• 한국콘텐츠학회논문지
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• 제14권11호
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• pp.467-475
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• 2014

최근 유전체학의 발전, 웨어러블 디바이스의 확산, IT/NT의 발전 등에 따라 방대한 양의 바이오-메디컬 데이터가 생산되고, 이에 따라 빅데이터를 활용한 헬스케어 산업이 급속히 발달하고 있으며, 이와 관련된 빅데이터 기술은 국민의 건강 증대와 건강한 고령 삶을 제공하는 핵심 기술로 급부상하고 있다. 패스웨이(Pathway)는 단백질, 유전자, 세포 등의 생체적 요소 간의 역학관계 혹은 상호작용 등을 네트워크 형식으로 표현한 생물학적 심층지식으로, 바이오-메디컬 빅데이터 분석에 있어서 널리 활용되고 있다. 하지만 패스웨이는 매우 다양한 형태를 갖고 용량이 매우 큰 빅데이터로 이를 분석하는데 많은 시간이 소요되며, 현재까지도 다양한 패스웨이를 통합 분석할 수 있는 시스템은 전무하다. 그래서 본 논문에서는 세계적으로 가장 우수하고 방대한 양의 패스웨이를 제공하는 KEGG 패스웨이 데이터베이스로부터 사용자가 관심 갖는 패스웨이만을 자동 수집하고 패스웨이 간 계층구조를 기반으로 네트워크를 구성 후, 해당 패스웨이 네트워크에 대한 클러스터링과 핵심 패스웨이 선정을 통해 패스웨이 간의 역학관계 또는 상호작용을 직관적으로 분석할 수 시스템을 제안했다. 마지막으로, 다양한 성능 평가 결과를 통해 개발한 분석 시스템의 우수성을 입증한다.

• Molecules and Cells
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• 제39권11호
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• pp.777-782
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• 2016

The innate immune system has evolved to detect and destroy invading pathogens before they can establish systemic infection. To successfully eradicate pathogens, including viruses, host innate immunity is activated through diverse pattern recognition receptors (PRRs) which detect conserved viral signatures and trigger the production of type I interferon (IFN) and pro-inflammatory cytokines to mediate viral clearance. Viral persistence requires that viruses co-opt cellular pathways and activities for their benefit. In particular, due to the potent antiviral activities of IFN and cytokines, viruses have developed various strategies to meticulously modulate intracellular innate immune sensing mechanisms to facilitate efficient viral replication and persistence. In this review, we highlight recent advances in the study of viral immune evasion strategies with a specific focus on how Kaposi's sarcoma-associated herpesvirus (KSHV) effectively targets host PRR signaling pathways.

• BMB Reports
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• 제34권5호
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• pp.421-427
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• 2001

Osteoclasts, cells primarily involved in bone resorption, originate from the hematopoietic precursor cells of the monocyte/macrophage lineage and differentiate into multinucleated mature forms. We developed an in vitro osteoclast culture system using embryonic chicken bone marrow cells. This culture system can be utilized in studies on the differentiation and function of osteoclasts. Phosphatidylinositol 3-kinase (PI3-kinase) and mitogen-activated protein kinases (MAPKs) have been implicated in diverse cellular functions including proliferation, migration, and survival. Using the developed avian osteoclast culture system, we examined the involvement of these kinases in osteoclast differentiation by employing specific inhibitors of the kinases. We Found that the inhibition of the PI 3-kinase, p38, or ERK interfered with osteoclast formation, suggesting that the signaling pathways that involve these molecules participate in the process of chicken osteoclast differentiation.

• Journal of Microbiology
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• 제38권2호
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• pp.53-61
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• 2000

Hydroxybenzoic acids are the most important intermediates in the degradative pathways of various aromatic compounds. Microorganisms catabolize aromatic compounds by converting them to hydroxylated intermediates and then cleave the benzene nucleus with ring dioxygenases. Hydroxylation of the benzene nucleus of an aromatic compound is an essential step for the initiation and subsequent disintegration of the benzene ring. The incorporation of two hydroxyl groups is essential for the labilization of the benzene nucleus. Monohydroxybenzoic acids such as 2-hydroxybenzoic acid, 3-hydroxybenzoic acid, and 4-hydrosybenzoic acid, opr pyrocattechuic acid that are susceptible for subsequent oxygenative cleavage of the benzene ring. These terminal aromatic intermediates are further degraded to cellular components through ortho-and/or meta-cleavage pathways and finally lead to the formation of constituents of the TCA cycle. Many groups of microorganisms have been isolated as degraders of hydroxybenzoic acids with diverse drgradative routes and specific enzymes involved in their metabolic pahtway. Various microorganisms carry out unusual non-oxidative decarboxylation of aromatic acids and convert them to respective phenols which have been documented. Futher, Pseudomonas and Bacillus spp. are the most ubiquitous microorganisms, being the principal components of microflora of most soil and water enviroments.

• Genomics & Informatics
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• 제14권2호
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• pp.46-52
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• 2016

Diverse somatic mutations have been reported to serve as cancer drivers. Recently, it has also been reported that epigenetic regulation is closely related to cancer development. However, the effect of epigenetic changes on cancer is still elusive. In this study, we analyzed DNA methylation data on colon cancer taken from The Caner Genome Atlas. We found that several promoters were significantly hypermethylated in colon cancer patients. Through clustering analysis of differentially methylated DNA regions, we were able to define subgroups of patients and observed clinical features associated with each subgroup. In addition, we analyzed the functional ontology of aberrantly methylated genes and identified the G-protein-coupled receptor signaling pathway as one of the major pathways affected epigenetically. In conclusion, our analysis shows the possibility of characterizing the clinical features of colon cancer subgroups based on DNA methylation patterns and provides lists of important genes and pathways possibly involved in colon cancer development.

• Molecules and Cells
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• 제42권2호
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• pp.166-174
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• 2019

Bacterial species in the genus Xanthomonas infect virtually all crop plants. Although many genes involved in Xanthomonas virulence have been identified through molecular and cellular studies, the elucidation of virulence-associated regulatory circuits is still far from complete. Functional gene networks have proven useful in generating hypotheses for genetic factors of biological processes in various species. Here, we present a genome-scale co-functional network of Xanthomonas oryze pv. oryzae (Xoo) genes, XooNet (www.inetbio.org/xoonet/), constructed by integrating heterogeneous types of genomics data derived from Xoo and other bacterial species. XooNet contains 106,000 functional links, which cover approximately 83% of the coding genome. XooNet is highly predictive for diverse biological processes in Xoo and can accurately reconstruct cellular pathways regulated by two-component signaling transduction systems (TCS). XooNet will be a useful in silico research platform for genetic dissection of virulence pathways in Xoo.

• Toxicological Research
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• 제22권1호
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• pp.23-30
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• 2006

Among poly aromatic hydrocarbons, dioxin and PCBs are the most controversial environmental pollutants in our modern life. These pollutants are known as human carcinogens, and liver is the most sensitive target in animal cancer models. Specific aims of the study were focused on the mechanism of carcinogenesis in hepatocytes and the structure-activity relation among these diverse environmental chemicals. Because key mechanisms of dioxin-induced carcinogenesis in human epithelial cell model are the alteration of signal transduction pathway and PKC isoforms, the alteration of the signal transduction pathways and other factors associated with carcinogenesis were studied. Rat hepatocytes cultured under the sandwich protocols were exposed with the various concentration of dioxins and PCBs, and signal transduction pathway, protein kinase C isoforms, oxidant stress, and apoptotic nuclei were evaluated. Since it is important to understand the structure-activity relation among these chemicals to properly assess the carcinogenic potentials, the study analyzed the parameters associated with carcinogenic processes, based on their structural characteristics. In addition, signal transduction pathways and PKC isoforms involved in inhibition of UV-induced apoptosis were also analyzed to elaborate the tumor promotion mechanism of these chemicals. Induction of apoptosis by UV irradiation was optimal at $60\;J/m^2$ in primary hepatocyte in culture. Compared to non coplanar PCBs such as PCB 114 and PCB 153, coplanar PCBs such as PCB 77 and PCB126 showed a stronger inhibition of apoptosis induced by UV irradiation. Production of reactive oxygen species (ROS) was more stimulated by non-coplanar PCBs than coplanar PCBs with the most potent induction of ROS by chlorinated non-coplanar PCB. As compared to the level of induction by PCB126, non-coplanar PCB153 showed a higher increase of intracellular concentrations. Besides the alteration of intracellular calcium concentration, translocation of PKC from cytosolic fraction to membrane fraction was clearly observed upon the exposure of non-coplanar PCB. Taken together, the present study demonstrated that there is a potent structure-activity relationship among PCB congeners and the mechanism of PAH-induced carcinogenesis is structure-specific. The study suggested that more diverse pathways of PAH-induced carcinogenesis should be taken into account beyond the boundary of Ah receptor dogma to assess the health impact of PAH with more accuracy.

• Archives of Pharmacal Research
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• 제23권1호
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• pp.1-16
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• 2000

Many natural products elicit diverse pharmacological effects. Using two classes of potential chemopreventive compounds, the phenolic compounds and the isothiocyanates, we review the potential utility of two signaling events, the mitogen-activated protein kinases (MAPKs) and the ICE/Ced-3 proteases (caspases) stimulated by these agents in mammalian cell lines. Studies with phenolic antioxidants (BHA, tBHQ), and natural products (flavonoids; EGCG, ECG, and isothiocyanates; PEITC, sulforaphane), provided important insights into the signaling pathways induced by these compounds. At low concentrations, these chemicals may activate the MAPK (ERK2, JNK1, p38) leading to gene expression of survival genes (c-Fos, c-Jun) and defensive genes (Phase II detoxifying enzymes; GST, QR) resulting in survival and protective mechanisms (homeostasis response). Increasing the concentrations of these compounds will additionally activate the caspase pathway, leading to apoptosis (potential cytotoxicity). Further increment to suprapharmacological concentrations will lead to nonspecific necrotic cell death. The wider and narrow concentration ranges between the activation of MAPK/gene induction and caspases/cell death exhibited by phenolic compounds and isothiocyanates, respectively, in mammalian cells, may reflect their respective therapeutic windows in vivo. Consequently, the studies of signaling pathways elicited by natural products will advance our understanding of their efficacy and safety, of which many man become important therapeuitc drugs of the future.

• Nutritional Sciences
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• 제7권1호
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• pp.23-30
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• 2004

As a central component of a novel protein kinase cascade, the activation of the mitogen-activated protein (MAP) kinase cascade has attracted considerable attention. We sought to determine the effect of exercise and diet on the activation of the extracellular-signal regulated protein kinase (ERK) 1/2 and the p38 MAP kinase pathways in rat soleus muscle. Forty-eight Sprague-Dawley rats were assigned to one of two dietary conditions: high-carbohydrate (CHO) or high-fat (FAT). Animals having each dietary condition were further divided into one of three subgroups: a sedentary control group that did not exercise (NT), a group that performed 8 weeks of treadmill running and was sacrificed 48 h after their final treadmill run (CE), and a group that was sacrificed immediately after their final routine exercise training (AE). A high-fat diet did not have any significant effect on phosphorylated and total forms of ERK 1/2 or p38 MAP kinase. In chronically trained muscle that was taken 48 h after the last training, phosphorylated ERK 1/2 significantly increased only in the FAT but not in the CHO groups. In the case of total ERK 1/2, it increased significantly for both groups. In contrast, both phosphorylated and total forms of p38 MAP kinase decreased markedly compared to sedentary muscle. In muscle that was taken immediately after a last bout of exercise, phosphorylated ERK 1/2 increased in both groups but statistical significance was seen only in the CHO group. Total ERK 1/2 in acutely stimulated muscle increased only in the CHO-AE group even though the degree was much lower than the phosphorylated status. Muscle that was taken immediately after the routine training increased in phosphorylation status of p38 MAP kinase for both dietary conditions. However, statistical significance was seen only in the CHO group owing to a large variation with FAT. In conclusion, a high-fat diet per se did not have any notable effect versus a high-carbohydrate diet on MAP kinase pathways. However, when diet (either CHO or FAT) was combined with exercise and/or training, there was differentiated protein expression in MAP kinase pathways. This indicates MAP kinase pathways have diverse control mechanisms in slow-twitch fibers.

• BMB Reports
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• 제47권5호
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• pp.241-248
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• 2014

CD1 molecules belong to non-polymorphic MHC class I-like proteins and present lipid antigens to T cells. Five different CD1 genes (CD1a-e) have been identified and classified into two groups. Group 1 include CD1a-c and present pathogenic lipid antigens to ${\alpha}{\beta}$ T cells reminiscence of peptide antigen presentation by MHC-I molecules. CD1d is the only member of Group 2 and presents foreign and self lipid antigens to a specialized subset of ${\alpha}{\beta}$ T cells, NKT cells. NKT cells are involved in diverse immune responses through prompt and massive production of cytokines. CD1d-dependent NKT cells are categorized upon the usage of their T cell receptors. A major subtype of NKT cells (type I) is invariant NKT cells which utilize invariant $V{\alpha}14-J{\alpha}18$ TCR alpha chain in mouse. The remaining NKT cells (type II) utilize diverse TCR alpha chains. Engineered CD1d molecules with modified intracellular trafficking produce either type I or type II NKT cell-defects suggesting the lipid antigens for each subtypes of NKT cells are processed/generated in different intracellular compartments. Since the usage of TCR by a T cell is the result of antigen-driven selection, the intracellular metabolic pathways of lipid antigen are a key in forming the functional NKT cell repertoire.