Difference between revisions of "Team:Aix-Marseille/Model"
| Line 1: | Line 1: | ||
| − | {{Aix-Marseille|title= | + | {{Aix-Marseille|title=Engineered M13 modelling|toc=__TOC__}} |
| − | + | ||
| − | + | ==What are we modeling ?== | |
| − | + | ||
| − | + | ||
| − | + | Reste à rédiger: décrire succintement le cycle de M13, idéalement avec un schéma (je peux m'en occuper. Du schéma aussi s'il n'y a pas de graphiste dispo) | |
| + | ==First iteration of the model== | ||
| − | + | We started with an excessively simple model to see wether our understanding of our system was profound enough to allow room for such simplifications. We made the following assumptions in this spirit: | |
| − | + | ||
| − | + | ||
| − | + | Which led to the following model: | |
| − | + | ||
| − | + | ||
| − | + | {| | |
| − | + | ! scope="col" |Assumption | |
| − | + | ! scope="col" |Reasonning | |
| − | + | |- | |
| − | + | |Neglecting cooperative effects | |
| − | + | | | |
| − | + | |- | |
| − | + | |Constant rate of p5 transcription/traduction | |
| − | + | | | |
| − | + | |- | |
| − | + | |One M13KO7 per factory cell | |
| − | + | | | |
| − | + | |- | |
| − | + | |Phage assembly isn't a limiting factor | |
| − | + | | | |
| − | + | |- | |
| − | + | |Neglecting stochasticity | |
| − | + | | | |
| − | + | |} | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | insérer image que j'ai dans la présentation que j'ai faite, mais en mieux dessinée / plus travaillée / classe / raccord avec le reste du thème graphique + comment je mets les images sur le site pour qu'elle s'intègrent dans le wiki? Est-ce que je les met sur internet sinon? | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ==Second iteration== | |
| − | + | ||
| − | + | ||
| − | </ | + | This time, we decided to adapt the model of a "wild-type" M13's biology <ref>Smeal ''et al'', Simulation of the M13 life cycle I: Assembly of a genetically-structured deterministic chemical kinetic simulation, Virology, 500, January 2017</ref><ref>Smeal ''et al'', Simulation of the M13 life cycle II: Investigation of the control mechanisms of M13 infection and establishment of the carrier state, Virology, 500, January 2017</ref> to fit our own engineered version of M13 and better inform wetlab experiments, as well as explain some of their preliminary findings! |
| − | + | Model validation: compare particle profile to that obtained in wetlab | |
| + | |||
| + | --> Insufficient p3 could cause the packing of several DNA molecules per phage. | ||
| + | |||
| + | What is the ideal number of plasmid copies if we produce p3 on a different plasmid? | ||
| + | |||
| + | ==Wet-lab and dry-lab back and forth== | ||
| + | |||
| + | Reste à rédiger, et ça je ne peux pas le faire seul | ||
| + | |||
| + | ==References== | ||
Revision as of 06:49, 24 October 2017
Engineered M13 modelling
Contents
What are we modeling ?
Reste à rédiger: décrire succintement le cycle de M13, idéalement avec un schéma (je peux m'en occuper. Du schéma aussi s'il n'y a pas de graphiste dispo)
First iteration of the model
We started with an excessively simple model to see wether our understanding of our system was profound enough to allow room for such simplifications. We made the following assumptions in this spirit:
Which led to the following model:
| Assumption | Reasonning |
|---|---|
| Neglecting cooperative effects | |
| Constant rate of p5 transcription/traduction | |
| One M13KO7 per factory cell | |
| Phage assembly isn't a limiting factor | |
| Neglecting stochasticity |
insérer image que j'ai dans la présentation que j'ai faite, mais en mieux dessinée / plus travaillée / classe / raccord avec le reste du thème graphique + comment je mets les images sur le site pour qu'elle s'intègrent dans le wiki? Est-ce que je les met sur internet sinon?
Second iteration
This time, we decided to adapt the model of a "wild-type" M13's biology [1][2] to fit our own engineered version of M13 and better inform wetlab experiments, as well as explain some of their preliminary findings!
Model validation: compare particle profile to that obtained in wetlab
--> Insufficient p3 could cause the packing of several DNA molecules per phage.
What is the ideal number of plasmid copies if we produce p3 on a different plasmid?
Wet-lab and dry-lab back and forth
Reste à rédiger, et ça je ne peux pas le faire seul
References
- ↑ Smeal et al, Simulation of the M13 life cycle I: Assembly of a genetically-structured deterministic chemical kinetic simulation, Virology, 500, January 2017
- ↑ Smeal et al, Simulation of the M13 life cycle II: Investigation of the control mechanisms of M13 infection and establishment of the carrier state, Virology, 500, January 2017
