• The Plant Pathology Journal
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• v.38 no.6
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• pp.616-628
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• 2022

Resistance to pyraclostrobin due to a single nucleotide polymorphism at 143rd amino acid position on the cytochrome b gene has been a major source of concern in red pepper field infected by anthracnose in Korea. Therefore, this study investigated the response of 24 isolates of C. acutatum and C. gloeosporioides isolated from anthracnose infected red pepper fruits using agar dilution method and other molecular techniques such as cytochrome b gene sequencing, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and allele-specific polymerase chain reaction (PCR). The result showed that four isolates were resistant to pyraclostrobin on agar dilution method and possessed GCT (alanine) codon at 143rd amino acid position, whereas the sensitive isolates possessed GGT (glycine). Furthermore, this study illustrated the difference in the cytochrome b gene structure of C. acutatum and C. gloeosporioides. The use of cDNA in this study suggested that the primer Cacytb-P2 can amplify the cytochrome b gene of both C. acutatum and C. gloeosporioides despite the presence of various introns in the cytochrome b gene structure of C. gloeosporioides. The use of allele-specific PCR and PCR-RFLP provided clear difference between the resistant and sensitive isolates. The application of molecular technique in the evaluation of the resistance status of anthracnose pathogen in red pepper provided rapid, reliable, and accurate results that can be helpful in the early adoption of fungicide-resistant management strategies for the strobilurins in the field.

• Journal of Life Science
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• v.20 no.5
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• pp.789-793
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• 2010

Artificial chromosome manipulation and amplification of single-copy yeast artificial chromosome (YAC) are usually required in order to use YACs for applications such as physical mapping and functional analysis in eukaryotes. We designed and implemented a Simultaneous YAC Manipulation-Amplification (SYMA) system that combines the copy number amplification system of YAC with a convenient YAC manipulation system. To achieve the desired split and to amplify a YAC clone-harboring plant chromosome, a pBGTK plasmid containing a conditional centromere and thymidine kinase (TK) gene was constructed as a template to amplify the splitting fragment via PCR. By splitting, new 490-kb and 100-kb split YACs containing the elements for copy number amplification were simultaneously generated from a 590-kb YAC clone. The 100-kb split YAC was then successfully amplified 14.4-fold by adding 3 mg/ml sulfanilamide and $50\;{\mu}g/ml$ methotrexate (S3/M50) as inducing substances.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.11
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• pp.1689-1693
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• 2007

The objective of this study was to develop a simplified, efficient, and accurate protocol for sexing goat embryos. Based on the amelogenin gene located on the conservation region of X- and Y- chromosomes, a pair of primers was utilized and the system of PCR was established to amplify a 262 bp fragment from the X- chromosome in female goats, and a 262 bp fragment from X- chromosome and 202 bp fragment from the Y- chromosome in male goats, respectively. The accuracy and specificity of the primers were assessed using DNA template extracted from goat whole blood sample of known sex. 100% (10/10) concordance was obtained by using the PCR assay. Fifty-one biopsied embryos were transferred into 25 recipient goats on the same day that the embryos were collected and sex of the kid was confirmed after parturition. Eighteen kids of predicted sex were born. The biopsied samples from 51 goat embryos were amplified with 100% efficiency and 94.7% accuracy. In conclusion, our results indicated that PCR sexing protocols based on the amelogenin gene is highly reliable and suitable for sex determination of goats.

• The Plant Pathology Journal
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• v.33 no.1
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• pp.80-86
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• 2017

One of the major problems in strawberry production is difficulty in diagnosis of anthracnose caused by Colletotrichum acutatum or Glomerella cingulata in latent infection stage. We here developed a diagnostic tool for the latent infection consisting of initial culturing of fungi, DNA extraction, synthesis of PCR-amplified probes and microtube hybridization (MTH) using a macroarray. The initial culturing step is convenient to lure the fungi out of the plant tissues, and to extract PCR-inhibitor-free DNA directly from fungal hyphae. For specific detection of the fungi, PCR primers were designed to amplify the fungal MAT1-2 gene. The subsequent MTH step using the PCR products as probes can replace the laborious electrophoresis step providing us sequence information and high-throughput screening. Using this method, we have conducted a survey for a few thousands nursery plants every year for three consecutive years, and finally succeeded in eliminating latent infection in the third year of challenge.

• Journal of Microbiology and Biotechnology
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• v.8 no.4
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• pp.310-317
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• 1998

Peptide synthetases are large multifunctional enzyme complexes that catalyze the nonribosomal synthesis of a structurally diverse family of peptide antibiotics. These enzymes are composed of functionally independent domains with independent enzymatic activities. Their specific linkage order of domains forms the protein template that defines the sequence of the incorporated amino acids. Within each domain, several motifs of highly conserved sequences have been identified from the sequence alignment of the various peptide synthetases ［30］. Taking advantage of the conserved nucleotide sequence of Core 1 and Core 2, we designed PCR primers to amplify the peptide synthetase genes from three different gram-positive bacterial strains. Nucleotide sequence analysis of the amplified PCR products from those three strains showed significant homology to various peptide synthetase genes, suggesting that the PCR products are parts of peptide synthetase genes. Therefore, this rapid and efficient PCR technique can be used for the isolation of peptide synthetase genes from various strains.

• Journal of Microbiology and Biotechnology
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• v.14 no.4
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• pp.737-744
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• 2004

A multiplex polymerase chain reaction (PCR) was developed for the simultaneous detection and differentiation among Vairimorpha spp. and Nosema spp. and identification of Vairimorpha necatrix from Lepidoptera insects. Three sets of primers were selected from different genomic sequences to specifically amplify an 831 bp amplicon within the SSU rRNA gene, specific for both Vairimorpha spp. and Nosema spp. (MSSR primer); a 542 bp amplicon within the SSU rRNA gene, specific for Vairimorpha spp. (VSSU primer); and a 476 bp amplicon within the actin gene, specific for Vairimorpha necatrix (VNAG primer). Using the primers in conjunction with multiplex PCR, it was possible to detect Vairimorpha spp. and Nosema spp. and to differentiate between them. The sensitivity of this PCR assay was approximately 10 spores per milliliter. It is proposed that the multiplex PCR is a sensitive, specific, and rapid tool that can serve as a useful differential diagnostic tool for detecting Vairimorpha spp. and Nosema spp. in Lepidoptera insect.

• Food Science of Animal Resources
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• v.26 no.3
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• pp.375-379
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• 2006

Food labeling regulations require that the meat species in various meat products are accurately declared to the consumer. Substitution or adulteration of costly meat with a cheaper one is one of the most common problems in the meat industry. In this study, PCR-restriction fragment length polymorphism(RFLP) method of the mitochondrial cytochrome b(mt cyt b) gene has been applied for identification of the origin of six mammalian meat species(beef, port horse, goat, mutton and deer) and three poultry meat species(chicken, turkey and duck) as raw materials for meat products. PCR was used to amplify a variable region of mt cyt b gene. Meat species differentiation was determined by digestion of the amplified products with a 359 bp fragment using HaeIII and HinfI restriction enzymes, which generated species-specific RFLP patterns. This PCR-RFLP DNA marker of mt cyt b gene could be very useful for the accurate and reliable identification and discrimination of animal meat species in routine analysis.

• Design & Manufacturing
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• v.11 no.3
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• pp.35-40
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• 2017

PCR(Polymerase chain reaction) is a technique to replicate and amplify a desired part of DNA. It is used in various aspects such as DNA fingerprint analysis and rare DNA amplification of an extinct animal. Especially in the medical diagnosis field, it provides various measurement methods at the molecular level such as genetic diagnosis, and is a basic tool for molecular diagnostics. The internal shape of the plastic vial tube for PCR analysis used in the DNA detection process, and the surface roughness and internal cleanliness can affect detection and discrimination results. The plastic vial tube demanded by the developer of the PCR analysis equipment should be changed to a structure that eliminates the residual washing solution in the washing process to ensure the internal cleanliness. Thus the internal structure and the internal surface design for improving the PCR amplification efficiency are key issues to develop the plastic vial tube for the DNA detection process.

• Journal of Microbiology and Biotechnology
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• v.27 no.3
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• pp.471-479
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• 2017

White spot syndrome virus (WSSV) is a major threat to the shrimp farming industry and so far there is no effective therapy for it, and thus early diagnostic of WSSV is of great importance. However, at the early stage of infection, the extremely low-abundance of WSSV DNA challenges the detection sensitivity and accuracy of PCR. To effectively detect low-abundance WSSV, here we developed a pre-amplification PCR (pre-amp PCR) method to amplify trace amounts of WSSV DNA from massive background genomic DNA. Combining with normal specific PCR, 10 copies of target WSSV genes were detected from ${\sim}10^{10}$ magnitude of backgrounds. In particular, multiple target genes were able to be balanced amplified with similar efficiency due to the usage of the universal primer. The efficiency of the pre-amp PCR was validated by nested-PCR and quantitative PCR, and pre-amp PCR showed higher efficiency than nested-PCR when multiple targets were detected. The developed method is particularly suitable for the super early diagnosis of WSSV, and has potential to be applied in other low-abundance sample detection cases.

• Journal of Plant Biology
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• v.38 no.3
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• pp.267-274
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• 1995

Based upon the nucleotide sequence of As strain of cucumber mosaic virus (CMV-As0 RNA4, coat protein (CP) gene was selected for the design of oligonucleotide primers of polymerase chain reaction (PCR) for detection and identification of the virus. Reverse transcription and polymerase chain reaction (RT-PCR) was performed with a set of 18-mer CMV CP-specific primers to amplify a 671 bp fragment from crude nucleic acid extracts of virus-infected leaf tissues as well as purified viral RNAs. The minimum concentrations of template viral RNA and crude nucleic acids from infected tobacco tissue required to detect the virus were 1.0 fg and 1:65,536 (w/v), respectively. No PCR product was obtained when potato virus Y-VN RNA or extracts of healthy plants were used as templates in RT-PCR using the same primers. The RT-PCR detected CMV-Y strain as well as CMV-As strain. Restriction analysis of the two individual PCR amplified DNA fragments from CMV-As and CMV-Y strains showed distinct polymorphic patterns. PCR product from CMV-As has a single recognition site for EcoRI and EcoRV, respectively, and the product from CMV-Y has no site for EcoRI or EcoRV but only one site for HindIII. The RT-PCR was able to detect the virus in the tissues of infected pepper, tomato and Chinese cabbage plants.