Team:Uppsala/Modeling PopulationLevel

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document.getElementById("tab1").innerHTML = '<h2>Introduction</h2><p>We wanted to evaluate the effectiveness of our system in the real intestine of a human. Since it requires a lot of ethical consideration and animal trials to test on real humans we decided to construct a model instead. The model will also give us insight into what parameters are most important when improving our system. Since the thought out medicine is thought of as a pill, see Policy & Practise, this is the premiss we will evaluate our modeling around.<br><br>Our final model is able to produce both a “density map” showing the small intestine as a two dimensional landscape and graphs of the total amount of cells and molecules over time. The first model is more heavy to run and can therefore only run at limited time intervals, while the later model is able to run at much longer intervals. The density map is good for analysing movement of molecules and cells in the domain, while the graphs are nice to show total effect of the system.</p><img src="https://static.igem.org/mediawiki/2014/7/73/Populationsummary1_Uppsala14.PNG"></img><p><i>Figure 1: Mathematical model of our system.</i></p><h2>Design</h2><p>To create our model we created a set of PDE:s to represent our system, see figure 1. The change of state is determined via a set of heaviside step functions(noted as theta) that are controlled by threshold concentrations noted as K_i, where i indicates which density is related to the threshold. Y.enterocolitica have been found to be immobile at 37 degrees celsius and do therefore not have a diffusion term. All parameters are defined in figure 2. You can read more about our design under the design page.</p><br><table id="partsT"><tr><th>Parameter</th><th>Value</th><th>Source</th></tr><tr><td>D_b</td><td>3*10^-4 mm^2/s</td><td>5</td></tr><tr><td>D_c</td><td>4.2*10^-5 mm^2/s</td><td>1</td></tr><tr><td>D_o</td><td>4.9*10^-6 mm^2/s</td><td>2</td></tr><tr><td>K_c</td><td>2.25*10^-7 molecules/mL</td><td>3</td></tr><tr><td>K_a</td><td>10^-8 molecules/mL</td><td>est.</td></tr><tr><td>beta_c</td><td>15.625 s^-1</td><td>1</td></tr><tr><td>beta_o</td><td>1 s^-1</td><td>est.</td></tr><tr><td>etac</td><td>1/1200</td><td>ets.</td></tr><tr><td>eta_o</td><td>1/1200</td><td>4</td></tr></table><p><i>Table 1. Table of parameter values</i></p><h2>Results</h2><p>The model was split into two scenarios depending if the Bactissile could coexist on the Y.enterocolitica or not. Being able to coexist with Y.enterocolitica was 6 times as effective as the case where the Bactissile could only surround the Y.enterocolitica, figure 1 and 2. Both models showed that the production of colicin is the rate limiting step, figure 3 and 4, while OHHL threshold and diffusion coefficients importance differed. In the coexist model it was only needed for the OHHL threshold to be less than the OHHL initial concentration. However in the non coexist model both OHHL and diffusion coefficients changes had a significant impact on the time to kill all Y.enterocolitica.</p><table><tr><td><img class="main_pic_left" src="https://static.igem.org/mediawiki/2014/4/48/Populationtest2_Uppsala14.jpg"></td><td><p><i>Figure 2: Bactissile and Y.enterocolitica coexists. 100s until elimination</i></p></td></tr></table><table><tr><td><img class="main_pic_left" src="https://static.igem.org/mediawiki/2014/8/83/Populationtest3_Uppsala14.jpg"></td><td><p><i>Figure 3: Bactissile and Y.enterocolitica does not coexist. 10% remains after 600s.</i></p></td></tr></table><table><tr><td><img class="main_pic_left" style="padding-right: 20px;" src="https://static.igem.org/mediawiki/2014/a/a0/Populationtest6_Uppsala14.png"></td><td><p><i>Figure 4:  Coexist model, Y-axis: Time to eliminate the initial Y.enterocolitica colony. X-axis: Multiplier of the original production rate.</i></p></td></tr></table><table><tr><td><img class="main_pic_left" style="padding-right: 20px;" src="https://static.igem.org/mediawiki/2014/0/0f/Populationtest9_Uppsala14.png"></td><td><p><i>Figure 5:  Non coexist model, Y-axis: Time to eliminate the initial Y.enterocolitica colony. X-axis: Multiplier of the original production rate.</i></p></td></tr></table><br><p>Based upon this, efforts should continue to form an adhesion system that ensures that the Bactissile can coexist. Further on measurements of the amount of colicin production rate should be taken to make better predictions, and work should be focused on increasing this production.<br><br>If no effective adhesion system can be built, improved effectivity could be achieved by taking another dose of Bactissiles within a short interval, e.g. every 20 minutes. This would act as a “reset” for the graph. Another alternative is to take the Bactissiles prior to sickness so that no Y.enterocolitica can infect in the first place. However unless the Bactissile can stay in the intestine for a long period of time you would frequently have to retake the bacteria. Having a large amount of cells in a living system is unstable since the amount of mutations increase, that could result in the system not working as intended.</p>';
document.getElementById("tab1").innerHTML = '<h2>Introduction</h2><p>We wanted to evaluate the effectiveness of our system in the real intestine of a human. Since it requires a lot of ethical consideration and animal trials to test on real humans we decided to construct a model instead. The model will also give us insight into what parameters are most important when improving our system. Since the thought out medicine is thought of as a pill, see Policy & Practise, this is the premiss we will evaluate our modeling around.<br><br>Our final model is able to produce both a “density map” showing the small intestine as a two dimensional landscape and graphs of the total amount of cells and molecules over time. The first model is more heavy to run and can therefore only run at limited time intervals, while the later model is able to run at much longer intervals. The density map is good for analysing movement of molecules and cells in the domain, while the graphs are nice to show total effect of the system.</p><img src="https://static.igem.org/mediawiki/2014/7/73/Populationsummary1_Uppsala14.PNG"></img><p><i>Figure 1: Mathematical model of our system.</i></p><h2>Design</h2><p>To create our model we created a set of PDE:s to represent our system, see figure 1. The change of state is determined via a set of heaviside step functions(noted as theta) that are controlled by threshold concentrations noted as K_i, where i indicates which density is related to the threshold. Y.enterocolitica have been found to be immobile at 37 degrees celsius and do therefore not have a diffusion term. All parameters are defined in figure 2. You can read more about our design under the design page.</p><br><table id="partsT"><tr><th>Parameter</th><th>Value</th><th>Source</th></tr><tr><td>D_b</td><td>3*10^-4 mm^2/s</td><td>5</td></tr><tr><td>D_c</td><td>4.2*10^-5 mm^2/s</td><td>1</td></tr><tr><td>D_o</td><td>4.9*10^-6 mm^2/s</td><td>2</td></tr><tr><td>K_c</td><td>2.25*10^-7 molecules/mL</td><td>3</td></tr><tr><td>K_a</td><td>10^-8 molecules/mL</td><td>est.</td></tr><tr><td>beta_c</td><td>15.625 s^-1</td><td>1</td></tr><tr><td>beta_o</td><td>1 s^-1</td><td>est.</td></tr><tr><td>etac</td><td>1/1200</td><td>ets.</td></tr><tr><td>eta_o</td><td>1/1200</td><td>4</td></tr></table><p><i>Table 1. Table of parameter values</i></p><h2>Results</h2><p>The model was split into two scenarios depending if the Bactissile could coexist on the Y.enterocolitica or not. Being able to coexist with Y.enterocolitica was 6 times as effective as the case where the Bactissile could only surround the Y.enterocolitica, figure 1 and 2. Both models showed that the production of colicin is the rate limiting step, figure 3 and 4, while OHHL threshold and diffusion coefficients importance differed. In the coexist model it was only needed for the OHHL threshold to be less than the OHHL initial concentration. However in the non coexist model both OHHL and diffusion coefficients changes had a significant impact on the time to kill all Y.enterocolitica.</p><table><tr><td><img class="main_pic_left" src="https://static.igem.org/mediawiki/2014/4/48/Populationtest2_Uppsala14.jpg"></td><td><p><i>Figure 2: Bactissile and Y.enterocolitica coexists. 100s until elimination</i></p></td></tr></table><table><tr><td><img class="main_pic_left" src="https://static.igem.org/mediawiki/2014/8/83/Populationtest3_Uppsala14.jpg"></td><td><p><i>Figure 3: Bactissile and Y.enterocolitica does not coexist. 10% remains after 600s.</i></p></td></tr></table><table><tr><td><img class="main_pic_left" style="padding-right: 20px;" src="https://static.igem.org/mediawiki/2014/a/a0/Populationtest6_Uppsala14.png"></td><td><p><i>Figure 4:  Coexist model, Y-axis: Time to eliminate the initial Y.enterocolitica colony. X-axis: Multiplier of the original production rate.</i></p></td></tr></table><table><tr><td><img class="main_pic_left" style="padding-right: 20px;" src="https://static.igem.org/mediawiki/2014/0/0f/Populationtest9_Uppsala14.png"></td><td><p><i>Figure 5:  Non coexist model, Y-axis: Time to eliminate the initial Y.enterocolitica colony. X-axis: Multiplier of the original production rate.</i></p></td></tr></table><br><p>Based upon this, efforts should continue to form an adhesion system that ensures that the Bactissile can coexist. Further on measurements of the amount of colicin production rate should be taken to make better predictions, and work should be focused on increasing this production.<br><br>If no effective adhesion system can be built, improved effectivity could be achieved by taking another dose of Bactissiles within a short interval, e.g. every 20 minutes. This would act as a “reset” for the graph. Another alternative is to take the Bactissiles prior to sickness so that no Y.enterocolitica can infect in the first place. However unless the Bactissile can stay in the intestine for a long period of time you would frequently have to retake the bacteria. Having a large amount of cells in a living system is unstable since the amount of mutations increase, that could result in the system not working as intended.</p>';
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document.getElementById("tab2").innerHTML = '<p>Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et rit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.</p>';
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document.getElementById("tab2").innerHTML = '<br><p>In this section we explain how we created our system of PDE:s, the parameters, the domain, the boundaries and the initial values. We also discuss how exact our model is and what its major flaws are. </p><h2>Inspiration</h2><p>A similar system that was controlled by switching on the CheZ-gene expression when the bacteria detected a specific chemical signal have been studied before (6). However no mathematical model was found. Although there are well established mathematical models for chemotaxis in <i>E.coli</i>, called Keller Segel(KS) models(7).The Keller Segel models are known to be intuitive and to capture the key-elements of chemotaxis, and many alterations are possible to improve upon the model(7).The KS model controls the movement via sensing a change in concentration of the sensed molecule, thereby following a gradient.A genetically controlled system can only return a expression result depending upon the rate of the chemical signal, or activates/deactivates once a threshold concentration has been reached. Our model can therefore not be based upon the KS model.</p><h2>Movement and target module</h2><p>Since we could not use the KS model we had to start from scratch, and the first step was the modeling of a random walk. Random walk was modeled as a diffusion via Fick’s law of diffusion, as is the convention when modeling large number of cells.<br><br>To model the activation of our system when a threshold concentration of chemical signal( K_o) is reached, an additional bacteria density (b_a) for attacking Bactissiles was introduced. This enables a visual representation of the amount of attacking Bactissiles. This also solves the problem to turn off the random walk when the Bactissiles are attacking. The activation and de-activation of bacteria is controlled via a heavieside-step function, notated as theta.</p>
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<img src="https://static.igem.org/mediawiki/2014/c/c8/Populationdesig1_Uppsala14.PNG"></img><h2>The <i>Y.enterocolitica</i></h2><p>The <i>Y.enterocolitica</i>, noted p, has been shown to be immobile at 37 degrees Celsius (8), and does therefore not need a term describing its random walk. Drift will be neglected since most bacteria attach to the intestinal wall and might therefore not be influenced by drift nor intestinal movement. Neither will growth of the <i>Y.enterocolitica</i> be included since the generation time is about 30min in optimal conditions for most bacteria. Considering the rough competitive climate in the intestine, it would be hard for the <i>Y.enterocolitica</i> to grow. It is therefore not worth to add a growth term due to its complexity.<br><br>The death of <i>Y.enterocolitica</i> due to sufficient concentrations of the colicin will be included in the model via a heaviside-step function. We can control when the <i>Y.enterocolitica</i> should be eliminated by setting up a threshold, K_c. When the colicin is above K_c the prey will be eliminated via the -p term, as seen in equation below.</p><img src="https://static.igem.org/mediawiki/2014/8/88/Populationdesign2_Uppsala14.PNG"></img><br><h2>The sensing module</h2><p>To incorporate the sensing of <i>Y.enterocolitica</i> we added a PDE to explain how the concentration of OHHL change over time. OHHL is produced by <i>Y.enterocolitica</i> at a constant production rate,( beta_p), in our formulas. The diffusion of the molecule is modeled via Fick’s law with the diffusion coefficient D_o. Since the OHHL is not stable in the intestine we also added a degradation constant, eta_o. Lastly we added consumption of the molecule by our Bactissile with a consumption rate, alpha_b.</p><img src="https://static.igem.org/mediawiki/2014/0/09/Populationdesign3_Uppsala14.PNG"></img><h2>The killing module</h2><p>Finally, we needed the killing module. Since the killing is determined by the concentration of colicin we added a PDE for the colicin. The colicin is produced by attacking Bactissiles with a production rate of, beta_c. As with the OHHL we also introduce both diffusion with diffusion constant, D_c, and degradation with constant, eta_c. However we have no consumption because the <i>Y.enterocolitica</i> will probably lyse upon death and the molecules can be reused.</p><img src="https://static.igem.org/mediawiki/2014/e/e5/Populationdesign4_Uppsala14.PNG"></img><h2>Domain and boundary</h2><p>Further, we need to define a domain for our system to be active in. The domain will consist of a rectangle representing the intestinal wall cut open and stretched out. This creates the advantageous 2D domain that could easily be studied. The intestine is folded over and over again, which creates opportunities for bacteria and cells to interact between the walls folded close together. Interactions between areas of the fold will however be neglected, due to high complexibility. Since most bacteria is attached to the intestinal wall they cannot diffuse over to the other wall and neglecting that diffusion will not be unrealistic.  The main loss is the diffusion of molecules over the surface. If the diffusion is fast enough the molecules would be able to reach the wall on the other side and trigger both detection and death of cells. If this would happen in real life it would not make our system less useful since the real life result will be better then the result proposed by the model.<br><br>The boundary of the domain was defined by setting the concentration of all molecules and bacteria to zero at the edges leading out of the defined part of the intestine. This is an approximation of the greater area outside the small intestine which will lead to concentrations approaching zero as the distance from the diffusion source increases . If the diffusion source would be set close to the domain boundaries this approximation would not be realistic, instead the domain should then be expanded to allow diffusion calculations to take place.</p><h2>Initial values</h2><p>To start our model we need to set up initial values, a time = 0 scenario, that is the moment before the medicine reached the intestine. We want to place a colony of <i>Y.enterocolitica</i> that has already built up a steady-state of OHHL around itself, in our model. Therefore we need to define the location x_p, y_p of the <i>Y.enterocolitica</i> and the radius of the colony, r_p. This can then be inserted via an if-statement into MATLAB initial code. The concentration of OHHL in the location can be calculated via running a simulation on a large time frame, eg. 3 hours, and then observe  at what value OHHL concentrations converges over time.<br><br>The position of the <i>Y.enterocolitica</i> colony was set to the middle of the system to make sure that the boundary conditions assumption would not effect our model too much. The radius of the colony was set to 3.16 (sqrt(10)) mm since no good data was found. The estimation originates from a test run to get nice results and internal guess.<br><br>The initial density of <i>Y.enterocolitica</i> was set to 1*10^8 cells/mL since it is known that they are constantly in their exponential phase during host infection(8). The initial concentration of our Bactissile was set to 1*10^7 cells/mL since it is likely that it is lower than the <i>Y. enterocolitica </i> concentration. One might suggest that the density should be set even lower, but due to restricted capacity to run long simulations we decided to go with 1*10^7 cells/mL.</p><h2>Parameters</h2><p>Some of the parameter values were found in articles while others were estimated, see table 1. A few parameters needed to be reworked, or did not precisely fit our system and will be discussed further.</p>';
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document.getElementById("tab3").innerHTML = '<p>Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et rit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.</p>';

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