• 한국전산유체공학회:학술대회논문집
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• 2009.11a
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• pp.164-169
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• 2009

Study on swimming of microorganisms like, sperm motility, cilia beating, bacterial flagellar propulsion has found immense significance in the field of biological fluiddynamics. Because of the complexity involved, it is challenging for the researchers to model such problems. Immersed boundary method has proved its efficacy in the field of biological fluiddynamics, The present work aims at performing a numerical study on the microorganism locomotion using the immersed boundary method proposed by Peskin[1]. A two-dimensional model of the microorganism is modeled as thin elastic filament described as a sine wave. The neutrally buoyant organism undergoing deformations is immersed in a viscous and incompressible fluid. The fluid quantities are described using Eulerian coordinates and the immersed body is represented by Lagrangian coordinates. The Eulerian and Lagrangian variables are connected by the Dirac delta function. The Navier-Stokes equations governing the fluid flow are solved using the fractional step method on a staggered Cartesian grid system. The developed numerical code in FORTRAN will be validated by comparing the numerical results with the available results.

• Microbiology and Biotechnology Letters
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• v.47 no.4
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• pp.651-661
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• 2019

Targeting the pathogen viability using drugs is associated with development of drug resistance due to selective pressure. Hence, there is an increased interest in developing agents that target bacterial virulence. In this study, the inhibitory effect of ciclopirox, an antifungal agent with iron chelation potential, on the microbial virulence factors was evaluated in 26 clinical MDR Pseudomonas aeruginosa isolates collected from Alexandria Main University Hospital, a tertiary hospital in Egypt. Treatment with 9 ㎍/ml ciclopirox inhibited the hemolytic activity in 70% isolates, reduced pyocyanin production, decreased protease secretion in 46% isolates, lowered twitching and swarming motility, and decreased biofilm formation by 1.5- to 4.5-fold. The quantitative real-time PCR analysis revealed that treatment with ciclopirox downregulated the expression levels of alkaline protease (aprA) and pyocyanin (phzA1). Ciclopirox is used to treat hematological malignancies and the systemic administration of ciclopirox is reported to have adequate oral absorption with a satisfactory drug safety profile. It is important to calculate the appropriate clinical dose and therapeutic index to reposition ciclopirox from a topical antifungal agent to a promising virulence-modifying agent agent against P. aeruginosa, a problematic Gram-negative pathogen.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.42 no.5
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• pp.461-467
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• 2009

A bacterial strain was screened and identified from sea sediments in Tongyeong coastal area in order to obtain proteases or peptidase cleaving C-terminal of glutamic acid. Strain TS0611, which showed the highest activity from 5 isolated protease producing strains, was selected and its properties investigated. Strain TS0611 was a gram-positive rod, $1.2\;{\mu}m$ in cell length, catalase positive, motility-positive, melanin-negative and grew at 15~$50^{\circ}C$, and hydrolyzed gelatin and casein. This strain was identified as Bacillus thuringiensis or Bacillus cereus based on results from the API system(API 50 CHB) which examined saccharides properties, fatty acid composition of cell wall, and 16S rRNA gene sequence.

• Journal of Microbiology and Biotechnology
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• v.20 no.2
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• pp.410-414
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• 2010

A bacterial strain, 13-$25^T$ with xylanolytic activity isolated from a single soil sample, was characterized with respect to its phenetic and phylogenetic characteristics. The cells of the isolate are Gram-staining variable rods, but spore formation was not observed. This strain is catalase- and oxidase-positive, and able to degrade starch and xylan. The predominant fatty acids are anteiso-$C_{15:0}$, $C_{16:0}$, and iso-$C_{16:0}$. The major respiratory quinone is menaquinone 7(MK-7), with a polar lipid profile consistent with the genus Cohnella. The DNA G+C content is 54.3 mol%. The 168 rRNA gene sequence analysis indicates that this organism belongs to the genus Cohnella, with Cohnella panacarvi as the closest phylogenetic neighbor. Low levels of 168 rRNA gene sequence similarity (<97.0%) with respect to other taxa with published names and the identification of distinctive phenetic features in the isolate indicate that the strain 13-$25^T$ represents a novel species of the genus Cohnella, for which the name Cohnella damensis sp. novo is proposed. The type strain is 13-$25^T$ (=CCTCC AB $208103^T$=KCTC $13422^T$).

• Journal of Microbiology and Biotechnology
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• v.27 no.11
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• pp.2028-2036
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• 2017

The Escherichia coli K-12 and B strains are among the most frequently used bacterial hosts for scientific research and biotechnological applications. However, omics analyses have revealed that E. coli K-12 and B exhibit notably different genotypic and phenotypic attributes, even though they were derived from the same ancestor. In a previous study, we identified a limited number of proteins from the two strains using two-dimensional gel electrophoresis and tandem mass spectrometry (MS/MS). In this study, an in-depth analysis of the physiological behavior of the E. coli K-12 and B strains at the proteomic level was performed using six-plex isobaric tandem mass tag-based quantitative MS. Additionally, the best lysis buffer for increasing the efficiency of protein extraction was selected from three tested buffers prior to the quantitative proteomic analysis. This study identifies the largest number of proteins in the two E. coli strains reported to date and is the first to show the dynamics of these proteins. Notable differences in proteins associated with key cellular properties, including some metabolic pathways, the biosynthesis and degradation of amino acids, membrane integrity, cellular tolerance, and motility, were found between the two representative strains. Compared with previous studies, these proteomic results provide a more holistic view of the overall state of E. coli cells based on a single proteomic study and reveal significant insights into why the two strains show distinct phenotypes. Additionally, the resulting data provide in-depth information that will help fine-tune processes in the future.

• Fisheries and Aquatic Sciences
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• v.15 no.1
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• pp.83-89
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• 2012

Flavobacterium johnsoniae was isolated from farmed rainbow trout Oncorhynchus mykiss in Korea, and its biochemical and molecular characterization was determined. Yellow-pigmented bacterial colonies were isolated from 18 of 64 fish samples (28.1%) on trypticase soy agar plates, and their biochemical profiles were characterized by API 20E and API 20NE test kits. F. johnsoniae was identified by biochemical phenotyping of factors including rapid gliding motility, Gram-negative condition, oxidase- and catalase-positive status, Congo red absorption, nitrate reduction, ${\beta}$-galactosidase production, acid production from glucose, and gelatin and casein hydrolysis. PCR and subsequent sequencing of 16S rRNA confirmed that the yellow-pigmented colonies were most similar to F. johnsoniae. The alignment analysis of 16S rRNA sequences also showed that all 18 rainbow trout isolates had highly similar homologies (97-99% identity). One isolate was selected and named FjRt09. This isolate showed 98% homology with previously reported F. johnsoniae isolates, and in phylogenetic analysis was more closely grouped with F. johnsoniae than with F. psychrophilum, F. columnare, or F. branchiophilum. This is the first report on the occurrence and biochemical characterization of F. johnsoniae isolated from rainbow trout in Korea.

• 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.39 no.1
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• pp.62-74
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• 2023

Plant pathogenic Pectobacterium species cause severe soft rot/blackleg diseases in many economically important crops worldwide. Pectobacterium utilizes plant cell wall degrading enzymes (PCWDEs) as the main virulence determinants for its pathogenicity. In this study, we screened a random mutant, M29 is a transposon insertion mutation in the metC gene encoding cystathionine β-lyase that catalyzes cystathionine to homocysteine at the penultimate step in methionine biosynthesis. M29 became a methionine auxotroph and resulted in growth defects in methionine-limited conditions. Impaired growth was restored with exogenous methionine or homocysteine rather than cystathionine. The mutant exhibited reduced soft rot symptoms in Chinese cabbages and potato tubers, maintaining activities of PCWDEs and swimming motility. The mutant was unable to proliferate in both Chinese cabbages and potato tubers. The reduced virulence was partially restored by a complemented strain or 100 µM of methionine, whereas it was fully restored by the extremely high concentration (1 mM). Our transcriptomic analysis showed that genes involved in methionine biosynthesis or transporter were downregulated in the mutant. Our results demonstrate that MetC is important for methionine biosynthesis and transporter and influences its virulence through Pcc21 multiplication in plant hosts.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.1
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• pp.166-176
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• 2020

Objective: An experiment was conducted to determine the effects of L-arginine (L-Arg) and N-carbamoylglutamic acid (NCG) on the growth, metabolism, immunity and community of cecal bacterial flora of weanling and young rabbits. Methods: Eighteen normal-grade male weanling Japanese White rabbits (JWR) were selected and randomly divided into 6 groups with or without L-Arg and NCG supplementation. The whole feeding process was divided into weanling stage (day 37 to 65) and young stage (day 66 to 85). The effects of L-Arg and NCG on the growth, metabolism, immunity and development of the ileum and jejunum were compared via nutrient metabolism experiments and histological assessment. The different communities of cecal bacterial flora affected by L-Arg and NCG were assessed using high-throughput sequencing technology and bioinformatics analysis. Results: The addition of L-Arg and NCG enhanced the growth of weanling and young rabbit by increasing the nitrogen metabolism, protein efficiency ratio, and biological value, as well as feed intake and daily weight gain. Both L-Arg and NCG increased the concentration of immunoglobulin A (IgA), IgM, and IgG. NCG was superior to L-Arg in promoting intestinal villus development by increasing villus height, villus height/crypt depth index, and reducing the crypt depth. The effects of L-Arg and NCG on the cecal bacterial flora were mainly concentrated in different genera, including Parabacteroides, Roseburia, dgA-11_gut_group, Alistipes, Bacteroides, and Ruminococcaceae_UCG-005. These bacteria function mainly in amino acid transport and metabolism, energy production and conversion, lipid transport and metabolism, recombination and repair, cell cycle control, cell division, and cell motility. Conclusion: L-Arg and NCG can promote the growth and immunity of weanling and young JWR, as well as effecting the jejunum and ileum villi. L-Arg and NCG have different effects in the promotion of nutrient utilization, relieving inflammation and enhancing adaptability through regulating microbial community.

• Korean Journal of Microbiology
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• v.46 no.3
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• pp.240-247
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• 2010

Pseudomonas aeruginosa is a Gram (-) opportunistic human pathogen causing a wide variety of infections on lung, urinary tract, eyes, and burn wound sites and quorum sensing (QS), a cell density-sensing mechanism plays an essential role in Pseudomonas pathogenesis. In order to investigate the importance of QS in the Pseudomonas infections of Korean patients, we isolated 189 clinical strains of P. aeruginosa from the patients in Pusan Paik Hospital, Busan, South Korea. The QS signal production of these clinical isolates was measured by signal diffusion assay on solid media using reporter strains. While most clinical strains (79.4%) produced the QS signals as similar level as a wild type strain, PAO1 did, where LasR, the initial QS signal sensor-regulator was fully activated, a minority of them (4.2%) produced much less QS signals at the level to which LasR failed to respond. Similarly, while 72.5% of the clinical isolates produced QS signals enough to activate QscR, an another QS signal sensor-regulator, some few of them (9%) produced the QS signals at much lower level where QscR was not activated. For further analysis, we selected 74 clinical strains that were obtained from the patients under suspicion of Pseudomonas infection and investigated the total protease activity that is considered important for virulence. Interestingly, significant portion of them showed very low protease activity (44.6%) or no detectable protease activity (12.2%). When the biofilm-forming ability that is considered very important in chronic infection was examined, most isolates showed lower biofilm-forming activity than PAO1. Similarly, significant portion of clinical isolates showed reduced motility (reduced swarming activity in 51.4% and reduced twitching activity in 41.9%), or non-detectable motility (swarming-negative in 28.4% and twitching-negative in 28.4%). Our result showed that the clinical isolates that produced QS signals at the similar level to wild type could have significantly reduced activities in the protease production, biofilm formation, and motility, and some clinical isolates had unique patterns of motility, biofilm formation, and protease production that are not correlated to their QS activity.