• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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• 2012.10a
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• pp.991-993
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• 2012

We analyzed RNA polymerase beta subunit gene (rpoB) mutation of rifampin-resistant Mycobacteria through analysis of nucleotide sequence of rpoB DNA (351 bp) containing rifampin resistant region, $rif^r$. For this study, we collected rifampin-resistant Mycobacteria that were identified by conventional culture methods from Masan National Hospital and The Korean Institute of Tuberculosis. We performed sequencing of DNA nucleotides and analyzed rpoB gene of those rifampin-resistant Mycobacteria. From this analysis, we invcestigated diverse mutations of rpoB gene included rifampin-resistant gene, which were not reported, from those rifampin-resistant Mycobacteria.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.17 no.4
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• pp.1005-1009
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• 2013

Using DNA sequencing method, we analyzed mutations of rpoB (RNA polymerase beta subunit) rifampin-resistant Mycobaterium tuberculosis strains which were identified by conventional test at Masan National Hospital and The Korean Institute of Tuberculosis. Though it has been reported different mutations of rpoB region of rifampin-resistant M. tuberculosis strains in the south of Korea, it is not confirmed whether these mutations of rpoB region actually express rifampin resistance through experiment. We confirmed experimentally these mutations of rpoB region of M. tuberculosis strains induced rifampin-resistance through ampified rpoB by polymerase chain reaction (PCR) and cloning of mutant rpoB into rifampin sensitive-M. tuberculosis strain.

• Journal of information and communication convergence engineering
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• v.10 no.2
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• pp.210-214
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• 2012

A microtiter well plate DNA hybridization method using Mycobacterium kansasii-specific rpoB DNA probe (kanp) were evaluated for the detection of M. kansasii from culture isolates. Among the 201 isolates tested by this method, 27 strains show positive results for M. kansasii, but the other 174 isolates were negative results for M. kansasii. This result was consistent with partial rpoB sequence analysis of M. kansasii and the result of biochemical tests. The negative strains by this DNA-DNA hybridization method were identified as Mycobacterium tuberculosis (159 strains), Mycobacterium avim (5 strains), Mycobacterium intracellulare (8 strains), and Mycobacterium flavescens (2 strain) by rpoB DNA sequence analysis. Due to high sensitivity and specificity of this test result, we suggest that DNA-DNA hybridization method using rpoB DNA probes of M. kansasii could be used for the rapid and convenient detection of M. kansasii.

• International Journal of Oral Biology
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• v.38 no.1
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• pp.29-36
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• 2013

Mitis group streptococci (MGS) were classified based on the nucleotide sequences 16S rRNA gene (16S rDNA) and comprised 13 Streptococcus species. However, 16S rDNA homogeneity among MGS was too high to discriminate between clinical strains at the species level, notably between Streptococcus mitis, Streptococcus oralis, Streptococcus pneumoniae, and Streptococcus pseudopneumoniae. The purpose of this study was to discriminate between 37 strains of MGS isolated from Korean oral cavities using phylogenetic analysis of the DNA-dependant RNA polymerase beta-subunit gene (rpoB). 16S rDNA and rpoB from clinical strains of MGS were sequenced using the dideoxy chain termination method and analyzed using MEGA version 5 software. The resulting phylogenetic data showed that the rpoB sequences could delineate clinical strains of MGS at the species level. Phylogenetic analysis of rpoB is therefore a useful approach for identifying MGS at the species level.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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• 2012.05a
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• pp.913-915
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• 2012

RNA polymerase beta subunit gene (rpoB) mutation of rifampin-resistant Mycobacteria was analyzed using nucleotide sequence of rpoB DNA (351 bp) containing rifampin resistant region, $rif^r$. For this purpose, we collected rifampin-resistant Mycobacteria that were identified by conventional culture method from Masan National Hospital and The Korean Institute of Tuberculosis and performed analysis of nucleotide sequence of rpoB of them. We found various mutations of rpoB linked rifampin resistant gene from rifampin-resistant Mycobacteria. From this study, we identified mutations of different codons from codons that have been reported recently.

• Korean Journal of Microbiology
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• v.46 no.3
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• pp.296-302
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• 2010

Microcystis (Cyanobacteria, Chroococcales) is one of the green tide-causing organisms in freshwaters, and some species produce microcystin that is hepatotoxin. In the aspects of freshwater quality controls and health concerns, therefore it is necessary to manage the harmful organisms. In the present study, RNA polymerase beta subunit (rpoB) gene sequences of Microcystis were determined and characterized in order to use a potential marker for the molecular detections of the species. Microcystis rpoB showed high divergences of DNA similarity and genetic distances when compared with those of 16S rRNA, and the molecular differences were statistically significant (Student t-test, p<0.05). Parsimony analyses showed the rpoB gene evolves more than 2-fold faster than 16S rRNA. In addition, phylogeny of the rpoB gene separated each M. aeruginosa strain more clearly compared with a 16S rRNA tree. This study found that the order Chroococcales, including Microcystis, has approximately two rRNA operons and single copy of the rpoB gene in their chromosomes. These results suggest that the rpoB gene is a useful marker for the molecular phylogenetics and the detection of Microcystis.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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• 2013.05a
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• pp.1012-1014
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• 2013

DNA-DNA hybridization method with four oligonucleotide-specific probes was used simultaneously for differentiation and identification of four Mycobacterium species (Mycobacterium tuberculosis, M. avium, M. intracellulare, and M. kansasii). This DNA-DNA hybridization method with 4 oligonucleotide-specific probes, which targets in the rpoB region of 4 Mycobacteria species, respectively, was tested on 322 clinical isolates. Using DNA-DNA hybridization method, we detected M. tuberculosis (282 strains), M. avim (7 strains), M. intracellulare (9 strains), and M. kansasii (3 strain) from 322 clinical isolates. This result was compared with conventional biochemical test and rpoB DNA sequence analysis of this clinical isolates. We confirmed identification of Mycobacterium tuberculosis, M. avium, M. intracellulare, and M. kansasii with high sensitivity (100 %) and specificity (100 %). This DNA-DNA hybridization method could be performed within 4 hours at least. Therefore, we suggest that DNA- DNA hybridization method using 4 rpoB DNA probes of Mycobacteria could be used for accurate, rapid, convenient detection and identification of Mycobacterium tuberculosis, M. avium, M. intracellulare, and M. kansasii in clinical samples.

• Korean Journal of Medicinal Crop Science
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• v.22 no.6
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• pp.489-496
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• 2014

Polygonatum is a genus placed in the family Liliaceae, distributed throughout the Northern Hemisphere and 16 of the species are grown naturally in Korea. In oriental medicine, the rhizomes of Polygonatum have been used as two different medicines, Okjuk (Polygonati odorati Rhizoma) and Hwangjeong (Polygonati Rhizoma). However, it is difficult to identify the morphological and chemical differences between the medicinal groups and thus easy to confuse the one with the other. Therefore, a clear classification standard needs to be established so as to be able to discriminate between them. In the study, the morphological characteristics of the plants, Polygonatum spp., were examined. Then, the differences in SNPs among the DNA sequences of 7 of the Polygonatum spp. and 1 of the Disporum spp. were analyzed by DNA barcoding with rpoC1, rpoB2, matK, and psbA-trnH of the cpDNA region. In the results, three regions, rpoC1, rpoB2, and matK were useful for discriminating the species, P. stenophyllum and P. sibiricum. Furthermore, it was possible to discriminate the individual germplasm within the species by using the combination of the results obtained from rpoB2, rpoC1, and matK.

• Korean Journal of Microbiology
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• v.47 no.3
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• pp.268-274
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• 2011

Anabaena (Cyanobacteria, Nostocales) are important for water quality controls, because they are often responsible for freshwater green tides; moreover, some species are reported to produce hepatotoxin. In this study, we sequenced RNA polymerase beta subunit (rpoB) gene of Anabaena, and evaluated their sequences for the potential use of a molecular taxonomic marker in this taxon. Anabaena rpoB showed low DNA similarity and high genetic divergences when compared those of 16S rRNA, and the molecular differences were statistically significant (Student t-test, p<0.01). Parsimony analyses showed the rpoB gene evolves 4.8-fold faster than 16S rRNA. In addition, phylogeny of the rpoB gene separated each Anabaena strain more clearly compared with a 16S rRNA tree. These results suggest that the rpoB gene is a useful marker for the molecular phylogenetics and the species discrimination of Anabaena.

• Korean Journal of Clinical Laboratory Science
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• v.38 no.3
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• pp.158-165
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• 2006

Although Mycobacterium tuberculosis complex strains remain responsible for the majority of diseases caused by mycobacterial infections worldwide, the increase in HIV infections has allowed for the emergence of other non-tuberculous mycobacteria as clinically significant pathogens. However, Mycobacterium species has a long period of incubation, and requires serious biochemical tests such as niacin, catalase, and nitrate test that are often tedious. The development of rapid and accurate diagnostics can aid in the early diagnosis of disease caused by Mycobacterium. The current DNA amplification and hybridization methods that have been developed target several genes for the detection of mycobacterial species such as hps65, 16S rDNA, rpoB, and dnaj. These methods produce rapid and accurate results. In this study, PCR-restriction fragment length polymorphism analysis(PCR-RFLP) based on the region of the rpoB gene was used to verify the identification of non-tuburculosis Mycobacterium species. A total of 8 mycobacterial reference strains and 13 clinical isolates were digested with restriction enzymes such as Msp I in this study. The results of using this process clearly demonstrated that all 13 specimens were identified by rpoB gene PRA method. The PCR-RFLP method based on the rpoB gene is a simple, rapid, and accurate test for the identification of Mycobacterium.