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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 201203 China shanghai-MOST Key Laboratory of Health and Disease Genomics Chinese National Human Genome Center Shanghai 201203 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

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 200235,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

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

miRNAs modulate the drug response of tumor cells

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Science china(Life Sciences) 2009年第9期52卷 797-801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 University of Chinese Academy of Sciences,shanghai 200031,china center of Functional Genomics Key Laboratory of System Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China national engineering center for biochip at shanghai Shanghai 201203 China Graduate University of Chinese Academy of Sciences Shanghai 200031 China

Chemotherapy is one of the major treatments of malignant carcinomas. However,its efficiency is affected by both intrinsic and acquired resistance to anticancer drugs. The cellular mechanisms of drug resistance include the overexpression of energy-dependent transporters that eject anticancer drugs from cells such as p-glycoprotein and multidrug resistance related protein (MRP),the mutation of drug targets,the activation of DNA repair pathways,the defects in cellular death pathways and so on. The genetic and epigenetic changes of these genes can lead to cancer drug resistance. Among these mechanisms,microRNAs (miRNAs) which are critical and essential for many important processes such as development,differentiation,and even carcinogenesis have been reported to regulate the chemosen-sitivity of tumor cells. In this paper we briefly review the relationship between miRNA and cancer drug resistance.

关键词： cancer drug resistance miRNAs

Finite element simulation of stretch forging using a mesh condensation method

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Science china(Technological Sciences) 2010年第1期53卷 227-234页

作者： CHEN Wen & CUI ZhenShan national Die & Mold CAD engineering Research center,shanghai Jiao Tong University,shanghai 200030,china 1. national Die & Mold CAD engineering Research center Shanghai Jiao Tong University Shanghai 200030 China

In order to reduce the computation time of finite element simulations of stretch forging process,a mesh condensation method is presented and applied to a three-dimensional rigid-viscoplastic finite element *** this method,a conventional mesh for the whole zone of a workpiece is condensed to a computational mesh for the active deformation *** vital problems are solved,which are automatic construction of the computational mesh and treatment of interfaces between the deformation zone and the rigid *** mesh condensation method is compared with conventional finite element method by simulations of a six-bite stretch forging *** simulation results including forging load,temperature distribution and effective strain distribution are *** efficiency and accuracy of this method are verified.

关键词： mesh condensation method finite element method stretch forging incremental forging

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

GATE TYPE SELECTION BASED ON FUZZY MAPPING

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Chinese Journal of Mechanical engineering 2002年第1期15卷 31-34,61页

作者： Wang Yu Xing Yuan Ruan Xueyu national Die & Mold CAD engineering Research center，shanghai Jiaotong University， shanghai 200030，china national Die & Mold CAD engineering Research center Shanghai Jiaotong University Shanghai 200030 China

Gate type selection is very important for mould design. Improper gate typemay lead to poor product quality and low production efficiency. Although numerical simulationapproach could be used to optimize gate location, the determination of gate type is still up todesigners' experience. A novel method for selecting gate type based on fuzzy logic is proposed. Theproposed methodology follows three steps: Design requirements for gate is extracted and generalized;Possible gate types (design schemes) are presented; The fuzzy mapping relationship between gatedesign requirements and gate design scheme is established based on fuzzy composition and fuzzyrelation transition matrices that are assigned by domain experts.

关键词： Gate type selection Fuzzy logic

A LINEAR DYNAMIC MODEL DESCRIBING LYMPH CIRCULATION

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Journal of Hydrodynamics 2009年第1期21卷 118-123页

作者： YAO Wei WANG Sheng-zhang DING Guang-hong SHEN Xue-yong Department of Mechanics and engineering Science Fudan University Shanghai 200433 China shanghai Research center of Acupuncture and Meridian Shanghai 201203 China Acupuncture Department of shanghai University of Traditional Chinese Medicine Shanghai 200032 China

The lymph circulation plays an important role in interstitial fluid balance, protein transport, and immune system. However, its mechanism is poorly understood, and associated pathologies are mostly untreatable. By following Sungawa＇s method of discussing the heart output, a hemodynamic model of lymph circulation was set up. The model was used to demonstrate how the lymphatic fluid formation, investigate the relationship between the lymph flow rate QL and physiological parameters, and explore how local massage influences QL Computer simulation results show that QL is linearly proportional to the interstitial fluid pressure P~, which is similar to experimental observations. Comparing the simulated value of QL during the massage of different frequency with the experimental data from Ikomi shows that they are identical, which indicates that the presented model is rational to explain the mechanism of massage treatment in traditional Chinese medicine （TCM）.

关键词： lymph circulation pressure-volume circle equivalent elastance massage treatment in TCM

Differential expression analysis and regulatory network reconstruction for genes associated with muscle growth and adipose deposition in obese and lean pigs

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Progress in Natural Science:Materials International 2008年第4期18卷 387-399页

作者： Mingzhou Li a, Xuewei Li a, Li Zhu a, Xiaokun Tengb, Huasheng Xiao b, Surong Shuaia, Lei Chen a, Qiang Li a, Yujiao Guo a a Laboratory of Pork Quality, College of Animal Science and Technology, Sichuan Agricultural University, Ya’an 625014, china b national engineering center for biochip at shanghai, shanghai 201203, china Laboratory of Pork Quality College of Animal Science and Technology Sichuan Agricultural University Ya’an 625014 China national engineering center for biochip at shanghai Shanghai 201203 China

During the growth and development of skeletal muscle cells and adipose cells, the regulatory mechanism of micro-effect polygenes determines porcine meat quality, carcass characteristics and other relative quantitative traits. Obese and lean type pig breeds show obvi- ous differences in muscle growth and adipose deposition; however, the molecular mechanism underlying this phenotypic variation remains unknown. We used pathway-focused oligo microarray studies to examine the expression changes of 140 genes associated with muscle growth and adipose deposition in longissimus dorsi muscle at six growth stages (birth, 1, 2, 3, 4 and 5 months) of Landrace (a leaner, Western breed) and Taihu pigs (a fatty, indigenous, Chinese breed). Variance analysis (ANOVA) revealed that differences in the expression of 18 genes in Landrace pigs and three genes in Taihu pigs were very significant (FDR-adjusted permutation, P < 0.01) and di?erences for 22 genes in Landrace pigs and seven genes in Taihu pigs were significant (FDR-adjusted permutation, P < 0.05) among six growth stages. Clustering analysis revealed a high level of signi?cance (FDR-adjusted, P < 0.01) for four gene expression patterns, in which genes that strongly up-regulated were mainly associated with the positive regulation of myofiber formation and fatty acid biogenesis and genes that strongly down-regulated were mainly associated with the inhibition of cell proliferation and positive regulation of fatty acid b-oxidation. Based on a dynamic Bayesian network (DBN) model, gene regulatory networks (GRNs) were reconstructed from time-series data for each pig breed. These two GRNs initially revealed the distinct differences in physiological and biochemical aspects of muscle growth and adipose deposition between the two pig breeds; from these results, some potential key genes could be identified. Quantitative real-time RT-PCR (QRT-PCR) was used to verify the microarray data for five modulated genes, and a good correlation betwee

关键词： Pig Muscle growth Adipose deposition Pathway-focused microarray Differential gene expression Gene regulatory network (GRN)