Fig 1.
Examples of different modes of yeast (S. cerevisiae) colony growth.
(a) A small filamentous colony grown in a low assimilable nitrogen (nutrient) environment. (b) A large filamentous colony in a high nitrogen environment. (c) A different strain of yeast under low nutrient conditions.
Fig 2.
Cell and colony-scale behaviour in filamentous yeast colonies [13].
(a) Schematic of a sated mother cell with two bud scars and a developing daughter cell under normal conditions. (b) Schematic of an elongated pseudohyphal cell. (c) A filamentous branch at the edge of a yeast colony, consisting of both sated and pseudohyphal cells.
Fig 3.
Spatiotemporal evolution of a filamentous yeast colony of AWRI 796 50 μm.
(a)–(f) Time series of images from a yeast growth experiment, showing the transition from Eden-like circular growth to filamentous growth. (g) Petri dish with many concurrent filamentous colony growth experiments, indicating the small scale of filamentous colonies.
Fig 4.
The yeast cell model and budding patterns.
(a) Yeast cells are represented as ellipses with centre m, major radius a, minor radius b and the angle between the x-axis and the major axis θ. The distal pole is m + v and the proximal pole m − v. New cells are produced at bud sites (red dots) along the border of the cell, which are located between angles of ±β at both ends of the cell. (b) The sated (green) cell gives birth to a daughter cell (blue), which in turn yields more pseudohyphal cells (purple). Environmental stressors trigger a transition from colonies containing only sated cells to pseudohyphal growth.
Table 1.
The cell half width a, cell half length b and budding angle β for sated and pseudohyphal cells [13].
Fig 5.
Flow chart outlining the process for deciding which type of new cell to propose when a cell proliferates.
When selecting a cell type, the probability of each event is indicated using the symbols that appear above the arrows.
Table 2.
Parameters that we vary in the off-lattice model.
All parameters in this table take values in the interval [0, 1].
Fig 6.
(a) Processed image of the experimental yeast colony in Fig 3f. (b) A binary image of the colony with the occupied central region removed from the image. The red marker is the colony centroid, such that the blue and orange curves indicate rcsr and rmax used to compute the radius ratio. (c) Skeletonised image of (b) obtained using Matlab’s bwmorph() command. This image is used to compute the sub-branch count summary statistic.
Fig 7.
Box plots of metrics to distinguish between experiments with varying nutrient (ammonium sulfate) concentrations and strains.
The red marker represents the sample mean. (a) Sub-branch count, IB, (b) Filament area ratio, IF, and (c) Radius ratio, IR. SW: Simi White.
Fig 8.
Posterior densities for average colony summary statistics and mean colony areas of AWRI 796 50 μm, AWRI 796 500 μm, and Simi White (SW) 50 μm.
The marker below the distribution shows the mean. The priors are as follows (a) n* ∼ Beta(5, 2), (b) pps ∼ Beta(2, 2), (c) psp ∼ Beta(2, 2), (d) γ ∼ Beta(2, 5), and (e) pa ∼ Beta(2, 5).
Table 3.
Mean and standard deviation of the normalised summary statistics for experimental images, where the normalisation is based on Eq (7).
Fig 9.
Posterior bivariate densities of γ vs n* for (a) AWRI 50 μm, (b) AWRI 500 μm and (c) Simi White 50 μm.
Fig 10.
Comparison between experiments and simulations with parameters inferred using the mean summary statistics from all replicates of given experimental conditions.
(a) Example experiment, AWRI strain with 50 μm initial nutrient (ammonium sulfate). (b) Simulation with θ = (n*, pa, psp, pps, γ) = (0.67, 0.14, 0.25, 0.58, 0.12). (c) Example experiment, Simi White strain with 50 μm initial nutrient. (d) Simulation with θ = (n*, pa, psp, pps, γ) = (0.62, 0.15, 0.23, 0.71, 0.16) (e) Example experiment, AWRI strain with 500 μm initial nutrient. (f) Simulation with θ = (n*, pa, psp, pps, γ) = (0.81, 0.16, 0.19, 0.49, 0.25).