• Fisheries and Aquatic Sciences
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• v.11 no.4
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• pp.205-208
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• 2008

The mixotrophic dinoflagellate Cochlodinium polykrikoides was reported to be linked to major fish kills in Korea and Japan since the 1990s. Rapid and sensitive detection of microalgae has been problematic because morphological identification of dinoflagellates requires light microscopic and scanning electron microscopic observations that are time consuming and laborious compared to real-time PCR. To address this issue, a real-time PCR probe targeting the ITS2 rRNA gene was used for rapid detection and quantification of C. polykrikoides. PCR inhibitors in water column samples were removed by dilution of template DNA for elimination of false-negative reactions. A strong association between cell quantification using real-time PCR and microscopic counts suggests that the real-time PCR assay is an alternative method for cell estimation of C. polykrikoides in environment samples.

• Korean Journal of Clinical Laboratory Science
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• v.41 no.4
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• pp.153-157
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• 2009

The production of extended-spectrum ${\beta}$-lactamases ($ESBL_S$) of the TEM or SHV type by bacterial pathogens is a major threat to the use of the clinically important expanded-spectrum cephalosporins. The characterization of the SHV ESBLs producing Klebsiella pneumoniae strains present in clinical isolates is time-consuming processes. We describe here in the development of a novel system, which consists of a real time PCR. We found 11 K. pneumoniae strains to be presumptive strains ESBLs producers by clinical and laboratory standards institute (CLSI) guidelines. The double disk synergy test showed 8 ESBL positive and conventional PCR showed 10 SHV ESBL positive, which were K. pneumoniae strains isolates. By real time PCR analysis, SHV gene in 11 of 11 strains were identified. When sequencing analysis was compared with real time PCR, both analysis were presented 99% similarity. In this study, we used a rapid, sensitive, and specific real-time PCR (RT-PCR) method for detection of the assay SHV ESBL producing K. pneumoniae strains in clinical isolates.

• Parasites, Hosts and Diseases
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• v.48 no.2
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• pp.99-103
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• 2010

Malaria is endemic in the Cukurova region while it is sporadic in other regions of Turkey. Therefore, the laboratory and clinical diagnosis of malaria is important for the treatment of malaria. In this study, 92 blood samples that were taken from the suspected malaria patients for routine diagnosis in a period of 10 years between 1999 and 2009 were analyzed. All of these blood samples were examined by microscopic examinations using Giemsa-stained thick blood films, nested PCR, and real-time PCR. The sensitivity-specificity and positive-negative predictive values for these diagnostic tests were then calculated. It was found that the positive predictive values of microscopic examination of thick blood films, nested PCR, and real-time PCR were 47.8%, 56.5%, and 60.9% for malaria, respectively. The real-time PCR was found to have a specificity of 75% and sensitivity of 100%, while specificity and sensitivity of nested PCR was found 81.2% and 97.7% according to the microscopic examination of thick blood films, respectively.

• Korean Journal of Veterinary Service
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• v.31 no.4
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• pp.485-492
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• 2008

Salmonella enterica serovars Gallinarum(SG, causative agent of fowl typhoid) and S Pullorum(SP, causative agent of pullorum disease) are very important bacterial pathogens in poultry industry. They share some common antigenic properties though the characteristics of outbreaks are quite different. To discriminate between SG and SP, we developed two rapid diagnostic methods, allele-specific real-time PCR and 3'-tailed PCR over 2 single nucleotide polymorphisms ($237^{th}\;and\;598^{th}$). In both methods, $237^{th}$ allele was found to be a good target for differential diagnosis, while $598^{th}$ allele produced some non-specific reactions.

• KSBB Journal
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• v.29 no.5
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• pp.361-371
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• 2014

Mycoplasma is well recognized as one of the most prevalent and serious microbial contaminants of biologic manufacturing processes. Conventional methods for mycoplasma testing, direct culture method and indirect indicator cell culture method, are lengthy, costly and less sensitive to noncultivable species. In this report, we describe a new TaqMan probe-based real-time PCR method for rapid and quantitative detection of mycoplasma contamination during manufacture of biologics. Universal mycoplasma primers were used for mycoplasma PCR and mycoplasma DNA was quantified by use of a specific TaqMan probe. Specificity, sensitivity, and robustness of the real-time PCR method was validated according to the European Pharmacopoeia. The validation results met required criteria to justify its use as a replacement for the culture method. The established real-time PCR assay was successfully applied to the detection of mycoplasma from human keratinocyte and mesenchymal stem cell as well as Vero cell lines artificially infected with mycoplasma. The overall results indicated that this rapid, specific, sensitive, and robust assay can be reliably used for quantitative detection of mycoplasma contamination during manufacture of biologics.

• Microbiology and Biotechnology Letters
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• v.36 no.1
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• pp.12-20
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• 2008

Validation of viral safety is essential in ensuring the safety of mammalian cell culture-derived biopharmaceuticals, because numerous adventitious viruses have been contaminated during the manufacture of the products. Mammalian cells are highly susceptible to minute virus of mice(MVM), and there are several reports of MVM contamination during the manufacture of biopharmaceuticals. In order to establish the validation system for the MVM safety, a real-time PCR method was developed for quantitative detection of MVM in cell lines, raw materials, manufacturing processes, and final products as well as MVM clearance validation. Specific primers for amplification of MVM DNA was selected, and MVM DNA was quantified by use of SYBR Green I. The sensitivity of the assay was calculated to be $6{\times}10^{-2}TCID_{50}/mL$. The real-time PCR method was proven to be reproducible and very specific to MVM. The established real-time PCR assay was successfully applied to the validation of Chinese hamster ovary (CHO) cell artificially infected with MVM. MVM DNA could be Quantified in CHO cell as well as culture supernatant. When the real-time PCR assay was applied to the validation of virus removal during a virus filtration process, the result was similar to that of virus infectivity assay. Therefore, it was concluded that this rapid, specific, sensitive, and robust assay could replace infectivity assay for detection and clearance validation of MVM.

• Journal of Life Science
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• v.20 no.8
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• pp.1201-1206
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• 2010

We performed a comparative analysis using a Real-time PCR (Polymerase Chain Reaction) and LC/MS (Liquid-Chromatograph/Mass Spectrometer) method in order to detect microcystin in environmental sources. Among the three different primer sets tested for microcystin using three positive strains of Microcystis aeruginosa by Real-time PCR assay, only TOX2P/TOX2M primer pairs were able to detect Microcystis aeruginosa. According to the results of a survey carried out from June 2009 to September 2009, 11 out of 11 (100%) raw water samples were were found to have microcystin when the Real-Time PCR and LC/MS method was used, with total microcystin concentration ranging from 5.98~219.0 ${\mu}g/l$. A microcystin removal treatment process was used to ensure entire removal, by passing it through a BAC filtration step. It was concluded that real-time PCR assay can be used to estimate micrucystin detection more rapidly and easily than the LC/MS method.

• Research in Plant Disease
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• v.18 no.4
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• pp.298-303
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• 2012

Tomato yellow leaf curl virus (TYLCV), transmitted exclusively by the whitefly (Bemisia tabaci) in a circulative manner is one of the most important virus in tomato. Since the first report of TYLCV incidence in Korea in 2008, the virus has rapidly spread nationwide. TYLCV currently causes serious economic losses in tomato production in Korea. Early detection of TYLCV is one of the most important methods to allow rouging of infected tomato plants to minimize the spread of TYLCV disease. We have developed an ultra-rapid and sensitive real-time polymerase chain reaction (PCR) using a new designed real-time PCR system, GenSpectorTM TMC-1000 that is a small and portable real-time PCR machine requiring only a $5{\mu}l$ reaction volume on microchips. The new system provides ultra-high speed reaction (30 cycles in less than 15 minutes) and melting curve analysis for amplified TYLCV products. These results suggest that the short reaction time and ultra sensitivity of the GenSpector$^{TM}$-based real-time PCR technique is suitable for monitoring epidemics and pre-pandemic TYLCV disease. This is the first report for plant virus detection using an ultra-rapid real-time PCR system.

• Food Science of Animal Resources
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• v.31 no.6
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• pp.851-857
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• 2011

This study was conducted to develop a real time reverse transcriptase-PCR (RT-PCR) method for the detection of viable Enterobacteriaceae in milk using primers based on the genes of ribosomal proteins S11 and S13 and to determine effects of heating and subsequent treatments on the threshold cycle (Ct) of the real time RT-PCR. Total RNA was isolated from 17 strains of bacteria including 11 strains of Enterobacteriaceae suspended in milk using a modified Tri reagent method. SYBR Green Master Mix was added to the RNA and the mixture was subjected to the real time RT-PCR. The Cts of eleven type strains of the Enterobacteriaceae in milk ($10^7$ cells) in the real time RT-PCR ranged from 21.5 to 24.6. However, the Cts of Pseudomonas fluorescens, Acinetobacter calcoaceticus, and three gram-positive bacteria were more than 40. The real time RT-PCR detected as low as $10^3$ cells in agarose gel electrophoresis. The Cts increased from 22.0 to 34.2 when milk samples contaminated with Escherichia coli ($10^7$ cells/mL) were heated at $65^{\circ}C$ for 30 min. In addition, subsequent incubation at $37^{\circ}C$ for 6 and 24 h increased the Cts further up to 36.2 and 37.2, respectively. Addition of RNase A to the bacterial suspension obtained from the heated milk and subsequent incubation at $37^{\circ}C$ for 1 h increased the Cts to more than 40. The results of this study suggests that pretreatment of bacterial cells heated in milk with RNase A before RNA extraction might enhance the ability to differentiate between viable and dead bacteria using real time RT-PCR.

• Korean Journal of Food Science and Technology
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• v.43 no.1
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• pp.119-123
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• 2011

In this study, performances of culture methods using two selective media and real-time PCR were evaluated for detection of Campylobacter jejuni (C. jejuni) in various food samples. Sausage, ground beef, and radish sprouts inoculated with C. jejuni were enriched in Hunt broth and then streaked onto modified cefoperazone charcoal deoxycholate agar and Preston agar, followed by incubation under microaerobic conditions. The enriched Hunt broth (1 mL) was used in real-time PCR assay. No statistical differences were observed in sensitivity among the two selective media and real-time PCR for sausage and ground beef. However, the number of positives by real-time PCR in radish sprouts was much higher than the two selective media (p<0.05). It appears that real-time PCR could be used as an effective screening tool to detect C. jejuni, particularly in foods with a high number of background microflora such as fresh vegetables.