• 한국균학회소식:학술대회논문집
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• 2015.11a
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• pp.41-41
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• 2015

Oomycetes belong to the kingdom Straminipila, a remarkably diverse group which includes brown algae and planktonic diatoms, although they have previously been classified under the kingdom Fungi. These organisms have evolved both saprophytic and pathogenic lifestyles, and more than 60% of the known species are pathogens on plants, the majority of which are classified into the order Peronosporales (includes downy mildews, Phytophthora, and Pythium). Recent phylogenetic investigations based on DNA sequences have revealed that the diversity of oomycetes has been largely underestimated. Although morphology is the most valuable criterion for their identification and diversity, morphological species identification is time-consuming and in some groups very difficult, especially for non-taxonomists. DNA barcoding is a fast and reliable tool for identification of species, enabling us to unravel the diversity and distribution of oomycetes. Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The mitochondrial cox2 gene has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. To determine which out of cox1 or cox2 is best suited as universal oomycete barcode, we compared these two genes in terms of (1) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (2) in terms of sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding type material. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. Including the two barcoding markers, ITS rDNA and cox2 mtDNA, the multi-locus phylogenetic analyses were performed to resolve two complex clades, Bremia lactucae (lettuce downy mildew) and Peronospora effuse (spinach downy mildew) at the species level and to infer evolutionary relationships within them. The approaches discriminated all currently accepted species and revealed several previously unrecognized lineages, which are specific to a host genus or species. The sequence polymorphisms were useful to develop a real-time quantitative PCR (qPCR) assay for detection of airborne inoculum of B. lactucae and P. effusa. Specificity tests revealed that the qPCR assay is specific for detection of each species. This assay is sensitive, enabling detection of very low levels of inoculum that may be present in the field. Early detection of the pathogen, coupled with knowledge of other factors that favor downy mildew outbreaks, may enable disease forecasting for judicious timing of fungicide applications.

• Journal of fish pathology
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• v.26 no.3
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• pp.149-161
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• 2013

Viral haemorrhagic septicaemia virus (VHSV), the causative agent of viral haemorrhagic septicaemia (VHS), is an epidemic virus of cultured olive flounder Paralichthys olivaceus in Korea. In the present study, the entire glycoprotein (G) gene including several hypervariable regions from 36 isolates of diverse geographic and host origin and 8 Korean VHSV isolates from cultured olive flounder were analyzed. Phylogenetic analysis indicated that most of Asian VHSV belong to the genotype IVa group, suggesting that they originated from a common ancestral virus. Comparative sequence analysis of the complete G protein from Korean VHSV isolates revealed 3 Korean strain-specific nucleotide residues (nucleotide number of G-region: A755, T834 and T1221). These results suggest that Korean VHSV originated from a common ancestor, but these regional specific nucleotide sequences suggest that genetic differences of VHSV are more related to geographic areas than to host fish species.

• Tuberculosis and Respiratory Diseases
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• v.50 no.1
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• pp.12-28
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• 2001

Background and Object : Immunostimulatory CpG-oligodeoxynucleotides (ISS CpG-ODN) up-regulate the $T_{H1}$-type immune response and down-regulate the $T_{H2}$-type response. This study was performed to investigate the immune response changes resulting from ISS CpG-ODN on bronchial hyperresponsiveness, eosinophilic inflammation and mucus hypersecretion in rat asthma. Materials and Methods : 10 normal controls(NC) and 26 asthmatic rats, which were generated by ovalbumin(OVA) sensitization and challenge, were studied. The asthmatic rats were randomized into 11 asthma controls(AC) and 15 in the asthma-CpG treatment group(CpG). The CpG group was administered ISS CpG-ODN intramuscularly and the AC group was administered a placebo(0.9% NaCl) on day 15 and 20. After CpG-ODN or placebo administration, we measured the IFN-${\gamma}$($T_{H1}$-type cytokine) and IL-4($T_{H2}$-type cytokine) levels in the bronchoalveolar lavage fluid(BALF), the specific airway resistance(sRaw), eosinophilic fraction in BALF, eosinophilic infiltration, goblet cell dysplasia and MUC5AC gene expression in the lung tissue. Results : In the BALF of the CpG group, the IFN-${\gamma}$ concentration was significantly high and the IL-4 concentration was significantly low when compared with the AC group. Both the sRaw and eosinophilic fraction, and infiltration into the BALF and lung tissue significantly lower in the CpG group when compared with the AC group. However, little difference in goblet cell dysplasia and MUC5AC gene expression was observed between the CpG group and the AC group. Conclusion : ISS CpG-ODN decreases bronchial hyperresponsiveness and eosinophilic inflammation in the rat asthma model through the up-regulation of the $T_{H1}$-type immune response with the down-regulation of the $T_{H2}$-type response. However, the effect of these immune response changes on mucus hypersecretion was is not remarkable in this study.

• Development and Reproduction
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• v.15 no.4
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• pp.273-279
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• 2011

Epigenetic regulation is a phenomenon that changes the gene function without changing the underlying DNA sequences. Epigenetic status of chromosome is regulated by mechanisms such as histone modification, DNA modification, and RNAi silencing. In this review, we focused on histone methylation for epigenetic regulation in ES cells. Two antagonizing multiprotein complexes regulate methylation of histones to guide expression of genes in ES cells. The Polycomb repressive complex 2 (PRC2), including EED, EZH2, and SUZ12 as core factors, contributes to gene repression by increasing trimethylation of H3K27 (H3K27me3). In contrast, the Trithorax group (TrxG) complex including MLL is related to gene activation by making H3K4me3. PRC2 and TrxG accompany a variety of accessory proteins. Most prominent feature of epigenetic regulation in ES cells is a bivalent state in which H3K27me3 and H3K4me3 appear simultaneously. Concerted regulation of PRC2, TrxG complex, and H3K4- or H3K27-specific demethylases activate expression of pluripotency-related genes and suppress development-related genes in ES cells. Modified balance of the regulators also enables ES cells to efficiently differentiate to a variety of cells upon differentiating signals. More detailed insights on the epigenetic regulators and their action will lead us to better understanding and use of ES cells for future application.

• Journal of Microbiology and Biotechnology
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• v.34 no.2
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• pp.457-466
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• 2024

Cellobiose dehydrogenases (CDHs) are a group of enzymes belonging to the hemoflavoenzyme group, which are mostly found in fungi. They play an important role in the production of acid sugar. In this research, CDH annotated from the actinobacterium Cellulomonas palmilytica EW123 (CpCDH) was cloned and characterized. The CpCDH exhibited a domain architecture resembling class-I CDH found in Basidiomycota. The cytochrome c and flavin-containing dehydrogenase domains in CpCDH showed an extra-long evolutionary distance compared to fungal CDH. The amino acid sequence of CpCDH revealed conservative catalytic amino acids and a distinct flavin adenine dinucleotide region specific to CDH, setting it apart from closely related sequences. The physicochemical properties of CpCDH displayed optimal pH conditions similar to those of CDHs but differed in terms of optimal temperature. The CpCDH displayed excellent enzymatic activity at low temperatures (below 30℃), unlike other CDHs. Moreover, CpCDH showed the highest substrate specificity for disaccharides such as cellobiose and lactose, which contain a glucose molecule at the non-reducing end. The catalytic efficiency of CpCDH for cellobiose and lactose were 2.05 × 10⁵ and 9.06 × 10⁴ (M^-1 s^-1), respectively. The result from the Fourier-transform infrared spectroscopy (FT-IR) spectra confirmed the presence of cellobionic and lactobionic acids as the oxidative products of CpCDH. This study establishes CpCDH as a novel and attractive bacterial CDH, representing the first report of its kind in the Cellulomonas genus.

• Journal of Food Hygiene and Safety
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• v.28 no.1
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• pp.50-55
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• 2013

Since 1 June 2012, it is prohibited to sell oilfish as a food material but there are still many illegal cases of selling oilfish as if it is tuna or grilled Patagonian toothfish. So it is absolutely crucial to construct the system to distinguish the real food material from oilfish. There are two sorts of oil fish called Ruvettus pretiosus and Lepidocybirium flavobrunneum involved in Percifomes order and Gempylidae class. 16S DNA gene region in mitochondria was selected to design the specific primers. For design species-specific primer, the theoretical experiment were performed for the sequences of R. pretiosus, L. flavobrunneum, Thunnus thynnus, Thunnus albacores, Makaira mitsukurii and Xiphias gladius, registered at the Gene bank from the National Centre for Biotechnology Information, using BioEdit 7.0.9.0. program. Through the analysis of the result from experiments, it was possible to design the 4 kinds of primers to distinguish R. pretiosus and L. flavobrunneum. As a comparison group, 3 kinds of tuna and 4 kinds of billfishes were selected and experimental verification was performed. As a result, for R. pretiosus and L. flavobrunneum, R.P-16S-006-F/R.P-16S-008-R and L.F-16S-004-F/L.F-16S-006-R primers were selected eventually and PCR condition was established. In addition, 178bp and 238bp of PCR products were confirmed from the established condition and non-specific band was not amplified among similar species. Therefore, the species-specific primers developed in this study would be very useful and used in various ways such as internet shopping mall and illegal distributions with fast and scientific results.

• Journal of Sericultural and Entomological Science
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• v.36 no.2
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• pp.138-146
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• 1994

The structural characteristics of Antheraea yamamai and Antheraea pernyi silk were investigated by using x-ray diffraction method, IR spectroscopy and polarizing microscopy. The amino acid composition, fiber density, thermal decomposition temperature and glass transition temperature were also measured for relating these physical properties to the structure in comparison with those of Bombyx mori silk fiber. There was no significant structural difference between A. yamamai and A. pernyi silk fiber on an examination of x-ray diffraction curve and IR spectrum. Both of these wild silk fibers showed double diffraction peaks at the Bragg angle 2Θ16.7˚ and 20.5˚by x-ray diffraction analysis as well as IR absorption peaks for the bending vibration of specific groups related to ala-ala amino acid sequence. On the other hand, the x-ray diffraction curve and IR spectrum of Bombyx mori silk fiber are different from those of wild silk fibers, indicating different crystal structure as well as amino acid sequences. It showed under the polarizing microscope examination that the birefringence and optical orientation factor of wild silk fibers are much lower than those of B. mori silk. Also, the surface of degummed wild silk fibers was characterized by the longitudinal stripes of microfibrils in the direction of fiber axies. The amino acid composition, which is strongly related to the fine structure and properties, was not significantly different between these two wild silk fibers. However, the alanine content was somewhat less and polar amino acid content more for A. yamamai. As a result of fiber density measurement, the specific gravities of B. mori, A. pernyi and A. yamamai were 1.355~1.356, 1.308~1.311, 1.265~1.301g/㎤ in the order, respectively. The calculated crystallinity(%) was 64% for B. mori and 51~52% for wild silk fibers, which showed same trend by IR method in spite of somewhat higher value. The thermal decomposition behaviour was examined by DSC and TGA, showing that the degradation temperature was in the order of B mori, A. prernyi and A. yamamai at around 350$^{\circ}C$. It was also observed by TGA that the decomposition seems to proceed step by step according to their specific regions in the fiber structure, resulting the difference in their thermal stabilities. The glass transition temperature was turned out to be 220$^{\circ}C$ for B. mori, 240$^{\circ}C$ A. yamamai and 255$^{\circ}C$ A. pernyi by the dynamic mechanical analysis. It is expected that the chemical properties are affected by the dynamic mechanical behavior in accordance with their structural characters.

• Research in Plant Disease
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• v.18 no.4
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• pp.387-390
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• 2012

Rice black-streaked dwarf virus (RBSDV) was reported to occur on maize plants in Gochang-gun of Jeonllabuk-do region in 2011. The symptoms typically include stunted and deformed leaves. Virus infected plants usually produce poor or no head. RT-PCR analysis of genomic dsRNA extracted from the plant confirmed the infection. Specific primers for full length genome of segments 8 and 10 were used for RNA amplification. Full-length genomes of S8 and S10 were cloned and sequenced. Sequence analysis revealed that the S8 and S10 sequences of the maize isolate were same with rice isolate in size, 1,936 nt and 1,801 nt, respectively. In comparison with rice RBSDV, S8 and S10 showed 94.9-99.6% and 94.1-98.4% sequence identity, respectively. Phylogenetic analysis showed that RBSDV S8 and S10 of maize plants are categorized into the same group as RBSDV of rice plant.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.7
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• pp.3223-3228
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• 2012

HMGN5 is a typical member of the HMGN (high mobility group nucleosome-binding protein) family which may function as a nucleosomal binding and transcriptional activating protein. Overexpression of HMGN5 has been observed in several human tumors but its role in tumorigenesis has not been fully clarified. To investigate its significance for human lung cancer progression, we successfully constructed a shRNA expression lentiviral vector in which sense and antisense sequences targeting the human HMGN5 were linked with a 9-nucleotide loop. Inhibitory effects of siRNA on endogenous HMGN5 gene expression and protein synthesis were demonstrated via real-time RT-PCR and western blotting. We found HMGN5 silencing to significantly inhibit A549 and H1299 cell proliferation assessed by MTT, BrdU incorporation and colony formation assays. Furthermore, flow cytometry analysis showed that specific knockdown of HMGN5 slowed down the cell cycle at the G0/G1 phase and decreased the populations of A549 and H1299 cells at the S and G2/M phases. Taken together, these results suggest that HMGN5 is directly involved in regulation cell proliferation in A549 and H1299 cells by influencing signaling pathways involved in cell cycle progression. Thus, our finding suggests that targeting HMGN5 may be an effective strategy for human lung cancer treatment.

• Journal of Microbiology and Biotechnology
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• v.25 no.1
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• pp.98-108
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• 2015

Staphylococcus aureus is an important foodborne pathogen that causes diverse diseases ranging from minor infections to life-threatening conditions in humans and animals. To further understand its pathogenesis, the genome of the strain S. aureus FORC_001 was isolated from a contaminated food. Its genome consists of 2,886,017 bp double-stranded DNA with a GC content of 32.8%. It is predicted to contain 2,728 open reading frames, 57 tRNAs, and 6 rRNA operons, including 1 additional 5S rRNA gene. Comparative phylogenetic tree analysis of 40 complete S. aureus genome sequences using average nucleotide identity (ANI) revealed that strain FORC_001 belonged to Group I. The closest phylogenetic match was S. aureus MRSA252, according to a whole-genome ANI (99.87%), suggesting that they might share a common ancestor. Comparative genome analysis of FORC_001 and MRSA252 revealed two non-homologous regions: Regions I and II. The presence of various antibiotic resistance genes, including the SCCmec cluster in Region I of MRSA252, suggests that this strain might have acquired the SCCmec cluster to adapt to specific environments containing methicillin. Region II of both genomes contains prophage regions but their DNA sequence identity is very low, suggesting that the prophages might differ. This is the first report of the complete genome sequence of S. aureus isolated from a real foodborne outbreak in South Korea. This report would be helpful to extend our understanding about the genome, general characteristics, and virulence factors of S. aureus for further studies of pathogenesis, rapid detection, and epidemiological investigation in foodborne outbreak.