• Parasites, Hosts and Diseases
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• v.34 no.4
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• pp.259-266
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• 1996

The taxonomic validity of morphological group III Accnthamoeba app. is uncertain. In the present study. six type strains of group III Aconthamoeba spry. , A. culbertsoni, A. heniyi, A. pustulosc, A. palestinensis, A. royrebn and A. lenticulnto were subjected for the evaluation or their taxonomic validity by comparison of the isoeneyme patterns by isoelectic focusing on polyacrylamide gels, mitochondrial DNA (Mt DNA) restriction fragment length polymorphism (RFLP) . and small subunit ribosomal DNA (ssu rDNA) PCR-RFLP patterns. The Mt DNA RFLP patterns were heterogeneous between the species. The type strains of A. pclestinensls and A. pustulosc showed almost identical patterns of isoenrymes and rDNA PCR-RFLP with an estimated sequence divergence of 2.6%. The other species showed heterogeneous patterns of isoenxymes and rDNA PCR- RFLP. It is likely that A. pustuLosc is closely related with A. palestinensis and that the former may be regarded as a junior synonym of the latter.

• Parasites, Hosts and Diseases
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• v.34 no.1
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• pp.15-20
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• 1996

Cysts of Entamoebn histoIMtica are still found from humans in Korea, but notall of the cysts are known as pathogenic. The non-pathogenic strain is regarded as a differenL species, E. nispnr. In this study, Korean isolates of conventional E. histolvticn were subjected for the differentiation by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis. Human stools were screened by routine microscopic examination, and cyst or trophozoite positive stools were inoculated into Robinson media. The cultivated trophozoites were prepared for DNA extraction, and the DNAs were used for PCR with common primers of Pl gene. The PCR products were divested with 3 restriction enzymes and RFLP was observed. Also anti-sense primers containing the cleavage site of each restriction eWe were designed for differentiation only by PCR. The PCR products of Korean isolates 59,512, YS-6, and YS-27 were spliced by Taq I and Xmnl but not byAccl, and the isolates S1, S3, S11, S15, S16, S17, S20, YS- l7, and YS-44 were spliced by Acc I but not by Taq I and Xmn I. These RFLP pattern correlated well with PCR products by the species specific primers. The findings confirm that the Korean isolates 59,512, YS-6, and YS-27 are E. histolwtico and others are E. dispar. In Korea, most of the asymptomatic cyst carriers are infected by E. dispar, not by E. histolytica. Key words: Entcmoebc histolytica, Entcmoebn dispar Korean isolates, polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP)

• Proceedings of the Microbiological Society of Korea Conference
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• 2002.10a
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• pp.15-21
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• 2002

Terminal-restriction fragment length polymorphism (T-RFLP) analysis has been optimized by using in vitro model community composed of genomic DNAs of known bacterial strains and has been applied to assess the bacterial community structure in marine sediments. The specific fluorescence-labeled terminal restriction fragments (T-RFs) between 39 and 839 base long specifying each strain were precisely measured for known bacterial strains. The addition of a co-solvent (dimethylsulfoxide or glycerol) into PCR reactions has reduced differential PCR amplification. Comparative bacterial community structure was investigated for pristine and polluted sediments. A complex T-RFLP pattern showing complex bacterial community structure was obtained in the pristine sediment, whereas simple T-RFLP pattern (low bacterial diversity) was shown in polluted sediments where caged aquaculture has been conducted for several years. The results of T-RFLP analysis were compared with that of cloning and sequencing 16S rDNA clones from the same sediments. Sequence analysis of 16S rDNA clones (72) of the pristine sediment revealed a diverse collection of lineages, largely of the class Proteobacteria ($6\%$ alpha subdivision, $46\%$ gamma subdivision, $13\%$ delta subdivision, and $3\%$ epsilon subdivision), Nitrospina $(8\%)$, high G+C gram positive $(8\%)$, Verrucomicrobia $(7\%)$, and Planctomycetes $(6\%)$. In the contaminated sediments, 17 $(59\%)$ of the 16S rDNA clones (29) were related to Campylobacter and symbiont of Rimicaris exoculata belonging to epsilon subdivision of Proteobacteria. The results obtained indicated that T-RFLP analysis is a rapid and precise technique for comparative bacterial community analysis.

• 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.

• Korean Journal of Veterinary Service
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• v.31 no.3
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• pp.369-374
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• 2008

The objective of this study was to differentiate the beef species between Hanwoo and Holstein from a total of 1,081 beef samples using PCR-RFLP of MC1R gene. When a PCR product of 403 bp specific band amplified from bovine MC1R gene sequence was digested with restriction enzyme MspA1I, Hanwoo type showed 2 bands, 220 bp and 183 bp size bands. Holstein type, however, showed three bands, 220 bp, 138 bp and 45 bp size band, respectively. The results of the differential test for beef species were as following; 7 samples (0.64%) were determined to Holstein type, of which 4 were submitted from administrative authorities, other 3 from self-collection planing, and none from civilian clients including school.

• 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.

• Korean Journal of Plant Taxonomy
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• v.34 no.1
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• pp.43-61
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• 2004

Molecular taxonomic studies were conducted to evaluate interspecific relationships in Korean Viola 34 taxa including two Japanese populations using RAPD(randornly amplified polymorphic DNA), ISSR(inter simple sequence repeat) and PCR-RFLP(restriction fragment length polymorphism) analysis. Only six and four primers out of 40 arbitrary and 12 ISSR primers were screened for 34 taxa, and were revealed 70 (98.6%) and 28 (96.6%) polymorphic bands, respectively. Fifteen restriction endonucleases produced 80 restriction sites and size variations from the large single copy region of cpDNA, 16 (20%) of which were polymorphic. The separate analyses from the RAPD, ISSR and PCR-RFLP data were incongruent in the relationships among 34 taxa, but combined data was in accordance with previous infrageneric classification system based on morphological characters, especially the subsection and series level. Section Chamaemelanium placed between subsect. Patellares and Vagimtae of section Nomimium was not formed as a distinct group. Viola alb ida complex including three very closely related taxa was recognized independent group within subsect. Patellares in combined data tree. This result strongly suggested that they should be treated to series Pinmtae. RAPD analysis was very useful to clarify the interspecific relationships among the species of Korean Viola than ISSH and PCR-RFLP analyses.

• 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.

• 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.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.10
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• pp.1487-1492
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• 2014

This research applied and evaluated a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using cytochrome b gene to detect pork contamination in meatballs from local markets in Surabaya and Yogyakarta regions, Indonesia. To confirm the effectiveness and specificity of this fragment, thirty nine DNA samples from different meatball shops were isolated and amplified, and then the PCR amplicon was digested by BseDI restriction enzyme to detect the presence of pork in meatballs. BseDI restriction enzyme was able to cleave porcine cytochrome b gene into two fragments (131 bp and 228 bp). Testing the meatballs from the local market showed that nine of twenty meatball shops in Yogyakarta region were detected to have pork contamination, but there was no pork contamination in meatball shops in Surabaya region. In conclusion, specific PCR amplification of cytochrome b gen and cleaved by BseDI restriction enzymes seems to be a powerful technique for the identification of pork presence in meatball because of its simplicity, specificity and sensitivity. Furthermore, pork contamination intended for commercial products of sausage, nugget, steak and meat burger can be checked. The procedure is also much cheaper than other methods based on PCR, immunodiffusion and other techniques that need expensive equipment.