• International Journal of Industrial Entomology and Biomaterials
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• v.20 no.1
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• pp.29-35
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• 2010

To compare the quality of manufactured goods distributed in the domestic markets, 6 isolates of Dongchongxiacao products, namely, 4 Paecilomyces tenuipes specimens (J2P, 901A, 901B, and 901C), 1 Cordyceps militaris specimen (901D), and 1 Cordyceps sinensis specimen (CI-1), were analyzed for their physicochemical properties and sequence-structure relationships. P. tenuipes (J2P), a kind of Dongchongxiacao, was successfully inoculated on silkworms by percutaneous infection of Rural Development AdminstraionNam et al., 1999); fruiting bodies were then formed on the complete surface of the pupa. Since P. tenuipes (J2P) from silkworm larva was also proved to have remarkable pharmacological activities, it has been produced in bulk and has been successfully sold to buyers in the Korean market. Additionally, imitation products such as 901A, 901B, 901C, 901D, and CI-1 were sold simultaneously, resulting in deterioration of product quality. This research focuses on establishing quality standards to discriminate between the original and imitation products circulating in the market. The products obtained for the experiments included J2P, 901A, 901B, 901C, 901D, and CI-1; proximate analysis was performed for these products. The hosts and methods of conidia inoculation for proliferation of mycelia differed among the products. P. tenuipes (J2P) was proliferated in live silkworm larvae, and dead silkworm pupae were used to produce 901A, 901B, and 901C. On the other hand, 901D was produced on hulled rice medium. Quality analysis of C. sinensis revealed that CI-1, which was imported from China, smelled bad and proved to be a counterfeit with the fruiting body glued to the insect by twigs. The results of the proximate analysis of 901A, 901B, 901C, and 901D were similar to those of J2P with respect to the moisture content. Otherwise, J2P contained higher crude protein than 901A, 901B, 901C, and 901D, but contained very low fat. C. militaris (901D) and C. sinensis (CI-1) had low crude protein content-12.79% and 9.78% respectively-as compared to that of J2P, which was 62.38%. In contrast to the crude ash content of 6.4% in J2P, the crude ash content of CI-1 was 18.51% and this specimen was found to contain many impurities. phylogenetic analysis of P. tenuipes revealed that the sequence similarity of J2P, 901B, and 901C was in the range of 92.3~92.7%. Additionally, differences in the sequences were found at the positions 65 bp, 436 bp, 441 bp, 463 bp, etc.

• Journal of Life Science
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• v.18 no.11
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• pp.1592-1599
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• 2008

The $\beta$-lactamase gene was cloned into E. coli DH5$\alpha$ from Bacillus sp. J105 with strong resistance against $\beta$-lactam antibiotics. The chromosomal DNA was partially digested with Sau3AI and ligated to BamHI digested pLAFR3. $\beta$-Lactamase positive clones were obtained by using in vitro packaging kit. The pKL11-${\Delta}4.6$ with $\beta$-lactamase activity was obtained by subcloning of the recombinant plasmid ($\beta$-lac +). The 6.5 kb fragment in the subcloned plasmid was sequenced. The DNA fragment that contains the $\beta$-lactamase gene encodes 309 amino acids. The 0.17 kb upstream region was similar to those of B. thuringinesis and B. cereus with 97% identity. The deduced amino acids sequence was also similar to those of $\beta$-lactamase from B. thuringinesis and B. cereus with 97% and 94% identity, respectively. The phylogenetic tree also showed the relationships of the $\beta$-lactamase gene of Bacillus sp. J105 to genetically related that of other Bacillus strains. Analysis of expression pattern of the pKL11-${\Delta}4.6$ in E. coli, revealed that the secretion efficiency of $\beta$-lactamase was $4{\sim}5%$ and the molecular weight was as same as that of original $\beta$-lactamase (31 kDa) from Bacillus sp. J105.

• Korean Journal of Ichthyology
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• v.2 no.2
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• pp.169-181
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• 1990

The development of eggs and larvae, and minute scale-like tubercles on the skin surface of larval Acantlaorhodeus gracilis from Korea were observed. They spawned from late March through the middle of June. A fish spawned at least 5 times and the number of eggs averaged 304 per oviposition. Unfertilized eggs are nearly ovoid-shaped(mean$\pm$SD=$2.09{\pm}0.04\;mm$ in length with range of 2.05 to 2.13 mm and mean$\pm$SD=$1.26{\pm}0.02\;mm$ in breadth with range of 1.24 to 1.30 mm measured for the 50 eggs) and opaque yellow color. The tip of egg membrane at the animal pole side swelled and formed a few hilly projections. The shape of the eggs was just like a loquat. Most of embryos began to hatch out in thirty-eight hours after insemination at $22{\pm}1^{\circ}C$ in water temperature. As regards the morphological characters of the eggs and larval development, Acan. gracilis was similar to Acan. asmussi, Acheilognathus rhombeus, A. longipinnis and Pseudoperilampus typus. The larvae of this species is unique particularly in the following two characters, i.e., 1) scale-like tubercles ellipsoided in a diagonal cross section on the whole body and 2) incessant wiggly movement pattern as that of fly maggot, with the larvae of the above mentioned species. These characters seem to reflect the phylogenetic relationships among acheilognathine fishes. On the other hand, this species and Acan. asmussi are spring-summer spawning bitterlings. And also these species never retard the larval growth in such larval stage as the duration from Stage B to Stage D.

• Horticultural Science & Technology
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• v.30 no.2
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• pp.178-184
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• 2012

This study was carried out to decide ITS (internal transcribed spacer) sequence of some Korean native $Aster$ species and to resolve their relationship among Korean native $Aster$, including $Kalimeris$, $Gymnaster$, $Heteropappus$ genus separated from $Aster$ in a previously study based on the pappus length. We registered 11 ITS sequences of $Aster$ species including $A.$ $glehni$ to GenBank and those sequences were used for the cluster analysis with $Kalimeris$ species. The size of ITS1 was varied from 248 to 256 bp, while ITS2 was varied from 220 to 222 bp. The G + C content of the ITS region ranged from 49.4 to 53.5%. Pairwise comparison results showed that the substitution rate of ITS1 and ITS2 region was 9% and 10%, respectively. $Kalimeris$ sensu strict substitution rate was lower than that of $Aster$ sensu strict species. The strict consensus parsimonious cluster analysis showed $A.$ $tripolium$ is the first branching from the clade and the next is $A.$ $scaber$. The $Kalimeris$ species except for the $A.$ $hispidus$ were grouped into the same clade with high bootstrap value (91%) within $Aster$. $Gymnaster$ and $Heteropappus$ that has been classified by morphological characters were also grouped into broad sense $Aster$ clade. These results implied these three genera could be merged together into $Aster$ based on the ITS sequences.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• v.8 no.2
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• pp.202-212
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• 2005

Purpose: Transfusion transmitted virus (TTV) is a newly discovered virus and to date the contribution of TTV to liver disease remains unclear. Little is known about the frequency of TTV infection in children in Korea. The purpose of this study was to investigate the prevalence and genotypic distribution of TTV carried by healthy children and patients with hepatitis in Korea. Methods: Eighty eight of healthy children and three groups of patients with hepatitis-14 patients with chronic hepatitis B, 12 patients with chronic hepatitis C and 25 patients with hepatitis of unknown etiology-were tested. TTV DNA was detected by semi-nested PCR using primer sets generated from N-22 region and from 5' noncoding region (NCR) of the viral genome. PCR products derived from 8 patients with hepatitis and from 11 healthy children were sequenced and a phylogenetic tree was constructed. Results: TTV was found by PCR with N22 primer in 11.3% of healthy children, 28.5% of children with hepatitis B, 25% of children with hepatitis C, 24% of children with hepatitis of unknown etiology. TTV DNA was found by PCR with 5'NCR primer in 32.9% of healthy children, 71.4% of patients with chronic hepatitis B, in 50% of patients with hepatitis C and in 48% of patients with hepatitis of unknown etiology. TLMV DNA was found in 48.9% of healthy children, 21.4% of patients with hepatitis B, 16.6% of patients with hepatitis C, 40% of patients with hepatitis of unknown etiology. Among the sequenced isolates, 10(52%) belonged to genotype 1 (G1) and others belonged to genotype 2 (G2) or genotype 3 (G3). Among the G1 sequences, 7 were grouped as G1a. Conclusion: TTV infection was common in healthy children and in patients with hepatitis. But, the prevalence of TTV DNA by 5'NCR primer was relatively high in patients with hepatitis B and there may be some association between TTV and hepatitis B virus infection. G1 was the major genotype of the studied population.

• Journal of Life Science
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• v.24 no.4
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• pp.461-466
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• 2014

Three plant species, Aster sphathulifolius, Sedum oryzifolium, and Lysimachia mauritiana, native to the Dokdo Islands in South Korea, were examined for rhizosphere microorganisms by using 16S rDNA sequences. Nine species of rhizosphere microorganisms were isolated from the three native plant species, respectively. Phylogenetic analysis showed that the microorganisms could be classified into 19 species belonging to four phyla (Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria), and the characteristics of the microbes were confirmed. Rhizosphere microorganisms from the six orders (Bacillales, Corynebacteriales, Flavobacteriales, Micrococcales, Oceanospirillales, and Rhodobacterales) were isolated from S. oryzifolium. From L. mauritiana, microbes belonging to the seven orders (Bacillales, Flavobacteriales, Micrococcales, Oceanospirillales, Rhizobiales, and Rhodobacterales) were isolated. From A. sphathulifolius, the six orders of rhizosphere microorganisms (Alteromonadales, Bacillales, Corynebacteriales, Flavobacteriales, Micrococcales, and Rhizobiales) were isolated. These data showed that Actinobacteria and Proteobacteria were the dominant phyla for the rhizosphere of all three plants. To confirm the bacterial diversity in rhizospheres, Shannon's diversity index (H') was used at the genus level. In these data, the rhizosphere from S. oryzifolium and L. mauritiana had more diverse bacteria compared to that from A. sphathulifolius.

• Korean Journal of Microbiology
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• v.52 no.3
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• pp.319-326
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• 2016

An antimicrobial bacterium to pathogenic microorganisms, strain $W5-1^T$ was isolated from Korean fermented-food Kimchi. The isolate was Gram-staining-variable, strictly aerobic, rod-shaped, endospore-forming, and motile with peritrichous flagella. It grew at $15-40^{\circ}C$, at pH 6.0-10.0, and in the presence of 0-4% NaCl. Strain $W5-1^T$ could hydrolyze esculin and xylan, and assimilate $\small{D}$-mannose, but not $\small{D}$-mannitol. Strain $W5-1^T$ showed antimicrobial activity against Listeria monocytogens, Pseudomonas aeruginosa, Staphylococcus aureus, and Salmonella typhi. The G+C content of the DNA of strains $W5-1^T$ was 52.6 mol%. The predominant respiratory quinone was menaquinone-7 (MK-7) and the major cellular fatty acids were $C_{16:0}$, antieiso-$C_{15:0}$, $C_{18:0}$, and $C_{12:0}$. The strain contained meso-diaminopimelic acid in cell-wall peptidoglycan. On the basis of 16S rRNA gene sequence and phylogenetic analysis, the strain W5-1 was shown to belong to the family Paenibacillaceae and was most closely related to Paenibacillus pinihumi $S23^T$ (98.4% similarity) and Paenibacillus tarimensis $SA-7-6^T$ (96.4%). The DNA-DNA relatedness between the isolate and Paenibacillus pinihumi $S23^T$ was 8.5%, indicating that strain $W5-1^T$ represented a species in the genus Paenibacillus. On the basis of the evidence from this polyphasic study, it is proposed that strain $W5-1^T$ is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus kimchicus sp. nov. is proposed. The type strain is $W5-1^T$ (=KACC $15046^T$ = $LMG 25970^T$).

• Korean Journal of Microbiology
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• v.52 no.3
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• pp.344-351
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• 2016

A marine bacterium, designated as strain 50C-3, was isolated from a seawater sample collected from the East Sea of South Korea. The strain is a Gram-negative, aerobic, yellow colored polar-flagellated bacterium that grows at $20-50^{\circ}C$ and pH 5.5-8.5. Optimal growth occurred at $40-50^{\circ}C$, at pH 6.5-7.5, and in the presence of 2% (w/v) NaCl. Based on 16S rRNA gene sequence similarity, the isolate was considered to represent a member of the genus Ruegeria. The result of this analysis showed that strain 50C-3 shared 99.4% and 96.98% sequence similarity with Ruegeria intermedia CC-GIMAT-$2^T$ and Ruegeria lacuscaerulensis ITI-$1157^T$, respectively. Furthermore, strain 50C-3 showed clear differences from related strains in terms of several characteristics such as motility, carbon utilization, enzyme production, etc. The DNA G+C content was 66.7 mol%. Chemotaxonomic analysis indicated ubiquinone-10 (Q-10) as the predominant respiratory quinone. Based on phenotypic, chemotaxonomic, and phylogenetic characteristics, the isolate represents a novel variant of the Ruegeria intermedia CC-GIMAT-$2^T$, for which we named Ruegeria sp. 50C-3 (KCTC23890=DSM25519). Strain 50C-3 did not produce cellulase and agarase, but produced alkaline phosphatase, ${\alpha}$-galactosidase, and ${\beta}$-galactosidase. The three enzymes showed stable activities even at $50^{\circ}C$ and thus regarded as thermostable enzymes. Especially, the ${\beta}$-galactosidase activity enhanced by 1.9 times at $50^{\circ}C$ than that at $37^{\circ}C$, which may be very useful for industrial application.

• Journal of Life Science
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• v.30 no.11
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• pp.947-955
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• 2020

The foot-and-mouth disease virus (FMDV), a member of the Aphthovirus genus in the Picornaviridae family, affects wild and domesticated ruminants and pigs. During replication of the FMDV RNA (ribonucleic acid) genome, FMDV-encoding RNA polymerase 3D acts in a highly location-specific manner. This suggests that specific RNA structures recognized by 3D polymerase within non-coding regions of the FMDV genome assist with binding during replication. One such region is the cis-acting replication element (CRE), which functions as a template for RNA replication. The FMDV CRE adopts a stem-loop conformation with an extended duplex stem, supporting a novel 15-17 nucleotide loop that derives stability from base-stacking interactions, with the exact RNA nucleotide sequence of the CRE producing different RNA secondary structures. Here, we show that CRE sequences of FMDVs isolated in Korea from 2010 to 2017 exhibit A and O genotypes. Interestingly, variations in the RNA secondary structure of the Korean FMDVs are consistent with the phylogenetic relationships between these viruses and reveal the specificity of FMDV infections for particular host species. Therefore, we conclude that each genetic clade of Korean FMDV is characterized by a unique functional CRE and that the evolutionary success of new genetic lineages may be associated with the invention of a novel CRE motif. Therefore, we propose that the specific RNA structure of a CRE is an additional criterion for FMDV classification dependent on the host species. These findings will help correctly analyze CRE sequences and indicate the specificity of host species for future FMDV epidemics.

• Journal of the Korea Organic Resources Recycling Association
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• v.16 no.4
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• pp.64-73
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• 2008

The cDNA of CCF (coelomic cytolytic factor)-like gene (EC 3.2.1.16), a kind of glycosyl hydorlase, was isolated and cloned from the midgut of the earthworm Eisenia anderi. The size of nucleotide sequence appeared to be 1,152 bp and its predicted coding region was composed of 384 amino acid residues including the initiation methionine. The 17 residues at N-terminal end in the deduced amino acid sequence were regarded to be a signal peptide. Based on the amino acid sequence analysis, it appeared that this CCF-like protein could belong to glycosyl hydrolase family 16 (GHF16) and showed a high sequence homology of about 79~99% with CCF and CCF-like proteins from other earthworm species. The CCFs and CCF-like proteins from various earthworm species exhibited a 100% homology in the polysacchride-binding motif and glucanase motif. It has been reported that the CCFs isolated from E. fedita appeared to show a broader pattern recognition specificity than those from other earthworm species because this species resides in decaying organic matter showing very high microbial activity, implying that CCF-like protein isolated in this study from E. andrei might exhibit a broad substrate specificity that is a useful characteristic for industrial application. A phylogenetic analysis using the deduced amino acid sequences of CCF-related proteins through the BLASTX revealed that GHF16 families could be divided into three groups of metazoa, viriplantae and eubacteria subfamily. Subsequently the CCF-related proteins of metazoa subfamily could clearly be subgroup into lophotrochozoan and edysozoan type including a deuterostome origin. Further understanding of the biological properties of E. andrei CCF-like protein should be addressed to regulate the ${\beta}$-D-glucan hydrolysis and production for the industrial uses.