Difference between revisions of "Team:UChile OpenBio-CeBiB/Model"
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Revision as of 23:52, 8 August 2017
UChile_OpenBio-CeBiB
Modeling
Modelling commission has the objective of giving information that contributes to implementation and designing of our project through mathematical representation of the metabolic pathways involved and genetic expression kinetics. To achieve this end, the following proposals will be accomplished:
- Elaborate a kinetic model to prove that the insertion of FBP/SBPase gene increases carbon dioxide fixation and quantify the amount.
- Construct a kinetic model of the ideas that we won’t be able to verify experimentally, these are the regulation of starch synthesis pathways by the means of metE operator sensible to vitamin B12. This would allow the usage of glucose for other economical purposes, and it the preferred method is through the use of antisense RNA. A comparison between the B12-sensible promoter and a light-induceable one will also be studied.
- Get an estimation or quantify the production of certain substances that could be generated in our microalgae by this genetic circuit.
- Carry out an economic analysis that could help evaluate the viability of the usage of this modified microalgae in bioreactors.
Methodology
To achieve each one of the previous proposals, we will follow this methodology:
Equations
For this model, it is firstly necessary to determine the reactions involved in the Calvin cycle, which are available in databases. Then, the kinetic characterization of them must be done through the search of parameters in scientific publications and other databases.
If you would like to see the equations, click the link below.
[[https://2017.igem.org/Team:UChile_OpenBio-CeBiB/Model/equations]]
Parameter selection
Due to the existence of various information regarding the same constant, an approximation to a single value can be done by assigning them a weight considering the similarity of the corresponding organism and environmental conditions.
If you would like to see the criterias, click the link below.
[[https://2017.igem.org/Team:UChile_OpenBio-CeBiB/Model/parameter_selection]]
Matlab simulation
Afterwards, all the collected data will be entered into Matlab and a contrast between the wild-type metabolism and the modified version will be studied.
If you would like to see the Matlab code, click the link below.
[[https://2017.igem.org/Team:UChile_OpenBio-CeBiB/Model/Matlab_code]]
Model fitting
Once the interesting questions are answered (selection between B12-sensitive promoter and light-sensitive promoter, quantity of B12 necessary to keep a sustainable amount of starch while glucose availability is increased, light level required to maximize carbon fixation), measurements of various physical and chemical magnitudes must be made to adjust the model, and establish a probability of a parameter to belong in a certain range. The fitting will be made by the least- square method.
After the model
Maximize glucose availability by carbon fixation through adjustment of environmental conditions.
Connection with human practice
- Once the information of Human Practices concerning the bioreactor is collected, the design of these systems will be done considering the best parameters obtained throughout the study.
- A possible collaboration with another iGEM team to model the effectiveness of a new biomolecule synthesis using our genetic circuit will be considered.
Results
From the previous procedures, we obtained the following results:
Calvin cycle
Starch synthesis pathway
