• The Plant Pathology Journal
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• v.28 no.1
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• pp.81-86
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• 2012

We developed a reassortant RNA virus vector derived from $Cucumber$ $mosaic$ $virus$ (CMV), which has advantages of very wide host range and can efficiently induce gene silencing in a few model plants. Certain CMV isolates, however, show limited host ranges presumably because they naturally co-evolved with their own hosts. We used a reassortant comprised of two strains of CMV, Y-CMV and Gn-CMV, to broaden the host range and to develop a virus vector for virus-induced gene silencing (VIGS). Gn-CMV could infect chili pepper and tomato more efficiently than Y-CMV. Gn-CMV RNA1, 3 and Y-CMV RNA2-A1 vector were newly reconstructed, and the transcript mixture of RNA1 and 3 genomes of Gn-CMV and RNA2 genome of Y-CMV RNA2 containing portions of the endogenous phytoene desaturase (PDS) gene (CMV2A1::PDSs) was inoculated onto chili pepper (cv. Chung-yang), tomato (cvs. Bloody butcher, Tigerella, Silvery fir tree, and Czech bush) and $Nicotiana$ $benthamiana$. All the tested plants infected by the reassortant CMV vector showed typical photo-bleaching phenotypes and reduced expression levels of $PDS$ mRNA. These results suggest that the reassortant CMV vector would be a useful tool for the rapid induction of the RNA silencing of endogenous genes in chili pepper and tomato plants.

• Journal of Plant Biotechnology
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• v.43 no.2
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• pp.164-173
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• 2016

To investigate the genetic basis of phenotypic differences, sequence variations were analyzed in 8 inbred watermelon lines by re-sequencing. The number of sequence variations differed depending on the chromosome. Only 12.9% of SNPs were found within genes, whereas the rest were detected in promoter or intergenic regions. SNP density analysis showed that there was a highly variable region at the end of chromosome 6, which is similar to previously published findings. However, this region with high SNP density did not show much variation between the lines. In contrast, highly conserved regions with a size of 6.5-10 Mb were found in chromosomes 10 and 11. Pathway analysis suggested that the DIMBOA (a natural antibiotic)-glucoside degradation pathway was significantly different between the lines, indicating that the eight lines may have different levels of pathogen resistance. Among the carbohydrate-related genes, the alpha-galactosidase gene was the most variable among the lines. Information from this study will be helpful in understanding the watermelon breeding process at the molecular level.

• Journal of fish pathology
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• v.11 no.2
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• pp.89-96
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• 1998

Marine birnavirus (MABV) has wide host range in marine organisms. To clarify various infection properties of MABV in different host species, in vitro study was performed by subculture for 10 passages in several fish cell lines. In CHSE-214, RTG-2 and RSBK-2 cells, the virus produced high yield of virus. Typical CPE with high protein expression was observed in these cells. On the contrary, the virus grown in EPC, FHM and BF-2 cells exhibited no CPE appearance although virus protein was detected. In EPC and FHM cells, the virus titer increased in later passages. The plaque size was distinctly bigger in CHSE-214, RTG-2 and RSBK-2 cells than in other cell lines. The nucleotide sequence of VP2/NS junction region on genome segment A exhibited one specific nucleotide change at 195. The different infection properties in several cell types performed in the present work might reflect in vivo MABV infection in various host species occurring in natural conditions.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.11
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• pp.1541-1546
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• 2016

Four carcass traits, namely carcass weight (CW), eye muscle area (EMA), back fat thickness (BF), and marbling score (MS), are the main price decision parameters used for purchasing Hanwoo beef. The development of DNA markers for these carcass traits for use in a beef management system could result in substantial profit for beef producers in Korea. The objective of this study was to validate the association of highly significant single nucleotide polymorphisms (SNPs) identified in a previous genome-wide association study (GWAS) with the four carcass traits in a commercial Hanwoo population. We genotyped 83 SNPs distributed across all 29 autosomes in 867 steers from a Korean Hanwoo feedlot. Six SNPs, namely ARS-BFGL-NGS-22774 (Chr4, Pos:4889229), ARS-BFGL-NGS-100046 (Chr6, Pos:61917424), ARS-BFGL-NGS-39006 (Chr27, Pos:38059196), ARS-BFGL-NGS-18790 (Chr10, Pos:26489109), ARS-BFGL-NGS-43879 (Chr9, Pos:39964297), and BTB-00775794 (Chr20, Pos:20476265), were found to be associated with CW, EMA, BF, and MS. The ARS-BFGL-NGS-22774, BTB-00775794, and ARS-BFGL-NGS-39006 markers accounted for 1.80%, 1.72%, and 1.35% (p<0.01), respectively, of the phenotypic variance in the commercial Hanwoo population. Many genes located in close proximity to the significant SNPs identified in this study were previously reported to have roles in carcass traits. The results of this study could be useful for marker-assisted selection programs.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.20
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• pp.8901-8904
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• 2014

Background: Genetic factors play important roles in the pathogenesis of human cancer. A recent genome wide association study (GWAS) identified an association between the rs2294008 polymorphism of the prostate stem cell antigen (PSCA) gene and bladder cancer risk in Caucasians. The aim of this study was to determine whether the rs2294008 polymorphism is similarly associated with bladder cancer susceptibility in a Korean population. Materials and Methods: We conducted a case-control study of 411 bladder cancer patients and 1,700 controls. Results: The frequencies of the CC, CT, and TT genotypes of the rs2294008 polymorphism were 16.9, 54.0, and 28.8% in bladder cancer patients and 24.4, 48.1, and 27.5% in controls, respectively. We found that the combined CT/TT genotypes were associated with a significantly increased risk of bladder cancer (OR CT/TT =1.58, 95% CI= 1.15-2.17), compared with the CC genotype. Smoking habits, tumor grade and tumor stage did not modify the association between rs2294008 and the risk of bladder cancer. Conclusions: Our study showed that the rs2294008 polymorphism in the PSCA gene is associated with the risk of bladder cancer in a Korean population, providing evidence that it may contribute to bladder carcinogenesis regardless of ethnicity.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.10
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• pp.6089-6094
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• 2013

Berberine, a common isoquinoline alkaloid, has been shown to possess anti-cancer activities. However, the underlying molecular mechanisms are still not completely understood. In the current study, we investigated the effects of berberine on cell growth, colony formation, cell cycle distribution, and whether it improved the anticancer efficiency of cisplatin and doxorubicin in human breast cancer estrogen receptor positive (ER+) MCF-7 cells and estrogen receptor negative (ER-) MDA-MB-231 cells. Notably, berberine treatment significantly inhibited cell growth and colony formation in the two cell lines, berberine in combination with cisplatin exerting synergistic growth inhibitory effects. Accompanied by decreased growth, berberine induced G1 phase arrest in MCF-7 but not MDA-MB-231 cells. To provide a more detailed understanding of the mechanisms of action of berberine, we performed genome-wide expression profiling of berberine-treated cells using cDNA microarrays. This revealed that there were 3,397 and 2,706 genes regulated by berberine in MCF-7 and MDA-MB-231 cells, respectively. Fene oncology (GO) analysis identified that many of the target genes were involved in regulation of the cell cycle, cell migration, apoptosis, and drug responses. To confirm the microarray data, qPCR analysis was conducted for 10 selected genes based on previously reported associations with breast cancer and GO analysis. In conclusion, berberine exhibits inhibitory effects on breast cancer cells proliferation, which is likely mediated by alteration of gene expression profiles.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.10
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• pp.4905-4908
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• 2012

Aim: Glioma cancer is the most common type of adult brain tumor. Recent genome-wide association studies (GWAS) have identified various new susceptibility regions and here we conducted an extensive analysis of associations between 12 single nucleotide polymorphisms (SNPs) and glioma risk. Methods: A total of 197 glioma cases and 197 health controls were selected, and 9 SNPs in 8 genes were analyzed using the Sequenom MassARRAY platform and Sequenom Assay Design 3.1 software. Results: We found the MAF among selected controls were consistent with the MAF from the NCBI SNP database. Among 9 SNPs in 8 genes, we identified four significant SNP genotypes associated with the risk of glioma, C/C genotype at rs730437 and T/T genotype at rs1468727 in ERGF were protective against glioma, whereas the T/T genotype at rs1799782 in XRCC1 and C/C genotype at rs861539 in XRCC3 conferred elevated risk. Conclusion: Our comprehensive analysis of nine SNPs in eight genes suggests that the rs730437 and rs1468727 in ERGF, rs1799782 in XRCC1 gene, and rs861539 in XRCC3 gene are associated with glioma risk. These findings indicate that genetic variants of various genes play a complex role in the development of glioma.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.4
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• pp.539-546
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• 2020

Objective: The Jeju native pig (JNP) found on the Jeju Island of Korea is a unique black pig known for high-quality meat. To investigate the genetic uniqueness of JNP, we analyzed the selection signature of the JNP in comparison to commercial pigs such as Berkshire and Yorkshire pigs. Methods: We surveyed the genetic diversity to identify the genetic stability of the JNP, using the linkage disequilibrium method. A selective sweep of the JNP was performed to identify the selection signatures. To do so, the population differentiation measure, Weir-Cockerham's F_st was utilized. This statistic directly measures the population differentiation at the variant level. Additionally, we investigated the gene ontologies (GOs) and genetic features. Results: Compared to the Berkshire and Yorkshire pigs, the JNP had lower genetic diversity in terms of linkage disequilibrium decays. We summarized the selection signatures of the JNP as GO. In the JNP and Berkshire pigs, the most enriched GO terms were epithelium development and neuron-related. Considering the JNP and Yorkshire pigs, cellular response to oxygen-containing compound and generation of neurons were the most enriched GO. Conclusion: The selection signatures of the JNP were identified through the population differentiation statistic. The genes with possible selection signatures are expected to play a role in JNP's unique pork quality.

• Biomedical Science Letters
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• v.21 no.3
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• pp.135-143
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• 2015

Electrocardiogram measures the electric impulses generated by the heart during its cycle. Recently genome-wide association studies on electrocardiogram traits revealed many relevant genetic loci. Therefore, these findings need to be validated and investigated to determine the underlying mechanisms using mouse models. Invasive radiotelemetry has been widely used to record the electrocardiogram in mice because it has several advantages over non-invasive measurements. However, radiotelemetry is expensive and requires complicated surgery. On the other hand, a non-invasive method using 3 electrodes (one for earth) for lead II is easy to establish and allows for rapid measurement. In this study, eleven mice were measured with this non-invasive method and no statistical difference among them was found in any ECG measurements. In addition, repeat measurement in the same mouse was performed in 9 sets of experiment and the results indicated that non-invasive method was reliable for reproducibility. Further it was shown that measurements for 1, 5, 10, and 15 minutes were not different so that a short recording such as 5 minutes was enough to estimate the ECG values including heart rate. Further this method was validated by measuring the ECG of Balb/c and FVB that were previously shown to differ in ECG values by radiotelemetry. Significant differences were found in heart rate, PR interval and corrected QT interval between these mouse strains. This study partially proved that non-invasive method also could provide the accuracy and reproducibility. Based on these results, the non-invasive ECG recordings of lead II is recommended as a useful method for quick test in mouse model.

• Biomedical Science Letters
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• v.18 no.4
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• pp.377-383
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• 2012

Recent genome-wide association studies (GWAS) have identified a number of common variants associated with blood pressure homeostasis and hypertension in population. In the previous study, single nucleotide polymorphisms (SNPs) in the SLC4A4 gene have been reported to be associated with hypertension in Han Chinese population. We aimed to confirm whether the genetic variation of SLC4A4 gene influence the susceptibility to blood pressure and hypertension in Korean population. We genotyped variants in or near SLC4A4 in a population-based cohort including 7,551 unrelated Korean from Ansan and Ansung. Here, we performed association analysis to elucidate the possible relations of genetic polymorphisms in SLC4A4 gene with blood pressure traits. By examining genotype data of a total of 7,551 subjects in the Korean Association REsource (KARE) study, we discovered the SLC4A4 gene polymorphisms are associated with blood pressure and hypertension. The common and highest significant polymorphism was rs6846301 (${\beta}$=0.839, additive P=0.032) with systolic blood pressure (SBP), rs6846301 (${\beta}$=0.588, additive P=0.027) with diastolic blood pressure (DBP), and rs6846301 (OR=1.23, CI: 1.09~1.40, additive $P=1.2{\times}10^{-3}$) with hypertension. Furthermore, the SNP rs6846301 was consistently associated with both blood pressure and hypertension. Consequently, we found statistically significant SNPs in SLC4A4 gene that are associated with both blood pressure and hypertension traits. In addition, these results suggest that the individuals with the minor alleles of the SNP in the SLC4A4 gene may be more susceptible to the development of hypertension in the Korean population.