• Korean Journal of Microbiology
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• v.39 no.3
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• pp.187-191
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• 2003

In an attempt to isolate myxobacteria from soil samples, we isolated swarm and fruiting body forming bacteria that have bacteriolytic activity on Coli-spot agar plate. For the classification of myxobacteria, 16S rDNA RFLP patterns were analyzed. Amplified 16S rDNAs of myxobacteria type strains (Family I, II, III and IV), negative control strains and soil-isolates were restricted with HaeIII, EcoRI and EcoRV, respectively. We found that the soil-isolates belongs to myxobacteria Family I, II, III.

• Journal of Environmental Science International
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• v.20 no.4
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• pp.551-554
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• 2011

The production of the sharp-toothed eel by commercial catch off waters of Korea is annually declined after 1978. This study was carried out to obtain the stock management of the sharp-toothed eel using the PCR-aided RFLP method. The mtDNA COI gene was amplified using species-specific primers and PCR product was observed to 700 bp. Amplified DNA fragments were treated with six kinds of restriction enzymes (BaeHI, EcoRI, PstI, Ksp22, HinfI and HaeIII). The treatment of HaeIII showed a distinct PCR product between Yeosu/Jinhae/Jeju/Goseoung and Jangheung/Haenam populations that were observed from 300 to 400 bp in reference to 100 bp molecular marker. However, DNA fragment within populations had an identical pattern. The phylogenetic homology is 82% between two populations inferred from RFLP PCR product pattern using NTsysPC ver. 2.1. The use of HaeIII plays an important role in discriminating populations. It is thought that adults after over-wintering in the southern part of Jeju migrate to the Yeosu, Jinhae and Goseoung regions to spawn instead of to southwestern waters. Individuals within populations showed a relatively active genetic mixing and migration regardless of geography. However, the genetic ancestor of Jangheung and Haenam populations is appeared to be more adjacent to China or Japan than Jeju.

• Journal of Life Science
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• v.15 no.6 s.73
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• pp.879-883
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• 2005

This study was differentiated between Korea and China arkshells using PCR-aided RFLP method which could identify the variation for inter-and intra-species of arkshell (Scapharca broughtonii Schrenck) at the level of DNA. The DNA fragment patterns were compared after digesting gene of mitochondrial 16S rDNA with 8 kinds of restriction enzymes. A 720 bp DNA fragment corresponding to 16S rDNA gene was amplified by PCR with primers ArkF-3 and ArkR-3. PCR products were cut by restriction enzymes (Pvull, BamHI, Hinfl, HaeIII, EcoRI, RsaI, Ksp221, and BstX21), and RFLP pattern was studied. A unique 275 bp DNA band was observed in the samples from Dukyang, Gamak, Namhae, Jinhae, and Taean in Korea when treated by Hinfl, but Chinese arkshell did not show. Treatment of HaeIII could discriminate the sample of Namhae and Jinhae from Dukyang/Gamak/Taean, as well as Korean and Chinese arkshell based on a 700 bp. However, PuvII, BamHI, EcoRI, RsaI, Ksp221, and BstX21 showed the same of 700 bp band in Korean and Chinese arkshell. The phylogenetic tree inferred from PCR-RFLP pattern comparsion in Korean arkshell was different that the distance between Dukyang/Gamak/Taean and Namhae/Jinhae was approximately 7. In particular, the distance between Korean and Chinese arkshell was 25. Consequently, HinfI and HaeIII played an important role in a reliable molecular tool for rapid discriminating Korean and Chinese arkshell, as well as a intra-species in Korea.

• Journal of Pharmacopuncture
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• v.12 no.1
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• pp.13-20
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• 2009

Objective : This study developed species-specific PCR and PCR-RFLP to detect the adulteration of Fel ursi products with cattle and pig bile juices. Methods : All the primers for PCR and PCR-RFLP in this study were designed based on nucleotide sequences of cytochrome b genes in the mitochondria. Results : The species-specific PCR amplified a DNA fragment of 214, 214, 295, and 167 bp from Fel ursi product, bear fur, cattle bile juice, and pig bile juice, respectively. The survey using the speciesspecific PCR indicated that some of commercial Fel ursi products were adulterated with cattle and pig bile juices. PCR-RFLP using the restriction endonucleases, HaeIII and HinfI enabled differentiation among Fel ursi product, cattle bile juice, and pig bile juice. Bear furs from two animals showed variations in PCR-RFLP patterns with HaeIII. Discussion : The detection methods of the species-specific PCR and PCR-RFLP could be useful in eliminating adulterated Fel ursi products from the market.

• Journal of Ginseng Research
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• v.27 no.3
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• pp.146-150
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• 2003

This study was carried out to obtain basic information on breeding using PCR-aided RFLP technology which can identify the variation inter- and intra-species of ginseng in the level of DNA. It was intended to investigate banding pattern on psbA and rbeL genes of chloroplast DNA in ginseng after treating with restriction enzymes. To isolate psbA and rbcL genes of chloroplast, both psbA-N, psbA-C primer and rbcL-N, PX-1 primer were used. As a result, 1,008 bp band of psbA gene and 1,336 bp band of rbcL gene were appeared, which was optimal and expected molecular weight. In addition, primers to isolate atpB, rpoB, trnL, and trnF genes were used, resulting in the expected 1366, 900, 1500 and 1008 bp bands. Genes of psbA and rbcL isolated by PCR were cut by restriction enzymes, Sau3A, TaqI, AluI, HaeIII, and RFLP pattern was investigated. KG line and other species of ginseng were cut by TaqI treatment, and bands were located in 800 bp. The treatment treated by AluI also showed the same 800 bp band in KG line and other species. In HaeIII treatment, 500 bp of faint bands were shown in case of KG line, whereas any bands were not observed in other species. All chloroplast genes formed bands by PCR amplification. However, it was not evident to distinguish intra-or inter-species of ginseng after restriction enzyme treatment. Therefore, more restriction enzyme treatment or sequence comparison method should be considered for further experiment.

• Korean Journal of Microbiology
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• v.36 no.4
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• pp.249-253
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• 2000

The genetic diversity among Korean cyanobacteria was assessed by restriction fragment length polymorphism(RFLP) analysis of PCR products from the phycocyanin locus. Strains of all the genera tested were successfully amplified, and the size of amplified fragments was approximately 700bp. The restriction patterns generated by AluI, MspI, and HaeIII were conserved for strains within each of genera studied and were specific to the genus level. Intrageneric delineation of strains was revealed by the enzyme, CfoI for members of genera Anabeana and Synechocystis. Phenogram derived from the different RFLP patterns revealed a coherent cluster among Anabeana, Chlorogloea, and Synechocystis strains. PC-RFLP methods provided useful tools for classification of cyanobacteria.

• Journal of fish pathology
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• v.37 no.1
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• pp.147-153
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• 2024

The World Organization for Animal Health (WOAH) recommends two protocols (ITS and COI) for conventional PCR of G. salaris diagnosis. However, ITS PCR protocol may yield false-positive results, leading to unnecessary countermeasures. It's difficult to distinguish between G. salaris and false-positive by similar amplicon size of PCR, since the amplicon size of ITS PCR in G. salaris and false-positive was 1,300 and 1,187 bp, respectively. The nucleotide sequences of ITS false-positive in rainbow trout is 99.7% identical to previously reported host genome sequences of rainbow trout (Oncorhynchus mykiss) and 95.3 to 89.1% identical to those of other salmonid fish species. To reduce false-positive PCR band, PCR was performed by the different annealing temperature, but PCR bands were still detected. In RFLP analysis by HaeIII, the PCR product of G. salaris was digested into four bands of 512, 399, 234 and 154 bp, while the false-positive was digested into seven bands of 297, 263, 242, 144, 93, 80 and 68 bp. In the RFLP patterns digested by HindIII, G. salaris showed two bands of 659 and 640 bp, while false-positive had one fragment of 1,187 bp without any digestion. Therefore, the RFLP method of ITS PCR with HaeIII and HindIII can be used for differentiation between G. salaris and false-positive. These results might provide important information on the improvement of PCR diagnostic method of G. salaris.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.9
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• pp.1226-1230
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• 2005

The present investigation was undertaken to study the genetic polymorphism of the DRB3 exon 2 in 75 crossbred cattle by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. Five genotypes i.e. HaeIII-a, HaeIII-b, HaeIII-e, HaeIII-ab and HaeIII-ae were observed when the 284 bp PCR products were digested with HaeIII restriction enzyme. The corresponding frequencies of these patterns were 0.53, 0.04, 0.01, 0.38 and 0.04, respectively. Digestion with RsaI restriction enzyme resolved 24 different restriction patterns. The frequencies of these patterns ranged from 0.013 (RsaI-f, RsaI-k and RsaI-c/n) to 0.120 (RsaI-n). The results revealed that the crossbred cows belonged to the RsaI patterns namely b, k, l, a/l, d/s, l/n, l/o and m/n, whose corresponding frequencies were 0.027, 0.013, 0.040, 0.027, 0.040, 0.067, 0.027 and 0.067, respectively. Digestion of the 284 bp PCR product of DRB3.2 gene with PstI in the crossbred cattle did not reveal any restriction site. These results suggested the absence of the recognition site in some of the animals. These results also revealed that the crossbred cows studied were in homozygous as well as heterozygous condition. On the basis of the above results it can be concluded that the DRB3.2 gene was found to be highly polymorphic in the crossbred cattle population.

• Korean Journal of Microbiology
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• v.35 no.3
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• pp.173-179
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• 1999

As a result of PCR-RFLP, the isolates used in this study were classified into five groups. Isolates 1 and 3 were included in AG-5 with 97% genetic similarity. Isolates 12 and 13 were included in AG-1 wilh 100% genetic similarily. Isolates 10 and AG-2-2 showed 97% similarity Isolates 7, 8, 11. 13, and 15 were included in AG-1. When isolates of 4, 5, 7 and 8 were restricted with Hae I. there was a single 700 bp fragment matched with AG-1. A 517 bp restriction fragment of isolate 9 was matched with AG-2-1. Based on the result of southem hybridization of genomic DNAs, all isolates restricted with Msp I showed more variable restriction differences than those restricted with Hae Ill. Isolates AG-2-1 and 9 showed 200 bp restriction fragment, and isolates 3 and AG-1 showed 1 kb restriction fragments.

• Journal of Life Science
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• v.22 no.2
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• pp.245-250
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• 2012

The 16S rDNA - RFLP types for six Vibrio species (V. fluvialis, V. proteolyticus, V. vulnificus, V. mimicus) including two core group members, V. alginolyticus and V. parahaemolyticu s, and Grimontia (Vibrio) hollisae were determined using PCR-RFLP analysis. Six tetrameric restriction enzymes (Alu I, Cfo I, Dde I, Hae III, Msp I, and Rsa I) were selected for RFLP analysis. V. alginolyticus, V. parahaemolyticus, and V. proteolyticus showed the same RFLP pattern following digestion with four of the six used restriction enzymes: CfoI, DdeI, MspI, and RsaI. Various restriction enzyme combinations generated digests recognizable as distinct RFLP types for each of the assayed Vibrio species. In particular, AluI single digestion produced species specific band patterns that enabled the differentiation between these Vibrio species. Dendrogram based on restriction patterns showed that two Vibrio core group members, V. alginolyticus and V. parahaemolyticus were closely related having a similarity over 90%. Although the observed RFLP pattern for Grimontia hollisae shared several common bands with other Vibrio spp., G. hollisae results were still clearly distinct from Vibrio spp. RFLP types for all restriction enzymes tested. If restriction enzymes are aptly selected, PCR-RFLP analysis is still a rapid and effective tool for differentiating Vibrio species.