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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 Sciences, Beijing Normal University, Beijing 100875. china 3. Institute of Viral Disease Control and Prevention, Chinese CDC, Beijing 10005., china 4. bioinformation center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, china 5. Shanghai center for bioinformation technology, Shanghai 200235, china 6. School of Life Sciences, Fudan University, Shanghai 2004.3, 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 23, 2004.. 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 4. 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

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In flight MTF monitoring and compensation for CCD camera on CBERS-02

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Science china(Technological Sciences) 2005年第S2期48卷 29-43页

作者： GU Xingfa1,2,3, LI Xiaoying1,2,4. MIN Xiangjun5. YU Tao1,2, SUN Jijuan5. ZENG Yong1,2,4. XU Hua1,2 & GUO Ding2,6 1. State Key Laboratory of Remote Sensing Science, Jointly Sponsored by the Institute of Remote Sensing Applications of Chinese Academy of Sciences and Beijing Normal University, Beijing 100101, china 2. The center for National Spaceborne Demonstration, Beijing 100101, china 3. Institut National de la Recherche Agronomique, Climat Sol Environnement, 84.14.Avignon, France 4. Graduate University of Chinese Academy of Sciences, Beijing 100039, china 5. china center for Resource Satellite Data and Application, Beijing 100830, china 6. University of Electronic Science and technology of china, Chengdu 61005., china State Key Laboratory of Remote Sensing Science Jointly Sponsored by the Institute of Remote Sensing Applications of Chinese Academy of Sciences and Beijing Normal University 100101 Beijing China The center for National Spaceborne Demonstration 100101 Beijing China Institut National de la Recherche Agronomique Climat Sol Environnement 84914 Avignon France Graduate University of Chinese Academy of Sciences 100039 Beijing China china center for Resource Satellite Data and Application 100830 Beijing China University of Electronic Science and technology of china 610054 Chengdu China

In this article, the approach of simulating ideal tarp scene was proposed to determine the MTF for CCD camera on CBERS-02. The MTF acquired from this technique was compared to those from some common methods. MTFs achieved from different approaches were employed to compensate the CCD images based on three restoration algorithms: the iterative method, the Wiener filter and the modified inverse filter (MIF). The two-dimensional MTF was established with the value at frequency 0.5.for 4.0} directional MTF as the value at its four corners. This article addressed the variations of the restored CCD images with different techniques of constructing two-dimensional MTF, restoring algorithms and determining the in-flight MTFs. Results showed images restored with the MTF determined from the technique of simulating ideal tarp scene represent the real scene best. And the restoration technique based on the MIF would produce better restored images than the other two techniques. This research also demonstrated that the two-dimensional MTF used for restoration should be interpolated under the control of the MTF for 4.0} axis, rather than by multiplying the cross-orbit MTF with along-orbit MTF.

关键词： CBERS-02 CCD MTF the technique of simulating ideal tarp scene.

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Southeastern extension of the Red River fault zone (RRFZ) and its tectonic evolution significance in western South china Sea

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Science china Earth Sciences 2006年第8期49卷 839-850页

作者： LIU Baoming1,2,3, XIA Bin1, LI Xuxuan1,3, ZHANG Minqiang1,3, NIU Binhua2, ZHONG Lifeng1, JIN Qinghuan1,4.& JI Shaocheng1,5.1. Key Laboratory of Marginal Sea Geology and Resources, Chinese Academy of Sciences,Guangzhou 5.064., china 2. china University of Geosciences (Beijing), Beijing 100083, china 3. Research center of Science & technology Department, CNOOC, Beijing 100027, china 4. Guangzhou Marine Geological Survey, Ministry of Land & Resources, Guangzhou 5.0075. china 5. Ecole Polytechnique Montreal, H3C3A7, Canada 1. Key Laboratory of Marginal Sea Geology and Resources Chinese Academy of Sciences Guangzhou 510640 China 2. china University of Geosciences (Beijing) Beijing 100083 China 3. Research center of Science & technology Department CNOOC Beijing 100027 China 4. Guangzhou Marine Geological Survey Ministry of Land & Resources Guangzhou 510075 China 5. Ecole Polytechnique Montreal H3C3A7 Canada

Recent geophysical surveys and basin modeling suggest that the No.1 fault in the Ying- gehai basin (YGHB) is the seaward elongation of the Red River fault zone (RRFZ) in the South china Sea (SCS). The RRFZ, which separates the South china and Indochina block, extends first along the Yuedong fault, offshore of Vietnam, and then continues southward and breaks off into two branches: the Lupar fault and the Tinjia fault. The southern extension of the Lupar fault dies out beneath the NW Borneo while the Tinjia fault extends southeast and reaches the Brunei-Sabah area. According to the gravity and geomagnetic data, and the tectonic evolution of the basins, there are different evolution histories between the Wan’an basin (WAB) and the basins in the Nansha block. The Tinjia fault may be the boundary between the Balingian block and the Nansha block. Hence, the line linking the Yue- dong fault and the Tinjia fault, which both are continental margin faults and strike-slip ones in the geological evolution histories, constitute the boundary between the Indochina and Nansha block. The Lupar fault, in contrast, is an intraplate fault within the Indochina block. The results provide new hints for reconstructing the tectonic evolution history of the RRFZ and the opening of the SCS, and also a framework for hydrocarbon prospecting in the region.

关键词： Red River fault zone, tectonic evolution, fault, extension, western South china Sea.

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Electron microscopy study of the sakhaite from endogenous borate deposit in Hunan, china

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Science china Earth Sciences 2004年第3期47卷 232-238页

作者： LIU Xiangwen1,2, YANG Guangming2, ZOU Huamin3, QU Jing1 & ZHAO Wenxia4.1. Graduate School, china University of Geosciences, Wuhan 4.0074. china 2. Test center, china University of Geosciences, Wuhan 4.0074. china 3. Physics and {5. College, Wuhan University, Wuhan 4.0072, china 4. Test center, Zhongshan University, Guangzhou 5.0275. china china Univ Geosci Grad Sch Wuhan 430074 Peoples R China china Univ Geosci Test Ctr Wuhan 430074 Peoples R China Wuhan Univ Phys & Technol Coll Wuhan 430072 Peoples R China Zhongshan Univ Test Ctr Guangzhou 510275 Peoples R China

Sakhaite specimens from an endogenous borate deposit in Hunan Province, china have been studied in detail by means of transmission electron microscopy (TEM). The selected area electron diffraction (SAED) patterns obtained with different crystal zone axes show that the crystal system is cubic, with a = 1.4.3 nm. The convergent beam electron diffraction (CBED) patterns indicate that the point group and space group of sakhaite is m3m and Fd3m, respec-tively. The space group of synthetic sakhaite determined by Chichagov (1974. is F4.32. The possible reasons why the space groups of the natural and the synthetic sakhaites are different are discussed.

关键词： sakhaite, space group, convergent beam electron diffraction (CBED).

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Functional analysis of schistosomes EF-hand domain-containing tegument proteins

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Chinese Science Bulletin 2007年第15期52卷 2100-2107页

作者： YU FuDong1,2,3,KANG Bin1,3,LI YuanYuan3,4.& LI YiXue1,3 1 Bioinformatics center,Key Laboratory of Systems Biology,Shanghai Institutes for Biological Sciences,Chinese Academy of Sci-ences,Shanghai 200031,china 2 Graduate University of Chinese Academy of Sciences,Shanghai 200031,china 3 Shanghai center for {4. {5.,Shanghai 200235,china 4.Key Laboratory of Systems Biology,Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences,Shanghai 200031,china Bioinformatics center Key Laboratory of Systems Biology Shanghai Institutesfor Biological Sciences Chinese Academy of Sciences Shanghai 200031 China

Schistosomes cause schistosomiasis disease which severely threatens human health. Little is known about the functions of EF-hand domain containing schistosomes tegument proteins other than as an-tigens. More possible functions of these tegument proteins were investigated with in silico analyses including protein-protein functional interaction,site-specific variation and glycosylation modification. The analysis results suggested that schistosomes could actively modulate host immune responses for its own favor through functional interactions with host proteins with immunomodulatory function,and passively regulate host immune responses through sequence variation under positive selection and glycosylating the recognition sites of host immune attack. In addition,the analysis of the C-terminal domain of these tegument proteins indicated that they could assist schistosomes in escaping host immune attacks through inhibiting chemotaxis and non-complement fixing antibody (IgG4. responses. In summary,our results suggested that these tegument antigen proteins could assist schistosomes in escaping and modulating host immune responses for self-protection during the process of host-para-site interaction.

关键词：寄生虫血吸虫皮蛋白质健康

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Quantitative detection of ING1 mRNA under different gene regulation based on molecular beacon

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Chinese Science Bulletin 2006年第17期51卷 2059-2064页

作者： LIU Bin1,2,3,4. WANG Kemin1,2,3,4. XIAO Zhiqiang5.6, WANG Wei1,3,4. TAN Weihong1,2,3,4. SUN Yi5.6, TANG Hongxing1,3,4.& YANG Xiaohai1,3,4.. State Key Laboratory of Chemo/Biosensing and Chemometrics, Hu- nan University, Changsha 4.0082, china 2. Life Science and Biotechnology Institute, Hunan University, Chang- sha 4.0082, china 3. Chemistry and Chemical Engineer College, Hunan University, Changsha 4.0082, china 4. Hunan Engineering Research center for Bio-Nanotechnology, Hunan University, Changsha 4.0082, china 5. Medical Experiment Research center, Xiangya Hospital, Central South University, Changsha 4.0008, china 6. Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Changsha 4.0008, china State Key Laboratory of Chemo/Biosensing and Chemometrics Hunan University Changsha China Life Science and Biotechnology Institute Hunan University Changsha China Chemistry and Chemical Engineer College Hunan University Changsha China Hunan Engineering Research center for Bio-Nanotechnology Hunan University Changsha China Medical Experiment Research center Xiangya Hospital Central South University Changsha China Key Laboratory of Cancer Proteomics of Chinese Ministry of Health Changsha China

The effects of drug treatment, gene transfection, and p5. RNA interference (RNAi) on level of ING1 mRNA in tumor cells were quantitatively detected with the help of ING1 molecular beacon (MB)/cRNA standard curve based on MB detection technology. Results showed that the level of ING1 mRNA could be upregulated by 5.FU treatment or ING1 transfection in low expression cell line of MCF-7 and be inhibited by silencing p5. with RNAi technology in normal expression cell line of CNE2. The level of ING1 varied from 7.7×10?16 to 5..4. 10?16 mol/μg total RNA of tumor cells. The results not only provided evidence for the regulation effects of gene expression but also were applied to investigat- ing the interaction of multigenes on signal transduc- tion pathway.

关键词： ING1 RT-PCR 定量分析分子信号 mRNA

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Contour representation based on wedgelet

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Journal of Systems Engineering and Electronics 2006年第2期17卷 251-257页

作者： Liu Zeyi~1, Sun Ziqiang~ 2,3 , Xu Ling~2 & Peng Xiang~ 4.5.1. Dept. of Mathematics of Science Coll., Shenzhen Univ., Shenzhen 5.8060, P.R. china 2. Dept. of Mathematics of Science Coll., Tianjin Univ., Tianjin 300072, P.R. Ch ina 3.Tianjin Foreign Studies Univ., Tianjin 300204. P.R. china 4. Inst. of Optoelectronics, Shenzhen Univ., Shenzhen 5.8060, P.R. china 5. National Lab of Precision Measurement technology and Instrumentation, Tianjin 300072, P.R. china Dept. of Mathematics of Science Coll. Shenzhen Univ. Shenzhen 518060 P. R. China Dept. of Mathematics of Science Coll. Tianjin Univ. Tianjin 300072 P. R. China Tianjin Foreign Studies Univ. Tianjin 300204 P. R. China Inst. of Optoelectronics Shenzhen Univ. Shenzhen 518060 P. R. China National Lab of Precision Measurement technology and Instrumentation Tianjin 300072 P. R. China

Aiming at the shortcomings of the existing wedgelet compression arithmetics, a novel contour-representing algorithm based on wedgelets is presented in this paper. Firstly the input image is binarized and the most optimized wedgelets are found by means of quadtree framework. Then the contours are reconstructed by applying the wedgelets, the data volume is compressed, and the shortcomings of the contour representation based on normal wavelet are ameliorated, the better effect for the visualization is obtained, too.

关键词： wedgelet binarization quadtree.

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A possible mode of the specific recognition of nucleic acids by proteins

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Chinese Science Bulletin 2001年第11期46卷 930-934页

作者： LI Xuqing & LIU CiquanDepartment of Computer Science, Kunming University of Science and technology, Kunming 65.04., china Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 65.223, china Yunnan Observatory, Chinese Academy of Sciences, Kunming 65.011, china 4. Modern Biological center, Yunnan University, Kunming 65.091, china Department of Computer Science Kunming University of Science and Technology Kunming China Yunnan Observatory Chinese Academy of Sciences Kunming China Laboratory of Cellular and Molecular Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China Modern Biological center Yunnan University Kunming China

Seven sets of protein target sites, which occur in several gene promoters, have been analyzed. The results suggest that there is a possible mode of specific recognition of double-helical nucleic acids by proteins. This recognition mode is related to a special topological property of double-helical DNA, which is termed base spatial pattern (BSP) of DNA segment. BSP is the spatial topological property determined only by the spatial arrangement of the bases on double-helical DNA segment.

关键词： protein nucleic acids recognition base spatial pattern (BSP) target sites.

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Semantic Search among Heterogeneous Biological Databases Based on Gene Ontology

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Acta Biochimica et Biophysica Sinica 2004年第5期36卷 365-370页

作者： Shun-Liang CAO, Lei QIN1, Wei-Zhong HE1, Yang ZHONG2, Yang-Yong ZHU, and Yi-Xue LI1,3* Department of Computing and Information technology, Fudan University, Shanghai 2004.3, china Shanghai center for bioinformation 1 technology, Shanghai {5., china School of Life Sciences, Fudan University, Shanghai 2004.3, china bioinformation center of Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai 200031, china Department of Computing and Information technology Fudan University Shanghai China

Semantic search is a key issue in integration of heterogeneous biological databases. In this paper, we present a methodology for implementing semantic search in BioDW, an integrated biological data warehouse. Two tables are presented: the DB2GO table to correlate Gene Ontology (GO) annotated entries from BioDW data sources with GO, and the semantic similarity table to record similarity scores derived from any pair of GO terms. Based on the two tables, multifarious ways for semantic search are provided and the corresponding entries in heterogeneous biological databases in semantic terms can be expediently searched.

关键词： Gene Ontology semantic search BioDW

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Fluorescence dynamics of interactions between polyamide PyPyPyβDp and DNA

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Science china Chemistry 2006年第1期49卷 75-80页

作者： ZHANG Huijuan1,2, WANG Jin3, WU Yishi1, YUAN Gu3, AI Xicheng1, WANG Li4.& ZHANG Jianping1 1. State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, china 2. School of Life Science and technology, Beijing Institute of technology, Beijing 100081, china 3. College of Chemistry and Molecular Engineering, Peking University, Beijing 100080, china 4. {5. for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080, china Correspondence should be addressed to Ai Xicheng and Zhang Jianping 1. State Key Laboratory for Structural Chemistry of Unstable and Stable Species Institute of Chemistry Chinese Academy of Sciences Beijing 100080 China 2. School of Life Science and technology Beijing Institute of Technology Beijing 100081 China 3. College of Chemistry and Molecular Engineering Peking University Beijing 100080 China 4. center for Condensed Matter Physics Institute of Physics Chinese Academy of Sciences Beijing 100080 China

The photophysical properties of the polyamide PyPyPyβDp (PPP) were investigated by means of steady-state absorption and fluorescence spectroscopies, as well as time-resolved fluo-rescence spectroscopy. It was found that the excited-state properties of PPP are very sensitive to solvents. In TKMC buffer PPP exhibited weak fluorescence with a decay time constant of 16 ps, while with the decrease of the solvent polarity PPP showed the blue-shifted peak position, increased inten-sity and lengthened life-time for its fluorescence behavior. In the presence of calf thymus DNA, it was observed that the fluorescence intensity was enhanced and the fluorescence lifetime increased from 16 to 32 ps for PPP, which verified that PPP bound into the minor groove of DNA duplex.

关键词： polyamide (PPP), calf thymus DNA (ctDNA), time-resolved fluorescence spectroscopy, recognition dynamics.

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