• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.131-131
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• 2017

Though the Platycodon grandiflorum, has a broad range of pharmacologic properties, but the mechanisms underlying these effects remain unclear. In order to profile proteins from the nodal segment, callus, root and shoot, high throughput proteome approach was executed in the present study. Two-dimensional gels stained with CBB, a total of 84 differential expressed proteins were confirmed out of 839 protein spots using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 58 differential expressed protein spots (${\geq}2-fold$) were analyzed using MASCOT search engine according to the similarity of sequences with previously characterized proteins along with the UniProt database. Out of 58 differential expressed protein, 32 protein spots were up-regulated such as ribulose-1,5-bisphosphate carboxylase, endoplasmic oxidoreductin-1, heat stress transcription factor A3, RNA pseudourine synthase 4, cysteine proteinase, GntR family transcriptional regulator, E3 xyloglucan 6-xylosyltransferase, while 26 differential protein spots were down-regulated such as L-ascorbate oxidase precursor, late embryogenesis abundant protein D-34, putative SCO1 protein, oxygen-evolving enhancer protein 3. However, the frequency distribution of identified proteins using iProClass databases, and assignment by function based on gene ontology revealed that the identified proteins from the explants were mainly associated with the nucleic acid binding (17%), transferase activity (14%) and ion binding (12%). Taken together, the protein profile may provide insight clues for better understanding the characteristics of proteins and its metabolic activities in various explants of this essential medicinal plant P. grandiflorum.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.132-132
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• 2017

Plants, including Platycodon grandiflorum have been used globally across varied cultures as a safe natural source of medicines. From time immemorial, humans have relied on plants that could meet their basic necessities such as food, shelter, fuel and health. This study was executed to profile proteins from the hormone induced diploid and tetraploid roots using high throughput proteome approach. Two dimensional gels stained with CBB, a total of 64 differential expressed proteins were identified from the diploid root using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 20 differential expressed protein spots ( ${\geq}1.5-fold$) were analyzed using LTQ-FTICR MS whereas a total of 13 protein spots were up regulated and 7 protein spots were down-regulated. However, in the case of tetraploid root, a total of 78 differential expressed proteins were identified from tetraploid root of which a total of 28 differential expressed protein spots (${\geq}1.5-fold$) were analyzed by mass spectrometry whereas a total of 16 protein spots were up regulated and a total of 12 protein spots were down-regulated. However, proteins identified using iProClass databases revealed that the identified proteins from the explants were mainly associated with the nucleic acid binding, oxidoreductase activity, transporter activity and isomers activity. The exclusive protein profile may provide insight clues for better understanding the characteristics of protein function and its metabolic activity that can help for the development of the nutritional and breeding aspects of this economically important medicinal plant.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.123-123
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• 2017

In spite of the potential medicinal significance and a wide range of pharmacologic properties of Platycodon grandiflorum, the molecular mechanism of its roots is still unknown. The present study was conducted to profile proteins from 3, 4 and 5 months aged diploid and tetraploid roots of Platycodon grandiflorum using high throughput proteome approach. Two-dimensional gels stained with CBB, a total of 68 differential expressed proteins were identified from the diploid root out of 767 protein spots using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 29 differential expressed protein spots (${\geq}2-fold$) were analyzed using LTQ-FTICR MS whereas a total of 24 protein spots were up-regulated and 5 protein spots were down-regulated. On the contrary, in the case of tetraploid root, a total of 86 differential expressed proteins were identified from tetraploid root out of 1033 protein spots of which a total of 39 differential expressed protein spots (${\geq}2-fold$) were analyzed using LTQ-FTICR MS whereas a total of 21 protein spots were up-regulated and a total of 18 protein spots were down-regulated. It was revealed that the identified proteins from the explants were mainly associated with the nucleotide binding, oxidoreductase activity, transferase activity. Taken together, the identified proteins may be helpful to identify key candidate proteins for genetic improvement of plants.

• Journal of Plant Biotechnology
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• v.47 no.3
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• pp.209-217
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• 2020

The presence of high amounts of seed storage proteins (SSPs) improves the overall quality of soybean seeds. However, these SSPs pose a major limitation due to their high abundance in soybean seeds. Although various technical advancements including mass-spectrometry and bioinformatics resources were reported, only limited information has been derived to date on soybean seeds at proteome level. Here, we applied a tandem mass tags (TMT)-based quantitative proteomic analysis to identify the significantly modulated proteins in the seeds of two soybean cultivars showing varying protein contents. This approach led to the identification of 5,678 proteins of which 13 and 1,133 proteins showed significant changes in Daewon (low-protein content cultivar) and Saedanbaek (high-protein content cultivar) respectively. Functional annotation revealed that proteins with increased abundance in Saedanbaek were mainly associated with the amino acid and protein metabolism involved in protein synthesis, folding, targeting, and degradation. Taken together, the results presented here provide a pipeline for soybean seed proteome analysis and contribute a better understanding of proteomic changes that may lead to alteration in the protein contents in soybean seeds.

• Proceedings of the Korean Society for Food Science of Animal Resources Conference
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• 2006.05a
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• pp.122-127
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• 2006

The innermost structures of synovium consist of one to three layers of cells generally identified as synovial lining cells(SLC). The present studies were initiated to determine the protein expression patterns of fibroblast-like synovial(FLS) cells derived from the synovia of rheumatoid arthritis. Post-traumatic arthritis(PTA) is one of the most common causes of secondary osteoarthritis, and usually affects younger people. The proteins were separated by two-dimensional polyacrylamide gel electrophoresis and RNA expression investigated by RT-PCR Proteome analyses led to the identification of more than 1,500 protein spots and of 11 differently expressed protein spots among them. Six proteins were down-regulated, and five proteins were up-regulated in ACL-transected synovial tissue. Among these, spots 3 and 8 were identified as cofilin-1 and smooth muscle protein $22-\alpha$, respectively, Therefore, the proteome analysis of synovial tissue is a useful approach to investigate a joint after an injury and can be used to understand the pathogenesis of PTA.

• Analytical Science and Technology
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• v.33 no.2
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• pp.98-107
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• 2020

Methamphetamine (MA) is currently the most abused illicit drug in Korea. MA is produced by chemical synthesis, and the final target drug that is produced contains small amounts of the precursor chemicals, intermediates, and by-products. To identify and quantify these trace compounds in MA seizures, a practical and feasible approach for conducting chromatographic fingerprinting with a suite of traditional chemometric methods and recently introduced machine learning approaches was examined. This was achieved using gas chromatography (GC) coupled with a flame ionization detector (FID) and mass spectrometry (MS). Following appropriate examination of all the peaks in 71 samples, 166 impurities were selected as the characteristic components. Unsupervised (principal component analysis (PCA), hierarchical cluster analysis (HCA), and K-means clustering) and supervised (partial least squares-discriminant analysis (PLS-DA), orthogonal partial least squares-discriminant analysis (OPLS-DA), support vector machines (SVM), and deep neural network (DNN) with Keras) chemometric techniques were employed for classifying the 71 MA seizures. The results of the PCA, HCA, K-means clustering, PLS-DA, OPLS-DA, SVM, and DNN methods for quality evaluation were in good agreement. However, the tested MA seizures possessed distinct features, such as chirality, cutting agents, and boiling points. The study indicated that the established qualitative and semi-quantitative methods will be practical and useful analytical tools for characterizing trace compounds in illicit MA seizures. Moreover, they will provide a statistical basis for identifying the synthesis route, sources of supply, trafficking routes, and connections between seizures, which will support drug law enforcement agencies in their effort to eliminate organized MA crime.

• Microbiology and Biotechnology Letters
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• v.39 no.1
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• pp.9-19
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• 2011

The Bacillus subtilis pyrimidine biosynthetic (pyr) operon encodes all of the enzymes for the de novo biosynthesis of Uridine monophosphate (UMP) and additional cistrones encoding a uracil permease and the regulatory protein PyrR. The PyrR is a bifunctional protein with pyr mRNA-binding regulatory funtion and uracil phosphoribosyltransferase activity. To study the global regulation by the pyrR deletion, the proteome comparison between Bacillus subtilis DB104 and Bacillus subtilis DB104 ${\Delta}$pyrR in the minimal medium without pyrimidines was employed. Proteome analysis of the cytosolic proteins from both strains by 2D-gel electrophoresis showed the variations in levels of protein expression. On the silver stained 2D-gel with an isoelectric point (pI) between 4 and 10, about 1,300 spots were detected and 172 spots showed quantitative variations in which 42 high quantitatively variant proteins were identified. The results showed that production of the pyrimidine biosynthetic enzymes (PyrAA, PyrAB, PyrB, PyrC, PyrD, and PyrF) were significantly increased in B. subtilis DB104 ${\Delta}$pyrR. Besides, proteins associated carbohydrate metabolism, elongation protein synthesis, metabolism of cofactors and vitamins, motility, tRNA synthetase, catalase, ATP-binding protein, and cell division protein FtsZ were overproduced in the PyrR-deficient mutant. Based on analytic results, the PyrR might be involved a number of other metabolisms or various phenomena in the bacterial cell besides the pyrimidine biosynthesis.

• 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.

• Genomics & Informatics
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• v.7 no.3
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• pp.141-147
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• 2009

Developed proteome-scale ortholog and paralog prediction methods are mainly based on sequence similarity. However, it is known that even the closest BLAST hit often does not mean the closest neighbor. For this reason, we added conserved interaction information to find orthologs. We propose a genome-scale, automated ortholog prediction method, named OrthoInterBlast. The method is based on both sequence and interaction similarity. When we applied this method to fly and yeast, 17% of the ortholog candidates were different compared with the results of Inparanoid. By adding protein-protein interaction information, proteins that have low sequence similarity still can be selected as orthologs, which can not be easily detected by sequence homology alone.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.6
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• pp.885-892
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• 2009

To investigate host defense mechanisms for protecting the mammary gland from mastitis infection, the membrane fraction of mammary tissues from Holstein cows was purified by differential velocity centrifugation, and then the sodium dodecyl sulfate-polyacrylamid gel electrophoresis (SDS-PAGE) separated proteins were identified by ion trap mass spectrometer equipped with a Surveyor high performance liquid chromatography (HPLC) system. A total of 183 proteins were identified. Bioinformatics software was applied to analyse physicochemical characteristics of the identified proteins and to predict biochemical function. These data may provide valuable information to investigate the mechanisms of mammary gland milk secretion and infectious disease, and enable a clear identification of proteins and potential protein targets for therapies.