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Sequence analysis of mRNA polyadenylation signals of rice genes

chinese Science Bulletin 2006年第9期51卷 1069-1077页

作者： LU Ying1, 2. GAO Chenxi1,2.3 & HAN Bin1,3,41. national center for {2. research, shanghai Institutes for Biological sciences, chinese academy of sciences, shanghai 2.02.3, china 2. Graduate School of the chinese academy of sciences, Beijing 100039, china 3. Institute of Plant Physiology and Ecology, shanghai Institutes for Biological sciences, chinese academy of sciences, shanghai 2.0032. china national center for {2. research Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200233 China Graduate School of the chinese academy of sciences Beijing 100039 China Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200032 China

The formation of eukaryotic mRNAs involves the cleavage and polyadenylation of pre- mRNAs. To investigate the sequence requirement of putative polyadenylation signals (PASs), poly(A) sites and downstream elements (DUEs) in 3′-end-pro- cessing in rice, we compared expressed sequences tags (ESTs) with poly(A) extremity to full-length cDNA sequences and constructed a database of 12.69 pre- mRNA sequences in ?40―+40 nt surrounding the poly(A) sites, which were from 9953 genes. The al- ternative poly(A) sites were revealed in approxi- mately 2.% of mRNAs. Nearly 80% of pre-mRNAs showed stringent requirement of the YA (CA or UA) at poly (A) sites for polyadenylation. About 7.9% had the AAUAAA signals on ?40―?1 nt upstream of the poly(A) sites. Over 60% of mRNAs probably used the one- or two-base variants of AAUAAA hexamers as their PASs in 3′ fragments. The single-base variants of AAUGAA revealed the high frequency in 11.5% of 3′ fragments. The DUEs were detected in 90% of pre- mRNAs, especially more than half of the pre-mRNAs with multi-base variants of AAUAAA had the DUEs surrounding the poly(A) site. The location of DUE is also important for defining the cleavage site. Al- though most of the rice pre-mRNAs did not contain AAUAAA signal, the existence of downstream ele- ments ensured the efficiency of cleavage-polyade-

关键词：多聚腺苷酸序列分析 mRNA 水稻基因工程

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Spectral analysis of quasi-stationary sea surface topography from GRACE mission

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Science china Earth sciences 2005年第11期48卷 2040-2048页

作者： ZHANG Zizhan1,2.& LU Yang1,3 1. Institute of Geodesy and Geophysics, chinese academy of sciences, Wuhan 430077, china 2. Graduate School of the chinese academy of sciences, Beijing 100039, china 3. Unite center for Astro-geodymics research, chinese academy of sciences, shanghai 2.0030, china 1. Institute of Geodesy and Geophysics Chinese Academy of Sciences 430077 Wuhan China 2. Graduate School of the chinese academy of sciences 100039 Beijing China 3. Unite center for Astro-geodymics research Chinese Academy of Sciences 200030 Shanghai China

During the last two decades satellite altimetry has offered an abundance of meas-urements of the sea surface resulting in the improvement of global mean sea surface height (MSSH) and marine geoid determination. On the other hand, with the launching of new genera-tion gravity satellites, some high accuracy long-wavelength gravity models are available. These breakthroughs give us a great opportunity for new estimation of quasi-stationary sea surface topography (QSST). In this paper, the new gravity model GGM01C derived from GRACE mission is briefly presented, and a new global high precision and high-resolution QSST is determined based on the GGM01C model and the global MSSH. The spectral features of the QSST esti-mated by GGM01C and EGM96 gravity model to degree/order 2.0 are discussed by spectral analysis. As a result, the QSST is mainly composed of long waves, medium waves partially and short waves scarcely, its power spectral structures are different between the zonal direction and the meridional direction, there are great differences between the two models, which maybe ex-plain why the ocean currents derived from the two gravity models by Tapley show different pat-terns.

关键词： quasi-stationary sea surface topography, mean sea surface height, GGM01, fast Fourier transform, spectral analysis

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Progress in the detection of human genome structural variations

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Science china(Life sciences) 2009年第6期52卷 560-567页

作者： WU XueMei1,3 & XIAO HuaSheng1,2.1 center of Functional Genomics,Key Laboratory of System Biology,shanghai Institutes for Biological {2.,chinese academy of {2.,shanghai 2.0031,china 2.national Engineering center for Biochip at shanghai,shanghai 2.12.3,china 3 Graduate School of the chinese academy of sciences,shanghai 2.0031,china 1. center of Functional Genomics Key Laboratory of System Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China 3. Graduate School of the chinese academy of sciences Shanghai 200031 China 2. national Engineering center for Biochip at {2. Shanghai 201203 China

The emerging of high-throughput and high-resolution genomic technologies led to the detection of submicroscopic variants ranging from 1 kb to 3 Mb in the human *** variants include copy number variations(CNVs),inversions,insertions,deletions and other complex rearrangements of DNA *** paper briefly reviews the commonly used technologies to discover both genomic structural variants and their potential ***,we highlight the array-based,PCR-based and sequencing-based assays,including array-based comparative genomic hybridization(aCGH),representational oligonucleotide microarray analysis(ROMA),multiplex amplifiable probe hybridization(MAPH),multiplex ligation-dependent probe amplification(MLPA),paired-end mapping(PEM),and next-generation DNA sequencing ***,we discuss the limitations and challenges of current assays and give advices on how to make the database of genomic variations more reliable.

关键词： structural variation cytogenetic microarray PCR paired end mapping(PEM) next-generation sequencing

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Entropy of three-dimensional BTZ black holes

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中国科学：物理学、力学、天文学英文版 2004年第3期47卷 277-283页

作者： GAO Changjun1,2.& SHEN Yougen1,2.3,4 1.shanghai Astronomical Observatory,chinese {2. of sciences,shanghai 2.0030,china(mailing address) 2.national Astronomical Observatories,chinese {2. of sciences,Beijing 100012.china 3.Institute of Theoretical Physics,chinese {2. of sciences,Beijing 100080,china 4.shanghai United center for Astrophysics,shanghai 2.02.4,china 1. shanghai Astronomical Observatory Chinese Academy of Sciences 200030 Shanghai China 2. national Astronomical Observatories Chinese Academy of Sciences 100012 Beijing China 3. Institute of Theoretical Physics Chinese Academy of Sciences 100080 Beijing China 4. shanghai United center for Astrophysics 200234 Shanghai China

The entropies of scalar field and neutrino field are calculated in the background of three-dimensional BTZ black hole. Considering statistical physics,we propose not to consider the superraradiant modes for bosons (Fermion fields do not display supperradiance).In fact,the nonsuperradiant modes do contribute exactly the area entropy for both bosons and fermions. The result shows that the neutrino field entropy is 3/2.times the scalar one.

关键词： BTZ black holes, entropy, supperradiant modes.

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miRNAs modulate the drug response of tumor cells

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Science china(Life sciences) 2009年第9期52卷 797-801页

作者： WU XueMei1,3 & XIAO HuaSheng1,2.1 center of Functional Genomics,Key Laboratory of System Biology,shanghai Institutes for Biological {2.,chinese academy of {2.,shanghai 2.0031,china 2.national Engineering center for Biochip at shanghai,shanghai 2.12.3,china 3 Graduate University of chinese academy of sciences,shanghai 2.0031,china center of Functional Genomics Key Laboratory of System Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China national Engineering center for Biochip at {2. Shanghai 201203 China Graduate University of chinese academy of sciences Shanghai 200031 China

Chemotherapy is one of the major treatments of malignant carcinomas. However,its efficiency is affected by both intrinsic and acquired resistance to anticancer drugs. The cellular mechanisms of drug resistance include the overexpression of energy-dependent transporters that eject anticancer drugs from cells such as p-glycoprotein and multidrug resistance related protein (MRP),the mutation of drug targets,the activation of DNA repair pathways,the defects in cellular death pathways and so on. The genetic and epigenetic changes of these genes can lead to cancer drug resistance. Among these mechanisms,microRNAs (miRNAs) which are critical and essential for many important processes such as development,differentiation,and even carcinogenesis have been reported to regulate the chemosen-sitivity of tumor cells. In this paper we briefly review the relationship between miRNA and cancer drug resistance.

关键词： cancer drug resistance miRNAs

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Calculation of the Surface Segregation of Cu-0.3 at. pct Au Alloy

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Journal of Materials Science & Technology 2000年第6期16卷 639-640页

作者： Liping ZHENG and Risheng LI (International center for Material Physics,{2., Shenyang 110015, china) Yuanxun ZHANG and Shi QIU (shanghai Institute of Nuclear research,{2., shanghai 2.1800, china) Bingyao JI Int. Cent. for Material Phys. Chinese Acad. of Sci. Shenyang 110015 China

Monte Carlo simulation technique with the energetics described by the embedded atom method has been used to calculate the surface segregation of Cu-0.3 at. pct Au alloy at T=800 K. It is found that the component Au in... 详细信息

关键词： Cu Calculation of the Surface Segregation of Cu-0.3 at pct Au Alloy

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Identification and Analysis of genes Present in Leptospira interrogans serovar lai but Absent in L. biflexa serovar monvalerio

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Acta Biochimica et Biophysica Sinica 2004年第12期36卷 832-839页

作者： Ping HE, Xiang-Yan ZHANG, Xiao-Kui GUO*, Bao-Yu HU, Xiao-Tian HUANG, Yang YANG, and Guo-Ping ZHAO1,2. Department of Microbiology and Parasitology, shanghai Second Medical University, shanghai 2.002.,{2. 1 research center of Biotechnology, Institutes for Biological sciences, chinese academy of sciences, shanghai 2.0031,{2. 2.9} national Human Genome center at shanghai, Zhangjiang High Tech Park, shanghai 2.12.3,{2. Department of Microbiology and Parasitology Shanghai Second Medical UniversityShanghai 200025 China research center of Biotechnology Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200031 China chinese national Human Genome {2. at shanghaiZhangjiang High Tech Park Shanghai 201203 China

genes present in virulent bacterial strains but absent in avirulent close relatives can be of great biologic and clinical interest. This project aimed to identify strain specific DNA sequences of Leptospira interrogans serovar lai, which is absent in the saprophytic L. biflexa serovar monvalerio, via suppression subtractive hybridization with the former as the tester while the latter as the driver. The mixture of PCR amplified DNA fragments from two subtractive hybridization experiments were cloned into pMD18-T vector and the positive clones were identified by dot blotting against the chromosome DNA of the two strains individually. After DNA sequencing and analysis, the distribution of these genomic fragment sequences in a panel of pathogenic and nonpathogenic leptospires was investigated employing dot blot analysis. Among the 188 positive clones randomly chosen, 2. contained the tester strain specific genomic regions, of which, 5 were non-coding fragments while the others contained 2. distinct protein coding sequences. Besides 9 genes encoding functional proteins, 12.genes encode unknown proteins and the rest two genes encode proteins with recognizable domain structures, one for a putative leucine-rich repeats (LRR) family protein while the other as an outer-membrane protein. Our experiment results indicated that suppression subtractive hybridiza- tion is effective for screening specific DNA sequences between two leptospiral strains, and some of these sequences might be responsible for virulence determination. Further analysis of these DNA sequences will provide important information on the pathogenesis of Leptospira.

关键词： Leptospira interrogans serovar lai suppression subtractive hybridization (SSH) specific genes

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Critical phenomena of a nuclear system in alternative ZM models

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Nuclear Science and Techniques 2000年第3期11卷 173-178页

作者： SONG Hong-Qiu (research center of Nuclear Theory of {2. Laboratory Of Heavy Ion Accelerator of Lanzhou, Lanzhou 730000 shanghai Institute of Nuclear research, the chinese academy of sciences, shanghai 2.1800) 兰州原子核理论研究中心重离子加速器国家实验室甘肃兰州 730000

Alternative versions of the ZM model are extended to asymmetric nuclear matter by including p meson degree of freedom in the Lagrangian. The extended models are then used to study the thermodynamical properties of asymmetric nuclear matter at finite temperature. The critical temperature for a liquid- gas phase transition in nuclear matter and its dependence on asymmetry parameter are calculated. The limiting temperature Tlim, which reflects Coulomb instability of hot nuclei, is studied. The calculated results are compared with that given by the original ZM model.

关键词：放射性核素临界现象 ZM模型固气相变热力学稳定性核子核反应临界温度

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Single crystal β-Ga_2._3: Cr grown by floating zone technique and its optical properties

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Science china(Technological sciences) 2007年第1期50卷 51-56页

作者： ZHANG JunGang1, 2. LI Bin3, XIA ChangTai1, XU Jun1, DENG Qun4, XU XiaoDong1, WU Feng1, XU WuSheng4, SHI HongSheng4, PEI GuangQing1, 2.& WU YongQing1,2.1 shanghai Institute of Optics and Fine Mechanics, chinese academy of sciences, shanghai 2.1800, china 2.Graduate School of the chinese academy of sciences, Beijing 100039, china 3 shanghai Institute of Applied Physics, chinese academy of sciences, shanghai 2.1800, china 4 GE (china) research and Development {12. Co. Ltd., shanghai 2.12.3, china 1. shanghai Institute of Optics and Fine Mechanics Chinese Academy of Sciences Shanghai 201800 China 2. Graduate School of the chinese academy of sciences Beijing 100039 China 3. shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China 4. GE (china) research and Development {2. Co. Ltd. Shanghai 201203 China

β-Ga2.3: Cr single crystals were grown by floating zone technique. Absorption spectra and fluorescence spectra were measured at room temperature. The values of field splitting parameter Dq and Racah parameter B were obtained by the peak values of absorption spectra. The value 10Dq/B=2..14 manifests that in β-Ga2.3 crystals Cr3+ ions are influenced by low energy crystal field. After high temperature annealing in air, the Cr3+ intrinsic emission was enhanced and the green lumines-cence disappeared. The strong and broad 691 nm emission was obtained at 42. nm excitation due to the electron transition occurred from 4T2.to 4A2. The studies manifest that the β-Ga2.3 crystals have the potential application for tunable laser.

关键词： β-Ga2.3: Cr single crystals floating zone technique tunable laser spectrum.

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Organic Solvents Mediate Self-assembly of GAV-9 Peptide on Mica Surface

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Acta Biochimica et Biophysica Sinica 2007年第4期39卷 285-289页

作者： Hai LI~(1,3) Feng ZHANG~1 Yi ZHANG~1* Jianhua HE~1 Jun HU~(1,2. 1 shanghai Institute of Applied Physics,chinese {2. of sciences,shanghai 2.1800,china 2.Bio-X Life sciences research center.College of Life Science and Biotechnology,shanghai Jiaotong University,shanghai 2.0030,china 3 Graduate School of the{12.,Beijing 100049,china shanghai Institute of Applied Physics Chinese Academy of SciencesShanghai 201800 China Graduate School of the chinese academy of sciencesBeijing 100049 China Bio-X Life sciences research {2. College of Life Science and Biotechnology Shanghai Jiaotong UniversityShanghai 200030 China

Self-assembly of peptides into fibrils and other morphologies has attracted much attention inmany fields,especially in nanofabrication,pathology and *** this paper,self-assembly of GAV-9peptide in organic solvents,ethanol and acetone,was investigated using atomic force microscopy(AFM)and attenuated total reflectance-Fourier transform infrared spectroscopy(ATR-FTIR).The results indicatedthat GAV-9 self-assembled into various nanostructures in both solvents after deposited and evaporated *** with β-sheet conformation were observed in both solvents when the peptide concentrationwas higher than 2.0 μ***,ordered fibrils with β-sheet conformation were formed in ethanol,butnot in acetone,with a peptide concentration ranging from 7 μM to 2. μ*** attribute the formation ofvarious nanostructures to the different physicochemical properties of the polar organic solvents on the self-assembly of GAV-9 peptide.

关键词： self-assembly GAV-9 peptide organic solvents ATR-FTIR AFM

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