• Korean Journal of Microbiology
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• v.53 no.2
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• pp.134-136
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• 2017

Lactobacillus salivarius KLW001, a species of lactic acid bacteria (LAB), was isolated from a weaning piglet in a swine farm, South Korea, to develop an antimicrobial probiotic strain for piglets. Herein, we report the draft genome sequence of the strain. The genome contains 2,326,706 bp with a G+C content of 33.0% in 166 contigs (${\geq}500bp$). From the genome, we found out 4 genes related to antibiotic resistance, 36 genes for phages, 3 genes for bile hydrolysis, and 27 CRISPR spacers.

• Journal of Photoscience
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• v.9 no.3
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• pp.49-50
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• 2002

N-Nitrosoproline(NPRO) is endogenously formed from proline and nitrite. NPRO has been reported to be nonmutagenic and noncarcinogenic. In this study, we have detected the direct mutagenicity of NPRO with UVA and UVB towards S. typhimurium. Formation of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), a mutagenic lesion, was observed in calf thymus DNA treated with NPRO plus simulated sunlight. Furthermore, the treatment with NPRO and sunlight induced single strand breaks in the superhelical replicative form of phage M13mp2 DNA. An analysis using scavengers suggested that both reactive oxygen species and NO radical mediate the strand breaks. The formation of nitric oxide was observed in NPRO solution irradiated with UVA. The co-mutagenic and co-toxic actions of NPRO and sunlight merit attention as possible mechanisms increasing the carcinogenic risk from UVA irradiation.

• Korean Journal of Microbiology
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• v.53 no.4
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• pp.337-339
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• 2017

Here we report the draft genome sequence of the Caballeronia sordidicola strain PAMC 26633, isolated from Psoroma species, a lichen material from Barton Peninsula, King George Island in Antarctica. As we have observed in previous genomic studies in the genus Caballeronia from polar lichen, draft genomic sequences of PAMC 26633 had an assortment of genes of ecological importance and of biotechnical potentials, which include diverse metabolic genes for carbohydrates, amino acids, and genes for nitrogen/sulfur metabolisms, stress responses, membrane transporters, antibiotic resistance, and heavy metal resistance. CRISPR genes and sequences were not found and there were some phage remnants and transposons.

• Journal of Radiation Industry
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• v.6 no.1
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• pp.17-21
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• 2012

The effects of gamma ray or electron beam irradiation on herbaceous medicinal plants were investigated in terms of the composition of volatile constituents using the aerial parts or leaves of Artemisia princeps Pamp. cv. Ganghwayakssuk and Artemisia argyi cvs. Namhaeyakssuk and Hwanghaessuk. The composition of volatile constituents in leaves was clearly distinguishable among the three Artemisia cultivars. However, the relative proportions of the major volatile constituents such as 1,8-cineole, ${\alpha}$-pinene, camphene, santolina triene, and artemesia triene, were similarly changed in two or three cultivars by gamma ray or electron beam irradiation. In particular, the proportion of 1,8-cineole was increased up to 1.29- to 1.71-fold in the three cultivars after irradiation with gamma ray. These results suggest that gamma ray or electron beam irradiation can be applied to modulate the composition of volatile constituents in the leaves of Artemisia plants.

• Current Optics and Photonics
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• v.1 no.1
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• pp.12-16
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• 2017

Color sensor systems based on M13 bacteriophage are being considerably researched. Although many studies on M13 bacteriophage-based chemical sensing of TNT, endocrine disrupting chemicals, and antibiotics have been undertaken, the fundamental physical and chemical properties of M13 bacteriophage-based nanostructures require further research. A simple M13 bacteriophage-based colorimetric sensor was fabricated by a simple pulling technique, and M13 bacteriophage was genetically engineered using a phage display technique to exhibit a negatively charged surface. Arrays of structurally and genetically modified M13 bacteriophage that can determine the polarity indexes of various alcohols were found. In this research, an M13 bacteriophage-based color sensor was used to detect various types of alcohols, including methanol, ethanol, and methanol/butanol mixtures, in order to investigate the polarity-related property of the sensor. Studies of the fundamental chemical sensing properties of M13 bacteriophage-based nanostructures should result in wider applications of M13 bacteriophage-based colorimetric sensors.

• Biodesign
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• v.6 no.4
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• pp.96-99
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• 2018

The gram-positive bacterium Staphylococcus aureus is a common cause of abscesses, sinusitis and food poisoning. The emergence of antibiotic-resistant strains has caused significant clinical issues worldwide. The HslU-HslV complex was first identified as a prokaryotic homolog of eukaryotic proteasomes. HslU is an unfoldase that mediates the unfolding of the substrate proteins, and it works with the protease HslV in the complex. To date, the protein complex has been mostly studied in gram-negative bacteria. In this study, we report the purification and crystallization of the full-length HslU from S. aureus. The crystal diffracted X-rays to a $3.5{\AA}$ resolution, revealing that the crystals belong to space group $P2_1$, with unit cell parameters of a = 166.5, b = 189.6, $c=226.6{\AA}$, and ${\beta}=108.1^{\circ}$. We solved the phage problem by molecular replacement using the structure of HslU from Haemophilus influenzae as a search model. The cell content analysis with this molecular replacement solution revealed that 24 molecules are contained in the asymmetric unit. This structure provides insight into the structural and mechanistic difference of the HslUV complex of gram-positive bacteria.

• Journal of Microbiology and Biotechnology
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• v.32 no.3
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• pp.333-340
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• 2022

Leuconostoc has been used as a principal starter in natural kimchi fermentation, but limited research has been conducted on its phages. In this study, prophage distribution and characterization in kimchi-derived Leuconostoc strains were investigated, and phage induction was performed. Except for one strain, 16 Leuconostoc strains had at least one prophage region with questionable and incomplete regions, which comprised 0.5-6.0% of the bacterial genome. Based on major capsid protein analysis, ten intact prophages and an induced incomplete prophage of Leu. lactis CBA3626 belonged to the Siphoviridae family and were similar to Lc-Nu-like, sha1-like, phiMH1-like, and TPA_asm groups. Bacterial immunology genes, such as superinfection exclusion proteins and methylase, were found on several prophages. One prophage of Leu. lactis CBA3626 was induced using mitomycin C and was confirmed as belonging to the Siphoviridae family. Homology of the induced prophage with 21 reported prophages was not high (< 4%), and 47% identity was confirmed only with TPA_asm from Siphoviridae sp. isolate ct3pk4. Therefore, it is suggested that Leuconostoc from kimchi had diverse prophages with less than 6% genome proportion and some immunological genes. Interestingly, the induced prophage was very different from the reported prophages of other Leuconostoc species.

• The Plant Pathology Journal
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• v.38 no.2
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• pp.102-114
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• 2022

Pectobacterium carotovorum subsp. carotovorum (Pcc) is a gram-negative, broad host range bacterial pathogen which causes soft rot disease in potatoes as well as other vegetables worldwide. While Pectobacterium infection relies on the production of major cell wall degrading enzymes, other virulence factors and the mechanism of genetic adaptation of this pathogen is not yet clear. In the present study, we have performed an in-depth genome-wide characterization of Pcc strain ICMP5702 isolated from potato and compared it with other pathogenic bacteria from the Pectobacterium genus to identify key virulent determinants. The draft genome of Pcc ICMP5702 contains 4,774,457 bp with a G + C content of 51.90% and 4,520 open reading frames. Genome annotation revealed prominent genes encoding key virulence factors such as plant cell wall degrading enzymes, flagella-based motility, phage proteins, cell membrane structures, and secretion systems. Whereas, a majority of determinants were conserved among the Pectobacterium strains, few notable genes encoding AvrE-family type III secretion system effectors, pectate lyase and metalloprotease in addition to the CRISPR-Cas based adaptive immune system were uniquely represented. Overall, the information generated through this study will contribute to decipher the mechanism of infection and adaptive immunity in Pcc.

• The Plant Pathology Journal
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• v.38 no.3
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• pp.248-253
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• 2022

Erwinia amylovora is a devastating bacterial plant pathogen that infects Rosaceae including apple and pear and causes fire blight. Bacteriophages have been considered as a biological control agent for preventing bacterial infections of plants. In this study, nine bacteriophages (ΦFifi011, ΦFifi044, ΦFifi051, ΦFifi067, ΦFifi106, ΦFifi287, ΦFifi318, ΦFifi450, and ΦFifi451) were isolated from soil and water samples in seven orchards with fire blight in Korea. The genetic diversity of bacteriophage isolates was confirmed through restriction fragment length polymorphism pattern analysis. Host range of the nine phages was tested against 45 E. amylovora strains and 14 E. pyrifoliae strains and nine other bacterial strains. Among the nine phages, ΦFifi044 and ΦFifi451 infected and lysed E. amylovora only. And the remaining seven phages infected both E. amylovora and E. pyrifoliae. The results suggest that the isolated phages were different from each other and effective to control E. amylovora, providing a basis to develop biological agents and utilizing phage cocktails.

• Animal cells and systems
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• v.15 no.4
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• pp.259-267
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• 2011

This study was undertaken to produce a $F_{ab}$ fragment of a human monoclonal antibody reactive to oxidized and carbamylated low-density lipoprotein (oxLDL and cLDL) using phage display technology. An analysis of DNA sequences of this $F_{ab}$, termed plaque 15,16-46 $F_{ab}$, revealed that the rearranged $V_H$ was highly mutated. Complementarity-determining regions of the $V_H$ showed a very high R/S ratio and contained many positively charged amino acids. In direct binding and competitive ELISA, the $F_{ab}$ reacted strongly with both MDA-LDL and Cu-oxLDL forms of oxLDL, and also showed high affinity for cLDL. Immunofluorescence and immunohistochemical analyses showed that this $F_{ab}$ positively stained atherosclerotic aortic plaques in $ApoE^{-/-}$ mice as well as those in patients with atherosclerosis. The $F_{ab}$ also showed positive staining in placental decidua from patients with preeclampsia. It is suggested that the plaque 15,16-46 $F_{ab}$ against oxLDL and cLDL might possibly be applicable for developing a diagnostic reagent for both human and rodent animal research to detect and characterize atherosclerotic disease progression in atherosclerotic lesions as well as exploring the pathogenesis of atherogenic diseases such as preeclampsia.