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Recent developments of nanoparticle-based enrichment methods for mass spectrometric analysis in proteomics

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Science china Chemistry 2010年第4期53卷 695-703页

作者： ZHANG LiJuan, LU HaoJie & YANG PengYuan Department of Chemistry and institutes of biomedical sciences, fudan university, shanghai 200433, china Department of Chemistry and institutes of biomedical sciences Fudan University Shanghai China

In proteome research, rapid and effective separation strategies are essential for successful protein identification due to the broad dynamic range of proteins in biological samples. Some important proteins are often expressed in ultra low abundance, thus making the pre-concentration procedure before mass spectrometric analysis prerequisite. The main purpose of enrichment is to isolate target molecules from complex mixtures to reduce sample complexity and facilitate the subsequent analyzing steps. The introduction of nanoparticles into this field has accelerated the development of enrichment methods. In this review, we mainly focus on recent developments of using different nanomaterials for pre-concentration of low-abundance peptides/ proteins, including those containing post-translational modifications, such as phosphorylation and glycosylation, prior to mass spectrometric analysis.

关键词： enrichment nanoparticles mass spectrometry proteomics phosphorylation glycosylation

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

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

A meta-analysis of oxidative stress markers in schizophrenia

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中国科学：生命科学英文版 2010年第1期53卷 112-124页

作者： ZHANG Ming1,2,ZHAO ZhongMing3,HE Lin1,2,4 & WAN ChunLing1,2 1 Bio-X Center,Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders(Ministry of Education),shanghai Jiao Tong university,shanghai 200030,china 2 institutes for Nutritional sciences,shanghai Institute of Biological sciences,Chinese Academy of sciences,shanghai 200031,china 3 Departments of biomedical Informatics,Psychiatry,and Cancer Biology,Vanderbilt university Medical Center,Nashville,TN 37232,USA 4 institutes of biomedical sciences,fudan university,shanghai 200032,china Bio-X Center Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) Shanghai Jiao Tong University Shanghai China institutes for Nutritional sciences Shanghai Institute of Biological Sciences Chinese Academy of Sciences Shanghai China Departments of biomedical Informatics Psychiatry and Cancer Biology Vanderbilt University Medical Center Nashville USA institutes of biomedical sciences Fudan University Shanghai China

Oxidative stress has been identified as a possible element in the neuropathological processes of schizophrenia(SCZ).Alteration of oxidative stress markers has been reported in SCZ studies,but with inconsistent *** evaluate the risk of oxidative stress to schizophrenia,a meta-analysis was conducted,including five markers of oxidative stress [thiobarbituric reactive substances(TBARS),nitric oxide(NO),catalase(CAT),glutathione peroxidase(GP) and superoxide dismutase(SOD)] in SCZ patients versus healthy *** study showed that TBARS and NO significantly increased in SCZ,while SOD activity significantly decreased in the disorganized type of SCZ *** significant effect size was found for the activities of GP and CAT in SCZ patients(P>0.05).Egger’s regression test observed no significant publication bias across the oxidative stress markers,but found high heterogeneities in all the 5 *** subgroup analysis suggested that the ethnicity,sample size of patients and sample sources may contribute to the heterogeneity of the results for TBARS,NO and *** result further demonstrated the involvement of oxidative stress in the pathophysiology of schizophrenia.

关键词： schizophrenia oxidative stress meta-analysis lipid peroxidation nitric oxide antioxidant enzymes

The contribution of cis-regulatory elements to head-to-head gene pairs' co-expression pattern

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Science china(Life sciences) 2009年第1期52卷 74-79页

作者： HAO Pei1,2,YU Yao2,3,ZHANG XiaoYan4,TU Kang2,FAN HaiWei2 & ZHONG Yang1 1 School of Life sciences,fudan university,shanghai 200433,china 2 Bioinformatics Center,Key Lab of Systems Biology,shanghai institutes for Biological sciences,Chinese Academy of sciences,shanghai 200031,china 3 shanghai Center for Bioinformation Technology,shanghai 200235,china 4 School of Life sciences,Tongji university,shanghai 200092,china School of Life sciences Fudan University Shanghai China Bioinformatics Center Key Lab of Systems Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China shanghai Center for Bioinformation Technology Shanghai China School of Life sciences Tongji University Shanghai China

Transcription regulation is one of the most critical pipelines in biological process,in which cis-elements play the role as gene expression *** attempt to deduce the principles underlying the co-expression of "head-to-head" gene pairs by analyzing activities or behaviors of the shared cis-elements.A network component analysis was performed to estimate the impact of cis-elements on gene promoters and their activities under different *** discoveries reveal how biological system uses those regulatory elements to control the expression pattern of "head-to-head" gene pairs and the whole transcription regulation system.

关键词： transcription regulation cis-elements "head-to-head" gene pairs

Computational neuroscience in china

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Science china(Life sciences) 2010年第3期53卷 385-397页

作者： WU Si1 & LIANG PeiJi2 1Institute of Neuroscience,shanghai institutes for Biological sciences,State Key Laboratory of Neurobiology,Chinese Academy of sciences,shanghai 200031,china 2Department of biomedical Engineering,shanghai Jiaotong university,shanghai 200240,china Institute of Neuroscience Shanghai Institutes for Biological Sciences State Key Laboratory of Neurobiology Chinese Academy of Sciences Shanghai China Department of biomedical Engineering Shanghai Jiaotong University Shanghai China

The ultimate goal of Computational Neuroscience(CNS) is to use and develop mathematical models and approaches to elucidate brain *** is a young and highly multidisciplinary *** heavily interacts with experimental neuroscience and such other research areas as artificial intelligence,robotics,computer vision,information science and machine *** paper reviews the history of CNS in china,its current status and the prospects for its future *** of CNS research in china are also presented.

关键词： computational neuroscience experimental neuroscience artificial intelligence

IL-12p40 is not required for islet allograft rejection

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Acta Pharmacologica Sinica 2006年第8期27卷 1065-1070页

作者： En-guang BI~(2,5) Wei SHI~(3,5) Jia ZOU~2 Zhen-hua HAO~3 Zhen-hu LI~2 Duan CAI~3 Hua-qun ZHANG~3 Bing SUN~(2,4,6) ~2Laboratory of Molecular Cell Biology shanghai institutes for Biological sciences,Chinese Academy of sciences,Graduate School of the Chinese Academy of sciences,shanghai 200031,china ~3the Huashan Hospital of fudan university,shanghai 200040,china ~4E-institutes of shanghai Universities Immunology Division,shanghai 200025.china Laboratory of Molecular Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of Sciences Shanghai China the Huashan Hospital of fudan university Shanghai China E-institutes of shanghai Universities Immunology Division Shanghai China

Aim:To investigate whether IL-12p40 plays a crucial role in regulating islet al-lograft rejection in a streptozotocin(STZ)-induced diabetes mouse ***:C57BL/6 and IL-12p40 gene knockout mice were selected as recipient mice,towhich the diabetes was induced with a treatment of STZ(150-200 mg/kg)by asingle ip ***/c mice were selected as donor mice and islet cells wereisolated from the *** 500 islets were transplanted into recipient mice be-neath the capsule of the left *** the islet transplantation the glu-cose from the mice sera was monitored and the rejection rate of islets was ***:STZ could induce diabetes in the recipient mice within 1 *** of allograft islets,the increased glucose in wild-type(WT)micereturned to normal level and was maintained for 10 ***,the rejectionrate of islet allograft between IL-12p40-deficient mice and WT mice was ***:The results suggested that,although islet allograft rejection is be-lieved to be Th1-cell predominant,the Th1 response inducer,IL-12 and IL-23 arenot essential to induce islet allograft rejection.

关键词： Th1 cells Th2 cells islets of Langerhans transplantation homologous transplantation IL-12p40-deficient mice

Identification and Characterization of glnA Promoter and its Corresponding Trans-regulatory Protein GlnR in the Rifamycin SV Producing Actinomycete,Amycolatopsis mediterranei U32

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Acta Biochimica et Biophysica Sinica 2006年第12期38卷 831-843页

作者： Hao YU~(1&) Wen-Tao PENG~1 Yang LIU~1 Ting WU~2 Yu-Feng YAO~1 Ming-Xue CUI~1 Wei-Hong JIANG~1 Guo-Ping ZHAO~(1,3,4*) 1 Laboratory of Molecular Microbiology,Institute of Plant Physiology and Ecology,shanghai institutes for Biological sciences,Chinese Academy of sciences,shanghai 200032,china 2 Department of Medicinal Chemistry,School of Pharmacy,fudan university,shanghai 200032,china 3 State Key Laboratory of Genetic Engineering & Department of Microbiology,School of Life Science,fudan university,shanghai 200433,china 4 Laboratory of Disease and Health Genomics,Chinese National Human Genome Center at shanghai,shanghai 201203,china Laboratory of Molecular Microbiology Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200032 China Department of Medicinal Chemistry School of Pharmacy Fudan University Shanghai 200032 China State Key Laboratory of Genetic Engineering & Department of Microbiology School of Life Science Fudan University Shanghai 200433 China Laboratory of Disease and Health Genomics Chinese National Human Genome Center at Shanghai Shanghai 201203 China

The genetic requirements for the transcription of glnA,encoding the major glutaminesynthetase in a rifamycin SV-producing Amycolatopsis mediterranei strain,U32,were *** experiments showed that the promoter of U32 glnA （pglnA） was likely to have two transcriptioninitiation sites:P1and P2,located 157 and 45 nucleotides （nt） upstream of the translational start codon,*** mobility shift and DNase I footprinting analyses revealed a 30 bp cis-element locatedat 45 to 75 nt downstream of P1,or 38 to 68 nt upstream of *** sequence of the cis-element displayedhigh similarity to the corresponding regions of pglnA from Streptomyces coelicolor and *** as a reporter gene,the expression levels of U32 pglnA and its deletion derivatives under differentnitrogen-source conditions were analyzed by detecting the catechol dioxygenase activities in ***54,*** J508 and *** FS10 （glnR mutant）.These in vivo studies showed that theactivation of U32 pglnA in *** required GlnR,and its binding to the U32 pglnA was furtherconfirmed by the gel mobility shift *** and heterologous expression of the U32 glnR allowed usto detect the in vitro interaction between the U32 GlnR and the corresponding pglnA *** shown by in vivo glnR inactivation and complementation indicated that GlnR is essential for theactive transcription of glnA in U32.

关键词： glnA promoter cis-element glnR Amycolatopsis mediterranei