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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 univer.ity, shanghai 200433, china 1. Department of Chemistry and institutes of biomedical sciences Fudan University Shanghai 200433 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 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

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 univer.ity,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 univer.ity Medical Center,Nashville,TN 37232,USA 4 institutes of biomedical sciences,fudan univer.ity,shanghai 2.0032.china 1. Bio-X Center Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) Shanghai Jiao Tong University Shanghai 200030 China2. Institutes for Nutritional Sciences Shanghai Institute of Biological Sciences Chinese Academy of Sciences Shanghai 200031 China3. Departments of Biomedical Informatics Psychiatry and Cancer Biology Vanderbilt University Medical Center Nashville TN 37232 USA4. Institutes of Biomedical Sciences Fudan University Shanghai 200032 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

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

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

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 univer.ity,shanghai 200240,china 1. Institute of Neuroscience Shanghai Institutes for Biological Sciences State Key Laboratory of Neurobiology Chinese Academy of Sciences Shanghai 200031 China2. Department of Biomedical Engineering Shanghai Jiaotong University Shanghai 200240 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

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 univer.ity,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 univer.ity,shanghai 200092,china 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

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

Biomarkers of neurodegenerative disorders: How good are they?

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Cell Research 2004年第5期14卷 347-358页

作者： Varun RACHAKONDA Department of Neurology Baylor College of Medicine Houston TX USA

Biomarkers are very important indicators of normal and abnormal biological processes. Specific changes in pathologies, biochemistries and genetics can give us comprehensive information regarding the nature of any particular disease. A good biomarker should be precise and reliable, distinguishable between normal and interested disease, and differential between different diseases. It is believed that biomarkers have great potential in predicting chances for diseases, aiding in early diagnosis, and setting standards for the development of new remedies to treat diseases. New technologies have enabled scientists to identify biomarkers of several different neurodegenerative diseases. The followings, for instance, are only a few of the many new biomarkers that have been recently identified: the phosphorylated tau protein and aggregated β-amyloid peptide for Alzheimer’s disease (AD), α-synuclein contained Lewy bodies and altered dopamine transporter (DAT) imaging for Parkinson’s disease (PD), SOD mutations for familial amyotrophic lateral sclerosis (ALS), and CAG repeats resulted from Huntington’s gene mutations in Huntington’s disease (HD). This article will focus on the most-recent findings of biomarkers belonging to the four mentioned neurodegenerative diseases.

关键词： Alzheimer’s disease Parkinson’s disease Amyotrophic Lateral Sclerosis Huntington’s disease biomarkers.

DNA羟甲基化在小鼠胚胎干细胞中的研究进展

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生物化学与生物物理进展 2011年第7期38卷 611-614页

作者：谭理复旦大学生物医学研究院表观遗传学实验室上海200032

简要总结DNA羟甲基化在小鼠胚胎干细胞(mouse embryonic stem cells,mESC)中的最新研究进展.DNA甲基化(DNAmethylation)影响染色质的结构与功能,在发育与疾病发生过程中具有重要作用.2009年Tahiliani等发现TET1可以催化甲基化胞嘧啶(5-m... 详细信息

简要总结DNA羟甲基化在小鼠胚胎干细胞(mouse embryonic stem cells,mESC)中的最新研究进展.DNA甲基化(DNAmethylation)影响染色质的结构与功能,在发育与疾病发生过程中具有重要作用.2009年Tahiliani等发现TET1可以催化甲基化胞嘧啶(5-methylcytosine,5mC)氧化为羟甲基化胞嘧啶(5-hydroxymethylcytosine,5hmC).DNA羟甲基化(DNAhydroxymethylation)被认为是调节DNA甲基化的一种重要方式,成为了表观遗传学的研究热点之一.

关键词：小鼠胚胎干细胞 DNA羟甲基化 Tet1