• Korean Journal of Microbiology
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• v.45 no.4
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• pp.425-429
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• 2009

Identification of virulent Bacillus cereus strains was examined by PCR using primers specific for the detection of plcR-papR, which encode regulatory proteins controlling the transcription of virulence factors in B. cereus. Total 96 strains of B. cereus that carried at least one of diarrheal toxin genes including hblACD, nheABC, and cytK showed all positive PCR products, while other 48 Bacillus strains that lacked the toxin genes were plcRpapR-negative. This PCR method targeting the plcR-papR genes appears to be simple and effective in identifying the enterotoxin genes-harboring B. cereus strains.

• Korean Journal of Microbiology
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• v.45 no.4
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• pp.430-434
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• 2009

Bacterial 16S rRNA gene sequences have been widely used for the studies on molecular phylogeny, evolutional history, and molecular detections. Bacterial genomes have multiple rRNA operons, of which gene sequences sometimes are variable. In the present study, heterogeneity of the Vibrio 16S rRNA gene sequences were investigated. Vibrio 16S rRNA sequences were obtained from GenBank databases, considering the completion of gene annotation of Vibrio genome sequences. These included V. cholerae, V. harveyi, V. parahaemolyticus, V. splendidus, and V. vulnificus. Chromosome 1 of the studied Vibrio had 7~10 copies of the 16S rRNA gene, and their intragenomic variations were less than 0.9% dissimilarity (more than 99.1% DNA similarity). Chromosome 2 had none or single 16S rRNA gene. Intragenomic 16S rRNA genotypes were detected at least 5 types (V. vulnificus #CMCP6) to 8 types (V. parahaemolyticus #RIMD 2210633, V. harveyi #ATCC BAA-1116). These suggest that Vibrio has high heterogeneity of the 16S rRNA gene sequences.

• Journal of KIISE:Software and Applications
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• v.31 no.4
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• pp.525-536
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• 2004

Gene expression profile is numerical data of gene expression level from organism, measured on the microarray. Generally, each specific tissue indicates different expression levels in related genes, so that we can classify disease with gene expression profile. Because all genes are not related to disease, it is needed to select related genes that is called feature selection, and it is needed to classify selected genes properly. This paper Proposes GA based method for searching optimal ensemble of feature-classifier pairs that are composed with seven feature selection methods based on correlation, similarity, and information theory, and six representative classifiers. In experimental results with leave-one-out cross validation on two gene expression Profiles related to cancers, we can find ensembles that produce much superior to all individual feature-classifier fairs for Lymphoma dataset and Colon dataset.

• Journal of the Korea Organic Resources Recycling Association
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• v.17 no.4
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• pp.48-58
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• 2009

Glycosyl hydrolases (GH, EC 3.2.1.-) are key enzymes which can hydrolyze the glycosidic bonds between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. The new enzyme nomenclature of glycoside hydrolases is based on their amino acid sequence similarity and structural features. Here, we examined the glycosyl hydrolase family(GHF) genes reported from earthworm species. Among overall 115 GHFs, 12 GHFs could be identified from earthworm species through CAZy database. Of 12 GHF group genes, five genes including GHF2, 5, 17, 18, 20 are thought to be potent for industrial applications. The alignment of these genes with same genes from other animal species exhibited high sequence homology and some important amino acid residues necessary for enzyme activity appeared to be conserved. These genes can be utilized as a pest control agent or applicable to the food industry, clinical therapeutics and organic wastes disposition.

• Korean Journal of Microbiology
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• v.30 no.6
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• pp.456-459
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• 1992

The genes of Halohacteria. gvpD and gvpE. take part in formation of gas vesicle. These mRNA cause a lot of experimental prohlems due to its eharacteristic instahility in the analysis of transcripts. This study allowed easy cloning and sequencing of RNA hy substituting a stable complementary DNA for the mRNA of the genes for an analysis. The weak 111 RNA was reverse transcribed to DNA using reverse transcriptase. and was amplified using PCR method. The transcripts confirmed in this ~,tudy have not heen round in the northern hybridization covering almost all ranges of ORF of the gene. gvpD.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.23 no.2
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• pp.1-7
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• 2023

Inherited metabolic disorders (IMD) are a group of disorders involving various metabolic pathways. Genetic diagnosis of IMD has been challenging because of extremely heterogeneous nature and extensive laboratory and/or phenotype overlap. Conventional genetic diagnosis was a gene-by-gene approach that needs a priori information on the causative genes that might underlie the IMD. Recent implementation of next-generation sequencing (NGS) technologies has changed the process of genetic diagnosis from a gene-by-gene approach to simultaneous analysis of targeted genes possibly associated with the IMD using gene panels or using whole exome/genome sequencing (WES/WGS) covering entire human genes. Clinical NGS tests can be a cost-effective approach for the rapid diagnosis of IMD with genetic heterogeneity and are becoming standard diagnostic procedures.

• Tuberculosis and Respiratory Diseases
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• v.44 no.4
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• pp.796-805
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• 1997

Background : It is clear that deregulation of cell cycle progression is a hallmark of neoplastic transformation and genes involved in the $G_1$/S transition of the cell cycle are especially frequent targets for mutations in human cancers, including lung cancer. p16 gene product, one of the G1 cell-cycle related proteins, that is recently identified plays an important role in the negative regulation of the the kinase activity of the cyclin dependent kinase (cdk) enzymes. Therefore p16 gene is known to be an important tumor suppressor gene and is also called MTS1 (multiple tumor suppressor 1). No more oncogenes have been reported to be frequently related to multiple different malignancies than the alterations of p16 gene. Especially when it comes to non-small cell lung cancer, there was no expression of p16 in more than 70% of cell lines examined. And also it is speculated that p16 gene could exert a key role in the development of non-small cell lung cancer. This study was designed to evaluate whether p16 gene could be used as a candidate for gene therapy of non-small cell lung cancer. Methods : After the extraction of total RNA from normal fibroblast cell line and subsequent reverse transcriptase reaction and polymerase chain reaction, the amplified p16 cDNA was subcloned into eukaryotic expression plasmid vector, pRC-CMV. The constructed pRC-CMV-p16 was transfected into the NCI-H441 NSCLC cell line using lipofectin. The changes of G1 cell-cycle related proteins were investigated with Western blot analysis and immunoprecipitation after extraction of proteins from cell lysates and tumor suppressive effect was observed by clonogenic assay. Results : (1) p16(-) NCI-H441 cell line transfected with pRC-CMV-p16 showed the formation of p16 : cdk 4 complex and decreased phosphorylated Rb protein, while control cell line did not. (2) Clonogenic assay demonstrated that the number of colony formation was markedly decreased in p16(-) NCI-H441 cell line transfected with pRC-CMV-p16 than the control cell line. Conclusion : It is confirmed that the expression of p16 protein in p16 absent NSCLC cell line with the gene transfection leads to p16 : cdk4 complex formation, subsequent decrease of phosphorylated pRb protein and ultimately tumor suppressive effects. And also it provides the foundation for the application of p16 gene as a important candidate for the gene therapy of NSCLC.

• Korean Journal of Acupuncture
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• v.24 no.2
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• pp.129-139
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• 2007

목적 : Signal transducers and activators of transcription 6 (Stat 6) 유전자는 면역세포의 발달에 있어서 중요한 유전인자이며, IL-4와 같은 사이토카인에 의해 유전자 발현이 조절된다. 본 연구에서는 Stat 6 유전자 제거 생쥐와 정상 (wild type, W/T) 생쥐에 carrageenan으로 염증을 유도한 후 족삼리에 침치료를 시행하여 시상하부에서의 유전자 발현 양상을 분석하고자 하였다. 방 법 : BALB/c (W/T, n=12) and BALB/c-Stat 6 유전자 제거 생쥐 (n=12)의 발뒤꿈치 표피에 1% carrageenan을 30 ul 주사하여 염증을 유도하였다. 침은 염증 유도 30분 후에 족삼리(ST36)에 시침하였으며, 염증유도에 의한 부종 증가율을 매 시간마다 측정하여 총 5시간동안 측정하였다. 마이크로에러이는 Stat 6 유전자 제거 생쥐를 염증 유발 군과 염증유발 후 침을 처치한 군으로 나누고, 시상하부를 적출하여 RNA를 분리한뒤 마이크로어레이 프로파일을 분석하였다. 결 과 : 염증에 의한 부종증가율을 비교한 결과, Stat 6 유전자 제거 생쥐 그룹의 부종증가율이 W/T 생쥐의 부종 증가율보다 약 50 % 정도 감소하였으며, 각 3, 4, 5시간째에 유의한 차이를 나타내었다. (각 p<0.05). W.T생쥐군과 Stat 6 유전자 제거 생쥐군 모두에서, 침 처치군이 염증 유발 군에 비해, 염증 유발 2시간 후부터 유의한 감소를 나타내었다. 시상하부의 유전자 발현을 관찰한 결과, 39개의 유전자가 3배 이상 감소하였으며, 19개의 유전자는 3배 이상 증가하였다. 결 론 : W/T 생쥐군과 Stat 6 유전자 제거 생쥐 모두에서 침의 진통효과는 나타나며, 이의 기전에는 시상하부에서의 침 치료에 의한 염증관련 유전자들의 감소와, 항염증과 관련된 유전자들이 증가가 관여하는 것으로 보인다., 10, 11), 내측전완피신경(TE5, 6, 7, 8, 9, 10, 11), 후상완피신경(TE12, 13), 상외측상완피신경(TE13), 외측쇄골상신경(TE14, 15),대이개신경(TE16, 17, 18, 19), 소후두신경(TE19, 20), 이개측두신경(TE20, 21, 22), 안면신경측두지(TE22, 23), 관골측두신경(TE23), 중층에 견갑상신경(TE15), 견갑배신경(TE15), 경상설골근신경(TE17), 후이개신경(TE18, 19, 20), 안면신경측두지(TE20, 21, 22), 심층에 후골간신경(TE5, 6, 7), 요골신경심지(TE8, 9, 12, 13), 견갑상신경(TE14), 액와신경가지(TE14), 부신경(TE16), 안면신경과 부신경가지(TE17), 설인신경(TE17), 설하신경(TE17), 경신경고리(TE17), 미주신경(TE17), 안면신경 (TE18). 3) 혈(血) 관(管) : 천층에 척측정맥배측지(TE1, 2), 고유수장지동맥배측지(TE1), 배측중수골동맥배측지(TE2), 배측중수골정맥(TE3), 척측피정맥(TE4, 5, 6, 7, 8, 9, 10, 11), 배측정맥궁(TE4), 부요측피정맥(TE6, 8, 9),요측피정맥(TE10, 11), 후견봉정맥가지(TE13, 14), 후이개동 ${\cdot}$ 정맥(TE16, 17, 18, 19, 20), 전이개동 ${\cdot}$ 정맥(TE20), 천측두동 ${\cdot}$ 정맥(TE22, 23), 중층에 후상완회선동맥(TE14), 견갑배동맥(TE15), 견갑상동맥(TE15),천측두동 ${\cdot}$ 정맥(TE21), 관골측두동 ${\cdot}$ 정맥(TE23), 심층에 배측중수골동맥(TE3), 배측수근동맥궁(TE4), 후골간동맥(TE4, 5, 6, 7, 8, 9), 전골간동맥(TE6, 7, 9)

• Korean Journal of Microbiology
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• v.41 no.3
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• pp.195-200
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• 2005

Comamonas sp. strain DJ-12 is a bacterial isolate capable of degrading of 4-chlorobiphenyl (4CB) as a carbon and energy source. The degradation pathway was characterized as being conducted by consecutive reactions of the meta-degradation of 4CB, hydrolytic dechlorination of 4-chlorobenzoate (4CBA), hydroxylation of 4-hydroxybenzoate, and meta-degradation of protocatechuate to product TCA metabolites. The 6.8 kb fragment from the chromosomal DNA of Comamonas sp. strain DJ-12 included the genes encoding for the meta-degradation of PCA; the genes of protocatechuate 4,5-dioxygenase alpha and beta subunits (pmcA and pmcB), 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase (pmcC), 2-pyrone-4,6-dicarboxylate hydrolase (pmcD), 4-oxalomesaconate (OMA) hydratase(pmcE), 4-oxalocitramalate (OCM) aldolase (pmcF), and transporter gene (pmcT). They were organized in the order of pmcT-pmcE-pmcF-pmcD-pmcA-pmcB-pmcC. The amino acid sequences deduced from the nucleotide sequences of pmcABCDEFT genes from Comamonas sp. strain DJ-12 exhibited 94 to $98\%$ homologies with those of Comamonas testosteroni BR6020 and Pseudomonas ochraceae NGJ1, but only 52 to $74\%$ with homologies Sphingomonas paucimobilis SYK-6, Sphingomonas sp. LB126, and Arthrobacter keyseri 12B.

• Journal of Sericultural and Entomological Science
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• v.51 no.2
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• pp.191-196
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• 2013

This study was aimed for development of a useful genes that has a transcript expressional specificity in the early embryonic stage of the silkworm, Bombyx mori. We constructed and analyzed a full-length cDNA library from silkworm's eggs which after a lapse of 2 ~ 6 hours post oviposit. A total 960 clones were randomly selected, and the 5' ends of the inserts were sequenced to generate 652 expressed sequence tags(EST). 334 unique ESTs were generated after the assembly of 652 ESTs. The annotation of 334 unique ESTs by BLAST search revealed that 156(47%) of the sequences represented known genes, whereas 178(53%) of the sequences has no matches in the database. Of the 156 known genes, the most abundant genes were heat shock protein hsp20.8 gene(12 times) and ubiqutin-like protein gene(11 times). The functional groups of these ESTs with matches in the database were constructed according to their putative molecular functions. Among thirteen functional categories, the largest groups were protein synthesis(9.6%) and cellular organization( 8.1%). Further defined studies on molecular functions and biological roles of their promoters will give us wellfined information and its application.