Difference between revisions of "Team:Chalmers-Gothenburg/Model"

As seen in the bottom right corner of Figure 1, the cascade ends with an activation of Ste12 which makes it possible for it to bind into DNA and begin transcriptional activation. This was therefore used as a first step into validating the function of the biosensor. The concentration of Ste12 should be higher in lung cancer patients compared to healthy people, due to the fact that they produce a higher amount of VOCs that can activate the pheromone pathway [7]. To check this, data on different VOC levels was used, both in in lung cancer patients and compared to a healthy control group and a group consisting of smokers [7]. The data of the median level of each group is presented in Table 1 and consists only of n-octanal levels. The choice of only studying the n-octanal levels is due to the fact that no data (kinetic rates v₁ to v₅ in Kofahl and Klipp’s model, see Figure 1) is available for the two receptors used in this project, thus the 2-butanone levels were omitted. The original yeast parameters of these reactions were used together with the n-octanal concentrations from the three patient groups.

The binding kinetics are assumed to be of Hill type with values found in the literature [2,8]. The initial concentrations of Fus1 and Cre recombinase are assumed to be zero. The time courses for Cre/Fus1 are shown in Figure 2b. Notice that we now have about double the Fus1/Cre recombinase amounts for the lung cancer patients compared to the controls. The Cre recombinase will flip a constitutive promoter P_TEF1 flanked between two LoxP sites. This will in turn activate transcription of the gRNA for ADE2 disruption in one mating type and transcription of the protein Cas9 in the other. Since the production rate of P_TEF1 is unknown, we set it to an arbitrary value of 1mmol/min/L. Setting an arbitrary production rate does not allow us to make any quantitative predictions about the gRNA/Cas9 levels. However, due to the fact that the original yeast parameters are used for the receptors, quantitative information is lost anyway. Although we can still estimate relative concentrations of these species between our patient groups.

The mating rate in this model is assumed to be proportional to the amount of haploid cells in the culture and the Fus1 concentration. Given an initial 1000 haploids, we produce the corresponding amount of diploids for each patient group, shown in Figure 2d. For the concentration of activated Cas9-gRNA complex per diploid cell we assumed it to be proportional to the amount of haploids, the gRNA concentration in each cell and the Cas9 concentration in each cell. The result from this simulation is shown in Figure 2e. After 24 hours there is about a 50% increase in Cas9:gRNA dimers compared with the controls. This increase will in turn promote deletion of the ADE2 gene, causing the cell to turn red. Although this can be modeled, since there were not any parameters at all for the ADE2 pathway in the literature, we decided to only model up until the Cas9:gRNA dimer formation.

From this we can conclude that it might be possible to differentiate between lung cancer patients and controls since we get a 50% higher level of Cas9:dimers after 24 hours.