• Korean Journal of Fisheries and Aquatic Sciences
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• v.27 no.5
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• pp.613-619
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• 1994

To investigate the population differences of small yellow croaker (Pseudosciaena polyactis BLEEKER) in the Yellow Sea, five catching sites (three from China; Zoushan, Shanghai and Qingdao, two from Korea; Inchon and Mokpo) were selected for sampling. The populations of small yellow croaker from all five catching sites were investigated to analyze their mtDNA's restriction fragment length polymorphism (RFLP) using 18 kinds of restriction enzymes. The average molecular size of the entire mtDNA was estimated at $16.9{\pm}0.6\;kb$. According to the results of RFLP analysis, a total of 40 restriction sites were identified in every population surveyed and the overall cleavage patterns of mtDNA, based on the RFLP, showed similar tendencies. However, the five restriction enzymes such as ApaI, EcoRI, PstI, SmaI and SstII showed slightly different cleavage patterns which could have resulted from individual variations between the populations of Korea and China.

• Restorative Dentistry and Endodontics
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• v.20 no.2
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• pp.577-609
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• 1995

Bacteria have been regarded as one of the most important factors in pulpal and periapical diseases. Streptococci are frequently isolated facultative anaerobes in infected root canals. Recently molecular biological techniques have been rapidly progressed. This study was designed to apply the molecular biological tools to the identification and classification of streptococci in the endodontic microbiology. Streptococci isolated from infected root canals were identified with both Vitek Systems and API 20 STREP. Identification results were somewhat different in several strains of streptococci. Eighteen streptococci and enterococcal was difficult so to digest plasmid DNA using Hind III and EcoRI to differentiate strains by restriction enzyme analysis of plasmid DNA. 16S rDNA of chromosome was amplified by polymerase chain reaction(PCR) and then restricition fragment length polymorphism(RFLP) using several restriction enzymes was observed. The molecular mass of 16S rDNA of chromosomal DNA was approximately 1.4kb. There were three to five RFLP patterns using eight restriction enzymes. RFLP patterns digested with CfoI which recognizes four base sequences were identical in all stains. Hind III which recognizes six base sequences could not digest the 16S rDNA. Restriction enzymes which recognize five base sequences were suitable for RFLP pattern analysis. At least three different restriction enzymes were needed to compare each strains. 16S rDNA PCR-RFLP was simple and rapid to differentiate and classify strains and could be used in the epidemiological study of root canal infections.

• Journal of Life Science
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• v.26 no.7
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• pp.819-825
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• 2016

The present study was done to assess the diversity of the bacterial community associated with Ulva pertusa collected from Jeju Island using Restriction Fragment Length Polymorphism (RFLP) marker analysis. For RFLP analysis, a total of 145 bacterial strains associated with Ulva pertusa were screened and cultivated using Marine agar and R2A agar. The PCR amplicons of the 16S rRNA gene from all the isolated strains were digested with HaeIII and RsaI restriction enzymes and then classified into different groups according to their restriction patterns. Strains selected based on the RFLP patterns showed more than 91% 16S rRNA gene sequence similarity when compared with known bacterial species, which include 4 phyla - proteobacteria (alpha-proteobacteria, beta-proteobacteria, gamma-proteobacteria - 63%), firmicutes (11%), actinobacteria (4%), bacteroidetes (22%)–as well as 7 classes (actinobacteria, flavobacteriia, cytophagia, bacilli, α-proteobacteria, γ-proteobacteria, β-proteobacteria), 13 orders, 18 families, and 27 genera. These results confirmed a wide diversity of bacterial communities as contrasted with other regions. The newly isolated 10 strains, which show 16S rRNA sequence similarity of <97% compared to previously identified bacteria, could be noble species. Further experiments, such as morphological, physiological, and biochemical classification, are necessary to confirm the novelty of the newly isolated 10 strains.

• Journal of Microbiology
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• v.38 no.2
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• pp.66-73
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• 2000

To investigate the genetic relationship among 12 species belonging to the Fusarium section Martiella, Dlaminia, Gibbosum, Arthrosporiella, Liseola and Elegans, the internal transcribed spacer(ITS) regions of ribosomal DNA (rDNA) were amplified with primer pITS1 and pITS4 using the polymerase chain reaction(PCR). After the amplified products were digested with 7 restriction enzymes, restriction fragment length polymorphism (RFLP) patterns were analyzed. The partial nucleotide sequences of the ITS region were determined and compared. Little variation was observed in the size of the amplified product having sizes of 550bp or 570bp. Based on the RFLP analysis, the 12 species studied were divided into 5 RFLP types. In particular, strains belonging to the section Martiella were separated into three RFLP types. Interestingly, the RFLP type of F. solani f. sp. piperis was identical with that of isolates belonging to the section Elegans. In the dendrogram derived from RFLP analysis of the ITS region, the Fusarium spp. examined were divided into two major groups. In general, section Martiella excluding F. solani f. sp. piperis showed relatively low similarity with the other section. The dendrogram based on the sequencing analysis of the ITS2 region also gave the same results as that of the RFLP analysis. As expected, 5.8S, a coding region, was highly conserved, whereas the ITS2 region was more variable and informative. The difference in the ITS2 region between the length of F. solani and its formae speciales excluding F. solani f. sp. piperis and that of other species was caused by the insertion/deletion of nucleotides in positions 143-148 and 179-192.

• Research in Plant Disease
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• v.17 no.1
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• pp.99-101
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• 2011

The ascomycetous fungus Taphrina wiesneri, the pathogen of cherry witches' broom, is highly pathogenic to Prunus yedoensis, the most widely planted cherry trees in Korea as park and roadside trees. A collection of 13 strains of the pathogen in Korea and Japan was characterized by 18S rDNA gene sequence and restriction fragment length polymorphism (RFLP) analysis. In cluster analysis based on 18S rDNA gene sequence the strains were divided into 2 clusters. In RFLP analysis of the rDNA-IGS region using HhaI, the strains were separated into four patterns, B, C, D and G, of which pattern G was new.

• Food Science of Animal Resources
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• v.26 no.3
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• pp.375-379
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• 2006

Food labeling regulations require that the meat species in various meat products are accurately declared to the consumer. Substitution or adulteration of costly meat with a cheaper one is one of the most common problems in the meat industry. In this study, PCR-restriction fragment length polymorphism(RFLP) method of the mitochondrial cytochrome b(mt cyt b) gene has been applied for identification of the origin of six mammalian meat species(beef, port horse, goat, mutton and deer) and three poultry meat species(chicken, turkey and duck) as raw materials for meat products. PCR was used to amplify a variable region of mt cyt b gene. Meat species differentiation was determined by digestion of the amplified products with a 359 bp fragment using HaeIII and HinfI restriction enzymes, which generated species-specific RFLP patterns. This PCR-RFLP DNA marker of mt cyt b gene could be very useful for the accurate and reliable identification and discrimination of animal meat species in routine analysis.

• Parasites, Hosts and Diseases
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• v.46 no.2
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• pp.105-108
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• 2008

Although the Korean isolate KI-1 of Toxoplasma gondii has been considered to be a virulent type I lineage because of its virulent clinical manifestations, its genotype is unclear. In the present study, genotyping of the KI-1 was performed by multilocus PCR-RFLP and microsatellite sequencing. For 9 genetic markers (c22-8, c29-2, L358, PK1, SAG2, SAG3, GRA6, BTUB, and Apico), the KI-1 and RH strains exhibited typical PCR-RFLP patterns identical to the type I strains. DNA sequencing of tandem repeats in 5 microsatellite markers (B17, B18, TUB2, W35, and TgM-A) of the KI-1 also revealed patterns characteristic of the type I. These results provide strong genetic evidence that KI-1 is a type I lineage of T. gondii.

• Journal of Periodontal and Implant Science
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• v.25 no.3
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• pp.679-693
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• 1995

The present study has been performed to see the intrafamilial transmission of periodontopathic organism Actinobacillus actinomycetemcomitans in Koreans having various froms of periodontal diseases. 17 clinical isolates from 8 periodontal patients and 20m clinical isolates from their 8 family members were grown anaerobically for the serotyping and the extraction of genomic DNA. The DNA was digested with restriction endonucleases (EcoRI+HindIII) and plasmid pAA 2097(kindly provided by Dr. DiRienzo, Univ. of Pennsylvania) including 4.7kb-size randlomly clone probe for restriction length pleomorphism analysis(RFLP). RFLP patterns of reference serotypes a, b, c, d, and e were used as the genotypes A, B, C, D, and E, respectively for comparison of genotypes of clinical isolates. 28 out of total 37 clinical isoltes belonged to either one of 5 basic gentotypes and 9 remaining isolats did not fall into any types, and hence were designate as non-type(NT). Genotype C were the most frequently found one(35.1%) and genotype B has not isolated. Intrafamilial transmission of bacteria between spouses, brothers and sisters, and parents and their offsprings, resepctively could well be demonstrated by comparing RFLP patterns. There were not any specific genotypes which showed predominance over others in terms of transmission.

• Korean Journal of Plant Resources
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• v.21 no.1
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• pp.41-46
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• 2008

Molecular relationship and genetic diversity of 21 wild tea collections which grown natural region in Korea were investigated based on PCR-RFLP analysis using DFR genes. Approximately 1.4kb fragment of the DFR gene from wild tea samples were successfully amplified use DFR 4+5 primer pair. On the bases of restriction fragment length polymorphism(RFLP) analysis using Hpa II and Mse I enzymes, three different band patterns shown from Hpa II enzyme and showed genetic diversity between same region wild tea group. Six kind of restriction enzyme profiles obtained from digested with restriction endonuclease Mse I and shown two kind of restriction enzyme profiles collected from same region wild tea at Ungpo. The results of RFLP analysis indicated that wild tea showed genetic diversity among different regions of tea groups, but also between same region wild tea.

• Journal of Microbiology and Biotechnology
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• v.22 no.6
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• pp.729-735
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• 2012

The PCR-RFLP method has been useful for detection of known genes and identification of novel genes. In the present study, degenerate primers were designed from five groups of cry1 genes for PCR-RFLP analysis. Bacillus thuringiensis (Bt) isolates from different regions were evaluated for PCR amplification of various cry1 genes using newly designed primers and cry2 genes using reported primers. PCR analysis showed an abundance of cry1A genes and especially cry1Ac genes in isolates from all regions. RFLP analysis revealed the presence of multiple cry1A genes in isolates from central and southern regions. Unique digestion patterns of cry1A genes were observed in isolates from each region. Few of the isolates represented a digestion pattern of cry1A genes that did match to any of the known cry1A genes. RFLP analysis suggested an abundance of cry2Ab along with a novel cry2 gene in Bt isolates from different regions of India. Sequence analysis of the novel cry2 gene revealed 95% sequence identity to cry2Ab and cry2Ah genes. Phylogenetic analysis revealed that the novel cry2 gene could have diverged earlier than the other cry2 genes. Our results encourage finding of more diverse cry2 genes in Bt isolates. Rarefaction analysis was used to compare cry1A gene diversity in isolates from different soil types. It showed a higher degree of cry1A gene diversity in isolates from central region. In the present study, we propose the use of novel degenerate primers for cry1 genes and the PCR-RFLP method using a single enzyme to distinguish multiple cry1A and cry2 genes as well as identify novel genes.