• Research in Plant Disease
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• v.23 no.4
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• pp.314-321
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• 2017

Acidovorax valerianellae had been reported a causal agent of bacterial black spot disease on corn salad in France, 2003 and on watermelon in Korea 2011. In this study, difference in host specificity between 2 groups, corn salad strains and watermelon strains, of Acidovorax valerianellae was recognized and compared. In the pathogenicity test, all 5 watermelon strains showed pathogenicity on the 6 Cucurbitaceae plants but not on corn salad, whereas 4 corn salad strains showed pathogenicity only on the corn salad. Utilization of Biolog substrates was different between watermelon strains and corn salad strains on 4 substrates, Malonic Acid, ${\alpha}-Hydroxybutyric$ Acid, ${\alpha}-Keto$ Butyric Acid, and Glycyl-L Glutamic Acid. The phylogenetic tree built with the 16S rDNA sequences showed that all of A. valerianellae stains was grouped into 1 clade separating from the other species of Acidovorax genus. Within A. valerianellae clade, watermelon strains and corn salad strains were separated into 2 sub-groups. REP-PCR analysis also separated the two groups. Host specificity, substrate utilization, and some genetic characteristics suggested that there are two pathogenic groups, watermelon group and corn salad group in A. valerianellae.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.48 no.6
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• pp.904-912
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• 2015

There is a great deal of research interest regarding substitutes for antibiotics because of various obstacles to the efficacy and use of antibiotics. We isolated and analyzed diversity of microbiota which exhibited antibacterial activity against 23 pathogenic bacteria, to develop alternative agent of antibiotics. By investigating the microbiota from rocks on the seashore, we characterized and obtained various antibacterial material-producing bacteria. Thirty-one isolates belong to four genera and seven species, according to 16S rDNA sequence analysis, showed antibacterial activities against 23 pathogenic bacteria. The Identity of 16S rDNA sequences indicated three species of Bacillus, one species of Paenibacillus, one species of Pseudomonas and two species of Enterobacter. Two isolates were similar to Bacillus aerophilus, four isolates were similar to Bacillus pumilus, seven isolates were similar to Bacillus safensis, 15 isolates were similar to Paenibacillus polymyxa, respectively. In addition, one isolate was similar with Pseudomonas poae, one isolate was similar to Enterobacter asburiae, and one isolate was similar to Enterobacter ludwigii, respectively. Variations of antibacterial activity and level among the same species were indicated the diverse strains of isolates. Vibrio vulnificus showed the highest degree of growth inhibition by 29 isolates. Further studies regarding antibacterial materials and bacteria suggest that development of probiotic strains or alternative agents to antibiotics.

• Microbiology and Biotechnology Letters
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• v.39 no.3
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• pp.210-217
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• 2011

In an effort to isolate novel bacteria for the bioremediation of over-fertilized soils, we identified 135 denitrifying cells out of 3,471 oligotrophic bacteria pools (3.9%) using a denitrification medium supplemented with potassium nitrate as the sole nitrogen source. Soil samples were taken from ecologically well-conserved areas, including a mountain swamp around the demilitarized zone (Yongneup), two ecoparks (Upo and the Mujechi bog), and ten representative islands around the Korean peninsula (Jejudo, Daecheongdo, Socheongdo, Baekryeongdo, Ulrungdo, Dokdo, Geomundo, Hongdo, Huksando and Yeonpyeongdo). All of the 135 bacteria produced nitrogen gas from the denitrification medium, and were proved to be nitrate reductase positive by API-BioLog tests. Phylogenetic analysis using 16S rDNA sequences revealed that the 135 bacteria consisted of 44 different genera. Along with the most prominent, Proteobacteria (87.4%), we identified denitrifying bacteria from Firmicutes (9.4%), Actinobacteria (2.4%), and Bacteroidetes (0.8%). Physiological analyses of the 44 representative denitrifying bacteria, under various pH levels, growth temperatures and salt stresses, revealed 12 favorable denitrifying strains for soil bioremediation.

• Applied Biological Chemistry
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• v.49 no.4
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• pp.276-280
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• 2006

Traditionally fermented Cheonggukjangs were collected from Gyeonggi and Gangwon provinces and 22 strains were isolated and identified by using 165 rDNA sequences. Most of the identified strains were Bacillus subtilis and B. licheniformis, B. subtilis and B. licheniformis are dominant in the Gyeonggi area and B. licheniformis in the Gangwon area. In the growth pattern of the isolated strains, the duration of lag phase was generally 5 to 7 hours and stationary phase was reached after 23 to 40 hours of incubation. Total cell populations at the stationary phase were between $1{\times}10^6\;CFU/ml$ and $5{\times}10^7\;CFU/ml$. The fermenting ability of carbohydrates of isolates showed some differences among the regions. The isolated strains from Yong-In, Gyeonggi showed higher fermenting abilities with D-xylose, xylitol, D-tagatose and Methyl-$\alpha$-D-mannopyranoside. D-lactose, D-tagatose, D-xylose, Methyl-$\alpha$-D-mannopyranoside, amygdalin, arbutin, esculin and 2-keto-gluconate were well fermented with the An-Seong's strains; L-rhamnose, inositol, D-mannitol, D-sorbitol, celibiose and gluconate with the Kawang-Ju's stains; and D-lactose with the Odaesan's strains.

• Journal of Life Science
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• v.24 no.4
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• pp.461-466
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• 2014

Three plant species, Aster sphathulifolius, Sedum oryzifolium, and Lysimachia mauritiana, native to the Dokdo Islands in South Korea, were examined for rhizosphere microorganisms by using 16S rDNA sequences. Nine species of rhizosphere microorganisms were isolated from the three native plant species, respectively. Phylogenetic analysis showed that the microorganisms could be classified into 19 species belonging to four phyla (Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria), and the characteristics of the microbes were confirmed. Rhizosphere microorganisms from the six orders (Bacillales, Corynebacteriales, Flavobacteriales, Micrococcales, Oceanospirillales, and Rhodobacterales) were isolated from S. oryzifolium. From L. mauritiana, microbes belonging to the seven orders (Bacillales, Flavobacteriales, Micrococcales, Oceanospirillales, Rhizobiales, and Rhodobacterales) were isolated. From A. sphathulifolius, the six orders of rhizosphere microorganisms (Alteromonadales, Bacillales, Corynebacteriales, Flavobacteriales, Micrococcales, and Rhizobiales) were isolated. These data showed that Actinobacteria and Proteobacteria were the dominant phyla for the rhizosphere of all three plants. To confirm the bacterial diversity in rhizospheres, Shannon's diversity index (H') was used at the genus level. In these data, the rhizosphere from S. oryzifolium and L. mauritiana had more diverse bacteria compared to that from A. sphathulifolius.

• Microbiology and Biotechnology Letters
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• v.39 no.2
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• pp.119-125
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• 2011

The Egr-1 gene is known to be a transcription factor for activating the expression of many tumor-repressing genes. In this study, three strains activating the promoter of the Egr-1 gene were selected, through the use of Egr-1 luciferase reporter assay and western blotting, from amongst approximately 3,800 oligotrophic bacteria isolated from the cultivated soils of various regions within Korea. These strains were identified as Pseudomonas koreensis on the basis of phylogenetic tree analysis of their 16S ribosomal DNA sequences and biochemical characteristics analyses using a variety of commercial kits (API 20NE, ID 32GN, API ZYM kits). In addition, we discovered that these strains produced anti-bacterial activity against Bacillus subtilis, Staphylococcus aureus and Listeria monocytogenes.

• Korean Journal of Environmental Agriculture
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• v.38 no.4
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• pp.269-272
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• 2019

BACKGROUND: Since 2015, fire blight disease caused by Erwinia amylovora has been devastating apple and pear orchards every year. To quickly block the disease spreading, infected apple and pear trees have been buried in soil. However, concern on the possibility of the pathogen survival urgently requires informative data on the buried host plants. Therefore, this study was conducted to investigate the survival of the pathogen from the buried host plants. METHODS AND RESULTS: Apple trees buried in 42 months ago in a Jecheon site and pear trees buried in 30 months ago in an Anseong site were excavated using an excavator. Plant samples were taken from stems and twigs of the excavated trees. The collected 120 samples were checked for rotting and used for bacterial isolation, using TSA, R2A, and E. amylovora selection media. The purely isolated bacteria were identified based on colony morphology and 16S rDNA sequences. Wood rotting and decay with off smells and discoloring were observed from the samples. A total of 17 genera and 48 species of bacteria were identified but E. amylovora was not detected. CONCLUSION: Our investigation suggests that the survival of E. amylovora doesn't seem possible in the infected hosts which have been buried in soil for at least 30 months. Therefore, the burial control can be considered as a safe method for fire blight disease.

• Korean Journal of Microbiology
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• v.52 no.4
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• pp.444-454
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• 2016

Sixteen lactic acid bacterial strains were isolated from silage and cow dung samples, and characterized to identify their potential as silage additives. They were identified as the members of the genera Lactobacillus, Enterococcus, and Weissella, and clustered into nine groups based on the sequences of the genes for 16S rRNA, RNA polymerase alpha subunit, 60-kDa heat shock protein, and phenylalanyl-tRNA synthase alpha subunit. Among them, the three strains which were genetically similar to L. plantarum showed the fastest growth and pH decrease in MRS and rye extract media, the highest numbers of available carbohydrates, and the widest ranges of pH, temperature, and salinity for growth. In addition, they showed no amplified DNA products in the PCR examination targeting the genes for the production of biogenic amines, and the MRS media where they had been cultured showed relatively high inhibition effect against the growth of silage-spoiling microorganisms, including fungi, yeast, and clostridia. The results suggest that these strains are good candidates for silage additives. However, the rye extract media where the lactic acid bacteria had been cultured had no effect on or stimulated the growth of the silage-spoiling microorganisms, and the causes must be established for the practical use of the lactic acid bacteria as silage additives.

• Animal cells and systems
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• v.15 no.4
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• pp.259-267
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• 2011

This study was undertaken to produce a $F_{ab}$ fragment of a human monoclonal antibody reactive to oxidized and carbamylated low-density lipoprotein (oxLDL and cLDL) using phage display technology. An analysis of DNA sequences of this $F_{ab}$, termed plaque 15,16-46 $F_{ab}$, revealed that the rearranged $V_H$ was highly mutated. Complementarity-determining regions of the $V_H$ showed a very high R/S ratio and contained many positively charged amino acids. In direct binding and competitive ELISA, the $F_{ab}$ reacted strongly with both MDA-LDL and Cu-oxLDL forms of oxLDL, and also showed high affinity for cLDL. Immunofluorescence and immunohistochemical analyses showed that this $F_{ab}$ positively stained atherosclerotic aortic plaques in $ApoE^{-/-}$ mice as well as those in patients with atherosclerosis. The $F_{ab}$ also showed positive staining in placental decidua from patients with preeclampsia. It is suggested that the plaque 15,16-46 $F_{ab}$ against oxLDL and cLDL might possibly be applicable for developing a diagnostic reagent for both human and rodent animal research to detect and characterize atherosclerotic disease progression in atherosclerotic lesions as well as exploring the pathogenesis of atherogenic diseases such as preeclampsia.

• Journal of the East Asian Society of Dietary Life
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• v.18 no.5
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• pp.753-759
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• 2008

The principal objective of this study was to develop the optimum oligonucleotide primers for the simple detection of Campylobacter in food samples. In order to achieve this goal, a variety of oligonucleotide primers were designed via the modification of 16S rDNA, ceuE and mapA sequences of Campylobacter. Through the subsequent analysis of the specificity and sensitivity of primers, two types of oligonucleotide primers, CB4 and CJ1, were selected for Campylobacter genus-specific and C. jejuni species-specific primers, respectively. The detection limit was found to be $10^0{\sim}10^1$ cells per reaction with the prepared cell suspension, however, the sensitivity in the meat samples was less, at $10^1{\sim}10^2$. We suggested that PCR inhibitors such as hemoglobin or immunoglobulin in pork or beef influenced.