• BMB Reports
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• v.37 no.5
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• pp.612-617
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• 2004

Autosomal dominant polycystic kidney disease (ADPKD) is a common genetic disorder characterized by the formation of fluid-filled cysts in the kidney and progressive renal failure. Other manifestations of ADPKD include the formation of cysts in other organs (liver, pancreas, and spleen), hypertension, cardiac defects, and cerebral aneurysms. The loss of function of the polycystin -1 and -2 results in the formation of epithelium-lined cysts, a process that depends on initial epithelial proliferation. cDNA microarrays powerfully monitor gene expression and have led to the discoveries of pathways regulating complex biological processes. We undertook to profile the gene expression patterns of epithelial cells derived from the cysts of ADPKD patients using the cDNA microarray technique. Candidate genes that were differently expressed in cyst tissues were identified. 19 genes were up-regulated, and 6 down-regulated. Semi-quantitative RT-PCR results were consistent with the microarray findings. To distinguish between normal and epithelial cells, we used the hierarchical method. The results obtained may provide a molecular basis for understanding the biological meaning of cytogenesis.

• Archives of Pharmacal Research
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• v.23 no.6
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• pp.613-619
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• 2000

We investigated the expression profiles of rat fibrotic liver induced by bile duct ligation and scission (BDL/S) using the 3'-directed cDNA libraries. The possibility that the 3'-directed cDNA library represents the mRNA population faithfully was examined by northern blots. During the northern analysis based on fibrotic liver expression profile, we found for the first time that purine specific sodium nucleoside cotransporter (SPNT) was upregulated in BDL/S-induced fibrotic liver. To determine whether the accumulation of bile juice could affect the expression of SPNT mRNA or not, we examined the change of SPNT mRNA expression at 3, 14, 28 days after BDL/S operation. No change in SPNT expression was observed in rat liver at 3 days after surgery. In contrast, there were significant increases in SPNT expression at 14 and 28 days after surgery. We also examined whether chronic liver damage affected SPNT mRNA expression. SPNT mRNA level was significantly increased in BDL/S-induced fibrotic rat liver, whereas no significant change was obserbed in fibrotic livers chronically exposed to carbon tetrachloride or dimethylnitrosamine. From the above results, although further study might be needed, it was considered that the increment of SPNT mRNA in BDL/S liver morphological compatibility to human was remarkable.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.10
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• pp.1406-1415
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• 2013

The study was conducted to correlate the periparturient immune status in terms of neutrophil functions and cytokine expression in peripheral blood mononuclear cell culture with impending postpartum reproductive disorders in buffaloes. Forty pregnant buffaloes were observed for occurrence of postpartum reproductive disorders (PRD), i.e., metritis, endometritis and delayed uterine involution etc., during one week prepartum to four weeks postpartum period. A representative number (n = 6) of buffaloes that did not develop any PRD were included in group I (healthy, control), while the animals which experienced PRD were assigned into group II (PRD, n = 8). The blood samples were collected at weekly interval from one week prepartum to four weeks postpartum period considering the day of calving as 'd 0'. Differential leucocytes counts, superoxide and hydrogen peroxide production activity in isolated neutrophils and the mRNA expression profile of cytokines i.e., IL-2, IL-4 and IFN-${\gamma}$ in PBMC culture were studied in all the samples. A higher total leucocytes, neutrophil and band cells count along with impaired neutrophil functions i.e., lowered level of production of superoxide and hydrogen peroxide before parturition and during early postpartum period were observed in buffaloes developing PRD. Further, a lower expression of IL-2, IFN-${\gamma}$ and IL-4 mRNA in PBMC culture was observed at calving in buffaloes that subsequently developed PRD at later postpartum. Thus, suppression in neutrophil function and cytokine expression at prepartum to early postpartum period predisposes the buffaloes to develop postpartum reproductive disorders. Hence, monitoring of neutrophils function and cytokine expression profile would be effective to predict certain reproductive disorders at late pregnancy or immediately after parturition in buffaloes. In future, this may be a novel approach for determining suitable management and therapeutic decisions for prevention of commonly occurring reproductive disorders in farm animals.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.161-164
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• 2005

Data mining techniques can be applied to identify patterns of interest in the gene expression data. One goal in mining gene expression data is to determine how the expression of any particular gene might affect the expression of other genes. To find relationships between different genes, association rules have been applied to gene expression data set [1]. A notable limitation of association rule mining method is that only the association in a single profile experiment can be detected. It cannot be used to find rules across different condition profiles or different time point profile experiments. However, with the appearance of time-series microarray data, it became possible to analyze the temporal relationship between genes. In this paper, we analyze the time-series microarray gene expression data to extract the sequential patterns which are similar to the association rules between genes among different time points in the yeast cell cycle. The sequential patterns found in our work can catch the associations between different genes which express or repress at diverse time points. We have applied sequential pattern mining method to time-series microarray gene expression data and discovered a number of sequential patterns from two groups of genes (test, control) and more sequential patterns have been discovered from test group (same CO term group) than from the control group (different GO term group). This result can be a support for the potential of sequential patterns which is capable of catching the biologically meaningful association between genes.

• Journal of the Korean Solar Energy Society
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• v.36 no.4
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• pp.11-20
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• 2016

For accurate wind resource assessment and wind turbine performance test, it is essential to secure wind data covering a rotor plane of wind turbine including a hub height. In general, we can depict wind speed profile by extrapolating or interpolating the wind speed data measured from a meteorological tower where multiple anemometers are mounted at different heights using a power-law of wind speed profile. The most important parameter of a power-law equation is a vertical wind profile exponent which represents local characteristics of terrain and land cover. In this study, we calculated diurnal vertical wind profile exponents of 8 locations in Jeju Island who possesses excellent wind resource according to the GUM (Guide to the Expression of Uncertainty in Measurement) to evaluate its uncertainty. Expanded uncertainty is calculated by combined standard uncertainty, which is the result of composing type A standard uncertainty with type B standard uncertainty. Although pooled standard deviation should be considered to derive type A uncertainty, we used the standard deviation of vertical wind profile exponent of each day avoiding the difficult of uncertainty evaluation of diurnal wind profile variation. It is anticipated that the evaluated uncertainties of diurnal vertical wind profile exponents at 8 locations in Jeju Island are to be registered as a national standard reference data and widely used in the relevant areas.

• The Korean Journal of Food And Nutrition
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• v.25 no.4
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• pp.863-870
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• 2012

Though hydrogen peroxide ($H_2O_2$) causes a deleterious effect to cells with its reactive oxygen species resulting in cell death, S-allyl cysteine (SAC, a bioactive organosulfur compound of aged garlic extract) has been known to have a cytoprotective effect. Few reported profiles of gene expression of $H_2O_2$ and SAC treated human cord blood derived mesenchymal stem cells (MSC). This study revealed changes in the profile of twenty-one genes grouped by oxidative stress, antioxidant, cell death, anti-apoptosis and anti-aging by quantitative real time PCR. A concentration of $100{\mu}M$ of SAC or $50{\mu}M$ of $H_2O_2$ was applied to MSC which show moderate growth and apoptosis pattern. $H_2O_2$ treatment enhanced expression of eleven genes out of twenty-one genes compared with that of control group, on the contrary SAC suppressed expression of eighteen genes out of twenty-one genes except C ros oncogene. SAC decreased expression of oxidative stress genes such as SOD1, CAT and GPX. These results seemed consistent with reports which elucidated over-expression of NF-${\kappa}$B by $H_2O_2$, and suppression of it by SAC. This study will confer basic information for further experiments regarding the effects of SAC on gene levels.

• Molecular & Cellular Toxicology
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• v.5 no.1
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• pp.44-50
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• 2009

This study was conducted to evaluate the inflammation mechanisms of tumor necrosis factor-$\alpha$ (TNF-$\alpha$), interleukin-4 (IL-4), and IL-$1{\beta}$-induced stimulation of A549 human epithelial cells. In the present study, A549 cells were stimulated with TNF-$\alpha$, IL-4 and IL-$1{\beta}$ to induce expression of chemokines and adhesion molecules involved in eosinophil chemotaxis. The effects of TNF-$\alpha$, IL-4 and IL-$1{\beta}$ on gene expression profiles in A549 cells were evaluated by oligonucleotide microarray and Real time RT-PCR. The gene expression profiles for the A549 cells varied depending on the cytokines. Also, the results of the microarray and Real time RT-PCR revealed that inflammatory-related genes were up-regulated in cytokine stimulated A549 cells. Cytokines can affect inflammation in A549 cells. A microarray-based genomic survey is a high-throughput approach that enables evaluation of gene expression in cytokine stimulated cell lines.

• Journal of the Institute of Electronics Engineers of Korea SP
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• v.41 no.3
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• pp.83-92
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• 2004

Gene expression profile is numerical data of gene expression level from organism measured on the microarray. Generally, each specific tissue indicates different expression levels in related genes, so that we can classify cancer with gene expression profile. Because not all the genes are related to classification, it is needed to select related genes that is called feature selection. This paper proposes a new gene selection method using forward selection method in regression analysis. This method reduces redundant information in the selected genes to have more efficient classification. We used k-nearest neighbor as a classifier and tested with colon cancer dataset. The results are compared with Pearson's coefficient and Spearman's coefficient methods and the proposed method showed better performance. It showed 90.3% accuracy in classification. The method also successfully applied to lymphoma cancer dataset.

• Molecular & Cellular Toxicology
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• v.2 no.4
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• pp.273-278
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• 2006

95 squamous cell lung carcinoma samples (normal tissue: 40 samples, tumor: 55 samples) were analyzed with 8 K cDNA microarray. 1-way ANOVA test was employed to select differentially expressed genes in tumor with FDR<0.01. Among the selected 1,655 genes, final 212 genes were chosen according to the expression fold change and used for following analysis. The expression of up-regulated 64 genes was verified with Reverse Transcription PCR and 10 genes were identified as candidates for SCC markers. In our opinion, those candidates can be exploited as diagnostic or therapeutic purposes. Gene Ontology (GO) based analysis was performed using those 212 genes, and following categories were revealed as significant biological processes: Immune response (GO: 0006955), antigen processing (GO: 0030333), inflammatory response (GO: 0006954), Cell adhesion (GO: 0007155), and Epidermis differentiation (GO: 0008544). Gene set enrichment analysis (GSEA) also carried out on overall gene expression profile with 522 functional gene sets. Glycolysis, cell cycle, K-ras and amino acid biosynthesis related gene sets were most distinguished. These results are consistent with the known characteristics of SCC and may be interconnected to rapid cell proliferation. However, the unexpected results from ERK activation in squamous cell carcinoma gripped our attention, and further studies are under progress.

• Archives of Pharmacal Research
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• v.27 no.4
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• pp.422-428
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• 2004

Expressed sequence tags (ESTs) were generated from two 3'-directed CDNA libraries constructed from quiescent and activated rat hepatic stellate cell (HSC) to analyze the expression profiles of active genes in both cells. From quiescent and activated HSC, 694 ESTs and 779 ESTs, respectively, were obtained after excluding those having shorter than 30 bp. Amonq ESTs obtained from quiescent and activated HSC, 68 and 73 kinds of ESTs (186 clones and 236 clones), respectively, appeared more than once, implying that their genes are expressed highly in each cell type. 52 among 73 ESTs appeared only in the activated HSC 47 amonq 68 ESTs only in the normal HSC, and 21 in both cells. The genes of these 52 ESTs were assumed to be expressed more highly in the activated HSC. To confirm the high expression of genes of which the ESTs appeared more than twice in the activated HSC, northern hybridization was carried out with RNAs derived from rat normal and fibrotic liver using each of 18 EST DNAs as probe. 13 ESTs showed more intense bands with RNA isolated from the fibrotic liver than normal liver. From these results, we confirm the positive correlation between abundance of transcript in activated HSCs and the expression level in fibrotic liver, The expression profile of the transcripts serves as an important tool in understanding the biological properties of HSC.