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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 {2., beijing 100101, china 2.3} genomics institute, the Chinese academy of {2., beijing 101300, 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.–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

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 academy of {2., Qingdao 2.6071,china 2. Graduate School of the Chinese academy of {2., beijing 100039, china 3. genomics & Bioinformatics institute, Chinese academy of {2., beijing 101300, 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

Palynological characters of Glycyrrhiza,Glycyrrhizopsis,and Meristotropis(Leguminosae),with special reference to their taxonomic significance

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Journal of Systematics and Evolution 2010年第6期48卷 455-463页

作者： 1,2.ei MENG 2.iang-Yun ZHU 1(College of Biological sciences,china Agricultural University,{2. 100094,china) 2.institute of Botany,Chinese academy of sciences,{2. 100093,china) (College of Biological sciences China Agricultural University Beijing 100094 China) (institute of Botany Chinese Academy of Sciences Beijing 100093 China)

The pollen morphology of 11 species of the genus Glycyrrhiza *** one from each of the genera Glycyrrhizopsis Boiss.& *** Meristotropis Fisch.& *** investigated by scanning electron *** pollen morphology,the main differences between Glycyrrhizopsis and Glycyrrhiza are:Glycyrrhizopsis-pollen grains 36.63 × 40.42.μm in size,oblate spheroidal in shape;and Glycyrrhiza-pollen grains 2..47-33.18 × 2..82.31.83 μm in size,prolate spheroidal in *** and Glycyrrhiza should be recognized as two distinct genera based on palynological and morphological *** and Glycyrrhiza are similar in many important palynological and morphological characters,suggesting that the two should be *** Glycyrrhiza,two types of pollen grains,3-lobed-circular or subtriangular in polar view,are found in different species,in accordance with morphological differences in the two groups,shedding light on the classification and evolution of the genus.

关键词： exine sculpture morphological character pollen morphology taxonomic revision.

^(40)Ar/^(39)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 academy of Geological {2., beijing 100081, china 2. institute of Geology, Chinese academy of Geological {2., beijing 100037, china 3. institute of Geology and Geophysics, Chinese academy of {2., 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 350℃. 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/39Ar dating, late Cenozoic.

Mineralogy and crystal structure determination of Mg-fillowite

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Science china Earth sciences 2005年第5期48卷 635-646页

作者： MA Zhesheng 1 , SHI Nicheng 1 & YE Danian 2.1. china University of Geosciences, {2. 100083, china 2. institute of Geology, Chinese academy of sciences, {2. 10002., china china University of Geosciences Beijing China institute of Geology Chinese Academy of Sciences Beijing China

Accurate crystal structure determination of complex phosphate Mg-fillowite ? Na2.a(Mn4Mg2.e)7[PO4]6 has been finished. Mg-fillowite occurs in muscovite-pegmatite in the Altay area, Xinjiang, china. It is of the trigonal lattice, with space group R-3, unit cell a=1.5143(3) nm, c=4.3191(2. nm, V=8.5736 nm3, Z = 18. The R-factor of the determination accuracy is R (I > 2. ( I )) = 0.0776. The cationic polyhedra consist of two kinds of structural units: compound col- umn and screw column. In three-dimensional space, they are linked with each other through corner sharing or edge sharing to build the entire structure. There are 45 atoms in an asymmetric unit and 72. atoms in a unit cell. In terms of types and connection manners of the coordination polyhedra, the degree of complicity is rarely seen in all mineral crystal structures. Study of such a structure is significant for the classification of phosphate and the building rule of coordination polyhedra in a complex crystal structure.

关键词： Mg-fillowite, complex phosphate, crystal structure, coordination polyhedron.

Some key technics of drop tower experiment device of National Microgravity Laboratory (china) (NMLC)

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Science china(Technological sciences) 2005年第3期48卷 305-316页

作者： ZHANG Xiaoqian 1 , YUAN Longgen 1 , WU Wendong 1 , TIAN Lanqiao 2.& YAO Kangzhuang 2.1. institute of Engineering Thermophysics, Chinese academy of {2., beijing 100080, china 2. institute of Mechanics, Chinese academy of {2., beijing 100080, china institute of Engineering Thermophysics Chinese Academy of Sciences Beijing China institute of Mechanics Chinese Academy of Sciences Beijing China

Drop tower is an important ground based facility for microgravity science experiment. The technical performances of the drop tower NMLC are advanced compared with similar facilities in the US, Germany and Japan. The main components such as drop capsule, deceleration devices, release mechanism present its advantages and creativities.

关键词： drop tower facility,drop capsule,deceleration devices,release mechanism.

Pattern phenomena in an rf discharge dusty plasma system

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Science china(Physics,Mechanics & Astronomy) 2006年第5期49卷 588-596页

作者： HUANG Feng1,2. YE Maofu2.& WANG Long2.1. College of Science, china Agricultural University, beijing 100083, china 2. institute of Physics, Chinese academy of sciences, beijing 100080, china College of Science China Agricultural University Beijing China institute of Physics Chinese Academy of Sciences Beijing China

Various dust patterns are observed in an rf discharge dusty plasma system. According to the dust growth process from small to large in size, the formation of different dust patterns can be divided into two stages: the small-particle stage (or dust cloud stage), and the large-particle stage (or dust crystal stage). The evolution relations between different dust patterns with gas pressure changing are investigated. Dust voids, dust acoustic waves and strong turbulence modes are presented at the small-particle stage. The self-organized dust lattices and dust clusters are investigated at the large-particle stage. The static structure of a dust lattice is characterized by means of the pair correlation function. Dust clusters formed by particles with different numbers and the regular evolution of the clusters with gas pressure are also investigated. The packing sequences of dust clusters are verified through two-dimensional confined molecular dynamics simulations.

关键词： dusty plasma dust patterns

Adjoint method for the optimum planning of industrial pollutant sources

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Science china Earth sciences 2005年第8期48卷 1270-1279页

作者： LIU Feng1,2. HU Fei2.& ZHU Jiang2.1. College of Environmental sciences, Peking University, beijing 100871, {2. 2. LAPC, institute of Atmospheric Physics, Chinese academy of sciences, beijing 10002., {2. College of Environmental sciences Peking University Beijing China LAPC Institute of Atmospheric Physics Chinese Academy of Sciences Beijing China

The optimum planning of industrial pollutant sources, which optimizes the economic object without violating environmental constraints, is an important and hard task to be conquered. In this paper, an adjoint method is developed to solve the problem. The penalty function is in-troduced to deal with the environmental inequality constraints, and Lagrange function is con-structed to derive the adjoint equation and the gradient of the object function. In this means, the gradient of the object function can be calculated by solving the adjoint equation, and the infor-mation from the gradient is used to make the object function descend and approach to an optimal solution after some iterations. A two-dimensional, simplified model is used for numerical experi-ments. The theoretical derivations are verified by the results of the experiments. Furthermore, the adjoint method is shown to be of excellent convergence and efficiency, which is adaptive to the fast development of air quality numerical models and super computers.

关键词： optimum planning, industrial pollutant sources, adjoint equation, penalty function, gradient.

The identity of some taxa of Schizophragma (Saxifragaceae)

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Journal of Systematics and Evolution 2009年第2期47卷 151-161页

作者： 1,2.ei LIU 1Xiang-Yun ZHU 1(institute of Botany,Chinese academy of {2.,beijing 100093,china) 2.Graduate University of Chinese academy of {2.,beijing 100049,china) institute of Botany Chinese Academy of Sciences Beijing 100093 China Graduate University of Chinese academy of sciences Beijing 100049 China

After examining a large number of type and authoritative specimens of Schizophragma Siebold & Zucc.,*** *** and *** *** Rehder were reduced to synonyms of *** Rehder and *** *** *** was reduced to synonym of *** *** crassum *** *** was treated as the correct name of *** ***(Chun) *** name *** *** Rehder is *** taxonomic treat-ment is supported by leaf epidermal characters.

关键词： leaf epidermis new synonym reinstatement Schizophragma