Use this URL to cite or link to this record in EThOS: https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.783842
Title: Effects of mechanical forces on the shape of confined E. Coli micro-colonies in Agarose
Author: Williams, Joshua Jon
ISNI:       0000 0004 7969 4235
Awarding Body: University of Edinburgh
Current Institution: University of Edinburgh
Date of Award: 2019
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Abstract:
Bacterial colonies and biofilms play an important role in many aspects of human life. Communities formed by harmful bacteria are responsible for human and animal infections and food spoilage, but beneficial bacteria find applications in water treatment and other waste processing. Rather unsurprisingly, a great deal of research has been undertaken into all aspects of their nature, especially into biofilm control and prevention. Traditional approaches to control bacterial growth have focused upon using chemicals to kill bacteria or inhibit their replication, such as antibiotics. However, bacteria can quickly develop resistance to antibiotics. This is because resistant mutants that emerge spontaneously in bacterial colonies outgrow sensitive cells. This process of Darwinian selection is making many antibiotics ineffective against infections. Recent work on evolution in bacterial populations has shown the importance of the spatial effects (colony shape) upon the fixation probabilities of mutants and the overall fitness of a population. For example, the roughness of a bacterial colony's front significantly affects the fixation probability of a new mutant. These and other studies have come to recognise the significance of mechanical interactions upon the colony morphology. This thesis considers how mechanical interaction can effect the colony shapes in two comparatively simple systems of confined, immotile E. Coli colonies. The first system (reffed to as "quasi-2D") is micro-colonies (< 500 cells) initiated from a single cell and grown at the interface of agarose gel and a glass slide. The second system studied (reffed to as "submerged") is colonies initiated from cells placed within the bulk of a stiff (> 0:6% w/w) agarose gel. In the "quasi-2D" system it has been found that different micro-colonies can vary greatly and apparently randomly in shape under identical growth conditions. In the "submerged" system, colonies are found to grow into oblate spheroid-like ("smartie") shapes. Here I use computer simulations and continuum mechanics approach to understand the origin of these shapes. Both systems are initially investigated by individual based models (IBMs). All IBMs used are based upon a "null" model simulating growth, division and contact between cells, to which other interactions are added as required to reproduce the experimental results. In particular I consider: cell-cell adhesion; cell-substrate adhesion; asymmetric friction; ageing of cells friction; a shifting center of mass during growth; compression from agarose; and phenotype switching between "sticky" and "non-sticky" cell types. Most interactions (cell-substrate adhesion, asymmetric friction, and variants thereof) are found to have some significant effect upon the colony shapes, but distributions of colony shapes do not correlate well with the experimental distribution. One interaction, cell-cell adhesion, is found to have no significant effect on the colony shape within a reasonable parameter range. The remaining interactions, compression from agarose and phenotype switching are capable of replicating the experimental colony shape distributions. In the case of the second system of "smartie" colonies, the colony shape appears to be principally determined by the interaction with the agarose gel. This is demonstrated in 2D simulations via a bead and spring agarose model added to the "null" model of bacterial colony. To get qualitatively similar shaped colonies to those seen experimentally, springs that represent agarose fibres must be robust and not break easily. Additionally, the model is able to qualitatively reproduce the experimental variation in the smartie aspect ratio with agarose gel concentration. To expand on simulations of "smartie" colonies a dynamical continuum model of agarose fracture is developed. The model predicts that cavity shape is significantly affected by the colony growth law (i.e. linear, exponential or cubic in time) and by critical strain. In particular, "smartie" shapes are only expected for cubic and sub-cubic colony growth laws. Other parameters of the model such as agarose or bacterial Young's moduli are also found to affect the cavity shape but to a lesser extent. The model also qualitatively reproduces the time dependence of the experimental colony shape for a growth law fitted to an experimental growth curve.
Supervisor: Waclaw, Bartlomiej ; Marenduzzo, Davide Sponsor: Engineering and Physical Sciences Research Council (EPSRC)
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID: uk.bl.ethos.783842  DOI: Not available
Keywords: biofilm control ; colony shape ; colony morphology ; E. coli ; individual based models ; smartie colonies ; agarose fibres
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