• Korean Journal of Plant Tissue Culture
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• v.28 no.6
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• pp.347-351
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• 2001

Panax ginseng C.A. Meyer is a well-known Korean traditional medicine. Until now, even though major research of ginseng has been focused on the pharmacological effect, clinical application and chemical analysis of extracted secondary metabolite for several years, the physiology and gene functions of ginseng were not well known. In this research, we have developed the protein extraction methods of ginseng root and hairy root for proteome analysis in order to elucidate the gene(s) function of ginseng. Using the liquid nitrogen (equation omitted) TCA method as protein extraction method, about 660 protein spots were detected on the 2-DE gel of hairy root. Additionally, comparative analysis result of 2-DEs of ginseng root (equation omitted) hairy root suggested that proteomes of same organism could be changeable according to the culture condition, growth stages and other stimulus.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.126-126
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• 2017

Mitochondria are important in wheat, as in all crops, as the main source of ATP for cell maintenance and growth including vitamin synthesis, amino acid metabolism and photorespiration. To investigate the mitochondrial proteome of the roots of wheat seedlings, a systematic and targeted analysis were carried out on the mitochondrial proteome from 15 day-old wheat seedling root material. Mitochondria were isolated by Percoll gradient centrifugation; and extracted proteins were separated and analyzed by Tricine SDS-PAGE along with LTQ-FTICR mass spectrometry. From the isolated the sample, 184 proteins were identified which is composed of 140 proteins as mitochondria and 44 proteins as other subcellular proteins that are predicted by the freeware subcellular predictor. The identified proteins in mitochondria were functionally classified into 12 classes using the ProtFun 2.2 server based on biological processes. Proteins were shown to be involved in amino acid biosynthesis (17.1%), biosynthesis of cofactors (6.4%), cell envelope (11.4%), central intermediary metabolism (10%), energy metabolism (20%), fatty acid metabolism (0.7%), purines and pyrimidines (5.7%), regulatory functions (0.7%), replication and transcription (1.4%), translation (22.1%), transport and binding (1.4%), and unknown (2.8%). These results indicate that many of the protein components present and functions of identifying proteins are common to other profiles of mitochondrial proteins performed to date. This dataset provides the first extensive picture, to our knowledge, of mitochondrial proteins from wheat roots. Future research is required on quantitative analysis of the wheat mitochondrial proteomes at the spatial and developmental level.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• v.34 no.2
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• pp.113-118
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• 2008

Temporomandibular joint disorder (TMD) can induce severe pain but, its pathogenic mechanisms remain poorly understood. In this study, we analyzed proteomes of human synovial fluid in the superior joint space in the patients with TMD, which is obtained during the treatment arthrocentesis. We've got this result that one of the spots was consistently down-regulated in synovial fluid of patients with TMD from analysis of protein pattern. Its molecular weight was estimated to be 33 kDa. Synoviolin was identified in our proteomics analysis of LC/MS/MS. This protein was recently reported as one of the proteins that might affect rheumatoid arthritis (RA). Synoviolin that might be associated with RA was detected in synovial fluid of patients with TMD. We can conclude that synoviolin might be involved not only in the pathogenesis of RA but also in TMD. In result, synoviolin might be involved in the pathogenesis of TMD and can be candidates as new therapeutic targets of TMD or early detection biomarkers.

• Plant Biotechnology Reports
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• v.3 no.2
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• pp.167-174
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• 2009

To identify genes involved in rice Pi5-mediated disease resistance to Magnaporthe oryzae, we compared the proteomes of the RIL260 rice strain carrying the Pi5 resistance gene with its susceptible mutants M5465 and M7023. Proteins were extracted from the leaf tissues of both RIL260 and the mutant lines at 0, 24, and 48 h after M. oryzae inoculation and separated by two-dimensional polyacrylamide gel electrophoresis (2-DE). Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis identified eight proteins that were differently expressed between the resistant and susceptible plants (three down- and five up-regulated proteins in the mutants). The down-regulated proteins included a triosephosphate isomerase (spot no. 2210), a 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (no. 3611), and an unknown protein (no. 4505). In addition, the five up-regulated proteins in the mutants were predicted to be a fructokinase I (no. 313), a glutathione S-transferase (no. 2310), an atpB of chloroplast ATP synthase (no. 3616), an aminopeptidase N (no. 3724), and an unknown protein (no. 308). These results suggest that proteomic analysis of rice susceptible mutants is a useful method for identifying novel proteins involved in resistance to the M. oryzae pathogen.

• Molecules and Cells
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• v.22 no.1
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• pp.119-125
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• 2006

The rat is an accepted model for studying human psychiatric/neurological disorders. We provide a protocol for total soluble protein extraction using trichloroacetic acid/acetone (TCA/A) from rat (female) whole brain, 10 brain regions and the pituitary gland, and show that two-dimensional gel electrophoresis (2-DGE) using precast immobilized pH (4-7) gradient (IPG) strip gels (13 cm) in the first dimension yields clean silver nitrate stained protein profiles. Though TCA/A precipitation may not be "ideal", the important choice here is the selection of an appropriate lysis buffer (LB) for solubilizing precipitated proteins. Our results reveal enrichment of protein spots by use of individual brain regions rather than whole brain, as well as the presence of differentially expressed spots in their proteomes. Thus individual brain regions provide improved protein coverage and are better suited for differential protein detection. Moreover, using a phosphoprotein-specific dye, ingel detection of phosphoproteins was demonstrated. Representative high-resolution silver nitrate stained proteome profiles of rat whole brain total soluble protein are presented. Shortcomings apart (failure to separate membrane proteins), gel-based proteomics remains a viable option, and 2-DGE is the method of choice for generating high-resolution proteome maps of rat brain and brain regions.

• Proceedings of the Microbiological Society of Korea Conference
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• 2006.05a
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• pp.29-31
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• 2006

In a previous report, we showed that enzyme $IIA^{Glc}(EIIA^{Glc}$ of Escherichia coli phosphotransferase system (PTS) interacts with and regulates activity of FrsA (fermentation/respiration switch protein). A BLAST search revealed that orthologs of FrsA exist only in some Gram-negative bacteria such as E. coli, Salmonella typhimurium, Shigella flexneri, Yersinia pestis, Vibrio cholerae, Vibrio vulnificus, Vibrio parahemeolyticus, and Photorhabdus luminescens and all of these species are facultative anaerobes belonging to the ${\gamma}-proteobacterial$ group, and most of them are highly pathogenic. Ligand-fishing experiments using $EIIA^{Glc}$ of Vibrio vulnificus ($vEIIA^{Glc}$) as bait revealed that $vEIIA^{Glc}$ also interacts with vFrsA in a phosphorylation state-dependent manner. The frsA mutant of Vibrio vulnificus showed remarkably reduced cytotoxicity to HeLa cells and reduced lethality to mice compared to wild type. Comparison of extracellular proteomes between the mutant and wild type indicated that hemolysin was not produced in the frsA mutant. Characterization of another protein interacting with $vEIIA^{Glc}$ will be discussed.

• Molecules and Cells
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• v.47 no.1
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• pp.100001.1-100001.8
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• 2024

In eukaryotes, a primary protein quality control (PQC) process involves the destruction of conformationally misfolded proteins through the ubiquitin-proteasome system. Because approximately one-third of eukaryotic proteomes fold and assemble within the endoplasmic reticulum (ER) before being sent to their destinations, the ER plays a crucial role in PQC. The specific functions and biochemical roles of several E3 ubiquitin ligases involved in ER-associated degradation in mammals, on the other hand, are mainly unknown. We identified 2 E3 ligases, ubiquitin protein ligase E3 component N-recognin 1 (UBR1) and ubiquitin protein ligase E3 component N-recognin 2 (UBR2), which are the key N-recognins in the N-degron pathway and participate in the ER stress response in mammalian cells by modulating their stability. Cells lacking UBR1 and UBR2 are hypersensitive to ER stress-induced apoptosis. Under normal circumstances, these proteins are polyubiquitinated through Lys48-specific linkages and are then degraded by the 26S proteasome. In contrast, when cells are subjected to ER stress, UBR1 and UBR2 exhibit greater stability, potentially as a cellular adaptive response to stressful conditions. Although the precise mechanisms underlying these findings require further investigation, our findings show that cytoplasmic UBR1 and UBR2 have anti-ER stress activities and contribute to global PQC in mammals. These data also reveal an additional level of complexity within the mammalian ER-associated degradation system, implicating potential involvement of the N-degron pathway.

• Clinical and Experimental Reproductive Medicine
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• v.44 no.2
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• pp.63-72
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• 2017

Objective: Hyperstimulation methods are broadly used for in vitro fertilization (IVF) in patients with infertility; however, the side effects associated with these therapies, such as ovarian hyperstimulation syndrome (OHSS), have not been well studied. N-glycoproteomes are subproteomes used for the remote sensing of ovarian stimulation in follicular growth. Glycoproteomic variation in human follicular fluid (hFF) has not been evaluated. In this study, we aimed to identify and quantify the glycoproteomes and N-glycoproteins (N-GPs) in natural and stimulated hFF using label-free nano-liquid chromatography/electrospray ionization-quad time-of-flight mass spectrometry. Methods: For profiling of the total proteome and glycoproteome, pooled protein samples from natural and stimulated hFF samples were selectively isolated using hydrazide chemistry to obtain the total proteomes and glycoproteomes. N-GPs were validated by the consensus sequence N-X-S/T (92.2% specificity for the N-glycomotif at p<0.05). All data were compared between natural versus hyperstimulated hFF samples. Results: We detected 41 and 44 N-GPs in the natural and stimulated hFF samples, respectively. Importantly, we identified 11 N-GPs with greater than two-fold upregulation in stimulated hFF samples compared to natural hFF samples. We also validated the novel N-GPs thyroxine-binding globulin, vitamin D-binding protein, and complement proteins C3 and C9. Conclusion: We identified and classified N-GPs in hFF to improve our understanding of follicular physiology in patients requiring assisted reproduction. Our results provided important insights into the prevention of hyperstimulation side effects, such as OHSS.

• Journal of Microbiology and Biotechnology
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• v.21 no.4
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• pp.366-373
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• 2011

We characterized the proteomes of murine N2a cells following infection with three rabies virus (RV) strains, characterized by distinct virulence phenotypes (i.e., virulent BD06, fixed CVS-11, and attenuated SRV9 strains), and identified 35 changes to protein expression using two-dimensional gel electrophoresis in whole-cell lysates. The annotated functions of these proteins are involved in various cytoskeletal, signal transduction, stress response, and metabolic processes. Specifically, a-enolase, prx-4, vimentin, cytokine-induced apoptosis inhibitor 1 (CIAPIN1) and prx-6 were significantly up-regulated, whereas Trx like-1 and galectin-1 were down-regulated following infection of N2a cells with all three rabies virus strains. However, comparing expressions of all 35 proteins affected between BD06-, CVS-11-, and SRV9-infected cells, specific changes in expression were also observed. The up-regulation of vimentin, CIAPIN1, prx-4, and 14-3-3 ${\theta}/{\delta}$, and down-regulation of NDPK-B and HSP-1 with CVS and SRV9 infection were ${\geq}2$ times greater than with BD06. Meanwhile, Zfp12 protein, splicing factor, and arginine/serine-rich 1 were unaltered in the cells infected with BD06 and CVS-11, but were up-regulated in the group infected with SRV9. The proteomic alterations described here may suggest that these changes to protein expression correlate with the rabies virus' adaptability and virulence in N2a cells, and hence provides new clues as to the response of N2a host cells to rabies virus infections, and may also aid in uncovering new pathways in these cells that are involved in rabies infections. Further characterization of the functions of the affected proteins may contribute to our understanding of the mechanisms of RV infection and pathogenesis.

• 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.