"
Team:KU Leuven/Project/Modelling/Cellular Level
From 2013.igem.org
| (4 intermediate revisions not shown) | |||
| Line 12: | Line 12: | ||
<div id="header" class="row-fluid"> | <div id="header" class="row-fluid"> | ||
<div class="span12"> | <div class="span12"> | ||
| - | <h3 class="bg-green">Modelling on | + | <h3 class="bg-green">Modelling on Cellular level</h3> |
</div> | </div> | ||
</div> | </div> | ||
| Line 21: | Line 21: | ||
<div class="row-fluid"> | <div class="row-fluid"> | ||
<div class="span12 white"> | <div class="span12 white"> | ||
| - | <p align = "justify">Synthetic biology designs new networks within | + | <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/> | Hence, several questions arise on our way to this goal:<br/><br/> | ||
| - | - Are there sufficient | + | - 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 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/> | - 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/> | - 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/> | 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 | + | 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! |
| - | + | ||
</p> | </p> | ||
</div> | </div> | ||
| Line 44: | Line 43: | ||
<div class="span10 icon-text "> | <div class="span10 icon-text "> | ||
| - | <h3>Flux Balance Analysis : Methyl Salicylate </h3> </a> | + | <h3>Flux Balance Analysis: Methyl Salicylate </h3> </a> |
<div class="row-fluid"> | <div class="row-fluid"> | ||
<div class="span12"> | <div class="span12"> | ||
| - | <p align="justify">We | + | <p align="justify">We checked whether the growth rate of our BanAphids will be affected when we introduce our methyl salicylate system. For this, we ran the Flux Balance Analysis using the COBRA Toolbox for MATLAB.</p> |
</div> | </div> | ||
</div> | </div> | ||
| Line 66: | Line 65: | ||
<div class="span10 icon-text "> | <div class="span10 icon-text "> | ||
| - | <h3>Kinetic Parameters Model : Methyl Salicylate</h3> </a> | + | <h3>Kinetic Parameters Model: Methyl Salicylate</h3> </a> |
<div class="row-fluid"> | <div class="row-fluid"> | ||
<div class="span12"> | <div class="span12"> | ||
Latest revision as of 03:59, 29 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!
