"
Team:KU Leuven/Project/StickerSystem
From 2013.igem.org
| Line 179: | Line 179: | ||
</div> | </div> | ||
| - | <!-- | + | <!-- Why an oscillator? --> |
<div class="row-fluid"> | <div class="row-fluid"> | ||
<div class="span12 white"> | <div class="span12 white"> | ||
<div class="row-fluid"> | <div class="row-fluid"> | ||
<div class="span8"> | <div class="span8"> | ||
| - | <h3> | + | <h3>Why would we use an oscillator?</h3> |
<p align="justify">An autonomous production system for β-farnesene might be a good solution in order to avoid having to put our systems directly on plants. However, a constitutive production of the pheromone, might rapidly render the aphids insensitive to it (Kunert, Reinhold and Gershenzon, 2010). Consequently we need a solution in which the production of β-farnesene is alternatingly on and off. In order to elaborate on the possibility of such a periodical production we investigated biological oscillating networks. A transcriptional network that exhibits oscillating behavior is the repressilator of Elowitz and Leibler (2000). This has been a cornerstone for synthetic biology since they were among the first to successfully introduce a synthetic model in a living organism. However, their paper mentions the lack of colony-wide synchronization. This is a necessity to achieve a periodical production, otherwise the variation will even out, resulting in a de facto constitutive expression. This means the repressilator does not suffice for a bacterial production unit with a periodical output.</p> | <p align="justify">An autonomous production system for β-farnesene might be a good solution in order to avoid having to put our systems directly on plants. However, a constitutive production of the pheromone, might rapidly render the aphids insensitive to it (Kunert, Reinhold and Gershenzon, 2010). Consequently we need a solution in which the production of β-farnesene is alternatingly on and off. In order to elaborate on the possibility of such a periodical production we investigated biological oscillating networks. A transcriptional network that exhibits oscillating behavior is the repressilator of Elowitz and Leibler (2000). This has been a cornerstone for synthetic biology since they were among the first to successfully introduce a synthetic model in a living organism. However, their paper mentions the lack of colony-wide synchronization. This is a necessity to achieve a periodical production, otherwise the variation will even out, resulting in a de facto constitutive expression. This means the repressilator does not suffice for a bacterial production unit with a periodical output.</p> | ||
</div> | </div> | ||
| Line 198: | Line 198: | ||
<br/> | <br/> | ||
| - | <!-- | + | <!-- Synchronized oscillator --> |
<div class="row-fluid"> | <div class="row-fluid"> | ||
<div class="span12 white"> | <div class="span12 white"> | ||
| Line 204: | Line 204: | ||
<div class="span4 greytext"> | <div class="span4 greytext"> | ||
<h3><br/></h3> | <h3><br/></h3> | ||
| - | <img src="https://static.igem.org/mediawiki/2013/ | + | <img src="https://static.igem.org/mediawiki/2013/0/09/KU_Leuven_team2.png" alt="Aphid milking"/> |
<p>Figure xǀ An ant 'milks' an aphid for his honeydew.</p> | <p>Figure xǀ An ant 'milks' an aphid for his honeydew.</p> | ||
</div> | </div> | ||
<div class="span8"> | <div class="span8"> | ||
| - | <h3> | + | <h3>A synchronized oscillator</h3> |
| - | <p align="justify"></p> | + | <p align="justify">The iGEM team from Wageningen tried to attain colony wide oscillations in 2011, by using the model proposed by Danino et al. (2010). This model provides a next step in the engineering of genetic circuits and is thoroughly described by the Wageningen 2011 iGEM team. As they mention on their wiki, this model heavily depends on the parameter values. Because we want to use an oscillator as a pace regulator, the eventual system will have multiple other inserted genes. The introduction of another set of genes besides an oscillator means an extra load on the current genetic circuit and this can influence the parameters of the oscillator-network (Shiue and Prather, 2012). To have a synchronized oscillator module that functions ‘independently’ on the presence of other modules, we need a system that gives oscillations for a broad range of parameters. This way it can preserve its oscillating behavior independently of possible other loads on the cell’s metabolism.</p> |
</div> | </div> | ||
</div> | </div> | ||
</div> | </div> | ||
</div> | </div> | ||
| + | |||
<br/> | <br/> | ||
Revision as of 16:33, 2 September 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!
The Oscillator
In this part we describe the design of an oscillator that could be useful in biological networks. We designed one ourselves since we have very specific demands and look forward to the challenge. We even tried to create a system that creates synchronized oscillations without depending heavily on the components used. So our proposal oscillates inherently, and only slightly depends on the parameters of the components used. In this text, we start with an explanation of how this oscillating model fits within the framework of our project. Second, we explain several necessities to obtain a synchronized oscillator, and how we managed to incorporate those within our network. For the thorough study of the network and to see what has been achieved in the lab, we refer to the modeling page and the wetlab page respectively.
Modeling
On this page we will talk about some more modeling stuff.
Wetlab
The C1 FFL coming to life.
Determining our requirements.
Why would we use an oscillator?
An autonomous production system for β-farnesene might be a good solution in order to avoid having to put our systems directly on plants. However, a constitutive production of the pheromone, might rapidly render the aphids insensitive to it (Kunert, Reinhold and Gershenzon, 2010). Consequently we need a solution in which the production of β-farnesene is alternatingly on and off. In order to elaborate on the possibility of such a periodical production we investigated biological oscillating networks. A transcriptional network that exhibits oscillating behavior is the repressilator of Elowitz and Leibler (2000). This has been a cornerstone for synthetic biology since they were among the first to successfully introduce a synthetic model in a living organism. However, their paper mentions the lack of colony-wide synchronization. This is a necessity to achieve a periodical production, otherwise the variation will even out, resulting in a de facto constitutive expression. This means the repressilator does not suffice for a bacterial production unit with a periodical output.
Figure xǀ Text
Figure xǀ An ant 'milks' an aphid for his honeydew.
A synchronized oscillator
The iGEM team from Wageningen tried to attain colony wide oscillations in 2011, by using the model proposed by Danino et al. (2010). This model provides a next step in the engineering of genetic circuits and is thoroughly described by the Wageningen 2011 iGEM team. As they mention on their wiki, this model heavily depends on the parameter values. Because we want to use an oscillator as a pace regulator, the eventual system will have multiple other inserted genes. The introduction of another set of genes besides an oscillator means an extra load on the current genetic circuit and this can influence the parameters of the oscillator-network (Shiue and Prather, 2012). To have a synchronized oscillator module that functions ‘independently’ on the presence of other modules, we need a system that gives oscillations for a broad range of parameters. This way it can preserve its oscillating behavior independently of possible other loads on the cell’s metabolism.
