• Korean Journal of Microbiology
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• v.55 no.3
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• pp.220-225
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• 2019

Studies based on microbial community analyses have increased in the recent decade since the development of next generation sequencing technology. Associations of gut microbiota with host's health are one of the major outcomes of microbial ecology filed. The major approach for microbial community analysis includes the sequencing of variable regions of 16S rRNA genes, which does not provide the information of bacterial activities. Here, we conducted RNA-based microbial community analysis and compared results obtained from DNA- and its cDNA-based microbial community analyses. Our results indicated that these two approaches differed in the ratio of Firmicutes and Bacteroidetes, known as an obesity indicator, as well as abundance of some key bacteria in gut metabolisms such as butyrate producers and probiotics strains. Therefore, cDNA-based microbial community may provide different insights regarding roles of gut microbiota compared to the previous studies where DNA-based microbial community analyses were performed.

• Analytical Science and Technology
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• v.21 no.4
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• pp.338-343
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• 2008

Extraction of DNA from skeletal material is of great importance in the identification of human remains, but is particularly difficult because the high amount of microbial DNA was often co-extracted with human bone DNA. We found that a phenol/chloroform extraction, followed by ultrafiltration, and cleanup by via the $QIAquick^{(R)}$ PCR purification kit yields higher amounts of human genomic DNA compared with extraction by the column affinity $method^{(R)}$ alone. Ultrafiltration extraction of human DNA from ten exhumed bone samples yielded $0.041-1.120ng/{\mu}L$ DNA (mean = $0.498ng/{\mu}L$ DNA), and purification using the column affinity resulted in $0.016-0.064ng/{\mu}L$ DNA (mean = $0.034ng/{\mu}L$ DNA). Although the STR genotyping by the column affinity method was partially successful, all DNA samples by the ultrafiltration method produced full profiles from the multiplex PCR. The efficiency of STR genotyping was in accordance with the amounts of the human DNA extracted.

• Korean Journal of Microbiology
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• v.37 no.2
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• pp.137-144
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• 2001

In order to investigate the diversity of bacterial community in the mud flat of Sunchon Bay, Chunnam province, diversity of amplified 16S rDNA was examined. Total DNA was extracted from sediment soils and 16S rDNAs were amplified using PCR primers based on the universally conserved sequences in bacteria. Clonal libraries were constructed and 111 clones were examined by amplified rDNA restriction analysis (ARDRA) using HaeIII. Clones were clustered based on restriction patterns using computer program, GelCompar II. One hundred different RFLP types were detected from 111 clones. The 20 clones were selected and sequenced according to dendrograms derived from ARDRA, to cover most of the bacterial diversity in the clone libraries. None of the clones were identical to any representatives in the Ribosomal Database Project small subunit RNA databases and GenBank. All sequences showed between 77 and 96.8% similarity to the known 16s rRNA sequence from cultured organisms. The 20 clones sequenced fell into seven major lineages of the domain Bacteria: alpha-, delta-, gamma-Proteobacteria, low G+C Gram positive bacteria, high G+C Gram positive bacteria, Sphingobacteria (Cytophaga) and Cyanobacteria (chloroplast). Among the clones, the Proteobacteria were dominant.

• Journal of fish pathology
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• v.30 no.2
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• pp.79-88
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• 2017

At the present, fish farms are suffering a lot of economic losses due to infectious diseases caused by various pathogens including aeromonad. Aeromonad is ubiquitous bacteria that causes infectious diseases. At least 26 species in the genus Aeromonas have been reported to cause fatal infections not only in salmonid fishes, but also in other freshwater and seawater fishes. Molecular techniques based on nucleic acid sequences of 16S rDNA and housekeeping genes can be used to identify the Aeromonas species. In this study, The genus Aeromonas was isolated from salmonid fishes of sixteen fish farms in Gangwon-Do, Korea and phylogenetically identified based on the sequences of 16S rDNA and housekeeping genes for Aeromonad, i.e. RNA polymerase sigma factor ${\sigma}^{70}$ (rpoD) or DNA gyrase subunit B (gyrB). Consequently, 96 strains were collected from Atlantic salmon (Salmo salar), coho salmon (Oncorhynchus kisutch), masou salmon (Oncorhynchus masou) and rainbow trout (Oncorhynchus mykiss), and 36 isolates were identified as the genus Aeromonas by 16S rDNA analysis. Thirty six Aeromonad isolates were further analysed based on rpoD or gyrB gene sequences and found Aeromonas salmonicida (24 isolates), A. sobria (10 isolates), A. media (1 isolates) and A. popoffii (1 isolates), indicating that A. salmonicida is a main infectious bacteria in Salmonid fishes in Gangwon-Do. It was also proved that the phylogenetic identification of Aeromonas species based on the sequences of housekeeping gene is more precise than the 16S rDNA sequence.

• Food Science of Animal Resources
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• v.27 no.2
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• pp.209-215
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• 2007

In order to develop a sensitive and reliable method for the species-specific molecular markers, PCR-RFLP assay of the mitochondrial DNA(mt DNA) 12S rRNA gene was exploited for the identification of the origin of animal meat species including cattle, pig, sheep, goat, horse, deer, chicken, duck and turkey. A specific primer pairs were designed, based on the nucleotide sequences of mt 12S rRNA gene, for the amplification of the highly conserved region in the gene of the animal species using PCR-RFLP technique. mt DNA was isolated from meat samples followed by DNA amplification using PCR with the specific primers. PCR amplification produced an approximately 455 bp fragment in each of these animal meats. To distinguish pleat species, the PCR amplicons were digested with restriction endonucleases Tsp5091 and MboI, respectively, which generates distinct RFLP profiles. The DNA profiles digested with Tsp5091 allowed the clear discrimination in the mammalian meat species and the DNA profiles digested with MboI in poultry meat species. Therefore, the PCR-RFLP profiles of mt 12S rRNA gene could be very useful to identify the origin of the raw materials in the raw meats as well as the processed meat products.

• Korean Journal of Medicinal Crop Science
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• v.18 no.4
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• pp.266-272
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• 2010

There is a considerable difference in morphological traits between Bokbunja cultivated in Korea (KCB) and Korea native Rubus coreanus, contrary to the conviction that the cultivated Bokbunja is the domestication of R. coreanus. To infer the phylogenetic relationship of KCB with other Rubus species, we compared the chloroplast DNA spacers of KCB with those of several Rubus species including black raspberry, R. occidentalis. The three chloroplast DNA spacers, atpB~rbcL, trnL~trnF, and trnT~trnL, were amplified using the specific primer pairs and converted to Single Strand Conformational Polymorphism (SSCP) markers. The SSCP makers of the chloroplast DNA spacers showed a considerable variation both within and among Rubus species. In the phylogenetic tree generated by the SSCP markers, KCB accessions were located in the same clade with R. occidentalis, but R. coreanus accessions in the different clade. Also, in the phylogenetic tree by the nucleotide sequences of the chloroplast DNA spacer trnL~trnF, KCB located in the same clade with R. occidentalis but not with R. coreanus. These results suggest that the three KCB accessions share higher similarity with R. occidentalis than with R. coreanus in the three chloroplast DNA spacers.

• Korean Journal of Environmental Biology
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• v.21 no.1
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• pp.45-51
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• 2003

Genetic diversity of local populations among geologically isolated groups of Rana amurensis was refined by sequence comparison of the mitochondrial (mt) 165 rDNA genes. Each 401 base pairs of DNA sequences, which was determined from four local populations of Rana amurensis, two local populations of R. nigromacutata, and three species of the genus Rana were used in this analysis. Despite morphological similarity of Rana amurensis, Korean populations were well distinguished from the other groups on the basis of 105 rDNA gene difference. Further analyses for additional local populations belonging to R. amurensis will be necessary to clarify the taxonomic status.

• The Korean Journal of Mycology
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• v.22 no.2
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• pp.117-121
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• 1994

Five strains of Pleurotus sajor-caju were collected from some countries including India and Papua New Guinea. Four strains produced brown fruitbody but the other strain from Papua New Guinea produced white fruitbody. Monokaryons obtained from both strains producing brown fruitbody and white fruitbody were mated each other. They showed different mating types such as brown strain of $A_1A_2B_1B_2$ and white strain of $A_3A_4B_3B_4$. DNAs were isolated from mycelia of five strains of P. sajor-caju. Mitochondrial DNA was seperated from nuclear DNA by bisbenzimide-CsCl ultracentrifugation. Digestion of the fungal mitochondrial DNA with Eco RI restriction endonuclease yielded from ten to fourteen fragments. Two strains of the five strains showed different restriction pattern of mitochondrial DNA from the other three strains. Summation of the fragment sizes gave a mitochondrial DNA size of about 60 to 65kb.

• Journal of Microbiology and Biotechnology
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• v.24 no.6
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• pp.812-822
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• 2014

Metagenomic analysis of the human intestinal microbiota has extended our understanding of the role of these bacteria in improving human intestinal health; however, a number of reports have shown that current total fecal DNA extraction methods and 16S rRNA universal primer sets could affect the species coverage and resolution of these analyses. Here, we improved the extraction method for total DNA from human fecal samples by optimization of the lysis buffer, boiling time (10 min), and bead-beating time (0 min). In addition, we developed a new long-range 16S rRNA universal PCR primer set targeting the V6 to V9 regions with a 580 bp DNA product length. This new 16S rRNA primer set was evaluated by comparison with two previously developed 16S rRNA universal primer sets and showed high species coverage and resolution. The optimized total fecal DNA extraction method and newly designed long-range 16S rRNA universal primer set will be useful for the highly accurate metagenomic analysis of adult and infant intestinal microbiota with minimization of any bias.

• ALGAE
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• v.39 no.2
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• pp.75-96
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• 2024

Rhodomonas (Cryptophyceae) and species assigned to this genus have undergone numerous taxonomic revisions. This also applies to R. marina studied here as it was originally assigned as a species of Cryptomonas and later considered a variation of R. baltica, the type species. Despite being described more than 130 years ago, R. marina still lacks a comprehensive characterization. Light and electron microscopy were employed to delineate a strain from western Greenland. The living cells were 18 ㎛ long and 9 ㎛ wide, elliptical in shape with a pointed to rounded posterior and truncated anterior in lateral view. Two sub-equal flagella emerged from a vestibulum, where also a furrow extended. In transmission electron microscopy, the furrow was associated with a tubular gullet and the pyrenoid embedded in a deeply lobed chloroplast. The chloroplast contained DNA in perforations and was surrounded by starch grains. A tubular nucleomorph was enclosed within the pyrenoid matrix. In scanning electron microscopy, the inner periplast consisted of rectangular plates with rounded edges and posteriorly these were replaced by a sheet-like structure. The water-soluble pigment was Crypto-Phycoerythrin type I (Cr-PE 545). A phylogenetic inference based on SSU rDNA confirmed the identity of strain S18 as a species of Rhodomonas as it clustered with congeners but also Rhinomonas, Storeatula, and Pyrenomonas. These genera formed a monophyletic clade separated from a diverse assemblage of other cryptophyte genera. To further explore the phylogeny of R. marina a concatenated phylogenetic analysis based on the SSU rDNA-ITS1-5.8S rDNA-ITS2-LSU rDNA region was performed but included only closely related species. The secondary structure of nuclear internal transcribed spacer 2 was predicted and compared to similar structures in related species. Using morphological and molecular signatures as diagnostic features the description of R. marina was emended.