• 한국축산식품학회지
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• 제31권4호
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• pp.530-536
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• 2011

It is well established that uncoupling protein 3 (UCP3) is expressed largely in skeletal muscle, white adipose tissue and brown adipose tissue and has been suggested to play important roles in regulating energy expenditure, body weight, thermoregulation as well as fatty acid metabolism and obesity. Therefore, the UCP3 gene was selected as a candidate gene for carcass and meat quality traits in Korean cattle. The objective of this study was to identify single nucleotide polymorphisms (SNPs) in the UCP3 gene and to evaluate the association of UCP3 SNP markers with carcass and meat quality traits in Korean cattle. The five exons in the UCP3 gene were sequenced, and ten SNPs were identified. The PCR-SSCP method was then developed to genotype the individuals examined. The g.3076A>G genotype was significantly associated with marbling score (MS) of Korean cattle. Animals with the AA genotype had a higher MS than those with the AG and GG genotypes. No significant associations of the SNP g.3076A>G were observed for any traits. In conclusion, although SNP g.3076A>G, which showed an association with MS, does not cause amino acid changes, this SNP may be used as a DNA marker to select animals that have higher intramuscular fat content.

• Asian Pacific Journal of Cancer Prevention
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• 제14권8호
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• pp.4553-4557
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• 2013

Objective: The purpose of this study was to identify genes related to bladder cancer with samples from normal and disease cases by microarray chip. Methods: After downloading the gene expression profile GSE3167 from Gene Expression Omnibus database which includes 50 bladder samples, comprising 9 normal and 41 disease samples, differentially expressed genes were identified with packages in R language. The selected differentially expressed genes were further analyzed using bioinformatics methods. Firstly, molecular functions, biological processes and cell component analysis were researched by software Gestalt. Then, software String was used to search interaction relationships among differentially expressed genes, and hub genes of the network were selected. Finally, by using plugins of software Cytoscape, Mcode and Bingo, module analysis of hub-genes was performed. Results: A total of 221 genes were identified as differentially expressed by comparing normal and disease bladder samples, and a network as well as the hub gene C1QBP was obtained from the network. The C1QBP module had the closest relationship to production of molecular mediators involved in inflammatory responses. Conclusion: We obtained differentially expressed genes of bladder cancer by microarray, and both PRDX2 and YWHAZ in the module with hub gene C1QBP were most significantly related to production of molecular mediators involved in inflammatory responses. From knowledge of inflammatory responses and cancer, our results showed that, the hub gene and its module could induce inflammation in bladder cancer. These related genes are candidate bio-markers for bladder cancer diagnosis and might be helpful in designing novel therapies.

• Tuberculosis and Respiratory Diseases
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• 제44권4호
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• pp.796-805
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• 1997

연구배경 : 세포주기의 활성화, 그 중에서도 특히 $G_1$/S 이행에 관여하는 세포주기관련 단백질들은 암발생에 있어서 매우 중요한 역할을 하는 것으로 알려져 있다. $G_1$ 세포주기 관련 단백질 중의 하나인 cdk4 (cyclin dependent kinase 4)의 억제제로 알려져 있는 p16 유전자는 최근에 밝혀진 종양억제유전자중의 하나로서 MTS1 (multiple tumor suppressor 1)이라고도 불린다. p16 유전자는 지금까지 알려진 어느 종양관련 유전자보다도 유전자변이의 빈도가 높은 암억제유전자인데, 특히 비소세포폐암인 경우는 70% 이상의 세포주에서 p16 단백질의 발현이 없는 것으로 밝혀져 있어 p16 유전자는 비소세포폐암 발생에 매우 중요한 역할을 할 것이라고 알려져 있다. 본 연구에서는 비소세포폐암에서 p16을 이용한 유전자치료의 타당성을 입증하기 위하여 다음과 같은 연구를 시행하였다. 방 법 : p16이 결여된 비소세포폐암 세포주 (NCI-H441)에, 정상섬유아세포에서 총 RNA를 추출하여 역전사효소 및 DNA 중합효소반응으로 증폭된 p16 cDNA를 유핵세포 발현 vector인 pRC-CMV plasmid에 subcloning하여 구축된 pRC-CMV-p16 plasmid vector를 lipofectin을 이용하여 유전자 이입한 후, 단백질을 추출하여 Western blot 분석과 면역침전법으로 $G_1$ 세포주기관련 단백질의 변동을 관찰하고, colony 형성능을 비교함으로써 암억제효과를 확인하였다. 결 과 : p16이 유전자주입된 NCI-H441 세포주에서 p16과 cdk4가 복합체를 형성하고 있고 인산화 Rb가 대조 세포주에 비해 감소되어 있음을 확인할 수 있어, p16이 cdk4와 결합함으로써 cdk4에 의한 Rb의 인산화를 방해하고 이에 따른 $G_1$ 세포주기 정체에 의해 종양억제효과가 나타난다는 설명을 뒷받침할 수 있었다. Clonogenic assay 결과는 p16 유전자주입된 NCI-H441 세포주의 colony 형성능이 대조 세포주에 비하여 현격히 감소함을 관찰하였다. 결 론 : 이상의 결과로 p16(MTS1) 유전자를 p16 단백질을 발현하지 못하는 비소세포폐암 세포주에 주입할 경우, 주입한 유전자에서 생성되는 p16 단백질이 cdk와 결합하여 Rb 단백질의 인산화를 저하시켜 궁극적으로 암억제 효과를 일으킬 수 있음이 확인되었고, 이는 향후 비소세포폐암의 유전자치료에 있어서 p16 유전자의 이용 가능성을 확인한 기초자료가 된다고 생각된다.

• Genomics & Informatics
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• 제15권4호
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• pp.128-135
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• 2017

As next-generation sequencing technologies have advanced, enormous amounts of whole-genome sequence information in various species have been released. However, it is still difficult to assemble the whole genome precisely, due to inherent limitations of short-read sequencing technologies. In particular, the complexities of plants are incomparable to those of microorganisms or animals because of whole-genome duplications, repeat insertions, and Numt insertions, etc. In this study, we describe a new method for detecting misassembly sequence regions of Brassica rapa with genotyping-by-sequencing, followed by MadMapper clustering. The misassembly candidate regions were cross-checked with BAC clone paired-ends library sequences that have been mapped to the reference genome. The results were further verified with gene synteny relations between Brassica rapa and Arabidopsis thaliana. We conclude that this method will help detect misassembly regions and be applicable to incompletely assembled reference genomes from a variety of species.

• Journal of Microbiology and Biotechnology
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• 제15권4호
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• pp.767-771
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• 2005

Expression in yeast may prove more amenable to generating large amounts of viral antigens for a vaccine candidate. We, therefore, cloned the gene encoding the Hepatitis C virus (HCV) structural proteins (C-El-E2, c740) fused in-frame with, and immediately 3' to, the chicken-lysozyme signal peptide (C-SIG) gene and under the control of the yeast glyceraldehyde-3-phosphate dehydrogenase gene promoter. In yeast, the HCV structural proteins were expressed in two different forms: a processed and a nonprocessed aggregated form. Biophysical characterization by sucrose linear gradient centrifugation revealed that both forms were present in the same fractions with a buoyant density of 1.127-1.176 g/$cm^3$. These findings suggest that the efficient synthesis of HCV structural proteins in yeast may be an important tool to study virus assembly and may lead to the development of an HCV vaccine.

• Nutrition Research and Practice
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• 제5권6호
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• pp.527-532
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• 2011

ESR1 has been listed in the Human Obesity Gene Map as candidate gene associated with obesity. Thus, in this study, we investigated the effect of the ESR1 rs1884051 polymorphism on obesity-related variables, together with their modulations by dietary intake in Korean men. The obesity-related variables and dietary intake of 3,039 Korean men aged 40-59 years from KoGES database were analyzed. Body weight (P = 0.007), BMI (P = 0.003), waist-hip ratio (= 0.011), fat body mass (P = 0.010), and body fat percentage (P = 0.040) were significantly lower in subjects with the minor T allele of ESR1 rs1884051 than in subjects carrying the C allele. Moreover, the rs1884051 T allele was associated with a decreased risk of obesity prevalence (P = 0.040). Among the subjects whose total energy intake was below the median, carrier of the minor T allele of ESR1 rs1884051 had a lower BMI (P = 0.003) when compared with subjects carrying the C allele. In addition, among subjects whose plant protein intake was above the median, carrier of the minor T allele of ESR1 rs1884051 had a lower BMI (P = 0.044) compared with subjects carrying the C allele. Our findings demonstrate that there is a significant association between the ESR1 rs1884051 variant and obesity-related variables and this association can be potentially modified by dietary energy and plant protein intake.

• 대한한방부인과학회지
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• 제19권3호
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• pp.1-12
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• 2006

Purpose : This study was aimed to investigate the inhibitory effect of Leonurus sibiricus on the proliferation of human uterine leiomyoma cells and the expression of gene related the mechanism of cell apoptosis. Methods : We counted the number of death cells treated with indicated concentration of Leonurus sibiricus and investigated cell death rate by MTS assay. Furthermore, flow cytometry analysis and DNA fragmentation assay were used to dissect between necrosis and apoptosis and then we observed the differential gene expression by western blot analysis. Results : Leonurus sibiricus significantly inhibited the proliferation of uterine leiomyoma cell in a dose-dependent and time dependent manner. Fluorescence activated cell sorter (FACS) analysis indicated that Leonurus sibiricus induced G1 cell cycle arrest. Leonurus sibiricus enhanced the expression of p27 and p53 with cell cycle arrest. Conclusion : These findings suggest that Leonurus sibiricus is a candidate agent for the treatment of uterine leiomyoma. p27, $p53^{1}$ may play an important role in Leonurus sibiricus-induced cell cycle arrest and cell growth inhibition.

• 한국인삼전략화협의회:학술대회논문집
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• 한국인삼전략화협의회 2003년도 제4차 한국인삼약초산업 전략화 세미나
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• pp.54-63
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• 2003

"Korea ginseng (Panax ginseng C.A Meyer) is an important medicinal plant. Its root has been used as an herbal medicine that provides resistance to stress and disease, and prevents exhaustion since the ancient time. Ginsenosides, glycosylated triterpene (saponin), are considered to be the main active compounds of the ginseng root. Despite of considerable commercial interests of ginsenosides, very little is known about the genes and their biochemical pathways for ginsenoside biosynthesis. This work will focus on the identification of genes involved in ginsenoside biosynthesis and the dissection of ginsenoside biosynthetic pathway using a functional genomics tool. Expression sequence tags (ESTs) provide a valuable tool to discovery the genes in secondary metabolite biosynthesis. We generated over 21,155 ginseng ESTs that is now sufficient to facilitate discovering the genes involved in ginsenoside biosynthesis such as oxidosqualene cyclase(OSC), cytochrome P450 and glycosyltransferase. With ESTs information, microarray technology will be used for the analysis of gene expression, and the identification of genes including transcription factors expressed in tissues under given experimental condition. Heterogous system such as yeast and plants will allow us to do the functional analysis. And selected ginseng hairy root which show variation in ginsenoside production will be used as a material for functional analysis of candidate gene. Functional genomics approach will successfully accelerate gene discovery, and also provide promises of metabolic engineering for the ginsenoside production."

• Toxicological Research
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• 제26권1호
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• pp.1-8
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• 2010

The process of new drug development consists of several stages; after identifying potential candidate compounds, preclinical studies using animal models link the laboratory and human clinical trials. Among many steps in preclinical studies, toxicology and safety assessments contribute to identify potential adverse events and provide rationale for setting the initial doses in clinical trials. Gene modulation is one of the important tools of modern biology, and is commonly employed to examine the function of genes of interest. Advances in new drug development have been achieved by exploding information on target selection and validation using genetically modified animal models as well as those of cells. In this review, a recent trend of genetically modified methods is discussed with reference to safety assessments, and the exemplary applications of gene-modulating tools to the tests in new drug development were summarized.

• 한국컴퓨터정보학회논문지
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• 제22권3호
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• pp.131-138
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• 2017

New drug development is time-consuming and costly. Hence, it is necessary to repurpose old drugs for finding new indication. We suggest the way that repurposing old drug using massive literature data and biological network. We supposed a disease-drug relationship can be available if signal pathways of the relationship include significant genes identified in literature data. This research is composed of three steps-identifying significant gene using co-occurrence in literature; analyzing the shortest path on biological network; and scoring a relationship with comparison between the significant genes and the shortest paths. Based on literatures, we identify significant genes based on the co-occurrence frequency between a gene and disease. With the network that include weight as possibility of interaction between genes, we use shortest paths on the network as signal pathways. We perform comparing genes that identified as significant gene and included on signal pathways, calculating the scores and then identifying the candidate drugs. With this processes, we show the drugs having new possibility of drug repurposing and the use of our method as the new method of drug repurposing.