• Molecular & Cellular Toxicology
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• v.4 no.2
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• pp.132-137
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• 2008

Differential gene expression profiling was carried out in the hepatic tissue of medaka fish, Oryzias latipes, after exposure to an organophosphorus pesticide (OPP), Iprobenfos (IBP), a widely used pesticide in agri- and fish-culture, using a medaka cDNA micro array. Twenty six kinds of differentially expressed candidate genes, with 15 and 11 induced and repressed in their gene expressions, respectively, were associated with cytoskeleton (3.8%), development (7.7%), immune (7.7%), metabolism (30.8%), nucleic acid/protein binding (42.3%) and reproduction (7.7%). Of these genes, changes at the transcription level of five were re-evaluated by real-time quantitative PCR (qRT-PCR). Considering the known function of authentic genes, the effects of IBP on the biological activity and pathological aspects in medaka fish were discussed. The identified genes could be used as molecular biomarkers for biological responses to OPPs contamination in an aquatic environment.

• Development and Reproduction
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• v.22 no.3
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• pp.253-262
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• 2018

The spermatogenesis is the process by which spermatozoa are generated in the testes. The spermatozoa travel male reproductive tract during which they meet many substances secreted from reproductive organs. One of the substances is epididymal protease inhibitor (EPPIN) that is involved in the post-testicular maturation including capability of fertilizing the eggs. The expression of EPPIN gene was investigated in various tissues of sexually mature and regressed male Syrian hamsters by reverse transcription polymerase chain reaction (RT-PCR). The EPPIN gene was identified in the testis and epididymis of the male Syrian hamsters and compared to the genes reported previously. There was no expression of EPPIN gene in reproductively and completely regressed testes of Syrian hamster. These results suggest that the expressions of the EPPIN gene are associated with the reproductive capability in the Syrian hamsters.

• Genomics & Informatics
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• v.3 no.1
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• pp.30-34
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• 2005

Microarray technology makes it possible to measure the expressions of tens of thousands of genes simultaneously under various experimental conditions. Identifying differentially expressed genes in each single experimental condition is one of the most common first steps in microarray gene expression data analysis. Reasonable choices of thresholds for determining differentially expressed genes are used for the next-stap-analysis with suitable statistical significances. We present a supervised model for identifying DEGs using pathway information based on the global connectivity structure. Pathway information can be regarded as a collection of biological knowledge, thus we are trying to determine the optimal threshold so that the consequential connectivity structure can be the most compatible with the existing pathway information. The significant feature of our model is that it uses established knowledge as a reference to determine the direction of analyzing microarray dataset. In the most of previous work, only intrinsic information in the miroarray is used for the identifying DEGs. We hope that our proposed method could contribute to construct biologically meaningful structure from microarray datasets.

• BMB Reports
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• v.29 no.5
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• pp.484-487
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• 1996

The matrix metalloproteinases (MMPs) are members of a unique family of proteolytic enzymes that degrade components of the extracellular matrix. Significant evidence has accumulated to directly implicate members of the MMPs in tumor invasion and metastasis formation. To investigate the correlation between ras oncogene and MMP gene expression in various tumor cells, we detected mRNAs for the ras, MMP-2 and MMP-9 (72 kD and 92 kD type IV collagenases, respectively) genes in nine human tumor cell lines. The ras gene was expressed in seven cell lines; MMP-2 in three; MMP-9 in two cell lines tested. There was no direct correlation between the ras oncogene and MMP expression. A clear difference in the mRNA expression between MMP-2 and MMP-9 was observed among the cell lines. As an approach to study the effect of the ras oncogene on metastasis, we examined the expressions of MMP-2 and MMP-9 in HT1080 cells transfected with the v-H-ras gene. MMP-9 expression was Significantly enhanced in the ras-transfected HT1080 cells compared with the nontransfectants while ras transfection did not affect the expression of MMP-2. These results suggest the possible inducing effect of the ras oncogene on the metastasis by activation of the MMP-9 gene in HT1080.

• Journal of Applied Biological Chemistry
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• v.49 no.3
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• pp.75-81
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• 2006

A full-length cDNA encoding dihydroflavonol 4-reductase (st-dfr) of potato was isolated by rapid amplification of cDNA ends, and their expression was investigated from purple-fleshed potato (Solanum tuberosum L. cv. Jashim). The st-dfr exists as a member of a small gene family and its transcripts was abundant in the order of tuber flesh, stem, leaf, and root. The expressions of st-dfr gene were light inducible and cultivar dependant. Transgenic potato plants harboring antisense st-dfr (AS-DFR) sequences were analyzed. The accumulation of mRNA was nearly completely inhibited as a result of introducing an AS-DFR gene under the control of the 35S CaMV promoter into the red tuber skin Solanum tuberosum L. cv. Desiree. The anthocyanin content of the tuber peels of the transgenic lines was dramatically decreased by up to 70%. The possible production of flavonols in the peels of AS-DFR transgenic potatoes was discussed.

• Genomics & Informatics
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• v.6 no.3
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• pp.136-141
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• 2008

A large number of studies have been performed to identify biomarkers that will allow efficient detection and determination of the precise status of a patient’s disease. The use of microarrays to assess biomarker status is expected to improve prediction accuracies, because a whole-genome approach is used. Despite their potential, however, patient samples can differ with respect to biomarker status when analyzed on different platforms, making it more difficult to make accurate predictions, because bias may exist between any two different experimental conditions. Because of this difficulty in experimental standardization of microarray data, it is currently difficult to utilize microarray-based gene sets in the clinic. To address this problem, we propose a method that predicts disease status using gene expression data that are transformed by their ranks, a concept that is easily applied to two datasets that are obtained using different experimental platforms. NCI and colon cancer datasets, which were assessed using both Affymetrix and cDNA microarray platforms, were used for method validation. Our results demonstrate that the proposed method is able to achieve good predictive performance for datasets that are obtained under different experimental conditions.

• Journal of Life Science
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• v.27 no.10
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• pp.1111-1120
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• 2017

This study was conducted to select pepper lines that were tolerant to excessive water injury among the pepper germplasm and investigate the genetic characteristics of those lines to contribute to the breeding of pepper cultivars with stable productivity in abnormal weather. Each of the tolerant and susceptible lines went through immersion treatment, and differentially expressed genes between them were analyzed. The tolerant line showed increased expression of the CA02g26670 gene, which is involved in the CONSTANS protein pathway and regulation of flowering by day length, but it exhibited decreased expressions of CA01g21450, CA01g22480, CA01g34470, CA02g00370 and CA02g00380. The susceptible line showed increased gene expressions of CA02g09720, CA02g21290, CA03g16520, CA07g 02110, and CA12g17910, which are involved in the inhibition of proteolytic enzyme activity, DNA binding, inhibition of cell wall-degrading enzyme, and inhibition of nodulin, respectively. Meanwhile the expressions of CA02g02820, CA03g21390, CA06g17700 and CA07g18230 decreased in the susceptible line, in relation to calcium-ion binding, high temperature, synthesis of phosphocholine and cold stress, respectively. The expressions of genes related to apoptosis and peroxidase increased, while that of CA02g16990, which functions as a nucleoside transporter, decreased in both the tolerant and susceptible lines. Based on the different gene expressions between the tolerant and susceptible lines, further studies are needed on breeding abiotic stress-tolerant lines.

• The Journal of Internal Korean Medicine
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• v.41 no.4
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• pp.668-675
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• 2020

Objectives: The aim of this study was to compare the effects of Galkunhwanglyeonhwanggum-tang (GGT), and Sopunghwalhyeol-tang (SPT) on gene expression of MCP-1, ICAM-1, VCAM-1, and eNOS in human umbilical vein endothelial cells (HUVECs). Methods: HUVECs were treated with GGT and SPT at concentrations of 50, 100, and 200 ㎍/mL. Gene expression of MCP-1, ICAM-1, VCAM-1, and eNOS in HUVECs was analyzed by the polymerase chain reaction (PCR), and electrophoresis was performed to verify the gene expression level. Results: 1. MCP-1 gene expression was more strongly decreased by SPT than by GGT. 2. ICAM-1 and VCAM-1 gene expressions were more strongly decreased by SPT than by GGT 3. GGT significantly increased eNOS gene expression, but SPT did not. Conclusions: These findings suggest that GGT and SPT regulate gene expression related to anti-inflammatory effects in HUVECs. Clinical application of these Korean medicines to diseases related to dyslipidemia, such as cardiovascular disease, will require additional in vivo experiments to verify the anti-inflammatory effects of GGT and SPT.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.2
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• pp.278-285
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• 2012

Poultry products are an important source of Salmonella enterica. An effective way to reduce food poisoning due to Salmonella would be to breed chickens more resistant to infection. Unfortunately host responses to Salmonella are complex with many factors involved. To learn more about responses to Salmonella in young chickens of 2 wk old, a cDNA Microarray containing 13,319 probes was performed to compare gene expression profiles between two chicken groups under control and Salmonella infected conditions. Newly hatched chickens were orally infected with S. enterica serovar Enteritidis. Since the intestine is one of the important barriers the bacteria encounter after oral inoculation, intestine gene expression was investigated at 2 wk old. There were 588 differentially expressed genes detected, of which 276 were known genes, and of the total number 266 were up-regulated and 322 were down-regulated. Differences in gene expression between the two chicken groups were found in control as well as Salmonella infected conditions indicating a difference in the intestine development between the two chicken groups which might be linked to the difference in Salmonella susceptibility. The differential expressions of 4 genes were confirmed by quantitative real-time PCR and the results indicated that the expression changes of these genes were generally consistent with the results of GeneChips. The findings in this study have lead to the identification of novel genes and possible cellular pathways, which are host dependent.

• Clinical and Experimental Reproductive Medicine
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• v.31 no.4
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• pp.217-223
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• 2004

Objective: To evaluate the effects of recombinant FSH (rFSH) and urinary FSH (uFSH) on the gene expressions of human endometrial stromal cells in vitro. Methods: Endometrial tissue was obtained from a pre-menopausal women undergoing hysterectomy. Primary endometrial stromal cells were isolated and in vitro cultured with FBS-free DMEM/F-12 containing 0, 10, 100, and 1, 000 mIU/ml of rFSH and uFSH for 48 hours, respectively. Total RNA was extracted from the cultured cells and subjected to real time RT-PCR for the quantitative analysis of progesterone receptor (PR), estrogen receptor $\alpha/\beta$ (ER-$\alpha/\beta$), cyclooxygenase 2 (Cox-2), leukemia inhibitory factor (LIF), homeobox A10-1 and -2 (HoxA10-1/-2). Results: Both hormone treatments slightly increased (< 3 folds) the expressions of PR, ER-$\beta$ and HoxA10-1/-2 gene. However, ER-$\alpha$ expression was increased up to five folds by treatments of both FSH for 48 hours. The LIF expression by the 10 mIU/ml of uFSH for 12 hours was significantly higher than that of rFSH (p<0.01). After 24 hours treatment of two kinds of hormones, the expression patterns of LIF were similar. The 100 and 1, 000 mIU/ml of rFSH induced significantly higher amount of Cox-2 expression than those of uFSH, respectively (p<0.05). Conclusion: This study represents no adversely effect of exogeneous gonadotropins, rFSH and uFSH, on the expression of implantation related genes. We suggest that rFSH is applicable for the assisted reproductive technology without any concern on the endometrial receptivity.