# Team:Lyon-INSA/modelling

(Difference between revisions)
 Revision as of 19:22, 25 October 2012 (view source)Xavier69 (Talk | contribs)← Older edit Latest revision as of 23:23, 26 October 2012 (view source) Line 39: Line 39:

- An interesting question when you are more biologist than mathematician (too many complicated equations!!!). And most of our team members are biologists/biochemists… Thus, we tried to explain modelling and our model in a comprehensive way for everyone.

+ An interesting question when you are more of a biologist than a mathematician (too many complicated equations!!!). And most of our team members are biologists/biochemists… Thus, we tried to explain modelling and our model in a comprehensive way for everyone.

This is our Biological Modelling for Dummies ! This is our Biological Modelling for Dummies ! Line 59: Line 59:

Definitions

Definitions

- A model is a symbolic representation of an object’s or phenomenon’s aspects in the real world.
+ A model is a symbolic representation of an object’s or a phenomenon’s aspects in the real world.

All models are false. Some are useful.” Georges Box

All models are false. Some are useful.” Georges Box

- Modelling is the process that allows the development of a model. It’s taking into account [1]:
+ Modelling is the process that enables the development of a model. It takes into account [1]:
• The phenomenon to represent
• The phenomenon to represent
• Line 79: Line 79:
• Have a formalization work, which is the model writing
• Have a formalization work, which is the model writing
• -
• Manipulate the model in the formal system to describe its properties (theoretical main behaviour independently on the values of the parameters)
• +
• Manipulate the model in the formal system to describe its properties (theoretical main behavior regardless of the values of the parameters)
• Establish relationships with other representations (computer program, graph function)
• Establish relationships with other representations (computer program, graph function)
• Line 102: Line 102:

Situation

Situation

- After the destruction of the biofilm by “Biofilm Killer” bacteria, we want to have the choice to either create a surfactant or establish a positive biofilm, both to prevent the recolonization of the surface by deleterious organisms. The toggle switch is done by environmental conditions : two inducers can be added to select one behaviour or another.
+ After the destruction of the biofilm by “Biofilm Killer” bacteria, we want to have the choice to either create a surfactant or establish a positive biofilm, both to prevent the recolonization of the surface by deleterious organisms. The toggle switch is done by environmental conditions : two inducers can be added to select one behavior or another.
Biological system to model
Biological system to model
Line 108: Line 108:

-
Figure 1: The construction of the biological model, with the following elements: 2 promoters (Pxyl and Plac), 2 repressors (LacI and XylR proteins)
and 2 inducers (IPTG and Xylose), and also sfp and abrB genes for Sfp and AbrB proteins.

+
Figure 1: The construction of the biological model, with the following elements: 2 promoters (Pxyl and Plac), 2 repressors (LacI and XylR proteins)
and 2 inducers (IPTG and Xylose), and also sfp and abrB genes for Sfp and AbrB proteins.

Line 120: Line 120:

-
Figure 2: The two possible states, surfactant formation for the top operon or biofilm formation for the bottom construction

+
Figure 2: The two possible states, surfactant formation for the top operon or biofilm formation for the bottom construction.

- LacI and XylR proteins are called repressors. They bind to their respective promoters (Plac and Pxyl), thus preventing RNA polymerase binding. So proteins under the inactivated promoter are not produced.
There are also two inducers in the system, IPTG (isopropyl β-D-1-thiogalactopyranoside) and Xylose (monosaccharide of the aldopentose type). In the absence of these inducers, both constructions are inhibited. If only one of them is present, the corresponding inhibition disappears and the associated construction is expressed.
+ LacI and XylR proteins are called repressors. They bind to their respective promoters (Plac and Pxyl), thus preventing RNA polymerase binding. So proteins under the inactivated promoter are not produced.
There are also two inducers in the system: IPTG (isopropyl β-D-1-thiogalactopyranoside) and Xylose (monosaccharide of the aldopentose type). In the absence of these inducers, both constructions are inhibited. If only one of them is present, the corresponding inhibition disappears and the associated construction is expressed.

Line 135: Line 135:

- For example, in the presence of Xylose, XylR proteins will form an enzymatic complex with their Xylose sugar. Thus, the inhibition of Pxyl caused by XylR binding will disappear, resulting in an enhanced production of Sfp, AbrB and LacI  proteins. Sfp production induces surfactin production, and AbrB production involves the repression of the formation of the biofilm. Eventually, LacI production will inhibit XylR production, so there will be stabilisation of Pxyl activation.
+ For example, in the presence of Xylose, XylR proteins will form an enzymatic complex with their Xylose sugar. Thus, the inhibition of Pxyl caused by XylR binding will disappear, resulting in an enhanced production of Sfp, AbrB and LacI  proteins. Sfp production induces surfactin production, and AbrB production involves the repression of the formation of the biofilm. Eventually, LacI production will inhibit XylR production, so there will be stabilisation of Pxyl activation.
- In opposition, in the presence of IPTG, LacI proteins will bind to their ligand, and Plac promoter will be free. So XylR proteins will be overproduced, limiting Sfp and AbrB productions. Thus, there will be no surfactin in the environment, biofilm formation can begin.
+ In opposition, in the presence of IPTG, LacI proteins will bind to their ligand, and Plac promoter will be free. So XylR proteins will be overproduced, limiting Sfp and AbrB productions. Thus, there will be no surfactin in the environment, biofilm formation can begin.

Line 144: Line 144: With this model, we pursue two main objectives :
With this model, we pursue two main objectives :
-
• 1) verify the design of the biological system, to be sure that the toggle switch is functional, +
• 1) Verify the design of the biological system, to be sure that the toggle switch is functional;
• -
• 2) predict the behaviour of this biological system depending on the presence of inducers to give usage guidelines for its industrialization

+
• 2) Predict the behaviour of this biological system depending on the presence of inducers to give usage guidelines for its industrialization.
• +

However...

However...

- We are working in a Bacillus subtilis strain and some parameters such as XylR values on binding/unbinding kinetics to both inducer and promoter or production rate from Pxyl promoter cannot be found in the literature and most of the existing values come from an E. coli strain rather than B. subtilis. + We are working in a Bacillus subtilis strain and some parameters such as XylR values on binding/unbinding kinetics to both inducer and promoter or production rate from Pxyl promoter cannot be found in the literature and most of the existing values come from an E. coli strain rather than B. subtilis. - Furthermore, we are finishing the biological system construction and its characterization is underway. Parameters will be measured very soon.
+ Furthermore, we are finishing the biological system construction and its characterization is on the way. Parameters will be measured very soon.

Because of this lack of information, we will create a theoretical model in order to characterize the global behavior of the system.
Because of this lack of information, we will create a theoretical model in order to characterize the global behavior of the system.

- Moreover, as we are mainly biologists in the team, we thought interesting to explain how we can easily obtain a mathematical model from a biological system.
+ Moreover, as we are mainly biologists in the team, we thought it could be interesting to explain how we can easily obtain a mathematical model from a biological system.
Line 178: Line 179:
Ordinary differential equation (ODE)
Ordinary differential equation (ODE)
-
• mathematical equation +
• mathematical equation;
• -
• format:  +
• format:
• -
• explanation: used in biology and physics to represent the growth or evolution of a quantity dx (i.e. population or concentration) proportional to the population size/effective concentration x during a period of time t +
• explanation: used in biology and physics to represent the growth or evolution of a quantity dx (i.e. population or concentration) proportional to the population size/effective concentration x during a period of time t;
• -
• x is called a variable +
• x is called a variable.

Line 187: Line 188:

First list of variables
First list of variables
- We want to have the concentration of LacI and XylR as output depending of the inducers concentrations input. We know that the repressors can bind either to their promoter (Plac and Pxyl respectively) or to their inducer (IPTG and xylose). Thus, first of all, we have the following variables in the system:

+ We want to have the concentration of LacI and XylR as outputs depending of the inducers concentrations input. We know that the repressors can bind either to their promoter (Plac and Pxyl respectively) or to their inducer (IPTG and xylose). Thus, first of all, we have the following variables in the system:

Line 193: Line 194:

Binding and unbinding kinetics
Binding and unbinding kinetics
- We decided to analyze the relation between repressors, promoters and inducers depending on the law of mass action. It is a branch of chemical kinetics, which states that the speed of a chemical reaction is proportional to the quantity of the reacting substances. These substances will bind with an association kinetic k and unbind with a dissociation kinetic km.

+ We decided to analyze the relation between repressors, promoters and inducers depending on the law of mass action. It is a branch of chemical kinetics, which states that the speed of a chemical reaction is proportional to the quantity of the reacting substances. These substances will bind with an association kinetic k and unbind with a dissociation kinetic km.

Line 209: Line 210:

-
It is working either for LacI binding to its Plac promoter than for XylR to Pxyl and also the inducers and LacI and XylR. This binding creates a new complex.

+
It is working either for LacI binding to its Plac promoter than for XylR to Pxyl and also the inducers and LacI and XylR. This binding creates a new complex.

Line 220: Line 221:
Promoters
Promoters
- As described above, there are two promoters, Plac and Pxyl, and each of them can be free (with no repressor binds on it) or occupied (with the corresponding repressor associated). + As described above, there are two promoters, Plac and Pxyl, and each of them can be free (with no repressor bound on it) or occupied (with the corresponding associated repressor).
Thanks to the law of mass action and binding and unbinding kinetics, we obtain the equations like this:

Thanks to the law of mass action and binding and unbinding kinetics, we obtain the equations like this:

Line 229: Line 230:
- So the equations for the promoters are this:

+ So the equations for the promoters are these:

Line 259: Line 260:
-
Figure 9: The repressors equations

+
Figure 9: Repressors' equations

Line 265: Line 266:

For this model, we need at least 12 parameters that characterize the variables and their relationship between each other. For this model, we need at least 12 parameters that characterize the variables and their relationship between each other. - The available values have been measure mainly in E. coli strain. + The available values have been measure mainly in an E. coli strain.

Line 370: Line 371: The following hypotheses have been made for this model. The following hypotheses have been made for this model.
-
• we just need LacI concentration for surfactant production and not Sfp and AbrB concentration because there is a proportional link between them. If there are LacI proteins produced, there will be also Sfp and AbrB proteins. +
• we just need LacI concentration for surfactant production and not Sfp and AbrB concentration because there is a proportional link between them. If there are LacI proteins produced, there will be also Sfp and AbrB proteins.
• -
• we assumed that there will be no degradation of IPTG due to its high stability[4] and no metabolism of Xylose in our condition[5]. +
• we assumed that there will be no degradation of IPTG due to its high stability[4] and no metabolism of Xylose in our condition[5].
• -
• we are aware of LacI[6] and XylR[7] dimerisation as fundamental functional unit but they are not taken into account in this model. +
• we are aware of LacI[6] and XylR[7] dimerisation as fundamental functional unit but they are not taken into account in this model.

Line 411: Line 412:
Experimentations
Experimentations
- So far, we can consider the values for the Plac promoter, LacI and IPTG that have been measured in E. coli to apply to our B. subtilis model. We have performed experiments with the Pxyl, xylose and XylR to evaluate whether this promoter can be modelled using similar values. When this step is performed, our model will allow us to determine two important concentration limits:
+ So far, we can consider the values for the Plac promoter, LacI and IPTG that have been measured in E. coli to apply to our B. subtilis model. We have performed experiments with the Pxyl, xylose and XylR to evaluate whether this promoter can be modelled using similar values. When this step is performed, our model will allow us to determine two important concentration limits:
-
• 1) the lowest IPTG concentration for the induction of the COAT option +
• 1) the lowest IPTG concentration for the induction of the COAT option;
• -
• 2) the lowest xylose concentration for the induction of the STICK option. +
• 2) the lowest xylose concentration for the induction of the STICK option.

# Modelling

An interesting question when you are more of a biologist than a mathematician (too many complicated equations!!!). And most of our team members are biologists/biochemists… Thus, we tried to explain modelling and our model in a comprehensive way for everyone.

This is our Biological Modelling for Dummies !

Click on the title to show/hide the text.

## What is modelling ?

### Definitions

A model is a symbolic representation of an object’s or a phenomenon’s aspects in the real world.

All models are false. Some are useful.” Georges Box

Modelling is the process that enables the development of a model. It takes into account [1]:
• The phenomenon to represent
• A specific formal system (equation, diagram..)
• Objectives (what we want to do with the model)
• Data (for variables) and knowledge (relation between variables) available or accessible by experimentation or observation

The tasks to obtain and use the model depend on the biological situation and the formal system chosen. Nevertheless, it must:
• Have a formalization work, which is the model writing
• Manipulate the model in the formal system to describe its properties (theoretical main behavior regardless of the values of the parameters)
• Establish relationships with other representations (computer program, graph function)
• Interpret and compare different representations obtained in the formal world with the biological reality (often that reality is seen through experimental data)

References:
• [1] Alain Pavé, Modélisation en biologie et en écologie, Aléas, 1994

## Biological System description

### Situation

After the destruction of the biofilm by “Biofilm Killer” bacteria, we want to have the choice to either create a surfactant or establish a positive biofilm, both to prevent the recolonization of the surface by deleterious organisms. The toggle switch is done by environmental conditions : two inducers can be added to select one behavior or another.
Biological system to model
For this, we have created the following construction, with a double regulation:

Figure 1: The construction of the biological model, with the following elements: 2 promoters (Pxyl and Plac), 2 repressors (LacI and XylR proteins)
and 2 inducers (IPTG and Xylose), and also sfp and abrB genes for Sfp and AbrB proteins.

This system is a gene-regulatory network, where two different states are possible:
• Formation of a naturally toxic bio-surfactant through sfp gene, which has antimicrobial properties that prevents the recolonization of the surface. The surfactant used is surfactin, whose production is activated by the sfp gene. This is the COAT option.
• Establishment of a positive biofilm by the inhibition of the main biofilm repressor gene abrB. This is the STICK option.

Figure 2: The two possible states, surfactant formation for the top operon or biofilm formation for the bottom construction.

LacI and XylR proteins are called repressors. They bind to their respective promoters (Plac and Pxyl), thus preventing RNA polymerase binding. So proteins under the inactivated promoter are not produced.
There are also two inducers in the system: IPTG (isopropyl β-D-1-thiogalactopyranoside) and Xylose (monosaccharide of the aldopentose type). In the absence of these inducers, both constructions are inhibited. If only one of them is present, the corresponding inhibition disappears and the associated construction is expressed.

For example, in the presence of Xylose, XylR proteins will form an enzymatic complex with their Xylose sugar. Thus, the inhibition of Pxyl caused by XylR binding will disappear, resulting in an enhanced production of Sfp, AbrB and LacI proteins. Sfp production induces surfactin production, and AbrB production involves the repression of the formation of the biofilm. Eventually, LacI production will inhibit XylR production, so there will be stabilisation of Pxyl activation.
In opposition, in the presence of IPTG, LacI proteins will bind to their ligand, and Plac promoter will be free. So XylR proteins will be overproduced, limiting Sfp and AbrB productions. Thus, there will be no surfactin in the environment, biofilm formation can begin.

Aim of the model:

With this model, we pursue two main objectives :
• 1) Verify the design of the biological system, to be sure that the toggle switch is functional;
• 2) Predict the behaviour of this biological system depending on the presence of inducers to give usage guidelines for its industrialization.

However...

We are working in a Bacillus subtilis strain and some parameters such as XylR values on binding/unbinding kinetics to both inducer and promoter or production rate from Pxyl promoter cannot be found in the literature and most of the existing values come from an E. coli strain rather than B. subtilis. Furthermore, we are finishing the biological system construction and its characterization is on the way. Parameters will be measured very soon.

Because of this lack of information, we will create a theoretical model in order to characterize the global behavior of the system.

Moreover, as we are mainly biologists in the team, we thought it could be interesting to explain how we can easily obtain a mathematical model from a biological system.

## Biological modelling for dummies !

### Basic knowledge

We want to transform the biological system into mathematical equations in order to be able to determine the quantity of inducers (input) needed to obtain a particular behavior (output).

Figure 3: The black box model:
there will be the STICK or COAT option depending on the inducers concentration

Ordinary differential equation (ODE)
• mathematical equation;
• format:
• explanation: used in biology and physics to represent the growth or evolution of a quantity dx (i.e. population or concentration) proportional to the population size/effective concentration x during a period of time t;
• x is called a variable.

### Elements of the model

First list of variables
We want to have the concentration of LacI and XylR as outputs depending of the inducers concentrations input. We know that the repressors can bind either to their promoter (Plac and Pxyl respectively) or to their inducer (IPTG and xylose). Thus, first of all, we have the following variables in the system:

Figure 4: The model variables at first glimpse

Binding and unbinding kinetics
We decided to analyze the relation between repressors, promoters and inducers depending on the law of mass action. It is a branch of chemical kinetics, which states that the speed of a chemical reaction is proportional to the quantity of the reacting substances. These substances will bind with an association kinetic k and unbind with a dissociation kinetic km.

Figure 5: Binding and unbinding kinetics in the model

It is working either for LacI binding to its Plac promoter than for XylR to Pxyl and also the inducers and LacI and XylR. This binding creates a new complex.

Figure 6: The model variables

### Equations of the model

Now, we can find the equations, based on the behavior of each element. There will be 3 types of equations, each of them related to the nature of the variable, i.e. a promoter, an inducer or a repressor.
Promoters
As described above, there are two promoters, Plac and Pxyl, and each of them can be free (with no repressor bound on it) or occupied (with the corresponding associated repressor).
Thanks to the law of mass action and binding and unbinding kinetics, we obtain the equations like this:

So the equations for the promoters are these:

Figure 7: Promoters' equations

Inducers
With the same method based on law of mass action and binding/unbinding kinetic, we obtain the inducers' equations.

Figure 8: Inducers' equations

Repressors
Now, for the repressors, the method is quite similar as before. However, we have to take into account that the proteins have a degradation rate (δ) depending on their nature and the environment. The quantity of protein produced at each time depends on the promoter under control (α).

LacI Equation

We obtain XylR's equation exactly as LacI's.

Figure 9: Repressors' equations

### Parameters of the model

For this model, we need at least 12 parameters that characterize the variables and their relationship between each other. The available values have been measure mainly in an E. coli strain.

Name Description Unit Value Reference
Prod_Plac Production rate from Plac promoter mol.s-1 1.66E23 1
Prod_Pxyl Production rate from Pxyl promoter mol.s-1 *** **
k1 binding kinetic of LacI and IPTG mol-1.s-1 1.2E5 2
km1 unbinding kinetic of LacI_IPTG s-1 2.1E-1 2
k2 binding kinetic of XylR and Xylose mol-1.s-1 *** **
km2 unbinding kinetic of XylR_Xylose s-1 *** **
k3 binding kinetic of LacI and Plac mol-1.s-1 5.1E6 2
km3 unbinding kinetic of PlacO s-1 3.7E-2 2
k4 binding kinetic of XylR and Plac mol-1.s-1 *** **
km4 unbinding kinetic of XylR and PlacO s-1 *** **
δ_LacI degradation rate of LacI s-1 3
δ_XylR degradation rate of XylR s-1 *** **

Model parameters. *** for no value and ** for no reference

### Hypotheses

The following hypotheses have been made for this model.
• we just need LacI concentration for surfactant production and not Sfp and AbrB concentration because there is a proportional link between them. If there are LacI proteins produced, there will be also Sfp and AbrB proteins.
• we assumed that there will be no degradation of IPTG due to its high stability[4] and no metabolism of Xylose in our condition[5].
• we are aware of LacI[6] and XylR[7] dimerisation as fundamental functional unit but they are not taken into account in this model.

References:
• [1] Nature. 2000 Jan 20;403(6767):335-8. A synthetic oscillatory network of transcriptional regulators. Elowitz MB, Leibler S.
• [2] Xu H.,Moraitis M., Reedstrom R. J., Matthews K. S. 1998. Kinetic and thermodynamic studies of purine repressor binding to corepressor and operator DNA. J. Biol. Chem. 273:8958–8964.
• [3] Tuttle et al. Model-Driven Designs of an Oscillating Gene Network., Biophys J 89(6):3873-3883, 2005
• [4] Herzenberg, L.A., Studies on the induction of beta-galactosidase in a cryptic strain of Escherichia coli. Biochim. Biophys. Acta, 31, 525 (1959)
• [5] http://bsubcyc.org/BSUB/NEW-IMAGE?type=PATHWAY&object=XYLCAT-PWY
• [6] Ramot, R. et al, Lactose Repressor Experimental Folding Landscape: Fundamental Functional Unit and Tetramer Folding Mechanisms. Biochemistry (2012)
• [7] Song S., Park C. Organization and regulation of the D-xylose operons in Escherichia coli K-12: XylR acts as a transcriptional activator. J Bacteriol. 1997 Nov;179(22):7025-32.

## Results

Expected results
Finally, we translated the biological system into mathematical equations. As we can see, there is a lot of paramaters for the binding and unbinding kinetics, degradation rates and productions from promoters. However, values for only a few of them are available. This is why we needed to simulate the behaviour of our system.
We want to have an overproduction of XylR in the presence of IPTG, for the STICK option. And an overproduction of LacI when there is xylose in the environment, for the COAT option.
According to the above theoretical model, we should generate the expected toggle switch (figure below), using the appropriate values for all parameters.

Figure 10: Expected results of the model

Experimentations
So far, we can consider the values for the Plac promoter, LacI and IPTG that have been measured in E. coli to apply to our B. subtilis model. We have performed experiments with the Pxyl, xylose and XylR to evaluate whether this promoter can be modelled using similar values. When this step is performed, our model will allow us to determine two important concentration limits:
• 1) the lowest IPTG concentration for the induction of the COAT option;
• 2) the lowest xylose concentration for the induction of the STICK option.

We also thought of a way to obtain binding and unbinding kinetics of the proteins. Some methods such as Isothermal titration calorimetry (ITC) permit to determine the thermodynamic parameters of interactions in solution