• Journal of Microbiology and Biotechnology
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• v.23 no.11
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• pp.1509-1518
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• 2013

An agar-degrading bacterium, designated as strain $G7^T$, was isolated from a coastal seawater sample from Gaya Island (Gayado in Korean), Republic of Korea. The isolated strain $G7^T$ is gram-negative, rod shaped, aerobic, non-motile, and non-pigmented. A similarity search based on its 16S rRNA gene sequence revealed that it shares 95.5%, 90.6%, and 90.0% similarity with the 16S rRNA gene sequences of Catenovulum agarivorans $YM01^T$, Algicola sagamiensis, and Bowmanella pacifica W3-$3A^T$, respectively. Phylogenetic analyses demonstrated that strain $G7^T$ formed a distinct monophyletic clade closely related to species of the family Alteromonadaceae in the Alteromonas-like Gammaproteobacteria. The G+C content of strain $G7^T$ was 41.12 mol%. The DNA-DNA hybridization value between strain $G7^T$ and the phylogenetically closest strain $YM01^T$ was 19.63%. The genomes of $G7^T$ and $YM01^T$ had an average ANIb value of 70.00%. The predominant isoprenoid quinone of this particular strain was ubiquinone-8, whereas that of C. agarivorans $YM01^T$ was menaquinone-7. The major fatty acids of strain $G7^T$ were Iso-$C_{15:0}$ (41.47%), Anteiso-$C_{15:0}$ (22.99%), and $C_{16:1}{\omega}7c/iso-C_{15:0}2-OH$ (8.85%), which were quite different from those of $YM01^T$. Comparison of the phenotypic characteristics related to carbon utilization, enzyme production, and susceptibility to antibiotics also demonstrated that strain $G7^T$ is distinct from C. agarivorans $YM01^T$. Based on its phenotypic, chemotaxonomic, and phylogenetic distinctiveness, strain $G7^T$ was considered a novel genus and species in the Gammaproteobacteria, for which the name Gayadomonas joobiniege gen. nov. sp. nov. (ATCC BAA-2321 = $DSM25250^T=KCTC23721^T$) is proposed.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• v.37 no.6
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• pp.550-555
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• 2011

Chromosomal loss of heterozygosity (LOH) is a common mechanism for the inactivation of tumor suppressor genes in human epithelial cancers. LOH patterns can be generated through allelotyping using polymorphic microsatellite markers; however, owing to the limited number of available microsatellite markers and the requirement for large amounts of DNA, only a modest number of microsatellite markers can be screened. Hybridization to single nucleotide polymorphism (SNP) arrays using Affymetarix GeneChip Mapping 10 K 2.0 Array is an efficient method to detect genome-wide cancer LOH. We determined the presence of LOH in oral SCCs using these arrays. DNA was extracted from tissue samples obtained from 10 patients with tongue SCCs who presented at the Hospital of Tokyo Dental College. We examined the presence of LOH in 3 of the 10 patients using these arrays. At the locus that had LOH, we examined the presence of LOH using microsatellite markers. LOH analysis using Affymetarix GeneChip Mapping 10K Array showed LOH in all patients at the 1q31.1. The LOH regions were detected and demarcated by the copy number 1 with the series of three SNP probes. LOH analysis of 1q31.1 using microsatellite markers (D1S1189, D1S2151, D1S2595) showed LOH in all 10 patients (100). Our data may suggest that a putative tumor suppressor gene is located at the 1q31.1 region. Inactivation of such a gene may play a role in tongue tumorigenesis.

• Journal of Life Science
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• v.14 no.5
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• pp.874-881
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• 2004

Angiogenesis has been implicated in progression of inflammation, arthritis, psoriasis, atherosclerosis as well as tumor growth and metastasis. Intensive studies have been carried out to develop a strategy for cancer treatment by blocking angiogenesis. During angiogenesis, endothelial proliferation and migration essentially occurs upon activation. In this study, we compared the expression profiles of human umbilical endothelial cells activated by incubating in vitro in the rich medium containing several growth factors, and non-activated ones. cDNA targets derived from total RNAs of HUVEC activated for 13 h in M199 medium containing endothelial cell growth supplement, 20% fetal bovine serum, and heparin, after reaching 70～80% confluency, or non-activated, were hybridized onto oligonucleotide microarrays containing 1,8864 genetic elements. Unsupervised hierarchical clustering analysis resulted in two subgroups on dendrogram exhibiting activated and non-activated HUVECs. We then extracted 122 outlier genes which were shown to be up-regulated or under-expressed by at least 2-folds in activated HUVECs. Among these, 32 annotated genes were up-regulated and 38 were down-regulated in activated HUVECs. Interestingly, genes involved in cell proliferation, motility, and inflammation/ immune response were up-regulated in activated HUVEC, whereas genes for cell adhesion or vessel morphogenesis/function were down-regulated. Unexpectedly, the expression of genes well-characterized as angiogenesis markers was not changed except Eph-B4, which was down-regulated about 4 folds. 52 unknown genes were also up- or down-regulated. Therefore, these results could provide an opportunity to targeting new vascular molecules for the development of anti-angiogenic molecules.

• Korean Journal of Ichthyology
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• v.29 no.1
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• pp.1-12
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• 2017

A natural hybrid of interspecific between the Coreoleuciscus splendidus and C. aeruginos (Cypriniformes: Cyprinidae) was captured in the Hwang-ji Stream, a tributary of the Nakdong River basin in Korea. An interspecific hybrid between C. splendidus and C. aeruginos was genetically identified based on morphological characteristics and the sequence analysis of nuclear recombination activating gene 1 (RAG1) gene (1,334 bp) and mitochondrial cytochrome c oxidase subunit 1 (CO1) gene (1,551 bp). As a result of morphological variations, the natural hybrid appeared to have an intermediate character between two parental species (C. splendidus and C. aeruginos) in three variations of black array (s) on dorsal, caudal and anal fin rays. Phylogenetic analysis inferred from RAG1 and CO1 sequence data revealed that Coreoleuciscus populations from Hwang-ji stream consist of two pure Coreoleuciscus species and a hybrid individual group. The individuals were clearly identified the cross and reciprocal hybrid by CO1 gene analysis. In RAG1 gene, 13 nucleotide variation loci were detected and the hybrid individuals displayed the double peaks of sequence chromatograms at the 9 diagnostic positions. In this study, molecular data and morphological variations were clearly demonstrated that hybridization did occur between C. splendidus and C. aeruginos. However, F2 hybrid generation and reproductive capacity of F1 hybrid individuals were not demonstrated.

• The Korean Journal of Food And Nutrition
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• v.15 no.2
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• pp.104-111
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• 2002

The peptidyl prolyl sis-trans isomerase (PPIase, EC 5.2.1.8) from bacillus stearothermophilus was extracted from the cells treated with by lysozyme. PPIase was purified from the cell extracts by heat treatment, ammonium sulfate precipitation, ion exchange chromatography and finally gel filtration, sodium dodecyl sulfate polyacrylamide gel electrophoresis(SDS-PAGE). The molecular weight of the purified PPIase was estimated as 18kDa by SDS-PAGE. The 39 amino acid residues from the N-terminus were determined by the protein sequencer. The enzyme showed the optimum pH at 8.0 and was stable at the range of pH 7.0∼8.0. The enzyme was considerably stable after heat treatment at 60$\^{C}$ for 30minutes, and the enzyme was quite stable up to 65$\^{C}$. The presence of the PPIase in the refolding solution accelerated the isomerization rate of the assay peptide. PPIase gene of Bacillus stearothermophilus was screened from a genomic library by plaque hybridization using the A-l primer as a probe. A PPIase positive plaque contained a 3.0kb insert of the chromosomal DNA. A 3.0kb fragment was subcloned into pUC18, resulting pPI-40. A DNA fragment encoding the N-terminal portion of the PPIase in pPI-40 was amplified by polymerase chain reaction(PCR) method using the A-1 and B-2 primers. The amplified fragment was cloned into the Sma I site of pUC18 and recombinant plasmid was designated as pSN-18. The nucleotide sequence of 167bp fragment was determined. The deduced amino acid sequence of PPIase was completely matched with the determined N-terminal amino acid sequence of PPIase B. stearothermophilus.

• Journal of Aquaculture
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• v.10 no.3
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• pp.363-371
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• 1997

Backcross hybridization between female cyprinid loach(Misgurnus anguillicaudatus) any male mud loach (M. mizolepis)$\times$cyjprinid loach hybrid were made, and its effect on early survival, cytogenetic traits, and gonad development were examined. Mean fertilization rate and hatching success of backcross hybrids were similar to those found in the maternal species, the cyprinid loach. However, the backcross hybrids revealed significantly improved early survival up to yolk sac absorption (86.0%) compared to cyprinid loach (0%) under low culture temperature ($15^{\circ}C$). the erythrocytic size and DNA content of backcross hybrids were nearly intermediate to those of the parents. Karyological analysis of backcross hybrids displayed two kinds of modal chromosome number of 2n=48 or 2n=49. Growth of backcross hybrids over 6 months after hatching was proven to be intermediate between their parental species. Although backcross hybrids had intermediate values between those of thier parents in most morphometric traits, overall external morphology of backcross hybrids was morer simlar to cyprinid loach than mud loach$\times$cyprinid loach hybrid. Histological examination of gonads at 2 and 4 months of age revealed that no female was obseved in backcross hybrid groups, suggesting the possibility of production of monosex male population.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.1
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• pp.19-24
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• 2008

The purpose of this study was to detect expression of genes related to egg production in Taiwan Country chickens by suppression subtractive hybridization. Liver samples of mRNA extraction from two Taiwan Country chicken strains (L2 and B), originated from the same population but with very distinct egg production rates after long-term selection for egg and meat production respectively. Two-way subtraction was performed. The hepatic cDNA from the low egg production chickens (B) was subtracted from the hepatic cDNA from the high egg production strain (L2). The reversed subtraction (L2 from B) was also performed. The resulting differentially expressed gene fragments were cloned and sequenced. We sequenced 288 clones from the forward subtraction and 96 clones from the reverse subtraction. These genes were subjected to further screening to confirm the differential expression between the two genetic breeds of chickens. The apolipoprotein B (apoB) was expressed to a greater extent in the liver of the L2 than in the B line chickens. The 5-aminoimidazole- 4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (PURH) was expressed to a greater extent in the liver of the B than in the L2 strain chickens. We demonstrated that both apoB and PURH were more highly expressed in the liver than that in other tissues (muscle, ovary, and oviduct) in laying Taiwan Country chickens. Taken together, these data suggest that after the selection for egg production, expression of apoB and PURH genes were also changed. Whether the changed expression of these genes is directly related to egg production is not known, but these two genes may be useful markers for egg laying performance in Taiwan Country chickens.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.3
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• pp.328-337
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• 2017

Objective: An experiment was conducted to determine the relationship between the KAP11.1 and the regulation wool fineness. Methods: In previous work, we constructed a skin cDNA library and isolated a full-length cDNA clone termed KAP11.1. On this basis, we conducted a series of bioinformatics analysis. Tissue distribution of KAP11.1 mRNA was performed using semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) analysis. The expression of KAP11.1 mRNA in primary and secondary hair follicles was performed using real-time PCR (real-time polymerase chain reaction) analysis. The expression location of KAP11.1 mRNA in primary and secondary hair follicles was performed using in situ hybridization. Results: Bioinformatics analysis showed that KAP11.1 gene encodes a putative 158 amino acid protein that exhibited a high content of cysteine, serine, threonine, and valine and has a pubertal mammary gland) structural domain. Secondary structure prediction revealed a high proportion of random coils (76.73%). Semi-quantitative RT-PCR showed that KAP11.1 gene was expressed in heart, skin, and liver, but not expressed in spleen, lung and kidney. Real time PCR results showed that the expression of KAP11.1 has a higher expression in catagen than in anagen in the primary hair follicles. However, in the secondary hair follicles, KAP11.1 has a significantly higher expression in anagen than in catagen. Moreover, KAP11.1 gene has a strong expression in inner root sheath, hair matrix, and a lower expression in hair bulb. Conclusion: We conclude that KAP11.1 gene may play an important role in regulating the fiber diameter.

• Korean Journal of Microbiology
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• v.45 no.1
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• pp.26-31
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• 2009

This study was aimed at the analysis of prokaryote communities in Korean traditional fermented food, jeotgal, and isolation of a novel strain from jeotgal by using culture-dependent and molecular biological approaches. Seventeen kinds of jeotgal were selected on the basis of its origins and sources. The samples were inoculated on 12 kinds of media. 308 isolates were selected randomly by morphological features, and its 16S rRNA gene sequences was amplified by PCR technique with bacteria and archaea specific primers (8F, 21F, and 1492R). The 16S rRNA gene sequences were compared with those in EzTaxon and GenBank databases. DNA-DNA hybridization was performed to identify a novel strain. As a result, the majority of the isolates were lactic acid bacteria (Leuconostoc, Weisella, Lactococcus, Lactobacillus, Carnobacterium, Marinilactibacillus), Bacillus, Pseudomonas, Micrococcus, Brevibacterium, Microbacterium and Kocuria in 17 kinds of jeotgal. The strains belonging to Salinicoccus, Halomonas, Cobetia, Lentibacillus, Paracoccus, and Psychrobacter were isolated as minor ones. Fourteen novel species were identified based on phylogenetic analysis.

• The Journal of Korean Society of Virology
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• v.27 no.1
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• pp.19-27
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• 1997

To develop the polymerase chain reaction (PCR) for the detection of type D simian retrovirus (SRV) infection, an oligonucleotide primer pair was designed to hybridize to the sequences within env gene of SRV subtype 1 (SRV-1). The 3' proximal env sequences annealing to the primers had been rather conserved among three different subtypes of SRV, SRV-1, SRV-2, and SRV-3 (Mason-Pfizer Monkey Virus: MPMV). The PCR using the primer pair targeting an env region successfully detected and amplified all three subtypes of SRV with excellent specificity after single round of reaction. The tests with peripheral blood mononuclear cells infected either with simian immunodeficiency virus or simian T-Iymphotropic virus type 1, major immunosuppressive viral agents together with SRV in simian, verified the specificity of the PCR by excluding any cross reactivity. Semiquantitative titration PCR, amplifying serially diluted plasmid DNA of each subtype, was performed to evaluate sensitivity limits of the reaction. Based on molecular weight of each cloned SRV genome, the PCR should be able to detect one SRV-infected cell per more than $5-7{\times}10^4$ uninfected cells after simple ethidium bromide staining of resulting products. The PCR must be very efficient screening system with its quickness, certainty, and sensitivity for SRV-infected animals used in human AIDS research model. Second round amplification of the reaction products from the first PCR, or Southern hybridization by radiolabeled probes shall render to compete its efficacy to ELISA which has been the most sensitive technique to screen SRV infection but with frequent ambiguity problem.