Team:Warwick/Project

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      <h1 class="title" align="center">The Project</h1>
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      <h2>The Problem</h2>
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<a href="https://2014.igem.org/Team:Warwick"style="color:#000000"> <b>  </b> </a> <a href=https://2014.igem.org/Team:Warwick><img src="https://static.igem.org/mediawiki/2014/9/9a/Home.png" border="20" align=20px" height ="20px" alt="Image and video hosting by TinyPic">
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Our modelling in this project has several aims :
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<li>To find the amount of DPP-IV reduction reached when the system reaches equilibrium</li>
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<li>To find a way to control the level of DPP-IV reduction</li>
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<li>To find the minimum number of RdRps, replicons, etc to be initially transfected into the cell, which are required to achieve a steady state for the system</li>
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<li>To find out how long does it take for the system to reach equilibrium</li>
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<li>To find out the level of reduction we need to treat diabetes</li>
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<li>To find out how stable the system is (i.e. will the system only work in very specific situations, or in lots of different systems?)
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<p><p>
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We are currently using Simbiology in Matlab and Copasi to model the system. We are currently adapting several different models, which come from research into HCV replicons, to our system. If our models can be made to fit our experiments well, we may extend our project to try and find a way to control the level of DPP-IV which is reduced. In addition modelling the system will allow it to be better optimised in the future, and optimum values for constants such as the strength of the ribosome binding sites, and the number of siRNAs produced by each degradation, so that the effect of our biobrick can be optimised.<p><p>
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Initially we determined that our system should reach some equilibrium after a certain amount of time. This is because firstly, HCV is a successful virus, so the replicons should not completely degrade away as time goes to infinity.  Secondly, since there are only a finite amount of resources within the cell, the number of replicons in the system cannot keep increasing forever. This means either the number of replicons must tend towards a certain constant (constant with respect to time), or the number of replicons should tend towards oscillations. <p><p>
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        The Sheffield iGEM 2014 team have chosen to address the challenge of reducing the amount of fats, oils and greases (FOGs) entering the sewage system. These contribute to major costs and blockages in the systems known as <a href="http://tinyurl.com/mdhrfmk"><i>fatbergs</i> </a>. At present, there are over 200,000 major UK sewage blockages per year, of which <sup>3</sup>/<sub>4</sub> are caused by FOGs, meaning this is a major challenge to infrastructure and clearly a global challenge as cities expand, particularly in developing countries. These drain blockages in the UK are a growing problem costing Thames Water (London) alone, £1 million per month to tackle. In addition to FOGs, human hair is a well-known problem in wastewater treatment, being among a range of difficult to degrade materials.
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      <h2>The Concept</h2>
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        Objectively, the team aim to build a genetically engineered, non-pathogenic strain of E. coli to responsively secrete lipase and keratinase in the presence of fats and hair in order to degrade and solubilise the components; this will ultimately prevent the blockages in the network. This will then be developed further in the future, by incorporating a transport system into the bacteria to uptake the lipid components to harvest and reuse as a potential energy source.
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      <h2>The Parts</h2>
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        The system being created in E. coli is composed of several key BioBrick parts from the iGEM registry:
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            <th>iGEM Registry Part Code</th>
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            <td>BBa_K258006</td>
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            <td>Thermostable lipase (TliA) of <i>P. fluorescens</i> SIK W1</td>
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            <td>The TliA lipase is secreted using an ABC transporter to degrade fats; it is thermostable and therefore efficient when functioning at high temperatures, such as within the water network.</td>
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            <td>BBa_K258008</td>
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            <td>ABC transporter of <i>E. chrysanthemi</i></td>
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            <td>A type I secretion system used to export proteins with C-terminal fragments, such as TliA</td>
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            <td>BBa_K861060</td>
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            <td>PfadR promoter</td>
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            <td>An artificial promoter containing a tandem FadR binding site which is not affected by glucose concentration, oxidative stress and several other factors.</td>
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            <td>BBa_K861061</td>
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            <td>RFP generator of PfadR</td>
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            <td>When placed downstream of K861060, efficacy of the promoter can be tested by allowing visualisation of red fluorescence protein.</td>
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            <td>BBa_K1149021</td>
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            <td>Composite used with BBa_K258008</td>
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            <td>This construct allows production of a promoter, RBS and lipase ABC transporter recognition domain to allow lipid secretion outside of the cell.</td>
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            <td>BBa_K215107</td>
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            <td>Lipase ABC transporter recognition domain</td>
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            <td>This domain will bind the lipase to allow secretion.</td>
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          <td>BBa_K215002</td>
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          <td>pLac + RBS + Secretion Signal and Streptavidin Binding Tags</td>
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          <td>This generator has a promoter which is IPTG-inducible and a strong RBS to allow expression of our transporter.</td>
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        Alongside these existing parts, we are developing our own keratinase enzyme part, which we will submit to the registry as a new, documented BioBrick.
 
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      <h2>The Approach</h2>
 
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        Alongside the laboratory work to construct this system, the team are collaborating with the water industry and potential users of the system in order to develop an implementation device for its application in society. The broader impact of this device will then be considered from many different aspects to evaluate the product. As well as this, outreach activities within and outside of the University to promote synthetic biology will be carrier out. These aim to deepen understanding of the new technology and gauge interest and support to allow successful incorporation of it into society.
 
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      <h1 class="title">Meet the Team</h1>
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            <div class="caption"><h1>Ben Madden</h1><p>Hi I'm Ben, a third year Chemical Engineer</p>
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            <div class="caption"><h1>Lara Grew</h1><p>Hi I'm Lara, a second year Geneticist</p>
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            <div class="caption"><h1>Ben Lomax</h1><p>Hi I'm Ben, a first year MBB student</p>
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            <div class="caption"><h1>Erika Otaviano</h1><p>Hi I'm Erika, a third year BioEngineer</p>
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            <div class="caption"><h1>Alex Simpson</h1><p>Hi I'm Alex, a second year Aerospace Engineer</p>
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Revision as of 13:07, 6 August 2014

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Our modelling in this project has several aims :
  • To find the amount of DPP-IV reduction reached when the system reaches equilibrium
  • To find a way to control the level of DPP-IV reduction
  • To find the minimum number of RdRps, replicons, etc to be initially transfected into the cell, which are required to achieve a steady state for the system
  • To find out how long does it take for the system to reach equilibrium
  • To find out the level of reduction we need to treat diabetes
  • To find out how stable the system is (i.e. will the system only work in very specific situations, or in lots of different systems?)

We are currently using Simbiology in Matlab and Copasi to model the system. We are currently adapting several different models, which come from research into HCV replicons, to our system. If our models can be made to fit our experiments well, we may extend our project to try and find a way to control the level of DPP-IV which is reduced. In addition modelling the system will allow it to be better optimised in the future, and optimum values for constants such as the strength of the ribosome binding sites, and the number of siRNAs produced by each degradation, so that the effect of our biobrick can be optimised.

Initially we determined that our system should reach some equilibrium after a certain amount of time. This is because firstly, HCV is a successful virus, so the replicons should not completely degrade away as time goes to infinity. Secondly, since there are only a finite amount of resources within the cell, the number of replicons in the system cannot keep increasing forever. This means either the number of replicons must tend towards a certain constant (constant with respect to time), or the number of replicons should tend towards oscillations.


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