• 한국미생물생명공학회:학술대회논문집
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• 한국미생물생명공학회 2005년도 2005 Annual Meeting & International Symposium
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• pp.230-232
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• 2005

The formation of insoluble aggregation of the recombinant kringle fragment of human apolipoprotein(a), rhLK8, in endoplasmic reticulum was identified as the rate-limiting step in the rhLK8 secretion in Saccharomyces cerevisiae. To analyze the protein secretion pathway, some of yeast genes closely related to protein secretion was rationally selected and their oligomer DNA were arrayed on the chip. The expression profiling of these genes during the induction of rhLK8 in fermentor fed-batch cultures revealed that several foldases including pdi1 gene were up-regulated in the early induction phase, whereas protein transport-related genes were up-regulated in the late induction phase. The coexpression of pdi1 gene increased rhLK8-folding capacity. Hence, the secretion efficiency of rhLK8 in the strain overexpressing pdi1 gene increased by 2-fold comparing in its parental strain. The oligomer DNA chip arrayed with minimum number of the genes selected in this study could be generally applicable to the monitoring system for the heterologous protein secretion and expression in Saccharomyces cerevisiae. With the optimization of fed-batch culture conditions and the alteration of genetic background of host, we obtained extracellular rhLK8 at higher yields than with Pichia pastoris systems, which was a 25-fold increased secretion level of rhLK8 compared to the secretion level at the initiation of this study.

• 동의생리병리학회지
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• 제19권6호
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• pp.1585-1593
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• 2005

The genetic effects of restraint stress challenge on HPA axis and the therapeutic effect of Boshimgeonbi-tang on the stress were studied with cDNA microarray analyses, RT-PCR on hypothalamus using an immobilization-stress mice as an animal model. Male CD-1 mice were restrained in a tightly fitted and ventilated vinyl holder for 2hrs once a day, and this challenge was repeated for seven· consecutive days. In the change of body weight it showed that the Boshimgeonbi-tang is effected recovery on weight loss caused by the immobilization-stress. Seven days later, total RNA was extracted from the organs of the mouse, body-labeled with $CyDye^{TM}$ fluorescence dyes and then hybridized to CDNA microarray chip. Scanning and analyzing the array slides were carried out using GenePix4000 series scanner and GenePix $Pro^{TM}$ analyzing program, respectively. The expression profiles of 109 genes out of 6000 genes on the chip were significantly modulated in hypothalamus by the immobilization stress. Energy metabolism-, lipid metabolism-, apoptosis-, stress protein, transcriptional factor, and signal transduction-related genes were transcriptionally activated whereas DNA repair-, protein biosysthesis-, and structure integrity-related genes were down-regulated in hypothalamus. The 58 genes were up-regulated by the mRNA expression folds of 1.5 to 7.9. and the 51 genes were down-regulated by 1.5 - 5.5 fold. The 11 genes among them were selected to confirm the expression profiles by RT-PCR. The mRNA expression levels of Tnfrsf1a (apoptosis), Calm2 (cell cycle), Bag3 (apoptosis), Ogg1 (DNA repair), Aatk (apoptosis), Dffa (apoptosis), Fkbp5 (protein folding) were restored to the normal one by the treatment of Boshimgeonbi-tang.

• 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.

• Journal of Veterinary Science
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• 제21권5호
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• pp.78.1-78.15
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• 2020

Background: Enteritis is one of the most frequently reported symptoms in piglets infected with porcine circovirus type 2 (PCV2), but the immunopathogenesis has not been reported. Objectives: This study examined the effect of a PCV2 infection on the intestinal mucosal immune function through morphological observations and immune-related molecular detection. Methods: Morphological changes within the ileum of piglets during a PCV2 infection were observed. The expression of the related-molecules was analyzed using a gene chip. The immunocyte subsets were analyzed by flow cytometry. The secretory immunoglobulin A (SIgA) content was analyzed by enzyme-linked immunosorbent assay. Results: The PCV2 infection caused ileal villus damage, intestinal epithelial cells exfoliation, and an increase in lymphocytes in the lamina propria at 21 days post-infection. Differentially expressed genes occurred in the defense response, inflammatory response, and the complement and coagulation cascade reactions. Most of them were downregulated significantly at the induction site and upregulated at the effector site. The genes associated with SIgA production were downregulated significantly at the induction site. In contrast, the expression of the Toll-like receptor-related genes was upregulated significantly at the effector site. The frequencies of dendritic cells, B cells, and CD8⁺T cells were upregulated at the 2 sites. The SIgA content decreased significantly in the ileal mucosa. Conclusions: PCV2 infections can cause damage to the ileum that is associated with changes in immune-related gene expression, immune-related cell subsets, and SIgA production. These findings elucidated the molecular changes in the ileum after a PCV2 infection from the perspective of intestinal mucosal immunity, which provides insights into a further study for PCV2-induced enteritis.

• 한국축산식품학회지
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• 제43권4호
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• pp.703-711
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• 2023

As an initial study to elucidate the molecular mechanism of how probiotics modulate macrophage activity, we monitored mRNA expression patterns in peritoneal macrophages (PMs) treated with two different strains of probiotics. After treatment with either Weissella cibaria WIKIM28 or Latilactobacillus sakei WIKIM50, total RNAs from PMs were isolated and subjected into gene chip analyses. As controls, mRNAs from vehicle (phosphate-buffered saline, PBS)-treated PMs were also subjected to gene chip analysis. Compared to vehicle (PBS)-treated PMs, WIKIM28-treated and WIKIM50-treated PMs exhibited a total of 889 and 432 differentially expressed genes with expression differences of at least 4 folds, respectively. Compared to WIKIM28-treated PMs, WIKIM50-treated PMs showed 25 up-regulated genes and 21 down-regulated genes with expression differences of more than 2 folds. Interestingly, mRNA transcripts of M2 macrophage polarization marker such as anxa1, mafb, and sepp1 were increased in WIKIM50-treated PMs comparing to those in WIKIM28-treated PMs. Reversely, mRNA transcripts of M1 macrophage polarization marker such as hdac9, ptgs2, and socs3 were decreased in WIKIM50-treated PMs comparing to those in WIKIM28-treated PMs. In agreement with these observations, mRNA expression levels of tumor necrosis factor-α and interleukin-1α were significantly reduced in WIKIM50-treated macrophages compared to those in WIKIM28-treated macrophages. These results may indicate that probiotics can be classified as two different types depending on their ability to convert macrophages into M1 or M2 polarization.

• 한국통신학회논문지
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• 제28권8C호
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• pp.803-810
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• 2003

본 논문은 여성 자궁경부암의 원인이 되는 인두유종 바이러스(papillomavirus)를 진단하기 위한 HPY-DNA 칩의 영상으로부터 탐촉자(probe)의 위치를 찾아내고 각 탐촉자에서의 교잡반응(hybridization) 여부를 결정하기 위한영상리 방법의 구현에 관한 것이다. HPV-DNA 칩은 22종의 HPV를 알아내기 위한 탐촉자들과 환자 샘플과 항상 반응하는 마커들로 구성되어 있다. 침 영상에서 탐촉자 들의 위치는 마커와 상대적으로 고정되어 있어서 도터(dotter)와 스캐너(scanner)의 정밀도에 따른 오차만을 갖는다. 한편 각 탐촉자는 진단신뢰도를 높이기 위하여 4번 씩 인쇄된다. 본 논문은 마커들간의 상대거리와 탐촉자의 중복 인쇄라는 사전정보를 템플릿 정합방법과 결합하여 안정적으로 마커를 찾고, 교잡반응 여부를 정확히 분류하는 방법을 제시한다. 정규화된 상관도를 정합도(matching measure)로 채택하여, 마커들의 상대적 위치에 대하여 평균을 취하면 안정적으로 마커를 찾을 수 있다는 것을 실험을 통하여 보인다. 또한 이미 계산된 정합도를 특징(feature) 값으로 사용하여 4개의 중복 탐촉자에 대한 평균 특징 값을 분류(classification)하면 탐촉자의 교잡반응 여부를 정확히 알아낼 수 있다는 실험 결과를 보인다.

• 동의신경정신과학회지
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• 제18권1호
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• pp.95-110
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• 2007

Objective : The purpose of this study was to investigate molecular basis of neuroprotective effect in total ginsenosides. After H202 induced neurotoxicity, gene expression profiling of SH-SY5Y neuroblastoma cells treated by total ginsenosides is analyzed. Method : After SH-SY5Y cells were cultured, they were damaged by H202 induced oxidative stress. After twenty four hours, experimental group is treated by total ginsenosides and control group is treated by 0.9% saline. A high density cDNA microarray chip is used to analyze the gene expression profiling of SH-SY5Y cells. The Significance Analysis of Microarray method is used for identifying genes on a microarray. Results : 1. According to the results of microarray experiment, 17 genes were up-regulated, 38 genes were down-regulated. 2. Expression of OPHNl, KTANl, ATM, PRKCE, MAPKs genes associated with cell proliferation, neural growth, and the prevention of apoptosis were increased. 3. Change of EPX gene was the greatest among all genes. EPX gene associated with oxidative stress, and tumor suppressor gene ADAM11 were decreased. Conclusion : According to this study, molecular basis of neuroprotective effect of total ginsenosides is as followings: the increase of gene expression associated with cell proliferation, neuron growth, the prevention of apoptotsis and decrease of gene expression associated with oxidative stress and tumor suppressor.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.53-55
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• 2000

Xenie is the JAVA application software that integrates and represents 'gene to function'information of human gene. Xenie extracts data from several heterogeneous molecular biology databases and provides integrated information in human readable and machine usable way. We defined 7 semantic frame classes (Gene, Transcript, Polypeptide, Protein_complex, Isotype, Functional_object, and Cell) as a common schema for storing and integrating gene to function information and relationship. Each of 7 semantic frame classes has data fields that are supposed to store biological data like gene symbol, disease information, cofactors, and inhibitors, etc. By using these semantic classes, Xenie can show how many transcripts and polypeptide has been known and what the function of gene products is in General. In detail, Xenie provides functional information of given human gene in the fields of semantic objects that are storing integrated data from several databases (Brenda, GDB, Genecards, HGMD, HUGO, LocusLink, OMIM, PIR, and SWISS-PROT). Although Xenie provide fully readable form of XML document for human researchers, the main goal of Xenie system is providing integrated data for other bioinformatic application softwares. Technically, Xenie provides two kinds of output format. One is JAVA persistent object, the other is XML document, both of them have been known as the most favorite solution for data exchange. Additionally, UML designs of Xenie and DTD for 7 semantic frame classes are available for easy data binding to other bioinformatic application systems. Hopefully, Xenie's output can provide more detailed and integrated information in several bioinformatic systems like Gene chip, 2D gel, biopathway related systems. Furthermore, through data integration, Xenie can also make a way for other bioiformatic systems to ask 'function based query'that was originally impossible to be answered because of separatly stored data in heterogeneous databases.

• 한국전기전자재료학회논문지
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• 제18권6호
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• pp.560-570
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• 2005

In this paper, a microelectrode away DNA chip was fabricated on glass slide using photolithography technology. Several probe DNAs consisting of mercaptohexyl moiety at their 5' end were immobilized on the gold electrodes by DNA arrayer utilizing the affinity between gold and sulfu. Then target DNAs were hybridized and reacted with Hoechst 33258, which is a DNA minor groove binder and electrochemically active dye. Cyclic voltammetry in 5mA ferricyanide/ferrocyanide solution at 100 mV/s confirmed the immobilization of probe DNA on the gold electrodes. Linear sweep voltammetry or cyclic voltammetry showed a difference between target DNA and control DNA in the anodic peak current values. It was derived from Hoechst 33258 concentrated at the electrode surface through association with formed hybrid. It suggested that this DNA chip could recognize the sequence specific genes. It suggested that multichannel electrochemical DNA microarray is useful to develop a portable device for clinical gene diagnostic system.

• Journal of Veterinary Science
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• 제21권1호
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• pp.4.1-4.9
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• 2020

Fast and accurate detection of viral RNA pathogens is important in apiculture. A polymerase chain reaction (PCR)-based detection method has been developed, which is simple, specific, and sensitive. In this study, we rapidly (in 1 min) synthesized cDNA from the RNA of deformed wing virus (DWV)-infected bees (Apis mellifera), and then, within 10 min, amplified the target cDNA by ultra-rapid qPCR. The PCR products were hybridized to a DNA-chip for confirmation of target gene specificity. The results of this study suggest that our method might be a useful tool for detecting DWV, as well as for the diagnosis of RNA virus-mediated diseases on-site.