Team:Paris/Modeling

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== DryLab ==
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<center> [[team:Paris/DryLab#DryLab| Main]] - [[team:Paris/Modeling#bottom|Introduction]] - [[Team:Paris/Production_modeling#bottom | Delay model]] - [[Team:Paris/Production_modeling2#bottom | Vesicle model]] - [[Team:Paris/Transduction_modeling#bottom | Fec simulation]] </center>
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<center> '''Introduction'''</center>
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== Modelling overview : DryLab - Introduction ==
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== Introduction ==
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Et un petit blabla d'intro sur les modélisations, ho que oui vous adorez ca .. Ca sent bon le blabla :d
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<font color=red>Non, ce n'est pas du blabla du tout. La raison pour laquelle vous avez passé tant de temps à faire de la modélisation n'est pas du tout accessoire. Fondamentale comme accompagnement à la réflexion sur le design du système et pour apprendre sur les mécanismes en jeu. Le travail de Piierre n'est peut être pasà ce stade immédiatement exploitable pour le projet, mais dans un perspective long terme une telle étude des mpécanismes biophysiques outre sont intérêt fondamental peut amener a des progrès importants pour les applicatiojns.</font>
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=='''Vesicles Maturation Modeling.'''==
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/DryLab#bottom"> Main </a>|
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<a class="menu_sub_active" href="https://2009.igem.org/Team:Paris/Modeling#bottom"> Introduction</a>|
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Production_modeling2#bottom"> Vesicle model</a>|
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Production_modeling#bottom"> Delay model</a>|
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_modeling#bottom"> Fec simulation</a>
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:*This part of the modelling works was dedicated to the vesicles creation understanding. Indeed if we want to control the emission of vesicles we need to discuss phenomenon which lead it. We decided to attach ourselves to the biophysics of the problem and especially on the biophysics of membranes. We finally linked the creation of vesicles to the free diffusion of PAL and TOL proteins in the membranes depending of the lipidic bilayer shapes.
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===Vesicles Maturation Modeling===
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This part of the modelling works was dedicated to the vesicles creation understanding. Indeed if we want to control the emission of vesicles we need to discuss phenomenon which lead it. We decided to attach ourselves to the biophysics of the problem and especially on the biophysics of membranes. We finally linked the creation of vesicles to the free diffusion of PAL and TOL proteins in the membranes depending of the lipidic bilayer shapes.
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::We demonstrate that two simple physical phenomenon and the Tol/pal binding can explain the creation of vesicles:
 
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=Osmotic pressure increase due to the Cell Wall turnover  and the Tol/Pal distinct location can explain the formation of blebbing=
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The conformation of the lippopolysaccharides and the normal phospholipids<font color=red> J'ai suggéré quelque part de faire des rappels de la biologie des membranes des gram-negatifs et E. coli en particulier. S'assurer que c'est le cas et y faire un lien. Sinon c'est l'endroit ici de faire quelques rappels sur la  question</font>can be seen as a lipid bilayer which conformed itself as a liquid crystal at the growth culture. The conformation of lipid bilayer has been well studied and a lot of theoretical results have been shown<font color=red>Quelques références alors d'articles de revue </font>. Some of them are of great interest for our project. This conformation is something <font color=red>Knowing some properties of this conformation enables us to... </font>which can enable us to understand the way vesicles can be produced and how they will be received.<font color=red> some simple basic calculs can already give us very interesting  results on...</font> In our project we first notice that from a basic calculus we can obtain very interesting results on the way outer membrane vesicles can be produced.<font color=red> annoncer déjà de quelle nature serontces résultats très intéressants. On ne rédige pas un roman à suspens...</font>
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===Osmotic pressure increase due to the Cell Wall turnover  and the Tol/Pal distinct location can explain the formation of blebbing===
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:the hypothesis made in []  about a link between vesicles creation and '''the turnover of the peptidoglycan act as  a physical ''motor'' for our model''' : Indeed during the division of the cell the peptidoglycan is degraded and reconstructed to be given a new shape. This turnover isn’t perfect: a part of the murrains components are released in the periplasm which make locally increased the pressure and so cause the local deformation of the outer membrane.
 
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:Defects in the TOL-PAL system leads to vesicles maturation. We can consider that '''TOL-PAL is acting as mooring ropes'''. So the distribution of TOL-PAL in the lipidic bilayer would be vital for the integrity of the outer membrane of the bacteria and any defect in those distributions can lead to vesicle maturation if there is any increase of the periplasm pressure. In vesicle creation '''Tol-Pal system act as counter forces to the osmotic pressure increase''' Using those type of information we create a 2 dimension model to explain the formation of blebbing
 
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=Brownian diffusion in the membranes can explains the affinity for concave region of outer membrane in bacteria and local clustering on the border of blebbing.=
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the hypothesis made in <font color=red>''Reference''</font> about a link between vesicles creation and '''the turnover of the peptidoglycan act as  a physical ''motor'' for our model''' : Indeed during the division of the cell, the peptidoglycan is degraded and reconstructed to be given a new shape. This turnover isn’t perfect: a part of the murrains components are released in the periplasm which make locally increased the pressure and so cause the local deformation of the outer membrane.
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Defects in the TOL-PAL system leads to vesicles maturation ''reference''. We can consider that '''TOL-PAL is acting as mooring ropes'''. So the distribution of TOL-PAL in the lipidic bilayer would be vital for the integrity of the outer membrane of the bacteria and any defect in those distributions can lead to vesicle maturation if there is any increase of the periplasm pressure. During vesicle creation '''Tol-Pal system act as counter forces to the osmotic pressure increase unabling a global swelling of the outer membrane'''. Using those types of information we create a 2 dimension model to explain the formation of blebbing
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===Brownian diffusion in the membranes can explains the affinity for concave region of outer membrane in bacteria and local clustering on the border of blebbing.===
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:Our hypothesis to this model is that '''simple Brownian diffusion on the surface can explain stable accumulation of TOL and PAL in the border of the blebbing''' ( Link toward Details). Indeed physically it appears that Brownian motion model on a non-plane surface doesn’t predict '''a non uniform concentration''' of particles. They will aggregate themselves in the '''highly concave areas of membrane'''. This prediction is in agreement with some observation about Tol/Pal ''Reference'' and some experiments were done which confirm a phenomena in [1] which is the accumulation of proteins in the septa region during E.coli division but not explained efficiently by simple biology mechanism.
 
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=Brownian Diffusion predict accumulation of TOL-PAL on the border of vesicles in creation phases.=
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Our hypothesis to this model is that '''simple Brownian diffusion on the surface can explain stable accumulation of TOL and PAL in the border of the blebbing''' ( Link toward Details). Indeed physically it appears that Brownian motion model on a non-plane surface doesn’t predict '''a non uniform concentration''' of particles. They will aggregate themselves in the '''highly concave areas of membranes'''. This prediction is in agreement with some observation about Tol/Pal <font color=red>''Reference''</font> and some experiments were done which confirm a phenomena in <font color=red> ''Reference'' </font> which is the accumulation of proteins in the septa region during E.coli division but not explained efficiently by simple biology mechanism.
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===Brownian Diffusion predict disparition of the borders of vesicles in creation phases.===
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The direct area caught inside the border of the blebbing is '''highly and negatively curved''' , so we can predict '''a migration of Tol-Pal complexes and Pal proteins toward this area : the Tol/Pal complexes are zippering back the membrane to the peptidoglycan''' but not efficiently enough to ensure the whole contrition of the blebbing: two different areas are separated.
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<b ="correction"> dessins </b>
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:::During the osmotic pressure increase if the TOL-PAL proteins complexes are not enough to create a tight net, blebbings can appear. On their border the curvature is negative and will be quickly populated by free PAL they will tend to attach themselves to the TOL complex localized in the inner membrane behind the cell wall and so the border of the blebbing is tightening itself. If the bleb is important enough the negative spontaneous curvature of the lipid bilayer of E.Coli ensures the tightening of the border would not retract the whole blebbing but just the border between the blebbing and the outer membrane. this end the maturation of the blebbing in a vesicle.
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Latest revision as of 23:31, 20 October 2009

iGEM > Paris > Home > DryLab > Modeling Introduction


Contents

Modelling overview : DryLab - Introduction

Vesicles Maturation Modeling

This part of the modelling works was dedicated to the vesicles creation understanding. Indeed if we want to control the emission of vesicles we need to discuss phenomenon which lead it. We decided to attach ourselves to the biophysics of the problem and especially on the biophysics of membranes. We finally linked the creation of vesicles to the free diffusion of PAL and TOL proteins in the membranes depending of the lipidic bilayer shapes.


The conformation of the lippopolysaccharides and the normal phospholipids J'ai suggéré quelque part de faire des rappels de la biologie des membranes des gram-negatifs et E. coli en particulier. S'assurer que c'est le cas et y faire un lien. Sinon c'est l'endroit ici de faire quelques rappels sur la questioncan be seen as a lipid bilayer which conformed itself as a liquid crystal at the growth culture. The conformation of lipid bilayer has been well studied and a lot of theoretical results have been shownQuelques références alors d'articles de revue . Some of them are of great interest for our project. This conformation is something Knowing some properties of this conformation enables us to... which can enable us to understand the way vesicles can be produced and how they will be received. some simple basic calculs can already give us very interesting results on... In our project we first notice that from a basic calculus we can obtain very interesting results on the way outer membrane vesicles can be produced. annoncer déjà de quelle nature serontces résultats très intéressants. On ne rédige pas un roman à suspens...

Osmotic pressure increase due to the Cell Wall turnover and the Tol/Pal distinct location can explain the formation of blebbing

the hypothesis made in Reference about a link between vesicles creation and the turnover of the peptidoglycan act as a physical motor for our model : Indeed during the division of the cell, the peptidoglycan is degraded and reconstructed to be given a new shape. This turnover isn’t perfect: a part of the murrains components are released in the periplasm which make locally increased the pressure and so cause the local deformation of the outer membrane. Defects in the TOL-PAL system leads to vesicles maturation reference. We can consider that TOL-PAL is acting as mooring ropes. So the distribution of TOL-PAL in the lipidic bilayer would be vital for the integrity of the outer membrane of the bacteria and any defect in those distributions can lead to vesicle maturation if there is any increase of the periplasm pressure. During vesicle creation Tol-Pal system act as counter forces to the osmotic pressure increase unabling a global swelling of the outer membrane. Using those types of information we create a 2 dimension model to explain the formation of blebbing

Brownian diffusion in the membranes can explains the affinity for concave region of outer membrane in bacteria and local clustering on the border of blebbing.

Our hypothesis to this model is that simple Brownian diffusion on the surface can explain stable accumulation of TOL and PAL in the border of the blebbing ( Link toward Details). Indeed physically it appears that Brownian motion model on a non-plane surface doesn’t predict a non uniform concentration of particles. They will aggregate themselves in the highly concave areas of membranes. This prediction is in agreement with some observation about Tol/Pal Reference and some experiments were done which confirm a phenomena in Reference which is the accumulation of proteins in the septa region during E.coli division but not explained efficiently by simple biology mechanism.

Brownian Diffusion predict disparition of the borders of vesicles in creation phases.

The direct area caught inside the border of the blebbing is highly and negatively curved , so we can predict a migration of Tol-Pal complexes and Pal proteins toward this area : the Tol/Pal complexes are zippering back the membrane to the peptidoglycan but not efficiently enough to ensure the whole contrition of the blebbing: two different areas are separated.

dessins



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