• Journal of Species Research
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• v.8 no.4
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• pp.319-336
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• 2019

During an investigation of unrecorded prokaryotic species in Republic of Korea, a total of 53 bacterial strains belonging to the class Gammaproteobacteria were isolated from soil, seawater, tidal flats, rhizosphere, salt ponds, beach sand, urine, manure, sediment, and animal intestine (Russian grayling butterfly [Hipparchia autonoe], mouse [Mus musculus], and sea bass [Lateolabrax japonicus]). Strains were identified to species using the 16S rRNA gene sequence, showing high similarity (>98.7%) with the closest bacterial species and forming a robust clade in the neighbor-joining phylogenetic tree. The 53 strains of Gammaproteobacteria in this study have not been report previously in Korea. Therefore, we describe 27 genera of 16 families in 7 orders: 13 strains in the order Alteromonadales, 1 strain in the order Chromatiales, 11 strains in the order Enterobacterales, 7 strains in the order Oceanospirillales, 10 strains in the order Pseudomonadales, 8 strains in the order Vibrionales, and 3 strains in the order Xanthomonadales. Gram reaction, strain ID, isolation source, and morphological and basic biochemical characteristics are described for each species.

• Journal of Applied Biological Chemistry
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• v.62 no.3
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• pp.247-250
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• 2019

Wheat is one of the most important grains. Its consumption is increasing globally. Many countries are making efforts to increase the extent of wheat harvest. It is known that plant growth promoting rhizobacteria (PGPRs) have beneficial effects on various plants. Two PGPRs including Paenibacillus pabuli strain P7S (PP7S) and Pseudomonas nitroreducens strain IHB (PnIHB) were employed to investigate effects of PGPRs on early growth of three wheat cultivars (Koso, Seakumkang, and Jokyung). While PP7S had adverse effects on Seakumkang and Jokyung, PP7S had positive effects on Koso except root length compared to control group having no treatment of PP7S. However, all treatments with PnIHB had adverse effects on germination rate, root/shoot lengths, vigor index, and dry root/shoot weights of all three wheat cultivars. These positive effects with PP7S on Koso might be related to the earlier emergence of wheat seed above soil which is known to be an indicator of increased yield. Results of the present study suggest that if proper PGPR strains are selected, they could have positive effects on early growth rate of a wheat cultivar.

• Journal of Species Research
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• v.8 no.2
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• pp.161-175
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• 2019

During a comprehensive investigation of indigenous prokaryotic species in Korea, a total of 46 bacterial strains assigned to the classes Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria were isolated from a diversity of habitats including freshwater, seawater, brackish water, ginseng soil, plant roots, natural caves, and tidal flats. Based on their high 16S rRNA gene sequence similarities (>98.7%) and formation of strongly-supported phylogenetic clades with the closest type species, each strain was assigned to an independent, predefined bacterial species. Since there were no published or official reports regarding the isolation of these 46 species in Korea, here we report them as new species to Korea: 34 species in 14 families in the five orders of Alphaproteobacteria, 10 species in five families in the three orders of Betaproteobacteria, one species of Deltaproteobacteria and one species of Epsilonproteobacteria. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are described in the species description section.

• Journal of Microbiology and Biotechnology
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• v.29 no.5
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• pp.794-808
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• 2019

Bacillus velezensis strain WRN014 was isolated from banana fields in Hainan, China. Bacillus velezensis is an important member of the plant growth-promoting rhizobacteria (PGPR) which can enhance plant growth and control soil-borne disease. The complete genome of Bacillus velezensis WRN014 was sequenced by combining Illumina Hiseq 2500 system and Pacific Biosciences SMRT high-throughput sequencing technologies. Then, the genome of Bacillus velezensis WRN014, together with 45 other completed genome sequences of the Bacillus velezensis strains, were comparatively studied. The genome of Bacillus velezensis WRN014 was 4,063,541bp in length and contained 4,062 coding sequences, 9 genomic islands and 13 gene clusters. The results of comparative genomic analysis provide evidence that (i) The 46 Bacillus velezensis strains formed 2 obviously closely related clades in phylogenetic trees. (ii) The pangenome in this study is open and is increasing with the addition of new sequenced genomes. (iii) Analysis of single nucleotide polymorphisms (SNPs) revealed local diversification of the 46 Bacillus velezensis genomes. Surprisingly, SNPs were not evenly distributed throughout the whole genome. (iv) Analysis of gene clusters revealed that rich gene clusters spread over Bacillus velezensis strains and some gene clusters are conserved in different strains. This study reveals that the strain WRN014 and other Bacillus velezensis strains have potential to be used as PGPR and biopesticide.

• Computers and Concrete
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• v.27 no.2
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• pp.163-173
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• 2021

In this paper, the parameters of haunch height, reinforcement ratio and site condition were evaluated for the influence on the seismic performance of a composite precast fabricated utility tunnel by shaking table test and numerical simulation. The dynamic response laws of acceleration, interlayer displacement and steel strain under unidirectional horizontal seismic excitation were analyzed through four specimens with a similarity ratio of 1:6 in the test. And a numerical model was established and analyzed by the finite element software ABAQUS based on the structure of utility tunnel. The results indicated that composite precast fabricated utility tunnel with the good anti-seismic performance. In a certain range, increasing the height of haunch or the ratio of reinforcement could reduce the influence of seismic wave on the utility tunnel structure, which was beneficial to the structure earthquake resistance. The clay field containing the interlayer of liquefied sandy soil has a certain damping effect on the structure of the utility tunnel, and the displacement response could be reduced by 14.1%. Under the excitation of strong earthquake, the reinforcement strain at the side wall upper end and haunches of the utility tunnel was the biggest, which is the key part of the structure. The experimental results were in good agreement with the fitting results, and the results could provide a reference value for the anti-seismic design and application of composite precast fabricated utility tunnel.

• Journal of Microbiology and Biotechnology
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• v.32 no.2
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• pp.176-186
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• 2022

Continued fenvalerate use has caused serious environmental pollution and requires large-scale remediation. Dibutyl phthalate (DBP) was discovered in fenvalerate metabolites degraded by Citrobacter freundii CD-9. Coculturing is an effective method for bioremediation, but few studies have analyzed the degradation pathways and potential mechanisms of cocultures. Here, a DBP-degrading strain (BDBP 071) was isolated from soil contaminated with pyrethroid pesticides (PPs) and identified as Stenotrophomonas acidaminiphila. The optimum conditions for DBP degradation were determined by response surface methodology (RSM) analysis to be 30.9 mg/l DBP concentration, pH 7.5, at a culture temperature of 37.2℃. Under the optimized conditions, approximately 88% of DBP was degraded within 48 h and five metabolites were detected. Coculturing C. freundii CD-9 and S. acidaminiphila BDBP 071 promoted fenvalerate degradation. When CD-9 was cultured for 16 h before adding BDBP 071, the strain inoculation ratio was 5:5 (v/v), fenvalerate concentration was 75.0 mg/l, fenvalerate was degraded to 84.37 ± 1.25%, and DBP level was reduced by 5.21 mg/l. In addition, 12 fenvalerate metabolites were identified and a pathway for fenvalerate degradation by the cocultured strains was proposed. These results provide theoretical data for further exploration of the mechanisms used by this coculture system to degrade fenvalerate and DBP, and also offer a promising method for effective bioremediation of PPs and their related metabolites in polluted environments.

• Journal of Microbiology and Biotechnology
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• v.31 no.11
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• pp.1591-1600
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• 2021

Streptomyces coelicolor is a filamentous soil bacterium producing several kinds of antibiotics. S. coelicolor abs8752 is an abs (antibiotic synthesis deficient)-type mutation at the absR locus; it is characterized by an incapacity to produce any of the four antibiotics synthesized by its parental strain J1501. A chromosomal DNA fragment from S. coelicolor J1501, capable of complementing the abs- phenotype of the abs8752 mutant, was cloned and analyzed. DNA sequencing revealed that two complete ORFs (SCO6992 and SCO6993) were present in opposite directions in the clone. Introduction of SCO6992 in the mutant strain resulted in a remarkable increase in the production of two pigmented antibiotics, actinorhodin and undecylprodigiosin, in S. coelicolor J1501 and abs8752. However, introduction of SCO6993 did not show any significant difference compared to the control, suggesting that SCO6992 is primarily involved in stimulating the biosynthesis of antibiotics in S. coelicolor. In silico analysis of SCO6992 (359 aa, 39.5 kDa) revealed that sequences homologous to SCO6992 were all annotated as hypothetical proteins. Although a metalloprotease domain with a conserved metal-binding motif was found in SCO6992, the recombinant rSCO6992 did not show any protease activity. Instead, it showed very strong β-glucuronidase activity in an API ZYM assay and toward two artificial substrates, p-nitrophenyl-β-D-glucuronide and AS-BI-β-D-glucuronide. The binding between rSCO6992 and Zn²⁺ was confirmed by circular dichroism spectroscopy. We report for the first time that SCO6992 is a novel protein with β-glucuronidase activity, that has a distinct primary structure and physiological role from those of previously reported β-glucuronidases.

• KSCE Journal of Civil and Environmental Engineering Research
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• v.42 no.4
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• pp.501-508
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• 2022

Required essential technique is to determine the maximum recharge pressure in the well with condition of non-ground failure for the recovery of the groundwater. Based on the classical soil mechanics, the maximum recharge pressure was estimated with the numerical anlaysis and laboratory triaxial test. In the numerical analysis, the maximum recharge pressure is defined as the ground failure stress. The ground failure of the sand was defined as the piping and the one of the caly was to the undrained failure by the confined pressure increment. In the triaxial test, the recharge pressure in the ground was modified by the back pressure in the specimen. In case of sand, the volume strain was dramatically increased at the 93 % of the maximum back pressure, same meaning of the 0 effective stress state. In case of clay, the only radial volume strain was to reached 1.5 % without failure. Therefore, The maximum recharge pressure could be determined with the numerical analysis and triaxial test.

• Journal of Microbiology and Biotechnology
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• v.33 no.1
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• pp.61-74
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• 2023

The global increase in multidrug-resistant (MDR) bacteria has inspired researchers to develop new strategies to overcome this problem. In this study, 23 morphologically different, soil-isolated actinomycete cultures were screened for their antibacterial ability against MDR isolates of ESKAPE pathogens. Among them, isolate BOGE18 exhibited a broad antibacterial spectrum, so it was selected and identified based on cultural, morphological, physiological, and biochemical characteristics. Chemotaxonomic analysis was also performed together with nucleotide sequencing of the 16S rRNA gene, which showed this strain to have identity with Streptomyces lienomycini. The ethyl acetate extract of the cell-free filtrate (CFF) of strain BOGE18 was evaluated for its antibacterial spectrum, and the minimum inhibitory concentration (MIC) ranged from 62.5 to 250 ㎍/ml. The recorded results from the in vitro anti-biofilm microtiter assay and confocal laser scanning microscopy (CLSM) of sub-MIC concentrations revealed a significant reduction in biofilm formation in a concentration-dependent manner. The extract also displayed significant scavenging activity, reaching 91.61 ± 4.1% and 85.06 ± 3.14% of 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), respectively. A promising cytotoxic ability against breast (MCF-7) and hepatocellular (HePG2) cancer cell lines was obtained from the extract with IC₅₀ values of 47.15 ± 13.10 and 122.69 ± 9.12 ㎍/ml, respectively. Moreover, based on gas chromatography-mass spectrometry (GC-MS) analysis, nine known compounds were detected in the BOGE18 extract, suggesting their contribution to the multitude of biological activities recorded in this study. Overall, Streptomyces lienomycini BOGE18-derived extract is a good candidate for use in a natural combating strategy to prevent bacterial infection, especially by MDR pathogens.

• KSCE Journal of Civil and Environmental Engineering Research
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• v.43 no.4
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• pp.469-476
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• 2023

Soil plasticity models for cyclic and dynamic loads are essential in non-linear numerical analysis of geotechnical structures. While a single yield surface model shows a linear behavior for cyclic loads, J₂-bounding surface plasticity model with zero elastic region can effectively simulate a nonlinearity of the ground response with the same material properties. The radius of the yield surface inside the boundary surface converged to 0 to make the elastic region disappear, and plastic hardening modulus and dilatancy define plastic strain increment. This paper presents the stress-strain incremental equation of the developed model, and derives plastic hardening modulus for the hyperbolic model. The comparative analyses of the triaxial compression test and the shallow foundation under the cyclic load can show stable numerical convergence, consistency with the theoretical solution, and hysteresis behavior. In addition, plastic hardening modulus for the modified hyperbolic function is presented, and a methodology to estimate model variables conforming 1D equivalent linear model is proposed for numerical modeling of the multi-dimensional behavior of the ground.