• Korean Journal of Environmental Biology
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• v.18 no.1
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• pp.53-61
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• 2000

In order to characterize the genetic diversity of bacterial community in groundwater, samples were collected from used for drinking water and polluted with heavy metal wastewater in Seoul city and natural cave of Kangwondo. The DNA was amplified with 165 rDNA-based primers by use of the PCR, and then analysed ARDRA (amplified ribosomal DNA restriction analysis). Restriction endonuclease analysis patterns of amplified 165 rDNA in drinking water and wastewater relatively showed high genetic diversity in situ and drinking groundwater. The number of DNA fragments varied with in situ and drinking water. This method of ARDRA of bacterial communities in groundwater could be used for a quick assessment of genotypic changes between different locations reflecting different environmental conditions and the diversity reflected pollution of groundwater (natural cave water>drinking water>waste water, as in order of grade). [Genetic diversity, Groundwater, 165 rDNA, PCR, ARDRA].

• Korean Journal of Microbiology
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• v.48 no.4
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• pp.275-283
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• 2012

Culture-dependent RFLP and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Asteropus simplex collected from Jeju Island. A total of 120 bacterial strains associated with the sponge were cultivated using modified Zobell and MA media. PCR amplicons of the 16S rDNA from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rDNA sequences derived from RFLP patterns showed more than 94% similarities compared with known bacterial species, and the isolates belonged to five phyla, Alphaproteobacteria, Gammaproteobacteria Actinobacteria, Bacteroidetes, and Firmicutes, of which Gammaproteobacteria was dominant. DGGE fingerprinting of 16S rDNAs amplified from the sponge-derived total gDNA showed 12 DGGE bands, and their sequences showed more than 90% similarities compared with available sequences. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of seven phyla, including Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Actinobacteira, Chloroflexi, and Nitrospira. Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were commonly found in bacteria associated with A. simplex by both RFLP and DGGE methods, however, overall bacterial community in the sponge differed depending on the analysis methods. Sponge showed more various bacterial community structures in culture-independent method than in culture-dependent method.

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.199-208
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• 2021

Environmental DNA (eDNA) metabarcoding is effective method with high detection sensitivity for evaluating fish biodiversity and detecting endangered fish from natural water samples. We compared the richness of operational taxonomic units(OTUs) and composition of freshwater fishes according to filters(cellulose nitrate filter vs. glass fiber filter), extraction kits(DNeasy2^® Blood & Tissue Kit vs. DNeasy2^® PowerWater Kit), primer sets (12S rDNA vs. 16S rDNA), and PCR methods (conventional PCR vs. touchdown PCR) to determine the optimal conditions for metabarcoding analysis of Korean freshwater fish. The glass fiber filter and DNeasy2^® Blood & Tissue Kit combination showed the highest number of freshwater fish OTUs in both 12S and 16S rDNA. Among the four types, the primer sets only showed statistically significant difference in the average number of OTUs in class Actinopterygii (non-parametric Wilcoxon signed ranks test, p=0.005). However, there was no difference in the average number of OTUs in freshwater fish. The species composition also showed significant difference according to primer sets (PERMANOVA, Pseudo-F=6.9489, p=0.006), but no differences were observed in the other three types. The non-metric multidimensional scaling (NMDS) results revealed that species composition clustered together according to primer sets based on similarity of 65%; 16S rDNA primer set was mainly attributed to endangered species such as Microphysogobio koreensis and Pseudogobio brevicorpus. In contrast, the 12S rDNA primer set was mainly attributed to common species such as Zacco platypus and Coreoperca herzi. This study provides essential information on species diversity analysis using metabarcoding for environmental water samples obtained from rivers in Korea.

• 한국생물공학회:학술대회논문집
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• 2003.04a
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• pp.710-712
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• 2003

A new species of Gram-negative halophilic cartenoid producing bacterium was isolated from the Haeundae Coast, Korea. This strain is non-motile, aerobic, orange-pigmented, rod-shaped, and produced carotenoids, mainly astaxanthin. All the type strains of the genus Paracoccus were compared with this strain using 16S rDNA sequence analysis, fatty acid patterns, and physiological reaction profiles. From the results obtained, this strain is classified as a new species, Paracoccus sp..

• Microbiology and Biotechnology Letters
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• v.31 no.2
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• pp.191-196
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• 2003

This study was carried out to investigate the isolation, identification, and antibacterial activity of lactic acid bacteria related to kimchi fermentation. Diluted kimchi soup was plated on the MRS agar media with CaCO$_3$ and incubated at $25^{\circ}C$ for 2 days. A total of 27 strains of lactic acid bacteria from various indigenous, spontaneously fermented vegetables (kimchi) were isolated. Combined methods of Bergey's manual of systematic bacteriology, BPB media analysis and 16S rDNA sequence analysis were applied for identification, however, their results did not coincide in several cases. Isolated lactic acid bacteria could be classified by the 16S rDNA sequence analysis as Leuconostoc mesenteriodes, Leu. carnosum, Lactobacillus curvatus, Lac. pentosus, Weisselia kimchi, W. cibaria, and Pediococcus pentosaceus. Leu. carnosum has not been reported in kimchi lactic acid bacteria. In addition, antibacterial activities of the isolates were tested with Bacillus subtilis, Escherichia coli, Salmonella enteritidis, S. paratyphica, S. typhi, Staphylococcus aureus, Shigella boydii, and S. sonnei. Some of isolates showed significant antibacterial activities to those pathogens.

• Korean Journal of Breeding Science
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• v.41 no.4
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• pp.468-473
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• 2009

Fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) were used for chromosome analysis of hybrids (2n=16) between onion (Allium cepa L., 2n=2X=16) and welsh onion (A. fistulosum L., 2n=2X=16). 5S rDNA, 45S rDNA, and tandemly repeated DNA (TSD) sequence were used as probes for FISH analysis. A. fistulosum specific DNA probe of telomeric repeats and A. fistulosum DNA were used for GISH analysis. In the analysis of meiotic chromosome GISH revealed that hybrids have 7 bivalants and 2 univalents chromosome and 2 univalents were derived from A. fistulosum chromosomes. In somatic chromosomes of hybrid each 8 chromosomes were derived from A. cepa and A. fistulosum, respectively. FISH signal of 45S rDNA probe in A. fistulosum was detected at secondary constriction of chromosomes, while FISH signal in A. cepa was observed in both secondary constriction and telomere of chromosomes. TDS signals in A. fistulosum chromosomes were detected at all subtelomeric of 8 chromosomes and also in 2 pericentromeric of the chromosomes, whereas TDS signals in A. cepa were observed only in subtelomeric in all chromosomes. The pattern of TDS signal in hybrid chromosomes was similar to those of A. fistulosum chromosomes.

• Korean Journal of Medicinal Crop Science
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• v.18 no.3
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• pp.186-190
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• 2010

The chromosome number was identified and fluorescence in situ hybridization(FISH) mapping of 5S and 45S rDNAs were conducted for C. minima and C. lanceolata in the genus Codonopsis from Jeju island. In this study, we have confirmed that the somatic metaphase chromosome number determined as 2n=2x=16 was the same as the findings from the previous studies. While the conventional staining method makes it rather difficult to distinguish satellite chromosomes due to high degree of variability, FISH analysis produced the exact number and location of 5S and 45S rDNAs. Both species in the genus Codonopsis have a pair of 5S rDNA and their gene loci were observed on chromosome 3. Although two pairs of 45S rDNAs (one on chromosome 1 and the other on chromosome 8) were identified in both species, the 45S rDNA signals on chromosome 8 in C. minima were significantly weaker than those on chromosome 1. In addition, the 45S rDNA signals on chromosome 1 in C. lanceolata showed that the chromosome is non-homologus. In this study, we have determined cytogenetic characteristics of C. minima and C. lanceolata according to their gene replication patterns.

• Korean Journal of Environmental Biology
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• v.22 no.1
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• pp.66-74
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• 2004

In order to clarify intra-and inter-specific variation of Korean Rana species, the partial DNA sequences of mitochondrial 16S rDNA gene were determined from 6 Korean and 1 Japanese Rana species, DNA sequences from Korean and Japanese species were comparison-analysed within, and also with the sequences from three species of Japanese brown frogs. DNA similarities were calculated as 91.3∼97.3％ among brown frog (R. amurensis coreana, R. dybowskii and R. huanrenensis), as 96.11∼97.26％ among pond frogs (R. nigromaculata and R. planeyi chosenica). Genetic distance of pond frog and wrinkle fyog (R. rugosa) were near than that of pond frog and brown frog. Two clusters were formed brown frogs and the other group by neigh-bor-joining and maximum-likelihood analysis, also the populations of R. nigromaculata were well distinguished between Korean peninsula and Korean island. But result from maximum-likelihood analysis slightly differed from neighbor-joining to cluster of R. rugosa. Further analyses for their population will be necessary to study the phylogenetic status.

• Korean Journal of Microbiology
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• v.46 no.4
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• pp.366-374
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• 2010

Culture-dependent RFLP and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Spirastrella abata. A total of 164 bacterial strains associated with the sponge were cultivated using Zobell and Natural sea salt media. PCR amplicons of the 16S rDNA from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rDNA sequences derived from RFLP patterns showed more than 95% similarities compared with known bacterial species, and the isolates belonged to four phyla, Proteobacteria (Alphaproteobacteria, Gammaproteobacteria), Actinobacteria, Firmicutes, and Bacteriodetes, of which Alphaproteobacteria was dominant. DGGE fingerprinting of 16S rDNAs amplified from the sponge- derived total gDNA showed five major DGGE bands, and their sequences showed more than 96% similarities compared with available sequences. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of four phyla, including Proteobacteria (Alphaproteobacteria, Gammaproteobacteria), Actinobacteria, Spirochetes, and Chloroflexi. Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were commonly found in bacteria associated with S. abata by both RFLP and DGGE methods; however, overall bacterial community in the sponge differed depending on the analysis methods.

• Food Engineering Progress
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• v.14 no.1
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• pp.7-13
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• 2010

A thermophilic microorganism, which is able to hydrolyze starch, was isolated from soil and compost in Korea. It was Gram-positive, rod-shaped, catalase positive, nonmotile, glucose and mannitol fermentative, xylose oxidative, and spore forming microorganism. It also has an ability to hydrolyze casein and gelatin. The color of colony was yellowish white. The sequence of 16S rDNA of strain 2719 showed 99.5% sequence homology with the sequence of 16S rDNA of Bacillus thermoglucosidasius. On the basis of biochemical and physiological properties and phylogenetic analysis, the isolated strain was named as Bacillus thermoglucosidasius 2719.