• Mycobiology
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• v.51 no.5
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• pp.281-287
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• 2023

The symbiotic association between fungus-gardening termites Macrotermes and its fungal symbiont has a moderate degree of specificity-although the symbiotic fungi (Termitomyces) form a monophyletic clade, there is not a one-to-one association between termite species and their fungus-garden associates. Here, we aim to determine the origin and phylogenetic relationships of Termitomyces in Oman. We used sequences of the internal transcribed spacer region (ITS) and the nuclear large subunit ribosomal RNA (LSU rRNA, 25S) gene and analyzed these with sequences of Termitomyces from other geographic areas. We find no evidence for more than a single colonization of Oman by Termitomyces. Unexpectedly, we find Termitomyces in Oman is most closely related to the symbiont of M. subhyalinus in West Africa rather than to those of geographically closer populations in East Africa.

• Molecules and Cells
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• v.20 no.3
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• pp.392-400
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• 2005

The genes encoding the DNA gyrase A (GyrA) and B subunits (GyrB) of Methylovorus sp. strain SS1 were cloned and sequenced. gyrA and gyrB coded for proteins of 846 and 799 amino acids with calculated molecular weights of 94,328 and 88,714, respectively, and complemented Escherichia coli gyrA and gyrB temperature sensitive (ts) mutants. To analyze the role of type II topoisomerases in the intrinsic quinolone resistance of methylotrophic bacteria, the sequences of the quinolone resistance-determining regions (QRDRs) in the A subunit of DNA gyrase and the C subunit (ParC) of topoisomerase IV (Topo IV) of Methylovorus sp. strain SS1, Methylobacterium extorquens AM1 NCIB 9133, Methylobacillus sp, strain SK1 DSM 8269, and Methylophilus methylotrophus NCIB 10515 were determined. The deduced amino acid sequences of the QRDRs of the ParCs in the four methylotrophic bacteria were identical to that of E. coli ParC. The sequences of the QRDR in GyrA were also identical to those in E. coli GyrA except for the amino acids at positions 83, 87, or 95. The $Ser^{83}$ to Thr substitution in Methylovorus sp. strain SS1, and the $Ser^{83}$ to Leu and $Asp^{87}$ to Asn substitutions in the three other methylotrophs, agreed well with the minimal inhibitory concentrations of quinolones in the four bacteria, suggesting that these residues play a role in the intrinsic susceptibility of methylotrophic bacteria to quinolones.

• Parasites, Hosts and Diseases
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• v.53 no.5
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• pp.641-645
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• 2015

Fascioliasis, a food-borne trematode zoonosis, is a disease primarily in cattle and sheep and occasionally in humans. Water dropwort (Oenanthe javanica), an aquatic perennial herb, is a common second intermediate host of Fasciola, and the fresh stems and leaves are widely used as a seasoning in the Korean diet. However, no information regarding Fasciola species contamination in water dropwort is available. Here, we collected 500 samples of water dropwort in 3 areas in Korea during February and March 2015, and the water dropwort contamination of Fasciola species was monitored by DNA sequencing analysis of the Fasciola hepatica and Fasciola gigantica specific mitochondrial cytochrome c oxidase subunit 1 (cox1) and nuclear ribosomal internal transcribed spacer 2 (ITS-2). Among the 500 samples assessed, the presence of F. hepatica cox1 and 1TS-2 markers were detected in 2 samples, and F. hepatica contamination was confirmed by sequencing analysis. The nucleotide sequences of cox1 PCR products from the 2 F. hepatica-contaminated samples were 96.5% identical to the F. hepatica cox1 sequences in GenBank, whereas F. gigantica cox1 sequences were 46.8% similar with the sequence detected from the cox1 positive samples. However, F. gigantica cox1 and ITS-2 markers were not detected by PCR in the 500 samples of water dropwort. Collectively, in this survey of the water dropwort contamination with Fasciola species, very low prevalence of F. hepatica contamination was detected in the samples.

• Korean Journal of Plant Resources
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• v.19 no.5
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• pp.628-633
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• 2006

ITS DNA sequences from five individuals, representative of five groups designated according to the degree of leaf teeth and lobes from simple to palmate compound leaf in the Viola albida complex, established and further analysed in order to solve the taxonomic difficulty. A total 702 bp was sequenced at the 5.8S ribosomal DNA and internal transcribed spacer 1 and 2. The 5.8S coding region is 163 bp, and has no sequence variations. The ITS1 and ITS2 noncoding regions have a little bit sequence variations, and those were further analysed by the methods of the analysis of variance (ANOVA), the analysis of sequence divergence and the phylogenetic analysis. The result of ANOVA showed no significant differences among individuals investigated. The analysis of sequence divergence with Kimura 2-parameter distance revealed that in-groups showed much less than 0.05 in absolute value among individuals, while two out groups more than 0.05, V. grypoceras and V. orientalis. This result appeared that the sequence divergence among in-groups was not yet occurred in the species level but situated at somewhere below the species level. In the phylogenetic analysis, two outgroups formed the basal clades in order. Five individuals in-groups formed a clade. The clade was, however, not very robust as around 50% in bootstrap value, suggesting that this result was not meaningful in the phylogenetic point of views.

• Journal of Microbiology and Biotechnology
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• v.9 no.4
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• pp.457-463
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• 1999

The physical map of bacteriophage $\PhiFC1$ DNA was constructed with the restriction endonucleases SalI, BamHI, EcoRI, XbaI, and AvaI. The 40.5-kb DNA restriction map is shown to be circularly permuted representing the headful packaging mechanism of the phage. The DNA restriction fragments containing the packaging initiation site(pac) was localized on the restriction map and the nucleotide sequences of the region were analyzed. Four open reading frames (ORFs), following one another with the same orientation, were found at the region. The 2nd ORF (ORF-ts) has significant amino acid sequence homologies to the previously known terminase small subunits of other bacteriophages. The putative terminase small subunit gene has a presumptive NTP-hydrolysis motif and a helix-turn-helix motif. The cleavage site for the first round of packaging was found to be located at the coding sequence of the putative terminase small subunit gene. The fourth ORF, even if partially sequenced, has a good amino acid sequence homology to the portal vertex proteins of other bacteriophages representing the evolutionarily conserved arrangements of genes near the pac site of this bacteriophage, $\PhiFC1$.

• Parasites, Hosts and Diseases
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• v.55 no.1
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• pp.95-98
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• 2017

Fasciola hepatica is a trematode that causes zoonosis, mainly in cattle and sheep, and occasionally in humans. Few recent studies have determined the infection status of this fluke in Korea. In August 2015, we collected 402 samples of freshwater snails at Hoenggye-ri (upper stream) and Suha-ri (lower stream) of Song-cheon (stream) in Daegwalnyeong-myeon, Pyeongchang-gun in Gangwon-do (Province) near many large cattle or sheep farms. F. hepatica infection was determined using PCR on the nuclear ribosomal internal transcribed spacer 2 (ITS-2). Among the 402 samples, F. hepatica 1TS-2 marker was detected in 6 freshwater snails; thus, the overall prevalence in freshwater snails was 1.5%. The prevalence varied between collection areas, ranging from 0.0% at Hoenggye-ri to 2.9% at Suha-ri. However, F. gigantica ITS-2 was not detected in the 6 F. hepatica-positive samples by PCR. The nucleotide sequences of the 6 F. hepatica ITS-2 PCR-positive samples were 99.4% identical to the F. hepatica ITS-2 sequences in GenBank, whereas they were 98.4% similar to F. gigantica ITS-2 sequences. These results indicated that the prevalence of F. hepatica in snail intermediate hosts was 1.5% in Gangwon-do, Korea; however the prevalence varied between collection areas. These results may help us to understand F. hepatica infection status in natural environments.

• Journal of fish pathology
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• v.6 no.2
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• pp.93-101
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• 1993

The RNAI mutation of Saccharomyces cerevisia is a recessive and temperature sensitive lethal mutation which interferes with the production of mRNA, rRNA, and tRNA. However, the precise role of RNAI gene have not been revealed until yet. We have cloned rna1-1 mutant gene from rna1-1 mutant yeast strain(R49 ; trpl, ura3-52, rna1-1). The 3.4kb BglII fragment of wild type RNAI clone(81-2-6) contains whole RNAI gene. The genomic southern blotting with BglII digested R49 genomic DNA as a probe shows the unique and identical band with wild type 3.4kb BglII fragment. Therefore, We prepared partial BglII genomic library(3~4kb BglII fragments) into BamH I site of pUC19. The rna 1-1 mutant clone was screened with Digoxigenin(DIG)-lableled probe by high density colony hybridization. The 5'-flanking region of rna1-1 gene was sequenced by dideoxy chain termination method. The 5'-flanking sequence of RNAI gene contains three TATA-like sequence ; TAATA, TATA and TTTTAA at position of -67, -45, and -36 from first ATG codon respectively. The 5'-flanking region of wild type RNA I gene from ATG codon to -103nt was deleted with Bal31 exonuclease digestion, generating $pUC{\Delta}$/RNA I. After constructing $pYEP{\Delta}RNA$ I (consists of -103nt deleting RNA I gene, URA3 gene, $2{\mu}m$ rep. origin), pYEPrna1-1(consists of Xba I fragment of pUCrna1-1. URA3 gene, $2{\mu}m$ rep. origin), and pYEPRNAI. each plasmid was transformed into host strain(trpl, ura3-52, rna1-1) by electroporation, respectively. Yeast transformant carrying $pYEP{\Delta}RNA$ I did not complement the thermal sensitivity of rna1-1 gene. It means that TATA-like sequences in 5'-flanking region is not TATA sequence for transcribing RNAI gene and there may be other essential sequence in upstream region for the transcription of RNAI gene.