• 한국통계학회:학술대회논문집
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• 한국통계학회 2002년도 춘계 학술발표회 논문집
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• pp.91-97
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• 2002

최근의 생물학 연구를 위한 기기의 자동화 및 고속화는 생물학 관련 정보량의 급증을 가져오고 있다. 예를 들어, DNA chip에서 얻어지는 마이크로어레이(microarray)는 수천 종류의 유전자의 발현량을 동시에 측정한다. 이러한 기술들은 생물의 세포나 조직에서 일어나는 일련의 다양한 현상을 전체적으로 조망하는 관점에서 관찰할 수 있는 기회를 제공하고 있으며, 이를 통한 생명공학의 전반적인 발전이 기대되고 있다. 따라서 대량의 생물학 관련 정보의 분석이나 데이터 마이닝이 행해지고 있으며 이를 위한 대표적인 기법들로는 각종 클러스터링(clustering) 및 신경망 계열의 모델 등이 있다. 본 논문에서는 확률그래프모델의 하나인 베이지안망(Bayesian network)을 생물정보분석에 이용한다. 구체적으로 유전자 발현패턴과 약물의 활성패턴 및 암 종류 사이의 확률적 관계를 모델링한다. 이러한 모델은 NCI60 dataset(http://discover.nci.nih.gov)에서 베이지안망을 학습함으로써 구성된다. 분석의 대상이 되는 데이터가 sparse하기 때문에 발생하는 어려움들을 해결하기 위한 기법들이 제시되며 학습된 모델에 대한 검증은 이미 생물학적으로 확인되어 있는 사실과의 비교를 통해 이루어진다. 학습된 베이지안망 모델은 각각의 유전자 간, 혹은 유전자와 처리된 약물 간의 실제 생물학적 관계를 다수 표현하며, 이는 제시되는 방법이 생물학적으로 유의미한 가설을 데이터 분석을 통해 효율적으로 생성하는데 유용하게 활용될 수 있음을 보인다.

• Genomics & Informatics
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• 제2권3호
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• pp.134-141
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• 2004

Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide and a typical hypervascular tumor. Therefore, it is important to find factors related to angiogenesis in the process of HCC malignancy. In order to find angiogenesis-related factors in HCC, we used combined methods of in silico prediction and an experimental assay. We analyzed 1457 genes extracted from cDNA microarray of HCC patients by text-mining, sequence similarity search and domain analysis. As a result, we predicted that 16 genes were likely to be involved in angiogenesis and then the effects of these genes were confirmed by hypoxia response element(HRE)-luciferase assay. For instant, we classified osteopontin into a potent angiogenic factor and coagulation factor XII into a significant anti­angiogenic factor. Collectively, we suggest that using a combination of in silico prediction and experimental approaches, we can identify HCC-specific angiogenesis­related factors effectively and rapidly.

• 한국식물생명공학회:학술대회논문집
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• 한국식물생명공학회 2003년도 추계학술대회 발표논문 초록집
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• pp.71-71
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• 2003

• Genomics & Informatics
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• 제14권1호
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• pp.34-40
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• 2016

Due to advances in omics technologies, numerous genome-wide studies on human samples have been published, and most of the omics data with the associated clinical information are available in public repositories, such as Gene Expression Omnibus and ArrayExpress. While analyzing several public datasets, we observed that errors in gender information occur quite often in public datasets. When we analyzed the gender description and the methylation patterns of gender-specific probes (glucose-6-phosphate dehydrogenase [G6PD], ephrin-B1 [EFNB1], and testis specific protein, Y-linked 2 [TSPY2]) in 5,611 samples produced using Infinium 450K HumanMethylation arrays, we found that 19 samples from 7 datasets were erroneously described. We also analyzed 1,819 samples produced using the Affymetrix U133Plus2 array using several gender-specific genes (X (inactive)-specific transcript [XIST], eukaryotic translation initiation factor 1A, Y-linked [EIF1AY], and DEAD [Asp-Glu-Ala-Asp] box polypeptide 3, Y-linked [DDDX3Y]) and found that 40 samples from 3 datasets were erroneously described. We suggest that the users of public datasets should not expect that the data are error-free and, whenever possible, that they should check the consistency of the data.

• Environmental Analysis Health and Toxicology
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• 제19권3호
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• pp.261-269
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• 2004

Although the biological functions of metallothioneins (MTs) are still being investigated, they have been suggested to be involved in detoxification of heavy metals, scavenging of free radicals, and protection against alkylating agents. MTs have been reported to be induced in most of animal tissues by heavy metals such as zinc, copper, mercury and cadmium, and the proteins have binding affinities to the metals. However, the presence or induction of MTs was reported not to be clear in leydig cells, which produce testosterone for the maturation of spermatozoa in male testes. In this study, we investigated the inducibility of metallothionein isomers by cadmium in cultured mouse leydig cells. Total RNA was extracted from the near confluent grown leydig cells and RT-PCR was Performed using the Primers which were synthesized on the basis of MT-1, 2, 3 and 4 cDNA from GenBank database. As results, MT-1 and MT-2 mRNA were found to be expressed in cadmium non-treated control cells and MT 1 mRNA expression was dose-dependent when leydig cells were treated with cadmium chloride. But MT-3 which is known to be brain specific and MT-4 which is another isoform of metallothionein, were not expressed. Other genes induced or depressed in cadmium treated leydig cells were also identified by microarray techniques.

• Plant Biotechnology Reports
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• 제2권4호
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• pp.233-238
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• 2008

Kadainou R-1, an interspecific hybrid grape derived from red (Vitis ficifolia var. ganebu) and white (V. vinifera cv. Muscat of Alexandria) grapes, accumulates high concentrations of anthocyanin in the berry skin. Hence, the expression of uridine 50 -diphosphate (UDP)-glucose:flavonoid 3-O-glucosyltransferase (UFGT), the key enzyme of the anthocyanin pathway, was examined in the berry skin of Kadainou R-1. As information on gene sequences of V. ficifolia var. ganebu and other wild grape species was unavailable, we performed GeneChip hybridization using biotin-labeled genomic deoxyribonucleic acid (DNA) to investigate how the genomic sequences of V. vinifera varieties and that of V. ficifolia var. ganebu differ. The study showed a lower correlation coefficient between V. vinifera cultivars and V. ficifolia var. ganebu than that among V. vinifera cultivars. The sequences of the UFGT gene derived from both parents of the red and white cultivars were sequenced in Kadainou R1 and revealed that both were expressed irrespective of the fact that it was not expressed in the white grape (male parent).

• 한방안이비인후피부과학회지
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• 제22권1호
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• pp.11-32
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• 2009

Objective : This study was designed to investigate anti-cancer and whitening activities (LC). So it was investigated the effects of LC on proliferation rates of melanoma genetic profile by LC. Methods : The genetic profile for the effect of LC on human derived melanoma cell, SK-MEL-2, was measured using microarray technique, and the functional analysis on these genes were conducted. Total 441 genes were up-regulated and 830 genes down-regulated in cells treated with LC. Genes induced or suppressed by LC were all mainly concerned with basic signalling pathways, which are involved in cell growth, differentiation and migration. Especially, many genes, which are related in apoptosis and cell cycle arrest were up-regulated by treatment with LC, and genes related in cell cycle were down-regulated. Result : The network of total protein interactions were identified by using cytoscape program, and some key molecules, such as BCL2L1, SIN3A, SMAD2 and c-myc that can be used for elucidation of therapeutical mechanism of medicine in the future. Conclusion : These results suggest possibility of LC as addition drug and whitening cosmetics. In addition, it was also suggested that related mechanisms are involved in BCL2L1, SIN3A, SMAD2 and c-myc related signalling pathways.

• Biotechnology and Bioprocess Engineering:BBE
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• 제10권5호
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• pp.451-461
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• 2005

The effect of carbon dioxide on yeast growth was investigated during the cultivation of pH 5.0 and pH 6.8. by replacing the nitrogen part with carbon dioxide under aerobic conditions. The values of the specific growth rate under pH 5.0 and pH 6.8 conditions became 64.0% and 46.9%, respectively, compared to those before the change in gas composition. This suggests that the effect of carton dioxide was greater pronounced in pH 6.8 than in pH 5.0. The genome-wide transcriptional response to elevated carbon dioxide was examined using a DNA microarray. As for upregulated genes, it was noteworthy that 3 genes were induced upon entry into a stationary phase and 6 genes were involved in stress response. Of 53 downregulated genes, 22 genes were involved in the ribosomal biogenesis and assembly and 5 genes were involved in the lipid metabolism. These facts suggest that carbon dioxide could bring the cell conditions partially to a stationary phase. The ALD6 gene encoding for cytosolic acetaldehyde dehydrogenase was downregulated, which would lead to a lack of cell components for the growth. The downregulation of ALD6 was greater in pH 6.8 than in pH 5.0. consistent with physiological response. This suggests that it might be the most effective factor for growth inhibition.

• 동의생리병리학회지
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• 제18권2호
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• pp.468-473
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• 2004

Psoriasis is a chronic inflammatory disease of the skin characterized by epidermal hyperplasia, dermal angiogenesis, infiltration of activated T cells, and increased cytokine levels, and affects 1-3% of the world-wide population. Although many immunological and clinical reports indicate a role for the immune system in the pathogenesis of psoriasis, puzzling questions about psoriasis remain unsolved. During the several decade, immunosuppressor and PUVA treatment are ubiquitously used to psoriasis therapy. But recently, to promote terminal differentiation of keratinocytes, block either NK-Tcell or T-cell activation, and interrupting the angiogenic switch represent another therapeutic opportunity in psoriasis. To keep face with immunological therapy, the needs of newly designed prescription on the psoriasis treatments were demanded. With the object of understand the psoriasis from an orient medical point of view, patients were administrated the GY during several weeks. We investigated the changes of gene expression in involved and uninvolved skin samples during the oriental remedy. Microarray data showed several important results. First, Gene expression profiling is similar to each patient. Second, precursor proteins that organize cornified envelops are decreased at the end of remedy. But genes which related to apoptosis, G-protein signalling, and lipid metabolism are increased. Third, 68.5% of clustering genes localized on the psoriasis susceptibility locus. In our results indicated that GY influence on the keratinocytes hyperproliferation by regulating the gene, which located on the psoriasis susceptibility locus.

• Journal of Microbiology and Biotechnology
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• 제16권12호
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• pp.1841-1848
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• 2006

Insights into gene expression have the potential for improvement of antibiotic yield and the development of robust production hosts for use in recombinant biomolecule production. $Cubicin^{TM}$ (daptomycin for injection) is a recently approved antibiotic active against many Gram(+) pathogens, including those resistant to methicillin, vancomycin, and fluoroquinolones. Daptomycin is produced as a secondary metabolite by Streptomyces roseosporus. A 128 kb region of DNA including the daptomycin biosynthetic gene cluster (dpt) has been cloned. and sequenced. Using a selected array of nucleic acid probes representing this region, we compared the expression levels of the dpt genes between S. roseosporus wild-type (WT) and derived S. roseosporus high-producer of daptomycin (HP). We observed that the majority of the biosynthetic genes were upregulated in HP compared with WT; a total of 12 genes, including those encoding daptomycin synthetase, showed consistently and significantly higher expression levels, at least 5-fold, in HP compared with WT. In contrast, some genes, flanking the dpt cluster, were expressed at higher levels in the WT strain. The expression of housekeeping genes such as S. roseosporus rpsL, rpsG, and 16S (positive controls) and presumptive intergenic regions in the dpt cluster (negative control) were identical in the two strains. In addition, we compared transcription during the early, mid-log, and early-stationary phases of growth in the HP strain. The same set of genes was upregulated and downregulated under all conditions examined; housekeeping genes showed no relative change in expression level over the periods of growth tested. Analyses of this type would be of value in studies of strain improvement and also for the identification of gene regulation processes that are important for secondary metabolite production.