Team:Cambridge/Bioluminescence/Firefly Modelling

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{{:Team:Cambridge/Templates/headerbar|colour=#96d446|linkcolour=#6bbe00|title=Project 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.
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:  
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|700px]]
[[Image:Modelluccycle.jpg|center|700px]]
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Some of the parameters could be found in the litterature, but some of the parameters (namely the diffusion of Luciferin into the cell and the regeneration rate were inferred from experimental data.)
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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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We modelled the system both with and without the effect of the [https://2010.igem.org/Team:Cambridge/Bioluminescence/Luciferin_Regeneration Luciferase Regenerating Enzyme] (LRE.) The 4 Figures below show a comparison the model and our data for both cases. 
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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:Modellight.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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[[Image:Datawithoutreg.png|thumb|center|700px|'''Figure 2 - Light output as a function of time for [http://partsregistry.org/Part:BBa_K325108 P.Pyralis luciferase] under pBad promoter. Arabinose concentration is 10mM and D-Luciferin concentration is 100µM''']]
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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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[[Image:Modellight_with_regen.png|thumb|center|700px|'''Figure 3 - Model of the light output as a function of time with the effect of the LRE. ''']]
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[[Image:Datawithreg.png|thumb|center|700px|'''Figure 4 - Light output as a function of time for [http://partsregistry.org/Part:BBa_K325219 L. Cruciata luciferase with LRE] under pBad promoter. Arabinose concentration is 100 µM and D-Luciferin concentration is 1µM''']]
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Latest revision as of 02:41, 28 October 2010