• 식물병연구
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• 제15권2호
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• pp.57-62
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• 2009

우리나라 벼에 발생하는 주요 바이러스 중 애멸구에 의하여 전염하는 벼줄무의잎마름병(RSV)과 벼검은줄오갈병(RBSDV)에 대한 간편한 유전자 진단법인 VCHT-PCR 방법을 개발하였다. 벼 잎의 경우 즙액 추출 완충액은 0.5% sodium sulfite를 첨가한 0.01 M 인산완충액(pH 7.0)을 기본 완충액으로 이용하고 애멸구를 진단할 경우에는 기본 완충액에 2% PVP을 첨가하였을 때 VC/RT-PCR 진단이 잘 되었다. VC/RT-PCR을 이용한 진단에 적합한 RSV와 RBSDV 프라이머를 선발하였고 이것을 이용하여 동시진단으로 경기도 김포, 평택, 시흥지역에서 채집한 애멸구의 RSV와 RBSDV의 보독충을 쉽고 경제적으로 진단 할 수 있었다. ELISA에 의한 진단결과와 비교할 때 세 지역을 합하여 RSV에 대한 평균 보독충률은 9.2%로 동일하였으나 보독충 중 일부가 ELISA와 VC/RT-PCR 두 방법에 의한 진단결과가 다르게 나온 것은 RSV의 혈청학적, 유전적 계통 존재 가능성을 제시하고 있다. 포장에서 채집한 애멸구의 VC/RT-PCR 진단효율은 RSV와 RBSDV를 동시에 진단하므로 써 RSV만 진단이 가능한 ELISA 결과 보다 3.2% 높았다.

• 한국식품위생안전성학회지
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• 제34권2호
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• pp.135-139
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• 2019

식품에 존재하는 병원균을 신속검출하기 위한 방법으로 LAMP와 real-time PCR 방법을 비교 평가 하였다. S. Typhimurium, L. monocytogenes, C. sakazakii의 3종에 대해 식품공전에서 권고하는 식품 종류를 선별하여 민감도를 분석하였다. S. Typhimurium에서는 11종의 식품(햄, 닭가슴살, 계란, 돼지고기, 소고기, 오리고기, 액상음료, 샐러드, 콘프레이크, 초콜릿, 사료)중 4종(햄, 돼지고기, 시리얼, 사료)에서 LAMP보다 real-time PCR에서 검출 민감도가 10배 이상 더 높았고, 6종(닭가슴살, 계란, 소고기, 오리고기, 음료, 샐러드)에서는 real-time PCR과 비슷한 수준을 그리고 초콜릿에서는 real-time PCR로는 검출되지 않았으며 LAMP로만 검출되는 결과가 나타났다. L. monocytogenes와 C. sakazakii에서는 9종 모두에서 LAMP보다 real-time PCR에서 검출 민감도가 더 높았다. 또한 L. monocytogenes에서 LAMP의 검출 민감도가 S. Typhimurium과 C. sakazakii 보다 10배 이상 낮았다. 3M MDS의 검출한계 향상을 위해 변형된 3M MDS의 민감도는 기존대비 10배 이상 증가되었다. 따라서 식품에 존재하는 병원균의 검출을 위해 식품의 구성성분에 따라 LAMP와 real-time PCR를 적절히 선택하는 것이 바람직할 것으로 생각되었다. 한편, 농축 방법을 이용해 LAMP방법의 민감도를 향상시킬 수 있음을 알 수 있었다.

• 대한수의학회지
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• 제36권1호
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• pp.119-129
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• 1996

The present study was conducted to rapidly detect Listeria monocytogenes in raw milk. Specificity and sensitivity of polymerase chain reaction(PCR) technique, and direct PCR were examinded in raw milk, also were compared the calssical culture methods with PCR technique. This method used a pair of primers based on a unique region in the 16S rRNA sequence of L nomocytogenes. In the PCR specificity tests, each of the 10 strains of L monocytogenes tested gave a single 70-bp band. But the other six Listera spp tested gave negative results. Results of the sensitivity tests showed that as few as 2 CFU of L monocytogenes in pure cultures could be detected with 16S rRNA-based primers, L-1 and L-2. In different PCR cycles, a PCR product was detected with $10^3$ cells of L monocytogenes from 25 cycles to 50 cycles and the concentration of PCR products was cycle-dependent. Raw milk samopes added L monocytogenes cells gave negative results. However, these samplers gave a single 70-bp band by pretreatment of pronase, and PCR products were detected with $10^1$ cells of L monocytogenes. To detemine the most sensitive culture protocol to use in conjunction with the PCR assay, raw milk samples were inoculated with L monocytogenes at concentrations ranging from 1 to $5.7{\times}10^4CFU/ml$. PCR assays from Listeria enrichment broth(LEB) containing raw milk samples added L monocytogene EGD could dtect 10 cells in pronase-pretreated samples without incubation, and 1 cell of L monocytogenes in both 12 hr and 24 hr incubation, respectively. Isolation raw of PCR assays was similar to that of classical culture methods, but required time for detection of L monocytogenes could remarkably be reduced compare to culture methods.

• 대한임상검사과학회지
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• 제36권1호
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• pp.33-37
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• 2004

In order to study the effect of temperature of denaturation, annealing and extension and cycles on amplification of DNA by PCR method, We isolated the hepatitis B virus DNA from hepatitis B patient blood and compared the density of DNA amplified by Reference PCR Program (denaturation at $94^{\circ}C$ for 30 sec., annealing at $60^{\circ}C$ for 1 min., extension at $72^{\circ}C$ for 1 min., holding at $72^{\circ}C$ for 5min., 30 cycles) that is usually used in laboratory to the density of DNA amplified by PCR program changed only the denaturation temperature or annealing temperature or extension temperature. We amplified about 341bp of hepatitis B virus DNA by Reference PCR Program from hepatitis patient blood, but the DNAs denatured at $72^{\circ}C$ or $60^{\circ}C$ were not detectable on photoradiography film. The DNA amplified at $37^{\circ}C$ of annealing temperature was not detectable, but the DNA annealed at $72^{\circ}C$ was detectable the lower density of DNA than the DNA amplified by Reference PCR Program. Each DNA amplified by PCR program changed only the extension temperature to $37^{\circ}C$ or $60^{\circ}C$ was almost same density as DNA amplified by Reference PCR Program. We compared the density of hepatitis B virus DNA amplified by Reference PCR Program for 30 cycles, 20 cycles, 10 cycles, and 5 cycles. The DNA cycled for 20 cycles was not amplified well as cycled for 30 cycles, but the DNA was detectable on the photoradiography film. The DNAs amplified for 10 cycles or 5 cycles were not detectable on photoradiorgaphy film. The concentration of hepatitis B virus DNA amplified in Reference PCR condition for 30 cycles, 20 cycles, 10 cycles, and 5 cycles were $72{\mu}g/m{\ell}$, $83{\times}10^{-3}{\mu}g/m{\ell}$, $27{\times}10^{-6}{\mu}g/m{\ell}$, and nondetectable, respectively.

• 산업기술연구
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• 제28권A호
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• pp.141-147
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• 2008

Several contaminated bacteria such as Lactobacillus brevis and Pediococcus damnosus in beer production cause beer spoilage by producing off flavours and turbidity. Detection of these organisms is complicated by the strict anaerobic conditions and lengthy incubation times required for their cultivation, consequently there is a need for more rapid detection methods. Recently, two contaminated strains were isolated from vessel of beer production and identified as Lactobacillus species by API kit identificaton as well as 16S-23S ITS sequencing analyses. Two isolated strains were named as Lactobacillus sp. HLA1 and Lactobacillus HLB2, respectively. A polymerase chain reaction (PCR) method was developed for the rapid and specific detection of Lactobacillus sp.. Two sets of primer pairs (HLA1-F/HLA1-R and HLB2-F/HLB2-R) were designed for the amplification of a 1576 base pair (bp) fragment of the HLA1 16S-23S rRNA gene and 1888 bp fragement of the HLB2 16S-23S rRNA. Amplified PCR products were highly specific to detect corresponding bacteria when other contaminated strains were used as PCR templates. However, detection of both strains were limited when $100{\mu}{\ell}$ of cultured samples were mixed with $100m{\ell}$ of beer sample in arbitrary manner. The sensitivity of the assay still needs to be improved for direct detection of the small amounts of bacteria present in beer.

• 한국미생물·생명공학회지
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• 제51권1호
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• pp.99-108
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• 2023

대기 입자상물질(particulate matter, PM) 시료의 곰팡이 메타게놈 분석을 위해 DNA 추출 및 유전자 증폭 시 여러 문제가 발생한다. 본 연구에서는 PM 시료로부터 DNA를 추출하는 방법과 polymerase chain reaction (PCR)을 위한 프라이머 및 온도 조건의 최적화를 위하여 다양한 조건으로 실험하였다. 여러 조건에서 DNA 추출 여부를 비교 평가한 결과, bufffer와 proteinase K를 이용하여 20분 동안 화학적 세포 용해 처리와 bead beating 처리를 한 후 상용 DNA 추출 kit를 사용하면 DNA를 효율적으로 추출할 수 있었다. PCR 조건을 최적화하기 위해 ITS2 유전자 영역을 증폭할 수 있는 10개 조합의 프라이머를 이용하여 PCR을 수행한 결과, ITS3tagmix3/ITS4 조합의 프라이머로 annealing 온도 58℃로 하였을 때 증폭된 PCR 산물의 농도가 상대적으로 높았다. 이 조건에서도 PCR 산물의 농도가 낮은 경우에는 1차 PCR 산물을 주형 DNA로 사용하여 nested PCR을 수행하면 만족스러운 농도로 ITS2 유전자를 증폭할 수 있었다. 본 연구에서 도출한 조건으로 서울 대기 PM2.5를 포집한 필터 시료 15종을 대상으로 DNA 추출과 PCR을 수행한 결과 성공적으로 ITS2 유전자 증폭이 가능하였다. 본 연구에서 최적화한 방법은 대기 PM 시료의 곰팡이 메타게놈을 분석하고 해석하는 연구에 활용 가능하다.

• 한국동물위생학회지
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• 제34권4호
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• pp.321-331
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• 2011

Mycobacterium bovis, a member of the M. tuberculosis complex (MTC), is the causative agent of bovine tuberculosis. Detection of M. bovis and M. tuberculosis using conventional culture- and biochemical-based assays is time-consuming. Therefore, a simple and sensitive molecular assay for rapid detection would be of great help in specific situations such as faster diagnosis of bovine tuberculosis (bTB) infection in the abattoirs. We developed a novel multiplex real-time PCR assay which was applied directly to biological samples with evidence of bTB and it was allowed to differentiate between M. bovis and M. tuberculosis. The primers and TaqMan probes were designed to target the IS1081 gene, the multi-copy insertion element in the MTC and the 12.7-kb fragment which presents in M. tuberculosis, not in the M. bovis genome. The assay was optimized and validated by testing 10 species of mycobacteria including M. bovis and M. tuberculosis, and 10 other bacterial species such as Escherichia coli, and cattle lymph nodes (n=113). The tests identified 96.4% (27/28) as M. bovis from the MTC-positive bTB samples using conventional PCR for specific insertion elements IS1081. And MTC-negative bTB samples (n=85) were tested using conventional PCR and the real-time PCR. When comparative analyses were conducted on all bovine samples, using conventional PCR as the gold standard, the relative accuracy of real-time PCR was 99.1%, the relative specificity was 100%, and the agreement quotient (kappa) was 0.976. The detection limits of the real-time PCR assays for M. bovis and M. tuberculosis genomic DNA were 10 fg and 0.1 pg per PCR reaction, respectively. Consequently, this multiplex real-time PCR assay is a useful diagnotic tool for the identification of MTC and differentiation of M. bovis and M. tuberculosis, as well as the epidemiologic surveillance of animals slaughtered in abattoir.

• Journal of Plant Biotechnology
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• 제5권2호
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• pp.83-86
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• 2003

A reverse transcription polymerase chain reaction (RT-PCR) protocol was developed using two specific 22-mer primers located in coat protein gene of SPFMV. A 411 bp PCR-product was detected in virus infected plants as well as tissue culture raised sweet potato but not in healthy plants. For optimization of RT-PCR protocol, the optimum crude nucleic acid concentration, annealing temperature, primer concentration and numbers of PCR-cycle for maximum sensitivity and specificity were determined. The optimum condition for RT-PCR was as follows: RT-PCR reaction mixture was one-step mixture, containing 50 pmol of primer, 30 units of reverse transcriptase, 5 units of RNasin, and the crude nucleic acid extracts (200 ng). In RT-PCR, cDNA was synthesized at $42^{\circ}C$ for 45 min before a quick incubation on ice after pre-denaturation at $95^{\circ}C$ for 5 min. The PCR reaction was carried out for 40 cycles at $96^{\circ}C$ for 30 see, $63^{\circ}C$ for 30 sec, $72^{\circ}C$ for 1 min, and finally at $72^{\circ}C$ for 10 min. The viral origin of the amplified product was confirmed by sequencing, with the sequence obtained having $95-98\%$ homology with published sequence data for SPFMV. The benefits of this RT-PCR based detection of SPFMV would be simple, rapid and specific.

• Mycobiology
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• 제38권1호
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• pp.33-38
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• 2010

We have successfully applied the nested PCR to detect Cylindrocarpon destructans, a major pathogen causing root rot disease from ginseng seedlings in our former study. The PCR assay, in this study, was used to detect the pathogen from soils. The nested PCR using internal transcribed spacer (ITS) 1, 4 primer set and Dest 1, 4 primer set maintained the specificity in soils containing various microorganisms. For a soil DNA extraction method targeting chlamydospores, when several cell wall disrupting methods were tested, the combination of lyophilization and grinding with glass beads, which broke almost all the chlamydospores, was the strongest. The DNA extraction method which was completed based on the above was simple and time-saving because of exclusion of unnecessary stages, and efficient to apply in soils. As three ginseng fields whose histories were known were analyzed, the PCR assay resulted as our expectation derived from the field information. The direct PCR method will be utilized as a reliable and rapid tool for detecting and monitoring C. destructans in ginseng fields.

• The Plant Pathology Journal
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• 제18권1호
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• pp.12-17
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• 2002

For the molecular detection of Sweet potaio feathery mottle virus (SPFMV) from diseased sweet potato plants, reverse transcription and polymerase chain reaction (RT-PCR) was performed with the use of a set of virus-specific primers to amplify an 816 bp product. The viral coat protein gene was selected for the design of the primers. No PCR product was amplified when Turnip mosaic virus, Potato vims Y or Cucumber mosaic virus were used as template in RT-PCR with the SPFMV-specific primers. The lowest concentration of template viral RNA required for detection was 10 fg. The vim was rapidly detected from total nucleic acids of leaves and roots from the virus-infected sweet potato plants as well as from the purified viral RNA by the RT-PCR. Twenty-four sweet potato samples were selected and analyzed by RT-PCR and restriction fragment length polymorphism (RFLP). RFLP analysis of the PCR products showed three restriction patterns, which resulted in some point mutations suggesting the existence of quasi-species for the vims in the infected sweet potato plants.