• Korean Journal of Microbiology
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• v.38 no.2
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• pp.107-112
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• 2002

To isolate the bacteria lysing cyanobacteria, the sediment samples were collected from Dochang and Pal'tang Reservoir and Seokchon Lake. Each sample was smeared on the Anabaena cylindrica lawn and incubated in light chamber for 11 days. Bacteria having cyanobacteria-Iysing activity were isolated from the samples of Seokchon reservoir. Confirmation of cyanobacteria-Iysing activity was carried out to measure chlorophyll a and bacterial cell counting in mixed culture of Anabaena cylindrica and bacteria. Lysis was detected when extracellular meterials was added to the Anabaena cylindrica culture. The isolate was identified by analysis based on 16S rDNA sequence and morphological and physiological properties. The bacterial strain was taxonomically studied by the phylogenetic analysis based on 165 rDNA sequence. This strain was identified as a member of the genus Bacillus and designated as Bacillus sp. CHS1.

• Biomedical Science Letters
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• v.17 no.2
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• pp.151-155
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• 2011

Short tandem repeats (STRs) loci are the genetic markers used for forensic human identity test. With multiplex polymerase chain reaction (PCR) assays, STRs are examined and measured PCR product length relative to sequenced allelic ladders. In the repeat region and the flanking region of the commonly-used STR may have DNA sequence variation. A mismatch due to sequence variation in the DNA template may cause allele drop-out (i.e., a "null" or "silent" allele) when it falls within PCR primer binding sites. The STR markers were co-amplified in a single reaction by using commercial PowerPlex$^{(R)}$ 16 system and AmpFlSTR$^{(R)}$ Identifiler$^{(R)}$ PCR amplification kits. Separation of the PCR products and fluorescence detection were performed by ABI PRISM$^{(R)}$ 3100 Genetic Analyzer with capillary electrophoresis. The GeneMapper$^{TM}$ ID software were used for size calling and analysis of STR profiles. Here, this study described a forensic human identity test in which allelic drop-out occurred in the STR system D18S51. During the course of human identity test, two samples with a homozygous (16, 16 and 21, 21) genotype at D18S51 locus were discovered using the PowerPlex$^{(R)}$ 16 system. The loss of alleles was confirmed when the samples were amplified using AmpFlSTR$^{(R)}$ Identifiler$^{(R)}$ PCR amplification kit and resulted in a heterozygous (16, 20 and 20, 21) genotype at this locus each other. This discrepancy results suggest that appropriate measures should be taken for database comparisons and that allele should be further investigated by sequence analysis and be reported to the forensic community.

• Journal of Microbiology and Biotechnology
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• v.13 no.1
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• pp.110-118
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• 2003

Pseudomonas syringae pv. actinidiae strains, which cause canker disease in kiwifruit, were collected from kiwifruit orchards in Korea and identified using biochemical and physiological tests. The nucleotide sequences of the 16s rDNA and 16s-23s internally transcribed spacer of the isolates were found to be Identical to those of' the pathotype strain, Kwl 1, of P syringae pv. actinidiae. Remarkably, no coding sequence for phaseolotoxin biosynthesis or phaseolotoxin- resistant ornithine carbamoyltransferase was found by PCR amplification in any of the new Korean isolates of pseudomonas syringae pv. actinidiae, although this was clearly identified in the control pathotype Kwl 1 reference strain. In contrast, three primer sets derived from the coronatine biosynthetic gene cluster and DNA from the Korean strains yielded amplified DNA fragments of the expected size. A sequence analysis of the PCR products revealed that P. syringae pv. actinidiae and the Korean strains of pv. actinidiae contain coronafncate ligase genes (cfl)with identical sequences, whereas their. corR genes exhibited 91% sequence similarity. The production of coronatine, instead of phaseolotoxin, by the Korean strains of P. syringae pv. actinidiae was confirmed by a bioassay using reference pathovars known to produce coronatine and phaseolotoxin. The genes for coronatine biosynthesis in the Korean strains of P. syringae pv. actinidiae were found to be present on plasmids.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 1999.10a
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• pp.63.2-63
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• 1999

• Journal of Microbiology and Biotechnology
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• v.14 no.2
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• pp.276-283
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• 2004

Screening was performed to isolate cellulose-producing microorganisms from the Korean traditional fermented persimmon vinegar. The resulting strain, KJ $145^{T}$, was then taxonomically investigated by phenotypic characterization, particularly chemotaxonomic, and by phylogenetic inference based on a 16S rDNA sequence analysis including other related taxa. Strain KJ $145^{T}$ was found to grow rapidly and form pale white colonies with smooth to rough surfaces on a GYC agar. Strain KJ $145^T$ also produced acetate from ethanol, and was tolerable to 10% ethanol in SM medium. In a static culture, a thick cellulose pellicle was produced, and in GYC broth, the strain grew at temperatures ranging from 28 to $40^\circ{C}$ with an optimum pH of 4.0. The genomic DNA G+C content of strain KJ $145^T$ was 61.9 mol%, and the predominant ubiquinone was Q 10 as the major quinone and Q9 as the minor quinone. The major cellular fatty acids were $C_{16:0}$ and the sum in feature 7 ($C_{18:1}$ w9c, w12t and/or w7c). A 16S rRNA-targeted oligonucleotide probe specific for strain KJ $145^T$was constructed, and the phylogenetic position of the new species was derived from a 16S rDNA-based tree. When comparing the 16S rDNA nucleotide sequences, strain KJ $145^T$ was found to be most closely related to G. hansenii LMG $1527^T$ (99.2%), although KJ $145^T$ was still distinct from G. hansenii LMG $l527^T$ and G. xylinus LMG $1515^T$ in certain phenotypic characteristics. Therefore, on the basis of 16S rDNA sequences and taxonomic characteristics, it is proposed that strain KJ $145^T$ should be placed in the genus Gluconacetobacter as a new species, Gluconacetobacter persimmonis sp. nov., under the type-strain KJ $145^T$ (=KCTC =$10175BP^T$=KCCM=$10354^T$).

• Journal of Microbiology and Biotechnology
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• v.20 no.9
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• pp.1322-1330
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• 2010

Three types of nuruk were made from rice, wheat, and a rice-glasswort (6:4) mixture. Nuruk, makgeolli, and vinegar were manufactured with rice nuruk (RN), wheat nuruk (WN), and rice-glasswort nuruk (RGN). The variable region of 18S or 16S rDNA amplified with genomic DNA extracted directly from nuruk-, makgeolli-, and vinegar-making cultures was analyzed via temperature gradient gel electrophoresis (TGGE). The sequence of the 18S rDNA variable region extracted from the TGGE gel for nuruk was 99% homologous with Aspergillus sp. and that for the makgeolli-making culture was 99% homologous with Saccharomyces sp. and Saccharomycodes sp. The sequence of the 16S rDNA variable region extracted from TGGE gel for the vinegar-making culture was 98% homologous, primarily with the Acetobacter sp. The eukaryotic and prokaryotic diversities in the nuruk-, makgeolli-, and vinegar-making cultures was not significantly altered by the addition of glasswort. Prokaryotic diversity was higher than eukaryotic diversity in the nuruk, but eukaryotic diversity was higher than prokaryotic diversity in the makgeolli-making culture, on the basis of the TGGE patterns. No 18S rDNA was amplified from the DNA extracted from the vinegar-making culture. The diversity of the microbial community in the process from nuruk to vinegar was slightly affected by the type of raw material utilized for nuruk-making. The saccharifying activity and ethanol productivity of nuruk, polyphenol content in makgeolli, and acetic acid and polyphenol content in the vinegar were increased as a result of the addition of glasswort. In conclusion, the glasswort may be not simply an activator for the growth of microorganisms during the fermentation of nuruk, makgeolli, or vinegar, but also a nutritional supplement that improves the quality of vinegar.

• Microbiology and Biotechnology Letters
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• v.32 no.1
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• pp.91-95
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• 2004

For the detection of the oil-degrading bacterium, Nocardia sp. Hl7-1, inoculated during the bioremediation of oil-contaminated soil, a species-specific primer was constructed based on the 16S rDNA sequence of this strain. Two forward primers and two reverse primers were designed and tested against both closely and distantly related bacterial strains. All the primers designed were specific to the Nocardia sp. H17-1. Particularly, primer sets NH169F-NH972R and NH575F-NH972R could be used to detect 50 fg of template DNA and TEX>$1.2${\times}$10^4$ CFU/g of sandy soil. These two PCR primer sets successfully detected the H 17-1 strain in the oil-con-laminated soil samples containing heterogeneous DNA. We also conformed the primer specificity by restriction-enzyme cleavage of the PCR products and denaturing gradient gel electrophoresis.

• Korean journal of applied entomology
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• v.45 no.3 s.144
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• pp.301-307
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• 2006

A ligniolytic bacterial strain was isolated from the digestive tract of a red dragonfly, Sympetrum dopressiusculum. It was identified as a Serratia marcescens HY-5 by 16S rDNA sequence analysis and physiological and biochemical analysis. The isolated strain showed proportional increase of ligninolytic activity to the cell growth in the culture media which include lignin compounds. It showed about 25-45% decomposition of lignin compound by 48 hr incubation especially, showed effective decomposition of monomer lignin compounds, vanillin and guaiacol, and a dimer, dealkaline lignin. PCR amplification of 16S rDNA followed by denaturing gradient gel electrophoresis analysis showed high density of S. marcescens HY-5 in the gut of the S. depressiusculum at both gut samples which collected at different site.

• Journal of Microbiology and Biotechnology
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• v.27 no.3
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• pp.535-541
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• 2017

Two Gram-staining-negative, red-pinkish, coccus-shaped, non-motile, and aerobic bacterial strains, designated $Ant21^T$ and Ant22, were isolated from the Antarctic coastal sea water. Strains $Ant21^T$ and Ant22 showed UVC and gamma radiation resistance. Phylogenetic analyses based on 16S rRNA gene sequences determined that these strains belong to the genus Deinococcus. Through the analyses of the 16S rRNA gene sequences, strains $Ant21^T$ and Ant22 were found to have 97.7% and 97.8% similarity to Deinococcus marmoris DSM $12784^T$ and 97.0% and 97.2% similarity to Deinococcus saxicola AA-$1444^T$, respectively. The sequence similarity with the type strains of other Deinococcus species was less than 96.9% for both strains. Strains $Ant21^T$ and Ant22 shared relatively high 16S rRNA gene sequence similarity (99.3%) and had a closely related DNA reassociation value of $84{\pm}0.5%$. Meanwhile, they showed a low level of DNA-DNA hybridization (<30%) with other closely related species of the genus Deinococcus. The two strains also showed typical chemotaxonomic features for the genus Deinococcus, in terms of the major polar lipid (phosphoglycolipid) and the major fatty acids ($C_{16:0}$, $C_{16:1}$ ${\omega}6c/{\omega}7c$, $iso-C_{17:0}$, and $iso-C_{15:0}$). They grew at temperatures between $4^{\circ}C$ and $30^{\circ}C$ and at pH values of 6.0-8.0. Based on the physiological characteristics, the 16S rRNA gene sequence analysis results, and the low DNA-DNA reassociation level with Deionococcus marmoris, strains $Ant21^T$ ($=KEMB\;9004-167^T$ $=JCM\;31436^T$) and Ant22 (KEMB 9004-168 =JCM 31437) represent novel species belonging to the genus Deinococcus, for which the name Deinococcus rubrus is proposed.

• Journal of Microbiology and Biotechnology
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• v.11 no.6
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• pp.1046-1054
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• 2001

Bioleaching is the process in which insoluble metal sulfide is oxidized by specialized iron- and/or sulfur-oxidizing lithotrophic bacteria in acidic, metal-rich environments. Most of these processes are carried out by the genus Thiobacillus. Three novel Thiobacillus strains (Thiobacillus thiooxidans AZ11, Thiobacillus thiooxidans MET, and thiobacillus thiooxidans TAS) associated with bioleaching have been isolated from soil and sludge (Korean patent No. 1999-0073060 for T. thiooxidans AZ11, Korean patent No. 1999-0005798 for T. thiooxidans MET, and Korean patent No. 1999-0073059 for T. thiooxidans TAS). A partial sequence of 16S ribosomal RNA gene (16S rDNA) and the entire sequence of 16S/23S intergenic spacer region (ISR) were determined in the three above novel strains and in Thiobacillus ferrooxidans ATCC19859 as a reference strain. When phylogenetic analysis was performed based on G+C contents and sequence alignments, T. ferroxidans ATCC19859 was found to be closely related to previously registered T. ferrooxidans strains in a monophyletic manner, while the three novel T. thiooxidans strains were classified in a paraphyletic manner. Close examination on the base composition of 16S/23S ISR revealed that the 5\` part (nucleotide residues 21-200) was specific for the genus Thiobacillus. On the other end, the 3\` part (nucleotide residues 201-520) showed specificity in T. ferrooxidans strains, but not in T. thiooxidans strains. These results suggest that the proximal and distal halves of 16S/23S could be used as a genetic marker for the identification of the genus Thiobacillus and the species T. ferrooxidans, respectively.