• Environmental Mutagens and Carcinogens
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• v.22 no.1
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• pp.54-59
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• 2002

We have used cDNA microarray hybridization to identify gene regulated in response to gamma-irradiation in U-937 cell. The cDNA-chip was composed entirely of 1,000 human cancer related gene including apoptosis and angiogenesis etc. In gamma-irradiated U-937 cell, highly charged protein, ribosomal protein L32, four and a half LIM domains 3, lipocalin 2 (oncogene 24p3) and interleukin 15, ataxia telangiectasia mutated (includes complementation groups A, C and D) genes showed increased level of its transcription, and cell division cycle 25A, dihydrofolate reductase, topoisomerase (DNA) II beta(180kD), kinase suppressor of ras and strarigin genes showed reduced level of its transcription compared to untreated U-937 cell. The significant change of level of transcription was not found in well-known ionizing radiation(IR)-responsive gene, such as transcription factor TP53 and p53 related gene, except ataxia telangiectasia mutated gene.

• Journal of Internet Computing and Services
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• v.15 no.1
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• pp.29-43
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• 2014

The development of NGS technologies, such as scientific workflows, has reduced the time required for decoding DNA sequences. Although the automated technologies change the genome sequence analysis environment, limited computing resources still pose problems for the analysis. Most scientific workflow systems are pre-built platforms and are highly complex because a lot of the functions are implemented into one system platform. It is also difficult to apply components of pre-built systems to a new system in the cloud environment. Cloud computing technologies can be applied to the systems to reduce analysis time and enable simultaneous analysis of massive DNA sequence data. Web service techniques are also introduced for improving the interoperability between DNA sequence analysis systems. The workflow-based middleware, which supports Web services, DBMS, and cloud computing, is proposed in this paper for expecting to reduceanalysis time and aiding lightweight virtual instances. It uses DBMS for managing the pipeline status and supporting the creation of lightweight virtual instances in the cloud environment. Also, the RESTful Web services with simple URI and XML contents are applied for improving the interoperability. The performance test of the system needs to be conducted by comparing results other developed DNA analysis services at the stabilization stage.

• Korean Journal of Ecology and Environment
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• v.53 no.1
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• pp.63-72
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• 2020

In this study, to discuss on the applicability of eDNA as a new method to investigate fish diversity at streams, we applied eDNA at 4 streams (Geum River, Ji Stream, Hwangji Stream, Seomjin River), where endangered species are inhabits, with conventional survey (cast net and kick net). The average (±standard deviation) number of species investigated by eDNA were 19 species (±4.4), and it was relatively higher than average of conventional survey, 10 species (±4.8). Most of case, in this study, eDNA was more efficient than conventional survey. However, there were errors on species identification of Korean endemic species and aliied species from eDNA, and it seems the universal primer (MiFish primer set) is not suitable for them. Furthermore, some of endangered species, caught by conventional method, was not detected by eDNA. As the present universal primer is not suitable for identify the every freshwater fish species in Korea, the complementing or development of universal primer is needed, and the eDNA application after species specific marker development for detecting specific species like endangered species should be considered. In conclusion, if the manual for field survey method by eDNA is developed, we expect applicability enlargement for water ecosystem survey.

• Korean Journal of Environmental Biology
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• v.22 no.1
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• pp.213-219
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• 2004

The bacterial community of water stream, soil and guano in Gossi cave was examined by using PCR amplified the 16S rDNA-denaturing gradient gel electrophoyesis (DGGE). In this study, the genetic diversity and the similarity of bacterial community between open area and non - open area toy cave tour were investigated, and the seasonable variation pattern was compared each other. DGGE is attractive technique, as it sepayate same length dsDNA according to sequence variation typical 16S rDNA genes. The diversity and similarity of bacterial community in cave was analyzed by GC341f and PRUN518r primer sets foy amplification of V3 region of eubacteria 16S rDNA. The specific DGGE band profile of the cave water gives the possibility that the specific bacterial cell can be adapting to the specific cave environment and living in the cave. The DGGE band profiles of all samples with guano were compared and analyzed by image analyzer, in which mutual band profile was compared to be and the band intensity of guano was the highest. From these result, it is thought that the guano was main nutrient source and influenced on the community structure of the cave environment where is nutritionally limited. Pseudomonas sp. NZ060, Pseudomonas pseudoalcaligenes, uncultured Variovorax sp. and soli bacterium NS7 were identified to be on some sample from analysing DNA sequence of some DGGE band.

• Environmental Analysis Health and Toxicology
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• v.29
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• pp.7.1-7.8
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• 2014

Objectives The present study was designed to systematically characterize the denaturation and the renaturation of double stranded DNA (dsDNA), which is suitable for DNA hybridization. Methods A series of physical and chemical denaturation methods were implemented on well-defined 86-bp dsDNA fragment. The degree of each denaturation was measured and the most suitable denaturation method was determined. DNA renaturation tendency was also investigated for the suggested denaturation method. Results Heating, beads mill, and sonication bath did not show any denaturation for 30 minutes. However probe sonication fully denatured DNA in 5 minutes. 1 mol/L sodium hydroxide (alkaline treatment) and 60% dimethyl sulfoxide (DMSO) treatment fully denatured DNA in 2-5 minutes. Conclusions Among all the physical methods applied, the direct probe sonication was the most effective way to denature the DNA fragments. Among chemical methods, 60% DMSO was the most adequate denaturation method since it does not cause full renaturation during DNA hybridization.

• Environmental Mutagens and Carcinogens
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• v.7 no.2
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• pp.59-64
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• 1987

Cytotoxic and genotoxic potential of monosodium glutamate (MSG) were evaluated in primary cultures of rat hepatocytes. When exposed to liver cell culture continuously for 24 hr, MSG did not show any cytotoxic effects up to 0.5% (w/v) level as determined by Tryphan Blue exclusion and lactic dehydrogenase release test. MSG also did not induce unscheduled DNA synthesis or DNA single-strand breaks in hepatocyte cultures up to 1% level. No synergistic effects of MSG were observed on aflatoxin B$_1$-induced DNA damage when 1% MSG was treated to liver cell culture along with aflatoxin B$_1$.

• Environmental Mutagens and Carcinogens
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• v.9 no.1
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• pp.13-22
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• 1989

The effect of novobiocin (NOV), and inhibitor of topoisomerase II, on ethyl methanesulfonate (EMS)-or bleomycin (BLM)-induced DNA repair synthesis was examined during the cell cycle of Chinese hamster ovary (CHO)-K1 cells. Three assays were employed in this study: cell survival, alkaline elution and unscheduled DNA synthesis. EMS was effective at killing CHO cells in G1 phase, wheras BLM preferentially killed cells in G2 and S phases. EMS induced the much more amount of DNA damage in G1 phase, while BLM induced in G2 phase than the other phases. The both of pre- and post-treatment with BOV inhibitied EMS- or BLM-induced DNA repair synthesis in G1 and G2 phases, and pretreatment with NOV inhibited more effectively than the post-treated group. These results suggested that CHO cells exhibited a differential sensitivity to cell lethality and DNA damage in relation to cell cycle according to used chemical agents, and that DNA topoisomerase II participated in an initial stage of DNA repair.

• Journal of the Korean Society of Environmental Restoration Technology
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• v.23 no.2
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• pp.69-89
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• 2020

Scientific trust and quantification of traditional species investigation and results that have been used in ecology for decades has always been a problem and concern for ecologists. Global ecologists have proposed DNA-based species investigation studies to find answers to problems. In this study, we reviewed the global trend of research on environmental DNA(eDNA), which is a method for monitoring species by detecting DNA of organisms naturally mixed in environmental samples such as water, soil, and feces. The first eDNA research confirmed the possibility of species investigation at the molecular level, and commercialization of NGS(Next Generation Sequencing) and DNA metabarcoding elicits efficient and quantitative species investigation results, and eDNA research is increasing in the filed of ecology. In this study, mammals and birds were detected using MiMammal universal primers from 23 samples(3 natural reserves; 20 water bowls) out of 4 patches to verify eDNA for urban ecosystems in Suwon, and eDNA was verified by performing camera trapping and field survey. Most terrestrial species were detected through eDNA, and particularly, mice(Mus musculus), and Vinous-throated Parrotbill (Sinosuthora webbiana) were identified only with eDNA, It has been confirmed to be highly effective by investigating techniques for small and internal species. However, due to the lack of resolution of the primer, weasels(Mustela sibirica) and squirrels(Melanochromis auratus) were not detected, and it was confirmed that the traditional investigation method was effective only for a few species, such as Mogera robusta(Mogera robusta). Therefore, it is judged that the effects of species investigation can be maximized only when eDNA is combined with traditional field survey and Camera trapping to complement each other.

• Environmental Mutagens and Carcinogens
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• v.20 no.1
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• pp.7-13
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• 2000

The mechanisms of benzene toxicity is not fully elucidated, although the metabolism of benzene is very well understood. In order to study the mechanism of benzene toxicity, we investigated DNA damage induced by benzene metabolite, 1,2,4-benzenetriol (BT) in HL-60 cells by alkaline comet assay. To investigate the mechanism of cellular DNA damage induced by BT, the cells were treated with antioxidant such as vitamin C, SOD, catalase, and chelating agent such as deferoxamine (DFO), bathocuproinedisulfonic acid (BCDS). BT induced DNA damage in dose-dependent manner at concentration between 10$\mu\textrm{m}$ and 100$\mu\textrm{m}$. The antioxidant vitamin C itself induced DNA damage at higher concentration. The DNA damage induced by BT in HL-60 cells was protected at low concentraiton of vitamin C whereas no protective effect was found at high concentration. In hibitory effect of SOD on DNA damage by BT was observed and this suggested that BT produce superoxide anion (O2-) causing DNA damage. Catalase protected BT-induced DNA damage suggesting that BT produce H2O2 during autooxidation of BT. Both Fe(II)-specific cheiating agent, deferoxamine (DFO) and Cu(I)-specific chelating agent, bathocuproinedisulfonic acid (BCDS) inhibited BT0induced DNA damage. This suggested that DNA damage was caused by active species which was produced DAN damage. This suggested that DNA damage was caused by active species which was produced by the autooxidation of BT in the presence of Cu(II) and Fe(III). These findings suggest that reactive oxygen species play an important role in the mechanism of toxicity induced by benzene metabolites.

• Environmental Mutagens and Carcinogens
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• v.9 no.2
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• pp.111-121
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• 1989

Ps. aeruginosa 의 DNA repair 기구 결손변이주인 rec-, Hcr- 그리고 R931 plasmid 를 가진 R2 (Carbenicillin, Kanamycin, Streptomycin) plasmid transconjugants 가 R2 Plasmid 획득에 의해서 Gamma선 및 돌연변이제 (4NQO, NTG)에 대해서도 내성을 증강시키는지를 검토함으로써 방사선에 대한 내성화 기구를 해명하고자 했다. 그리고, DNA repair 기구에 작용하는 DNA polymerase I 생산에 관여하는 유전자가 R2 plasmid에 code 되어 있는지를 검토하여 다음과 같은 결과를 얻었다. 1) Ps. aeruginosa PAO균주의 R2 plasmid transconjugants는 R2 plasmid 획득에 의해 자외선, Gamma선 및 돌연변이제에 대한 내성을 부여받았으나 transconjugant 균주에 따라 다른 종류의 내성결과를 얻어졌다.