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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 100052, 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,{16., shanghai 200433, 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 42 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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The fundamental solution of the Keldysh typeoperator

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Science china Mathematics 2009年第9期52卷 1829-1843页

作者： CHEN ShuXing school of Mathematical sciences, fudan university, shanghai 200433, china 1. school of Mathematical sciences Fudan University Shanghai 200433 China

In this paper we discuss the fundamental solution of the Keldysh type operator $ L_\alpha u \triangleq \frac{{\partial ^2 u}} {{\partial x^2 }} + y\frac{{\partial ^2 u}} {{\partial y^2 }} + \alpha \frac{{\partial u}} {{\partial y}} $ , which is a basic mixed type operator different from the Tricomi operator. The fundamental solution of the Keldysh type operator with $ \alpha > - \frac{1} {2} $ is obtained. It is shown that the fundamental solution for such an operator generally has stronger singularity than that for the Tricomi operator. Particularly, the fundamental solution of the Keldysh type operator with $ \alpha < \frac{1} {2} $ has to be defined by using the finite part of divergent integrals in the theory of distributions.

关键词： mixed type equation Keldysh operator fundamental solution finite part of divergent integral 35M10 35A08

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Local Existence of Smooth Solutions to the FENE Dumbbell Model

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Chinese Annals of Mathematics,Series B 2012年第4期33卷 501-520页

作者： Ge YANG11school of Mathematical sciences, fudan university, shanghai 200433, china. school of Mathematical sciences Fudan University Shanghai 200433 China

The author proves the local existence of smooth solutions to the finite extensible nonlinear elasticity (FENE) dumbbell model of polymeric flows in some weighted spaces if the non-dimensional parameter b > 2.

关键词： Fokker-Planck equation FENE model Degenerate parabolic equations Regularity

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RADIAL BASIS FUNCTION INTERPOLATION IN SOBOLEV SPACES AND ITS APPLICATIONS

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Journal of Computational Mathematics 2007年第2期25卷 201-210页

作者： Manping Zhang (school of Mathematical sciences,fudan university,shanghai 200433,{6. Institute of Computational Mathematics,Chinese Academy of sciences,Beijing 100080,{6. school of Mathematical sciences Fudan University Shanghai 200433 China Institute of Computational Mathematics Chinese Academy of Sciences Beijing 100080 China

In this paper we study the method of interpolation by radial basis functions and give some error estimates in Sobolev space H^k（Ω）（k 〉 1）. With a special kind of radial basis function, we construct a basis in H^k（Ω） and derive a meshless method for solving elliptic partial differential equations. We also propose a method for computing the global data density.

关键词： Sobolev space Radial basis function Global data density Meshless method

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Hyperbolic positive mass theorem under modified energy condition

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Science china Mathematics 2008年第12期51卷 2189-2197页

作者： XIE NaQing Institute of Mathematics, school of Mathematical sciences, fudan university, shanghai 200433, china Institute of Mathematics School of Mathematical Sciences Fudan University Shanghai 200433 China

We provide two new positive mass theorems under respective modified energy conditions allowing T00 negative on some compact set for certain modified asymptotically hyperbolic manifolds. This work is analogous to Zhang... 详细信息

关键词： positive mass theorem modified energy condition modified asymptotically hyperbolic 83C40 53C27

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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, {6. of life sciences, fudan university, shanghai 200433, china Department of Physics Fudan University Shanghai 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 6.9 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

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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 {6., Chengdu 6.006., china Department of Applied Mathematics, shanghai {6. of Finance & Economics, shanghai 200433, china 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

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-

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Global Existence of Classical Solutions for Some Oldroyd-B Model via the Incompressible Limit

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Chinese Annals of Mathematics,Series B 2006年第5期27卷 565-580页

作者： Zhen LEI school of Mathematical sciences, fudan university, shanghai 200433, china school of Mathematics and Statistics, Northeast Normal {6., Changchun 130024, china. school of Mathematical sciences Fudan University Shanghai 200433 China school of Mathematics Statistics Northeast Normal University Changchun 130024 China

In this paper, we prove local and global existence of classical solutions for a system of equations concerning an incompressible viscoelastic fluid of Oldroyd-B type via the incompressible limit when the initial data ... 详细信息

关键词： Incompressible limit Global existence Oldroyd model

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Invariant tori for asymptotically linear impact oscillators

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Science china Mathematics 2006年第5期49卷 669-687页

作者： QIAN Dingbian & SUN Xiying school of Mathematical sciences, Suzhou university, Suzhou 215006. china Laboratory of Mathematics for Nonlinear sciences, fudan university,{6., china school of Mathematical sciences Suzhou University Suzhou 215006 China Laboratory of Mathematics for Nonlinear sciences Fudan University Shanghai 200433 China

The existence of invariant tori and quasi-periodic solutions for asymptotically linear impact oscillators is proved by using the successor map and some generalized versions of the Moser's twist theorem.

关键词： invariant tori, boundedness of solutions, quasi-periodic solution, impact oscillator.

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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 1. Department of life Science Fudan University Shanghai 200433 China4. Department of Food Science Shanghai Business School Shanghai 200235 China2. Department of Chemistry Fudan University Shanghai 200433 China3. Institutes of Biomedical Sciences Fudan University Shanghai 200433 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

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