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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 2012.3,china 2 shanghai-MOST Key Laboratory of Health and Disease Genomics,Chinese national Human Genome center,shanghai 2012.3,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

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 2012.3,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 2012.3,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

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 2012.3, 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 constructed 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)

A measurement error model for microarray data analysis

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Progress in Natural Science:Materials International 2005年第7期15卷 614-620页

作者： ZHOU Yiming and CHENG Jing ( Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, china State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, china national engineering research center for Beijing biochip technology, 18 Life Science Parkway, Beijing 102206, china) Department of Biological Sciences and Biotechnology Tsinghua University Beijing 100084 China. State Key Laboratory of Biomembrane and Membrane Biotechnology Tsinghua University Beijing 100084 China. national engineering research center for Beijing biochip technology 18 Life Science Parkway Beijing 102206 China

Microarray technology has been widely used to analyze the gene expression levels by detecting fluorescence intensity in a high throughput fashion. However, since the measurement error produced from various sources in microarray experiments is heterogeneous and too large to be ignored, we propose here a measurement error model for microarray data processing, by which the standard deviation of the measurement error is demonstrated to be linearly increased with fluorescence intensity. A robust algorithm, which estimates the parameters of the measurement error model from a single microarray without replicated spots, is provided. The model and algorithm for estimating of the parameters from a given data set are tested on both the real data set and the simulated data set, and the result has been proven satisfactory. And, combining the measurement error model with traditional Z-test method, a full statistical model has been developed It can significantly improve the statistical inference for identifying differentially expressed genes.

关键词： microarray measurement error model parameter estimation differentially expressed genes.

General Properties of Low-frequency Power Losses in Fe-based Nanocrystalline Soft Magnetic Alloys

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Journal of Materials Science & technology 2000年第1期16卷 37-44页

作者： Yanzhong ZHANG, Huijuan JIN and Ying SHI (shanghai Key Laboratory for research and Developing and Applications of Metallic Function Materials, research center, shanghai Iron and Steel research institute,shanghai 200940, china) shanghai Key Lab. for research and Developing and Applications of Metallic Function Materials Research Center Shanghai Iron and Steel Research Institute Shanghai 200940 China

The dependences of the power loss per cycle on frequency f and amplitude flux density Bm have been investigated for the three main original magnetic states in five sorts of Fe-based nanocrystalline soft magnetic alloys in the ranges of 10 Hzcomposed into the sum of the hysteresis loss Physt, the classical eddy current loss Pel and the excess loss Pexc. Physt has been found to be proportional to Bm^2 and f. The behavior of Pexc/f vs f being equivalent to P/f vs f clearly exhibits nonlinearity in the range not more than about 120 Hz, whereas the behavior of P/f vs f roughly shows linearity in the range far above 100 Hz and not more than 1000 Hz. In the range up to 1000 Hz, Physt is dominant in the original high permeability state and the state of low residual flux density, whereas Pexc in the state of high residual flux density is dominant in the wider range above about 100 Hz. The framework of the statistical theory of power loss has been used for representing the behavior of Pexc/f vs f. It has been found that the number n of the simultaneously active 'Magnetic Objects' linearly varies as n = n0 + Hexc/H0 as a function of the dynamic field Hexc in the range below about 120 Hz, whereas n approximately follows a law of the form n = n0 + (Hexc/H0)^m with 1 < m < 2 in the range far above 100 Hz and not more than 1000 Hz. The values of the field HO in principle related to the microstructure and the domain structure have been calculated for the three states.

关键词： General Properties of Low-frequency Power Losses in Fe-based Nanocrystalline Soft Magnetic Alloys Fe

Effects of Ho on the microstructure and mechanical properties of Mg-Zn-Ho-Zr magnesium alloys

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Rare Metals 2011年第2期30卷 131-136页

作者： LI Daquan WANG Qudong DING Wenjiang national engineering research center for Nonferrous Metals compositions General Research Institute for Nonferrous Metals Beijing 100088 China national engineering research center of Light Alloys Net Forming and State Key Laboratory of Metal Matrix composites School of Materials Science and Engineering Shanghai Jiaotong University Shanghai 200240 China

The microstructure and mechanical properties of Mg-Zn-Ho-Zr alloys have been investigated in detail. The grain size of the as-cast Mg-Zn-Ho-Zr alloy was greatly decreased by the addition of Ho, and the grain growth during solution treatment was suppressed by Mg-Zn-Ho phases formed at grain boundaries. These thermally stable Mg-Zn-Ho phases could not completely dissolve into the matrix dur- ing solution treatment, and the strengthening effect of solution-plus-ageing treatment weakened. The addition of Ho can greatly enhance the high-temperature elongation of the Mg-Zn-Ho-Zr alloy, but the increase of high-temperature tensile strength was just a little.

关键词： magnesium alloys holmium rare earth additions heat treatment microstmcture mechanical properties

Accurate tracking control in LOM application

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Journal of University of Science and technology Beijing 2003年第1期10卷 74-78页

作者： Yadong Liu, congxin Li, Xingui Guo, and Decai Wangnational Die & Mould CAD engineering research center, shanghai Jiaotong University, shanghai 200030, china national Die & Mould CAD engineering research center Shanghai Jiaotong University Shanghai 200030 China

The fabrication of accurate prototype from CAD model directly in short time depends on the accurate tracking control and reference trajectory planning in (Laminated Object Manufacture) LOM application. An improvement on contour accuracy is acquired by the introduction of a tracking controller and a trajectory generation policy. A model of the X-Y positioning system of LOM machine is developed as the design basis of tracking controller. The ZPETC (Zero Phase Error Tracking controller) is used to eliminate single axis following error, thus reduce the contour error. The simulation is developed on a Maltab model based on a retrofitted LOM machine and the satisfied result is acquired.

关键词： tracking control LOM ZPETC trajectory planning

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 2012.3, china 1. Department of computer Science & engineering Shanghai Jiao Tong University Shanghai 200030 China2. School of National Information Security Nanjing University Nanjing 210093 China3. BIOCOMPLEX 4915 Bathurst St. Unit# 209-366 Toronto ON M2R 1X9 Canada4. National Engineering Center for BioChip at Shanghai Shanghai 201203 China

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