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Team:British Columbia/modeling description
From 2010.igem.org
Introduction
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 explored.
Model Description
Basic Biofilm GeometryThe 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. The total biofilm population in a biofilm can be estimated:
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, BL. The total population, BT, undergo logistic growth at rate ΡT limited by the carrying capacity, K; the uninfected, Bu, and infected, Bi, subpopulations grow at rates Ρu and Ρi, respectively. The following differential equations describe the dynamics of the two infected subpopulations, where p is the portion of latent bacteria, Π the rate of transition from latent to lytic phase, and Λ the rate of lysis:
EquationsThe carrying capacity is related to the maximum biofilm thickness, since both are determined by the genetic predisposition of the constituent bacteria and environmental factors. The carrying capacity can be coarsely estimated using Equation 1 by letting D equal to the maximum thickness.
Phage ParticlesInitially, only the engineered S. aureus bacteria will be introduced to the biofilm. In response to the presence of AIP, they will generate and release the first batch of phage particles. A proportion of these phage particles, Κ, will successfully infect and integrate its genetic information into the host genome. Once infected, a bacterium is subject to lysis probability of Λ; upon lysis, the bacterium will release R number of phage particles. The dynamics of the phage particles is governed by half-life, t1/2.
Phage Diffusion and Invasion
Lysis of the infected host cells forms a pool of newly produced phage particles. This phage population diffuses out 1) towards the bulk liquid at rate rout or 2) into the biofilm structure through EPS at rate rin. We assume that the new phage pool is concentrated in a defined layer immediately after lysis. This layer serves as the initial point of diffusion. The diffusion of phage particles into the biofilm can be modeled by Fick’s second law of diffusion, where Φ is the phage concentration and x the distance from the concentrated layer:
Equations
Let us redefine the concentration, Φ, to be relative to the initial phage concentration, Φ0, at time t = 0 such that EQUATION:
Equations
Solving for ϕr, we derive:
The distance of phage diffusion within one time step (i.e. from t = 0 to t = 1) can be estimated by letting Φr = 0 and solving for x, which is dependent on the constant, Θ, and diffusion coefficient, rin (Equation 10.1) Note that the integral cannot be solved analytically in closed form. Numerical methods such as the adaptive Simpson quadrature are required to estimate it.
Equations
Since we are treating this as a one-dimensional problem, the distance of phage diffusion can be roughly estimated by the diffusion length for a certain time period Δt:
Equations
This distance reflects the depth of the phage-infested layer and is related to the proportion of the total biofilm susceptible to infection. We simplify this relationship by using information about the geometry of the biofilm bacteria and biofilm structure. The following represents the relationship between the depth of the remaining biofilm (i.e. not disintegrated by phage) and the total biofilm population.
Figure 1: Schematic diagram of the biofilm structure. A cylindrical (or rectangular) container of depth, D, and cross-sectional area, A, holds the biofilm mass. Each bacterium occupies a spherical volume of diameter, d, corrected by a constant representing the space filled by surrounding EPS, Α.
Figure 2: Flow diagram indicating the interactions among the components of the biofilm system. The total biofilm population BT is divided into subpopulations (inside the rounded box). The phage particle population P directly interacts with only the subpopulation infected with latent phage.
