• Journal of Microbiology and Biotechnology
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• 제28권2호
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• pp.210-217
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• 2018

A one-step multiplex reverse transcription PCR (RT-PCR) method comprising six primer sets (for the detection of norovirus GI and GII, hepatitis A virus, rotavirus, and astrovirus) was developed to simultaneously detect four kinds of pathogenic viruses. The size of the PCR products for norovirus GI and GII, hepatitis A virus (VP3/VP1 and P2A regions), rotavirus, and astrovirus were 330, 164, 244, 198, 629, and 449 bp, respectively. The RT-PCR with the six primer sets showed specificity for the pathogenic viruses. The detection limit of the developed multiplex RT-PCR, as evaluated using serially diluted viral RNAs, was comparable to that of one-step single RT-PCR. Moreover, this multiplex RT-PCR was evaluated using food samples such as water, oysters, lettuce, and vegetable product. These food samples were artificially spiked with the four kinds of viruses in diverse combinations, and the spiked viruses in all food samples were detected successfully.

• Journal of Microbiology
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• 제34권3호
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• pp.229-235
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• 1996

Microgram quantities of DNA per gram soil were recovered with SDS- based and freeze-and thaw procedures. The average DNA fragment size was > 23 Kb. This method generated minimal shearing of extracted DNA. However, the DNA extracts still contained considerable amounts of humic impurities sufficient to inhibit PCR. Several approaches were used to reduce the interferences with the PCR (use of CTAF in extraction step, Elutip-d column purification, addition of BSA to PCR buffer) to accomplish PCR with DNA extract as a template. Most of the DNA extracts were not digested completely by restriction endonuclease, and CTAB-TREATED ane Elutip-d column purified DNA extracts were partially digested. Regarding as restriction enzyme digestion, all PCRs failed to amplify 16S rRNA gene fragments in the DNA extracts. In the case of DNA extracts only where BSA was added to PCR buffer, PCR was successfully conducted whether the DNA extracts were treated with CTAB or purified with columns. However, these two treatments were indispensable for humic impurity-rich DNA extracts to generate the PCR-compatible DNA samples. Direct extraction of DNA, coupled with these procedures to remove and relieve interferences by humic impurities and followed by the PCR, can be rapid and simple method for molecular microbiological study on soil microorganisms.

• 한국축산식품학회지
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• 제41권1호
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• pp.85-94
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• 2021

A pig-specific real-time PCR assay based on the mitochondrial ND5 gene was developed to detect porcine material in food and other products. To optimize the performance of assay, seven commercial TaqMan master mixes and two real-time PCR platforms (Applied Biosystems StepOnePlus and Bio-rad CFX Connect) were used to evaluate the limit of detection (LOD) as well as the PCR efficiency and specificity. The LODs and PCR efficiencies for the seven master mixes on two platforms were 0.5-5 pg/reaction and 84.96%-108.80%, respectively. Additionally, non-specific amplifications of DNA from other animal samples (human, dog, cow, and chicken) were observed for four master mixes. These results imply that the sensitivity and specificity of a real-time PCR assay may vary depending on master mix and platform used. The best combination of master mix and real-time PCR platform can accurately detect 0.5 pg porcine DNA, with a PCR efficiency of 100.49%.

• 한국산림과학회지
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• 제100권4호
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• pp.623-629
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• 2011

파이토플라스마에 감염된 뽕나무의 각 부위를 nested-PCR법과 경쟁 PCR법을 이용하여 파이토플라스마의 검출 범위 및 밀도 변화를 조사하였다. 파이토플라스마에 부분 감염된 뽕나무를 총 5부위(A. 빗자루병이나 오갈병 증상을 보인 잎의 엽병, B. 병징을 보인 잎이 있는 가지의 아래쪽 건전해 보이는 잎의 엽병, C. 병징을 보인 잎의 가지 부위, D. 병징을 보이지 않은 가지 쪽의 영병이나 가지, E. 잔뿌리)로 구분하였다. AS-1/AS-2 프라이머를 이용한 nested-PCR 결과, 파이토플라스마는 모든 시료에서 검출되었으며, 파이토플라스마의 검출범위는 P1/P7 프라이머를 이용한 direct-PCR 산물에서는 희석액이 $10^4$배까지 검출되었고, AS-1/AS-2 프라이머를 이용하여 nested-PCR를 수행한 결과, PCR 산물을 $10^{13}$배 희석한 시료까지 파이토플라스마가 검출되었다. 경쟁 PCR 결과, 뽕나무 파이토플라스마의 밀도는 $7.94{\times}10^{18}-10^{12}copies/{\mu}L$의 범위내에 존재하였으며, 년 중 파이토플라스마가 모든 시료에서 존재하였다. 초기생장시기에는 "B"부위와 "C"부위에서 파이토플라스마 밀도가 높게 나타났으나 "A"부위와 "D"부위에서는 이보다 낮게 나타났다. 휴면기에는 "C"부위와 "E"부위가 "D"부위보다 밀도가 높았다. 모든 시료 중 "C"부위와 "A"부위에서 년 중 파이토플라스마 밀도가 안전적으로 존재하였다. 본 연구 결과, nested-PCR 법과 경쟁 PCR법은 식물체내의 파이토플라스마의 정확한 검출과 밀도변화를 알아볼 수 있는 유용한 방법이다.

• KSBB Journal
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• 제29권5호
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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.

• BMB Reports
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• 제40권3호
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• pp.444-447
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• 2007

Polymerase chain reaction (PCR) is a powerful technique in molecular biology and is widely used in various fields. By amplifying DNA fragments, PCR has facilitated gene cloning procedures, as well as molecular genotyping. However, the extraction of DNA from samples often acts as a limiting step of these reactions. In particular, the extraction of PCR-compatible genomic DNA from higher plants requires complicated processes and tedious work because plant cells have rigid cell walls and contain various endogenous PCR inhibitors, including polyphenolic compounds. We recently developed a novel solution, referred to as AnyDirect, which can amplify target DNA fragments directly from whole blood without the need for DNA extraction. Here, we developed a simple lysis system that could produce an appropriate template for direct PCR with AnyDirect PCR buffer, making possible the direct amplification of DNA fragments from plant leaves. Thus, our experimental procedure provides a simple, convenient, non-hazardous, inexpensive, and rapid process for the amplification of DNA from plant tissue.

• 분석과학
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• 제32권4호
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• pp.155-162
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• 2019

Analysis techniques using DNA profiling are widely used in various fields including forensic science and new technologies such as the Direct PCR amplification method are being developed continuously in order to acquire the DNA profiles efficiently. However, it has a limits such as non-specific amplification according to the quality of crime scene evidence samples. Especially, split peaks caused by excessive DNA samples are one of the important factors that could cause the debate to allow researchers to interpret the DNA profile results. In this study, we confirmed the occurrence rate of split peaks in each STR (short tandem repeats) locus of the $GlobalFiler^{TM}$ kit and investigated the possibility of improving the split peaks using several PCR additives such as DMSO (dimethylsulfoxide), $MgCl_2$, Betaine and Tween-20. As a result, we could make three groups according to the occurrence rate of split peaks in Direct PCR and it was confirmed that the ratio of split peaks could be reduced by DMSO (87.4 %), $MgCl_2$ (84.5 %) and Betaine (86.1 %), respectively. These results indicate that PCR additives such as DMSO, $MgCl_2$ and Betaine can be improve the split peaks in Direct PCR and thereby facilitate subsequently a successful DNA profile results.

• 미생물학회지
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• 제43권1호
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• pp.23-30
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• 2007

조류 인플루엔자바이러스(AIV) H5N1 아형을 Real-time PCR법을 이용하여 가장 빠르게 진단할 수 있는 방법을 개발하였다. 검색 대상의 염기서열은 AIV H5N1 아형의 hemagglutinin 유전자 중 가장 상동성이 높은 387 bp의 부위를 선택하였고, 실험의 안전을 위하여 인공합섬의 방법으로 제작하였다. Microchip을 기반으로 한Real-time PCR법을 사용하였으며, 총PCR 반응액의 양을 $1{\mu}l$로, PCR 과정 중 각 단계, 즉 해리, 접합, 신장의 시간을 각1초, 1초, 3초로 하여 총 실험시간을 단축하였다. 진단을 위한 실험과정에서 PCR 및 융점분식에 소요된 최단 시간은 12분28초였으며, 민감도측정에서 최소2.4개의 hemaggutinin 유전자를 기질로 하여 목적한 특이 189 bp의 PCR 산물을 증폭할 수 있었기에, 본 연구에서는 이런 초고속 PCR 실험방식을 Quick Real-time PCR이라 명명하였다. 이 결과들은 가금류 및 사람에게 전파된 AIV H5N1아형의 진단에 적용될 수 있을 뿐 아니라, PCR이 사용되는 다른 신속검색법에도 널리 적용 될 수 있을 것으로 기대한다.

• Journal of Microbiology
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• 제41권4호
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• pp.320-326
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• 2003

In order to identify Vibrio vulnificus in the Yellow Sea near Gunsan, Korea during the early and late summers, the efficiency of the real-time quantitative TaqMan PCR was compared to the efficiency of the conventional PCR and Biolog identification system^TM. Primers and a probe were designed from the hemolysin/cytolysin gene sequence of V. vulnificus strains. The number of positive detections by real-time quantitative TaqMan PCR, conventional PCR, and the Biolog identification system from seawater were 53 (36.8%), 36 (25%), and 10 strains (6.9%), respectively, among 144 samples collected from Yellow Sea near Gunsan, Korea. Thus, the detection method of the real-time quantitative TaqMan PCR assay was more effective in terms of accuracy than that of the conventional PCR and Biolog system. Therefore, our results showed that the real-time TaqMan probe and the primer set developed in this study can be applied successfully as a rapid screening tool for the detection of V. vulnificus.

• 미생물학회지
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• 제38권3호
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• pp.198-204
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• 2002

폴리오 바이러스는 전형적인 장관계 바이러스로 마비, 무균성 수막염, 뇌염 등을 유발한다. 폴리오 바이러스는 분변-구강 경로를 통해 전파되며, 오염된 물을 음용수로 사용할 시 공중 보건에 문제가 될 수 있으므로 먹는 물에서 폴리오 바이러스를 검출하는 것은 중요하다. 감염성이 있는 바이 러스와 불활성화(열처리와 자외선 처리)시킨 바이러스를 세포배양법, 역전사 중합효소 연쇄반응법(reverse transcription-polymerase chain reaction: RT-PCR)그리고 세포배양-중합효소 연쇄반응 통합법(integrated cell culture-PCR: ICC-PCR)으로 검출 실험을 했다. 감염성이 있는 폴리오 바이러스는 세 가지 방법으로 모두 검출이 되었으며, 이 중에서 바이러스를 검출하는데 ICC-PCR 방법이 가장 민감했다. 세포배양법은 적은 수의 바이러스를 검출하는데 약 2주의 긴 시간이 걸렸다. 열처리나 자외선 처리로 불활성화된 바이 러스는 세포배양과 ICC-PCR방법으로는 검출이 되지 않았다. 자외선 처리한 바이러스는 RT-PCR 방법으로 검출되지 않았으나 열처리한 바이러스는 검출되었다. RT-PCR 방법은 감염성 바이러스뿐 아니라 불활성화된 바이러스도 검출할 수 있으므로 감염성이 있는지 없는지를 구분할 수 없는 단점이 있다. 이와 같은 결과는 감염성 있는 바이러스를 가장 민감하고 효과적으로 검출하는 방법이 ICC-PCR 방법이라는 것을 제시하여 준다.