Modelling of Nutrient Gradients in a Bacterial Colony

Fraleigh, Steven P.; Bungay, Henry R.

doi:10.1099/00221287-132-7-2057

Cited by 8 publications

(6 citation statements)

References 8 publications

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“…Fraleigh & Bungay (1986) have simulated O2 and substrate gradients as a first step in obtaining a detailed colony growth model. Despite major simplifications in the definition of the colony system the model yielded results which were similar to those from microelectrode studies.…”

Section: Results a N D Discussionmentioning

confidence: 99%

Oxygen Profiles in, and in the Agar Beneath, Colonies of Bacillus Cereus, Staphylococcus Albus and Escherichia Coli

Peters

Wimpenny²,

Coombs³

1987

Microbiology

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The paper reports the use of microelectrodes to measure O2 penetration in different aged colonies of Bacillus cereus, Escherichia coli and Staphylococcus albus. In young (18 h) colonies of B. cereus and E. coli O2 disappeared at depths of 25-30 micron and 35-40 micron respectively. In young S. albus colonies, O2 reached a minimum but was never completely absent. As colonies aged (24-168 h) the depth to which O2 penetrated increased.

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Section: Results a N D Discussionmentioning

confidence: 99%

Oxygen Profiles in, and in the Agar Beneath, Colonies of Bacillus Cereus, Staphylococcus Albus and Escherichia Coli

Peters

Wimpenny²,

Coombs³

1987

Microbiology

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“…Oxygen profiles in colonies and in the solid medium have been measured using microelectrodes (Wimpenny & Coombs, 1983;Bungay et al, 1983;Peters et al, 1987). Fraleigh & Bungay (1986) modelled oxygen and substrate gradients in the colony. Wimpenny (1979) found that near the periphery or leading edge of a growing colony, the height rises relatively steeply to a ridge.…”

Section: Introductionmentioning

confidence: 99%

Growth of Yeast Colonies on Solid Media

Kamath

Bungay²

1988

Microbiology

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Colonies on nutrient agar of the aerobic yeast Candida utilis show linear increases in diameter and height with time throughout most of the growth cycle. The concentration of glucose in the agar has a negligible effect on radial growth rate although an increase in the glucose concentration prolongs the linear radial growth phase. The rate of increase in height of the colony is proportional to the square root of the initial glucose concentration. A new model that considers both glucose diffusion and oxygen diffusion in the colony is consistent with the observed colony profiles.

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“…In spatially constrained cell populations the shape of the growth profile

depends both upon the biochemical environment and mechanical constraints (Andersen and von Meyenburg, 1980 ; Matsushita and Fujikawa, 1990 ; Tuson et al, 2012 ; Farrell et al, 2013 ; Rudge et al, 2013 ; Smith et al, 2017 ; Winkle et al, 2018 ). At the typical bacterial microcolony scale the biochemical environment is essentially uniform in space due to the fast diffusion of small molecules like sugars and aminoacids (Matson and Characklis, 1976 ; Fraleigh and Bungay, 1986 ; Guélon et al, 2012 ). Using microfluidic devices cells can be maintained in constant fresh media allowing observation of the long term dynamics of genetic circuits (Danino et al, 2010 ; Long et al, 2013 ; Potvin-Trottier et al, 2016 ).…”

Section: Resultsmentioning

confidence: 99%

Novel Tunable Spatio-Temporal Patterns From a Simple Genetic Oscillator Circuit

Feliú

Vidal

Silva

et al. 2020

Front. Bioeng. Biotechnol.

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Multicellularity, the coordinated collective behavior of cell populations, gives rise to the emergence of self-organized phenomena at many different spatio-temporal scales. At the genetic scale, oscillators are ubiquitous in regulation of multicellular systems, including during their development and regeneration. Synthetic biologists have successfully created simple synthetic genetic circuits that produce oscillations in single cells. Studying and engineering synthetic oscillators in a multicellular chassis can therefore give us valuable insights into how simple genetic circuits can encode complex multicellular behaviors at different scales. Here we develop a study of the coupling between the repressilator synthetic genetic ring oscillator and constraints on cell growth in colonies. We show in silico how mechanical constraints generate characteristic patterns of growth rate inhomogeneity in growing cell colonies. Next, we develop a simple one-dimensional model which predicts that coupling the repressilator to this pattern of growth rate via protein dilution generates traveling waves of gene expression. We show that the dynamics of these spatio-temporal patterns are determined by two parameters; the protein degradation and maximum expression rates of the repressors. We derive simple relations between these parameters and the key characteristics of the traveling wave patterns: firstly, wave speed is determined by protein degradation and secondly, wavelength is determined by maximum gene expression rate. Our analytical predictions and numerical results were in close quantitative agreement with detailed individual based simulations of growing cell colonies. Confirming published experimental results we also found that static ring patterns occur when protein stability is high. Our results show that this pattern can be induced simply by growth rate dilution and does not require transition to stationary phase as previously suggested. Our method generalizes easily to other genetic circuit architectures thus providing a framework for multi-scale rational design of spatio-temporal patterns from genetic circuits. We use this method to generate testable predictions for the synthetic biology design-build-test-learn cycle.

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Modelling of Nutrient Gradients in a Bacterial Colony

Cited by 8 publications

References 8 publications

Oxygen Profiles in, and in the Agar Beneath, Colonies of Bacillus Cereus, Staphylococcus Albus and Escherichia Coli

Oxygen Profiles in, and in the Agar Beneath, Colonies of Bacillus Cereus, Staphylococcus Albus and Escherichia Coli

Growth of Yeast Colonies on Solid Media

Novel Tunable Spatio-Temporal Patterns From a Simple Genetic Oscillator Circuit

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