• Proceedings of the Korean Information Science Society Conference
• /
• 2006.10a
• /
• pp.516-521
• /
• 2006

DNA칩의 성능은 칩을 구성하는 probe에 의해 결정된다. 좋은 probe는 homogeneity, sensitivity, specificity와 같은 속성을 갖추어야 한다. 이중 specificity는 probe의 특정 유전자에 대한 선별적 결합 능력을 나타내는 것으로 이를 계산하는데 가장 많은 시간이 요구된다. 본 논문은 유전자의 개별 후보 probe들에 대한 선정 작업을 실행하기 전에 q-gram을 이용하여 비교가 필요한 유전자들만을 전체 유전자의 길이가 n인 경우 O(1/$4^an^2$)의 시간에 선별하는 전처리 알고리즘을 제안한다. 그리고 제안한 알고리즘을 사용함으로써 기존 방법들보다 빠른 probe 선정이 가능함을 실제 데이터를 사용하여 보인다.

• Journal of Acupuncture Research
• /
• v.20 no.3
• /
• pp.34-44
• /
• 2003

Objective : Bone homeostasis is maintained by balance of bone formation and resorption. Therefore, bone related diseases arose by disturbance of this balance between osteoblast and osteoclast activities. To develop a successful screening system the therapeutic components based on oriental medicine is essential to set up systematic approach for that purpose. The purpose of this study is to the know the gene expression using cDNA microarray assay. Methods : Cervi Pantotricuhum Cornu Herbal-acupuncture extract was prepared by boiling. human osteosarcoma cells(HOS) were treated with Cervi Pantotricuhum Cornu Herbal-acupuncture solution. Then mRNA was extracted and cDNA microarray assay was performed. Results : Human osteosarcoma cells(HOS) treated with Cervi Pantotricuhum Cornu Herbal-acupuncture solution($500{\mu}g/m{\ell}$) showed that thioredoxin, TAFII31 and two novel genes were increased. However many genes decreased their expression by Cervi Pantotricuhum Cornu Herbal-acupuncture. Conclusions : This type of approach will give a good chance to explore the favorable effects of Cervi Pantotricuhum Cornu Herbal-acupuncture. Further study is needed for investigating the effect of Cervi Pantotricuhum Cornu Herbal-acupuncture.

• Journal of Sensor Science and Technology
• /
• v.27 no.4
• /
• pp.237-241
• /
• 2018

The real-time enrichment and detection of pathogens are serious issues and rapidly evolving field of research because of the ability of these pathogens to cause infectious diseases. In general, bacterial detection is accomplished by conventional colony counting or by polymerase chain reaction (PCR) after DNA extraction. As colony counting requires considerable time to cultivate, PCR is an attractive method for rapid detection. A small number of pathogens can cause diseases. Hence, a pretreatment process, such as enrichment is essential for detecting bacteria in an actual environment. Thus, in this study, we developed a microfluidic chip capable of performing rapid enrichment of bacteria and the extraction of their genes. A lectin, i.e., Concanavalin A (ConA), which shows binding affinity to the surface of most bacteria, was coated on the surface of magnetic particles to nonspecifically capture bacteria. It was subsequently concentrated through magnetic forces in a microfluidic channel. To lyse the captured bacteria, magnetic particles were irradiated by a wavelength of 532nm. The photo-thermal effect on the particles was sufficient for extracting DNA, which was consequently utilized for the identification of bacteria. Our device will help monitor the existence of bacteria in various environmental situations such as water, air, and soil.

• Journal of Physiology & Pathology in Korean Medicine
• /
• v.19 no.6
• /
• pp.1585-1593
• /
• 2005

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, RT-PCR on hypothalamus using an immobilization-stress mice as an animal model. Male CD-1 mice were restrained in a tightly fitted and ventilated vinyl holder for 2hrs once a day, and this challenge was repeated for seven· consecutive days. In the change of body weight it showed that the Boshimgeonbi-tang is effected recovery on weight loss caused by the immobilization-stress. Seven days later, total RNA was extracted from the organs of the mouse, body-labeled with $CyDye^{TM}$ fluorescence dyes and then hybridized to CDNA microarray chip. Scanning and analyzing the array slides were carried out using GenePix4000 series scanner and GenePix $Pro^{TM}$ 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-, stress protein, transcriptional factor, and signal transduction-related genes were transcriptionally activated whereas DNA repair-, protein biosysthesis-, 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 - 5.5 fold. The 11 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), Ogg1 (DNA repair), Aatk (apoptosis), Dffa (apoptosis), Fkbp5 (protein folding) were restored to the normal one by the treatment of Boshimgeonbi-tang.

• Journal of Food Hygiene and Safety
• /
• v.33 no.1
• /
• pp.50-57
• /
• 2018

Salmonella continue to be a major cause of food poisoning worldwide. The rapid detection method of food-borne Salmonella is an important food safety tool. A real-time polymerase chain reaction (PCR) has been used as a rapid method for the detection of pathogens. It has been recently reported that NBS LabChip real-time PCR is a novel, ultrafast, and chip-type-convenient real-time PCR system. We developed the assay method based on NBS LabChip real-time PCR for the rapid detection of Salmonella, which its reaction time was within 20 minutes. Two target genes (invA and stn) were selected to design target specific primers and probes. The new method was validated by checking specificity and sensitivity (limit of detection). This study included forty-two target and twenty-one non-target strains to assess the specificity. This assay was able to identify the 42 Salmonella strains correctly. The limit of detection (LOD) was $10^1copies/{\mu}L$ in Salmonella genomes DNA, while LOD incubated for 4 hr in the inoculated sausage sample ranged from $10^1CFU/g$ to $10^2CFU/g$ as an inoculated cell count. The assay developed in this study could be applied for the investigation of food poisoning pathogens.

• Journal of Physiology & Pathology in Korean Medicine
• /
• v.17 no.6
• /
• pp.1393-1403
• /
• 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.

• Genomics & Informatics
• /
• v.5 no.2
• /
• pp.83-87
• /
• 2007

The analysis of DNA microarray data is a rapidly evolving area of bioinformatics, and various types of microarray are emerging as some of the most exciting technologies for use in biological and clinical research. In recent years, microarray technology has been utilized in various applications such as the profiling of mRNAs, assessment of DNA copy number, genotyping, and detection of methylated sequences. However, the analysis of these heterogeneous microarray platform experiments does not need to be performed separately. Rather, these platforms can be co-analyzed in combination, for cross-validation. There are a number of separate laboratory information management systems (LIMS) that individually address some of the needs for each platform. However, to our knowledge there are no unified LIMS systems capable of organizing all of the information regarding multi-platform microarray experiments, while additionally integrating this information with tools to perform the analysis. In order to address these requirements, we developed a web-based LIMS system that provides an integrated framework for storing and analyzing microarray information generated by the various platforms. This system enables an easy integration of modules that transform, analyze and/or visualize multi-platform microarray data.

• Bulletin of the Korean Chemical Society
• /
• v.34 no.4
• /
• pp.1035-1038
• /
• 2013

Rolling circle amplification (RCA) of DNA on an aligned-carbon nanotube (a-CNT) surface was electrically interfaced by the a-CNT based filed effect transistor (FET). Since the electric conductance of the a-CNT will be dependent upon its local electric environment, the electric conductance of the FET is expected to give a very distinctive signature of the surface reaction along with this isothermal DNA amplification of the RCA. The a-CNT was initially grown on the quartz wafer with the patterned catalyst by chemical vapor deposition and transferred onto a flexible substrate after the formation of electrodes. After immobilization of a primer DNA, the rolling circle amplification was induced on chip with the a-CNT based FET device. The electric conductance showed a quite rapid increase at the early stage of the surface reaction and then the rate of increase was attenuated to reach a saturated stage of conductance change. It took about an hour to get the conductance saturation from the start of the conductance change. Atomic force microscopy was used as a complementary tool to support the successful amplification of DNA on the device surface. We hope that our results contribute to the efforts in the realization of a reliable nanodevice-based measurement of biologically or clinically important molecules.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2006.02a
• /
• pp.98-107
• /
• 2006

Chromosomal copy number changes (aneuploidies) are common in human populations. The extra chromosome can affect gene expression by whole-genome level. By gene expression microarray analysis, we want to find aberrant gene expression due to aneuploidies in Klinefelter (+X) and Down syndrome (+21). We have analyzed the inactivation status of X-linked genes in Klinefelter Syndrome (KS) by using X-linked cDNA microarray and cSNP analysis. We analyzed the expression of 190 X-linked genes by cDNA microarray from the lymphocytes of five KS patients and five females (XX) with normal males (XY) controls. cDNA microarray experiments and cSNP analysis showed the differentially expressed genes were similar between KS and XX cases. To analyze the differential gene expressions in Down Syndrome (DS), Amniotic Fluid (AF)cells were collected from 12 pregnancies at $16{\sim}18$ weeks of gestation in DS (n=6) and normal (n=6) subjects. We also analysis AF cells for a DNA microarray system and compared the chip data with two dimensional protein gel analysis of amniotic fluid. Our data may provide the basis for a more systematic identification of biological markers of fetal DS, thus leading to an improved understanding of pathogenesis for fetal DS.

• Journal of the Optical Society of Korea
• /
• v.10 no.3
• /
• pp.130-142
• /
• 2006

Lab-on-a-chip technology is attracting great interest because the miniaturization of reaction systems offers practical advantages over classical bench-top chemical systems. Rapid mixing of the fluids flowing through a microchannel is very important for various applications of microfluidic systems. In addition, highly sensitive on-chip detection techniques are essential for the in situ monitoring of chemical reactions because the detection volume in a channel is extremely small. Recently, a confocal surface enhanced Raman spectroscopic (SERS) technique, for the highly sensitive biological analysis in a microfluidic sensor, has been developed in our research group. Here, a highly precise quantitative measurement can be obtained if continuous flow and homogeneous mixing condition between analytes and silver nano-colloids are maintained. Recently, we also reported a new analytical method of DNA hybridization involving a PDMS microfluidic sensor using fluorescence energy transfer (FRET). This method overcomes many of the drawbacks of microarray chips, such as long hybridization times and inconvenient immobilization procedures. In this paper, our recent applications of the confocal Raman/fluorescence microscopic technology to a highly sensitive lab-on-a-chip detection will be reviewed.