• International Journal of Industrial Entomology and Biomaterials
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• 제27권1호
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• pp.142-158
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• 2013

The bumblebee, Bombus ignitus (Hymenoptera: Apidae), is a valuable natural resource that is widely utilized for greenhouse pollination in South Korea. Understanding the magnitude of genetic diversity and geographic relationships is of fundamental importance for long term preservation and utilization. As a first step, we sequenced a partial COI gene of mitochondrial DNA (mtDNA) corresponding to the "DNA barcode" region and the complete internal transcribed spacer 2 (ITS2) of nuclear ribosomal DNA from 88 individuals collected in nine South Korean localities. The complete ITS2 sequences were longest among known insects, ranging in size from 2,034 bp ~ 2,052 bp, harboring two duplicated 112-bp long repeats. The 658-bp long mtDNA sequences provided only six haplotypes with a maximum sequence divergence of 0.61% (4 bp), whereas the ITS sequences provided 84 sequence types with a maximum sequence divergence of 1.02% (21 sites). The combination of the current COI data with those of published data suggest that the B. ignitus in South Korea and China are genetically a large group, but those in Japan can be roughly separated into another group. Overall, a very high per generation migration ratio, a very low level of genetic fixation, and no discernable hierarchical population were found to exist among the South Korean populations of B. ignitus, which suggests panmixia. This finding is consistent with our understanding of the dispersal capability of the species.

• Journal of Microbiology and Biotechnology
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• 제17권7호
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• pp.1090-1097
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• 2007

Genomic analysis of Thermococcus sp. NA1 revealed the presence of a 3,927-base-pair (bp) family B-type DNA polymerase gene, TNA1_pol. TNA1_pol, without its intein, was overexpressed in Escherichia coli, purified using metal affinity chromatography, and characterized. TNA1_pol activity was optimal at pH 7.5 and $75^{\circ}C$. TNA1_pol was highly thermostable, with a half-life of 3.5h at $100^{\circ}C$ and 12.5h at $95^{\circ}C$. Polymerase chain reaction parameters of TNA1_pol such as error-rate, processivity, and extension rate were measured in comparison with rTaq, Pfu, and KOD DNA polymerases. TNA1_pol averaged one incorrect bp every 4.45 kilobases (kb), and had a processivity of 150 nucleotides (nt) and an extension rate of 60 bases/s. Thus, TNA1_pol has a much faster elongation rate than Pfu DNA polymerase with 7-fold higher fidelity than that of rTaq.

• Bulletin of the Korean Chemical Society
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• 제28권12호
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• pp.2203-2208
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• 2007

Three possible binding modes of cationic meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) to d[(GCATATATGC)2] duplex were investigated by the molecular dynamics (MD) simulation. Among the three binding modes namely, “along the groove”, “across the groove” and “face on the groove”, the “across the groove” model exhibited the largest negative binding free energy and the DNA backbone remained as the B form. In this model, the molecular plain of the TMPyP tilts 45o with respect to the DNA helix axis and is largely exposed to the solvent. TMPyP was stabilized mainly by the interaction between the positively charged neighboring pyridinium moieties of TMPyP and negatively charged phosphate groups of DNA. The result obtained in this work by MD and the report (Jin, B. et al., J. Am. Chem. Soc. 2005, 127, 2417.) that the spectral properties of poly[d(A-T)2] bound TMPyP in the presence and absence of the minor groove binding drug 4',6- diamidino-2-phenylindole are similar, we propose that TMPyP bind across the minor groove of the AT rich- DNA.

• Journal of Preventive Medicine and Public Health
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• 제38권2호
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• pp.170-174
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• 2005

Objectives: The aim of this study was to evaluate the response to a hepatitis B vaccination, and investigate the HBV DNA in subjects with isolated anti-HBc. Methods: 34 subjects with persistent isolated anti-HBc were included in the study. 32 subjects negative for HBsAg, anti-HBs and anti-HBc were included as a control group. They were all vaccinated with Hepaccine at 0, 1 and 2 months, and anti-HBs titers were measured 1 month after the 1st and 3rd vaccinations (1 and 3 months). The HBV-DNA was tested by polymerase chain reaction in subjects with isolated anti-HBc. Results: After the 1st & 3rd vaccinations, the anti-HBs titers$\geq$10mIU/ml were 70.6 & 70.6% in isolated anti-HBc group, and 34.4 & 81.2% in the control group, respectively. There were statistically significant differences after the 1st vaccination, but none after the 3rd, between the two groups. In the isolated anti-HBc and control groups, the primary, amnestic and no responses were 0 vs. 46.9%, 55.9 vs. 6.3% and 29.4 vs. 18.8%, respectively. The HBV DNA was not detected in all subjects with isolated anti-HBc. Conclusion: None of the subjects with isolated anti-HBc had a false positive result (primary response); therefore, they should be excluded from vaccination programs in Korea. To differentiate between immunity and occult infections, a single dose of vaccine, with a follow-up anti-HBs test, is preferable for subjects with isolated anti-HBc. An amnestic response indicates late immunity, and no response a suspect occult infection.

• Microbiology and Biotechnology Letters
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• 제22권5호
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• pp.467-476
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• 1994

Lactobacillus casei HY 2782, prophage cured strain was characterized to be stable as much as L casei YIT 9018, parent strain. By southern hybridization, it was confirmed that the temperate phage was incorporated in chromosomal DNA of L. casei YIT 9018 as a prophage. It was also proved that the prophage was cured from chromosomal DNA of L casei HY 2782. The growth rate, lactic acid producing ability, carbohydrates fermentation, and enzymatic activity of L. casei HY 2782 were found to be similar to those of L. casei YIT 9018. When L casei HY 2782 was used as a host, the multiplicity of infection (M.O.I.) of the temperate phage for L. casei HY 2782 was 1.0~5.0. Restriction enzyme analysis of pLC90 plasmid from L. casei HY 2782 was shown that the size was an approximately 68.22 kb. The plasmid profiles, genomic DNA patterns, and cellular fatty acids composition of L. casei HY 2782 were similar to those of L casei YIT 9018. And the major fatty acids composition of these strains were C$_{14;0}$,C$_{16;1}$, C$_{16;0}$, C$_{18;1}$ and C$_{19;cyclo-}$ 10 sets of arbitrary primer in the PCR were screened to find differentiation against two strains of L. casei. Among them, b$_{5}-1/17-1 primer was produced an approximately 1.3 kb DNA band of only L casei YIT 9018. And b$_{5}-2/17-2 primer was produced an approximately 1.0 kb DNA band of only L casei HY 2782.

• Bulletin of the Korean Chemical Society
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• 제27권4호
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• pp.568-572
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• 2006

To study the effect of sequence on DNA structure, the two decamer crystal structures one alternating,d(GTACGCGTAC), and the other non-alternating, d(GGCCGCGGCC), were solved. Crystals of both decamers belong to the hexagonal space group $P6_122$, with one strand in the asymmetric unit. The unit cell constants of the alternating decamer are a = b = 39.26 $\AA$, c = 77.70 $\AA$. The structure was refined with 1,828 reflections from 8.0 to 2.0 Aresolution to an R value of 21.3% with all DNA atoms and 63 water molecules. The isomorphous non-alternating decamer had unit cell dimensions of a = b = 39.05 $\AA$, c = 82.15 $\AA$. The structure was refined with 2,423 reflections from 8.0 to 2.0 $\AA$ resolution to a final R value of 22.2% for all DNA atoms and 65 water molecules. Although the average helical parameters of the decamers are typical of A-DNAs, there are some minor differences between them. The helical twist, rise, x-displacement, inclination and roll alternate in the alternating decamer, but do not in the non-alternating decamer. The backbone conformations in both structures show some differences; the residue G(7) of the alternating decamer is trans for $\alpha$ and $\gamma$ while the trans conformations are observed at the residue G(8) of the non-alternating decamer.

• Journal of the Korean Chemical Society
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• 제57권2호
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• pp.246-251
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• 2013

With -$OCH_2CO$- as a linker, a non ${\beta}$-substituted cationic bisporphyrin (4a) and a ${\beta}$-substituted cationic bisporphyrin (4b) were prepared through methylation of the intermediate which was obtained from ${\beta}$-amino-5,10,15,20-tetra (4-cyanophenyl) porphyrin or 5-hydroxylphenyl-10,15,20-tris(4-cyanophenyl) reacting with 5-hydroxy-10,15,20-trispyridinylporphyrin. Their structures were confirmed by $^1H$ NMR, IR, UV-vis, MS and elemental analysis. DNA photocleavage ability and the singlet oxygen ability of those cationic bisporphyrins were investigated. DNA photocleavage activity of ${\beta}$-substituted cationic bisporphyrin was significantly weaker than that of $H_2TMPyP$, but similar to that of non ${\beta}$-substituted cationic bisporphyrin. While 4a and 4b showed substantial photocleavage activities toward DNA, with 68% and 66% observed at 10 ${\mu}M$. The assessment of indirectly measured $^1O_2$ production rates against $H_2TMPyP$ were described and the relative singlet oxygen production yields were: free cationic bisporphyrins > $H_2TMPyP$. The results showed the cationic bisporphyrins with ${\beta}$-substitution and non ${\beta}$-substitution could be developed as potential photodynamic agents.

• YAKHAK HOEJI
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• 제51권6호
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• pp.415-423
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• 2007

This study was to evaluate the genotoxic effects of airborne particulate matters using single cell gell elec trophoresis (comet assay) in A549 human lung carcinoma cells. The total suspended particulate (TSP) was collected on back-up filter in Chuncheon, Kangwon Do, South Korea from April, 2003 to February, 2005. The concentrations of TSP, B(a)p and most of heavy metals seemed to be higher in spring and winter, and lower in summer. And they showed higher concentration in the commercial areas and the residential area having more traffics than in the rural area. It was found that A549 cells interacting with the organic extract of TSP showed more DNA single-strand breaks compare to untreated cells. The genotoxicity of the organic extract of TSP was increased with the pre-treatment of S-9 mixture during the culture or with the treatment of endonuclease after cell lysis. The DNA damage by the organic extract of TSP was higher in winter and the commercial area than in summer and the rural area. This study suggests that TSP, heavy metals and B(a)P analyzed showed significant variation depend on the seasons and the areas which are correlated with the DNA damage evaluated by Comet assay, indicating that genotoxic biomarker is useful for toxicological evaluation of air quality.

• Journal of Microbiology and Biotechnology
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• 제10권5호
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• pp.643-650
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• 2000

A new aniline-utilizing microorganism, strain HY1 obtained from an orchard soil, was characterized by using the BIOLOG system, an analysis of the total cellular fatty acids, and a 16S rDNA sequence. Strain HY1 was identified as a Burkholderia species, and was designated Burkholderia sp. HY1. GC and HPLC analyses revealed that Burkholderia sp. HY1 was able to degrade aniline to produce catechol, which was subsequently converted to cis,cis-muconic acid through an ortho-ring fission pathway under aerobic conditions. Strain HY1 exhibited a drastic reduction in the rate of aniline degradation when glucose was added to the aniline media. However, the addition of peptone or nitrate to the aniline media dramatically accelerated the rate of aniline degradation. A fatty acid analysis showed that strain HY1 was able to produce lipids 16:0 2OH, and 11 methyl 18:1 ${\omega}7c$ approximately 3.7-, 2.2-, and 6-fold more, respectively, when grown on aniline media than when grown on TSA. An analysison the alignment of a 1,435 bp fragment. A phylogenetic analysis of the 16S rDNA sequence based on a 1,420 bp multi-alignment sowed of the 16s rDNA sequence revealed that strain HY1 was very closely related to Burkholderia graminis with 95% similarity based that strain HY1 was placed among three major clonal types of $\beta$-Proteobacteria, including Burkholderia graminis, Burkholderia phenazinium, and Burkholderia glathei. The sequence GAT(C or G)${\b{G}}$, which is highly conserved in several locations in the 16S rDNA gene among the major clonal type strains of $\beta$-Proteobacteria, was frequently replaced with GAT(C or G)${\b{A}}$ in the 16S rDNA sequence from strain HY1.

• Microbiology and Biotechnology Letters
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• 제31권4호
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• pp.334-341
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• 2003

This study was carried out to investigate the cause of cholera outbreak in Gyeongbuk province in 2001.90 strains of Vibrio cholerae O1 El Tor serotype Inaba were isolated from diarrheal patients. By multiplex-PCR, all of the isolated strains revealed positive for detection ctxA, hlyA and tcpA genes. There were DNA sequence difference of the cholera-toxin subunit A gene and subunit B gene between isolated V. cholerae O1 and the strain of GenBank. In analysis of PFGE patterns, all of the isolated strains were showed the same DNA fragments. We also collected plankton samples in the east coast of Gyeongbuk to isolate V. cholerae O1 and V. cholerae O139 from August to October 2002. The samples were examined to detect the rfb gene and cholera-toxin gene by multiplex-PCR. The cholera-toxin gene was detected and then we tried to isolate V. cholerae O1 and V. cholerae O139, but they were not isolated.