#soc{

margin-left:-15px;

.soc_1{

.soc_2{

.soc_3{

height:37vh;

<ul class="nav navbar-nav">

<li><div id="links_drop" class="dropdown">

<li><a id="links" href="https://2016.igem.org/Team:Exeter/Interlab">InterLab</a></li>

<li><div id="links_drop" class="dropdown">

<li><a id="links" style="background:none;line-height:0.7vh;margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Engagement">Public Engagement<br /><br /><br /> & Education</a></li><li><a id="links" style="margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Log">Log</a></li>

<li><div id="links_drop" class="dropdown">

<li><a id="links" style="margin:10px 0 30px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Awards">Awards</a></li>

<li><span style="margin:10px 0 30px 2px;padding:0;">Special pages</span></li>

<ul class="nav navbar-nav navbar-right">

<li style="height:50px;width:48px;"class="soc_1">

<a href="https://www.youtube.com/channel/UC31qfG4hnm8gRHDCkrBtAiQ">

<img id = "soc" src="https://static.igem.org/mediawiki/2016/2/23/You.png"/></a>

</li>

<li style="height:50px;width:48px;"class="soc_2">

<a href="https://www.facebook.com/ExeteriGEM2016/?ref=aymt_homepage_panel">

<img id = "soc" src="https://static.igem.org/mediawiki/2016/5/51/Fb.png"/></a>

</li>

<li style="height:50px;width:48px;"class="soc_3">

<a href="https://twitter.com/exeter_igem">

<img id = "soc" src="https://static.igem.org/mediawiki/2016/7/76/Twit.jpg"/></a>

</li>

</ul>

<a href="#section_1" class="banner_link col-xs-6 col-sm-3"><span class="oneline">Introduction</span></a>

<a href="#section_2" class="banner_link col-xs-6 col-sm-3"><span class="twoline">KillerRed/<br />KillerOrange</span></a>

<a href="#section_3" class="banner_link col-xs-6 col-sm-3"><span class="twoline">Enzymatic <br /> Killswitches</span></a>

<a href="#section_4" class="banner_link col-xs-6 col-sm-3"><span class="oneline">Section 4</span></a>

                 <p id="pp">At the outset, multiple assumptions were made to simplify the the system, enabling suitable definition of  appropriate variables and rates. Mutations were also ignored to eradicate this further layer of complexity. Mindful that the timeframe considered was much larger than the replication time of <i>E. coli</i>,  the amount of mRNA, Protein etc was adjusted accordingly by assuming that it splits evenly and halving the amount every time replication occurs, also affecting the amount of plasmids. However,  as cited in (Nordström and Dasgupta, 2006), the frequency of replication is variable to maintain a constant amount. Therefore, in the case of our plasmid pSB1C3, which had a high copy number ~300, the amount was kept constant even after replication of the <i>E. Coli</i>.</p>

.wrap ul{

.wrap ul li {

.wrap ul li:before {

                     <li>k6 is the rate of ros production</li>

                 <p id="pp">K1 was calculated to be 22.175s. This was achieved by taking the total number of base pairs of the plasmid (887) and dividing through by the transcription rate of 40 base pairs per second for the T7 promoter (García and Molineux, 1995).</p>

                 <p id="pp">K2 was found to be 3-8 minutes for 80% of mrna (Bernstein et al., 2002). 5 minutes was used as an approximation of the median time as the actual number fluctuates.</p>

                 <p id="pp">Simbiology, a modelling app for matlab, was used to model the flow diagram with the above rate parameters. Running the simulation, a rate for mrna production and protein production could be found. A few issues were initially identified, these being that the degradation times affected the transcription/translation rate directly and also that as soon as mrna production started, protein production was initialised. This suggested that even when the mrna is in the process of being transcribed, translation has started and we know this not to be the case as you can’t start transcription with a non integer amount of mRNA.

                 <p id="pp">To correct this, the mRNA needed to be a step function, so limiting the amount to whole integers and meaning that production of the protein was restricted until the first mrna was produced. However, this only served to add a delay onto the overall protein production and multiply it by the mRNA amount as seen in Figure 1. This highlights another problem. As we can see in Figure 2 below, we know that it takes ~28 s to produce a protein (K3) after the mRNA has been made, suggesting that it should occur at  ~54s. However, the second mRNA is produced in advance of this, increasing the rate at which the protein are produced and making the first protein at  ~53s. This correctly describes the overall rate of the system in producing proteins but is incorrect for finding the time at which they are made, as each mRNA is independent of any other. This means that each mRNA required  individual consideration based on each having a separate protein production mechanism that contributes to a total protein quantity. </p>

 

                <div class="col-xs-12" style="width:100%;position:relative;margin:auto;padding:0;">

<div class="graph_box_single col-xs-12">

<img src="https://static.igem.org/mediawiki/2016/1/17/T--Exeter--Modelling_GraphKRone.png">

<span>Figure 1: A graph showing the mRNA amount in blue over 100 seconds and the overall rate of Protein production in red over 100 seconds.</span>

</div>

</div>

 

                <div class="col-xs-12" style="width:100%;position:relative;margin:auto;padding:0;">

<div class="graph_box_single col-xs-12">

<img src="https://static.igem.org/mediawiki/2016/0/03/T--Exeter--Modelling_GraphKRtwo.png">

<span>Figure 1: A graph showing the mRNA amount in blue over 100 seconds and the overall rate of Protein production in red over 100 seconds.</span>

</div>

</div>

         <mi>&#x03BD;<!-- ν --></mi>

         <mo stretchy="false">&#x2192;<!-- → --></mo>

           <mo>&#x2217;<!-- ∗ --></mo>

           <mo>&#x2217;<!-- ∗ --></mo>

         <mo stretchy="false">&#x2192;<!-- → --></mo>

         <mi>&#x03BD;<!-- ν --></mi>

           <mo>&#x2217;<!-- ∗ --></mo>

         <mo stretchy="false">&#x2192;<!-- → --></mo>

             <mo>&#x2212;<!-- − --></mo>

           <mo>&#x2217;<!-- ∗ --></mo>

         <mo stretchy="false">&#x2192;<!-- → --></mo>

           <mo>&#x2217;<!-- ∗ --></mo>

             <mo>&#x2212;<!-- − --></mo>

           <mo>&#x2217;<!-- ∗ --></mo>

         <mo stretchy="false">&#x2192;<!-- → --></mo>

             <mo>&#x2212;<!-- − --></mo>

           <mo>&#x2217;<!-- ∗ --></mo>

         <mo stretchy="false">&#x2192;<!-- → --></mo>

             <mo>&#x2219;<!-- ∙ --></mo>

             <mo>&#x2212;<!-- − --></mo>

             <mo>&#x2212;<!-- − --></mo>

             <mo>&#x2212;<!-- − --></mo>

           <mo>&#x2217;<!-- ∗ --></mo>

         <mo stretchy="false">&#x2192;<!-- → --></mo>

             <mo>&#x2219;<!-- ∙ --></mo>

             <mo>&#x2212;<!-- − --></mo>

             <mo>&#x2212;<!-- − --></mo>

             <mo>&#x2212;<!-- − --></mo>

<div class="col-xs-12" style="width:100%;position:relative;margin:auto;padding:0;">

<div class="graph_box_single col-xs-12">

<img src="https://static.igem.org/mediawiki/2016/2/24/T--Exeter--Modelling_Enzyme_Graph3.png">

<span>Fig. 1. Using Michaelis-Menten kinetics the reaction rate of each lysozyme enzyme has  

been plotted for each peptidoglycan substrate concentration. The  

average reaction rate of $0.43\text{s}^{-1}$ occurs when the concentration is equal to $K_M = 0.0056\text{M}$.  

The maximum or initial concentration $[Pep]_{int} = 0.0083\text{M}$ of the substrate causes a reaction rate of $0.51\text{s}^{-1}$.</span>

</div>

<div class="graph_box col-xs-12">

<div class="graph_box col-xs-12">

between the two child cells, hence cell damage drops from almost 100% to 50%. The immediate concern  

<div>