• Journal of Life Science
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• v.9 no.3
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• pp.262-267
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• 1999

Mitochondrial DNA (mtDNA) polymorphism of the blue mussel (Mytilus edulis) species complex sampled from the east coast of Korean was studied using a partial sequence of COIII gene (336 bp). Samples obtained from three localities on the east coast of Korea revealed four haplotypes with two clearly differentiated mitochondrial clades (termed clades B and E), separated by 4.2% of minimum sequence divergence. This pattern indicates no difference between east and south coasts of Korea. According to population genetic theory on evolutionary characteristics of mtDNA, we concluded that mtDNA introgression from M. edulis to M. gallprovincialis might be a source for mtDNA polymorphism found in mussels on the east coast of Korea.

• Journal of Environmental Impact Assessment
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• v.32 no.2
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• pp.94-111
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• 2023

In order to establish an effective management strategy for invasive species early detection and regular monitoring are required to assess their introduction or dispersal. Environmental DNA (eDNA) is actively applied to evaluate the fauna including the presence of invasive species as it has high detection sensitivity and can detect multiple species simultaneously. In Korea, the applicability evaluation of metabarcoding is being conducted mainly on fish, and research on other taxa is insufficient. Therefore, this study identified the feasibility of detecting invasive species in Korea using eDNA metabarcoding. In addition, to confirm the possibility of detection by taxa, the detection of target species was evaluated using four universal primers (MiFish, MiMammal, Mibird, Amp16S) designed for fish, mammals, birds, and amphibians. As a result, target species (Trachemys scripta, 3 sites; Cervus nippon, 3 sites; Micropterus salmoides, 7 sites; Rana catesbeiana, 4 sites) were detected in 17 of the total 55 sites. Even in the selection of dense sampling sites within the study area, there was a difference in the detection result by reflecting the ecological characteristics of the target species. A comparison of community structures (species richness, abundance and diversity) based on the presence of invasive species focused on M.salmoides and T.scripta, showed higher diversity at the point where invasive species were detected. Also, 1 to 4 more species were detected and abundance was also up to 1.7 times higher. The results of invasive species detection through metabarcoding and the comparison of community structures indicate that the accumulation of large amounts of monitoring data through eDNA can be efficiently utilized for multidimensional ecosystem evaluation. In addition, it suggested that eDNA can be used as major data for evaluation and prediction, such as tracking biological changes caused by artificial and natural factors and environmental impact assessment.

• Proceedings of the Korea Society of Environmental Toocicology Conference
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• 2000.12a
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• pp.54-54
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• 2000

• Environmental Mutagens and Carcinogens
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• v.23 no.3
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• pp.99-102
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• 2003

IARC classified areca quid as a human carcinogen. Areca quid chewed in Taiwan includes Piper betle inflorescence, which contains high concentrations of safrole (15 mg/fresh weight). Safrole is a documented rodent hepatocarcinogen, and chewing areca quid may contribute to human exposure (420 $\mu$m in saliva). The carcinogenicity of safrole is mediated through 1'-hydroxysafrole formation, followed by sulfonation to an unstable sulfate that reacts to form DNA adducts. Using human liver microsomes and Escherichia coli membranes expressing bicistronic human P450s, CYP2E1 and CYP2C9 were identified as the main P450s involved in the activation of safrole. We have demonstrated the presence of stable safrole-dGMP adducts in human oral tissues following areca quid chewing using $^{32}$ P-postlabeling and HPLC mass spectrometry methods. By studying 88 subjects with a known AQ chewing history and 161 matched controls, we have demonstrated that the presence of safrole-DNA adducts in peripheral blood cells was correlated to AQ chewing, and CYP2E1 seemed to play an important role in the modulation of safrole-DNA adduct formation. We have also shown that safrole can form stable safrole-DNA adducts as well as oxidative damages in rodent liver. However, the stable safrole-DNA adducts may represent a more significant initial lesion as compared to the rapidly repaired safrole-induced 8-hydroxy-2'-deoxyguanosine. This oxidative DNA damage is mediated through the formation of hydoryxchavicol, the major safrole metabolite in human urine. Hydroxychavicol may have gone through two-electron oxidation to the o-quinone; then via one-electron reduction to semiquinone radicals to generate oxidative DNA damage. However, these reactive metabolites can be efficiently conjugated by GSH. These data suggest that safrole may contribute to the initiation of oral carcinogenesis through safrole-DNA adduct and not oxidative DNA damage. In addition, CYP2E1 may modulate this adduct formation.

• Journal of Microbiology and Biotechnology
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• v.33 no.8
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• pp.1084-1090
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• 2023

The strain KIST612, initially identified as E. limosum, was a suspected member of E. callanderi due to differences in phenotype, genotype, and average nucleotide identity (ANI). Here, we found that E. limosum ATCC 8486^T and KIST612 are genetically different in their central metabolic pathways, such as that of carbon metabolism. Although 16S rDNA sequencing of KIST612 revealed high identity with E. limosum ATCC 8486^T (99.2%) and E. callanderi DSM 3662^T (99.8%), phylogenetic analysis of housekeeping genes and genome metrics clearly indicated that KIST612 belongs to E. callanderi. The phylogenies showed that KIST612 is closer to E. callanderi DSM 3662^T than to E. limosum ATCC 8486^T. The ANI between KIST612 and E. callanderi DSM 3662^T was 99.8%, which was above the species cut-off of 96%, Meanwhile, the ANI value with E. limosum ATCC 8486^T was not significant, showing only 94.6%. The digital DNA-DNA hybridization (dDDH) results also supported the ANI values. The dDDH between KIST612 and E. callanderi DSM 3662^T was 98.4%, whereas between KIST612 and E. limosum ATCC 8486^T , it was 57.8%, which is lower than the species cut-off of 70%. Based on these findings, we propose the reclassification of E. limosum KIST612 as E. callanderi KIST612.

• Parasites, Hosts and Diseases
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• v.45 no.4
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• pp.301-306
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• 2007

We attempted to identify parasite DNA in the biliary stones of humans via PCR and DNA sequencing. Genomic DNA was isolated from each of 15 common bile duct (CBD) stones and 5 gallbladder (GB) stones. The patients who had the CBD stones suffered from cholangitis, and the patients with GB stones showed acute cholecystitis, respectively. The 28S and 18S rDNA genes were amplified successfully from 3 and/or 1 common bile duct stone samples, and then cloned and sequenced. The 28S and 18S rDNA sequences were highly conserved among isolates. Identity of the obtained 28S D1 rDNA with that of Clonorchis sinensis was higher than 97.6%, and identity of the 18S rDNA with that of other Ascarididae was 97.9%. Almost no intra-specific variations were detected in the 28S and 18S rDNA with the exception of a few nucleotide variations, i.e., substitution and deletion. These findings suggest that C. sinensis and Ascaris lumbricoides may be related with the biliary stoneformation and development.

• Korean Journal of Ichthyology
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• v.34 no.3
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• pp.208-217
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• 2022

We wanted to develop a real-time PCR assay capable of detecting Liobagrus obesus in environmental DNA (eDNA) extracted from freshwater samples using a pair of species-specific primers and probe for the endangered fish, L. obesus. The species-specific primers and probe were designed in consideration of single nucleotide polymorphisms between 65 species of freshwater fish living in the Republic of Korea within the cytochrome b (cytb) gene of mitochondrial DNA. The species-specific primers and probe, in the real-time PCR assay, showed high specificity as only the L. obesus genomic DNA (gDNA) was found to be positive in the specificity verification using 65 species gDNA of freshwater fish in the Republic of Korea. In addition, in the detection limit analysis using the serial dilution concentrations of L. obesus gDNA, it was found that it was possible to detect up to 0.2 pg, showing high sensitivity. Afterwards, using the species-specific primers and probe, real-time PCR assay was performed on freshwater samples obtained from 8 stations in the mid-upper basin of Geum River. As a result, the cytb gene of L. obesus was detected in total 5 stations including all 3 stations where this species was collected at the time of field survey. Therefore, the species-specific primers and probe developed in present study, and the real-time PCR assay using them, can accurately detect the cytb gene of L. obesus from eDNA samples, which can be utilized to monitor the existing habitats of this species and to discover potential new habitats.

• Korean Journal of Environmental Biology
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• v.40 no.2
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• pp.199-205
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• 2022

Two tree frogs, Dryophytes suweonensis and Dryophytes japonicus, inhabiting Korea, are morphologically similar and share the same habitats. Therefore, they are identified mainly through their calls, especially for males. Dryophytes suweonensis is registered as an endangered (IUCN: EN grade) and protected species in South Korea. Thus, it is necessary to develop a method to rapidly identify and discriminate the two species and establish efficient protection and restoration plans. We identified significant genetic variation between them by sequencing a maternally-inherited mitochondrial 12S ribosomal DNA region. Based on the sequence data, we designed a pair of primers containing 7bp differences for high resolution melting(HRM) analysis to rapidly and accurately characterize their genotypes. The HRM analysis using genomic DNA showed that the melting peak for D. suweonensis was 76.4±0.06℃, whereas that of D. japonicus was 75.0±0.05℃. The differential melt curve plot further showed a distinct difference between them. We also carried out a pilot test for the application of HRM analysis based on immersing D. suweonensis in distilled water for 30 min to generate artificial environmental DNA(eDNA). The results showed 1.10-1.31℃ differences in the melting peaks between the two tree frog samples. Therefore, this HRM analysis is rapid and accurate in identifying two tree frogs not only using their genomic DNA but also using highly non-invasive eDNA.

• Journal of the Korean Society of Fisheries and Ocean Technology
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• v.58 no.1
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• pp.39-48
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• 2022

Using environmental DNA (eDNA) in the fisheries and oceanography fields, research on the diversity of biological species, the presence or absence of specific species and quantitative evaluation of species has considerably been performed. Up to date, no study on eDNA has been tried in the area of fisheries acoustics in Korea. In this study, the biomass of a dominant species in the northwestern waters of Jeju Island was examined using 1) the catch ratio of the species from trawl survey results and 2) the ranking ratio of the species from the eDNA results. The dominant species was Zoarces gillii, and its trawl catch ratio was 68.2% and its eDNA ratio was 81.3%. The Zoarces gillii biomass from the two methods was 7199.4 tons (trawl) and 8584.6 tons (eDNA), respectively. The mean and standard deviation of the acoustic backscattering strength values (120 kHz) from the entire survey area were 135.5 and 157.7 m²/nm², respectively. The strongest echo signal occurred at latitude 34° and longitude 126°15' (northwest of Jeju Island). High echo signals were observed in a specific oceanographic feature (salinity range of 32-33 psu and the water temperature range of 19-20℃). This study was a pilot study on evaluating quantitatively aquatic resources by applying the eDNA technique into acoustic-trawl survey method. Points to be considered for high-quality quantitative estimation using the eDNA to fisheries acosutics were discussed.

• Toxicological Research
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• v.17 no.4
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• pp.249-253
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• 2001

Fumonisin B1, a mycotoxin, is thought to induce esophageal cancer in humans and apoptosis in animal cells by inhibiting ceramide synthase. Dumonisin Bl may also generate reactive oxygen species directly or indirectly, leading to DNA damage and lipid peroxidation. In this study, a DNA fragmentation assay, dichlorofluorescein (DCF) analysis, and single cell gel electrophoresis (SCGE) were used to investigate the involvement of cellular free radicals, specifically hydrogen peroxide, in the DNA damaging activity of fumonisin B1. From an in vitro DNA fragmentation assay, E. coli DNA, damage by fumonisin Bl was increased by the addition of superxide dismutase (SOD) and decreased by catalase. SCGE and DCF analysis in vivo showed that the nuclear DNA damage and intracellular free radicals in cultured rat hepatocytes treated with fumonisin B1 were increased with the concentration of fumonisin Bl . DNA damage and free radical generation were inhibited by the addition of catalase. Fumonisin Bl , in the presence of SOD, produces hydrogen peroxide causing oxidative DNA damage and protein malfunction, leading to genotoxicity and cytotoxicity of the toxin.