• Journal of the korean society of oceanography
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• v.35 no.3
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• pp.158-160
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• 2000

The relativity of four isolates of C. polykrikoides was determined by comparative sequence analysis based on direct sequencing of PCR amplified ribosomal DNA (the internal transcribed spacer region and the 5.8S rDNA). Sequence comparisons indicated that four isolates had the same nucleotide sites in the ITS regions, as well as a total of 585 nucleotide length and 100% homology. The molecular data revealed that C. polykrikoides in Korean coastal waters show no genetical difference.

• Journal of Applied Biological Chemistry
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• v.56 no.2
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• pp.119-129
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• 2013

Thirteen different Streptomyces isolates were evaluated for their ability to produce keratinase using chicken feather as a sole carbon and nitrogen sources under solid state fermentation (SSF). Streptomyces sp. NRC 13S produced the highest keratinase activity [1,792 U/g fermented substrate (fs)]. The phenotypic characterization and analysis of 16S rDNA sequencing of the isolate were studied. Optimization of SSF medium for keratinase production by the local isolate, Streptomyces sp. NRC13S, was carried out using the one-variable-at-a-time and the statistical approaches. In the first optimization step, the effect of incubation period, initial moisture content, initial pH value of the fermentation medium, and supplementation of some agro-industrial by-products on keratinase production were evaluated. The strain produced about 2,310 U/gfs when it grew on chicken feather with moisture content of 75% (w/w), feather: fodder yeast ratio of 70:30 (w/w), and initial pH 7 using phosphate buffer after 8 days. Based on these results, the Box-Behnken design and response surface methodology were applied to find out the optimal conditions for the enzyme production. The corresponding maximal production of keratinase was about 2,569.38 U/gfs.

• Korean Journal of Medicinal Crop Science
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• v.26 no.2
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• pp.113-118
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• 2018

Background: Gastrodia elata Blume is a saprophytic perennial plant in the Orchidaceae family, because of its agricultural and medicinal effectiveness, researchers focus on its genome and chemical components. However, cytogenetic information based on the chromosome structure and composition to construct chromosomal backbone for genome sequencing research and for the development and breeding of plants is very limited. Methods and Results: We determined the metaphase chromosome composition of the G. elata genome by fluorescence in situ hybridization (FISH) using 5S and 45S rDNAs and telomeric repeat probes. The nuclear genome of G. elata was organized into 2 n = 36, with relatively small ($2.71-5.50{\mu}m$)chromosomes that showed gradual decrease in size. Conglutination phenomenon was observed among the metaphase chromosomes, and it was distinguished from that in other plant metaphase chromosome spreads. One pair of signal was detected for each 5S and 45S rDNA in the pericentromeric region and interstitial region on the short arm of chromosomes 10 and 4, respectively, and telomeric DNA signals were detected in the terminal region of most chromosomes. Conclusions: To our knowledge, this is the first FISH chromosome composition result in G. elata and could be useful in more comprehensive molecular cytogenetic and genomic analyses as well as breeding programs of the medicinal plant G. elata.

• Proceedings of the Korean Aquaculture Society Conference
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• 2003.10a
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• pp.134-135
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• 2003

The geographic expansion of the toxic dinoflagellates genus Alexandrium has been shown to be world wide ranging. The members of the genus Alexandrium ocnstituted of 20-30 species did not show substantial differences in their morphology, which is mostly referred in the 'tamarensis species complex', except some species. Though rDNA sequences variations are very few and pseudogene types are so diverse that it is difficult to use them as the specific markers. In this study, we outlined Korean and Japanese A, tamarense and A. catenella regional isolates by phylogenetic analysis inferred from no cutting alignments of LSU rDNA D1-D2 and SSU rDNA sequences to group these regional isolates. The results were compared to RFLP patterns of PCR products targeted chloroplast DNA. Lastly screening of highly repeated microsatellite DNA which is frequently used for population analysis in eukaryotes was conducted. A. catenella regional strains identified by the sequencing of rDNA D1-D2 domain were divided into at least 3 groups of type E, CMC and Chinese type, divergence root may not be deep comparing with that of A. tamarense whose pseudogenes are very variable. Results of RFLP pattern and the phylogeny of the unknown gene targeting chloroplast showed that Korean and Japanese A. catenella regional isolates were divided into 3 types: Korean, Japanese and the third CMC types. Population-specific PCR amplification with Japanese A. catenella type-specific PCR primers was useful method for population analysis of A. catenella. Various types of satellite sequences such as 5 nucleotides repeats were obtained from A. tamarense and A. catenella. The 5 nucleotides repeats were primed at the both 3'and 5' ends, and these repeats were prominent as longer repeated motifs. This repeated DNA was intercalated as internal sequences containing various types subrepeats. It is expected that these satellite DNA would be a useful molecular population marker through detail comparison among Alexandrium regional isolates to trace their transferring pathway and to prevent their human-associated their regional extents.

• The Plant Pathology Journal
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• v.26 no.1
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• pp.83-89
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• 2010

Taxonomic position of 46 Korean isolates of Rhizoctonia solani which were classified into nine intraspecific groups by anastomosis and cultural characteristics was analyzed by randomly amplified polymorphic DNA (RAPD) and sequence analyses of the internal transcribed spacer (ITS) regions of ribosomal DNA. All the isolates within each group showed highly similar band patterns in RAPD. The ITS regions of the isolates within the same groups showed a high level of sequence similarity above 96.0% whereas similarities among different groups were below 94.4%. When compared with several reference strains of R. solani from foreign countries, all the Korean isolates were clustered with the foreign isolates belonging to the same groups in the phylogenetic tree. All six Korean strains of AG-4 were identified as HG-1 out of 3 subgroup of AG-4. We discussed taxonomic position of Korean isolates of R. solani and showed that sequence analysis with ITS regions could be a rapid and useful method for identification of intraspecific group of R. solani.

• Genomics & Informatics
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• v.10 no.4
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• pp.249-255
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• 2012

In this study, fosmid cloning strategies were used to assess the microbial populations in water from the International Space Station (ISS) drinking water system (henceforth referred to as Prebiocide and Tank A water samples). The goals of this study were: to compare the sensitivity of the fosmid cloning strategy with that of traditional culture-based and 16S rRNA-based approaches and to detect the widest possible spectrum of microbial populations during the water purification process. Initially, microbes could not be cultivated, and conventional PCR failed to amplify 16S rDNA fragments from these low biomass samples. Therefore, randomly primed rolling-circle amplification was used to amplify any DNA that might be present in the samples, followed by size selection by using pulsed-field gel electrophoresis. The amplified high-molecular- weight DNA from both samples was cloned into fosmid vectors. Several hundred clones were randomly selected for sequencing, followed by Blastn/Blastx searches. Sequences encoding specific genes from Burkholderia, a species abundant in the soil and groundwater, were found in both samples. Bradyrhizobium and Mesorhizobium, which belong to rhizobia, a large community of nitrogen fixers often found in association with plant roots, were present in the Prebiocide samples. Ralstonia, which is prevalent in soils with a high heavy metal content, was detected in the Tank A samples. The detection of many unidentified sequences suggests the presence of potentially novel microbial fingerprints. The bacterial diversity detected in this pilot study using a fosmid vector approach was higher than that detected by conventional 16S rRNA gene sequencing.

• Microbiology and Biotechnology Letters
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• v.31 no.4
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• pp.421-428
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• 2003

To develop the functional-compost containing antifungal substance by using antagonistic microorganisms, Spinacia oleracea L and Rhizoctonia solani Kuhn O-28 were used as a model plant and phytopathogen, respectively. Total 80 strains were isolated from the compost of various waste foods mixture processed for a year. Among them, No.15-2 strain was selected due to its highest antifungal activity against R. solani Kuhn O-28 and was identified phyno- and phylogenotypically as Burkholderia cepacia genomovar V. which is rare probability in pathogen, by 16S rDNA sequencing and specific primer pair PCR method. B. cepacia No.15-2 preferentially dominated during the compost and its cell numbers were maintained almost $${\times}$10^{13}$ cuf/g for 15 days. The morbidity caused by R. solani Kuhn O-28 in S. oleracea L cultivation was reduced to 40% by addition of B. cepacia No.15-2. In conclusion, the antifungal compost using B. cepacia No.15-2 could be applied to biocontrol of various crops blights caused by fungal pathogen.

• Food Science of Animal Resources
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• v.37 no.4
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• pp.535-541
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• 2017

This study investigated the psychrotrophic bacteria isolated from chicken meat to characterize their microbial composition during refrigerated storage. The bacterial community was identified by the Illumina MiSeq method based on bacterial DNA extracted from spoiled chicken meat. Molecular identification of the isolated psychrotrophic bacteria was carried out using 16S rDNA sequencing and their putrefactive potential was investigated by the growth at low temperature as well as their proteolytic activities in chicken meat. From the Illumina sequencing, a total of 187,671 reads were obtained from 12 chicken samples. Regardless of the type of chicken meat (i.e., whole meat and chicken breast) and storage temperatures ($4^{\circ}C$ and $10^{\circ}C$), Pseudomonas weihenstephanensis and Pseudomonas congelans were the most prominent bacterial species. Serratia spp. and Acinetobacter spp. were prominent in chicken breast and whole chicken meat, respectively. The 118 isolated strains of psychrotrophic bacteria comprised Pseudomonas spp. (58.48%), Serratia spp. (10.17%), and Morganella spp. (6.78%). All isolates grew well at $10^{\circ}C$ and they induced different proteolytic activities depending on the species and strains. Parallel analysis of the next generation sequencing and culture dependent approach provides in-depth information on the biodiversity of the spoilage microbiota in chicken meat. Further study is needed to develop better preservation methods against these spoilage bacteria.

• Journal of Aquaculture
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• v.10 no.4
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• pp.403-407
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• 1997

Intraspecific sequence variation was detected by polymerase chain reaction (PCR) and direct sequencing of a 350-nucleotide region of the mitochondrial 12S rRNA gene of two natural populations (Han River and Nakdong River) and one hatchery stock (Jinhae Inland Fisheries Institute) of local strain common carp, one Israeli strain of common carp stock from Pukyong National University (PKU), and one hybrid between Israeli strain of common carp female and local strain common carp male from PKU stock. There is little variation in 350 bases of the mitochondrial 12S rRNA gene sequences among 2 natural and 1 hatchery local strain common carp populatins, representing abut 7 to 20 nucleotide differences (less than 6%). The sequence of specimens from Han River was more similar to that from Nakdong River (identity=98.0%) than to that from Jinhae Inland Fisheries Institute (identity=96.3%). Sequence variation between Israeli strain and wild local strain common carp was higher than the variation within natural stocks. The level of variation was ranged from 15.7 to 17.7%. The hybrid showed very similar nucleotide4 sequence of 12S rRNA gene to the sequence of Israeli strain with the identity of 98.9%.

• 한국생물공학회:학술대회논문집
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• 2000.11a
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• pp.77-80
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• 2000

Various analytical methods such as electron microscopy, quinone analysis, and 16S rDNA sequencing studies were used to investigate the microbial communities and to identify the microorganisms responsible for enhanced biological phosphorus removal (EBPR) in an anaerobic/aerobic sequencing batch reactor (SBR) fed with acetate. Electron photomicrographs showed that oval-shaped microorganisms of about $0.7\;{\sim}\;1\;{\mu}m$ in diameter dominated the microbial sludge. These microorganisms contained polyphosphate granules and glycogen inclusions, which suggests that they are a kind of phosphorus accumulating organism. Quinone and 16S rRNA sequence analyses showed that the members of Proteobacteria beta subclass were the most abundant species, which were affiliated with the Rhodocyclus-likes group. Phylogenetic analysis revealed that the two dominating clones of the beta subclass were most distantly related to Propionivibrio dicarboxylicus DSM 5885 and Rhodocyclus tenuis DSM 109 with about 95% and 96% sequence similarity, respectively. Therefore, it was concluded that the oval-shaped organisms related to the Rhodocyclus-likes group are likely to be responsible for biological phosphorus removal in SBR operation supplied with acetate.