• Korean Journal of Veterinary Service
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• v.30 no.4
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• pp.489-496
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• 2007

An oligonucleotide microarray system was developed for the simultaneous detection of porcine epidemic diarrhea virus, transmissible gastroenteritis virus, porcine enteric calicivirus, porcine group A and C rotavirus. RNAs of the reference viruses and porcine diarrhea samples were extracted and amplified using one-step multiplex RT-PCR in the presence of cyanine 5-dCTP and hybridized on the microarray chip that spotted the virus-specific oligonucleotides. This system were approximately 10-to 100-fold higher in sensitivity than conventional RT-PCR, and the assay time was less than 3 hours. The relative sensitivity and specificity were 92% and 72.2%, respectively, based on 102 porcine diarrhea samples using RT-PCR as gold standard. These results suggested that the oligonucleotide microarray system in this study be probably more reliable and reproducible means for detecting porcine enteric viruses and that it could be of substantial use in routine diagnostic laboratories.

• Biomolecules & Therapeutics
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• v.14 no.4
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• pp.240-245
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• 2006

The primary use for glycidol is as a stabilizer in the manufacture of vinylpolymers, however, it is also used as an intermediate in the production of pharmaceuticals, as an additives for oil and synthetic hydraulic fluids, and as a diluting agent is same epoxy resins. In this study, we have carried out in vitro genetic toxicity test of glycidol and microarray analysis of differentially expressed genes in response to glycidol. The result of Ames test showed mutations with glycidol treatment in base substitution strain TA1535 both with and without exogenous metabolic activation. Likewise, glycidol showed mutations in frame shift TA98 both with and without exogenous metabolic activation. The result of COMET assay in L5178Y cells with glycidol treatment showed DNA damage both with and without exogenous metabolic activation. Glycidol increased micronuclei in CHO cells both with and without exogenous metabolic activation. 150 Genes were selected as differentially expressed genes in response to glycidol by microarray analysis and these genes would be candidate biomarkers of genetic toxic action of glycidol.

• Journal of Pharmacopuncture
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• v.8 no.3
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• pp.57-69
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• 2005

Objectives : Neurological disorders have been one of main therapeutic targets of acupuncture. The present study investigated the protective effects of Gwakhyangjeonggisan herbal acupuncture solution (GHAS). Methods : We performed 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay in glioblastoma cells, and did microarray analysis with cells exposed to reactive oxigen species (ROS) of hydrogen peroxide by 8.0 k Human cDNA, with cut-off level of 2-fold changes in gene expression. Results : MTT assay showed protective effect of GHAS on the glioblastoma cells exposed to hydrogen peroxide. When glioblastoma cells were exposed to hydrogen peroxide, 24 genes were downregulated. When the cells were pretreated with GHAS before exposure to hydrogen peroxide, 46 genes were downregulated. Many of the genes downregulated by hydrogen peroxide stimulation were decreased in the amount of downregulation or reversed to upregulation. Conclusions : The gene expression changes observed in the present study are supposed to be related to the protective molecular mechanism of GHAS in the glioblastoma cells exposed to ROS stress.

• International Journal of Industrial Entomology and Biomaterials
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• v.35 no.1
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• pp.7-13
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• 2017

In this study, changes in gene expression after administration of silk fibroin fragments ($size{\approx}30kDa$) were evaluated in MG63 cells using a cDNA microarray assay. In addition, the level of alkaline phosphatase (ALP) activity and cellular proliferation in the group administered moderately sized silk fibroin fragments ($size{\approx}30kDa$) (MSF) were compared to those in the group administered smaller silk fibroin fragments (size < 1 kDa) (SSF). The results of the cDNA microarray assay show increased expression of genes that are related to the cell cycle and inflammation. ALP, bone morphogenetic protein-7, bone morphogenetic protein receptor type IA, and runt-related transcription factor 2 exhibited significantly lower expression compared to control cells (fold ratio < 0.5). Relative ALP activity of the $100{\mu}g/mL$ MSF group was significantly lower than that of the SSF group (P < 0.05). Thus, the MSF group showed increased expression of genes associated with cellular proliferation and inflammation but decreased expression of genes associated with osteogenesis.

• Journal of Acupuncture Research
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• v.22 no.6
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• pp.111-123
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• 2005

Objectives : Neurological disorders have been one of main therapeutic targets of acupuncture. The present study investigated the protective effects of Gwakhyangjeonggisan herbal acupuncture solution (GHAS). Methods : We performed 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay in glioblastoma cells, and did microarray analysis with cells exposed to reactive oxigen species (ROS) of hydrogen peroxide by 8.0 k Human cDNA, with cut-off level of 2-fold changes in gene expression. Results : MTT assay showed protective effect of GHAS on the glioblastoma cells exposed to hydrogen peroxide. When glioblastoma cells were exposed to hydrogen peroxide, 16 genes were upregulated. When the cells were pretreated with GHAS before exposure to hydrogen peroxide, 22 genes were upregulated. Most of the genes upregulated by hydrogen peroxide stimulation were reversed to downregulation by GHAS. Conclusion : The gene expression changes observed in the present study are supposed to be related to the protective molecular mechanism of GHAS in the glioblastoma cells exposed to ROS stress.

• Genomics & Informatics
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• v.3 no.1
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• pp.8-14
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• 2005

Although much is known about the molecular biology of platelets, the megakaryocytes' (MKs) molecular biology was not understood so well because of their rareness. By the cloning and characterization of thrombopoietin (TPO), which is the principal regulator of the growth and development of the MKs, researches on the MKs have been growing rapidly. To understand megakaryocytopoiesis, we investigated the gene expression profile of the MKs using oligonucleotide microarray where 10,108 unique genes were spotted. Comparing the fluorescence intensities of which ratio is $\ge$ ${\mid}2{\mid}$, 372 genes were up-regulated and 541 genes were down-regulated in MKs. For confirmatory expression, RNase protection assay (RPA) establishing abundant apoptotic gene expression was carried out. In MKs, many of the known genes, including several platelet related genes, GATA binding protein were highly expressed. Particularly, TGF beta, clusterin (complement lysis inhibitor), and thymosin beta 4 (actin-sequestering molecules) were expressed highly in MKs. As MKs specific expressed genes may regulate normal and pathologic platelet (and/or MK) functions, the transcript profiling using microarray was useful on molecular understanding of MKs,

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.20
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• pp.8957-8961
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• 2014

Background: Promoter hypermethylation leads to altered gene functions and may result in malignant cellular transformation. Thus, identification of biomarkers for hypermethylated genes could be useful for diagnosis, prognosis, and therapeutic treatment of oral squamous cell carcinoma (OSCC). Objectives: To screen hypermethylated genes with a microarray approach and to validate selected hypermethylated genes with the methylation-specific polymerase chain reaction (MSPCR). Materials and Methods: Genome-wide analysis of normal oral mucosa and OSCC tissues was conducted using the Illumina methylation microarray. The specified differential genes were selected and hypermethylation status was further verified with an independent cohort sample of OSCC samples. Candidate genes were screened using microarray assay and run by MSPCR analysis. Results: TP73, PIK3R5, and CELSR3 demonstrated high percentages of differential hypermethylation status. Conclusions: Our microarray screening and MSPCR approaches revealed that the signature candidates of differentially hypermethylated genes may possibly become potential biomarkers which would be useful for diagnostic, prognostic and therapeutic targets of OSCC in the near future.

• BMB Reports
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• v.37 no.5
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• pp.546-551
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• 2004

The increasing pace of development in molecular biology during the last decade has had a direct effect on mass testing and diagnostic applications, including blood screening. We report the model Microarray that has been developed for Hepatitis B virus (HBV) and Hepatitis D virus (HDV) detection. The specific primer pairs of PCR were designed using the Primer Premier 5.00 program according to the conserved regions of HBV and HDV. PCR fragments were purified and cloned into pMD18-T vectors. The recombinant plasmids were extracted from positive clones and the target gene fragments were sequenced. The DNA microarray was prepared by robotically spotting PCR products onto the surface of glass slides. Sequences were aligned, and the results obtained showed that the products of PCR amplification were the required specific gene fragments of HBV, and HDV. Samples were labeled by Restriction Display PCR (RD-PCR). Gene chip hybridizing signals showed that the specificity and sensitivity required for HBV and HDV detection were satisfied. Using PCR amplified products to construct gene chips for the simultaneous clinical diagnosis of HBV and HDV resulted in a quick, simple, and effective method. We conclude that the DNA microarray assay system might be useful as a diagnostic technique in the clinical laboratory. Further applications of RD-PCR for the sample labeling could speed up microarray multi-virus detection.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2006.02a
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• pp.71-76
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• 2006

Comparative genomic hybridization (CGH) is a technique for studying chromosomal changes in cancer. As cancerous cells multiply, they can undergo dramatic chromosomal changes, including chromosome loss, duplication, and the translocation of DNA from one chromosome to another. Chromosome aberrations have previously been detected using optical imaging of whole chromosomes, a technique with limited sensitivity, resolution, quantification, and throughput. Efforts in recent years to use microarrays to overcome these limitations have been hampered by inadequate sensitivity, specificity and flexibility of the microarray systems. The oligonucleotide CGH microarray system overcomes several scientific hurdles that have impeded comparative genomic studies of cancer. This new system can reliably detect single copy deletions in chromosomes. The system includes a whole human genome microarray, reagents for sample preparation, an optimized microarray processing protocol, and software for data analysis and visualization. In this study, we determined the sensitivity, accuracy and reproducibility of the new system. Using this assay, we find that the performance of the complete system was maintained over a range of input genomic DNA from 5 ug down to 0.15 ug.

• BMB Reports
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• v.43 no.11
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• pp.750-755
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• 2010

Crude Orostachys japonicus polysaccharide extract (OJP) was prepared by hot steam extraction. Polysaccharides (OJPI) were separated from OJP by gel filtration chromatography and phenol-sulfuric acid assay. The average molecular weight of the OJPI was 30-50 kDa. The anti-proliferative effect of OJPI on HT-29 human colon cancer cells was investigated via morphology study, cell viability assay, apoptosis assay, cell cycle analysis, and cDNA microarray. OJPI inhibited proliferation and growth of HT29 cells and also stimulated apoptosis in a dose- and time-dependent manner. In cell cycle analysis, treatment with OJPI resulted in a marked increase of cells in the G0 (sub G1) and G2/M phases. To screen for genes involved in the induction of cell cycle arrest and apoptosis, the gene expression profiles of HT-29 cells treated with OJPI were examined by cDNA microarray, revealing that a number of genes were up- or down-regulated by OJPI. Whereas several genes involved in anti-apoptosis, cell proliferation and growth, and cell cycle regulation were down-regulated, expression levels of several genes involved in apoptosis, tumor suppression, and other signal transduction events were up-regulated. These results suggest that OJPI inhibits the growth of HT-29 human colon cancer cells by various apoptosis-aiding activities as well as apoptosis itself. Therefore, OJPI deserve further development as an effective agent exhibiting anticancer activity.