• Journal of Microbiology and Biotechnology
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• 제16권2호
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• pp.205-211
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• 2006

A quantitative analytical method to detect new lines of genetically modified (GM) maize, NK603 and TC1507, has been developed by using a real-time polymerase chain reaction (PCR). To detect these GM lines, two specific primer pairs and probes were designed. A plasmid as a reference molecule was constructed from an endogenous DNA sequence of maize, a universal sequence of a cauliflower mosaic virus (CaMV) 35S promoter used in most GMOs, and each DNA sequence specific to the NK603 and TC1507 lines. For the validation of this method, the test samples of 0, 0.1, 0.5, 1.0, 3.0, 5.0, and 10.0% each of the NK603 and TC1507 GM maize were quantitated. At the 3.0% level, the biases (mean vs. true value) for the NK603 and TC1507 lines were 3.3% and 15.7%, respectively, and their relative standard deviations were 7.2% and 5.5%, respectively. These results indicate that the PCR method developed in this study can be used to quantitatively detect the NK603 and TC1507 lines of GM maize.

• Journal of Microbiology and Biotechnology
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• 제22권10호
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• pp.1350-1358
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• 2012

Viral pathogens, alongside other pathogens, have major effects on crustacean aquaculture. Hepatopancreatic parvovirus (HPV) is an emerging virus in the shrimp industry and has been detected in shrimp farms worldwide. The HPV genome has greater diversity than other shrimp viruses owing to its wide host range and geographical distribution. Therefore, developing diagnostic tools is essential to detect even small copy numbers from the target region of native HPV isolates. We have developed two easy to use quantitative real-time PCR kits, called Green Star and Dual Star, which contain all of the necessary components for real-time PCR, including HPV primers, using the primers obtained from the sequences of HPV isolates from Korea, and analyzed their specificity, efficiency, and reproducibility. These two kits could detect from 1 to $1{\times}10^9$ copies of cloned HPV DNA. The minimum detection limits obtained from HPV-infected shrimp were $7.74{\times}10^1$ and $9.06{\times}10^1$ copies in the Green Star and Dual Star assay kits, respectively. These kits can be used for rapid, sensitive, and efficient screening for HPV isolates from Korea before the introduction of postlarval stages into culture ponds, thereby decreasing the incidence of early development of the disease.

• International Journal of Oral Biology
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• 제46권1호
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• pp.1-6
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• 2021

Since the outbreak of coronavirus disease 2019 (COVID-2019), the infection has spread worldwide due to the highly contagious nature of severe acute syndrome coronavirus (SARS-CoV-2). To manage SARS-CoV-2, the development of diagnostic assays that can quickly and accurately identify the disease in patients is necessary. Currently, nucleic acid-based testing and serology-based testing are two widely used approaches. Of these, nucleic acid-based testing with quantitative reverse transcription-PCR (RT-qPCR) using nasopharyngeal (NP) and/or oropharyngeal (OP) swabs is considered to be the gold standard. Recently, the use of saliva samples has been considered as an alternative method of sample collection. Compared to the NP and OP swab methods, saliva specimens have several advantages. Saliva specimens are easier to collect. Self-collection of saliva specimens can reduce the risk of infection to healthcare providers and reduce sample collection time and cost. Until recently, the sensitivity and accuracy of the data obtained using saliva specimens for SARS-CoV-2 detection was controversial. However, recent clinical research has found that sensitive and reliable data can be obtained from saliva specimens using RT-qPCR, with approximately 81% to 95% correspondence with the data obtained from NP and OP swabs. These data suggest that self-collected saliva is an alternative option for the diagnosis of COVID-19.

• Asian-Australasian Journal of Animal Sciences
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• 제26권12호
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• pp.1665-1671
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• 2013

Real-time quantitative PCR (qRT-PCR) is one of the important methods for investigating the changes in mRNA expression levels in cells and tissues. Selection of the proper reference genes is very important when calibrating the results of real-time quantitative PCR. Studies on the selection of reference genes in goat tissues are limited, despite the economic importance of their meat and dairy products. We used real-time quantitative PCR to detect the expression levels of eight reference gene candidates (18S, TBP, HMBS, YWHAZ, ACTB, HPRT1, GAPDH and EEF1A2) in ten tissues types sourced from Boer goats. The optimal reference gene combination was selected according to the results determined by geNorm, NormFinder and Bestkeeper software packages. The analyses showed that tissue is an important variability factor in genes expression stability. When all tissues were considered, 18S, TBP and HMBS is the optimal reference combination for calibrating quantitative PCR analysis of gene expression from goat tissues. Dividing data set by tissues, ACTB was the most stable in stomach, small intestine and ovary, 18S in heart and spleen, HMBS in uterus and lung, TBP in liver, HPRT1 in kidney and GAPDH in muscle. Overall, this study provided valuable information about the goat reference genes that can be used in order to perform a proper normalisation when relative quantification by qRT-PCR studies is undertaken.

• Clinical and Experimental Reproductive Medicine
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• 제34권4호
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• pp.275-283
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• 2007

목 적: 본 연구에서는 생리혈에 존재하는 탈락된 자궁내막조직에서의 자궁내막증 관련 유전자들의 발현 양상과 자궁내막증 병태생리와의 관련성을 살펴보고자 하였다. 연구방법: 자궁내막증으로 확진된 환자 (n=16)와 정상 대조군 (n=26)에서 생리주기 2$\sim$3일째 Wallace catheter로 채취한 생리혈로부터 탈락된 자궁내막조직을 분리하였다. 기존의 연구들에서 보고된 12종류의 자궁내막증 관련 유전자들의 mRNA 발현 양상을 semi-quantitative RT-PCR 방법으로 비교, 분석하였다. 결 과: 생리혈에서 분리한 탈락된 자궁내막조직은 조직학적 관찰을 통해 자궁내막조직임을 확인하였다. 총 12가지 종류의 자궁내막증 관련 유전자에 대한 RT-PCR 분석에서 telomerase, c-kit, aromatase등의 mRNA 발현이 관찰되지 않았다. 세포사멸 (apoptosis)과 관련성이 있는 fas, fas ligand, bcl-2, bax 유전자와 stem cell factor, ER-$\alpha$/$\beta$, endometriosis protein-I, secretory leukocyte protease inhibitor 등의 mRNA 발현 양상은 자궁내막증으로 확진된 환자군과 대조군에서 통계적으로 유의한 차이를 나타내지 않았다. 결 론: 결론적으로 자궁내막증과 관련된 다양한 유전자들의 발현 양상을 생리혈에 존재하는 탈락된 자궁내막조직에서 분석하였지만 의미성이 있는 유전자를 동정하지는 못하였다. 이는 자궁내막조직의 생리학적 특징인 생리주기에 따른 유전자 발현의 역동적인 변화와 관련이 있을 것으로 생각된다.

• Journal of Microbiology and Biotechnology
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• 제24권8호
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• pp.1026-1033
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• 2014

The fecal microbiotas were investigated in 13 healthy Thai subjects using polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE). Among the 186 DNA bands detected on the polyacrylamide gel, 37 bands were identified as representing 11 species: Bacteroides thetaiotaomicron, Bacteroides ovatus, Bacteroides uniformis, Bacteroides vulgatus, Clostridium colicanis, Eubacterium eligenes, E. rectale, Faecalibacterium prausnitzii, Megamonas funiformis, Prevotella copri, and Roseburia intestinalis, belonging mainly to the groups of Bacteroides, Prevotella, Clostridium, and F. prausnitzii. A dendrogram of the PCR-DGGE divided the subjects; vegetarians and non-vegetarians. The fecal microbiotas were also analyzed using a quantitative real-time PCR focused on Bacteroides, Bifidobacterium, Enterobacteriaceae, Clostrium coccoides-Eubacterium rectale, C. leptum, Lactobacillus, and Prevotella. The nonvegetarian and vegetarian subjects were found to have significant differences in the high abundance of the Bacteroides and Prevotella genera, respectively. No significant differences were found in the counts of Bifidabacterium, Enterobacteriaceae, C. coccoides-E. rectale group, C. leptum group, and Lactobacillus. Therefore, these findings on the microbiota of healthy Thais consuming different diets could provide helpful data for predicting the health of South East Asians with similar diets.

• 대한의생명과학회지
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• 제25권4호
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• pp.407-416
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• 2019

Recent years have seen an increase in the incidence of candidiasis caused by non-albicans Candida (NAC) species. In fact, C. glabrata is now second only to C. albicans as the most common cause of invasive candidiasis. Therefore, the rapid genotyping specifically for C. glabrata is required for early diagnosis and treatment of candidiasis. A number of genotyping assays have been developed to differentiate C. glabrata sequence types (STs), but they have several limitations. In the previous study, multi-locus sequence typing (MLST) has performed with a total of 101 C. glabrata clinical isolates to analyze the prevalent C. glabrata STs in Korea. A total of 11 different C. glabrata STs were identified and, among them, ST-138 was the most commonly classified. Thus, a novel probe-based quantitative PCR (qPCR) assay was developed and evaluated for rapid and accurate identification of the predominant C. glabrata ST-138 in Korea. Two primer pairs and hybridization probe sets were designed for the amplification of internal transcribed spacer 1 (ITS1) region and TRP1 gene. Analytical sensitivity of the probe-based qPCR assay was 100 ng to 10 pg and 100 ng to 100 pg (per 1 μL), which target ITS1 region and TRP1 gene, respectively. This assay did not react with any other Candida species and bacteria except C. glabrata. Of the 101 clinical isolates, 99 cases (98%) were concordant with MLST results. This novel probe-based qPCR assay proved to be rapid, sensitive, highly specific, reproducible, and cost-effective than other genotyping assay for C. glabrata ST-138 identification.

• 한국육종학회지
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• 제43권5호
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• pp.448-456
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• 2011

적색 과육 '홍양' 품종에서 차등발현하는 유전자를 찾기 위하여 mirror orientation selection (MOS)과 결합된 suppression subtractive hybridization (SSH) 실험을 수행하였다. 그 결과, 288개의 cDNA clone을 확보하였으며, colony PCR을 통해 192개의 positive clone을 선발하였고, 이들을 sequencing하였다. NCBI/Genbank 데이터베이스의 BLAST 검색를 이용하여 염기서열을 분석한 결과, 30개의 clone에서 기존에 알려진 유전자기능과의 유사성을 확인할 수 있었으며, 10개의 clone이 특이유전자였다. 그 중 3개의 clone(AcF21, AcF42, AcF106)은 과실 후숙과 관련된 ACC-oxidase와 상동성이 있었다. SSH의 결과를 통해 얻어진 이 유전자들의 차등발현양상을 확인하기 위하여 reverse transcription PCR(RT-PCR)과 quantitative real-time PCR(qReal-time PCR) 분석을 실시하였다. qReal-time PCR분석과 RT-PCR분석에서 모두 동일한 결과를 확인할 수 있었으며, 3개 clone 모두 '홍양'에서의 유전자발현수준이 '헤이워드'보다 더 높았다. AcF21은 다른 유전자들보다 가장 높은 발현수준을 나타내었는데, 만개 후 120일과 160일 모두 '홍양'에서의 발현수준이 높았다.

• 공업화학
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• 제33권3호
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• pp.235-241
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• 2022

유엔이 발표한 세계 물개발 보고서는 2030년까지 식수가 현재보다 40% 감소할 것으로 전망하고 있다. 이는 물의 양이 감소하는 것이 아니라, 환경오염으로 인해 상수원이 오염되는 것을 말한다. 미생물이 수질에 깊은 연관이 있기 때문에 미생물의 분석은 수질관리에 매우 중요하다. 현재 미생물 분석에 사용되는 방법은 배양 후 현미경을 통한 모양과 형태를 분석하는 것이 가장 일반적이나, 유전자분석 기술이 발달함에 따라 현미경을 통한 미생물 분석 방식에 qPCR(quantitative polymerase chain reaction) 적용이 가능해졌고 활용방법 등이 연구되었다. 그 중에는 역전사 단계를 추가하여 RNA 분석에 용이성을 부여한 RT-qPCR법과 미생물 배양분석에 접목시켜 검사시간을 단축시키는 ICC-qPCR, 자연에서 채취한 샘플의 위양성율을 감소시키는 데 용이한 viability qPCR, 다중분석에 용이한 multiplex qPCR, 소량의 샘플만으로 분석이 가능한 microfluidic qPCR법 등이 있다. 본 논문에서는 이처럼 qPCR 방법이 미생물 분석에 적용되는 사례와 방식의 원리, 그리고 발전 방향에 대해 소개하고자 한다.

• Journal of Microbiology and Biotechnology
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• 제21권12호
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• pp.1280-1286
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• 2011

A quantitative, real-time PCR method was developed to enumerate Lactobacillus plantarum IWBT B 188 during the malolactic fermentation (MLF) in Grauburgunder wine. The qRT-PCR was strain-specific, as it was based on primers targeting a plasmid DNA sequence, or it was L. plantarum-specific, as it targeted a chromosomally located plantaricin gene sequence. Two 50 l wine fermentations were prepared. One was inoculated with 15 g/hl Saccharomyces cerevisiae, followed by L. plantarum IWBT B 188 at $3.6{\times}10^6$ CFU/ml, whereas the other was not inoculated (control). Viable cell counts were performed for up to 25 days on MRS agar, and the same cells were enumerated by qRT-PCR with both the plasmid or chromosomally encoded gene primers. The L. plantarum strain survived under the harsh conditions in the wine fermentation at levels above $10^5$/ml for approx. 10 days, after which cell numbers decreased to levels of $10^3$ CFU/ml at day 25, and to below the detection limit after day 25. In the control, no lactic acid bacteria could be detected throughout the fermentation, with the exception of two sampling points where ca. $1{\times}10^2$ CFU/ml was detected. The minimum detection level for quantitative PCR in this study was $1{\times}10^2$ to $1{\times}10^3$ CFU/ml. The qRT-PCR results determined generally overestimated the plate count results by about 1 log unit, probably as a result of the presence of DNA from dead cells. Overall, qRT-PCR appeared to be well suited for specifically enumerating Lactobacillus plantarum starter cultures in the MLF in wine.