• 한국정보통신학회논문지
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• 제12권7호
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• pp.1243-1248
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• 2008

최근 생명 정보학 기술의 발달로 마이크로 단위의 실험조작이 가능해짐에 따라 하나의 chip상에서 전체 genome의 expression pattern을 관찰할 수 있게 되었고, 동시에 수 만개의 유전자들 간치 상호작용도 연구 가능하게 되었다. 본 논문에서는 암에 걸린 흰쥐 외피 기간 세포 분화 실험에서 얻어진 3840 유전자의 마이크로어레이 cDNA를 이용해 데이터의 정규화를 거쳐 본 논문에서 제안한 유사성 척도 조합 방법으로 정보력 있는 유전자들을 추출한 후, 유사성 척도 조합 방법과 결합한 멀티퍼셉트론 신경망 분류기와 기존의 DT, NB, SVM 분류기를 이용하여 클래스 분류 시스템을 구축하고, 성능을 비교분석하였다. 피어슨 적률 상관 계수와 유클리디안 거리 계수 조합을 이용하여 선택된 200 유전사들을 멀티퍼셉트론 신경망 분류기로 분류한 결과 98.84%의 정확도를 보여 다른 분류기를 이용하여 실험을 수행한 경우보다 향상된 분류 성능을 보였다.

• 한국식품영양과학회:학술대회논문집
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• 한국식품영양과학회 2004년도 Annual Meeting and International Symposium
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• pp.271-274
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• 2004

Nutritional genomics is a new field of study of how nutrition interacts with an individual's genome or individual responds to individual diets. Systematic approach of nutritional genomics will likely provide important clues about responders and non-responders. The current interest in personalizing health stems from the breakthroughs emerging in integrative technologies of genomics and epigenomics and the identification of genetic and epigentic diversity in individual's genetic make-up that are associated with variations in many aspects of health, including diet-related diseases. Microarray is a powerful screen system that is being also currently employed in nutritional research. Monitoring of gene expression at genome level is now possible with this technology, which allows the simultaneous assessment of the transcription of tens of thousands of genes and of their relative expression of pathological cells such tumor cells compared with that of normal cells. Epigenetic events such as DNA methylation can result in change of gene expression without involving changes in gene sequence. Recent developed technology of DNAarray-based methylation assay will facilitate wide study of epigenetic process in nutrigenomics. Some of the areas that would benefitfrom these technologies include identifying molecular targets (Biomarkers) for the risk and benefit assessment. These characterized biomarkers can reflect expose, response, and susceptibility to foods and their components. Furthermore the identified new biomarker perhaps can be utilized as a indicator of delivery system fur optimizing health.

• 식물병연구
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• 제20권3호
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• pp.173-181
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• 2014

The early and accurate detection of plant viruses is an essential component to control those. Because the globalization of trade by free trade agreement (FTA) and the rapid climate change promote the country-to-country transfer of viruses and their hosts and vectors, diagnosis of viral diseases is getting more important. Because symptoms of viral diseases are not distinct with great variety and are confused with those of abiotic stresses, symptomatic diagnosis may not be appropriate. From the last three decades, enzyme-linked immunosorbent assays (ELISAs), developed based on serological principle, have been widely used. However, ELISAs to detect plant viruses decrease due to some limitations such as availability of antibody for target virus, cost to produce antibody, requirement of large volume of sample, and time to complete ELISAs. Many advanced techniques allow overcoming demerits of ELISAs. Since the polymerase chain reaction (PCR) developed as a technique to amplify target DNA, PCR evolved to many variants with greater sensitivity than ELISAs. Many systems of plant virus detection are reviewed here, which includes immunological-based detection system, PCR techniques, and hybridization-based methods such as microarray. Some of techniques have been used in practical, while some are still under developing to get the level of confidence for actual use.

• 한국수정란이식학회지
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• 제22권4호
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• pp.199-208
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• 2007

Although many studies have focused on the biological and toxicological effects of phenol products, in particular, in reproductive tracts, the data about their effects in this estrogenic responsive tissue are much less clear. In addition, the in vitro and in vivo data concerning ED-adverse impacts in other endocrine organs, i.e. pituitary gland, are not understood well either. Thus, a further study is needed for providing a new insight into possible impacts of estrogenic EDs including phenol products in humans and wildlife. A combination of in vitro and in vivo system for examining EDs may bring better understanding into the regulatory mechanisms underlying EDs-induced events. In addition, this information may support for developing optimal screening methods of estrogenic EDs, in particular, phenol products.

• BMB Reports
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• 제38권2호
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• pp.151-160
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• 2005

By a cDNA array representing 2308 signal transduction related genes, we studied the expression profiles of HeLa cells stably transfected by Hepatitis C virus nonstructural protein 4B (HCV-NS4B). The alterations of the expression of four genes were confirmed by real-time quantitative RT-PCR; and the aldo-keto reductase family 1, member C1 (AKR1C1) enzyme activity was detected in HCV-NS4B transiently transfected HeLa cells and Huh-7, a human hepatoma cell line. Of the 2,308 genes we examined, 34 were up-regulated and 56 were down-regulated. These 90 genes involved oncogenes, tumor suppressors, cell receptors, complements, adhesions, transcription and translation, cytoskeletion and cellular stress. The expression profiling suggested that multiple regulatory pathways were affected by HCV-NS4B directly or indirectly. And since these genes are related to carcinogenesis, host defense system and cell homeostatic mechanism, we can conclude that HCV-NS4B could play some important roles in the pathogenesis mechanism of HCV.

• 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
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• 제43권3호
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• pp.308-312
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• 2005

The global RNA transcription profiles of Bacillus lentimorbus WJ5 under an in vitro co-culture with Colletotrichum gloeosporioides were analyzed in order to study the antagonistic bacteria-fungi interactions. Using a filter membrane system, B. lentimorhus WJ5 was exposed to the spores of C. gloeosporioides at the late exponential stage. The transcription profiles of the B. lentimorhus WJ5, both with and without a challenge from C. gloeosporioides, were analyzed using custom DNA chips containing 2,000 genome fragments. A total of 337 genes were expressed, with 87 and 47 up- and down-regulated, respectively. Of these, 12 genes, which were involved in central carbon metabolisms, and 7 from minor catabolism were relatively highly up-regulated (> 10 fold) and down-regulated (< 0.2 fold), respectively. Nine genes, which were thought to be related to the antifungal activity, were also up-regulated, but their levels were not so high (2.0 - 9.7 folds). From the results, during the early stage of the co-culture of B. lentimorbus WJ5 and C. gloeosporioides, nutrient competition seemed to occur; therefore, the genes from central carbon metabolisms could be up-regulated, while those from minor catabolism could be down-regulated.

• Genomics & Informatics
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• 제10권1호
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• pp.33-39
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• 2012

High-throughput genomic technologies (HGTs), including next-generation DNA sequencing (NGS), microarray, and serial analysis of gene expression (SAGE), have become effective experimental tools for cancer genomics to identify cancer-associated somatic genomic alterations and genes. The main hurdle in cancer genomics is to identify the real causative mutations or genes out of many candidates from an HGT-based cancer genomic analysis. One useful approach is to refer to known cancer genes and associated information. The list of known cancer genes can be used to determine candidates of cancer driver mutations, while cancer gene-related information, including gene expression, protein-protein interaction, and pathways, can be useful for scoring novel candidates. Some cancer gene or mutation databases exist for this purpose, but few specialized tools exist for an automated analysis of a long gene list from an HGT-based cancer genomic analysis. This report presents a new web-accessible bioinformatic tool, called CaGe, a cancer genome annotation system for the assessment of candidates of cancer genes from HGT-based cancer genomics. The tool provides users with information on cancer-related genes, mutations, pathways, and associated annotations through annotation and browsing functions. With this tool, researchers can classify their candidate genes from cancer genome studies into either previously reported or novel categories of cancer genes and gain insight into underlying carcinogenic mechanisms through a pathway analysis. We show the usefulness of CaGe by assessing its performance in annotating somatic mutations from a published small cell lung cancer study.

• Molecular & Cellular Toxicology
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• 제4권2호
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• pp.164-169
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• 2008

Methylmercury (MeHg) is known to have devastating effects on the mammalian nervous system. In order to characterize the mechanism of MeHg-induced neurotoxicity, we investigated the analysis of transcriptional profiles on human 8k cDNA microarray by treatment of $1.4{\mu}M$ MeHg at 3, 12, 24 and 48h in human neuroblastoma SH-SY5Y cell line. Some of the identified genes by MeHg treatment were significant at early time points (3h), while that of others was at late time points (48h). The early response genes that may represent those involved directly in the MeHg response included pantothenate kinase 3, a kinase (PRKA) anchor protein (yotiao) 9, neurotrophic tyrosine kinase, receptor, type 2 gene, associated with NMDA receptor activity regulation or perturbations of central nervous system homeostasis. Also, when SH-SY5Y cells were subjected to a longer exposure (48h), a relative increase was noted in a gene, glutamine-fructose-6-phosphate transaminase 1, reported that overexpression of this gene may lead to the increased resistance to MeHg. To confirm the alteration of these genes in cultured neurons, we then applied real time-RT PCR with SYBR green. Thus, this result suggests that a neurotoxic effect of the MeHg might be ascribed that MeHg alters neuronal receptor regulation or homeostasis of neuronal cells in the early phase. However, in the late phase, it protects cells from neurotoxic effects of MeHg.

• Journal of Acupuncture Research
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• 제22권3호
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• pp.37-51
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• 2005

비만세포는 염증 및 알레르기 반응과 관련하여 우리 몸에서 주요한 작용을 하는 세포이다. 봉독은 현재까지 진통기전에 관련된 모델로 연구가 진행되어 왔으나, 최근에는 항염증이나 항알러지반응 둥에서 면역세포와 관련 한 연구가 진행 중에 있다. 본 연구는 봉독의 주요성분인 melittin과 MCD Peptide가 비만세포주에서의 유전자 발현에 미치는 영향을 연구함으로써 향후 유전자 언구에 관련한 기초를 제시하고자 하였다. 본 연구에서는 사람의 비만세포주를 이용하여, 세포독성 실험을 거쳐서 얻은 유효농도에서 각각 melittin과 MCD Peptide를 처치하고, 이때 변화하는 유전자의 발현양상을 microarray분석기법을 통하여 정보를 얻었다. 실험적 통계에 의하여 global M이 1 또는 -1 이상인 것을 유의한 것으로 보았을 때, melittin에서는 모두 7개 의 유전자가 항진되고, 8개의 유전자가 어제되었다. MCDP에서는 7개의 유전자가 항진되고 17개의 유전자가 억제되었다. 이들 유전자들이 주로 관련하는 체내의 작용은 세포내에서 단백결합, lymphocyte 기능의 활성화, macrophage 항원관련 및 세포핵의 수용체, GABA A receptor 관련물질, cAMP 반응요소와 연관된 단백질, 보체계 8번 및 B-cell 관련물질, 다낭성 신질환에 관련된 단백물질, 염증관련물질, 혈액응고에 영향을 주는 단백물질등과 연관이 되었다. 이러한 분석결과를 통하여 동복에서의 주요약리작용을 담당하는 melittin과 MCD peptide의 작용기전을 밝히는데 보다 유용한 자료를 얻을 수 있었으며, 향후에 봉독의 주요성분 및 전체봉 독액이 항알레르기반응이나 항염증작용에 미치는 영향에 대한 심도있는 연구가 필요할 것으로 사료된다.