• Clinical and Experimental Pediatrics
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• v.48 no.7
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• pp.779-788
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• 2005

Purpose : Echinacea, a traditional plant medicine has been used as immune-stimulant. Recent studies have revealed that extract of Echinacea has immunostimulatory effects on human blood mononuclear cells. This study was designed for the purpose of screening the genes associated with immunologic effects of Echinacea on monocytes and dendritic cells using a cDNA microarray chip. Methods : $CD14^+$ monocyte cells were cultured for one day with Echinacea extract(final concentration : $50{\mu}g/mL$) in experiment 1, but were cultured without Echinacea in experiment 2. The gene expression of these cultured monocytes was analyzed using the cDNA microarray chip. Dendritic cells produced from $CD14^+$ monocyte were cultured for five days with GM-CSF and IL-4, and then cultured for one day with Echinacea in experiment 3, but were done without Echinacea in experiment 4. Results : In experiments 1 and 2, there were 17 significantly expressed genes with average expression ratios above 2.5, including interferon gamma-inducible protein 30(IFI 30), CDC(cell-division-cylcle)-like kinase 2(CLK 2), syndecan binding protein(syntenin), superoxide dismutase 2, etc. In experiments 3 and 4, there were 24 gene, with significantly expressed genes were 24 genes, which were insulin-like growth factor 2(somatomedin A), methyl-CpG binding domain protein 3, IFI 30, small inducible cytokine subfamily A, member 22, etc. The genes encoding CD44, IFI 30, mannose receptor C type 1(MRC 1), chemokine receptor 7(CCR 7), CLK 2, syntenin and cytochrome C oxidase subunit VIII were significantly expressed in both monocytes and dendritic cells cultured with Echinacea. Conclusion : This study employed a cDNA microarray chip to elicit the immune-associated gene profile; the expression was enhanced by Echinacea in CD14+ monocytes and dendritic cells. Thus we laid the basis for the quantitative and functional analysis of genes induced by Echinacea in monocytes and monocyte-derived dendritic cells.

• Microbiology and Biotechnology Letters
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• v.44 no.4
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• pp.563-570
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• 2016

Two Streptomyces griseus strains, a wild-type strain and an A-factor-dependent transcriptional activator mutant strain harboring multiple copies of a gene, dasA, that encodes a substrate-binding protein of the ATP-binding cassette transporter, showed severe ectopic sporulation of young substrate hyphae in response to glucose. The effect of dasA overexpression on the ectopic sporulation of Streptomyces strains was evaluated by comparing the transcriptomes of the strain harboring multiple copies of dasA and a strain harboring empty vector. By DNA microarray, 4 genes (SGR794, SGR2469, SGR3656, and SGR3657) and 3 clusters (SGR795-797, SGR2377-2378, and SGR6997-6998) were differentially expressed by more than 2-fold in S. griseus strains harboring dasA. The DNA microarray result was validated by low-resolution S1 nuclease mapping.

• Parasites, Hosts and Diseases
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• v.49 no.4
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• pp.341-347
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• 2011

Acanthamoeba infection is difficult to treat because of the resistance property of Acanthamoeba cyst against the host immune system, diverse antibiotics, and therapeutic agents. To identify encystation mediating factors of Acanthamoeba, we compared the transcription profile between cysts and trophozoites using microarray analysis. The DNA chip was composed of 12,544 genes based on expressed sequence tag (EST) from an Acanthamoeba ESTs database (DB) constructed in our laboratory, genetic information of Acanthamoeba from TBest DB, and all of Acanthamoeba related genes registered in the NCBI. Microarray analysis indicated that 701 genes showed higher expression than 2 folds in cysts than in trophozoites, and 859 genes were less expressed in cysts than in trophozoites. The results of real-time PCR analysis of randomly selected 9 genes of which expression was increased during cyst formation were coincided well with the microarray results. Eukaryotic orthologous groups (KOG) analysis showed an increment in T article (signal transduction mechanisms) and O article (posttranslational modification, protein turnover, and chaperones) whereas significant decrement of C article (energy production and conversion) during cyst formation. Especially, cystein proteinases showed high expression changes (282 folds) with significant increases in real-time PCR, suggesting a pivotal role of this proteinase in the cyst formation of Acanthamoeba. The present study provides important clues for the identification and characterization of encystation mediating factors of Acanthamoeba.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.1
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• pp.11-18
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• 2008

We created a cDNA microarray representing approximately 3,500 pig genes for functional genomic studies. The array elements were selected from 6,494 cDNA clones identified in a large-scale expressed sequence tag (EST) project. These cDNA clones came from normalized and subtracted porcine adipose tissue cDNA libraries. Sequence similarity searches of the 3,426 ESTs represented on the array using BLASTN identified 2,790 (81.4%) as putative human orthologs, with the remainder consisting of "novel" genes or highly divergent orthologs. We used the gene microarray to profile transcripts expressed by adipose tissue of fatty Chinese Xiang pig (XP) and muscley Large White (LW). Microarray analysis of RNA extracted from adipose tissue of fatty XP and muscley LW identified 81 genes that were differently expressed two fold or more. Transcriptional differences of four of these genes, adipocyte fatty acid binding protein (aP2), stearyl-CoA desaturase (SCD), sterol regulatory element binding transcription factor 1 (SREBF1) and lipoprotein lipase (LPL) were confirmed using SYBR Green quantitative RT-PCR technology. Our results showed that high expression of SCD and SREBF1 may be one of the reasons that larger fat deposits are observed in the XP. In addition, our findings also illustrate the potential power of microarrays for understanding the molecular mechanisms of porcine development, disease resistance, nutrition, fertility and production traits.

• Journal of the Society of Cosmetic Scientists of Korea
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• v.30 no.4 s.48
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• pp.479-483
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• 2004

An attempt was made to develop a proteinchip for screening of MITF (microphthalmia transcription factor) inhibitor. Binding of MITF to E-box causes transcription of several pigmenting genes including tyrosinase gene. We investigated binding of MITF and its DNA binding site (E-box) using a protein-DNA chip with various detection methods including flurorescence (Cyt3). SPR (surface plasmon resonance) and SPRi (surface plasmon resonance imaging). A fusion protein (MITF-Maltose Binding Protein) was attached on the glass plate by chemical modification. An inhibitory synthetic DNA oligomer, artificially designed based on the E-box sequence, inhibited the binding of MITF and E-box. These results showed the potentials of flurorescence-based MITF protein chip as a microarray for high throughput screening (HTS) system of depigmenting agents.

• Journal of Life Science
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• v.17 no.8 s.88
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• pp.1115-1120
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• 2007

In the present study, we investigated whether several phytochemicals (resveratrol, genistein, epicatechin gallate, dially disulfide, caffeic acid phenetyl ester) and sulindac sulfide could induce expression of tumor suppressor p53 protein in human colorectal HCT116 cells. We found that p53 was dramatically induced by all phytochemical treatments except sulindac sulfide. Among treated phytochemicals, we selected resveratrol for further experiments because it is one of the highest p53 inducer. Using a Western blot analysis, we found that resveratrol induced p53 in a dose- and time-dependent manner. Additionally, using membrane-based microarray analysis, we found that twenty-five genes were up-regulated and two genes were down-regulated by resveratrol treatment. Among the up-regulated genes, we selected 4 genes and performed reverse-transcription-PCR to confirm microarray data. The results of RT-PCR were highly accorded with those of membrane microarray. In addition, we found that thrombospondin-1 (TSP-1) expression was not dependent on p53 presence, whereas mammary serine protease inhibitor (MASPIN) expression was dependent on p53 expressed by resveratrol treatment. The results of this study may help to promote our understandings of the molecular mechanisms of chemoprevention that are mediated by resveratrol in human colorectal cancer.

• Genomics & Informatics
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• v.11 no.4
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• pp.200-210
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• 2013

Studying biological networks, such as protein-protein interactions, is key to understanding complex biological activities. Various types of large-scale biological datasets have been collected and analyzed with high-throughput technologies, including DNA microarray, next-generation sequencing, and the two-hybrid screening system, for this purpose. In this review, we focus on network-based approaches that help in understanding biological systems and identifying biological functions. Accordingly, this paper covers two major topics in network biology: reconstruction of gene regulatory networks and network-based applications, including protein function prediction, disease gene prioritization, and network-based genome-wide association study.

• Journal of Gastric Cancer
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• v.5 no.1
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• pp.34-39
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• 2005

Purpose: KLF6, a member of the KLF family, is a ubiquitous zinc finger tumor suppressor protein that is mutated in several human cancers. Our aim was to determine whether the expression pattern of KLF6 might be associated with gastric cancer development and, if so, to determine to which pathologic parameter it is linked. Materials and Methods: For the construction of the gastric cancer tissue microarray, 85 paraffin-embedded tissues containing gastric cancer areas were cored 3 times and transferred to the recipient master block. The expression pattern of KLF6 was examined on tissue microarray slides by using immunohistochemistry and was compared with pathologic parameters, including histologic type, depth of invasion, lymph node metastasis, and peritoneal dissemination. Results: The KLF6 protein was expressed on superficial and foveolar epithelial cells in the gastric mucosa. We found loss of KLF6 expression in 28 ($32.9\%$) of the 85 gastric cancer tissues. There was a significant correlation between loss of KLF6 expression and lymph-node metastasis. However, other pathologic parameters, such as histologic type, depth of invasion, and peritoneal dissemination, were not statistically associated with loss of KLF6 expression. Conclusion: Our findings suggest that loss of KLF6 expression may contribute to abnormal regulation of gastrointestinal epithelial cell growth and differentiation and to the development and/or progression of Korean gastric cancer.

• Proceedings of the Korean Nutrition Society Conference
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• 2003.10a
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• pp.84-84
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• 2003

• Journal of Acupuncture Research
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• v.20 no.5
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• pp.50-62
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• 2003

Objective: Bee Venom(BV) has been used for various kinds of inflammatory or painful conditions in Oriental Medicine clinics, and there publishes reports on its therapeutic effects and the probable mechanism of those therapeutic effects, where CDs and cytokines plays important role. This study investigated the influences of bee venom on the expressions of CDs and cytokines of HMC cell line Methods: In this study we analysed the expression profile of HMC cell line treated with BV of 10-2ug/ml in relation to that of HMC cell line treated with vehicle by way of CD/cytokine microarray hybridization with 342 genes on it. Results: There were no upregulated genes by more than 3 fold, while there showed some downregulated genes by less than 1/3 fold as follows: colony stimulating factor 2, CD122, IL-7, CD112, TNF-alpha, CD138, CD166, TGFbetaR2, CD42b, CD62L, CD111, interleukin 10 receptor alpha, colony stimulating factor 1(macrophage), CD38 antigen(p45), CD121a, CD33 antigen(gp67), colony stimulating factor 1 receptor, B cell linker protein (SLP65) mRNA, CD94, alanyl(membrane) aminopeptidase, immunoglobulin(CD79A) binding protein 1, CD205, CD241, CD207, CDw121b, integrin alpha L(CD11a), integrin beta 1(CD29), CD91, CD42b. Conclusions: Bee venom treatment induced downregulation of some CDs or cytokines including $TNF-{\alpha}$. IL-1R with its possible implication in an antiinflammatory action of BV. Further research on expression profile changes induced by BV treatment is expected.