• Korean Journal of Plant Resources
• /
• v.19 no.1
• /
• pp.161-168
• /
• 2006

To investigate the origin of backyeoncho (Opuntia ficus-indica var. saboten), we isolated 685 bp clone using ITS primer pairs. The rDNA consists of the genes coding for the partial 54 bp 185, 162 bp 5.8S, and partial 56 bp 26S. The coding regions are interrupted by two internal transcribed spacers, 193 bp ITS1 and 220 bp ITS2. The ITS2 of backnyeoncho in length was shorter than that previously registered in Cucurbitoideae plants. The GC contents was 66.8% in ITS1, and 67.7% in ITS2. The rDNA of backnyeoncho matched to the previously reported genes and showed a high similarity with the 95% identity with Pereskiopsis porteri (L708037). In the phylogenetic analysis, the backnyeoncho rDNA was clustered with Pereskiopsis porteri (L708037).

• Journal of Life Science
• /
• v.20 no.4
• /
• pp.578-583
• /
• 2010

It has been reported that extracts of globe thistle (Echinops spp.) and thistle (Circium spp., Carduus spp. and Onopordum spp.) have anti-bacterial and anti-fungal activities. Methanol extracts of Echinops setifer and Carduus spp. were used to test and see if the extracts of these plants could suppress growth of Mycobacterium smegmatis and Mycobacterium fortuitum. Although extract of Echinops setifer showed no anti-mycobacterial activities, extract of Carduus spp. showed inhibition zones when tested with filter discs. Genomic DNA was isolated from Carduus spp. and PCR was performed to clone a DNA fragment containing ITS1, 5.8S rRNA gene and ITS2. A 733-bp PCR product was obtained and its DNA sequence was reported to the GenBank (accession number GU188570). BLAST search of the obtained DNA sequence did not show a match with any DNA sequences in the Genbank. Carduus crispus and Carduus defloratus had the closest phylogenetic relationships to this plant.

• Journal of Life Science
• /
• v.21 no.6
• /
• pp.838-844
• /
• 2011

The purpose of this study was to investigate gender-specific changes of plasma MDA, SOD, and lymphocyte DNA damage during high intensity exercise. In this study, 17 healthy male and 18 healthy female college students ran on a treadmill at 85%$VO_{2max}$ until the point of all-out. Blood-collecting was carried out five times (Rest, Ex-Exha, R0.5h, R4h and R24h), and with the collected blood, plasma malondialdehyde (MDA), superoxide dismutase (SOD), and lymphocyte DNA damage were analyzed. Plasma MDA and SOD concentration increased significantly at the Ex-Exha (p<0.05), and there were no significant differences in gender. For the degree of lymphocyte DNA damage, all %DNA in the tail, tail length and tail moment increased significantly at the Ex-Exha (p<0.05), and %DNA in the tail and tail length were significantly higher in the male group than in the female group (p<0.05). These results suggest that acute high intensity exercise not only causes oxidative stress but also brings about lymphocyte DNA damage. In addition, it was found that males showed higher DNA damage than females in terms of oxidative stress subject to high intensity exercise. Nevertheless, further subsequent studies are required in order to better understand the mechanism behind DNA damage varying with gender, in a way that takes into consideration physical fitness, hormonal level, exercise intensity and duration - additional factors which might affect DNA damage.

• Journal of Animal Science and Technology
• /
• v.46 no.6
• /
• pp.917-924
• /
• 2004

Using PCR-RFLP haplotyping for the mitochondrial DNA(mtDNA) fragment containing the NADH dehydrogenase 2 gene(ND2) and three tRNA genes(tRNA-Met, tRNA-Trp and tRNA-Ala), we characterized the genetic diversity of five pig breeds including Jeju native pigs. mtDNA polymorphisms showing distinct cleavage patterns were found in the pig breeds. Two digestion patterns were detected when HaeIII- and Hinfl-RFLP, and four in the Tsp5091-RFLP analyses. Combining the three restriction enzyme digestion patterns found in five different pig breeds, four mtDNA haplotypes were observed and the haplotype frequencies were significantly different by the pig breeds. A monomorphic haplotype, mtWB, was observed in both Korean wild boars and Large White pigs. Both Duroc and Landrace pigs contained two haplotypes suggesting their multiple maternal lineages. Jeju native pig has two haplotypes(mtJN and mtJD). Of these, mtJN is identified as a Jeju native pig specific haplotype. This study suggested that more than two progenitor populations have been taken part in the domestication process of the Jeju native pig population, and/or probably subsequent crossing with other pig breeds from near east Asia. Unlike with our prediction, there was no direct evidence under molecular levels on the maternal introgression of Korean wild boar in the domestication of Jeju native pigs. In conclusion, specificity of mtDNA haplotypes related to pig breeds win be useful for identifying the maternal lineage as wen as constructing the genealogical pedigree in pigs.

• The Korean Journal of Mycology
• /
• v.27 no.2 s.89
• /
• pp.124-131
• /
• 1999

This study was carried out to identify the phylogenetic relationship among Phellinus species by comparing the DNA sequences of the 5.8S ribosomal DNA (rDNA) and the internal transcribed spacers (ITSs), ITS1 and ITS2 regions. Two primers from the 3' end of 18S rDNA and the 5' end of 28S rDNA sequences were chosen to amplify the specific ITS regions of Phellinus spp. Phellinus strains used in the study were divided into four clusters by the phylogenetic tree based on the amplified regions of ITS and 5.8S rDNA sequences. The first cluster consist of Phellinus hartigii IMSNU 32041 and Phellinus robustus IMSNU 32068, and the second cluster consists of Phellinus linteus strains and Phellinus weirianus IMSNU 32021. Phellinus laevigatus KCTC 6229, KCTC 6230 and Phellinus igniarius KCTC 6227, KCTC 6228 belong to the third cluster. Finally, Phellinus chrysoloma KCTC 6225 and Phellinus chrysoloma KCTC 6226 are the fourth cluster. In the second cluster the differentiation between Phellinus linteus strains and Phellinus weirianus species were not possible by the comparison of the ITS sequences. These results revealed that Phellinus linteus and Phellinus weirianus cannot be established the concept of species level only by the ITS sequences. Therefore, both physiological and molecular biological methods as well as the sequences of type strains are necessary to classify the strains of these two species accurately. The comparison of the ITS sequences of four Phellinus species indicated that the sequences of the ITS1 generally are more divergent than those of the ITS2. Although the ITS sequences are varied in some species, the conserved regions in both ITS1 and ITS2 are useful tool to differentiate the species. Phellinus linteus and related species have their specific sequences in the ITS1 compared to the other species.

• Journal of Animal Science and Technology
• /
• v.52 no.5
• /
• pp.367-374
• /
• 2010

Telomeres at the end of chromosomes consist of tandem repeats of (TTAGGG)n DNA sequence and associated proteins. Telomeres have the essential functions in chromosome stability and genome integrity and are hence related to cell senescence and cancer. This study was carried out to quantify the amount of telomeric DNA and establish age prediction equations by using the quantity of telomeric DNA for cattle. Analysis of the telomere quantity of the lymphocytes was performed at different age, across breeds and between different sexes of cattle. We quantified the amount of telomeric DNA by the Q-FISH technique using the telomeric DNA probe in 460 cattle at age of 1~166 months in Korean Cattle and Holstein breeds. In results, we found that the amount of telomeric DNA decreased gradually with age. The amount of telomeric DNA of Korean Cattle was significantly higher than that of Holstein breed (P<0.01). In addition, the amount of telomeric DNA in male was significantly higher than that in female (P<0.01). Using the relationship between age and the amount of telomeric DNA in cattle, age predicting equations were established as a result of regression analysis. Because sex and breeds influenced telomeric DNA quantity, the age prediction equations were estimated separately in Korean Cattle females and Holstein females. The regression equations were $\hat{Y}$=$38.102X^2$-220.103X + 318.309 (P<0.0001, $R^2$=0.8019) in Korean Cattle females and $\hat{Y}$ = $42.799X^2$ - 199.682X + 242.106 (P<0.0001, $R^2$ = 0.8379) in Holstein females, where the X was quantity of telomeric DNA and Y was predicted age in months. These equations predicted the age of cattle with high significance and accuracy and have high R square values. Thus, it could be possible to scientifically predict the age using the above equations for Korean Cattle and Holstein females.

• Microbiology and Biotechnology Letters
• /
• v.32 no.1
• /
• pp.91-95
• /
• 2004

For the detection of the oil-degrading bacterium, Nocardia sp. Hl7-1, inoculated during the bioremediation of oil-contaminated soil, a species-specific primer was constructed based on the 16S rDNA sequence of this strain. Two forward primers and two reverse primers were designed and tested against both closely and distantly related bacterial strains. All the primers designed were specific to the Nocardia sp. H17-1. Particularly, primer sets NH169F-NH972R and NH575F-NH972R could be used to detect 50 fg of template DNA and TEX>$1.2${\times}$10^4$ CFU/g of sandy soil. These two PCR primer sets successfully detected the H 17-1 strain in the oil-con-laminated soil samples containing heterogeneous DNA. We also conformed the primer specificity by restriction-enzyme cleavage of the PCR products and denaturing gradient gel electrophoresis.

• Korean Journal of Soil Science and Fertilizer
• /
• v.33 no.4
• /
• pp.266-274
• /
• 2000

Understanding of microbial community structure in soil-root system is necessary to use beneficial soil and rhizosphere microbes for improvement of crop production and biocontrol. The knowledge of behavior and function of microbes in soil-root system plays a key role for the application of beneficial inocula. Because the majority of the intact bacteria in soil are unable to grow on nutrient media, both culturable and nonculturable bacteria have to be studied together. In our study, culture-independent survey of bacterial community in the soil-root system of red pepper fields was conducted by the sequence analysis of three universal clone libraries of genes which code for small-subunit rRNA (rDNA). Universal small subunit rRNA primers were used to amplify DNA extracted from each sample and PCR products were cloned into pGEM-T. Out of 27 clones sequenced, 25 clones were from domain bacteria. Two of the rDNA sequences were derived from eukaryotic organelles. Within the domain bacteria, several kingdoms were represented : the Proteobacteria (16 clones). Cytophyga-Flexibacter-Bacteroides group (2 clones). the high G+C content gram-positive group(1 clone) and 4 unknown clones.

• Korean Journal of Ichthyology
• /
• v.25 no.3
• /
• pp.149-156
• /
• 2013

Phylogenetic relationships and DNA polymorphism among local populations of two Korean gobiidae species: Boleophthalmus pectinirostris and Scartelaos gigas were investigated based on 12S and 16S mitochondrial DNA and mitochondrial cytochrome b DNA sequences. DNA polymorphisms of B. pectinirostris between Suncheon and Gunsan populations were 100% identity from 434 bp segment of 12S rRNA gene and from 444 bp segment of mitochondrial cytochrome b genes, and 99.6% (2 bp different) identity from 484 bp segments of 16S rRNA genes. These results indicated the long period of geographic isolation between two populations of B. pectinirostris in Korea caused such high degrees of DNA polymorphisms. Based on the phylogenetic tree constructed from the two gobiid species in Korea, two genetically distinct groups of B. pectinirostris and S. gigas groups were recognized.

• Journal of Korean society of Dental Hygiene
• /
• v.6 no.4
• /
• pp.311-324
• /
• 2006

The purpose of this investigation was to evaluate of the specificity of Fusobacterium nucleatum subspecies-specific DNA probes using dot blot hybridization. To confirm whether the clinical isolates were F. nucleatum or not, 16S rDNA of them were cloned and sequenced. The sequencing data were used in homology search with database of GenBank. When the homology was above 98% compared with the nucleotide sequence of a certain bacteria, it was judged as the same species with the bacteria. 23 strains of F. nucleatum were isolates from subgingival plaque of periodontitis patient. The clinical isolates of F. nucleatum were classified into 10 groups using phylogenetic analysis of 16S rDNA sequence. F. nucleatum subspecies nucleatum-specific DNA probe Fu4(1.3 kb) reacted with genomic DNAs from 8 type strains of F. nucleatum and it reacted strongly with those from 8 clinical isolates. The Fp4(0.8 kb) reacted with F. nucleatum subsp. polymorphum ATCC 10953 and one clinical isolates. Fv35(1.9 kb) and Fs17(8.2 kb) probes reacted with genomic DNAs from F. nucleatum subsp. vincentii ATCC 49256 and F. nucleatum subsp. fusiform ATCC 51190, respectively. Our results showed that it is not enough to evaluate the specificity of F. nucleatum subspecies-specific DNA probes with only dot blot hybridization. Therefore, Southern blot analysis will be necessary to confirm the specificity of F. nucleatum subspecies-specific DNA probes.