• 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.

• Journal of fish pathology
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• v.22 no.3
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• pp.391-400
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• 2009

Genetic identification of 17 fish-derived Aeromonas strains was attempted using 5 housekeeping genes. 16S rRNA, gyrB, rpoD, dnaJ and recA genes from the 17 strains were amplified, and total of 85 amplicons were sequenced. DNA sequences of the strains and type strains of the 17 Aeromonas homology groups were used for genetic identification and phylogenetic analyses. None of the strains was identified as a single species using the 16S rRNA gene, showing the same identities (average = 99.7%) with several Aeromonas species. According to gyrB, rpoD, dnaJ, and recA, 9 strains and RFAS-1 used in this study were identified as A. hydrophila and A. salmonicida, respectively. However, the other strains were closely related to 2 or more Aeromonas species (i.e., A. salmonicida, A. veronii, A. jandaei, A. media and A. troda) depending on the genetic marker used. In this study, gyrB, rpoD, dnaJ and recA gene sequences proved to be advantageous over 16S rRNA for the identification of field Aeromonas isolates obtained from fish. However, there are discrepancies between analyses of different phylogenetic markers, indicating there are still difficulties in genetic identification of the genus Aeromonas using the housekeeping genes used in this study. Advantages and disadvantages of each housekeeping gene should be taken into account when the gene is used for identification of Aeromonas species.

• Korean Journal of Microbiology
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• v.54 no.1
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• pp.81-83
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• 2018

We sequenced the genome of the Neisseria sp. KEM232 isolated from the smooth surface caries of human cavity of a 7-year old male in Republic of Korea by using the standard dilution plating technique. The genome comprises a single circular 2,371,912 bp chromosome with a G + C content of 58.5%, 2,210 protein-coding genes, 108 pseudo genes, 51 RNA genes, and one CRISPR array. Based on the 16S rRNA gene sequence similarity and average nucleotide identity, the strain KEM232 is most closely related to Neisseria baciliformis.

• Ocean Science Journal
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• v.41 no.4
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• pp.315-318
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• 2006

Three Synechococcus strains were isolated from seawater near the Ieodo Ocean Research Station (IORS), and their 16S rDNA genes and the internal transcribed spacer (ITS) between the 16S and 23S rRNA genes were sequenced to investigate their phylogenetic relationships. Phylogenetic trees based on the 16S rDNA and ITS sequences showed that they clustered in the main MC-A Synechococcus group (subcluster 5.1), but formed branches differentiating them from the described clades. As the IORS is located in an area affected by diverse water masses, high Synechococcus diversity is expected in the area. Therefore, the IORS might be a good site to study the diversity, physiology, and distribution of the Synechococcus group.

• Korean Journal of Breeding Science
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• v.42 no.2
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• pp.163-168
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• 2010

This study was carried out to determine the chromosomal localization of the 5S and 18S-26S ribosomal DNA(rDNA) genes by means of fluorescence in situ hybridization(FISH) techniques, and the constitutive heterochromatin detected by means of Gimsa C-banding technique in rye(Secale cereale L.). The somatic chromosomes number was 2n=14. The karyotype consists of four pairs of metacentrics(chromosomes 1, 2, 3, and 7) and three pairs of submetacentrics(chromosomes 4, 5, and 6). Secondary constrictions appeared in the short arm of chromosome 1. The 5S rDNA genes have been located on two pairs of chromosomes 1 and 5, and 18S-26S rDNAs genes have been located on one pair of chromosome 1. 5S rDNA genes were detected on the distal region of the secondary constrictions in nucleolus organizer regions(NOR) in chromosome 1, and other detected on the intercalary region in the short arm of chromosome 5.

• 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.

• Korean Journal of Environmental Biology
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• v.30 no.1
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• pp.54-63
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• 2012

This study characterizes three $Anabaena$ strains and 5 $Trichormus$ strains isolated from Korean waters and 3 $Anabaena$ $flos-aquae$ strains procured from the UTEX based on morphological features and molecular analyses. The $Anabaena$ and $Trichormus$ isolates were morphologically assigned to $A.$ $variabilis$ K$\ddot{u}$tzing and $T.$ $variabilis$(K$\ddot{u}$tzing ex Bornet et Flahault) Kom$\acute{a}$rek et Anagnostidis, respectively. The $Anabaena$ and $Trichormus$ strains differed significantly in the mean length of their vegetative cells. The 16S rRNA genes from the $Anabaena$ strains showed a 100% identity to that from $A.$ $variabilis$ ATCC 29413, while the 16S rRNA genes from the $Trichormus$ strains showed a 99.9% identity to that from $T.$ $variabilis$ GREIFSWALD. The overall topology was in agreement for the 16S rRNA gene and $cpcBA$-IGS trees in the both tree-constructing methods. In a neighbor-joining tree based on the 16S rRNA gene, the 3 $Anabaena$ strains were asso-ciated with $A.$ $variabilis$, the 5 $Trichormus$ strains with $T.$ $variabilis$, and the 3 $Anabaena$ (UTEX) strains were with $Nostoc$. To date, this is the first report on $A.$ $variabilis$ and $T.$ $variabilis$ strains originating from Korea.

• Journal of Life Science
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• v.31 no.8
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• pp.710-718
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• 2021

Placenta-derived mesenchymal stem cells (PD-MSCs) are promising candidates for cell-based therapy in regenerative medicine. The migration and homing potential of PD-MSCs to injured sites is a critical property of MSC engraftment. MicroRNAs (miRNAs) have recently been shown to regulate the critical functions of MSCs, such as proliferation, survival, and migration. The objective of the present study was to identify the miRNA and target genes involved in PD-MSCs homing in a bile duct ligation (BDL) rat model. We selected candidate miRNAs targeting genes for PD-MSCs homing based on microarray analysis. PD-MSC engraftment in BDL-injured rat liver was identified by immunofluorescence assay and human-specific Alu gene expression by quantitative real-time polymerase chain reaction (qRT-PCR) one week after transplantation. Compared with migrated naïve PD-MSCs under hypoxic and normoxic conditions (Hyp/Nor), the transplanted group with PD-MSCs (Tx) showed distinct differences in miRNA expressions in BDL-injured rat liver. We also validated the miRNAs and their target genes for PD-MSCs homing. The expressions of integrin α4 (ITGA4) and integrin α5 (ITGA5) target genes for miR-199a-5p and miR-148a-3p were significantly upregulated in the Tx group (p<0.05). In addition, integrin β1 (ITGB1) and integrin β8 (ITGB8) were upregulated by suppressing miR-183-5p and miR-145-5p, respectively. These results demonstrated that PD-MSCs regulate miRNA expression related to the integrin family for their homing effects on the BDL-injured rat liver. The findings further suggest that miRNA-mediated regulation of the integrin family contributes to the therapeutic efficacy of PD-MSCs in the rat hepatic fibrosis model by BDL.

• Journal of Microbiology and Biotechnology
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• v.31 no.7
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• pp.921-932
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• 2021

LINC01272 is a long non-coding RNA (lncRNA) that has been considered as a biomarker for many diseases including lung squamous cell carcinoma. Here, we investigated the function and mechanism of LINC01272 on lung cancer (LC). The differential expression of LINC01272 in LC and normal samples was analyzed by GEPIA based on the data from TCGA-LUAD database, as survival prognosis was analyzed through Kaplan-Meier Plotter. LINC01272 overexpression plasmid and miR-7-5p mimic were transfected into A549 and PC-9 cells. LINC01272, miR-7-5p and cardiolipin synthase 1 (CRLS1) mRNA expression was measured by quantitative reverse transcription-polymerase chain reaction. Cell viability was detected through MTT assay. Cell multiplication was evaluated by cell formation assay. Cell apoptosis was assessed through flow cytometry assay. Through bioinformatics, the target miRNA of LINC01272 and downstream genes of miR-7-5p were predicted. The targeting relationship was tested by dual luciferase reporter analysis. CRLS1, B-cell lymphoma-2 (Bcl-2), BCL2-associated X (Bax) and cleaved caspase-3 protein levels were detected through western blot. LINC01272 was downregulated in LC and low LINC01272 expression had poor prognosis. In A549 and PC-9 cells, LINC01272 inhibited cell viability and multiplication and induced apoptosis. LINC01272 negatively regulated miR-7-5p and CRLS1 was a target of miR-7-5p. MiR-7-5p reversed the effect of LINC01272 on viability, multiplication, apoptosis and expression of miR-7-5p and CRLS1 as well as apoptosis-related factors (Bcl-2, Bax and cleaved caspase-3). LINC01272 suppressed cell multiplication and induced apoptosis via regulating the miR-7-5p/CRLS1 axis in LC.

• International Journal of Industrial Entomology and Biomaterials
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• v.44 no.2
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• pp.55-64
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• 2022

Bombyx shini Park & Sohn, 2002 (Lepidoptera: Bombycidae), which was listed as an endemic species in South Korea has recently been renamed as the East Asian silk moth Rotunda rotundapex Miyata & Kishida, 1990 (Lepidoptera: Bombycidae). In this study, we sequenced the complete mitochondrial genome (mitogenome) of the R. rotundapex to announce genomic characteristics and to clarify its validity with a new name. The 15,294-bp long complete mitogenome comprises a typical set of genes [13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes] and one major noncoding, A + T-rich region, with an arrangement identical to that observed in most lepidopteran mitogenomes. The A/T content of the whole mitogenome was 79.22%; however, it varied among the regions/genes as follows: A + T-rich region, 91.62%; srRNA, 84.67%; lrRNA, 83.01%; tRNAs, 81.43%; and PCGs, 77.46%. Phylogenetic analyses of 35 species in the Bombycoidea superfamily showed the sister relationship between the families Sphingidae and Bombycidae s. str., with the higher nodal support [bootstrap support (BS) = 78%]. The Saturniidae was placed as the sister to the two families, but the nodal support for this relationship was low (BS = 53%). Current R. rotundapex was placed together with previously reported con-species with the highest nodal support, forming a separate clade from Bombyx, validating that B. shini can have a new genus name, Rotunda. However, the Korean R. rotundapex showed a substantial sequence divergence at 5.28% to that originated from an individual of type locality Taiwan in 1,459-bp of COI sequences. Considering such a high sequence divergence an additional study, which includes morphological and DNA barcoding data from further extensive distributional range maybe is needed for further robust taxonomic conclusion.