Team:KU Leuven/Project/Modelling/Cellular Level

From 2013.igem.org

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   <p align = "justify">Synthetic biology designs new networks within/ on top of the existing cellular network of your favourite organism.The key question, however, is whether the cell/tissue/organism will actually be able to produce this network?!
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Ultimately our project aims to reduce crop loss due to aphid infestations. With an environmental project like ours, the computer is our best friend: through modelling and prediction algorithms we can reduce the real costs of field tests.
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Hence, several questions arise on our way to this goal:
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Our first step in the modelling was to predict the effect of our pheromones on the environment and the ecosystem through a series of modelling steps. You can find this in our ecological model page. The pheromones E-β-farnesene and methyl salicylate will not only affect the environment but also the bacterial cell itself. To figure out the impact of our system on our E. coli we performed a Flux Balance Analysis. Once we knew that our bacteria could handle the production of the pheromones we tried to predict the exact production amounts and find the rate limiting steps. Here our goal was also to feed wet-lab data into our algorithms. Finally, to optimise the impact of the released pheromones on the aphids and the ladybugs, we designed an oscillating transcription factor network to regulate their production. This oscillator also communicates between cells, enforcing the oscillating rhythm onto the whole colony.
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- Are there sufficient tRNA’s to build these new proteins, or should we codon optimise our strains?
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Summarised, these algorithms allow us to model our system from the cellular metabolism throughout to the environmental impact. Based on our models, we adapted the actual building of the system towards the most effective circuit. Finally, our mathematical predictions will provide significant benefits once we prepare our E. coligy for field tests.</p>
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- Will the cell be able funnel off enough precursor material to build significant amounts of this new network?
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- Will the series of proteins and enzymes produce our final, desired product?
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- Won’t the cell make toxic side-products in the process, possibly reducing growth and thus production rate?
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Revision as of 12:16, 28 October 2013

iGem

Secret garden

Congratulations! You've found our secret garden! Follow the instructions below and win a great prize at the World jamboree!


  • A video shows that two of our team members are having great fun at our favourite company. Do you know the name of the second member that appears in the video?
  • For one of our models we had to do very extensive computations. To prevent our own computers from overheating and to keep the temperature in our iGEM room at a normal level, we used a supercomputer. Which centre maintains this supercomputer? (Dutch abbreviation)
  • We organised a symposium with a debate, some seminars and 2 iGEM project presentations. An iGEM team came all the way from the Netherlands to present their project. What is the name of their city?

Now put all of these in this URL:https://2013.igem.org/Team:KU_Leuven/(firstname)(abbreviation)(city), (loose the brackets and put everything in lowercase) and follow the very last instruction to get your special jamboree prize!

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Synthetic biology designs new networks within/ on top of the existing cellular network of your favourite organism.The key question, however, is whether the cell/tissue/organism will actually be able to produce this network?! Hence, several questions arise on our way to this goal: - Are there sufficient tRNA’s to build these new proteins, or should we codon optimise our strains? - Will the cell be able funnel off enough precursor material to build significant amounts of this new network? - Will the series of proteins and enzymes produce our final, desired product? - Won’t the cell make toxic side-products in the process, possibly reducing growth and thus production rate?

Methyl Salicylate - Modelling: Flux Balance Analysis

We ran the Flux Balancing Analysis using the COBRA Toolbox for MATLAB. With this analysis we checked whether the growth rate of our cells will be affected when we introduce our methyl salicylate system.

Methyl Salicylate - Modelling: Kinetic Parameters Model

We have modelled the production system of methyl salicylate by using the transcription, translation and protein degradation rates in order to calculate the mRNA and protein fluxes. We also brought the kinetics of methyl salicylate synthesis into account.

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