• Journal of Animal Science and Technology
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• v.66 no.4
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• pp.702-716
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• 2024

The objective of this study was to identify genomic regions and candidate genes associated with productive traits using a total of 37,099 productive records and 6,683 single nucleotide polymorphism (SNP) data obtained from five Great-Grand-Parents (GGP) farms in Landrace. The estimated of heritabilities for days to 105 kg (AGE), average daily gain (ADG), backfat thickness (BF), and eye muscle area (EMA) were 0.49, 0.49, 0.56, and 0.23, respectively. We identified a genetic window that explained 2.05%-2.34% for each trait of the total genetic variance. We observed a clear partitioning of the four traits into two groups, and the most significant genomic region for AGE and ADG were located on the Sus scrofa chromosome (SSC) 1, while BF and EMA were located on SSC 2. We conducted Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), which revealed results in three biological processes, four cellular component, three molecular function, and six KEGG pathway. Significant SNPs can be used as markers for quantitative trait loci (QTL) investigation and genomic selection (GS) for productive traits in Landrace pig.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.9
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• pp.4315-4320
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• 2012

Background: The P53 tumor suppressor gene plays a pivotal role in maintaining cellular homeostasis by preventing the propagation of genome mutations. P53 in its transcriptionally active form is capable of activating distinct target genes that contribute to either apoptosis or growth arrest, like P21. However, the MDM2 gene is a major negative regulator of P53. Single nucleotide polymorphisms (SNP) in codon Arg72Pro of P53 results in impairment of the tumor suppressor activity of the gene. A similar effect is caused by a SNP in codon 31 of P21. In contrast, a SNP in position 309 of MDM2 results in increased expression due to substitution of thymine by guanine. All three polymorphisms have been associated with increased risk of tumorigenesis. Aim of the study: We aimed to study the prevalence of SNPs in the P53 pathway involving the three genes, P53, P21 and MDM2, among acute myeloid leukemia (AML) patients and to compare it to apparently normal healthy controls for assessment of impact on risk. Results: We found that the P21 ser31arg heterozygous polymorphism increases the risk of AML (P value=0.017, OR=2.946, 95% CI=1.216-7.134). Although the MDM2 309G allele was itself without affect, it showed a synergistic effect with P21 ser/arg polymorphism (P value=0.003, OR=6.807, 95% CI=1.909-24.629). However, the MDM2 309T allele abolish risk effect of the P21 polymorphic allele (P value=0.71). There is no significant association of P53 arg72pro polymorphism on the risk of AML. Conclusion: We suggest that SNPs in the P53 pathway, especially the P21 ser31arg polymorphism and combined polymorphisms especially the P21/MDM2 might be genetic susceptibility factors in the pathogenesis of AML.

• International Journal of Industrial Entomology and Biomaterials
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• v.8 no.1
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• pp.113-115
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• 2004

Six generations (P$_1$, P$_2$, F$_1$, BC$_1$, BC$_2$ and F$_2$) of four bivoltine silkworm crosses (SKAU-R-1 ${\times}$ Yakwei, SKAU-R-6 ${\times}$ Yakwei, CSR$_2$ ${\times}$ CSR$_4$ and SH$_{6}$${\times}$ NB$_4$D$_2$) were evaluated in a completely randomized block design with 5 replications for each treatment. The generation mean 2 in respect of 3 metric traits (single cocoon weight, single shell weight, and shell ratio ％), were subjected to Cavallis joint scaling test. Additive dominance model was found to be adequate in CSR$_2$${\times}$CSR$_4$ and SH$_{6}$${\times}$ NB$_4$D$_2$ for single cocoon weight and shell weight and SKAU-R-6 ${\times}$ Yakwei for shell ratio(％). Whereas, in rest of the crosses epistasis was evident in the traits under investigation. Magnitude of additive gene effect (d) was greater than dominance(h) in SH$_{6}$${\times}$NB$_4$D$_2$ and SKUA-R-6${\times}$Yakwei for shell ratio (％) and in CSR$_2$${\times}$ CSR$_4$ for shell weight. Thus selection for these traits in early segregating generations of these crosses would be effective for obtaining considerable genetic gain. gain.

• Journal of Microbiology and Biotechnology
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• v.26 no.12
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• pp.2184-2191
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• 2016

The time-consuming and high-cost preparation of soluble peptide-major histocompatibility complexes (pMHC) currently limits their wide uses in monitoring antigen-specific T cells. The single-chain trimer (SCT) of peptide-${\beta}2m$-MHC class I heavy chain was developed as an alternative strategy, but its gene fusion is hindered in many cases owing to the incompatibility between the multiple restriction enzymes and the restriction endonuclease sites of plasmid vectors. In this study, overlap extension PCR and one-step cloning were adopted to overcome this restriction. The SCT gene of the $OVA_{257-264}$ peptide-$(GS_4)_3-{\beta}2m-(GS_4)_4-H-2K^b$ heavy chain was constructed and inserted into plasmid pET28a by overlap extension PCR and one-step cloning, without the requirement of restriction enzymes. The SCT protein was expressed in Escherichia coli, and then purified and refolded. The resulting $H-2K^b/OVA_{257-264}$ complex showed the correct structural conformation and capability to bind with $OVA_{257-264}$-specific T-cell receptor. The overlap extension PCR and one-step cloning ensure the construction of single-chain MHC class I molecules associated with random epitopes, and will facilitate the preparation of soluble pMHC multimers.

• Research in Plant Disease
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• v.14 no.3
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• pp.165-170
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• 2008

One hundred and three isolates of Xanthomonas oryzae pv. oryzae in Korea were evaluated for their virulence on four near-isogenic lines (NILs) containing a single resistance gene, and Korean differential varieties. The resistant gene backgrounds of Cheongcheongbyeo, Pungsanbyeo, Hangangchalbyeo, Milyang42 were not completely understood and they were not suited for the classification of X. oryzae pv. oryzae. Four NILs, IRBB101, IRBB103, IRBB105, and IRBB107 were difference for characterizing races of X. oryzae pv. oryzae because they have a single resistance gene. These NILs may be useful differential set in examining pathogenic races of X. oryzae pv. oryzae in Korea. Based on the virulence of 103 isolates to new differential varieties, they were classified into 3 races.

• Journal of Animal Science and Technology
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• v.51 no.6
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• pp.453-458
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• 2009

Prion protein (PRNP) is known to be a causative protein for transmissible spongiform encephalopathy (TSE), a disease occurring in human and animals. Previous results indicate that the genetic variability can affect the resistance and susceptibility of goat scrapie and can give the guideline for reducing the risk of this disease. Until now, 35 single nucleotide polymorphisms (SNPs) were identified in goat PRNP gene from many countries such as Great Britain, Italy, United States of America and Asian countries etc. In this study, SNPs in PRNP gene have been investigated to research the PRNP variations and their possible TSE risks in 60 Korean native goats. Based on the sequencing results, we identified four SNPs and three of those polymorphisms (G126A, C414T and C718T) were synonymous and the A428G polymorphism was non-synonymous which changes the amino acid histidine to arginine. Previously, all of these four SNPs were identified in Asian native goats. Specifically, five polymorphisms were identified in Asian native goats and two of them (G126A and C414T) were silent mutations, and the other SNPs (T304G, A428G and T718C) caused amino acid changes (W102G, H143R and S240P). Comparing with SNP results from other breeds, this study is an initial step to understand resistance and susceptibility of this disease in Korean native goats.

• Journal of Periodontal and Implant Science
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• v.42 no.5
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• pp.151-157
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• 2012

Purpose: Cyclooxygenase (COX) enzyme catalyzes the production of prostaglandins, which are important mediators of tissue destruction in periodontitis. Single nucleotide polymorphisms of $COX_2$ enzyme have been associated with increasing susceptibility to inflammatory diseases. The present study evaluates the association of two single nucleotide polymorphisms in $COX_2$ gene (-1195G>A and $8_{473}$C>T) with chronic periodontitis in North Indians. Methods: Both SNPs and their haplotypes were used to explore the associations between $COX_2$ polymorphisms and chronic periodontitis in 56 patients and 60 controls. Genotyping was done by polymerase chain reaction followed by restriction fragment length polymorphism. Chi-square test and logistic regression analysis were performed for association analysis. Results: By the individual genotype analysis, mutant genotypes (GA and AA) of $COX_2$-1195 showed more than a two fold risk (odds ratio [OR]>2) and $COX_2$ $8_{473}$ (TC and CC) showed a reduced risk for the disease, but the findings were not statistically significant. Haplotype analysis showed that the frequency of the haplotype AT was higher in the case group and a significant association was found for haplotype AT (OR, 1.79; 95% confidence interval, 1.03 to 3.11; P=0.0370) indicating an association between the AT haplotype of $COX_2$ gene SNPs and chronic periodontitis. Conclusions: Individual genotypes of both the SNPs were not associated while haplotype AT was found to be associated with chronic periodontitis in North Indians.

• Journal of Microbiology and Biotechnology
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• v.27 no.2
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• pp.335-341
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• 2017

The complexity of the bacterial recombination system is a barrier for the construction of bacterial mutants for the further functional investigation of specific genes. Several protocols have been developed to inactivate genes from the genus Pseudomonas. Those protocols are complicated and time-consuming and mostly do not enable easy construction of multiple knock-ins/outs. The current study describes a single and double crossover-recombination system using an optimized vector-free allele-exchange protocol for gene disruption and gene replacement in a single species of the family Pseudomonadaceae. The protocol is based on self-ligation (circularization) for the DNA cassette which has been obtained by overlapping polymerase chain reaction (Fusion-PCR), and carries an antibiotic resistance cassette flanked by homologous internal regions of the target locus. To establish the reproducibility of the approach, three different chromosomal genes (ncRNA31, rpoN, rpoS) were knocked-out from the root-associative bacterium Pseudomonas stutzeri A1501. The results showed that the P. stutzeri A1501 mutants, which are free of any plasmid backbone, could be obtained via a single or double crossover recombination. In order to optimize this protocol, three key factors that were found to have great effect on the efficiency of the homologous recombination were further investigated. Moreover, the modified protocol does not require further cloning steps, and it enables the construction of multiple gene knock-in/out mutants sequentially. This work provides a simple and rapid mutagenesis strategy for genome editing in P. stutzeri, which may also be applicable for other gram-negative bacteria.

• Journal of Preventive Medicine and Public Health
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• v.39 no.2
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• pp.177-183
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• 2006

Objectives : In this study we examined the association between the genetic markers ACE (A-240T, C-93T, I/D, A2350G), AGT (M235T), AT1R (A1166C), CYP11B2 (T344C, V386A), REN (G2646A), ADRB2 (G46A, C79G, T47C, T1641), GNB3 (C825T) and ADD1 (G460W) and the presence of essential hypertension in adolescents. Methods : The Kangwha Study is an 18-year prospective study that is aimed at elucidating the determinants of the blood pressure level from childhood to early adulthood. For this study, we constructed a case-control dataset of size of 277 and 40 family trios data from the Kangwha Study. For this purpose, we perform a single locus-based case-control association study and a single locus-based TDT (transmission/disequilibrium test) study. Results : In the case-control study, the single locus-based association study indicated that the ADD1 (G460W) (p=0.0403), AGT (M235T) (p=0.0002), and REN (G2646A) (p=0.0101) markers were significantly associated with the risk of hypertension. These results were not confirmed on the TDT study. This study showed that genetic polymorphisms of the ADD1, AGT and REN genes might be related to the hypertension in Korean adolescents. Conclusions : This study provided useful information on genetics markers related to blood pressure. Further study will be needed to confirm the effect of the alpha adducin gene, the angiotensinogen gene and the renin gene on essential hypertension.

• International Journal of Industrial Entomology and Biomaterials
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• v.18 no.2
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• pp.113-120
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• 2009

Embryonic lethal abnormal visual (elav) is a lethal gene in Drosophila inducing the abnormal development and function of nervous system. We cloned a Bm-elav gene by bioinformatics and biological experiment, based on sequence of ELAV protein and dbEST of Bombyx mori. The full-length of Bm-elav cDNA is 1498 bp, contains a 906 bp open read frame (ORF) encoding a precursor of 301 amino acid residues with a calculated molecular weight of 34 kDa and pI of 8.99. Bm-ELAV protein precursor contains three RNA recognition motifs (RRM) in $24{\sim}91$, $110{\sim}177$ and $222{\sim}295$ bit amino acid residues respectively, and belongs to RNA-binding protein family. Bm-ELAV shared varying positives, ranging from 56% to 60% (Identities from 41% to 45%), with RRM from other species of Xenopus tropicalis, Apis mellifera, Tribolium castaneum, Branchiostoma belcheri and Drosophila. Gene localization indicated that Bm-elav is a single-copy gene, gene mapping within 12-chromosome from 7916.68 knt to 7918.16 knt region of nscaf2993. Spatiotemporal expressions pattern analysis revealed that Bm-elav expressed higher in most tested tissues and developmental stages in whole generation, such as silk gland, fat body, midgut, hemopoietic organ and ovary, but almost no expression in terminated diapause eggs. This suggested that the expression of Bm-elav in early developmental embryonic stages might induce abnormal development like in Drosophila. Cloning of the Bm-elav gene enables us to test its potential role in controlling pests by transferring the gene into field lepidopteran insects in the future.