• Microbiology and Biotechnology Letters
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• v.47 no.3
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• pp.359-363
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• 2019

Meju is a spontaneously fermented soybean product produced in Korea. We isolated the bacteria of the genera Bacillus, Enterococcus, and Staphylococcus from 12 meju samples collected from five regions of Korea using selective media, and we identified them based on the sequence analysis of 16S ribosomal RNA and gmk (guanylate kinase) genes. Bacillus and Enterococcus strains were identified from all samples and the numbers of Bacillus strains in the 11 samples were >15% of the total cell number. Therefore, the genus Bacillus was confirmed as the predominant bacterial group of meju. Staphylococcus strains were identified from six samples. The identified 151 Bacillus isolates predominated in the following order: B. velezensis, B. sonorensis, B. subtilis, and B. licheniformis. Among the 165 Enterococcus isolates, 163 strains were identified as E. faecium. Eighty-two Staphylococcus isolates were classified into six species of coagulase-negative Staphylococcus group and S. xylosus was the predominant species.

• International Journal of Industrial Entomology and Biomaterials
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• v.2 no.1
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• pp.37-53
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• 2001

Two regions of mtDNA genome, cytochrome oxidase subunit I (COI) and 165 ribosomal RNA (165 rRNA) genes, were sequenced for 15 species of the long-horned beetle belonging to four subfamilies and geographic samples of mulberry longicorn beetle, Apriona germari, from two localities in Korea. Ten samples of A. germari collected from Suwon and Busan revealed three COI haplotypes ranging in nucleotide divergence of 0.3% to 0.5%, and the two populations shared one common COI haplotype (80%). The sequence divergence among 15 species of the long-horned beetle was much higher in COI gene (12.3%∼39.4%) than 16S rRNA gene (7.2% to 23.1), and the maximum value in the COI gene is exceptional compared with other relevant studies, including that of Coleoptera. The greatly increased divergence in the COI gene, in facto was stemmed from a peculiar sequence of Prionus insularis belonging to Prioninne, divergence of which ranges from 31.2% to 39.3% from other species. We discussed possible reason of the divergence in this species. Due to the abnormality of COI gene divergence, decrease in phylogenetic signal was severe in COI nucleotide and, subsequently, the converted amino acid sequences, rendering us to put more confidence on the 16S5 rRNA gene data. Although the molecular phylogeny confidently supports the monophyletic origin of Lepturinae, the presence of discrepancy between molecular data and traditional taxonomic views also is a testable hyothesis. One such discrepancy includes taxonomic position of Sophronica obrioides and Theophilea cylindricollis belonging to Lamiinae.

• 한국생물공학회:학술대회논문집
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• 2005.04a
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• pp.495-495
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• 2005

• Korean Journal of Veterinary Service
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• v.44 no.4
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• pp.305-308
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• 2021

A female Chinese hamster with unknown age was referred for acute onset of anorexia, depression, and large cyst from the head to body. After referring, the patient died shortly. During necropsy, severe hemorrhage in the cyst, multiple mass on liver, and transformed right kidney were found. The infection was confirmed by cytology, cultures and PCR of 16S ribosomal RNA gene. This report describes a first case of naturally occurred systemic Klebsiella oxytoca infection in a household Chinese hamster.

• Research in Plant Disease
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• v.29 no.1
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• pp.94-99
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• 2023

Blueberry red ringspot virus (BRRSV) and blueberry scorch virus (BlScV) are included in the quarantine virus list managed by the Korean Animal and Plant Quarantine Agency. A multiplex polymerase chain reaction (PCR) assay with an internal control was developed for the simultaneous detection of both viruses. The specific primers used here were designed based on the highly conserved regions of the genomic sequences of each virus, obtained from the National Center for Biotechnology Information nucleotide databases. The primers were designed to amplify a partial sequence within coat protein (CP) for detecting BRRSV and a partial sequence within the CP-16 kDa for detecting BlScV. 18S ribosomal RNA (rRNA) was used as internal control, and the primer set used in a previous study was modified in this study for detecting 18S rRNA. Each conventional PCR using the BRRSV, BlScV, and 18S rRNA primers exhibited a sensitivity of approximately 1 fg plasmid DNA. The multiplex PCR assay using the BRRSV, BlScV, and 18S rRNA primers was effective in simultaneously detecting the two viruses and 18S rRNA with a sensitivity of 1 fg plasmid DNA, similar to that of conventional PCR assays. The multiplex PCR assay developed in this study was performed using 14 blueberry cultivars grown in South Korea. BRRSV and BlScV were not detected, but 18S rRNA was all detected in all the plants tested. Therefore, our optimized multiplex PCR assay could simultaneously detect the two viruses and 18S rRNA in field samples collected from South Korea in a time-efficient manner. This approach could be valuable in crop protection and plant quarantine management.

• Molecules and Cells
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• v.22 no.1
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• pp.78-88
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• 2006

The phylogeny of the subfamily Tephritinae (Diptera: Tephritidae) was reconstructed from mitochondrial 16S ribosomal RNA gene sequences using 53 species representing 11 currently recognized tribes of the Tephritinae and 10 outgroup species. The minimum evolution and Bayesian trees suggested the following phylogenetic relationships: (1) monophyly of the Tephritinae was strongly supported; (2) a sister group relationship between the Tephritinae and Plioreocepta was supported by the Bayesian tree; (3) the tribes Tephrellini, Myopitini, and Terelliini (excluding Neaspilota) were supported as monophyletic groups; (4) the non-monophyletic nature of the tribes Dithrycini, Eutretini, Noeetini, Tephritini, Cecidocharini, and Xyphosiini; and (5) recognition of 10 putative tribal groups, most of which were supported strongly by the statistical tests of the interior branches. Our results, therefore, convincingly suggest that an extensive rearrangement of the tribal classification of the Tephritinae is necessary. Since our sampling of taxa heavily relied on the current accepted classification, some lineages identified by the present study were severely under-sampled and other possible major lineages of the Tephritinae were probably not even represented in our dataset. We believe that our results provide baseline information for a more rigorous sampling of additional taxa representing all possible major lineages of the subfamily, which is essential for a comprehensive revision of the tephritine tribal classification.

• Journal of Life Science
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• v.2 no.2
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• pp.108-119
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• 1992

근년에 개발된 효소적인 DNA증폭법을 이용하면 일차구조상의 단편적인 정보만 알면 단 수시간내 해석에 필요한 양의 DNA가 증폭되어 cDNA의 염기배열결정의 신속화, 간편화가 가능하게 되었다. 그러므로 유전자증폭법으로써 PCR법에 관해 기술한다. 그리고 리보좀 RNA는 분자시계로서 생물의 계통을 논하는 데에 있어서는 최적의 조건을 갖춘 고분자화합물이다. 이에 PCR법을 이용한 16S like 리보좀DNA의 증폭법을 다루고, PCR증폭산물의 염기배열결정법에 대해 서술한다. 또한 인위적인 leading error 등을 배제하고 신속한 자동해독과 시간적인 절약이 자동 DNA sequencer의 개발과 시판으로 가능하게 되어 cDNA의 형광색소표식 염기배열결정법에 대해서도 서술한다.

• International Journal of Oral Biology
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• v.44 no.3
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• pp.96-100
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• 2019

The purpose of this study was to develop Peptoniphilus mikwangii-specific quantitative real-time polymerase chain reaction (qPCR) primers based on the 16S ribosomal RNA (16S rDNA) gene. The specificity of the primers was determined by conventional PCR using 29 strains of 27 oral bacterial species including P. mikwangii. The sensitivity of the primers was determined by qPCR using the purified genomic DNA of P. mikwangii KCOM $1628^T$ (40 ng to 4 fg). The data showed that the qPCR primers (RTB134-F4/RTB134-R4) could detect P. mikwangii strains exclusively and as little as 40 fg of the genomic DNA of P. mikwangii KCOM $1628^T$. These results suggest that the developed qPCR primer pair can be useful for detecting P. mikwangii in epidemiological studies of oral bacterial infectious diseases.

• Restorative Dentistry and Endodontics
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• v.36 no.6
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• pp.498-505
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• 2011

Objectives: The purpose of this in vivo study was to investigate the microbial diversity in symptomatic and asymptomatic canals with primary endodontic infections by using GS FLX Titanium pyrosequencing. Materials and Methods: Sequencing was performed on 6 teeth (symptomatic, n = 3; asymptomatic, n = 3) with primary endodontic infections. Amplicons from hypervariable region of the small-subunit ribosomal RNA gene were generated by polymerized chain reaction (PCR), and sequenced by means of the GS FLX Titanium pyrosequencing. Results: On average, 10,639 and 45,455 16S rRNA sequences for asymptomatic and symptomatic teeth were obtained, respectively. Based on Ribosomal Database Project Classifier analysis, pyrosequencing identified the 141 bacterial genera in 13 phyla. The vast majority of sequences belonged to one of the seven phyla: Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria, Spirochetes, and Synergistetes. In genus level, Pyramidobacter, Streptococcus, and Leptotrichia constituted about 50% of microbial profile in asymptomatic teeth, whereas Neisseria, Propionibacterium, and Tessaracoccus were frequently found in symptomatic teeth (69%). Grouping the sequences in operational taxonomic units (3%) yielded 450 and 1,997 species level phylotypes in asymptomatic and symptomatic teeth, respectively. The total bacteria counts were significantly higher in symptomatic teeth than that of asymptomatic teeth (p < 0.05). Conclusions: GS FLX Titanium pyrosequencing could reveal a previously unidentified high bacterial diversity in primary endodontic infections.

• Research in Plant Disease
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• v.17 no.3
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• pp.265-271
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• 2011

Seven phytoplasma diseases have been occurred on floricultural crops in Korea : Ph-ch1 and Ph-ch2 of chrysanthemum, Ph-lily of lily, petunia flat stem-Korean (PFS-K) of petunia, poinsettia branch inducing- Korean (PoiBI-K) of poinsettia, statis witches' broom-Korean (SWB-K) of statis and azalea witches broom (AWB). Classification of the seven phytoplasmal diseases based on 16S ribosomal RNA (rRNA) sequences showed that floricultural crop phytoplasma disease were widespread in order of aster yellow (AY), stolbur and X-disease in Korea. In phenotypic characters, the fasciation was occurred in both monocotyledon plant of lily and dicotyledon plants of petunia and poinsettia. Besides, the fascination was occurred in Ph-lily of stolbur, petunia PFS-K of AY and PoiBI-K of X-disease. This result indicated that phytoplasma classification based on 16S rRNA and symptoms are not consistently related. The comparison of 16S rRNA sequence of the seven floricultural crop phytoplasma with five tree phytoplasmal diseases of jujube witches' broom, paulownia witches' broom, wild jujube witches' broom, mulberry dwarf, golden rain phytoplasma occurred in Korea showed as high as 88.5-99.9% homology. Among them, especially mulberry dwarf showed the highest homology with the seven floricultural crop phytoplasms. Based on this result, floricultural crop phytoplasmas were assumed to be transmitted by insect vectors from tree phytoplasmas in Korea.