• Mycobiology
• /
• v.31 no.1
• /
• pp.19-22
• /
• 2003

The primary objective of the current research was to detect genetic variations within the Indonesian isolates of Cochliobolus heterostrophus collected from ecologically different places of the country at molecular level using PCR-RFLP analyses. The primer pair of NS3 and NS6 produced amplification fragment in all of the isolates tested. A single fragment of estimated 907 bp was observed in the PCR product pattern. RFLP analysis of the PCR product employing three restriction enzymes, HaeIII, HhaI, and RsaI, respectively, did not reveal intraspecific variations within the fungus. Similarly, nucleotide sequences of portion of small subunit of the ribosomal DNA gene of two of the isolates collected showed no appreciable differences, indicating the absence of genetic diversities among the isolates tested. A phylogenetic tree was constructed and the Indonesian C. heterostrophus, represented by SM-1 isolate, was found to be phylogenetically located near C. sativus, a closely related species.

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

• The Plant Pathology Journal
• /
• v.24 no.2
• /
• pp.159-163
• /
• 2008

Accurate identification of pine wood nematode, Bursaphelenchus xylophilus is a prerequisite to diagnose the pine wilt disease. However, a fungivorous nematode, B. mucronatus is highly similar to B. xylophilus and it is difficult to differentiate these two species by morphological features. A molecular diagnosis method, ITSRFLP was applied for the identification of B. xylophilus and B. mucronatus from Korea. Genomic DNA was extracted from a single individual nematode and ITS DNA was amplified by PCR. The size of PCR product was approximately 900bp and the sequence data were obtained after cloning. Amplified ITS was digested by 5 different restriction enzymes (Rsa I, Hae III, Msp I, Hinf I, and Alu I) and provided a discriminatory profile for B. xylophilus and B. mucronatus. Besides, B. mucro- natus was determined to have 2 different genotypes, East Asian type and European type also clearly separated by Rsa I and Hae III digestion. European type of B. mucronatus is recently collected from Pinus koraiensis and has not been reported before. ITS sequnce data were analyzed by Restriction Mapper program and the result supported ITS-RFLP pattern. These data indicated that PCRRFLP method is an accurate and simple way for identification of Bursaphelenchus species.

• Journal of Microbiology and Biotechnology
• /
• v.15 no.6
• /
• pp.1170-1177
• /
• 2005

Terminal-restriction fragment length polymorphism (T-RFLP) analysis was used to monitor inoculated oil-degrading microorganisms during bioremedial treatability tests. A pair of universal primers, fluorescently labeled 521F and 1392R, was employed to amplify small subunit rDNA in order to simultaneously detect two bacterial strains, Corynebacterium sp. IC10 and Sphingomonas sp. KH3-2, and a yeast strain, Yarrowia lipolytica 180. Digestion of the 5'-end fluorescence/labeled PCR products with HhaI produced specific terminal-restriction fragments (T-RFs) of 185 and 442 bases, corresponding to Corynebacterium sp. IC10 and Y. lipolytica 180, respectively. The enzyme NruI produced a specific T-RF of 338 bases for Sphingomonas sp. KH3-2. The detection limit for oildegrading microorganisms that were inoculated into natural environments was determined to be $0.01\%$ of the total microbial count, regardless of the background environment. When three oil-degrading microorganisms were released into oil-contaminated sand microenvironments, strains IC10 and 180 survived for 35 days after inoculation, whereas strain KH3-2 was detected at 8 days, but not at 35 days. This result implies that T-RFLP could be a useful tool for monitoring the survival and relative abundance of specific microbial strains inoculated into contaminated environments.

• Asian-Australasian Journal of Animal Sciences
• /
• v.18 no.10
• /
• pp.1368-1374
• /
• 2005

To investigate the genetic relationships among various cattle breeds, bovine mtDNA D-loop region was used in 411 animals of 18 cattle breeds, including 8 Asian Bos taurus, 7 European Bos taurus, 1 Asian Bos indicus, and 2 African Bos indicus. The size of amplified PCR products from mtDNA D-loop region was 964 bp and the products were digested by 15 different restriction enzymes. Two different band patterns were identified in eight restriction enzymes (BstXI, Hae III, Msp I, Apa I, Taq I, Alu I, BamH I, EcoN I) and the rest of restriction enzymes showed more than 3 different band patterns among which Apo I and MspR9 resulted in 7 different restriction patterns. The genotypes, number of haplotype, effective number of haplotype, and degree of heterozygosity were analyzed. Based on all the PCR-RFLP data, different haplotypes were constructed and analyzed for calculating genetic distances between these breeds using Nei's unbiased method and constructing a phylogenetic tree.

• Asian-Australasian Journal of Animal Sciences
• /
• v.20 no.6
• /
• pp.817-820
• /
• 2007

The effects of diacylglycerol O-acyltransferase (DGAT1) candidate gene polymorphism on the economic traits of Hanwoo were studied. Through sequencing analysis, two polymorphism sites at K232A and T11993C were established and were analyzed by PCR-RFLP. The PCR-RFLP analysis for K232A showed that the frequencies of alleles K and A were 0.75 and 0.25, respectively, and the frequencies of genotypes for K/K, K/A and A/A were estimated as 0.509, 0.491 and 0, respectively. In the PCR-RFLP analysis for T11993C, we found allele frequencies of 0.773 and 0.227 for T and A, respectively, and 0.546, 0.454 and 0 for the T/T, T/C and C/C genotype frequencies, respectively. No significant effects on economic traits in Hanwoo were found in the separate analysis of K232A and T11993C polymorphisms, but the interaction between K232A and T11993C showed a significant effect (p<0.005) on marbling score. The DGAT1 candidate gene was found to have a significant effect not only on milk yield and component traits but also on the metabolism of intramuscular fat.

• Korean Journal of Veterinary Research
• /
• v.43 no.1
• /
• pp.95-102
• /
• 2003

Because Staphylococcus aureus (S. aureus) has variable number of short sequence repeat region in coagulase gene, it has been used to investigate the relatedness of S. aureus isolates. In this study, we isolated S. aureus strains from 20 dairy farms with bovine mastitis from September 2000 to August 2001. PCR-RFLP analysis of coagulase gene revealed 10 different patterns. Most of the S. aureus isolates showed only one coagulase gene RFLP pattern per farm. However, there were several S. aureus clones spreading between dairy farms. All the farms showed poor management conditions of milking machine and milker, indicating that managements for mastitis control program include use of proper milking matching, premilking sanitation, and segregation in the S. aureus infection herd. Our data suggest that PCR-RFLP analysis of coagulase gene might be applicable for the epidemiological investigations of S. aureus isolated from bovine mastitis cows.

• Journal of Ecology and Environment
• /
• v.29 no.2
• /
• pp.143-149
• /
• 2006

This study was conducted to identify native ectomycorrhizal (ECM) fungi colonizing Pinus densiflora for revegetation of abandoned coal mines in Korea. Seedlings of P. densiflora growing on coal mining spoils of a study site in Samcheok were collected. ECM roots were observed under stereomicroscope and their DNA were extracted from each root tip for a seedling for molecular identification. A PCR primer pair specific to fungi, ITS1F and ITS4, was used to amplify fungal DNA. Restriction enzymes, Alul and Hinfl were used for restriction fragment length polymorphism (RFLP). Combined with RFLP profiles and sequence analysis, total twenty one taxa were identified from the ECM root tips. Basidiomycetous fungi including Thelephoraceae, Pezizales, Laccaria, Pisolithus and Ascomycetous fungi including ericoid mycorrhizal fungi were identified from this study. Results showed that the most frequently found in the study sites was a species in Thelephoraceae. A possible use of ECM fungi identified in this study for the revegetation of abandoned coal mines with P. densiflora was discussed.

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

• Proceedings of the Korean Society for Food Science of Animal Resources Conference
• /
• 2004.10a
• /
• pp.132-136
• /
• 2004

본 연구는 근육 및 지방세포 분화에 관여하는 leptin, MYF5 및 H-FABP의 3개 기능성 후보 유전자가 한우의 도체특성 및 육질에 미치는 영향을 분석하기 위하여 이들 유전자의 PCR-RFLP marker와 도체형질과의 관련성을 분석하였다. Leptin, MYF5 및 H-FABP 유전자에서 AA, AB 및 BB 3종류의 RFLP 유전자형이 각각 검출되었고 A와 B 대립유전자 빈도는 각각 0.57과 0.43, 0.61과 0.39 그리고 0.90과 0.10으로 추정되었다. 육질 등급에 따라 고급육과 저급육으로 분리 선발한 두 그룹간의 대립유전자 출현빈도를 비교한 결과 leptin과 MYF5 유전자에서 각각 통계적 유의차(P< .05)가 인정되었다. 또한 각 후보유전자의 RFLP marker 유전자형이 도체형질에 미치는 효과를 분석한 결과 leptin 유전자는 등지방 두께 그리고 MYF5유전자는 배장근 단면적에 각각 유의적인 영향(P< .05)을 미치는 것으로 분석되었다. 그러나 H-FABP 유전자는 도체형질들과 유의성이 인정되지 않았다. 따라서, leptin과 MYF5 유전자는 한우의 도체특성 및 육질 개선을 위한 DNA marker로 이용 가능할 것으로 사료된다.