Team:ULB-Brussels/Modelling/2A-Peptid

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Revision as of 06:14, 10 October 2014

$~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ \newcommand{\MyColi}{{\small Mighty\hspace{0.12cm}Coli}} \newcommand{\Stabi}{\small Stabi}$ $\newcommand{\EColi}{\small E.coli} \newcommand{\SCere}{\small S.cerevisae}\\[0cm] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ \newcommand{\PI}{\small PI}$ $\newcommand{\Igo}{\Large\mathcal{I}} \newcommand{\Tgo}{\Large\mathcal{T}} \newcommand{\Ogo}{\Large\mathcal{O}} ~$

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Previous Years 2012 : InteGreator 2011 : Pindel 2010 : HydroColi 2009 : GluColi

-News to compare with & without p2A? Yes, now we get it !

- Université Libre de Bruxelles - Bioreactor and 2A Peptide $\newcommand{\Tox}{\small Tox} \newcommand{\AnTox}{\small Anti\hspace{0.08cm} Tox} \newcommand{\EColi}{\small E.Coli}$ Improve $\Stabi$ to $\MyColi$ The objective of $\Stabi$ is to stabilize the presence of the plasmids that contain the $\PI$ gene sequence. E.Coli can insert other plasmids, f.e. containing the $\Tox$ and the $\AnTox$ genes; in this case, these two proteins are produced at same rate (contitutive promoter: T7) and the $\PI$ is independently produced in the classical system. The objective of $\MyColi$ is a little bit different: The T7 promoter iniciates the transcription of the $\PI$ $\small\&$ the $\AnTox$ genes, but another promoter, pBAD, controls the transcription of the $\Tox$ gene, situated in another plasmid than the $\PI$ $\small\&$ the $\AnTox$ genes. The problem with the classical system is that if there're a lot of mutations or a lot of heterogeneity in the E.Coli population, the $\PI$ is not produced at high rate. In a bioreactor built to product a special kind of $\PI$, this system's not optimal because there're $\PI$ losses, especially if the $\PI$ gene sequence is long or if the $\PI$ is cumbersome for E.Coli. With our $\MyColi$ system, the sub-producing bacteria are eliminated from the bioreactor because these E.Coli don't produce the $\PI$ in sufficient quantity (the $\PI$ is produced at same rate than the $\AnTox$, thanks to the $2A$ $peptid$). The presence of the $p\small 2A$ is necessary with $\MyColi$, so the losses can be divided in two classes: (1) bacteria without cleavage of $p\small 2A$ $\hspace{0.1cm}\small\&\hspace{0.1cm}$ (2) bacteria killed by TA system, when there's more $\Tox$ than $\AnTox$ (this's when the fraction [$\Tox$]/[$\AnTox$] is bigger than one, this happens when a lot of $\AnTox$ are degraded and when $\Tox$ are produced at high rate). Hypothesis To only take a sight in the $\MyColi$ mechanism, we will assume that E.Coli is virtually immortal (no relation between the producing rate of proteins and the old age of some members of the population), that E.Coli has food enough when the bioreactor is working and that $\Tox$ and $\AnTox$ recombine rapidly in TA-complex (no dependence with the mean free path of proteins into the cytoplasm). Parameters Our 4 parameters are $(a)$ the probability of mutations in comparison with the length of the genes, $(b)$ the estimator of the heterogeneity in populations, $(c)$ the cleavage rate of $p\small 2A$, $(d)$ the proportion of bacteria died by the TA-system in comparison with the fraction [$\Tox$]/[$\AnTox$]. Be careful with the bioreactor A problem with $\MyColi$ is that the bioreactor cannot stop, because when it stops, the antitoxin is not produced and bacteria die. A solution solving this is to thoughtfully tranfer the bacteria from a growth medium with arabinose to a growth medium with glucose, because $ara$ activates pBAD and $glu$ stops pBAD (as proven by experiments in our previous Results page).
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