• Title, Summary, Keyword: proteomic

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Proteomic Application in Cell Biology (세포생물학과 Proteomics 응용)

  • 김동욱
    • Korean Journal of Microbiology
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    • v.37 no.2
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    • pp.109-113
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    • 2001
  • As the complete genomic sequences accumulate, the use of global techniques became possible. DNA microarray is a powerful technology for measuring global mRNA levels. This method, however, does not provide information on post-translational modifications of proteins. In addition, mRNA levels do not strictly correlate with protein concentrations, especially for lower-abundance proteins. Therefore, studies at the level of transcription are not sufficient to understand cellular activity. Proteomic techniques to analyze protein expression and function at the large-scale have been developed and used. This review introduces a simple explanation for proteomic analysis and examples of how proteomics is applied in cell biology.

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Effects of Hyperbaric Pressure on Cellular Morphology, Proliferation and Protein Expression of Jurkat Cell

  • Oh, Eun-Ha;Oh, Sang-Nam;Im, Ho-Sub;Lee, Joo-Hyun;Kim, Jin-Young;Moon, Joo-Hee;Hong, Eun-Young;Kim, Yang-Hee;Yang, Min-Ho;Lim, Yong-Chul;Park, Sun-Young;Lee, Eun-Il;Sul, Dong-Geun
    • Molecular & Cellular Toxicology
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    • v.1 no.2
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    • pp.116-123
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    • 2005
  • The application of high pressure on cellular morphology, proliferation and protein expression of Jurkat cells (human T lymphocyte cell line) has been extensively investigated. In the present study, we manufactured a novel pressure chamber that modulates 5% $CO_{2}$, temperature and pressure (up to 3 ATA). Jurkat cells was incubated 2 ATA pressure and analyzed cellular morphology and growth using an electron microscopy and MTT assay. The cells showed the morphological changes in the cell surface, which appeared to cause a severe damage in cell membrane. The growth rate of the cells under 2 ATA pressure decreased as cultured time got increased. Furthermore, a long term exposure of high pressure on Jurkat cells may act as one of the important cellular stresses that leads to inducing cell death. Cellular proteomes were separated by 2-dimensional electrophoresis with pH 3-10 ranges of IPG Dry strips. And many proteins showed significant up-and-down expressions with hyperbaric pressure. Out of all, 10 spots were identified significantly using matrix-assisted laser desorption/ionization-time of fight (MALDI-TOF) mass spectrometry. We and found that 9 protein expressions were decreased and one protein, heat shock protein HSP 60, was increased in Jurkat cells under 2 ATA. Identified proteins were related to lipid metabolism and signal transduction.

Comprehensive Analysis of Proteomic Differences between Escherichia coli K-12 and B Strains Using Multiplexed Isobaric Tandem Mass Tag (TMT) Labeling

  • Han, Mee-Jung
    • Journal of Microbiology and Biotechnology
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    • v.27 no.11
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    • pp.2028-2036
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    • 2017
  • The Escherichia coli K-12 and B strains are among the most frequently used bacterial hosts for scientific research and biotechnological applications. However, omics analyses have revealed that E. coli K-12 and B exhibit notably different genotypic and phenotypic attributes, even though they were derived from the same ancestor. In a previous study, we identified a limited number of proteins from the two strains using two-dimensional gel electrophoresis and tandem mass spectrometry (MS/MS). In this study, an in-depth analysis of the physiological behavior of the E. coli K-12 and B strains at the proteomic level was performed using six-plex isobaric tandem mass tag-based quantitative MS. Additionally, the best lysis buffer for increasing the efficiency of protein extraction was selected from three tested buffers prior to the quantitative proteomic analysis. This study identifies the largest number of proteins in the two E. coli strains reported to date and is the first to show the dynamics of these proteins. Notable differences in proteins associated with key cellular properties, including some metabolic pathways, the biosynthesis and degradation of amino acids, membrane integrity, cellular tolerance, and motility, were found between the two representative strains. Compared with previous studies, these proteomic results provide a more holistic view of the overall state of E. coli cells based on a single proteomic study and reveal significant insights into why the two strains show distinct phenotypes. Additionally, the resulting data provide in-depth information that will help fine-tune processes in the future.

Chip-based microcapillary HPLC for proteomic analysis (칩 기반 미세관 HPLC를 이용한 단백체 분석)

  • Kim, Bo-Ra;Park, Jong-Moon;Lee, Hoo-Keun
    • Analytical Science and Technology
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    • v.24 no.6
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    • pp.407-413
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    • 2011
  • Over the last decade sophisticated and powerful microcapillary HPLC for proteomic analysis have been developed increasingly and interfaced with high resolution tandem mass spectrometers. Separation prior to mass spectrometric (MS) analysis removes impurities, and concentrates analytes in the narrow elution peaks, resulting in increased sensitivity of MS analysis. This review will focus on the recent advances of on-line highperformance separation techniques based on microfluidic chips for complex proteomic analysis.

Genomic and Proteomic Profiling of the Cadmium Cytotoxic Response in Human Lung Epithelial Cells

  • Choi, Kwang-Man;Youn, Hyung-Sun;Lee, Mi-Young
    • Molecular & Cellular Toxicology
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    • v.5 no.3
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    • pp.198-206
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    • 2009
  • Microarray and proteomic expression patterns in response to cadmium exposure were analyzed in human lung epithelial cells. Among 35,000 genes analyzed by cDNA microarray, 228 genes were up-regulated and 99 genes were down-regulated, based on a fold change cut-off value of ${\geq}2$. Combining two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry (MALDI-ToF-MS), 25 of 629 protein spots showed fold changes in expression ${\geq}2$ (17 up-regulated, 8 down-regulated). After comparing the cDNA microarray and proteomic analyses, only transglutaminase 2, translation elongation factor 1 alpha 1, and glyceraldehyde-3-phosphate dehydrogenase showed overlapping signals in the cDNA microarray and proteomic analyses, whereas the remaining differentially expressed proteins showed large discrepancies with respect to mRNA expression.

Pituitary Adenoma Biomarkers Identified Using Proteomic Fingerprint Technology

  • Zhou, Kai-Yu;Jin, Hang-Huang;Bai, Zhi-Qiang;Liu, Chi-Bo
    • Asian Pacific Journal of Cancer Prevention
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    • v.13 no.8
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    • pp.4093-4095
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    • 2012
  • Objective: To determine whether pituitary adenomas can be diagnosed by identifying protein biomarkers in the serum. Methods: We compared serum proteins from 65 pituitary adenoma patients and 90 healthy donors using proteomic fingerprint technology combining magnetic beads with matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS). Results: A total of 42 M/Z peaks were identified as related to pituitary adenoma (P<0.01). A diagnostic model established based on three biomarkers (3382.0, 4601.9, 9191.2) showed that the sensitivity of diagnosing pituitary adenoma was 90.0% and the specificity was 88.3%. The model was further tested by blind analysis showing that the sensitivity was 88.0% and the specificity was 83.3%. Conclusions: These results suggest that proteomic fingerprint technology can be used to identify pituitary adenoma biomarkers and the model based on three biomarkers (3382.0, 4601.9, 9191.2) provides a powerful and reliable method for diagnosing pituitary adenoma.

Effect of Carthami Tinctorii Fructus Herbal-acupuncture Solution(CTF-HAS) on Gene Expression in HepG2 carcinomar cells by Proteomic Analysis (Proteomic Analysis기법을 이용한 홍화자약침액(紅花子藥鍼液)이 간암세포주(肝巖細胞柱)의 유전자(遺傳子) 발현(發顯)에 미치는 영향(影響))

  • Lee, Kyung-Min;Lim, Seong-Chul;Jeong, Tae-Young;Seo, Jung-Chul;Han, Sang-Won
    • Journal of Pharmacopuncture
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    • v.8 no.2
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    • pp.23-28
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    • 2005
  • Objective : It has long been known about the osteogenic effect of CTF-HAS on bone tissues. However, it has not been determined the effect of CTF-HAS on cancer cells. The purpose of this study is to screen the CTF-HAS mediated differentially expressed genes in cancer cells such as HepG2 hepatoma cells lines. Methods : CTF-HAS was prepared by boiling and stored at $-70^{\circ}C$ until use. For proteomic analysis, total protein was analyzed by 2D gel electrophoresis and Q-TOF mass spectrometer. Results : In proteomic analysis, three spots were identified by 2D-gel electrophoresis and Q-TOF analysis. One down-regulated protein was heat shock 70kDa protein 5 and up-regulated proteins were chaperonin and 2-phospho -pyruvate-hydratase ${\alpha}-enolase$ by 1.5mg/ml of CTF-HAS. Discussion : Proteomic analysis approach were performed to screen the differential expression genes. The screened genes will be used for the better understanding in therapeutic effect of CTF-HAS on cancer field.

Proteomic Analysis of the GacA Response Regulator in Pseudomonas chlororaphis O6

  • Anderson, Anne J.;Kim, Young Cheol
    • Research in Plant Disease
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    • v.24 no.2
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    • pp.162-169
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    • 2018
  • The GacS/GacA system in the root colonizer Pseudomonas chlororaphis O6 is a key regulatory system of many traits relevant to the plant probiotic nature of this bacterium. The work in this paper elucidates proteins using proteomics approach in P. chlororaphis O6 under the control of the cytoplasmic regulatory protein, GacA. A gacA mutant of P. chlororaphis O6 showed loss in production of phenazines, acyl homoserine lactones, hydrogen cyanide, and protease, changes that were associated with reduced in vitro antifungal activity against plant fungal pathogens. Production of iron-chelating siderophore was significantly enhanced in the gacA mutant, also paralleling changes in a gacS mutant. However, proteomic analysis revealed proteins (13 downregulated and 7 upregulated proteins in the mutant compared to parental strain) under GacA control that were not apparent by a proteomic study of a gacS mutant. The putative identity of the downregulated proteins suggested that a gacA mutant would have altered transport potentials. Notable would be a predicted loss of type-VI secretion and PEP-dependent transport. Study of mutants of these GacA-regulated proteins will indicate further the features required for probiotic potential in this rhizobacterium.

Proteomic Dissection of Abiotic Stress Response in Crop Plants

  • Alam, Iftekhar;Sharmin, Shamima Akhtar;Lee, Byung-Hyun
    • 한국환경농학회:학술대회논문집
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    • pp.196-204
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    • 2011
  • Abiotic stress is the primary cause of crop loss worldwide, reducing average yields for most major crop plants by more than 50%. In addition, future agricultural production and management will encounter multifaceted challenges from global climate change. Therefore, it is necessary to study the molecular response of crop plants to the stresses in order to develop appropriate strategies to sustain food production under adverse environmental conditions. We carried out a large scale proteomic analysis of soybean plants in response to various abiotic stresses, including drought, salinity, waterlogging and their interactions. Proteins were analyzed by two dimensional polyacrylamide gel electrophoresis followed by matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry. The identified proteins are involved in a wide range of cellular functions. In addition to the well known stress-associated proteins, we identified several novel proteins, which were not reported before. In many cases our proteomic data bridges the gap between mRNA and metabolite data. Our studie provides new insights into identification of abiotic stress responsive proteins in soybean, and demonstrates the advantages of proteomic analysis in dissecting metabolic and regulatory networks.

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