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Team:KU Leuven/Project/Modelling/Colony Level
From 2013.igem.org
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| + | <h3 class="bg-green">Modelling on cellular level</h3> | ||
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| + | <p align = "justify">Synthetic biology designs new networks within and 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:<br/><br/> | ||
| + | - Are there sufficient tRNAs to build these new proteins, or should we codon optimise our strains?<br/> | ||
| + | - Will the cell be able to funnel off enough precursor material to build significant amounts of this new network?<br/> | ||
| + | - Will the series of proteins and enzymes produce our final, desired product?<br/> | ||
| + | - Won’t the cell make toxic side-products in the process, possibly reducing growth and thus production rate?<br/><br/> | ||
| + | The answer to these questions lies in <b>modelling</b> but also in designing the <b>appropriate wet-lab experiments</b> to support, verify and improve our modelling.<br/><br/> | ||
| + | On a <b>cellular level</b>, we used <b>2 modelling suites to obtain more insight in our BanAphids</b>. First we worked out the Flux Balance Analysis for methyl salicylate and secondly we employed a Kinetic Parameter Model for Methyl Salicylate. Obviously, both suites can be used to verify E-beta-farnesene production and limits while <b>other iGEM teams</b> can fill in their favourite compound! | ||
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Revision as of 19:09, 28 October 2013
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!
Modelling on cellular level
Synthetic biology designs new networks within and 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 tRNAs to build these new proteins, or should we codon optimise our strains?
- Will the cell be able to 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?
The answer to these questions lies in modelling but also in designing the appropriate wet-lab experiments to support, verify and improve our modelling.
On a cellular level, we used 2 modelling suites to obtain more insight in our BanAphids. First we worked out the Flux Balance Analysis for methyl salicylate and secondly we employed a Kinetic Parameter Model for Methyl Salicylate. Obviously, both suites can be used to verify E-beta-farnesene production and limits while other iGEM teams can fill in their favourite compound!
Design
In this part we describe the design of an oscillator that could be useful in biological networks. We created a system that creates synchronized oscillations without depending heavily on the components used. We explain several necessities to obtain a synchronized oscillator, and how we managed to incorporate those within our network.
