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| | <li> | | <li> |
| | <a href="https://2016.igem.org/Team:UofC_Calgary/Model">Model</a> | | <a href="https://2016.igem.org/Team:UofC_Calgary/Model">Model</a> |
| | + | </li><li> |
| | + | <a href="https://2016.igem.org/Team:UofC_Calgary/Design">Applied Design</a> |
| | </li> | | </li> |
| | <li> | | <li> |
| | <a href="https://2016.igem.org/Team:UofC_Calgary/Parts">Parts Registry</a> | | <a href="https://2016.igem.org/Team:UofC_Calgary/Parts">Parts Registry</a> |
| | </li> | | </li> |
| | + | <li> |
| | + | <a href="https://2016.igem.org/Team:UofC_Calgary/Composite_Part">Composite Parts</a> |
| | + | </li> |
| | + | |
| | </ul> | | </ul> |
| | </li> | | </li> |
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| | <a href="https://2016.igem.org/Team:UofC_Calgary/HP/Gold">Gold</a> | | <a href="https://2016.igem.org/Team:UofC_Calgary/HP/Gold">Gold</a> |
| | </li> | | </li> |
| | + | <li> |
| | + | <a href="https://2016.igem.org/Team:UofC_Calgary/Policy"> Policy Brief </a> |
| | + | </li> |
| | </ul> | | </ul> |
| | </li> | | </li> |
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| | | | |
| | <li> | | <li> |
| − | <a href="https://2016.igem.org/Main_Page" data-toggle="modal" data-target="#login-form" class="c-btn-border-opacity-04 c-btn btn-no-focus c-btn-header btn btn-sm c-btn-border-1x c-btn-white c-btn-circle c-btn-uppercase c-btn-sbold"><i class="icon-chemistry"></i> iGEM </a> | + | <a href="https://2016.igem.org/Main_Page" data-toggle="modal" data-target="#login-form" class="c-btn-border-opacity-04 c-btn btn-no-focus c-btn-header btn btn-sm c-btn-border-1x c-btn-white c-btn-circle c-btn-sbold"><i class="icon-chemistry"></i> iGEM </a> |
| | </li> | | </li> |
| | <li class="c-quick-sidebar-toggler-wrapper"> | | <li class="c-quick-sidebar-toggler-wrapper"> |
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| | <!-- BEGIN: PAGE CONTENT --> | | <!-- BEGIN: PAGE CONTENT --> |
| | <!--BEGIN: SLIDE #1 --> | | <!--BEGIN: SLIDE #1 --> |
| − | <img alt="" src="https://static.igem.org/mediawiki/2016/8/87/T--UofC_Calgary--humanpractices.jpg" data-bgposition="center center" data-bgfit="cover" data-bgrepeat="no-repeat" style="width: 100%; height: 100%;"> | + | <img alt="" src="https://static.igem.org/mediawiki/2016/d/d2/T--UofC_Calgary--project.jpg" data-bgposition="center center" data-bgfit="cover" data-bgrepeat="no-repeat" style="width: 100%; height: 100%;"> |
| | <!-- END: LAYOUT/SLIDERS/REVO-SLIDER-1 --> | | <!-- END: LAYOUT/SLIDERS/REVO-SLIDER-1 --> |
| | | | |
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| | <!-- Begin: Title 1 component --> | | <!-- Begin: Title 1 component --> |
| | <div class="c-content-title-1"> | | <div class="c-content-title-1"> |
| − | <h3 class="c-font-uppercase c-font-bold">Model</h3> | + | <h3 class="c-font-uppercase c-font-bold"><a href="https://static.igem.org/mediawiki/2016/a/af/T--UofC_Calgary--ModellingPDF.pdf">Model</a></h3> |
| | <div class="c-line-left c-theme-bg"> | | <div class="c-line-left c-theme-bg"> |
| | </div> | | </div> |
| | </div> | | </div> |
| − | <!-- End--> | + | <!-- End--> <center><object data="https://static.igem.org/mediawiki/2016/a/af/T--UofC_Calgary--ModellingPDF.pdf" type="application/pdf" width="100%" height="600px"> |
| − | <!-- PASTE --> | + | Your device does not support embed PDFs. Please click the following link to open up the PDF. <a href="https:// static. igem. org/ mediawiki/ 2016/a/ af/ T-- UofC_Calgary-- ModellingPDF. pdf"> Modelling. pdf</ a> |
| − | <p><strong>Best Model Websites</strong></p>
| + | </object> </center> |
| − | <p><a href="https://2015.igem.org/Team:Waterloo/Modeling"><span style="font-weight: 400;">https://2015.igem.org/Team:Waterloo/Modeling</span></a></p>
| + | |
| − | <p><a href="https://2015.igem.org/Team:Oxford/Modeling"><span style="font-weight: 400;">https://2015.igem.org/Team:Oxford/Modeling</span></a></p>
| + | |
| − | <p><a href="https://2015.igem.org/Team:Czech_Republic/Software"><span style="font-weight: 400;">https://2015.igem.org/Team:Czech_Republic/Software</span></a></p>
| + | |
| − | <h2> </h2>
| + | |
| − | <p><span style="font-weight: 400;">Look at “Modelling Story” in Google Drive for ideas</span></p>
| + | |
| − | <h2> </h2>
| + | |
| − | <p><span style="font-weight: 400;">*Talk to Syed (for a modelling page) and Christine (for layout)</span></p>
| + | |
| − | <h2> </h2>
| + | |
| − | <p><strong>Table of Contents</strong></p>
| + | |
| − | <h2> </h2>
| + | |
| − | <ul>
| + | |
| − | <li style="font-weight: 400;"><span style="font-weight: 400;">Introduction</span></li>
| + | |
| − | <li style="font-weight: 400;"><span style="font-weight: 400;">Growth Curves</span></li>
| + | |
| − | <li style="font-weight: 400;"><span style="font-weight: 400;">Diffusion Model</span></li>
| + | |
| − | <li style="font-weight: 400;"><span style="font-weight: 400;">Production Rate</span></li>
| + | |
| − | <li style="font-weight: 400;"><span style="font-weight: 400;">Degradation Rate</span></li>
| + | |
| − | <li style="font-weight: 400;"><span style="font-weight: 400;">Summary</span></li>
| + | |
| − | <li style="font-weight: 400;"><span style="font-weight: 400;">Improvements</span></li>
| + | |
| − | </ul>
| + | |
| − | <p> </p>
| + | |
| − | <h2> </h2>
| + | |
| − | <p><strong>Introduction</strong></p>
| + | |
| − | <p><em><span style="font-weight: 400;">How long can a patch last on an astronaut? </span></em></p>
| + | |
| − | <p><em><span style="font-weight: 400;">How much radioactive peptide will be diffused through in the astronaut’s system?</span></em></p>
| + | |
| − | <p><em><span style="font-weight: 400;"> When should the astronaut pop the extra media packet? </span></em></p>
| + | |
| − | <h2> </h2>
| + | |
| − | <p><span style="font-weight: 400;">These were the types of questions we were able to answer by using a combination of lab experiments and mathematical models. These computative/analytical models / modelling / numerical techniques were used to evaluate how realistic our patch is, how beneficial it would be in space applications and where to make improvements, so that, one day, we can make our project a reality. </span><br /><br /></p>
| + | |
| − | <p><strong><math xmlns="http://www.w3.org/1998/Math/MathML"><mfrac><mn>1</mn><mn>2</mn></mfrac></math></strong></p>
| + | |
| − | <p><strong>Growth Curves</strong></p>
| + | |
| − | <p><span style="font-weight: 400;">Our first step was to determine the lifetime of our bacteria, </span><em><span style="font-weight: 400;">Bacillus subtilis</span></em><span style="font-weight: 400;">, as it would determine the nature of how our peptide would be produced how long the peptide would be produced for, and therefore, the lifetime of our patch. This was done through experimental growth curves:</span><br /><br /></p>
| + | |
| − | <p><strong><em>Figure 1: Raw data of growth curves at different temperatures. Three replicates of growth at various temperatures was measured every hour over a period of 24 hours. Optical density was measured by spectrophotometry at a wavelength of 600 nm (OD 600). The most relevant growth curve is the one in orange, as this is the average temperature of the surface of the skin.</em></strong></p>
| + | |
| − | <p> </p>
| + | |
| − | <p><span style="font-weight: 400;">The growth curves revealed that </span><em><span style="font-weight: 400;">B. subtilis</span></em><span style="font-weight: 400;">, under expected conditions,</span><span style="font-weight: 400;"> underwent death phase after 16-18 hours. This established the process when the packets of super-rich media in our patch needed to be added to increase the bacteria’s lifetime. For ease of remembrance for the user, we decided that the packets should be popped every 12 hours.</span></p>
| + | |
| − | <p><span style="font-weight: 400;">To simulate our patch, another experiment was conducted in which a packet of super rich media was added to the bacteria every 12 hours. This was in triplicates as there are three packets in our patch. Through this, we determined that the bacteria’s lifetime in our patch is 60 hours (about 2.5 days). Since </span><em><span style="font-weight: 400;">B. subtilis</span></em><span style="font-weight: 400;"> begins to release toxic material that may pass into the skin during its death phase (i.e. after 60 hours), we determined that the patch must be disposed of at this time. </span></p>
| + | |
| − | <p><span style="font-weight: 400;">The complete experiments can be found here (link).</span></p>
| + | |
| − | <p><strong>�</strong></p>
| + | |
| − | <p><strong>Diffusion Model</strong></p>
| + | |
| − | <p><span style="font-weight: 400;">MATLAB was used to develop a diffusion model to numerically represent the diffusion of our peptide, </span><span style="font-weight: 400;">Bowman–Birk protease inhibitor (BBI)</span><span style="font-weight: 400;">, from the patch, through the skin and into the blood. This diffusion model was developed with the hopes to answer questions, such as:</span></p>
| + | |
| − | <ul>
| + | |
| − | <li style="font-weight: 400;"><span style="font-weight: 400;">Does the peptide reach a constant concentration in the blood while the patch is on the user?</span></li>
| + | |
| − | <li style="font-weight: 400;"><span style="font-weight: 400;">Literature values show that the minimum required amount of peptide needed for radioprotection is 10 micromolar (link). Does the concentration in the blood reach 10 micromolar or higher?</span></li>
| + | |
| − | <li style="font-weight: 400;"><span style="font-weight: 400;">How long does it take for the concentration in the blood to reach zero after the patch has been removed?</span></li>
| + | |
| − | </ul>
| + | |
| − | <p><span style="font-weight: 400;">The following is a visual representation of what the system looks like.<br /></span><em><span style="font-weight: 400;"><br /></span></em><strong><em>Figure 2: A visual representation of the diffusion model system. Note that the main barriers in this diffusion system are the patch’s rate-controlling membrane and the skin. The skin was assumed to be one homogeneous layer (other factors, such as accounting differences in cellular structure of the skin, any absorption by cells and sweat ducts, enzymes, etc. were not considered).<br /><br /></em></strong></p>
| + | |
| − | <p><span style="font-weight: 400;">To start developing our model, Fick’s first and second law were used:</span></p>
| + | |
| − | <p><span style="font-weight: 400;">J = -D </span><span style="font-weight: 400;">dC</span><span style="font-weight: 400;">dx</span> <span style="font-weight: 400;">(1)</span></p>
| + | |
| − | <p><span style="font-weight: 400;">dC</span><span style="font-weight: 400;">dt</span><span style="font-weight: 400;"> = D </span><span style="font-weight: 400;">d</span><span style="font-weight: 400;">2</span><span style="font-weight: 400;">C</span><span style="font-weight: 400;">dx</span><span style="font-weight: 400;">2</span> <span style="font-weight: 400;"> (2)</span></p>
| + | |
| − | <h2> </h2>
| + | |
| − | <p><span style="font-weight: 400;">Where:</span></p>
| + | |
| − | <p><span style="font-weight: 400;">J</span><span style="font-weight: 400;"> = concentration flux (</span><span style="font-weight: 400;">mol</span><span style="font-weight: 400;">m</span><span style="font-weight: 400;">2</span><span style="font-weight: 400;">s</span><span style="font-weight: 400;">)</span></p>
| + | |
| − | <p><span style="font-weight: 400;">D</span><span style="font-weight: 400;"> = diffusion coefficient (</span><span style="font-weight: 400;">m</span><span style="font-weight: 400;">2</span><span style="font-weight: 400;">s</span><span style="font-weight: 400;">)</span></p>
| + | |
| − | <p><span style="font-weight: 400;">C</span><span style="font-weight: 400;"> = concentration (</span><span style="font-weight: 400;">mol</span><span style="font-weight: 400;">m</span><span style="font-weight: 400;">3</span><span style="font-weight: 400;">)</span></p>
| + | |
| − | <p><span style="font-weight: 400;">x</span><span style="font-weight: 400;"> = distance (</span><span style="font-weight: 400;">m</span><span style="font-weight: 400;">)</span></p>
| + | |
| − | <p><span style="font-weight: 400;">t</span><span style="font-weight: 400;"> = time (</span><span style="font-weight: 400;">s</span><span style="font-weight: 400;">)<br /><br /></span></p>
| + | |
| − | <p><span style="font-weight: 400;">We were able to develop three equations (one for each section - see Figure 2) which were used to determine the concentration in the patch, </span><span style="font-weight: 400;">C</span><span style="font-weight: 400;">0</span><span style="font-weight: 400;">, the concentration in the adhesive, </span><span style="font-weight: 400;">C</span><span style="font-weight: 400;">1</span><span style="font-weight: 400;">, and the concentration in the blood, </span><span style="font-weight: 400;">C</span><span style="font-weight: 400;">2</span><span style="font-weight: 400;">. These equations were developed on the basis that the change in concentration over time for a block is defined as the flux of peptide entering the block minus the flux of peptide leaving the block. To ensure that the units match, the flux variables were multiplied by the cross-sectional area and divided by the respective volume of the section.<br /><br /></span></p>
| + | |
| − | <p><span style="font-weight: 400;">dC0</span><span style="font-weight: 400;">dt</span><span style="font-weight: 400;">=production rate - J</span><span style="font-weight: 400;">1</span><span style="font-weight: 400;"> (3)</span></p>
| + | |
| − | <p><span style="font-weight: 400;"> </span><span style="font-weight: 400;"> = </span><span style="font-weight: 400;">production rate - (</span><span style="font-weight: 400;">-Dm </span><span style="font-weight: 400;">(C</span><span style="font-weight: 400;">1</span><span style="font-weight: 400;">-C</span><span style="font-weight: 400;">0</span><span style="font-weight: 400;">) </span><span style="font-weight: 400;">x</span><span style="font-weight: 400;">m</span><span style="font-weight: 400;">x-area</span><span style="font-weight: 400;">V</span><span style="font-weight: 400;">patch</span><span style="font-weight: 400;">)</span><span style="font-weight: 400;">(4)<br /><br /></span></p>
| + | |
| − | <p><span style="font-weight: 400;">dC1</span><span style="font-weight: 400;">dt</span><span style="font-weight: 400;">= J</span><span style="font-weight: 400;">1</span><span style="font-weight: 400;"> -J</span><span style="font-weight: 400;">2</span> <span style="font-weight: 400;">(5)</span></p>
| + | |
| − | <p><span style="font-weight: 400;"> = </span><span style="font-weight: 400;">(</span><span style="font-weight: 400;">-Dm </span><span style="font-weight: 400;">(C</span><span style="font-weight: 400;">1</span><span style="font-weight: 400;">-C</span><span style="font-weight: 400;">0</span><span style="font-weight: 400;">) </span><span style="font-weight: 400;">x</span><span style="font-weight: 400;">m</span><span style="font-weight: 400;">x-area</span><span style="font-weight: 400;">V</span><span style="font-weight: 400;">adhesive</span><span style="font-weight: 400;">)</span><span style="font-weight: 400;"> - </span><span style="font-weight: 400;">(</span><span style="font-weight: 400;">-Ds </span><span style="font-weight: 400;">(C</span><span style="font-weight: 400;">2</span><span style="font-weight: 400;">-C</span><span style="font-weight: 400;">1</span><span style="font-weight: 400;">) </span><span style="font-weight: 400;">x</span><span style="font-weight: 400;">s</span><span style="font-weight: 400;">x-area</span><span style="font-weight: 400;">V</span><span style="font-weight: 400;">adhesive</span><span style="font-weight: 400;">)</span><span style="font-weight: 400;"> (6)<br /><br /></span></p>
| + | |
| − | <p><span style="font-weight: 400;">dC2</span><span style="font-weight: 400;">dt</span><span style="font-weight: 400;">= J</span><span style="font-weight: 400;">2</span><span style="font-weight: 400;"> - degradation rate</span><span style="font-weight: 400;"> (7)</span></p>
| + | |
| − | <p><span style="font-weight: 400;"> </span><span style="font-weight: 400;">= (</span><span style="font-weight: 400;">-Ds </span><span style="font-weight: 400;">(C</span><span style="font-weight: 400;">2</span><span style="font-weight: 400;">-C</span><span style="font-weight: 400;">1</span><span style="font-weight: 400;">) </span><span style="font-weight: 400;">x</span><span style="font-weight: 400;">s</span><span style="font-weight: 400;">x-area</span><span style="font-weight: 400;">V</span><span style="font-weight: 400;">blood</span><span style="font-weight: 400;">)</span><span style="font-weight: 400;">- </span><span style="font-weight: 400;">degradation rate</span><span style="font-weight: 400;">(8)<br /><br /></span></p>
| + | |
| − | <p><span style="font-weight: 400;">Where the values are the following:</span></p>
| + | |
| − | <h2> </h2>
| + | |
| − | <p><strong><em>Table 1: Values Used In Equations (4), (6) and (8) </em></strong></p>
| + | |
| − | <table>
| + | |
| − | <tbody>
| + | |
| − | <tr>
| + | |
| − | <td>
| + | |
| − | <p><strong>Parameter</strong></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><strong>Value</strong></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><strong>Where Value Is Obtained From</strong></p>
| + | |
| − | </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">Cross sectional area, </span><span style="font-weight: 400;">x-area</span></p>
| + | |
| − | <p><span style="font-weight: 400;">(</span><span style="font-weight: 400;">m</span><span style="font-weight: 400;">2</span><span style="font-weight: 400;">)</span></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">4.9 </span><span style="font-weight: 400;">10</span><span style="font-weight: 400;">-3 </span></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">Patch is 7 cm by 7 cm</span></p>
| + | |
| − | </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">Diffusion coefficient of membrane, </span><span style="font-weight: 400;">D</span><span style="font-weight: 400;">m</span><span style="font-weight: 400;">(</span><span style="font-weight: 400;">m</span><span style="font-weight: 400;">2</span><span style="font-weight: 400;">s</span><span style="font-weight: 400;">)</span></p>
| + | |
| − | </td>
| + | |
| − | <td> </td>
| + | |
| − | <td>
| + | |
| − | <p><strong>?</strong></p>
| + | |
| − | </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">Thickness of membrane, </span><span style="font-weight: 400;">x</span><span style="font-weight: 400;">m</span><span style="font-weight: 400;"> (</span><span style="font-weight: 400;">m</span><span style="font-weight: 400;">)</span></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">50.8 </span><span style="font-weight: 400;">10</span><span style="font-weight: 400;">-6 </span></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">3M information sheet </span></p>
| + | |
| − | </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">Volume of patch,</span><span style="font-weight: 400;">V</span><span style="font-weight: 400;">patch</span><span style="font-weight: 400;"> (</span><span style="font-weight: 400;">m</span><span style="font-weight: 400;">3</span><span style="font-weight: 400;">)</span></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">1 </span><span style="font-weight: 400;">10</span><span style="font-weight: 400;">-5 </span></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">10 mL</span></p>
| + | |
| − | </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">Diffusion coefficient of skin, </span><span style="font-weight: 400;">D</span><span style="font-weight: 400;">s</span><span style="font-weight: 400;"> (</span><span style="font-weight: 400;">m</span><span style="font-weight: 400;">2</span><span style="font-weight: 400;">s</span><span style="font-weight: 400;">)</span></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><strong>1 </strong><strong>10</strong><strong>-10</strong></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><strong>Based on 1-slab model from analytical model from Nelly</strong></p>
| + | |
| − | </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">Thickness of skin, </span><span style="font-weight: 400;">x</span><span style="font-weight: 400;">s</span><span style="font-weight: 400;"> (</span><span style="font-weight: 400;">m</span><span style="font-weight: 400;">)</span></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">0.001</span></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">Ask Tiffany?</span></p>
| + | |
| − | </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">Volume of adhesive,</span><span style="font-weight: 400;">V</span><span style="font-weight: 400;">adhesive</span><span style="font-weight: 400;"> (</span><span style="font-weight: 400;">m</span><span style="font-weight: 400;">3</span><span style="font-weight: 400;">)</span></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">100 </span><span style="font-weight: 400;">10</span><span style="font-weight: 400;">-6 </span></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">Cross - sectional area </span><span style="font-weight: 400;"> thickness of adhesive (estimated to be 100 micrometers)</span></p>
| + | |
| − | </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">Volume of blood,</span><span style="font-weight: 400;">V</span><span style="font-weight: 400;">blood</span><span style="font-weight: 400;"> (</span><span style="font-weight: 400;">m</span><span style="font-weight: 400;">3</span><span style="font-weight: 400;">)</span></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">0.005</span></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">Volume of blood ranges from 4.7 L to 5 L (according to Google)</span></p>
| + | |
| − | </td>
| + | |
| − | </tr>
| + | |
| − | </tbody>
| + | |
| − | </table>
| + | |
| − | <h2> </h2>
| + | |
| − | <p><span style="font-weight: 400;">*An important note is that we were not able to find literature values for the diffusion of our peptide, BBI, through our patch’s size controlling membrane and the skin. For this reason, we used literature values for ____, to represent the diffusion of BBI through the skin. For the diffusion coefficient through the size-controlling membrane, which works . <br /><br /></span></p>
| + | |
| − | <p><span style="font-weight: 400;">Although this does not produce data that exactly represents the diffusion process of BBI in our system, it does reveal the general pattern of how it would diffuse. This was important to analyze as well.</span></p>
| + | |
| − | <p><span style="font-weight: 400;">The </span><strong>production rate</strong><span style="font-weight: 400;"> is the amount of peptide (BBI) produced by the bacteria (</span><em><span style="font-weight: 400;">B. subtilis</span></em><span style="font-weight: 400;">)</span><span style="font-weight: 400;"> in a given period of time.</span></p>
| + | |
| − | <p><span style="font-weight: 400;">The </span><strong>degradation rate</strong><span style="font-weight: 400;"> is the amount of peptide lost in a given period of time through enzyme degradation in the liver and excretion through the kidneys. The equation to represent the degradation rate is determined to be:<br /><br /></span></p>
| + | |
| − | <p><span style="font-weight: 400;">degradation rate = k</span><span style="font-weight: 400;">C</span><span style="font-weight: 400;">2</span><span style="font-weight: 400;"> (9)<br /><br /></span></p>
| + | |
| − | <p><span style="font-weight: 400;">Where:</span></p>
| + | |
| − | <p><span style="font-weight: 400;">k</span><span style="font-weight: 400;">= decay constant (</span><span style="font-weight: 400;">s</span><span style="font-weight: 400;">-1</span><span style="font-weight: 400;">)<br /><br /></span></p>
| + | |
| − | <p><span style="font-weight: 400;">To determine the decay constant, the exponential decay equation was used:</span></p>
| + | |
| − | <p><span style="font-weight: 400;">N(t) = N</span><span style="font-weight: 400;">0</span><span style="font-weight: 400;">e</span><span style="font-weight: 400;">-kt</span><span style="font-weight: 400;"> (10)<br /><br /></span></p>
| + | |
| − | <p><span style="font-weight: 400;">Rearranging equation (10) for </span><span style="font-weight: 400;">k</span><span style="font-weight: 400;">:</span></p>
| + | |
| − | <p><span style="font-weight: 400;">k = </span><span style="font-weight: 400;">ln (</span><span style="font-weight: 400;">N(t)</span><span style="font-weight: 400;">N</span><span style="font-weight: 400;">0</span><span style="font-weight: 400;">)</span><span style="font-weight: 400;">-t</span><span style="font-weight: 400;"> (11)<br /><br /></span></p>
| + | |
| − | <p><span style="font-weight: 400;">Half-life conditions for the peptide were used in equation (11) to solve for </span><span style="font-weight: 400;">k</span><span style="font-weight: 400;">. The values used were the following:<br /><br /></span></p>
| + | |
| − | <p><strong><em>Table 2: Values Used in Equation (11)</em></strong></p>
| + | |
| − | <table>
| + | |
| − | <tbody>
| + | |
| − | <tr>
| + | |
| − | <td>
| + | |
| − | <p><strong>Parameter</strong></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><strong>Value</strong></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><strong>Where Value Is Obtained From</strong></p>
| + | |
| − | </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">Time, </span><span style="font-weight: 400;">t</span><span style="font-weight: 400;"> ( </span><span style="font-weight: 400;">s</span><span style="font-weight: 400;">)</span></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">16200</span></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">The half life of the peptide</span></p>
| + | |
| − | </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">(</span><span style="font-weight: 400;">Concentration at time t, N(t) </span><span style="font-weight: 400;">Initial concentration, N</span><span style="font-weight: 400;">0</span> <span style="font-weight: 400;">)</span></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">0.5</span></p>
| + | |
| − | </td>
| + | |
| − | <td>
| + | |
| − | <p><span style="font-weight: 400;">It doesn’t matter what the initial concentration is… at the half life, this ratio is always 0.5?</span></p>
| + | |
| − | </td>
| + | |
| − | </tr>
| + | |
| − | </tbody>
| + | |
| − | </table>
| + | |
| − | <h2> </h2>
| + | |
| − | <p><span style="font-weight: 400;">After solving for </span><span style="font-weight: 400;">k</span><span style="font-weight: 400;">, we found that its value was </span><span style="font-weight: 400;">4.2786863 </span><span style="font-weight: 400;">10</span><span style="font-weight: 400;">-5 </span><span style="font-weight: 400;">s</span><span style="font-weight: 400;">-1</span><span style="font-weight: 400;">. Thus, equation (9) can be rewritten to be:<br /><br /></span></p>
| + | |
| − | <p><span style="font-weight: 400;">degradation rate = 4.2786863 </span><span style="font-weight: 400;">10</span><span style="font-weight: 400;">-5 </span><span style="font-weight: 400;">s</span><span style="font-weight: 400;">-1</span><span style="font-weight: 400;">C</span><span style="font-weight: 400;">2</span><span style="font-weight: 400;"> (12)<br /><br /></span></p>
| + | |
| − | <p><span style="font-weight: 400;">Now that we have determined both the production and degradation rate, we could plug in these values, as well as table 1, into equations (4), (6) and (8):<br /><br /></span></p>
| + | |
| − | <p><span style="font-weight: 400;">(13)</span></p>
| + | |
| − | <p><span style="font-weight: 400;">(14)</span></p>
| + | |
| − | <p><span style="font-weight: 400;">(15)<br /><br /></span></p>
| + | |
| − | <p><span style="font-weight: 400;">These equations were then solved through MATLAB by using the following codes (link?/download code). The following graphs for the concentration in each section vs time for the different locations were determined:</span></p>
| + | |
| − | <p> </p>
| + | |
| − | <p><strong><em>Figure 3: Concentration of BBI in the patch vs time</em></strong></p>
| + | |
| − | <h2> </h2>
| + | |
| − | <p><strong><em>Figure 4: Concentration of BBI in the adhesive vs time</em></strong></p>
| + | |
| − | <h2> </h2>
| + | |
| − | <p><strong><em>Figure 5: Concentration of BBI in the blood vs time</em></strong></p>
| + | |
| − | <h2> </h2>
| + | |
| − | <p><span style="font-weight: 400;">From these graphs, we were able to make the following conclusions to our initial problems:</span></p>
| + | |
| − | <ul>
| + | |
| − | <li style="font-weight: 400;"><span style="font-weight: 400;">The peptide does reach a constant concentration in the blood while the patch is on the user; from Figure 3, we can also determine exactly at what time this happens (from Figure 3, it shows this happens at ___. However, recall that this number does not represent when BBI reaches equilibrium in the system).</span></li>
| + | |
| − | </ul>
| + | |
| − | <ul>
| + | |
| − | <li style="font-weight: 400;"><span style="font-weight: 400;">We are also able to determine whether the peptide will reach 10 micromolar (the radioprotection minimum). From Figure 3, it shows that the peptides reaches a maximum of _____, and since this is greater than 10 micromolar, it means that the patch will provide radioprotection for the user.</span></li>
| + | |
| − | </ul>
| + | |
| − | <ul>
| + | |
| − | <li style="font-weight: 400;"><span style="font-weight: 400;">From Figure 3, we are also able to determine that it takes roughly ____ hours for the concentration of peptide in the blood to reach zero (or 10 micromolar?). Hence, we can determine that a new patch should be applied after ____ hours, when the peptide concentration has reached zero micromolar (or 10 micromolar?).</span></li>
| + | |
| − | </ul>
| + | |
| − | <h2> </h2>
| + | |
| − | <p><span style="font-weight: 400;">Some other interesting results from the model were:</span></p>
| + | |
| − | <ul>
| + | |
| − | <li style="font-weight: 400;"><span style="font-weight: 400;">There was an </span><strong>exponential increase</strong><span style="font-weight: 400;"> in the concentration of the peptide. </span></li>
| + | |
| − | </ul>
| + | |
| − | <h2> </h2>
| + | |
| − | <p><span style="font-weight: 400;">References (for Diffusion Model):</span></p>
| + | |
| − | <p><a href="http://serc.carleton.edu/quantskills/methods/quantlit/expGandD.html"><span style="font-weight: 400;">http://serc.carleton.edu/quantskills/methods/quantlit/expGandD.html</span></a><span style="font-weight: 400;"> (exponential decay equation)</span></p>
| + | |
| − | <p><span style="font-weight: 400;">________ (literature value for when bacteria starts creating its peptide)</span></p>
| + | |
| − | <h2> </h2>
| + | |
| − | <p><a href="https:// solutions. 3m. com/ 3MContentRetrievalAPI/ BlobServlet?locale=en_WW&lmd=1219086637000&assetId=1114279699559&assetType=MMM_Image&blobAttribute=ImageFile"><span style="font-weight: 400;">https://solutions.3m.com/3MContentRetrievalAPI/BlobServlet?locale=en_WW&lmd=1219086637000&assetId=1114279699559&assetType=MMM_Image&blobAttribute=ImageFile</span></a ></ p> | + | |
| − | <p><span style="font-weight: 400;">Value for the patch (3m info sheet)</span></p>
| + | |
| − | <p><strong>�</strong></p>
| + | |
| − | <p><strong>Improvements???</strong></p>
| + | |
| − | <p><span style="font-weight: 400;">E.g. change the diffusion coefficient and see what the result is and put in the graph</span></p>
| + | |
| − | <h2> </h2>
| + | |
| − | <p><strong>Summary of Results</strong></p>
| + | |
| − | <p><span style="font-weight: 400;">Here is a summary of how the patch works, based on our results and conclusions from the lab experiments and computational models:</span></p>
| + | |
| − | <p><em><span style="font-weight: 400;">Timeline picture - Christine … caption it “Our patch’s story”<br /><br /><br /></span></em></p>
| + | |
| − | <p><strong><em>Figure 6: A visual representation of how the patch works.</em></strong></p>
| + | |
| − | <ul>
| + | |
| − | <li style="font-weight: 400;"><span style="font-weight: 400;">The patch can be applied for 60 hours (about 2.5 days)</span></li>
| + | |
| − | <li style="font-weight: 400;"><span style="font-weight: 400;">The packets need to be popped every 12 hours</span></li>
| + | |
| − | <li style="font-weight: 400;"><span style="font-weight: 400;">The steady state concentration of radioactive peptide in the blood is _____, which is. This is __inbetween? than the required amount for radioprotective effects in the human body. It reaches this steady state concentration at ____ hours. </span></li>
| + | |
| − | <li style="font-weight: 400;"><span style="font-weight: 400;">It takes ___ hours for the peptide concentration in the blood to reach zero </span></li>
| + | |
| − | <li style="font-weight: 400;"><span style="font-weight: 400;">A new patch can be applied after ____ hours</span></li>
| + | |
| − | </ul>
| + | |
| − | <!-- PASTE -->
| + | |
| | </div> | | </div> |
| | </div> | | </div> |
| | + | |
| | + | <br><br><p><center><font size="4"><a href="https://static.igem.org/mediawiki/2016/a/af/T--UofC_Calgary--ModellingPDF.pdf">Click here to view the above PDF</a></font></center></p> |
| | + | |
| | </div> | | </div> |
| | <!-- END: CONTENT/MISC/ABOUT-1 --> | | <!-- END: CONTENT/MISC/ABOUT-1 --> |
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| − | <h3 class="c-font-uppercase c-font-bold c-font-white">i<span class="c-theme-font">GEM</span></h3> | + | <h3 class="c-font-bold c-font-white">i<span class="c-theme-font">GEM</span></h3> |
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| − | Lorem ipsum dolor sit amet, consectetuer adipiscing elit, s ed elit diam nonummy ad minim veniam quis nostrud exerci et tation diam.
| + | iGEM is an international competition promoting synthetic biology as a means to solve social, economic and humanitarian problems around the globe. The iGEM Jamboree is held in Boston annually. In 2016, over 300 teams are competing against each other. |
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| − | </div>
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| − | <div class="c-post-content">
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| − | <h4 class="c-post-title"><a href="#">BBI & KTI Have Arrived!</a></h4>
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| | <h4 class="c-post-title"><a href="#">Fully Trained!</a></h4> | | <h4 class="c-post-title"><a href="#">Fully Trained!</a></h4> |
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| − | Lorem ipsum dolor ipsum sit ipsum amet, consectetuer sit adipiscing elit ipsum elit elit ipsum elit | + | Our entire team received a full BioSafety education from the University of Calgary! This entailed going to classes to prepare for a final quiz that tested our ability to be safe in the lab. Several of our members also had radiation training and clearance to ensure that work done with radiation was safe! |
| | </p> | | </p> |
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