Team:Paris Saclay/Modeling

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[[Team:Paris_Saclay/PCBs|What are PCBs ?]]
[[Team:Paris_Saclay/PCBs|What are PCBs ?]]
[[Team:Paris_Saclay/Project|Overview]]
[[Team:Paris_Saclay/Project|Overview]]
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[[Team:Paris_Saclay/Modeling|Modeling]]
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<html><a class="selflink">Modeling</a></html>
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[[Team:Paris_Saclay/PS-PCR|PS-PCR]]
[[Team:Paris_Saclay/Achievements|Achievements]]
[[Team:Paris_Saclay/Achievements|Achievements]]
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[[Team:Paris_Saclay/PSPCR|PSPCR]]
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{{Team:Paris_Saclay/incl_fin_menu_navigation}}
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Modeling
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[[Team:Paris_Saclay/Modeling|Overview]]
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[[Team:Paris_Saclay/Modeling/Simulator|Simulator]]
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[[Team:Paris_Saclay/Modeling/FNR|Oxygen sensor]]
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='''Modeling'''=
 
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"La modélisation, c'est comme le sexe, plus y'a d'inconnues, plus c'est chaud." ---damdam_du_91
 
<big>
<big>
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<p>Before you start, maybe those words could make you understand more quickly our project.</p>
 
==''What do we model?''==
==''What do we model?''==
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<p>This modeling is about the simulation of FNR aero/anaerobic regulation system which we have successfully achieved in our experiments. The second part of our experiment: the PCBs sensor system is not touched in the modeling.</p>
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<p>The degradation of PCBs demands multi bio-chemical reactions performing successively in aerobic or anaerobic condition. The regulator FNR is the key to control the processus. In different condition, FNR activated or desactivated, and foster or prevent some gene expression. So our super bacterium PCBs buster can be regulated by our will, and does the right thing at the right time.</p>
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<p>The FNR aero/anaerobic regulation system, briefly, we try to rebuild mathematically a system which can simulate the alternate expression of FNR in aerobic or anaerobic situation, from the translation of fnr to the production of reporter protein.</p>
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<p>This modeling is about the simulation of FNR aero/anaerobic regulation system that we have successfully achieved in our experiments. Briefly, we try to build bio-informatically a model which can reveal the alternate expression of FNR and its reporter, a virtuel system include bio-chemical phenomenons from the translation of fnr to the production of reporter protein.</p>
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==''What’s our purpose for this modeling?''==
==''What’s our purpose for this modeling?''==
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<p>The main aim of our modeling is recreate the aero/anaerobic reporter protein expression system. By alternating the oxygen concentration, activated or inactivated FNR combine (or not) with potential sensor gene sequence and make blue or red color. Our job is to see if we can observe the alternating red and blue curve when we change the oxygen condition.</p>
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<p>The main aim of our modeling is to create the aero/anaerobic reporter protein expression system which corresponds to our experiments. By alternating the oxygen concentration, active or inactive FNR combines (or not) with potential reporter sensor gene sequence and make green or red color. Anyway the simulation for experimental experiences works well, we can observe the alternating red and green prtein in our model when we change the oxygen condition, so we add  some additional scenarios for further test.</p>
 +
 
==''How do we model?''==
==''How do we model?''==
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<p>As the research of FNR regulation system is a well-studied territory, we found some excellent scientific paper in library especially [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2867928/ Regulation of Aerobic to Anaerobic Transitions by the FNR cycle in Escherichia coli by Dean A.Tolla and Michael A.Savageau]. This is a differential equation model. And in our modeling we decided to redo what they have done but use a different method: a stochastic system created by new modeling tool: Hsim. Hsim is a stochastic automation simulator, it simulate chemical or enzymatic reactions between molecules and based on reactions it can simulate whole system.</p>
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<p>As the research of FNR regulation system is a well-studied territory, we found some excellent scientific paper in library especially the paper of Dean A.Tolla and Michael A.Savageau. They have built successfully a differential equation system. And in our modeling we decided to redo what they have done but using a different method: a stochastic system created by a new modeling tool: [https://2013.igem.org/Team:Paris_Saclay/Modeling/Simulator Hsim]. We have also programed a online simulator which is able to perform our model on wiki without any installation in your computer. Thic online simulator works the same way as Hsim, but it is lighter and quicker. You can DIY your own simulation in this [https://2013.igem.org/Team:Paris_Saclay/Modeling/FNR page]. </p>
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=='''Oxygen censor, FNR regulator system modeling'''==
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<p>As we use Hsim for the modeling, if you want to dig in our model we suggest you to read [https://www.lri.fr/~pa/Hsim/ this page] written by Mr. Patrick Amar the developer of Hsim.</p>
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<p>Roughly speaking, we define a sampling volume, size in nanometer and we declare some molecules with their sizes, their moving speed and their number. Once the simulation starts, those molecules move randomly in the space and trigger some possible reaction between them with some probabilities. There is always somehow deviation from the reality, but we are all excited about this particular simulating modeling.</p>
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<p>We represent our FNR regulator model to you by 3 steps. We have chosen HSIM, a multi-agents programme developped at our university in order to follow the assembly, movements and dissociation of a large number of molecules in a virtual cell. HSIM replaces the Ordinary Differential Equations and mimics chemical reactions of the real system by rewriting rules. Following our modeling process, we provided the list of molecules, the rewriting rules, and the initial values of each molecule quantity in a configuration file to HSIM. We also have developed a web version of Hsim which allows user change and test the system parameters.</p>
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=='''Steps of modeling'''==
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==='''Step 1: translate biological knowledges into functional scheme'''===
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[[File:PSFNRcycle.jpg|800px]]<p>This scheme from the Dean A.Tolla and Michael A.Savageauthe's paper shows clearly the FNR transformation cycle. After the fnr mRNA translation, apoFNR is produced and a dimerization of 2 apoFNR catalyzed by ClpXP forme create the 4Fe-FNR. The 4Fe-FNR can be oxidized by oxygen to 2Fe-FNR then to apoFNR. 2Fe-FNR plus ClpXP can generate 4Fe-FNR. And all 3 FNR derivatives sustain a degradation effect. Those proteins will dissimilate in a while.</p>
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<br>
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<p>If we combine the FNR cycle and color reporter system :</p>
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[[File:PSFNRmodel.jpg|800px|alt Claire]]<p>The FNR behave differently for aerobic and anaerobic condition. In the case that oxygen is absent, a pair of 4Fe-FNR fix on the reporter DNA sequence and the blue reporter gene is expressed so we will see the blue color for those colonies. But a group of 4 4Fe-FNR come to fix at red reporter’s gen and prevent the expression of red color. If oxygen is sufficient, FNR derivatives keep in inactive form, the red reporter’s gene continue to produce the red color.</p>
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==='''Step 2: transcribe functional description into equation system'''===
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<br>
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==Summary for equations:==
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<p>
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*translation of Pfnr gene into FNR protein (FNR without Fe)
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*dimerisation of 4Fe-FNR (action of Ise protein)
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*oxydation: in aerobic conditions, oxygen inactivates FNR but cell continues to reactivate it (action of Ise protein)
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degradation of each kind of FNR (FNR without Fe, FNR activated, and FRN inactivated), a green protein, and a red protein (action of ClpXP
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protein)
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*activation/inactivation of a gene under a repressor promotor (green) and production or not of the cognate protein
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*activation/inactivation of a gene under an activator promotor (red) and production or not of the cognate protein
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</p>
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==Details==
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<br>
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*Translating fnr to FNR
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: fnr mRNA generates steadily apoFNR(inactived).  
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::''fnr -> fnr + apoFNR [probability]''
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<br>
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*Dimerization of apoFNR
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:2 apoFNRs form 4Fe-FNR(activated) with catalyzer Ise.
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::''{apoFNR}apoFNR + Ise -> QFeFNRa + Ise[probability]''
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<br>
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*Oxidation, from 4Fe-FNR to apoFNR(inactivated)
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: Aerobically, oxygen inactivates FNR, from 4Fe-FNR to 2Fe-FNR(inactivated)
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::''QFeFNRa + o2 -> DFeFNRi +o2 [probability]''
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:Then, oxidize from 2Fe-FNR to apoFNR
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::''DFeFNRi + o2 -> apoFNR +o2 [probability]''
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:2Fe-FNR can be reactivate by Ise
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::''DFeFNRi + Ise -> QFeFNRa + Ise [probability]''
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<br>
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*Degradation FNR
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:Protein FNR and its derivation submit a steady degrading rate
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::''apoFNR + ClpXP -> ClpXP [probability]''
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::''DFeFNRi + ClpXP -> ClpXP [probability]''
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::''QFeFNRa + ClpXP -> ClpXP [probability]''
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<br>
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*Activation/inactivation of green gene
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: Association between 4Fe-FNR(activated) and green protein gene
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::''QFeFNRa + GPV -> QFeFNRa_GPV_binded [probability]''
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: Dissociation between 4Fe-FNR(activated) and green protein gene
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::''QFeFNRa_GPV_binded -> QFeFNRa + GPV [probability]''
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::''QFeFNRa_GPV_binded -> PV + QFeFNRa_GPV_binded [probability]''
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<br>
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*Green protein degradation :catalyzed by ClpXP
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::''PV + ClpXP -> ClpXP [probability]''
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<br>
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*Repression of red protein gene : Association between 4Fe-FNR(activated) and red protein gene
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::''QFeFNRa + GPR -> QFeFNRa_GPR_binded [probability]''
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: Dissociation between 4Fe-FNR(activated) and red protein gene
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::''QFeFNRa_GPR_binded -> QFeFNRa + GPR [probability]''
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:Association of 4 4Fe-FNR(activated)
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::''{QFeFNRa_GPR_binded}QFeFNRa_GPR_binded -> rep [probability] ''
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:Dissociation of 4 4Fe-FNR(activated)
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::''rep -> QFeFNRa_GPR_binded + QFeFNRa_GPR_binded [probability]''
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<br>
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*Expression the red gene in aerobic condition
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: Production of red protein without repression
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::''GPR -> GPR + PR [probability]''
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::''QFeFNRa_GPR_binded -> QFeFNRa_GPR_binded + PR [probability]''
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<br>
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*Degradation of red protein
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::''PR + ClpXP -> ClpXP [probability]''
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<br>
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<p>Here you will find our configuration files to launch HSIM: [https://2013.igem.org/Team:Paris_Saclay/simulation#simulation.hsim links].</p>
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==='''3rd step: HSim on a web simulator'''===
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Damir has conceived and implemented the web simulations
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<br>
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<p>We provide 2 web versions of the HSIM simulator. Each of them implements a different set of rules. The "Simple simulation" describes the following reactions:</p>
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*translation of Pfnr gene into FNR protein (FNR without Fe)
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*dimerisation of 4Fe-FNR (action of Ise protein)
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*oxydation: in aerobic conditions, oxygen inactivates FNR but cell continues to reactivate it (action of Ise protein)
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*degradation of each kind of FNR (FNR without Fe, FNR activated, and FRN inactivated), a green protein, and a red protein (action of ClpXP
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protein)
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*activation/inactivation of a gene under a repressor promotor (green) and production or not of the cognate protein
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*activation/inactivation of a gene under an activator promotor (red) and production or not of the cognate protein
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<p>We used the simple simulation to explore different combinations of initial values. The complex simulation itemizes more rules than the simple simulation. en cours</p>
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<p>Here you will find our configuration files to launch HSIM: [https://2013.igem.org/Team:Paris_Saclay/simulation#simulation.hsim links].</p>
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=='''How to launch the simulations?'''== When simulation is launched, curve of molecule quantities appear with time.
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The "START/PAUSE" and "RESET" buttons give control to the simulation time.
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You may change the oxygen quantities with the "O2" panel.
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== Oxygen sensing system ==
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=== Simple simulation ===
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{{Team:Paris_Saclay/simbox|width=785|height=300|load=modeling/fnr0.xml}}
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=== Complex simulation ===
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{{Team:Paris_Saclay/simbox|width=785|height=300|load=modeling/fnr1.xml}}
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=='''Results and discussion'''==
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en cours
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==''What does our model look like?''==
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<p>In our model, we establish a virtual cell. Inside of this cell, we simulate some different reactions about different molecules. We observe those molecules reacting in some scenarios which are prepared for testing our system. Of cause, we also reveal our experiments in the model.  </p>
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{| align="center"
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|-
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|[[File:PSecolivert.jpg|400px]]
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|[[File:PSecolirouge.jpg|400px]]
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|-
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|<center>In anaerobic condition</center>
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|<center>In aerobic condition</center>
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|}
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<p>In the model here we only reveal 2 kinds of reporter protein (green and red, respectivelly regulated by activator and repressor promotor). In anaerobic condition, active FNR leads to the production of the green reporter protein and suppress the expression of the red one. In aerobic condition, FNR is inactivated by oxygen, there is no production of green reporter protein while the red reporter protein is synthetised. </p>
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</big>
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Writing by Zhou and Damir
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==''Reference''==
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*Wenmao Meng, Jeffrey Green and John R.Guest FNR-dependent repression of ndh gene expression requires two upstream FNR-binding sites Microbiology (1997), 143, 1521-1532
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*Parick Amar, Gilles Bernot, Victor Norris HSIM: a simulation programme to study large assemblies of proteins
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*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2867928/ Dean A.Tolla and Michael A.Savageau Regulation of Aerobic to Anaerobic Transitions by the FNR cycle in Escherichia coli] 
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written by Zhou
{{Team:Paris_Saclay/incl_fin}}
{{Team:Paris_Saclay/incl_fin}}

Latest revision as of 21:39, 4 October 2013

Project What are PCBs ? Overview Modeling PS-PCR Achievements


Modeling Overview Simulator Oxygen sensor


Contents

What do we model?

The degradation of PCBs demands multi bio-chemical reactions performing successively in aerobic or anaerobic condition. The regulator FNR is the key to control the processus. In different condition, FNR activated or desactivated, and foster or prevent some gene expression. So our super bacterium PCBs buster can be regulated by our will, and does the right thing at the right time.

This modeling is about the simulation of FNR aero/anaerobic regulation system that we have successfully achieved in our experiments. Briefly, we try to build bio-informatically a model which can reveal the alternate expression of FNR and its reporter, a virtuel system include bio-chemical phenomenons from the translation of fnr to the production of reporter protein.

What’s our purpose for this modeling?

The main aim of our modeling is to create the aero/anaerobic reporter protein expression system which corresponds to our experiments. By alternating the oxygen concentration, active or inactive FNR combines (or not) with potential reporter sensor gene sequence and make green or red color. Anyway the simulation for experimental experiences works well, we can observe the alternating red and green prtein in our model when we change the oxygen condition, so we add some additional scenarios for further test.

How do we model?

As the research of FNR regulation system is a well-studied territory, we found some excellent scientific paper in library especially the paper of Dean A.Tolla and Michael A.Savageau. They have built successfully a differential equation system. And in our modeling we decided to redo what they have done but using a different method: a stochastic system created by a new modeling tool: Hsim. We have also programed a online simulator which is able to perform our model on wiki without any installation in your computer. Thic online simulator works the same way as Hsim, but it is lighter and quicker. You can DIY your own simulation in this page.

What does our model look like?

In our model, we establish a virtual cell. Inside of this cell, we simulate some different reactions about different molecules. We observe those molecules reacting in some scenarios which are prepared for testing our system. Of cause, we also reveal our experiments in the model.

PSecolivert.jpg PSecolirouge.jpg
In anaerobic condition
In aerobic condition

In the model here we only reveal 2 kinds of reporter protein (green and red, respectivelly regulated by activator and repressor promotor). In anaerobic condition, active FNR leads to the production of the green reporter protein and suppress the expression of the red one. In aerobic condition, FNR is inactivated by oxygen, there is no production of green reporter protein while the red reporter protein is synthetised.

Reference

  • Wenmao Meng, Jeffrey Green and John R.Guest FNR-dependent repression of ndh gene expression requires two upstream FNR-binding sites Microbiology (1997), 143, 1521-1532
  • Parick Amar, Gilles Bernot, Victor Norris HSIM: a simulation programme to study large assemblies of proteins
  • [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2867928/ Dean A.Tolla and Michael A.Savageau Regulation of Aerobic to Anaerobic Transitions by the FNR cycle in Escherichia coli]

written by Zhou

Retrieved from "http://2013.igem.org/Team:Paris_Saclay/Modeling"