• Parasites, Hosts and Diseases
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• 제48권2호
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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.

• 한국연초학회지
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• 제37권1호
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• pp.25-33
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• 2015

Genome walking is a par ticular application for identifying sequences of unknown genomic regions adjacent to a known region. Many genome walking methods based on polymerase chain reaction (PCR) are available. Even if earlier techniques suffer from low reproducibility, inefficiency, and non-specificity, improved strategies have been developed. In this study, we present an alternative strategy: the genomic DNA is digested with restriction enzymes. After cytosine overhangs at 5' ends, the fragments are ligated to linker adaptor s had guanine overhang at 3' ends. Then nested PCR is performed. The improvements in this strategy focus on two points. The first is the C tailing method using Pfu polymerase instead of the A tailing method based on nontemplate-dependent terminal transferase activity of Taq polymerase. Therefore unintended modification of target DNA can be prevented without A tailing error. The second point is the use of C/G-specific ligation had advantage in the ligation efficiency compared with A/T-specific ligation. Therefore, the C-G linker PCR method increases ligation efficiency between digested genomic DNA and adaptor DNA. As a result, the quantity of target DNA to amplify by PCR is enriched. We successfully used G-C linker PCR to retrieve flanking regions bordering the phophinothricin resistance gene in genetically modified tobacco (GMO).

• 미생물학회지
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• 제38권2호
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• pp.103-106
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• 2002

사상균류의 세포자체로부터 직접 PCR을 하는 방법은 세포벽 파괴의 어려움 때문에 모든 곰팡이에 적용될 수 없다. 극초단파 조사는 사상균류의 DNA를 추출함에 있어서 그 유용함이 이미 검중된 바 있는데, 본 논문에서는 극초단파 조사를 이용하여 Aspergillus nidulans의 포자로부터 손쉽게 주형 DNA를 얻어 PCR증폭하는 방법을 소개하고자 한다. 본 실험에서는 극초단파 조사시간과 PCR에 필요한 주형 DNA의 양 등을 최적화하였으며, 이렇게 수행된 PCR결과는 single copy유전자를 대상으로도 약 3 kb크기의 산물가지 증폭 가능하여, 형질전환체를 선별하기에 충분한 크기의 산물들도 효과적으로 얻어짐을 보여주었다. 따라서 이 방법은A. nidulans의 형질전환체를 보다 손쉽게, 시간을 절약하여 선별할 수 있는 효과적인 방법이라 생각된다.

• Clinical and Experimental Pediatrics
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• 제49권7호
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• pp.745-750
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• 2006

목 적 : 장바이러스는 모든 연령층에서 무균성 뇌막염의 가장 흔한 원인으로 확진은 뇌척수액에서 직접 바이러스를 검출하는 것이나 시일이 많이 걸리고 민감도가 낮아 뇌척수액, 대변 등 환자의 검체에서 바이러스 RNA를 탐지하는 PCR법이 대두되었다. 무균성 뇌막염 환자에서 뇌척수액과 대변의 채취 시기에 따라 검체별 PCR 양성률이 달라서 이에 관한 평가가 필요하다. 이에 저자들은 소아 환자에서 무균성 뇌막염을 진단함에 있어 증상 발현 후 뇌척수액과 대변 검체의 채취 시기에 따른 검체별 PCR의 유용성을 알고자하였다. 방 법 : 2005년 6월 11일부터 8월 30일까지 부산 일신기독병원에 입원하여 무균성 뇌막염으로 진단 받은 42례를 대상으로 임상 증상의 발현 시점에서 뇌척수액과 대변 채취 시기에 따른 검체별 PCR 결과를 조사하였다. 결 과 : 뇌척수액의 경우 증상 발현 시점부터 검체 채취 시기까지의 기간이 2일 이내였던 18례 중 PCR 양성은 9례(50.0%)로 2일이 지나 채취된 검체 24례 중 PCR 양성 1례(4.2%)에 비해 유의하게 높았다(P=0.001). 반면 대변의 경우는 일주일까지 채취 시점에 관계없이 PCR 양성률이 평균 90.5%로 지속적으로 높았다. 뇌척수액 10례(23.8%)에서 장바이러스 PCR이 양성이었고, 바이러스가 밝혀진 9례(21.4%)에서 coxsackievirus B5 6례, coxsackievirus B3 3례였다. 대변의 경우 42례 중 38례(90.5%)에서 장바이러스 PCR이 양성으로 echovirus 18 7례, echovirus 9 3례, coxsackievirus B5 8례, coxsackievirus B3 3례였다. 뇌척수액과 대변에서 동시에 배양된 경우는 6례로 모두 coxsackievirus B5였다. 결 론 : 대변을 이용한 PCR은 장바이러스 뇌막염 동안 장바이러스를 검출하는 임상적으로 민감한 검사법으로 질병 경과 동안 진단을 예측하게 한다. 결정적인 진단은 뇌척수액 PCR에 의해 얻어지나 발병 2일 후 얻어진 검체에서는 그 유용성이 매우 낮아서 임상 증상이 2일 이상 경과하였을 때는 뇌척수액 PCR 이외에 대변을 이용한 PCR을 같이 검사하는 것이 도움이 된다.

• Journal of Microbiology and Biotechnology
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• 제24권7호
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• pp.1004-1007
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• 2014

Culture is the gold standard for diagnosis of tuberculosis, but it takes 6 to 8 weeks to confirm the result. This issue is complemented by the detection method using polymerase chain reaction, which is now widely used in a routine microbiology laboratory. In this study, we evaluated the performance of the Seegene Anyplex TB PCR to assess its diagnostic sensitivity and specificity, and compared its results with the Roche Cobas TaqMan MTB PCR, one of the most widely used assays in the world. Five university hospitals located in the Chungcheong area in South Korea participated in the study. A total of 1,167 respiratory specimens ordered for acid-fast bacilli staining and culture were collected for four months, analyzed via the Seegene Anyplex TB PCR, and its results were compared with the Roche Cobas TaqMan MTB PCR. For detection of Mycobacterium tuberculosis, the diagnostic sensitivity and specificity of the Anyplex TB PCR were 87.5% and 98.2% respectively, whereas those of the Cobas TaqMan were 92.0% and 98.0% respectively (p value > 0.05). For smear-positive specimens, the sensitivity of the Anyplex TB PCR was 95.2%, which was exactly the same as that of the Cobas TaqMan. For smear-negative specimens, the sensitivity of the Anyplex TB PCR was 69.2%, whereas that of the Cobas TaqMan TB PCR was 84.6%. For detection of MTB, the Seegene Anyplex TB PCR showed excellent diagnostic performance, and high sensitivity and specificity, which were comparable to the Roche Cobas TaqMan MTB PCR. In conclusion, the Anyplex TB PCR can be a useful diagnostic tool for the early detection of tuberculosis in clinical laboratories.

• 농업과학연구
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• 제42권2호
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• pp.99-103
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• 2015

Potato virus T (PVT) is a plant pathogen in the family Betaflexiviridae, group IV single-stranded positive sense RNA viruses. The major host of PVT is potato, and it has been reported in Ullucus tuberosus, Oxalis tuberosa and Tropaeolum tuberosum. This study aimed at developing reverse transcription (RT)-polymerase chain reaction (PCR) and nested PCR techniques for specific detection of PVT. Finally, Two RT-PCR primer sets were developed and verified. The RT-PCR products were amplified to 734 (PVT RT-PCR primer set 6) and 828 bp (PVT RT-PCR primer set 29) long to detect PVT. The nested PCR primer sets [PVT-N70/C20 ($734{\rightarrow}315bp$) and PVT-N75/C30 ($828{\rightarrow}529bp$)] were developed which are high sensitivity and verification for detection of PVT. Furthermore, a modified-positive control plasmid is use to verify contamination of laboratory in PVT detection. This study supported the diagnose PVT in potato or PVT related hosts.

• 대한의생명과학회지
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• 제10권4호
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• pp.473-477
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• 2004

Methicillin-Resistant Staphylococcus aureus (MRSA) strains are resistant to a wide range of antibiotics and are a major cause of nosocomial infections. Accurate and rapid typing of MRSA is needed to implement effective infection control measures. Arbitrarily Primed PCR (AP-PCR) is a very useful method in rapid typing. AP-PCR is not necessary information about target DNA sequence because this is basically DNA amplification and could be useful in epidemiological typing by classified band pattern. In this study, MRSA were isolated and identified from ICU, Neu, IM and Ped environments and investigated molecular typing by AP-PCR. Ped, the MRSA pattern determines the la, IIa type, 1M is Ib type, Neu is IIa type and ICU determines the IIa, lIb types. All MRSA in this study were typeable by AP-PCR, which was easy to perform and reproduce with evidence of MRSA for purposes of nosocomial infection control.

• 연구논문집
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• 통권33호
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• pp.17-25
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• 2003

In this work, thermal design of a PCR chip for LOC is systematically conducted. From the numerical simulation of a PCR chip based on the finite volume method, how to control the average temperature of a PCR chip and the temperature difference between the denaturation zone and the annealing zone is presented. The average temperature is shown to be controlled by adjusting heat input and a cooler as well as a heater is shown to be necessary to obtain three individual temperature zones for polymerase chain reaction. To reduce the time required, a heat sink for the cooler is not included in the calculation domain for the PCR chip and heat sink design is conducted separately by using a compact modeling method, the porous medium approach.

• 한국동물생명공학회지
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• 제34권4호
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• pp.259-266
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• 2019

Emulsion polymerase chain reaction (PCR) is performed on compartmentalized DNA, allowing a large number of PCR reactions to be carried out in parallel. Emulsion PCR has unique advantages in DNA amplification. It can be applied in many molecular biological assays, especially those requiring highly sensitive and specific DNA amplification. This review discusses the principle of emulsion PCR and its applications in biotechnology. Related technologies are also discussed.

• Journal of Microbiology and Biotechnology
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• 제25권5호
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• pp.745-752
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• 2015

Tuberculosis (TB) is the most common mycobacterial infection in developing countries, requiring a rapid, accurate, and well-differentiated detection/diagnosis. For the rapid detection and discrimination of Mycobacterium tuberculosis complex (MTC) from non-tuberculous mycobacteria (NTM), a novel, simple, and primer-combined single-step multiplex PCR using three primer pairs (6110F-6110R, 1081F-1081R, and 23SF-23SR; annealing on each of IS6110, IS1081, and 23S rDNA targets), hereafter referred to as a triplex PCR, has been developed and evaluated. The expected product for IS6110 is 416 bp, for IS1081 is 300 bp, and for 23S rDNA is 206 bp by single PCR, which was used to verify the specificity of primers and the identity of MTC using DNA extracted from the M. tuberculosis H37Rv reference strain (ATCC, USA) and other mycobacteria other than tuberculosis (MOTT) templates. The triplex PCR assay showed 100% specificity and 96% sensitivity; the limit of detection for mycobacteria was ~100 fg; and it failed to amplify any target from DNA of MOTT (50 samples tested). Of 307 blinded clinical samples, overall 205 positive M. tuberculosis samples were detected by single PCR, 142 by conventional culture, and 90 by AFB smear methods. Remarkably, the triplex PCR could subsequently detect 55 positive M. tuberculosis from 165 culture-negative and 115 from 217 AFB smear-negative samples. The triplex PCR, targeting three regions in the M. tuberculosis genome, has proved to be an efficient tool for increasing positive detection/discrimination of this bacterium from clinical samples.