• Korean Journal of Microbiology
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• v.32 no.4
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• pp.245-251
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• 1994

Ten strains of 7 species from the genus Ganoderma, G. lucidum ATCC 64251, FP-103561-T, and ES70701, G. applanatum ATCC 44053 and FP-57035-T. G. lobatum ATCC 42985, G. resinaceum ATCC 52416, G. subamboinense var. laevisporum ATCC 52420, G. meredithae ATCC 64492, and G. microsporum ATCC 76024, were studied to discuss their phylogenetic relationships by utilizing restriction fragment length polymorphisms (RFLPs) of mitochondrial DNAs (mtDNAs). Six restriction enzymes, BamHI, BglII, EcoRI, HindIII, PvuII, and XbaI which digested mtDNAs into adequate numbers of restriction fragments for cluster analysis, were used in this study. Restriction profiles of strains for each restriction enzyme were treated as analysis characters to calculate similarity coefficients, which were converted into nucleotide sequence divergence values whose mean values were then arranged in a matrix table. This table was utilized for a phylogenetic analysis using the Neighborjoining method of the PHYLIP package to construct phylogenetic tree. Three strains of G. lucidum and two strains of G. applanatum exhibited different lineages each but one of G. applanatum strains showed a close relationship with G. lobatum, which reflected the species complexity of these species whose strains were phenotypically indistinguishable but genetically distinct. The present results suggest that the natural classification of Ganoderma needs to be considered from the viewpoints of molecular biology-based systematics as well as morphological classifications and cultural identifications for better phylogenetic conclusions.

• Proceedings of the Zoological Society Korea Conference
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• 1994.10a
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• pp.90.2-90
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• 1994

No Abstract, See Full Text

• The Journal of the Korean Society for Microbiology
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• v.22 no.4
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• pp.463-471
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• 1987

The genomes of leptospiral field isolates from Korea belonging to serogroup Icterohaemorrhagiae (21 strains) and serogroup Canicola (1 strain) were analysed and compared by restriction enzyme analysis with EcoRI and HindIII as digesting enzymes. One isolate belonging to serogroup Canicola showed the same pattern as serovar portlandvere. All 21 isolates belonging to serogroup Icterohaemorrhagiae showed almost same patterns as Leptospira serovar lai from China, But with very slight differences 21 isolates could be classified into 8 subtypes and these grouping seems to reflect the differences in epidemiological niche. And also the geographical data consisted with the grouping into 8 subtypes. According to our results, we concluded that the restriction endonuclease analysis of chromosomal DNA will be an accurate and reliable method to compare and classify pathogenic leptospires.

• 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.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.44 no.3
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• pp.253-255
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• 1999

Reverse transcription and polymerase chain reaction (RT-PCR) assay was used to detect SMV strains. A pair of oligonucleotide primers were designed to include the cylindrical inclusion (CI) coding region between 4,176 to 5,560 nt. Amplification from the total RNA extracted from infected plants with SMV yielded a 1,385 bp DNA fragment. RT-PCR was shown to be $10^3$ times more sensitive than the ELISA assay and it could detect a virus in $10^{-6}$ dilution. Restriction enzyme analysis of RT- PCR products using EcoR I showed that SMV isolates were classified into six groups according to the patterns of restriction fragments.

• Journal of Microbiology
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• v.43 no.5
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• pp.417-423
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• 2005

In this study, the nematode-trapping fungus, Monacrosporium sphaeroides, was transformed with a plasmid harboring the hygromycin B phosphotransferase gene, via restriction enzyme-mediated integration (REMI). Frequencies of up to 94 transformants ${\mu}g^{-1}$ per linearized plasmid DNA were obtained by optimizing the PEG concentration, as well as the category and quantity of the added restriction enzyme. $90\%$ of the transformants were determined to be stable for drug resistance when 20 randomly selected transformants were tested. Southern analyses revealed that the transforming DNA was integrated into the M. sphaeroides genome either with or without rearrangement. Five mitotic stable mutant strains were obtained using this approach, all of which had been altered with regard to sporulation capacity and pathogenicity toward nematodes. Southern blot analyses of the five mutants revealed that foreign plasmid DNA had integrated into the genome. Three of the mutants, Tms2316, Tms3583 and Tms1536, exhibited integration at a single location, whereas the remaining two, Tms32 and Tms1913, manifested integration at double or multiple locations. Our results suggest that the transformation of M. sphaeroides via REMI will facilitate insertional mutagenesis, the functional analysis of a variety of genes, and the tagging or cloning of genes of interest.

• Korean Journal Plant Pathology
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• v.14 no.4
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• pp.308-313
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• 1998

Reverse transcription and polymerase chain reaction (RT-PCR) techiniques were used to identification and differentiation of cucumber mosaic virus isolated from Forsythia koreana (CMV-Fk). RT-PCT used by two set of 20-mer primers one was CMV-common primers and another was CMV subgroup I-specific primers designed in a conserved region of the 3' end of CMV RNA3, amplified about 490 bp and 200 bp DNA fragments from CMV-Fk, respectively. CMV could be detected by RT-PCR at a dilution as low as 10-4 in forsythia crude sap extracts. Restriction enzyme analysis of RT-PCR products using EcoRI and MspI showed that CMV-Fk belonged to CMV subgroup I. But, analysis of RNA fingerprinting by arbitrarily primed polymerase chain reaction (RAP-PCR) showed heterogeneity of RNA3 between CMV-Fk and CMV-Y as a member of subgroup I.

• Parasites, Hosts and Diseases
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• v.55 no.6
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• pp.653-658
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• 2017

Hypoderma spp. larvae cause subcutaneous myiasis in several animal species. The objective of the present investigation was to identify and characterize morphologically and molecularly the larvae of Hypoderma spp. collected from cattle (Bos taurus taurus) and red deer (Cervus elaphus) in the district of Castelo Branco, Portugal. For this purpose, a total of 8 larvae were collected from cattle (n=2) and red deer (n=6). After morphological identification of Hypoderma spp. larvae, molecular characterization was based on PCR-RFLP and mitochondrial CO1 gene sequence analysis. All larvae were morphologically characterized as the third instar larvae (L3) of H. actaeon. Two restriction enzymes were used for molecular identification of the larvae. TaqI restriction enzyme was not able to cut H. actaeon. However, MboII restriction enzyme differentiated Hypoderma species showing 210 and 450 bp bands in H. actaeon. Furthermore, according to the alignment of the mt-CO1 gene sequences of Hypoderma species and to PCR-RFLP findings, all the identified Hypoderma larvae were confirmed as H. actaeon. This is the first report of identification of Hypoderma spp. (Diptera; Oestridae) from cattle and red deer in Portugal, based on morphological and molecular analyses.

• The Plant Pathology Journal
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• v.27 no.2
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• pp.148-155
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• 2011

Our previous sequence and phylogenetic analyses of the Korean Rice stripe virus (RSV) suggested possible genetic reassortment of RNA segments, but whether this RNA variation contributed to the recent RSV outbreaks in Korea is yet unclear. To further clarify these RSV-RNA segment variations, we developed a reverse transcription-polymerase reaction/restriction enzyme (RT-PCR/RE) analysis-based method. We identified five REs, including DraI, EcoR1, NdeI/AseI, and SpeI, that could differentiate RSV RNA 1-4 subtypes, respectively. Our RT-PCR/RE results provided a clear pattern of RNA reassortment, i.e., different groups of isolates having their RNA segments derived from two to three different RSV ancestors, such as from Eastern and Southwestern Chinese or Japanese M and T isolates. We also found that the migratory small brown planthopper from Eastern China caught by aerial net traps that possesses RSV-RNA3 genotypes corresponds mainly to Eastern China, with a few for Southwestern China based on RT-PCR/RE, sequence and phylogenetic analyses, indicating that RSV populations in Eastern China may also have strong RNA variation. The development of an RE analysisbased method proved a useful epidemiological tool for rapid genotyping and identification of mixed infections by RSV strain and by different subtype.

• Journal of Microbiology and Biotechnology
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• v.21 no.12
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• pp.1336-1344
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• 2011

This study details and examines a novel ligation-mediated polymerase chain reaction (LM-PCR) method. Named the LM-PCR/Shifter, it relies on the use of a Class IIS restriction enzyme giving restriction fragments with different 4-base, 5' overhangs, this being the Shifter, and the ligation of appropriate oligonucleotide adapters. A sequence of 4-base, 5' overhangs of the adapter and a 4-base sequence of the 3' end of the primer(s) determine a subset of the genomic restriction fragments, which are amplified by PCR. The method permits the differentiation of bacterial species strains on the basis of the different DNA band patterns obtained after electrophoresis in polyacrylamide gels stained with ethidium bromide and visualized in UV light. The usefulness of the LM-PCR/Shifter method for genotyping is analyzed by a comparison with the restriction endonuclease analysis of chromosomal DNA by the pulsed-field gel electrophoresis (REA-PFGE) and PCR melting profile (PCR MP) methods for isolates of clinical origin. The clustering of the LM-PCR/Shifter fingerprinting data matched those of the REA-PFGE and PCR MP methods. We found that the LM-PCR/Shifter is rapid, and offers good discriminatory power and excellent reproducibility, making it a method that may be effectively applied in epidemiological studies.