• Analytical Science and Technology
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• v.22 no.6
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• pp.498-503
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• 2009

Lung cancer is the main cancer on the world today, due to the high case fatality. Lung cancer can devide into two major types, such as small-cell lung cancer (SCLC) and non-small-cell lung cancer (NSCLC). Mutations in the epidermal growth factor receptor (EGFR) have been described in patients with advanced NSCLC. Mutations in the EGFR are associated with clinical and radiographic responses to EGFR tyrosine kinase inhibitors gefitinib and erlotinib. Thus, the detection of EGFR mutation can offer an effective information in clinical decision-making. In this study, We developed very simple, cheep and rapid mutation detection system by chip-based isothermal amplification method. The method described here has shown the advantages of rapid amplification, high sensitivity, and specificity. Also, it will be useful for rapid and reliable clinical diagnosis of EGFR mutation.

• Tuberculosis and Respiratory Diseases
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• v.55 no.1
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• pp.41-58
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• 2003

Background : The resurgence of tuberculosis and the widespread emergence of multidrug-resistant M. tuberculosis have emphasized the importance of rapid and accurate diagnostic procedures. Recently, the oligonucleotide chip has proven to be a useful tool in the rapid diagnosis of infectious diseases. The purpose of this study was to rapidly and accurately detect specific mutations in the rpoB, katG and rpsL genes associated with rifampin, isoniazid and streptomycin resistance in M. tuberculosis, respectively, using a single oligonucleotide chip. Method : For detection of drug-resistance, 7 wild-type and 13 mutant-type probes for rifampin, 2 wild-type and 3 mutant-type probes for isoniazid, and 2 wild-type and 2 mutant-type probes for streptomycin were designed and spotted onto glass slides. Fifty-five cultured samples of M. tuberculosis were amplified by PCR, and then underwent hybridization and scanning. Direct sequencing was done to verify the results from the oligonucleotide chip and to analyze the types of mutations. Result : Thirty-five cases out of 40 rifampin-resistant strains(~88%) had mutations in the rpoB gene. One case had a new mutation(D516F, GAC R TTC) and another known mutation together. Twenty cases out of 42 isoniazid-resistant strains(~50%) had mutations in the katG gene, while 7 cases out of 9 streptomycin-resistant strains(~78%) had mutations in the rpsL gene. From these results, the oligonucleotide chip was confirmed to be able to detect the most frequent mutations from the genes associated with rifampin, isoniazid and streptomycin resistance. The results proved that the drug-resistance detection probes were specific. When the results from the oligonucleotide chip and DNA sequencing were compared, the types of mutations were exactly matched. Conclusion : The diagnostic oligonucleotide chip with mutation specific probes for drug resistance is a very reliable and useful tool for the rapid and accurate diagnosis of drug resistance against rifampin, isoniazid and streptomycin in M. tuberculosis infections.

• Horticultural Science & Technology
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• v.33 no.4
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• pp.575-584
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• 2015

Drought stress is a crucial environmental factor determining crop survival and productivity. The goal of this study was to clearly identify a new drought stress-tolerance gene in Brassica rapa. From KBGP-24K microarray data with the B. rapa ssp. pekinensis inbred line 'Chiifu' under drought stress treatment, a gene which was named BrDSR (B. rapa Drought Stress Resistance) was chosen among 738 drought-responsive unigenes. BrDSR function has yet to be determined, but its expression was induced over 6-fold by drought. To characterize BrDSR, the gene was isolated from B. rapa inbred line 'CT001' and found to contain a 438-bp open reading frame encoding a 145 amino acid protein. The full-length cDNA of BrDSR was used to construct an over-expression vector, 'pSL100'. Tobacco transformation was then conducted to analyze whether the BrDSR gene can increase drought tolerance in plants. The BrDSR expression level in T1 transgenic tobacco plants selected via PCR and DNA blot analyses was up to 2.6-fold higher than non-transgenic tobacco. Analysis of phenotype clearly showed that BrDSR-expressing tobacco plants exhibited more tolerance than wild type under 10 d drought stress. Taking all of these findings together, we expect that BrDSR functions effectively in plant growth and survival of drought stress conditions.

• Journal of Plant Biotechnology
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• v.44 no.3
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• pp.264-270
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• 2017

Brassinosteroid (BR), a plant steroid hormone, plays a critical role in the growth and developmental processes through its canonical signaling and crosstalk with various internal and external signaling pathways. Recent studies have revealed the essential interplay mechanisms between BR and ABA during seed germination and early seedling establishment. However, molecular mechanisms for this important signaling crosstalk are largely unknown. To understand the crosstalk between BR-mediated signaling pathways and ABA functions during early seedling development, we carried out a comparative genome-wide transcriptome analysis with an Agilent Arabidopsis $4{\times}44K$ oligo chip. We selected and compared the expression patterns of ABA response genes in ABA-insensitive bes1-D mutant with wild type seedlings on which ABA was exogenously applied. As a result, we identified 2,353 significant differentially expressed genes (DEGs) in ABA-treated bes1-D and wild type seedlings. GO enrichment analysis revealed that ABA signaling, response, and metabolism were critically down-regulated by BR-activated signaling pathways. In addition, the genome-wide transcriptome analysis data revealed that BR-regulated signaling pathways were tightly connected to diverse signal cues including abiotic/biotic stress, auxin, ROS etc. In this study, we newly identified the molecular mechanisms of BR-mediated repression of ABA signaling outputs. Also, our data suggest that interplay among diverse signaling pathways is critical for the adaptive response of the plant to various environmental factors.

• Korean Journal of Food Science and Technology
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• v.35 no.4
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• pp.591-597
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• 2003

To compare the quality of genomic DNA extracted from potato for PCR detection, four different methods, such as silica-based membrane method, silica-coated bead method, STE solution treatment, and CTAB-phenol/chloroform method, were evaluated. Also, to remove an excessive carbohydrate from the potato, ${\alpha}$- and ${\beta}$-amylase were used individually and in combination. When used both silica-based membrane method and silica-coated bead method combined with enzymes, the genomic DNAs were extracted from the raw potato with high purity for PCR. However, the silica-coated head method combined with enzyme treatment was the most efficient for extraction of the genomic DNA from the frozen fried potatoes. When applied with STE solution, the highly purified DNA was extracted from the raw potatoes without enzyme treatment in adequate yield for PCR. In cases of processed potatoes, such as frozen-fried potato and fabricated potato chips, CTAB-phenol/chloroform method is mostly feasible for DNA extraction and PCR efficacy at high sensitivity. As the results of PCR amplification, 216bp of PCR product was detected on 2% agarose gel electrophoresis, but any amplicons derived from New leaf and New leaf Y gene was not detected in any sample.

• The Journal of the Korea institute of electronic communication sciences
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• v.8 no.12
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• pp.1875-1882
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• 2013

Micro-array technology contributes numerous achievements such as ordering of gene network and integration of genomic. This technology is well established as means for investigating patterns of gene expression. DNA micro-arrays utilize Affymetric chips where a large quantity of DNA sequences may be synthesized. There are two general type of conventional DNA array spotter: contact and piezoelectric. The contact technology used spotting pin technology to make contact with the glass slide surface. This may caused damage or scratches to the surface matrix where protein will be contaminated and may not bind specifically. Piezoelectric technology available at this present time on the other hand requires the analyzer to print the result that can only be done within the laboratory despite of mass production. Therefore, in this paper, high-throughput technology is developed for providing greater consistency in feature spot without touching the glass slide surface.

• Korean Journal of Oriental Medicine
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• v.6 no.1
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• pp.89-98
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• 2000

Cerebral ischemia, the most prevalent form of clinical stroke, is a medical problem of the first magnitude. Substantial efforts are being made to develop drugs which will protect the brain from the neurodegeneration followed by an ischemic stroke. A key factor in this process is the development of animal models that mimic the neuropathological consequences of stroke. Recently, there is increasing an evidence that free radical is involved in the mechanisms of ischemic brain damage. We investigated the macro scale gene expression analysis on the global ischemia induced by 4-vessel occlusion in Wister rats. The recent availability of microarrays provides an attractive strategy for elaborating an unbiased molecular profile of large number of genes during ischemic injury. This experimental approach offers the potential to identify molecules or cellular pathways not previously associated with ischemia. Ischemia was induced by 4-vessel occlusion for 10 minutes and reperfused again. RNA from sham control brain and time-dependent ischemed brain were hybridized to microarrays containing 4,000 rat genes. 589 genes were found to be at least 2 fold regulated at one or more time points. These survey data provide the foundation studies that should provide convincing proof for ischemia and oxidative stress on gene expression.

• Journal of Sasang Constitutional Medicine
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• v.18 no.3
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• pp.131-144
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• 2006

1. Objectives This research uses the DNA chip, which includes 16,383 gene code, and various statistic prediction way that shows objectification index for the objectification of constitution diagnosis. 2. Methods Drawing blood whose constitution is confirmed, and analyze its gene information by using 1.7k DNA chip to find the gene correlation through multivariate statistical method. 3. Results and Conclusions Distinctive genes such as AK001919, U09384, NM_001805, X99962, NM_004796, AK026738, AL050148, BC002538, AK027074, AK026219, AF087962, AL390142, NM_015372, AL157466, NM_002446, AK024523, NM_014706, NM_014746 and AL137544 were related to Taeumin; AL157448, NM_005957, NM_005656, NM_017548, AK027246, NM_003025, NM_012302 and NM_005905 were represented in Soeumin, while AK026503, AF147325, NM_002076, AF147307, AK001375, NM_003740, NM_005114, AB007890, NM_005505, NM_015900, NM_014936, Z70694, AB023154, U52076, NM_004360, NM_005835, NM_017528, AF087987, NM_014897, AK021720, NM_006420, AJ277915, AK002118 and AK021918 were for Soyangin. This study figured out the possibility to develop the prediction system by sorting each constitution's gene, and research each constitution's distinctive character of manifestation pattern.

• Clean Technology
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• v.21 no.2
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• pp.90-95
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• 2015

Digital microfluidic electroporation system was used for the transformation of microalgae and we have obtained higher transformation efficiency and viability than that of conventional method. Key parameters of electroporation such as pulse voltage, number, and duration time were systematically investigated for two different microalgal strains with and without cell wall. We have found that cell wall does not always have negative effects on the gene transformation of microalgae. Parallel processing of proposed digital microfluidic electroporation was demonstrated together with on chip culture of microalgae.

• Journal of Life Science
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• v.13 no.1
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• pp.99-104
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• 2003

Aromatic compounds are of major concern among environmental pollutants due to their toxicity and persistence. To monitor aromatic compounds in a real time with a better sensitivity, a new method of SPR (surface plasmon resonance) based on DNA chip (Biacore 3000) was developed here. It is thought that CapR regulatory protein as a complex with phenol, could bind to their corresponding promoter, Po. Biotinylated DNA oligomers for the promoter was synthesized by PCR and coupled onto streptoavidin-linked CM5-chip. CapR regulatory proteins were purified after cloning their genes in pET21a (+) vector and expressing proteins. The interaction was assessed by the system where the regulatory proteins flowed with or without phenol through the cells of DNA chip. CapR regulatory protein even in the presence of phenol had no response to its promoter, Po, suggesting that other factor(s) might be required for the activation of Po promoter. The present work reveals a promising possibility of the SPR-based DNA chip in monitoring specific environmental pollutants in a real time.