• Environmental Engineering Research
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• v.14 no.1
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• pp.63-67
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• 2009

Escherichia coli K-12 (E. coli K-12) is a representative indicator globally used for distinguishing and monitoring dynamic fates of pathogenic microorganisms in the environment. This study investigated how to most critically quantify lacZ ($\beta$-galactosidase) gene in E. coli K-12 by two different real-time polymerase chain reaction (real-time PCR) in association with three different DNA extraction practices. Three DNA extractions, i.e., sodium dodecyl sulfate (SDS)/proteinase K, magnetic beads and guanidium thiocyanate (GTC)/silica matrix were each compared for extracting total genomic DNA from E. coli K-12. Among them, GTC/silica matrix and magnetic beads beating similarly worked out to have the highest (22-23 ng/${\mu}L$) concentration of DNA extracted, but employing SDS/proteinase K had the lowest (10 ng/${\mu}L$) concentration of DNA retrieved. There were no significant differences in the quantification of the copy numbers of lacZ gene between SYBR Green I qPCR and QProbe-qPCR. However, SYBR Green I qPCR obtained somewhat higher copy number as $1{\times}10^8$ copies. It was decided that GTC/silica matrix extraction or magnetic beads beating in combination with SYBR Green I qPCR can be preferably applied for more effectively quantifying specific gene from a pure culture of microorganism.

• Korean Journal of Environmental Biology
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• v.29 no.3
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• pp.236-240
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• 2011

Mercury known as quicksilver, is the most common cause of heavy metal toxicity. Toxicity caused by excessive mercury exposure is now being recognized as a widespread environmental problem and is continuing to attract a great deal of public concerns. The mercury genotoxicity could be its effect on DNA repair mechanisms, which constitute the defense system designated to protect genome integrity. The objective of this study is to confirm that mercuric chloride inhibits the repair of gamma ray-induced DNA damage. The earthworm of Eisenia fetida was chosen for this study because it is an internationally accepted model species for toxicity testing with a cosmopolitan distribution. Experiments were done to identify the levels of DNA damage and the repair kinetics in the coelomocytes of E. fetida irradiated with 20 Gy gamma rays alone or with gamma rays after 40 mg $kg^{-1}$ $HgCl_2$ treatment by means of the single cell gel electrophoresis assay. The Olive tail moments were measured during 0~96 hours after irradiation. The repair time in the animals treated with the combination of $HgCl_2$ and ionizing radiation was nearly five times longer than that in the animals treated with ionizing radiation alone. Also, E. fetida exposed to mercury showed a statistically lower repair efficiency of gamma ray-induced DNA damage. The results suggest that the mercury could even have deleterious effects on the DNA repair system. Influence of mercury on the DNA repair mechanisms has been confirmed by this study.

• Korean Journal of Medicinal Crop Science
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• v.23 no.6
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• pp.489-499
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• 2015

Background : Plants belonging to 5 species of the genus Eleutherococcus are currently distributed in the Korean peninsula. The traditional medicine 'Ogapi', derived from Eleutherococcus sessiliflorus and other related species, and 'Gasiogapi', derived from Eleutherococcus senticosus, are frequently mixed up and marketed. Therefore, accurated identification of their origins in urgently required. Methods and Results : Candidate genes from nuclear ribosomal DNA (nrDNA) and chloroplast DNA (cpDNA) of Eleutherococcus plants were analyzed. Whereas the nrDNA-internal transcribed spacer (ITS) regions were useful in elucidating the phylogenetic relationships among the plants, the cpDNA regions were not as effective. Therefore, a combined analysis with nrDNA-ITS was performed. Various combinations of nrDNA and matK were effective for discriminating among the plants. However, the matK and rpoC1 combination was ineffective for discriminating among some species. Based on these results, it was found that OG1, OG4, OG5, OG7, GS1, GS2, and GS3 were derived from E. sessiliflorus. In particular, it was confirmed that GS1, GS2, and GS3 were not derived from E. senticosus. However, more samples need to be analyzed because identification of the origins of OG2, OG3, OG6 and GS4 was not possible. Conclusion : The ITS2, ITS5a, and matK combination was the most effective in identifying the phylogenetic relationship among Eleutherococcus plants and traditional medicines based on Eleutherococcus.

• Toxicological Research
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• v.7 no.2
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• pp.157-163
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• 1991

The effect of patulin, a mycotoxin, on the growth of Escherichia coli cell was investigated. E. coli cell elongation usually shown in SOS-response for DNA repair was induced by 20 mg of patulin per ml. After staining the E. coli chromosome with fluorescence dye(DAPI, 4', 6-diamino-2-phenyl-indole), chromosomal DNA partitioning was not affected by patulin. The observation indicateds that patulin acts as a DNA damaging agent which is effective for E. coli cell elongation introduced by the inhibition of septum formation.

• Journal of Ecology and Environment
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• v.48 no.1
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• pp.32-48
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• 2024

Background: Longitudinal connectivity in river systems strongly affects biological components related to ecosystem functioning, thereby playing an important role in shaping local biodiversity and ecosystem health. Environmental DNA (eDNA)-based metabarcoding has an advantage of enabling to sensitively diagnose the presence/absence of species, becoming an efficient/effective approach for studying the community structure of ecosystems. However, little attention has been paid to eDNA-based biomonitoring for river systems, particularly for assessing the river longitudinal connectivity. In this study, by using eDNA we analyzed and compared species diversity and composition among artificial barriers to assess the longitudinal connectivity of the fish community along down-, mid- and upstream in the Hotancheon from the Geum River basin. Moreover, we investigated temporal variation in eDNA fish community structure and species diversity according to season. Results: The results of species detected between eDNA and conventional surveys revealed higher sensitivity for eDNA and 61% of species (23/38) detected in both methods. The results showed that eDNA-based fish community structure differs from down-, mid- and upstream, and species diversity decreased from down to upstream regardless of season. We found that there was generally higher species diversity at the study sites in spring (a total number of species across the sites [n] = 29) than in autumn (n = 27). Nonmetric multidimensional scaling and heatmap analyses further suggest that there was a tendency for community clusters to form in the down-, mid- and upstream, and seasonal variation in the community structure also existed for the sites. Dominant species in the Hotancheon was Rhynchocypris oxycephalus (26.07%) regardless of season, and subdominant species was Nipponocypris koreanus (16.50%) in spring and Odontobutis platycephala (15.73%) in autumn. Artificial barriers appeared to negatively affect the connectivity of some fish species of high mobility. Conclusions: This study attempts to establish a biological monitoring system by highlighting the versatility and power of eDNA metabarcoding in monitoring native fish community and further evaluating the longitudinal connectivity of river ecosystems. The results of this study suggest that eDNA can be applied to identify fish community structure and species diversity in river systems, although some shortcomings remain still need to be resolved.

• Journal of Environmental Impact Assessment
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• v.30 no.1
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• pp.1-12
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• 2021

This study focused on verifying the identification of freshwater fish species in Korea using Environmental DNA (eDNA) technique. The research of DNA is increasing in the field of ecology, since this is more sensitive of identify rather than traditional investigation method. Which is difficult to detect species hidden in water and be easily influenced by diverse factors (sites, bad weather, researchers and so on). We applied the pilot test in aquarium (Freshwater Fish Ecological Learning Center in Yangpyeong, Gyeonggi Do), where freshwater fish species are inhabits. We conducted to sampling and analyzing the sixteen water samples (50 species from 7 orders and 13 families) using MiFish primer set. The results showed that 45 species (90%) was investigated by eDNA. It highlight that eDNA with universal primer is possible to detect freshwater fish species of Korean. However, the errors on species identification seems to be caused by the primer that be not suited perfectly and the pollution such as aquarium, sampling collectors.

• Korean Journal of Environmental Biology
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• v.41 no.4
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• pp.637-656
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• 2023

River estuaries are dynamic and productive ecosystems with high regional biodiversity. Environmental DNA (eDNA) has become a useful approach to assessing biodiversity in aquatic ecosystems. This study was conducted to investigate fish community characteristics and species diversity in two river estuary ecosystems, the Taehwa River and Changwon Stream. We further compared conventional and eDNA metabarcoding analyses of the fish communities. The conventional survey was performed in May, July, and October 2022, while the eDNA analysis was conducted only in May. We observed various fish species with different life histories, including carp, goby, and marine fish. We also found that migratory fish, such as dace Tribolodon hakonensis, sweetfish Plecoglossus altivelis, and eel Auguilla japonica, occurred in the Taehwa River, suggesting high river connectivity. Marine fish species were predominant in the Changwon Stream, as this river is located close to the sea. The diversity indices showed that the Taehwa River generally had higher species richness, evenness, and diversity values than the Changwon Stream. A total of 9-19 species were detected in the conventional survey for the three sites, whereas 11-18 species were found from eDNA analysis. The findings indicate that the sensitivity of eDNA was similar to or higher than that of the conventional method. Our study findings suggest the efficiency and efficacy of eDNA-based fish community monitoring, although with some shortcomings in applying the genetic marker to Korean fish, including no clear-cut distinction for Korean endemic species and/or genetically closely related species groups.

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.156-169
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• 2021

Traditional morphological identification difficulties, such as phenotypic plasticity, misidentification of cryptic species, and larval stage species, can be compensated for by using DNA analysis techniques, such as DNA barcoding, in surveying zooplankton populations, including species identification. Recently, the rapid development of DNA sequencing techniques has allowed DNA-based community analysis not only for zooplankton assemblages in various aquatic ecosystems but also for the gut contents of zooplankton that are limited by conventional methods such as visual and microscopic identification. Therefore, the application of DNA sequencing can help understand biological interactions through the analysis of zooplankton food sources. The present paper introduces the major DNA-based approaches in zooplankton research topics, including taxonomic approaches by DNA barcoding, community-level approaches by metabarcoding, and gut content analyses, summarizes the analysis methods, and finally suggests the methodological topics that need to be considered for future applications.

• Environmental Mutagens and Carcinogens
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• v.19 no.2
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• pp.112-115
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• 1999

The action mechanism of the inhibitory effect of some natural products on the DNA strand break and DNA damage was investigated in vitro and in vivo. In the E. coli chromosomal DNA strand break experiment in vitro, three mushroom water extracts were effective on the DNA strand breaking by daunorubicin. Phellinus linteus water extract inactivated daunorubicin, a DNA strand breaking agent, but did not protect DNA from daunorubicin-induced DNA strand breaking. Agaricus blazei water extract inhibited DNA strand breaking action of daunorubicin not only by daunorubicin inactivation, but also by DNA protection from daunorubicin. An inhibitory effect of Ganoderma lucidum water extract on the DNA strand break was based on the DNA protection rather than daunorubicin inactivation. In vivo mutagen assay system (SOS-chromotest), among three mushroom water extracts Phellinus linteus water extract was the most effective one on the inhibition of DNA damage by 4-NQO. The results suggest that all three mushroom water extracts inhibit daunorubicin-induced DNA damage and in vivo DNA damaging action of 4-NQO by the reaction of mutagen inactivation or DNA protection from the mutagen.

• Proceedings of the National Institute of Ecology of the Republic of Korea
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• v.3 no.1
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• pp.54-65
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• 2022

Species distribution models are a useful tool for predicting future distribution and establishing a preemptive response of invasive species. However, few studies considered the possibility of habitat for the aquatic organism and the number of target sites was relatively small compared to the area. Environmental DNA (eDNA) is the emerging tool as the methodology obtaining the bulk of species presence data with high detectability. Thus, this study applied eDNA survey results of Micropterus salmoides and Lepomis macrochirus to species distribution modeling by seasons in the Anyang stream network. Maximum Entropy (MaxEnt) model evaluated that both species extended potential distribution area in October compared to July from 89.1% (12,110,675 m²) to 99.3% (13,625,525 m²) for M. salmoides and 76.6% (10,407,350 m²) to 100% (13,724,225 m²) for L. macrochirus. The prediction value by streams was varied according to species and seasons. Also, models elucidate the significant environmental variables which affect the distribution by seasons and species. Our results identified the potential of eDNA methodology as a way to retrieve species data effectively and use data for building a model.