• Korean Journal of Microbiology
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• v.35 no.3
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• pp.180-184
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• 1999

Molecular spslemaucs of Agaricus species was investigated on the base of the sequences of the internal transcribed spaceriITS) regions in ribosomal DNA (rDNA). The sequences of the ITS region in 5 species and two group of Agaricus genus were resolved. In the phylogenetic trees. the species generally divided inlo two subclusters, refered to here as the group I and group 11. The group I consisted of Agaricus blazei ATCC 76739, Agarictrs blazei species cultivated in Korean hmings. Ago/-icus anmensis IMSNU 32049 and Agaricus can~pestris VPI-OKM 25665. Between Agaricus blazei NCC 76739 and the Agaricus blazei species cultivated in Korean farmings had the variation in lhe 5 nucleotide on the ITS regions. These varieties were presumed the variation by the geographic and cultivated conditions. In addition the subgroup of group I was formed by Agaricus arvensis LMSNU 32049 and Agaricus carnpests VPI-OKM 25665. The group IT included Agnrictrs bispoms CH 3004 and Agaricus pocillotor DUKE-J 173.

• The Korea Journal of Herbology
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• v.21 no.2
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• pp.9-13
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• 2006

Objectives : To determine the DNA sequence of the 18S rRNA gene of the Rehmannia glutinosa and analyze it phylogenetically Methods : Dried root of the Rehmannia glutinosa was ground with a mortar and pestle. Glass beads(0.5 mm in diameter), TE buffer and SDS solution were added to that. The mixture was vortexed vigorously and extracted with the mixture of phenol, chloroform and isoamyl alcohol and with the mixture of the chloroform and isoamyl alcohol. The nucleic acids were precipitated with ethanol and resuspended in TE buffer. Contaminating RNA was digested with RNAse A and the DNA was purified further with the Geneclean Turbo Kit. This DNA was used as a template for amplification of the 18S rRNA gene by PCR. The PCR product was cloned in the pBluescript SK II plasmid by blunt-end ligation and the DNA sequence of the insert was determined. This DNA sequence was analyzed phylogenetically by the BLAST program. Results and Conclusion : Vortexing the ground powder of the dried plant root with glass beads during cell lysis improved recovery of DNA. The DNA sequence of the Rehmannia glutinosa 18S rRNA gene was determined and deposited at the GenBank as the accession number DQ469606. Phylogenetic analysis of that sequence showed the relationship between the members of the family of Scrophulariaceae and also the close relationship of the Buddleja davidii to the members of the Scrophulariaceae family.

• The Korean Journal of Mycology
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• v.22 no.4
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• pp.366-377
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• 1994

The base composition of DNA of Aspergillus phoenicis, Rhizopus acidus and Candida albicans treated with cycloheximide and nalidixic acid during the culture was analyzed to compare with the control. The contents of base in the DNA were inhibited by cycloheximide, 20.4% of adenine, 43.1% of thymine, 40.9% of cytosine, 35.3% of guanine, 32.2% of purine, and 42.7% of pyrimidine for A. phoenicis. In R. acidus, 34.2% of adenine, 42.1% of thymine, 38.0% of cytosine, 18.1% of guanine, 24.1% of purine and 40.0% of pyrimidine were depressed by cycloheximide. In the antibiotic treatment of C. albicans, 58.3% of adenine, 58.5% of thymine, 58.1% of cytosine, 42.4% of guanine, 46.8% of purine and 58.8% of pyrimidine were inhibited to compare with the control. The nalidixic acid treatments were showed that, in A. phoenicis 41.6% of adenine, 47.1% of thymine, 59.3% of cytosine, 46.3% of guanine, 45.6% of purine and 57.2% of pyrimidine were inhibited. When R. acidus was treated with nalidixic acid, 59.1% of adenine, 54.7% of thymine, 35.3% of cytosine, 37.4% of guanine, 45.9% of purine and 44.9% of pyrimidine decreased. In treatment of nalidixic acid, the content of DNA was depressed 60.1% of adenine, 68.6% of thymine, 60.7% of cytosine, 40.0% of guanine, 45.8% of purine and 63.5% of pyrimidine for C. albicans In the DNA synthesis of three fungal cells, cycloheximide and nalidixic acid treatments were analyzed obviously that the biosynthesis of pyrimidine was depressed than that of purine. Therefore, it was showed that the DNA contents in the various fungal cells were inhibited remarkably in nalidixic acid treatment than cycloheximide.

• International Journal of Oral Biology
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• v.38 no.1
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• pp.29-36
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• 2013

Mitis group streptococci (MGS) were classified based on the nucleotide sequences 16S rRNA gene (16S rDNA) and comprised 13 Streptococcus species. However, 16S rDNA homogeneity among MGS was too high to discriminate between clinical strains at the species level, notably between Streptococcus mitis, Streptococcus oralis, Streptococcus pneumoniae, and Streptococcus pseudopneumoniae. The purpose of this study was to discriminate between 37 strains of MGS isolated from Korean oral cavities using phylogenetic analysis of the DNA-dependant RNA polymerase beta-subunit gene (rpoB). 16S rDNA and rpoB from clinical strains of MGS were sequenced using the dideoxy chain termination method and analyzed using MEGA version 5 software. The resulting phylogenetic data showed that the rpoB sequences could delineate clinical strains of MGS at the species level. Phylogenetic analysis of rpoB is therefore a useful approach for identifying MGS at the species level.

• Journal of Microbiology
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• v.35 no.2
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• pp.79-86
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• 1997

For the phylogenetic study of the genus Trichaptum, nuclear ribosomal DNA sequences from eight strains of four Trichaptium species were examined. Phylogenetic trees were constructed using molecular data on 18 rDNA and 5.8S rDNA and thei ITSs. Parsimony analyses of the Trichaptum species showed that T. biforme and T. laricinum made a monophyletic group respectively, suggesting that each species is phylogenetically independent. However, T. abietum represented a polyphyletic group and T. fusco-violaceum formed a polytomous group, suggesting that these species could be in the process of evolutionary differentiation. Examination of base substitutions of the 18S rRNA gene reveals that the C-T transition is most predominant and that there is a stronger transition bias between closely related organisms rather than between distantly related ones.

• Journal of Korean society of Dental Hygiene
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• v.13 no.5
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• pp.889-900
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• 2013

Objectives : Molecular biology techniques were employed to assess diversity of bacterial in children's dental caries. Methods : DNA of germs was extracted and the diversity of the 16S rRNA clones was analyzed by amplified rDNA restriction analysis and sequencing. The experimental samples were pit and fissure caries (PC), deep dentinal caries (DC), smooth surface caries (SC), and supragingival plaque (PQ) from 50 children of age less than 12 years old. The control group was healthy teeth supragingival plaque (HT). Thirty clones from each 16S rRNA clone library of 5 samples were randomly selected, thus a total of 150 clones were analyzed. Results : Amplified rDNA restriction analysis uncovered 18, 20, 11, 17, and 22 phylotypes from healthy teeth, pit and fissure caries, deep dentinal caries, smooth surface caries, and supragingival plaque, respectively. Sequencing analysis found the dominance of Actinomycs naeslundii and Fusobacterium nucleatum in the healthy teeth; Leptotrichia sp. in the pit and fissure caries; Actinomyces sp., Streptococcus mutans, and Rahnella aquatilis in the deep dentinal caries; Streptococcus mutans and Actinomyces sp. in the smooth surface caries; Enterobacter hormaechei and Streptococcus sanguinis in the supragingival plaque. Conclusions : Clonal analysis identified 6 phyla, 20 genera, and 51 species.

• Korean Journal of Microbiology
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• v.50 no.2
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• pp.152-157
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• 2014

The aim of this study was to investigate the bacterial community inhabited in Callyspongia elegans. Marine bacteria were isolated from the marine sponge C. elegans using marine agar. The resulting 112 isolated pure cultures were then used for further study. They were characterized by determining morphological characteristics through Gram's staining and morphological observation. The colony pigments of bacterial isolates were characterized as yellow, brown, ivory, and white. Thirty-seven strains were found to be Gram-positive and 75 strains were Gram-negative. Seventy-nine strains were coccus-shaped, while 16 strains were rod-shaped. On the basis of the results of the comparative analyses of 16S rDNA gene sequences, the 112 isolated bacteria were divided into 5 major groups: Alphaproteobacteria (39%), Gammaproteobacteria (22%), Actinobacteria (14%), Fimicutes (9%), and Bacteroidetes (6%). It is strongly suggested that fifteen isolates are candidates for a new genera or species, based on the analyses of 16S rDNA gene sequences.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.35 no.6
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• pp.633-638
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• 2002

Nuclear 18S ribosomal RNA gene (185 rDNA) from the aquaculturable seaweed Porphya yezoensis (Bangiales, Rhodophyta) was amplified using the polymerase chain reaction and its sequence was analysed. Complete 185 rDNA has an 1823 bp exon and a 514 bp intron. The G+ C contents of exon and intron were $48\%$ and $51.4\%$, respectively. The exon sequence showed $99.5\%$ homology to the GenBank accession number AB013177 of the Japanese p. yezoensis. The intron region that was inserted upstream between 568 and 1083 showed $93.4\%$ homology to the AB013177.

• Mycobiology
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• v.34 no.3
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• pp.154-157
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• 2006

A fungal isolate collected from infected paprika (Capsicum annuum var. grossum) was characterized as Sclerotinia sclerotiorum based on its ability of sclerotium formation, physiological and molecular properties. When the isolate was grown on potato dextrose agar, oatmeal agar, and malt extract agar, it grew most well on PDA. Optimal temperature and pH for its growth were $25^{\circ}C$ and pH 7, respectively. The fungal isolate produced sclerotia on PDA within 10 days, and the color and shape of the sclerotia were similar to those of S. sclerotiorum. The ITS rDNA regions including ITS1 and ITS2 and 5.8S sequences were amplified using ITS1F and ITS4 primers from the genomic DNAs of the paprika isolate and other known pathogenic S. sclerotiorum isolated from different crops in Korea, and their nucleotide sequences were determined. Sequence comparison analysis showed the ITS rDNA of the paprika isolate shares 100% sequence identity with those of S. sclerotiorum isolated from red pepper, lettuce and a S. sclerotiorum isolate registered in GenBank DNA database. Neighbor joining analysis based on the ITS rDNA sequence revealed the paprika isolate has very close phylogenetic relationships with known Sclerotinia sclerotiorum isolates. This is the first report that S. sclerotiorum has been found associated with paprika rot in paprika growing countries.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.33 no.6
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• pp.489-495
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• 2000

The 185 ribosomal RNA gene (185 rDNA) of the marine alga Porphyra sp. 723 (Bangiales, Rhodophyta) was amplified using the polymerase chain reaction and its sequence was analysed. The Porphyra species was a summer strain collected on rocks in upper intertidal zone at Ikidae, Pusan on 23rd July 1999. The fronds were $1{\~}5 cm$ long, monostromatic, and orbicular or ovate shaped, They had spinulate processes at margin of the frond, Comparison of this 185 rDNA sequence with the other Forphyra species indicates that Porphyra sp. 723 has the same 185 rDNA sequence derived from Porphyra suborbiculata (NCBI access number; AB 013180) except one base pair substitution in 2327 base pairs.