• Journal of Microbiology and Biotechnology
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• v.33 no.1
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• pp.83-95
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• 2023

These days, bacterial detection methods have some limitations in sensitivity, specificity, and multiple detection. To overcome these, novel detection and identification method is necessary to be developed. Recently, NGS panel method has been suggested to screen, detect, and even identify specific foodborne pathogens in one reaction. In this study, new NGS panel primer sets were developed to target 13 specific virulence factor genes from five types of pathogenic Escherichia coli, Listeria monocytogenes, and Salmonella enterica serovar Typhimurium, respectively. Evaluation of the primer sets using singleplex PCR, crosscheck PCR and multiplex PCR revealed high specificity and selectivity without interference of primers or genomic DNAs. Subsequent NGS panel analysis with six artificially contaminated food samples using those primer sets showed that all target genes were multi-detected in one reaction at 10⁸-10⁵ CFU of target strains. However, a few false-positive results were shown at 10⁶-10⁵ CFU. To validate this NGS panel analysis, three sets of qPCR analyses were independently performed with the same contaminated food samples, showing the similar specificity and selectivity for detection and identification. While this NGS panel still has some issues for detection and identification of specific foodborne pathogens, it has much more advantages, especially multiple detection and identification in one reaction, and it could be improved by further optimized NGS panel primer sets and even by application of a new real-time NGS sequencing technology. Therefore, this study suggests the efficiency and usability of NGS panel for rapid determination of origin strain in various foodborne outbreaks in one reaction.

• Journal of the Korean Geotechnical Society
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• v.24 no.2
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• pp.87-97
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• 2008

Behaviors of cemented engineered soils, composed of rigid sand particle and soft rubber particle, are investigated under $K_o$ condition. The uncemented and cemented specimens are prepared with various sand volume fractions to estimate the effect of the cementation in mixtures. The vertical deformation and elastic wave velocities with vertical stress are measured. The bender elements and PZT sensors are used to measure elastic wave velocities. After cementation, the slope of vertical strain shows bilinear and is similar to that of uncemented specimen after decementation. Normalized vertical strains can be divided into capillary force, cementation, and decementation region. The first deflection of the shear wave in near field matches the first arrival of the primary wave. The elastic wave velocities dramatically increase due to cementation hardening under the fixed vertical stress, and are almost identical with additional stress. After decementation, the elastic wave velocities increase with increase in the vertical stress. The effect of cementation hinders the typical rubber-like, sand-like, and transition behaviors observed in uncemented specimens. Different mechanism can be expected in decementation of the rigid-soft particle mixtures due to the sand fraction. a shape change of individual particles in low sand fraction specimens; a fabric change between particles in high sand fraction specimens. This study suggests that behaviors of cemented engineered soils, composed of rigid-soft particles, are distinguished due to the cementation and decementation from those of uncemented specimens.

• Korean Journal of Environmental Biology
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• v.40 no.3
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• pp.290-300
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• 2022

A strain of Alexandrium species was established by isolating cells from Jangmok Bay, Korea. Its morphology and molecular phylogeny based on LSU rRNA gene sequences were examined. In addition, growth responses of this Alexandrium species to changes in temperature, salinity, and nutrient concentrations were investigated. This Alexandrium species from Jangmok Bay had a ventral pore on the 1', which was morphologically consistent with previously described Alexandrium tamarense and A. catenella. Phylogenetic analyses revealed that this isolate was assigned to A. pacificum (Group IV) within A. tamarense species complex. In growth experiments, relatively high growth rates and cell densities of A. pacificum (Group IV) were observed at 15℃ and 20℃. This species also grew under a wide range of salinity. This indicates that this Korean isolate of A. pacificum (Group IV) is a stenothermic and euryhaline species. In growth responses to changes in nutrient levels, enhanced growth rates and cell densities of A. pacificum(Group IV) were observed with additions of nitrate and phosphate. In particular, rapid uptakes of phosphate by A. pacificum (Group IV) were observed in experimental treatments, indicating that the increase in phosphate concentration could stimulate the growth of A. pacificum(Group IV).

• Journal of Microbiology and Biotechnology
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• v.33 no.4
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• pp.552-558
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• 2023

Levulinic acid (LA) is a valuable chemical used in fuel additives, fragrances, and polymers. In this study, we proposed possible biosynthetic pathways for LA production from lignin and poly(ethylene terephthalate). We also created a genetically encoded biosensor responsive to LA, which can be used for screening and evolving the LA biosynthesis pathway genes, by employing an LvaR transcriptional regulator of Pseudomonas putida KT2440 to express a fluorescent reporter gene. The LvaR regulator senses LA as a cognate ligand. The LA biosensor was first examined in an Escherichia coli strain and was found to be non-functional. When the host of the LA biosensor was switched from E. coli to P. putida KT2440, the LA biosensor showed a linear correlation between fluorescence intensity and LA concentration in the range of 0.156-10 mM LA. In addition, we determined that 0.156 mM LA was the limit of LA detection in P. putida KT2440 harboring an LA-responsive biosensor. The maximal fluorescence increase was 12.3-fold in the presence of 10 mM LA compared to that in the absence of LA. The individual cell responses to LA concentrations reflected the population-averaged responses, which enabled high-throughput screening of enzymes and metabolic pathways involved in LA biosynthesis and sustainable production of LA in engineered microbes.

• KSCE Journal of Civil and Environmental Engineering Research
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• v.29 no.4A
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• pp.385-393
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• 2009

This study grasped the relationship between relative humidity in concrete and concrete shrinkage followed by pre-absorbed water of porous lightweight aggregates through measurements of concrete shrinkage and humidity and comparisons with established research results. It was showed that shrinkage reduction effect of lightweight concrete is 36% at 7 days early ages and 25% at 180 days long-term ages when water-binder ratio is 0.3. It also showed that shrinkage reduction effect is 19% at 7 days and 16% at 180 days when water-binder ratio is 0.4 and 37%, 32% when water-binder ratio is 0.5. The moisture supply effect of lightweight aggregates was remarkable at early age within 7~10 days irrespective of water-binder ratio. In case of waterbinder ratio is 0.3, the relationship between shrinkage and internal humidity of concrete has been underestimated regardless of applied existing model type and in case of water-binder ratio is 0.4, 0.5, measurement values are relatively similar with existing model equations. Finally this study did regression analyses about the relation among the humidity change and the shrinkage strain as a high-degree polynomial and derived parameters that can connect moisture movement analysis with differential shrinkage analysis in case of considering relative humidity at the time by moisture movement analysis of concrete.

• KSCE Journal of Civil and Environmental Engineering Research
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• v.26 no.3C
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• pp.201-207
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• 2006

Soil tests are generally conducted using a membrane to measure a pore water pressure. However, it has also been recognized that the membrane penetrates into the specimen by the change of the confining pressure, and it results in the erroneous measurement in the pore water pressure and the volumetric strain. This study examined the effectiveness of the correction equation of the membrane penetration on the basis of the experimental data acquired during the isotropic unloading and the cyclic shear process using the hollow cylindrical shear test equipment. The results showed that the membrane penetration by the correction equation could be overestimated when the mean effective stress was lower than 20kPa in this study. The limitations originated from the sudden increase near the zero effective stress, and in order to prevent the overestimation in low effective stress condition, the use of the constant a was proposed in this study. Furthermore, the correction equation for the membrane penetration had to be applied carefully when the initial relative density was high and the density changes were occurred by the relocation of the soil particle by the liquefaction.

• Journal of Life Science
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• v.33 no.11
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• pp.944-949
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• 2023

The purpose of this study was to identify conserved metabolic pathways and conserved genes in 122 archaeal species. Using the Clusters of Orthologous Groups of Proteins (COG) database of conserved genes, we analyzed whether 122 species had 63 COG metabolic pathways, the 822 COGs that compose them, and a total of 4,877 COGs. Archaeal ribosomal proteins were the most conserved in metabolic pathways. 46 COGs in seven COG pathways among 63 COG pathways and 20 COGs in others were conserved in 122 species. Some genes involved in cell wall and extracellular matrix synthesis, replication, transcription, translation, and protein metabolism were common to all 122 species. When the distance value of the phylogenetic tree was analyzed at the phylum level or class level, the average was the lowest at the class Halobacteria of the phylum Euryarchaeota. Standard deviation was high for the class Nitosospharia of the phylum Thaumarchaeota, the unclassified members of phylum Thaumarchaeota, the class Halobacteria of the phylum Euryarchaeota, the class Thermoprotei of the phylum Crenarchaeota, and other archaea. Furthermore, the phylogenetic tree analysis revealed six commonalities. The results of this study, along with data on conserved genes, could be used for drug development and gene selection for strain improvement.

• Journal of Mushroom
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• v.21 no.4
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• pp.261-265
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• 2023

We aimed to develop outstanding domestic varieties suitable for both columnar and cylindrical-shape substrates, aiming to replace foreign varieties. and bred a high-quality new strain named 'Charmjon', using genetic resources collected from Japan and China. The optimal cultivation temperature for Charmjon's mycelial growth was found to be 25℃, and its mycelial growth at 15℃ and 25℃ was superior to the control variety. In terms of mycelial growth characteristics based on the substrate, Charmjon exhibited excellent mycelial strength on PDA medium compared to the control variety. Through columnar and cylindrical-shape substrates cultivation, we assessed the quantity and morphological characteristics of the fruiting bodies. The results confirmed that Charmjon can be produced stably using both cultivation methods, and it showed higher yields and individual weights than the control variety. In addition, the color of the pileus was notably darker, and the shape of the pileus varied depending on the cultivation method. The test of genetic diversity revealed that Charmjon has distinct genetic characteristics compared to the control varieties.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.12 no.3
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• pp.178-185
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• 2007

Myrionecta rubra Jankowski 1976(=Mesodinium rubrum Lohmann 1908), a mixotrophic ciliate, is very common and often causes recurrent red tides in diverse marine environments. Since the report on the first laboratory strain of this species in 2000, papers on its novel ecological role and evolutionary importance have been high lighted. This review paper is prepared to promote the de novo recognition M. rubra as a marine mixotrophic species. M. rubra is a ciliate which is able to photosynthesize using plastids originated from cryptophyte (including Teleaulax sp. and Geminigera sp.) prey cells (i.e. kleptoplastidic ciliate). Recently, novel bacterivory of M. rubra was firstly reported. Thus, the nutritional modes of M. rubra include photosynthesis, bacterivory, and algivory. In turn, M. rubra was reported as the prey species of metazoan predators such as calanoid copepods, mysids, larvae of ctenophore and anchovy, and spats of bivalves. In addition, it was reported that dinoflagellate Dinophysis causing diarrhetic shellfish poisoning is one among the predators of M. rubra. Thus, M. rubra, a marine mixotrophic ciliate, may play a pivotal role as a common linking ciliate for the flow of energy and organic material in pelagic food webs.

• Journal of the Korea Institute of Military Science and Technology
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• v.27 no.4
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• pp.507-515
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• 2024

Microbial forensics is a scientific discipline for analyzing evidence related to biological crimes by identifying the origin of microorganisms. Multiple locus variable number tandem repeat analysis(MLVA) is one of the microbiological analysis methods used to specify subtypes within a species based on the number of tandem repeat in the genome, and advances in next generation sequencing(NGS) technology have enabled in silico anlysis of full-length whole genome sequences. In this paper, we analyzed unknown samples provided by Robert Koch Institute(RKI) through The United Nations Secretary-General's Mechanism(UNSGM)'s external quality assessment exercise(EQAE) project, which we officially participated in 2023. We confirmed that the 3 unknown samples were B. anthracis through nucleic acid isolation and genetic sequence analysis studies. MLVA results on 32 loci of B. anthracis were analysed by using genome sequences obtained from NGS(NextSeq and MinION) and Sanger sequencing. The MLVA typing using short-reads based NGS platform(NextSeq) showed a high probability of causing assembly error when a size of the tandem repeats was grater than 200 bp, while long-reads based NGS platform(MinION) showed higher accuracy than NextSeq, although insertion and deletion was observed. We also showed hybrid assembly can correct most indel error caused by MinION. Based on the MLVA results, genetic identification was performed compared to the 2,975 published MLVA databases of B. anthracis, and MLVA results of 10 strains were identical with 3 unkonwn samples. As a result of whole genome alignment of the 10 strains and 3 unknown samples, all samples were identified as B. anthracis strain A4564 which is associated with injectional anthrax isolates in heroin users.