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Discovery of immune related factors in Fenneropenaeus chinensis by annotation of ESTs

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Progress in Natural Science:Materials International 2004年第1期14卷 48-55页

作者： SHEN Yaoqing 1,2. , XIANG Jianhai 1*, WANG Bing 1,2. , LI Fuhua 1 and TONG Wei 3.1. Experimental Marine Biology Laboratory, institute of Oceanology, Chinese {2. of Sciences, Qingdao 2.6071,China 2. Graduate School of the Chinese {2. of Sciences, {3. 10003., China 3. genomics & Bioinformatics institute, Chinese {2. of Sciences, {3. 1013.0, China) Chinese Acad Sci Inst Oceanol Expt Marine Biol Lab Qingdao 266071 Peoples R China Chinese Acad Sci Grad Sch Beijing 100039 Peoples R China Chinese Acad Sci Geonom & Bioinformat Inst Beijing 101300 Peoples R China

A total of 10446 expressed sequence tags (ESTs) are obtained by a large scale sequencing of a cDNA library from cephalothorax of adult Fenneropenaeus chinensis . An EST analysis platform was built up based on local computers and bioinformatic techniques were used to annotate these ESTs in order to promptly find possible functional genes, especially for immune related factors. About 4% of the ESTs show similarity to the coding sequences of such factors, including lectin, serine protease, serpin, lysozyme, etc. These ESTs provide a partial profile of the immune system in F. chinensis and useful information for further study on these genes.

关键词： Fenneropenaeus chinensis bioinformatics ESTs immune factors

^(40)Ar/^(3.)Ar dating of shear deformation of the Xianshuihe fault zone in west Sichuan and its tectonic significance

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Science China Earth Sciences 2004年第9期47卷 794-803页

作者： ZHANG Yueqiao1, CHEN Wen2. 3.& YANG Nong1 1. institute of Geomechanics, Chinese {2. of Geological Sciences, beijing 100081, China 2. institute of Geology, Chinese {2. of Geological Sciences, beijing 10003., China 3. institute of Geology and Geophysics, Chinese {2. of Sciences, beijing 10002., China institute of Geomechanics Chinese Academy of Geological Sciences Beijing China institute of Geology Chinese Academy of Geological Sciences Beijing China institute of Geology and Geophysics Chinese Academy of Sciences Beijing China

Based on field geological survey, structural measurements and classical Ar/Ar dating of mica, biotite and K-feldspar, we obtain cooling ages for Miocene left-lateral shear along the Xianshuihe fault zone. The results document two thermal events during the sinistral shear. The early event (12.10 Ma) corresponds to rapid cooling of the Zheduoshan granitic massif from above 700℃ to below 3.0℃. The late event (5-3.5 Ma) corresponds to cooling of granites intruded along the eastern side of the fault zone. These dating results provide important thermochronological constraint on the timing of late Cenozoic eastward extrusion of the Chuan-Dian Block in the SE Tibetan margin.

关键词： Xianshuihe fault zone, Zheduoshan granitic massif, sinistral shear deformation, 40Ar/3.Ar dating, late Cenozoic.

A new DNA algorithm to solve graph coloring problem

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Progress in Natural Science:Materials International 2007年第6期17卷 733-738页

作者： Jiang Xingpeng1, Li Yin2. Meng Ya3.and Meng Dazhi2.1. National Laboratory of Pattern Recognition,institute of Automation, Chinese {2. of Sciences, beijing 100080, China 2. College of Applied Sciences, beijing University of Technology, beijing 10002., China 3. School of Science, beijing institute of Technology, beijing 100081, China) National Laboratory of Pattern Recognition Institute of Automation Chinese Academy of Sciences Beijing 100080 China College of Applied Sciences Beijing University of Technology Beijing 100022 China School of Science Beijing Institute of Technology Beijing 100081 China

Using a small quantity of DNA molecules and little experimental time to solve complex problems successfully is a goal of DNA computing. Some NP-hard problems have been solved by DNA computing with lower time complexity than conventional computing. However, this advantage often brings higher space complexity and needs a large number of DNA encoding molecules. One example is graph coloring problem. Current DNA algorithms need exponentially increasing DNA encoding strands with the growing of problem size. Here we propose a new DNA algorithm of graph coloring problem based on the proof of four-color theorem. This algorithm has good properties of needing a relatively small number of operations in polynomial time and needing a small number of DNA encoding molecules (we need only 6R DNA encoding molecules if the number of regions in a graph is R).

关键词： DNA computing NP-hard problem graph coloring problem.

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, {2. 100101, China 2.2. genomics institute, the Chinese academy of Sciences, {2. 1013.0, China The institute of Genetic and Developmental Biology the Chinese Academy of SciencesBeijing 100101 China beijing genomics {2. 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 2.–3. 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

Compression behavior of Zr_(41)Ti_(14.Cu_(12.5)Ni_(10)Be_(2..5) bulk metallic glass up to 2. GPa

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Science China(Physics,Mechanics & Astronomy) 2005年第3期48卷 319-324页

作者： LI Gong 1, 2., ZHAN Zaiji 2., LIU Jing 3., YUN Jinku 1 , SUN Liling 2., LIU Riping 1 , ZHANG Jun 2.& WANG Wenkui 1, 2.1. Key Laboratory of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao 066004, China 2. Center for Condensed Matter Physics, institute of Physics, Chinese {2. of Sciences, beijing 100080, China 3. BSRF, institute of High Energy Physics, Chinese {2. of Sciences, beijing 10003., China Key Laboratory of Metastable Materials Science and Technology Yanshan University Qinhuangdao China Center for Condensed Matter Physics Institute of Physics Chinese Academy of Sciences Beijing China BSRF Institute of High Energy Physics Chinese Academy of Sciences Beijing China

The compression of a Zr41Ti14.u12.5Ni10Be2..5 bulk metallic glass (BMG) is investigated at room temperature up to 2. GPa using in-situ high pressure energy dispersive X-ray diffraction with a synchrotron radiation source. The pressure-induced structural relaxation is exhibited. It is found that below about 8 GPa, the existence of excess free volume contributes to the rapid structural relaxation, which gives rise to the rapid volumetric change, and the structural relaxation results in the structural stiffness under higher pressure.

关键词： bulk metallic glass, high pressure, structural relaxation, synchrotron radiation.

Preparing a re-sequencing DNA library of 2.cancer candidate genes using the ligation-by-amplification protocol by two PCR reactions

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Science China(Life Sciences) 2009年第5期52卷 483-491页

作者： SU YeYang1,2,3. LIN Lin1,2,3. TIAN Geng1,2,3. CHEN Chen2,3. LIU Tao2,3. XU Xingya3. QI XinPeng1,2,3. ZHANG XiuQing2,3. YANG HuanMing2,3.1 Graduate School of Chinese academy of Sciences, beijing 100049, China 2.beijing {3. of genomics, Chinese academy of Sciences, beijing 100029, China 3.beijing genomics {3., beijing 1013.0, China Graduate School of Chinese academy of Sciences Beijing China beijing institute of {2. Chinese Academy of Sciences Beijing China beijing genomics {2. Beijing China

To meet the needs of large-scale genomic/genetic studies, the next-generation massively parallelized sequencing technologies provide high throughput, low cost and low labor-intensive sequencing service, with subsequent bioinformatic software and laboratory methods developed to expand their applications in various types of research. PCR-based genomic/genetic studies, which have significant usage in association studies like cancer research, haven't benefited much from those next-generation sequencing technologies, because the shortgun re-sequencing strategy used by such sequencing machines as the Illumina/Solexa Genome Analyzer may not be applied to direct re-sequencing of short-length target regions like those in PCR-based genomic/genetic studies. Although several methods have been proposed to solve this problem, including microarray-based genomic selections and selector-based technologies, they require advanced equipment and procedures which limit their applications in many laboratories. By contrast, we overcame such potential drawbacks by utilizing a ligation by amplification (LBA) protocol, a method using a pair of Universal Adapters to randomly ligate target regions in a two-step-PCR procedure, whose Long LBA products were easily fragmented and sequenced on the next-generation sequencing machine. In this concept-proven study, we chose the consensus coding sequences of two human cancer genes: BRCA1 and BRCA2.as target regions, specifically designed LBA primer pairs to amplify and randomly ligate them. 70 target sequences were successfully amplified and ligated into Long LBA products, which were then fragmented to construct DNA libraries for sequencing on both a conventional Sanger sequencer ABI 3.3.xl DNA Analyzer and the next-generation 'synthesis by sequencing technology' Illumina/Solexa Genome Analyzer. Bioinformatic analysis demonstrated the utility and efficiency (including the coverage and depth of each target sequence and the SNPs detection effectiveness) o

关键词： health genomics the next-generation sequencing techonology sequencing technology large-scale genomics PCR

A mixed method for measuring low-frequency acoustic properties of macromolecular materials

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Science China(Physics,Mechanics & Astronomy) 2006年第6期49卷 729-739页

作者： LIU Hongwei1,YAO Lei1,3.ZHAO Hong1,3.ZHANG Jichuan2.3.& XUE Zhaohong2.1. National Key Laboratory of Acoustics,institute of Acoustics,Chinese academy of Sciences,beijing 100080,China 2. institute of Chemistry,Chinese academy of Sciences,beijing 100080,China 3. Graduate University of Chinese academy of Sciences,beijing 100049,China National Key Laboratory of Acoustics Institute of Acoustics Chinese Academy of Sciences Beijing China Graduate University of Chinese academy of Sciences Beijing China institute of Chemistry Chinese Academy of Sciences Beijing China

A mixed method for measuring low-frequency acoustic properties of macro-molecular materials is presented. The dynamic mechanical parameters of materials are first measured by using Dynamic Mechanical Thermal Apparatus(DMTA) at low frequen-cies,usually less than 100 Hz; then based on the Principles of Time-Temperature Super-position (TTS),these parameters are extended to the frequency range that acousticians are concerned about,usually from hundreds to thousands of hertz; finally the extended dynamic mechanical parameters are transformed into acoustic parameters with the help of acoustic measurement and inverse analysis. To test the feasibility and accuracy,we measure a kind of rubber sample in DMTA and acquire the basic acoustic parameters of the sample by using this method. While applying the basic parameters to calculating characteristics of the sample in acoustic pipe,a reasonable agreement of sound absorp-tion coefficients is obtained between the calculations and measurements in the acoustic pipe.

关键词： low-frequency acoustic properties,dynamic mechanical properties,Principles of Time-Temperature Superposition,acoustic pipe,sound absorption coefficient.

Interannual variability of Antarctic Oscillation and its influence on East Asian climate during boreal winter and spring

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Science China Earth Sciences 2006年第5期49卷 554-560页

作者： FAN Ke1,2.3.& WANG Huijun2.1. Nansen-Zhu International Research Center, institute of Atmospheric Physics, Chinese {2. of Sciences, beijing 10002., China 2. Department of Atmospheric Science, Yunnan University, Kunming 650091, China 3. Graduate University of the Chinese {2. of Sciences, beijing 100049, China Nansen-Zhu International Research Center Institute of Atmospheric Physics Chinese Academy of Sciences Beijing China Department of Atmospheric Science Yunnan University Kunming China Graduate University of the Chinese academy of Sciences Beijing China

The interannual variability of Antarctic Oscillation (AAO) and its influence on East Asian climate during both boreal winter and spring are addressed. The results show that the positive AAO anomaly decreases the cold activity over East Asia during both boreal winter and spring. AAO-related barotropic meridional teleconnection from Antarctic to Arctic is found through analysis of mean me- ridional circulations. This meridional teleconnection is remarkable over Eurasia during boreal winter and over the Pacific Ocean during boreal spring. The results also show that zonal mean zonal wind at high latitudes in Southern Hemisphere has well positive correlation with that of Eurasia during boreal winter and has negative correlation with Pacific North American teleconnection (PNA) during boreal spring, which again display the meridional teleconnection. Thus, local meridional teleconnection is a possible linkage for interaction of circulations at mid-high latitudes between both hemispheres.

关键词： Antarctic Oscillation, Eurasian west wind, meridional teleconnection, mean meridional circulation.

Cloning and expression of putative ethylene receptor genes in soybean plant

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Progress in Natural Science:Materials International 2007年第10期17卷 1152-1160页

作者： Xie Zongming1,2.3. Lei Gang1,2. Wuriyanghan Hada1,2. Tian Aiguo1, Zhang Jinsong1 and Chen Shouyi1(1. National Key Laboratory of Plant genomics, {2. of Genetics and Developmental Biology, Chinese academy of Sciences, {3. 100101, China 2. Graduate School of Chinese academy of Sciences, {3. 10003., China 3. Xinjiang academy of Agricultural and Reclamation Science, Shihezi 83.000, China) National Key Laboratory of Plant genomics Institute of Genetics and Developmental Biology Chinese Acad. of Sci. Beijing 100101 China Graduate School Chinese Acad. of Sci. Beijing 100039 China Xinjiang academy of Agricultural and Reclamation Science Shihezi 832000 China

Ethylene plays important roles in plant growth, development, and stress responses, and ethylene receptors have been identified and studied extensively in various plant species. Here we report the cloning of four ethylene receptor genes from soybean, i.e. GmETR1, GmERS1, GmETR2.and GmEIN4. Construction of the phylogenic tree showed that GmETR1 and GmERS1 belong to subfamily I whereas GmETR2.and GmEIN4 belong to subfamily II. The four ethylene receptor genes showed different tissue-specific expression patterns in roots, stems, leaves, cotyledons, flowers, pods and seeds of soybean. These genes were differentially regulated by various abiotic stresses and plant hormones. The possible roles of the four genes in soybean plant were also discussed.

关键词： abiotic stress expression analysis ethylene receptor plant hormone soybean.