• Journal of the korean academy of Pediatric Dentistry
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• v.41 no.4
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• pp.292-297
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• 2014

DNA extraction is a prerequisite for the identification of pathogens in clinical samples. Commercial DNA extraction kits generally involve time-consuming and laborious multi-step procedures. In the present study, our modified DNA isolation method for saliva samples allows for the quick detection of pathogens associated with dental caries or periodontitis by PCR within 1 h. To release DNA from the bacteria, 1 min of boiling was adequate, and the resulting isolated DNA can be used many times and is suitable for long term storage of at least 13 months at $4^{\circ}C$, and even longer at $-20^{\circ}C$. In conclusion, our modified DNA extraction method is simple, rapid, and cost-effective, and suitable for preparing DNA from clinical samples for PCR for the rapid detection of oral pathogens from saliva.

• Environmental Analysis Health and Toxicology
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• v.22 no.4
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• pp.349-355
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• 2007

장수풍뎅이 유충(Allomyrina dichotoma larva, ADL)은 중국의 전통 약재로서, 특히 항산화 효과가 우수하여 항당료 제재로 사용되고 있다. 본 연구에서는 이러한 ADL의 추출물을 이용하여 헴스터 췌장의 ${\beta}$-세포(HIT-T15)에서 Streptozotocin에 의해 유발된 산화적 손상에 대한 보호효과 및 그 작용기전을 조사하였다. ADL추출물은 처리농도 의존적으로 Streptozotocin에 의해 유발된 지질과산화 및 세포 내 자유산 소종의 양을 억제함으로서 ${\beta}$-세포의 산화적 스트레스에 의한 손상을 보호하였다. 또한 DNA laddering 방법을 사용하여 Streptozotocin에 의해 유발된 DNA 손상을 조사한 결과, ADL추출물 처리농도에 비례하여 Streptozotocin에 의해 유발된 DNA 손상이 감소하였다. 이러한 산화적 손상의 억제능 관련 작용 기전을 조사하기 위해 DPPH free radical 소거능을 실시하였다. 그 결과 ADL추출물 자체가 DPPH 자유 레디컬 소거능이 있음을 확인하였으며, 또한 플라스미드를 이용한 Single-strand break 방법을 통한 DNA 손상 보호능을 측정한 결과도 $Fe^{3+}$ 및 $H_2O_2$에 의해 유발된 DNA 손상이 ADL추출물 처리농도에 비례하여 감소하였다. 이러한 결과들을 종합하여 볼 때, 장수풍뎅이 유충의 추출물들이 자체의 레디컬 소거능 및 산화적 손상에 의한 DNA손상을 억제함으로써, Streptozotocin에 의해 유발된 산화적 손상을 억제할 수 있을 것이라 사료된다.

• Korean Journal of Food Science and Technology
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• v.30 no.4
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• pp.964-969
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• 1998

To investigated the anticarcinogenic activity of 70% ethanol extracts from various cereal in vitro, antimutagenic activity, inhibitory effect of DNA strand scission and tumor promotion were examined. The antimutagenic activity of the beans such as black bean and small red bean was generally higher than that of cereals examined. However inhibitory activity of 70% ethanolic extracts against DNA strand scission induced mitomycin C showed that millet, job's tear, black bean and soy bean among cereals and beans tested in this study inhibited effectively the DNA strand scission. Antioxidative activity of some cereal extracts determined by using linoleic acid model system showed that Job's tear, millet and black bean were higher antioxidative activity than other cereals and beans. Conventional short-term antipromoter assay system using activation of Epstein Barr virus (EBV) clearly demonstrated that sorghum, buckwheat, black bean and small red bean have inhibitory effects on promotion in cellular carcinogenesis.

• Korean Journal of Plant Resources
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• v.22 no.5
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• pp.461-466
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• 2009

This study was carried out to evaluate the effects of yam (Dioscorea batatas Dence) extracts on the cell viability, growth and nucleus-DNA damage of tobacco cells which were exposed to $\gamma$-radiation stress. The viability and growth of tobacco cells exposed to 20 Gy of radiation stress were effectively recovered by pretreatment of 10 mg/L ethylacetate (EtOAc) yam extract. Pretreatment of EtOAc extract showed 20% higher cell viability and fresh weight growth than that of cells without pretreatment in 20 Gy radiation treated tobacco cells. Nucleus-DNA damage was measured as the ratio of tail length (T) to head length (H) in individual comet image isolated from tobacco cells. The T/H ratio of control-cells and treated-cells at 20 Gy were 1.05 and 1.68, and % head DNA of those cell were 86.7 and 71.3%, respectively, suggesting that nuclei of tobacco cells were severely damaged in the integrity of DNA by the treatment of $\gamma$-radiation. However, pretreatment of MeOH, EtOAc and n-BuOH extracts decreased radiation induced DNA-damage in the tobacco cells, showing T/H ratio of 1.37, 1.01 and 1.10 and % head DNA of 81.5, 87.6 and 88.7%, respectively.

• Applied Biological Chemistry
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• v.39 no.5
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• pp.403-408
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• 1996

Total bacterial community DNA, which was extracted from microcosm soil and field soil after 2,4-D amendments, was analyzed on Southern blots, using the tfdA gene probe derived from plasmid pJP4 and the Spa probe from Sphingomonas paucimobilis. Southern blot analyses with total bacterial DNA extracted from soils Inoculated with Pseudomonas cepacia/pJP4 revealed that DNA probe method could detect the 2,4-D degrading bacteria down to $10^5\;cells/g$ dry soil. In the microcosm experiment, there was a good correlation between 2,4-D degradation and banding patterns in hybridization analyses performed after each 2,4-D treatment using the two probes. When bacterial DNA extracted from microcosm soil was hybridized with the Spa probe, a change in the position of hybrid bands was observed over time in a Southern blot, suggesting that population change or possibly genetic rearrangement in 2,4-D degrading microbial populations occurred in this soil. With the Spa probe, one hybrid DNA band was persistently observed throughout the five 2,4-D additions. When bacterial DNA isolated from the field soil was probed with the tfdA and Spa, strong hybridization signal was observed in the 100 ppm-treated subplot, weak signal In the 10 ppm-treated subplot, and no significant signal in the 1 ppm-treated and control subplots. The data show that DNA probe analyses were capable of detecting and discriminating the indigenous 2,4-D degrading microbial populations in soil amended with 2,4-D under laboratory and field conditions.

• Proceedings of the Korea Contents Association Conference
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• 2016.05a
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• pp.185-186
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• 2016

최근 DNA 복구 기작 저해가 암 전이를 억제한다는 연구결과가 발표되었다. 이번 연구에서는 DNA 복구 기작을 효율적으로 저해시킬 수 있는 단백질을 선정하고자 했다. 먼저 HPRD에서 59개의 DNA repair 단백질 정보를 얻고 각각의 도메인 정보를 추출하였다. 이 단백질과 상호작용하는 단백질을 KEGG로 부터 추출하고 추출한 단백질의 도메인 정보는 HPRD에서 얻었다. Cytoscape를 통하여 DNA 복구 단백질-상호작용 단백질-도메인의 네트워크를 시각화하였다. 네트워크 상에서 보존적이며 핵심적인 단백질 후보 및 도메인 후보를 선정 하였다. KEGG에서 제공하는 암의 경로(pathways in cancer)을 이용하여 후보의 적용 가능성을 확인하였다. 선정한 최종 후보들은 향후 암 전이 억제에 사용될 수 있는 타깃이 될 수 있을 것으로 기대한다.

• Journal of Korean Society of Forest Science
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• v.112 no.4
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• pp.554-560
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• 2023

To prevent illegal timber distribution, DNA markers have been used to identify the species and origin. However, extracting high-quality DNA from timber is difficult because of its physical and chemical properties. In this study, we investigated whether the age of timber tissue influences the yield of DNA extraction and the success rate of polymerase chain reaction (PCR) to understand the relationship between the establishment time of the wood annual ring and the extracted DNA concentration (ng/μl), purity (A260/A280), and PCR success rate (%) from pinewood, a major Korean domestic species. According to the results, it was observed that as the distance from the cambium increased, indicating that the tissue was older, the concentration and purity of the extracted DNA decreased significantly. For the trnM-trnV (285 bp) and rpoC1 (298 bp) regions, the PCR success rate was 100%. However, for the rbcL (1.3 kb) region, the PCR success rate was 66.67%. Moreover, PCR amplification of the rbcL region failed at all points older than 30 years. Thus, it is deduced that as time passes, along with the decay of timber cells, DNA is degraded, leading to a decrease in DNA concentration, purity, and PCR success rate. The results of this study are expected to be beneficial for future applications, such as the species identification of timber, providing valuable insights and potential utilization in this field.

• Journal of Genetic Medicine
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• v.7 no.1
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• pp.53-58
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• 2010

Purpose: To find the most effective method for extraction of cell-free DNA (cf-DNA) from maternal plasma, we compared a blood DNA extraction system (blood kit) and a viral DNA extraction system (viral kit) for non-invasive first-trimester fetal gender determination. Materials and Methods: A prospective cohort study was conducted with maternal plasma collected from 44 women in the first-trimester of pregnancy. The cf-DNA was extracted from maternal plasma using a blood kit and a viral kit. Quantitative fluorescent-polymerase chain reaction (QF-PCR) was used to detect the SRY gene and AMEL gene. The diagnostic accuracy of the QF-PCR results was determined based on comparison with the final delivery records. Results: A total of 44 women were tested, but the final delivery record was only obtained in 36 cases which included 16 male-bearing and 20 female-bearing pregnancies. For the blood kit and viral kit, the diagnostic accuracies for fetal gender determination were 63.9% (23/36) and 97.2% (35/36), respectively. Conclusion: In non-invasive first-trimester fetal gender determination by QF-PCR, using a viral kit for extraction of cf-DNA may result in a higher diagnostic accuracy.

• Journal of Food Hygiene and Safety
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• v.34 no.6
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• pp.557-561
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• 2019

This study investigated the efficacy of DNA extraction methods for real-time PCR detection of foodborne pathogenic bacteria in livestock manure composts. Livestock manure composts were inoculated with Escherichia coli O157:H7, Salmonella Typhimurium, Listeria monocytogenes, Bacillus cereus and incubated in enrichment broth. For DNA extraction, enriched samples were treated following boiling method, by chloroform, C₁₈ powder, and proteinase K. As a result, 4 species of bacteria were detected by real-time PCR when subjected to boiling for 30 min and treated with proteinase K. These results suggest that detection of foodborne pathogens by real-time PCR from livestock manure composts could be applicable using effective DNA extraction methodology such as the boiling method or proteinase K.

• Journal of Life Science
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• v.23 no.1
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• pp.31-37
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• 2013

The present study aimed to investigate effects of ethanol extracts from Hydropsyche kozhantschikovi on cell and DNA damage caused by oxidative stress. In a radical scavenging assay, compared with ascorbic acid used as a control, the level of DPPH (1,1-diphenyl-2-picrylhydrazyl) and that of hydroxyl radicals in H. kozhantschikovi extracts were 60.0% and 43.7%, respectively. The ferrous iron chelating level was 37.5% compared to the chelating value of EDTA (ethylenediaminetetraacetic acid) as a positive control at the same concentration. To verify inhibitory effects of oxidative cell damage induced by reactive oxygen species (ROS), the relative level of lipid peroxidation and the expression level of the p21 protein were compared in extracts-treated and untreated groups. Lipid peroxidation was completely inhibited in the extracts-treated group compared with the radical-only treated group. The level of p21 protein expression was restored to 92.2% of p21 protein expression in the control sample. In addition, DNA cleavage inhibition in the H. kozhantschikovi extracts was 74.1% compared with that of the control group, suggesting that H. kozhantschikovi extracts repress DNA cleavage induced by ROS. Moreover, the phosphorylation ratio of the H2AX protein was 16.7% in the radical-treated group, indicating that the ethanol extracts inhibited 83.3% of DNA damage. Our findings suggest that ethanol extracts from H. kozhantschikovi are effective not only in repressing the oxidation of free radicals and highly toxic hydroxyl radicals, but also in decreasing cell and DNA damage caused by oxidative stress.