Team:Manchester/Modelling

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            <p>
 
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The team planned and delivered 12 workshops for children aged 11-13 years old as part of the University of Manchester’s Science Stars event. We also held a poster stand at a Community Open Day that saw hundreds of people through its doors. Click here to learn more...
 
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                        <img src="https://static.igem.org/mediawiki/2013/2/26/Outreachthumb.jpg" height="230" width="150"/>     
 
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<a href="https://2013.igem.org/Team:Manchester/Outreach" class="myButton" >PUBLIC OUTREACH</a>
 
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  <img src="https://static.igem.org/mediawiki/2013/e/ea/Ethics.jpg" height="230" width="150"/>     
 
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Due to the nature of our chosen topic, ethics has played a major role in the development of the project. Here we address the potential problems of using synbio to produce a synthetic alternative to a natural project, and the ways that we would try to overcome them.
 
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            <a href="https://2013.igem.org/Team:Manchester/Ethics" class="myButton" > ETHICS </a>
 
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When the methods have been optimised, our project will have the potential to reach commercial success. Here we outline a business plan based around our synthetic alternative to palm oil, including likely start-up time, potential product markets and patenting information.
 
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                        <img src="https://static.igem.org/mediawiki/2013/2/25/Businessplan.jpg" height="230" width="150"/>     
 
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<a href="https://2013.igem.org/Team:Manchester/Collaboration" class="myButton" >MODELLING COLLABORATION </a>
 
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The Knowledge Deficit model describes the common misconception by scientists that ‘The Public’ is simply ignorant of science, and this is the root of all opposition. We had dialogue with numerous industry representatives and environmental activists, and learned that the truth is not as simple as this...
 
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            <a href="https://2013.igem.org/Team:Manchester/KnowledgeDeficit" class="myButton" > KNOWLEDGE DEFICIT ASSUMPTION </a>
 
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  <b><u>Key Achievements</u></b><br>
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<li>Produced the first kinetic model of the fatty acid biosynthesis pathway using uncertainty modelling</li>
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<li>Used molecular dynamics simulations to determine the optimal location for His-tag addition onto FabA</li>
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<li>Modelled the population dynamics of the sumatran orangutan to examine the effect of our project on the endangered species</li>
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<li>Generated a repository of modelling tutorials in collaboration with other UK iGEM teams</li>
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       <a href="https://2013.igem.org/Team:Manchester/Enzyme"><img src="https://static.igem.org/mediawiki/2013/4/4e/Enzymesensitivities.png" width="120" height="210" class="left"/></a>
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                 <p> Enzymes in the FAB pathway showed a lack of experimentally determined kinetic parameters. To account for this, we used probability distributions for each individual parameter defined with respect to the uncertainty of the value. We were then able to generate not one but a <i>series</i> of unbiased models to illustrate the FAB pathway. We believe that this innovative approach to modelling appropriately addresses uncertainties in biology and is important for use in future computational investigations.  
                 <p> Enzymes in the FAB pathway showed a lack of experimentally determined kinetic parameters. To account for this, we used probability distributions for each individual parameter defined with respect to the uncertainty of the value. We were then able to generate not one but a <i>series</i> of unbiased models to illustrate the FAB pathway. We believe that this innovative approach to modelling appropriately addresses uncertainties in biology and is important for use in future computational investigations.  
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         <a href="https://2013.igem.org/Team:Manchester/FabProteinModel"><img src="https://static.igem.org/mediawiki/2013/4/46/FabAman.png" width="120" height="210" class="left"/></a>
         <img src="https://static.igem.org/mediawiki/2013/4/48/FabA_cartoon_mesh.png" width="300" height="210" class="right"/>     
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                 <p> Trying to experimentally study the overexpression of some enzymes critically involved in palm oil synthesis, as predicted by our “system” level model isn’t easy, particularly when they are involved in cyclic reactions like FabA. Our strategy was to simply add a His-tag to the N-terminus and C-terminus of FabA, but to make it even more complex FabA is a homodimer. Therefore, we did another model but this time of the molecular dynamics kind to see which terminal, if any, would be best to add the His-tags to.
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                 <p>Trying to experimentally study the overexpression of some enzymes involved in palm oil synthesis, as predicted by our “system” level model isn’t easy, particularly when they are involved in cyclic reactions (eg FAB pathway). Our strategy was to simply add a His-tag to the N- and C-terminus of βHACdH, but to make it even more complex βHACdH is a homodimer. Therefore, we did another model but this time of the molecular dynamics kind to see which terminal, if any, would be best to add the His-tags to.
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       <a href="https://2013.igem.org/Team:Manchester/PopulationDynamics"><img src="https://static.igem.org/mediawiki/2013/8/84/DynamicMan.png" width="120" height="210" class="left"/></a>
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                 <p> As part of our Human Practices investigations, we created a series of in depth population dynamics models to show the impact that the palm oil industry has on the population of the  Sumatran Orangutan. We were then able to project this into the future to demonstrate a series of likely scenarios. Sadly, things are looking pretty bleak for the Orangutan - however, it appears there could be a way to save them...
                 <p> As part of our Human Practices investigations, we created a series of in depth population dynamics models to show the impact that the palm oil industry has on the population of the  Sumatran Orangutan. We were then able to project this into the future to demonstrate a series of likely scenarios. Sadly, things are looking pretty bleak for the Orangutan - however, it appears there could be a way to save them...
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       <a href="https://2013.igem.org/Team:Manchester/Collaboration"><img src="https://static.igem.org/mediawiki/2013/b/b1/ModellingMan1.png" width="120" height="210" class="left"/></a>
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                 <p> Here at Manchester iGEM team, we believe that modelling is a vital step in the production of any synthetic biology system. However, often the production of such models can be hindered or left out altogether due to lack of expertise and outside help. With this in mind, we enlisted the help of another two UK iGEM teams in a quest to educate the iGEM community about the software available to them.      </p>         
                 <p> Here at Manchester iGEM team, we believe that modelling is a vital step in the production of any synthetic biology system. However, often the production of such models can be hindered or left out altogether due to lack of expertise and outside help. With this in mind, we enlisted the help of another two UK iGEM teams in a quest to educate the iGEM community about the software available to them.      </p>         
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Latest revision as of 18:19, 27 October 2013

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Safety

Key Achievements
  • Produced the first kinetic model of the fatty acid biosynthesis pathway using uncertainty modelling
  • Used molecular dynamics simulations to determine the optimal location for His-tag addition onto FabA
  • Modelled the population dynamics of the sumatran orangutan to examine the effect of our project on the endangered species
  • Generated a repository of modelling tutorials in collaboration with other UK iGEM teams
  • Enzymes in the FAB pathway showed a lack of experimentally determined kinetic parameters. To account for this, we used probability distributions for each individual parameter defined with respect to the uncertainty of the value. We were then able to generate not one but a series of unbiased models to illustrate the FAB pathway. We believe that this innovative approach to modelling appropriately addresses uncertainties in biology and is important for use in future computational investigations.

    Trying to experimentally study the overexpression of some enzymes involved in palm oil synthesis, as predicted by our “system” level model isn’t easy, particularly when they are involved in cyclic reactions (eg FAB pathway). Our strategy was to simply add a His-tag to the N- and C-terminus of βHACdH, but to make it even more complex βHACdH is a homodimer. Therefore, we did another model but this time of the molecular dynamics kind to see which terminal, if any, would be best to add the His-tags to.

    As part of our Human Practices investigations, we created a series of in depth population dynamics models to show the impact that the palm oil industry has on the population of the Sumatran Orangutan. We were then able to project this into the future to demonstrate a series of likely scenarios. Sadly, things are looking pretty bleak for the Orangutan - however, it appears there could be a way to save them...

    Here at Manchester iGEM team, we believe that modelling is a vital step in the production of any synthetic biology system. However, often the production of such models can be hindered or left out altogether due to lack of expertise and outside help. With this in mind, we enlisted the help of another two UK iGEM teams in a quest to educate the iGEM community about the software available to them.