Lattice-based Monte Carlo simulation of the effects of nutrient concentration and magnetic field exposure on yeast colony growth and morphology

Abstract

Yeasts exist in communities that expand over space and time to form complex structures and patterns. We developed a lattice-based framework to perform spatial-temporal Monte Carlo simulations of budding yeast colonies exposed to different nutrient and magnetic field conditions. The budding patterns of haploid and diploid yeast cells were incorporated into the framework, as well as the filamentous growth that occurs in yeast colonies under nutrient limiting conditions. Simulation of the framework predicted that magnetic fields decrease colony growth rate, solidity, and roundness. Magnetic field simulations further predicted that colony elongation and boundary fluctuations increase in a nutrient- and ploidy-dependent manner. These in-silico predictions are an important step towards understanding the effects of the physico-chemical environment on microbial colonies and for informing bioelectromagnetic experiments on yeast colony biofilms and fungal pathogens.

Fitness effects of a demography-dispersal trade-off in expanding Saccharomyces cerevisiae mats

“…[26]); machine learning may be able to quantify growth rates from images of TBR1, tbr1, and TBR5 strains on semi-solid media [44]. Our model could be augmented to incorporate nutrient diffusion and depletion [45], which results in spatial heterogeneity of the resource supply and slows mat expansion due to an increasingly nutrient-depleted environment (figure C9). In contrast, the steppingstone model assumes that the carrying capacity is constant in all demes and that cells have unlimited resources as they expand exponentially (figure C10).…”

A Novel Magnetic Field Device: Effects of Magnetic Fields on Planktonic Yeasts and Fungal Mats

“…By using two large Neodymium magnets, we are able to provide a sufficient volume to generate a homogeneous MF throughout exposure region, which will facilitate MF exposure experiments on yeast mats/biofilms on agar plates and yeast cells in liquid culture. Additionally, while many previous MF exposure experiments were conducted for no longer than 2 days [12, 13, 14, 11], our MF exposure device is able to maintain an uninterrupted MF for longer-term experiments, the importance of which has been previously emphasized [19]. Finally, our device can be placed inside of a standard microbiological incubator or environmental chamber to control for confounding variables, such as temperature, that affect growth and gene expression in yeast [42].…”

“…The decreased expansion rate of MF-exposed TBR1 yeast mats may be attributed to spatial hindrance due the expression of the flo11 surface adhesion gene in this strain [30] combined with the magnetic properties of microtubules [11, 43, 44]. As the mitotic spindle is composed of [45] and oriented [46] by microtubules, the presence of a horizontal MF may cause the budding yeast cells to align their long axis along the direction of the MF [19, 11]. Partial or complete alignment of cells to the MF at the expanding boundary of a yeast mat may introduce competition among cells attempting to bud into unoccupied space on the agar surface.…”

“…Another study found that exposing non-pathogenic S. cerevisiae cells to stronger EMFs (50 Hz with inductions up to 10 mT , with exposure times up to 24 minutes) decreased the viability of yeasts cells and slowed their growth [18]. More recently, a lattice-based Monte Carlo simulation framework was developed to investigate the effects of nutrient concentration and MF exposure on yeast colony growth and morphology [19]. Simulation of this framework predicted that prolonged MF exposure will decrease colony growth and alter colony morphology in a nutrient- and ploidy-dependent manner.…”

An off-lattice discrete model to characterise filamentous yeast colony morphology

“…We use agent-based mathematical modelling to simulate filamentous colony growth. Agent-based models (ABMs) [9,10,[14][15][16][17][18][19][20][21] track movement, proliferation, and death of individual cells in the colony.…”