• Journal of Preventive Medicine and Public Health
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• v.39 no.2
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• pp.130-134
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• 2006

Objectives : Oxidative DNA damage is a known risk factor of lung cancer. The glutathione peroxidase (GPX) antioxidant enzyme that reduces hydrogen peroxide and lipid peroxides plays a significant role in protecting cells from the oxidative stress induced by reactive oxygen species. The aim of this case-control study was to investigate effects of oxidative stress and genetic polymorphisms of the GPX1 genes and the interaction between them in the carcinogenesis of lung cancer. Methods : Two hundreds patients with lung cancer and 200 age- and sex-matched controls were enrolled in this study. Every subject was asked to complete a questionnaire concerning their smoking habits and their environmental exposure to PAHs. The genotypes of the GPX1 and 8-oxoguanine glycosylase 1 (hOGG1) genes were examined and the concentrations of urinary hydroxypyrene (1-OHP), 2-naphthol and 8-hydroxydeoxyguanosine (8-OH-dG) were measured. Results : Cigarette smoking was a significant risk factor for lung cancer. The levels of urinary 8-OH-dG were higher in the patients (p<0.001), whereas the urinary 1-OHP and 2-naphthol levels were higher in the controls. The GPX1 codon 198 polymorphism was associated with an increased risk of lung cancer. Individuals carrying the Pro/Leu or Leu/Leu genotype of GPX1 were at a higher risk for lung cancer (adjusted OR=2.29). In addition, these individuals were shown to have high urinary 8-OH-dG concentrations compared to the individuals with the GPX1 Pro/Pro genotype. On the other hand, the polymorphism of the hOGG1 gene did not affect the lung cancer risk and the oxidative DNA damage. Conclusions : These results lead to a conclusion that individuals with the GPX1 Pro/Leu or Leu/Leu genotype would be more susceptible to the lung cancer induced by oxidative stress than those individuals with the Pro/Pro genotype.

• Journal of Life Science
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• v.22 no.3
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• pp.398-406
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• 2012

This study aimed to examine whether the polygenic profile of ACE ID and ACTN3 R577X polymorphisms is associated with muscle power performance in Korean athletes. For this study, 106 top-class power athletes (top-class group), 158 elite power athletes (elite-class group), and 676 healthy adults (control) aged 18-39 yrs were recruited and their genotypes were analyzed. The top-class group showed higher frequencies of the II genotype and I allele in ACE, as well as higher frequencies of the RR genotype and R allele in ACTN3 (top-class vs. control: 41.4% vs. 32.1% for II genotype, 67.1% vs. 57.7% for I allele, p<0.05; 42.3% vs. 29.0% for RR genotype, 65.3% vs. 54.8% for I allele, p<0.05). In the polygenic profile, the top-class group had significantly higher frequencies of combined-II/ID+RR/RX genotype than the control group (top-class vs. control: 82.9% vs. 66.7% for II/ID+RR/RX, p<0.05), and there was even a sharp increase in total genotype score (TGS) in this group compared to the elite-class and control groups ($66{\pm}0.9$ vs. $58{\pm}1.9$ vs. $56{\pm}2.3$, p<0.05). The combined-II/ID+RR/RX genotype showed the possibility of succussion in the top-class muscle power performance with an odds ratio of 2.3 (CI:1.4-4.1, p<0.05). These results suggested that ACE and ACTN3 need to interact with each other to affect muscle-power performance in an additive form. Furthermore, the polygenic profile of ACE and ACTN3 can predict muscle performance with high success in a homogeneous dominant combined genotype (II/ID+RR/RX). A further study could identify and combine other genes into ACE and ACTN3 for muscle strength.

• Korean Journal of Clinical Laboratory Science
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• v.38 no.2
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• pp.99-104
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• 2006

Human Papilloma viruses (HPVs) are etiological agents for cervical cancer and are classified into low- and high-risk categories. The aim of this study was to determine the frequency of the HPV genotype in the HPV screening test of Korean women using PCR-direct sequencing. Consensus primers of L1 legion were used for the amplification of HPV DNA and the PCR products (450 bps) obtained were analyzed by automatic sequencing. Sequences were compared with those in GenBank by using the BLAST program. Cervical swab samples of 3,978 women (20-73 years) were tested and the average age was 37.6 years. In this study, 1,174 samples were HPV positive out of 3,978 cervical swab samples screened (29.5%) and 136 samples (11.6%) showed a double infection. A total of 1,310 HPV genotypes were analyzed. The HPV positive rate was the lowest in the 20 years group (69.5%) and most of the samples of the > 60 years group were found HPV positive. Among thirty seven different HPV types identified by sequencing, 21 were HPV high risk types and 16 HPV low risk types were 69.8% (914/1,310) and 26.0% (340/1,310), respectively. In HPV high-risk types, 16 (13.21%), was the most frequently found. HPV 53 (9.62%) and 58 (9.24%) were also frequently found. This group was followed by HPV types 70 (5.50%), 33 (4.73%), 66 (4.20%), 18 (4.05%), 52 (4.05%), 31 (3.97%) and 56 (3.51%) in descending order of frequency. Among HPV low-risk types, 62 (4.20%), 6 (3.59%), 81 (3.59%), 84 (3.51%), and 11 (2.6%) were frequently found. In conclusion, PCR-direct sequencing could be used for quick and reliable typing of known and novel HPVs from clinical specimens. This data could be useful for epidemiological study of HPV and it also allows type-specific follow-up of women who have been treated for cervical intraepithelial neoplasia.

• Journal of Yeungnam Medical Science
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• v.12 no.2
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• pp.366-385
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• 1995

Epidemiological studies are important in both the prevention and treatment of mycobacterial infections. This study was initiated to establish the pulsed-field gel electrophoresis (PFGE) method, which are not yet extensively studied. The most apprpriate restriction endonucleases included DraI, AsnI, and XbaI. The optimal PFGE condition was different according to the enzymes used. Two stage PFGE was performed, in case of DraI first stage was performed with 10 seconds of initial pulse and 15 seconds of final pulse, while the second stage was performed with 60 seconds of initial pulse and 70 seconds of final pulse. The electrophoresis time for DraI-PFGE was 14 hours for each stage. Electrophoresis was performed for 22 hours, in case of XbaI, with 3 seconds of initial pulse and 12 seconds of final pulse. Electrophoresis was performed for 22 hours, in case of AsnI, with 5 seconds of initial pulse and 25 seconds of final pulse. In all cases the voltage of the electrophoresis was maintained constantly at 200 voltage. Standard mycobacterial strains, which included Mycobacterium bovis BCG, M. tuberculosis, and M. fortuitum, could not be differentiated by PFGE analysis. PFGE analysis was performed to differentiate 9 clinically isolated M. fortuitum strains using AsnI. All M. fortuitum strains showed different genotypes except 2 strains. Cluster analysis divided M. fortuitum strains into 2 large groups. PFGE analysis was performed to further differentiate M. fortuitum isolates using XbaI. The undifferentiated 2 M. fortuitum strains showed different PFGE patterns with Xba I. Cluster analysis of the XbaI-PFGE patterns showed more complex grouping than AsnI-PFGE patterns, which showed that XbaI-PFGE analysis was better than AsnI-PFGE in M. fortuitum genotyping. The top dissimilarity values of AsnI-PFGE and XbaI-PFGE were 0.74 and 0.75, respectively. This value was higher than that of arbitrarily primed polymerase chain reaction (AP-PCR) analysis and lower than that of restriction fragment length polymorphism (RFLP) analysis. This suggested that PFGE can be used as a supportive or alternative genotyping method to RFLP analysis.

• Korean Journal of Breeding Science
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• v.42 no.4
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• pp.397-406
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• 2010

Field screening method has been commonly used for purity test of $F_1$ hybrid seeds in melon and oriental melon. However, as this method takes a lot of time and cost, molecular marker-based purity test is necessary. To develop molecular markers for purity test, thirty pairs of SNP (single nucleotide polymorphism) primers were obtained from melon EST sequences, and 10 polymorphic markers showing HRM (high resolution melting) polymorphisms between parents of two melon cultivars and one oriental melon cultivar were selected. Blind tests were performed to validate usefulness of the selected markers for purity test. Blind test results showed that HRM genotypes were matched with the expected identity of individual sample, $F_1$ hybrid, male or female parents. Three HRM-based SNP markers were converted to CAPS markers for general use which is favor to breeders. We expect that SNP markers developed in this study will be useful for purity test of $F_1$ hybrid seeds in melon and oriental melon.

• Journal of Life Science
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• v.28 no.11
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• pp.1255-1261
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• 2018

Whole genome analysis have been made possible with the development of DNA sequencing technologies and discovery of many single nucleotide polymorphisms (SNPs). Large number of SNP can be analyzed with SNP chips, since SNPs of human as well as livestock genomes are available. Among the various missing nucleotide imputation programs, Minimac3 software is suggested to be highly accurate, with a simplified workflow and relatively fast. In the present study, we used Minimac3 program to perform genomic missing value substitution 1,226 animals 770K SNP chip and imputing missing SNPs with next generation sequencing data from 311 animals. The accuracy on each chromosome was about 94~96%, and individual sample accuracy was about 92~98%. After imputation of the genotypes, SNPs with R Square ($R^2$) values for three conditions were 0.4, 0.6, and 0.8 and the percentage of SNPs were 91%, 84%, and 70% respectively. The differences in the Minor Allele Frequency gave $R^2$ values corresponding to seven intervals (0, 0.025), (0.025, 0.05), (0.05, 0.1), (0.1, 0.2), (0.2, 0.3). (0.3, 0.4) and (0.4, 0.5) of 64~88%. The total analysis time was about 12 hr. In future SNP chip studies, as the size and complexity of the genomic datasets increase, we expect that genomic imputation using Minimac3 can improve the reliability of chip data for Hanwoo discrimination.

• Journal of the Korean Society of International Agriculture
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• v.30 no.4
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• pp.277-284
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• 2018

Meat quality has always been one of the most important factors that controls the choice of pork consumers and is of great interest in the pig industry. In this study, we identified a single nucleotide polymorphism (SNP) in the enoyl-CoA delta isomerase 2 (ECI2) gene in Berkshire pigs (n = 430) by analyzed the association between the SNP and meat quality traits. The non-synonymous SNP in the ECI2 gene is located at c.608 C > G and resulted in an amino acid change from threonine to serine. Significant associations between the SNP and meat quality traits, such as redness (CIE a), and the $pH_{24hr}$, were revealed in both the dominant and co-dominant models, whereas carcass weight, drip loss, and fat content and moisture content were significantly associated only with the dominant model. In barrow, the SNP was significantly associated with CIE a, drip loss, and $pH_{24hr}$, whereas in gilt, only a significant relationship with moisture content was observed. GG genotype pigs had a higher $pH_{24hr}$ and lower drip loss. Because $pH_{24hr}$ and drip loss are considered the most important meat quality traits, GG genotype pork is high-quality meat compared to that from other genotypes. In conclusion, the SNP in the ECI2 gene is significantly associated with several meat quality traits. These traits and could be as genetic markers in molecular breeding programs for improving meat quality.

• Journal of Life Science
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• v.31 no.12
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• pp.1088-1093
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• 2021

Jeju horse (Equus ferus caballus) is a Korean horse breed that has been native to Jeju Island for a long time. Jeju horses are used as racehorses, and their racing ability is a major economic trait. The role of the myostatin (MSTN) gene in skeletal muscle mass has been studied in various mammals, and mutations in the MSTN gene are known to affect the racing ability and stamina of thoroughbreds. In this study, we compared the frequency of mutations in the MSTN gene in several horse breeds, including 1,433 Jeju horses. Among the mutations (ECA18 g.66493737C>T) in the MSTN gene, the long-distance aptitude genotype (TT) was found to have a frequency of 0.826 in Jeju horses, which was higher than that in Halla horses (0.285) and thoroughbreds (0.252). The genotypes and arrival records of Jeju horses were compared according to various distances (400 m, 800 m, 900 m, 1,000 m, 1,110 m, and 1,200 m). According to the results, the CT type showed a faster-reaching record than the TT type in races of less than 1,000 m. However, almost identical results were confirmed in races over 1,110 m. This study suggests that the MSTN mutation in Jeju horses may be related to race distance aptitude. In future research, the data in this study can be used for developing markers related to race distance aptitude and racing abilities in Jeju horses.

• Journal of Food Hygiene and Safety
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• v.37 no.5
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• pp.317-322
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• 2022

Corynebacterium pseudotuberculosis is the causative agent of caseous lymphadenitis (CLA), a chronic contagious disease in small ruminants. The prevalence of CLA has been reported to be >50% in Korean black goats. CLA is difficult to control due to a lack of efficient vaccines and treatment methods. Effective disinfection of the farm environment may be an alternative strategy for reducing the spread of C. pseudotuberculosis. The objective of this study was to evaluate the efficacy of commercial disinfectants against CLA. The six commercial disinfectants, largely composed of sodium dichloroisocyanurate, sodium hypochlorite, potassium monopersulfate triple salt, quaternary ammonium, citric acid, and copper sulfate, were tested against five different genotypes of C. pseudotuberculosis isolated from goat farms in Korea. Efficacy tests were performed in accordance with the disinfectant efficacy test guidelines recommended by the Animal and Plant Quarantine Agency of Korea with slight modifications. All disinfectants except for copper sulfate exhibited >99.99% killing efficacy under hard water conditions following 30 min of incubation, which is the recommended standard treatment time according to guidelines. The minimum bactericidal treatment time was evaluated by employing treatments for durations of 1, 5, and 15 min. The most effective compounds under hard water conditions were sodium dichloroisocyanurate, potassium monopersulfate triple salt, and sodium hypochlorite, exhibiting >99.99% killing efficacy after 1 min of treatment. In the aqueous solution forms, citric acid and the quaternary ammonium compound were the most effective, but required at least 5 min to kill >99.99% of the bacteria. The current study characterizes the killing efficacy of six commercial disinfectant active compounds against C. pseudotuberculosis. Thus, this study provides essential information regarding the efficacy of the disinfectants used to control CLA in goat farms.

• Journal of Korean Society of Forest Science
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• v.112 no.2
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• pp.157-172
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• 2023

Controlled pollination (CP) is an important method in tree breeding programs because CP quickly generates desirable genotypes and rapidly maximizes genetic gains. However, few studies have evaluated the efficiency and success rate of CP in the breeding program of Pinus densiflora. To evaluate CP and the management of control pollinated progenies, we used 159 individuals in CB2 × KW40 or KW40 × CB2 populations that were established in 2015. After genotyping microsatellite loci, we estimated whether the number of primers was sufficient or not. Then, we performed pedigree analysis. The result showed that the number of primers was sufficient. By pedigree analysis, we found out that 60 of 159 individuals had been generated by the mating between CB2 and KW40. In the maternity analysis, there was evidence to indicate the possibility of management problems. Therefore, we excluded 54 individuals and repeated the pedigree analysis. In the second analysis, 47 of 105 individuals were generated by the mating between CB2 and KW40. To increase the efficiency of CP in tree breeding programs, several precautions are required. It is necessary to identify the exact clone names of the mother and father trees. In addition, CP processes should be performed properly, including deciding on the schedule of CP and the isolation of female strobili or flowers. Finally, the monitoring of hybrid progenies management after mating is important. Molecular markers should be used to identify the clone names of the mother and father trees and for monitoring post hoc management. This study provides a reference for tree breeding programs for the future control pollination of pine species.