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Genomic research for important pathogenic bacteria in china

Science china(Life Sciences) 2009年第1期52卷 50-63页

作者： YANG RuiFu1,GUO XiaoKui2,YANG Jian3,JIANG YongQiang1,PANG Bo4,CHEN Chen5,YAO YuFeng2,QIN JinHong2 & LI QingTian2 1 Laboratory of Analytical Microbiology,State Key Laboratory of Pathogen and Biosecurity,beijing institute of Microbiology and Epidemiology,beijing 100071,china 2 Department of Medical Microbiology and Parasitology,institutes of Medical Sciences,Shanghai Jiao Tong University School of Medicine,Shanghai 200025,china 3 State Key Laboratory for Molecular Virology and Genetic engineering,institute of Pathogen Biology,Chinese Academy of Medical Sciences,beijing 100176,china 4 State Key Laboratory for Infectious Disease Prevention and Control,institute for Communicable Disease Control and Prevention,Chinese Center for Disease Control and Prevention,beijing 102206,china 5 beijing genomics institute at shenzhen,shenzhen 518083,china Laboratory of Analytical Microbiology State Key Laboratory of Pathogen and Biosecurity Beijing Institute of Microbiology and Epidemiology Beijing China Department of Medical Microbiology and Parasitology Institutes of Medical Sciences Shanghai Jiao Tong University School of Medicine Shanghai China State Key Laboratory for Molecular Virology and Genetic engineering Institute of Pathogen Biology Chinese Academy of Medical Sciences Beijing China State Key Laboratory for Infectious Disease Prevention and Control Institute for Communicable Disease Control and Prevention Chinese Center for Disease Control and Prevention Beijing China beijing genomics institute at shenzhen Shenzhen China

Rapid accumulation of bacterial genomic data offered an unprecedented opportunity to understand bacterial biology from a holistic view of *** can thus closely look at the way in which a pathogen is evolved,and these data has been applied to molecular epidemiology and microbial forensics,and screening of novel diagnostic,vaccine and drug *** newly developed high-throughput low-cost sequencing technologies,such as 454,Solexa and SOLiD,will promote the acquisition and application of genomic data in new research areas that we dared not imagine previously,such as the metagenomics of human gastric-intestinal tract,for better and comprehensive understanding of human health and disease.

关键词： genome pathogenic bacteria sequencing application

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Sequencing and analysis of the giant panda genome

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Science china(Life Sciences) 2010年第8期53卷 1047-1048页

作者： YANG HuanMing BGI-shenzhen (beijing genomics institute shenzhen), shenzhen 518083, china BGI-shenzhen (beijing genomics institute shenzhen) Shenzhen China

The giant panda (Ailuropoda melanoleuca) is loved all over the world and is considered a symbol of china, as illustrated by its being one of the

关键词： Sequencing and analysis of the giant panda genome

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Antisense expression of a rice cellular apoptosis susceptibility gene (OsCAS} alters the height of transgenic rice

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Progress in Natural Science:Materials International 2007年第1期17卷 39-43页

作者： XU Chunxiao and HE Chaozu ( National Key Laboratory of Plant genomics, institute of Microbiology, Chinese Academy of Sciences, beijing 100080, china Graduate University of Chinese Academy of Sciences, beijing 100039, china shenzhen Laboratory of Superhybrid Rice Research, Graduate School at shenzhen, Tsinghua University, shenzhen 518055, china) National Key Laboratory of Plant genomics Institute of Microbiology Chinese Academy of Sciences Beijing 100080 China Graduate University Chinese Academy of Sciences Beijing 100039 China shenzhen Laboratory of Superhybrid Rice Research Graduate School at Shenzhen Tsinghua University Shenzhen 518055 China

Cellular apoptosis susceptibility (CAS) gene plays important roles in mitosis, development and export of importin a from the nucleus, but its function in plant is unknown. In this study, a rice CAS ortholog (OsCAS), which encodes a predicted protein of 983 amino acids with 62% similarity to human CAS, was identified. DNA gel blot analysis revealed a single copy of OsCAS in the rice genome. A 973 bp fragment at the 3' end of OsCAS cDNA was cloned from rice cDNA library and transferred into rice in the antisense direction under the control of CaMV 35S promoter via Agrobacterium-mediated transformation method, 105 transgenic lines were obtained. Expression of OsCAS was suppressed in the antisense transgenic lines as revealed by semi-quantitative RT-PCR. The antisense transgenic lines showed dwarf phenotypes. The results indicated that OsCAS was involved in culm development of rice.

关键词： antisense dwarf ortholog OsCAS rice.

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LONG TIME ASYMPTOTIC BEHAVIOR OF SOLUTION OF DIFFERENCE SCHEME FOR A SEMILINEAR PARABOLIC EQUATION (Ⅱ)

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Journal of Computational Mathematics 1998年第5期16卷 571-576页

作者： Hui Feng(shenzhen University Normal College, shenzhen 518060, china Laboratorp of Computational Physics, institute of Applied Physics and Computational Mathematics,P.O.Box 8009, beijing 100088, china )Long-jnn Shen(Laboratory of Computational Physics, In 深圳大学师范学院广东深圳

In this paper we prove the solution of explicit difference scheme for a semilinear parabolic equation converges to the solution of difference scheme for the relevant nonlinear stationary problem as t→∞. For nonlinear parabolic problem, we obtain the long time asymptotic behavior of its discrete solution which is analogous to that of its continuous solution. For simplicity, we discuss one-dimensional problem.

关键词： Asymptotic behavior Explicit difference scheme Semilinear parabolic equation.

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Sequencing,annotation and comparative analysis of nine BACs of the giant panda(Ailuropoda melanoleuca)

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Science china(Life Sciences) 2010年第1期53卷 107-111页

作者： ZHENG Yang1,2,3,CAI Jing4,LI JianWen3,6,LI Bo3,LIN RunMao3,TIAN Feng3,WANG XiaoLing3 & WANG Jun3,5 1beijing institute of genomics,Chinese Academy of Sciences(CAS),beijing 100029,china 2College of Life Science,Graduate University of Chinese Academy of Sciences,beijing 100049,china 3beijing genomics institute at shenzhen,shenzhen 518083,china 4CAS-Max Planck Junior Research Group on Evolutionary genomics,State Key Laboratory of Genetic Resources and Evolution,Kunming institute of Zoology,Chinese Academy of Sciences(CAS),Kunming 650223,china 5Department of Biology,University of Copenhagen,Copenhagen DK-2200,Denmark 6School of Biological Science and Engineering,South china University of Technology,Guangzhou 510006,china beijing institute of genomics Chinese Academy of Sciences (CAS) Beijing China College of Life Science Graduate University of Chinese Academy of Sciences Beijing China beijing genomics institute at shenzhen Shenzhen China CAS-Max Planck Junior Research Group on Evolutionary genomics State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences (CAS) Kunming China School of Biological Science and Engineering South China University of Technology Guangzhou China Department of Biology University of Copenhagen Copenhagen Denmark

A 10-fold BAC library for the giant panda was constructed and nine BACs were selected to generate finish *** BACs could be used as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of the giant panda newly generated by Illumina GA sequencing *** Sanger sequencing,assembly,annotation and comparative analysis were carried out on the selected BACs of a joint length 878 *** search and de novo prediction methods were used to annotate genes and *** protein coding genes were predicted,seven of which could be functionally *** seven genes have an average gene size of about 41 kb,an average coding size of about 1.2 kb and an average exon number of 6 per ***,seven tRNA genes were *** 27 percent of the BAC sequence is composed of repeats.A phylogenetic tree was constructed using a neighbor-join algorithm across five species,including the giant panda,human,dog,cat and mouse,which reconfirms dog as the most closely related species to the giant *** results provide detailed sequence and structure information for new genes and repeats of the giant panda,which will be helpful for further studies about the giant panda.

关键词： giant panda BAC sequencing assembly annotation evolution

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Generation of pancreatic islet cells from human embryonic stem cells

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Science china(Life Sciences) 2009年第7期52卷 615-621页

作者： ZHANG DongHui1,2,JIANG Wei1,SHI Yan2 & DENG HongKui1,2 1 Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education,College of Life Sciences,Peking University,beijing 100871,china 2 Laboratory of Chemical genomics,shenzhen Graduate School of Peking University,shenzhen 518055,china Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education College of Life Sciences Peking University Beijing China Laboratory of Chemical genomics Shenzhen Graduate School of Peking University Shenzhen China

Efficiently obtaining functional pancreatic islet cells derived from human embryonic stem(hES) cells not only provides great potential to solve the shortage of islets sources for type I diabetes cell therapy,but also benefits the study of the development of the human pancreas and diabetes *** 2001,hES cells were reported to have the capacity to generate insulin-producing cells by spontaneous differentiation in *** then,many strategies(such as overexpression of key transcription factors,delivery of key proteins for pancreatic development,co-transplantation of differentiated hES cells along with fetal pancreas,stepwise differentiation by mimicking in vivo pancreatic development) have been employed in order to induce the differentiation of pancreatic islet cells from hES ***,patient-specific induced pluripotent stem(iPS) cells can be generated by reprogramming somatic *** cells have characteristics similar to those of ES cells and offer a new cell source for type I diabetes cell therapy that reduces the risk of immunologic *** this review,we summarize the recent progress made in the differentiation of hES and iPS cells into functional pancreatic islet cells and discuss the challenges for their future study.

关键词： human embryonic stem(hES) pancreatic islet cells differentiation induced pluripotent stem(iPS) cells

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Positioning localities from spatial assertions based on Voronoi neighboring

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Science china(Technological Sciences) 2010年第S1期53卷 143-149页

作者： GONG YongXi 1,2,3,LI GuiCai 1,LIU Yu 2 & YANG Jian 1 1 shenzhen Key Lab of Recycling Economy,Peking University shenzhen Graduate School,shenzhen 518055,china 2institute of Remote Sensing and Geographical Information Systems,Peking University,beijing 100871,china 3College of Urban and Environmental Science,Peking University,beijing 100871,china shenzhen Key Lab of Recycling Economy Peking University Shenzhen Graduate School Shenzhen China institute of Remote Sensing and Geographical Information Systems Peking University Beijing China College of Urban and Environmental Science Peking University Beijing China

With the rapid development of Internet,much spatial information contained in non-structured or semi-structured documents is available on the World Wide *** such documents,localities are always textually described using spatial relationships and named places,instead of numerical ***,extracting positional information from locality descriptions is an important *** this paper,we bridge two aspects of locality descriptions,namely generating locality descriptions and positioning localities,and provide a method to compute probability density according to the selection probability of a reference object to describe the position of the target *** operation on uncertainty field is used to deal with locality description involving multiple reference *** metrics are introduced to measure the results of positioning *** choose the mixed selection probability function based on Euclidean distance and Voronoi stolen-area to compute probability density ***,we use three cases to demonstrate the proposed methods.

关键词： geographic information science positioning locality Voronoi neighboring probability density function

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人居地理学的理论与实践及融合与发展

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地理学报 2024年第8期79卷 2115-2140页

作者：田深圳张悦李雪铭杨俊李航丛雪萍孙慧颖辽宁师范大学地理科学学院大连116029 辽宁师范大学人居环境研究中心大连116029 中国城市群研究基地联盟辽中南城市群研究基地大连116029 辽宁省“海洋经济高质量发展”高校协同创新中心大连116029 中国科学院地理科学与资源研究所北京100101

人居地理学既传承了国内外地理学的学科优势,是学科交叉融合发展到高级阶段的必然产物,又是面向人民群众对美好人居环境向往、面向国家重大需求的重要指向标。目前人居地理学相较于城市地理学、经济地理学、行为地理学,其理论框架、实... 详细信息

人居地理学既传承了国内外地理学的学科优势,是学科交叉融合发展到高级阶段的必然产物,又是面向人民群众对美好人居环境向往、面向国家重大需求的重要指向标。目前人居地理学相较于城市地理学、经济地理学、行为地理学,其理论框架、实践应用、融合发展等学科脉络主线尚未进行系统性探究。建构人居地理学的学科框架,基于学理基础、理论框架、地理尺度、研究范式、主题脉络5大视角阐释人居地理学的理论;厘定以人居关系为核心的学科布局,从“三维”“三元”两大维度发掘人居地理学的实践;结合“三态”相互关系这一独特优势,提出人居地理学的开放式学科融合;未来立足新的科学议题、新的数据与方法、新的发展设想三大方向,启迪人居地理学由“小学科”的交叉融合向“大地理”“大学科”的发展格局迈进。人居地理学的理论、实践、融合与发展以期推动人居地理学与相关领域的学科交叉与范式革新,服务居民对人居环境多样化的现实需要与国家发展战略的科学决策,提升中国在全球人居环境体系中的话语权与决策权。

关键词：人居地理学理论与实践融合与发展人居关系 “三态”人居环境

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High Throughput SNP Genotyping with Two Mini-sequencing Assays

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Acta Biochimica et Biophysica Sinica 2004年第6期36卷 379-384页

作者： Chunqing LUO1,2#, Libin DENG1#, and Changqing ZENG1,2* The institute of Genetic and Developmental Biology, the Chinese Academy of Sciences, beijing 100101, china 2beijing genomics institute, the Chinese Academy of Sciences, beijing 101300, china The institute of Genetic and Developmental Biology the Chinese Academy of SciencesBeijing 100101 China beijing genomics institute the Chinese Academy of SciencesBeijing 101300 China

Two mini-sequencing methods, FP-TDI (template-directed dye-terminator incorporation with fluorescence-polarization) and MassArray (matrix assisted laser desorption ionization time of flight detection mass spectrometry), were optimized. A numeric standard was introduced to evaluate the SNP scoring quality of FP-TDI assay, thus made the optimization work easier. At the same time, using multi-PCR technology, 8-plex genotyping of MassArray assay was successfully carried out, some softwares were developed and the data process of MassArray was highly automated. Then these two methods were applied to high throughput SNP genotyping, the accuracy, efficiency and robustness were compared. The result shows FP-TDI is more sensitive to the concentration of SNPprimer and PCR product, as well as extension cycles, the SNPprimer length of FP-TDI should be 24–30 bp long, whereas MassArray assay prefers to be as short as only 16 *** 6440 SNP sites of human chromosome 3 were genotyped in a sample of 90 individuals, 4792 sites by FP-TDI assay and 1648 sites by MassArray assay, the success rates of FP-TDI and MassArray were 67.7% and 93.6% respectively. The throughput of MassArray was higher than FP-TDI, and the cost of MassArray was lower, MassArray was more suitable for high throughput SNP genotyping.

关键词： SNP genotyping FP-TDI MassArray high throughput

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Mesozoic subduction-accretion zone in northeastern South china Sea inferred from geophysical interpretations

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Science china Earth Sciences 2006年第5期49卷 471-482页

作者： ZHOU Di1, WANG Wanyin2, WANG Jialin3, PANG Xiong4, CAI Dongsheng5 & SUN Zhen1 1. Key Laboratory of Marginal Sea Geology, South china Sea institute of Oceanology, Chinese Academy of Sciences, Guang- zhou 510301, china 2. College of Geological and Topographical Engineering, Chang’an University, Xi’an 710054, china 3. Key Laboratory of Marine Geology, Tongji University, Shanghai 200092, china 4. china National Offshore Oil Co. Limited – shenzhen Branch, shenzhen 518067, china 5. china National Offshore Oil Co. Limited – Research Center, beijing 100027, china Key Laboratory of Marginal Sea Geology South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou China College of Geological and Topographical Engineering Chang’an University Xi’an China Key Laboratory of Marine Geology Tongji University Shanghai China china National Offshore Oil Co. Limited — shenzhen Branch Shenzhen China china National Offshore Oil Co. Limited — Research Center Beijing China

A segment of Mesozoic subduction-accretion zone was inferred across thenortheastern South china Sea at approximately NE450 orientation. Basic evidence includes thefollowing: A belt of peek gross horizontal Bouguer gravity gradient (PGHGBA) is comparable in sizeand intensity to that of the Manila subduction-accretion zone. A belt of high positive magneticanomalies appears to the north and sub-parallel to the PGHGBA, representing the volcanic arcassociated to the subduction zone. The PGHGBA crosses obliquely both Cenozoic structures and presentseafloor topography, indicating a pre-Cenozoic age. The segment is offset left-laterally byNW-running strike-slip faults, in concord with the Mesozoic stress field of South china. Inaddition, the existence of the subduction zone is supported by wide-angle seismic data obtained indifferent years by different institutions. At approximate localities, a north-dipping ramp of Mohosurface is indicated by records of ocean-bottom seismometers, and a strong reflector about 8 kmbeneath the Moho reflector is indicated by both OBS and long-cable seismic records. Theidentification of a segment of Mesozoic subduction zone in NE South china Sea fills nicely the gapof the Great Late Mesozoic Circum SE Asia Subduction-acrretion Zone, which extended from Sumatra,Java, SE Kalimantan to N Palawan, and from Taiwan, Ryukyu to SW Japan.

关键词： Mesozoic, subduction zone, SE Asia, NE South china Sea, geophysics.

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