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Science Bulletin 2010年第33期 3829-3834页

作者： ZHAO YingChun1,2,MING Ming1,HONG Jie2,MA DeWang1,WU Jia1,LI QingGuo3,HUANG WeiDa2 & DING JianDong1 1 Key Laboratory of Molecular Engineering of Polymers of Ministry of Education,department of Macromolecular Science,fudan university,shanghai 200433,china 2 department of Biochemistry,school of life sciences,fudan university,shanghai 200433,china 3 department of physiology and biophysics,school of life sciences,fudan university,shanghai 200433,china

Bacteriorhodopsin(BR)exhibits,as a membrane protein in Halobacterium salinarum,unique photoresponsive behaviors,and shows promise as a functional information material.A new mutant of BR with the 96th aspartic acid replaced by valine(BR-D96V)was obtained and then a composite film of BR-D96V in a synthetic polymer matrix was prepared in this *** mutant BR-D96V was expressed in a bacterio-opsin deficient halobacterial strain(L33)by gene *** valine is very hydrophobic,this point mutant keeps the basic biological activities,namely,photoelectric and photochromic ***,the lifetime of M intermediate in the BR mutant is nearly two orders of magnitude longer than that of wild-type BR in neutral aqueous solution,which benefits its potential application as an information *** M lifetime is further significantly prolonged after embedding BR-D96V into poly(vinyl alcohol)(PVA).It was also found that BR-D96V is very sensitive to water content in comparison with wild-type BR and another BR mutant.

关键词： synthetic polymer organic photoelectric material composite film bacteriorhodopsin site-specific mutagenesis photore-sponsive protein

Dynamics of Primary Events in the Photocycle of Excited Bacteriorhodopsin

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Acta Biochimica et Biophysica Sinica 2004年第11期36卷 724-728页

作者： Jun-Jun LU, Ming MING, Yi YANG, Jia WU, Bo LI, Jian-Dong DING, Qing-Guo LI, and Shi-Xiong QIANdepartment of Physics, fudan university, shanghai 200433, china department of Macromolecular Science, Key Laboratory of Molecular Engineering of Polymers, fudan university, shanghai 200433, china department of physiology and biophysics, school of life sciences, fudan university, shanghai 200433, china department of Physics Fudan UniversityShanghai 200433 China department of Macromolecular Science Key Laboratory of Molecular Engineering of Polymers Fudan UniversityShanghai 200433 China department of physiology and biophysics School of Life Sciences Fudan UniversityShanghai 200433 China

Transient dynamic behavior of the excited bacteriorhodopsin (BR), which was isolated from the strain H. salinarum, was studied at excitation wavelength from 585 to 639 nm. With the one-color femtosecond (fs) pump-probe technique, we revealed the primary events in BR's photocycle that took place in an ultrafast time scale. From the analysis of the decay components of the dynamical traces, it was evident that the isomerization of the retinal

关键词： bacteriorhodopsin transient dynamics primary events femtosecond laser pump-probe technique

Induction of Epstein-Barr Virus Lytic Replication by Recombinant Adenoviruses Expressing the Zebra Gene with EBV Specific Promoters

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Acta Biochimica et Biophysica Sinica 2005年第4期37卷 215-220页

作者： Lu CHEN Juan YIN Yi CHEN Jiang ZHONG department of Microbiology and Microbial Engineering,school of life sciences,fudan university,shanghai 200433,china department of Microbiology and Microbial Engineering School of Life Sciences Fudan University Shanghai 200433 China

The latent Epstein-Barr virus (EBV) is found in the cells of many *** example,EBVis detectable in almost all cases,and in almost all tumor cells,of non-keratinizing nasopharyngeal *** the latent virus,which will result in its lytic replication and the death of tumor cells,is a potentialapproach for the treatment of EBV-associated *** this study,three recombinant adenoviruses wereconstructed to express the Zebra gene,an EBV gene responsible for switching from the latent state to ***-specific promoters were used in order to limit Zebra expression in EBV-positive cells,andreduce the potential side *** EBV promoters used were Cp,Zp and a dual promoter combining *** Zebra protein was detected in HEK293 cells as well as the EBV-positive D98-HR1cells infected with recombinant *** EBV lyric replication early antigen,EA-D,was also detected ininfected D98-HR1,implying the initiation of lytic *** the cell viability assay,Zebra-expressingadenoviruses had little effect on EBV-negative HeLa cells,while significantly reducing the cell viability andproliferation of D98-HR1 *** results indicate that EBV virus promoters can be used in adenovirusvectors to express the Zebra gene and induce EBV lytic replication in D98-HR1 cells.

关键词： Epstein-Barr virus recombinant adenovirus lytic replication cancer

Proteomic dissection of biological pathways/processes through profiling protein-protein interaction networks

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Science china Chemistry 2010年第4期53卷 737-746页

作者： CHEN Xian Institutes for Biomedical sciences, fudan university, shanghai 200433, china department of Biochemistry & biophysics, school of Medicine, university of North Carolina-Chapel Hill, USA Institutes for Biomedical sciences Fudan University Shanghai China department of Biochemistry & biophysics School of Medicine University of North Carolina-Chapel Hill Chapel Hill USA

Cellular functions, either under the normal or pathological conditions or under different stresses, are the results of the coordinated action of multiple proteins interacting in macromolecular complexes or assemblies. The precise determination of the specific composition of protein complexes, especially using scalable and high-throughput methods, represents a systematic approach toward revealing particular cellular biological functions. In this regard, the direct profiling protein-protein interactions (PPIs) represent an efficient way to dissect functional pathways for revealing novel protein functions. In this review, we illustrate the technological evolution for the large-scale and precise identification of PPIs toward higher physiologically relevant accuracy. These techniques aim at improving the efficiency of complex pull-down, the signal specificity and accuracy in distinguishing specific PPIs, and the accuracy of identifying physiological relevant PPIs. A newly developed streamline proteomic approach for mapping the binary relationship of PPIs in a protein complex is introduced.

关键词： Chen Proteomic dissection of biological pathways/processes through profiling protein-protein interaction networks

Mass spectrometry analysis of melanoma related O-glycans in sera

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Science china Chemistry 2010年第4期53卷 807-811页

作者： BAI Chen1,4, WU Gang1 & ZHAO Liang2,3 1department of life Science, fudan university, shanghai 200433, china 2department of Chemistry, fudan university, shanghai 200433, china 3Institutes of Biomedical sciences, fudan university, shanghai 200433, china 4department of Food Science, shanghai Business school, shanghai 200235, china department of life Science Fudan University Shanghai China department of Food Science Shanghai Business School Shanghai China department of Chemistry Fudan University Shanghai China Institutes of Biomedical sciences Fudan University Shanghai China

Glycomics comparison was carried out by screening melanoma serum biomarkers between C57 mice with and without B16 implanted. O-glycans were released from 10 μL sera by β-elimination, purified by Graphitized Carbon Cartridge Solid Phase Extraction (GCC-SPE) and analyzed by MALDI-QIT-TOF-MS. MS raw data were acquired and exported by Launchpad software. MATLAB was then applied for further data analysis. 10 Glycans were considered to have stable changes after B16 implantation and 5 of them were under structural analysis via MS/MS.

关键词： mass spectrometry glycomics melanoma biomarkers

Regulation of swelling-activated chloride channels in embryonic chick heart cells

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Cell Research 2003年第1期13卷 21-28页

作者： HUA WEI, VAN AI MEI, JIA TING SUN, HAN QING ZHOU, ZHI HONG ZHANGdepartment of physiology and biophysics, Liren Laboratory, school of life sciences, fudan university, shanghai 200433, china Fishery College, shanghai Fisheries university, shanghai 200090, china department of physiology and biophysics Liren Laboratory School of Life Sciences Fudan University Shanghai China Fishery College Shanghai Fisheries University Shanghai China

Swelling-activated Cl- currents, I(ci,swell), were measured during hyposmotic shock in white Leghorn embryonic chick heart cells using the whole-cell recording of patch-clamp technique. Genistein, an inhibitor of protein tyrosine kinase (PTK), suppressed I(ci,swell), Under isosmotic condition phorbol 12-myristate 13-acetate (PMA), an activator of PKC, elicited the Cl~ current similar to that in hyposmotic solution, whereas hyposmotic shock did not elicit I(ci,swell) in chelerythrine chloride(an inhibitor of PKC)-treated cells. Con-focal microscopy experiments using FITC-phalloidin as a fluorescent label of F-actin showed that the actin network was moved from cortical region of the cell to the center after hyposmotic shock as compared with the image under isosmotic condition. When the cells were treated with cytochalasin B (CB) or cytochalasin D (CD) under isosmotic condition the disruption of the F-actin integrity was observed, and I(ci,Sweii) was not elicited. With combination treatment of CB with PMA,

关键词： swelling activation myocardium chloride current F-actin phosphorylation.

Approximate solutions to infinite dimensional LQ problems over infinite time horizon

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Science china Mathematics 2006年第7期49卷 865-876页

作者： PAN Liping, ZHANG Xu & CHEN Qihong school of Mathematical sciences, fudan university, shanghai 200433, china school of Mathematics, Sichuan university, Chengdu 610064, china department of Applied Mathematics, shanghai university of Finance & Economics, shanghai 200433, china school of Mathematical sciences Fudan University Shanghai China school of Mathematics Sichuan University Chengdu China department of Applied Mathematics Shanghai University of Finance & Economics Shanghai China

This paper is addressed to develop an approximate method to solve a class of infinite dimensional LQ optimal regulator problems over infinite time horizon. Our algorithm is based on a construction of approximate solutions which solve some finite dimensional LQ optimal regulator problems over finite time horizon, and it is shown that these approximate solutions converge strongly to the desired solution in the double limit sense.

关键词： approximate solution LQ problem infinite dimensional infinite time hori-

Modern thermodynamics-New concepts based on the second law of thermodynamics

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Progress in Natural Science:Materials International 2009年第1期19卷 125-135页

作者： Jitao Wang department of Microelectronics,fudan university,shanghai 200433,china department of Microelectronics Fudan University Shanghai 200433 China

Thermodynamics is a core part of *** all scientists should have a basic knowledge of *** is a science of development,and is a viewpoint of scientific development in natural *** of thermodynamics has influence not only on natural sciences,but also on social sciences and *** concepts and definitions are very important for any discipline of science,so what is classical thermodynamics and what is modern thermodynamics have become the key points of puzzledom in *** this paper,after clarification of fundamental concept in thermodynamics,a complete basic modern classification of thermodynamics is naturally *** is suggested that extended Carnot theorem and dissipation decrease theorem,together with the laws of thermodynamics,are the most fundamental theorems in thermodynamics *** thermodynamics is a new field besides equilibrium thermodynamics belonging to the equal part of the second law of thermodynamics.

关键词： Modern thermodynamics Second law of thermodynamics Thermodynamic coupling Spiral reactions Chemical oscillation Low-pressure diamond growth

A NONLOCAL NONLINEAR BOUNDARYVALUE PROBLEM FOR THE HEAT EQUATIONS

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Chinese Annals of Mathematics,Series B 1996年第3期17卷 365-374页

作者： YAN JINHAI(department of Mathematics, fudan university, shanghai 200433, china) department of Mathematics Fudan University Shanghai 200433 China

The existence and limit behaviour of the solution for a kind of nonlocal nonlinear boundaryvalue condition on a part of the boundary is studied for the heat equation, which physicallymeans that the potential is the function of the total flux. When this part of boundary shrinksto a point in a certain wayt this condition either results in a Dirac measure or simply disappearsin the corresponding problem.

关键词： Heat equation Nonlinear boundary problem Potential Limit behavior

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 200433, china shanghai Center for Bioinformation 1 Technology, shanghai 200235, china school of life sciences, fudan university, shanghai 200433, 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 200433 China shanghai Center for Bioinformation Technology shanghai 200235 China school of life sciences Fudan University Shanghai 200433 China Bioinformation Center of shanghai Institutes for Biological sciences the Chinese Academy of Sciences Shanghai 200031 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