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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 {2.,{2. 2.12.3,china 2.{2.-MOST Key Laboratory of Health and Disease Genomics,chinese national Human Genome center,{2. 2.12.3,china national Engineering center for Biochip at {2. 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 2.03,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

Reconstruction of the most recent common ancestor sequences of SARS-Cov S gene and detection of adaptive evolution in the spike protein

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chinese Science Bulletin 2004年第12期49卷 1311-1313页

作者： ZHANG Yuan1, ZHENG Nan2.3, HAO Pei4,5 & ZHONG Yang6 1. Laboratory of Systematic and Evolutionary Botany, Institute of Bot- any, chinese academy of sciences, Beijing 100093, china 2. College of Life {2., Beijing Normal University, Beijing 100875, china 3. Institute of Viral Disease Control and Prevention, chinese CDC, Beijing 100052. china 4. Bioinformation center, shanghai Institutes for Biological {2., chinese academy of sciences, shanghai 2.0031, china 5. shanghai center for Bioinformation Technology, shanghai 2.02.5, china 6. School of Life {2., Fudan University, shanghai 2.0433, china 1. Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences 100093 Beijing China 2. College of Life sciences Beijing Normal University 100875 Beijing China 3. Institute of Viral Disease Control and Prevention Chinese CDC 100052 Beijing China 4. Bioinformation center Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 200031 Shanghai China 5. shanghai center for Bioinformation Technology 200235 Shanghai China 6. School of Life sciences Fudan University 200433 Shanghai China

The genome oiganization and expression strategy of severe acute respiratory syndrome coronavirus (SARS-CoV) have been described extensively. As a structural glycoprotein on the virion surface, the spike protein is responsible for binding to host cellular receptors and for the fusion between the viral envelope and the cellular membrane. It also induces neutralizing antibodies in the host and mediates cellular immunity. Previous studies suggested that amino acid replacements in the spike protein coulddramatically alter the pathogenesis and virulence of some coronaviruses. It is therefore reasonable to test the hypothesis that radical amino acid replacements in the spike protein, favored by environmental selective pressure during the process of SARS-CoV interspecific transmission, might make this pathogen adapt to a new host, In this study, we investigated a total of 108 complete sequences of the SARS-CoV S gene from Gen-Bank (until March 2., 2.04). After omission of those records containing frame-shift mutations or low quality sequences, e.g. ZJ01, and selection of one sequence for identical records, an alignment of 42.sequences was obtained using the program Clustal-X. Then, we reconstructed the most recent common ancestor (MRCA) sequences of theSARS-CoV S gene and detected the adaptive evolution in the spike protein.

关键词： SARS冠状病毒自适应进化基因表达糖蛋白分子免疫学波峰病毒

Modeling the impact of Australian Plate drift on Southern Hemisphere climate and environment

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chinese Science Bulletin 2005年第14期50卷 1495-1502页

作者： ZHOU Botao1,5, ZHAO Ping2. JIAN Zhimin3 & HE Jinhai4 1. Nansen-Zhu International research {2., Institute of Atmospheric Physics, chinese academy of sciences, Beijing 10002., china 2. Institute of Climate and Environment, chinese academy of Meteoro- logical sciences, Beijing 100081, china 3. Laboratory of Marine Geology, Tongji University, shanghai 2.0092. china 4. Department of Atmospheric sciences, Nanjing Institute of Meteorol- ogy, Nanjing 2.0044, china 5. Graduate School of the chinese academy of sciences, Beijing 100039, china Nansen-Zhu International research {2. Institute of Atmospheric Physics Chinese Academy of Sciences Beijing 100029 China Graduate School of the chinese academy of sciences Beijing 100039 China Institute of Climate and Environment Chinese Academy of Meteorological Sciences Beijing 100081 China Laboratory of Marine Geology Tongji University Shanghai 200092 China Department of Atmospheric sciences Nanjing Institute of Meteorology Nanjing 210044 China

Using a global atmosphere-ocean coupled model with the present-day and 14 MaB.P. oceanic topogra- phy respectively, two experiments are implemented to inves- tigate the effect of different locations of Australian Plate on the atmospheric circulation in middle-high latitudes of the Southern Hemisphere. The results show that when Austra- lian Plate lay south at 14 MaB.P., both anticyclone circula- tions in the subtropical oceans and cyclone circulation around 60°-70°S are strengthened. Subtropical highs and circumpolar low pressure appear stronger, which results in much stronger Antarctic Oscillation and shorter period of Antarctic Oscillation Index (AOI) at 14 MaB.P. The rainfall and the surface air temperature also change correspondingly. The precipitation decreases around 40°S and increases around 60°-70°S, and the surface air temperature rises in high latitudes of the South Pacific and descends over the Weddell Sea and its north side. Besides, due to the changes of the temperatures and winds, Antarctic sea ice coverage also changes with its increasing in the Ross Sea and its west re- gions and decreasing in the Weddell Sea.

关键词：半球气候地球环球澳大利亚漂流物海洋地形学

Cloning and characterization of two putative seven-transmembrane receptor genes from cotton

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Progress in Natural Science:Materials International 2008年第10期18卷 1225-1231页

作者： Peng Gao Piming Zhao Juan Wang Haiyun Wang Guiling Wang Guixian Xia national Key Laboratory of Plant Genomics,Institute of Microbiology,chinese {2. of sciences,Datun Road,Chaoyang District,Beijing 100101,china national center for Plant gene research,Beijing 100101,china national Key Laboratory of Plant Genomics Institute of Microbiology Chinese Academy of Sciences Datun Road Chaoyang District Beijing 100101 China national center for Plant {2. research Beijing 100101 China

Using rapid amplification of cDNA ends (RACE)-PCR,two full-length cDNAs encoding putative seven-transmembrane receptors (designated Gh7TMpRI and Gh7TMpR2. were cloned from cotton *** blot and an ApaL1 restriction site polymorphism analyses revealed that Gh7TMpRI was derived from the ancestral A diploid genome,while Gh7TMpR2.was from the D subgenome. Northern blot hybridization indicated that both Gh7TMpR1 and GhTTMpR2.were expressed preferentially in the elongation phase of fiber *** of the Gh7TMpRl proteins were located within the membrane structure and displayed a punctuate pattern of *** of Gh7TMpR1 in fission yeast disrupted the polar growth and caused the formation of rounded cells. These results suggest that GhT7MpRl may play a critical role in cotton fiber development,perhaps as a signaling receptor that is involved in controlling fiber elongation.

关键词： Cotton Seven-transmembrane protein Fiber elongation Alloalleles

Determination of chinese mobile SLR sites'coordinates

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chinese Science Bulletin 2003年第21期48卷 2300-2302页

作者： FENG Chugang, CAI Wusan, ZHU Yuanlan & YANG Fumin shanghai Astronomical Observatory, chinese academy of sciences {2. for Astro-Geodynamical research, chinese academy of sciences, shanghai 2.0030, china Correspondence should be addressed to Feng Chugang (e-mail: fcg@***) shanghai Astronomical Observatory Chinese Academy of Sciences Shanghai China center for Astro-Geodynamical research Chinese Academy of Sciences Shanghai China

The geocentric coordinates of three mobile sites including Fangshan in Beijing, Urumqi in the Xinjiang Uy-gur Autonomous Region and Lhasa in Tibet are determinedin the ITRF2.00 frame by means of both the global SLRdata and the mobile (SLR) data obtained by a mobile satel-lite laser ranging (SLR) apparatus from Aug. 2.00 to Dec.2.01. The results showed that the geometrical performance of chinese SLR network has been significantly improved.

关键词：中国卫星激光修正设备数据处理几何学

Morphology and mapping analysis of rice(Oryza sativa L.)clustered spikelets(Cl)mutant

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chinese Science Bulletin 2003年第6期48卷 559-562页

作者： ZHENG Leiying1, ZHU Xudong2. QIAN Qian2. ZHAO Zhong1, ZHANG Jianjun3, HU Xiaohe1, LIN Hongxuan1,4 & LUO Da1 1. national Key Laboratory of Plant Molecular genetics, {2. In-stitute of Plant Physiology and Ecology, chinese academy of Sci-ences, {2. 2.0032. china 2. china national Rice research Institute, Hangzhou 310006, china 3. Crop Institute of Breeding and Cultivation, {2. Agricultural academy, {2. 2.1106, china 4. {2. Anxin research Foundation Laboratory, {2. 2.0032. china national Key Laboratory of Plant Molecular genetics Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences China china national Rice {2. Institute China Crop Institute of Breeding and Cultivation Shanghai Agricultural Academy China shanghai Anxin research Foundation Laboratory China

The rice clustered spikelets (Cl) mutant exhib-its a phenotype that most of branch apical have 2.3 spikelets clustered together. SEM (scanning electron microscope) ob-servation suggested that the Cl gene controlled branch apical development, and influenced the terminal spikelets elonga-tion. The spikelet number was reduced in mutant, indicating that Cl may also have an effect on spikelet number. To map Cl locus, two F2.mapping populations derived from the crosses between the Cl and ZhongHua11, and Cl and ZheFu802.were constructed, respectively. The Cl locus was roughly mapped between two CAPS markers, CK02.4 and SS032.. A further fine mapping analysis showed that the Cl locus was mapped between makers R0674E and Cl2.60, with genetic distances of 0.2.and 2.1 cM, respectively. Then we found a PAC contig spanning Cl locus, the region was delim-ited to 196 kb. This result was useful for cloning of the Cl gene. Allelism test demonstrated that Cl was allelic to Cl2. another rice clustered spikelets mutant.

关键词：水稻簇生小穗突变体分子标记基因图遗传分析植物形态 SEM

Orbit determination for geostationary satellites with the combination of transfer ranging and pseudorange data

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Science china(Physics,Mechanics & Astronomy) 2010年第9期53卷 1746-1754页

作者： GUO Rui1,2.3,4,HU XiaoGong2.4,LIU Li1,WU XiaoLi1,HUANG Yong2.4 & HE Feng1 1 Beijing Global Information Application and Development center,Beijing 100094,china 2.{2. Astronomical Observatory,chinese academy of sciences,{2. 2.0030,china 3 Graduate University of chinese academy of sciences,Beijing 100049,china 4 Space Navigation and Positioning Technology,Laboratory of {2. Municipal,{2. 2.0030,china 1. Beijing Global Information Application and Development center Beijing 100094 China2. Shanghai Astronomical Observatory Chinese Academy of Sciences Shanghai 200030 China3. Graduate University of Chinese Academy of Sciences Beijing 100049 China4. Space Navigation and Positioning Technology Laboratory of Shanghai Municipal Shanghai 200030 China

Geostationary satellites(GEOs) play a significant role in the regional satellite navigation *** experiments show that the clock corrections could be mitigated through a single strategy or double differencing strategies for a navigation constellation,but for the mode of individual GEO orbit determination,high precision orbit and clock correction could not be obtained in the orbit determination based on the pseudorange data.A new GEO combined precise orbit determination(POD) strategy is studied in this paper,which combines pseudorange data and C-band transfer ranging *** strategy overcomes the deficiency of C-band transfer ranging caused by limited stations and tracking time *** the combination of transfer ranging and pseudorange data,clock corrections between the GEO and the stations can be estimated simultaneously along with orbital parameters,maintaining self-consistency between the satellite ephemeris and clock correction *** error covariance analysis is conducted to illuminate the contributions from the transfer ranging data and the psudoranging *** data collected for a chinese GEO satellite with 3 C-band transfer ranging stations and 4 L-band pseudorange tracking stations,POD experiments indicate that a meter-level accuracy is *** root-mean-square(RMS) of the post-fit C-band ranging data is about 0.2.3 m,and the RMS of the post-fit pseudorange is 0.408 *** component errors of the POD experiments are independently evaluated with the satellite laser ranging(SLR) data from a station in Beijing,with the residual RMS of 0.076 *** SLR evaluation also suggests that for 2.h orbital predication,the predicted radial error is about 0.404 m,and the clock correction error is about 1.38 *** for the combination of one C-band transfer ranging station and 4 pseudorange stations,POD is able to achieve a reasonable accuracy with the radial error of 0.2.0 m and the 2.h predicted radial error of 0.888 *** syn

关键词： satellite navigation precise orbit determination pseudorange equipment ranging delay GEO SLR

水稻逆转录转座子RIRE10拷贝数与LTR区转录活性的鉴定

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生物化学与生物物理学报 2003年第8期35卷 768-773页

作者：王嵘洪国藩韩斌中国科学院上海生命科学研究院国家基因研究中心中国科学院上海生命科学研究院国家基因研究中心上海2.02.3 中国科学院上海生命科学研究院生物化学与细胞生物学研究所上海2.0031

在水稻第四号染色体的长臂上鉴定了一个结构完整的Ty3型逆转录转座子RIRE10。RIRE10两LTR间的中间区域在gag pol的上游还包含另一个开放阅读框。通过RT PCR与Northern印迹杂交检测到来自LTR区的转录产物 ;根据点杂交结果 ,鉴定出包含中... 详细信息

在水稻第四号染色体的长臂上鉴定了一个结构完整的Ty3型逆转录转座子RIRE10。RIRE10两LTR间的中间区域在gag pol的上游还包含另一个开放阅读框。通过RT PCR与Northern印迹杂交检测到来自LTR区的转录产物 ;根据点杂交结果 ,鉴定出包含中间区域的RIRE10成员的个数以及LTR区的拷贝数。除了 6 5个完整的逆转录转座子所具备的两个LTR外 ,水稻基因组还含有近 90 0个RIRE10的solo LTR。LTR区的转录以及导致solo LTR产生的同源重组可能影响了RIRE10成员在水稻基因组中的转座活性

关键词：栽培稻 Ty3型逆转录转座子转录

Agrobacterium tumefaciens-mediated transformation of rice with the spider insecticidal gene conferring resistance to leaffolder and striped stem borer

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Cell research 2001年第2期11卷 149-155页

作者： HUANG JIAN QIU, ZHI MING WEI, HAI LONG AN, YU XIAN ZHU national Laboratory of Plant Molecular genetics, Institute of Plant Physiology and Ecology, {2. Institutes for Biological sciences, chinese academy of sciences, {2. 2.0032. china national La national Laboratory of Plant Molecular genetics Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai. jqhuang@***

Immature embryos of rice varieties 'Xiushui11' and 'Chunjiang 11' precultured for 4d were infected and transformed by Agrobacterium tumefaciens strain EHA101/pExT7 (containing the spider insecticidal gene). The resistant cant were transferred onto the differentiation medium and plants were regenerated. The transformation frequency reached 56%-72. measured as numbers of geneticin (G418)-resistant calli produced and 36%-60% measured as numbers of transgenic plants regenerated, respectively. PCR and Southern blot analysis of transgenic plants confirmed that the T-DNA had been integrated into the rice genome. Insect bioassays using T1 transgenic plants indicated that the mortality of the leaffolder (Cnaphalocrasis medinalis) after 7d of leaf feeding reached 38%-61% and the corrected mortality of the striped stem borer (Chilo suppressalis) after 7d of leaf feeding reached 16%-75%. The insect bioassay results demonstrated that the transgenic plants expressing the spider insecticidal protein conferred enhanced resistance to these pests.

关键词： Rice Agrobacterium tumefaciens spider insecticidal gene transgenic plant Leaffolder striped stem borer insect bioassay.