Team:KU Leuven/Project/StickerSystem

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    <a href="https://2013.igem.org/Team:KU_Leuven/Project/Aphid_Background">
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    <h3>Aphid Background</h3>
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    <p>Crashcourse in aphid biology</p>
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    <a href="https://2013.igem.org/Team:KU_Leuven/Project/HoneydewSystem">
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    <h3>Honeydew System</h3> </a>
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    <p>Our BanAphids react to honeydew</p>
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    <a href="https://2013.igem.org/Team:KU_Leuven/Project/StickerSystem">
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    <h3>Sticker System</h3>
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    <p>You are here!</p>
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    <a href="https://2013.igem.org/Team:KU_Leuven/Project/E.coligy">
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    <h3><i>E. coligy</i></h3>
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    <p>Validating the BanAphids in vivo</p>
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  <a href="https://2013.igem.org/Team:KU_Leuven/Parts">
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    <h3>Parts</h3> </a>
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    <p>BioBrick 'm all!</p>
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    <h3>Data Page</h3> </a>
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    <p>All our achievements on one small page!</p>
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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.</p>
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Our initial system for the production of methyl salicylate and β-farnesene relied on direct interaction between the bacteria and the aphids, our BanAphids would be sprayed on the plant. This is ethically and practically challenging since our <b>BanAphids</b> could end up in the environment. <b>We therefore designed an alternative pheromone production system, where the bacteria are kept in semi-permeable pouches</b>. These allow the pheromones to disperse in the air yet the bacteria themselves remain in the bags. Consequently, the presence of aphids secreting honeydew cannot be used as a trigger for the production of both pheromones. <b>Since constitutive production of β-farnesene rapidly renders aphids insensitive, concentrations should fluctuate to prevent habituation. This is typically achieved in an oscillator.</b> The oscillator is extensively elaborated in the <b><a href="https://2013.igem.org/Team:KU_Leuven/Project/Modelling/Colony_Level">oscillator model section</a></b>. Here we will mainly focus on the design of a β-farnesene oscillator, a part of it will be actually made in the lab. The production of methyl salicylate can be regulated similarly.</p>
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       <p align="justify">On this page we will talk about some more modeling stuff.</p>
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       <p align="justify">In this part we explain the necessity of the sticker system, as well as its practical execution, such as the properties of the sticker and the implementation of an oscillator. </p>
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       <p align="justify">A part of the oscillator was implemented in the wetlab. You can find the genes we chose for our oscillator here, as well as the results of the wetlab experiments. </p>
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    <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>
 
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    <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>
 
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Latest revision as of 03:19, 29 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!

tree ladybugcartoon

Aphid Background

Crashcourse in aphid biology

Honeydew System

Our BanAphids react to honeydew

Sticker System

You are here!

E. coligy

Validating the BanAphids in vivo

Parts

BioBrick 'm all!

Data Page

All our achievements on one small page!

Our initial system for the production of methyl salicylate and β-farnesene relied on direct interaction between the bacteria and the aphids, our BanAphids would be sprayed on the plant. This is ethically and practically challenging since our BanAphids could end up in the environment. We therefore designed an alternative pheromone production system, where the bacteria are kept in semi-permeable pouches. These allow the pheromones to disperse in the air yet the bacteria themselves remain in the bags. Consequently, the presence of aphids secreting honeydew cannot be used as a trigger for the production of both pheromones. Since constitutive production of β-farnesene rapidly renders aphids insensitive, concentrations should fluctuate to prevent habituation. This is typically achieved in an oscillator. The oscillator is extensively elaborated in the oscillator model section. Here we will mainly focus on the design of a β-farnesene oscillator, a part of it will be actually made in the lab. The production of methyl salicylate can be regulated similarly.

Design

In this part we explain the necessity of the sticker system, as well as its practical execution, such as the properties of the sticker and the implementation of an oscillator.

Integrating the oscillator into the wetlab

A part of the oscillator was implemented in the wetlab. You can find the genes we chose for our oscillator here, as well as the results of the wetlab experiments.

Retrieved from "http://2013.igem.org/Team:KU_Leuven/Project/StickerSystem"