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Construction of Chromosome-Specific BAC Libraries from the Filamentous Ascomycete Ashbya gossypii
Choi Sang-Dun Korea Genome Organization 2006 Genomics & informatics Vol.4 No.2
It is clear that the construction of large insert DNA libraries is important for map-based gene cloning, the assembly of physical maps, and simple screening for specific genomic sequences. The bacterial artificial chromosome (BAC) system is likely to be an important tool for map-based cloning of genes since BAC libraries can be constructed simply and analyzed more efficiently than yeast artificial chromosome (YAC) libraries. BACs have significantly expanded the size of fragments from eukaryotic genomes that can be cloned in Escherichia coli as plasmid molecules. To facilitate the isolation of molecular-biologically important genes in Ashbya gossypii, we constructed Ashbya chromosome-specific BAC libraries using pBeloBAC11 and pBACwich vectors with an average insert size of 100 kb, which is equivalent to 19.8X genomic coverage. pBACwich was developed to streamline map-based cloning by providing a tool to integrate large DNA fragments into specific sites in chromosomes. These chromosome-specific libraries have provided a useful tool for the further characterization of the Ashbya genome including positional cloning and genome sequencing.
Single and Dual Ligand Effects on Gene Expression Changes in Mouse Macrophage Cells
Choi Sang-Dun,Seo Jeong-Sun Korea Genome Organization 2006 Genomics & informatics Vol.4 No.2
We identified differentially expressed genes in RAW264.7 cells in response to single and double ligand treatments (LPS, $IFN{\gamma}$, 2MA, LPS plus $IFN{\gamma}$, and LPS plus 2MA). The majority of the regulated transcripts responded additively to dual ligand treatment. However, a significant fraction responded in a non-additive fashion. Several cytokines showing non-additive transcriptional responses to dual ligand treatment also showed non-additive protein production/secretion responses in separately performed experiments. Many of the genes with non-additive responses to LPS plus 2MA showed enhanced responses and encoded pro-inflammatory proteins. LPS plus $IFN{\gamma}$ appeared to induce both non-additive enhancement and non-additive attenuation of gene expression. The affected genes were associated with a variety of biological functions. These experiments reveal both dependent and independent regulatory pathways and point out the specific nature of the regulatory interactions.
철도역사 사상사고 예방대책 수립을 위한 기초 연구 (Development of Railway Station Safety Measures for Passenger)
곽상록(Sang-Log Kwak),최돈범(Dun-Bum Choi),박찬우(Chan-Woo Park),조연옥(Yun-Ok Cho) 한국철도학회 2011 한국철도학회 학술발표대회논문집 Vol.2011 No.5
As accident rate have been reduced into half since 2005, no train accident fatality occurred in recent year. Level crossing accident also been reduced that no more than 5 fatalities occurred every year. As a result 98% of accident fatalities occurred in station and track. So railway station safety measures are more and more important but only few research have been done on railway station safety. In this study status on safety measures on railway stations are reviewed and basic research have been done based on expert interview for the development of new safety measures.
Fluorescence Quenching Causes Systematic Dye Bias in Microarray Experiments Using Cyanine Dye
Jeon, Ho-Sang,Choi, Sang-Dun Korea Genome Organization 2007 Genomics & informatics Vol.5 No.3
The development of microarray technology has facilitated the understanding of gene expression profiles. Despite its convenience, the cause of dye-bias that confounds data interpretation in dual-color DNA microarray experiments is not well known. In order to economize time and money, it is necessary to identify the cause of dye bias, since designing dye-swaps to reduce the dye-specific bias tends to be very expensive. Hence, we sought to determine the reliable cause of systematic dye bias after treating murine macrophage RAW 264.7 cells with 2-keto-3-deoxyoctonate (KDO), interferon-beta $(IFN-{\beta})$, and 8-bromoadenosine (8-BR). To find the cause of systematic dye bias from the point of view of fluorescence quenching, we examined the correlation between systematic dye bias and the proportion of each nucleotide in mRNA and oligonucleotide probe sequence. Cy3-dye bias was highly correlated with the proportion of adenines. Our results support the fact that systematic dye bias is affected by fluorescence quenching of each feature. In addition, we also found that the strength of fluorescence quenching is based on not only dye-dye interactions but also dye-nucleotide interactions as well.
Fluorescense Quenching Causes Systematic Dye Bias in Microarray Experiments Using Cyanine Dye
Jeon Ho Sang,Choi Sang Dun 한국유전체학회 2007 Genomics & informatics Vol.5 No.3
The development of microaray technology has facilitated the understanding of gene expresion profiles. Despite its convenience, the cause of dye-bias that confounds data interpretation in dual-color DNA microarray experiments it is necessary to identify the cause of dye bias, since designing dye-swaps to reduce the dye-specific bias tends to be very expensive. Hence, we sought to determine the reliable cause of systematic dye bias after treating murine macrophage RAW 264.7 cells with 2-keto-3-deoxyoctonate (KDO), interferon-beta (IFN-β), and 8-bromoadenosine (8-BR). To find the cause of systematic dye bias from the point of view of fluorescence quenching, we examined the correlation betwen systematic dye bias and the proportion of each nucleotide in mRNA and oligonucleotide probe sequence. Cy3-dye bias was highly correlated with the systematic dye bias is affected by fluorescence quenching of each feature. In addition, we also found that the strength of fluorescence quenching is based on not only dye-dye interactions but also dye-nucleotide interactions as well.
Krishnan, Jayalakshmi,Choi, Sang-Dun Korea Genome Organization 2012 Genomics & informatics Vol.10 No.3
A variety of ligands differ in their capacity to bind the receptor, elicit gene expression, and modulate physiological responses. Such receptors include Toll-like receptors (TLRs), which recognize various patterns of pathogens and lead to primary innate immune activation against invaders, and G-protein coupled receptors (GPCRs), whose interaction with their cognate ligands activates heterotrimeric G proteins and regulates specific downstream effectors, including immuno-stimulating molecules. Once TLRs are activated, they lead to the expression of hundreds of genes together and bridge the arm of innate and adaptive immune responses. We characterized the gene expression profile of Toll-like receptor 4 (TLR4) in RAW 264.7 cells when it bound with its ligand, 2-keto-3-deoxyoctonate (KDO), the active part of lipopolysaccharide. In addition, to determine the network communications among the TLR, Janus kinase (JAK)/signal transducer and activator of transcription (STAT), and GPCR, we tested RAW 264.7 cells with KDO, interferon-${\beta}$, or cAMP analog 8-Br. The ligands were also administered as a pair of double and triple combinations.
Park, Ji-Hwan,Choi, Sang-Dun Korea Genome Organization 2011 Genomics & informatics Vol.9 No.4
Angiogenesis is regulated by a large number of molecules and complex signaling mechanisms. The G protein $G{\alpha}_{13}$ is a part of this signaling mechanism as an endothelial cell movement regulator. Gene expression analysis of $G{\alpha}_{13}$ knockout mouse embryos was carried out to identify the role of $G{\alpha}_{13}$ in angiogenesis signaling during embryonic development. Hypoxia-inducible response factors including those acting as regulators of angiogenesis were over expressed, while genes related to the cell cycle, DNA replication, protein modification and cell-cell dissociation were under expressed. Functional annotation and network analysis indicate that $G{\alpha}_{13}{^{-/-}}$ embryonic mice were exposed to hypoxic conditions. The present analysis of the time course highlighted the significantly high levels of disorder in the development of the cardiovascular system. The data suggested that hypoxia-inducible factors including those associated with angiogenesis and abnormalities related to endothelial cell division contributed to the developmental failure of $G{\alpha}_{13}$ knockout mouse embryos.
Piras, Vincent,Selvarajoo, Kumar,Fujikawa, Naoki,Choi, Sang-Dun,Tomita, Masaru,Giuliani, Alessandro,Tsuchiya, Masa Korea Genome Organization 2007 Genomics & informatics Vol.5 No.3
MicroRNAs (miRNAs) are known to negatively control protein-coding genes by binding to messenger RNA (mRNA) in the cytoplasm. In innate immunity, the role of miRNA gene silencing is largely unknown. In this study, we performed microarray-based experiments using lipopolysaccharide (LPS)-stimulated macrophages derived from wild-type, MyD88 knockout (KO), TRIF KO, and MyD88/TRIF double KO mice. We employed a statistical approach to determine the importance of the commonality and specificity of miRNA binding sites among groups of temporally co-regulated genes. We demonstrate that both commonality and specificity are irrelevant to define a priori groups of co-down regulated genes. In addition, analyzing the various experimental conditions, we suggest that miRNA regulation may not only be a late-phase process (after transcription) but can also occur even early (1h) after stimulation in knockout conditions. This further indicates the existence of dynamic interactions between miRNA and signaling molecules/transcription factor regulation; this is another proof for the need of shifting from a 'hard-wired' paradigm of gene regulation to a dynamical one in which the gene co-regulation is established on a case-by-case basis.