• Korean Journal of Veterinary Service
• /
• v.30 no.4
• /
• pp.505-510
• /
• 2007

This study was conducted to detect ${\beta}$-lactam antibiotic-resistant genes in the 400 E coli isolates from porcine fecal samples in Korea by a DNA chip. The DNA chip contains the specific probe DNAs of the ${\beta}$-lactam antibiotic-resistant genes that had been labeled with a mixture of primer set designed to amplify specific genes (PSE, OXA, FOX, MEN, CMY, TEM, SHV, OXY and AmpC) using a multiplex polymerase chain reaction (PCR). Of 400 isolates 339 contained at least one ${\beta}$-lactamases gene. Resistance to ${\beta}$-lactamases was mediated mainly by AmpC (n = 339, 100%), and followed by TEM (n = 200, 59.0%), CMY (n = 101, 29.8%), PSE (n = 30, 8.9%) and both OXA and SHV genes (n = 20, 5.9%), while the FOX, MEN and OXY genes were not detected. The other sixty-one did not contain any ${\beta}$-lactamase genes even though they were resistant to antimicrobial drugs. In conclusion, the DNA chip system can be used as a rapid and reliable method for detecting of ${\beta}$-lactamases genes, which will help veterinarians select the antibiotics for monitoring and treating of animal diseases.

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

• Proceedings of the Korean Society of Veterinary Pathology Conference
• /
• 2003.10a
• /
• pp.32-32
• /
• 2003

Intestinal infections are common in growing pigs and can be caused by multiple pathogens, environmental and management factors [1]. Among the most important viruses in swine enteritis are porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine enteric calicivirus (PECV), porcine group A rotavirus (PRV gp A) and bacteria are Escherichia coli and Salmonella spp. and protozoa is Isospora suis [1]. The DNA chip system can serve as a powerful tool that can be utilized for simultaneous detection of specific pathogenic bacteria strains and viruses [2,3]. The combination of PCR and DNA chip technology will provide a novel method for the detection of porcine enteric pathogens thus revolutionize the diagnosis and management of the disease. The aim of this study is to develop DNA chip system for the rapid and reliable detection of five major porcine enteric pathogens based on oligonucleotide DNA chip hybridization. (omitted)

• Genomics & Informatics
• /
• v.21 no.4
• /
• pp.52.1-52.10
• /
• 2023

Accurate and efficient microbial diagnosis is crucial for effective molecular diagnostics, especially in the field of human healthcare. The gold standard equipment widely employed for detecting specific microorganisms in molecular diagnosis is quantitative real-time polymerase chain reaction (qRT-PCR). However, its limitations in low metagenomic DNA yield samples necessitate exploring alternative approaches. Digital PCR, by quantifying the number of copies of the target sequence, provides absolute quantification results for the bacterial strain. In this study, we compared the diagnostic efficiency of qRT-PCR and digital PCR in detecting a particular bacterial strain (Staphylococcus aureus), focusing on skin-derived DNA samples. Experimentally, specific primer for S. aureus were designed at transcription elongation factor (greA) gene and the target amplicon were cloned and sequenced to validate efficiency of specificity to the greA gene of S. aureus. To quantify the absolute amount of microorganisms present on the skin, the variable region 5 (V5) of the 16S rRNA gene was used, and primers for S. aureus identification were used to relative their amount in the subject's skin. The findings demonstrate the absolute convenience and efficiency of digital PCR in microbial diagnostics. We suggest that the high sensitivity and precise quantification provided by digital PCR could be a promising tool for detecting specific microorganisms, especially in skin-derived DNA samples with low metagenomic DNA yields, and that further research and implementation is needed to improve medical practice and diagnosis.

• The Transactions of the Korean Institute of Electrical Engineers C
• /
• v.55 no.11
• /
• pp.544-547
• /
• 2006

In this paper, we present a temperature-controlled system for MEMS electrical resistance heaters without a temperature sensor. To rapidly control the heater temperature, the microheater system developed consists of a power supply, power amplifier, digital ${\underline{P}}roportional-{\underline{I}}ntegral-{\underline{D}}ifferential$ (PID) controller, and a quarter bridge circuit with the microheater and three resistors are nominally balanced. The microheaters are calibrated inside a convection oven to obtain the temperature coefficient with a linear or quadratic fit. A voltage amplifier applies the supply voltage proportional to the control signal from the PID controller. Small changes in heater resistance generate a finite voltage across the quarter bridge circuit, which is fed back to the PID controller to compare with the set-point and to generate the control signal. Two MEMS microheaters are used for evaluating the developed control system - a NiCr serpentine microheater for a preconcentrator and a Nickel microheater for ${\underline{P}}olymerase\;{\underline{C}}hain\;{\underline{R}}eaction$ (PCR) chip.

• Proceedings of the Korean Society of Veterinary Pathology Conference
• /
• 2003.10a
• /
• pp.33-33
• /
• 2003

There prevalence of $\beta$-lactamases bacteria in animals has been increased since 1990s [1]. The resistance in E coli which is mediated by $\beta$-lactamases hydrolyze the $\beta$-lactam ring eventually inactivate the antibiotics [2]. Generally, $\beta$-lactamases can be classified into four main groups and eight subgroups according to their functional and structural characteristics [3]. The detection of $\beta$-lactam antibiotic-resistant bacteria by DNA chip has been described [4]. The chip has a specific probe DNAs that contained the $\beta$-lactam antibiotic-resistant genes which was labeled by multiplex PCR reaction with a mixture of primer sets that were designed to amplify specific gene. Here we report the susceptibility of enteropathogenic E. coli isolated from pigs in Korea using the DNA chip in detecting $\beta$-lactam antibiotic-resistant genes. (omitted)

• Horticultural Science & Technology
• /
• v.31 no.6
• /
• pp.748-755
• /
• 2013

This study was conducted to find a salt tolerance gene in Brassica rapa. In order to meet this objective, we analyzed data from a KBGP-24K oligo chip [BrEMD (Brassica rapa EST and microarray database)] of the B. rapa ssp. pekinensis 'Chiifu' under salt stress (250 mM NaCl). From the B. rapa KBGP-24K microarray chip analysis, 202 salt-responsive unigenes were primarily selected under salt stress. Of these, a gene with unknown function but known full-length sequence was chosen to closely investigate the gene function. The selected gene was named BrSSR (B. rapa salt stress resistance). BrSSR contains a 285 bp open reading frame encoding a putative 94-amino acid protein, and a DUF581 domain. The pSL94 vector was designed to over-express BrSSR, and was used to transform tobacco plants for salt tolerance analysis. T1 transgenic tobacco plants that over-expressed BrSSR were selected by PCR and DNA blot analyses. Quantitative real-time RT PCR revealed that the expression of BrSSR in transgenic tobacco plants increased by approximately 3.8-fold. Similar results were obtained by RNA blot analysis. Phenotypic characteristics analysis showed that transgenic tobacco plants with over-expressed BrSSR were more salt-tolerant than the wild type control under 250 mM NaCl for 5 days. Based on these results, we hypothesized that the over-expression of BrSSR may be closely related to the enhancement of salt tolerance.

• Transactions of the Korean Society of Mechanical Engineers A
• /
• v.34 no.12
• /
• pp.1785-1791
• /
• 2010

This paper describes a separable microfluidic device fabricated with PDMS (polydimethylsiloxane) and glass. The device is used for sample preparation involving cell lysis and the DNA purification process. The cell lysis was performed for 2 min at $80^{\circ}C$ in a serpentine-type microreactor ($20 {\mu}l$) using a Au microheater that was integrated with a thermal microsensor on a glass substrate. The DNA that was mixed with other residual products during the cell lysis process was then filtered through a new filtration system composed of microbeads (diameter: $50 {\mu}m$) and PDMS pillars. Since the entire process (sample loading, cell lysis reaction, DNA purification, and sample extraction) was performed within 5 min in a microchip, we could reduce the sample preparation time in comparison with that for the conventional methods used in biochemistry laboratories. Finally, we verified the performance of the sample preparation chip by conducting PCR (polymerase chain reaction) analysis of the chip product.

• 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.

• Asian Pacific Journal of Cancer Prevention
• /
• v.14 no.3
• /
• pp.1687-1689
• /
• 2013

We performed a case-control study to investigate whether SNPs of CHIP might affect the development of IA in Chinese Han nationality. We believe we are the first to have screened IA patients for mutations in the CHIP gene to determine the association with these variants. The study group comprised 224 Chinese Han nationality patients with at least one intracranial aneurysm and 238 unrelated healthy Han nationality controls. Genomic DNA was isolated from blood leukocytes. The entire coding regions of CHIP were genotyped by PCR amplification and DNA sequencing. Differences in genotype and allele frequencies between patients and controls were tested by the chi-square method. Genotype and allele frequencies of the SNP rs116166850 was demonstrated to be in Hardy-Weinberg equilibrium. No significant difference in genotype or allele frequencies between case and control groups was detected at the SNP. Our data do not support the hypothesis of a major role for the CHIP gene in IA development in the Chinese Han population.