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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

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

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 center of Functional Genomics Key Laboratory of System Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 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

Allelic distributions of CYP2D6 gene copy number variation in the Eastern Han Chinese population

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Acta Pharmacologica Sinica 2007年第2期28卷 279-286页

作者： Hai-hui SHENG~(2,6) Ai-ping ZENG~(3,6) Wen-xiang ZHU~2 Ren-fang ZHU~3 Hong-mei LI~2 Zhi-dong ZHU~2 Ying QIN~2 Wei JIN~4 Yan LIU~4 Yun-lan DU~5 Jian SUN~5 Hua-sheng XIAO~(2,7)2 national engineering center for biochip at shanghai,shanghai 201203,china 3 Department of Clinical Laboratory,Wenling No 1 People's Hospital,Wenzhou Medical College,Wenzhou 317500,china 4 Department of Cardiology,Ruijin Hospital,Medical College,shanghai Jiaotong University,shanghai 200025 5 Department of Neurology,shanghai Gongli Hospital,shanghai 200135,china nationalengineeringcenterforbiochipatshanghai Shanghai201203China DepartmentofClinicalLaboratory WenlingNo1People'sHospitalWenzhouMedicalCollegeWenzhou317500China

Aim:The human cytochrome P450 2D6(CYP2D6)gene copy number variation,involving CYP2D6 gene deletion(CYP2D6*5)and duplication or multiduplication(CYP2D6*×N),can result in reduced or increased metabolism of many clinicallyused *** identification of CYP2D6*5 and CYP2D6*xN and the investi-gation of their allelic distributions in ethnic populations can be important in deter-mining the right drug and dosage for each ***:The CYP2D6*5 andCYP2D6 genes,and CYP2D6 gene duplication were identified by 2 modified longPCR,*** determine duplicated alleles,a novel long PCR was devel-oped to amplify the entire duplicated CYP2D6 gene which was used as templatefor subsequent PCR amplification.A total of 363 unrelated Eastern Han Chineseindividuals were analyzed for CYP2D6 gene copy number ***:Thefrequency of CYP2D6*5 and CYP2D6*xN were 4.82%(n=35)and 0.69%(n=5)inthe Eastern Han Chinese population,*** the 5 duplicated alleles,3were CYP2D6*1×Nand 2 were CYP2D6*IO×*** individual was a carrier ofboth CYP2D6*5 and CYP2D6*I×*** together,the CYP2D6 gene rear-rangements were present in 10.74% of ***:Allelic distributionsof the CYP2D6 gene copy number variation differ among Chinese from differentregions,indicating ethnic variety in *** PCR are convenient,costeffective,specific and semiquantitative for the detection of the CYP2D6 genecopy number variation,and amplification of the entire duplicated CYP2D6 gene isnecessary for the accurate identification of duplicated alleles.

关键词： CYP2D6 long PCR deletion duplication copy number variation rearrangement

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微芯片电泳紫外检测系统分析蛋白质

生物化学与生物物理进展 2004年第11期31卷 1045-1049页

作者：刘菁庄贵生徐良基贾春平金庆辉赵建龙中国科学院上海微系统与信息技术研究所生物芯片上海国家工程研究中心上海201203

微芯片电泳是基于微机电加工技术 (MEMS)工艺 ,在芯片上的微管道中完成电泳检测过程的新型技术 .依据紫外吸光度分析法 ,对蛋白质样品进行电泳分离与紫外检测 .实验采用自控接口模板对进样及分离电压进行了系统的程序化控制 ,从而准确... 详细信息

微芯片电泳是基于微机电加工技术 (MEMS)工艺 ,在芯片上的微管道中完成电泳检测过程的新型技术 .依据紫外吸光度分析法 ,对蛋白质样品进行电泳分离与紫外检测 .实验采用自控接口模板对进样及分离电压进行了系统的程序化控制 ,从而准确地控制整个电泳、检测流程 ,提高了微芯片电泳的分离效率和检测灵敏度 .实验结果表明 ,夹流进样的方法可以有效分离混合蛋白 ,可用于蛋白质样品的分离检测 .

关键词：微芯片电泳紫外检测蛋白质

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 1shanghai-MOST Key Laboratory for Disease and Health Genomics Chinese National Human Genome Center at Shanghai Shanghai 201203 China. 2Lab 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. 4School of Life Sciences Fudan University Shanghai 200433 China. 5shanghai 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

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 national Die & Mold CAD engineering Research center Shanghai Jiao Tong University Shanghai 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

Asymmetric encryption and signature method with DNA technology

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Science china(Information Sciences) 2010年第3期53卷 506-514页

作者： LAI XueJia1, LU MingXin2, QIN Lei3, HAN JunSong4 & FANG XiWen11Department of Computer Science & engineering, shanghai Jiao Tong University, shanghai 200030, china 2School of national Information Security, Nanjing University, Nanjing 210093, china 3BIOCOMPLEX, 4915 Bathurst St. Unit# 209-366, ON M2R 1X9, Canada 4national engineering center for biochip at shanghai, shanghai 201203, china Department of Computer Science & engineering Shanghai Jiao Tong University School of national Information Security Nanjing University BIOCOMPLEX 4915 Bathurst St. Unit# 209-366

This paper proposes DNA-PKC, an asymmetric encryption and signature cryptosystem by combining the technologies of genetic engineering and cryptology. It is an exploratory research of biological cryptology. Similar to conventional public-key cryptology, DNA-PKC uses two pairs of keys for encryption and signature, respectively. Using the public encryption key, everyone can send encrypted message to a specified user, only the owner of the private decryption key can decrypt the ciphertext and recover the message; in the signature scheme, the owner of the private signing key can generate a signature that can be verified by other users with the public verification key, but no else can forge the signature. DNA-PKC differs from the conventional cryptology in that the keys and the ciphertexts are all biological molecules. The security of DNA-PKC relies on diffcult biological problems instead of computational problems; thus DNA-PKC is immune from known attacks, especially the quantum computing based attacks.

关键词： cryptology asymmetric encryption digital signature biological cryptology DNA