• Proceedings of the Zoological Society Korea Conference
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• 2003.08a
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• pp.195.2-195
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• 2003

No Abstract, See Full Text

• Molecular & Cellular Toxicology
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• v.3 no.4
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• pp.231-237
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• 2007

Exposure to DNA-damaging agents can elicit a variety of stress-related responses that may alter the expression of genes associated with numerous biological pathways. We used 19 k whole human genome chip to detect gene expression profiles and potential signature genes in human normal hepatocytes (THLE-3) by treatment of five direct acting mutagens, furylfuramide (AF-2), N-nitroso-N-methylurea (MNU), methylmethanesulfonate (MMS), 4-nitroquinoline-N-oxide (4-NQO) and 2-nitrofluorene (2NF) of the $IC_{20}$ concentration for 3 h. Fifty one up-regulated common genes and 45 down-regulated common genes above 1.5-fold by five direct-acting mutagens were identified by clustering analysis. Many of these changed genes have some association with apoptosis, control of cell cycle, regulation of transcription and signal transduction. Genes related to these functions, as TP73L, E2F5, MST016, SOX5, MAFB, LIF, SII3, TFIIS, EMR1, CYTL1, CX3CR1 and RHOH are up-regulated. Down-regulated genes are ALOX15B, xs155, IFITM1, BATF, VAV2, CD79A, DCDC2, TNFSF8 and KOX8. We suggest that gene expression profiling on mutagens by toxicogenomic analysis affords promising opportunities to reveal potential new mechanistic markers of genotoxicity.

• Genomics & Informatics
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• v.10 no.4
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• pp.244-248
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• 2012

Oxidative stress, which results in an excessive product of reactive oxygen species (ROS), is one of the fundamental mechanisms of the development of hypertension. In the vascular system, ROS have physical and pathophysiological roles in vascular remodeling and endothelial dysfunction. In this study, ROS-hypertension-related genes were collected by the biological literature-mining tools, such as SciMiner and gene2pubmed, in order to identify the genes that would cause hypertension through ROS. Further, single nucleotide polymorphisms (SNPs) located within these gene regions were examined statistically for their association with hypertension in 6,419 Korean individuals, and pathway enrichment analysis using the associated genes was performed. The 2,945 SNPs of 237 ROS-hypertension genes were analyzed, and 68 genes were significantly associated with hypertension (p < 0.05). The most significant SNP was rs2889611 within MAPK8 (p = $2.70{\times}10^{-5}$; odds ratio, 0.82; confidence interval, 0.75 to 0.90). This study demonstrates that a text mining approach combined with association analysis may be useful to identify the candidate genes that cause hypertension through ROS or oxidative stress.

• Journal of Microbiology and Biotechnology
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• v.28 no.7
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• pp.1217-1224
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• 2018

Seaweeds produce antioxidants to counteract environmental stresses, and these antioxidant genes are regarded as important defense strategies for marine algae. In this study, the expression of Pyropia yezoensis (Bangiales, Rhodophyta) ascorbate peroxidase (PyAPX) and manganese-superoxide dismutase (PyMnSOD) was examined by qRT-PCR in P. yezoensis blades under abiotic stress conditions. Furthermore, the functional relevance of these genes was explored by overexpressing them in Chlamydomonas. A comparison of the different expression levels of PyAPX and PyMnSOD after exposure to each stress revealed that both genes were induced by high salt and UVB exposure, being increased approximately 3-fold after 12 h. The expression of the PyAPX and PyMnSOD genes also increased following exposure to $H_2O_2$. When these two genes were overexpressed in Chlamydomonas, the cells had a higher growth rate than control cells under conditions of hydrogen peroxide-induced oxidative stress, increased salinity, and UV exposure. These data suggest that Chlamydomonas is a suitable model for studying the function of stress genes, and that PyAPX and PyMnSOD genes are involved in the adaptation and defense against stresses that alter metabolism.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.61-68
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• 2000

Now that the complete genomes of numerous organisms have been ascertained, key problems in molecular biology include determining the functions of the genes in each organism, the relationships that exist among these genes, and the regulatory mechanisms that control their operation. These problems can be partially addressed by using machine learning methods to induce predictive models from available data. My group is applying and developing machine learning methods for several tasks that involve characterizing gene regulation. In one project, for example, we are using machine learning methods to identify transcriptional control elements such as promoters, terminators and operons. In another project, we are using learning methods to identify and characterize sets of genes that are affected by tumor promoters in mammals. Our approach to these tasks involves learning multiple models for inter-related tasks, and applying learning algorithms to rich and diverse data sources including sequence data, microarray data, and text from the scientific literature.

• Plant Breeding and Biotechnology
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• v.7 no.3
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• pp.272-286
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• 2019

Developing elite hybrid rice varieties is one important objective of rice breeding programs. Several genes related to male sterilities, restores, and pollinators have been identified through map-based gene cloning within natural variations of rice. These identified genes are good targets for introducing genetic traits in molecular breeding. This study was conducted to breed elite hybrid lines with major genes related to hybrid traits and disease/insect resistance in 240 genetic resources and F₁ hybrid combinations of rice. Molecular markers were reset for three major hybrid genes (S5, Rf3, Rf4) and thirteen disease/insect resistant genes (rice bacterial blight resistance genes Xa3, Xa4, xa5, Xa7, xa13, Xa21; blast resistance genes Pita, Pib, Pi5, Pii; brown planthopper resistant genes Bph18(t) and tungro virus resistance gene tsv1). Genotypes were then analyzed using molecular marker-assisted selection (MAS). Biological assay was then performed at the Red River Delta region in Vietnam using eleven F₁ hybrid combinations and two control vatieties. Results showed that nine F₁ hybrid combinations were highly resistant to rice bacterial blight and blast. Finally, eight F₁ hybrid rice varieties with resistance to disease/insect were selected from eleven F₁ hybrid combinations. Their characteristics such as agricultural traits and yields were then investigated. These F₁ hybrid rice varieties developed with major genes related to hybrid traits and disease/insect resistant genes could be useful for hybrid breeding programs to achieve high yield with biotic and abiotic resistance.

• Molecular & Cellular Toxicology
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• v.4 no.1
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• pp.22-30
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• 2008

Malachite Green (MG), a toxic chemical used as a dye, topical antiseptic and antifungal agent for fish, is highly soluble in water, cytotoxic to various mammalian cells and also acts as a liver tumor promoter. In view of its industrial importance and possible exposure to human beings, MG possesses a potential environmental health hazard. So, we performed with HepG2, a human hepatocellular carcinoma cell line, to identify the differentially expressed genes (DEGs) related to toxicity of MG. And we compared gene expression between control and MG treatment to identify genes that are specifically or predominantly expressed by employing annealing control primer (ACP)-based $GeneFishing^{TM}$ method. The cytotoxicity $(IC_{20})$ of MG was determined above the $0.867{\mu}M$ in HepG2 cell for 48 h treatment. And the DEGs of MG were identified that 5 out of 6 DEGs were upregulated and 1 out of 6 DEGs was down-regulated by MG. Also, MG induced late apoptosis and necrosis in a dose dependent in flow cytometric analysis. Through further investigation, we will identify more meaningful and useful DEGs on MG, and then can get the information on mechanism and pathway associated with toxicity of MG.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.8
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• pp.3601-3606
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• 2014

Single nucleotide polymorphisms located at microRNA (miRNA)-binding sites are likely to affect the expression of miRNA targets and may contribute to the susceptibility of humans to common diseases. Here 335 candidate lung cancer-related inflammatory genes were selected according to the existing literature and database. We identified putative miRNA-binding sites of 149 genes by specialised algorithms and screened SNPs in the 3'UTRs of these genes. By calculating binding free energy, we sorted 269 SNPs on the basis of the possibility of prediction. The proposed approach could help to easy the identification of functionally relevant SNPs and minimize the workflow and the costs.

• Molecules and Cells
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• v.26 no.4
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• pp.368-372
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• 2008

Recent molecular and genetic studies in rice, a short-day plant, have elucidated both conservation and divergence of photoperiod pathway genes and their regulators. However, the biological roles of rice genes that act within the autonomous pathway are still largely unknown. In order to better understand the function of the autonomous pathway genes in rice, we conducted molecular genetic analyses of OsFVE, a rice gene homologous to Arabidopsis FVE. OsFVE was found to be ubiquitously expressed in vegetative and reproductive organs. Overexpression of OsFVE could rescue the flowering time phenotype of the Arabidopsis fve mutants by up-regulating expression of the SUPPRESSOR OF OVEREXPRESSION OF CO1 (SOC1) and down-regulating FLOWERING LOCUS C (FLC) expression. These results suggest that there may be a conserved function between OsFVE and FVE in the control of flowering time. However, OsFVE overexpression in the fve mutants did not rescue the flowering time phenotype in in relation to the response to intermittent cold treatment.

• Molecules and Cells
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• v.43 no.2
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• pp.188-197
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• 2020

Cells are designed to be sensitive to a myriad of external cues so they can fulfil their individual destiny as part of the greater whole. A number of well-characterised signalling pathways dictate the cell's response to the external environment and incoming messages. In healthy, well-ordered homeostatic systems these signals are tightly controlled and kept in balance. However, given their powerful control over cell fate, these pathways, and the transcriptional machinery they orchestrate, are frequently hijacked during the development of neoplastic disease. A prime example is the Wnt signalling pathway that can be modulated by a variety of ligands and inhibitors, ultimately exerting its effects through the β-catenin transcription factor and its downstream target genes. Here we focus on the interplay between the three-member family of RUNX transcription factors with the Wnt pathway and how together they can influence cell behaviour and contribute to cancer development. In a recurring theme with other signalling systems, the RUNX genes and the Wnt pathway appear to operate within a series of feedback loops. RUNX genes are capable of directly and indirectly regulating different elements of the Wnt pathway to either strengthen or inhibit the signal. Equally, β-catenin and its transcriptional co-factors can control RUNX gene expression and together they can collaborate to regulate a large number of third party co-target genes.