• Korean Journal of Medicinal Crop Science
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• v.17 no.1
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• pp.26-32
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• 2009

The region containing 18S rRNA gene, ITS 1 and part of the 5.8S rRNA gene of the Atractylodes japonica Koidz was amplified by PCR and the product cloned in a pBluescript SK II plasmid. DNA sequence of the cloned DNA was determined and submitted to the GenBank (accession number EU678363). Phylogenetic analysis of the ITS 1 DNA showed close similarity with the other plant species of the family Compositae. The extract of the plant materials of five different members of the family Compositae was analyzed by HPLC to detect atractylon. Extract of the A. japonica Koidz showed presence of significant amount of atractylon. However, noticeable amount of atractylon was not detected by the same analyses from the extracts of the other plants belonging to the family Compositae including Artemisia capillaris, Chrysantemum zawadskii, Eclipta prostrata or Taraxacum platycarpum.

• Korean Journal of Microbiology
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• v.26 no.4
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• pp.312-317
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• 1988

The genes for ribosomal RNA in Rhizobium meliloti and Bradyrhizobium japonicum were analyzed by southern hybridization of BamHI, EcoRI, HindIII digested chromosomal DNA with purified 5' $^{32}P$-labeled 16S and 23S rRNA. The big differences in the hybridization pattern of both rhizobia were found. The comparative results were discussed in relation to the copy number and conservativity of restriction sites in the rRNA genes of both rhizobia.

• Microbiology and Biotechnology Letters
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• v.40 no.3
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• pp.268-273
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• 2012

Microbial diversity analyses were performed in several geothermal areas in Indonesia using a culture-independent approach with 16S rRNA gene sequencing. All areas and the majority of samples were noted as being affiliated with Proteobacteria. In addition, unclassified bacteria with no phylum affiliation were detected at an incidence rate of 20.0-26.5% in every location. The majority groupings in the geothermal hot stream in Cisolok belonged to ${\beta}$-Proteobacteria (27.1%) and Cyanobacteria (11.0%), whereas the majority from the volcanic area in Kamojang was ${\gamma}$-Proteobacteria (51.5%) followed by Aquificales (12.9%). The predominant groups around an underwater thermal vent in the sea at Likupang were ${\gamma}$-Proteobacteria (33.3%) and then Bacteroidetes (27.6%). This detailed microbial community analyses of each area strongly support a possible association with plausible community groups and environmental habitats, such as extremely geothermal or marine habitats. This study has significantly contributed to the expansion of scientific knowledge of the microbial community in Indonesia.

• 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.

• Genomics & Informatics
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• v.13 no.2
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• pp.26-30
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• 2015

nc886 (=vtRNA2-1, pre-miR-886, or CBL3) is a newly identified non-coding RNA (ncRNA) that represses the activity of protein kinase R (PKR). nc886 is transcribed by RNA polymerase III (Pol III) and is intriguingly the first case of a Pol III gene whose expression is silenced by CpG DNA hypermethylation in several types of cancer. PKR is a sensor protein that recognizes evading viruses and induces apoptosis to eliminate infected cells. Like viral infection, nc886 silencing activates PKR and induces apoptosis. Thus, the significance of the nc886:PKR pathway in cancer is to sense and eliminate pre-malignant cells, which is analogous to PKR's role in cellular innate immunity. Beyond this tumor sensing role, nc886 plays a putative tumor suppressor role as supported by experimental evidence. Collectively, nc886 provides a novel example how epigenetic silencing of a ncRNA contributes to tumorigenesis by controlling the activity of its protein ligand.

• Journal of fish pathology
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• v.26 no.2
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• pp.77-88
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• 2013

Starry flounder, Platichthys stellatus (body length $4.4{\pm}0.51cm$) that became sick during an outbreak of disease at mariculture facilities at Ulsan, Korea in August of 2012, were examined to identify the cause of the disease. Diseased fish didn't show a unique sign, but the oxidase-positive and gram negative rod was isolated from moribund fish. The bacterium was revealed as Photobacterium damselae subsp. piscicida by biochemical analysis and sequence analysis of the 16S rRNA and capsular polysaccharide (CPS) genes. The isolates (AD5) was carrying susceptible to ofloxacin and gentamycin and showed high growth value at $18^{\circ}C$ and $25^{\circ}C$ compared to four other P. damsela strains.

• ALGAE
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• v.38 no.1
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• pp.1-22
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• 2023

An enormous body of research is focused on finding ways to commercialize carotenoids produced by the unicellular green alga, Haematococcus, often without the benefit of a sound phylogenetic assessment. Evidence of cryptic diversity in the genus means that comparing results of pigment studies may be confounded by the absence of a phylogenetic framework. Moreover, previous work has identified unnamed strains that are likely candidates for species status. We reconstructed the phylogeny of an expanded sampling of Haematococcus isolates utilizing data from nuclear ribosomal markers (18S rRNA gene, 26S rRNA gene, internal transcribed spacer [ITS]-1, 5.8S rRNA gene, and ITS-2) and the rbcL gene. In addition, we gathered morphological, ultrastructural and pigment data from key isolates of Haematococcus. Our expanded data and taxon sampling support the concept of a new species, H. privus, found exclusively in North America. Despite overlap in numerous morphological traits, results indicate that ratios of protoplast length to width and akinete diameter may be useful for discriminating Haematococcus lineages. High growth rate and robust astaxanthin yield indicate that H. rubicundus (SAG 34-1c) is worthy of additional scrutiny as a pigment source. With the description of H. privus, the evidence supports the existence of at least five, species-level lineages in the genus. Our phylogenetic assessment provides the tools to frame future pigment investigations of Haematococcus in an updated evolutionary context. In addition, our investigation highlighted open questions regarding polyploidy and sexuality in Haematococcus which demonstrate that much remains to be discovered about this green flagellate.

• Journal of Species Research
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• v.8 no.3
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• pp.249-258
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• 2019

Owing to a distinct environmental regime and anthropogenic effects, freshwater bacterial communities of urban streams are considered to be different from those of large freshwater lakes and rivers. To obtain unrecorded, freshwater bacterial species in Korea, water and sediment samples were collected from various urban streams of the Han River watershed in 2018. After plating the freshwater samples on R2A agar, approximately 1000 bacterial strains were isolated from the samples as single colonies and identified using 16S rRNA gene sequence analyses. A total of 26 strains, with >98.7% 16S rRNA gene sequence similarity with validly published bacterial species but not reported in Korea, were determined to be unrecorded bacterial species in Korea. The unrecorded bacterial strains were phylogenetically diverse and belonged to four phyla, six classes, 12 orders, 16 families, and 21 genera. At the generic level, the unreported species were assigned to Nocardioides, Streptomyces, Microbacterium, Kitasatospora, Herbiconiux, Corynebacterium, and Microbacterium of the class Actinobacteria; Paenibacillus and Bacillus of the class Bacilli; Caulobacter, Methylobacterium, Novosphingobium, and Porphyrobacter of the class Alphaproteobacteria; Aquabacterium, Comamonas, Hydrogenophaga, Laribacter, Rivicola, Polynucleobacter, and Vogesella of the class Betaproteobacteria; Arcobacter of the class Epsilonproteobacteria; and Flavobacterium of the class Flavobacteriia. The details of the 26 unreported species, including Gram reaction, colony and cell morphology, biochemical properties, and phylogenetic position are also provided in the strain descriptions.

• Journal of Species Research
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• v.13 no.1
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• pp.100-104
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• 2024

The purpose of this study was to isolate and identify wild yeasts from soil samples collected in Daegu and Cheongju city, Republic of Korea. To identify the wild yeast strains, pairwise sequence comparisons of D1/D2 region of the 26S rRNA gene sequence were done using Basic Local Alignment Search Tool (BLAST). The cell morphologies were observed by phase contrast microscope and assimilation test are done using API 20C AUX kit. All strains were assigned to the phylum Basidiomycota. Among 13 strains, 11 strains were previously reported, but two strains were unreported from the Republic of Korea. The two unrecorded yeast strains, GW1-3 and PG1-1-10C, belong to the genus Solicoccozyma (family Piskurozymaceae, order Filobasidiales, class Tremellomycetes). The two strains had oval-shaped and polar budding cells. This research showed the morphological and biochemical properties of the two unreported yeast species that had not officially reported in Korea.

• Biomedical Science Letters
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• v.26 no.3
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• pp.149-156
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• 2020

We developed a simple and rapid method for detecting vancomycin resistance genes, such as vanA and vanB, using loop-mediated isothermal amplification (LAMP). To identify not only vancomycin resistance genes, but also the genus Enterococcus, primers were designed for vanA, vanB, and 16S rRNA. Screening for vancomycin susceptibility in Enterococcus was performed using Etest (bioMérieux Inc). The results of the LAMP assay were compared to those of real-time RT-PCR. The optimal conditions for the LAMP assay were 65℃ for 60 min. The detection limits of the LAMP assay for vanA, and vanB were 2 × 10² copies/reaction. Compared to RT-PCR, the sensitivities and specificities of LAMP for 16S rRNA, vanA, and vanB were 100/100%, 100/100%, and 100/100%, respectively. The vanA genotype-vanB phenotype accounted for 57.5% (46/80) of the vancomycin-resistant Enterococci samples collected from 2016 to 2019. In conclusion, the LAMP assay developed in this study showed high sensitivity and specificity for vancomycin-resistant genes. Moreover, due to the simplicity and rapidity of the LAMP assay, its use can be very useful in clinical microbiology laboratories.