• 동의생리병리학회지
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• 제19권4호
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• pp.913-921
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• 2005

In this study, we investigated gene expression patterns induced by Ailanthus altissima extract and compared it with Gleevec, a well-known anti-leukemia drug, in K562 chromic leukemia cells. Ailanthus altissima extract(100 ug/ml) and Gleevec(50 ug/ml) were treated to cells for 1h, 2h, 4h, and 16h and total RNA was extracted. Gene expressions were evaluated using cDMA microarray, in which 24,000 genes were spotted. Hierarchical clustering analysis showed that expression of genes included in two clusters were increased or decreased time dependently by both Ailanthus altissima extract and Gleevec. Genes included in another cluster were induced by Ailanthus altissima extract but not by Gleevec. In biological process analysis, expression of genes involved in apoptosis, growth arrest and DNA-damage were increased, but genes stimulating cell cycle were decreased. This study provides comprehensive comparison of the patterns of gene expression changes induced by Ailanthus altissima extract and Gleevec in K-562 leukemia cells.

• Molecular & Cellular Toxicology
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• 제3권4호
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• pp.306-313
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• 2007

The welding fume has been implicated as a causal agent in respiratory disease such as pneumoconiosis. The molecular mechanism by which welding fume induces toxicity in the lung is still unknown, but studies have focused on histological structure and indirect approach measuring the pulmonary damage markers. In the present study, gene expression profiles were analyzed in the lung of rats exposed by manual metal-arc stainless-steel (MMA-SS) welding fume for 30 days using Affymetrix GeneChip$^{(R)}$. Totally, 379 genes were identified as being either up- or down-regulated over 2-fold changes (P<0.01) in the lung of low- or high-dose group and were analyzed by using hierarchical clustering. We focused on genes involved in immune/inflammation responses were differentially regulated during lung injury induced by welding fume exposure. The information of these deregulated genes may contribute in elucidation of the inflammation mechanism during lung injury such as lung fibrosis.

• Molecular & Cellular Toxicology
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• 제3권1호
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• pp.60-67
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• 2007

Gentamicin is a broad-spectrum aminoglycoside antibiotic used in the treatment of bacterial infection. Although side effects of gentamicin such as nephrotoxicity and ototoxicity have been investigated, the information on the hepatic effects of gentamicin is still limited. In the present study, gene expression profiles were analyzed in the liver of gentamicin treated mice using Affymetrix GeneChip$^{(R)}$ Mouse Expression 430A 2.0 Array. Totally, 400 genes were identified as being either up- or down-regulated over 1.5-fold changes (P<0.01) in the liver of gentamicin treated mice. Among these deregulated genes, 16 up-regulated genes mainly involved in transport (Kif5b, Pex14, Rab14, Clcn3, and Necap1) and 20 down-regulated genes involved in lipid and other metabolisms (Hdlbp, Gm2a, Uroc1, and Dak) were selected using k-means clustering algorithm. The functional classification of differentially expressed genes represented that several stress-related genes were regulated in the liver by gentamicin treatment. This data may contribute in understanding the molecular mechanism in the liver of gentamicin treated mice.

• 대한한의학방제학회지
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• 제29권4호
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• pp.267-275
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• 2021

Objectives : Previously, we reported that compound K isolated from fermented ginseng by Aspillus oryzae has a wide biochemical and pharmacological effect, including anti-cancer activity in prostate cancer PC-3 cells. Despite these findings, its signaling pathway and gene expression pattern are not clearly understood. Methods : To confirm the gene expression study of treated with compound K in PC-3 cells, a cDNA microarray chip composed of 44K human cDNA probes was used. MTT assay, western blot analysis, propidium iodide staining, and annexin V/propidium iodide staining were analyzed. Results : We confirmed the differences of gene expression profiles. Then, we analyzed with the cell cycle arrest, cell death and cell proliferation related genes using DAVID database. Conclusions : Our finding should be useful for understanding genome-wide expression patterns of compound K-mediated cell cycle arrest toward induction of cell death and be helpful for finding future cancer therapeutic targets for prostate cancer cells.

• Reproductive and Developmental Biology
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• 제37권1호
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• pp.1-8
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• 2013

In order to investigate genetic stability and gene expression profile after cloning procedure, two groups of cloned pigs were used for swine leukocyte antigen (SLA) gene nucleotide alteration and microarray analyses. Each group was consist of cloned pigs derived from same cell line (n=3 and 4, respectively). Six SLA loci were analyzed for cDNA sequences and protein translations. In total, 16 SLA alleles were identified and there were no evidence of SLA nucleotide alteration. All SLA sequences and protein translations were identical among the each pig in the same group. On the other hand, microarray assay was performed for profiling gene expression of the cloned pigs. In total, 43,603 genes were analyzed and 2,150~4,300 reliably hybridized spots on the each chip were selected for further analysis. Even though the cloned pigs in the same group had identical genetic background, 18.6~47.3% of analyzed genes were differentially expressed in between each cloned pigs. Furthermore, on gene clustering analysis, some cloned pigs showed abnormal physiological phenotypes such as inflammation, cancer or cardiomyopathy. We assumed that individual environmental adaption, sociality and rank in the pen might have induced these different phenotypes. In conclusion, the results of the present study indicate that SLA locus genes appear to be stable following SCNT. However, gene expressions and phenotypes between cloned pigs derived from the same cell line were not identical even under the same rearing conditions.

• 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.

• 동의생리병리학회지
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• 제23권3호
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• pp.645-661
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• 2009

The water extract of Dohongsamul-Tang(DHSMT) has been traditionally used to stroke and brain injuries in Oriental Medicine. The present study was designed to investigate the effects of DHSMT on the gene expression profile of cerebral infarction by cDNA microarray in photothrombotic ischemia mouse model. Photothrombotic ischemia was induced in stereotactically held male BALB/c mice using rose bengal and cold light. MRI was performed 24 hours after inducing photothrombosis using 1.5 T MRI and 47 mm surface coil to obtain T2-weighted, and contrast-enhanced images. After MRI test, animal was sacrificed and the brain sections were stained for hematoxylin and eosin and immunohistochemistry. MRI and histological analysis revealed that lesion of thrombotic ischemia was well induced in the cortex with the evidence of biological courses of infarction. The target area of thrombotic infarction was 1 mm anterior to bregma and 3 mm lateral to midline with 2 mm in diameter, which were decreased by administration of DHSMT. To assess gene expression pattern of cerebral infarction, mRNA was isolated and reacted with microarray chip(Agilant's DNA Microarray 44K). Scatter and MA plot analysis were performed to clustering of each functional genes. M value [M=log2(R/G), A={log2(R ${\times}$ G)}/2] was between -0.5 and +0.5 with 40% difference. After pretreatment with DHSMT, the expression levels of mRNA of many genes involved in various signaling pathway such as apoptosis, cell cycle, cell proliferation, response to oxidative stress, immune response, angiogenesis, and inflammatory cytokine were markedly inhibited in photothrombotic ischemia lesion compared to the control group. These results suggest that DHSMT prevent ischemic death of brain on photothrombotic ischemia model of mice through modulation of gene expression at the transcriptional level.

• Molecular & Cellular Toxicology
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• 제5권1호
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• pp.58-66
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• 2009

The 2-year rodent carcinogenicity test involves long-term, repetitive dosing of animals that is both time consuming and expensive. Alternative approaches have been attempted using specific transgenic or knockout mice or toxicogenomics to predict carcinogenicity without conducting a 2-year rodent test. In addition, toxicogenomic analysis of carcinogen-treated animals could also enhance our understanding of molecular mechanisms and aid in the diagnosis of acute toxicity induced by carcinogens. Therefore, we investigated transcription profiles after administering the carcinogens 4,4-dimethylformamide (DMF) and 4-biphenylamine (ABP). BALB/c male mice were treated once with DMF (650 mg/kg i.p.) or ABP (120 mg/kg p.o.). Standard blood biochemistry and histological changes were observed. Gene expression profiles in the livers of mice treated with either vehicle or the carcinogens were analyzed using the Affymetrix $GeneChip^{(R)}$ assay. In all, 1,474 differentially expressed genes in DMF- or ABP-treated mice were identified as being either up- or down-regulated over 1.5-fold (P< 0.01), and these genes were analyzed using hierarchical clustering and Ingenuity Pathways Analysis. Of these, 107 genes were consistently regulated in both carcinogen-treated groups. Genes associated with cancer were upregulated (Por, S100a10, Tes, Ctcf, Ddx21, Eapp, Nel, and Pa2g4) or downregulated (Cbs and Gch1). Toxicological function analysis also identified genes involved in organ toxicity, including hepatotoxicity. These data may help to identify molecular markers for acute hepatotoxicity induced by carcinogens.

• 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.

• Korean Journal of Acupuncture
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• 제23권2호
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• pp.125-136
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• 2006

Objectives: It has long been known about the osteogenic effect of CPC-HAS(cervi parvum cornu herbal-acupuncture solution) on bone tissues. However, it has not been determined the effect of CPC-HAS on cancer cells. The purpose of this study is to screen the CPC-HAS mediated differentially expressed genes..in cancer cells such as SNU484 gastric cancer cell lines. Oligonucleotide microarray approache was employed to screen the differential expression genes. Methods: CPC-HAS was prepared by boiling and stored at $-70^{\circ}C$ until use. Cells were treated with various concentrations of CPC-HAS (0.1, 0.5, 1.5, 10, 20 mg/ml) for 24 h. Cell toxicity was tested by MTT assay. To screen the differentially expressed genes in cancer cells, cells were treated with 1.5 mg/ml of CPC-HAS. For oligonucleotide microarray assay, total RNA was used for gene expression analysis using oligonucleotide Genechip(Human genome U133 Plus 2.0., Affimatrix Co.). Results: It has no cytotoxic effects on SNU484 cell in all concentrations(0.l, 0.5, 1.5, 10, 20 mg/ml). In oligonucleotide microarray assay, in SNU484 cells, the number of more than twofold up-regulated genes was 5 while, the number of more than twofold down-regulated genes was 10. Conclusions: This study showed the screening of CPC-HAS mediated differentially regulated genes using combined approaches of oligonucleotide microarray. The screened genes will be used for the better understanding of the therapeutic effects of CPC-HAS on cancer fields.