• Journal of Species Research
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• v.12 no.3
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• pp.229-239
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• 2023

We isolated and identified 25 unrecorded bacterial species belonging to the phylum Actinomycetota found in the Republic of Korea. Sequence comparison of 16S rRNA was performed using the NCBI BLAST and EzBioCloud database to identify 25 species, which had a 16S rRNA gene sequence similarity of >98.8% and were allocated as unrecorded species in the Republic of Korea. Among the 25 unrecorded bacterial strains, Streptomyces was the most common with nine species, followed by Leifsonia with two species. Isoptericola, Nocardioides, Dermacoccus, Sinomonas, Patulibacter, Marmoricola, Allobranchiibius, Aldersonia, Actinokineospora, Agromyces, Aeromicrobium, Cellulomonas, and Gordonia with one species each were also found. Twenty-five unrecorded species were excavated in various environments, such as tidal flats, ferns, soil, pine cones, moss, mud, wetlands, and plants. These isolates were characterized on the basis of their phylogenetic, biochemical properties, and morphological data, and species descriptions were provided.

• Journal of Life Science
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• v.26 no.7
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• pp.819-825
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• 2016

The present study was done to assess the diversity of the bacterial community associated with Ulva pertusa collected from Jeju Island using Restriction Fragment Length Polymorphism (RFLP) marker analysis. For RFLP analysis, a total of 145 bacterial strains associated with Ulva pertusa were screened and cultivated using Marine agar and R2A agar. The PCR amplicons of the 16S rRNA gene from all the isolated strains were digested with HaeIII and RsaI restriction enzymes and then classified into different groups according to their restriction patterns. Strains selected based on the RFLP patterns showed more than 91% 16S rRNA gene sequence similarity when compared with known bacterial species, which include 4 phyla - proteobacteria (alpha-proteobacteria, beta-proteobacteria, gamma-proteobacteria - 63%), firmicutes (11%), actinobacteria (4%), bacteroidetes (22%)–as well as 7 classes (actinobacteria, flavobacteriia, cytophagia, bacilli, α-proteobacteria, γ-proteobacteria, β-proteobacteria), 13 orders, 18 families, and 27 genera. These results confirmed a wide diversity of bacterial communities as contrasted with other regions. The newly isolated 10 strains, which show 16S rRNA sequence similarity of <97% compared to previously identified bacteria, could be noble species. Further experiments, such as morphological, physiological, and biochemical classification, are necessary to confirm the novelty of the newly isolated 10 strains.

• Korean Journal of Microbiology
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• v.48 no.1
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• pp.42-47
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• 2012

Hydrothermal vents (HTV) provide special environments for evolution of lives independent on solar energy. HTV samples were gained from Tofua arc trench in Tonga, South Pacific. We investigated archaeal diversity enriched using combinations of various electron donors (yeast extract and $H_2$) and electron acceptors [Iron (III), elemental sulfur ($S^0$) and nitrate. PCR amplification was performed to detect archaeal 16S rRNA genes after the cultures were incubated $65^{\circ}C$ and $80^{\circ}C$ for 2 weeks. The cultures showing archaeal growth were transferred using the dilution-to-extinction method. 16S rRNA gene PCR-Denaturing Gradient Gel Electrophoresis was used to identify the enriched archaea in the highest dilutions where archaeal growth was observed. Most of cultured archaea belonged to genus of Thermococcus (T. alcaliphilius, T. litoralis, T. celer, T. barossii, T. thoreducens, T. coalescens) with 98-99% 16S rRNA gene similarities. Interestingly, archaeal growth was observed in the cultures with Iron (III) and nitrate as an electron acceptor. It was supposed that archaea might use the elemental sulfur generated from oxidation of the reducing agent, sulfide. To cultivate diverse archaea excluding Thermococcus, it would be required to use other reducing agents instead of sulfide.

• Journal of Marine Life Science
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• v.8 no.2
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• pp.128-135
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• 2023

The present study was tried to identify whether the eel's larva was close to a conger (Conger myriaster), a pipe conger (Muraenesox cinereus) or four species of Anguilla. Experimental fishes were collected by set net in the gulf of enggang, Namhae, Korea from May to June. Their morphological characteristics were compared with adult fishes of a conger, a pipe conger and four species of Anguilla. For genetic classification, DNA was isolated and amplified by using 12S rRNA and 16S rRNA primer set. The PCR products were direct sequencing in both directions. The nucleotide sequences were analyzed using softwares. As results of morphological measurement on eel's larva, the percentages of head length and preanal length against total length were similar with a conger. Based on the nucleotide sequences, the phylogenetic tree also revealed a close relationship to a conger. Therefore, eel's larva, caught in Namhae from May to June, was identified into a conger's larva.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.242-247
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• 2019

Biological factors (e.g. microorganism activity) in wastewater treatment plant (WWTP) play essential roles for degradation and/or removal of organic matters. In this study, to understand the microbial functional roles in WWTP, we tried to isolate and characterize a bacterial strain from activated sludge sample. Strain S16 was isolated from the activated sludge of a municipal WWTP in Daejeon metropolitan city, the Republic of Korea. The cells were a Gram-stain-positive, non-motile, facultative anaerobe, and rod-shaped. Strain S16 grew at a temperature of $15{\sim}40^{\circ}C$ (optimum, $30^{\circ}C$), with 0~9.0% (w/v) NaCl (optimum, 1.0~2.0%), and at pH 5.5~9.0 (optimum, pH 7.0~7.5). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S16 was most closely related to the unique species Miniimonas arenae NBRC $106267^T$ (99.79%, 16S rRNA gene sequence similarity) of the genus Miniimonas. The cell wall contained alanine, glutamic acid, serine, and ornithine. Although the isolation source of the type strain NBRC $106267^T$ which considered as a marine microorganism is sea sand, that of strain S16 is terrestrial environment. It might raise an ecological question for habitat transition. Therefore, comparative genome analysis will be valuable investigation for shedding light on their potential metabolic traits and genomic streamlining.

• Korean Journal of Microbiology
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• v.47 no.3
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• pp.209-217
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• 2011

Archaeal communities were investigated using 454 pyrosequencing technology based on 16S rRNA gene in 11 samples collected from six different full-scale anaerobic digesters. Observed operational taxonomic units (OTUs) estimated from the archaeal 16S rRNA gene sequences were 13-55 OTUs (3% cutoff) which was corresponded to 29-89% of Chao1 richness estimates. In the anaerobic digesters there were archaeal sequences within the orders Thermoproteales, Thermoplasmatales, Desulfurococcales as well as within the orders Methanomicrobiales, Methanobacteriales, Methanococcales, Methanosarcinales, and Methanocellales, which are known to produce methane. Among these orders, Methanococcales known to produce methane using hydrogen was the predominant taxon and constituted 51.8-99.7% of total sequences. All samples showed a very similar community structure (Pearson correlation coefficient=0.99) except for one sample based on a heat map analysis. In addition, canonical correspondence analysis correlating archaeal communities to the environmental variables demonstrated that digester temperature and total solids removal rate were the two important explanatory variables. Overall results suggested that environmental and operational variables of anaerobic digester are important factors determining archaeal diversity and community structure.

• The Plant Pathology Journal
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• v.23 no.3
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• pp.151-154
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• 2007

Phytoplasma was identified from leaf lettuce (Lactuca sativa) cultivated in commercial green-house in Korea. Diseased leaf lettuce revealed proliferation of shoots, and yellowing and shrinking of leaves (lettuce proliferation-K). Polymerase chain reaction (PCR) with universal primer pair P1/P6, and aster yellows (AY) specific primer pair R16F1/R1 amplified 1.5kb and 1.1kb length of DNA fragments, respectively. Nucleotide sequences of 16S rRNA gene were determined (Gen Bank accession no EF489024). Phylogenetic analysis of 16S rDNA showed the closest relationship with AY phytoplasma (GenBank accession no. AY389822 and AY389826), indicating that lettuce proliferation-K is a member of AY. Phytoplasma bodies were detected in phloem sieve tubes of diseased lettuce by transmission electron microscopy. The structures had round or pleomorphic shapes with a diameter of 130-300nm. Phylogenetic analysis of 16S rRNA gene, microscopic observation of phytoplasma bodies and symptomatology indicated that lettuce proliferation-K is caused by phytoplasma in the AY group. This is the first report of phytoplasma disease in lettuce in Korea.

• The Korean Journal of Physiology and Pharmacology
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• v.26 no.4
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• pp.239-253
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• 2022

Epithelial-mesenchymal transition (EMT) is known to be involved in airway remodeling and fibrosis of bronchial asthma. However, the molecular mechanisms leading to EMT have yet to be fully clarified. The current study was designed to reveal the potential mechanism of microRNA-21 (miR-21) and poly (ADP-ribose) polymerase-1 (PARP-1) affecting EMT through the PI3K/AKT signaling pathway. Human bronchial epithelial cells (16HBE cells) were transfected with miR-21 mimics/inhibitors and PARP-1 plasmid/small interfering RNA (siRNA). A dual luciferase reporter assay and biotin-labeled RNA pull-down experiments were conducted to verify the targeting relationship between miR-21 mimics and PARP-1. The migration ability of 16HBE cells was evaluated by Transwell assay. Quantitative real-time polymerase chain reaction and Western blotting experiments were applied to determine the expression of Snail, ZEB1, E-cadherin, N-cadherin, Vimentin, and PARP-1. The effects of the PI3K inhibitor LY294002 on the migration of 16HBE cells and EMT were investigated. Overexpression of miR-21 mimics induced migration and EMT of 16HBE cells, which was significantly inhibited by overexpression of PARP-1. Our findings showed that PARP-1 was a direct target of miR-21, and that miR-21 targeted PARP-1 to promote migration and EMT of 16HBE cells through the PI3K/AKT signaling pathway. Using LY294002 to block PI3K/AKT signaling pathway resulted in a significant reduction in the migration and EMT of 16HBE cells. These results suggest that miR-21 promotes EMT and migration of HBE cells by targeting PARP-1. Additionally, the PI3K/AKT signaling pathway might be involved in this mechanism, which could indicate its usefulness as a therapeutic target for asthma.

• Journal of Korean Society on Water Environment
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• v.35 no.1
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• pp.28-34
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• 2019

This study analyzed the occurrence pattern of Dolichospermum (= Anabaena) in the Bukhan river from March 2012 to December 2014 in order to identify the genotypes of Dolichospermum. Furthermore, 16S rRNA were analyzed to identify the genotypes of Dolichospermum that occurred in 2015 which were then compared to the reference sequence deposited at NCBI. During this period, the occurrence of Dolichospermum was highly correlated to water temperature. In the year 2012 and 2013, Dolichospermum appeared in Lake Cheongpyeong (CP), Sambong (SB), and Lake Paldang (P2) between July and August. However, in 2014, it appeared in SB and P2, but not in CP. This reduction in appearance was attributed to the decreased inflow to Lake Uiam as a result of low rainfall in 2014 as compared to 2012. In July 2015, the Dolichospermum 16S rRNA genotype was confirmed in five locations; Lake Cheongpyeong (CP), Seojong (SJ), Songchon Sewage Treatment Plant (SC), Joan (P4), and Lake Paldang (PD). Anabaena crassa of spiral clone, A. planctonica of linear clone, and A. circinalis of spiral clone exhibited high genetic similarity with the reference sequence. The 16r RNA genotype showed approximately 3 % sequence variation between the locations and were more similar to each other in locations that were closer.

• BMB Reports
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• v.37 no.3
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• pp.351-355
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• 2004

Separate protocols are commonly used to prepare plasmid DNA, chromosomal DNA, or total RNA from E. coli cells. Various methods for the rapid preparation of plasmid DNA have been developed previously, but the preparation of the chromosomal DNA and total RNA are usually laborious. We report here a simple, fast, reliable, and cost-effective method to extract total nucleic acids from E. coli by direct lysis of the cells with phenol. Five distinct and sharp bands, which correspond to chromosomal DNA, plasmid DNA, 23S rRNA, 16S rRNA, and a mixture of small RNA, were observed when analyzing the prepared total nucleic acids on a regular 1-2% agarose gel. The simple and high-quality preparation of the total nucleic acids in a singe tube allowed us to rapidly screen the recombinant plasmid, as well as to simultaneously monitor the change of the plasmid copy number and rRNA levels during the growth of E. coli in the liquid medium.