• Journal of KIISE:Computing Practices and Letters
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• v.15 no.5
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• pp.375-379
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• 2009

Protein domain is the conserved unit of compact tree-dimensional structure and evolution, which carries specific function. Domains may appear in patterns in proteins, since they have been conserved through the evolution for functional formation of proteins. In this paper, we propose a formulated method for conservation analysis of domain combination based on association rule. Proposed method measures mutual dependency of domains in a combination, as well as co-occurrence frequency of them, which is conventionally used. Based on the method, we extracted conserve domain combinations in S.cerevisiae proteins and analyzed their functions based on Gene Ontology. From the results, we drew conclusions that domains in S.cerevisiae proteins form patterns whose members are highly affiliated to one another, and that extracted patterns tend to be associated with molecular function. Moreover, the results testified to proposed method superior to conventional ones for identifying domain combinations conserved for functional cooperation.

• Biomolecules & Therapeutics
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• v.30 no.4
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• pp.348-359
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• 2022

Gastric adenocarcinoma is among the top causes of cancer-related death and is one of the most commonly diagnosed carcinomas worldwide. Benzyl isothiocyanate (BITC) has been reported to inhibit the gastric cancer metastasis. In our previous study, BITC induced apoptosis in AGS cells. The purpose of the present study was to investigate the effect of BITC on autophagy mechanism in AGS cells. First, the AGS cells were treated with 5, 10, or 15 μM BITC for 24 h, followed by an analysis of the autophagy mechanism. The expression level of autophagy proteins involved in different steps of autophagy, such as LC3B, p62/SQSTM1, Atg5-Atg12, Beclin1, p-mTOR/mTOR ratio, and class III PI3K was measured in the BITC-treated cells. Lysosomal function was investigated using cathepsin activity and Bafilomycin A1, an autophagy degradation stage inhibitor. Methods including qPCR, western blotting, and immunocytochemistry were employed to detect the protein expression levels. Acridine orange staining and omnicathepsin assay were conducted to analyze the lysosomal function. siRNA transfection was performed to knock down the LC3B gene. BITC reduced the level of autophagy protein such as Beclin 1, class III PI3K, and Atg5-Atg12. BITC also induced lysosomal dysfunction which was shown as reducing cathepsin activity, protein level of cathepsin, and enlargement of acidic vesicle. Overall, the results showed that the BITC-induced AGS cell death mechanism also comprises the inhibition of the cytoprotective autophagy at both initiation and degradation steps.

• The KIPS Transactions:PartB
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• v.16B no.5
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• pp.359-366
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• 2009

Analysis of 3-dimensional (3D) protein structure plays an important role of structural bioinformatics. The protein structure alignment is the main subjects of the structural bioinformatics and the most fundamental problem. Protein Structures are flexible and undergo structural changes as part of their function, and most existing protein structure comparison methods treat them as rigid bodies, which may lead to incorrect alignment. We present a new method that carries out the flexible structure alignment by means of finding SSPs(Similar Substructure Pairs) and flexible points of the protein. In order to find SSPs, we encode the coordinates of atoms in the backbone of protein into RDA(Relative Direction Angle) using local similarity of protein structure. We connect the SSPs with Floyd-Warshall algorithm and make compatible SSPs. We compare the two compatible SSPs and find optimal flexible point in the protein. On our well defined performance experiment, 68 benchmark data set is used and our method is better than three widely used methods (DALI, CE, FATCAT) in terms of alignment accuracy.

• Journal of KIISE:Computer Systems and Theory
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• v.33 no.5
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• pp.267-281
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• 2006

PPI(Protein-Protein Interaction) data has information about the organism has maintained a life with some kind of mechanism. So, it is used in study about cure research back, cause of disease, and new medicine development. This PPI data has been increased by geometric progression because high throughput methods are developed such as Yeast-two-hybrid, Mass spectrometry, and Correlated mRNA expression. So, it is impossible that a person directly manage and analyze PPI data. Fortunately, PPI data is able to abstract the graph which has proteins as nodes, interactions as edges. Consequently, Graph theory plentifully researched from the computer science until now is able to be applied to PPI data successfully. In this paper, we introduce Proteinca(PROTEin INteraction CAbaret) workbench system for easily managing, analyzing and visualizing PPI data. Proteinca assists the user understand PPI data intuitively as visualizing a PPI data in graph and provide various analytical function on graph theory. And Protenica provides a simplified visualization with gravity-rule.

• Biomedical Science Letters
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• v.15 no.1
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• pp.97-99
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• 2009

Geldanamycin is a benzoquinone ansamycin antibiotic that binds to cytosol HSP90 (Heat Shock Protein 90) and changes its biological function. HSP90 is involved in the intracellular important roles for the regulation of the cell cycle, cell growth, cell survival, apoptosis, angiogenesis and oncogenesis. To identify genes expressed during geldanamycin treatment against neurons of rats (PC12 cells), DNA microarray method was used. We have isolated 2 gene groups (up-or down-regulated genes) which are geldanamycin differentially expressed in neurons. Granzyme B is the gene most significantly increased among 204 up-regulated genes (more than 2 fold over-expression) and Chemokine (C-C motif) ligand 20 is the gene most dramatically decreased among 491 down-regulated genes (more than 2 fold down-expression). The gene increased expression of Cxc110, Cyp11a1, Gadd45a, Gja1, Gpx2, Ifua4, Inpp5e, Sox4, and Stip1 are involved stress-response gene, and Cryab, Dnaja1, Hspa1a, Hspa8, Hspca, Hspcb, Hspd1, Hspd1, and Hsph1 are strongly associated with protein folding. Cell cycle associated genes (Bc13, Brca2, Ccnf, Cdk2, Ddit3, Dusp6, E2f1, Illa, and Junb) and inflammatory response associated genes (Cc12, Cc120, Cxc12, Il23a, Nos2, Nppb, Tgfb1, Tlr2, and Tnt) are down-regulated more than 2 times by geldanamycin treatment. We found that geldanamycin is related to expression of many genes associated with stress response, protein folding, cell cycle, and inflammation by DNA microarray analysis. Further experimental molecular studies will be needed to figure out the exact biological function of various genes described above and the physiological change of neuronal cells by geldanamycin. The resulting data will give the one of the good clues for understanding of geldanamycin under molecular level in the neurons.

• Reproductive and Developmental Biology
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• v.38 no.1
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• pp.53-62
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• 2014

The objective of this study was to investigate the relationship between fertility and protein pattern change using in vitro fertilization, analysis of sperm characteristics and two-dimensional gel electrophoresis in different pig types. In results, the viability and mitochondria integrity of sperm were higher significantly (p<0.05) but the portions of acrosome reaction was lower significantly (p<0.05) in Duroc and $F_1$ (potbellied ${\times}$ PWG miniature pig) than PWG miniature. On in vitro fertilization to investigate fertility, the fertility of $F_1$ semen war higher significantly (p<0.05) than in Duroc and PWG miniature pig. On the other hand, protein patterns showed similar function among the different boar semen. Especially, the heat shock 70 kDa 1-like and G patch domain-containing protein 4 were significantly (p<0.05) higher expressed in $F_1$ than in Duroc and PWG miniature pig. The proteins associated with mitochondria in Duroc were significantly (p<0.05) higher expressed than in $F_1$ and PWG miniature pig. The developmental rates to blastocyst stage of oocytes fertilized with sperm of $F_1$ pig were significantly (p<0.05) higher than in PWG miniature pig. However, phosphoglycerate kinase 2 and zinc finger protein 431 were significantly (p<0.05) higher expressed in PWG miniature pig than in $F_1$ and Duroc pigs. In conclusion, the results of the present study indicate that different proteins were expressed in different pig types, and were associated with a sperm functions and embryo development.

• The Korean Journal of Physiology and Pharmacology
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• v.26 no.5
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• pp.325-333
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• 2022

Heart failure (HF) has become one of the severe public health problems. The detailed role of mitochondrial function in HF was still unclear. Benzoylaconine (BAC) is a traditional Chinese medicine, but its role in HF still needs to be explored. In this study, oxygen-glucose deprivation and reperfusion (OGD/R) was executed to mimic the injury of H9C2 cells in HF. The viability of H9C2 cells was assessed via MTT assay. OGD/R treatment markedly decreased the viability of H9C2 cells, but BAC treatment evidently increased the viability of OGD/R-treated H9C2 cells. The apoptosis of H9C2 was enhanced by OGD/R treatment but suppressed by BAC treatment. The mitochondrial membrane potential was evaluated via JC-1 assay. BAC improved the mitochondrial function and suppressed oxidative stress in OGD/R-treated H9C2 cells. Moreover, Western blot analysis revealed that the protein expression of p-AMPK and PGC-1α were reduced in OGD/R-treated H9C2 cells, which was reversed by BAC. Rescue assays indicated that AMPK attenuation reversed the BAC-mediated protective effect on OGD/R-treated cardiomyocytes. Moreover, BAC alleviated myocardial injury in vivo. In a word, BAC modulated the mitochondrial function in OGD/R-induced cardiomyocyte injury by activation of the AMPK/PGC-1 axis. The findings might provide support for the application of BAC in the treatment of HF.

• 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.

• Restorative Dentistry and Endodontics
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• v.29 no.4
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• pp.399-408
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• 2004

Odontoblasts are responsible for the formation and maintenance of dentin. They are known to synthesize unique gene products including dentin sialophosphoprotein (DSPP). Another unique genes of the cells remain unclear. OD314 was isolated from the odontoblasts/pulp cells of rats and partially characterized as an odontoblast-enriched gene (Dey et al., 2001). This study aimed to elucidate the biological function of OD314, relating to odontoblast differentiation and dentinogenesis. After determining the open reading frame (ORP) of OD314 by transient transfection analysis using green fluorescent protein (GPP) expression vector, mRNA in-situ hybridization, immunohistochemistry, reverse transcription-polymerase chain reaction (RT-PCR) and western analysis were performed. The results were as follows: 1. In in-situ hybridization, OD314 mRNAs were expressed in odontoblasts of developing coronal and root pulp. 2. OD314 was a novel protein encoding 154 amino acids, and the protein was mainly expressed in cytoplasm by transient transfection analysis. 3. Mineralized nodules were associated with multilayer cell nodules in the culture of human dental pulp cells and first detected from day 21 using alizarin-red S staining. 4. In RT-PCR analysis, OD314, osteocalcin (OC) and DSPP strongly expressed throughout 28 days of culture. Whereas, osteonectin (ON) mRNA expression stayed low up to day 14, and then gradually decreased from day 21. 5. Western blots showed an approximately 17 kDa band. OD314 protein was expressed from the start of culture and then increased greatly from day 21. In conclusion, OD314 is considered as an odontoblast-enriched gene and may play important roles in odontoblast differentiation and dentin mineralization.

• The Journal of the Korea Contents Association
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• v.19 no.11
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• pp.632-643
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• 2019

In recent years, large scale damages from arbovirus infections by mosquitoes have been reported worldwide due to factors such as change in global climate, increased overseas travel, and increased logistics movement between countries. Among them, Zika virus and dengue virus belonging to genus Flavivirus are representative. In this study, we performed in-depth analyses of the envelope (E) protein that perform essential functions for host infection of Zika virus and dengue virus based on bioinformatics databases. The domain analysis of E protein was performed to determine the type, location, and function, and homology analysis for each domain. From these results, EDIII showing low homology was identified. The homology and immunogenicity of each peptide constituting EDIII were analyzed and three-dimensional structures were modeled. Furthermore, we discussed their biological meaning and how they could be used.