• Proceedings of the Korean Society of Computer Information Conference
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• 2009.01a
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• pp.77-84
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• 2009

Intracellular signal transduction is achieved by protein-protein interaction. In this paper, we suggest performance algorithm based on Yeast protein-protein interaction and protein location information. We compare if pathways predicted with high valued weights indicate similar tendency with pathways provided in KEGG.

• Interdisciplinary Bio Central
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• v.4 no.4
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• pp.13.1-13.6
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• 2012

The advanced glycation endproducts receptor (AGER) is a multiligand signal transduction receptor. One of its ligands, S100b molecules activates vascular smooth muscle cells and endothelial cells via its receptor, thus triggering activation of signaling cascades and generation of cytokines and proinflammatory molecules. Ubiquitin-conjugating enzyme Ubc9 is an E2 conjugating enzyme that transfers the activated small ubiquitin-related modifier to protein substrates, and thus it plays a critical role in SUR-Mylation-mediated cellular pathways. Previous studies have shown that both AGE-R and Ubc9 play roles in diverse cellular signaling pathways. However, until recently, little attention has been paid to interactions between AGE-R and Ubc9. In this study, sequence database searches allowed us to identify a potential interaction motif between AGE-R and Ubc9. The subsequent biochemical and molecular biological analysis suggested that there may be specificity in AGE-R and Ubc9 complex signaling in atherosclerosis and cancer cells in a cell-type specific manner. Although the determinant for specificity in AGE-R and Ubc9 complex signaling in cancer cells and atherosclerosis is yet to be determined, this study provides the basis to develop a specific therapeutic application of AGE-R, SURM (small ubiquitin-related modifier)-1, and Ubc9 complex activation pathways in atherosclerosis, diabetes, cancer and inflammatory diseases.

• Plant Biotechnology Reports
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• v.5 no.1
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• pp.19-25
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• 2011

Tocopherols belong to the plant-derived poly phenolic compounds known for antioxidant functions in plants and animals. Activation of mitogen-activated protein kinases (MAPK) is a common reaction of plant cells in defense-related signal transduction pathways. We report a novel non-antioxidant function of ${\alpha}$-tocopherol in higher plants linking the physiological role of tocopherol with stress signalling pathways. Pre-incubation of a low concentration of $50{\mu}M$ ${\alpha}$-tocopherol negatively interferes with MAPK activation in elicitor-treated tobacco BY2 suspension culture cells and wounded tobacco leaves, whereas pre-incubated BY2 cells with ${\alpha}$-tocopherol phosphate did not show the inhibitory effect on stimuli-induced MAPK activation. The decreased MAPK activity was neither due to a direct inhibitory effect of ${\alpha}$-tocopherol nor due to the induction of an inhibitory or inactivating activity directly affecting MAPK activity. The data support that the target of ${\alpha}$-tocopherol negatively regulates an upstream component of the signaling pathways that leads to stress dependent MAPK activation.

• Genomics & Informatics
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• v.4 no.3
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• pp.118-124
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• 2006

For the direct understanding of flow, pathway data are usually represented as directed graphs in biological journals and texts. Databases of metabolic pathways or signal transduction pathways inevitably contain these kinds of graphs to show the flow. KEGG, one of the representative pathway databases, uses the manually drawn figure which can not be easily maintained. Graph layout algorithms are applied for visualizing metabolic pathways in some databases, such as EcoCyc. Although these can express any changes of data in the real time, it exponentially increases the edge crossings according to the increase of nodes. For the understanding of genome scale flow of metabolism, it is very important to reduce the unnecessary edge crossings which exist in the automatic graph layout. We propose a metabolic pathway drawing algorithm for reducing the number of edge crossings by considering the fact that metabolic pathway graph is scale-free network. The experimental results show that the number of edge crossings is reduced about $37{\sim}40%$ by the consideration of scale-free network in contrast with non-considering scale-free network. And also we found that the increase of nodes do not always mean that there is an increase of edge crossings.

• Molecules and Cells
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• v.44 no.5
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• pp.335-341
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• 2021

Zinc is an essential micronutrient with crucial roles in multiple facets of biological processes. Dysregulated zinc homeostasis impairs overall immune function and resultantly increases susceptibility to infection. Clinically, zinc supplementation is practiced for treatment of several infectious diseases, such as diarrhea and malaria. Recent focus on zinc as a beneficial element for immune system support has resulted in investigation of the immunomodulatory roles of zinc in a variety of immune cells. Besides its classical role as a cofactor that regulates the structural function of thousands of proteins, accumulating evidence suggests that zinc also acts, in a manner similar to calcium, as an ionic regulator of immune responses via participation as an intracellular messenger in signaling pathways. In this review, we focus on the role of zinc as a signaling molecule in major pathways such as those downstream of Toll-like receptors-, T cell receptor-, and cytokine-mediated signal transduction that regulate the activity and function of monocytes/macrophages and T cells, principal players in the innate and adaptive immune systems.

• Genomics & Informatics
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• v.21 no.1
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• pp.6.1-6.8
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• 2023

Glaucoma is the second leading cause of irreversible blindness, and primary open-angle glaucoma (POAG) is the most common type. Due to inadequate diagnosis, treatment is often not administered until symptoms occur. Hence, approaches enabling earlier prediction or diagnosis of POAG are necessary. We aimed to identify novel drugs for glaucoma through bioinformatics and network analysis. Data from 36 samples, obtained from the trabecular meshwork of healthy individuals and patients with POAG, were acquired from a dataset. Next, differentially expressed genes (DEGs) were identified to construct a protein-protein interaction (PPI) network. In both stages, the genes were enriched by studying the critical biological processes and pathways related to POAG. Finally, a drug-gene network was constructed, and novel drugs for POAG treatment were proposed. Genes with p < 0.01 and |log fold change| > 0.3 (1,350 genes) were considered DEGs and utilized to construct a PPI network. Enrichment analysis yielded several key pathways that were upregulated or downregulated. For example, extracellular matrix organization, the immune system, neutrophil degranulation, and cytokine signaling were upregulated among immune pathways, while signal transduction, the immune system, extracellular matrix organization, and receptor tyrosine kinase signaling were downregulated. Finally, novel drugs including metformin hydrochloride, ixazomib citrate, and cisplatin warrant further analysis of their potential roles in POAG treatment. The candidate drugs identified in this computational analysis require in vitro and in vivo validation to confirm their effectiveness in POAG treatment. This may pave the way for understanding life-threatening disorders such as cancer.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2021.04a
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• pp.56-56
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• 2021

Nypa fruticans Wurmb is a mangrove plant belonging to Araceae family. N. fruticans is typically found in Southeast Asia, and in some parts of Queensland, Australia. N. fruticans has phytochemicals, phenolics, and flavonoids. In this study, we investigated the anti-inflammatory effects of the ethyl acetate fraction of N. fruticans (ENF) on the production and expression of cytokines and inflammatory mediators through the major signal transduction pathways. ENF attenuated the level of cytokines in a dose-dependent manner and decreased the production of nitric oxide (NO). ENF decreased the expression of cyclooxygenase-2 (COX-2) and inducible nitric oxide synthase (iNOS) via alleviating transcription of nuclear factor-kappa B (NF-κB) by an inhibitor of nuclear factor-kappa B (IκB) degradation. Furthermore, mitogen-activated protein kinase (MAPK) signaling pathways (ERK1/2, JNK1/2, and p38) are known to be involved in the inflammatory response. Phosphorylations of ERK1/2, JNK1/2, and p38 were significantly decreased compared with the ENF-untreated control. Conclusively, ENF was related to alleviating various pro-inflammatory mediators through IκB/NF-κB and MAPK signaling pathways, including p65 translocation to the nucleus.

• Proceedings of the Korean Society of Veterinary Pathology Conference
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• 2003.10a
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• pp.42-42
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• 2003

The contamination of the environment with pollutants is one of the main problems of modern life, and the levels pollution in industrialized regions are giving raise to increased public concern. The mitogen-activated protein kinase (MAP kinase) are playa pivotal role in the regulation of important cellular functions by activation of specific signal transduction pathways from cell the surface to the nuclei. Three major subgroups of MAP kinases have been identified, and these comprise the extracellular signal-regulated kinase (ERK), the c-Jun amino-terminal kinase (JNK), and the p38 MAP kinases [1-3]. Herein, we investigated the effect of regulation of phospho-JNK (p-JNK), phospho-p38 (p-p38) and phospho-ERK (p-ERK) by TCDD. (omitted)

• Journal of Environmental Health Sciences
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• v.42 no.1
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• pp.27-33
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• 2016

Objectives: Alumina nanoparticles ($Al_2O_3$, Al-NPs) are used for various purposes, including as coating agents and paint additives. Their potential toxicity has raised concern for human health. This study focuses on exploring the toxic effects on the brain and kidneys caused by Al-NPs exposure in rats. Methods: The animals were orally administered Al-NPs at 10, 50 and 100 mg/kg body weight for 28 days following OECD TG 407. To determine the targeted toxicity of Al-NPs, histopathological examination and gene expression analysis were conducted on the rats. Results: The Al-NPs treatment induced kidney tubular dilatation. In the rat cerebrums, the expression levels of 126 genes experienced two-fold or greater increases in response to Al-NPs, including other genes encoding proteins involved in cell differentiation, transcription and signal transduction. In the rat kidneys, the expression levels of 152 genes also showed two-fold or greater increases in response to Al-NPs, including other genes encoding proteins involved in apoptosis, transcription and signal transduction. Conclusion: These results suggest that exposure to Al-NPs influences cellular signal pathways of kidney and cerebrum, and it can be a toxic indicators of nanometrials.

• BMB Reports
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• v.31 no.1
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• pp.83-88
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• 1998

Recently a B cell surface molecule, CD40, has emerged as a receptor mediating a co-stimulatory signal for B cell proliferation and differentiation. To investigate the mechanism of synergy between interleukin-4 (IL-4) and CD40 ligation in B cell activation, we have examined the effect of CE40 cross-linking on the IL-4 receptor expression in human B cells using anti-CE40 antibody. We observed that IL-4 and anti-CD40 both induce IL-4 receptor gene expression with a rapid kinetics resulting in a noticeable accumulation of IL-4 receptor mRNA within 4 h. While IL-4 caused a dose-dependent induction of surface IL-4 receptor expression, the inclusion of anti-CD40 in the IL-4-treated culture, further up-regulated the IL-4-induced IL-4 receptor expression as analyzed by flow cytometry. Pretreatment of B cells with inhibitors of protein tyrosine kinase (PTK) resulted in a significant inhibition of both the IL-4- and anti-CD40-induced IL-4 receptor mRNA levels, while protein kinase C (PKC) inhibitors had no effects. These results suggest that IL-4 and CD40 ligation generate B cell signals, which via PTK-dependent pathways, lead to the synergistic induction of IL-4 receptor gene expression. The rapid induction of IL-4 receptor gene expression through the tyrosine kinase-mediated signal transduction by B cell activating stimuli, would provide cells capacity for an efficient response to IL-4 in the early phase of IL-4 action, and may in part constitute the molecular basis of the reported anti-CD40 co-stimulatory effect on the IL-4-induced response.