• Korean Journal of Food Science and Technology
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• v.33 no.5
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• pp.521-524
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• 2001

A method using PCR was developed for the monitoring of glyphosate tolerant soybean (GTS) produced by the DNA recombination technique. We designed 3 pairs of specific oligonucleotide primers based on the gene sequences inserted in soybean and in lectin and ferritin genes as internal standards. Template DNAs were isolated from soybeans by the modified hexadecyl trimethyl ammonium bromide (CTAB)method and used for PCR with different primer sets. PCR, used with specific primer sets for GTS detection, showed the amplified DNA fragments with GTS template DNA but no product showed with non-GTS template. PCR amplified products were confirmed by DNA sequencing and were detected for up to 0.05% of GTS template DNA.

• Korean Journal of Microbiology
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• v.41 no.1
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• pp.60-66
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• 2005

To select the rapid and efficient molecular subtyping method for epidemiologic monitoring of Staphylococcus aureus (S. aureus) strains at clinical laboratory levels, a total 116 of S. aureus and MRSA (methicillin-resistant S. aureus) strains from diverse animal species [Korean cattle, goat, pig, dog, chicken, mouse] and also humans were analyzed. To evaluate the discriminatory ability (DA) of individual PCR methods, random amplified polymorphic of DNA [RAPD; 4M & RA primer], repetitive extragenic palindromic sequences PCR (REP-PCR), and enterobacterial repetitive intergenic consensus sequences PCR (ERIC-PCR) methods were conducted and then compared on their Simpson's index of diversity (SID) values based on the dendrogram patterns, which was produced by software program (BiolD2+ & GelCompar II). In first, RAPD using the 4M primer (SID 0.915) was expressed more higher SID value than that of RA primer (SID 0.874). 4M primer was expressed more powerful DA than RA. Both REP-PCR (SID 0.930) and ERIC-PCR (SID 0.929) methods showed much more higher DA than that of RAPD. According to the present results, both REP-PCR and ERIC-PCR among the tested analysis methods were found as the most reliable and discriminative molecular subtyping method, because they expressed the highest DA for the present S. aureus and MRSA strains.

• The Korean Journal of Mycology
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• v.36 no.2
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• pp.138-143
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• 2008

Botrytis cinerea, gray mold pathogen, causes serious losses in greenhouse tomato crop. In this study, a primer set was developed for identification and specific PCR detection of B. cinerea from tomato plants. The primer pair (BTF1/BTR1) was designed from polymorphic sequence region in pyruvate carboxylase gene (pyc) of B. cinerea. A PCR product (112 bp) was amplified on genomic DNA of 13 B. cinerea isolates from 10 different host plants, but not on those from 6 other Botrytis spp., 4 Botryotinia spp., 5 Sclerotinia spp. and 16 other genus of phytopathogenic fungi. The sensitivity limit of the primer set was 2 pg of genomic DNA of B. cinerea, approximately. The PCR assay using species-specific primer set was specifically able to detect the pathogen on naturally infected tomato plants and artificially infected plants. These results suggest that the sensitivity and specificity of this primer set can be applied in a rapid and accurate diagnosis of tomato disease caused by B. cinerea.

• Journal of Life Science
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• v.28 no.9
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• pp.1062-1067
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• 2018

Reliable labeling of fish products can reassure consumers regarding the identity and quality of seafoods. Therefore, techniques that can identify adulteration or mislabeling are valuable. To rapidly identify two Trachurus species, Trachurus japonicus and Trachurus novaezelandiae, a highly efficient, rapid, duplex polymerase chain reaction (PCR) having two species-specific primers simultaneously was identified. This species-specific primer focused on a single nucleotide mismatch in the 3'-terminal base of a primer designed in the mitochondrial cytochrome c oxidase (COI) subunit I DNA. To optimize the duplex PCR condition, gradient PCR reactions were conducted to determine the primer annealing temperature and the primer concentration. The PCR's product was observed on the gel, suggesting that DNA molecules may be useful in differentiating the two species. The length of the amplification fragments were 103 bp for Trachurus japonicus and 214 bp for Trachurus novaezelandiae, which, along with the species-specific primer visualized by agarose gel electrophoresis, enabled accurate distinction of the species of the Trachurus genus. These results indicate that the duplex PCR, which has a species-specific primer based on single nucleotide polymorphism (SNP), can be useful for rapidly differentiating the two species of Trachurus. This duplex PCR analysis is simple, rapid, and reliable, and could be beneficial to protecting consumers' rights.

• Mycobiology
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• v.30 no.4
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• pp.202-207
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• 2002

This study was carried out to develop specific primers for PCR detection of Phellinus linteus. Diverse genomes of 15 Phellinus spp. including five Phellinus linteus isolates were fingerprinted by Primer Universal rice primer(URP)1F. The URP-PCR pattern differentiated P. linteus isolates from other phellinus spp. A polymorphic band(2.8 kb), which is unique for P. linteus isolates, was isolated and sequenced. Twenty four-oligonucleotide primer pairs were designed based on information of DNA sequence. The primer set(PLSPF2/PLSPR1) amplified single band(2.2 kb) of expected size with genomic DNA from seven Phellinus linteus, but not with that of other Phellinus species tested. The primers could be used identically in both DNA samples from mycelium and fruit bodies. This specific primers could offer a useful tool for detecting and identifying P. linteus rapidly.

• Journal of fish pathology
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• v.23 no.2
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• pp.145-153
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• 2010

Prevalence of a protozoan parasite Perkinsus olseni in Manila clam Ruditapes philippinarum was surveyed from July to December 2009 on the west and south coast of Korea. P. olseni infection was diagnosed using two primer sets, P.olseni NTS Forward/P.olseni NTS Reverse set and PolsITS-140F/PolsITS-600R set in polymerase chain reaction(PCR). The results using PolsITS-140F and PolsITS-600R primer set was retained up to 60% at all stations from July to December, except for Padori. Especially, Goheung showed 100% prevalence from October to December. The results about comparison of the 4 station's DNA sequences which were analyzed from PCR products(457bp) using PolsITS-140F and PolsITS-600R primer set, there were only 2base differences at Sunjedo.

• The Plant Pathology Journal
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• v.27 no.4
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• pp.367-371
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• 2011

Multiplex PCR assays were developed for the simultaneous detection of ten important Korean quarantine phytoplasmas. The species-specific primers were designed based on ribosomal protein, putative preprotein translocase Y, immunodominant protein, elongation factor TU, chaperonin protein and the 16S rRNA genes of 'Candidatus (Ca.) Phytoplasma' species. Three main primer sets were prepared from ten designed primer pairs to limit nonspecific amplification as much as possible. The multiplex PCR assay using the three primer sets successfully amplified the correct conserved genes for each 'Ca. Phytoplasma' species. In addition, ten important 'Ca. Phytoplasma' species could be easily determined by recognizing band patterns specific for each phytoplasma species from three primer sets. Moreover, a high sensitivity of multiplex PCR for each primer set was observed for samples containing a low DNA concentration (10 ng/${\mu}l$). This study provides the useful multiplex PCR assay as a convenient method to detect the presence of ten important quarantine phytoplasmas in Korea.

• Journal of fish pathology
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• v.22 no.1
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• pp.85-90
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• 2009

A method for the identification of Nocardia seriolae, the causative agent of nocardiosis in cultured fishes, using PCR was developed in the study. A PCR primer set specific to N. seriolae was designed based on 16S-23S rRNA sequence of various Nocardia species accessed in GenBank. Designed PCR primer set, Nseri-F (5'-GCA AAC TCT TCG AAC AGT CG-3') and Nseri-R (5'-GGA TAT CAG GAC TTA CCG GC-3'), amplifies the target regions of N. seriolae only, but not 4 other Nocardia species, N. asteroides, N. crassostreae, N. farcinica and N. salmonicida.

• Research in Plant Disease
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• v.23 no.2
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• pp.193-201
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• 2017

Major tomato viruses in Korea are Tomato chlorosis virus (ToCV), Tomato spotted wilt virus (TSWV), Cucumber mosaic virus (CMV), Pepper mottle virus (PepMoV), and Tomato mosaic virus (ToMV). RT-PCR conditions for the viruses were examined, especially in primer set and RT-PCR mixture. Total 46 primer sets from the unique sequence of the viruses were tested for nonspecific background products in a RT-PCR mixture without template. Among them 16 primer sets were applied to healthy tomato RNA, resulting the compatibility between RT-PCR mixture and primer set influenced RT-PCR to reduce nonspecific background products. Based on the combinations among cDNA synthesis parameters and RT-PCR mixtures, two reaction mixtures were finally selected for ToCV detection. The condition allowed to determine more specific primer sets; C029 (ToCV), C072 (TSWV), C070 (CMV), C048 (PepMoV), and C065 (ToMV). These primer sets are expected to be of use to specific detection of the major viruses in tomato plants.

• The Plant Pathology Journal
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• v.21 no.1
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• pp.55-58
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• 2005

In order to diagnose and differentiate jujube witches' broom (JWB) phytoplasma rapidly, oligonucleotide primer pair, 16Sr(V) F/R, for polymerase chain reactions (PCRs) was designed on the basis of 16S rRNA sequences of JWB phytoplasma. The PCR employing phytoplasma universal primer pair P1/P7 consistently amplified DNA in all tested phytoplasma isolates. But no phytoplasma DNA was detected from healthy jujube seedlings. The nested PCR, the primer pair 16S(V) F/R, about 460 bp fragment, amplified DNA in all tested JWB and related phytoplasmas including ligustrum witches' broom phytoplasma of the 16S rRNA group V, but no DNA amplification was detected from other phytoplasma strains such as groups 16SrI (Aster yellows) and 16SrXII (Stolbur group) in which mulberry dwarf phytoplasma and chrysanthemum witches' broom phytoplasma belong to, respectively. The same results were obtained from both Korean and Chinese isolates of JWB phytoplasma. Nested-PCR using phytoplasma universal primer pair P1/P7 and 16SrV group-specific primer pair 16S(V) F/R could detect group V phytoplasmas rapidly and easily, in particular JWB phytoplasma.