Difference between revisions of "Team:IIT Kanpur/TestPage"

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<h1><font color="#008080">Model Overview</font> </h1></font></h1>
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<h2>1. Abstract</h2>
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<div class="Unindented">
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<p>In modeling, we obtain mathematical relationships between quantities in the system. Then, one can easily obtain the initial conditions that would lead to the desired outcome. The main variation in the inital condition is variation in the initial concentration of the inducer (AHL - Acyl-Homoserine-lactone), which can (mainly) vary the total bacteria living time. Because of the complexity of our model, we use an ODE (Ordinary Differential Equations) numerical solver we’ve written in matlab for obtaining final and graphical results. We present our system briefly and reactions, and then we compare the model and the experimental results for validation and conclusions.</p>
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</div>
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<h2>2.Introduction</h2>
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<div class="Unindented"><p>
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Our model has 2 main aspects: 1. Gene expression; 2. Plasmid loss. For the first aspect, we obtained the equations by applying enzyme kinetics and mass action on our reactions. For the second aspect, we obtain the equations from a typcial bacterial population growth and plasmid loss models.</p>
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</div>
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<h3 class="Subsection">
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2.1. Why Do We Need a Model?
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</h3>
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<div class="Unindented"><p>
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Our model is an integral part of our biological system. In order to use our kill switch properly, one needs to know exactly which initial conditions match the expected result. Using our model, one can easily obtain the initial concentrations to put in the kill switch activate it for the appropriate time. </p>
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</div>
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<div class="Indented"><p>
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The plasmid loss aspect of our model is an additional model that takes into account the fact that plasmid loss can occur and cause unexpected results. For example, Satellite Colonies (see &ldquo;Plasmid Loss&rdquo; page for more details), which can hurt the functioning of the kill switch.</p>
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</div>
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<h3 class="Subsection">
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2.2. Methods
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</h3>
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<div class="Unindented"><p>
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In this model, we described all the reactions and processes by ODEs (Ordinary Differential Equations). This method is suitable for describing dynamic systems and for easy simulation. This is the common procedure for describing dynamic systems in science, especially in biology. It enables predicting the behaviour of very complex dynamic systems, as long as we can describe how the system change at any given time. Our system is for sure complex and dynamic, so we use a set of ODE to describe it.</p>
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</div>
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<div class="Indented"><p>
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In order to achive a quantitive description of the reactions and processes, we use mainly the Law of Mass Action. This law, or principle, states that the rate of a reaction is proportional to the product of the masses (hence the name) or concentrations of the reactant. This law holds for system in a steady state and since we assume that are system is in a quasi steady state, i.e. the changes in it are relatively slow, we can use it. There are a few reaction for which we use other kinetic laws.</p>
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</div>
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<h3 class="Subsection">
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2.3. Our System
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</h3>
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<h4>
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2.3.1. In General
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</h4>
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<div class="Unindented"><p>
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Our system consists of an inducer (AHL from the Homoserine-Lactones group) and the genetic circuit that is inserted in a plasmid. In the circuit, there is a &ldquo;death protein&rdquo; (in this case, ccdB) which is responsible for the actual death. The precence of the inducer in the bacteria represses the expression of the death protein. Therefore, after the inducer is degraded, there is nothing that can repress the expression of the death gene, and the bacteria die.</p>
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</div>
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<h4>
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2.3.2. In Detail
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</h4>
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<div class="Unindented"><p>
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The AHL (inducer) binds to the protein LuxR and they form a complex. This complex binds to the pLux promoter and activates it. Then, the tetR protein is expressed, binds to the pTet promoter and deactivates it. As a result, the ccdb (&ldquo;death protein&rdquo;) will not be expressed. When the AHL is fully degreaded, there will be not AHL-LuxR complex to activate the pLux promoter, thus no tetR will be expressed, thus ccdB will be expressed, which will kill the bacteria.</p>
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</div>
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<h4>
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2.3.3. Note About Notations
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</h4>
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<div class="Unindented"><p>
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In this page we’ll use the (relatively) full  names for the substances and complexes. In the equations page we’ll use abbreviations which will be explained there. Please note that we sometime call the TetR repressor TRLV (TetR with tag LVA). It’s so because during the process of modelling our system we didn’t knew for sure which version of TetR we’ll finally use. In other words, for any purposes of the modelling TRLV and TetR are equivalent and are used interchangeably in this wiki. As you've seen in the description page, in the end we used TetR in our biological circuit.</p>
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</div>
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<div class="Indented"><p>
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Furthermore, the notations of in, out and sum are used in this page without much explanation, although they aren’t crucial for understanding our model. Thorough explanation of them available in the Documents section</p>
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</div>
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<h3 class="Subsection">
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3. Reactions
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</h3>
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<img src="https://static.igem.org/mediawiki/2015/7/70/Technion_HS_2015_reactions.png" style="width:80%">
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<p class=MsoListParagraphCxSpFirst dir=LTR style='margin-top:0cm;margin-right:
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.minipic {
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0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
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cursor:pointer;}
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direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
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115%'>i.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
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115%'>AHL self-degradation. </span></p>
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<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
 
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direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
 
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115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
 
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
 
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115%'>Law: Mass action</span></p>
 
  
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<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
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body {
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0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
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width:100%;
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direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
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margin:0 auto;
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115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
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}
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
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115%'>Explanation: Each molecule of AHL has a certain probability to degrade,
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hence the corresponding change rate in the amount of the AHL is proportional to
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the amount of AHL in all the cells. The coefficient is noted by C2 for cell
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internal AHL and C2' for cell external AHL. </span></p>
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<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
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.minipic {
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0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
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cursor:pointer;}
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direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
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115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
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115%'>Results:<br>
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<img src="https://static.igem.org/mediawiki/2015/1/1d/Technion_HS_2015_Reaction_1.png" class="term"><br/><img src="https://static.igem.org/mediawiki/2015/0/04/Technion_HS_2015_Reaction_2.png
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" class="term"></span></p>
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<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
 
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0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
 
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
 
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115%'>ii.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
 
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115%'>Diffusion of AHL</span></p>
 
  
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<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
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.unit {
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0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
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display:inline-block;
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direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
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vertical-align: top;
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115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
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padding:0px;
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
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height:300px;
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115%'>Law: Simple passive diffusion</span></p>
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<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
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}
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0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
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direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
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115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
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115%'>Explanation: Will be explained in the processes section.</span></p>
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<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
 
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0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
 
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direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
 
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115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
 
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
 
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115%'>Results:<br>
 
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Change in external AHL concentration:<br>
 
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<img src="https://static.igem.org/mediawiki/2015/1/16/Technion_HS_2015_Reaction_3.png" class="term"><br>
 
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Change in total amount inside of AHL inside all the cells:<br>
 
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<img src="https://static.igem.org/mediawiki/2015/7/7d/Technion_HS_2015_Reaction_4.png" class="term"> </span></p>
 
  
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<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
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#hover-contentone, #hover-contenttwo, #hover-contentthree, #hover-contentfour, #hover-contentfive {
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0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
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    opacity:0;
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direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
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    position:absolute;
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115%'>iii.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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}
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
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115%'>AHL degradation by AiiA</span></p>
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<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
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.parent:hover {
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0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
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transform:scale(1.3)
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direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
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}
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115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
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115%'>Law: Michaelis Menten</span></p>
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<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
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</style>
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0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
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</head>
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direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
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115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
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115%'>Explanation: AiiA is an enzyme, and simple Mass Action doesn't work well
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for enzymatic reactions. The reason for it is the fact that the enzyme and the
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substrate form a complex, which is then converted to a product and the original
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enzyme. Therefore, two mass actions are required to describe this process, but
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under quasi-steady-state assumption we can derive a single equation, which is
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the Michaelis Menten law. It has two parameters, the maximal reaction rate and
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the turnover number.</span></p>
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<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
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<body>
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<center><div>
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direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
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<h3 style="text-align:center;">Click on the collaboration to read about it.</h3>
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115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
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<div class = "unit" style = "margin:0px 125px 0px 0px">
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
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    <div id = "parentfour" class = "parent">
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115%'>Results:<br>
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    <center id = "minfour"  class = "mini" style = "color:#760E18; padding:30px 0px; font-size:300%;">Survey</center>
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<img src="https://static.igem.org/mediawiki/2015/4/40/Technion_HS_2015_Reaction_5.png" class="term"></span></p>
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    <center><img class = "minipic" id = "minifour" src = "https://static.igem.org/mediawiki/2018/thumb/e/e6/T--IIT_Kanpur--Collab_SurveyIcon.png/600px-T--IIT_Kanpur--Collab_SurveyIcon.png" style = "width:170px; padding:0px;"></center>
 +
    </div>  
  
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<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
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</div>
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0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
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direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
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115%'>iv.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
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115%'>Pairing of AHL and LuxR into AHL-LuxR complex</span></p>
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<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
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<div class = "unit">
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0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
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    <div id = "parentone" class = "parent">
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direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
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    <center id = "minone"  class = "mini" style = "color:#0071a7; padding:30px 0px; font-size:300%;">Ruia-Mumbai</center>
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115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
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    <center><img class = "minipic" id = "minione" src = "https://static.igem.org/mediawiki/2018/thumb/5/57/T--IIT_Kanpur--Collab_RuiaIcon.png/611px-T--IIT_Kanpur--Collab_RuiaIcon.png" style = "width:170px; padding:0px;"></center>
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
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    </div>  
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115%'>Law: Mass action</span></p>
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<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
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</div>
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direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
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<div class = "unit" style = "margin:0px 125px 0px 125px;">
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115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
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    <div id = "parenttwo" class = "parent">
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
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    <center id = "mintwo" class = "mini" style = "color:#bd162a; padding:30px 0px; font-size:300%;">IISER-Bhopal</center>
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115%'>Explanation: The chance of a molecule of AHL to meet a molecule of LuxR
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    <center><img class = "minipic" id = "minitwo" src = "https://static.igem.org/mediawiki/2018/6/66/T--IIT_Kanpur--Collab_iiserbIcon.png" style = "width:170px; padding:0px;"></center>
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is proportional to both the concentration of AHL and LuxR (the more AHL you
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    </div>
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have, the higher the chance for reaction between AHL and LuxR). We get that the
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reaction rate is proportional to the product of the concentrations of AHL and
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LuxR.</span></p>
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<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
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</div>
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direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
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115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
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115%'>Results:<br>
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<img src="https://static.igem.org/mediawiki/2015/d/d4/Technion_HS_2015_Reaction_6.png" class="term"></span></p>
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<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
 
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0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
 
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direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
 
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115%'>v.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
 
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115%'>Disassociation of the AHL-LuxR complex to its components</span></p>
 
  
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<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
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<div class = "unit" style = "margin:0px 125px 0px 0px;">
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    <div id = "parentthree" class = "parent">
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direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
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    <center id = "minthree" class = "mini" style = "color:#507f54; padding:30px 0px; font-size:300%;">IISER-Mohali</center>
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115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
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    <center><img class = "minipic" id = "minithree" src = "https://static.igem.org/mediawiki/2018/5/53/T--IIT_Kanpur--Collab_iisermIcon.png" style = "width:170px; padding:0px;"></center>
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
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    </div>
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115%'>Law: Mass action</span></p>
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<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
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</div>
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0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
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direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
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115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
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115%'>Explanation: Each AHL-LuxR complex has a certain probability to
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disassociate, hence the corresponding change rate in the amount of the AHL is
+
−
proportional to the amount of AHL-LuxR. The coefficient is denoted by C4.</span></p>
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<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
 
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0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
 
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direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
 
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115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
 
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</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
 
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115%'>Results:<br>
 
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<img src="https://static.igem.org/mediawiki/2015/8/8a/Technion_HS_2015_Reaction_7.png" class="term"></span></p>
 
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
<div class = "unit">
−
0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
+
    <div id = "parentfive" class = "parent">
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
    <center id = "minfive" class = "mini" style = "color:#507f94; padding:30px 0px; font-size:300%;">TecCEM</center>
−
115%'>vi.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+
    <center><img class = "minipic" id = "minifive" src = "https://static.igem.org/mediawiki/2018/d/db/T--IIT_Kanpur--Collab_teccemIcon.png" style = "width:170px; padding:0px;"></center>
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
    </div>
−
115%'>Pairing of 2 AHL-LuxR complexes into the dimer (AHL-LuxR)<sub>2</sub></span></p>
+
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
</div>
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Law: Mass action</span></p>
+
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
</div></center>
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Explanation: The chance of a molecule of AHL-LuxR complex to meet another
+
−
one is proportional, again, to the product of their concentrations, (which this
+
−
time are equal and we get [AHL-LuxR]^2).</span></p>
+
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
 
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
 
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
 
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
 
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
 
−
115%'>Results:<br>
 
−
<img src="https://static.igem.org/mediawiki/2015/8/8e/Technion_HS_2015_Reaction_8.png" class="term"></span></p>
 
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
 
−
0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
 
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
 
−
115%'>vii.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
 
−
115%'>Disassociation of (AHL-LuxR)<sub>2</sub> to its components</span></p>
 
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
<div id="hover-contentone" style="padding:0px 250px 150px 150px;">
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
<div>
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
    <center style = "font-size:280%; font-family:Trebuchet MS; color:#0071A7">Mentoring Team Ruia-Mumbai</center>
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
    <br>
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
    <center><hr style= "width:500px; height: 3px; background-color:#0071A7"></center>
−
115%'>Law: Mass action</span></p>
+
</div>
 +
<p style = "color:#0071A7; font-size:150%; padding:0% 8% 3% 5%;">Team Ruia-Mumbai have been working to create a synthetic biological device to degrade catechu, by extracellular expression of genes responsible for breaking the flavan 3,4-diol bonds in polyphenols which is one of the compounds responsible for the red stains caused by the same.<br>
 +
They approached us regarding mentorship at the beginning of July 2018. In our first meeting we got acquainted with their project and suggested different methodologies they could follow to make their project more robust for example, we discussed in detail about secretion tag to facilitate extracellular secretion of their protein of interest and suggested corresponding literature. After that, we organized regular video conference meetings between July and October to discuss the progress of their project and other aspects of iGEM competition such as Interlab and Human Practices. We discussed technical doubts they faced in Interlab and also shared data to validate the results.<br>
 +
Our team also helped Team Ruia-Mumbai with experimentation protocols like we shared our protocol for preparing competent cells. We suggested changes to their protocols to optimize experimentation for cloning of their construct. We also thoroughly discussed modeling kinetics of their enzyme but weren’t able to continue it due to time constraints.
 +
</p>
 +
<img src = "https://static.igem.org/mediawiki/2018/1/14/T--IIT_Kanpur--Collab_Ruia2.png" height="200" width="300" style = "margin-left: auto;margin-right: auto;padding:0% 0% 0% 0%;border:3px solid black"></img>
 +
<img src = "https://static.igem.org/mediawiki/2018/1/1d/T--IIT_Kanpur--Collab_Ruia1.png" height="200" width="300" style = "margin-left: auto;margin-right: auto;padding:0% 0% 0% 0%;border:3px solid black"></img>
 +
</div>
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
 
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
 
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
 
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
 
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
 
−
115%'>Explanation: Each (AHL-LuxR)<sub>2</sub> dimer has a certain probability
 
−
to disassociate, hence the corresponding change rate in the amount of the AHL
 
−
is proportional to the total amount of AHL-LuxR in the cells. The coefficient
 
−
is denoted by C6.</span></p>
 
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
<div id="hover-contenttwo" style="padding:0px 250px 50px 150px;">
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
<div>
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
    <center style = "font-size:280%; font-family:Trebuchet MS; color:#bd162a;">Discussions with IISER-Bhopal</center>
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
    <br>
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
    <center><hr style= "width:500px; height: 3px; background-color:#bd162a;"></center>
−
115%'>Results:<br>
+
−
<img src="https://static.igem.org/mediawiki/2015/0/0b/Technion_HS_2015_Reaction_9.png" class="term"></span></p>
+
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
<p style = "color:#bd162a; font-size:150%; padding:2% 5% 1% 8%;">We have been in constant touch with Team IISER-Bhopal starting from the month of May. We discussed each other’s project and helped sort out technical problems related to it.<br>
−
0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
+
IISER Bhopal suggested an initiative to increase the outreach of each other’s projects. In this initiative both the teams exchanged slides mentioning brief overview about their project and introduced each other’s idea in public engagement events like Lecture Series conducted by IIT Kanpur and iGEM Day (25th August 2018) organized by IISER Bhopal.<br>
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
Both teams shared each others’ Interlab data and interpretations to get a deeper understanding of the acquired data from experiments.  <br>
−
115%'>viii.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+
We also helped Team IISER-Bhopal with their US VISA procedures which eased their application process.    
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
Along the way, we also cleared their other technical doubts and both the teams helped each other out whenever possible.
−
115%'>(AHL-LuxR)<sub>2</sub> binds to the pLuxR promoter</span></p>
+
</p>
 +
<br>
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
<img src = "" width = 40% style = "padding:5% 5% 10% 3%; float:center;">
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
</div>
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
</div>
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Law: Mass action</span></p>
+
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
<div id="hover-contentthree" style="padding:0px 250px 50px 150px;">
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
<div>
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
    <center style = "font-size:280%; font-family:Trebuchet MS; color:#507f54;">Meeting with IISER-Mohali</center>
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
    <br>
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
    <center><hr style= "width:500px; height: 3px; background-color:#507f54;"></center>
−
115%'>Explanation: The activation rate is proportional to the product of the
+
−
concentrations of the dimer and the number of plasmid plasmids with pLuxR
+
−
promoters. It will be explained later in the processes section.</span></p>
+
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
 
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
 
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
 
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
 
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
 
−
115%'>Results:<br>
 
−
<img src="https://static.igem.org/mediawiki/2015/c/c3/Technion_HS_2015_Reaction_10.png" class="term"></span></p>
 
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
<p style = "color:#507f54; font-size:150%; padding:0% 8% 0% 5%;">We recently had a discussion with Team IISER-Mohali in which we discussed each other’s project. It was an interesting session, and we found their project an innovative one. Our session was focussed on critically analyzing each other’s project and discussing potential questions that can come up during Jamboree presentation. It helped both our teams to prepare robustly for the same.
−
0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
+
Since the team had participated in iGEM 2017, they shared their experience about judging criteria, presentation and poster session at the Giant Jamboree which was helpful and gave us additional insight into the competition.
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
</p>
−
115%'>ix.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+
<br>
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
</div>
−
115%'>(AHL-LuxR)<sub>2 </sub>unbinds from the pLuxR promoter</span></p>
+
</div>
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
 
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
 
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
 
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
 
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
 
−
115%'>Law: Mass action</span></p>
 
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
 
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
 
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
 
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
 
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
 
−
115%'>Explanation: Each activated promoter has a certain probability to
 
−
deactivate and to release its (AHL-LuxR)<sub>2</sub>, and therefore the rate of
 
−
this process is proportional to the number of activated promoters. It will be
 
−
explained later in the processes section.</span></p>
 
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
 
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
 
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
 
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
 
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
 
−
115%'>Results:<br>
 
−
<img src="https://static.igem.org/mediawiki/2015/0/01/Technion_HS_2015_Reaction_11.png" class="term"></span></p>
 
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
 
−
0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
 
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
 
−
115%'>x.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
 
−
115%'>Transcription of RNA<sub>TRLV</sub> by pLuxR promoter without the complex</span></p>
 
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
<div id="hover-contentfive" style="padding:0px 250px 50px 150px;">
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
<div>
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
    <center style = "font-size:280%; font-family:Trebuchet MS; color:#507f54;">Accepting BioBrick Part from Team TecCEM</center>
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
    <br>
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
    <center><hr style= "width:500px; height: 3px; background-color:#507f54;"></center>
−
115%'>Law: Mass action</span></p>
+
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
<p style = "color:#507f54; font-size:150%; padding:0% 8% 0% 5%;">In iGEM 2015, Team TecCEM_HS participated and worked upon developing a system to degrade SDS, similar to our project in idea. A member of their team, Borreguin JC,  is participating in this year’s Team TecCEM as well, and he was helpful in figuring out the issues they faced in past project so that we could avoid committing them.<br>
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
Since isolating the sdsA gene from Pseudomonas aeruginosa was difficult, we contacted them if they could provide us with the plasmid containing the same. They gifted us the BioBrick(BBa_K1629002) which they had submitted in iGEM with the corresponding gene, thus helping us move forward with our project.
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
</p>
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
<br>
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Explanation: Each inactivated promoter transcripts mRNA in a certain rate.
+
−
This rate is called leakiness. We multiply it by the number of inactivated LuxR
+
−
promoters to get the total rate. It will be explained further in the processes
+
−
section.</span></p>
+
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
<img src = "" width = 40% style = "padding:5% 5% 10% 3%; float:center;">
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
</div>
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
</div>
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Results:<br>
+
−
<img src="https://static.igem.org/mediawiki/2015/a/a0/Technion_HS_2015_Reaction_13.png" class="term"></span></p>
+
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
 
−
0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
 
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
 
−
115%'>xi.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
 
−
115%'>Transcription of RNA<sub>TRLV</sub> by pLuxR promoter with the complex</span></p>
 
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
<div id="hover-contentfour" style="padding:0px 250px 50px 150px;">
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
<div>
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
<center style = "font-size:280%; font-family:Trebuchet MS; color:#760E18;">Survey amongst iGEM 2018 teams</center>
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
    <br>
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
    <center><hr style= "width:500px; height: 3px; background-color:#760E18;"></center>
−
115%'>Law: Mass action</span></p>
+
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
<p style = "color:#760E18; font-size:150%; padding:0% 8% 0% 5%;">A great idea is great not because of its technicalities, but because of the impact it has on the people around it.<br>
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
To gather an understanding of how water pollution affects different parts of the world, we conducted a survey amongst iGEM 2018 teams to get their views on the problem in their regions. Members of 18 teams filled us in with their knowledge which has given us a wider perspective of the problem around the globe.<br>
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
</p><embed src="https://static.igem.org/mediawiki/2018/a/a0/T--IIT_Kanpur--Collab_Survey.pdf" width="550px" height="600px" /><p style="float:right;color:#760E18; font-size:150%;">
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
The teams that did the needful are:<br><br>
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
&#8594;Team Ruia-Mumbai<br>
−
115%'>Explanation: Each activated promoter transcripts mRNA in a certain rate.
+
&#8594;CPU_CHINA<br>
−
We multiply it by the number of activated LuxR promoters to get the total rate.
+
&#8594;Pasteur Paris 2018<br>
−
It will be explained further in the processes section.</span></p>
+
&#8594;METU HS Ankara iGEM 2018<br>
 +
&#8594;Hawaii iGEM Team<br>
 +
&#8594;UPF_CRG_Barcelona<br>
 +
&#8594;Lambert iGEM<br>
 +
&#8594;AFCM-Egypt<br>
 +
&#8594;iGEM Bielefeld-CeBiTec 2018<br>
 +
&#8594;Tacoma_RAINMakers<br>
 +
&#8594;NWU-China<br>
 +
&#8594;TecCem Mexico<br>
 +
&#8594;TecCEM<br>
 +
&#8594;iGEM Pasteur Paris 2018<br>
 +
&#8594;SKLMT-China<br>
 +
&#8594;TUST China<br>
 +
&#8594;METU_HS_Ankara<br>
 +
&#8594;ICT-Mumbai<br>
 +
</p>
 +
</div>
 +
</div>
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
 
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
 
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
 
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
 
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
 
−
115%'>Results:<br>
 
−
<img src="https://static.igem.org/mediawiki/2015/f/f8/Technion_HS_2015_Reaction_14.png" class="term"></span></p>
 
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
 
−
0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
 
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
 
−
115%'>xii.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
 
−
115%'>Translation of TRLV from RNA<sub>TRLV</sub></span></p>
 
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
<div style = "height:500px;"></div>
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
</body>
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Law: Mass action</span></p>
+
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
  <script type="text/javascript">
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
$(document).ready(
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
    function(){
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
  $("#parentone").click(function () {
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
      $('#parentone').removeClass('parent');
−
115%'>Explanation: mRNA of TetR translates to the protein TetR in a certain
+
      $('#parenttwo').addClass('parent');
−
rate. We multiply it by the concentration of RNA to get the total rate. It will
+
      $('#parentthree').addClass('parent');
−
be explained further in the processes section.</span></p>
+
      $('#parentfour').addClass('parent');
 +
      $('#parentfive').addClass('parent');
 +
            $('#minone').animate({'font-size':'200%'}, 500);
 +
            $('#minone').animate({'padding':'10px 0px 20px 0px'}, 500);
 +
            $('#minone').css('padding', '10px 0px 20px 0px');
 +
            $('#minione').animate({"width":"150px"}, 500);
 +
            $('#minfour').animate({'font-size':'150%'}, 500); 
 +
            $('#minfour').css('padding', '20px 0px');      
 +
            $('#minifour').animate({"width":"100px"}, 500);
 +
        $('#minfive').animate({'font-size':'150%'}, 500); 
 +
            $('#minfive').css('padding', '20px 0px');       
 +
            $('#minifive').animate({"width":"100px"}, 500);
 +
            $('#minthree').animate({'font-size':'150%'}, 500); 
 +
            $('#minthree').css('padding', '20px 0px');      
 +
            $('#minithree').animate({"width":"100px"}, 500);
 +
            $('#mintwo').animate({'font-size':'150%'}, 500); 
 +
            $('#mintwo').css('padding', '20px 0px');      
 +
            $('#minitwo').animate({"width":"100px"}, 500);
 +
            $('#hover-contentone').animate({'opacity':'1'}, 1000);
 +
            $('#hover-contenttwo').animate({'opacity':'0'}, 1000);
 +
            $('#hover-contentthree').animate({'opacity':'0'}, 1000);
 +
            $('#hover-contentfour').animate({'opacity':'0'}, 1000);
 +
        $('#hover-contentfive').animate({'opacity':'0'}, 1000);
 +
 
 +
      $('#instruct').hide(600);
 +
        });
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
    });
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
</script>
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Results:<br>
+
−
<img src="https://static.igem.org/mediawiki/2015/b/b3/Technion_HS_2015_Reaction_15.png" class="term"></span></p>
+
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
<script type="text/javascript">
−
0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
+
$(document).ready(
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
    function(){
−
115%'>xiii.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+
  $("#parenttwo").click(function () {
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
      $('#parenttwo').removeClass('parent');
−
115%'>TRLV self-degradation</span></p>
+
      $('#parentone').addClass('parent');
 +
      $('#parentthree').addClass('parent');
 +
      $('#parentfour').addClass('parent');
 +
      $('#parentfive').addClass('parent');
 +
            $('#mintwo').animate({'font-size':'200%'}, 500);
 +
            $('#mintwo').animate({'padding':'10px 0px 20px 0px'}, 500);
 +
            $('#mintwo').css('padding', '10px 0px 20px 0px');
 +
            $('#minitwo').animate({"width":"150px"}, 500);
 +
            $('#minfour').animate({'font-size':'150%'}, 500); 
 +
            $('#minfour').css('padding', '20px 0px');      
 +
            $('#minifour').animate({"width":"100px"}, 500);
 +
        $('#minfive').animate({'font-size':'150%'}, 500); 
 +
            $('#minfive').css('padding', '20px 0px');       
 +
            $('#minifive').animate({"width":"100px"}, 500);
 +
            $('#minthree').animate({'font-size':'150%'}, 500);
 +
            $('#minthree').css('padding', '20px 0px');      
 +
            $('#minithree').animate({"width":"100px"}, 500);
 +
            $('#minone').animate({'font-size':'150%'}, 500);
 +
            $('#minone').css('padding', '20px 0px');      
 +
            $('#minione').animate({"width":"100px"}, 500);
 +
            $('#hover-contenttwo').animate({'opacity':'1'}, 1000);
 +
            $('#hover-contentone').animate({'opacity':'0'}, 1000);
 +
            $('#hover-contentthree').animate({'opacity':'0'}, 1000);
 +
            $('#hover-contentfour').animate({'opacity':'0'}, 1000);
 +
        $('#hover-contentfive').animate({'opacity':'0'}, 1000);
 +
 
 +
      $('#instruct').hide(600);
 +
        });
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
    });
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
</script>
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
<script type="text/javascript">
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
$(document).ready(
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
    function(){
−
115%'>Law: Mass action</span></p>
+
  $("#parentthree").click(function () {
 +
      $('#parentthree').removeClass('parent');
 +
      $('#parentone').addClass('parent');
 +
      $('#parenttwo').addClass('parent');
 +
      $('#parentfour').addClass('parent');
 +
      $('#parentfive').addClass('parent');
 +
            $('#minthree').animate({'font-size':'200%'}, 500);
 +
            $('#minthree').animate({'padding':'10px 0px 20px 0px'}, 500);
 +
            $('#minthree').css('padding', '10px 0px 20px 0px');
 +
            $('#minithree').animate({"width":"150px"}, 500);
 +
            $('#minfour').animate({'font-size':'150%'}, 500); 
 +
            $('#minfour').css('padding', '20px 0px');      
 +
            $('#minifour').animate({"width":"100px"}, 500);
 +
        $('#minfive').animate({'font-size':'150%'}, 500);
 +
            $('#minfive').css('padding', '20px 0px');       
 +
            $('#minifive').animate({"width":"100px"}, 500);
 +
            $('#mintwo').animate({'font-size':'150%'}, 500); 
 +
            $('#mintwo').css('padding', '20px 0px');       
 +
            $('#minitwo').animate({"width":"100px"}, 500);
 +
            $('#minone').animate({'font-size':'150%'}, 500); 
 +
            $('#minone').css('padding', '20px 0px');       
 +
            $('#minione').animate({"width":"100px"}, 500);
 +
            $('#hover-contentthree').animate({'opacity':'1'}, 1000);
 +
            $('#hover-contentone').animate({'opacity':'0'}, 1000);
 +
            $('#hover-contenttwo').animate({'opacity':'0'}, 1000);
 +
            $('#hover-contentfour').animate({'opacity':'0'}, 1000);
 +
        $('#hover-contentfive').animate({'opacity':'0'}, 1000);
 +
 
 +
      $('#instruct').hide(600);
 +
        });
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
    });
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
</script>
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
<script type="text/javascript">
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
$(document).ready(
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
    function(){
−
115%'>Explanation: Each molecule of TRLV has a certain probability to degrade,
+
  $("#parentfour").click(function () {
−
hence the corresponding change rate in the amount of the TRLV is proportional
+
      $('#parentfour').removeClass('parent');
−
to the amount of TRLV all the cells.</span></p>
+
      $('#parentone').addClass('parent');
 +
      $('#parenttwo').addClass('parent');
 +
      $('#parentthree').addClass('parent');
 +
      $('#parentfive').addClass('parent');
 +
            $('#minfour').animate({'font-size':'200%'}, 500);
 +
            $('#minfour').animate({'padding':'10px 0px 20px 0px'}, 500);
 +
            $('#minfour').css('padding', '10px 0px 20px 0px');
 +
            $('#minifour').animate({"width":"150px"}, 500);
 +
            $('#minthree').animate({'font-size':'150%'}, 500); 
 +
            $('#minthree').css('padding', '20px 0px');      
 +
            $('#minithree').animate({"width":"100px"}, 500);
 +
        $('#minfive').animate({'font-size':'150%'}, 500);
 +
            $('#minfive').css('padding', '20px 0px');       
 +
            $('#minifive').animate({"width":"100px"}, 500);
 +
            $('#mintwo').animate({'font-size':'150%'}, 500); 
 +
            $('#mintwo').css('padding', '20px 0px');       
 +
            $('#minitwo').animate({"width":"100px"}, 500);
 +
            $('#minone').animate({'font-size':'150%'}, 500); 
 +
            $('#minone').css('padding', '20px 0px');       
 +
            $('#minione').animate({"width":"100px"}, 500);
 +
            $('#hover-contentfour').animate({'opacity':'1'}, 1000);
 +
            $('#hover-contentone').animate({'opacity':'0'}, 1000);
 +
            $('#hover-contenttwo').animate({'opacity':'0'}, 1000);
 +
            $('#hover-contentthree').animate({'opacity':'0'}, 1000);
 +
        $('#hover-contentfive').animate({'opacity':'0'}, 1000);
 +
 
 +
      $('#instruct').hide(600);
 +
        });
  
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
    });
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
</script>
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
<script type="text/javascript">
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
$(document).ready(
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
    function(){
−
115%'>Results:<br>
+
  $("#parentfive").click(function () {
−
<img src="https://static.igem.org/mediawiki/2015/d/d3/Technion_HS_2015_Reaction_16.png" class="term"></span></p>
+
      $('#parentfive').removeClass('parent');
−
 
+
      $('#parentone').addClass('parent');
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
      $('#parenttwo').addClass('parent');
−
0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
+
      $('#parentthree').addClass('parent');
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
      $('#parentfour').addClass('parent');
−
115%'>xiv.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+
            $('#minfive').animate({'font-size':'200%'}, 500);
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
            $('#minfive').animate({'padding':'10px 0px 20px 0px'}, 500);
−
115%'>TRLV binds to the pTetR repressor </span></p>
+
            $('#minfive').css('padding', '10px 0px 20px 0px');
−
 
+
            $('#minifive').animate({"width":"150px"}, 500);
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
            $('#minthree').animate({'font-size':'150%'}, 500);
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
            $('#minthree').css('padding', '20px 0px');      
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
            $('#minithree').animate({"width":"100px"}, 500);
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
        $('#minfour').animate({'font-size':'150%'}, 500);
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
            $('#minfour').css('padding', '20px 0px');      
−
115%'>Law: Mass action</span></p>
+
            $('#minifour').animate({"width":"100px"}, 500);
−
 
+
            $('#mintwo').animate({'font-size':'150%'}, 500);
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
            $('#mintwo').css('padding', '20px 0px');      
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
            $('#minitwo').animate({"width":"100px"}, 500);
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
            $('#minone').animate({'font-size':'150%'}, 500);
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
            $('#minone').css('padding', '20px 0px');      
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
            $('#minione').animate({"width":"100px"}, 500);
−
115%'>Explanation: The activation rate is proportional to the product of the
+
            $('#hover-contentfive').animate({'opacity':'1'}, 1000);
−
concentrations of the dimer and the number of plasmid plasmids with pTetR promoters.
+
            $('#hover-contentone').animate({'opacity':'0'}, 1000);
−
It will be explained later in the processes section.</span></p>
+
            $('#hover-contenttwo').animate({'opacity':'0'}, 1000);
−
 
+
            $('#hover-contentthree').animate({'opacity':'0'}, 1000);
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
        $('#hover-contentfour').animate({'opacity':'0'}, 1000);
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
 
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
      $('#instruct').hide(600);
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
        });
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Results:<br>
+
−
<img src="https://static.igem.org/mediawiki/2015/6/67/Technion_HS_2015_Reaction_17.png" class="term"></span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%'>xv.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>TRLV unbinds from the pLuxR repressor</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Law: Mass action</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Explanation: Each activated promoter has a certain probability to
+
−
deactivate and to release its TRLV, and therefore the rate of this process is proportional
+
−
to the number of activated promoters. It will be explained later in the
+
−
processes section.</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Results:<br>
+
−
<img src="https://static.igem.org/mediawiki/2015/e/e0/Technion_HS_2015_Reaction_18.png" class="term"></span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%'>xvi.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Transcription of RNA<sub>ccdB</sub> by ptetR promoter without the TRLV</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Law: Mass action</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Explanation: For each inactivated repressor there is transcription to mRNA
+
−
in a certain rate. We multiply it by the number of inactivated ptetR promoters
+
−
to get the total rate. It will be explained further in the processes section.</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Results:<br>
+
−
<img src="https://static.igem.org/mediawiki/2015/7/74/Technion_HS_2015_Reaction_19.png" class="term"></span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%'>xvii.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Transcription of RNA<sub>ccdB</sub> by ptetR promoter with the TRLV</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Law: Mass action</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Explanation: For each activated repressor there is still transcription to
+
−
mRNA in a certain rate. We multiply it by the number of activated ptetR promoters
+
−
to get the total rate. It will be explained further in the processes section.</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Results:<br>
+
−
<img src="https://static.igem.org/mediawiki/2015/d/d6/Technion_HS_2015_Reaction_20.png" class="term"></span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%'>xviii.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Translation of ccdB from RNA<sub>ccdB</sub></span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Law: Mass action</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Explanation: mRNA of ccdb translates to the protein ccdb in a certain
+
−
rate. We multiply it by the concentration of RNA to get the total rate. It will
+
−
be explained further in the processes section.</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Results:<br>
+
−
<img src="https://static.igem.org/mediawiki/2015/d/d1/Technion_HS_2015_Reaction_21.png" class="term"></span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%'>xix.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>ccdB self-degradation</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Law: Mass action</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Explanation: Each molecule of ccdB has a certain probability to degrade,
+
−
hence the corresponding change rate in the amount of the ccdB is proportional
+
−
to the amount of ccdB all the cells.</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Results:<br>
+
−
<img src="https://static.igem.org/mediawiki/2015/3/3e/Technion_HS_2015_Reaction_22.png" class="term"></span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%'>xx.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>producing of the desired protein x by the pCONST promoter</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Law: Mass Action</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Explanation: Each plasmid with our circuit produces the desired enzyme, X,
+
−
in a certain amount.</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Results:<br>
+
−
<img src="https://static.igem.org/mediawiki/2015/a/a8/Technion_HS_2015_Reaction_23.png" class="term"></span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%'>xxi.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>producing of LuxR by the pCONST promoter</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Law: Mass Action</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Explanation: Each plasmid with our circuit produces LuxR in a certain amount.</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Results:<br>
+
−
<img src="https://static.igem.org/mediawiki/2015/3/35/Technion_HS_2015_Reaction_24.png" class="term"></span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%'>xxii.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>producing of AiiA by the pCONST promoter</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Law: Mass Action</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Explanation: Each plasmid with our circuit produces AiiA in a certain amount.</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Results:<br>
+
−
<img src="https://static.igem.org/mediawiki/2015/2/20/Technion_HS_2015_Reaction_25.png" class="term"></span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%'>xxiii.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>plasmid loss</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>We model the effect of plasmid loss on the system. It affects the
+
−
equations by having both bacteria with plasmids (N+) and without plasmid (N-).</span></p>
+
−
 
+
−
<p class=MsoListParagraphCxSpLast dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Further explanation is <a
+
−
href="https://2015.igem.org/Team:Technion_HS_Israel/PlasmidLoss">here</a>. </span>
+
−
<span dir=LTR></span>
+
−
<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
−
0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
+
−
direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
+
−
115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
+
−
</span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
+
−
115%'>Results:<br>
+
−
<img src="https://static.igem.org/mediawiki/2015/9/97/Technion_HS_2015_Reaction_26.png" class="term"></span></p>
+
−
 
+
−
</p>
+
−
 
+
−
</p>
+
−
<h2>
+
−
4. Processes
+
−
</h2>
+
−
<h3 class="Subsection">
+
−
4.1. AHL Diffusion
+
−
</h3>
+
−
<div class="Unindented"><p>
+
−
Our system is based on controlling the initial amount of AHL inside the cells in order to control the life span of the bacteria. However, we can’t put the AHL directly inside the cells. We put it in the test tube together with the bacteria. Therefore, it’s important to model how this process, of AHL entering the cell, accure and how it affects our system. It is part of seeing our system as an integrated complex, whose parts interect with each other and affect the result: the external AHL diffuse inside the cells, inside the cells the AHL is degraded by the AiiA, and as AHL is decreasing inside the cells, the external AHL diffuses accordingly into the cells in order to maintain equilibrium.</p>
+
−
</div>
+
−
<div class="Indented"><p>
+
−
As AHL diffuse rather quickly through the membrane of E. Coli, we use a rather simplified model. We assume that each seperated part of our system (external environment, inside each cell, etc) is homogenous, which is quite true as AHL diffuses quickly, and it’s suffeciant to our needs.</p>
+
−
</div>
+
−
<div class="Indented"><p>
+
−
We base our diffusion model on <a class="URL" href="http://www.tiem.utk.edu/~gross/bioed/webmodules/diffusion.htm">this document</a>. Essentially, it says that the rate of the diffusion is proportional to the concetration gradient.</p>
+
−
</div>
+
−
<h3 class="Subsection">
+
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4.2. Transcription and Translation
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We have two proteins whose production is a part of our biological circuit: the TetR and the ccdb (or the RFP in the experiments). In our model, each of this processes is described using 4 equations. The first two describe the number of plasmids with an activated promoter (or repressor, depends on the processes) using regular Mass Action. In the third we assume that RNA is transcripted in a certain constant rate for each actiivated binding site and the same for unactivated, and get an expression for the change in the concentration of RNA strands. In the last one we desscribe the translation rate of the protein, using the Mass Action law, as a function of the RNA. We assume that the translation rate is proportional to the concentration of the RNA. </p>
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4.3. Plasmid Loss
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Read the full explanation and description of the plasmid loss model <a class="URL" href="https://2015.igem.org/Team:Technion_HS_Israel/PlasmidLoss">here</a>.</p>
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5. Documents
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During our work, we’ve made a documents describing different aspects and parts of our model. We put them here in hope that whomever want to dive into our model will be able to do so and will find these documents interesting.</p>
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<a class="URL" href="https://static.igem.org/mediawiki/2015/8/8c/Technion_HS_2015_Scopes_ofModelling.pdf">Scopes in biological systems modelling.</a>
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<a class="URL" href="https://static.igem.org/mediawiki/2015/9/9b/Simulation.pdf">Solving dynamic systems numerically</a>
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Partial modelling notebook: <a class="URL" href="https://static.igem.org/mediawiki/2015/9/9c/Technion_HS_2015_Summary_Modelling1.pdf">1</a> <a class="URL" href="https://static.igem.org/mediawiki/2015/2/2c/Technion_HS_2015_Summary_Modelling2.pdf">2</a> <a class="URL" href="https://static.igem.org/mediawiki/2015/8/84/Technion_HS_2015_Summary_Modelling3.pdf">3</a>.
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6. Simulation
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We simulated our system a few times using our numerical solver. Description and documentation of our solver can be found <a class="URL" href="https://2015.igem.org/Team:Technion_HS_Israel/Software/Simulation">here</a>. The results we’ve got are in the <a class="URL" href="https://2015.igem.org/Team:Technion_HS_Israel/Modelling/Results">Modelling Results page</a>.</p>
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<h3>Parameters</h3>
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<p>In order to describe our biological system, we need the right parameters. We looked up in literature and in iGEM projects from previous years (using our <a href="https://2015.igem.org/Team:Technion_HS_Israel/Constants_Database"> Constant Database</a>!) and found almost all the 40 required parameters and constants, and estimated the rest. Check our parameter table <a href="https://2015.igem.org/Team:Technion_HS_Israel/Modelling/Parameters">here</a></p>
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Revision as of 12:22, 17 October 2018

Click on the collaboration to read about it.

Survey
Ruia-Mumbai
IISER-Bhopal
IISER-Mohali
TecCEM
Mentoring Team Ruia-Mumbai

Team Ruia-Mumbai have been working to create a synthetic biological device to degrade catechu, by extracellular expression of genes responsible for breaking the flavan 3,4-diol bonds in polyphenols which is one of the compounds responsible for the red stains caused by the same.
They approached us regarding mentorship at the beginning of July 2018. In our first meeting we got acquainted with their project and suggested different methodologies they could follow to make their project more robust for example, we discussed in detail about secretion tag to facilitate extracellular secretion of their protein of interest and suggested corresponding literature. After that, we organized regular video conference meetings between July and October to discuss the progress of their project and other aspects of iGEM competition such as Interlab and Human Practices. We discussed technical doubts they faced in Interlab and also shared data to validate the results.
Our team also helped Team Ruia-Mumbai with experimentation protocols like we shared our protocol for preparing competent cells. We suggested changes to their protocols to optimize experimentation for cloning of their construct. We also thoroughly discussed modeling kinetics of their enzyme but weren’t able to continue it due to time constraints.

Discussions with IISER-Bhopal

We have been in constant touch with Team IISER-Bhopal starting from the month of May. We discussed each other’s project and helped sort out technical problems related to it.
IISER Bhopal suggested an initiative to increase the outreach of each other’s projects. In this initiative both the teams exchanged slides mentioning brief overview about their project and introduced each other’s idea in public engagement events like Lecture Series conducted by IIT Kanpur and iGEM Day (25th August 2018) organized by IISER Bhopal.
Both teams shared each others’ Interlab data and interpretations to get a deeper understanding of the acquired data from experiments.
We also helped Team IISER-Bhopal with their US VISA procedures which eased their application process. Along the way, we also cleared their other technical doubts and both the teams helped each other out whenever possible.


Meeting with IISER-Mohali

We recently had a discussion with Team IISER-Mohali in which we discussed each other’s project. It was an interesting session, and we found their project an innovative one. Our session was focussed on critically analyzing each other’s project and discussing potential questions that can come up during Jamboree presentation. It helped both our teams to prepare robustly for the same. Since the team had participated in iGEM 2017, they shared their experience about judging criteria, presentation and poster session at the Giant Jamboree which was helpful and gave us additional insight into the competition.


Accepting BioBrick Part from Team TecCEM

In iGEM 2015, Team TecCEM_HS participated and worked upon developing a system to degrade SDS, similar to our project in idea. A member of their team, Borreguin JC, is participating in this year’s Team TecCEM as well, and he was helpful in figuring out the issues they faced in past project so that we could avoid committing them.
Since isolating the sdsA gene from Pseudomonas aeruginosa was difficult, we contacted them if they could provide us with the plasmid containing the same. They gifted us the BioBrick(BBa_K1629002) which they had submitted in iGEM with the corresponding gene, thus helping us move forward with our project.


Survey amongst iGEM 2018 teams

A great idea is great not because of its technicalities, but because of the impact it has on the people around it.
To gather an understanding of how water pollution affects different parts of the world, we conducted a survey amongst iGEM 2018 teams to get their views on the problem in their regions. Members of 18 teams filled us in with their knowledge which has given us a wider perspective of the problem around the globe.

The teams that did the needful are:

→Team Ruia-Mumbai
→CPU_CHINA
→Pasteur Paris 2018
→METU HS Ankara iGEM 2018
→Hawaii iGEM Team
→UPF_CRG_Barcelona
→Lambert iGEM
→AFCM-Egypt
→iGEM Bielefeld-CeBiTec 2018
→Tacoma_RAINMakers
→NWU-China
→TecCem Mexico
→TecCEM
→iGEM Pasteur Paris 2018
→SKLMT-China
→TUST China
→METU_HS_Ankara
→ICT-Mumbai