• Proceedings of the Microbiological Society of Korea Conference
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• 2005.05a
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• pp.200.1-200
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• 2005

• 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.

• Korean Circulation Journal
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• v.54 no.8
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• pp.468-481
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• 2024

Background and Objectives: Although the clinical consequences of advanced heart failure (HF) may be similar across different etiologies of cardiomyopathies, their proteomic expression may show substantial differences in relation to underlying pathophysiology. We aimed to identify myocardial tissue-based proteomic characteristics and the underlying molecular pathophysiology in non-ischemic cardiomyopathy with different etiologies. Methods: Comparative extensive proteomic analysis of the myocardium was performed in nine patients with biopsy-proven non-ischemic cardiomyopathies (3 dilated cardiomyopathy [DCM], 2 hypertrophic cardiomyopathy [HCM], and 4 myocarditis) as well as five controls using tandem mass tags combined with liquid chromatography-mass spectrometry. Differential protein expression analysis, Gene Ontology (GO) analysis, and Ingenuity Pathway Analysis (IPA) were performed to identify proteomic differences and molecular mechanisms in each cardiomyopathy type compared to the control. Proteomic characteristics were further evaluated in accordance with clinical and pathological findings. Results: The principal component analysis score plot showed that the controls, DCM, and HCM clustered well. However, myocarditis samples exhibited scattered distribution. IPA revealed the downregulation of oxidative phosphorylation and upregulation of the sirtuin signaling pathway in both DCM and HCM. Various inflammatory pathways were upregulated in myocarditis with the downregulation of Rho GDP dissociation inhibitors. The molecular pathophysiology identified by extensive proteomic analysis represented the clinical and pathological properties of each cardiomyopathy with abundant proteomes. Conclusions: Different etiologies of non-ischemic cardiomyopathies in advanced HF exhibit distinct proteomic expression despite shared pathologic findings. The benefit of tailored management strategies considering the different proteomic expressions in non-ischemic advanced HF requires further investigation.

• 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.

• 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.

• 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.

• 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.

• 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.

• BMB Reports
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• v.48 no.1
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• pp.19-24
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• 2015

A mouse homozygous for the spontaneous mutation uncovered (Uncv) has a hairless phenotype. A 309-bp non-frameshift deletion mutation in the N-terminal cytoplasmic domain of iRhom2 was identified in Uncv mice ($iRhom2^{Uncv}$) using target region sequencing. The detailed molecular basis for how the iRhom2 mutation causes the hairless phenotype observed in the homozygous $iRhom2^{Uncv}$ mouse remains unknown. To identify differentially expressed proteins in the skin of wild-type and homozygous $iRhom2^{Uncv}$ littermates at postnatal day 5, proteomic approaches, including two-dimensional gel electrophoresis and mass spectrometry were used. Twelve proteins were differentially expressed in the skin in a comparison between wild-type and homozygous $iRhom2^{Uncv}$ mice. A selection of the proteomic results were tested and verified using qRT-PCR, western blot and immunohistochemistry. These data indicate that differentially expressed proteins, especially KRT73, MEMO1 and Coro-1, might participate in the mechanism by which iRhom2 regulates the development of murine skin.

• Environmental Analysis Health and Toxicology
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• v.29
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• pp.19.1-19.10
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• 2014

Objectives Lysosome is the cell-organelle which is commonly used as biomonitoring tool in environmental pollution. In this study, the lysosomal proteomic of the yeast Saccharomyces cerevisiae was analyzed for utilization in the detection of toxic substances in mine water samples. Methods This work informs the expression of lysosomal proteomic in yeast in response with toxic chemicals, such as sodium meta-arsenite and tetracycline, for screening specific biomarkers. After that, a recombinant yeast contained this biomarker were constructed for toxic detection in pure toxic chemicals and mine water samples. Results Each chemical had an optimal dose at which the fluorescent protein intensity reached the peak. In the case of water samples, the yeast showed the response with sample 1, 3, 4, and 5; whereas there is no response with sample 2, 6, and 7. Conclusions The recombinant yeast showed a high ability of toxic detection in response with several chemicals such as heavy metals and pharmaceuticals. In the case of mine water samples, the response varied depending on the sample content.