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Analysis of tandem repeats in the genome of chinese shrimp Fenneropenaeus chinensis

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chinese Science Bulletin 2005年第14期50卷 1462-1469页

作者： KONG Jie1 & GAO Huan2.3 1. Key Laboratory for Sustainable Utilization of Marine Fisheries Re- sources, Ministry of Agriculture, Yellow Sea Fisheris Research Insti- tute, chinese academy of Fishery {2., Qingdao 2.6071, china 2. Institute of Oceanology, chinese academy of sciences, Qingdao 2.6071, china 3. The Graduate school of the chinese academy of sciences, beijing 10003., china Key Laboratory for Sustainable Utilization of Marine Fisheries Resources Ministry of Agriculture Yellow Sea Fisheris Research Institute Chinese Academy of Fishery Sciences Qingdao China Institute of Oceanology Chinese Academy of Sciences Qingdao China The Graduate school of the chinese academy of sciences Beijing China

Through random sequencing, we found a total of 884000 base-pairs (bp) of random genomic sequences in the genome of chinese shrimp (Fenneropenaeus chinensis). Using bio-soft Tandem Repeat Finder (TRF) software, 2.59 tandem repeats were found, in which there were 1714 mi- crosatellites and 445 minisatellites, accounting for 79.4% and 2..6% of repeat sequences, respectively. The cumulative length of repeat sequences was found to be 116685 bp, ac- counting for 13.2. of the total DNA sequence; the cumula- tive length of microsatellites occupied 9.78% of the total DNA sequence, and that of minisatellites occupied 3.42.. In decreasing order, the 2. most abundant repeat sequence classes were as follows: AT (557), AC (471), AG (2.4), AAT (92., A (56), AAG (2.), ATC (2.), ATAG (2.), AGG (18), ACT (15), C (11), AAC (11), ACAT (11), CAGA (10), AGAA (9), AGGG (7), CAAA (7), CGCA (6), ATAA (6), AGAGAA (6). Dinucleotide repeats, not only in the aspect of the number, but also in cumulative length, were the preponderant repeat type. There were few classes and low copy numbers of repeat units of the pentanucleotide repeat type, which included only three classes: AGAGA, GAGGC and AAAGA. The classes and copy numbers of heptanucleotide, eleven-nucleotide and thirteen-nucleotide primer-number-composed repeats were distinctly less than that of repeat types beside them.

关键词：虾遗传特性遗传基因 DNA

Representation of microscale ocean wavenumber spectrum correct to the second order

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Science china Earth sciences 2005年第4期48卷 549-554页

作者： YUAN Yeli2.& HUA Feng1,2.3 1. Institute of Oceanology, chinese academy of sciences, Qingdao 2.6071, china 2. Key Laboratory of Marine Science and Numerical Modeling, State Oceanic Administration, Qingdao 2.6061, china 3. Graduate school of the chinese academy of sciences, beijing 10003., china 1. Key Laboratory of Marine Science and Numerical Modeling State Oceanic Administration 266061 Qingdao China 2. Institute of Oceanology Chinese Academy of Sciences 266071 Qingdao China 3. Graduate school of the chinese academy of sciences 100039 Beijing China

In this paper, the analytical representations of four wave source functions in high-frequency spectrum range are given on the basis of ocean wave theory and dimensional analysis, and the perturbation method is used to solve the governing equations of ocean wave high-frequency spectrum on the basis of the temporally stationary and locally homogeneous scale relations of microscale wave. The microscale ocean wavenumber spectrum correct to the second order has an explicit structure, its first order part represents the equilibrium between dif- ferent source functions, and its second order part represents the contribution of microscale wave propagation.

关键词： temporally stationary and locally homogeneous, source function in high-frequency spectrum range, microscale ocean wavenumber spectrum.

THE DUAL MIXED METHOD FOR AN UNILATERAL PROBLEM

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Journal of Computational Mathematics 2003年第6期21卷 733-746页

作者： Lie-heng Wang(LSEC, ICMSEC, academy of Mathematics and System sciences,{2.,beijing 100080, china) LSEC ICMSEC Academy of Mathematics and System Sciences Chinese Academy of Sciences Beijing 100080 China

In this paper, the dual mixed method for an unilateral problem, which is the simplified modelling of scalar function for the friction-free contact problem, is considered. The dual mixed problem is introduced, the existence and uniqeness of the solution of the problem are presented, and error bounds O(h3/4) and O(h3/2. are obtained for the dual mixed finite element approximations of Raviart-Thomas elements for k = 0 and k = 1 respectively.

关键词： Dual Mixed Method Unilateral Problem.

Identification of novel SINEs from Cyprinidae and their evolutionary significance

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Progress in Natural Science:Materials International 2007年第3期17卷 270-279页

作者： HAN Yawei, HE Slumping and CHEN Yiyu ( Institute of Hydrobiology, chinese academy of sciences, Wuhan 430072. china. Graduate {2., chinese academy of sciences, beijing 10003., china) [a]Institute of Hydrobiology Chinese Academy of Sciences Wuhan China [b]Graduate school Chinese Academy of Sciences Beijing China

Short interspersed nuclear elements (SINEs) are widespread among eukaryotic genomes. They are repetitive DNA sequences that have been amplified by retrotransposition. In this study, a class of SINEs were isolated from the Opsariichthys bidens genome, and named Opsar. Sequence analysis confirmed that Opsar is a new class of typical SINEs derived from tRNA molecules. With the tRNA-derived region of Opsar and through BLASTN search, we further identified Zb-SINEs from the zebrafish genome, which includes two groups: Zb-SINE-A and Zb-SINE-B. The Zb-SINE-A. group comprises subfamilies of -Al--A5, and the Zb-SINE-B group is a dimer of the tRNA -derived region and shares a similar dimeric composition to Alu. Zb-SINEs are composed of three distinct regions: a 5’ end tRNA-derived region, a tRNA-unrelated region and a 3’ end AT-rich region. The flanking regions are AT rich. The average length of Zb-SINEs elements is about 340 bp. Zb-SINEs account for as much as 0.1 % of the whole zebrafish genome. About 70% of the Zb-SINEs are on chromosomes 11, 18, and 19. These Zb-SINEs were characterized by PCR and dot hybridization. The distribution pattern of Zb-SINEs in genome strongly supports the master genes model. The tRNA-derived regions of Opsar and Zb-SINEs were compared with the tRNAAla gene, and they showed 76% similarity, indicating that Opsar and Zb-SINEs originated from an inactive tRNA sequence or a tRNA -like sequence. In view of the evolutionary status of zebrafish in the Cyprinidae, we deduced that Zb-SINEs were a very old class of interspersed sequences.

关键词： short interspersed nuclear elements (SINEs) master gene model Opsar Zb-SINEs and Cyprinidae.

Characteristics of air particulate matter and their sources in urban and rural area of beijing, china

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Journal of Environmental sciences 2000年第4期12卷 402-409页

作者： YANG Shao jin, DONG Jin quan, CHENG Bing ru (Institute of High Energy Physics, chinese academy of sciences, beijing 100080,{2.) Institute of High Energy Physics Chinese Academy of Sciences Beijing 100080 China

During October 1993 and March 1996, the samples of fine and coarse air particulate matter have been collected at representative urban and rural site of beijing with the Gent Stacked Filter Unit Sampler. Instrumental neutron activation analysis (INAA) and proton induced X ray emission (PIXE) method were used to determine the elemental composition of the particulate matter. Average elemental concentrations and enrichment factors were calculated for the fine and coarse size fractions. Based on the particulate matter data obtained at urban and rural site together with the chemical constituents of the aerosol from the different sources are discussed. The results show that the relative particulate mass and elemental concentrations of crustal and pollutant elements in the air particulate matter collected over the urban are higher than rural and winter heating period are higher than in ordinary season. beijing atmosphere is polluted by aerosols from regional and faraway sources. It was noticed that the toxic or harmful elements such as As, Sb, Pb, Cu, Ni, S and Zn were mainly enriched in fine particles with diameter less than 2.μm. A receptor model was used to assess the relative contribution of major air pollution sources at receptor sites in beijing. Trace elements were used as the markers for the above assessment. Factor analysis method was used to identify possible emission sources of air particles. The major sources of dust soil, coal burning, motor vehicle emission, industry emission and refuse incineration were identified.

关键词： atmospheric particulate matter urban rural source aerosol

Artificial coordinating field and its application to motion planning of robots in uncertain dynamic environments

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Science china(Technological sciences) 2004年第5期47卷 577-594页

作者： JING Xingjian1, 2. WANG Yuechao1 & TAN Dalong1 1. Robotics Laboratory, Shenyang Institute of Automation, chinese academy of sciences, Shenyang 110016, china 2. Graduate {2., chinese academy of sciences, beijing 10003., china Correspondence should be addressed to Jing Xingjian 1. Robotics Laboratory Shenyang Institute of Automation Chinese Academy of Sciences 10016 Shenyang China 2. Graduate school Chinese Academy of Sciences 10039 Beijing China

Artificial coordinating fields (ACF) are proposed to deal with the motion planning problems of mobile robots in uncertain dynamic environments. An ACF around an obstacle can generate two orthogonal force vectors to a robot: one is called the coordinating force vector which is purposively designed in this paper, and the other is the repulsive force vector which is the same as that in a conventional artificial potential field. The ACF is designed according to the updated motion purpose and the relative states of the robot with respect to its local environment, and it also satisfies the robot’s dynamic constraints. The direction of the coordinating force can be determiend on line according to an optimal evaluation function. The ACF can effectively remove the local minima, and reduce the oscillation of the planned trajectory between multiple obstacles. Only local knowledge of the environments is needed in the ACF-based motion planning. The properties of the ACF such as controllability, adaptability, safety and reachability are studied and discussed in detail in this paper. Theoretical analysis and simulations are given to illustrate our main results.

关键词： artificial coordinating fields, artificial potential fields, mobile robots, motion planning, uncertain dynamic environments.

Cytotoxicity of carbon nanotubes

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Science china Chemistry 2008年第11期51卷 1021-1029页

作者： ZHU Ying1,2.& LI WenXin1 1 Laboratory of Nano-biology and Medicine, Shanghai Institute of Applied Physics, chinese academy of sciences, Shanghai 2.1800, china 2.Graduate {2. of chinese academy of sciences, beijing 100049, china 1. Laboratory of Nano-biology and Medicine Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China 2. Graduate school of chinese academy of sciences Beijing 100049 China

With large-scale production and application at large scale, carbon nanotubes (CNTs) may cause ad-verse response to the environment and human health. Thus, study on bio-effects and safety of CNTs has attracted great attention from scientists and governments worldwide. This report briefly summa-rizes the main results from the in vitro toxicity study of CNTs. The emphasis is placed on the descrip-tion of a variety of factors affecting CNTs cytotoxicity, including species of CNTs, impurities contained, lengths of CNTs, aspect ratios, chemical modification, and assaying methods of cytotoxicity. However, experimental information obtained thus far on CNTs' cytotoxicity is lacking in comparability, and some-times there is controversy about it. In order to assess more accurately the potential risks of CNTs to human health, we suggest that care should be taken for issues such as chemical modification and quantitative characterization of CNTs in cytotoxicity assessment. More importantly, studies on physical and chemical mechanisms of CNTs' cytotoxicity should be strengthened; assaying methods and evaluating criteria characterized by nanotoxicology should be gradually established.

关键词： carbon nanotubes (CNTs) cell bio-security

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, Institute of Genetics and Developmental Biology, chinese academy of sciences, beijing 100101,{2. 2. Graduate school of chinese academy of sciences, beijing 10003.,{2. 3. Xinjiang academy of Agricultural and Reclamation Science, Shihezi 832.00,{2.) National Key Laboratory of Plant Genomics Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China Graduate school of chinese academy of sciences 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.

A CLASS OF NEW PARALLEL HYBRID ALGEBRAIC MULTILEVEL ITERATIONS

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Journal of Computational Mathematics 2001年第6期19卷 651-672页

作者： Zhong-zhi Bai (LSEC ICMSEC, academy of Mathematics and Systems sciences,{2., beijing 100080, china) 中科院计算数学与科学工程计算所北京 100080

Presents preconditioning matrices having parallel computing function for the coefficient matrix and a class of parallel hybrid algebraic multilevel iteration methods for solving linear equations. Solution to elliptic ... 详细信息

关键词： elliptic boundary value problem system of linear equations symmetric positive definite matrix multilevel iteration parallel method