• Genomics & Informatics
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• v.14 no.4
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• pp.187-195
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• 2016

In genetic association studies with high-dimensional genomic data, multiple group testing procedures are often required in order to identify disease/trait-related genes or genetic regions, where multiple genetic sites or variants are located within the same gene or genetic region. However, statistical testing procedures based on an individual test suffer from multiple testing issues such as the control of family-wise error rate and dependent tests. Moreover, detecting only a few of genes associated with a phenotype outcome among tens of thousands of genes is of main interest in genetic association studies. In this reason regularization procedures, where a phenotype outcome regresses on all genomic markers and then regression coefficients are estimated based on a penalized likelihood, have been considered as a good alternative approach to analysis of high-dimensional genomic data. But, selection performance of regularization procedures has been rarely compared with that of statistical group testing procedures. In this article, we performed extensive simulation studies where commonly used group testing procedures such as principal component analysis, Hotelling's $T^2$ test, and permutation test are compared with group lasso (least absolute selection and shrinkage operator) in terms of true positive selection. Also, we applied all methods considered in simulation studies to identify genes associated with ovarian cancer from over 20,000 genetic sites generated from Illumina Infinium HumanMethylation27K Beadchip. We found a big discrepancy of selected genes between multiple group testing procedures and group lasso.

• Genomics & Informatics
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• v.14 no.4
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• pp.166-172
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• 2016

Although a large number of genetic variants have been identified to be associated with common diseases through genome-wide association studies, there still exits limitations in explaining the missing heritability. One approach to solving this missing heritability problem is to investigate gene-gene interactions, rather than a single-locus approach. For gene-gene interaction analysis, the multifactor dimensionality reduction (MDR) method has been widely applied, since the constructive induction algorithm of MDR efficiently reduces high-order dimensions into one dimension by classifying multi-level genotypes into high- and low-risk groups. The MDR method has been extended to various phenotypes and has been improved to provide a significance test for gene-gene interactions. In this paper, we propose a simple method, called accelerated failure time (AFT) UM-MDR, in which the idea of a unified model-based MDR is extended to the survival phenotype by incorporating AFT-MDR into the classification step. The proposed AFT UM-MDR method is compared with AFT-MDR through simulation studies, and a short discussion is given.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.2
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• pp.149-153
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• 2017

Objective: This study was to determine the relationship between estimated breeding value and phenotype information after farrowing when juvenile selection was made in candidate pigs without phenotype information. Methods: After collecting phenotypic and genomic information for the total number of piglets born by Landrace pigs, selection accuracy between genomic breeding value estimates using genomic information and breeding value estimates of best linear unbiased prediction (BLUP) using conventional pedigree information were compared. Results: Genetic standard deviation (${\sigma}_a$) for the total number of piglets born was 0.91. Since the total number of piglets born for candidate pigs was unknown, the accuracy of the breeding value estimated from pedigree information was 0.080. When genomic information was used, the accuracy of the breeding value was 0.216. Assuming that the replacement rate of sows per year is 100% and generation interval is 1 year, genetic gain per year is 0.346 head when genomic information is used. It is 0.128 when BLUP is used. Conclusion: Genetic gain estimated from single step best linear unbiased prediction (ssBLUP) method is by 2.7 times higher than that the one estimated from BLUP method, i.e., 270% more improvement in efficiency.

• BMB Reports
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• v.31 no.3
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• pp.269-273
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• 1998

The objective of this study was to evaluate the reversal of multi drug resistance of human cell lines by specific inhibitors of ${\alpha}-glycosidase$ and mannosidases that had been reported to be involved in N-linked oligosaccharide processing of glycoproteins. N-methyldeoxynojirimycin, I-deoxynojirimycin, and castanospermine, which were known to be potent inhibitors of both ${\alpha}-glycosidase$ I and II, showed no activity against the multidrug resistant phenotype of the cell lines of SNU1DOX, KB-V1, and MCF-7/ADR. In contrast, I-deoxymannojirimycin, an inhibitor of mannosidase I, resulted in a slight reversal for the vinblastine resistance of the KB-V1 cell line, but did not show any activity toward the other cell lines. Parallel experiments with tunicamycin, an inhibitor of N-linked glycosylation, also resulted in no significant changes in multidrug resistant (MDR) phenotype of the cell lines tested in this work. These observations suggest that the unglycosylation of P-glycoprotein associated with the inhibitor treatments might not be correlated with the reversal of multidrug resistance of the cell lines tested in this study.

• BMB Reports
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• v.42 no.11
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• pp.725-730
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• 2009

Cyclin E1 (CCNE1), a positive regulator of the cell cycle, controls the transition of cells from G1 to S phase. In numerous human tumors, however, CCNE1 expression is frequently dysregulated, while the mechanism leading to its dysregulation remains incompletely defined. Herein, we showed that CCNE1 expression was subject to post-transcriptional regulation by a microRNA miR-16-1. This was evident at protein level of CCNE1 as well as its mRNA level. Further evident by dual luciferase reporter assay revealed that two evolutionary conserved binding sites on 3' UTR of CCNE1 were the direct functional target sites. Moreover, we showed that miR-16-1 induced G0/G1 cell cycle arrest by targeting CCNE1 and siRNA against CCNE1 partially phenocopied miR-16-1-induced cell cycle phenotype whereas substantially rescued anti-miR-16-1- induced phenotype. Together, all these results demonstrate that miR-16-1 plays a vital role in modulating cellular process in human cancers and indicate the therapeutic potential of miR-16-1 in cancer therapy.

• Korean Journal of Clinical Laboratory Science
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• v.40 no.2
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• pp.106-112
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• 2008

Bone marrow derived mesenchymal stem cells (BMSCs) are largely studied for their potential clinical use. But it is hard to get enough number of those cells for clinical trials and give serious pain to the patients. Adipose tissue is derived from the embryonic mesenchyme and contains a stroma that is easily isolated with large amount. This cell population (adipose derived stem cells: ADSCs) can be isolated from human lipoaspirates and like MSCs, differentiate toward the osteogenic, adipogenic, myogenic and chondrogenic lineages. To confirm whether adipose tissue contains stem cells, the ADSCs extracted from omental or subcutaneous fat tissue were expanded during third to fifth passages. The phenotype of the ADSCs was identified by the conventional cell surface markers using flow cytometry: positive for CD29 and CD44, but negative for CD34, CD45, CD117 and HLA-DR that similar to those observed on BMSCs. The ADSCs were able to differentiate into the osteoblast or adipocytes with induction media. Finally, ADACs expressed multiple CD marker antigens similar to those observed on BMSCs and differentiated into osteoblast, adipocyte. With this, human adipotissue contains multipotent cells and may represent an alternative stem cell source to bone marrow-derived MSCs.

• Biomedical Science Letters
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• v.10 no.2
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• pp.153-161
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• 2004

Antibiotic resistance is often associated with the production of inner membrane proteins (for example, AcrAB/TolC efflux pump) that are capable to extrude antibiotics, detergents, dyes and organic solvents. In order to evaluate the unknown MarB function of Escherichia coli, especially focused on the function of OmpF porin, several mutants were construted by T4GT7 transduction. MarA plays a major roles in mar (multiple antibiotic resistance) phenotype with AcrAB/TolC efflux pump in E. coli K-12. Futhermore, MarA decreases OmpF porin expression via micF antisense RNA. Expression of acrAB is increased in strains containing mutation in marR, and in those carrying multicopy plasmid expressing marA. MarB protein of E. coli K-12 showed its activity at OmpF porin & TolC protein as target molecule. Some paper reported MarB positively regulates OmpF function. MarA shows mar phenotype, and MarB along with MarA show decreased MIC through OmpF function. By this experiment, MarB could decrease MIC through the OmpF porin & TolC protein as target.

• Korean Journal of Microbiology
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• v.29 no.2
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• pp.75-79
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• 1991

The yeast L-A virus (4.6 kb dsRNA genome) encodes the major coat protein and a "gag-pol" fusion minor coat protein that separately encapsidate itself and $M_{1}$, a 1.8 kb dsRNA satellite virus encoding a secreted protein toxin (the killer toxin). The teast chromosomal SKI genes prevent viral cytopathology by lowering the virus copy number. Thus, $ski^{-}$ mutants are ts and cs for growth. We transformed a ski2-2 virus-infested mutant with a yeast bank in a high copy cloning vector and selected the rare healthy transformants for analysis. One type of transformant segregated M-O L-A-O cells with high frequency. Elimination of the DNA clone from the ski2-2 strain eliminated this phinotype and introduction of the DNA clone recovered from such transformants into the parent ski2-2 strain, or into ski3 or ski6 mutants gave the same phenotype. This killer-curing phenotype was due to the curing of the helper L-A dsRNA virus. The 6.5 kb insert only had this activity when carried on a high copy vector and in $ski^{-}$ cells (not in $SKI^{+}$ cells). This 6.5 kb insert acts as a mutagen on L-A dsRNA producing a high rate of deletion mutations.mutations.

• Korean Journal of Microbiology
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• v.29 no.5
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• pp.290-295
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• 1991

N4 phage, which infects E. coli K-12 strains, could not infect E. coli K-12 strains containing rtn(resistant to N4) gene on plasmids, which was isolated from Proteus vulgaris ATCC 13315. The region of rtn gene for Rtn phenotype was reduced to the 1.7 kb HincII-AccI fragment, and rtn gene seemed to have its own promoter. This putative promoter was present in 107 bp HindII-DraI fragment, and known to be functional in E. cole K-12, which is supported by the fact that phenotype of a subclone, pRMG103A1B which does not contain the 107 bp fragment, was dependent on the existance of a functional promoter in the upstream of rtn gene, and that the 107 bp fragment had promoter activity when located in the upstream of structural gene of galactodinase of E. coli. The promoter-bearing fragment contains two overlapping putative promoter sequences, both of which show a fit in eight of twelve nucleotides with consensus sequences of E. coli promoters at the -35 and -10 regions.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2004.10a
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• pp.48-52
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• 2004

We have found the role of rice mitogen-activated protein kinase kinase kinase (MAPKKK), OsEDR1, as controling hypersensitive response (HR) and increased disease resistance to rice blast fungus Magnaporthe grisea. Generation of transgenic rice plants through introduction of the over-expression construct of OsEDR1 using Agrobacterium-mediated transformation results in lesion mimic phenotype. Up-regulation of defense mechanism was detected through detection of increased transcription level of rice PBZ1 and PR1a. Inoculation of rice blast fungus on the lesion mimic transgenic lines displayed significantly increased resistance. The disease symptoms were arrested like HR responses which are commonly detected in the incompatible interactions. High accumulation of phenolic compounds around developing lesions was detected under UV light. There was variation among transgenic lines on the timing of lesion progression as well as the lesion numbers on the rice leaves. Transgenic lines with few lesions also show increased resistance as well as equal amount of grain yields compared to that of wild type rice cultivar Nipponbare. This is the first report of the MAPKKK as a positive regulator molecule on defense mechanism through inducing HR-like cell death lesion mimic phenotype. The application of OsEDR1 is highly expected for the development of resistant cultivars against rice pathogens.