• Journal of Microbiology and Biotechnology
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• v.30 no.11
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• pp.1688-1696
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• 2020

Soil physical and chemical characteristics, soil potential denitrification rates (PDR), community composition and nirK-, nirS- and nosZ-encoding denitrifiers were studied by using MiSeq sequencing, quantitative polymerase chain reaction (qPCR), and terminal restriction fragment polymorphism (T-RFLP) technologies base on short-term (5-year) tillage field experiment. The experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue retention (NT), and rotary tillage with crop residue removed as control (RTO). The results indicated that soil organic carbon, total nitrogen and NH₄⁺-N contents were increased with CT, RT and NT treatments. Compared with RTO treatment, the copies number of nirK, nirS and nosZ in paddy soil with CT, RT and NT treatments were significantly increased. The principal coordinate analysis indicated that tillage management and crop residue returning management were the most and the second important factors for the change of denitrifying bacteria community, respectively. Meanwhile, this study indicated that activity and community composition of denitrifiers with CT, RT and NT treatments were increased, compared with RTO treatment. This result showed that nirK, nirS and nosZ-type denitrifiers communities in crop residue applied soil had higher species diversity compared with crop residue removed soil, and denitrifying bacteria community composition were dominated by Gammaproteobacteria, Deltaproteobacteria, and Betaproteobacteria. Therefore, it is a beneficial practice to increase soil PDR level, abundance and community composition of nitrogen-functional soil microorganism by combined application of tillage with crop residue management.

• Korean Journal of Agricultural Science
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• v.38 no.4
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• pp.689-693
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• 2011

The purpose of this study was to investigate the Cytochrome P450 (CYP2A6) gene as a candidate gene for the traits related with meat fatty acid composition traits in pigs. Porcine CYP2A6 polymorphisms were detected and PCR-RFLP was performed for genotyping of Korean native pig (n=14), Landrace (n=3), Duroc (n=3), Berkshire (n=3), Yorkshire (n=8) and F2 population composed of 202 individuals from an intercross between Korean Native pig and Yorkshire. PCR primer set amplified a 612 bp fragment of CYP2A6 and digestion of the PCR products was performed with the restriction enzymes SchI. The CYP2A6 SchI polymorphism was only found in the KNP breed. The genotype frequencies of TT, TC and CC genotypes were 0.36, 0.56 and 0.08 in the KNP respectively and the other pig breeds were fixed with CC genotype (Duroc, Landrace, Berkshire and Yorkshire). Statistical association between genotypes and fatty acid composition traits were tested in the Korean native pig and Yorkshire crossed F2 pigs. The CYP2A6 SchI polymorphism was associated with only fatty acid composition C20:3n3 level (cis11,14,17-Eicosatrienoic acid, p=0.0252). The 'T' allele was associated with lower C20:3n3 level. Further study is required to validate the genotypic association and biological consequence of the CYP2A6 gene polymorphism in pigs.

• Journal of Pharmaceutical Investigation
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• v.37 no.6
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• pp.369-376
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• 2007

Cyclosporine (CsA) and tacrolimus (FK506) have a narrow therapeutic range, and their pharmacokinetic (PK) characteristic varies among individual. They are also substrates for cytochrome P450 (CYP) 3A4, 3A5 genes, and P-glycoprotein, the product of the multidrug resistance 1 (MDR1). The aims were to investigate the relationship between CYP3A and MDR1 genotypes and their PK parameters among healthy subjects. We investigated the genotype for CYP3A and MDR1 gene in human using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. After oral administration of CsA and FK506 (100 mg and 1 mg, respectively), whole blood samples were taken up to 24 hours. Blood CsA and FK506 concentrations were measured by LC/MS/MS. Each PK parameters were compared using Kruskal-Wallis test according to the CYP3A and MDR1 genotype. We found that the values of AVC for CsA were significantly different among CYP3A5 and MDR1 exon 26 (C3435T) genotypes (P=0.037 and P=0.049). On the other hand, the AUC for FK506 was significantly different only among CYP3A5 genotypes (P=0.013). The results clearly demonstrate the effects of CYP3A5 and MDR1 exon 26 on Cys and FK506 disposition.

• Animal Bioscience
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• v.36 no.6
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• pp.840-850
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• 2023

Objective: This study aimed to investigate the polymorphisms of the dopa decarboxylase (DDC) gene and association analysis with lamb quality and expression quantification of the DDC gene in phenotypically divergent Indonesian sheep. Methods: The totals of 189 rams with an average body weight of 24.12 kg at 10 to 12 months were used to identify DDC gene polymorphism using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Among 189 rams, several rams representing various sheep genotypes were used for an association study between genotypes and phenotypic traits with proc general linear model (GLM) analysis. In addition, the gene expression analysis of the DDC mRNA in the phenotypically divergent sheep population was analyzed using quantitative reverse-transcription PCR. Results: The DDC gene (g. 5377439 G>A) showed polymorphisms that indicated three genotypes: AA, AG, and GG. The DDC gene polymorphism was significantly associated (p≤0.05) with carcass characteristics including carcass percentage, carcass length, hot and cold carcass; physical properties of lamb quality including pH value; retail cut carcass; fatty acid composition such as fat content, pentadecanoic acid (C15:0), tricosylic acid (C23:0), lignoceric acid (C24:0), oleic acid (C18:1n9c), elaidic acid (C18:1n9t), nervonic acid (C24:1), linoleic acid (C18:2n6c), arachidonic acid (C20:4n6), cervonic acid (C22:6n3); and mineral content including potassium (K). The GG genotype of the DDC gene had the best association with lamb quality traits. The DDC gene expression analysis mRNA showed no significant difference (p≥0.05) between lamb quality traits. Conclusion: The DDC gene could be used as a potential candidate gene to improve lamb quality.

• Research in Plant Disease
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• v.29 no.4
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• pp.420-424
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• 2023

In 2020, within the Dongbaekdongsan area in Jeju Island, a Septobasidium sp. associated with a felt disease in Castanopsis sieboldii (Makino) Hatus. ex T. Yamaz. & Mashiba was identified. The symptom included the presence of brown, thin, and silk-like mycelial mats attached to the tree's bark, displaying variations in size from large to small. To induce hyphal growth, the samples collected were incubated in a moist chamber, and the newly formed hyphae were subjected to genomic DNA extractions. The nucleotide sequences of the internal transcribed spacer and small subunit rDNA genes were determined, and molecular characteristics among the isolates were investigated through polymerase chain reaction-based restriction fragment length polymorphism analysis. This Septobasidium sp. exhibited distinct morphological and phylogenetic features compared to those that were previously reported in South Korea. Consequently, this strain is taxonomically classified as a provisionally novel species of Septobasidium. Furthermore, the observed felt disease exhibited a high degree of host specificity, as it was exclusively identified in C. sieboldii without occurrence in other tree species at the time of observation.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.8
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• pp.3785-3791
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• 2016

Background: Previous studies have assessed the association between the Cytotoxic T-lymphocyte Antigen-4(CTLA-4) polymorphism with the risk of malignant bone tumor, but the conclusions were inconsistent. We aimed to clarify association of cytotoxic T-lymphocyte antigen-4 polymorphisms with malignant bone tumors risk by performing a meta-analysis. Materials and Methods: The databases including PubMed, EMBase databases and the Cochrane Library were searched to identify the eligible studies prior to January 30 2016. Odds ratio (OR) with 95% confidence interval (95%CI) were used to estimate the strengths of the association between the CTLA-4 polymorphism and the malignant bone tumor risks. The meta-analysis was performed by STATA 12.0. Results: Four individual studies with a total of 1003 cases with malignant bone tumor and 1162 controls were included in our meta-analysis. The results of meta-analysis on those data demonstrated that CTLA-4 +49G>A polymorphism was associated with the risk of Ewing's sarcoma and osteosarcoma strongly (A vs. G: OR=1.36, 95%CI:1.20-1.54, p=0.000; AA+AG vs. GG: OR=1.35, 95%CI:1.14-1.61, p=0.001; AA vs. GG: OR=2.24, 95%CI:1.67-2.99, p=0.000; AA vs. AG+GG: OR=2.00, 95%CI:1.53-2.62, p=0.000), but CTLA-4 -318C/T polymorphism was not associated with the risk of malignant bone tumor (C vs. T: OR=0.76, 95%CI:0.76-1.08, p= 0.262; CC+CT vs. TT: OR=0.70, 95%CI:0.41-1.20, p= 0.198; CC vs. TT: OR=0.69, 95%CI:0.40-1.19, p= 0.183; CC vs. CT+TT: OR=0.92, 95%CI:0.75-1.13, p= 0.419). Subgroup analysis showed that there are significantly positive correlations between CTLA-4 +49G>A polymorphism and increased risks of malignant bone tumors in large size of sample (A vs. G: OR=1.347, 95%CI: 1.172,1.548, p=0.000; AA vs. GG: OR=2.228, 95%CI: 1.608,3.085, p=0.000), Ewing's Sarcoma or Osteosarcoma (A vs. G: OR=1.361, 95%CI: 1.201,1.540, p=0.000; AA vs. GG: OR=2.236, 95%CI: 1.674,2.986, p=0.000), and PCR-RFLP or Sequencing(A vs. G: OR=1.361, 95%CI: 1.201,1.540, p=0.000; AA vs. GG: OR=2.236, 95%CI: 1.674,2.986, p=0.000), but CTLA-4 -318C/T polymorphism was not associated with the risk of malignant bone tumors in diagnosis, genotype method, and sample size (all p>0.05). Conclusions: CTLA-4 +49A/G variant was associated with an increased risk of developing the malignant bone tumors, such as Ewing's sarcoma and osteosarcoma. However, it failed to show the association between CTLA-4 -318C/T polymorphism and the risk of malignant bone tumors. Future large-scale studies remain to be done to confirm our conclusions.

• Journal of Genetic Medicine
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• v.5 no.2
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• pp.119-124
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• 2008

Purpose: Aneuploidy is the cause of diseases such as Down syndrome or Edward syndrome and, more generally, is a major cause of mental retardation and fetal loss. The purpose of this study was to evaluate the association between MTHFR (C677T) or MTRR (A66G) polymorphisms and fetal aneuploidy. Materials and Methods: Data was collected from 37 women who had a fetus with aneuploidy (cases) and 78 women who had previously delivered at least two healthy children without aneuploidy and did not have a history of miscarriage or abnormal pregnancy (controls). The MTHFR (C677T) or MTRR (A66G) polymorphisms were analyzed by PCR-restriction fragment length polymorphism assay. Results: The frequencies of the MTHFR 677 CC, CT, and TT genotypes were 30.7%, 48.7%, and 20.6% in the control group and 37.8%, 48.6%, and 13.5% in the case group, respectively. There were no significant differences in genotype frequencies between the two groups. For the MTRR A66G polymorphism, the frequencies of the AA, AG and GG genotypes were 50%, 46.1%, and 3.9% in the control group and 13.5%, 81.1%, and 5.4% in case group, respectively. The frequency of the MTRR AG mutant was significantly increased in the case group, with an odds ratio of 6.5 (95% CI: 2.3-18.6, P<0.05). Conclusion: The results of this study suggest that mother carriers with the MTRR G allele have an increased risk of fetal aneuploidy, while the MTHFR T allele is not associated with increased risk of fetal aneuploidy. The MTRR A66G polymorphism may be a risk factor for producing a child with chromosomal aneuploidy.

• Tuberculosis and Respiratory Diseases
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• v.62 no.6
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• pp.492-498
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• 2007

Background: Several lines of evidence suggest that a host's genetic factors influence the outcome of exposure to Mycobacterium tuberculosis. The aim of this study was to determine whether polymorphism in NRAMP1 (natural resistance associated macrophage protein 1) gene is associated with the susceptibility or resistance to tuberculosis infection for patients with drug-sensitive pulmonary tuberculosis (DS-TB) and multi-drug resistant pulmonary tuberculosis (MDR-TB). Methods: Eight genetic polymorphisms of the NRAMP1 gene were investigated in patients suffering with DS-TB (n=100) or MDR-TB (n=102), and in healthy normal controls (NC, n=96). The genetic polymorphisms of NRAMP1 were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Results: The frequency of D543N A/G heterogygotes was significantly higher in the DS-TB subjects than the NCs (OR=2.10, 95% CI: 1.00 to 4.41, p=0.049). The frequency of 823C/T T/C heterozygotes was significantly higher in the DS-TB subjects (OR=2.79, 95% CI: 1.11 to 7.04, p=0.029) and the MDR-TB subject (OR=3.30, 95% CI 1.33 to 8.18, p=0.010) than in the NCs. However, the frequency of these genotypes was not different between the DS-TB and MDR-TB subjects. Conclusion: A significant association was found between NRAMP1 823 C/T polymorphism and pulmonary tuberculosis. This result suggests that NRAMP1 polymorphism may be involved in the development of pulmonary tuberculosis in Koreans.

• Clinical and Experimental Reproductive Medicine
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• v.33 no.2
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• pp.85-95
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• 2006

Objective: To investigate whether polymorphisms of gene encoding CYP1B1 is associated with the risk of endometriosis in Korean women. Methods: We investigated 199 patients with histopathologically confirmed endometriosis rAFS stage III/IV and 183 control group women who were surgically proven to have no endometriosis. The genetic distribution of four different CYP1B1 polymorphisms at $G^{119}-T$, $G^{432}-C$, $T^{449}-C$, and $A^{453}-G$ were analyzed by polymerase chain reaction(PCR) and restriction fragment length polymorphism of PCR products. Results: We found no overall association between each individual CYP1B1 genotype and the risk of endometriosis. The odds ratio of genotype GG/GC+GG/TC+TT/AA compared to GG/CC/CC/AA(reference) was calculated as 2.06 with a 95% confidence interval of 1.003~4.216. Conclusion: This results suggest that CYP1B1 genetic polymorphism may be associated with development of endometriosis in Korean women.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.8
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• pp.4017-4023
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• 2012

Background and Aim: Polymorphisms in methylenetetrahydrofolate reductase (MTHFR) are known to be associated with predisposition for certain cancers. This study aimed to evaluate the effects of lifestyle factors, family history and genetic polymorphisms in MTHFR C677T and A1298C on rectal cancer risk and possible interactions with lifestyle factors in Northeast Thailand. Methods: A hospital-based case-control study was conducted during 2002-2006 with recruitment of 112 rectal cancer cases and 242 non-rectal cancer patient controls. Information was collected using a structured-questionnaire. Blood samples were obtained for assay of MTHFR C677T and A1298C genotypes by polymerase chain reaction with restriction fragment length polymorphism (PCR-RFLP) techniques. Associations between lifestyle factors, family history and genetic polymorphisms v.s. rectal cancer risk were assessed using logistic regression analysis. Results: Subjects with frequent and occasional constipation had a higher risk ($OR_{adj.}$=14.64; 95%CI=4.28-50.04 and $OR_{adj.}$=2.15; 95%CI=1.14-4.06), along with those who reported ever having hemorrhoids ($OR_{adj.}$=2.82; 95%CI=1.36-5.84) or a family history of cancer ($OR_{adj.}$=1.90; 95%CI=1.06-3.39). Consumption of a high level of pork was also associated with risk ($OR_{adj.}$=1.82; 95%CI=1.05-3.15). Interactions were not observed between MTHFR and other risk factors. Conclusions: This study suggested that the risk factors for rectal cancer in the Thai population are bowel habits, having had hemorrhoids, a family history of cancer and pork consumption.