9 research outputs found
Characterizing the shape patterns of dimorphic yeast pseudohyphae
© 2018 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.Pseudohyphal growth of the dimorphic yeast Saccharomyces cerevisiae is analysed using two-dimensional top-down binary images. The colony morphology is characterized using clustered shape primitives (CSPs), which are learned automatically from the data and thus do not require a list of predefined features or a priori knowledge of the shape. The power of CSPs is demonstrated through the classification of pseudohyphal yeast colonies known to produce different morphologies. The classifier categorizes the yeast colonies considered with an accuracy of 0.969 and standard deviation 0.041, demonstrating that CSPs capture differences in morphology, while CSPs are found to provide greater discriminatory power than spatial indices previously used to quantify pseudohyphal growth. The analysis demonstrates that CSPs provide a promising avenue for analysing morphology in high-throughput assays
TAMMiCol: Tool for analysis of the morphology of microbial colonies.
Many microbes are studied by examining colony morphology via two-dimensional top-down images. The quantification of such images typically requires each pixel to be labelled as belonging to either the colony or background, producing a binary image. While this may be achieved manually for a single colony, this process is infeasible for large datasets containing thousands of images. The software Tool for Analysis of the Morphology of Microbial Colonies (TAMMiCol) has been developed to efficiently and automatically convert colony images to binary. TAMMiCol exploits the structure of the images to choose a thresholding tolerance and produce a binary image of the colony. The images produced are shown to compare favourably with images processed manually, while TAMMiCol is shown to outperform standard segmentation methods. Multiple images may be imported together for batch processing, while the binary data may be exported as a CSV or MATLAB MAT file for quantification, or analysed using statistics built into the software. Using the in-built statistics, it is found that images produced by TAMMiCol yield values close to those computed from binary images processed manually. Analysis of a new large dataset using TAMMiCol shows that colonies of Saccharomyces cerevisiae reach a maximum level of filamentous growth once the concentration of ammonium sulfate is reduced to 200 μM. TAMMiCol is accessed through a graphical user interface, making it easy to use for those without specialist knowledge of image processing, statistical methods or coding
Diffusion-Limited Growth of Microbial Colonies.
The emergence of diffusion-limited growth (DLG) within a microbial colony on a solid substrate is studied using a combination of mathematical modelling and experiments. Using an agent-based model of the interaction between microbial cells and a diffusing nutrient, it is shown that growth directed towards a nutrient source may be used as an indicator that DLG is influencing the colony morphology. A continuous reaction-diffusion model for microbial growth is employed to identify the parameter regime in which DLG is expected to arise. Comparisons between the model and experimental data are used to argue that the bacterium Bacillus subtilis can undergo DLG, while the yeast Saccharomyces cerevisiae cannot, and thus the non-uniform growth exhibited by this yeast must be caused by the pseudohyphal growth mode rather than limited nutrient availability. Experiments testing directly for DLG features in yeast colonies are used to confirm this hypothesis
Extensional and surface-tension-driven fluid flows in microstructured optical fibre fabrication
Microstructured optical fibres (MOFs) are a design of optical fibre comprising a series of longitudinal air channels within a thread of material that form a waveguide for light. The flexibility of this design allows optical fibres to be created with adaptable and previously unrealised optical properties. A MOF is typically constructed by first creating a macroscopic version of the design, known as a preform, with a centimetre-scale diameter that is later drawn into a fibre with a micrometer-scale diameter. There are several methods for constructing a preform. In the extrusion method molten material is forced through a die containing an array of blocking elements that match the required pattern of channels. Preforms may also be constructed by stacking tubes and fusing them together with heat. In both processes the fluid flow that arises can deform the air channels, rendering the fibre useless. At present there is only a limited understanding of the relative importance of the various physical parameters in determining the final preform geometry, which means that the development of new MOF technology requires time-consuming and costly experimentation. This thesis develops mathematical models of the fluid flows that occur during the extrusion and stacking methods of MOF preform fabrication. These models are used to determine which physical mechanisms are important during the manufacturing process so as to inform the fabrication of MOF preforms. A model is constructed of a fixed slender fluid cylinder with internal structure stretching under gravity and with surface-tension-driven deformation. The molten material is modelled as a Newtonian fluid with a temperature-dependent viscosity, which is assumed known. The variables are expanded as series in powers of a slenderness parameter so that, after dropping higher-order terms, the resulting equations partially decouple into a one-dimensional model for the axial ow and a two-dimensional model for the transverse flow. Under a suitable transformation of variables the transverse equations are precisely the Stokes equations with unit surface tension. After reviewing the use of complex variables to represent the transverse problem, three numerical solution methods are considered: two based upon spectral methods and one using the method of fundamental solutions (MFS). These methods are compared for their efficiency and accuracy. Several example solutions for stretching cylinders are presented and the role of surface tension is investigated using approximate solutions derived for zero and small surface tension. The model is validated against experimental data and found to be in good agreement. The stretching model is extended to the case of an extruded fluid cylinder, neglecting extrudate-swell effects, where again the fluid flow decouples in axial and transverse models. The results are compared with experimental observations and the model used to analyse the formation of distortions during preform extrusion and how these may be controlled. Two problems related to preform fabrication are considered that feature cross sections with non-circular initial outer boundaries. A technique is developed for deriving initial conformal maps describing such domains, which are used in the stretching and extrusion models to analyse the proposed problems.Thesis (Ph.D.) -- University of Adelaide, School of Mathematical Sciences, 2016
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Diffusion-Limited Growth of Microbial Colonies.
The emergence of diffusion-limited growth (DLG) within a microbial colony on a solid substrate is studied using a combination of mathematical modelling and experiments. Using an agent-based model of the interaction between microbial cells and a diffusing nutrient, it is shown that growth directed towards a nutrient source may be used as an indicator that DLG is influencing the colony morphology. A continuous reaction-diffusion model for microbial growth is employed to identify the parameter regime in which DLG is expected to arise. Comparisons between the model and experimental data are used to argue that the bacterium Bacillus subtilis can undergo DLG, while the yeast Saccharomyces cerevisiae cannot, and thus the non-uniform growth exhibited by this yeast must be caused by the pseudohyphal growth mode rather than limited nutrient availability. Experiments testing directly for DLG features in yeast colonies are used to confirm this hypothesis
Driving script from Quantifying the dominant growth mechanisms of dimorphic yeast using a lattice-based model
MATLAB code that calls the model code to run the different scenarios considered in this study
Processed images from: TAMMiCol: Tool for analysis of the morphology of microbial colonies
Images processed by TAMMiCol used in TAMMiCol: Tool for analysis of the morphology of microbial colonies. The images are taken over time and show yeast colonies exhibiting filamentous growth
Processed binary image of a filamentous colony from Quantifying the dominant growth mechanisms of dimorphic yeast using a lattice-based model
A processed binary image of the filamentous colony shown in figure 10a