• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2004.04a
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• pp.255-258
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• 2004

본 연구는 유전자 기능예측에 있어서 유사성 검색과 비교유전체학이 가진 한계를 극복하기 위하여 9종의 Human Herpesvirus를 대상으로 COG와 계통유전학적 방법을 적용하여 향상된 유전자 기능예측을 하고자 하였다. COG의 방법을 이용하여 114 HCOGs (Human Herpesvvirus COGs)를 구축하고, HCOGs를 바탕으로 유전자 컨텐츠트리를 제작하였다. 이 트리를 통하여 각 HCOG는 $\alpha$-특이적 그룹, $\beta$-특이적 그룹, $\alpha$, $\beta$, ${\gamma}$ -특이적 그룹 중 하나에 속함을 보였다. 계통유전체학의 적용을 위하여 u, $\beta$, ${\gamma}$ -특이 그룹에 속하는 ORF중 DNA polymerase를 이용하여 종트리를 제작하였다. SDI (Speciation and Duplication) 알고리즘을 통하여 148개의 당단백질에서 47개의 복제점을 예측하였고, 초기 HCOG의 제작에서 제외되었던 7 ORF는 당단백질과 관련된 5개의 HCOG로 재 정의 하였다. 이 연구를 통하여 COG는 ortholog 그룹을 를러스터링하는데 효과적인 방법이며, 이를 더욱 보완할 수 있는 방법으로 비교유전체학이 사용될 수 있음을 확인하였다. 이는 비교유전체학의 방법과 계통유전체학적 방법을 조화시켜 유전자 기능 예측을 보완할 수 있음을 보여 주었다.

• Development and Reproduction
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• v.13 no.4
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• pp.249-256
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• 2009

The estrogen receptor-related receptors (ERRs) are a group of nuclear receptor superfamily of transcription factors. ERRs and estrogen receptors (ERs) have overlapping affinities for coactivators and DNA binding sites, but differ markedly in ligand binding and activation. The three mammalian ERR genes have been implicated in diverse physiological processes ranging from placental development to maintenance of bone density, whereas the molecular diversity, function, and regulation of ERRs in non-mammalian species are not well understood. In the present study, to investigate the involvement of ERR in transcription and embryogenesis in marine invertebrates, a cDNA encoding ERR (SnERR) was cloned from the gonad in Strongylocentrotus nudus, by polymerase chain reaction (PCR). The amino acid sequence of SnERR showed high homology with that of S. purpuratus (91%). A phylogenetic tree clearly showed that SnERR is a member of the ERR family and clustered in echinodermata group as supported by a high bootstrap value. We examined gene expression of SnERR during embryonic development of S. nudus using real-time PCR. During the embryonic development, the mRNA of ERR was significantly high levels in early development stages (4~64 cell) and larval stages. The SnERR slightly activated transcription through the classical estrogen response elements (EREs) in the presence of genistein. In addition, peroxisome proliferator-activated receptor $\gamma$ coactivator (PGC)-$1\alpha$ knwon as a coactivator of ERR enhanced the snERR-mediated transactivation, suggesting that the PGC-$1\alpha$ is a coactivator of SnERR.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.10
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• pp.1493-1498
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• 2014

Epigenetic factors, such as DNA methylation status, may regulate adipogenesis and lipogenesis, thus affecting intramuscular fat (IMF) deposition in longissimus dorsi muscle (LM) of beef cattle. In Korean cattle steers, the LM consists mainly of muscle tissue. However, the LM tissue also contains IMF. We compared the gene expression levels between the IMF and muscle portions of the LM after tissue separation. Real-time polymerase chain reaction analysis showed that the mRNA levels of both adipogenic peroxisome proliferator-activated receptor gamma isoform 1 (PPARG1) and lipogenic fatty acid binding protein 4 (FABP4) were higher (p<0.01) in the IMF than in the muscle portion of the LM. We determined DNA methylation levels of regulatory regions of the PPARG1 and FABP4 genes by pyrosequencing of genomic DNA. DNA methylation levels of two of three CpG sites in the PPARG1 gene promoter region were lower (p<0.05) in the IMF than in the muscle portion of the LM. DNA methylation levels of all five CpG sites from the FABP4 gene promoter region were also lower (p<0.001) in the IMF than in the muscle portion. Thus, mRNA levels of both PPARG1 and FABP4 genes were inversely correlated with DNA methylation levels in regulatory regions of CpG sites of the corresponding gene. Our findings suggest that DNA methylation status regulates tissue-specific expression of adipogenic and lipogenic genes in the IMF and muscle portions of LM tissue in Korean cattle.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• v.20 no.4
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• pp.259-262
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• 2017

Mitochondria play essential role in eukaryotic cells including in the oxidative phosphorylation and generation of adenosine triphosphate via the electron-transport chain. Therefore, defects in mitochondrial DNA (mtDNA) can result in mitochondrial dysfunction which leads to various mitochondrial disorders that may present with various neurologic and non-neurologic manifestations. Mutations in the nuclear gene polymerase gamma (POLG) are associated with mtDNA depletions, and Alpers-Huttenlocher syndrome is one of the most severe manifestations of POLG mutation characterized by the clinical triad of intractable seizures, psychomotor regression, and liver failure. The hepatic manifestation usually occurs late in the disease's course, but in some references, hepatitis was reportedly the first manifestation. Liver transplantation was considered contraindicated in Alpers-Huttenlocher syndrome due to its poor prognosis. We acknowledged a patient with the first manifestation of the disease being hepatic failure who eventually underwent liver transplantation, and whose neurological outcome improved after cocktail therapy.

• Journal of Life Science
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• v.19 no.8
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• pp.1047-1054
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• 2009

Oral squamous carcinoma (OSC) cells present resistance to chemotherapeutic agents-mediated apoptosis in the late stages of malignancy. Advances in the understanding of bacterial toxins have produced new strategies for the treatment of cancers. It was demonstrated here that Pseudomonas aeruginosa exotoxin A (PEA) significantly decreased the viability of chemoresistant YD-9 cells in the apoptosis mechanism. Apoptotic manifestations were evident through changes in nuclear morphology and generation of DNA fragmentation. PEA treatment induced caspase-3, -6 and -9 cleavage, and activation. These events preceded proteolysis of the caspase substrates poly (ADP-ribose) polymerase (PARP), DNA fragmentation factor 45 (DFF45), and lamin A in YD-9 cells. The reduction of mitochondrial membrane potential, release of cytochrome c and SmacjDlABLO from mitochondria to cytosol, andtranslocation of AlF into nucleus were shown. While p53, p21 and $14-3-3{\gamma}$ were upregulated, cyclin Band cdc2 were downregulated by PEA treatment. Taken together, PEA induces apoptosis in chemoresistant YD-9 cells via activation of caspases, mitochondrial events and regulation of cell cycle genes.

• Journal of Korean Society on Water Environment
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• v.24 no.1
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• pp.19-29
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• 2008

Hot air sparging is a groundwater remediation technique, in which organic contaminants volatilized into hot air from the saturated to vadose zone. In the laboratory diesel (10,000 mg TPH/kg) was spiked in contaminated saturated aquifer soil. The hot air ($34.9{\pm}2.7^{\circ}C$) was injected in intermittent (Q=1,500 mL/min, 10 minute injection and 10 minute idle) modes. We performed microcosm tests using the groundwater samples to assess TPH reductive remediation activity. For Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis of eubacterial communities in sludge of wastewater treatment plants and soil of experiment site, the 16S rDNA was amplified by Polymerase Chain Reaction (PCR) from the sludge and the soil. The obtained 16S rDNA fragments were digested with Msp I and separated by electrophoresis gel. We found various sequence types for hot air sparging experiment with sludge soil samples that were closely related to Bacillus (149 bp, Firmicutes), Methlobacterium (149 bp, Euryarchaeotes), Pseudomonas (492 bp, ${\gamma}$-Proteobacteria), etc., in the clone library. In this study we find that TPH-water was reduced to 78.9% of the initial value in this experiment aquifer. The results of the present study suggests that T-RFLP method may be applied as a useful tool for the monitoring in the TPH contaminated soil fate of microorganisms in natural microbial community.

• Journal of Periodontal and Implant Science
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• v.34 no.3
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• pp.671-681
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• 2004

Genomic Project 이후로 다양한 질환에 있어서 유전적인 영향에 관한 연구가 진행되고 있다. 이 연구의 목적은 한국인 치주질환 환자에서 Fc ${\gamma}R$ 유전자의 유전자다형성과 치주질환 특성과의 관련성을 알아보는 것이다. 치주적으로 건강한 한국인 90명(대조군, 남자64명, 여자26명), 중도 만성 치주염환자 40명(severe chronic periodontitis patients; severe CP, 남자 24명, 여자 16명)을 대상으로 임상지수(치주낭 깊이, 입상부착소실, 치은지수, 치태지수, 탐침 후 출혈지수, 치조골소실)를 측정하였다. 또한 이들의 정맥혈에서 추출한 DNA를 PCR(Polymerase Chain Reaction)법, 전기영동법 등을 이용하여 Fc ${\gamma}RIIIa$ , Fc ${\gamma}RIIIb$의 대립유전자의 존재여부를 확인하였다. 이를 바탕으로 각 유전자의 다형성 및 Fc ${\gamma}R$ 복합유전자형 (Fc ${\gamma}R$ composite genotype)을 확인하여, 각 군 간을 비교하였다. 치주질환의 특성과 유전자 다형성과의 관련성을 알아보기 위하여 Fc ${\gamma}R$ 유전자에 대한 유전자다형성을 조사한 결과 다음과 같은 결과를 얻을 수 있었다. 1. Fc ${\gamma}RIIla$에 대한 유전자다형성 연구결과 대조군과 severe CP, AgP군 사이에서, severe CP와 AgP군 사이에서는 대립유전자분포가 서로 유의성 있는 차이를 나타내었지만(p<0.05), Fc ${\gamma}RIIlb$에서는 유의성 있는 차이를 보이지 않았다(p>0.05). 2. Fc ${\gamma}R$ 복합유전자형간의 비교에서 유의성 있는 차이를 발견할 수 없었다(p>0.05). 이와 같은 결과를 종합하여 볼 때 실험대상 한국인 치주염환자에서 Fc ${\gamma}R$ 유전자에 대한 다형성분석에서 Fc ${\gamma}RIIIa$ 대립유전자가 치주염에 대한 감수성과 관련되어 있다고 생각된다. 이 연구의 결과는 유전자의 차이가 치주질환의 감수성 판단의 자료로 활용할 수 있는 가능성을 보여주고 있다.

• Journal of Physiology & Pathology in Korean Medicine
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• v.21 no.6
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• pp.1513-1519
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• 2007

Yukwool-tang (YWT) is a traditional Chinese medicine, which has been used for patients suffering from a uterine disease in Oriental medicine. In the present study, it was examined the biochemical mechanisms of apoptosis by YWT in human cervical carcinoma HeLa cells. It was found that YWT could inhibit the cell growth of HeLa cells in a dose-dependent manner, which was associated with apoptotic cell death such as formation of apoptotic bodies and DNA fragmentation. Flow cytometry analysis confirmed that YWT treatment increased populations of apoptotic-sub-G1 phase of the cell cycle. We observed the p53-independent induction of p21 proteins, down-regulation of anti apoptotic Bcl-2 expression and proteolytic activation of caspase-3 in YWT-treated HeLa cells. YWT treatment also concomitant degradation and/or inhibition of poly (ADP-ribose) polymerase (PARP), phospholipase C-1 ($PLC{\gamma}1$), ${\beta}-catenin$ and DNA fragmentation factor 45/inhibitor of caspase-activated DNase (DFF45/ICAD). Taken together, these findings partially provide novel insights into the possible molecular mechanism of the anti-cancer activity of YWT.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.8
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• pp.3117-3120
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• 2015

Objective: Interferon-${\gamma}$ (IFN-${\gamma}$) and signal transducers and activators of transcription (STATs) each play an important role in carcinogenesis associated with viral infection. Cervical cancer is almost invariably associated with infection by human papillomavirus (HPV), and previous studies suggested that dysregulation of the signal pathway involved in IFN-${\gamma}$ and STATs is associated. Our objective was to evaluate the association of SNPs in STAT2, STAT3, and IFN-${\gamma}$ with cervical cancer susceptibility in Chinese Han women in Hunan province. Materials and Methods: Genomic DNA was extracted from peripheral blood samples of 234 cervical cancer patients and 216 healthy female controls. STAT2 and STAT3 genotyping was performed using polymerase chain reaction-restriction enzyme (PCR-RE) analysis. IFN-${\gamma}$ genotyping was detected by PCR-amplification of specific allele (PASA). Results: For STAT2 rs2066807 polymorphisms, there was no significant difference of genotype distribution (P=0.827) and allele frequencies (P=0.830, OR=1.09, 95% CI: 0.51-2.31) between cases and controls. For STAT3 rs957970 polymorphisms, there was no significant difference of genotype distribution (P=0.455) and allele frequencies (P=0.560, OR=0.92, 95% CI: 0.71-1.20) between cases and controls. For IFN-${\gamma}$ +874A/T polymorphisms, there was no significant difference of genotype distribution (P=0.652) and allele frequencies (P=0.527, OR=1.12, 95% CI: 0.79-1.59) between cases and controls. Conclusion: These results suggest that polymorphisms in STAT2, STAT3 and IFN-${\gamma}$ genes are not likely to be strong predictors of cervical cancer in Han women in southern China.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.04a
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• pp.68-68
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• 2018

In this study, we investigated whether S. baicalensis rhizome ethanol extract (SBRE) has antioxidant capacities against oxidative stress induced cellular damage in the HaCaT keratinocytes. Our results revealed that treatment with SBRE prior to hydrogen peroxide ($H_2O_2$) exposure significantly increased the HaCaT cell viability. SBRE also effectively attenuated $H_2O_2$ induced comet tail formation, and inhibited the $H_2O_2$ induced phosphorylation levels of the histone ${\gamma}H2AX$, as well as the number of apoptotic bodies and Annexin V positive cells. In addition, SBRE exhibited scavenging activity against intracellular ROS generation and restored the mitochondria membrane potential loss induced by $H_2O_2$. Moreover, $H_2O_2$ enhanced the cleavage of caspase-3 and degradation of poly (ADP-ribose)-polymerase as well as DNA fragmentation; however, these events were almost totally reversed by pretreatment with SBRE. Furthermore, SBRE increased the levels of HO-1 associated with the induction of Nrf2. Therefore, we believed that SBRE may potentially serve as an agent for the treatment and prevention of neurodegenerative diseases caused by oxidative stress.