Data-driven multiscale modeling reveals the role of metabolic coupling for the spatio-temporal growth dynamics of yeast colonies

Jukka Intosalmi*, Adrian C. Scott, Michelle Hays, Nicholas Flann, Olli Yli-Harja, Harri Lähdesmäki, Aimée M. Dudley, Alexander Skupin

*Corresponding author for this work

Research output: Contribution to journalArticleScientificpeer-review

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Abstract

Background: Multicellular entities like mammalian tissues or microbial biofilms typically exhibit complex spatial arrangements that are adapted to their specific functions or environments. These structures result from intercellular signaling as well as from the interaction with the environment that allow cells of the same genotype to differentiate into well-organized communities of diversified cells. Despite its importance, our understanding how this cell-cell and metabolic coupling lead to functionally optimized structures is still limited. Results: Here, we present a data-driven spatial framework to computationally investigate the development of yeast colonies as such a multicellular structure in dependence on metabolic capacity. For this purpose, we first developed and parameterized a dynamic cell state and growth model for yeast based on on experimental data from homogeneous liquid media conditions. The inferred model is subsequently used in a spatially coarse-grained model for colony development to investigate the effect of metabolic coupling by calibrating spatial parameters from experimental time-course data of colony growth using state-of-the-art statistical techniques for model uncertainty and parameter estimations. The model is finally validated by independent experimental data of an alternative yeast strain with distinct metabolic characteristics and illustrates the impact of metabolic coupling for structure formation. Conclusions: We introduce a novel model for yeast colony formation, present a statistical methodology for model calibration in a data-driven manner, and demonstrate how the established model can be used to generate predictions across scales by validation against independent measurements of genetically distinct yeast strains.

Original languageEnglish
Article number59
JournalBMC Molecular and Cell Biology
Volume20
Issue number1
DOIs
Publication statusPublished - 19 Dec 2019
MoE publication typeA1 Journal article-refereed

Keywords

  • Bayesian optimization
  • Diauxic shift
  • Markov chain Monte Carlo
  • Metabolic coupling
  • Multicellular systems
  • Multiscale modeling
  • Yeast colony

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