• Title, Summary, Keyword: PCR

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Emulsion PCR Improves the Specificity and Sensitivity of PCR-based Pathogen Detection (식중독균 검출의 민감도 향상을 위한 Emulsion PCR 적용)

  • Chai, Changhoon
    • Journal of Dairy Science and Biotechnology
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    • v.34 no.1
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    • pp.43-49
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    • 2016
  • Emulsion PCR (ePCR) has recently gained interest in the areas of food safety and biotechnology owing to its highly specific and sensitive performance in the amplification of target DNA. To facilitate the applications of ePCR to food safety and biotechnology, this paper describes the principles of ePCR and the factors that should be considered in designing ePCR. In addition, current research and applications related to ePCR are discussed.

Development of In situ PCR Method Using Primer Polymers (프라이머 중합체를 이용한 원위치 중합효소 연쇄반응 In situ PCR 방법의 개발)

  • 장진수;이재영
    • Korean Journal of Microbiology
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    • v.40 no.2
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    • pp.167-171
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    • 2004
  • Reduction in the leakage of the amplified PCR product out of cell is required for effective in situ PCR. For this purpose, primers with complementary tail sequences at their 5' sides were utilized to synthesize high molecular weight PCR products, but it is time-consuming and causes deterioration of cellular appearance with many PCR cycles. Therefore, it is required to optimize the PCR condition with minimal PCR cycles. To achieve the pur-pose, primer polymers were made without the target DNA in tube from nonspecific amplification with tailed primers and treated onto the fixed Molt/LAV cells on the glass slide for the 20 cycle-in situ PCR, in which the appropriate target signals were observed for the possible use of primer polymers in in situ PCR.

Detection of Giardia lamblia in River Water Samples Using PCR and RT-PCR (PCR 및 RT-PCR을 이용한 하천수 중 Giardia lamblia 검출)

  • Cho, Eun-Ju;Lee, Mok-Young;Byun, Seung-Heun;Han, Sun-Hee;Ahn, Seoung-Koo
    • Journal of Korean Society of Environmental Engineers
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    • v.29 no.8
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    • pp.904-908
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    • 2007
  • The protozoan pathogen Giardia lamblia has been major cause of waterborne enteric disease. In this study, we tried to identify G. lamlbia of human infectious species and to detect viable C. lamblia in river water samples including three sites of Han River mainstream and an its creek using PCR and RT-PCR technique. The PCR/RT-PCR methods were performed by using giardin primer based on the giardin gene targeting ventral disk of Giardia. Sensitivity testing in the DNA/RNA extraction and PCR/RT-PCR amplification steps showed that it was possible to detect a single cyst of G. lamblia and viable G. lamblia. The PCR/RT-PCR methods were compared with immunofluorescence(IF) assay by analyzing 48 samples collected from the mainstream water and the creek water. The mean concentration of the total cysts were 6.3 cysts/10 L(arithmetic mean, n = 48) and the positive detection rate were 62.5%(30/48). And the mean concentration of the cysts excluding empty cysts were 4.5 cysts/10 L and the positive detection rate were 52.1%(25/48). It resulted that 24 of 48 samples included Giardia lamblia by PCR assay and 10 of 48 samples included viable G. lamblia by RT-PCR assay. It resulted that the PCR/RT-PCR technique would be available to river water samples with low concentration of Giardia cysts. And it could support the Korean protozoan standard method, which provides useful information for species and viability.

PCR detection of food-borne pathogenic microorganisms in milk

  • Kim, Gyeong-Ju;Lee, Gi-Se
    • 한국생물공학회:학술대회논문집
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    • pp.204-205
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    • 2001
  • Milk is easily contaminated by pathogenic microorganisms and contains many ingredients that inhibit normal PCR. In this study, we developed a detection mothed for pathogenic microorganisms existing in milk by usting PCR. 'Sample pretreatment prior to PCR were compared to overcome the inhibition. A high PCR efficiency was achieved by SDS lysis pretreatment. without further purification of DNA for PCR.

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UNG-based direct polymerase chain reaction (udPCR) for the detection of porcine circovirus 2 (PCV2) (UNG 기반 direct polymerase chain reaction (udPCR)을 이용한 돼지 써코바이러스 2형 진단법)

  • Kim, Eun-Mi;Park, Choi-Kyu
    • Korean Journal of Veterinary Service
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    • v.37 no.4
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    • pp.253-261
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    • 2014
  • Porcine circovirus disease (PCVD) is a major problem of swine industry worldwide, and diagnosis of PCV2, causal agent of PCVD, has been doing in clinical laboratories of pig disease by polymerase chain reaction (PCR) methods. But the PCR analyses have a serious problem of misdiagnosis by contamination of DNA, in particular, from carryover contamination with previously amplified DNA or extracted DNA from field samples. In this study, an uracil DNA glycosylase (UNG)-based direct PCR (udPCR) without DNA extraction process and DNA carryover contamination was developed and evaluated on PCV2 culture and field pig samples. The sensitivity of the udPCR combined with dPCR and uPCR was same or better than that of the commercial PCR (cPCR) kit (Median diagnostics, Korea) on PCV2-positive serum, lymph node and lung samples of the pigs. In addition, the udPCR method confirmed to have a preventing ability of mis-amplification by contamination of pre-amplified PCV2 DNA from previous udPCR. In clinical application, 170 pig samples (86 tissues and 84 serum) were analysed by cPCR kit and resulted in 37% (63/170) of positive reaction, while the udPCR was able to detect the PCV2 DNA in 45.3% (77/170) with higher sensitivity than cPCR. In conclusion, the udPCR developed in the study is a time, labor and cost saving method for the detection of PCV2 and providing a preventing effect for DNA carryover contamination that can occurred in PCR process. Therefore, the udPCR assay could be an useful alternative method for the diagnosis of PCV2 in the swine disease diagnostic laboratories.

Identification of Fel ursi and Cattle and Pig Bile Juices by speciesspecific PCR and PCR-RFLP (종 특이 PCR과 PCR-RFLP를 이용한 웅담과 기타 담류의 감별 방법)

  • Kwon, Ki-Rok;Baek, Seung-Il;Choi, Suk-Ho
    • Journal of Pharmacopuncture
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    • v.12 no.1
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    • pp.13-20
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    • 2009
  • Objective : This study developed species-specific PCR and PCR-RFLP to detect the adulteration of Fel ursi products with cattle and pig bile juices. Methods : All the primers for PCR and PCR-RFLP in this study were designed based on nucleotide sequences of cytochrome b genes in the mitochondria. Results : The species-specific PCR amplified a DNA fragment of 214, 214, 295, and 167 bp from Fel ursi product, bear fur, cattle bile juice, and pig bile juice, respectively. The survey using the speciesspecific PCR indicated that some of commercial Fel ursi products were adulterated with cattle and pig bile juices. PCR-RFLP using the restriction endonucleases, HaeIII and HinfI enabled differentiation among Fel ursi product, cattle bile juice, and pig bile juice. Bear furs from two animals showed variations in PCR-RFLP patterns with HaeIII. Discussion : The detection methods of the species-specific PCR and PCR-RFLP could be useful in eliminating adulterated Fel ursi products from the market.

Detection of Marine Birnavirus (MBV) from Rockfish Sebastes schlegeli Using Reverse Transcription and Nested PCR

  • Joh, Seong-Joon;Kim, Doo-Won;Kim, Jeong-Ho;Heo, Gang-Joon
    • Journal of Microbiology
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    • v.38 no.4
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    • pp.260-264
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    • 2000
  • Reverse transcription (RT)-PCR and nested PCR methods (2-step PCR) were tested for their ability to detect marine birnavirus (MBV) in cultured rockfish, Sebastes schlegeli. One set of primers for RT-PCR was designed, based on a gene of infectious pancreatic necrosis virus (IPNV), and another set of primers for nested PCR was designed based on the VP2/NS junction region of MBV. This 2-step PCR method was specific for MBV and sensitivity was heightened when nested PCR was combined to RT-PCR. This 2-step PCR method was useful for detecting MBV not only in diseased fish, but also in asymptomatic fish. These results indicate that this 2-step PCR method is useful for detecting MBV in rockfish.

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Usefulness of PCR to Mycobacterium Tuberculous and Nontuberculous Mycobacteria from Paraffin-embedded Tissues

  • Choi, Yeon-Il;Kim, Hye-Young
    • Korean Journal of Clinical Laboratory Science
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    • v.46 no.2
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    • pp.47-53
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    • 2014
  • The purpose of this study was to evaluate the clinical utility of TB/NTM PCR by comparing the results of TB PCR to detect Mycobacterium tuberculous (MTB) and nontuberculous mycobacteria (NTM) from paraffin-embedded tissue specimens. A total of 60 cases were tested using TB PCR and TB/NTM PCR. The MTB and NTM rate of TB/NTM PCR was 84.2% (16/19), 10.5% (2/19) in TB positive of TB PCR. The NTM rate of TB/NTM PCR was 29.3% (12/41) in TB negative of TB PCR. Fourteen different species of NTM were identified, the common isolate was M. gordonae (21.4%), M. avium (14.3%), M. ulcerans (7.1%), M. interjectum (7.1%), M. gilvum (7.1%), M. fortuitum (7.1%), M. mucogenicum (7.1%). The rare species identified were M. farcinogenes (7.1%), M. tokaiense (7.1%). Therefore, TB/NTM PCR is useful to differentiate MTB and NTM from paraffin-embedded tissue specimens and it is more effective in detecting NTM with TB PCR.

Comparison of Different PCR-Based Genotyping Techniques for MRSA Discrimination Among Methicillin-Resistant Staphylococcus aureus Isolates

  • Kim, Keun-Sung;Seo, Hyun-Ah;Oh, Chang-Yong;Kim, Hong
    • Journal of Microbiology and Biotechnology
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    • v.11 no.5
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    • pp.788-797
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    • 2001
  • The usefulness of three PCR methods were evaluated for the epidemiological typing of Staphylococcus aureus: an enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR), repetitive extragenic palindromic element PCR (REP-PCR), and 16S-23S intergenic spacer PCR (ITS-PCR). The analysis was performed using a collection of S. aureus strains comprised of 6 reference and 79 isolates from patients with various diseases. Among the 85 S. aureus strains tested, 6 references and 6 isolates were found to be susceptible to methicillin, whereas the remaining 73 isolates were resistant to it. PCR methods are of special concern, as conventional phenotypic methods are unable to clearly distinguish among methicillin-resistant S. aureus (MRSA) strains. The ability of the techniques to detect different unrelated types was found to be as follows: ERIC-PCR, 19 types; REP-PCR, 36 types; and ITS-PCR, 14 types. On the basis of combining the ERIC, REP, and ITS fingerprints, the 85 S. aureus strains were grouped into 56 genetic types (designated G1 to G56). The diversities for the 85 S. aureus strains, calculated according to Simpson\`s index, were 0.88 for an ERIC-PCR, 0.93 for a REP-PCR, and 0.48 for an ITS-PCR, and the diversity increased up to 0.97 when an ERIC-PCR and REP-PCR were combined. The above discrimination indices imply that the genetic heterogeneity of S. aureus strains is high. Accordingly, this study demonstrates that DNA sequences from highly conserved repeats of a genome, particularly a combination of ERIC sequences and REP elements, are a convenient and accurate tool for the subspecies-specific discrimination and epidemiologic tracking of S. aureus.

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Development of Nested PCR Primer Set for the Specific and Highly Sensitive Detection of Human Parvovirus B19

  • Cho, Kyu-Bong
    • Biomedical Science Letters
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    • v.24 no.4
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    • pp.390-397
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    • 2018
  • For the specific detection of human Parvovirus B19 (HuPaV-B19), we designed ten specific PCR primers from 3,800~4,500 nucleotides of HuPaV-B19 complete genome (NC_000883.2). Seventeen candidate PCR primer sets for specific detecting HuPaV-B19 were constructed. In specific reaction of HuPaV-B19, seventeen PCR primer sets showed specific band, however five PCR primer sets were selected basis of band intensity, amplicon size and location. In non-specific reaction with seven reference viruses, four PCR primer sets showed non-specific band, however one PCR primer set is not. Detection sensitivity of final selective PCR primer set was $100fg/{\mu}L$ for 112 minute, and PCR amplicon is 539 base pairs (bp). In addition, nested PCR primer set was developed, for detection HuPaV-B19 from a low concentration of contaminated samples. Selection of nested PCR primer set was basis of sensitivity and groundwater sample tests. Detection sensitivity of final selective PCR and nested PCR primer sets for the detection of HuPaV-B19 were $100fg/{\mu}L$ and $100ag/{\mu}L$ basis of HuPaV-B19 plasmid, it was able to rapid and highly sensitive detection of HuPaV-B19 than previous reports. We expect developed PCR primer set in this study will used for detection of HuPaV-B19 in various samples.