• Microbiology and Biotechnology Letters
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• v.42 no.4
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• pp.393-401
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• 2014

A bacterium producing antimicrobial substance was isolated from cheonggukjang. The bacterium was identified as a strain of Bacillus subtilis by 16S rDNA sequencing and designated as Bacillus subtilis HH28. The antimicrobial substance produced from Bacillus subtilis HH28 was purified by 0-80% ammonium sulfate precipitation, DEAE-sepharose FF column chromatography, and Sephacryl S-200 HR gel chromatography. The molecular weight of the purified antimicrobial substance was estimated to be approximately 3,500 Da using Tricine sodium dodecyl sulfate-polyacrylamide gel electrophoresis and direct detection analysis. Antimicrobial substance from B. subtilis HH28 not only inhibited B. cereus, but also Listeria monocytogenes and Vibrio parahaemolyticus. The purified antimicrobial substance was stable at $40-80^{\circ}C$, and between pH 2 and 8. Antimicrobial activity of the purified substance was completely destroyed by treatment of protease, proteinase K, and pronase E, indicating that it is proteinaceous.

• The Journal of Advanced Prosthodontics
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• v.7 no.6
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• pp.468-474
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• 2015

PURPOSE. The aim of this study was to characterize and compare bacterial diversity on the removable partial denture (RPD) framework over time. MATERIALS AND METHODS. This descriptive pilot study included five women who were rehabilitated with free-end mandibular RPD. The biofilm on T-bar clasps were collected 1 week ($t_1$) and 4 months ($t_2$) after the RPD was inserted ($t_0$). Bacterial 16S rDNA was extracted and PCR amplified. Amplicons were cloned; clones were submitted to cycle sequencing, and sequences were compared with GenBank (98% similarity). RESULTS. A total of 180 sequences with more than 499 bp were obtained. Two phylogenetic trees with 84 ($t_1$) and 96 ($t_2$) clones represented the bacteria biofilm at the RPD. About 93% of the obtained phylotypes fell into 25 known species for $t_1$ and 17 for $t_2$, which were grouped in 5 phyla: Firmicutes ($t_1=82%$; $t_2=60%$), Actinobacteria ($t_1=5%$; $t_2=10%$), Bacteroidetes ($t_1=2%$; $t_2=6%$), Proteobacteria ($t_1=10%$; $t_2=15%$) and Fusobacteria ($t_1=1%$; $t_2=8%$). The libraries also include 3 novel phylotypes for $t_1$ and 11 for $t_2$. Library $t_2$ differs from $t_1$ (P=.004); $t_1$ is a subset of the $t_2$ (P=.052). Periodontal pathogens, such as F. nucleatum, were more prevalent in $t_2$. CONCLUSION. The biofilm composition of the RPD metal clasps changed along time after RPD wearing. The RPD framework may act as a reservoir for potentially pathogenic bacteria and the RPD wearers may benefit from regular follow-up visits and strategies on prosthesis-related oral health instructions.

• Journal of Life Science
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• v.17 no.10
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• pp.1426-1433
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• 2007

To investigate the antibiotic resistant patterns of the bacteria producing ESBL, we isolated one organism of Klebsiella pneumoniae from a clinical laboratory in Busan. The organism that produces ESBL gene was detected by double disk synergy test and the presence of three ESBL genes (TEM-1, SHV-12, CTX-M-15) was confirmed by polymerase chain reaction and DNA sequencing analysis. To analyse the characteristics of three ESBL genes, we performed transconjugation, transformation and cloning experiment with the organism. The MIC of Klebsiella pneumoniae was revealed that ceftazidime, cefotaxime and ceftriaxone were $256\;{\mu}g/ml,\;128\;{\mu}g/ml\;and\;128\;{\mu}g/ml$ respectively. The MIC of conjugant (E. coli $RG176^{Na(r)}$) af was revealed that ceftazidime, cefotaxime and ceftriaxone were $256\;{\mu}g/ml,\;64\;{\mu}g/ml\;and\;128\;{\mu}g/ml$ respectively. The MIC of transformant (E. cofi $DH5{\alpha}$) was revealed that ceftazidime, cefotaxime and ceftriaxone were $128\;{\mu}g/ml,\;32\;{\mu}g/ml,\;and\;32\;{\mu}g/ml$ respectively, The MIC of cloned organism of SHV-12 gene (E. coli $DH5{\alpha}$) was revealed that ceftazidime, cefotaxime and ceftriaxone were $128\;{\mu}g/ml,\;8\;{\mu}g/ml,\;and\;32\;{\mu}g/ml$ respectively. The results indicated that MIC of conjugant was higher than MIC of transformant and also SHV-12 gene were not resistant against cefotaxime antibiotic.

• Journal of Microbiology
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• v.45 no.3
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• pp.246-255
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• 2007

Mutans streptococci have been implicated as cariogenic bacteria in dental caries because they can produce high levels of dental caries-causing lactic acid and extracellular polysaccharide. The aim of this study was to isolate and characterize the mutans streptococci from the dental plaque obtained from Koreans. The dental plaque samples were collected from the anterior and molar teeth of both jaws in 155 subjects (aged 2 to 33.2 years, average age $13.7{\pm}4.7\;years$). The samples were diluted by 100-fold in $1{\times}\;PBS$ and plated on mitis-salivarius bacitracin (MSB) agar plates. The mutans streptococci grown on MSB plates were screened by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) targeting dextranase gene (dex). The mutans streptococci were identified at the species level using a 16S rDNA sequencing comparison method. The biochemical tests were carried out to biotype the mutans streptococci. Ninety-five strains of the mutans streptococci out of 358 colonies, which were derived from 141 subjects, were isolated. Of them, 77 strains and 18 strains were Streptococcus mutans and Streptococcus sobrinus, respectively. The biotyping data showed that 62, 1, 20, 10, and 2 strains were biotypes I, II, IV, V and variant, respectively. Of the two strains of variant biotype, one strains was similar to biotype IV except that it was positive to the arginine hydrolysis test. We considered this one strain a new biotype, and classified it as biotype VII. In conclusion, S. mutans and its biotype I was most frequently isolated in Korean dental plaque. The mutans streptococci strains isolated in this study might be useful for the study of the pathogenesis and the prevention of dental caries.

• Research in Plant Disease
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• v.12 no.2
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• pp.134-138
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• 2006

A new bacterial disease of broccoli (Brassica oleracea var. italica) was observed on field-grown plants in Pyungchang during 2003 and 2004. Seedling infections first appeared as a blackening along the margins of the cotyledon. Cotyledon shriveled and dropped off. Infected seedlings were stunted and yellowed and eventually died. The disease was easily recognized by the presence of yellow, V-shaped, or U-shaped areas extending inward from margin of the leaf. As the disease progressed, the yellow lesions turned brown and the tissues died. Isolations made from diseased leaves on yeast extract dextrose calcium carbonate agar yielded nearly pure cultures of a yellow-pigmented bacterium typical of a xanthomonad. Two bacterial strains were purified and used for further tests. Pathogenicity of strains was confirmed on 3-week-old crucifer (cabbage, Chinese cabbage, kale, radish and broccoli) plants cut by scissors with bacterial suspensions containing $10^8 cfu/ml$ of phosphate buffered saline. The Biolog and fatty acid analyses and 16S rDNA sequencing of two strains (SL4797 and SL4800) from broccoli black rot showed that they could be identified as X. campestris pv. campestris because of their high similarity to the tester strain (X. campestris pv. campestris NCPPB528) with a match probability of 100%. This is the first report of black rot of broccoli in Korea.

• Journal of Biomedical and Translational Research
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• v.19 no.4
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• pp.116-124
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• 2018

Korean Native Pig (KNP) has a uniform black coat color, excellent meat quality, white colored fat, solid fat structure and good marbling. However, its growth performance is low, while the western origin Yorkshire pig has high growth performance. To take advantage of the unique performance of the two pig breeds, we raised crossbreeds (KNP ${\times}$ Yorkshire to make use of the heterotic effect. We then analyzed the liver transcriptome as it plays an important role in fat metabolism. We sampled at two stages: 10 weeks and at 26 weeks. The stages were chosen to correspond to the change in feeding system. A total of 16 pigs (8 from each stage) were sampled and RNA sequencing was performed. The reads were mapped to the reference genome and differential expression analysis was performed with edgeR package. A total of 324 genes were found to be significantly differentially expressed (${\left|log2FC\right|}$ > 1 & q < 0.01), out of which 180 genes were up-regulated and 144 genes were down-regulated. Principal Component Analysis (PCA) showed that the samples clustered according to stages. Functional annotation of significant DEGs (differentially expressed genes) showed that GO terms such as DNA replication, cell division, protein phosphorylation, regulation of signal transduction by p53 class mediator, ribosome, focal adhesion, DNA helicase activity, protein kinase activity etc. were enriched. KEGG pathway analysis showed that the DEGs functioned in cell cycle, Ras signaling pathway, p53 signaling pathway, MAPK signaling pathway etc. Twenty-nine transcripts were also part of the DEGs, these were predominantly Cys2His2-like fold group (C2H2) family of zinc fingers. A protein-protein interaction (PPI) network analysis showed that there were three highly interconnected clusters, suggesting an enrichment of genes with similar biological function. This study presents the first report of liver tissue specific gene regulation in a cross-bred Korean pig.

• Horticultural Science & Technology
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• v.34 no.6
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• pp.912-923
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• 2016

Watermelon production is often limited by powdery mildew in areas with a large daily temperature range. Development of resistant watermelon cultivars can protect against powdery mildew; however, little is known about the characteristics of its causal agents. Here, we identified the genus and race of a causal pathogen of powdery mildew in Ansung province of South Korea, and developed molecular markers for the generation of resistant watermelon cultivars. The causal pathogen was determined to be Podosphaera xanthii based on multiple sequence alignments of internal transcribed spacers (ITS) of rDNA. The physiological race was identified as 1W, and the Ansung isolate was named P. xanthii 1W-AN. Following inoculation with the identified P. xanthii 1W-AN, we found inheritance of the resistant gene fitting a single dominant Mendelian model in a segregated population ('SBA' ${\times}$ PI 254744). To develop molecular markers linked to fungus-resistant loci, random amplified polymorphic DNA (RAPD) was accomplished between DNA pooled from eight near-isogenic lines (NILs; $BC_4F_6$), originated from PI 254744 and susceptible 'SBB' watermelon. After sequencing bands from RAPD were identified in all eight NILs and PI254744, 42 sequence-characterized amplifiedregion (SCAR) markers were developed. Overall, 107 $F_2$ plants derived from $BC_4F_6$ NIL-1 ${\times}$ 'SBB' were tested, and one SCAR marker was selected. Sequence comparison between the SCAR marker and the reference watermelon genome identified three Nco I restriction enzyme sites harboring a single nucleotide polymorphism, and codominant cleavage-amplified polymorphic site markers were subsequently developed. A CAPS marker was converted to a high-resolution melt (HRM) marker, which can discriminate C/T SNP (254PMR-HRM3). The 254PMR-HRM3 marker was evaluated in 138 $F_{2:3}$ plants of a segregating population ('SBA' ${\times}$ PI254744) and was presumed to be 4.3 cM from the resistance locus. These results could ensure P. xanthii 1W-AN resistance in watermelon germplasm and aid watermelon cultivar development in marker-assist breeding programs.

• Journal of The Korean Society of Grassland and Forage Science
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• v.38 no.2
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• pp.106-111
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• 2018

This study was conducted to investigate the relationship between changes of rumen microflora and bloat in Jersey cow. Jersey cows (control age: 42 months, control weight: 558kg; treatment age: 29 months, treatment weight 507kg) were fed on the basis of dairy feeding management at dairy science division in National Institute of Animal Science. The change of microbial population in rumen was analyzed by using next generation sequencing (NGS) technologies due to metabolic disease. The diversity of Ruminococcus bromii, Bifidobacterium pseudolongum, Bifidobacterium merycicum and Butyrivibrio fibrisolvens known as major starch fermenting bacteria was increased more than 36-fold in bloated Jersey, while cellulolytic bacteria community such as Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens was increased more than 12-fold in non-bloated Jersey. The proportion of bacteroidetes and firmicutes was 33.4% and 39.6% in non-bloated Jersey's rumen, while bacteroidetes and firmicutes were 24.9% and 55.1% in bloated Jersey's. In conclusion, the change of rumen microbial community, in particular the increase in starch fermenting bacteria, might have an effect to occur the bloat in Jersey cow.

• Korean Journal of Microbiology
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• v.42 no.3
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• pp.185-194
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• 2006

The aim of this study was to identify the bacteria isolated from endodontic lesions by cell culture and to determine the antimicrobial susceptibility of them against 8 antibiotics. The necrotic pulpal tissues were collected from 27 infected root canals, which were diagnosed as endodontic infection. Samples were collected aseptically from the infected pulpal tissue of the infected root canals using a barbed broach and a paper point. The cut barbed broaches and paper points were transferred to an eppendorf tube containing $500{\mu}l\;of\;1{\times}PBS$. The sample solution was briefly mixed and plated onto a BHI-agar plate containing 5% sheep blood. The agar plates were incubated in a $37^{\circ}C$ anaerobic chamber for 2 to 5 days. The bacteria grown on the agar plates were identified by comparison of 16S rRNA gene (rDNA) sequencing method at the species level. To test the sensitivity of the bacteria isolated from the infected root canals against 8 antibiotics, minimum inhibitory concentrations (MIC) were determined using broth dilution assay. The data showed that 101 bacterial strains were isolated and were identified. Streptococcus spp. (29.7%) and Actinomyces spp. (21.8%) were predominantly isolated. The 9 strains were excluded in antimicrobial susceptibility test because they were lost during the experiment or were not grown in broth culture. The percentage of bacteria susceptible for each antibiotic in this study was clindamycin, 87.0% (80 of 92); tetracycline, 75.0% (69 of 92); cefuroxime axetil, 75.0% (69 of 92); amoxicillin + clavulanic acid (5:1), 71.7% (66 of 92); penicillin G, 66.3% (61 of 92); erythromycin, 66.3% (61 of 92); amoxicillin, 44.6% (41 of 92); and ciprofloxacin, 31.5% (29 of 92). The susceptibility pattern of 8 antibiotics was dependent on the host of the bacteria strains rather than the kinds of bacterial species. These results indicate that antibiotic susceptibility test should be performed when antibiotics are needed for the treatment of infected root canals.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.11
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• pp.4555-4561
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• 2014

Background: Silencing due to methylation of suppressor of cytokine signaling-3 (SOCS-3), a negative regulator gene for the JAK/STAT signaling pathway has been reported to play important roles in leukemogenesis. Imatinib mesylate is a tyrosine kinase inhibitor that specifically targets the BCR-ABL protein and induces hematological remission in patients with chronic myeloid leukemia (CML). Unfortunately, the majority of CML patients treated with imatinib develop resistance under prolonged therapy. We here investigated the methylation profile of SOCS-3 gene and its downstream effects in a BCR-ABL positive CML cells resistant to imatinib. Materials and Methods: BCR-ABL positive CML cells resistant to imatinib (K562-R) were developed by overexposure of K562 cell lines to the drug. Cytotoxicity was determined by MTS assays and $IC_{50}$ values calculated. Apoptosis assays were performed using annexin V-FITC binding assays and analyzed by flow cytometry. Methylation profiles were investigated using methylation specific PCR and sequencing analysis of SOCS-1 and SOCS-3 genes. Gene expression was assessed by quantitative real-time PCR, and protein expression and phosphorylation of STAT1, 2 and 3 were examined by Western blotting. Results: The $IC_{50}$ for imatinib on K562 was 362nM compared to 3,952nM for K562-R (p=0.001). Percentage of apoptotic cells in K562 increased upto 50% by increasing the concentration of imatinib, in contrast to only 20% in K562-R (p<0.001). A change from non-methylation of the SOCS-3 gene in K562 to complete methylation in K562-R was observed. Gene expression revealed down-regulation of both SOCS-1 and SOCS-3 genes in resistant cells. STAT3 was phosphorylated in K562-R but not K562. Conclusions: Development of cells resistant to imatinib is feasible by overexposure of the drug to the cells. Activation of STAT3 protein leads to uncontrolled cell proliferation in imatinib resistant BCR-ABL due to DNA methylation of the SOCS-3 gene. Thus SOCS-3 provides a suitable candidate for mechanisms underlying the development of imatinib resistant in CML patients.