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Energy Metabolism Disorder and Myocardial Injury in Chronic Myocardial Ischemia with Qi Deficiency and Blood Stasis Syndrome Based on 2-DE proteomics

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Chinese Journal of Integrative Medicine 2013年第8期19卷 616-620页

作者： Yong Wang 王勇 (11230) Wen-jing Chuo 啜文静 (11230) Chun Li 李春 (11230) Shu-zhen Guo 郭淑贞 (11230) Jian-xin Chen 陈建新 (11230) Jun-da Yu 余俊达 (11230) Wei Wang 王伟 (11230) 11230. Beijing University of Chinese Medicine Beijing 100029 China

Objective： To inquire the characteristic proteins in chronic myocardial ischemia by testing twodimensional electrophoresis （2-DE） map to explore the possible inherent pathological mechanism and the therapeutic intervention of qi deficiency and blood stasis syndrome. Methods： Ameroid constrictor ring was placed on the first interval of left anterior descending coronary artery to prepare chronic myocardial ischemia model on Chinese miniature swine. Animals were randomly divided into sham group and model group with 10 animals in each group, respectively. The dynamic symptoms observation of the four diagnostic information was collected from 0 to 12 weeks. Echocardiography was employed to evaluate cardiac function and the degree of myocardial ischemia, 2-DE and matrix-assisted laser desorption/ionization-time of flight mass spectrometry （MALDI-TOF-MS） were used to carry out proteomics research on animals. Enzyme-linked immunosorbent assay was applied to identify the relevant differential proteins on chronic myocardial ischemia with qi deficiency and blood stasis syndrome. Results： The preliminary study found that at the 12th week, chronic myocardial ischemia with qi deficiency and blood stasis syndrome model was established stably. Compared with the sham group, there were 8 different proteins down-regulated, 22 proteins up-regulated significantly. After validated by MALDI- TOF-MS/MS, 11 protein spots were identified. Distinct proteins were mainly associated with energy metabolism and myocardial structural injury, including isocitrate dehydrogenase 3 （NAD＋） alpha, NADH dehydrogenase （NAD） Fe-S protein 1, chain A （crystal structure of aidose reductase by binding domain reveals a new Nadph）, heat shock protein 27 （HSP27）, oxidoreductase （NAD-binding protein）, antioxidant protein isoform, cardiac troponin T （cTnT）, myosin （myosin light polypeptide）, cardiac alpha tropomyosin, apolipoprotein A- I and albumin. Conclusion： Down-regulated energy metabolism disorder mediated by NADH respiratory chain and myocardial injury may

关键词： chronic myocardial ischemia Chinese medicine qi deficiency and blood stasis syndrome proteomics

Mass spectrometry-based proteomics and peptidomics for systems biology and biomarker discovery

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Frontiers in Biology 2012年第4期7卷 313-335页

作者： Robert CUNNINGHAM Di MA Lingjun LI Department of Chemistry University of Wisconsin-Madison 777 Highland Avenue 1101 University Avenue Madison WI 53706 USA School of Pharmacy University of Wisconsin-Madison 777 Highland Avenue Madison WI 53 705-2222 USA

The scientific community has shown great interest in the field of mass spectrometry-based proteomics and peptidomics for its applications in biology. proteomics technologies have evolved to produce large data sets of proteins or peptides involved in various biologic and disease progression processes generating testable hypothesis for complex biologic questions. This review provides an introduction to relevant topics in proteomics and peptidomics including biologic material selection, sample preparation, separation techniques, peptide fragmentation, post-translational modifications, quantification, bioinformatics, and biomarker discovery and validation. In addition, current literature, remaining challenges, and emerging technologies for proteomics and peptidomics are presented.

关键词： mass spectrometry proteomics peptidomics review post-translational modifications fragmentation separation,protein quantitation sample preparation biomarker discovery validation bioinforrnatics

Comparative proteomics analysis of lanthanum citrate complex-induced apoptosis in HeLa cells

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Science China Chemistry 2009年第11期52卷 1814-1820页

作者： SHEN LiMing LIU Qiong NI JiaZuan College of Life Sciences Shenzhen UniversityShenzhen 518060China

In a previous study,the lanthanum citrate complex([LaCit2]3-) has been found to induce apoptosis in the human HeLa cervical cancer cell line.To clarify the mechanism,we carried out comparative proteomics analysis between treated and control cells.Differentially expressed proteins were separated electrophoretically and identified by MALDI-TOF/TOF tandem mass spectrometry.There were profound changes in 14 proteins related to mitochondrial function and oxidative stress,suggesting that mitochondrial dysfunction plays a key role in [LaCit2]3--induced apoptosis.This was confirmed by a decrease in the mitochondrial transmembrane potential,and increases in cytochrome c release and reactive oxygen species generation in [LaCit2]3--treated cells.Western blotting analyses show that [LaCit2]3--induced apoptosis was accompanied by the activation of caspase-9 and the specific proteolytic cleavage of PARP,leading to an increase in the proapoptotic protein Bax and a decrease in the antiapoptotic protein Bcl-2.These results suggest that [LaCit2]3-induced the apoptosis of HeLa cells through oxidative stress mediated pathway involving MT participation.

关键词： lanthanum citrate complex HeLa cells proteomics

Transcriptomics and proteomics in the Study of H1N1 2009

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Genomics, proteomics & Bioinformatics 2010年第3期8卷 139-144页

作者： Lijun Zhang Xiaojun Zhang Qing Ma Fang Ma Honghao Zhou Department of Pharmacogenetics Institute of Clinical Pharmacology Central South University Changsha 410078 China Shanghai Public Health Clinical Center Fudan University Shanghai 201508 China Department of Neurosurgery Fuzhou General Hospital Fuzhou 350025 China School of Pharmacy and Pharmaceutical Sciences University at Buffalo NY 14260 USA.

Influenza A virus （H1N1） 2009, a new swine-origin influenza A virus, has been spread worldwidely and caused great public fear. High-throughput transcriptomics and proteomics methods are now being used to identify H1N1 and H1Nl-host interaction. This article reviews recent transcriptomics and proteomics research in H1N1 diagnosis, treatment, and H1N1 virus-host interaction, to offer some help for further understanding the infection mechanism and controlling H1N1 transmission.

关键词： H 1N 1 proteomics transcriptomics host

Hands-on Workshops as An Efective Means of Learning Advanced Technologies Including Genomics,proteomics and Bioinformatics

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Genomics, proteomics & Bioinformatics 2013年第6期11卷 368-377页

作者： Nichole Reisdorph Robert Stearman Katerina Kechris Tzu Lip Phang Richard Reisdorph Jessica Prenni David J.Erle Christopher Coldren Kevin Schey Alexey Nesvizhskii Mark Geraci Department of Immunology National Jewish Health Department of Medicine Division of Pulmonary Sciences and Critical Care MedicineUniversity of Colorado School of Medicine Department of Biostatistics and Informatics Colorado School of Public Health Department of Pediatrics National Jewish Health Department of Biochemistry and Molecular Biology Proteomics and Metabolomics FacilityColorado State University Lung Biology Center Department of MedicineUniversity of California Bioinformatics PathgroupNashvilleTN 37027 USA Department of Biochemistry and Mass Spectrometry Research Center Vanderbilt School of Medicine Department of Pathology University of Michigan Medical School

Genomics and proteomics have emerged as key technologies in biomedical research, resulting in a surge of interest in training by investigators keen to incorporate these technologies into their research. At least two types of training can be envisioned in order to produce meaningful results, quality publications and successful grant applications：（1） immediate short-term training workshops and （2） long-term graduate education or visiting scientist programs. We aimed to fill the former need by providing a comprehensive hands-on training course in genomics, proteomics and informatics in a coherent, experimentally-based framework. This was accomplished through a National Heart, Lung, and Blood Institute （NHLBI）-sponsored 10-day Genomics and proteomics Hands-on Workshop held at National Jewish Health （NJH） and the University of Colorado School of Medicine （UCD）. The course content included comprehensive lectures and laboratories in mass spectrometry and genomics technologies, extensive hands-on experience with instrumentation and software, video demonstrations, optional workshops, online sessions, invited keynote speakers, and local and national guest faculty. Here we describe the detailed curriculum and present the results of short- and long-term evaluations from course attendees. Our educational program consis- tently received positive reviews from participants and had a substantial impact on grant writing and review, manuscript submissions and publications.

关键词： proteomics Mass spectrometry Genomics Bioinformatics Hands-on Workshops

Application of proteomics in the Study of Tumor Metastasis

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Genomics, proteomics & Bioinformatics 2004年第3期2卷 152-166页

作者： Zhen Cai Jen-Fu Chiu Qing-Yu He Department of Surgery The University of Hong KongHong KongChina Open Laboratory of Chemical Biology of the Institute of Molecular Technology for Drug Discovery and Synthesis The University of Hong KongHong KongChina Institute of Molecular Biology The University of Hong KongHong KongChina Department of Chemistry The University of Hong KongHong KongChina

Tumor metastasis is the dominant cause of death in cancer patients. However, the molecular and cellular mechanisms underlying tumor metastasis are still elusive. The identi?cation of protein molecules with their expressions correlated to the metastatic process would help to understand the metastatic mechanisms and thus facilitate the development of strategies for the therapeutic interventions and clini- cal management of cancer. proteomics is a systematic research approach aiming to provide the global characterization of protein expression and function under given conditions. Proteomic technology has been widely used in biomarker discovery and pathogenetic studies including tumor metastasis. This article provides a brief review of the application of proteomics in identifying molecular factors in tumor metastasis process. The combination of proteomics with other experimental ap- proaches in biochemistry, cell biology, molecular genetics and chemistry, together with the development of new technologies and improvements in existing method- ologies will continue to extend its application in studying cancer metastasis.

关键词： proteomics metastasis tumor mechanism protein identification MALDI-TOF SELDI-ProteinChip

Application of proteomics in environmental science

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Frontiers of Environmental Science & Engineering 2009年第4期3卷 393-403页

作者： Xiaona CHU Jiangyong HU Say Leong ONG Center for Water Research Division of Environmental Science and Engineering National University of Singapore10 Kent Ridge CrescentSingapore 119260Singapore

proteomics involves the separation of proteins,identification of the amino acid sequence of the interested or target proteins,study of the function of the proteins,modification,structure and ultimate assignments to functional pathways in the cell.The proteomic investigations have contributed greatly to human diseases studies,new drugs discovery researches,and environmental science in recent years.This article provides a review on the development of the main proteomic technologies,including both the gel based and non-gel based technologies,and their applications in environmental science.Proteomic technologies have been utilized in the environmental stresses studies to analyze the induction or reduction of proteins at expression level and identify the target proteins to investigate their function in response to environmental stresses,such as high or low pH,oxidation stress,and toxic chemicals.Such protein responses are also helpful to understand the mechanisms of some cellular activities and the functions of some proteins.

关键词： proteomics environmental stress two dimensional(2D)gel electrophoresis mass spectrometry

New clues concerning pigment biosynthesis in green colored fiber provided by proteomics-based analysis

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Journal of Integrative Agriculture 2018年第1期17卷 46-53页

作者： LI Yan-jun SUN Shi-chao ZHANG Xin-yu WANG Xiang-fei LIU Yong-chang XUE Fei SUN Jie Key Laboratory of Oasis Eco-agriculture College of AgricultureShihezi University College of Pharmacy Shihezi University

To separate the proteins related to pigment synthesis in green colored fiber （GCF）, we performed a comparative proteomic analysis to identify the differentially expressed proteins between green cotton fiber and a white near-isogenic line （NIL）. One differential spot identified as phenylocumaran benzylic ether redutase-like protein （PCBER） was expressed only in GCF, but was not found in white colored fiber （WCF） at any time points. Since PCBER was a key enzyme in lignans biosynthesis, total lignans were extracted from GCF and WCF and their content was determined by using a chromotropic acid spectrophotometric method. The results showed that total lignans content in GCF was significantly higher than that in WCF. The qPCR analysis for two PLR genes associated with lignans biosynthesis showed that the expression level of two genes was much higher in GCF than that in WCF at 24 and 27 days post anthesis （DPA）, which may be responsible for the higher lignans content in GCF. Our study suggested that PCBER and lignans may be responsible for the color difference between GCF and WCF. Additionally, p-dimethylaminocinnamaldehyde （DMACA） staining demonstrated that the pigment in GCF was not proanthocyanidins, and was different from that in brown colored fiber （BCF）. This study provided new clues for uncovering the molecular mechanisms related to pigment biosynthesis in GCF.

关键词： green colored cotton proteomics upland cotton pigment biosynthesis phenylocumaran benzylic ether redutase- like protein

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