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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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| − | <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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| − | <h3 class="Subsection">
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| − | 2.1. Why Do We Need a Model?
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| − | </h3>
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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 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 “Plasmid Loss” page for more details), which can hurt the functioning of the kill switch.</p>
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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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| − | 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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| − | 2.3. Our System
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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 “death protein” (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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| − | 2.3.2. In Detail
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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 (“death protein”) 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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| − | 2.3.3. Note About Notations
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| − | </h4>
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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:
| + | /*GOOGLE FONTS*/ |
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| − | 115%'>i.<span style='font:7.0pt "Times New Roman"'>
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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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| − | </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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| − | </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,
| + | src: local('Raleway'), local('Raleway-Regular'), url(https://static.igem.org/mediawiki/2018/5/59/T--MIT--raleway2.woff) format('woff'); |
| − | 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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| − | </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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| − | 115%'>Diffusion of AHL</span></p>
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| | + | @media (max-width:768px){.w3-modal-content{width:500px}.w3-modal{padding-top:50px}} |
| | + | @media (min-width:993px){.w3-modal-content{width:900px}.w3-hide-large{display:none!important}.w3-sidebar.w3-collapse{display:block!important}} |
| | + | @media (max-width:992px) and (min-width:601px){.w3-hide-medium{display:none!important}} |
| | + | @media (max-width:992px){.w3-sidebar.w3-collapse{display:none}.w3-main{margin-left:0!important;margin-right:0!important}} |
| | + | .w3-top,.w3-bottom{position:fixed;width:100%;z-index:1}.w3-top{top:0}.w3-bottom{bottom:0} |
| | + | .w3-overlay{position:fixed;display:none;width:100%;height:100%;top:0;left:0;right:0;bottom:0;background-color:rgba(0,0,0,0.5);z-index:2} |
| | + | .w3-display-topleft{position:absolute;left:0;top:0}.w3-display-topright{position:absolute;right:0;top:0} |
| | + | .w3-display-bottomleft{position:absolute;left:0;bottom:0}.w3-display-bottomright{position:absolute;right:0;bottom:0} |
| | + | .w3-display-middle{position:absolute;top:50%;left:50%;transform:translate(-50%,-50%);-ms-transform:translate(-50%,-50%)} |
| | + | .w3-display-left{position:absolute;top:50%;left:0%;transform:translate(0%,-50%);-ms-transform:translate(-0%,-50%)} |
| | + | .w3-display-right{position:absolute;top:50%;right:0%;transform:translate(0%,-50%);-ms-transform:translate(0%,-50%)} |
| | + | .w3-display-topmiddle{position:absolute;left:50%;top:0;transform:translate(-50%,0%);-ms-transform:translate(-50%,0%)} |
| | + | .w3-display-bottommiddle{position:absolute;left:50%;bottom:0;transform:translate(-50%,0%);-ms-transform:translate(-50%,0%)} |
| | + | .w3-display-container:hover .w3-display-hover{display:block}.w3-display-container:hover span.w3-display-hover{display:inline-block}.w3-display-hover{display:none} |
| | + | .w3-display-position{position:absolute} |
| | + | .w3-circle{border-radius:50%} |
| | + | .w3-round-small{border-radius:2px}.w3-round,.w3-round-medium{border-radius:4px}.w3-round-large{border-radius:8px}.w3-round-xlarge{border-radius:16px}.w3-round-xxlarge{border-radius:32px} |
| | + | .w3-row-padding,.w3-row-padding>.w3-half,.w3-row-padding>.w3-third,.w3-row-padding>.w3-twothird,.w3-row-padding>.w3-threequarter,.w3-row-padding>.w3-quarter,.w3-row-padding>.w3-col{padding:0 8px} |
| | + | .w3-container,.w3-panel{padding:0.01em 16px}.w3-panel{margin-top:16px;margin-bottom:16px} |
| | + | .w3-code,.w3-codespan{font-family:Consolas,"courier new";font-size:16px} |
| | + | .w3-code{width:auto;background-color:#fff;padding:8px 12px;border-left:4px solid #4CAF50;word-wrap:break-word} |
| | + | .w3-codespan{color:crimson;background-color:#f1f1f1;padding-left:4px;padding-right:4px;font-size:110%} |
| | + | .w3-card,.w3-card-2{box-shadow:0 2px 5px 0 rgba(0,0,0,0.16),0 2px 10px 0 rgba(0,0,0,0.12)} |
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| | + | .w3-animate-left{position:relative;animation:animateleft 0.4s}@keyframes animateleft{from{left:-300px;opacity:0} to{left:0;opacity:1}} |
| | + | .w3-animate-right{position:relative;animation:animateright 0.4s}@keyframes animateright{from{right:-300px;opacity:0} to{right:0;opacity:1}} |
| | + | .w3-animate-bottom{position:relative;animation:animatebottom 0.4s}@keyframes animatebottom{from{bottom:-300px;opacity:0} to{bottom:0;opacity:1}} |
| | + | .w3-animate-zoom {animation:animatezoom 0.6s}@keyframes animatezoom{from{transform:scale(0)} to{transform:scale(1)}} |
| | + | .w3-animate-input{transition:width 0.4s ease-in-out}.w3-animate-input:focus{width:100%!important} |
| | + | .w3-opacity,.w3-hover-opacity:hover{opacity:0.60}.w3-opacity-off,.w3-hover-opacity-off:hover{opacity:1} |
| | + | .w3-opacity-max{opacity:0.25}.w3-opacity-min{opacity:0.75} |
| | + | .w3-greyscale-max,.w3-grayscale-max,.w3-hover-greyscale:hover,.w3-hover-grayscale:hover{filter:grayscale(100%)} |
| | + | .w3-greyscale,.w3-grayscale{filter:grayscale(75%)}.w3-greyscale-min,.w3-grayscale-min{filter:grayscale(50%)} |
| | + | .w3-sepia{filter:sepia(75%)}.w3-sepia-max,.w3-hover-sepia:hover{filter:sepia(100%)}.w3-sepia-min{filter:sepia(50%)} |
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| | + | .w3-xlarge{font-size:24px!important}.w3-xxlarge{font-size:36px!important}.w3-xxxlarge{font-size:48px!important}.w3-jumbo{font-size:64px!important} |
| | + | .w3-left-align{text-align:left!important}.w3-right-align{text-align:right!important}.w3-justify{text-align:justify!important}.w3-center{text-align:center!important} |
| | + | .w3-border-0{border:0!important}.w3-border{border:1px solid #ccc!important} |
| | + | .w3-border-top{border-top:1px solid #ccc!important}.w3-border-bottom{border-bottom:1px solid #ccc!important} |
| | + | .w3-border-left{border-left:1px solid #ccc!important}.w3-border-right{border-right:1px solid #ccc!important} |
| | + | .w3-topbar{border-top:6px solid #ccc!important}.w3-bottombar{border-bottom:6px solid #ccc!important} |
| | + | .w3-leftbar{border-left:6px solid #ccc!important}.w3-rightbar{border-right:6px solid #ccc!important} |
| | + | .w3-section,.w3-code{margin-top:16px!important;margin-bottom:16px!important} |
| | + | .w3-margin{margin:16px!important}.w3-margin-top{margin-top:16px!important}.w3-margin-bottom{margin-bottom:16px!important} |
| | + | .w3-margin-left{margin-left:16px!important}.w3-margin-right{margin-right:16px!important} |
| | + | .w3-padding-small{padding:4px 8px!important}.w3-padding{padding:8px 16px!important}.w3-padding-large{padding:12px 24px!important} |
| | + | .w3-padding-16{padding-top:16px!important;padding-bottom:16px!important}.w3-padding-24{padding-top:24px!important;padding-bottom:24px!important} |
| | + | .w3-padding-32{padding-top:32px!important;padding-bottom:32px!important}.w3-padding-48{padding-top:48px!important;padding-bottom:48px!important} |
| | + | .w3-padding-64{padding-top:64px!important;padding-bottom:64px!important} |
| | + | .w3-left{float:left!important}.w3-right{float:right!important} |
| | + | .w3-button:hover{color:#000!important;background-color:#ccc!important} |
| | + | .w3-transparent,.w3-hover-none:hover{background-color:transparent!important} |
| | + | .w3-hover-none:hover{box-shadow:none!important} |
| | + | /* Colors */ |
| | + | .w3-amber,.w3-hover-amber:hover{color:#000!important;background-color:#ffc107!important} |
| | + | .w3-aqua,.w3-hover-aqua:hover{color:#000!important;background-color:#00ffff!important} |
| | + | .w3-blue,.w3-hover-blue:hover{color:#fff!important;background-color:#2196F3!important} |
| | + | .w3-light-blue,.w3-hover-light-blue:hover{color:#000!important;background-color:#87CEEB!important} |
| | + | .w3-brown,.w3-hover-brown:hover{color:#fff!important;background-color:#795548!important} |
| | + | .w3-cyan,.w3-hover-cyan:hover{color:#000!important;background-color:#00bcd4!important} |
| | + | .w3-blue-grey,.w3-hover-blue-grey:hover,.w3-blue-gray,.w3-hover-blue-gray:hover{color:#fff!important;background-color:#607d8b!important} |
| | + | .w3-green,.w3-hover-green:hover{color:#fff!important;background-color:#4CAF50!important} |
| | + | .w3-light-green,.w3-hover-light-green:hover{color:#000!important;background-color:#8bc34a!important} |
| | + | .w3-indigo,.w3-hover-indigo:hover{color:#fff!important;background-color:#3f51b5!important} |
| | + | .w3-khaki,.w3-hover-khaki:hover{color:#000!important;background-color:#f0e68c!important} |
| | + | .w3-lime,.w3-hover-lime:hover{color:#000!important;background-color:#cddc39!important} |
| | + | .w3-orange,.w3-hover-orange:hover{color:#000!important;background-color:#ff9800!important} |
| | + | .w3-deep-orange,.w3-hover-deep-orange:hover{color:#fff!important;background-color:#ff5722!important} |
| | + | .w3-pink,.w3-hover-pink:hover{color:#fff!important;background-color:#e91e63!important} |
| | + | .w3-purple,.w3-hover-purple:hover{color:#fff!important;background-color:#9c27b0!important} |
| | + | .w3-deep-purple,.w3-hover-deep-purple:hover{color:#fff!important;background-color:#673ab7!important} |
| | + | .w3-red,.w3-hover-red:hover{color:#fff!important;background-color:#f44336!important} |
| | + | .w3-sand,.w3-hover-sand:hover{color:#000!important;background-color:#fdf5e6!important} |
| | + | .w3-teal,.w3-hover-teal:hover{color:#fff!important;background-color:#009688!important} |
| | + | .w3-yellow,.w3-hover-yellow:hover{color:#000!important;background-color:#ffeb3b!important} |
| | + | .w3-white,.w3-hover-white:hover{color:#000!important;background-color:#fff!important} |
| | + | .w3-black,.w3-hover-black:hover{color:#fff!important;background-color:#000!important} |
| | + | .w3-grey,.w3-hover-grey:hover,.w3-gray,.w3-hover-gray:hover{color:#000!important;background-color:#9e9e9e!important} |
| | + | .w3-light-grey,.w3-hover-light-grey:hover,.w3-light-gray,.w3-hover-light-gray:hover{color:#000!important;background-color:#f1f1f1!important} |
| | + | .w3-dark-grey,.w3-hover-dark-grey:hover,.w3-dark-gray,.w3-hover-dark-gray:hover{color:#fff!important;background-color:#616161!important} |
| | + | .w3-pale-red,.w3-hover-pale-red:hover{color:#000!important;background-color:#ffdddd!important} |
| | + | .w3-pale-green,.w3-hover-pale-green:hover{color:#000!important;background-color:#ddffdd!important} |
| | + | .w3-pale-yellow,.w3-hover-pale-yellow:hover{color:#000!important;background-color:#ffffcc!important} |
| | + | .w3-pale-blue,.w3-hover-pale-blue:hover{color:#000!important;background-color:#ddffff!important} |
| | + | .w3-text-amber,.w3-hover-text-amber:hover{color:#ffc107!important} |
| | + | .w3-text-aqua,.w3-hover-text-aqua:hover{color:#00ffff!important} |
| | + | .w3-text-blue,.w3-hover-text-blue:hover{color:#2196F3!important} |
| | + | .w3-text-light-blue,.w3-hover-text-light-blue:hover{color:#87CEEB!important} |
| | + | .w3-text-brown,.w3-hover-text-brown:hover{color:#795548!important} |
| | + | .w3-text-cyan,.w3-hover-text-cyan:hover{color:#00bcd4!important} |
| | + | .w3-text-blue-grey,.w3-hover-text-blue-grey:hover,.w3-text-blue-gray,.w3-hover-text-blue-gray:hover{color:#607d8b!important} |
| | + | .w3-text-green,.w3-hover-text-green:hover{color:#4CAF50!important} |
| | + | .w3-text-light-green,.w3-hover-text-light-green:hover{color:#8bc34a!important} |
| | + | .w3-text-indigo,.w3-hover-text-indigo:hover{color:#3f51b5!important} |
| | + | .w3-text-khaki,.w3-hover-text-khaki:hover{color:#b4aa50!important} |
| | + | .w3-text-lime,.w3-hover-text-lime:hover{color:#cddc39!important} |
| | + | .w3-text-orange,.w3-hover-text-orange:hover{color:#ff9800!important} |
| | + | .w3-text-deep-orange,.w3-hover-text-deep-orange:hover{color:#ff5722!important} |
| | + | .w3-text-pink,.w3-hover-text-pink:hover{color:#e91e63!important} |
| | + | .w3-text-purple,.w3-hover-text-purple:hover{color:#9c27b0!important} |
| | + | .w3-text-deep-purple,.w3-hover-text-deep-purple:hover{color:#673ab7!important} |
| | + | .w3-text-red,.w3-hover-text-red:hover{color:#f44336!important} |
| | + | .w3-text-sand,.w3-hover-text-sand:hover{color:#fdf5e6!important} |
| | + | .w3-text-teal,.w3-hover-text-teal:hover{color:#009688!important} |
| | + | .w3-text-yellow,.w3-hover-text-yellow:hover{color:#d2be0e!important} |
| | + | .w3-text-white,.w3-hover-text-white:hover{color:#fff!important} |
| | + | .w3-text-black,.w3-hover-text-black:hover{color:#000!important} |
| | + | .w3-text-grey,.w3-hover-text-grey:hover,.w3-text-gray,.w3-hover-text-gray:hover{color:#757575!important} |
| | + | .w3-text-light-grey,.w3-hover-text-light-grey:hover,.w3-text-light-gray,.w3-hover-text-light-gray:hover{color:#f1f1f1!important} |
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| | + | .w3-border-amber,.w3-hover-border-amber:hover{border-color:#ffc107!important} |
| | + | .w3-border-aqua,.w3-hover-border-aqua:hover{border-color:#00ffff!important} |
| | + | .w3-border-blue,.w3-hover-border-blue:hover{border-color:#2196F3!important} |
| | + | .w3-border-light-blue,.w3-hover-border-light-blue:hover{border-color:#87CEEB!important} |
| | + | .w3-border-brown,.w3-hover-border-brown:hover{border-color:#795548!important} |
| | + | .w3-border-cyan,.w3-hover-border-cyan:hover{border-color:#00bcd4!important} |
| | + | .w3-border-blue-grey,.w3-hover-border-blue-grey:hover,.w3-border-blue-gray,.w3-hover-border-blue-gray:hover{border-color:#607d8b!important} |
| | + | .w3-border-green,.w3-hover-border-green:hover{border-color:#4CAF50!important} |
| | + | .w3-border-light-green,.w3-hover-border-light-green:hover{border-color:#8bc34a!important} |
| | + | .w3-border-indigo,.w3-hover-border-indigo:hover{border-color:#3f51b5!important} |
| | + | .w3-border-khaki,.w3-hover-border-khaki:hover{border-color:#f0e68c!important} |
| | + | .w3-border-lime,.w3-hover-border-lime:hover{border-color:#cddc39!important} |
| | + | .w3-border-orange,.w3-hover-border-orange:hover{border-color:#ff9800!important} |
| | + | .w3-border-deep-orange,.w3-hover-border-deep-orange:hover{border-color:#ff5722!important} |
| | + | .w3-border-pink,.w3-hover-border-pink:hover{border-color:#e91e63!important} |
| | + | .w3-border-purple,.w3-hover-border-purple:hover{border-color:#9c27b0!important} |
| | + | .w3-border-deep-purple,.w3-hover-border-deep-purple:hover{border-color:#673ab7!important} |
| | + | .w3-border-red,.w3-hover-border-red:hover{border-color:#f44336!important} |
| | + | .w3-border-sand,.w3-hover-border-sand:hover{border-color:#fdf5e6!important} |
| | + | .w3-border-teal,.w3-hover-border-teal:hover{border-color:#009688!important} |
| | + | .w3-border-yellow,.w3-hover-border-yellow:hover{border-color:#ffeb3b!important} |
| | + | .w3-border-white,.w3-hover-border-white:hover{border-color:#fff!important} |
| | + | .w3-border-black,.w3-hover-border-black:hover{border-color:#000!important} |
| | + | .w3-border-grey,.w3-hover-border-grey:hover,.w3-border-gray,.w3-hover-border-gray:hover{border-color:#9e9e9e!important} |
| | + | .w3-border-light-grey,.w3-hover-border-light-grey:hover,.w3-border-light-gray,.w3-hover-border-light-gray:hover{border-color:#f1f1f1!important} |
| | + | .w3-border-dark-grey,.w3-hover-border-dark-grey:hover,.w3-border-dark-gray,.w3-hover-border-dark-gray:hover{border-color:#616161!important} |
| | + | .w3-border-pale-red,.w3-hover-border-pale-red:hover{border-color:#ffe7e7!important}.w3-border-pale-green,.w3-hover-border-pale-green:hover{border-color:#e7ffe7!important} |
| | + | .w3-border-pale-yellow,.w3-hover-border-pale-yellow:hover{border-color:#ffffcc!important}.w3-border-pale-blue,.w3-hover-border-pale-blue:hover{border-color:#e7ffff!important} |
| | | | |
| − | <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"'>
| |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| |
| − | 115%'>Law: Simple passive diffusion</span></p>
| |
| | | | |
| − | <p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
| + | #contentSub, #footer-box, #catlinks, #search-controls, #p-logo, #sideMenu, #menubar, .logo_2017, .printfooter, .firstHeading,.visualClear { |
| − | 0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
| + | display: none; |
| − | direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
| + | } /*-- hides default wiki settings --*/ |
| − | 115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>
| + | |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | |
| − | 115%'>Explanation: Will be explained in the processes section.</span></p>
| + | |
| | | | |
| − | <p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
| + | #top-section { /*-- styling for default menu bar (edit, page, history, etc.) --*/ |
| − | 0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
| + | border: 0 none; |
| − | direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
| + | height: 3vw; |
| − | 115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>
| + | z-index: 100; |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | top: 0; |
| − | 115%'>Results:<br>
| + | position: fixed; |
| − | Change in external AHL concentration:<br>
| + | width: 975px; |
| − | <img src="https://static.igem.org/mediawiki/2015/1/16/Technion_HS_2015_Reaction_3.png" class="term"><br>
| + | left: 50%; |
| − | Change in total amount inside of AHL inside all the cells:<br>
| + | margin-left: -487px; |
| − | <img src="https://static.igem.org/mediawiki/2015/7/7d/Technion_HS_2015_Reaction_4.png" class="term"> </span></p>
| + | } |
| | | | |
| − | <p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
| + | #top_title, #top { |
| − | 0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
| + | display: none; |
| − | direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
| + | z-index: -1000; |
| − | 115%'>iii.<span style='font:7.0pt "Times New Roman"'>
| + | } |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | |
| − | 115%'>AHL degradation by AiiA</span></p>
| + | |
| | | | |
| − | <p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
| + | .logo_2018 { |
| − | 0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
| + | display: none; |
| − | direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
| + | z-index: -1000; |
| − | 115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>
| + | } |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | |
| − | 115%'>Law: Michaelis Menten</span></p>
| + | |
| | | | |
| − | <p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
| + | #globalWrapper, #content { /*-- changes default wiki settings --*/ |
| − | 0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
| + | width: 100%; |
| − | direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
| + | height: 100%; |
| − | 115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>
| + | border: none; |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | background-color: #7267e8; |
| − | 115%'>Explanation: AiiA is an enzyme, and simple Mass Action doesn't work well
| + | margin: 0px; |
| − | for enzymatic reactions. The reason for it is the fact that the enzyme and the
| + | padding: 0px; |
| − | substrate form a complex, which is then converted to a product and the original
| + | letter-spacing: normal; |
| − | enzyme. Therefore, two mass actions are required to describe this process, but
| + | |
| − | under quasi-steady-state assumption we can derive a single equation, which is
| + | font-weight: light; |
| − | the Michaelis Menten law. It has two parameters, the maximal reaction rate and
| + | } |
| − | the turnover number.</span></p>
| + | |
| | | | |
| − | <p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
| + | html, body, .wrapper { /*-- changes default wiki settings --*/ |
| − | 0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
| + | width: 100%; |
| − | direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
| + | height: 100%; |
| − | 115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>
| + | background-color: #7267e8; |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | } |
| − | 115%'>Results:<br>
| + | |
| − | <img src="https://static.igem.org/mediawiki/2015/4/40/Technion_HS_2015_Reaction_5.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%'>iv.<span style='font:7.0pt "Times New Roman"'>
| |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| |
| − | 115%'>Pairing of AHL and LuxR into AHL-LuxR complex</span></p>
| |
| | | | |
| − | <p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
| + | .menu { |
| − | 0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
| + | list-style-type: none; |
| − | direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
| + | margin: 0vw; |
| − | 115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>
| + | padding: .3vw; |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | /*overflow: hidden;*/ |
| − | 115%'>Law: Mass action</span></p>
| + | background-color: #333; |
| | + | position: fixed; |
| | + | width: 100%; |
| | + | height: 4.5vw; |
| | + | -webkit-box-shadow: 0 8px 6px -6px #2c2c2c; |
| | + | -moz-box-shadow: 0 8px 6px -6px #2c2c2c; |
| | + | box-shadow: 0 8px 6px -6px #2c2c2c; |
| | + | top: 1.1vw; |
| | + | z-index: 20; |
| | + | } |
| | | | |
| − | <p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
| + | .sub { |
| − | 0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
| + | font-family: 'Dosis', sans-serif;; |
| − | direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
| + | font-size: 1.5vw; |
| − | 115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>
| + | float: left; |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | height: 4.5vw; |
| − | 115%'>Explanation: The chance of a molecule of AHL to meet a molecule of LuxR
| + | |
| − | is proportional to both the concentration of AHL and LuxR (the more AHL you
| + | } |
| − | have, the higher the chance for reaction between AHL and LuxR). We get that the
| + | |
| − | reaction rate is proportional to the product of the concentrations of AHL and
| + | |
| − | LuxR.</span></p>
| + | |
| | | | |
| − | <p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
| + | .sub a { |
| − | 0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
| + | display: block; |
| − | direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
| + | color: white; |
| − | 115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>
| + | text-align: center; |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | padding: 1vw 1.5vw; |
| − | 115%'>Results:<br>
| + | text-decoration: none; |
| − | <img src="https://static.igem.org/mediawiki/2015/d/d4/Technion_HS_2015_Reaction_6.png" class="term"></span></p>
| + | } |
| | | | |
| − | <p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
| + | .sub a:hover { |
| − | 0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
| + | background-color: #410081; |
| − | direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
| + | } |
| − | 115%'>v.<span style='font:7.0pt "Times New Roman"'>
| + | |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | |
| − | 115%'>Disassociation of the AHL-LuxR complex to its components</span></p>
| + | |
| | | | |
| − | <p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
| + | .active { |
| − | 0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
| + | background-color: #9055ff; |
| − | 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"'>
| + | |
| − | </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:
| + | .dropdown { |
| − | 0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
| + | position: relative; |
| − | direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
| + | display: inline-block; |
| − | 115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>
| + | } |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | |
| − | 115%'>Explanation: Each AHL-LuxR complex has a certain probability to
| + | |
| − | 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>
| + | |
| | | | |
| − | <p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
| + | .dropdown-content { |
| − | 0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
| + | font-family: 'Raleway', sans-serif;; |
| − | direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
| + | font-size: 1.2vw; |
| − | 115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>
| + | display: none; |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | position: absolute; |
| − | 115%'>Results:<br>
| + | top: 4vw; |
| − | <img src="https://static.igem.org/mediawiki/2015/8/8a/Technion_HS_2015_Reaction_7.png" class="term"></span></p>
| + | background-color: #2c2c2c; |
| | + | min-width: 10vw; |
| | + | box-shadow: 0px 8px 16px 0px rgba(0,0,0,0.2); |
| | + | z-index: 1; |
| | + | } |
| | | | |
| − | <p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
| + | .dropdown-content a { |
| − | 0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
| + | color: white; |
| − | direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
| + | padding: .6vw .9vw; |
| − | 115%'>vi.<span style='font:7.0pt "Times New Roman"'>
| + | text-decoration: none; |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | display: block; |
| − | 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:
| + | .dropdown-content a:hover {background-color: #474747;} |
| − | 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"'>
| + | |
| − | </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:
| + | .dropdown:hover .dropdown-content {display: block;} |
| − | 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"'>
| + | |
| − | </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:
| + | body{ |
| − | 0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
| + | margin:0; |
| − | 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"'>
| + | .h3{ |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | color: white; |
| − | 115%'>Results:<br>
| + | font-family: 'Dosis', sans-serif;; |
| − | <img src="https://static.igem.org/mediawiki/2015/8/8e/Technion_HS_2015_Reaction_8.png" class="term"></span></p>
| + | font-size: 3.7vw; |
| | + | position: absolute; |
| | + | line-height: 2.8vw; |
| | + | } |
| | | | |
| − | <p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
| + | .h4{ |
| − | 0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
| + | color: #410081; |
| − | direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
| + | font-family: 'Dosis', sans-serif;; |
| − | 115%'>vii.<span style='font:7.0pt "Times New Roman"'>
| + | font-size: 2.5vw; |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | position: absolute; |
| − | 115%'>Disassociation of (AHL-LuxR)<sub>2</sub> to its components</span></p>
| + | line-height: 2.8vw; |
| | + | } |
| | + | .p{ |
| | + | color: white; |
| | + | font-family: 'Raleway', sans-serif;; |
| | + | font-size: 1.5vw; |
| | + | line-height: 2.8vw; |
| | + | z-index: 5; |
| | + | } |
| | + | </style> |
| | + | </head> |
| | + | <body > |
| | | | |
| − | <p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right: | + | <div class="menu"> |
| − | 0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
| + | <div class="sub"><a href="https://2018.igem.org/Team:MIT">Home</a></div> |
| − | direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
| + | <div class="dropdown"> |
| − | 115%;font-family:"Courier New"'>o<span style='font:7.0pt "Times New Roman"'>
| + | <div class="sub"><a href="https://2018.igem.org/Team:MIT/Team">Team</a></div> |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height: | + | <div class="dropdown-content"> |
| − | 115%'>Law: Mass action</span></p>
| + | <a href="https://2018.igem.org/Team:MIT/Team">Team Members</a> |
| | + | <a href="https://2018.igem.org/Team:MIT/Collaborations">Collaborations</a> |
| | + | </div> |
| | + | </div> |
| | + | <div class="dropdown"> |
| | + | <div class="sub"><a href="https://2018.igem.org/Team:MIT/Description">Project</a></div> |
| | + | <div class="dropdown-content"> |
| | + | <a href="https://2018.igem.org/Team:MIT/Design">Design</a> |
| | + | <a href="https://2018.igem.org/Team:MIT/Results">Results</a> |
| | + | <a href="https://2018.igem.org/Team:MIT/InterLab">InterLab</a> |
| | + | <a href="https://2018.igem.org/Team:MIT/Notebook">Notebook</a> |
| | + | <a href="https://2018.igem.org/Team:MIT/Experiments">Protocols</a> |
| | + | <a href ="https://2018.igem.org/Team:MIT/Attributions"> Attributions </a> |
| | + | </div> |
| | + | </div> |
| | + | <div class="dropdown"> |
| | + | <div class="sub"><a href="https://2018.igem.org/Team:MIT/Parts">Parts</a></div> |
| | + | <div class="dropdown-content"> |
| | + | <a href="https://2018.igem.org/Team:MIT/Basic_Part">Basic Parts</a> |
| | + | <a href="https://2018.igem.org/Team:MIT/Composite_Part">Composite Parts</a> |
| | + | </div> |
| | + | </div> |
| | + | <div class="sub"><a class="active" href="https://2018.igem.org/Team:MIT/Safety">Safety</a></div> |
| | + | <div class="dropdown"> |
| | + | <div class="sub"><a href="https://2018.igem.org/Team:MIT/Human_Practices">Human Practices</a></div> |
| | + | <div class="dropdown-content"> |
| | + | <a href="https://2018.igem.org/Team:MIT/Human_Practices">Integrated Human Practices</a> |
| | + | <a href="https://2018.igem.org/Team:MIT/Public_Engagement">Public Engagement</a> |
| | + | </div> |
| | + | </div> |
| | + | <div class="sub"><a href="https://2018.igem.org/Team:MIT/Model">Model</a></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"'>
| |
| − | </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 class="h3"style="position: absolute; top: 7vw; left: 2vw; margin-right: 4vw;"> |
| − | 0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
| + | Safety |
| − | 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"'>
| + | |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | |
| − | 115%'>Results:<br>
| + | |
| − | <img src="https://static.igem.org/mediawiki/2015/0/0b/Technion_HS_2015_Reaction_9.png" class="term"></span></p>
| + | |
| | | | |
| − | <p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right: | + | <div class="h4"style="position: absolute; top: 11vw; left: 2vw; margin-right: 4vw;"> |
| − | 0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
| + | Safe Project Design |
| − | direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
| + | </div> |
| − | 115%'>viii.<span style='font:7.0pt "Times New Roman"'>
| + | |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | |
| − | 115%'>(AHL-LuxR)<sub>2</sub> binds to the pLuxR promoter</span></p>
| + | |
| | | | |
| − | <p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right: | + | <div class="p" style="position: absolute; top: 14vw; left: 2vw; margin-right: 4vw;"> |
| − | 0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
| + | In our project we are using HEK293 Cells which are a well documented line of cells that the team has been trained to handle properly. We are also using Streptococcus Mutans UA159, which is a strain of bacteria that is commonly found in the mouth. This strain of bacteria poses little to no threat to those that it could come in contact with unless they are immunocompromised. We also are not changing the S.Mutans’ DNA in any way to give them antibiotic resistance due to the chance that it could get out of the lab and cause harm to the environment. |
| − | 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"'>
| + | |
| − | </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 class="h4"style="position: absolute; top: 29vw; left: 2vw; margin-right: 4vw;"> |
| − | 0cm;margin-bottom:10.0pt;margin-left:72.0pt;text-align:left;text-indent:-18.0pt;
| + | Safe Lab Work |
| − | 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"'>
| + | |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | |
| − | 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"'>
| |
| − | </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: | + | <div class="p" style="position: absolute; top: 32vw; left: 2vw; margin-right: 4vw;"> |
| − | 0cm;margin-bottom:10.0pt;margin-left:54.0pt;text-align:left;text-indent:-36.0pt;
| + | In our lab we consistently used proper PPE depending on what materials we were working with. Every team member was also required to go through lab specific trainings to be allowed to work with anything in the lab, and some of the team members were trained separately to deal with the s.mutans in the lab. While using the S.mutans we had a different set of procedures due to the bacteria’s vulnerability to contamination. This made it so that we used multiple sets of gloves during our experiments and also used a bunsen burner to decrease the likelihood of contamination. |
| − | direction:ltr;unicode-bidi:embed'><span style='font-size:16.0pt;line-height:
| + | |
| − | 115%'>ix.<span style='font:7.0pt "Times New Roman"'>
| + | |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | |
| − | 115%'>(AHL-LuxR)<sub>2 </sub>unbinds from the pLuxR 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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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:
| + | |
| − | 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"'>
| + | |
| − | </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"'>
| + | |
| − | </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:
| + | |
| − | 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"'>
| + | |
| − | </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"'>
| + | |
| − | </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:
| + | |
| − | 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"'>
| + | |
| − | </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"'>
| + | |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | |
| − | 115%'>Explanation: Each activated promoter transcripts mRNA in a certain rate.
| + | |
| − | We multiply it by the number of activated 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:
| + | |
| − | 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"'>
| + | |
| − | </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"'>
| + | |
| − | </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:
| + | |
| − | 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"'>
| + | |
| − | </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"'>
| + | |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | |
| − | 115%'>Explanation: mRNA of TetR translates to the protein TetR 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"'>
| + | |
| − | </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:
| + | |
| − | 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%'>xiii.<span style='font:7.0pt "Times New Roman"'>
| + | |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | |
| − | 115%'>TRLV 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"'>
| + | |
| − | </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"'>
| + | |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | |
| − | 115%'>Explanation: Each molecule of TRLV has a certain probability to degrade,
| + | |
| − | hence the corresponding change rate in the amount of the TRLV is proportional
| + | |
| − | to the amount of TRLV 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"'>
| + | |
| − | </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/d3/Technion_HS_2015_Reaction_16.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%'>xiv.<span style='font:7.0pt "Times New Roman"'>
| + | |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | |
| − | 115%'>TRLV binds to the pTetR 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"'>
| + | |
| − | </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"'>
| + | |
| − | </span></span><span dir=LTR></span><span style='font-size:16.0pt;line-height:
| + | |
| − | 115%'>Explanation: The activation rate is proportional to the product of the
| + | |
| − | concentrations of the dimer and the number of plasmid plasmids with pTetR 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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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"'>
| + | |
| − | </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> |
| − | <div class="Indented"><p>
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| − | 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>
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| − | </div>
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| − | <div class="Indented"><p>
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| − | 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>
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| − | </div>
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| − | <h3 class="Subsection">
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| − | 4.2. Transcription and Translation
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| − | </h3>
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| − | <div class="Unindented"><p>
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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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| − | </div>
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| − | <h3 class="Subsection">
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| − | 4.3. Plasmid Loss
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| − | </h3>
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| − | <div class="Unindented"><p>
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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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| − | </div>
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| − | <h2 class="Section">
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| − | 5. Documents
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| − | </h2>
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| − | <div class="Unindented"><p>
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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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| − | </div>
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| − | <ul>
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| − | <li>
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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>
| |
| − | </li>
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| − | <li>
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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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| − | </li>
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| − | <li>
| |
| − | 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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| − | </li>
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| − |
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| − | </ul>
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| − | <h2 class="Section">
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| − | 6. Simulation
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| − | </h2>
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| − | <div class="Unindented"><p>
| |
| − | 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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