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Xiaoling Wang – One of the best experts on this subject based on the ideXlab platform.

  • Simulation of Bacillus subtilis biofilm growth on Agar Plate by diffusion–reaction based continuum model
    Physical biology, 2016
    Co-Authors: Xianlong Zhang, Xiaoling Wang, Kai Nie, Qingping Sun
    Abstract:

    Various species of bacteria form highly organized spatially-structured aggregates known as biofilms. To understand how microenvironments impact biofilm growth dynamics, we propose a diffusion-reaction continuum model to simulate the formation of Bacillus subtilis biofilm on an Agar Plate. The extended finite element method combined with level set method are employed to perform the simulation, numerical results show the quantitative relationship between colony morphologies and nutrient depletion over time. Considering that the production of polysaccharide in wild-type cells may enhance biofilm spreading on the Agar Plate, we inoculate mutant colony incapable of producing polysaccharide to verify our results. Predictions of the glutamate source biofilm‘s shape parameters agree with the experimental mutant colony better than that of glycerol source biofilm, suggesting that glutamate is rate limiting nutrient for Bacillus subtilis biofilm growth on Agar Plate, and the diffusion-limited is a better description to the experiment. In addition, we find that the diffusion time scale is of the same magnitude as growth process, and the common-employed quasi-steady approximation is not applicable here.

  • simulation of bacillus subtilis biofilm growth on Agar Plate by diffusion reaction based continuum model
    Physical Biology, 2016
    Co-Authors: Xianlong Zhang, Xiaoling Wang, Mingpeng Li
    Abstract:

    Various species of bacteria form highly organized spatially-structured aggregates known as biofilms. To understand how microenvironments impact biofilm growth dynamics, we propose a diffusion–reaction continuum model to simulate the formation of Bacillus subtilis biofilm on an Agar Plate. The extended finite element method combined with level set method are employed to perform the simulation, numerical results show the quantitative relationship between colony morphologies and nutrient depletion over time. Considering that the production of polysaccharide in wild-type cells may enhance biofilm spreading on the Agar Plate, we inoculate mutant colony incapable of producing polysaccharide to verify our results. Predictions of the glutamate source biofilm‘s shape parameters agree with the experimental mutant colony better than that of glycerol source biofilm, suggesting that glutamate is rate limiting nutrient for Bacillus subtilis biofilm growth on Agar Plate, and the diffusion-limited is a better description to the experiment. In addition, we find that the diffusion time scale is of the same magnitude as growth process, and the common-employed quasi-steady approximation is not applicable here.

Shinobu Oda – One of the best experts on this subject based on the ideXlab platform.

  • Efficient production of fungal spores by the combination of reduction of nitrogen source content and embedding of hydrophobic polymer in an Agar Plate.
    Journal of bioscience and bioengineering, 2021
    Co-Authors: Kyoko Sugimoto, Shinobu Oda
    Abstract:

    Fungal sporulation is affected by many environmental factors, for example, we previously observed that embedding of a hydrophobic polypolymer net in an Agar Plate medium significantly accelerates spore formation of some fungi. Here, it was found that the fungal spore formation depended on the surface hydrophobicity of cultivation vessels used for the Plate cultivation. In a polypropylene (PP) vessel, six fungal strains produced spores of 1.5 to 514.8 times of those growing in a glass vessel. The contact of vegetative hyphae on the surface of the vessels might trigger the fungal spore formation. Moreover, the spore formation was synergistically accelerated by the reduction of nitrogen source content in an Agar Plate medium and by the contact to hydrophobic polymers. The synergistic effect depended on the surface area of the hydrophobic polypolymer. Thus, the combination of the reduction of nitrogen source and the embedding of hydrophobic polypolymer is expected as a novel and effective procedure for production of fungal sporspores which are useful for the inoculum in fermentation industry and biocontrol agent in agriculture.

  • Acceleration of fungal spore production by embedding a hydrophobic polymer net in a nutrient Agar Plate
    Fungal biology, 2018
    Co-Authors: Shinobu Oda, Ryosuke Kido
    Abstract:

    Abstract A simple and novel procedure for the acceleration of fungal spore production was developed. A net of hydrophobic polypolymer such as polypropylene (PP) and polytetrafluoroethylene (PTFE) was embedded in a nutrient Agar Plate, and effect of the polymer net on spore production by 6 fungal strains, such as Aspergillus terreus, Penicillium multicolor, and Trichoderma virens were estimated. The effect of hydrophobic polypolymer net was insufficient in a liquid-surface immobilization (LSI) system with fungal cells immobilized on a ballooned microsphere layer formed on a liquid medium surface. On the other hand, the embedding of a PTFE net in an Agar Plate remarkably enhanced the spore production in all 6 strains tested to produce 2.0–8.5 × 107 spores/cm2-Agar Plate surface. Especially, the spore production by A. terreus ATCC 20542 in the presence of a PTFE net was 7.7 times as much than that in no net. Positive correlations between the hydrophobicity of net and the spore production were observed in all 6 strains (R2, 0.653–0.999).

  • Solvent-tolerance of fungi located on an interface between an Agar Plate and an organic solvent.
    Bioscience biotechnology and biochemistry, 2014
    Co-Authors: Shinobu Oda, Ayaka Sugitani, Shinichi Ohashi
    Abstract:

    While 6 by 20 of type culture fungi could grow on an interface between organic solvent (log P, 4.12) and Agar Plate, 13 by 20 of strains could form a large colony after the removal of more toxic solvent, such as styrene (log P, 2.95) and tert-butyl acetate (log P, 1.76) because of viability of spores on the interface.

Xianlong Zhang – One of the best experts on this subject based on the ideXlab platform.

  • Simulation of Bacillus subtilis biofilm growth on Agar Plate by diffusion–reaction based continuum model
    Physical biology, 2016
    Co-Authors: Xianlong Zhang, Xiaoling Wang, Kai Nie, Qingping Sun
    Abstract:

    Various species of bacteria form highly organized spatially-structured aggregates known as biofilms. To understand how microenvironments impact biofilm growth dynamics, we propose a diffusion-reaction continuum model to simulate the formation of Bacillus subtilis biofilm on an Agar Plate. The extended finite element method combined with level set method are employed to perform the simulation, numerical results show the quantitative relationship between colony morphologies and nutrient depletion over time. Considering that the production of polysaccharide in wild-type cells may enhance biofilm spreading on the Agar Plate, we inoculate mutant colony incapable of producing polysaccharide to verify our results. Predictions of the glutamate source biofilm’s shape parameters agree with the experimental mutant colony better than that of glycerol source biofilm, suggesting that glutamate is rate limiting nutrient for Bacillus subtilis biofilm growth on Agar Plate, and the diffusion-limited is a better description to the experiment. In addition, we find that the diffusion time scale is of the same magnitude as growth process, and the common-employed quasi-steady approximation is not applicable here.

  • simulation of bacillus subtilis biofilm growth on Agar Plate by diffusion reaction based continuum model
    Physical Biology, 2016
    Co-Authors: Xianlong Zhang, Xiaoling Wang, Mingpeng Li
    Abstract:

    Various species of bacteria form highly organized spatially-structured aggregates known as biofilms. To understand how microenvironments impact biofilm growth dynamics, we propose a diffusion–reaction continuum model to simulate the formation of Bacillus subtilis biofilm on an Agar Plate. The extended finite element method combined with level set method are employed to perform the simulation, numerical results show the quantitative relationship between colony morphologies and nutrient depletion over time. Considering that the production of polysaccharide in wild-type cells may enhance biofilm spreading on the Agar Plate, we inoculate mutant colony incapable of producing polysaccharide to verify our results. Predictions of the glutamate source biofilm’s shape parameters agree with the experimental mutant colony better than that of glycerol source biofilm, suggesting that glutamate is rate limiting nutrient for Bacillus subtilis biofilm growth on Agar Plate, and the diffusion-limited is a better description to the experiment. In addition, we find that the diffusion time scale is of the same magnitude as growth process, and the common-employed quasi-steady approximation is not applicable here.

Jung Kyung Kim – One of the best experts on this subject based on the ideXlab platform.

  • visualization of biosurfactant film flow in a bacillus subtilis swarm colony on an Agar Plate
    International Journal of Molecular Sciences, 2015
    Co-Authors: Kyunghoon Kim, Jung Kyung Kim
    Abstract:

    Collective bacterial dynamics plays a crucial role in colony development. Although many research groups have studied the behavior of fluidic swarm colonies, the detailed mechanics of its motion remains elusive. Here, we developed a visualization method using submicron fluorescent beads for investigating the flow field in a thin layer of fluid that covers a Bacillus subtilis swarm colony growing on an Agar Plate. The beads were initially embedded in the Agar Plate and subsequently distributed spontaneously at the upper surface of the expanding colony. We conducted long-term live cell imaging of the B. subtilis colony using the fluorescent tracers, and obtained high-resolution velocity maps of microscale vortices in the swarm colony using particle image velocimetry. A distinct periodic fluctuation in the average speed and vorticity of flow in swarm colony was observed at the inner region of the colony, and correlated with the switch between bacterial swarming and growth phases. At the advancing edge of the colony, both the magnitudes of velocity and vorticity of flow in swarm colony were inversely correlated with the spreading speed of the swarm edge. The advanced imaging tool developed in this study would facilitate further understanding of the effect of micro vortices in swarm colony on the collective dynamics of bacteria.

  • long term visualization of micro vortices in bacillus subtilis bacterial biofilm on Agar Plate using particle image velocimetry
    Biophysical Journal, 2014
    Co-Authors: Kyunghoon Kim, Jung Kyung Kim
    Abstract:

    The collective dynamics of bacteria has a crucial role in the development of biofilm. Although the behavior of the fluidic biofilm was studied by many research groups, detailed mechanics of its motion still remains elusive. Previously, we developed a method for visualization of vortical flow in the Bacillus Subtilis (B. subtilis) colony using 200-nm fluorescent microbeads, which were initially embedded in the Agar Plate and distributed spontaneously at the upper surface of the growing colony. Here, we conducted a long-term live imaging of B. subtilis colony with the fluorescent beads and obtained high-resolution velocity maps of microscale vortices in the biofilm using particle image velocimetry (PIV). At the tip of the colony, a distinct periodic fluctuation of average speed and vorticity revealed by Micro-PIV analysis was correlated with switching between bacterial swarming and growth phases. Our advanced imaging tool helps to explain the effect of micro vorticies in the biofilm on the collective dynamics of bacteria.

Qingping Sun – One of the best experts on this subject based on the ideXlab platform.

  • Simulation of Bacillus subtilis biofilm growth on Agar Plate by diffusion–reaction based continuum model
    Physical biology, 2016
    Co-Authors: Xianlong Zhang, Xiaoling Wang, Kai Nie, Qingping Sun
    Abstract:

    Various species of bacteria form highly organized spatially-structured aggregates known as biofilms. To understand how microenvironments impact biofilm growth dynamics, we propose a diffusion-reaction continuum model to simulate the formation of Bacillus subtilis biofilm on an Agar Plate. The extended finite element method combined with level set method are employed to perform the simulation, numerical results show the quantitative relationship between colony morphologies and nutrient depletion over time. Considering that the production of polysaccharide in wild-type cells may enhance biofilm spreading on the Agar Plate, we inoculate mutant colony incapable of producing polysaccharide to verify our results. Predictions of the glutamate source biofilm’s shape parameters agree with the experimental mutant colony better than that of glycerol source biofilm, suggesting that glutamate is rate limiting nutrient for Bacillus subtilis biofilm growth on Agar Plate, and the diffusion-limited is a better description to the experiment. In addition, we find that the diffusion time scale is of the same magnitude as growth process, and the common-employed quasi-steady approximation is not applicable here.