuang shanghai-MOST Key Laboratory for Disease and Health Genomics,chinese national human genome center at shanghai,shanghai 201203,china shanghai-MOST Key Laboratory for Disease and Health Genomics Chinese National Human Genome Center at Shanghai Shanghai China

Along the course of occurrence and development of liver cancer,the corresponding somatic cells accumulate some important genetic *** variations may be divided into two *** the genetic changes closely related to etiology of liver cancer,the well-known cases include insertion and integration of the hepatitis B virus(HBV) DNA after infection,and mutations at site 249 of the tumor suppressor gene p53 induced by exposure to aflatoxin *** secondary genetic changes include amplification and deletion of certain chromosome regions,mutations in p53 at the sites other than 249,as well as the mutational activation of the Wnt/β-catenin signal *** tumor cells with these genetic variations may gradually become the dominant clones under evolutionary ***,identification of genetic susceptible against risk of liver malignancy is also an important aspect of research in this field.

关键词： hepatocellular carcinoma chromosomal instability gene mutation oncogene tumor suppressor gene

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Development and application of genotyping technologies

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Science china(Life Sciences) 2009年第1期52卷 17-23页

作者： SHI JinXiu,WANG Ying & HUANG Wei shanghai-MOST Key Laboratory of Health and Disease Genomics,chinese national human genome center at shanghai,shanghai 201203,china shanghai-MOST Key Laboratory of Health and Disease Genomics Chinese National Human Genome Center at Shanghai Shanghai China

With the completion of human genome Project,International HapMap Project and the publication of copy number variation in human genome,a great number of accurate,rapid,and cost-effective technologies for SNP analysis have been developed,promoting the research of the complex *** article presents a review of widely used genotyping techniques,and the progress and prospect in the study of complex diseases in terms of the projects and achievements of chinese national human genome center at shanghai(CHGCs).

关键词： single nucleotide polymorphism copy number variation complex disease

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Perspectives of DNA microarray and next-generation DNA sequencing technologies

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Science china(Life Sciences) 2009年第1期52卷 7-16页

作者： TENG XiaoKun1 & XIAO HuaSheng1,2 1 national Engineering center for Biochip at shanghai,shanghai 201203,china 2 shanghai-MOST Key Laboratory of Health and Disease Genomics,chinese national human genome center,shanghai 201203,china national Engineering center for Biochip at shanghai Shanghai China shanghai-MOST Key Laboratory of Health and Disease Genomics Chinese National Human Genome Center Shanghai China

DNA microarray and next-generation DNA sequencing technologies are important tools for high-throughput genome research,in revealing both the structural and functional characteristics of *** the past decade the DNA microarray technologies have been widely applied in the studies of functional genomics,systems biology and *** next-generation DNA sequencing method was first introduced by the 454 Company in 2003,immediately followed by the establishment of the Solexa and Solid techniques by other biotech *** it has not been long since the first emergence of this technology,with the fast and impressive improvement,the application of this technology has extended to almost all fields of genomics research,as a rival challenging the existing DNA microarray *** paper briefly reviews the working principles of these two technologies as well as their application and perspectives in genome research.

关键词： DNA microarray next generation DNA sequencing genome

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Current progress in epigenetic research for hepato-carcinomagenesis

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Science china(Life Sciences) 2009年第1期52卷 31-42页

作者： HUANG Jian national human genome Research center at shanghai-Ministry of Science and Technology to build a healthy and disease Ge-nomics Laboratory,shanghai 201203,china national human genome Research center at shanghai-Ministry of Science and Technology to build a healthy and disease Genomics Laboratory Shanghai China

Hepatocellular carcinoma is the main type of primary liver cancer,and also one of the most malignant *** present,the pathogenesis mechanisms of liver cancer are not entirely *** has been shown that inactivation of tumor suppressor genes and activation of oncogenes play a significant role in carcinogenesis,caused by the genetic and epigenetic *** the past,people generally thought that genetic mutation is a key event of tumor pathogenesis,and somatic mutation of tumor suppressor genes is in particular closely associated with *** deeper understanding of tumors in recent years,increasing evidence has shown that epigenetic silencing of those genes,as a result of aberrant hypermethylation of CpG islands in promoters and histone modification,is essential to carcinogenesis and *** term epigenetics refers to heritable changes in gene expression caused by regulation mechanisms,other than changes in the underlying DNA *** epigenetic processes include DNA methylation,genome imprinting,chromotin remodeling,histone modification and microRNA *** paper reviews recent epigenetics research progress in the hepatocellular carcinoma study,and tries to depict the relationships between hepatocellular carcinomagenesis and DNA methylation as well as microRNA regulation.

关键词： tumor heaptocellular carcinoma epigenetics DNA methylation microRNA

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Expression and Comparative Analysis of Genes Encoding Outer Membrane Proteins LipL21,LipL32 and OmpL1 in Epidemic Leptospires

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Acta Biochimica et Biophysica Sinica 2005年第10期37卷 7+650-656页

作者： Xiang-Yan ZHANG~(1#) Yang YU~(2,3#) Ping HE~1 Yi-Xuan ZHANG~(2,3) Bao-Yu HU~1 Yang YANG~1 Yi-Xin NIE~4 Xiu-Gao JIANG~4 Guo-Ping ZHAO~(2,3) Xiao-Kui GUO~(1*) 1 Department of Medical Microbiology and Parasitology,shanghai Jiaotong University,shanghai 200025,china 2 Research center of Biotechnology,shanghai Institutes for Biological Sciences,chinese Academy of Sciences,shanghai 200031,china 3 chinese national human genome center at shanghai,Zhangjiang High Tech Park,shanghai 201203,china 4 Institute for Infectious Disease Control and Prevention,chinese center for Disease Control and Prevention,Beijing 102206,china Department of Medical Microbiology and Parasitology Shanghai Jiaotong UniversityShanghai 200025 China Research center of Biotechnology Shanghai Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200031 China chinese national human genome center at shanghai Zhangjiang High Tech ParkShanghai 201203 China Institute for Infectious Disease Control and Prevention Chinese Center for Disease Control and PreventionBeijing 102206 China

Leptospiral outer membrane proteins (OMPs) are highly conserved in different species,andplay an essential role in the development of new immunoprotection and serodiagnosis *** genesencoding LipL21,LipL32 and OmpL1 were cloned from the complete genome sequence of Leptospirainterrogans serovar lai strain Lai and expressed in *** comparison analysis revealed that the threegenes were highly conserved among distinct epidemic leptospires,including three major epidemic speciesLeptospira interrogans,Leptospira borgpetersenii and Leptospira weilii,in *** analysis wasfurther performed to scrutinize 15 epidemic Leptospira reference strains using the antisera of the *** immunoblot assay and reverse transcription-polymerase chain reaction demonstrated that thesethree OMPs were conservatively expressed in pathogenic *** strains and other pathogenic ***,the use of these recombinant OMPs as antigens in enzyme-linked immunosorbent assay (ELISA)for serodiagnosis of leptospirosis was *** recombinant LipL32 and OmpL1 proteins showed ahigh degree of ELISA reactivity with sera from patients infected with *** strain Lai and otherpathogenic *** results may contribute to the identification of candidates for broad-rangevaccines and immunodiagnostic antigens in further research.

关键词： outer membrane protein expression comparative analysis epidemic leptospire

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Identification and classification of all potential hemolysin encoding genes and their products from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai

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Acta Pharmacologica Sinica 2005年第4期26卷 453-461页

作者： Yi-xuan ZHANG~(2,3,4,5) Yan GENG(2,3,4,5) Bo BI~(2,4) Jian-yong HE~4 Chun-fu WU~4 Xiao-kui GUO~3 Guo-ping ZHAO~(2,4,6,7) 2 Research center of Biotechnology,shanghai Institutes for Biological Sciences,chinese Academy of Sciences,shanghai 200233,china 3 Department of Microbiology and Parasitology,shanghai Second Medical University,shanghai 200025,china 4 The School of Pharmaceutical Engineering,Shenyang Pharmaceutical University,Shenyang 110016,china 6 chinese national human genome center at shanghai,ZhangJiang High Tech Park,shanghai 201203,china Research center of Biotechnology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China Department of Microbiology and Parasitology Shanghai Second Medical University Shanghai China The School of Pharmaceutical Engineering Shenyang Pharmaceutical University Shenyang China chinese national human genome center at shanghai ZhangJiang High Tech Park Shanghai China

Aim:To identify and classify all potential hemolysin candidates of Leptospirainterrogans serogroup Icterohaemorrhagiae serovar ***:All of thepotential hemolysin encoding genes were characterized in *** geneswere cloned and expressed in Escherichia *** hemolytic activities of theexpressed proteins were assayed observing the hemolysis on sheep blood *** activities of the hemolysin candidates were measuredby thin-layer chromatography(TLC)and HPLC for *** and secretion of the hemolysins in L interrogans were studied byreverse transcription polymerase chain reaction,Western blot,and enzyme-linkedimmunosorbent *** and Conclusion:The hemolytic activities ofhemolysin candidates(LA0327,LA0378,LA1027,LA1029,LAI650,LA3050,LA3937,LA4004)from L interrogans strain Lai were *** were furtherdivided into two groups,sphingomyelinase hemolysins and non-sphingomyelinasehemolysins,based on their ability to hydrolyze *** of thesehemolysins were actually expressed in living L interrogans and some of themwere secreted into the *** study establishes an essential findcomplete basis for further studying the contribution of hemolysins to the patho-genesis of L interrogans.

关键词： hemolysin Leptospira interrogans sphingo myelinase

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Identification and Analysis of Genes Present in Leptospira interrogans serovar lai but Absent in L. biflexa serovar monvalerio

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Acta Biochimica et Biophysica Sinica 2004年第12期36卷 832-839页

作者： Ping HE, Xiang-Yan ZHANG, Xiao-Kui GUO*, Bao-Yu HU, Xiao-Tian HUANG, Yang YANG, and Guo-Ping ZHAO1,2* Department of Microbiology and Parasitology, shanghai Second Medical University, shanghai 200025, china 1 Research center of Biotechnology, Institutes for Biological Sciences, chinese Academy of Sciences, shanghai 200031, china 2chinese national human genome center at shanghai, Zhangjiang High Tech Park, shanghai 201203, china Department of Microbiology and Parasitology Shanghai Second Medical UniversityShanghai 200025 China Research center of Biotechnology Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200031 China chinese national human genome center at shanghaiZhangjiang High Tech Park Shanghai 201203 China

Genes present in virulent bacterial strains but absent in avirulent close relatives can be of great biologic and clinical interest. This project aimed to identify strain specific DNA sequences of Leptospira interrogans serovar lai, which is absent in the saprophytic L. biflexa serovar monvalerio, via suppression subtractive hybridization with the former as the tester while the latter as the driver. The mixture of PCR amplified DNA fragments from two subtractive hybridization experiments were cloned into pMD18-T vector and the positive clones were identified by dot blotting against the chromosome DNA of the two strains individually. After DNA sequencing and analysis, the distribution of these genomic fragment sequences in a panel of pathogenic and nonpathogenic leptospires was investigated employing dot blot analysis. Among the 188 positive clones randomly chosen, 24 contained the tester strain specific genomic regions, of which, 5 were non-coding fragments while the others contained 23 distinct protein coding sequences. Besides 9 genes encoding functional proteins, 12 genes encode unknown proteins and the rest two genes encode proteins with recognizable domain structures, one for a putative leucine-rich repeats (LRR) family protein while the other as an outer-membrane protein. Our experiment results indicated that suppression subtractive hybridiza- tion is effective for screening specific DNA sequences between two leptospiral strains, and some of these sequences might be responsible for virulence determination. Further analysis of these DNA sequences will provide important information on the pathogenesis of Leptospira.

关键词： Leptospira interrogans serovar lai suppression subtractive hybridization (SSH) specific genes

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Development of a quantitative,cell-based,high-content screening assay for epidermal growth factor receptor modulators

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Acta Pharmacologica Sinica 2007年第10期28卷 1698-1704页

作者： Jue WANG~2,Xin XIE~(2,3)~2 The national center for Drug Screening,shanghai Institute of Materia Medica,chinese Academy of Sciences Graduate School of chinese Academyof Sciences shanghai 201203,china The national center for Drug Screening Shanghai Institute of Materia Medica Chinese Academy of Sciences Graduate School of chinese Academy of Sciences Shanghai China

Aim:To develop a robust,cell-based,high-content screening （HCS） assay basedon receptor internalization for the identification of novel modulators of the epi-dermal growth factor receptor （EGFR）.Methods:Agonist-induced receptorinternalization is part of the signaling cascade of ***-taggedepidermal growth factor （EGF） was used to visualize the internalized receptor-ligand *** fluorescent intracellular spots were detected and mea-sured with an ArrayScan HCS *** that can competitively bind toEGFR or interfere with EGFR internalization process would result in a reducednumber and intensity of intracellular fluorescent *** assay was validated,optimized,and applied to a large-scale screening of a library containing 48 000synthetic ***:The competition between fluorescent EGF andunlabeled EGF reveals the IC50of unlabeled EGF is approximately 0.2 nmol/L,which is comparable with other published *** compounds with arelatively high degree of interference with EGFR internalization were *** of the compounds was proven to be agonist of the EGFR since it inducedphosphorylation of the receptor and extracellular signal-regulated protein ki-nase （ERK）.Conclusion:This automated,objective,and easy-to-use assay pro-vided abundant information,quantitative results,and demonstrated the potentialuse of HCS methods in searching membrane receptor modulators.

关键词： high-content screening epidermal growth factor receptor receptor internalization competitive binding

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Identification and Characterization of glnA Promoter and its Corresponding Trans-regulatory Protein GlnR in the Rifamycin SV Producing Actinomycete,Amycolatopsis mediterranei U32

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Acta Biochimica et Biophysica Sinica 2006年第12期38卷 831-843页

作者： Hao YU~(1&) Wen-Tao PENG~1 Yang LIU~1 Ting WU~2 Yu-Feng YAO~1 Ming-Xue CUI~1 Wei-Hong JIANG~1 Guo-Ping ZHAO~(1,3,4*) 1 Laboratory of Molecular Microbiology,Institute of Plant Physiology and Ecology,shanghai Institutes for Biological Sciences,chinese Academy of Sciences,shanghai 200032,china 2 Department of Medicinal Chemistry,School of Pharmacy,Fudan University,shanghai 200032,china 3 State Key Laboratory of Genetic Engineering & Department of Microbiology,School of Life Science,Fudan University,shanghai 200433,china 4 Laboratory of Disease and Health Genomics,chinese national human genome center at shanghai,shanghai 201203,china Laboratory of Molecular Microbiology Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200032 China Department of Medicinal Chemistry School of Pharmacy Fudan University Shanghai 200032 China State Key Laboratory of Genetic Engineering & Department of Microbiology School of Life Science Fudan University Shanghai 200433 China Laboratory of Disease and Health Genomics Chinese National Human Genome Center at Shanghai Shanghai 201203 China

The genetic requirements for the transcription of glnA,encoding the major glutaminesynthetase in a rifamycin SV-producing Amycolatopsis mediterranei strain,U32,were *** experiments showed that the promoter of U32 glnA （pglnA） was likely to have two transcriptioninitiation sites:P1and P2,located 157 and 45 nucleotides （nt） upstream of the translational start codon,*** mobility shift and DNase I footprinting analyses revealed a 30 bp cis-element locatedat 45 to 75 nt downstream of P1,or 38 to 68 nt upstream of *** sequence of the cis-element displayedhigh similarity to the corresponding regions of pglnA from Streptomyces coelicolor and *** as a reporter gene,the expression levels of U32 pglnA and its deletion derivatives under differentnitrogen-source conditions were analyzed by detecting the catechol dioxygenase activities in ***54,*** J508 and *** FS10 （glnR mutant）.These in vivo studies showed that theactivation of U32 pglnA in *** required GlnR,and its binding to the U32 pglnA was furtherconfirmed by the gel mobility shift *** and heterologous expression of the U32 glnR allowed usto detect the in vitro interaction between the U32 GlnR and the corresponding pglnA *** shown by in vivo glnR inactivation and complementation indicated that GlnR is essential for theactive transcription of glnA in U32.

关键词： glnA promoter cis-element glnR Amycolatopsis mediterranei

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