• Fisheries and Aquatic Sciences
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• v.11 no.1
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• pp.32-35
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• 2008

The Suminoe oyster, Crassostrea ariakensis, occurs in estuaries where rivers meet seawater. In Korea, it is one of the most popular fisheries resources in the Nam River and Sumjin River. However, the genetic identification of this species has been questioned, because specimens are often mis-identified as other species. To identify the species, we conducted polymerase chain reaction (PCR) amplification of the internal transcribed spacer-1 (ITS-1) region, followed by digestion with the restriction enzyme HaeIII. Restriction profiles for oysters collected from Korea, Japan, and China (north and south) were determined by comparing the PCR-restriction fragment length polymorphism (RFLP) patterns of the ITS-1 regions. Our study verified that the oysters collected from Korea were C. ariakensis based on the PCR-RFLP patterns. These results emphasize the value of molecular markers for identifying morphologically uncertain species.

• Korean Journal Plant Pathology
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• v.14 no.2
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• pp.157-163
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• 1998

Genetic diversity among 27 isolates of Rhizoctonia solani, which were obtained from diseased crops in Korea and classified into 9 intraspecific groups by anastomosis test and cultural characteristics, was studied by PCR-RFLP. Gene regions of nuclear 17S ribosomal DNA and internal transcribed spacers including 5.8S rDNA of the isolates were amplified with polymerase chain reaction and digested with 12 restriction enzymes. Differences of restriction patterns were not shown among isolates within each intraspecific groups, however, each anastomosis group and culturala type sowed unique restriction fragment length polymorphisms by restriction patterns using HaeIII, Cfr13I and MspI. The results suggest that PCR-FRLP of rDNA using three restriction enzymes could be used to differentiate intraspecific groups of Rhizoctonia solani in Korea.

• 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.

• The Plant Pathology Journal
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• v.15 no.4
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• pp.228-235
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• 1999

Genetic diversity of ninety-five Korean isolates of Phytophthora was investigated on the basis of PCR-RFLP of ribosomal DNA. The isolates were previously identified as following fifteen species by mycological and cultural characteristics; P. boehmeriae, P. cactorum, P. cambivora, P. capsici, P. cinnamoni, P. citricola, P. citrophthora, P. cryptogea, P. drechsleri, P. erythroseptica, P. infestans, P. megasperma, P. nicotianae, P. palmivora and P. sojae. The regions of small subunit (SSU) and internal transcribed spacer (ITS) of rDNA were amplified with primer pair, NS1 and ITS4, by polymerase chain reaction (PCR) and digested with nine restriction enzymes. P. boehmeriae, P. cactorum, P. cambivora, P. capsici, P. cinnamomi, P. citricola, P. citrphthora, P. infestans, P. nicotianae and P. palmivora showed specific band patterns for each species. However, P. sojae and P. erythroseptica presented identical band patterns and P. cryptogea, P. drechsleri and P. megasperma were divided into six groups, which were not compatible with delineation of the species. A group originated from cucurbits showed distinct band patterns from other groups, but the other five groups were closely related within 96.0% similarity, forming one complex group. Consequently, Korean isolates of Phytophthora were divided into thirteen genetic groups and each group was readily differentiated by comparing digestion patterns of AvaII, HaeIII, MboI, HhaI and MspI. Therefore, PCR-RFLP of rDNA using the five enzymes can be used to differentiate or identify the Phytophthora species reported in Korea so far.

• Parasites, Hosts and Diseases
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• v.39 no.2
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• pp.161-170
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• 2001

We conducted both the small subunit ribosomal DNA (SSU rDNA) polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and mitochondrial (mt) DNA RFLP analyses for a genetic characterization of Acanthamoeba isolates from contact lens storage cases of students in Seoul, Korea. Twenty-three strains of Acanthamoeba from the American Type Culture Collection and twelve clinical isolates from Korean patients were used as reference strains. Thirty-nine isolates from contact lens storage cases were classified into seven types (KA/LS1 , KA/LS2, KA/LS4, KA/LS5, KA/LS7 KA/LS18, KA/LS31). Four types (KA/LS1 , KA/LS2, KA/LS5, KA/LS18) including 33 isolates were regarded as A. castellanii complex by riboprints. KA/LS1 type was the most predominant (51.3%) in the present survey area, followed by KA/LS2 (20.9%), and KA/LSS (7.7%) types. Amoebae of KA/LS1 type had the same mtDNA RFLP and riboprint patterns as KA/E2 and KA/E12 strains, clinical isolates from Korean keratitis patients. Amoebae of KA/LS2 type had the identical mtDNA RFLP patterns with A. castellanii Ma strain, a corneal isolate from an American patient as amoebae of KA/LS5 type, with KA/E3 and KA/E8 strains from other Korean keratitis patients. Amoebae of KA/LS 18 type had identical patterns with JAC/E1, an ocular isolate from a Japanese patient. Three types , which remain unidentified at species level, were not corresponded with any clinical isolate in their mtDNA RFLP and riboprint patterns. Out of 39 isolates analyzed in this study, mtDNA RFLP and riboprint patterns of 33 isolates (84.6%) were identical to already known clinical isolates, and therefore, they may be regarded as potentially keratopathogenic. These results suggest that contact lens wearers in Seoul should pay more attention to hygienic maintenance of contact lens storage cases for the prevention of Acanthamoeba keratitis.

• 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.

• Mycobiology
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• v.30 no.1
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• pp.1-4
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• 2002

Genetic relatedness of medically important Exophiala species such as E. dermatitidis, E. mansonii, and three E. jeanselmei varieties: jeanselmei, lecanii-corni, and heteromorpha was examined using PCR-RFLP(restriction fragment length polymorphism) of ribosomal DNA, M-13, $(GTG)_5$ and nucleotide sequences of ribosomal ITS(internal transcribed space) II regions. Three E. jeanselmei varieties showing distinct band patterns for each DNA markers as well as different nucleotide sequences of ribosomal ITS II regions could be considered as a separate species. E. dermatitidis and E. mansonii demonstrated the identical band patterns of RFLP of ribosomal DNA, M-13, and $(GTG)_5$ markers. However, nucleotides sequences of ribosomal ITS II region were different between these two species.

• 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.

• Korean Journal of Agricultural Science
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• v.38 no.2
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• pp.249-255
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• 2011

This study was performed to investigate the characterization of infectious BLV env gene isolated form Korean Holstein Cattle and to determine its incoming origin. Gp51 region of BLV env gene known as having important role in immunological function was characterized using PCR-RFLP sequencing and phylogenetic analysis. BLV env gene was grouped into PCR-RFLP patterns with three restriction endonucleases including Pvu II, BamHI and Hae III, and we identified two new RFLP patterns from nucleotide sequences of each group. Phylogenetic analysis showed that 80% of the Korean Holstein was included in the USA and Japanese group. These results here can provide a valuable information about the character of the BLV env gene and research on infection route of BLV.

• Fisheries and Aquatic Sciences
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• v.7 no.3
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• pp.130-135
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• 2004

The marine dinoflagellate genus Alexandrium, which produces PSP toxins, has a global distribution. As human-assisted dispersal of the species has been suggested, it is important to develop molecular tools to trace the dispersal pathway. To screen population-specific DNA sequences that differentiate Korean and Japanese A. catenella, we targeted the area downstream of the chloroplast psbA gene using PCR with population-specific DNA primers followed by RFLP (restriction fragment length polymorphism) analysis and sequencing. The RFLP patterns of the PCR products divided Korean and Japanese A. catenella regional isolates into three types: Korean, Japanese, and type CMC3, isolated from Korea. We sequenced the PCR products, but found no similar gene in a homology search. The molecular phylogeny inferred from the sequences separated the Korean and Japanese A. catenella strains, as did the RFLP patterns. However, the Japanese isolates included two slightly different sequences (types J and K), while the Korean sequence was the same as the Japanese K type. In addition, a unique sequence was found in the Korean strains CMC2 and CMC3. Population-specific PCR amplification with Japanese A. catenella type-specific PCR primers designed from the type J sequence yielded PCR products for Japanese strains only, showing that the unknown gene can be used for a population analysis of Korean and Japanese A. catenella.