Team:Evry/Model/phenol model

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IGEM Evry 2014

Phenol Model

Phenol sensor model


Introduction

In this section we model the phenol sensor in Kappa. Kappa is a rule based language allowing the expression of protein-protein interactions in order to build executable models of protein networks. according to literature, the phenol sensor is composed of phosphoriled Dmpr dimers forming hexamers and binding on the P0 site as described in the schemas bellow from


More precisely we are interested in finding: what is the quantity of compound that is in contact with our bacterium ?

With this quantity and the number of bacteria in the sponge, we can the connect with the models developed for PCB and phenol (TODO) sensing and then relate the sensing capacity to the concentration of compound in the surrounding water.

To answer this question, we built two different model :

  1. A simple model where we consider only water flows without trying to take into acount the very specific geometry of the sponge.
  2. A 2D diffusion model where we take into acount the geometry of the sponge.

Throughout this section we base our study on the Spongia Officinalis species, because i) there are evidences that pseudovibrio bacteria live inside (TODO: cite) and ii) its is a quite common type of sponge.

Model 1: Simple Fluxes

For this model, we make simple computations based on the intake and expeled quantities of water. Our main assumptions are the following :

  1. Bacteria are uniformely distributed in the sponge
  2. Compounds diffuse instantly inside the sponge (the quantity of compound in the same everywhere inside)
These two assumptions imply that each bacterium is in contact with the same quantity of compound.

Model Formulation

We call φin (in ml/h/cm3) the quantity of compounds (<= 0.2 μm) filtered by a sponge of volume V (cm3). The compound is present at concentration C (mol.ml-1). Then the quantity of compound in contact with the bacteria, Q (mol.h-1), is:

Q = φinVC

Parameters

Name Value Unit Ref
φin [0.1-0.3] cm3(water).cm-3(sponge).s-1 WATER TRANSPORT, RESPIRATION AND ENERGETICS OF THREE TROPICAL MARINE SPONGES
V [66.8-116] cm3 Filtering activity of Spongia officinalis var. adriatica (Schmidt) (Porifera, Demospongiae) on bacterioplankton: Implications for bioremediation of polluted seawater

Results

We present in Figure1 the results obtained for different parameter sets (min, mean and max values). The value of Q increases linearly with the concentration and is in the range of the μmol.

IMAGE
Figure 1: Quantity of compound in contact with the bacteria inside the sponge (Q) as a function of the external compound concentration. Three different parameter sets used: red minimal parameter values; gree: mean parameter values; blue: max parameter values.

The equations for the three lines in Figure1 are the following:

  • Red: y = 0.00668x
  • Green: y = 0.01828x
  • Blue: y = 0.0348x

Model 2: 2D diffusion

For this second model we want to take into account the geometry of the sponge. For the equations and geometry to be tractable we will consider a 2D slice of a sponge. Our assumptions are the following :

  1. Bacteria are uniformely distributed in the sponge (as for model 1)
  2. Sponge geometry is approximated as a sphere
  3. The interior of the sponge is a uniform medium in which the compound diffuse isotropically with a coefficient D

We emphasize that assumption 2 may not be a pure mathematician's idealization, some spongia officinalis sponges have approximately spherical shapes as presented in Figure2a (Although others do not, a wide variety of shapes depending on the environment are exhibited). Some articles also represent some species of sponges as ellipsoidal, see Figure2 b (TODO cite).

IMAGE
Figure 2: Sponge morphology and functionning. a) Illustration of different sponge morphology of S. officinalis. b) Sponge morphology approximated as an ellipsoid and functionning of the sponge. Sources: a)Corriero et al., aquaculture (2004); b) Webster, Environmental Microbiology (2007)

Geometry
For the simplicity of the simulations, we represent only a slice of a spherical sponge, the slice going through its center. We thus have the following geometry presented in Figure3.
IMAGE
Figure 2: Sponge morphology and functionning. a) Illustration of different sponge morphology of S. officinalis. b) Sponge morphology approximated as an ellipsoid and functionning of the sponge. Sources: a)Corriero et al., aquaculture (2004); b) Webster, Environmental Microbiology (2007)
Model Formulation
Parameters
Results