• Journal of Radiation Industry
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• v.3 no.1
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• pp.25-29
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• 2009

Microarrays can be used to screen thousands of binding events in a parallel and high throughput fashion and are of major importance in disease diagnosis and drug discovery. The use of radioisotope is conventionally regarded as one of the most sensitive detection methods. Atherosclerosis is a common disorder affecting arterial blood vessels. It happens when fat, cholesterol, and other substances made in the arterial blood vessels form a hard substances called plaque. Lipoprotein-associated phospholipase $A_2$ ($Lp-PLA_2$), a phospholipase $A_2$ enzyme, is used as a marker for cardiac disease. The detection of $Lp-PLA_2$ was accomplished by using radioactive [$^3H-acetyl$] PAF as a substrate and a feasibility study on RI biochip application to detection of $Lp-PLA_2$, a risk factors of atherosclerosis was performed. Inhibitive activity of a native plant extract was also determined by using the RI biochip. It was found to be applicable to a high-throughput screening of inhibitors for developing atherosclerosis therapeutic agents.

• Journal of Radiation Industry
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• v.6 no.3
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• pp.281-287
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• 2012

The model plant, Arabidopsis thaliana is the subject of an international genome research project. Massive doses of ionizing radiation have been shown to induce physiological changes in plants. The wild-type (Ler) Arabidopsis plants were irradiated with 100 Gy and 800 Gy of gamma-ray. Gibberellin (GA) affects developmental processes and responses according to the various environment conditions in diverse plant. The 13 GA isomers were analyzed at vegetative (VE) and reproductive (RE) stages by HPLC. Total GA contents were reduced with the increase in radiation doses at VE and RE stages. Specifically, levels of GA3, GA4, GA12, and GA34 were significantly reduced with the increase of radiation doses. Oligonucleotide microarrays analysis was performed with Arabidopsis plants at different developmental stages and doses of gamma-ray. Through the microarray data, we isolated 41 genes related to GA biosynthesis and signaling transduction. Expression of these genes was also decreased as the reduction of GA contents. Interestingly, in GA signaling related gene expression, gibberellin-responsive protein, putative (At2g18420) was down-regulated at VE and RE stages. Myb21 (At3g27810), Myb24 (At5g40350), and Myb57 (At3g01530) was down-regulated at RE stage. In GA biosynthesis related gene expression, YAP169 (At5g07200) and GA20ox2 (At5g51810) were down-regulated at 100 Gy treatment of VE stage and 800 Gy treatment of RE stage in cytoplasm, respectively. However, exceptively, GA3ox2 (At1g80340) was up-regulated at 100 Gy treatment of RE stage in cytoplasm. In this study, the wild type (Ler) Arabidopsis plants showed differences in response with development stage at the various doses of gamma-rays. GA contents change was reported in gamma irradiated plant.

• Animal cells and systems
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• v.5 no.2
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• pp.153-156
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• 2001

A key aspect of genomic research in the “post-genome era”is to associate sequence variations with heritable phenotypes. The most common variations in the human genome are single nucleotide polymorphisms (SNPs) that occur approximately once in every 500 to 1,000 bases. Although analyzing the phenotypic outcome of these SNPs is crucial to facilitate large-scale association studies of genetic diseases, detection of SNPs from an extended number of human DNA samples is often difficult, labor-intensive and time-consuming. Recent development in SNP detection methods using DNA microarrays and mass spectrophotometry has allowed automated high throughput analyses, but such equipments are not accessible to many scientists. In this study, we demonstrate that a simple PCR-based method using primers with a mismatched base at the 3'-end provides a fast and easy tool to identify known SNPs from human genomic DNA in a regular molecular biology laboratory. Results from this PCR amplification of specific alleles (PASA) analysis efficiently and accurately typed the Q576R polymorphism of human IL4 receptor from the genomic DNAs of 29 Koreans, including 9 samples whose genotype could not be discerned by the conventiona1 PCR-SSCP (single strand conformation polymorphism) method. Given the increasing attention to disease-associated polymorphisms in genomic research, this alternative technique will be very useful to identify SNPs in large-scale population studies.

• Toxicological Research
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• v.35 no.3
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• pp.257-270
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• 2019

Silver nanoparticles (AgNPs) have been widely used in a variety of applications in innovative development; consequently, people are more exposed to this particle. Growing concern about toxicity from AgNP exposure has attracted greater attention, while questions about nanosilver-responsive genes and consequences for human health remain unanswered. By considering early detection and prevention of nanotoxicology at the genetic level, this study aimed to identify 1) changes in gene expression levels that could be potential indicators for AgNP toxicity and 2) morphological phenotypes correlating to toxicity of HepG2 cells. To detect possible nanosilver-responsive genes in xenogenic targeted organs, a comprehensive systematic literature review of changes in gene expression in HepG2 cells after AgNP exposure and in silico method, connection up- and down-regulation expression analysis of microarrays (CU-DREAM), were performed. In addition, cells were extracted and processed for transmission electron microscopy to examine ultrastructural alterations. From the Gene Expression Omnibus (GEO) Series database, we selected genes that were up- and down-regulated in AgNPs, but not up- and down-regulated in silver ion exposed cells, as nanosilver-responsive genes. HepG2 cells in the AgNP-treated group showed distinct ultrastructural alterations. Our results suggested potential representative gene data after AgNPs exposure provide insight into assessment and prediction of toxicity from nanosilver exposure.

• Yonsei Medical Journal
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• v.59 no.9
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• pp.1041-1048
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• 2018

Purpose: Heat shock factor 1 (HSF1) is a key regulator of the heat shock response and plays an important role in various cancers. However, the role of HSF1 in gastric cancer is still unknown. The present study evaluated the function of HSF1 and related mechanisms in gastric cancer. Materials and Methods: The expression levels of HSF1 in normal and gastric cancer tissues were compared using cDNA microarray data from the NCBI Gene Expression Omnibus (GEO) dataset. The proliferation of gastric cancer cells was analyzed using the WST assay. Transwell migration and invasion assays were used to evaluate the migration and invasion abilities of gastric cancer cells. Protein levels of HSF1 were analyzed using immunohistochemical staining of tissue microarrays from patients with gastric cancer. Results: HSF1 expression was significantly higher in gastric cancer tissue than in normal tissue. Knockdown of HSF1 reduced the proliferation, migration, and invasion of gastric cancer cells, while HSF1 overexpression promoted proliferation, migration, and invasion of gastric cancer cells. Furthermore, HSF1 promoted the proliferation of gastric cancer cells in vivo. In Kaplan-Meier analysis, high levels of HSF1 were associated with poor prognosis for patients with gastric cancer (p=0.028). Conclusion: HSF1 may be closely associated with the proliferation and motility of gastric cancer cells and poor prognosis of patients with gastric cancer. Accordingly, HSF1 could serve as a prognostic marker for gastric cancer.

• Korean Journal of Clinical Laboratory Science
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• v.52 no.4
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• pp.310-316
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• 2020

Microarray technology represents a critical new advance in molecular cytogenetics. The development of this approach has provided fundamental insights into the molecular pathogenesis in clinical cytogenetics and has provided a clue to many unidentified or unexplained diseases. The approach allows a comprehensive investigation of thousands and millions of genomic loci simultaneously and enables the efficient detection of copy number alterations. The application of this technology has shown tremendous fluidity and complexity of the human genome, and has provided accurate diagnosis and appropriate clinical management in a timely and efficient manner for identifying genomic alterations. The clinical impact of the genomic alterations identified by microarrays is evolving into a diagnostic tool to identify high-risk patients better and predict patient outcomes from their genomic profiles. The transformation of conventional cytogenetics into an automated discipline will improve diagnostic yield significantly, leading to accurate diagnosis and genetic counseling. This article reviews cytogenetic technologies used to identify human chromosome alterations and highlights the potential utility of present and future genome microarray technology in the diagnosis.

• Journal of Life Science
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• v.30 no.9
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• pp.772-782
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• 2020

Skeletal muscle differentiation or myogenesis is important to maintain muscle mass and metabolic homeostasis. Muscle-specific microRNAs (miRNAs) are known to play a critical role in skeletal myogenic differentiation. In this study, we examined the expression profiling of miRNAs during myogenic differentiation in rat L6 myoblasts using rat miRNA microarrays. We identified the upregulated expression of miR-128 as well as several well-known myogenic miRNAs, including miR-1, miR-133b, and miR-206. We additionally confirmed the increased expression of miR-128 observed on microarray through quantitative real-time PCR (qRT-PCR), which showed similarly upregulated expression of both primary miR-128 and mature miR-128, consistent with the microarray findings. Furthermore, transfection of miR-128 into rat L6 myoblasts induced gene expression of myogenic markers such as muscle creatine kinase (MCK), myogenin, and myosin heavy chain (MHC). Protein expression of MHC was increased as well. Inhibition of miR-128 by inhibitory peptide nucleic acids (PNAs) blocked the expression of those myogenic markers. In addition, the transfection of miR-128 into rat L6 myoblasts enhanced the phosphorylation of Erk and Akt proteins stimulated by insulin, while simultaneously reversing the inhibited phosphorylation of Erk and Akt due to insulin resistance. These findings suggest that miR-128 may play important roles in myogenic differentiation and insulin signaling.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2001.08a
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• pp.129-137
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• 2001

We used cDNA microarrays to assess gene expression profiles in 60 human cancer used in a drug discovery screen by the National Cancer Institute. Using these data, we linked bioinformatics and chemoinformatics by correlating gene expression and drug activity pattens in the NCI60 lines. Clustering the cell lines on the basis of gene expression yielded relationships very different from those obtained by clustering the cell lines on the basis of their response to drugs. Gene-drug relationships for the clinical agents 5-fluorouracil and L-asparaginase exemplify how variations in the transcript levels of particular genes relate to mechanisms of drug sensitivity and resistance. This is the first study to intergrate large databases on gene expression and molecular pharmacology.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.15 no.11
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• pp.6774-6781
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• 2014

This study examined the efficacy and the mechanism of action of biological response modifiers, ginsenosides Rb1 and Rg1 isolated from Panax ginseng C.A. Meyer on human keratinocytes HaCaT cell lines. A non-significant cytotoxic response was obtained in the HaCaT cell lines on treatment with various concentrations of ginsenosides Rb1 and Rg1 for different time durations. Furthermore, the global changes in the mRNA profile of HaCaT cells were investigated using DNA microarrays after stimulation with the ginsenosides Rb1 and Rg1. Ginsenosides Rb1 and Rg1 strongly increased FGF2 in HaCaT cells, and were found to be a candidate gene for antioxidant activity and elasticity. Other key candidate genes for antioxidant activity, such as FANCD2, LEPR, and FAS, also show enhanced regulation in HaCaT cells treated with ginsenoside Rb1. This study will be useful for understanding the regulatory genes involved in skin elasticity and signal transduction pathway stimulated by the ginsenoside Rb1. This paper currently focuses on the key factors regulating the interaction of anti-aging principles and skin elasticity.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.23
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• pp.10217-10223
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• 2015

Hyperactivated ${\alpha}2$-6-sialylation on N-glycans due to overexpression of the Golgi enzyme ${\beta}$-galactoside: ${\alpha}2$-6-sialyltransferase (ST6Gal-I) often correlates with cancer progression, metastasis, and poor prognosis. This study was aimed to determine the association between ST6Gal-I expression and the risk of recurrence and survival of patients with localized clear-cell renal cell carcinoma (ccRCC) following surgery. We retrospectively enrolled 391 patients (265 in training cohort and 126 in validation cohort) with localized ccRCC underwent nephrectomy at a single center. Tissue microarrays were constructed for immunostaining of ST6Gal-I. Prognostic value and clinical outcomes were evaluated. High ST6Gal-I expression was associated with Fuhrman grade (p<0.001 and p=0.016, respectively) and the University of California Los-Angeles Integrated Staging System (UISS) score (p=0.004 and p=0.017, respectively) in both cohorts. Patients with high ST6Gal-I expression had significantly worse overall survival (OS) (p<0.001 and p<0.001, respectively) and recurrence free survival (RFS) (p<0.001 and p=0.002, respectively) than those with low expression in both cohorts. On multivariate analysis, ST6Gal-I expression remained associated with OS and RFS even after adjusting for the UISS score. Stratified analysis suggested that the association is more pronounced among patients with low and intermediate-risk disease defined by the UISS score. High ST6Gal-I expression is a potential independent adverse predictor of survival and recurrence in ccRCC patients, and the prognostic value is most prominent in those with low and intermediate-risk disease defined by the UISS score.