Today we discussed the following with Miguel:
BIOPARTS:
There was information in regards to the transformation of the bioparts. Chiba’s team explained to us that their biopart’s DNA was not in the registry however it was mistakenly set as available. However they assured us that they have the functional bioparts, so we will have to request some DNA directly to the team.
ELECTRODES:
Miguel thinks that measuring a conductivity change in the medium will be sufficient. The temporary plan is to create a document gathering everything we know on the subject and that everyone helps investigating as much as possible.
PARAMETERS FOR THE MODEL:
This is further explained below, in modeling session, but basically what Miguel told us is that we can’t count with experimental data for the moment. He suggested that we should search for average half-lives and protein kinetics in general and use those parameters as a first approach.
CONTROLS:
Now that the experimental work has inevitably been delayed, that time can be invested in defining controls, both positive and negative for the experiment.
MODELING:
Defining parameters:
Obtaining the kinetic parameters experimentally is impossible right now; we first need the working bioparts. Right now we could get an average half-life of other proteins, which share characteristics with our desired protein (for example, average half-life of membrane proteins to define RcnA’s half-life) and trust that they won’t differ much. Once the experimental work resumes we could compare our parameters with those obtained experimentally.
The concentrations that will be experimentally determined (such as aiiA) will be calculated using the average synthesis rate of the given promoter, and the proteins degradation rate.
In the case of nickel and AHL, whose concentrations are arbitrary, we’ll use the model itself to estimate the range that will be experimentally tested; it is also necessary to evaluate if this concentrations are biologically feasible.
Notes on the model:
- Rules are apparently unnecessary, at least in our case, given that the declared properties naturally occur in our model; for example, in the case of total nickel, it is unnecessary to specify that it will be constant, given that for every lost molecule of internal nickel one molecule of external nickel is gained, and vice versa. Therefore the sum will be constant. The rules will therefore only be used to illustrate this phenomenon.
- Null is a special variable of the program to define the degradation of a protein, the model was corrected to use this variable.
TO-DO LIST:
Parameters: We are going to focus on this.
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