• Asian Pacific Journal of Cancer Prevention
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• 제13권10호
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• pp.5069-5074
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• 2012

Objectives: The purpose of this study was to determine the relationship between methylation status of the Dact1 gene and MTHFR a1298c polymorphic forms in transitional cell carcinoma tissues in a Chinese population. Methods: Polymorphisms of folate metabolism enzyme gene MTHFR were assessed by restrictive fragment length polymorphism (RFLP) methods and PCR-based DNA methylation analysis was used to determine the CpG island methylation status of the Dact1 gene. Associations between the methylation status of the Dact1 gene and clinical characteristics, as well as MTHFR a1298c polymorphisms, were analyzed. Results: aberrant methylation of the Dact1 gene was found in 68.3% of cancer tissues and 12.4% of normal tissues,. The methylation rate of the Dact1 gene in cancer tissues was significantly higher in patients with lymph node metastasis than in those without lymph node metastasis (46.3% vs. 17.2%, P = 0.018). No association was found between aberrant DNA methylation and selected factors including sex, age, tobacco smoking, alcohol consumption and green tea consumption. After adjusting for potential confounding variables, variant allele of MTHFR a1298c was found to be associated with methylation of the Dact1 gene. Compared with wild type CC, the odds ratio was 4.33 (95% CI: 1.06-10.59) for AC and 4.95 (95% CI: 1.18-12.74) for AA. The N stage in TNM staging and the occurrence of lymph node metastasis were associated with an MTHFR 1298 AA+AC genotype (P<0.05). Conclusion: MTHFR 1298 AC and AA genotypes might help maintain a normal methylation status of the Dact1 gene, aberrant CpG island methylation of which is closely related to the genesis and progression of transitional cell carcinoma.

• Asian-Australasian Journal of Animal Sciences
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• 제29권12호
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• pp.1675-1681
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• 2016

The aim of this study was to detect positional candidate genes located within the support interval (SI) regions based on the results of red blood cell, mean corpuscular volume (MCV), and mean corpuscular hemoglobin quantitative trait locus (QTL) in Sus scrofa chromosome 13, and to verify the correlation between specific single-nucleotide polymorphisms (SNPs) located in the exonic region of the positional candidate gene and the three genetic traits. The flanking markers of the three QTL SI regions are SW38 and S0215. Within the QTL SI regions, 44 genes were located, and runt-related transcription factor 1, dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A (DYRK1A), and potassium inwardly-rectifying channel, subfamily J, member 15 KCNJ15-which are reported to be related to the hematological traits and clinical features of Down syndrome-were selected as positional candidate genes. The ten SNPs located in the exonic region of the three genes were detected by next generation sequencing. A total of 1,232 pigs of an $F_2$ resource population between Landrace and Korean native pigs were genotyped. To investigate the effects of the three genes on each genotype, a mixed-effect model which is the considering family structure model was used to evaluate the associations between the SNPs and three genetic traits in the $F_2$ intercross population. Among them, the MCV level was highly significant (nominal $p=9.8{\times}10^{-9}$) in association with the DYRK1A-SNP1 (c.2989 G$F_2$ intercross, our approach has limited power to distinguish one particular positional candidate gene from a QTL region.

• Journal of Crop Science and Biotechnology
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• 제10권3호
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• pp.147-158
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• 2007

Xanthomonas axonopodis pv. glycines(Xag) is a pathogen that causes bacterial leaf pustule(BLP) disease in soybeans grown in Korea and the southern United States. Typical and early symptoms of the disease are small, yellow to brown lesions with raised pustules that develop into large necrotic lesions leading to a substantial loss in yield due to premature defoliation. After Xag infects PI 96188, only pustules without chlorotic haloes were observed, indicating the different response to Xag. To identify differentially expressed genes prior to and 24 hr after Xag inoculation to PI 96188 and BLP-resistant SS2-2, an oligonucleotide macroarray was constructed with 100 genes related to disease resistance and metabolism from soybean and Arabidopsis. After cDNAs from each genotype were applied on the oligonucleotide macroarrays with three replicates and dye swapping, 36 and 81 genes were expressed as significantly different between 0 hr and 24 hr in PI 96188 and SS2-2, respectively. Six UniGenes, such as the leucine-rich repeat protein precursor or 14-3-3-like protein, were selected because they down-regulated in PI 96188 and up-regulated in SS2-2 after Xag infection, simultaneously. Using tubulin and cDNA of Jangyeobkong(BLP-susceptible) as controls, the oligonucleotide macroarray data concurred with quantitative real-time RT-PCR(QRT RT-PCR) results in most cases, supporting the accuracy of the oligonucleotide macroarray experiments. Also, QRT RT-PCR data suggested six candidate genes that might be involved in a necrotic response to Xag in PI 96188.

• Parasites, Hosts and Diseases
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• 제53권3호
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• pp.271-277
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• 2015

The genetic diversity of Schistosoma haematobium remains largely unstudied in comparison to that of Schistosoma mansoni. To characterize the extent of genetic diversity in S. haematobium among its definitive host (humans), we collected S. haematobium eggs from the urine of 73 infected schoolchildren at 5 primary schools in White Nile State, Sudan, and then performed a randomly amplified polymorphic DNA marker ITS2 by PCR-RFLP analysis. Among 73 S. haematobium egg-positive cases, 13 were selected based on the presence of the S. haematobium satellite markers A4 and B2 in their genomic DNA, and used for RFLP analysis. The 13 samples were subjected to an RFLP analysis of the S. haematobium ITS2 region; however, there was no variation in size among the fragments. Compared to the ITS2 sequences obtained for S. haematobium from Kenya, the nucleotide sequences of the ITS2 regions of S. haematobium from 4 areas in Sudan were consistent with those from Kenya (> 99%). In this study, we demonstrate for the first time that most of the S. haematobium population in Sudan consists of a pan-African S. haematobium genotype; however, we also report the discovery of Kenyan strain inflow into White Nile, Sudan.

• Genomics & Informatics
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• 제10권3호
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• pp.184-193
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• 2012

Gastric cancer is ranked as the most common cancer in Koreans. A recent molecular biological study about the folate pathway gene revealed the correlation with a couple of cancer types. In the folate pathway, several genes are involved, including methylenetetrahydrofolate reductase (MTHFR), methyltetrahydrofolate-homocysteine methyltransferase reductase (MTRR), and methyltetrahydrofolate-homocysteine methyltransferase (MTR). The MTHFR gene has been reported several times for the correlation with gastric cancer risk. However, the association of the MTRR or MTR gene has not been reported to date. In this study, we investigated the association between the single nucleotide polymorphisms (SNPs) of the MTHFR, MTRR, and MTR genes and the risk of gastric cancer in Koreans. To identify the genetic association with gastric cancer, we selected 17 SNPs sites in folate pathway-associated genes of MTHFR, MTR, and MTRR and tested in 1,261 gastric cancer patients and 375 healthy controls. By genotype analysis, estimating odds ratios and 95% confidence intervals (CI), rs1801394 in the MTRR gene showed increased risk for gastric cacner, with statistical significance both in the codominant model (odds ratio [OR], 1.39; 95% CI, 1.04 to 1.85) and dominant model (OR, 1.34; 95% CI, 1.02 to 1.75). Especially, in the obese group (body mass index ${\geq}25kg/m^2$), the codominant (OR, 9.08; 95% CI, 1.01 to 94.59) and recessive model (OR, 3.72; 95% CI, 0.92 to 16.59) showed dramatically increased risk (p < 0.05). In conclusion, rs1801394 in the MTRR gene is associated with gastric cancer risk, and its functional significance need to be validated.

• 농업과학연구
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• 제45권2호
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• pp.238-247
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• 2018

The overall consumption of meat is increasing as the level of national income increases. The end weight is a trait closely associated with dressed meat. Genome-wide association study (GWAS) is an effective method of analyzing genetic variation and gene identification associated with a number of natural alternative traits because it can detect variations. So this paper did a GWAS analysis to identity the location on the genome related to the end weight in purebred landrace pigs and to explore the relevant candidate gene. This study identified a significant single nucleotide poly morphism (SNP) marker in chromosome 6 (ASGA0029422, $p=1.22{\times}10^{-6}$). Adhesion G protein-coupled receptor L2 (ADGRL2) was found to be the candidate gene at the identified SNP marker location. ADGRL2 genes have been found to be associated with cell development in relation to the external and internal environment of a cell. In addition, genotype and statistical analyses were done on nine variations on the exon of ADGRL2. The results show that the SNP marker (ASGA0029422, $p=1.32{\times}10^{-6}$) was significant, but the significance of the nine variations on the ADGRL2 exon was not verified. However, by performing further experiments and functional studies on other SNPs showing possible genetic ADGRL-Exon mutations, objects with high associations of high-end weights can be selected.

• Journal of the Korean Data and Information Science Society
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• 제25권6호
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• pp.1385-1395
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• 2014

가축의 경제적인 특성은 환경적인 요인과 유전적인 요인의 영향을 받으며, 또한 하나의 유전자가 아닌 여러 유전자의 상호작용의 영향을 받는다고 알려져 있다. 본 논문에서는 선형회귀모형을 활용하여 환경적인 요인을 보정한 자료로 한우의 맛과 육질에 영향을 준다고 밝혀진 지방산합성효소의 단일염기다형성 5개를 이용해 한우의 경제 형질에 영향을 미치는 우수 유전자 조합을 선별하고 우수 유전자형을 밝힌다. 이를 위해 데이터마이닝 기법인 인공신경망, 로지스틱 회귀모형, C5.0, CART 기법을 이용하였다. 공정한 모형 평가를 위해 전체 데이터를 훈련용 데이터 (60%)와 검증용 데이터 (40%)로 나누었고, 훈련용 데이터에서 설정된 모형을 검증용 데이터에 적용시켜 정확도를 비교하였다. 그 결과 C5.0이 최적 모형으로 선정되었으며, C5.0의 의사결정나무를 통해 우수 유전자 조합을 선별하였다.

• Journal of Plant Biotechnology
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• 제41권4호
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• pp.236-241
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• 2014

An efficient regeneration protocol for stem disc culture of Populus euramericana, which is important species for bioenergy resource in agroforestry, was established. The number of explants that were obtained and the number of explants that regenerated varied with the genotypes. However, in all the genotypes, stem disc culture produced more regenerated shoots than did in axillary bud culture. A comparison of the effects of cytokinin type and concentration on shoot regeneration in different explants (i.e., petiole, leaf, and root segments of P. euramericana) revealed that a concentration of $0.002mg\;l^{-1}$ thidiazuron (TDZ) used on petiole segments resulted in the greatest shoot regeneration (95.83%). The hormonal requirements for the greatest shoot regeneration in the three explant types varied. Different concentrations of $AgNO_3$ and $CoCl_2$ were added separately to the medium to stop the yellowing and subsequent necrosis of the regenerated shoots. Lower concentrations (3 and $5mg\;l^{-1}$) of these compounds improved shoot regeneration and elongation, compared with the control. The in vitro-regenerated shoots were transferred to rooting medium and subsequently acclimatized. The highly efficient regeneration system of P. euramericana reported here can be used for mass propagation of this recalcitrant for regeneration, economically important tree species.

• 대한의생명과학회지
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• 제25권2호
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• pp.190-195
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• 2019

Hemoglobin (Hb) concentrations and hematocrit (Hct) values can be changed by factors such as erythrocyte production, destruction, and bleeding. In addition, variants in the protein expression involved in the amount of red blood cells that determine Hb metabolism or Hct value can increase susceptibility to complex blood diseases. Previous studies have reported significant single nucleotide polymorphisms (SNPs) by applying a genome-wide association study (GWAS) on Hb levels and Hct values in European population. In this study, we confirmed whether the significant SNPs are replicated in Koreans. In previous studies, 26 and 18 SNPs with a significant correlation Hb and Hct were identified in Korean genotype data, and 21 and 12 SNPs were selected, respectively. The SNPs of PRKCE (rs10495928), TMPRSS6 (rs2235321, rs5756505, rs855791) were significantly associated with Hb (P<0.05). In the association analysis of Hct, the SNPs of HBS1L (rs6920211, rs9389268, rs9483788), PRKCE (rs4953318), SCGN (rs9348689) and TMPRSS6 (rs2413450) genes showed a significant correlation (P<0.05). Replicated SNPs and not replicated SNPs showed the difference of genetic distance calculated by Fst. The replicated SNPs with a significant correlation showed similar allele frequencies, whereas the not replicated SNPs showed a large difference in allele frequency. All replicated SNPs with significant correlations had Fst values less than 0.05, indicating that the genetic distance between the groups was close. On the other hand, the not replicated SNPs showed that the Fst value was 0.05 or more and the genetic distance was relatively large.

• Tuberculosis and Respiratory Diseases
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• 제82권2호
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• pp.143-150
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• 2019

Background: The purpose of this study was to analyze the relationship between the gene mutation patterns by the GenoType MTBDRplus (MTBDRplus) assay and the phenotypic drug susceptibility test (pDST) results of isoniazid (INH) and prothionamide (Pto). Methods: A total of 206 patients whose MTBDRplus assay results revealed katG or inhA mutations were enrolled in the study. The pDST results were compared to mutation patterns on the MTBDRplus assay. Results: The katG and inhA mutations were identified in 68.0% and 35.0% of patients, respectively. Among the 134 isolated katG mutations, three (2.2%), 127 (94.8%) and 11 (8.2%) were phenotypically resistant to low-level INH, high-level INH, and Pto, respectively. Among the 66 isolated inhA mutations, 34 (51.5%), 18 (27.3%) and 21 (31.8%) were phenotypically resistant to low-level INH, high-level INH, and Pto, respectively. Of the 34 phenotypic Pto resistant isolates, 21 (61.8%), 11 (32.4%), and two (5.9%) had inhA, katG, and both gene mutations. Conclusion: It is noted that Pto may still be selected as one of the appropriate multidrug-resistant tuberculosis regimen, although inhA mutation is detected by the MTBDRplus assay until pDST confirms a Pto resistance. The reporting of detailed mutation patterns of the MTBDRplus assay may be important for clinical practice, rather than simply presenting resistance or susceptibility test results.