• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.45-52
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• 2000

Genomic approach produces massive amount of data within a short time period, New high-throughput automatic sequencers can generate over a million nucleotide sequence information overnight. A typical DNA chip experiment produces tens of thousands expression information, not to mention the tens of megabyte image files, These data must be handled automatically by computer and stored in electronic database, Thus there is a need for systematic approach of data collection, processing, and analysis. DNA sequence information is translated into amino acid sequence and is analyzed for key motif related to its biological and/or biochemical function. Functional genomics will play a significant role in identifying novel drug targets and diagnostic markers for serious diseases. As an enabling technology for functional genomics, bioinformatics is in great need worldwide, In Korea, a new functional genomics project has been recently launched and it focuses on identi☞ing genes associated with cancers prevalent in Korea, namely gastric and hepatic cancers, This involves gene discovery by high throughput sequencing of cancer cDNA libraries, gene expression profiling by DNA microarray and proteomics, and SNP profiling in Korea patient population, Our bioinformatics team will support all these activities by collecting, processing and analyzing these data.

• The Plant Pathology Journal
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• 제30권4호
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• pp.343-354
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• 2014

Rice blast disease caused by Magnaporthe oryzae is one of the most serious diseases of cultivated rice (Oryza sativa L.) in most rice-growing regions of the world. In order to investigate early response genes in rice, we utilized the transcriptome analysis approach using a 300 K tilling microarray to rice leaves infected with compatible and incompatible M. oryzae strains. Prior to the microarray experiment, total RNA was validated by measuring the differential expression of rice defense-related marker genes (chitinase 2, barwin, PBZ1, and PR-10) by RT-PCR, and phytoalexins (sakuranetin and momilactone A) with HPLC. Microarray analysis revealed that 231 genes were up-regulated (>2 fold change, p < 0.05) in the incompatible interaction compared to the compatible one. Highly expressed genes were functionally characterized into metabolic processes and oxidation-reduction categories. The oxidative stress response was induced in both early and later infection stages. Biotic stress overview from MapMan analysis revealed that the phytohormone ethylene as well as signaling molecules jasmonic acid and salicylic acid is important for defense gene regulation. WRKY and Myb transcription factors were also involved in signal transduction processes. Additionally, receptor-like kinases were more likely associated with the defense response, and their expression patterns were validated by RT-PCR. Our results suggest that candidate genes, including receptor-like protein kinases, may play a key role in disease resistance against M. oryzae attack.

• 생명과학회지
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• 제19권9호
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• pp.1294-1298
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• 2009

콩의 대표적인 이소플라본인 genistein과 daidzein에 의해 암세포 생존율에 미치는 영향을 확인하기 위하여, HCT116 세포주에 genistein과 daidzein을 농도 의존적으로 처리하였다. Genistein은 처리한 농도 의존적으로 암세포 생존율을 감소시켰으며, 이에 반해 daidzein은 세포생존율에 큰 변화를 보여주지는 못하였다. 이전의 마이크로어레이 실험 결과에 의하면, $50{\mu}M$의 genistein에 의해 2배 이상 증가되는 유전자 71개, 2배 이상 감소되는 유전자 64개가 검색되었다. 이중 3개의 유전자(DKK-1, ATF3 그리 고 NAG-1)를 선택하여, 마이크로어레이 실험 결과를 검증하기 위하여 RT-PCR을 수행하였다. RT-PCR 결과 마이크로어레이 결과와 모두 일치함을 증명하였다. 한편, genistein과 daidzein에 의한 병합처리에 의해 암세포생존에 미치는 영향을 확인하였다. 그 결과 병합처리에 의한 상승적인 세포독성 효과를 확인하였다. RT-PCR과 real-time PCR의 결과 genistein과 daidzein의 병합처리에 의해 항암유전자인 NAG-1 유전자가 상승적으로 발현이 증가됨을 확인하였다. 이러한 결과는 이소플라본뿐만 아니라 대두제품에 의한 암 화학예방법의 기전을 이해하는 도움을 줄 것으로 생각된다.

• 생물정신의학
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• 제12권1호
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• pp.42-61
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• 2005

Objectives:The ginsenoside Rg1 and Rb1, the major components of ginseng saponin, have neurotrophic and neuroprotective effects including promotion of neuronal survival and proliferation, facilitation of learning and memory, and protection from ischemic injury and apoptosis. In this study, to investigate the molecular basis of the effects of ginsenoside on neuron, we analyzed gene expression profiling of SH-SY5Y human neuroblastoma cells treated with ginsenoside Rg1 or Rb1. Methods:SH-SY5Y cells were cultured and treated in triplicate with ginsenoside Rg1 or Rb1($80{\mu}M$, $40{\mu}M$, $20{\mu}M$). The proliferation rates of SH-SY5Y cells were determined by MTT assay and microscopic examination. We used a high density cDNA microarray chip that contained 8K human genes to analyze the gene expression profiles in SH-SY5Y cells. We analyzed using the Significance Analysis of Microarray(SAM) method for identifying genes on a microarray with statistically significant changes in expression. Results:Treatment of SH-SY5Y cells with $80{\mu}M$ ginsenoside Rg1 or Rb1 for 36h showed maximal proliferation compared with other concentrations or control. The results of the microarray experiment yielded 96 genes were upregulated(${\geq}$3 fold) in Rg1 treated cells and 40 genes were up-regulated(${\geq}$2 fold) in Rb1 treated cells. Treatment with ginsenoside Rg1 for 36h induced the expression of some genes associated with protein biosynthesis, regulation of transcription or translation, cell proliferation and growth, neurogenesis and differentiation, regulation of cell cycle, energy transport and others. Genes associated with neurogenesis and neuronal differentiation such as SCG10 and MLP increased in ginsenoside Rg1 treated cells, but such changes did not occur in Rb1-group. Conclusion:Our data provide novel insights into the gene mechanisms involved in possible role for ginsenoside Rg1 or Rb1 in mediating neuronal proliferation or cell viability, which can elicit distinct patterns of gene expression in neuronal cell line. Ginsenoside Rg1 have more broad and strong effects than ginsenoside Rb1 in gene expression and related cellular physiology. In addition, we suggest that SCG10 gene, which is known to be expressed in neuronal differentiation during development and neuronal regeneration during adulthood, may have a role in enhancement of activity dependent synaptic plasticity or cytoskeletal regulation following treatment of ginsenoside Rg1. Further, ginsenoside Rg1 may have a possible role in regeneration of injured neuron, promotion of memory, and prevention from aging or neuronal degeneration.

• 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.

• 한방안이비인후피부과학회지
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• 제21권3호
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• pp.52-68
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• 2008

Objectives and Methods : Salviae miltiorrhizae Radix (SMR) promotes blood circulation to remove blood stasis, cools the blood to relieve carbuncle, clears away heat from the heart and tranquilizes the mind. This study was designed to investigate the effects of SMR on immuno-potentiative action in terms of changes in the genetic profile of dendritic cells (DC) using by microarray analysis. Results and Conclusion: In this experiment, treatments with more than 250 ${\mu}g/ml$ upto 1000 ${\mu}g/ml$ of SMR elevated the proliferation rates of DC. Microscopic observations confirmed the tendency on proliferation rates. Expression levels of genes related with cellular methabolic process, cell communication, and macromolecule metabolic process were elevated by treatment with SMR in comparison of functional distribution in a Biological Process. In molecular functions, expression levels of genes related with receptor activation, nucleotide binding and nucleic acid binding were elevated. In cellular components, expression levels of genes related to cellular membrane-bound organelles were elevated. In addition, expression levels of genes related to Wnt signalling pathways and the glycerophospholipid metabolism were elevated through analysis using pathway analysis between up-and down-regulated genes in cells treated with SMR. Finally, genes related to JAK2, GRB2, CDC42, SMAD4, B2M, FOS and ESRI located the center of Protein interaction network of genes through treatment with SMR.

• 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.

• Reproductive and Developmental Biology
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• 제37권4호
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• pp.185-192
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• 2013

Many countries have implemented genetic evaluation for fertility traits in recent years. In particular, reproductive trait is a complex trait and need to require a system-level approach for identifying candidate genes related to the trait. To find the candidate gene associated with reproductive trait, we applied a weighted gene co-expression network analysis from expression value of bovine genes. We identified three co-expressed modules associated with reproductive trait from bovine microarray data. Hub genes (ZP4, FHL2 and EGR4) were determined in each module; they were topologically centered with statistically significant value in the gene co-expression network. We were able to find the highly co-expressed gene pairs with a correlation coefficient. Finally, the crucial functions of co-expressed modules were reported from functional enrichment analysis. We suggest that the network-based approach in livestock may an important method for analyzing the complex effects of candidate genes associated with economic traits like reproduction.

• Genomics & Informatics
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• 제15권2호
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• pp.56-64
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• 2017

We have previously reported that NS-398, a cyclooxygenase-2 (COX-2)-selective inhibitor, inhibited replicative cellular senescence in human dermal fibroblasts and skin aging in hairless mice. In contrast, celecoxib, another COX-2-selective inhibitor, and aspirin, a non-selective COX inhibitor, accelerated the senescence and aging. To figure out causal factors for the senescence-modulating effect of the inhibitors, we here performed cDNA microarray experiment and subsequent Gene Set Enrichment Analysis. The data showed that several senescence-related gene sets were regulated by the inhibitor treatment. NS-398 up-regulated gene sets involved in the tumor necrosis factor ${\beta}$ receptor pathway and the fructose and mannose metabolism, whereas it down-regulated a gene set involved in protein secretion. Celecoxib up-regulated gene sets involved in G2M checkpoint and E2F targets. Aspirin up-regulated the gene set involved in protein secretion, and down-regulated gene sets involved in RNA transcription. These results suggest that COX inhibitors modulate cellular senescence by different mechanisms and will provide useful information to understand senescence-modulating mechanisms of COX inhibitors.

• Nutrition Research and Practice
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• 제9권1호
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• pp.22-29
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• 2015

BACKGROUND/OBJECTIVES: Recently, anthocyanins have been reported to have various biological activities. Furthermore, anthocyanin-rich purple corn extract (PCE) ameliorated insulin resistance and reduced diabetes-associated mesanginal fibrosis and inflammation, suggesting that it may have benefits for the prevention of diabetes and diabetes complications. In this study, we determined the anthocyanins and non-anthocyanin component of PCE by HPLC-ESI-MS and investigated its anti-diabetic activity and mechanisms using C57BL/KsJ db/db mice. MATERIALS/METHODS: The db/db mice were divided into four groups: diabetic control group (DC), 10 or 50 mg/kg PCE (PCE 10 or PCE 50), or 10 mg/kg pinitol (pinitol 10) and treated with drugs once per day for 8 weeks. During the experiment, body weight and blood glucose levels were measured every week. At the end of treatment, we measured several diabetic parameters. RESULTS: Compared to the DC group, Fasting blood glucose levels were 68% lower in PCE 50 group and 51% lower in the pinitol 10 group. Furthermore, the PCE 50 group showed 2-fold increased C-peptide and adiponectin levels and 20% decreased HbA1c levels, than in the DC group. In pancreatic islets morphology, the PCE- or pinitol-treated mice showed significant prevention of pancreatic ${\beta}$-cell damage and higher insulin content. Microarray analyses results indicating that gene and protein expressions associated with glycolysis and fatty acid metabolism in liver and fat tissues. In addition, purple corn extract increased the phosphorylation of AMP-activated protein kinase (AMPK) and decreased phosphoenolpyruvate carboxykinase (PEPCK), glucose 6-phosphatase (G6pase) genes in liver, and also increased glucose transporter 4 (GLUT4) expressions in skeletal muscle. CONCLUSIONS: Our results suggested that PCE exerted anti-diabetic effects through protection of pancreatic ${\beta}$-cells, increase of insulin secretion and AMPK activation in the liver of C57BL/KsJ db/db mice.