• 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.

• 한국환경과학회지
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• 제24권5호
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• pp.623-631
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• 2015

Microarray technology provides a unique tool for the determination of gene expression at the level of messenger RNA (mRNA). This study, the mRNA expression profiles provide insight into the mechanism of action of cadmium in Fleshy shrimp (Fenneropenaeus chinensis). The ability of genomic technologies was contributed decisively to development of new molecular biomarkers and to the determination of new possible gene targets. Also, it can be approach for monitoring of trace metal using oligo-chip microarray-based in potential model marine user level organisms. 15K oligo-chip for F. chinensis that include mostly unique sets of genes from cDNA sequences was developed. A total of 13,971 spots (1,181 mRNAs up- regulated and 996 down regulated) were identified to be significantly expressed on microarray by hierarchical clustering of genes after exposure to cadmium for different conditions (Cd24-5000 and Cd48-1000). Most of the changes of mRNA expression were observed at the long time and low concentration exposure of Cd48-1000. But, gene ontology analysis (GO annotation) were no significant different between experiments groups. It was observed that mRNA expression of main genes involved in metabolism, cell component, molecular binding and catalytic function. It was suggested that cadmium inhibited metabolism and growth of F. chinensis.

• Journal of Plant Biotechnology
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• 제43권2호
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• pp.231-239
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• 2016

담배에서 후성유전관련 유전자의 발현연구를 위해 담배유래 시토신 DNA 탈메틸화 관련 NtROS2a 유전자를 과발현 및 RNAi 식물체를 육성하였다. 이들 형질전환체들은 고염 및 산화 스트레스하에서 내성이 증진되었으며, 다양한 표현형변이를 보였다(Lee et al. 2015). 본연구에서는 선발된 과발현 (OX1), RNAi 식물체(RNAi 13) 및 대조식물체(WT)를 이용하여 Agilent Tobacco 4 X 44K Oligo chip으로 microarray분석을 수행하였다. OX1과 RNAi13 계통을 이용하여 WT과 함께 비교 분석한 결과, 대부분 세포 내 이온 수송, 영양 공급 등과 같은 물질대사와 생물적 비생물적 스트레스 및 methylation과 관련되어 영향을 주는 유전자들에서 up-regulation 되었고, 물질대사관련 유전자와 세포 내 기능유전자의 역할을 담당하는 조효소, 그리고 다양한 스트레스 및 메틸레이션 관련 유전자군에서 또한 down-regulation되었다. 각각의 up-, down-regulation된 유전자들을 WT과 비교하여 qRT-PCR을 수행한 결과, KH domain-containing protein, MADS-box protein 및 Zinc phosphodiesterase ELAC protein 유전자들에서 발현이 높게 나타났으며, 반면에 pentatricopeptide (PPR) repeat-containing protein, histone deacetylase HDAC3 protein 및 protein kinase는 0.4 ~ 1.0-fold 발현양이 감소되었다. 따라서 DNA glycosylase를 암호화하는 NtROS2a 유전자는 demethylation과 관련되어 담배 식물체에서 다양한 전사레벨을 조절하는 것으로 판단된다.

• 대한화장품학회지
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• 제30권4호
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• pp.479-483
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• 2004

MITF는 미백관련 유전자의 대표적인 조절 인자 단백질로서 미백관련 유전자의 E-box와의 결합정도를 단백질 칩을 이용하여 측정하였다. 융합 단백질 형태의 MITF를 유리 칩에 고정시켰고 E-box를 포함하는 DNA oligomer가 결합하는 것을 확인하였다. 형광법, SPR (surface plasmon resonance), SPRi (surface plasmon resonance imaging)방법 중 형광법이 가장 효과적이었으며, DNA 저해제를 사용시 결합이 감소하는 것을 확인하였다. 이 결과 MITF를 이용한 미백원료의 고속스크리닝(HTS)의 가능성을 보여주었다.

• Toxicological Research
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• 제20권2호
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• pp.109-116
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• 2004

For the safety evaluation of adenovirus-mediated gene transfer, we investigated differential gene expressions after transfecting adenoviral vector containing p16 tumor suppressor gene (Ad5CMV-p16) into human non-small cell lung cancer cells. In the previous study, we showed adenovirus-mediated $p16^{INK4a}$ gene transfer resulted in significant inhibition of cancer cell growth. We investigated gene expression changes after transfecting Ad5CMV-p16, Ad5CMV (null type, a mock vector) into A549 cells by using cDNA chip and oligonucleotide microarray chip (1200 genes) which carries genes related with signal transduction pathways, cell cycle regulations, oncogenes and tumor suppressor genes. We found that $p16^{INK4a}$ gene transfer down regulated 5 genes (cdc2, cyclin D3, cyclin B, cyclin E, cdk2) among 26 genes involved in cell cycle regulations. Compared with serum-free medium treated cells, Ad5CMV-p16 changed 27 gene expressions, two fold or more on oligonucleotide chip. In addition, Ad5CMV-p16 did not seem to increase the tumorigenicity-related gene expression in A549 cells. Further studies will be needed to investigate the effect of Ad5CMV-p16 on normal human cells and tissues for safety evaluation.

• 한국어업기술학회:학술대회논문집
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• 한국어업기술학회 2003년도 춘계 수산관련학회 공동학술대회발표요지집
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• pp.311-312
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• 2003

Microarray를 해석하는데 있어서 방해가 되는 요인에는 여러 가지가 있을 수 있다. 예를 들면 probe DNA의 농도, spotting 시의 습도, spot의 크기 및 모양, slide blocking 과정, lab리ing technique, hybri야zation 온도와 시간 그리고 background signal 등이 그것이다(Hegde et at., 2000). 본 연구에서는 전보에서 선정된 rhabdovirus의 96개 probe로 실제 oligonucleotide chip을 만들어 spot의 모양이나 크기에 관계되는 spotting 조건을 확립하고, slide blocking과 slide washing에 따른 background signal을 낮추기 위한 과정을 도입하였다. (중략)

• Asian Pacific Journal of Cancer Prevention
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• 제17권5호
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• pp.2519-2525
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• 2016

There are several existing reports of microarray chip use for assessment of altered gene expression in different diseases. In fact, there have been over 1.5 million assays of this kind performed over the last twenty years, which have influenced clinical and translational research studies. The most commonly used DNA microarray platforms are Affymetrix GeneChip and Quality Control Software along with their GeneChip Probe Arrays. These chips are created using several quality controls to confirm the success of each assay, but their actual impact on gene expression profiles had not been previously analyzed until the appearance of several bioinformatics tools for this purpose. We here performed a data mining analysis, in this case specifically focused on ovarian cancer, as well as healthy ovarian tissue and ovarian cell lines, in order to confirm quality control results and associated variation in gene expression profiles. The microarray data used in our research were downloaded from ArrayExpress and Gene Expression Omnibus (GEO) and analyzed with Expression Console Software using RMA, MAS5 and Plier algorithms. The gene expression profiles were obtained using Partek Genomics Suite v6.6 and data were visualized using principal component analysis, heat map, and Venn diagrams. Microarray quality control analysis showed that roughly 40% of the microarray files were false negative, demonstrating over- and under-estimation of expressed genes. Additionally, we confirmed the results performing second analysis using independent samples. About 70% of the significant expressed genes were correlated in both analyses. These results demonstrate the importance of appropriate microarray processing to obtain a reliable gene expression profile.

• BMB Reports
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• 제37권5호
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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.

• Fisheries and Aquatic Sciences
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• 제5권1호
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• pp.36-42
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• 2002

Microarrayer is used to make DNA chip and microarray that contain hundreds to thousands of immobilized DNA probes on surface of a microscope slide. This paper shows the develop-ment results for a printing type of microarrayer. It realizes a typical, low-cost and efficient microarrayer for generating low density micro array. The microarrayer is developed by using a prependicular type robot with three axes. It is composed of a computer-controlled three-axes robot and a pen tip assembly. The key component of the arrayer is the print-head containing the tips to immobilize cDNA, genomic DNA or similar biological material on glass surface. The robot is designed to automatically collect probes from two 96-well plates with up to 12 pens at the same time. To prove the performance of the developed microarrayer, we use the general water types of inks such as black, blue and red. The inks are distributed at proper positions of 96 well plates and the three color inks are immobilized on the slide glass under the operation procedure. As the result of the test, we can see that it has sufficient performance for the production of low integrated DNA chip consisted of 96 spots within $1cm^2$ area.

• 동의생리병리학회지
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• 제17권6호
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• pp.1393-1403
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• 2003

The genetic effects of restraint stress challenge on HPA axis and the therapeutic effect of Boshimgeonbi-Tang on the stress were studied with cDNA microarray analyses on hypothalamus using an immobilization-stress mouse as stress model. Male CD-1 mice were restrained in a tightly fitted and ventilated vinyl holder for 2hours once a day, and this challenge was repeated for seven consecutive days. The body weights of the immobilization-stress mice were diminished about 25 percent degree as compared to normal ones. Seven days later, total RNA was extracted from the organs of the mouse, body-labeled with CyDye/sup TM/ fluorescence dyes (Amersham Bioscience Co., NJ), and then hybridized to cDNA microarray chip. Scanning and analyzing the array slides were carried out using GenePix 4000 series scanner and GenePix Pro/sup TM/ analyzing program, respectively. The expression profiles of 109 genes out of 6000 genes on the chip were significantly modulated in hypothalamus by the immobilization stress. Energy metabolism-, lipid metabolism-, apoptosis- and signal transduction-related genes were transcriptionally activated whereas DNA repair-, protein biosynthesis-, and structure integrity-related genes were down-regulated in hypothalamus. The 58 genes were up-regulated by the mRNA expression folds of 1.5 to 7.9. and the 51 genes were down-regulated by 1.5 - 3.5 fold. The 20 genes among them were selected to confirm the expression profiles by RT-PCR. The mRNA expression levels of Tnfrsf1a (apoptosis), Calm2 (cell cycle), Bag3 (apoptosis), Hspe1 (protein folding), Aatk (apoptosis), Dffa (apoptosis), Itgb1 (cell adhesion), Vcam1 (cell adhesion), Fkbp5 (protein folding), BDNF (neuron survival) were restored to the normal one by the treatment of Boshimgeonbi-Tang.