• Journal of Marine Life Science
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• v.3 no.2
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• pp.45-50
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• 2018

Rock bream iridovirus (RBIV) is a megalocytivirus widely infected in various fish species in Korea, causing symptoms of acute inflammation and enlargement of spleen. In our previous study, RBIV induced the initial upregulation but later down-regulation of proinflammatory cytokines and IFN1 gene expression. Signal transducers and activators of transcriptions (STAT) are transcription factors involved in the regulation of immune genes including IFNs. This study was conducted to analyse the expression of STAT2. The expressional study of STAT2 gene was performed in head kidney and spleen upon RBIV infection and immune stimulants like LPS or poly I:C in vitro. Consequently, STAT2 gene expression pattern was different in head kidney and spleen as it was significantly up-regulated by LPS from 4 h to 8 h but down-regulated at 24 h while up-regulated by poly I:C at 8 h in head kidney while, in spleen, STAT2 gene expression was down regulated by LPS but significantly up-regulated by poly I:C. Upon RBIV stimulation, STAT2 gene expression was significantly down-regulated by high dose RBIV at 4 h but up-regulated at 8 h and 24 h in head kidney. In spleen cells, it was up-regulated by medium dose RBIV at 4 h and by high dose RBIV at 4 h and 8 h but down regulated later then. In vivo, STAT2 gene expression was not significantly affected by RBIV infection while significant up-regulated by vaccination at day 7 post-vaccination, indicating STAT2 gene can be involved in adaptive immune response in rock bream.

• Journal of Periodontal and Implant Science
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• v.41 no.4
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• pp.192-200
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• 2011

Purpose: The aim of this study is to compare the gene expression profile in mesenchymal stem cells derived from dental tissues and bone marrow for characterization of dental stem cells. Methods: We employed GeneChip analysis to the expression levels of approximately 32,321 kinds of transcripts in 5 samples of bone-marrow-derived mesenchymal stem cells (BMSCs) (n=1), periodontal ligament stem cells (PDLSCs) (n=2), and dental pulp stem cells (DPSCs) (n=2). Each cell was sorted by a FACS Vantage Sorter using immunocytochemical staining of the early mesenchymal stem cell surface marker STRO-1 before the microarray analysis. Results: We identified 379 up-regulated and 133 down-regulated transcripts in BMSCs, 68 up-regulated and 64 down-regulated transcripts in PDLSCs, and 218 up-regulated and 231 down-regulated transcripts in DPSCs. In addition, anatomical structure development and anatomical structure morphogenesis gene ontology (GO) terms were over-represented in all three different mesenchymal stem cells and GO terms related to blood vessels, and neurons were over-represented only in DPSCs. Conclusions: This study demonstrated the genome-wide gene expression patterns of STRO-$1^+$ mesenchymal stem cells derived from dental tissues and bone marrow. The differences among the expression profiles of BMSCs, PDLSCs, and DPSCs were shown, and 999 candidate genes were found to be definitely up- or down-regulated. In addition, GOstat analyses of regulated gene products provided over-represented GO classes. These data provide a first step for discovering molecules key to the characteristics of dental stem cells.

• The Plant Pathology Journal
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• v.25 no.2
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• pp.172-178
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• 2009

To obtain global gene expression profiles of Arabidopsis thaliana by acid stress, seedlings were subjected to low pH stress. Using Affymetrix AH1 chips covering 24,000 genes, we analyzed gene expression patterns. Fifty-four genes were up-regulated, and 38 were down-regulated more than 3-fold after 2 h of acid stress (pH 3.0). Several defense and abiotic stress-related genes were recognized among the up-regulated genes and peroxidase and extensin genes were identified among the down-regulated genes. After 12 h treatment, relatively fewer genes showed changed expression, indicating that plants seem to adjust themselves to this abiotic stress. Most of the up-regulated genes are already known to be involved in abiotic stress responses and pathogen attacks, especially wounding. However, down-regulated genes for the members of extensins and peroxidases are specific to the acid treatment. These results suggest that acid treatment turns on genes involved in stress responses, especially in wounding and turns off genes very specific for the acid stress.

• Reproductive and Developmental Biology
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• v.31 no.3
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• pp.207-213
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• 2007

This study was carried out to examine gene expression altered in endometrium of Korean cattle (Hanwoo) with endometritis using microarray. In this study, 4,560 diferentially expressed genes (DEGs) were identified in the endometrium of Hanwoo. Of 4,560 DEGs, 2,026 genes were up-regulated, while 2,536 genes were down-regulated in endometritis. Of them, top 10 regulated genes were listed. Filamin A, pancreatic anionic trypsinogen, Rho GDP dissociation inhibitor alpha, collagen type VI alpha 1, butyrate response factor 2, aggrecanses-2, annexin 14, aminopeptidease A, orphan transporter v7-3, and epithelial stromal interaction 1 were up-regulated, while MHC class II antigen, integrin-binding sialoprotein, uterine milk protein precursor, down-regulated in colon cancer 1, glycoprotein 330, dickkopf-1, cfh protein, $Ca^{2+}-dependent$ secretion activator, UL16 binding protein 3, and proenkephalin were down-regulated in the endometritis. Our results suggest that these genes could be useful biomarkers for diagnosis Hanwoo's endometritis.

• Korean Journal of Veterinary Research
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• v.52 no.2
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• pp.99-104
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• 2012

The present study was performed to evaluate the relationship between the neurotoxicity of acrylamide and the differential gene expression pattern in mice. Both locomotor test and rota-rod test showed that the group treated with higher than 30 mg/kg/day of acrylamide caused impaired motor activity in mice. Based on cDNA microarray analysis of mouse brain, myelin basic protein gene, kinesin family member 5B gene, and fibroblast growth factor (FGF) 1 and its receptor genes were down-regulated by acrylamide. The genes are known to be essential for neurofilament synthesis, axonal transport, and neuroprotection, respectively. Interestingly, both FGF 1 and its receptor genes were down-regulated. Genes involved in nucleic acid binding such as AU RNA binding protein/enoyl-coA hydratase, translation initiation factor (TIF) 2 alpha kinase 4, activating transcription factor 2, and U2AF 1 related sequence 1 genes were down-regulated. More interesting finding was that genes of both catalytic and regulatory subunit of protein phosphatases which are important for signal transduction pathways were down-regulated. Here, we propose that acrylamide induces neurotoxicity by regulation of genes associated with neurofilament synthesis, axonal transport, neuro-protection, and signal transduction pathways.

• The Journal of Korean Medicine Ophthalmology and Otolaryngology and Dermatology
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• v.22 no.3
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• pp.47-62
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• 2009

Glenditsia spina (GS) can resolve carbuncle, relive swelling, dispel wind and destroy parasites. For these reasons, GS has been widely used as dermatologic agent clinically. In this study, the specific pathways of anti-proliferative effect of GS on human derived melanoma cells were identified. The molecular profile was measured using microarray technique to identify up- or down-regulated genes in SK-MEL-2 cell line. Pathway analysis was done by listing percentage of pathway involvement, and the represented pathways were obtained from KEGG. The transcription factor binding sequences were obtained by Transfac database. By the promoter analysis, up-regulated genes by GS were mainly associated with MAPK, Regulation of actin cytoskeleton, Wnt, Focal adhesion and Long term potentiation pathway. Down-regulated genes by GS were mainly associated with MAPK and Antigen processing and presentation pathway. And some of the transcription factors like Sp1 and NF-Y in up-regulated genes and Oct-1 in down-regulated genes by GS also identified.

• Journal of Plant Biotechnology
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• v.43 no.1
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• pp.37-48
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• 2016

The transcriptional profiles of 'Tamnara' grapevine (Vitis labruscana L.) to Rhizobium vitis were determined using 12,000 gene oligonucleotide microarray chips constructed with 6,776 unigenes based on the EST sequencing. Among them, 95 clones were up-regulated more than three times and 90 were down-regulated more than 5-times in the R. vitis-inoculated grapevines relative to the control vines. Treatment of salicylic acid showed that 337 clones were upregulated and 52 clones were down regulated in grapevines. Microarray analysis, reverse transcription-polymer chain reaction, and slot blot hybridization analysis revealed that 5, 14, and 64 clones were up-regulated and 10, 12, and 61 clones were down-regulated in wounded, salicylic acid-treated, and R. vitis-inoculated 'Tamnara' grapevine leaves, respectively. The expression patterns of ${\beta}$-1,3-glucanase, proline-rich protein, and lipoxygenase genes of 'Tamnara' moderately resistant to R. vitis were similar to those of resistant 'Concord' and 'Delaware' grapevines. However, chalcone synthase genes in 'Tamnara' grapevines showed similar expression patterns to susceptible grapevines 'Neomuscat' and 'Rizamat'. Further expression studies with various clones for each gene should be conducted to elucidate their roles in resistant responses against pathogens or other stimuli in grapevines. These results could provide better resources for understanding the mechanism of defense responses against crown gall disease and clues for identifying new genes that may play a role in defense against R. vitis in grapevines.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.12
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• pp.6319-6325
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• 2012

We previously found cytotoxic effects of tomato leaf extract (TLE) on the MCF-7 breast cancer cell line. The aim of this study was to ascertain the molecular mechanisms associated with the usage of TLE as an anticancer agent by microarray analysis using mRNA from MCF-7 breast cancer cells after treatment with TLE for 1 hr and 48 hrs. Approximately 991 genes out of the 30,000 genes in the human genome were significantly (p<0.05) changed after the treatment. Within this gene set, 88 were significantly changed between the TLE treated cells and the untreated MCF-7 cells (control cells) with a cut-off fold change >2.00. In order to focus on genes that were involved in cancer cell growth, only twenty-nine genes were selected, either down-regulated or up-regulated after treatment with TLE. Microarray assay results were confirmed by analyzing 10 of the most up and down regulated genes related to cancer cells progression using real-time PCR. Treatment with TLE induced significant up-regulation in the expression of the CRYAB, PIM1, BTG1, CYR61, HIF1-${\alpha}$ and CEBP-${\beta}$ genes after 1 hr and 48 hrs, whereas the TXNIP and THBS1 genes were up-regulated after 1 hr of treatment but down-regulated after 48 hrs. In addition both the HMG1L1 and HIST2H3D genes were down-regulated after 1 hr and 48 hrs of treatment. These results demonstrate the potent activity of TLE as an anticancer agent.

• Molecular & Cellular Toxicology
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• v.2 no.3
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• pp.202-211
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• 2006

Our objective is to identify molecular factors which contribute to the increased risk of smoke in human. About 677 workers who had control and experimental groups according to their urinary Naphthol levels were enrolled in our study. In the present study, we investigated the effects of smoking on gene expression profiles in human. We determined differential gene expression patterns in smoker versus non-smoker using cDNA microarray. Specific genes were up-or down-regulated according to smoking and age. Inflammatory related genes such as cytokine, interleukin, and tumor necrosis factor were up-regulated, DNA repair related genes such as high-mobility group (nonhistone chromosomal) protein 1, and protein 2 were down-regulated, apoptosis related genes such as myeloperoxidase and Bcl-2-associated athanogene were down-regulated, and cell cycle related genes were down-regulated. In our epidemiological study, notably, inflammatory, DNA repair, apoptosis, signal transduction, metabolism, cell cycle, cell proliferation, transcription related genes were regulated.

• The Journal of Korean Obstetrics and Gynecology
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• v.24 no.3
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• pp.28-47
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• 2011

Objectives: This study was performed to investigate the effects of Angelicae gigantis Radix (AGR) which is one of the most useful herbal-drug to treat patients with Polycystic Ovary Syndrome (PCOS) in Oriental medicine on gene expression of ovary tissue. Methods: The effects of AGR on gene expression of ovary tissue resected from PCOS induced rats using single injection of $\ss$-Estradiol 17-valerate (EV) was measured using microarray technique, and the functional analysis on these genes was conducted. Results: Total 2,812 genes were up-regulated or down-regulated, 1,421 genes were up-regulated, 1,391 genes were down-regulated by induction of PCOS. Up-regulated genes were mainly involved in biological function such as cell signalling pathways and inflammatory response. Expression levels of 1,442 genes were restored to those of naive animals by administration of AGR. 558 genes were restored to those of naive animals, which were lowered by induction of PCOS. 884 genes were lowered to naive levels, which were elevated by induction of PCOS. The functions of restored genes were partially involved in the restoration of expression levels, which were changed by induction of PCOS. Especially, up-regulated gene by induction of PCOS were mainly involved in these changes. These results mean restorative effects of AGR on damaged functions by induction of PCOS. The network of total protein interactions was measured using cytoscape program, and some key molecules, such as IRS2, MCM10, ORC2L related in up-regulated genes, CTBP2, CD44, RHOA, related in down-regulated genes that can be used for elucidation of therapeutical mechanism of medicine in future were identified. Conclusion: Restored genes by AGR were thought to have common pathways related in regulation of gene expressions. Especially, genes in restored expression levels by AGR, which were up-regulated by induction of PCOS, were regulated by 9 of common transcription factors, genes in restored expression levels by AGR, which were down-regulated by induction of PCOS, were involved in 25 of common transcription factors.