• BMB Reports
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• v.42 no.11
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• pp.737-742
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• 2009

Hypoxia-inducible factor-$1{\alpha}/{\beta}$ (HIF-$1{\alpha}/{\beta}$) is a heterodimeric transcriptional activator that mediates gene expression in response to hypoxia. HIF-$1{\alpha}$ has been noted as an effective therapeutic target for ischemic diseases such as myocardiac infarction, stroke and cancer. By using a yeast two-hybrid system and a random peptide library, we found a 16-mer peptide named F29 that directly interacts with the bHLH-PAS domain of HIF-$1{\alpha}$. We found that F29 facilitates the interaction of the HIF-$1{\alpha/\beta}$ heterodimer with its target DNA sequence, hypoxia-responsive element (HRE). The transient transfection of an F29-expressing plasmid increases the expression of both an HRE-driven luciferase gene and the endogenous HIF-1 target gene, vascular endothelial growth factor (VEGF). Taken together, we conclude that F29 increases the DNA-binding ability of HIF-$1{\alpha}$, leading to increased expression of its target gene VEGF. Our results suggest that F29 can be a lead compound that directly targets HIF-$1{\alpha}$ and increases its activity.

• The Plant Pathology Journal
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• v.18 no.2
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• pp.57-62
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• 2002

In vivo expression technology (IVET) has been developed to study bacterial gene expression in Salmonella typhimurium during host infection. The expression of selected genes by IVET has been elevated in vivo but not in vitro. The selected genes turned out to be important for bacterial virulence and/or pathogenicity. IVET depends on a synthetic operon with a promoterless transcriptional fusion between a selection marker gene and a reporter gene. The IVET approach has been successfully adapted in other bacterial pathogens and plant-associated bacteria using different selection markers. Pseudomonas putida suppresses citrus root rot caused by Phytophthora parasitica and enhances citrus seedling growth. The WET strategy was adapted based on a transcriptional fusion, pyrBC'-lacZ, in P. putida to study the bacterial traits important far biocontrol activities. Several genes appeared to be induced on P. parasitica hyphae and were found to be related with metabolism and regulation of gene expression. It is likely that the biocontrol strain took a metabolic advantage from the plant pathogenic fungus and then suppressed citrus root rot effectively. The result was parallel with those from the adaptation of IVET in P. fluorescens, a plant growth promoting rhizobacteria (PGPR). Interestingly, genes encoding components for type III secretion system have been identified as rhizosphere-induced genes in the PGPR strain. The type III secretion system may play a certain role during interaction with its counterpart plants. Application of IVET has been demonstrated in a wide range of bacteria. It is an important strategy to genetically understand complicated bacterial traits in the environment.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.6
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• pp.817-820
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• 2007

The effects of diacylglycerol O-acyltransferase (DGAT1) candidate gene polymorphism on the economic traits of Hanwoo were studied. Through sequencing analysis, two polymorphism sites at K232A and T11993C were established and were analyzed by PCR-RFLP. The PCR-RFLP analysis for K232A showed that the frequencies of alleles K and A were 0.75 and 0.25, respectively, and the frequencies of genotypes for K/K, K/A and A/A were estimated as 0.509, 0.491 and 0, respectively. In the PCR-RFLP analysis for T11993C, we found allele frequencies of 0.773 and 0.227 for T and A, respectively, and 0.546, 0.454 and 0 for the T/T, T/C and C/C genotype frequencies, respectively. No significant effects on economic traits in Hanwoo were found in the separate analysis of K232A and T11993C polymorphisms, but the interaction between K232A and T11993C showed a significant effect (p<0.005) on marbling score. The DGAT1 candidate gene was found to have a significant effect not only on milk yield and component traits but also on the metabolism of intramuscular fat.

• Interdisciplinary Bio Central
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• v.3 no.2
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• pp.8.1-8.6
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• 2011

Background: Thanks to the development of the mathematical/statistical reverse engineering and the high-throughput measuring biotechnology, lots of biologically meaningful genegene interaction networks have been revealed. Steady-state analysis of these systems provides an important clue to understand and to predict the systematic behaviours of the biological system. However, modeling such a complex and large-scale system is one of the challenging difficulties in systems biology. Results: We introduce a new stochastic modeling approach that can describe gene regulatory mechanisms by dividing two (DNA and protein) layers. Simple queuing system is employed to explain the DNA layer and the protein layer is modeled using G-networks which enable us to account for the post-translational protein interactions. Our method is applied to a transcription repression system and an active protein degradation system. The steady-state results suggest that the active protein degradation system is more sensitive but the transcription repression system might be more reliable than the transcription repression system. Conclusions: Our two layer stochastic model successfully describes the long-run behaviour of gene regulatory networks which consist of various mRNA/protein processes. The analytic solution of the G-networks enables us to extend our model to a large-scale system. A more reliable modeling approach could be achieved by cooperating with a real experimental study in synthetic biology.

• Journal of Microbiology
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• v.39 no.4
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• pp.314-320
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• 2001

Macrophages stimulated by lipopolysaccharide(LPS) from gram negative bacteria undergo activation of a group of immediate early genes including Rantes. The mouse Rantes gene promoter region contains an LPS rsponsive element(LPE) We detected 3 specific bands termed B1, B2 and 3 formed by the interaction of the LPE and proteins found in LPS-stimulated RAW 367.7 cells. An additional band B4 was determined to be an Ap-1 binding protein. The B1 band appears within 1 hour of LPS nuclear extracts from LPS-stimulation, and this protein kinase enhances B1 and formation. The B1 band can be converted to band B2/B3 by adding specific heparin column fraction purified Ser/Thr specific protein phosphatases PP-1 and PP-2A can stimulate the same conversion to about the same extent. Thus, the formation of the LRE sequence binding complex appears to be regulated by Ser/Thr protein kinase and one or more Ser/Thr specific phosphatases. At least four proteins are involved in the trgulation of the LRE-dependent Rants experssion: two binding factors that bind directly to the target sequences. and two factors that control their binding. The future purification and characterization of these binding pro-teins will reveal in detail the mechanism of Rantes gene activation after LPS stimulation.

• Proceedings of the Zoological Society Korea Conference
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• 1995.10b
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• pp.82-82
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• 1995

Regulation of enzyme synthesis by transcriptional and translational control systems provides rather stable adaptation to change of amino acid level in the growth medium, while manipulation of enzyme activity through endproduct feedback inhibition represents rather short-term and reversible ways of adjusting metabolic fluctuation of amino acid level. Various control mechanisms interplay to regulate genes encoding enzymes for amino acid biosynthesis in the yeast, Sacchromyces cerevisiae. When amino acids are in short supply, genes under a cross-pathway regulatory mechanism Or general amino acid control (general control) increase their action, in which Gcn4p is the major positive regulator of gene expression. When cells are cultured in minimal medium, basal level expression is also regulated by supplementary control elements, where inorganic phosphate level is additionally involved. Most of amino acid biosynthetic genes are also regulated by the level of endproduct of the pathway. This pathway-specific regulatory mechanism is called specific amino acid control (specific controD, under which gene expression is reduced when endproduct is present in the medium. Derepression of a gene through general control can be usually overridden by repression through specific control, where the endproduct level of that particular pathway is high and not limiting. In this presentation, regulatory factors for basal level expression and general control of yeast amino acid biosynthesis will be discussed, m addition to pathway-specific repression patterns and interaction between CrOSS- and specific-control mechanisms. Preliminary results are also presented from the investigation of the cloned genes in the threonine biosynthetic pathway of the yeast. yeast.

• Journal of the Korean Society of International Agriculture
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• v.23 no.5
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• pp.503-506
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• 2011

In order to analyze the resistant gene to Xanthomonas oryzae pv. oryzae in Korean native rices. Six Korean native rice varieties were crossed with IR-BB 101 contains Xa1 resistant gene and inoculated Japanese isolates IA(T7174). Cheonggunbyeo has Xa1 resistant gene only, and Yukseongjaerae, Agukdo, Heukpi and Icheon7ilchal have Xa1 and another one dominant gene. Ginggaragshare has Xa1 and another two dominant genes and two of those genes concerned complementary interaction against Japanese isolates IA(T7174).

• Genomics & Informatics
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• v.10 no.1
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• pp.33-39
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• 2012

High-throughput genomic technologies (HGTs), including next-generation DNA sequencing (NGS), microarray, and serial analysis of gene expression (SAGE), have become effective experimental tools for cancer genomics to identify cancer-associated somatic genomic alterations and genes. The main hurdle in cancer genomics is to identify the real causative mutations or genes out of many candidates from an HGT-based cancer genomic analysis. One useful approach is to refer to known cancer genes and associated information. The list of known cancer genes can be used to determine candidates of cancer driver mutations, while cancer gene-related information, including gene expression, protein-protein interaction, and pathways, can be useful for scoring novel candidates. Some cancer gene or mutation databases exist for this purpose, but few specialized tools exist for an automated analysis of a long gene list from an HGT-based cancer genomic analysis. This report presents a new web-accessible bioinformatic tool, called CaGe, a cancer genome annotation system for the assessment of candidates of cancer genes from HGT-based cancer genomics. The tool provides users with information on cancer-related genes, mutations, pathways, and associated annotations through annotation and browsing functions. With this tool, researchers can classify their candidate genes from cancer genome studies into either previously reported or novel categories of cancer genes and gain insight into underlying carcinogenic mechanisms through a pathway analysis. We show the usefulness of CaGe by assessing its performance in annotating somatic mutations from a published small cell lung cancer study.

• Journal of the Korean Data and Information Science Society
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• v.26 no.3
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• pp.677-685
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• 2015

Disease of human and economic traits of livestocks are affected a lot by gene combination effect rather than a single gene effect. In this study, we used SNPHarvester method that supplement existing method in order to investigate the interaction of these genes. The used genes are SREBPs (g.3270+10274 C>T, g.13544 T>C) and FABP4 (g.2634+1018 A>T, g.2988 A>G, g.3690 G>A, g.3710 G>C, g.3977-325 T>C, g.4221 A>G) that are closely related to the fatty acid composition affecting the meatiness of Korean cattle. The economic traits which are used are oleic acid (C18:1), monounsaturated fatty acid (MUFA), marbling score (MS). First, we have utilized the SNPHarvester method in order to find excellent gene combination, and then used the multifactor dimensionality reduction method in order to identify excellent genotype in gene combination.

• Korean Journal of Biological Psychiatry
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• v.8 no.2
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• pp.220-225
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• 2001

As numbers of serotonin's function are so many, studies of serotonin are numerous nowadays. In the beginning, concentration of metabolites such as 5-HIAA was a key issue, but recent studies have been challenged for serotonin receptor genes and their relation to mood disoder. Serotonin transporter(5-HTT) gene is a strong candidate gene of mood disoder for following reason. Serotonin transporter is a key protein in the serotonin pathway as it regulate the concentration of serotonin in the synaptic clept and essential pathophysiology of depression is dysregulation of 5-HTT so that all antidepressants have effect of 5-HTT antagonist. The decrease of 5-HTT in the platelet and in brain of the depressive patients is much consistent results in the studies of the pathophysiology of mood disorder till now. By this, we will be able to develop simple and easy marker for diagnosis, type, and treatment monitoring of depression. Many psychiatrists have sought the independent genes in relation to depression or schizophrenia. Obviously, the hereditary vulnerability contributes to etiology of mood disorders, but it is difficult to discriminate the independent genes because of many environmental factors. Moreover, in the hereditarily complex diseases such as mood disorder, the only vulnerability of gene can not sufficiently explain the etiology. In the future, to exclude the role of the gene-environmental interaction, the methods such as gene transfer can be considered. In the opposite direction, by using the gene destruction method, the role of target genes can be examined. As yet the concept of the gene expression, neural plasticity, neurogenesis and etc, is the elementary stage. The development of this field will help to establish the treatment strategy of chronic and refractory mood disorders.