• 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

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.319-324
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• 2005

An integrated approach for prostate cancer detection using proteomic data is presented. Due to the high-dimensional feature of proteomic data, the discrete wavelet transform (DWT) is used in the first-stage for data reduction as well as noise removal. After the process of DWT, the dimensionality is reduced from 43,556 to 1,599. Thus, each sample of proteomic data can be represented by 1599 wavelet coefficients. In the second stage, a voting method is used to select a common set of wavelet coefficients for all samples together. This produces a 987-dimension subspace of wavelet coefficients. In the third stage, the Autoassociator algorithm reduces the dimensionality from 987 to 400. Finally, the artificial neural network (ANN) is applied on the 400-dimension space for prostate cancer detection. The integrated approach is examined on 9 categories of 2-class experiments, and also 3- and 4-class experiments. All of the experiments were run 10 times of ten-fold cross-validation (i. e. 10 partitions with 100 runs). For 9 categories of 2-class experiments, the average testing accuracies are between 81% and 96%, and the average testing accuracies of 3- and 4-way classifications are 85% and 84%, respectively. The integrated approach achieves exciting results for the early detection and diagnosis of prostate cancer.

• Proceedings of the PSK Conference
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• 2005.04a
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• pp.71-71
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• 2005

• Bulletin of the Korean Chemical Society
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• v.35 no.3
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• pp.933-937
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• 2014

A derivative of Mycobacterium bovis Bacillus Calmette-Guerin (BCG) has been used for the preparation of tuberculosis vaccines. To establish a Korean tuberculosis vaccine derived from BCG-Pasteur $1173P_2$, genome sequencing of a BCG-Korea strain was completed by Joung and coworkers. A comparison analysis of the genome sequences of the BCG-Pasteur $1173P_2$ and BCG-Korea strains showed marginal increases in the total genome length (~0.05%) and the number of genes (~4%) in the BCG-Korea genome. However, how the genomic changes affect the BCG-Korea protein expression levels remains unknown. Here, we provide evidence of the proteomic alterations in the BCG-Korea strain by using a SWATH-based mass spectrometric approach (Sequential Window Acquisition of all THeoretical mass spectra). Twenty BCG proteins were selected by top-rank identification in the BCG proteome analysis and the proteins were quantified by the SWATH method. Thirteen of 20 proteins showing significant changes were enough to discriminate between the two BCG proteomes. The SWATH method is very straightforward and provides a promising approach owing to its strong reliability and reproducibility during the proteomic analysis.

• Molecular & Cellular Toxicology
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• v.4 no.3
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• pp.253-259
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• 2008

Human follicular fluid (HFF) is the in vivo microenvironment for oocyte maturation and includes a variety of proteins that could be involved in oocyte development and fertilization. We therefore used a proteomic approach to identify new HFF proteins. HFF from mature human follicles was obtained from five women following oocyte collection for in vitro fertilization (IVF). Ethanol-precipitated HFF run on two-dimensional gel electrophoresis (2DE) produced approximately 250 Coomassie brilliant blue-stained spots, 64 of which were identified using matrix-assisted laser desorption/ionization-mass spectrometry (MALDIMS). In this study, several proteins including complement factor H, inter-${\alpha}$ (globulin) inhibitor H4, inter-${\alpha}$-trypsin inhibitor heavy chain H4 precursor, human zinc-${\alpha}$-2-glycoprotein chain B, PRO2619, PRO02044, and complex-forming glycoprotein HC were new proteins that have not been previously reported in HFF using proteomic methods. Additionally, we identified alloalbumin venezia for the first time from trichloroacetic acid (TCA)-precipitated HFF. These HFF proteins could serve as new biomarkers for important human reproductive processes.

• Biotechnology and Bioprocess Engineering:BBE
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• v.11 no.3
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• pp.187-198
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• 2006

The aromatic hydrocarbons (AHs), which include benzene, polycyclic aromatic hydrocarbons, and dioxin, are important chemical and environmental contaminants in industry that usually cause various diseases. Over the years, numerous studies have described and evaluated the adverse health effects induced by AHs. Currently, "Omics" technologies, transcriptomics and proteomics, have been applied in AH toxicity studies. Proteomics has been used to identify molecular mechanisms and biomarkers associated with global chemical toxicity. It could enhance our ability to characterize chemical-induced toxicities and to identify noninvasive biomarkers. The proteomic approach (e.g. 2-dimensional electrophoresis [2-DE]), can be used to observe changes in protein expression during chemical exposure with high sensitivity and specificity. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) and electrospray ionization-quadrupole (ESI-Q)-TOF MS/MS are recognized as the most important protein identification tools. This review describes proteomic technologies and their application in the proteomic analysis of AH toxicity.

• Mycobiology
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• v.45 no.3
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• pp.226-231
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• 2017

Coprinopsis cinerea was employed to investigate the fungal response to gravity. Mycelium growth revealed a consistent growth pattern, irrespective of the direction of gravity (i.e., horizontal vs. perpendicular). However, the fruiting body grew in the direction opposite to that of gravity once the primordia had formed. For the proteomic analysis, only curved-stem samples were used. Fifty-one proteins were identified and classified into 13 groups according to function. The major functional groups were hydrolases and transferases (16%), signal transduction (15%), oxidoreductases and isomerases (11%), carbohydrate metabolism (9%), and transport (5%). To the best of our knowledge, this is the first report on a proteomic approach to evaluate the molecular response of C. cinerea to gravity.

• 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.

• 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.

• Journal of Microbiology and Biotechnology
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• v.11 no.6
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• pp.1111-1114
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• 2001

An extracellular fibrinolytic-enzyme-producing bacterium was isolated from Doen-Jang, a Korean traditional fermented flood, and identified as Bacillus sp. DJ based on its morphology and cellular fatty acid composition. The total extracellular fibrinase (EF) from Bacillus sp. DJ was analyzed using three fibrin zymographic techniques, SDS-fibrin zymography (SDS-FZ), isoelectrofocucing-fibrin zymographs(IEF-FZ), and a two-dimensional SDS-fibrin zymographic analysis (2D SDS-FZ). As a result, the EP map of Bacillus sp. DJ was established. The results suggest that the 2D SDS-FZ method will be a useful tool for the proteomic approach for many other bacterial pretenses.