• Korean Journal of Microbiology
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• v.41 no.1
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• pp.24-37
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• 2005

This study was conducted to analyze the molecular epidemiological properties and to select the most efficient and reliable PCR method on 116 of Staphylococcus aureus (S. aureus) isolates from Korean cattle, black goat, pig, dog, chicken, mouse and also human clinical cases from hospital. The distribution patterns of SSG [species specific genes; coagulase (coa), protein A (spa), nuclease (nuc) and aroA (RsaI) gene] were analyzed by PCR method. Among the SSGs, the nuc-gene was found in all strains $(100\%)$ tested and followed by coa-gene $(87.9\%)$, spa-gene $(91.4\%)$ and aroA-gene $(26.7\%)$, in order. The genetic subtyping by RFLP method was performed on the coa [AluI] and aroA-gene [RsaI] PCR products. The mecA-gene PCR and PCR-RFLP techniques were chosen to detect and verify of MRSA strains. Only the human strains $(12.1\%)$ were detected the positive mecA-gene products (533 bp), which were divided into two specific bands [201 & 332 bp] by HhaI enzyme digestion. On coa-gene and spa-gene typing, coa-gene was typed with ten kinds of genotype and coa-3 type were determined as the most predominant genotype, while spa-gene was divided into eleven kinds of genotype and also spa-7 type were selected the most prevalent genotype based on their genetic variations. On the aroA and coa-gene subtyping by PCR-RFLP, aroA-gene products were discriminated with only seven types of genotype, while coa-gene products were further divided into an eleven genotype, respectively. In comparison of SID values of five PCR based typing methods, the coa-PCR-RFLP (SID0.894) was evaluated the most efficient and reliable tools and followed by coa-PCR (SID0.883) and aroA-PCR-RFLP (SID0.462), in order. In conclusion, we could determined that the coa-PCR-RFLP method was the most suitable genetic analysis tool for S. aureus and MRSA strains from domestic animals and humans.

• The Plant Pathology Journal
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• v.24 no.1
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• pp.17-23
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• 2008

A total of 33 isolates of Colletotrichum species obtained from pepper, apple, and strawberry in 2001 and 2002 were identified based on mycological characteristics, responses to fungicides carbendazim and the mixture of carbendazim and diethofencarb, and nucleotide sequence analysis of internal transcribed spacer (ITS) regionMost of the Colletotrichum isolates from pepper could be identified as C. acutatum. The pepper isolates produced grey white mycelia that gradually changed to dark gray. The conidia were variable in size, and almost cylindrical in shape with at least one rounded end. They could grow on PDA amended with carbendazim or with the mixture of carbendazim and diethofencarb at $10{\mu}g/ml$, to which the isolates from apple and strawberry were very sensitive. A part of the ITS regions from the Colletotrichum isolates was amplified with the specific primers designed for C. acutatum (Ca1-1) or C. gloeosporioides (Cg1-3). A primer pair of Ca1-1 and a universal primer (ITS4) amplified a 496-bp DNA fragment from all of the pepper isolates examined and one apple isolate. Taken together, it is conclusive that the Colletotrichum isolates causing the typical lesion of anthracnose on pepper fruits are C. acutatum.

• Korean Journal of Head & Neck Oncology
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• v.12 no.2
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• pp.169-176
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• 1996

Tuberculous cervical lymphadenitis is still an important cause of neck mass in Korea. Tuberculosis is an important differential diagnosis in patients of cervical lymphadenopathy. Rapid and sensitive test for the diagnosis of tuberculosis is essential for the approapiate treatment. Up to now, conventional diagnostic methods for M. tuberculosis were acid-fast bacilli(AFB) stain and culture of M. tuberculosis. The direct microscopic examination of AFB by Ziehl-Neelsen stain is rapid, but often negative. The culture for M. tuberculosis is time-consuming, taking 4 to 8 weeks. Recently various methods to detect Mycobacterial DNA, including PCR and restriction fragment length polymorphism(RFLP) analysis have been reported. Here we represent a simple method for the confirmation of M. tuberculosis and exclusion of the other Mycobacterial species by RFLP analysis and silver staining of polyacrylamide gel electrophoresis after nested PCR for a repetitive DNA sequence(IS986) specific for M. tuberculosis from fresh or paraffin-embedded biopsy specimens. This result leads us to conclude that this method is simple, rapid and possibly applicable to confirm M. tuberculosis and rule out the other Mycobacteria species from the clinical specimens in the clinical laboratories.

• Mycobiology
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• v.51 no.6
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• pp.452-462
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• 2023

Opportunistic infections due to Cryptococcus neoformans and C. gattii species complexes continue to rise unabated among HIV/AIDS patients, despite improved antifungal therapies. Here, we collected a total of 20 environmental and 25 presumptive clinical cryptococcal isolates from cerebrospinal fluid (CSF) samples of 175 patients enrolled in an ongoing clinical trial Ambition 1 Project (Botswana-Harvard Partnership). Identity confirmation of the isolates was done using MALDI-TOF MS and PCR. We describe the diversity of the isolates by PCR fingerprinting and sequencing (Oxford Nanopore Technology) of the intergenic spacer region. Mating types of the isolates were determined by amplification of the MAT locus. We report an unusual prevalence of 42.1% of C. neoformans × C. deneoformans hybrids Serotype AD (n = 16), followed by 39.5% of C. neoformans Serotype A (n = 15), 5.3% of C. deneoformans, Serotype D (n = 2), 7.9% of C. gattii (n = 3), and 5.3% of C. tetragattii (n = 2) in 38 representative isolates that have been characterized. Mating type-specific PCR performed on 38 representative environmental and clinical isolates revealed that 16 (42.1%) were MATa/MAT𝛼 hybrids, 17 (44.7%) were MAT𝛼, and five (13.2%) possessed MATa mating type. We used conventional and NGS platforms to demonstrate a potential link between environmental and clinical isolates and lay a foundation to further describe mating patterns/history in Botswana.

• Proceedings of the Korean Society of Fisheries Technology Conference
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• 2001.05a
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• pp.334-335
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• 2001

Common carp (Cyprinus carpio) and Israeli carp(C. carpio) samples were obtained from a aquaculture facility in the Kunsan National University, Korea. Genomic DNA was isolated from the common carp and Israeli carp representing genetic characteristics and genomic polymorphisms by polymerase chain reaction amplification of DNA as arbitrary primers. There were observed a total of 90 species-specific genetic markers within Israeli carp. On average, each random RAPD primer produced amplified 7.9 products from 1 to 17 bands. An average genetic similarity within Israeli carp showed -.60$\pm$0.05. The average level of bandsharing was some 0.57$\pm$0.03 between common carp and Israeli carp. Accordingly, two carp species were genetically a little distant. The electrophoretic analysis of PCR-RAPD proudcts showed high levels of variation between two fish species. The RAPD polymorphism generated by primer may be used as a genetic marker for species or lines identification in important aquacultural carp.

• Journal of Animal Science and Technology
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• v.46 no.3
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• pp.315-324
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• 2004

Cytochrome P450 aromatase is the enzyme responsible for biosynthesis of female sex hormone(estrogen) and 19-nortestosterone(nandrolone), a unique steroid hormone endogenously synthesized in the pig. By use of RT-PCR coupled with DHPLC technique (WAVE analysis), expression pattern of isoforms of porcine cytochrome P450 aromatase gene was investigated. Relatively higher expression of aromatase mRNA was observed in testis than in ovary and this result accounted for the previous findings of higher blood estrogen level in male compared with female in this species. The result from the DHPLC demonstrated that PCR amplified DNA fragments of ovary and testis tissues. using unique PCR primers for all three types of aromatase genes, were different from those of type II and ill genes. Further nucleotide sequence analyses of the plasmid clones containing the PCR products revealed that nucleotide sequences of all clones were identical to type I aromatase gene(ovary type). Thus, the result from the present study indicates that the ovary and testis express the same type of aromatase gene. Therefore, the efficacy of DHPLC techniques used for this study helped us to analyze tissue-specific expression of isoform of genes containing the nucleotide sequences with high homology.

• Journal of Food Hygiene and Safety
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• v.28 no.2
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• pp.124-129
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• 2013

The method for detection foods containing allergenic materials by PCR was developed in this study. To detect allergenic raw material from processed food, species specific primer which up to 200bp for PCR product were designed or selected from advanced research. As target materials, 14 items were selected (12 target materials for allergen in Korea, 2 target materials for allergen in foreign countries). The amplicon size for eggs, milk, buckwheat, peanuts, beans, wheat, mackerel, crab, shrimp, pork, peach, tomato, almond, and sesame were confirmed 281, 131, 138, 120, 118, 127, 211, 174, 231, 138, 174, 132, 103, and 220bp, respectively. And any non-specific bands were not detected among each others. Detection method for allergenic material developed in this study could be used to investigate inaccurate goods for allergen labeling or non-intentional contaminant during processed foods manufacturing. In addition, the system will be usefully to detection accurate allergenic raw materials of export for other countries.

• Genomics & Informatics
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• v.3 no.4
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• pp.133-141
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• 2005

Most of the endogenous retroviral genes integrated into the primate genome after the split of New World monkeys in the Oligocene era, approximately 33 million years ago. Because they can change the structure of adjacent genes and move between and within chromosomes they may play important roles in evolutionas well as in many kinds of disease and the creation of genetic polymorphism. Comparative analysis of HERVs (human endogenous retroviruses) and their LTR (long terminal repeat) elements in the primate genomes will help us to understand the possible impact of HERV elements in the evolution and phylogeny of primates. For example, HERV-K LTR and SINE-R elements have been identified that have been subject to recent change in the course of primate evolution. They are specific elements to the human genome and could be related to biological function. The HERV-M element is related to the superfamily of HERV-K and is integrated into the periphilin gene as the truncated form, 5'LTR-gag-pol-3'LTR. PCR and RT-PCR approaches indicated that the insertion of various retrotransposable elements in a common ancestor genome may make different transcript variants in different primate species. Examination of the HERV-W elementrevealed that env fragments were detected on human chromosomes 1, 3-7, 12, 14, 17, 20, and X, whilst the pol fragments were detected on human chromosomes 2-8, 10-15, 20, 21, X, and Y. Bioinformatic blast search showed that almost full-length of the HERV-W family was identified on human chromosomes 1-8, 11-15, 17, 18, 21, and X. Expression analysis of HERV-W genes (gag, pol, and env) in human tissues by RT-PCR indicated that gag and pol were expressed in specific tissues, whilst env was constituitively expressed in all tissues examined. DNA sequence based phylogenetic analysis indicated that the gag, pol and env genes have evolved independently during primate evolution. It will thus be of considerable interest to expand the current HERV gene information of various primates and disease tissues.

• Animal cells and systems
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• v.11 no.2
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• pp.165-168
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• 2007

The nucleotide sequences of a male-specific marker sex determining region Y (SRY) gene and a mitochondrial cytochrome B (CYTB) gene were characterized and analyzed to establish a molecular method for identification of species and sex of Korean roe deer (Capreolus pygargus tianschanicus). Similarity search result of SRY sequences showed very similar result to those reported in Moose (Alces alces) and Reindeer (Rangifer tarandus), both of which had 95.9% similarity in identity. CYTB genes were very similar to those reported in Siberian roe deer (C. pygargus pygargus) which had 98.6% similarity and not to European roe deer (C. capreolus), suggesting that the DNA samples tested were of Siberian roe deer lineage. Polymerase chain reaction (PCR)-based sex typing successfully discriminated between carcasses of male and female roe deer. Males had SRY band on agarose gels and females did not. The result of this molecular sex typing provided similar information with that obtained by genital organ observation. Therefore, this molecular method using male specific marker SRY and mitochondrial CYTB genes would be very useful for identification of the species and sex of the carcass remains of roe deer.

• The Korean Journal of Malacology
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• v.25 no.1
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• pp.41-49
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• 2009

Random amplified polymorphic DNA (RAPD) marker and sequence analyses of the internal transcribed spacer (ITS) region of ribosomal DNA were used to assess phylogenetic relationships of four Korean oyster species. The average number of species-specific markers identified from five universal rice primers (URPs) by RAPD-PCR was 1.8 for Crassostrea gigas, 3.2 for C. nippona, 3.6 for C. ariakensis, and 4.6 for Ostrea denselamellosa. The length of the ITS (ITS1-5.8S-ITS2) region ranged from 1,001 to 1,206 bp (ITS1, 426-518 bp; 5.8S, 157 bp; and ITS2, 418-536 bp), while the GC content ranged from 55.5-61.1% (ITS1, 56.8-61.8%; 5.8S, 56-57.3%; and ITS2, 54.1-62.2%). A phylogenetic analysis of the oysters based on our RAPD, ITS1, and ITS2 sequence data revealed a close relationship between C. gigas and C. nippona and a distant relationship between the genera Crassostrea and Ostrea. Our results indicated that RAPD and ITS sequence analysis was a useful tool for the elucidation of phylogenetic relationships and for the selection of species-specific markers in Korean oysters.