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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 {2., fudan University, shanghai 200433, china Department of Chemistry and institutes of biomedical {2. 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

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, {2. 2.epartment of Chemistry, fudan University, shanghai 200433, {2. 3institutes of biomedical sciences, fudan University, shanghai 200433, {2. 4Department of Food Science, {12. Business School, {12. 2.02.5, {2. 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 {2. 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

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 {2., fudan University, shanghai 200433, china Department of Biochemistry & Biophysics, School of Medicine, University of North Carolina-Chapel Hill, USA institutes for biomedical {2. 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

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, {2. shanghai Center for Bioinformation 1 Technology, shanghai 2.02.5, {2. School of Life sciences, fudan University, shanghai 200433, {2. Bioinformation Center of shanghai institutes for Biological sciences, the Chinese Academy of sciences, shanghai 2.0031, {2. Department of Computing and Information Technology Fudan University Shanghai 200433 China shanghai Center for Bioinformation Technology shanghai 2.02.5 China School of Life sciences Fudan University Shanghai 200433 China Bioinformation Center of shanghai institutes for Biological {2. 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 DB2.O 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 2.0030,{2. 2.institutes for Nutritional sciences,shanghai Institute of Biological sciences,Chinese Academy of sciences,shanghai 2.0031,{2. 3 Departments of biomedical Informatics,Psychiatry,and Cancer Biology,Vanderbilt University Medical Center,Nashville,TN 372.2.USA 4 institutes of biomedical sciences,fudan University,shanghai 2.0032.{2. 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 {2. 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,{2.,china 2.Bioinformatics Center,Key Lab of Systems Biology,shanghai institutes for Biological sciences,Chinese Academy of sciences,shanghai 2.0031,china 3 shanghai Center for Bioinformation Technology,shanghai 2.02.5,china 4 School of Life sciences,Tongji University,shanghai 2.0092.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 {2.,State Key Laboratory of Neurobiology,Chinese Academy of {2.,shanghai 2.0031,china 2.epartment of biomedical Engineering,shanghai Jiaotong University,shanghai 2.02.0,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-12.40 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) ~2.aboratory of Molecular Cell Biology shanghai institutes for Biological {2.,Chinese Academy of {2.,Graduate School of the Chinese Academy of {2.,shanghai 2.0031,china ~3the Huashan Hospital of fudan University,shanghai 2.0040,china ~4E-institutes of shanghai Universities Immunology Division,shanghai 2.002..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-12.40 plays a crucial role in regulating islet al-lograft rejection in a streptozotocin(STZ)-induced diabetes mouse ***:C57BL/6 and IL-12.40 gene knockout mice were selected as recipient mice,towhich the diabetes was induced with a treatment of STZ(150-2.0 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-12.40-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-2. arenot essential to induce islet allograft rejection.

关键词： Th1 cells Th2.cells islets of Langerhans transplantation homologous transplantation IL-12.40-deficient mice

Inhibition of Tumor Growth in Mice by Endostatin Derived from Abdominal Transplanted Encapsulated Cells

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Acta Biochimica et Biophysica Sinica 2007年第4期39卷 278-284页

作者： Huaining TENG~(1.3) Ying ZHANG~2.Wei WANG~2.Xiaojun MA~2. Jian FEI~1* 1 Laboratory of Molecular Cell Biology,Institute of Biochemistry and Cell Biology,Model Organism Research Center,shanghai institutes for Biological {2.,Chinese Academy of {2.,shanghai 2.0031,china 2.Laboratory of biomedical Material Engineering,Dalian Institute of Chemical Physics,Chinese Academy of {2.,Dolian 11602.,china 3 Department of Urology,Changzheng Hospital,Second Military Medical University,shanghai 2.0003,china Laboratory of Molecular Cell Biology Institute of Biochemistry and Cell Biology Model Organism Research Center Shanghai Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200031 China Department of Urology Changzheng Hospital Second Military Medical UniversityShanghai 200003 China Laboratory of biomedical Material Engineering Dalian Institute of Chemical Physics Chinese Academy of SciencesDalian 116023 China

Endostatin,a C-terminal fragment of collagen 18a,inhibits the growth of established tumorsand metastases in vivo by inhibiting ***,the purification procedures required for large-scale production and the attendant cost of these processes,together with the low effectiveness in clinicaltests,suggest that alternative delivery methods might be required for efficient therapeutic use of *** the present study,we transfected Chinese hamster ovary(CHO)cells with a human endostatin geneexpression vector and encapsulated the CHO cells in alginate-poly-L-lysine *** release ofbiologically active endostatin was confirmed using the chicken chorioallantoic membrane *** encap-sulated endostatin-expressing CHO cells can inhibit the growth of primary tumors in a subcutaneous B 16tumor model when injected into the abdominal cavity of *** results widen the clinical applicationof the microencapsulated cell endostatin delivery system in cancer treatment.

关键词： microencapsulation endostatin CHO tumor gene therapy