Team:Yale/Parts

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<h1 >WELCOME TO iGEM 2014! </h1>
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<p>Your team has been approved and you are ready to start the iGEM season!
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<br>On this page you can document your project, introduce your team members, document your progress <br> and share your iGEM experience with the rest of the world! </p>
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<p style="color:#E7E7E7"> <a href="https://2014.igem.org/wiki/index.php?title=Team:Yale/Parts&action=edit"style="color:#FFFFFF"> Click here  to edit this page!</a> </p>
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<a href="https://igem.org/Team.cgi?year=2014&team_name=Yale"style="color:#000000"> Official Team Profile </a></td>
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<a href="https://2014.igem.org/Team:Yale/Parts"style="color:#000000"> Parts</a></td>
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<h1 style="margin-top:22px; font-size:50px;">Modeling</h1>
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<tr><td colspan="4"><h2>Modeling E. coli growth producing a toxic compound</h2>
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We sought out to determine the optimal time to induce the E. coli in order to produce the largest quantity of antimicrobial peptides.  We hypothesized that the optimal induction time would be around mid-log, when the E. coli are growing fastest and there are enough bacteria to produce a significant amount of peptide before the population levels drop. To test this theory, we created a theoretical model using MATLAB, using E. coli logistical growth combined with exponential decay (due to the antimicrobial peptide) at different induction times, as represented in the graphic below.
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<td > <h3>What information do I need to start putting my parts on the Registry? </h3></td>
 
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An important aspect of the iGEM competition is the use and creation of standard  biological parts. Each team will make new parts during iGEM and will submit them to the <a href="http://partsregistry.org"> Registry of Standard Biological Parts</a>. The iGEM software provides an easy way to present the parts your team has created. The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. 
 
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<strong>Note that if you want to document a part you need to document it on the <a href="http://partsregistry.org Registry"> Registry</a>, not on your team wiki.</strong> Future teams and other users and are much more likely to find parts on the Registry than on your team wiki.
 
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Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without a need to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.
 
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<tr><td colspan="2"><h2>Determining Optimal Time to Induce Expression</h2>
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As soon as possible! We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better recall you will have of all details surrounding your parts. Remember you don't need to send us the DNA to create an entry for a part on the Registry. However, you must send us the sample/DNA before the Jamboree. Only parts for which you have sent us samples/DNA are eligible for awards and medal requirements.  
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We simulated a 24 hour period and determined the optimal time to induce the cells is around mid-log (~7.5 hours). Inducing at this time maximizes production of the peptide. The graph below shows E. coli growth with induction at different times.  They follow a logistic growth model until the inducer is added and then there is an exponential decay. </p>
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<p>Overlayed with this graph is a plot of <strong>total production of of the peptide vs. time of induction</strong>, (with induction at every 6 minutes over a 24 hour period). The highest production of peptide over the lifespan of these bacteria is represented by the peak of this plot, which corresponds to induction at mid-log, as we previously hypothesized.<br/> The MATLAB code for our model can be found <strong>Here</strong>.
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The information needed to initially create a part on the Registry is:
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We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. Check out part <a href="http://parts.igem.org/Part:BBa_K404003">BBa_K404003</a> for an excellent example of a highly characterized part.
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You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry"> Add a Part to the Registry</a> link.
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<tr><td colspan="3" > <h3> Parts Table</h3></td></tr>
 
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Any parts your team has created will appear in this table below:</td></tr>
 
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<groupparts>iGEM013 Yale</groupparts>
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Revision as of 01:27, 17 October 2014

Modeling

Modeling E. coli growth producing a toxic compound

We sought out to determine the optimal time to induce the E. coli in order to produce the largest quantity of antimicrobial peptides. We hypothesized that the optimal induction time would be around mid-log, when the E. coli are growing fastest and there are enough bacteria to produce a significant amount of peptide before the population levels drop. To test this theory, we created a theoretical model using MATLAB, using E. coli logistical growth combined with exponential decay (due to the antimicrobial peptide) at different induction times, as represented in the graphic below.

Determining Optimal Time to Induce Expression

We simulated a 24 hour period and determined the optimal time to induce the cells is around mid-log (~7.5 hours). Inducing at this time maximizes production of the peptide. The graph below shows E. coli growth with induction at different times. They follow a logistic growth model until the inducer is added and then there is an exponential decay.

Overlayed with this graph is a plot of total production of of the peptide vs. time of induction, (with induction at every 6 minutes over a 24 hour period). The highest production of peptide over the lifespan of these bacteria is represented by the peak of this plot, which corresponds to induction at mid-log, as we previously hypothesized.
The MATLAB code for our model can be found Here.

Main Campus:
Molecular, Cellular & Developmental Biology
219 Prospect Street
P.O. Box 208103
New Haven, CT 06520
Phone: 203.432.3783
igem@yale.edu
natalie.ma@yale.edu (Graduate Advisor)
Copyright (c) 2014 Yale IGEM