Team:Imperial College London/Drylab/Protein production/Analysis

Mathematical models are useful in two ways: In this model, we made several assumptions, followed by predictions. These are listed below.
 * In the absence of experimental data they provide predictions about the behaviour of a system, and rely on a set of assumptions.
 * When experimental data is available they can be refined and provide explanations about the results we see.

 Model assumptions
--Mabult 17:19, 17 October 2009 (UTC) get rid of the blah-blah above...


 * LacI assumptions:
 * The lac operon represses by constitutively synthesizing the LacI gene product [1].
 * Here we have assumed that all the other complicated dynamical pathways are at dynamic equilibrium [2] and the lacI gene product is the only repressing entity in the system. For more details on the theory see our section on Chemical induction.
 * If these effects were included, the dynamics of the entire system will be more complicated, and the outcome of the model will be different.

--Mabult 17:34, 17 October 2009 (UTC)Do not say something like this!!!!!
 * In a culture grown overnight, levels of LacI expression will have reached steady state. We can assume that this is the case before we add in IPTG.


 * IPTG assumptions:
 * LacI and IPTG undergo a secondary set of reactions when IPTG is added in. We assume that 1 molecule of IPTG binds to 1 molecule of LacI, creating an intermediate reaction complex:
 * We also assume that the concentration of IPTG we put in is below the threshold of toxicity that could significantly start killing our cells. (Literature review on IPTG)
 * In this model we have neglected the natural degradation rate of IPTG and also of the [IPTG-LacI] complex.

Model Predictions Taking these assumptions into account, we can predict what the overall Qualitative behavior of the system will be.
 * In the absence of IPTG, the output amount of our protein of interest will depend on the steady state of LacI protein.
 * If the levels of LacI at steady state are low, we get a relatively high basal production of protein of interest, as the steady state is dependent on the lac promoter strength and its degradation. A weak promoter does not repress sufficiently the production of protein of interest.
 * If the levels of LacI at steady state are high, we are repressing more the production of protein of interest, so we will get a lower initial rate of protein production as the Lac promoter is stronger (higher PoPs output)
 * If we take into account leakiness of the Lac promoter, we will see a higher basal amount of protein of interest initially than in the non-leaky case.
 * When IPTG is added in, it will undergo a secondary reaction with LacI, thus, de-repressing the pathway, so we will see a bump in production of the protein of interest.
 * These effects are transient. LacI has a constitutive equilibrium, so after sometime, it will return to its original state and repress production of protein of interest once again.
 * The more IPTG we add in, the more LacI we will remove initially from the system, so the more output protein produced for a given period of time.

The actual model... Click here for details. Genetic circuit models are explained extensively in [3].

--Mabult 17:39, 17 October 2009 (UTC)Why don't you include the content on this page? Make it another subsection! Alternative is to create another thumbnail for the details on the model