• Korean Journal of Microbiology
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• v.53 no.4
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• pp.242-250
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• 2017

Actinobacteria tolerating extreme conditions can be a rich source of bioactive compounds and enzymes. In this study filamentous actinobacteria were isolated from soils of Ulleung Island, and their physiological properties were examined. Soil samples were collected, serially diluted and spread on various agar media. The average viable counts of total bacteria were $1.28{\times}10^7CFU/g$ for soil sample 1 (ULS1) and $2.05{\times}10^7CFU/g$ for soil sample 2 (ULS2). As a result, 34 strains of actinobacteria were isolated and assigned to the genera Streptomyces (16 strains), Isoptericola (5 strains), Rhodococcus (4 strains), Agromyces (3 strains), Micrococcus (2 strains), Arthrobacter (1 strain), Williamsia (1 strain), Microbacterium (1 strain), and Oerskovia (1 strain) based on 16S rRNA gene sequence analysis. Enzyme activity and plant growth promoting potential were tested for representative isolates. Multiple strains of Streptomyces degraded starch, casein and Tween 80. As for plant growth promoting potential, strains of Oerskovia, Williamsia, Isoptericola, and Streptomyces solubilized phosphate, and those of Agromyces, Oerskovia, Micrococcus, Rhodococcus, Streptomyces, and Isoptericola produced 3-indole-acetic acid (IAA), respectively. Selected strains of Streptomyces exhibited strong antagonistic activity against Staphylococcus aureus and Bacillus subtilis as well as Candida albicans. This study confirms that actinobacteria from Ulleung Island can be a good source of novel bioactive compounds.

• Journal of Life Science
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• v.29 no.5
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• pp.524-529
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• 2019

Medicinal plants resources are becoming important assets since their usages have been expanded to the development of functional foods for human health, cosmetics and pharmaceutical industries. However, their phylogenetic origins and names are different from each country and quite often they are mixed each other resulting in the confusion for consumers. Particularly when they are very similar based on their morphological characteristics and distributed, it is extremely difficult to differentiate their origins even by specialists. Therefore, identification of each plant species is important for standardizing herbal medicine. Thistle is a medicinal and perennial plant. Obtaining information about the genetic diversity of plant populations is highly important for conservation and germplasm utilization. Although thistle is an important medicinal plant species registered in South Korea, no molecular markers are currently available to distinguish from other similar species from different countries. In this study, we developed single nucleotide polymorphism (SNP) markers derived from chloroplast genomic sequences to identify distinct Korean-specific thistle species via high resolution melting (HRM) curve analyses. We performed molecular authentication of four different kinds of thistle species from different regions using DNA sequences in the trnL-F and matK chloroplast intergenic region. The SNP markers developed in this study are useful for rapidly identifying specific thistle species from different country.

• Korean Journal of Environmental Agriculture
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• v.41 no.4
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• pp.335-343
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• 2022

BACKGROUND: Antibiotics used in animal husbandry for disease prevention and treatment have resulted in the rapid progression of antibiotic resistant bacteria which can be introduced into the environment through livestock feces/manure, disseminating antibiotic resistant genes (ARGs). In this study, fecal samples were collected from the livestock farms located in Jeju Island to investigate the relationship between microbial communities and ARGs. METHODS AND RESULTS: Illumina MiSeq sequencing was applied to characterize microbial communities within each fecal sample. Using quantitative PCR (qPCR), ten ARGs encoding tetracycline resistance (tetB, tetM), sulfonamide resistance (sul1, sul2), fluoroquinolone resistance (qnrD, qnrS), fluoroquinolone and aminoglycoside resistance (aac(6')-Ib), beta-lactam resistance (bla_TEM, bla_CTX-M), macrolide resistance (ermC), a class 1 integronsintegrase gene (intI1), and a class 2 integrons-integrase gene (intI2) were quantified. The results showed that Firmicutes and Bacteroidetes were dominant in human, cow, horse, and pig groups, while Firmicutes and Actinobacteria were dominant in chicken group. Among ARGs, tetM was detected with the highest number of copies, followed by sul1 and sul2. Most of the genera belonging to Firmicutes showed positive correlations with ARGs and integron genes. There were 97, 34, 31, 25, and 22 genera in chicken, cow, pig, human, and horse respectively which showed positive correlations with ARGs and integron genes. In network analysis, we identified diversity of microbial communities which correlated with ARGs and integron genes. CONCLUSION(S): In this study, antibiotic resistance patterns in human and livestock fecal samples were identified. The abundance of ARGs and integron genes detected in the samples were associated with the amount of antibiotics commonly used for human and livestocks. We found diverse microbial communities associated with antibiotics resistance genes in different hosts, suggesting that antibiotics resistance can disseminate across environments through various routes. Identifying the routes of ARG dissemination in the environment would be the first step to overcome the challenge of antibiotic resistance in the future.

• Journal of Life Science
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• v.33 no.10
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• pp.808-819
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• 2023

This study was conducted to develop a selection marker for the identification of the Bacillus licheniformis K12 strain in microbial communities. The strain not only demonstrates good growth at moderate temperatures but also contains enzymes that catalyze the decomposition of various polymer materials, such as proteases, amylases, cellulases, lipases, and xylanases. To identify molecular markers appropriate for use in a microbial community, a search was conducted to identify variable gene regions that show considerable genetic mutations, such as recombinase, integration, and transposase sites, as well as phase-related genes. As a result, five areas were identified that have potential as selection markers. The candidate markers were two recombinase sites (BLK1 and BLK2), two integration sites (BLK3 and BLK4), and one phase-related site (BLK5). A PCR analysis performed with different Bacillus species (e.g., B. licheniformis, Bacillus velezensis, Bacillus subtilis, and Bacillus cereus) confirmed that PCR products appeared at specific locations in B. licheniformis: BLK1 in recombinase, BLK2 in recombinase family protein, and BLK3 and BLK4 as site-specific integrations. In addition, BLK1 and BLK3 were identified as good candidate markers via a PCR analysis performed on subspecies of standard B. licheniformis strains. Therefore, the findings suggest that BLK1 can be used as a selection marker for B. licheniformis species and subspecies in the microbiome.

• Korean Journal of Ichthyology
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• v.22 no.2
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• pp.115-120
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• 2010

Genetic variation and population structure of the slender bitterling Acheilognathus lanceolatus of Korea (the Han, Geum, Dongjin, Seomjin and Nakdong Rivers) and Japan (the Katsura River) were assessed by amplified fragment length polymorphism (AFLP) analysis. Five combinations of selective primers generated 345~374 DNA fragments, of which 55~131 were polymorphic. The Nakdong River population had the highest genetic diversity and the Han River population had the lowest genetic diversity. Dendrogram based on the distance matrix revealed that individuals from each population consistently clustered together and bifurcated into two distinct clades (or population groups) composed of the Han, Geum, Dongjin and Seomjin River populations and of the Nakdong and Katsura River populations, supported with high bootstrap values. The pairwise genetic differentiation ($F_{ST}$) estimates showed that the six populations were genetically well differentiated (P<0.01). The analysis of molecular variance (AMOVA) after partitioning the six populations into two population groups revealed very strong biogeographic structuring between them with 25.49% of total variance (P<0.01). Taken together, the AFLP markers clearly divided six A. lanceolatus populations into two population groups.

• Journal of Life Science
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• v.22 no.7
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• pp.970-980
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• 2012

Native halophytes, such as Suaeda maritima, Limonium tetragonum, S. japonica, Zoysia sinica, and Phragmites australis were collected from the Muan salt marsh. Ninety endophytic fungi were isolated from the roots of the collected halophytes. Molecular insights inferred by internal transcribed spacer containing ITS1, 5.8s, and the ITS2 region showed that all the fungal strains belong to ten orders, i.e., Capnodiales (4.44%), Cystofilobasidiales (1.11%), Dothideales (3.33%), Eurotiales (53.33%), Glomerellales (3.33%), Hypocreales (8.89%), Mucorales (1.11%), Pleosporales (15.56%), Sordariales (1.11%), and Trichosphaeriales (1.11%). The rest (6.67%) of all fungal isolates were not identified. Ninety fungal strains were confirmed at the genus level, containing Acremonium, Alternaria, Aspergillus, Aureobasidium, Cephalosporium, Chaetomium, Cladosporium, Colletotrichum, Cryptococcus, Didymella, Dothideomycete, Emericellopsis, Epicoccum, Eupenicillium, Fusarium, Gibberella, Gongronella, Macrophoma, Microsphaeropsis, Nigrospora, Paecilomyces, Paraconiothyrium, Penicillium, Phaeomyces, Phoma, Pleosporales, Purpureocillium, and Talaromyces. Of all the endophytic fungi identified from the various halophytes, Aspergillus and Penicillium of Eurotiales had the highest abundance.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.21 no.4
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• pp.158-170
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• 2016

We investigated the occurrence of the dinoflagellate genus Alexandrium in the nineteen Korean coastal sites from July to October 2013. Alexandrium-like planktonic cells were microscopically observed only in four out of the 19 sampling sites. From the samples containing Alexandrium-like cells 22 clonal cultures of Alexandrium species were established by single cell or single chain isolation method. Taxonomic identity of the 4 different strains ascertained by the robust analyses of morphological and molecular genetic characteristics were confirmed to be A. catenella, A. affine, A. fraterculus and an unidentified Alexandrium sp. for which strain WEB-Alex-01 was assigned. It was ascertained that in spite of hot summer diverse Alexandrium species attaining up to four were distributed in the study area, in contrast with the long empirical recognition that the emergence of Alexandrium species is restricted to cooler seasons like spring or autumn in Korean coastal waters. Morphology and genetic characteristics of Alexandrium sp. strain WEB-Alex-01 are different from any other previously reported Alexandrium species from Korean seas, which implies that further studies on taxonomic, physiological, ecological and toxicological properties of the newly recorded Alexandrium species are needed.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.51 no.3
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• pp.259-268
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• 2006

Miniature inverted transposable elements (MITEs) are abundant genomic components in plant including rice. MITE-transposon display (MITE-TD) is an Amplified Fragment Length Polymorphism (AFLP)-related technique based on MITE sequence. In this study, we used the MITE-AFLP for the analysis of diversity and relation-ship of the 114 japonica accessions. Of the several MITEs, the mPing family was applied to detect polymorphisms based on PCR amplification. The BfaI adaptor primer and the specific primer derived from mPing terminal inverted repeat (TIR) region were used to PCR amplification of 114 accessions. Nine primer pairs produced a total of 160 polymorphic bands. PIC values of the polymorphic bands generated by nine primer pairs ranged from 0.269 (BfaI + ACT) to 0.426 (BfaI + T). Each accession revealed a distinct fingerprint with two primer combinations, BfaI + G and BfaI + C. Cluster analysis using marker-based genetic similarity classified 114 accessions into five groups. MITE-AFLP markers were genetically mapped using a population of 80 BILs (BC1F7) derived from a cross between the rice accessions, Milyang 23 and Hapcheonaengmi 3. Eight of the markers produced with the primer pair BfaI + 0 were mapped on chromosomes 1, 2, 4, 5, 7, and 9. Considering that one MITE-AFLP marker on chromosome 7 was tightly linked to the Rc gene, the MITE-AFLP markers will be useful for gene tagging and molecular cloning.

• Journal of Crop Science and Biotechnology
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• v.11 no.1
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• pp.17-22
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• 2008

Aromatic rice has become popular owing to its aroma. Growing demand for aromatic rice has spurred interest in the development of domestic cultivars that offer similar combinations of grain attributes such as texture, cooking characteristics, aroma, and taste. In this study, the most important agronomic attributes and aroma of 26 cultivars from Afghanistan, Iran, and Uzbekistan, and controls from Japan, Thailand, and India were characterized. Also $F_2$ populations derived from the cross between(Jasmine 85 aromatic$\times$Nipponbare non-aromatic) and(Jasmine 85$\times$Basmati 370 aromatic) were obtained. Tasting individual grains, cooking test, 1.7% KOH sensory test, and molecular marker analysis have been applied to distinguish between aromatic and non-aromatic rice. Diversity for some traits of agronomic importance, such as plant height was detected among countries, e.g. Afghan cultivars classified as tall, and Iranian and Uzbek intermediate and short, respectively. Differentiations of panicle, grain, leaf, basal internode, and culm dimension among rice cultivars, indicating the source of rice diversity in Central Asia. According to the results, 6 of 10, 2 of 7, and 0 of 6 of Afghan, Iranian, and Uzbek rice cultivars were scored as aromatic, respectively. Therefore, Afghan cultivars are a good source of aromatic rice germplasm for Central Asia. The expression between aromatic and non-aromatic, and aromatic and aromatic combinations has been evaluated. The observed segregation ratio of these crosses in the $F_2$ populations was tested by $x^2$ analysis against the expected ratio for a single gene. A segregation ratio of 3:1 between non-aromatic and aromatic combination has been detected, while segregation has not been detected between the aromatic and aromatic combinations. Also, parallel results were obtained from the tested aromatic rice cultivars. Thus, our results suggest that a single recessive gene controls aroma in all aromatic rice cultivars.

• Journal of Environmental Health Sciences
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• v.39 no.2
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• pp.166-177
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• 2013

Objectives: The genus Legionella is common in aquatic environments. Some species of Legionella are recognized as potential opportunistic pathogens for human, notably Legionella pneumophila that causes, Legionellosis. Thus, we investigated the contamination of Legionella pneumophila on water supply systems in Seoul, including cooling towers, public baths, hospitals and fountains. Methods: The existence of 16S rRNA and mip gene of L. pneumophila was confirmed in the genome of the isolated strains by PCR. Results: During the summer season of 2010 and 2011, Legionella pneumophila were detected from 163 samples (21.1%) out of 772 samples collected. Among the 163 strains of L. pneumophila, eighty one isolates belonged to serogroup 1 (57.4%), 23 isolates were serogroup 5 (16.3%), 21 isolates were serogroup 6 (14.9%), 8 isolates were serogroup 2 (5.79%), and 8 isolates were identified in serogroup 3 (5.7%). Through PFGE (pulsed-field gel electrophoresis) analysis using Sfi I, genetic types of L. pneumophila were classified into five (A to E) patterns by the band similarity with excess of 70% from public baths. Conclusions: The PFGE patterns of the serotypes showed a tendency for diversity of L. pneumophila. Our results suggest the existence of serological and genetic diversity among the L. pneumophila isolates.