• Molecular & Cellular Toxicology
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• 제1권2호
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• pp.78-86
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• 2005

Dioxins, especially 2, 3, 7, 8-Tetrachlorodibenzo-p-dioxin (TCDD or dioxin), are ubiquitous environmental contaminants. TCDD is known that it has toxic effects in animals and humans, including chloracne, immune, reproductive and developmental toxicities, carcinogenicity, wasting syndrome and death. TCDD induces a broad spectrum of biological responses, including disruption of normal hormone signaling pathways, reproductive and developmental defects, immunotoxicity, liver damage, wasting syndrome and cancer. Many researches showed that TCDD induces gene expression of transcriptional factors related cell proliferation, signal transduction, immune system and cell cycle arrest at molecular and cellular levels. These toxic actions of TCDD are usually mediated with AhR (receptor, resulted from cell culture, animal and clinical studies). cDNA microarray can be used as a highly sensitive and informative marker for toxicity. Additionally, microarray analysis of dioxin-toxicity is able to provide an opportunity for the development of candidate bridging biomarkers of dioxin-toxicity. Through microarray technology, it is possible to understand the therapeutic effects of agonists within the context of toxic effects, classify new chemicals as to their complete effects on biological systems, and identify environmental factors that may influence safety.

• 한국수의병리학회:학술대회논문집
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• 한국수의병리학회 2002년도 추계학술대회초록집
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• pp.142-142
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• 2002

돼지의 주요 장염 유발 바이러스인 돼지 전염성 위장염 바이러스 (transmissible gastroenteritis virus; TGEV), 돼지 유행성 설사증 바이러스 (porcine epidemic diarrhea virus; PEDV), 돼지 칼리시 바이러스 (porcine enteric calicivirus; PECV), 돼지 로타바이러스 A 형과 C 형 (porcine rotavirus; PRY, group A and C)을 동시에 감별 진단 할 수 있는 신속하고 정확한 oligonucleotide microarray 진단법을 개발하였다. 이 진단법은 유리슬라이드에 각각의 바이러스에 특이적인 부위에서 제작된 oligonucleotide probe를 찍은 DNA chip을 제작하여 여기에 각각의 바이러스를 역전사하고 cy5-dCTP를 포함한 multiplex PCR을 수행한 다음 hybridization 하였다. 이후 hybridization 결과는 fluorescence scanner를 이용하여 확인하였다. 이 새로운 microarray system은 RT-PCR과 같은 기존의 진단방법보다 소량의 바이러스를 민감하게 검사할 수 있을 뿐 아니라 hybridization을 통해 검사결과의 정확성을 확인할 수 있었다. 따라서 본 연구에서 개발한 microarray system은 돼지의 설사 유발 바이러스를 진단하는데 매우 유용한 진단 방법임을 확인하였다.

• Journal of Microbiology
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• 제45권1호
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• pp.21-28
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• 2007

In order to search for specific genotypes related to this unique phenotype, we used whole genomic DNA microarray to characterize the genomic diversity of Helicobacter pylori (H. pylori) strains isolated from clinical patients in China. The open reading frame (ORF) fragments on our microarray were generated by PCR using gene-specific primers. Genomic DNA of H. pylori 26695 and J99 were used as templates. Thirty-four H. pylori isolates were obtained from patients in Shanghai. Results were judged based on In(x) transformed and normalized Cy3/Cy5 ratios. Our microarray included 1882 DNA fragments corresponding to 1636 ORFs of both sequenced H. pylori strains. Cluster analysis, revealed two diverse regions in the H. pylori genome that were not present in other isolates. Among the 1636 genes, 1091 (66.7%) were common to all H. pylori strains, representing the functional core of the genome. Most of the genes found in the H. pylori functional core were responsible for metabolism, cellular processes, transcription and biosynthesis of amino acids, functions that are essential to H. pylori's growth and colonization in its host. In contrast, 522 (31.9%) genes were strain-specific genes that were missing from at least one strain of H. pylori. Strain-specific genes primarily included restriction modification system components, transposase genes, hypothetical proteins and outer membrane proteins. These strain-specific genes may aid the bacteria under specific circumstances during their long-term infection in genetically diverse hosts. Our results suggest 34 H. pylori clinical strains have extensive genomic diversity. Core genes and strain-specific genes both play essential roles in H. pylori propagation and pathogenesis. Our microarray experiment may help select relatively significant genes for further research on the pathogenicity of H. pylori and development of a vaccine for H. pylori.

• Journal of Microbiology and Biotechnology
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• 제17권2호
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• pp.244-252
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• 2007

Escherichia coli has a PhoR-PhoB two-component regulatory system to detect and respond to the changes of environmental phosphate concentration. For the E. coli W3110 strain growing under phosphate-limiting condition, the changes of global gene expression levels were investigated by using DNA microarray analysis. The expression levels of some genes that are involved in phosphate metabolism were increased as phosphate became limited, whereas those of the genes involved in ribosomal protein or amino acid metabolism were decreased, owing to the stationary phase response. The upregulated genes could be divided into temporarily and permanently inducible genes by phosphate starvation. At the peak point showing the highest expression levels of the phoB and phoR genes under phosphate-limiting condition, the phoB- and/or phoR-dependent regulatory mechanisms were investigated in detail by comparing the gene expression levels among the wild-type and phoB and/or phoR mutant strains. Overall, the phoB mutation was epistatic over the phoR mutation. It was found that PhoBR and PhoB were responsible for the upregulation of the phosphonate or glycerol phosphate metabolism and high-affinity phosphate transport system, respectively. These results show the complex regulation by the PhoR-PhoB two-component regulatory system in E. coli.

• Journal of Microbiology and Biotechnology
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• 제10권1호
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• pp.21-26
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• 2000

A microarrayer system was developed mainly for manufacturing DNA chips. The 3-axis robot was designed to automatically collect samples from 96-or 384-well microtiter plates using up to 16 simultaneously moving pens and to deposit them on a surface-modified slide glass. This is followed by a wash/dry operation in a clean station. The cycle is repeated with a new set of samples, This system can deposit cDNA or oligonucleotides with spot intervals of $150{\;}\mu\textrm{m}$ and the spot size of $80\mu\textrm{m}$, thus allowing a high density DNA chip containing about 5,000 spots per $\textrm{cm}^2$. The entire procedure is controlled by the Visual C++ program that was written in our laboratory by using a personal computer with Pentium 100 CPU.

• 대한전기학회:학술대회논문집
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• 대한전기학회 2006년도 제37회 하계학술대회 논문집 C
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• pp.1324-1326
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• 2006

In this study, an integrated microelectrode array was fabricated on glass slide using microfabrication technology. Probe DNAs consisting of mercaptohexyl moiety at their 5-end were spotted on the gold electrode using micropipette or DNA arrayer utilizing the affinity between gold and sulfur. Cyclic voltammetry in 5mM ferricyanide/ferrocyanide solution at 100 mV/s confirmed the immobilization of probe DNA on the gold electrodes. When several DNAs were detected electrochemically, there was a difference between target DNA and control DNA in the anodic peak current values. It was derived from specific binding of Hoechst 33258 to the double stranded DNA due to hybridization of target DNA. It suggested that this DNA chip could recognize the sequence specific genes. It suggested that multichannel electrochemical DNA microarray is useful to develop a portable device for clinical gene diagnostic system.

• 대한전기학회:학술대회논문집
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• 대한전기학회 2006년도 제37회 하계학술대회 논문집 C
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• pp.1319-1321
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• 2006

This research aims to develop the multiple channel electrochemical DNA chip that has the above characteristic and be able to solve the problems. At first, we fabricated a high integration type DNA chip array by lithography technology. It is able to detect a plural genes electrochemically after immobilization of a plural probe DNA and hybridization of non-labeling target DNA on the electrodes simultaneously. It suggested that this DNA chip could recognize the sequence specific genes. It suggested that multichannel electrochemical DNA microarray is useful to develop a portable device for clinical gene diagnostic system.

• Biotechnology and Bioprocess Engineering:BBE
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• 제8권4호
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• pp.221-226
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• 2003

With the current rapid development of nanotechnology and synthesis technology for designed oligonucleotides or oligonucleotide-modified nanoparticle conjugates, the combined strategies have become one of the most valuable methods in detection technology for DNA analysis. Using the uniquely recognizable interactions of pre-designed DNA molecules in assembling nanoparticles, various novel approaches have been recently developed towards detecting specific DNA sequences. Here we describe the key fundamentals and issues of this promising strategies ranging from the initial findings of rationally designed DNA-based assembly of nanoparticles to the extended chip-based detection system. Some limitations of these new strategies and possible approaches will be also discussed for the practical application in the area of DNA microarray detection.

• 한국환경독성학회:학술대회논문집
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• 한국환경독성학회 2003년도 추계국제학술대회
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• pp.176-176
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• 2003

Methylmercury is known to have devastating effects on the mammalian nervous system. When human neuroblastoma SH-SY5Y cells were treated with methylmercury at sublethal concentrations (6.25 uM), up-regulated genes (39) ＆ down-regulated genes (19) were identified by human 8k cDNA microarray. These genes are related with microtubule process, signal transduction pathway and cell death (apoptosis), Apoptosis-associated genes, HSP70, CDK inhibitor 1, FOS-like antigen were up-regulated and microtubule related genes like villin and dynein down-regultaed. To confirm the presence of apoptosis in cultured SH-SY5Y cells treated 6.25 and 1 uM methylmercury, we applied Annexin V-FITC assay followed by flow cytometric measurements after 6 and 24h. Studies on transcriptional and molecular effect by methylmercury may provide an insight into the neurotoxic effects of methylmercury in human neuronal cells and a possibility to develop more efficient and exact monitoring system of heavy metals as ubiquitous environmental pollutants.

• Molecular & Cellular Toxicology
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• 제1권4호
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• pp.256-261
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• 2005

The recent DNA microarray technology enables us to understand gene expression profiling in cell line and animal models. The technology has potential possibility to comprehend mechanism of multiple genes were related to compounds which have toxicity in biological system. So, microarray system has been used for the prediction of toxicity through gene expression induced by toxicants. It has been shown that compounds with similar toxic mechanisms produce similar changes in gene expression in vivo system. Here we focus on the use of toxicogenomics for the determination of gene expression analysis associated with hepatotoxicity in rat liver and cell line (WB-F344). Methotrexate (MTX) is a chemotherapy agent that has been used for many years in the treatment of cancer because it affects cells that are rapidly dividing. Also it has been known the toxicity of MTX, in a MTX abortion, it stops embryonic cells from dividing and multiplying and is a non-surgical method of ending pregnancy in its early stages. We have shown DNA microarray analyses to assess MTX-specific expression profiles in vivo and in vitro. Male Sprague-Dawely VAF+ albino rats of 5-6 weeks old and WB-F344 cell line have been treated with MTX. Total RNA was isolated from Rat liver and cell line that has treated with MTX. 4.8 K cDNA microarray in house has been used for gene expression profiling of MTX treatment. We have found quite distinct gene expression patterns induced by MTX in a cell line and in vivo system.