Team:Paris Saclay/Modeling

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=Modeling=
=Modeling=
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At this step of the wiki, the careful readers has certainly understand that the goal is to rise up ethical question by creating a agar lemon covered with bacteria - ''E.coli'' in practice. But, before start more investigation and experimentation there is a real need to ensure that our project is feasable. And that's why we thought that modeling is so much important in an iGEM project.
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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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* Firstly, we wonder if bacteria could live and develop them-solves correctly in the agar media.
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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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Actually, ultimatly we hope create our lemon with the help of 3D-printer wich would use a mix of melted agar media and bacteria solution. A first ingredient which is desirable is oxygen. That's why we decided to model the [https://2014.igem.org/Team:Paris_Saclay/Modeling/oxygen_diffusion oxygen diffusion] in an agar medium.
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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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* 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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For all these reasons, modeling is really important for the concrete realization of our artwork and in general in an iGEM project!
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Without spoiling, we can just say that the previous model confirm the intution we could have : while oxygen couldn't easily go into the medium, the growth on the surface area is sufficiently more important than in the medium to neglect the first one. More precisly, our bacteria is colorfull and the surface will be whole covered before intern-colony have time to develop enought to be visible. Finaly, when we could hope observe intern-bacteria the surface-one have allready done an opaque layer.
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==[https://2014.igem.org/Team:Paris_Saclay/Modeling/oxygen_diffusion Oxygen Diffusion]==
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So, this part aims to predict the bacterial population growth on an ellipsoidal object - a fake lemon in practice - over time.
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More precisely, we have te 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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[[File:Paris_Saclay_oxygenpenetration.png|left|150px]]
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* An important aspect of our project is the transition from green to yellow in order to emulate the lemon maturation. To do this, we use a [https://2014.igem.org/Team:Paris_Saclay/Modeling/Fusion_Proteine fusion protein]. Before start the fusion of the two -blue and yellow- chromoproteins, we have to check the compatibility of the both. That's why we will then discuss the structural modeling of the it. 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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''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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We would have like modeling the salycilate inducible system to better understand this system but, unfortunatly, we do not have time anymore at last...
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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.
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==[https://2014.igem.org/Team:Paris_Saclay/Modeling/bacterial_Growth Bacterial Growth]==
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* Last but not least, the [https://2014.igem.org/Team:Paris_Saclay/Modeling/odor lemon scent] !
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[[File:Paris_Saclay_Pure_Birth_Process.png|left|150px]]
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Actually, we have modify ''E.coli'' in order to let her produce ''pinene'', ''limonene'' and ''Geraniol'' but thus do not ensure us that we will smell the lemon : the concentrations of this three fragance have to stay compatible and that's why we will study the evolution of these concentrations over time.
+
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].
 +
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!''
 +
==[https://2014.igem.org/Team:Paris_Saclay/Modeling/Fusion_Proteine Fusion Protein]==
 +
[[File:Paris_Saclay_BlueChromoSwissModStruct.png|left|150px]]
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'''Note''' : We have tried to illustrate our work with figures which could be understood for themselves, without knowing the method to get it. Morever, we will just add one or two -for the warrior- star(s) to parts which need more mathematical background in order to don't disgust not-mathematical readers from mathematics.  
+
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 [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.
 +
 
 +
==[https://2014.igem.org/Team:Paris_Saclay/Modeling/odor Lemon Scent]==
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[[File:Paris_Saclay_odor_60.png|left|150px]]
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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 three fragrances over time.
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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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----
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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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