Team:Paris Saclay/Modeling

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{{Team:Paris_Saclay/modeling_header}}
{{Team:Paris_Saclay/modeling_header}}
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=Modelling=
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=Modeling=
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comment : mettre les points en + gros ou des trucs en gras car ça fait trop bloc
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    Je pense que t'auras du mal à le faire. Je propose qu'on mettre une image en miniature (pas trop quand même) assez representative des parties. Par exemple votre dernier graphe de bacterial growth.
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==Overview==
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An important part of our [https://2014.igem.org/Team:Paris_Saclay/Project project] is devoted to the concrete realization of a lemon by moulding it from agar gel. It is well explained in the [https://2014.igem.org/Team:Paris_Saclay/Project/Lemon_Shaping lemon shaping] part.
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But, before starting more investigations and more experimentation, there is a real need to ensure that our project is feasible. We will tackle these following points :
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At this step of the wiki, the attentive reader has certainly understood that the goal of our project is to raise up ethical questions by creating an agar lemon covered with bacteria - ''E.coli'' in practice. But, before starting more investigations and more experimentation, there is a real need to ensure that our project is feasible.
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*By cutting a lemon, there is a slight  yellow/green color on the surface and white on the inside. To reproduce this effect, we use a kill-switch system based on oxygen and had been achieved by the team iGEM Paris Saclay 2013. The more we penetrate into the gel, the less oxygen is present, the less kill-switch system is activated, the less bacteria will produce desired color, and the whiter the interior. For this, we must ensure that oxygen does not penetrate completely into the lemon. We decided to model [https://2014.igem.org/Team:Paris_Saclay/Modeling/oxygen_diffusion oxygen diffusion] into the gel.  
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For this reason, we think modelling is really important in an iGEM project.
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*A major issue is the development of our bacteria in an agar medium. We noticed that the bacteria inside the gel grew less than those on the outside. We model the bacterial growth
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*To be even closer to the reality, we will imitate the [https://2014.igem.org/Team:Paris_Saclay/Project/Salicylate_Inducible_System ripening process] of a real lemon. We wanted to test if we could get a green color by fusion of two chromoproteins one yellow and one blue.
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*Lastly, we obtain the [https://2014.igem.org/Team:Paris_Saclay/Project/Lemon_Scent lemon scent] by modifying ''E.coli'' in order to let it produce ''pinene'', ''limonene'' and ''geraniol'' but this does not ensure us that we will smell the lemon fragrance.
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For all these reasons, modeling is really important for the concrete realization of our artwork and in general in an iGEM project!
==[https://2014.igem.org/Team:Paris_Saclay/Modeling/oxygen_diffusion Oxygen Diffusion]==
==[https://2014.igem.org/Team:Paris_Saclay/Modeling/oxygen_diffusion Oxygen Diffusion]==
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[[File:Paris_Saclay_oxygenpenetration.png|left|100px]]
 
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The construction of our lemon requires the introduction of bacteria in an agar gel.
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[[File:Paris_Saclay_oxygenpenetration.png|left|150px]]
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This poses several technical problems:
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''Is it possible to have a crust on the surface of the lemon by producing a "lemon coloration-like" by our bacteria ?''
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* bacteria need access to oxygen for respiration.
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* We want our bacteria produce a "lemon coloration-like" in order to have a crust on the surface.
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We will make a compromise to solve these two problems. The first one is easy to solve because ''E.coli'' can live in an anaerobic environment. Thus, with the property of anaerobic combined with the ease of access to oxygen, we solve the second problem by reacting our ''E.coli'' only in contacts with oxygen. Since we just want a crust, it is not necessary that all our bacteria react. Hence the necessity to estimate the penetration of oxygen into the gel.
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We invite you to discover how we modelled the [https://2014.igem.org/Team:Paris_Saclay/Modeling/oxygen_diffusion oxygen diffusion].
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We invite you to discover how we modelled the [https://2014.igem.org/Team:Paris_Saclay/Modeling/oxygen_diffusion oxygen diffusion] in order to answer this question.
==[https://2014.igem.org/Team:Paris_Saclay/Modeling/bacterial_Growth Bacterial Growth]==
==[https://2014.igem.org/Team:Paris_Saclay/Modeling/bacterial_Growth Bacterial Growth]==
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[[File:Paris_Saclay_Pure_Birth_Process.png|left|100px]]
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[[File:Paris_Saclay_Pure_Birth_Process.png|left|150px]]
Now that we know if bacteria could develop in agar or not, a natural issue is to predict the [https://2014.igem.org/Team:Paris_Saclay/Modeling/bacterial_Growth bacterial growth].
Now that we know if bacteria could develop in agar or not, a natural issue is to predict the [https://2014.igem.org/Team:Paris_Saclay/Modeling/bacterial_Growth bacterial growth].
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Without spoiling, we can just say that the previous model confirms the intuition we could have : while oxygen can't easily move into the medium, the growth on the surface area is sufficiently more important than into the medium to neglect the latter. More precisely, our bacteria is colorful and the surface will be entirely covered before internal bacteria have time to develop enough to be visible. Finaly, when we could hope to observe internal bacteria due to their color, the surface bacteria have already done an opaque layer.
 
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So, this part aims at predicting over time the bacterial population growth on an ellipsoidal object - a fake lemon in practice -.
So, this part aims at predicting over time the bacterial population growth on an ellipsoidal object - a fake lemon in practice -.
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More precisely, we have to determine the threshold of the initial proportion of bacteria for which we are sure that the population will never extinct... ''if this threshold exists!''
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More precisely, we have to determine the initial proportion of bacteria threshold from which we are sure that the population will never extinct...if this threshold exists !  
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==[https://2014.igem.org/Team:Paris_Saclay/Modeling/Fusion_Proteine Fusion Protein]==
==[https://2014.igem.org/Team:Paris_Saclay/Modeling/Fusion_Proteine Fusion Protein]==
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[[File:Paris_Saclay_BlueChromoSwissModStruct.png|left|100px]]
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[[File:Paris_Saclay_BlueChromoSwissModStruct.png|left|150px]]
An important aspect of our project is the color transition from green to yellow, in order to emulate the lemon maturation.
An important aspect of our project is the color transition from green to yellow, in order to emulate the lemon maturation.
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To do this, we use a [https://2014.igem.org/Team:Paris_Saclay/Modeling/Fusion_Proteine fusion protein]. Before starting the fusion of the two chromoproteins -yellow and blue-, we have checked for their respective compatibility. That's why we discuss the structural modeling of the proteins.
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To do this, we use a [https://2014.igem.org/Team:Paris_Saclay/Modeling/Fusion_Proteine fusion protein]. Before starting the fusion of the two chromoproteins -blue and yellow-, we have checked for their respective compatibility. That's why we will then discuss the structural modeling of the proteins. We used here the bioinformatics tools developed by the Swiss Institute of Bioinformatics and by the Xu group of Chicago University.
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We would have like modeling the salicylate inducible system in order to better understand this system but, unfortunately, we did not have time anymore at last...
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==[https://2014.igem.org/Team:Paris_Saclay/Modeling/odor Lemon Scent]==
==[https://2014.igem.org/Team:Paris_Saclay/Modeling/odor Lemon Scent]==
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[[File:Paris_Saclay_odor_60.png|left|100px]]
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[[File:Paris_Saclay_odor_60.png|left|150px]]
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Last but not least, the [https://2014.igem.org/Team:Paris_Saclay/Modeling/odor lemon scent] !
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Actually, we have modified ''E.coli'' in order to let her produce ''pinene'', ''limonene'' and ''geraniol'' but this do not ensure us that we will smell the lemon fragrance.
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As '''''De gustibus non est disputandum !''''', we need criteria to assess the scent of lemon; we have process as follows:
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We need criteria to assess the scent of lemon. For this, we have process as follow:
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* We evaluate the evolution of the concentrations of this three fragrances over time.
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* We evaluate the evolution of the concentrations of three fragrances over time.
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* Give a procedure for estimating a suitable time interval in which we can say that we got the smell citronel as desired.
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* We give a procedure for estimating a suitable time interval in which we can say that we got the lemon smell as desired.
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'''Note''' : Do not not be afraid and run away because of seing mathematical formulae : ''Maths is fun'' and we have made a real effort to be as precise as possible in order non-mathematicians to understand. For example, in order not to disgust poor mathematical readers of others, we will just add one or two -for the warrior- star(s) to parts which need more mathematical background. Morever, we illustrated our work with figures which could be understood for themselves, without knowing the method to get them.
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'''Note''' : Do not be afraid and run away because of seing mathematical formulae : ''Maths is fun'' and we have made a real effort to be as precise as possible in order non-mathematicians to understand. For example, in order not to disgust poor mathematical readers of others, we will just add one or two -for the warrior- star(s) to parts which need more mathematical background. Morever, we illustrated our work with figures which could be understood for themselves, without knowing the method to get them.
{{Team:Paris_Saclay/default_footer}}
{{Team:Paris_Saclay/default_footer}}

Latest revision as of 01:18, 18 October 2014

Contents

Modeling

Overview

An important part of our project is devoted to the concrete realization of a lemon by moulding it from agar gel. It is well explained in the lemon shaping part.

But, before starting more investigations and more experimentation, there is a real need to ensure that our project is feasible. We will tackle these following points :

  • By cutting a lemon, there is a slight yellow/green color on the surface and white on the inside. To reproduce this effect, we use a kill-switch system based on oxygen and had been achieved by the team iGEM Paris Saclay 2013. The more we penetrate into the gel, the less oxygen is present, the less kill-switch system is activated, the less bacteria will produce desired color, and the whiter the interior. For this, we must ensure that oxygen does not penetrate completely into the lemon. We decided to model oxygen diffusion into the gel.
  • A major issue is the development of our bacteria in an agar medium. We noticed that the bacteria inside the gel grew less than those on the outside. We model the bacterial growth
  • To be even closer to the reality, we will imitate the ripening process of a real lemon. We wanted to test if we could get a green color by fusion of two chromoproteins one yellow and one blue.
  • Lastly, we obtain the lemon scent by modifying E.coli in order to let it produce pinene, limonene and geraniol but this does not ensure us that we will smell the lemon fragrance.

For all these reasons, modeling is really important for the concrete realization of our artwork and in general in an iGEM project!

Oxygen Diffusion

Paris Saclay oxygenpenetration.png

Is it possible to have a crust on the surface of the lemon by producing a "lemon coloration-like" by our bacteria ?

We invite you to discover how we modelled the oxygen diffusion in order to answer this question.

Bacterial Growth

Paris Saclay Pure Birth Process.png

Now that we know if bacteria could develop in agar or not, a natural issue is to predict the bacterial growth. So, this part aims at predicting over time the bacterial population growth on an ellipsoidal object - a fake lemon in practice -. More precisely, we have to determine the threshold of the initial proportion of bacteria for which we are sure that the population will never extinct... if this threshold exists!

Fusion Protein

Paris Saclay BlueChromoSwissModStruct.png

An important aspect of our project is the color transition from green to yellow, in order to emulate the lemon maturation. To do this, we use a fusion protein. Before starting the fusion of the two chromoproteins -yellow and blue-, we have checked for their respective compatibility. That's why we discuss the structural modeling of the proteins.

Lemon Scent

Paris Saclay odor 60.png

We need criteria to assess the scent of lemon. For this, we have process as follow:

  • We evaluate the evolution of the concentrations of three fragrances over time.
  • We give a procedure for estimating a suitable time interval in which we can say that we got the lemon smell as desired.



Note : Do not be afraid and run away because of seing mathematical formulae : Maths is fun and we have made a real effort to be as precise as possible in order non-mathematicians to understand. For example, in order not to disgust poor mathematical readers of others, we will just add one or two -for the warrior- star(s) to parts which need more mathematical background. Morever, we illustrated our work with figures which could be understood for themselves, without knowing the method to get them.

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