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Team:British Columbia/modeling description
From 2010.igem.org
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<b>Introduction</b> | <b>Introduction</b> | ||
| - | <p>We developed a mathematical model that describes the dynamics of the biofilm structure (in terms of bacterial population size) and the interactions | + | <p>We developed a mathematical model that describes the dynamics of the biofilm structure (in terms of bacterial population size) and the interactions among the major components, including the engineered phage and DispersinB (DspB) protein. We used numerical simulations to predict the impact of phage and DspB release on the biofilm structure. We also investigated the weight of each parameter to the design of our system with sensitivity analysis. Possible scenarios of biofilm degradation suggested by our model are investigated.</p> |
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<b>Model Description</b> | <b>Model Description</b> | ||
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<i>Basic Biofilm Geometry</i> | <i>Basic Biofilm Geometry</i> | ||
<p>The biofilm system assumes a simple planar geometry characterized by depth, D, and cross-sectional area, A (Figure 1). The density and distribution of the biofilm bacterial population, extracellular polymeric substance (EPS), and dissolved components (e.g. AIP and metabolites) are uniform throughout the biofilm structure. Assuming that each biofilm bacterium occupies a spherical volume of diameter, d, and the surrounding EPS extends this volume by a constant, Α, each bacterium takes up a cubic volume of (Α + d)^3.</p> | <p>The biofilm system assumes a simple planar geometry characterized by depth, D, and cross-sectional area, A (Figure 1). The density and distribution of the biofilm bacterial population, extracellular polymeric substance (EPS), and dissolved components (e.g. AIP and metabolites) are uniform throughout the biofilm structure. Assuming that each biofilm bacterium occupies a spherical volume of diameter, d, and the surrounding EPS extends this volume by a constant, Α, each bacterium takes up a cubic volume of (Α + d)^3.</p> | ||
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| + | <i>Biofilm Bacteria</i> | ||
| + | The total bacterial population, B, is divided into two subpopulations: 1) the carrier bacteria, B<sub>i</sub>, which are infected with the engineered phage and 2) the non-carrier bacteria, B<sub>u</sub>, which are uninfected but susceptible to phage infection upon exposure. We separate the carrier bacteria subpopulation further into two subpopulations: 1) the bacteria infected with the phage in latent phase, B<sub>l</sub> , and 2) those infected with the phage in lytic phase, . The total population, B<sub>L</sub> , undergo logistic growth at rate limited by the carrying capacity, K; the uninfected, , and infected, , subpopulations grow at rates and , respectively. The following differential equations describe the dynamics of the two infected subpopulations, where is the portion of latent bacteria, the rate of transition from latent to lytic phase, and the rate of lysis:</p> | ||
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Revision as of 00:20, 9 October 2010
Introduction
Model Description
Basic Biofilm Geometry
Biofilm Bacteria The total bacterial population, B, is divided into two subpopulations: 1) the carrier bacteria, Bi, which are infected with the engineered phage and 2) the non-carrier bacteria, Bu, which are uninfected but susceptible to phage infection upon exposure. We separate the carrier bacteria subpopulation further into two subpopulations: 1) the bacteria infected with the phage in latent phase, Bl , and 2) those infected with the phage in lytic phase, . The total population, BL , undergo logistic growth at rate limited by the carrying capacity, K; the uninfected, , and infected, , subpopulations grow at rates and , respectively. The following differential equations describe the dynamics of the two infected subpopulations, where is the portion of latent bacteria, the rate of transition from latent to lytic phase, and the rate of lysis:
We developed a mathematical model that describes the dynamics of the biofilm structure (in terms of bacterial population size) and the interactions among the major components, including the engineered phage and DispersinB (DspB) protein. We used numerical simulations to predict the impact of phage and DspB release on the biofilm structure. We also investigated the weight of each parameter to the design of our system with sensitivity analysis. Possible scenarios of biofilm degradation suggested by our model are investigated.
Model Description
Basic Biofilm Geometry
The biofilm system assumes a simple planar geometry characterized by depth, D, and cross-sectional area, A (Figure 1). The density and distribution of the biofilm bacterial population, extracellular polymeric substance (EPS), and dissolved components (e.g. AIP and metabolites) are uniform throughout the biofilm structure. Assuming that each biofilm bacterium occupies a spherical volume of diameter, d, and the surrounding EPS extends this volume by a constant, Α, each bacterium takes up a cubic volume of (Α + d)^3.
Biofilm Bacteria The total bacterial population, B, is divided into two subpopulations: 1) the carrier bacteria, Bi, which are infected with the engineered phage and 2) the non-carrier bacteria, Bu, which are uninfected but susceptible to phage infection upon exposure. We separate the carrier bacteria subpopulation further into two subpopulations: 1) the bacteria infected with the phage in latent phase, Bl , and 2) those infected with the phage in lytic phase, . The total population, BL , undergo logistic growth at rate limited by the carrying capacity, K; the uninfected, , and infected, , subpopulations grow at rates and , respectively. The following differential equations describe the dynamics of the two infected subpopulations, where is the portion of latent bacteria, the rate of transition from latent to lytic phase, and the rate of lysis:
