• Journal of Life Science
• /
• v.16 no.2 s.75
• /
• pp.240-244
• /
• 2006

We present a fast and simple protocol for purification of mitochondria, mitochondrial DNA, and RNA from small amounts of tomato leaves. This method uses a high ionic strength medium to isolate mitochondria and extract mitochondrial DNA and RNA from a single preparation and is easily adaptable to other plant species. Mitochondria was confirmed by MitoTracker. The mitochondrial DNA was not contaminated by plastid DNA, was successfully used for PCR. Similarly, the isolated mitochondrial RNA was not contaminated only slightly contaminated (leaves) by plastid RNA. RNA prepared according to our method was acceptable for RT-PCR analysis

• Korean Journal of Microbiology
• /
• v.34 no.1_2
• /
• pp.51-57
• /
• 1998

A study was carried out to understand some parameters affecting on RAPD analysis with Lactobacillus species. From the results, we found that appearance of specific DNA bands were very influenced by the concentration of $MgCl_2$ but it was overcome by applying enough amount of Taq DNA polymerase. Other parameters such as concentrations of template DNA, random primers and Taq DNA polymerase have enhanced the production of specific DNA bands by increasing their concentration applied. However, we noticed that G/C contents of random primers did not show any correlations with number of specific RAPD bands generated but the RAPD results were heavily influenced by the characteristics of the random primers, that is, the sequences of the oli.

• Tuberculosis and Respiratory Diseases
• /
• v.42 no.3
• /
• pp.314-321
• /
• 1995

Background: Flow cytometric study has been used to measure the DNA content of solid tumors for the last decade. DNA ploidy is an important property commonly measured by flow cytometry. The possibility to study archival paraffin-embedded tumors has hastened an appreciation of prognostic utility of this method. The aim of this study is to look for biologic prognostic indicator for survival time of patients with small cell carcinoma of lung in addition to the well known clinical prognostic factors. Method: DNA ploidy was measured by flow cytometric method using tumor cells isolated from paraffin embedded tissue. To evaluate the prognostic significance, DNA ploidy of small cell lung cancer was analysed in 42 patients who died after receiving anticancer chemotherapy. Results: 1) Mean survival time of all patients was 190(${\pm}156$) days. Survival time was shortened, when TNM stage and PS scale were advanced. 2) 62% of all patients was DNA aneuploidy. DNA ploidy had nothing to do with advance of TNM stage and PS scale. 3) Mean survival time of aneuploid tumor was significantly shorter($138{\pm}90$ days) than that of diploid tumors($272{\pm}197$ days).(p<0.001) 4) To exclude the influence of clinical prognostic factors such as TNM stage and PS scale, the analysis was restricted to subgroups of identical stage. We were able to find the same tendency. Conclusion: DNA ploidy is an independent prognostic factor in small cell lung cancer.

• Journal of the Korean Society of Food Science and Nutrition
• /
• v.46 no.5
• /
• pp.545-551
• /
• 2017

Curcuma longa L. (CL) is widely used as a spice and coloring agent in several foods, such as curry and mustard, as well as cosmetics and drugs. In this study, we investigated the protective effects of CL extracted with various solvents [methanol (MC), ethanol (EC), acetone (AC)] on $H_2O_2-induced$ DNA damage in human leukocytes along with total polyphenol contents (TPC) and antioxidant properties. The antioxidant effects of CL were determined by measuring 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity (RSA) and superoxide dismutase (SOD)-like activity. The preventive effect of CL on oxidative stress-induced DNA damage and DNA repair capacities were assessed using comet assay. MC showed the highest TPC (11.17 g gallic acid equivalents/100 g) and antioxidant properties among the solvent extracts. The $SC_{50}$ for DPPH RSA was MC: 35.0 > AC: 45.8 > EC: $57.8{\mu}g/mL$ and SOD-like activity was MC: 46.6 > EC: 141.5 > AC: $296.4{\mu}g/mL$. In the comet assay, the $ED_{50}$ value of MC showed the highest inhibition ($86.7{\mu}g/mL$) of $H_2O_2-induced$ DNA damage, followed by AC ($110.0{\mu}g/mL$) > EC ($115.8{\mu}g/mL$). Analysis of the percentage of damaged cells showed that repair capacity significantly decreased at 4, 8, and 12 h from $H_2O_2-induced$ oxidative stress in each extract. After 12 h, level of DNA damage recovery was similar to the negative control level. These results suggest that CL has potential antioxidant activity and a protective effect against oxidation-induced DNA damage, and the methanol extract of CL was the most effective.

• Journal of Soil and Groundwater Environment
• /
• v.14 no.3
• /
• pp.57-67
• /
• 2009

In soil and sediment environment, microorganisms play major roles in biochemical cycles of ecological significant elements. Because of its ecological significance, microbial diversity and community structure information are useful as indexes for assessing the quality of subsurface ecological environment and bioremediation. To achieve more accurate assessment, it is requested to gain sufficient yield and purity of DNA extracted from various soil and sediment samples. Although there have been a large number of basic researches regarding soil and sediment DNA extraction methods, little guideline information is given in literature when choosing optimal DNA extraction methods for various purposes such as environmental ecology impact assessment and bioremediation capability evaluation. In this study, we performed a thorough literature review to compare the characteristics of the current DNA extraction methods from soil and sediment samples, and discussed about considerations when selecting and applying DNA extraction methods for environmental impact assessment and bioremediation capability evaluation. This review suggested that one approach is not enough to gain the suitable quantity and yield of DNA for assessing microbial diversity, community structure and population dynamics, and that a careful attention has to be paid for selecting an optimal method for individual environmental purpose.

• Analytical Science and Technology
• /
• v.31 no.2
• /
• pp.65-70
• /
• 2018

This study compared two methods for preparing ancient DNA (aDNA) for the construction of successful shotgun libraries that may be applied to massive parallel sequencing. For the comparative analysis, the DNA of prehistoric rib samples from Hungary was extracted using either a manually prepared silica suspension or the Amicon Ultracel-15 10K ultracentrifugal device (Millipore). After the extraction of the same amount of bone powder (about 150 mg) from three samples by each method, the amount of extracted double-stranded DNA and the subsequent degree of construction of the shotgun library were analyzed. The Amicon device method was rapid and easier to perform and resulted in an approximately 11-fold higher DNA recovery than that obtained using the silica suspension. The shotgun library constructed using DNA templates prepared by the Amicon device was more successful than that constructed from templates isolated using the silica suspension. The comparative study of these two aDNA extraction methods showed that the Amicon device has the advantages of saving time, process simplicity, and high efficiency.

• KSBB Journal
• /
• v.22 no.6
• /
• pp.387-392
• /
• 2007

Recently, microfluidic biochips for DNA microarray are providing a number of advantages such as, reduction in reagent volume, high-throughput parallel sample screening, automation of processing, and reduction in hybridization time. Particularly, the enhancement of target probe hybridization by decrease of hybridization time is an important aspect highlighting the advantage of microfluidic DNA microarray platform. Fundamental issues to overcome extremely slow diffusion-limited hybridization are based on physical, electrical or fluidic dynamical mixing technology. So far, there have been some reports on the enhancement of the hybridization with the microfluidic platforms. In this review, their principle, performance, and outreaching of the technology are overviewed and discussed for the implementation into many bio-applications.

• Journal of Life Science
• /
• v.27 no.11
• /
• pp.1331-1339
• /
• 2017

DNA barcoding is the identification of a species based on the DNA sequence of a fragment of the cytochrome C oxidase subunit I (COI) gene in the mitochondrial genome. It is widely applied to assist with the sustainable development of fishery-product resources and the protection of fish biodiversity. This study attempted to verify horse-head fish (Branchiostegus japonicus) and fake horse-head fish (Branchiostegus albus) species, which are commonly consumed in Korea. For the validation of the two species, a real-time PCR method was developed based on the species' mitochondrial DNA genome. Inter-species variations in mitochondrial DNA were observed in a bioinformatics analysis of the mitochondrial genomic DNA sequences of the two species. Some highly conserved regions and a few other regions were identified in the mitochondrial COI of the species. In order to test whether variations in the sequences were definitive, primers that targeted the varied regions of COI were designed and applied to amplify the DNA using the real-time PCR system. Threshold-cycle (Ct) range results confirmed that the Ct ranges of the real-time PCR were identical to the expected species of origin. Efficiency, specificity and cross-reactivity assays showed statistically significant differences between the average Ct of B. japonicus DNA ($21.85{\pm}3.599$) and the average Ct of B. albus DNA ($33.49{\pm}1.183$) for confirming B. japonicus. The assays also showed statistically significant differences between the average Ct of B. albus DNA ($22.49{\pm}0.908$) and the average Ct of B. japonicus DNA ($33.93{\pm}0.479$) for confirming B. albus. The methodology was validated by using ten commercial samples. The genomic DNA-based molecular technique that used the real-time PCR was a reliable method for the taxonomic classification of animal tissues.

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

• Journal of Plant Biotechnology
• /
• v.31 no.3
• /
• pp.225-230
• /
• 2004

We employed single cell gel electrophoresis method (comet assay) to analyze the degree of nucleus-DNA damage in the leaves of red pepper (Capsicum annuum L.) seedlings exposed to $^{60}$ CO v-radiation stress. Nucleus-DNA damage was measured as the ratio of tail length (T) to head length (H) in individual comet image isolated from pepper leaf cell. The T/H ratio of control-cells and treated-cells at 50 or 100 Gy were 1.28 and 3.54 or 3.39, respectively, suggesting that nuclei of pepper cells were severely damaged in the integrity of DNA strand by the treatment of enhanced v-radiation. The percentage of head-DNA in control-cells was 76.8%, whereas those of 50 and 100 Gy treated-cells were 55.9% and 59.9%, respectively. Pretreatment of low dose (4 to 20 Gy) radiation to seeds decreased DNA-damage in the leaves of seedlings treated with high dose radiation at 50 or 100 Gy. In this experiment, we developed a sensitive, reliable and rapid method for evaluating genotoxic effect in the nuclei of plant cells by employing comet assay.