Team:Cambridge/Bioluminescence/Firefly Modelling

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{{:Team:Cambridge/Templates/Topheader|header=Introduction}}
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<a href="http://cambridgeigem.org/igem10/In Vivo Cycle.xml" style="display:block; width:300px; padding-top:100px; margin-left:30px; margin-bottom:30px; background-image:url('https://static.igem.org/mediawiki/2010/7/76/Downloadsbml.png');background-repeat:no-repeat; background-position:top left;">Download model in SBML format
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We set out to build a mathematical model of our firefly system, featuring the activity of luciferase and luciferin regenerating enzyme.
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We modelled the Luciferin cycle as described in the [http://www.ncbi.nlm.nih.gov/pubmed/18949818 literature] We used data from [http://www.ncbi.nlm.nih.gov/pubmed/19859663 S. Inouye]'s review and the paper on [http://www.ncbi.nlm.nih.gov/pubmed/20655239 firefly luciferase inhibition] from J.M Leitão ''et al.''
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We modelled the Luciferin cycle as described by [http://www.ncbi.nlm.nih.gov/pubmed/18949818 Marques 2009] and others. We were assisted by data from [http://www.ncbi.nlm.nih.gov/pubmed/19859663 S. Inouye (2010)] on the catlysis of light emission by luciferase and  information [http://www.ncbi.nlm.nih.gov/pubmed/20655239 J.M Leitão ''et al.'' (2010)] on the inhibition of the enzyme.
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A Diagram of the model can be found below:  
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We used the [http://www.mathworks.com/products/simbiology/ Matlab Simbiology toolbox] to model the cycle. A diagram of the model we developed can be found below:  
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[[Image:Modelluccycle.jpg|center|500px]]
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[[Image:Modelluccycle.jpg|center|700px]]
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Some parameters were taken from literature.  However there was no clear data for others, such that we were only able to define some parameters in the light of experimental data.
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==Effect of LRE==
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While attempting to optimise our system we modelled the effect of [https://2010.igem.org/Team:Cambridge/Bioluminescence/Luciferin_Regeneration Luciferin Regenerating Enzyme (LRE)].
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[[Image:Cambridge-LREmodel.png|thumb|center|700px|'''Figure 1 - Model of the light output as a function of time without the effect of the LRE. ''']]
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Our model suggested that the LRE would make light output increase faster, peak higher and decay more slowly.  These were all qualities which suited us.
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==Validity of model==
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<p><h2 class="noline" style="margin-top:30px;">Luciferase alone</h2>
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<td><div class="center"><div class="thumb tnone"><div class="thumbinner" style="width:352px;"><a href="/Image:Modellight.png" class="image" title="Modellight.png"><img alt="" src="/wiki/images/thumb/b/b5/Modellight.png/350px-Modellight.png" width="350" height="234" border="0" class="thumbimage" /></a>  <div class="thumbcaption"><div class="magnify"><a href="/Image:Modellight.png" class="internal" title="Enlarge"><img src="/wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div></div></div></div></div>
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</td><td><div class="center"><div class="thumb tnone"><div class="thumbinner" style="width:352px;"><a href="/Image:Datawithoutreg.png" class="image" title="Datawithoutreg.png"><img alt="" src="/wiki/images/thumb/d/dd/Datawithoutreg.png/350px-Datawithoutreg.png" width="350" height="211" border="0" class="thumbimage" /></a>  <div class="thumbcaption"><div class="magnify"><a href="/Image:Datawithoutreg.png" class="internal" title="Enlarge"><img src="/wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div></div></div></div></div>
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<td><div style="margin:10px">Figure 1 - Model of the light output as a function of time without the effect of the LRE. </div>
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</td><td><div style="margin:10px">Figure 2 - Light output as a function of time for <a href="http://partsregistry.org/Part:BBa_K325108" class="external text" title="http://partsregistry.org/Part:BBa_K325108" rel="nofollow">P.Pyralis luciferase</a> under pBad promoter. Arabinose concentration is 10mM and D-Luciferin concentration is 100µM</div>
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<p><h2 class="noline" style="margin-top:30px;">Luciferase and LRE</h2>
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<td><div class="center"><div class="thumb tnone"><div class="thumbinner" style="width:352px;"><a href="/Image:Modellight_with_regen.png" class="image" title="Modellight with regen.png"><img alt="" src="/wiki/images/thumb/6/6d/Modellight_with_regen.png/350px-Modellight_with_regen.png" width="350" height="241" border="0" class="thumbimage" /></a>  <div class="thumbcaption"><div class="magnify"><a href="/Image:Modellight_with_regen.png" class="internal" title="Enlarge"><img src="/wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div></div></div></div></div>
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</td><td><div class="center"><div class="thumb tnone"><div class="thumbinner" style="width:352px;"><a href="/Image:Datawithreg.png" class="image" title="Datawithreg.png"><img alt="" src="/wiki/images/thumb/6/6b/Datawithreg.png/350px-Datawithreg.png" width="350" height="211" border="0" class="thumbimage" /></a>  <div class="thumbcaption"><div class="magnify"><a href="/Image:Datawithreg.png" class="internal" title="Enlarge"><img src="/wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div></div></div></div></div>
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<td><div style="margin:10px">Figure 3 - Model of the light output as a function of time with the effect of the LRE. </div>
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</td><td><div style="margin:10px"> Figure 4 - Light output as a function of time for <a href="http://partsregistry.org/Part:BBa_K325219" class="external text" title="http://partsregistry.org/Part:BBa_K325219" rel="nofollow">L. Cruciata luciferase with LRE</a> under pBad promoter. Arabinose concentration is 100 µM and D-Luciferin concentration is 1µM</div>
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Latest revision as of 02:41, 28 October 2010