• Communications for Statistical Applications and Methods
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• v.29 no.5
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• pp.591-601
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• 2022

In gene set analysis with microarray expression data, a group of genes such as a gene regulatory pathway and a signaling pathway is often tested if there exists either differentially expressed (DE) or differentially co-expressed (DC) genes between two biological conditions. Recently, a statistical test based on covariance estimation have been proposed in order to identify DC genes. In particular, covariance regularization by hard thresholding indeed improved the power of the test when the proportion of DC genes within a biological pathway is relatively small. In this article, we compare covariance thresholding methods using four different regularization penalties such as lasso, hard, smoothly clipped absolute deviation (SCAD), and minimax concave plus (MCP) penalties. In our extensive simulation studies, we found that both SCAD and MCP thresholding methods can outperform the hard thresholding method when the proportion of DC genes is extremely small and the number of genes in a biological pathway is much greater than a sample size. We also applied four thresholding methods to 3 different microarray gene expression data sets related with mutant p53 transcriptional activity, and epithelium and stroma breast cancer to compare genetic pathways identified by each method.

• Proceedings of the Korean Society of Life Science Conference
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• 2002.12a
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• pp.13-19
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• 2002

To elucidate the regulatory mechanism for expression of sialyl-glycoconjugates and their biological functions, ninetheen sialyltransferase cDNAs including eleven by our group or co-works have been cloned and characterized so far. The cloned sialyltransferases are classified into four families according to the carbohydrate linkages they synthesize: ${\alpha}2,3-sialyltransferase$ (ST3Gal I-VI), ${\alpha}$ 2,6-sialyltransferase (ST6Gal I), GalNAc ${\alpha}$ 2,6-sialyltransferase (ST6GalNAc I-VI), and ${\alpha}2,8-sialyltransferase$ (ST8Sia I-VI). Each of the sialyltransferase genes is differentially expressed in a tissue-, cell type-, and stage-specific manner. These enzymes differ in their substrate specificity and various biochemical parameters. However, enzymatic analysis conducted in vitro with recombinant enzyme revealed that one linkage can be synthesized by multiple enzymes. We present here an overview of structure and function of sialyltransferases performed by our group and co-works. Genomic structures and transcriptional regulation of two kinds of human sialyltransferase gene are also presented.

• KSBB Journal
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• v.17 no.3
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• pp.311-313
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• 2002

Lactobacillus spry. are Gram-positive bacteria playing important roles in human health. In this study, we successfully isolated the total RNA from the cells broken by glass beads using hot phenol method. Moreover, we were able to omit lysozyme and proteinase K treatment by using glass beads to break cell more efficiently. This method was more rapid and simple when compared to the previous one. Prepared RNA can be used for the transcriptional analysis of Lactobacillus spp.

• BMB Reports
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• v.42 no.12
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• pp.823-828
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• 2009

Techniques for analyzing protein-DNA interactions on a genome-wide scale have recently established regulatory roles for distal enhancers. However, the large sizes of higher eukaryotic genomes have made identification of these elements difficult. Information regarding sequence conservation, exon annotation and repetitive regions can be used to reduce the size of the search region. However, previously developed resources are inadequate for consolidating such information. CONVIRT is a web resource for the identification of transcription factor binding sites and also features comparative genomics. Genomic information on ortholog-independent conserved regions, exons, repeats and sequences is integrated into the virtual chromosome, and statistically over-represented single or combinations of transcription factor binding sites are sought. CONVIRT provides regulatory network analysis for several organisms with long promoter regions and permits inter-species genome alignments. CONVIRT is freely available at http://biosoft.kaist.ac.kr/convirt.

• Journal of Microbiology and Biotechnology
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• v.4 no.3
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• pp.176-182
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• 1994

The light-organ symbiont of pine cone fish, Vibrio fischeri, senses its presence in the host and responds to environmental changes by differentially expressing its symbiosis-related luminescence genes. The V. fischeri luminescence genes are activated by LuxR protein in the presence of an autoinducer. In an effort to elucidate the mechanism of regulation of luxR, a plasmid containing luxR was mutagenized in vitro with hydroxylamine and a luxR mutant plasmid was isolated by its ability to activate luminescence genes cloned in E. coli in the absence of the autoinducer. The specific base change identified by DNA sequencing was only single base transition at ＋78 from the transcriptional start of luxR. Based on a Western immunoblot analysis, the nucleotide change directed the synthesis of much higher level of LuxR protein without any amino acid substitutions. The results suggest that the region including the ＋78th base is presumably internal operator required for autorepression of luxR, and the increased cellular level of LuxR results in activation of luminescence genes by autoinducer independent fashion.

• Journal of Microbiology and Biotechnology
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• v.16 no.8
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• pp.1292-1300
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• 2006

Aeromonas encheleia, a potential human intestinal pathogen, was shown to infect a human intestinal epithelial cell line (Caco-2) in a noninvasive manner. The transcriptional profile of the Caco-2 cells after infection with the bacteria revealed an upregulated expression of genes involved in chloride secretion, including that of phospholipase A2 (PLA2) and platelet-activating factor (PAF) acetylhydrolase (PAFAH2). This was also confirmed by a real-time RT-PCR analysis. As expected from PLA2 induction, PAF was produced when the Caco-2 cells were infected with the bacteria, and PAF was also produced when the cells were treated with a bacterial culture supernatant including bacterial extracellular proteins, yet lacking lipopolysaccharides. Bacterial aerolysin was shown to induce the production of PAF.

• 대한생식의학회:학술대회논문집
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• 2007.11a
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• pp.138-138
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• 2007

• Toxicological Research
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• v.21 no.4
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• pp.285-290
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• 2005

We demonstrate that radicicol, a macrocyclic antifungal antibiotic originally isolated from Monosporium bonorden, inhibits LPS-induced expression of iNOS gene in RAW 264.7 cells. Treatment of peritoneal macrophages and RAW 264.7 cells with radicicol inhibited LPS-stimulated nitric oxide production in a dose-related manner. Immunohistochemical staining of iNOS and RTPCR analysis showed that the decrease of NO was due to the inhibition of iNOS gene expression in RAW 264.7 cells. Immunostaining of p65, EMSA, and reporter gene assay showed that radicicol inhibited $NF-\kappa/Rel$ nuclear translocation. DNA binding, and transcriptional activation, respectively. Collectively, these series of experiments indicate that radicicol inhibits iNOS gene expression by blocking $NF-\kappa/Rel$ nuclear translocation. Due to the critical role that NO release plays in mediating inflammatory responses, the inhibitory effects of radicicol on iNOS suggest that radicicol may represent a useful anti-inflammatory agent.

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.11a
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• pp.356-360
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• 2005

Xanthine dehydrogenase (XDH), a classic enzyme involved in purine catabolism, can catalyze the formation of redox-signaling reactive oxygen and nitrogen species such as superoxide and nitric oxide. We generated transgenic plants of Arabidopsis in which XDH was knocked out by introduction of hairpin RNA-expression vector. Expression analysis by reverse transcription-PCR and in-gel staining of XDH activity revealed that transgenic lines efficiently suppressedXDH expression at the transcriptional level, demonstrating that RNA interference was successfully induced. XDH-suppressed transgenic lines exhibitedincreased biomass production during the growth of seedlings.

• BMB Reports
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• v.50 no.4
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• pp.201-207
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• 2017

Alternations in usage of polyadenylation sites during transcription termination yield transcript isoforms from a gene. Recent findings of transcriptome-wide alternative polyadenylation (APA) as a molecular response to changes in biology position APA not only as a molecular event of early transcriptional termination but also as a cellular regulatory step affecting various biological pathways. With the development of high-throughput profiling technologies at a single nucleotide level and their applications targeted to the 3'-end of mRNAs, dynamics in the landscape of mRNA 3'-end is measureable at a global scale. In this review, methods and technologies that have been adopted to study APA events are discussed. In addition, various bioinformatics algorithms for APA isoform analysis using publicly available RNA-seq datasets are introduced.