• Journal of Life Science
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• v.12 no.2
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• pp.158-163
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• 2002

For axenic isolation of the cyanobacterium Microcystis aeruginosa, water bloom at the Mulgum station from the Nakdong River was pretreated by shaking with distilled water. Removal of bacteria was accomplished using antibiotics (150 $\mu$g/$m\ell$ ampicillin and 25 $\mu$g/$m\ell$ neomycin) and colonizing on CB solid medium prepared from 0.7% agarose at 3$0^{\circ}C$ under 40 $\mu$ mol m$^{-2}$ s$^{-1}$ light. Among 26 strains of the Microcystis species, only three strains were axenically established. The three strains were examined by PCR-amplified 16S rRNA gene and 16S rRNA sequencing. The similarities were 99.5 ~100% with M. aeruginosa AF 139292.

• Korean Journal of Food Science and Technology
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• v.53 no.3
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• pp.334-343
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• 2021

Various vegetables, including cucumbers, have a high probability of foodborne illness because they are usually eaten raw. In this study, we analyzed the 16S rRNA gene sequences of the cucumber (Cucumis sativus L.) microbiota. The diversity indices of cucumber cultivated in May were higher than in cucumber cultivated in November. At the phylum level, Proteobacteria, Firmicutes, and Actinobacteria were predominant. The classes generally comprised Gammaproteobacteria, Bacilli, Alphaproteobacteria, and Actinobacteria. At the genus level, the proportions of Aureimonas, Escherichia, and Microbacterium in samples from May were relatively high, whereas Enterococcus, Pseudomonas, and Rhizobium accounted for a higher proportion in samples from November. Moreover, it is noteworthy that potential pathogenic genera such as Acinetobacter, Aerococcus, Aureimonas, Enterobacter, Enterococcus, Escherichia, Pantoea, Pseudomonas, and Staphylococcus were detected. Although further studies on the characteristics of potential pathogens are required, our results can be used to improve the food safety of vegetables.

• Plant Biotechnology Reports
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• v.5 no.3
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• pp.289-295
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• 2011

The SpoU family of proteins catalyzes the methylation of transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs). We characterized a putative tRNA/rRNA methyltransferase, VaSpoU1 of the SpoU family, from Viscum album (mistletoe). VaSpoU1 and other plant SpoU1s exhibit motifs of the SpoU methylase domain that are conserved with bacterial and yeast SpoU methyltransferases. VaSpoU1 transcripts were detected in the leaves and stems of V. album. VaSpoU1-GFP fusion proteins localized to both chloroplasts and mitochondria in Arabidopsis protoplasts. Sequence analysis similarly predicted that the plant SpoU1 proteins would localize to chloroplasts and mitochondria. Interestingly, mitochondrial localization of VaSpoU1 was inhibited by the deletion of a putative N-terminal presequence in Arabidopsis protoplasts. Therefore, VaSpoU1 may be involved in tRNA and/or rRNA methylation in both chloroplasts and mitochondria.

• Microbiology and Biotechnology Letters
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• v.38 no.3
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• pp.263-272
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• 2010

One hundred sixty three strains showing different colony morphological characteristics on different concentration of marine agar (MA) plates were isolated from ambient seawater near Dokdo island. Bacterial diversity and distributions were studied by phylogenetic analysis of the partial 16S rRNA gene sequences. One hundred sixty three strains were partially sequenced and analyzed phylogenetically. They were composed of 5 phyla, of which gamma-proteobacteria (58%), alpha-proteobacteria (20%), bacteriodetes (16%) were predominant. They were affiliated with 90 species. The 16S rRNA sequence similarity of the isolates was in 93.3 to 100 % range to reported sequence data. Thirty six isolates of among them were assumed to be novel species candidates based on similarity analysis of the 16S rRNA gene sequences. Overall, Proteobacteria and Bacteriodetes of the Dokdo coastal sea water showed a high diversity.

• Molecules and Cells
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• v.43 no.8
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• pp.718-727
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• 2020

The imbalance between the proliferation and apoptosis of B-cell precursors is an important contributor to the pathogenesis of B-cell precursor acute lymphoblastic leukemia (BCP-ALL), while its specific regulatory mechanism remains perplexing. This study aimed to expound the underlying mechanism of the proliferation and apoptosis of BCP-ALL cells from the perspective of non-coding RNA. In this study, long non-coding RNA colorectal neoplasia differentially expressed (LncRNA CRNDE) was upregulated in the bone marrow of BCP-ALL patients and BCP-ALL cell lines (NALM-6 and RS4;11). Functionally, LncRNA CRNDE knockdown restrained cell proliferation and boosted cell apoptosis in NALM-6 and RS4;11 cells. The subsequent investigation confirmed that LncRNA CRNDE bound to miR-345-5p and negatively regulated miR-345-5p expression. The overexpression of miR-345-5p suppressed cell proliferation and boosted cell apoptosis in NALM-6 and RS4;11 cells. Further experiments revealed that miR-345-5p downregulated cyclic AMP response element-binding protein (CREB) expression by targeting its mRNA directly. CREB overexpression reversed the effect of miR-345-5p mimic on cell proliferation and apoptosis in NALM-6 and RS4;11 cells. Finally, in vivo experiments showed that LncRNA CRNDE knockdown prolonged the survival of mice xenotransplanted with NALM-6 cells. In conclusion, LncRNA CRNDE upregulated CREB expression by suppressing miR-345-5p, thus promoting cell proliferation and reducing cell apoptosis in BCP-ALL.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.303-305
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• 2019

An actinobacterial strain designated Gordonia sp. MMS17-SY073 (=KCTC 49257) was isolated from a coastal soil of an island, and its complete genome was analyzed. A single contig consisting of 5,962,176 bp with the G + C content of 67.4% was obtained, and the annotation resulted in 5,201 protein-coding genes, 6 rRNA genes and 45 tRNA genes. Strain MMS17-SY073 was closest to the type strain of Gordonia soli based on the 16S rRNA gene sequence comparison, sharing 98.5% sequence similarity. A number of biosynthetic gene clusters for secondary metabolites, non-ribosomal peptide synthetase types in particular, could be identified from the genome.

• Journal of Microbiology
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• v.44 no.5
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• pp.566-571
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• 2006

An archaeal 16S rRNA gene library was constructed from mangrove soil. Phylogenetic analysis revealed archaea in mangrove soil including the Crenarchaeota (80.4%) and Euryarchaeota (19.6%) phyla. The archaeal community in mangrove soil appears to be a mixture of organisms found in a variety of environments with the majority being of marine origin.

• Journal of Korean Society on Water Environment
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• v.20 no.5
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• pp.506-511
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• 2004

Maintaining dissolved oxygen (DO) at sufficiently low concentration in the aeration tank at a wastewater treatment plant (WWTP) is essential for reduction of the costs of operation and maintenance. On the other hand, the low DO level may result in adverse effect on the integrity of the activated sludge, A typical and disastrous outcome frequently experienced is the outgrowth of filamentous microorganisms, which is called as filamentous bulking, In addition to the traditional methods such as sludge settleability and microscopic observation of the culture, molecular techniques including polymerase chain reaction (PCR) amplification followed by 16S rRNA sequencing were applied to identify filamentous bacteria present in bulking sludge under a condition of low DO concentration, Two morphologically distinct groups, presumably consisting of Sphaerofilus nafans, and Eikelboom Type 1701 or Type 1851, were identified through microscopic observation. They were further confirmed by subsequent 16S rRNA sequencing. Dominant filamentous bacteria identified by the molecular techniques were consisted of three major groups. Sequences of partial 16S rRNA cloned showed that the filamentous bulking organisms were closely related to Eikelboom Type 021N and Eikelboom Type 1701, and Sphaerotilus natans, respectively. Molecular methods were found to possess a strong potential of direct examination of the microbial community of an activated sludge system.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.33 no.2
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• pp.103-109
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• 2000

Complete senuences of the mitochondrial rRNA Benes were determined among six salmonines in Korean Waters (Brachpmystax lenok, Onoorhpchus keta, O. masou mason, O. mason ishikawae, O. mykiss, and albino mutant of O. mykiss). The purposes of this study were to provide the basic information on levels of mtDNA polymorphism among these species for genetic characterization; discuss phylogentic relationships among three Oncorhynchus sepecies; demonstrate the utility of rRNA gene sequence data as a genetic marker for disringuishinf among Korean salmonines. PCR/direct sequencing data indicated the following consistent results; 1) 12S rRNA genes was 945 bases long in Oncorhynchus species, and 946 bases in B. lenot including one insertion. 2) Of sequence variation in mitochondrial rRNA regions, transitional substitutions were superior to transversion. 3) The significant differences were not shown in the intraspecific variation values in these gene regions. The percentage sequence divergence values were ranged from $0.066 to 0.212{\%}$. 4) The interspecific divergences were greater than the intraspecific variation. Nevertheless, ribosomal RMh genes were more conserved among species than the other mitochondrial genes, and they showed potentiality as an intergenic marker for systematics. In addition, phylogenetic trees, constructed from this data, supported that cherry salmon was closer to chum salmon than to rainbow trout, and that lenok was most distantly related species in six salmonid species.

• Clinical and Experimental Pediatrics
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• v.53 no.2
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• pp.178-183
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• 2010

Purpose : The aim of this study was to identify mutations associated with macrolide resistance in Mycoplasma pneumoniae (MP) and to establish a cultural method to determine antimicrobial susceptibility. Methods : Nasopharyngeal aspirates (NPAs) were collected from 62 children diagnosed with MP pneumonia by a serologic method or polymerase chain reaction. The 23S rRNA and L4 ribosomal protein genes of MP were amplified and sequenced. To identify mutations in these 2 genes, their nucleotide sequences were compared to those of the reference strain M129. MP cultivation was carried out for 32 (28 frozen and 5 refrigerated) NPAs and M129 strain using Chanock's glucose broth and agar plate in a 5% $CO_2$ incubator at $37^{\circ}C$ and examined at 2-3 day intervals for 6 weeks. Results : Among the 62 specimens, 17 had M144V mutations in ribosomal protein L4. The A2064G mutation was observed in 1 specimen; its 23S rRNA gene was successfully sequenced. Culture for MP was successful from the M129 strain and 2 of the 5 NPAs that were refrigerated for no longer than 3 days. However, MP did not grow from the 28 NPAs that were kept frozen at $-80^{\circ}C$ since 2003. Conclusion : We found the M144V mutation of L4 protein to be common and that of domain V of 23S rRNA gene was relatively rare among MP. Studies on the prevalence of macrolide-resistant MP and the relationship between the mutations of 23S rRNA gene and ribosomal protein L4 will aid in understanding the mechanism of macrolide resistance in MP.