• Tuberculosis and Respiratory Diseases
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• v.41 no.4
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• pp.339-353
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• 1994

Background : The p53 gene codes for a DNA-binding nuclear phosphoprotein that appears to inhibit the progression of cells from the G1 to the S phase of the cell cycle. Mutations of the p53 gene are common in a wide variety of human cancers, including lung cancer. In lung cancers, point mutations of the p53 gene have been found in all histological types including approximately 45% of resected NSCLC and even more frequently in SCLC specimens. Mutant forms of the p53 protein have transforming activity and interfere with the cell-cycle regulatory function of the wild-type protein. The majority of p53 gene mutations produce proteins with altered conformation and prolonged half life; these mutant proteins accumulate in the cell nucleus and can be detected by immunohistochemical staining. But protein overexpression has been reported in the absence of mutation. p53 protein overexpression or gene mutation is reported poor prognostic factor in breast cancer, but in lung cancer, its prognostic significance is controversial. Method : We investigated the p53 abnormalities by nucleotide sequencing, polymerase chain reaction-single strand conformation polymorphism(PCR-SSCP), and immunohistochemical staining. We correlated these results with each other and survival in 75 patients with NSCLC resected with curative intent. Overexpression of the p53 protein was studied immunohistochemically in archival paraffin- embedded tumor samples using the D07(Novocastra, U.K.) antibody. Overexpression of p53 protein was defined by the nuclear staining of greater than 25% immunopositive cells in tumors. Detection of p53 gene mutation was done by PCR-SSCP and nucleotide sequencing from the exon 5-9 of p53 gene. Result: 1) Of the 75 patients, 36%(27/75) showed p53 overexpression by immunohistochemical stain. There was no survival difference between positive and negative p53 immunostaining(overall median survival of 26 months, disease free median survival of 13 months in both groups). 2) By PCR-SSCP, 27.6%(16/58) of the patients showed mobility shift. There was no significant difference in survival according to mobility shift(overall median survival of 27 in patients without mobility shift vs 20 months in patients with mobility shift, disease free median survival of 8 months vs 10 months respectively). 3) Nucleotide sequence was analysed from 29 patients, and 34.5%(10/29) had mutant p53 sequence. Patients with the presence of gene mutations showed tendency to shortened survival compared with the patients with no mutation(overall median survival of 22 vs 27 months, disease free median survival of 10 vs 20 months), but there was no statistical significance. 4) The sensitivity and specificity of immunostain based on PCR-SSCP was 67.0%, 74.0%, and that of the PCR-SSCP based on the nucleotide sequencing was 91.8%, 96.2% respectively. The concordance rate between the immunostain and PCR-SSCP was 62.5%, and the rate between the PCR-SSCP and nucleotide sequencing was 95.3%. Conclusion : In terms of detection of p53 gene mutation, PCR-SSCP was superior to immunostaining. p53 gene abnormalities either overexpression or mutation were not a significant prognostic factor in NSCLC patients resected with curative intent. However, patients with the mutated p53 gene showed the trends of early relapse.

• Journal of Animal Science and Technology
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• v.44 no.2
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• pp.181-190
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• 2002

This study was performed to determine sequences of the mt DNA D-loop region, including $tRNA^{Pro}$ and $tRNA^{Pre}$ and to analysis sequence variation polymorphism in Korean cattle. The resulting sequencies were compared with previously published sequences for other cattle breeds(GenBank J01394). The PCR was used to amplify an 1142bp between nucleotides 15061 and 404 within the D-loop region of mt DNA using specific primers. Korean cattle showed 24 polymorphic sites by nucleotide substitutions and insertions of single base pairs. About 50% of polymorphic sites were found in positions 16042 to 16122 with the most variable region. Among these polymorphic sites, variations at 16055, 16230 and 16260 bp were detected as new sequence variants in Korean cattle. These specific polymorphic sites have not been reported in the Japanese black cattle and European cattle. Therefore, mt DNA variants in the D-loop region may be used as genetic markers for specifying Korean cattle. The frequencies of positions 169, 16302, 16093, 16042, 16119 with a high level of sequence polymorphism were 0.81, 0.56, 0.56, 0.50 and 0.43, respectively. In comparison of genetic distances, Korean cattle showed the more closely to European cattle as Bos taurus than Bos indicus such as African and India breeds. In conclusion, these mt DNA sequence polymorphisms in the D-loop region for Korean cattle may be useful for the analysis of cytoplasmic genetic variation and associations with economic important traits and genetic analysis of maternal lineage.

• Korean Journal of Poultry Science
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• v.40 no.2
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• pp.139-145
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• 2013

There are several loci controlling the feather color of birds, of which one of the most studied is Extended black (E) encoding the melanocortin 1-receptor (MC1R). Mutations in this gene affect the relative distribution of eumelanin, phaeomelanin. The association of feather color and sequence polymorphism in the melanocortin 1-receptor (MC1R) gene was investigated using Korean native chicken H breed (H_PL) and 'Woorimatdag' commercial chickens (Woorimatdag_CC). In order to correlate gene mutation to Korean native chicken feather color, single nucleotide polymorphism (SNP) from MC1R gene sequence were investigated. A total of 307 birds from H_PL and Woorimatdag_CC were used. H_PL have black, black-brown feather color and Woorimatdag_CC have black with brown spots or brown with black spots. There are 6 SNPs in MC1R gene, locus T69C, C212T, A274G, G376A, G636A, T637C. 3 SNPs are nonsynonymous that change amino acid. But it is difficult to find correlation of feather color and polymorphisms. It will be needed to increase the population of Korean native chicken H breed and correlation analysis of genetic variation with feather colors.

• Sleep Medicine and Psychophysiology
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• v.22 no.1
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• pp.25-29
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• 2015

Objectives: The pathophysiology of restless legs syndrome (RLS) has not been fully elucidated. Oxidative stress might play a role in the development of RLS and other antipsychotic-induced side effects such as tardive dyskinesia. In the present study, we investigated whether the glutathione S-transferase (GST) gene polymorphisms are associated with antipsychotic-induced RLS in schizophrenia. Methods: We assessed antipsychotic-induced RLS symptoms in 190 Korean schizophrenic patients using the diagnostic criteria of the International Restless Legs Syndrome Study Group. The GST-M1, GST-T1 and GST-P1 loci were analyzed using PCR-based methods. Results: We divided the subjects into 2 groups: those with RLS symptoms (n = 96) and those without RLS symptoms (n = 94). There were no significant differences in the distributions of the GST-M1 genotypes (${\chi}^2=3.56$, p = 0.059), GST-T1 (${\chi}^2=0.51$, p = 0.476) and GST-P1 (${\chi}^2=0.57$, p = 0.821) between the 2 groups. Comparison of the RLS score among genotypes of the GST-M1 (t = -1.54, p = 0.125), GST-T1 (t = -0.02, p = 0.985) and GST-P1 (F = 0.58, p = 0.560) revealed no significant difference. Conclusion: These data suggest that GST gene polymorphisms do not confer increased susceptibility to RLS symptoms in schizophrenic patients. Future studies are necessary to evaluate the possible influences of other candidate genes involved in the reactive oxygen species system.

• Journal of Animal Science and Technology
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• v.53 no.1
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• pp.1-6
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• 2011

This simulation study was performed to investigate the accuracy of the estimated breeding value by using genomic information (GEBV) by way of Bayesian framework. Genomic information by way of single nucleotide polymorphism (SNP) from a chromosome with length of 100cM were simulated with different marker distance (0.1cM, 0.5cM), heritabilities (0.1, 0.5) and half sibs families (20 heads, 4 heads). For generating the simulated population in which animals were inferred to genomic polymorphism, we assumed that the number of quantitative trait loci (QTL) were equal with the number of no effect markers. The positions of markers and QTLs were located with even and scatter distances, respectively. The accuracies of estimated breeding values by way of indicating correlations between true and estimated breeding values were compared on several cases of marker distances, heritabilities and family sizes. The accuracies of breeding values on animals only having genomic information were 0.87 and 0.81 in marker distances of 0.1cM and 0.5cM, respectively. These accuracies were shown to be influenced by heritabilities (0.87 at $h^2$ =0.10, 0.94 at $h^2$ =0.50). According to half sibs' family size, these accuracies were 0.87 and 0.84 in family size of 20 and 4, respectively. As half sibs family size is high, accuracy of breeding appeared high. Based on the results of this study it is concluded that the amount of marker information, heritability and family size would influence the accuracy of the estimated breeding values in genomic selection methodology for animal breeding.

• Korean Journal of Breeding Science
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• v.50 no.4
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• pp.424-433
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• 2018

Watermelon (Citrullus lanatus) is an economically important vegetable crop all over the world, which has functional compounds such as lycopene and citrulline. Gummy stem blight caused by Didymella bryoniae is one of the most devastative diseases in watermelon. Single nucleotide polymorphisms (SNPs), which are genetic variations occurring between individuals with respect to a single base, were often used to construct genetic linkage maps and develop molecular markers linked to a variety of horticultural traits and resistance to several diseases. In this study, we developed high-resolution melting (HRM) markers based on SNPs generated from NGS resequencing of two parents in watermelon. Plant materials were C. lanatus '920533' (female and susceptible parent), C. amarus 'PI 189225' (male and resistant parent), and their $F_1$ and $F_2$ progenies. A total of 13.6 Gbp ('920533') and 13.1 Gbp ('PI 189225') of genomic sequences were obtained using NGS analysis. A total of 6.09 million SNPs between '920533' and 'PI 189225' were detected, and 354,860 SNPs were identified as potential HRM primer sets. From these, a total of 330 primer sets for HRM analysis were designed. As a result, a total of 61 HRM markers that have polymorphic melting curves were developed. These HRM markers can be used for the construction of SNP-based linkage maps and for the analysis of quantitative trait loci (QTLs) related to gummy stem blight resistance.

• Journal of Life Science
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• v.30 no.3
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• pp.230-238
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• 2020

Carcass traits are the most economically important traits in Hanwoo (Korean cattle). Recently, the development of the field of genomics has made it possible to identify DNA markers for the genetic evaluation of carcass and meat quality traits in beef cattle. The objective of this study was to assess the genetic effects of single nucleotide polymorphism (SNP) markers related to carcass traits by field evaluations in a commercial Hanwoo population. We evaluated 15 SNP markers (TG g.371T>C, APM1 g.1454G>A, FABP4 g.2834C>G, FABP4 g.3533T>A, FABP4 g.3691G>A, SCD g.10153A>G, SCD g.10329T >C, CPE g.601T>C, EDG1 g.166A>G, NPY g.4271T>C, GPD1 g.2766C>T, PDE1B g.17122A>G, PDE1B g.17507A>C, TNNT1 g.6650C>T, and RORC g.20152A>G) related to carcass traits in Hanwoo. Genotyping of these SNP markers was performed using PCR-RFLP analysis in Hanwoo steers (n = 1,536) to evaluate their association with carcass traits. Seven SNPs, APM1 g.1454G>, FABP4 g.3691G>A, SCD g.10153A>G, CPE g.601T>C, PDE1B g.17122A>G, TNNT1 g.6650C>T, and RORC g.20152A>G, were significantly associated with carcass traits such as marbling score (MS), backfat thickness (BF), musculus longissimus dorsi area (LDA), carcass weight (CW), meat grade (MG), meat color (MC), and maturity score (MA). The results suggest that these SNPs may be used as DNA markers for the selection of Hanwoo with higher meat quality.

• Journal of Life Science
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• v.28 no.7
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• pp.795-801
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• 2018

This study was conducted to investigate the association of single nucleotide polymorphism (SNP) markers on equine chromosomes (ECA) 3 and 9 with body weight in Jeju horses. We used DNA samples and body weight data of 320 horses provided by the Livestock Promotion Agency, Jeju Special Self-Governing Province, and the Korean Racing Association, respectively. We genotyped all the experimental animals using nine SNP markers located on ECA 3 (BIEC2-808466, BIEC2-808543, BIEC2-808967, and BIEC2-809370) and ECA 9 (BIEC2-1105370, BIEC2-1105372, BIEC2-1105377, BIEC21105505, and BIEC2-1105840). These markers were selected due to their effects on body conformation traits in horses. The joint effect of the genotypes of the two SNP markers (BIEC2-808467 and BIEC2-1105377) regarding body weight were also evaluated. The estimated breeding value (EBV) of body weight was obtained as the dependent variable for association analyses using a linear mixed model. Significant associations were detected between SNP markers (BIEC2-808543, BIEC2-808967, BIEC2-809370, BIEC2-1105370, BIEC2-1105372, and BIEC2-1105377) and the body weight EBV. In addition, the joint genotype effect of the BIEC2-808467 and BIEC2-1105377 on the body weight EBV was significant. These results indicate that the SNP markers, which showed their significant effects on body conformation, can be used as genetic markers to improve the efficiency of the selective breeding program for the body weight traits in Jeju horses.

• Journal of Animal Science and Technology
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• v.52 no.1
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• pp.9-16
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• 2010

A previous study has shown that the g.17924G>A polymorphism of fatty acid synthase (FASN) is associated with unsaturated fatty acid composition in the Hanwoo beef, hence this study was conducted to evaluate the effect of single nucleotide polymorphisms (SNPs) within FASN gene on the selection phenotypes of Hanwoo breeding stock. A total of 925 progeny test steers were used to genotype g.11280G>A, g.13125T>C, and g.17924G>A polymorphisms and significant associations were found among g.11280G>A, g.17924G>A, and carcass traits, such as carcass weight, backfat thickness, and beef quantity index. No significant association was found between g.13125T>C and carcass traits. Although the degree of linkage disequilibrium (LD) was not strong among g.11280G>A, g.13125T>C, and g.17924G>A in the LD analysis, four major haplotype classes were formed with the genotypic information within the FASN gene; the frequencies of the halpotypeswere -GCG-[0.378], -ATG-[0.301], -GTA-[0.191], and -ACG-[0.063], respectively. Phenotypic association was performed among these haploptypes, and the haplotype 2 (-ATG-)was significantly associated with higher carcass weight when compared to the other haplotypes, i.e. haplotype 1 (-GCG-) and haplotype 3 (-GTA-). A copy number of the FASN haplotype 3 (-GTA-) had also a significant association with carcass weight of subjects. In conclusion, it was observed that two polymorphisms (g.11280G>A and g.17924G>A) and their haplotypes within the FASN gene are consistently associated with carcass traits. Therefore, it is desirable to use the FASN polymorphisms for pre-selection program as genetic marker with improved carcass yield and beef quality of the Hanwoo sire at the Hanwoo Improvement Center as well as for commercial Hanwoo producers, the FASN genotypic information can be used for a part of selecting Hanwoo dam for superior calf production.

• Journal of Life Science
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• v.26 no.11
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• pp.1232-1236
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• 2016

Mitochondrial calcium uptake 1 (MICU1) including two canonical EF hands, located in the mitochondrial inner membrane, is known to play a crucial role in the calcium uptake in mitochondria. Mitochondrial calcium uptake in muscular cells is related to post mortem shortening by calcium release from muscles. Therefore, the porcine MICU1 gene has been estimated as a genetic candidate for meat quality traits. In this study, variations on the exonic regions of the porcine MICU1 gene were investigated by sequencing cDNAs and tested for their association with meat quality traits. A total of 667 Berkshire heads (347 sows and 320 castrated boars) were used for this association test. Three SNPs were detected on the 3' untranslated region (UTR) of the porcine MICU1 gene. SNP1 (c.*136G>A) was associated with drip loss (p=0.017) and intramuscular fat content (p=0.039). In addition, SNP2 (c.*222G>A) and SNP3 (c.*485G>A) were associated with drip loss (p=0.018) and intramuscular fat content (p<0.001), respectively. In conclusion, it was verified that three variations on the 3' UTR of the porcine MICU1 gene were significantly associated with meat quality traits. It was also suggested that molecular biological analyses are needed to validate the function of variations on the 3 UTR of the porcine MICU1 gene.