• Korean Journal of Clinical Laboratory Science
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• 제37권3호
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• pp.139-142
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• 2005

Most expressed HLA(human leukocyte antigen) loci exhibit a remarkable degree of allelic polymorphism, which is derived from sequenceing differences predominantly localized to discrete hypervariable regions of the amino-terminal domain of the molecule. In this study, the HLA-DRB1 genotypes were determined in twenty students using the PCR-SSP (polymerase chain reaction-sequence specific primer) technique. Two specific primer pairs in assigning the DRB1 gene were used. The results of PCR-SSP, the $HLA-DRB1^{\ast}0101$ primer detected nine and $HLA-DRB1^{\ast}1501$ primer detected three people. This study shows that the PCR-SSP technique is relatively simple, fast and a practical tool for the determination of the HLA-DRB1 genotypes. Moreover, these genotype frequency results of the HLA DRB1 gene could be useful for database study before being applied to individual identification and transplantation immunity.

• Parasites, Hosts and Diseases
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• 제55권3호
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• pp.333-336
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• 2017

Avian trichomoniasis caused by Trichomonas gallinae is a serious protozoan disease worldwide. The domestic pigeon (Columba livia domestica) is the main host for T. gallinae and plays an important role in the spread of the disease. Based on the internal transcribed spacers of nuclear ribosomal DNA of this parasite, a pair of primers (TgF2/TgR2) was designed and used to develop a PCR assay for the diagnosis of T. gallinae infection in domestic pigeons. This approach allowed the identification of T. gallinae, and no amplicons were produced when using DNA from other common avian pathogens. The minimum amount of DNA detectable by the specific PCR assay developed in this study was 15 pg. Clinical samples from Guangzhou, China, were examined using this PCR assay and a standard microscopy method, and their molecular characteristics were determined by phylogenetic analysis. All of the T. gallinae-positive samples detected by microscopic examination were also detected as positive by the PCR assay. Most of the samples identified as negative by microscopic examination were detected as T. gallinae positive by the PCR assay and were confirmed by sequencing. The positive samples of T. gallinae collected from Guangzhou, China, were identified as T. gallinae genotype B by sequencing and phylogenetic analyses, providing relevant data for studying the ecology and population genetic structures of trichomonads and for the prevention and control of the diseases they cause.

• Tuberculosis and Respiratory Diseases
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• 제75권4호
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• pp.150-156
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• 2013

Background: Thoracoscopic pleural biopsy is often required for rapid and confirmative diagnosis in patients with suspected pleural tuberculosis (PL-TB). However, this method is more invasive and costly than its alternatives. Therefore, we evaluated the clinical utility of the chest computed tomography (CT)-based bronchial aspirate (BA) TB-polymerase chain reaction (PCR) test in such patients. Methods: Bronchoscopic evaluation was performed in 54 patients with presumptive PL-TB through diagnostic thoracentesis but without a positive result of sputum acid-fast bacilli (AFB) smear, pleural fluid AFB smear, or pleural fluid TB-PCR test. Diagnostic yields of BA were evaluated according to the characteristics of parenchymal lesions on chest CT. Results: Chest radiograph and CT revealed parenchymal lesions in 25 (46%) and 40 (74%) of 54 patients, respectively. In cases with an absence of parenchymal lesions on chest CT, the bronchoscopic approach had no diagnostic benefit. BA TB-PCR test was positive in 21 out of 22 (95%) patients with early-positive results. Among BA results from 20 (37%) patients with patchy consolidative CT findings, eight (40%) were AFB smear-positive, 18 (90%) were TB-PCR-positive, and 19 (95%) were culture-positive. Conclusion: The BA TB-PCR test seems to be a satisfactory diagnostic modality in patients with suspected PL-TB and patchy consolidative CT findings. For rapid and confirmative diagnosis in these patients, the bronchoscopic approach with TB-PCR may be preferable to the thoracoscopy.

• The Journal of Korean Society of Virology
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• 제30권2호
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• pp.151-159
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• 2000

Hepatitis C virus (HCV) is one of the important human pathogen that can cause acute and chronic hepatitis, liver cirrhosis and hepatocellular carcinoma. Recently, the third generation radiation immuno assay (RIA) method has been developed as a very sensitive test to detect anti-HCV antibody. However, false positive is the problem with RIA test. To solve this the RIA results were compared to those of 5-antigen recombinant immunoblot assay (5-RIBA) and reverse transcription-polymerase chain reaction (RT-PCR). Among 12,767 serum samples tested from clinic visitors, total 275 (2.2%) samples were antibody positive by RIA. RIBA was performed with 148 RIA positives cases but among them was shown eighty five was antibody positive and sixty three (42.6%) was negative result. However, nested RT-PCR test was shown also carried out with 43 positive, 6 intermediates and 25 negatives of RIBA. As a result of the nested RT-PCR results, HCV antigen were detected in RIBA positive, 33.3% (2/6) RIBA intermediate and 12% (3/25). Clinical syndrome of all 148 patients as a with chronic active hepatitis (46.0%), cirrhosis (18.9%), hepatocellular carcinoma (8.1%) and others (27.0%) and they were positive in reaction by RIA test. But RIBA positive patients with 34.9% of chronic active hepatitis, 18.6% of cirrhosis, 4.6% of hepatocellular carcinoma and 41.9% of others were detected to be positive case by nested RT-PCR.

• Journal of Life Science
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• 제9권1호
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• pp.15-21
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• 1999

The random amplified ploymorphic DNAs (RAPD) assay is a simple and useful tool in identification of appropriate genetic markers, that requires no knowledge of target DNA sequence. RAPD products were generated directly from seaweed tissues, without prior nucleic acid extraction, of Porphyra yezoensis, Ulva pertusa and Undaria pinnatifida. The nuclear rDNA internal transcribed spacer (ITS) fragment however was not amplified directly from the seaweed tissues. Using DNA extracted by the LiCl method, both the ITS and RAPD's have been amplified by the polymerase chain reaction. RAPD of P yezoensis, thallus (n) and conchocelis (2n) produced lots of different polymorphic bands (36-50$\%$) depending on the arbitrary primers used. Difference was also observed between direct tissues amplification and DNA extracts amplification (53-57$\%$). Thus it is important to use the same ploidy of tissue for DNA extraction and as a RAPD template.

• Biomedical Science Letters
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• 제25권4호
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• pp.407-416
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• 2019

Recent years have seen an increase in the incidence of candidiasis caused by non-albicans Candida (NAC) species. In fact, C. glabrata is now second only to C. albicans as the most common cause of invasive candidiasis. Therefore, the rapid genotyping specifically for C. glabrata is required for early diagnosis and treatment of candidiasis. A number of genotyping assays have been developed to differentiate C. glabrata sequence types (STs), but they have several limitations. In the previous study, multi-locus sequence typing (MLST) has performed with a total of 101 C. glabrata clinical isolates to analyze the prevalent C. glabrata STs in Korea. A total of 11 different C. glabrata STs were identified and, among them, ST-138 was the most commonly classified. Thus, a novel probe-based quantitative PCR (qPCR) assay was developed and evaluated for rapid and accurate identification of the predominant C. glabrata ST-138 in Korea. Two primer pairs and hybridization probe sets were designed for the amplification of internal transcribed spacer 1 (ITS1) region and TRP1 gene. Analytical sensitivity of the probe-based qPCR assay was 100 ng to 10 pg and 100 ng to 100 pg (per 1 μL), which target ITS1 region and TRP1 gene, respectively. This assay did not react with any other Candida species and bacteria except C. glabrata. Of the 101 clinical isolates, 99 cases (98%) were concordant with MLST results. This novel probe-based qPCR assay proved to be rapid, sensitive, highly specific, reproducible, and cost-effective than other genotyping assay for C. glabrata ST-138 identification.

• Journal of Microbiology and Biotechnology
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• 제22권7호
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• pp.1021-1028
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• 2012

In this study, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the rapid, sensitive, and inexpensive detection of nervous necrosis virus (NNV) in olive flounder, Paralichthys olivaceus, in Korea. A set of six specific primers was designed to target the RNA 2 gene encoding the coat protein of Korean NNV strains. The RT-LAMP reaction successfully detected NNV after 30 min at $65^{\circ}C$. When the sensitivities among RT-LAMP, RT-PCR, and nested RTPCR were compared, the RT-LAMP was shown to be able to detect the RNA template at $2.58{\times}10^{-2}\;TCID_{50}/ml$, whereas the RT-PCR and nested RT-PCR were only able to detect the RNA template at $2.58{\times}10^2\;TCID_{50}/ml$ and $2.58TCID_{50}/ml$, respectively. Thus, the sensitivity of the RT-LAMP assay was higher than those of the RT-PCR assays. In the specificity test of the RT-LAMP, 2 genotypes of NNVs (SJNNV and RGNNV) were positive; however, no other fish viruses were positive with the primers, indicating that the RT-LAMP assay is only specific to NNV. A total of 102 olive flounder were collected from hatcheries between 2009 and 2011. The occurrence of NNV in olive flounder was determined to be 53.9% (55/102) by the RT-LAMP. On the other hand, the prevalence based on the nested RT-PCR and RT-PCR results was 33.8% (34/102) and 20.6% (21/102), respectively. This result indicates that the RT-LAMP assay developed in this study is suitable for early field diagnosis of NNV with high sensitivity.

• Journal of Korean Society of Water and Wastewater
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• 제23권2호
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• pp.199-205
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• 2009

It is very important to differentiate of DNA derived from live or dead bacteria within mixed microbial communities in aquatic environments. Ethidium monoazide (EMA) is a DNA intercalating agent and the treatment of EMA with strong visible light cleaves the genomic DNA of bacteria. In dead bacterial cells, EMA intercalates into the genomic DNA, induces the cleavage of DNA, and inhibits the PCR amplification. In this study, we developed the EMA-PCR and EMA real-time PCR to detect the DNA derived from viable Escherichia coli (E.coli) in mixed cultures of live and dead E.coli. The treatment of EMA, $50{\mu}g/mL$, and 650 W visible halogen light exposure for 2 minutes cleaved the genomic DNA derived from heat killed E.coli but did not those of live E.coli. EMA-PCR could detect the DNA from live E.coli in mixed culture samples of live and dead E.coli at various ratio and there was no DNA amplification in only dead E.coli cultures. Similar results were observed in EMA real-time PCR. Further studies are needed to develop various EMA-PCR methods to detect viable waterborne pathogens such as Helicobacter pylori, Giardia lamblia, and so on.

• Food Science and Biotechnology
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• 제17권4호
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• pp.761-765
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• 2008

Bacillus cereus causes two different types of food poisoning syndromes: diarrhea and emesis. The diarrheal syndrome is attributed to various enterotoxins, including nonhemolytic enterotoxin, hemolytic enterotoxin, and enterotoxin-T, whereas the emetic syndrome is caused by the dodecadepsipeptide toxin cereulide. A multiplex polymerase chain reaction (PCR) assay was developed to rapidly detect and identify B. cereus strains. Three primer pairs specific to regions within genes encoding nonhemolytic enterotoxin (nheA), molecular chaperonin (groEL), and cereulide synthetase (ces) were used to identify and differentiate between the enterotoxin-producing and emetic toxin-producing B. cereus strains. The cereulide-producing emetic B. cereus showed 3 PCR products of 325, 405, and 685 bp for the groEL, ces, and nheA genes, respectively, whereas the enterotoxin-producing B. cereus showed 2 PCR products without a ces gene specific DNA fragment. Specific amplifications and differentiations by multiplex PCR assay were obtained using 62 B. cereus strains and 13 strains' of other bacterial species. The detection limit of this assay for enterotoxin-producing strain and emetic toxin-producing strain from pure cultures were $2.4{\times}10^1$ and $6.0{\times}10^2\;CFU/tube$, respectively. These results suggest that our multiplex PCR method may be useful for the rapid detection and differentiation of B. cereus strains in foods.

• Restorative Dentistry and Endodontics
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• 제33권6호
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• pp.537-544
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• 2008

Polymerase chain reaction (PCR) can detect bacteria more rapidly than conventional plate counting. However DNA-based assays cannot distinguish between viable and dead cells due to persistence of DNA after cells have lost their vitality. Recently, propidium monoazide (PMA) treatment has been introduced. The purpose of this study is to evaluate the applicability of the PMA treatment and real-time PCR method for cell counting in comparison with plate counting and to evaluate the antibacterial efficacy of 2% CHX on E. faecalis using PMA treatment in combination with real-time PCR. Firstly, to elucidate the relationship between the proportion of viable cells and the real-time PCR signals after PMA treatment, mixtures with different ratios of viable and dead cells were used. Secondly, relative difference of viable cells using PMA treatment in combination with real-time PCR was compared with CFU by plate counting. Lastly, antibacterial efficacy of 2% CHX on E. faecalis was measured using PMA treatment in combination with real-time PCR. The results were as follows : 1. Ct value increased with decreasing proportion of viable E. faecalis. 2. There was correlation between viable cells measured by real-time PCR after PMA treatment and CFU by plate counting until Optical density (OD) value remains under 1.0. However, viable cells measured by real-time PCR after PMA treatment have decreased at 1.5 of OD value while CFU kept increasing. 3. Relative difference of viable E. faecalis decreased more after longer application of 2% CHX.