• Proceedings of the Korea Society of Poultry Science Conference
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• 2000.11a
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• pp.78-80
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• 2000

A new murine TGF-$\beta$ family member, myostatin(growth/differentiation factor-8) is expressed specifically in developing and adult skeletal muscle and may be a negative regulator of skeletal muscle development. This study aims at characterization and identification of genomic organization of chicken myostatin gene. In thi study, we identified the genomic organization and sequence of chicken myostatin gene. Results of RT-PCR and Northern blots from various tissues showed different mRNA expression levels in developmental stages of chick embryos and demonstrated strong expression of myostatin mRNA in skeletal muscle. These facts suggest that chicken myostatin gene would play an important role not only in skeletal muscle cell but also in other tissues.

• BMB Reports
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• v.37 no.2
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• pp.177-184
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• 2004

The Crustacean hyperglycemic hormone (CHH) has been shown to exist as multiple molecular forms in several crustacean species. In Penaeus monodon, a gene encoding CHH (so-called Pem-CHH1) was recently described. In this study, the molecular structures of two other CHH genes (Pem-CHH2 and Pem-CHH3) are reported. Both the Pem-CHH2 and Pem-CHH3 genes contain three exons that are separated by two introns that are similar to the structure of other genes in the same family. An analysis of the upstream nucleotide sequences of each Pem-CHH gene has identified the putative promoter element (TATA box) and putative binding sites for several transcription factors. The binding sites for CREB, Pit-1, and AP-1 were found upstream of all three Pem-CHH genes. A Southern blot analysis showed that at least one copy of each Pem-CHH gene was located within the same 10 kb genomic DNA fragment. These results suggest that the CHH genes are arranged in a cluster in the genome of P. monodon, and that their expression may be modulated by similar mechanisms.

• Journal of Microbiology and Biotechnology
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• v.4 no.2
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• pp.108-112
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• 1994

The genetic organization of the urease gene cluster from an alkalophilic Bacillus pasteurii was determined by subcloning and Tn5 transposon mutagenesis of a 10.7 kilobasepair cloned fragment. A region of DNA between 5.0 and 6.0 kb in length is necessary for urease activity. In vitro transcription-translation analysis of transposon insertion mutants of the cloned urease genes demonstrated that the major ($M_r$ 67,000) and minor ($M_r$ 20,000) structural peptides of urease are encoded at one end of the urease gene cluster and at least 3 additional polypeptides are encoded by adjacent DNA sequences.

• Genomics & Informatics
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• v.2 no.1
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• pp.19-29
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• 2004

Gene expression profiles may offer more information than morphology and provide an alternative to morphology- based tumor classification systems. Informative gene selection is finding gene subsets that are able to discriminate between tumor types, and may have clear biological interpretation. Gene selection is a fundamental issue in gene expression based tumor classification. In this report, techniques for selecting informative genes are illustrated and supervised shaving introduced as a gene selection method in the place of a clustering algorithm. The supervised shaving method showed good performance in gene selection and classification, even though it is a clustering algorithm. Almost selected genes are related to leukemia disease. The expression profiles of 3051 genes were analyzed in 27 acute lymphoblastic leukemia and 11 myeloid leukemia samples. Through these examples, the supervised shaving method has been shown to produce biologically significant genes of more than $94\%$ accuracy of classification. In this report, SVM has also been shown to be a practicable method for gene expression-based classification.

• Journal of Microbiology
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• v.42 no.3
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• pp.188-193
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• 2004

Xanthobacter flavus strain UE15 was isolated in wastewater obtained from the Ulsan industrial complex, Korea. This strain functions as a 1,2-dichloroethane (1,2-DCA) degrader, via a mechanism of hydrolytic dechlorination, under aerobic conditions. The UE15 strain was also capable of dechlorinating other chloroaliphatics such as 2-chloroacetic acid and 2-chloropropionic acid. The dhlA gene encoding 1,2-DCA dechlorinase was cloned from the genomic DNA of the UE15 strain, and its nucleotide sequence was determined to consist of 933 base pairs. The deduced amino acid sequence of the DhlA dechlorinase exhibited 100％ homology with the corresponding enzyme from X. autotrophicus GJ10, but only 27 to 29％ homology with the corresponding enzymes from Rhodococcus rhodochrous, Pseudomonas pavonaceae, and Mycobacterium sp. strain GP1, which all dechlorinate haloalkane compounds. The UE15 strain has an ORF1 (1,356 bp) downstream from the dhlA gene. The OFR1 shows 99％ amino acid sequence homology with the transposase reported from X. autotrophicus GJ10. The transposase gene was not found in the vicinity of the dhlA in the GJ10 strain, but rather beside the dhlB gene coding for haloacid dechlorinase. The dhlA and dhlB genes were confirmed to be located at separate chromosomal loci in the Xanthobacter flavus UE15 strain as well as in X. autotrophicus GJ10. The dhlA and transposase the UE15 strain were found to be parenthesized by a pair of insertion sequences, 181247, which were also found on both sides of the transposase gene in the GJ10 strain. This unique structure of the dhlA gene organization in X. flavus strain UE15 suggested that the dechlorinase gene, dhlA, is transferred with the help of the transposase gene.

• Journal of Korean Neurosurgical Society
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• v.46 no.4
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• pp.385-388
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• 2009

Objective : We analyzed the methylation status of the O6-methylguanine-DNA methyltransferase (MGMT) gene promoter in World Health Organization (WHO) grade III gliomas in association with other molecular markers to evaluate their prevalence. Methods : The samples of a total of 36 newly WHO grade III glioma patients including 19 anaplastic oligodendrogliomas (AO), 7 anaplastic oligoastrocytomas (AOA), and 10 anaplastic astrocytomas (AA) were analyzed. The methylation status of the MGMT gene promoter was confirmed by methylation-specific polymerase chain reaction. The 1p/19q chromosomal deletion status and EGFR amplification were assessed by Fluorescence In-Situ Hybridization. MGMT, EGFR, EGFRvlll, and p53 expression were analyzed by immunohistochemical staining. Results : The MGMT gene promoter was methylated in 32 (88.9%) and unmethylated in 4 (11.2%) Among them, all of the AO and AOA had methylated MGMT gene promoter without exception. Significant associations between MGMT gene promoter hypermethylation and 1p/19q deletion was observed (p=0.003). Other molecular markers failed to show significant associations between MGMT gene promoter statuses. Conclusion : There was extensive epigenetic silencing of MGMT gene in high grade gliomas with oligodendroglial component. Together with frequent 1p/19q co-deletion in oligodendroglial tumors, this may add plausible explanations supporting the relative favorable prognosis in oligodendroglial tumors compared with pure astrocytic tumors.

• Genomics & Informatics
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• v.16 no.4
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• pp.37.1-37.3
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• 2018

Gene-gene interaction is a key factor for explaining missing heritability. Many methods have been proposed to identify gene-gene interactions. Multifactor dimensionality reduction (MDR) is a well-known method for the detection of gene-gene interactions by reduction from genotypes of single-nucleotide polymorphism combinations to a binary variable with a value of high risk or low risk. This method has been widely expanded to own a specific objective. Among those expansions, fuzzy-MDR uses the fuzzy set theory for the membership of high risk or low risk and increases the detection rates of gene-gene interactions. Fuzzy-MDR is expanded by a maximum likelihood estimator as a new membership function in empirical fuzzy MDR (EFMDR). However, EFMDR is relatively slow, because it is implemented by R script language. Therefore, in this study, we implemented EFMDR using RCPP ($c^{{+}{+}}$ package) for faster executions. Our implementation for faster EFMDR, called EMMDR-Fast, is about 800 times faster than EFMDR written by R script only.

• The Korea Genome Conference
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• 2005.09a
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• pp.65-65
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• 2005

• Proceedings of the Korean Aquaculture Society Conference
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• 2003.10a
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• pp.42-42
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• 2003

The far eastern catfish (Silurus asotus) growth hormone (GH) gene was cloned and characterized. The complete nucleotide sequences of genomic GH gene sequences as well as a catfish GH cDNA were obtained by RT-PCR and gene filter screening. The GH cDNA and genomic gene span 1.0 and 1.8 kb from the start codon to the polyadenylation signal, respectively. Both on cDNA and gDNA GH genes, the sequence polymorphism was detected including various silence mutations. The genomic GH gene comprised of only four exons and three introns, which was novel type of fish GH gene structure. The evolutionary relation of the catfish GH gene was inferred based on the comparative phylogenic analysis using the gene structures and sequences.

• Genomics & Informatics
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• v.16 no.4
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• pp.38.1-38.3
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• 2018

Gene-gene interaction (GGI) analysis is known to play an important role in explaining missing heritability. Many previous studies have already proposed software to analyze GGI, but most methods focus on a binary phenotype in a case-control design. In this study, we developed "Hierarchical structural CoMponent analysis of Gene-Gene Interactions" (HisCoM-GGI) software for GGI analysis with a continuous phenotype. The HisCoM-GGI method considers hierarchical structural relationships between genes and single nucleotide polymorphisms (SNPs), enabling both gene-level and SNP-level interaction analysis in a single model. Furthermore, this software accepts various types of genomic data and supports data management and multithreading to improve the efficiency of genome-wide association study data analysis. We expect that HisCoM-GGI software will provide advanced accessibility to researchers in genetic interaction studies and a more effective way to understand biological mechanisms of complex diseases.