• Journal of the korean academy of Pediatric Dentistry
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• v.29 no.2
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• pp.278-284
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• 2002

To examine the global gene expression of osteoclastogenesis-related genes in RAW 264.7 and its differentiated OCLs through the use of Atlas Mouse cDNA Array 2.1 membranes printed with 1176 well-characterized mouse genes involved in biology. Both samples were screened in parallel using cDNA expression arrays. The array results were additionally validated using RT-PCR. The results of cDNA arrays showed that 6 genes were up-regulated >2.5-fold (PKC beta II. POMC, PTEN, etc) and 16 genes were down-regulated >2.5-fold (Osteopontin, Cyclin D1, Cathepsin C, PTMA, etc) in both samples at the mRNA level. RT-PCR analysis of PKC beta II of these differentially expressed genes gave result consistent with cDNA array findings. The result of osteoclastogenesis showed that the PKC beta II gene was overexpressed in OCLs compared with RAW264.7 cell line. Osteoclastogenesis-related genes are differentially expressed in RAW264.7 cell line and its differentiated OCLs. its gene overexpression correlates with osteoclast differentiation in RAW264.7 cell line.

• KIEE International Transactions on Electrophysics and Applications
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• v.4C no.4
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• pp.133-136
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• 2004

This research aims to develop a DNA chip array without an indicator. We fabricated a microelectrode array through photolithography technology. Several DNA probes were immobilized on an electrode. Then, target DNA was hybridized and measured electrochemically. Cyclic-voltammograms (CVs) showed a difference between the DNA probe and mismatched DNA in an anodic peak. This indicator-free DNA chip resulted in a sequence-specific detection of the target DNA.

• Journal of Korean Society of Occupational and Environmental Hygiene
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• v.20 no.1
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• pp.29-40
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• 2010

This study was aimed at investigating the gene expression profile in basal ganglia of cadmium exposed rat based on cDNA array analysis. For cDNA array analysis, adult Sprague-Dawley male rats (350 ${\pm}$ 25 g) were intraperitoneally injected with 2.0 mg/kg body weight/day of CdCl2 (0.3 ml) for 5 days. For doserelated gene expression analysis rats were intraperitoneally injected with 0.0, 0.1, 0.3, 1.0 mg/kg body weight/day of CdCl$_2$ for 5 days. Control rats were injected with equal volume of saline. Cadmium concentration of brain was analyzed by atomic absorption spectrophotometer. For cDNA array, RNA samples were extracted from basal ganglia and reverse-transcribed in the presence of [${\alpha}$32P]-dATP. Membrane sets of the Atlas Rat 1.2 array II and Toxicology array 1.2 (Clontech, Palo Alto, CA) were hybridized with cDNA probe sets. RT-PCR was employed to validate the relative gene expression patterns obtained from the cDNA array. Northern blot hybridization methods were employed to assess the dose-related gene expression. Among the 2352 cDNAs, 671 genes were detected in both array sets and 63 genes of 38 classes showed significant (more than two fold) changes in expression. Thirty five of these genes were up-regulated and twenty eight were down-regulated in the cadmium exposed group. According to the dose-related gene expression analysis, heat shock 27 kDa protein (HSP27), neurodegeneration-associated protein 1 (Neurodap 1) genes were significantly up-regulated and melatonin receptor 1a (Mel1a), Kinesin family member 3C (KIF3C), novel kinesinrelated protein (KIF1D) genes were significantly downregulated even in the low-dose of cadmium exposed group (0.1 mg/kg body weight/day). Conclusions Sixty three genes detected in this study can give some more useful informations about the cadmium-induced neurotoxicity in the basal ganglia. As well as, HSP27, Neurodap1, Mel1a, KIF3C and KIF1D genes may be useful for the study of the cadmium-induced neurotoxicity because these genes showed dramatic changes of mRNA levels in response to the low dose of cadmium exposure.

• The Transactions of the Korean Institute of Electrical Engineers C
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• v.53 no.5
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• pp.286-292
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• 2004

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 ㎷/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.

• KIEE International Transactions on Electrophysics and Applications
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• v.4C no.4
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• pp.145-148
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• 2004

In this study, a DNA chip with a microelectrode array was fabricated using microfabrication technology. Several probe DNAs consisting of mercaptohexyl moiety at their 5' end were immobilized on the gold electrodes by a DNA arrayer. Then target DNAs were hybridized and reacted with Hoechst 33258, which is a DNA minor groove binder and electrochemically active dye. Linear sweep voltammetry or cyclic voltammetry showed a difference between target DNA and control DNA in the anodic peak current values. It was derived from Hoechst 33258 and concentrated at the electrode surface through association with the formed hybrid. This suggested that this DNA chip could recognize the sequence specific genes.

• KIEE International Transactions on Electrophysics and Applications
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• v.11C no.2
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• pp.23-27
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• 2001

Microarray-based DNA chips provide an architecture for multi-analyte sensing. In this paper, we report a new approach for DNA chip microarray fabrication. Multifunctional DNA chip microarrays were made by immobilizing many kinds if DNAs on transducers (particles). DNA chip microarrays were prepared by randomly distributing a mixture of the particles on a chip pattern containing thousands of micro meter-scale sites. The particles occupied different sites from array to array. Each particle cam be distinguished by a tag that is established on the particle. The particles were arranged on the chip pattern by the random fluidic self-assembly (RFSA) method, using hydrophobic interaction.

• Molecular & Cellular Toxicology
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• v.5 no.1
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• pp.51-57
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• 2009

Quantum Dot (QD) nanoparticles are used in various industrial applications, such as diagnostic, drug delivery, and imaging agents of biomedicine. Although QDs are extensively used in many medical science, several studies have been demonstrated the potential toxicity of nanoparticles. The first objective of this study was to investigate the nanotoxicity of QDs in the HaCaT human keratinocyte cell line by focusing on gene expression pattern. In order to evaluate the effect of QDs on gene expression profile in HaCaT cells, we analyzed the differential genes which related to oxidative stress and antioxidant defense mechanisms by using human cDNA microarray and PCR array. A human cDNA microarray was clone set, which was sorted for a list of genes correlated with cell mechanisms. We tried to confirm results of cDNA microarray by using PCR array, which is pathway-focused gene expression profiling technology using Real-Time PCR. Although we could not find the exactly same genes in both methods, we have screened the effects of QDs on global gene expression profiles in human skin cells. In addition, our results show that QD treatment somehow regulates cellular pathways of oxidative stress and antioxidant defense mechanisms. Therefore, we suggest that this study can enlarge our knowledge of the transcriptional profile and identify new candidate biomarker genes to evaluate the toxicity of nanotoxicology.

• 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.

• The Korean Journal of Nuclear Medicine
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• v.37 no.1
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• pp.43-52
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• 2003

Microarray technology allows the simultaneous analysis of gene expression patterns of thousands of genes, in a systematic fashion, under a similar set of experimental conditions, thus making the data highly comparable. In some cases arrays are used simply as a primary screen loading to downstream molecular characterization of individual gene candidates. In other cases, the goal of expression profiling is to begin to identify complex regulatory networks underlying developmental processes and disease states. Microarrays were originally used with ceil lines or other simple model systems. More recently, microarrays have been used in the analysis of more complex biological tissues including neural systems and the brain. The application of cDNA arrays in neuropsychiatry has lagged behind other fields for a number of reasons. These include a requirement for a large amount of input probe RNA In fluorescent-glass based array systems and the cellular complexity introduced by multicellular brain and neural tissues. An additional factor that impacts the general use of microarrays in neuropsychiatry is the lack of availability of sequenced clone sets from model systems. While human cDNA clones have been widely available, high qualify rat, mouse, and drosophilae, among others are just becoming widely available. A final factor in the application of cDNA microarrays in neuropsychiatry is cost of commercial arrays. As academic microarray facilitates become more commonplace custom made arrays will become more widely available at a lower cost allowing more widespread applications. in summary, microarray technology is rapidly having an impact on many areas of biomedical research. Radioisotope-nylon based microarrays offer alternatives that may in some cases be more sensitive, flexible, inexpensive, and universal as compared to other array formats, such as fluorescent-glass arrays. In some situations of limited RNA or exotic species, radioactive membrane microarrays may be the most practical experimental approach in studying psychiatric and neurodegenerative disorders, and other complex questions in the brain.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.51-56
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• 2005

There are many sources of systematic variations in cDNA microarray experiments which affect the measured gene expression levels like differences in labeling efficiency between the two fluorescent dyes. Print-tip lowess normalization is used in situations where dye biases can depend on spot overall intensity and/or spatial location within the array. However, print-tip lowess normalization performs poorly in situation where error variability for each gene is heterogeneous over intensity ranges. We proposed the new print-tip normalization methods based on support vector machine regression(SVMR) and support vector machine quantile regression(SVMQR). SVMQR was derived by employing the basic principle of support vector machine (SVM) for the estimation of the linear and nonlinear quantile regressions. We applied our proposed methods to previous cDNA micro array data of apolipoprotein-AI-knockout (apoAI-KO) mice, diet-induced obese mice, and genistein-fed obese mice. From our statistical analysis, we found that the proposed methods perform better than the existing print-tip lowess normalization method.