• 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).

• 한국토양비료학회지
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• 제37권4호
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• pp.259-265
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• 2004

사과의 영양진단에서 사과잎 분석을 신속히 하기 위한 방법을 모색하기 위해 생잎과 건조잎을 이용해 근적의 스펙트럼을 측정하고 이를 질소 함량과의 최적의 상관관계를 도출하기 위해 부분소자승(PLS)과 주성분회귀(PCR)과 같은 다변량 분석법을 이용하여 비파괴 검량식을 작성하였다. 또한 검량식 작성에서 비파괴 측정 정확도를 향상시키기 위하여 smoothing, mean normalization, multiplicative scatter correction (MSC). derivative 등의 다양한 데이터 전처리 조작을 수행하여 정확도 향상 가능성을 조사하였다. 사과 건조잎의 비파괴 측정 가능성을 조사한 결과 PLS-1 모델에서 Norris first derivate하였을 태 RMSEP가 $0.6999g\;kg^{-1}$ 로 가장 좋았으며, 생잎은 Savitzky-Golay first derivate하였을 때에 RMSEP 가 $1.202g\;kg^{-1}$으로 가장 좋았다. 건조잎의 PCR 모델은 mean normalization 처리 후 Savitzky-Golay first derivative하였을 때가 RMSEP 가 $0.553g\;kg^{-1}$, 이었으며 생잎에서도 RMSEP는 $1.047g\;kg^{-1}$로 나타났다. 이와 같은 견과로서 사과의 생잎과 건조잎의 분석이 근적외분석기술에 의해 가능할 것으로 판단된다.

• Applied Biological Chemistry
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• 제49권3호
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• pp.192-195
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• 2006

국내에서 개발된 비타민 E 강화 유전자변형 들깨의 정성 PCR 분석법의 개발을 위해 들깨의 내재 유전자로써 KAS-I (Beta-ketoacyl-ACP synthase I)를 선별하였고, 이러한 내재유전자를 특이적으로 증폭시킬 수 있는Primer(Pfru3-F/R)쌍을 이용한 PCR에서 95 bp의 PCR증폭 산물을 얻었으며, 들깨를 포함한 16개 작물에 대해 PCR을 수행한 결과에서 들깨만이 특이적으로 증폭되는 것을 확인하였다. 또한, 비타민 E 강화 유전자변형 들깨에 삽입된 TMT(${\gamma}$-tocopherol methyltransferase) 유전자와 OCS(Octopine synthase) terminator 연결 부위를 증폭시켜 148 bp의 PCR 산물을 얻을 수 있는 primer(TMTO-F/R)를 제작하였으며, 이러한 두 쌍의 primer를 이용하여 국내 개발된 비타민 E 강화 유전자변형 들깨의 PCR 정성 분석법을 확립하였다.

• The Plant Pathology Journal
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• 제17권6호
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• pp.329-335
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• 2001

Yellowing disease of palms caused by phytoplasma is spreading in the Arabian Gulf region. Surveys were conducted to determine the occurrence of the disease. Electron and fluorescence microscopy, and polymerase chain reaction (PCR) techniques were used to detect the phytoplasma associated with the yellowing disease of ornamental palm Washingtonia sp. grown in Kuwait. An accumulation of phytoplasmal DNA was observed by fluorescence microscopy in phloem tissues of diseased palms. Electron microscopy showed that phytoplasma cells were primarily confined to the phloemsieve elements of tissue samples collected from infected mature palms in the field. The pathogen was identified on the basis of molecular analysis using universal and specific nested primers in PCR amplifications. Prokaryotic 16S rDNA gene was detected in amplified PCR products. Nested PCR resulted in DNA amplification of 1.2 kbp fragment. This is the first report of a phytoplasmal rDNA gene identified from the putative causal pathogen of yellows in ornamental palms in the Arabian Gulf region.

• 대한수의학회지
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• 제43권3호
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• pp.471-476
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• 2003

Malignant catarrhal fever (MCF) is a systemic disease of ruminants caused by ovine herpesvirus 2 (OvHV-2). OvHV-2 is a gamma herpesvirus, which induces frequent latent infection and often difficult to detect its antigens and even specific nucleic acids because of its low viral copies in the infected tissues. Histopathology, serology and polymerase chain reaction (PCR) were compared for the diagnosis of MCF using 10 bison infected with OvHV-2. Histopathological diagnosis was performed using the criteria which was based upon the pathognomic lesions. Serological diagnosis was conducted using its serum with competitive ELISA for the detection of antibodies of OvHV-2. Also, the nest PCR was performed with peripheral blood leukocytes for the detection of OvHV-2-specific DNAs. Primers 556 and 775 were used for the primary amplification, and primers 556 and 555 were used for the secondary amplification. As the results, positive cases were 6 by histopahology, 9 by serology and 10 by PCR. As comparing with other diagnostic methods, PCR was found to be more sensitive than histopathology and serology. The recent development of molecular diagnostic assays has provided powerful tools for investigating how viruses survive in nature. Development of PCR specific for viruses has dramatically improved the accuracy of diagnosis of viruses in clinically infected animals. Furthermore, amplification of viral genomic material by nest PCR represents the most sensitive method for the detection of viruses and might be detected successfully even though very low viral DNA copies. So, it could be used as the first choice for the detection of viral DNAs with low copies such as the status of latent infection. However, it has also some limitation of application like as false negative results by PCR inhibitors and false positive results by contamination. The results of this study suggest that the use of molecular biological methods like PCR may increase the accuracy for the diagnosis of infectious diseases. However, in diagnostic laboratory, it is recommended that PCR assay must be conducted with other diagnostic methods for more reliable diagnosis.

• 한국균학회지
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• 제49권4호
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• pp.455-467
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• 2021

Macrofungi are valuable resources as novel drug candidates, new biomaterials, and edible materials. Recently, genetic approaches pertaining to macrofungi have been continuously growing for their identification, molecular breeding, and genetic engineering. However, purification and amplification of fungal DNA is challenging because of the rigid cell wall and presence of PCR inhibitory metabolites. Here, we established a direct PCR method to provide a rapid and efficient method for PCR-grade macrofungal DNA preparation applicable to both conventional PCR and real-time PCR. We first optimized the procedure of lysis and PCR using the mycelia of Lentinula edodes, one of the most widely consumed macrofungal species. Lysates prepared by neutralizing with (NH₄)₂SO₄ after heating the mycelia in a mixture of TE buffer and KOH at 65℃ for 10 min showed successful amplification in both conventional and real-time PCR. Moreover, the addition of bovine serum albumin to the PCR mixture enhanced the amplification in conventional PCR. Using this method, we successfully amplified not only internal transcribed spacer fragments but also low-copy genes ranging in length from 500 to 3,000 bp. Next, we applied this method to 62 different species (54 genera) of macrofungi, including edible mushrooms, such as Pleurotus ostreatus, and medicinal mushrooms such as Cordyceps militaris. It was found that our method is widely applicable to both ascomycetes and basidiomycetes. We expect that our method will contribute to accelerating PCR-based approaches, such as molecular identification, DNA marker typing, gene cloning, and transformant screening, in macrofungal studies.

• Fisheries and Aquatic Sciences
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• 제16권2호
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• pp.93-99
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• 2013

In 2009, a systemic megalocytivirus infection associated with high mortality was detected for the first time in cultured starry flounder Platichthys stellatus in Korea. Diseased starry flounder had pale bodies and gill coloring and enlarged spleens. Histopathological examinations revealed basophilic enlarged cells in various organs of diseased starry flounder. Polymerase chain reaction (PCR) was performed on tissue samples using three published primer sets developed for the red sea bream iridovirus. PCR products were detected for all primer sets, except 1-F/1-R, which are registered by the World Organization for Animal Health (OIE). The part of the gene corresponding to the full open reading frame encoding the viral major capsid protein (MCP) was amplified by PCR. PCR products of approximately 1,581 bp were cloned, and the nucleotide sequences were analyzed phylogenetically. The MCP gene of the starry flounder iridovirus, designated SFIV0909, was identical to that of the turbot reddish body iridovirus (AB166788).

• Asian Pacific Journal of Cancer Prevention
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• 제16권7호
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• pp.2851-2855
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• 2015

Background: Recent reports have shown that nuclear enriched abundant transcript 1 (NEAT1), a long noncoding RNA (lncRNA), contributes to the precise control of gene expression and is related to several human malignancies. However, limited data are available on the expression and function of NEAT1 in lung cancer. The major objective of the current study was to profile the expression and clinicopathological significance of NEAT1 in non-small cell lung cancers (NSCLCs). Materials and Methods: NEAT1 expression in 125 NSCLC cases and paired adjacent non-cancer tissues was assessed by real-time quantitative reverse transcription-PCR (qRT-PCR). Relationships between NEAT1 and clinicopathological factors were also investigated. Results: The relative level of NEAT1 was $6.98{\pm}3.74$ in NSCLC tissues, significantly elevated as compared to that of the adjacent non-cancer lung tissues ($4.83{\pm}2.98$, p<0.001). The area under curve (AUC) of high expression of NEAT1 to diagnose NSCLC was 0.684 (95% CI: 0.619~0.750, p<0.001). NEAT1 expression was positively correlated with patient age (r=-2.007, p=0.047), lymphatic metastasis (r=-2.731, p=0.007), vascular invasion (r=-3.617, p=0.001) and clinical TNM stage (r=-4.134, p<0.001). Conclusions: This study indicates that NEAT1 might be associated with oncogenesis and progression in NSCLC, and suggests application in molecular targeted therapy.

• Journal of Microbiology
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• 제45권2호
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• pp.168-170
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• 2007

In this research 26 Shigella isolates were examined by PCR and direct nucleotide sequencing for genetic alterations in the quinolone-resistance determining regions (QRDRs). We tested for the presence of qnr genes by PCR in 91 strains, but no qnr genes were found. The results did show, however, some novel mutations at codon 83 of gyrA ($Ser{\rightarrow}Ile$) and codon 64 of parC ($Ala64{\rightarrow}Cys,\;Ala64{\rightarrow}Asp$), which were related to fluroquinolone resistance.

• Applied Biological Chemistry
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• 제50권4호
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• pp.245-252
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• 2007

FTA(fault tree analysis)는 system 오류 관리를 위한 정성적/정량적 기법으로 적용되고 있다. FTA를 적용한 PCR의 오류 관리 system의 구축을 위한 시범적 단계로서 PCR 실행의 여러 단계 중 가장 간단한 단계인 '반응액의 제조 및 PCR 기기 사용 단계'를 모델로 하여 분석하였다. PCR 실행시 발생할 수 있는 오류를 연역적 논리 방식에 의해 fault tree의 형태로 규명하였다. Fault tree는 오류 관리의 최상위 요소인 top event를 중심으로 중간 계층을 이루는 intermediate events와 최하위의 요소인 basic events로 세분하여 구성하였다. Top event는 '반응액의 제조 및 PCR 기기 사용 단계에서의 오류'; 중간계층 events는 '기기 유래 오류', '실험행위 유래 오류'; basic events는 '정전상황', 'PCR 기기 선정', '기기 사용 관리', '기기 내구성', '조작의 오류', '시료 구분의 오류'로 분석되었다. 이로부터 top event의 원인 분석 및 중요 관리점을 도출하기 위하여 정성적/정량적 분석을 실시하였다. 정성적 기법으로 minimal cut sets, structural importance, common cause vulnerability를 분석하였고, 정량적 기법으로 simulation, cut set importance, item importance, sensitivity를 분석하였다. 정성적 분석과 정량적 분석의 결과에서 '시료 구분의 오류'와 '기기 조작의 오류'가 제 1중요관리점; '기기 관리의 오류'와 '내구성에 의한 오류'는 제 2중요관리점으로 일치되게 나타났다. 그러나 '정전상황'과 '기기 선정의 오류'는 정성적 분석에서만 중요관리점으로 분석되었다. 특히 sensitivity 분석에서 '기기 관리의 오류'는 사용 시간이 경과함에 따라 가장 중요한 관리점으로 부각되었다. 결론적으로 FTA는 PCR 모델 case에 대한 오류의 원인 분석 및 그 방지를 위한 중요관리점을 제시함에 따라, 궁극적으로 미래에 PCR의 오류 관리 system을 완성할 수 있는 효과적인 방법으로 사료된다.