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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 univer.ity, shanghai 200433, china 2Department of Chemistry, fudan univer.ity, shanghai 200433, china 3institutes of biomedical sciences, fudan univer.ity, 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

Metalloproteins/metalloenzymes for the synthesis of acetyl-CoA in the Wood-Ljungdahl pathway

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Science china Chemistry 2009年第12期52卷 2071-2082页

作者： ZHU XiaoFei1 & TAN XiangShi1,2 1 Department of Chemistry,fudan univer.ity,shanghai 200433,china 2 institutes of biomedical sciences,fudan univer.ity,shanghai 200433,china 1. Department of Chemistry Fudan University Shanghai 200433 China 2. institutes of biomedical sciences Fudan University Shanghai 200433 China

This paper focuses on the group of metalloproteins/metalloenzymes in the acetyl-coenzyme A synthesis pathway of anaerobic microbes called Wood-Ljungdahl pathway,including formate dehydrogenase (FDH),corrinoid iron sulfur protein (CoFeSP),acetyl-CoA synthase (ACS) and CO dehydrogenase (CODH). FDH,a key metalloenzyme involved in the conversion of carbon dioxide to methyltetrahydrofolate,catalyzes the reversible oxidation of formate to carbon dioxide. CoFeSP,as a methyl group transformer,accepts the methyl group from CH3-H4 folate and then transfers it to ACS. CODH reversibly catalyzes the reduction of CO2 to CO and ACS functions for acetyl-coenzyme A synthesis through condensation of the methyl group,CO and coenzyme A,to finish the whole pathway. This paper introduces the structure,function and reaction mechanisms of these enzymes.

关键词： Wood-Ljungdahl pathway formate dehydrogenase corrinoid iron sulfur protein acetyl-CoA synthase CO dehydrogenase

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 univer.ity, shanghai 200433, china Department of Biochemistry & Biophysics, School of Medicine, univer.ity of North Carolina-Chapel Hill, USA 1. institutes for biomedical sciences Fudan University Shanghai 200433 China2. 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

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 univer.ity, shanghai 200433, china shanghai Center for Bioinformation 1 Technology, shanghai 200235, china School of Life sciences, fudan univer.ity, 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 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

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 univer.ity, 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

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 univer.ity,shanghai 200433,china Institute of Computational Mathematics,Chinese Academy of sciences,Beijing 100080,china 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

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 univer.ity, 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

THE MODULI SPACE OF COMPLEX LAGRANGIAN SUBMANIFOLDS IN THE HYPER-KAEHLER MANIFOLD

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Chinese Annals of Mathematics,Series B 1999年第4期20卷 393-400页

作者： FU JIXIANG(Institute of Mathematics, fudan univer.ity, shanghai 200433, china) fudan Univ Inst Math Shanghai 200433 Peoples R China

The deformation of a compact complex Lagrangian submanifold in a hyper-Kaehler manifold and the moduli space are studied. It is proved that the moduli space Mc1 is a special Kaehler manifold, where special means that there is a real flat torsionfree symplectic connection satisfying dI = 0 (I is a complex structure of Mcl). Thus, following [4], one knows thatT*Mcl is a hyper-Kaehler manifold and then that Mcl is a complex Lagrangian submanifold in T* Mcl.

关键词： Moduli space Complex Lagrangian submanifold Hyper-Kaehler manifold Special Lagrangian submanifold Special Kaehler manifold Deformation

THE OCCUPATION DENSity FIELD FOR THE CATALYTIC SUPER-BROWNIAN MOTION

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Chinese Annals of Mathematics,Series B 1999年第4期20卷 447-454页

作者： HONG WENMING(Institute of Mathematics, fudan univer.ity shanghai 200433, china) fudan Univ Inst Math Shanghai 200433 Peoples R China

It is proved that the occupation time of the catalytic super-Brownian motion is absolutely continuous for d = 1, and the occupation density field is jointly continuous and jointly Holder continuous.

关键词： Branching rate functional Brownian collision local time Catalytic super-Brownian motion Occupation time Occupation density field