• YAKHAK HOEJI
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• v.59 no.3
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• pp.113-119
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• 2015

Protein phosphorylation is one of most important post-translational modifications (PTMs) and plays an important role in regulation of protein function. Here we develop a method for a global identification of phosphopeptides and phosphorylation sites using nano-LC MS/MS. We compared two separation methods, C4 and strong cation ion exchange (SCX). Before phosphopeptides enrichment with $TiO_2$, total proteins from Rat 1 cells have been separated using C4 column or tryptic peptides of proteins from the cells have been separated using SCX column. Finally, we have detected 52 phosphorylation sites on 41 proteins from SCX method and 375 phosphorylation sites on 252 proteins from C4 method, and determined the function and localization of identified phosphoproteins using DAVID software. In particular, we showed new phosphorylation sites from membrane proteins related to various cell signaling mechanisms. This method may contribute to study global signal networks induced by various signals including ligands and drugs.

• Biomedical Science Letters
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• v.29 no.4
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• pp.336-343
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• 2023

Lung cancer is one of the cancers with high mortality and incidence rates worldwide. Although, various anticancer research efforts are underway to completely treat cancer, the challenge against it remains in the inability to eliminate cancer stem cells (CSCs), leading to difficulties in curing the cancer and resulting in recurrence. As a result, there is a growing interest in the discovery of new biomarkers and therapeutic molecules that can simultaneously target both cancer cells and CSCs. From this point of view, we focused on fibronectin leucine rich transmembrane protein 3 (FLRT3), one of the genes known to be present in human lung cells and the discovery from our previous cancer proteomic analysis study. This study aimed to evaluate the potential of FLRT3 as a specific therapeutic biomarker for lung cancer and Lung Cancer-derived-Stem Cells (LCSC). Also, to estimate the biological function of FLRT3 in cancer and LCSC, short hairpin RNA (shRNA) was generated and showed the ability of the decreased-cell migration and cell proliferation of lung cancer through ERK signaling pathway when FLRT3 was knock-downed. In conclusion, our study is the first to report that FLRT3 has the potential as therapeutic biomarker for the treatment of lung cancer and LCSC.

• Biomedical Science Letters
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• v.21 no.2
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• pp.60-68
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• 2015

NecroX-7 is a novel small compound of the NecroX series based on the indole moiety, which has potent cytoprotective and antioxidant properties. We previously detected potential immune regulatory effects of NecroX-7 in immune related diseases like Graft-versus-Host Disease. However, the function and the underlying mechanisms of immunological effects of NecroX-7 in the immune system have not been well established. In this study, we investigated the immune response characterization of differentially expressed genes of NecroX-7 administration in $CD4^+$ T cells by microarray analysis. $CD4^+$ T cells stimulated with NecroX-7 ($40{\mu}M$) or vehicle for 72 hours resulted in the identification of 337 differentially expressed genes (1.5 fold, P<0.05) by expression profiling analysis. Twenty eight of the explored NecroX-7-regulated genes were related to immune system processes. These genes were validated by quantitative real-time PCR. The most significant genes were glutathione reductase, eukaryotic translation elongation factor 1, lymphotoxin-alpha, heat shock protein 9 and chloride intracellular channel protein 4. These findings demonstrate the strongly immune response of NecroX-7 in $CD4^+$ T cells, suggesting that cytoprotection and immune regulation may underlie the critical aspects of NecroX-7 exposure.

• International Journal of Control, Automation, and Systems
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• v.4 no.3
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• pp.382-393
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• 2006

Mechanical system dynamics plays an important role in the area of computational structural biology. Elastic network models (ENMs) for macromolecules (e.g., polymers, proteins, and nucleic acids such as DNA and RNA) have been developed to understand the relationship between their structure and biological function. For example. a protein, which is basically a folded polypeptide chain, can be simply modeled as a mass-spring system from the mechanical viewpoint. Since the conformational flexibility of a protein is dominantly subject to its chemical bond interactions (e.g., covalent bonds, salt bridges, and hydrogen bonds), these constraints can be modeled as linear spring connections between spatially proximal representatives in a variety of coarse-grained ENMs. Coarse-graining approaches enable one to simulate harmonic and anharmonic motions of large macromolecules in a PC, while all-atom based molecular dynamics (MD) simulation has been conventionally performed with an aid of supercomputer. A harmonic analysis of a macroscopic mechanical system, called normal mode analysis, has been adopted to analyze thermal fluctuations of a microscopic biological system around its equilibrium state. Furthermore, a structure-based system optimization, called elastic network interpolation, has been developed to predict nonlinear transition (or folding) pathways between two different functional states of a same macromolecule. The good agreement of simulation and experiment allows the employment of coarse-grained ENMs as a versatile tool for the study of macromolecular dynamics.

• Physical Therapy Korea
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• v.19 no.3
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• pp.72-80
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• 2012

The purpose of the present study was to investigate the effects of familiar exercise and novel exercise on motor function after intracerebral hemorrhage (ICH) in rats. The rats were subjected to a unilateral striatal ICH via collagenase infusion. The rats were randomly divided into the following three groups: the CON (control group; rested one week post-ICH), the FE (familiar exercise group; familiar exercise was performed two weeks after one-week post-ICH period), and NE (novel exercise group; novel exercise was performed two weeks after one-week post-ICH period). We measured neurological behavior using a ladder rung walking test and a beam walking test; we measured the level of nerve growth factor (NGF) using immunohistochemistry and western blot analysis. We performed a one-way ANOVA test to analyze the scores obtained from the neurological behavior tests and the differences of NGF protein levels among the three groups. In the present study, the FE group and the NE group showed significant improvement during the neurological behavior tests and in their expression of NGF protein level, as compared to the CON group. Especially, NE group more increase than FE group in neurological behavior tests, the expression of NGF on motor cortex. In conclusion, these results suggest that, after ICH, familiar exercise and novel exercise enhance motor function and, novel exercise is more effective than familiar exercise.

• Journal of Physiology & Pathology in Korean Medicine
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• v.36 no.1
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• pp.18-22
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• 2022

To investigate effects of cognitive function improvement whether against Taegeuk ginseng on scopolamine-induced memory impairment in rats. All experiments were conducted in three groups: the control group (CTR), the scopolamine 0.4mg/kg (SCP), and the scopolamine (SCP+T) treated with Taegeuk ginseng 100 mg/kg. Taegeuk ginseng 100 mg/kg daily was orally administered for one month and treated with scopolamine was only for 7 consecutive days on the Morris water maze task. 3 weeks after oral administration of Taegeuk ginseng, subjects were performed the Morris water maze test for 8 days and then the open-field exploration test which to assessed for cognitive function improvement. After behavioral testing, subjects were sacrificed and microdissected brains for neurochemical analysis. In the cognitive-behavioral test, long-term administration of Taegeuk ginseng improved spatial navigation learning task compared with the impeded by scopolamine treatment. In neurochemistry, the expression of the synaptic marker PSD95 (postsynaptic density protein 95) was increased in the hippocampus compared to the scopolamine group. Also, brain-derived neurotrophic factor (BDNF) expression was significantly increased in the taegeuk ginseng administration group. These data suggested that long-term administration of taegeuk ginseng might improve cognitive-behavioral functions on hippocampal related spatial learning memory, and it was correlated with neurotropic and synaptic reinforcement. In conclusion, treatment with taegeuk ginseng may positive outcome on learning and memory deficit disorders.

• Journal of Veterinary Science
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• v.25 no.4
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• pp.54.1-54.16
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• 2024

Importance: As one of the main etiologic agents of infectious diseases in pigs, pseudorabies virus (PRV) infections have caused enormous economic losses worldwide. EP0, one of the PRV early proteins (EP) plays a vital role in PRV infections, but the mechanisms are unclear. Objective: This study examined the function of EP0 to provide a direction for its in-depth analysis. Methods: In this study, the EP0-deleted PRV mutant was obtained, and Tandem Mass Tag-based proteomic analysis was used to screen the differentially expressed proteins (DEPs) quantitatively in EP0-deleted PRV- or wild-type PRV-infected porcine kidney 15 cells. Results: This study identified 7,391 DEPs, including 120 and 21 up-regulated and down-regulated DEPs, respectively. Western blot analysis confirmed the changes in the expression of the selected proteins, such as speckled protein 100. Comprehensive analysis revealed 141 DEPs involved in various biological processes and molecular functions, such as transcription regulator activity, biological regulation, and localization. Conclusions and Relevance: These results holistically outlined the functions of EP0 during a PRV infection and might provide a direction for more detailed function studies of EP0 and the stimulation of lytic PRV infections.

• Herbal Formula Science
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• v.32 no.3
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• pp.247-261
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• 2024

Objectives : Zuojin Pill, recognized as an effective herbal remedy, has undergone investigation for its potential in alleviating symptoms like indigestion, vomiting, and abdominal distension. The purpose of this study was to investigate the mechanism of digestive function activation through network pharmacology, particularly focused on improving functional dyspepsia. Methods : The two components, Coptidis Rhizoma and Evodiae Fructus, constituting Zuojin Pill were analyzed based on broad information on chemical and pharmacological properties, confirming 40 active compounds and 115 digestive-related molecular targets. Concentration analysis revealed impacts on various pathways related to digestive functions. Results : According to network pharmacological analysis of Zuojin Pill, quercetin and beta-sitosterol were exhibited relatively numerous targets, suggesting their potential significance in the therapeutic activity of Zuojin Pill and by a Protein-Protein Interaction (PPI) network, JUN, RELA, MAPK1, HSP90AA1, TP53, TNF, AKT1, IL6, MAPK14, ESR1, FOS, MYC were identified. Also, berberine exhibited the highest contribution index (92.58%), indicating that this compound may be a major contributor to the digestive activity of Zuojin Pill. Additionally, functional interaction analysis by GeneMANIA indicated that targets of Zuojin Pill could functionally interact through various mechanisms, implying similarities in pharmacological roles. Conclusions : These findings contribute valuable insights into the digestive function activation mechanism and highlight the therapeutic potential of Zuojin Pill in improving functional dyspepsia.

• Journal of Nutrition and Health
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• v.31 no.9
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• pp.1457-1467
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• 1998

The relationship between cognitive function and dietary patterns in Korean elderly women was investigated in this study. Twenty-four-hour dietary recall and cognitive function tests were performed in 170 elderly women aged over 60 years. Average age of the subjects was 71 years and the average number of family members was 3.3. Most of the subjects had less than seven years of education and their monthly income was much lower than the Korean average. Most of the subjects engaged in regular exercise and did not indulge in drinking and smoking. The average cognitive function score of the subjects was 58.4. Most of the subjects appeared to consume insufficient amount of food ; average intakes of energy, Ca, iron, vitamin A, and riboflavin were lower than RDA for the elderly. Cognitive function score was positively related to education level and regularity of exercise. Also, cognitive function score had a strong relationship with food intake such as total amounts of foods, fish and shellfish, milk and dairy products, total animal food, fruit, bread and sugar. Energy, protein, Ca, p, riboflavin, and niacin were also shown to have positive relationships to cognitive function score, while carbohydrate caloric ratio had a negative relationship with cognitive function. According to the results of multiple regression analysis, factors that most influenced on cognitive function were education level and riboflavin intake. The subjects who had more than seven years of education had significantly higher cognitive function scores than those with no school education. And cognitive function scores f3r those who consumed more than 2/3 of the RDA for most nutrients were significantly higher than the ones fir the subjects who consumed less than 2/3 of the RDA. These results suggest that proper education and adequate nutrient intake in quantity and quality by achieving food diversity are essential in maintaining cognitive function in later life (Korean J Nutrition 31(9) : 1457-1467, 1998)

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.21-22
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• 2000

Expressed sequence tags (EFTs) are the partial segments of cDNA produced from 5 or 3 single-pass sequencing of cDNA clones, error-prone and generated in highly redundant sets. Advancement and expansion of Genomics made biologists to generate huge amount of ESTs from variety of organisms-human, microorganisms as well as plants, and the cumulated number of ESTs is over 5.3 million, As the EST data being accumulate more rapidly, it becomes bigger that the needs of the EST analysis tools for extraction of biological meaning from EST data. Among the several needs of EST analyses, the extraction of protein sequence or functional motifs from ESTs are important for the identification of their function in vivo. To accomplish that purpose the precise and accurate identification of the region where the coding sequences (CDSs) is a crucial problem to solve primarily, and it will be helpful to extract and detect of genuine CD5s and protein motifs from EST collections. Although several public tools are available for EST analysis, there is not any one to accomplish the object. Furthermore, they are not targeted to the plant ESTs but human or microorganism. Thus, to correspond the urgent needs of collaborators deals with plant ESTs and to establish the analysis system to be used as general-purpose public software we constructed the pipelined-EST analysis system by integration of public software components. The software we used are as follows - Phred/Cross-match for the quality control and vector screening, NCBI Blast for the similarity searching, ICATools for the EST clustering, Phrap for EST contig assembly, and BLOCKS/Prosite for protein motif searching. The sample data set used for the construction and verification of this system was 1,386 ESTs from human intrathymic T-cells that verified using UniGene and Nr database of NCBI. The approach for the extraction of CDSs from sample data set was carried out by comparison between sample data and protein sequences/motif database, determining matched protein sequences/motifs that agree with our defined parameters, and extracting the regions that shows similarities. In recent future, in addition to these components, it is supposed to be also integrated into our system and served that the software for the peptide mass spectrometry fingerprint analysis, one of the proteomics fields. This pipelined-EST analysis system will extend our knowledge on the plant ESTs and proteins by identification of unknown-genes.