Team:Davidson-MissouriW

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    <div id="orangeBox"><h3>Optimizing Codons</h3><br>
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        <p>Building weighted items for the Knapsack through codon variation of the TetA gene led to Foundational Advances&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</p>
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        <a href="http://2010.igem.org/Team:Davidson-MissouriW/OptimizingCodons">Details</a>
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    <div id="greenBox"><h3>Characterizing Cre/Lox</h3><br>
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    <p>Foundational Advances were made as 11 novel lox sites for Cre recombination were built for randomly choosing Knapsack objects
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    <a href="http://2010.igem.org/Team:Davidson-MissouriW/CreLox">Details</a>
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  <div id="blueBox"><h3>Measuring Gene Expression</h3><br>
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    <p>Design and construction of a Knapsack biological computer required Foundational Advances in the measurement of gene expression</p>
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    <a href="http://2010.igem.org/Team:Davidson-MissouriW/MeasuringExpression">Details</a>
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         <div id="mission_box"> <h3> iGEM Davidson – MWSU 2010: Tools </h3>
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         <div id="mission_box"> <h3> iGEM Davidson – Missouri Western 2010:<br>Foundational Advances in Biology and the Knapsack Problem </h3>
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            <p>The team has created several tools in conjunction with our iGem project.</p>
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          <p> The Davidson/Missouri Western multidisciplinary team is using synthetic biology to address a mathematical problem in <i>Escherichia coli</i>.  Specifically, we are addressing the Knapsack Problem, an NP-complete problem that asks, “Given a finite number of weighted items, can one find a subset of these items that completely fills a knapsack of fixed capacity?” </p>
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            <a href="http://gcat.davidson.edu/igem10/index.html"
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                <h3>The Oligator</h3>
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                            <p>Designing and building DNA sequences is a fundamental tool for anyone who works in synthetic biology.  The Oligator is designed to choose oligos to create any desired sequence between 20 and 20,000 base pairs.  The program allows the user to choose oligo lengths between 20 and 160 bp and overlap lengths of between 20 and 80 bp. 
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The program will also check for and remove BioBrick restriction sites at the request of the user. Choosing the first checkbox will tell the user if BioBrick restriction sites exist anywhere in the entered DNA sequence and embolden where they occur. The second checkbox will remove the sites, leaving the amino acid sequence intact. Since keeping the amino acid sequence the same involves knowing the reading frame, a radio button must be filled in indicating where the reading frame begins.
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The final option is to add BioBrick ends to your sequence. This is helpful when cloning your sequence into a BioBrick plasmid. Simply choose which site you want to add to the 5' end. The options are a prefix digested with XbaI, a prefix digested with EcoRI or the entire prefix. You then choose which site you want to add to the 3' end. The options are a suffix digested with SpeI, a suffix digested with PstI or the entire suffix. However, if you choose to add a prefix, you must choose a suffix, and vice-versa. Furthermore, you also have the ability to add a custom prefix and suffix.</p>
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                            <img src="http://2010.igem.org/wiki/images/3/33/Davidson-MoWOligator.png" width=409 height=305 alt="gator"/>
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            <a href="http://gcat.davidson.edu/igem10/opt/opt_index.html">
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                <h3>The Optimoose</h3>
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                            <p>The Optimoose is a tool designed to allow the user to evaluate the expression level of a sequence from ecoli using either RCBS-PC or the CAI formula. The RCBS-PC, or Relative Codon Bias value takes the observed codon frequency and substract it to the expected codon frequency and divides by the expected frequency.
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The CAI, or Codon Adaptation Index takes the frequency of each codon in a host organism and divides it by the frequency of each codon that appears the most in the host organism; and raise that result to the 1 over L power.  The user has then the option to either optimized or deoptimized the sequence by using one of those two formulas. If the optimize or deoptimize option is selected the user will be given a new sequence in which the codons have been changed to reflect the best, or worst, codons as determined by the selected formula. However, the amino acid sequence is preserved.
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The Optimoose was designed to allow us to assign a given weight to the items to fill up the knapsack.  Based on how optimized or deoptimized the sequence is , and based on the capacity of the knapsack; we could give every items a weight to satisfy our goals.</p>
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                            <img src="http://2010.igem.org/wiki/images/a/a4/Optimoose.png" alt="Tools" width=400 height=298/>
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                <h3>Construct Simulation</h3>
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                            <p> In order to be able to better understand how to build our constructs to give us the best system for solving the knapsack problem we created a simulation of the cre-lox systemThis simulation allows the user to test several pre-determined constructs that out team came up with.  In addition, one can create their own custom construct from any number of promoters, lox sites, fluorescent proteins, essential genes, and/or terminators.  The program will then show either a single, animated simulation that will allow the user to see how the lox sites interact, or it will run many simulations and then create a histogram that shows the distribution of what fluorescent proteins were expressed.  In addition, if the user chooses to include weights for the "items" and a capacity for the knapsack the program will tell you whether or not your construct has exceeded the capacity.  In order to run the program, <a href="http://gcat.davidson.edu/igem10/opt/opt_index.html">download the jar file</a> .  To see the actual percentages behind the histogram, the program needs to be run through a command line tool, but other than that simply double clicking the jar file to run it should be sufficient.</p>
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                            <img src="http://2010.igem.org/wiki/images/1/13/Davidson-MisouriW-SimE.png" alt="sim" width=400 height=225/>
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        <div id="VeriPart">
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                <h3>VeriPart</h3>
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                            <p>Verifying BioBrick parts can be difficult and tedious by hand.  To solve this problem, we have developed a tool to identify BioBrick parts and devices in a given DNA sequence.  When a sequence is entered, the program checks the last archived version of the BioBrick Parts Registry.  If your desired part is not found, you can attempt to align the sequence you entered with the part you desire.  Since this search uses a real-time version of the registry, it can potentially find additional parts.  When a device is found in your sequence, you can click to view the sequences of individual parts.</p>
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                            <img src="http://2010.igem.org/wiki/images/7/72/Veripart.png" alt="Veri" width=253 height=300/>
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                <a href="http://72.22.219.205/knapsack"></a>
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            <a href="http://72.22.219.205/knapsack">
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                <h3>Knapsack Game</h3>
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                            <p>In order to aid in the understanding of the Knapsack Problem, we created a game.  The game has two modes: tutorial and challenge, each of which asks the player to fill a knapsack of a certain capacity with given weighted items. The tutorial gives tips about the type of problem and only uses six weighted items.  The challenge offers no help and asks the player to choose from nine weighted items. </p>
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                            <img src="http://2010.igem.org/wiki/images/9/92/Knapsack.png" alt=""/>
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<p>In our design, weighted items are represented by versions of <i>TetA</i> genes that confer measurably distinct levels of tetracycline resistance.  We have altered the codons of the wild type <i>TetA</i> gene, optimizing and de-optimizing several segments of the coding sequence.  Each <i>TetA</i> variant is coupled with a distinctive fluorescent gene, and each pair of genes is flanked by <i>lox</i> sites.  In the presence of Cre protein, the <i>lox</i> mechanism either inverts or excises the coding sequence, yielding different combinations of expressed <i>TetA</i> variants.  An expressed variant corresponds to an item being placed in the knapsack.  Over-expression of <i>TetA</i> results in cell death, which represents exceeding the capacity of the knapsack.  Under-expression of <i>TetA</i> causes the cells to stop growing due to tetracycline in the growth medium, which represents not completely filling the knapsack.  Surviving cells correspond to cells within a certain range of <i>TetA</i> production and the fluorescence tag allows for comparative measurement within this range.</p>
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<p>The team is also working to develop software tools relevant to the specific project and applicable to projects in the wider synthetic biology community.</p><br>
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    </div>
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    <div id="team_box"><center><a href="http://2010.igem.org/Team:Davidson-MissouriW/Team"><img src="http://2010.igem.org/wiki/images/8/86/Davidson-MissouriWTeam.png" alt="Team" width="174px" height="36px"/></center>
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        <h3>Team</h3></a>
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        <p>The 2010 iGEM team from Davidson College and Missouri Western State University is composed of approximately 15 multidisciplinary undergraduate students and 4 professors – 2 biologists and 2 mathematicians. The team includes math, biology, computer science, and chemistry majors. The team has traveled back and forth across the country and research was conducted on both campuses. View the Davidson- Missouri Western <a href="http://2010.igem.org/Team:Davidson-MissouriW/Team">team </a>page. </p>
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    <div id="zoo_box"><center><a href="http://2010.igem.org/Team:Davidson-MissouriW/Project"><img src="http://igem.org/wiki/images/3/3e/Davidson-MissouriW_Project.jpeg" alt="Project"/></center>
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        <h3>Project</h3></a>
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        <p>In an attempt to solve the knapsack problem, we explored a variety of different topics. We optimized the codons for a portion of the TetA gene in order to produce variant genes that confer differing amounts of tetracycline resistance. We also created 11 variant lox sites that have differing recombination frequencies. Finally, we explored gene expression of RFP and the TetA gene. View the <a href="http://2010.igem.org/Team:Davidson-MissouriW/Project">work </a> done by Davidson and Missouri Western undergrads.</p>
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    <div id="notebook_box"><center><a href="http://2010.igem.org/Team:Davidson-MissouriW/Notebook"><img src="http://2010.igem.org/wiki/images/0/0b/Davidson-MissouriWNotebook.png" alt="Notebook"/></center>
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        <h3>Notebook</h3></a>
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        <p>Lab notebooks are an integral part of conducting scientific research because the results of a scientific experiment must be reproducible.  In an effort to properly document our efforts, each team member kept a detailed record of their daily activities.  We have condensed the information from all of these sources so that each entry in this virtual notebook contains the highlights of each day’s work.  View the daily progress of our project via the lab <a href="http://2010.igem.org/Team:Davidson-MissouriW/Notebook">Notebook</a>.</p>
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    <div id="parts_box"> <center><a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2010&group=Davidson-MissouriW"><img src="http://2010.igem.org/wiki/images/2/26/Davidson-MissouriWParts.jpg" alt="Parts"/></center>
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        <h3>Parts</h3></a>
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        <p>BioBricks are the foundation of iGEM.  We have created more than 40 basic and composite parts that are now available for the entire synthetic biology community to use.  Among these parts are 11 new variant lox sites in both forward and reverse versions. Using these variants, we have constructed “modules” consisting of RFP floxed by multiple different combinations. Furthermore, we have assembled new cre recombinase expression cassettes and added them to the RFP modules. View the <a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2010&group=Davidson-MissouriW">parts</a> built by our team.</p>
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    <div id="gallery_box"><center><a href="http://2010.igem.org/Team:Davidson-MissouriW/Tools"><img src="http://2010.igem.org/wiki/images/9/90/Davidson-MissouriW_Tools.png" alt="Tools"/></center>
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        <h3>Tools</h3></a>
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        <p> We have designed many programs that will be useful to the public.  VeriPart will identify the BioBrick part associated with any DNA sequence thus eliminating the tedious process of manually confirming sequences.  The Oligator suggests which oligos are needed to assemble the submitted sequence.  The Optimus allows users to choose different equations to optimize a given segment of DNA.  The Construct Simulator models how floxed modules behave when exposed to cre.  The Knapsack Game is an educational tool intended to explain the problem.  View our<a href="http://2010.igem.org/Team:Davidson-MissouriW/Tools"> Tools </a>page.</p>
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    <div id="sponsors_box"> <center><a href="http://2010.igem.org/Team:Davidson-MissouriW/Sponsors"><img src="http://2010.igem.org/wiki/images/a/ab/Davidson-MissouriWsponsorship.jpg" alt="Acknowledgements"/></center>
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        <h3>Acknowledgements</h3></a>
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        <p> This project and our participation in iGEM 2010 would not have been possible without help from numerous sources.  We have received invaluable assistance from numerous people both at Davidson College and at Missouri Western State University.  Furthermore, many organizations have contributed generously to our efforts, and without their help, we could not have come this far.  This section is a thank you to our <a href="http://2010.igem.org/Team:Davidson-MissouriW/Sponsors"> sponsors </a> and all of those who have helped us in any way.</p>
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Latest revision as of 07:02, 27 October 2010

Optimizing Codons


Building weighted items for the Knapsack through codon variation of the TetA gene led to Foundational Advances        

Details

Characterizing Cre/Lox


Foundational Advances were made as 11 novel lox sites for Cre recombination were built for randomly choosing Knapsack objects

Details

Measuring Gene Expression


Design and construction of a Knapsack biological computer required Foundational Advances in the measurement of gene expression

Details

iGEM Davidson – Missouri Western 2010:
Foundational Advances in Biology and the Knapsack Problem

The Davidson/Missouri Western multidisciplinary team is using synthetic biology to address a mathematical problem in Escherichia coli. Specifically, we are addressing the Knapsack Problem, an NP-complete problem that asks, “Given a finite number of weighted items, can one find a subset of these items that completely fills a knapsack of fixed capacity?”

In our design, weighted items are represented by versions of TetA genes that confer measurably distinct levels of tetracycline resistance. We have altered the codons of the wild type TetA gene, optimizing and de-optimizing several segments of the coding sequence. Each TetA variant is coupled with a distinctive fluorescent gene, and each pair of genes is flanked by lox sites. In the presence of Cre protein, the lox mechanism either inverts or excises the coding sequence, yielding different combinations of expressed TetA variants. An expressed variant corresponds to an item being placed in the knapsack. Over-expression of TetA results in cell death, which represents exceeding the capacity of the knapsack. Under-expression of TetA causes the cells to stop growing due to tetracycline in the growth medium, which represents not completely filling the knapsack. Surviving cells correspond to cells within a certain range of TetA production and the fluorescence tag allows for comparative measurement within this range.

The team is also working to develop software tools relevant to the specific project and applicable to projects in the wider synthetic biology community.


Team

Team

The 2010 iGEM team from Davidson College and Missouri Western State University is composed of approximately 15 multidisciplinary undergraduate students and 4 professors – 2 biologists and 2 mathematicians. The team includes math, biology, computer science, and chemistry majors. The team has traveled back and forth across the country and research was conducted on both campuses. View the Davidson- Missouri Western team page.

Project

Project

In an attempt to solve the knapsack problem, we explored a variety of different topics. We optimized the codons for a portion of the TetA gene in order to produce variant genes that confer differing amounts of tetracycline resistance. We also created 11 variant lox sites that have differing recombination frequencies. Finally, we explored gene expression of RFP and the TetA gene. View the work done by Davidson and Missouri Western undergrads.

Notebook

Notebook

Lab notebooks are an integral part of conducting scientific research because the results of a scientific experiment must be reproducible. In an effort to properly document our efforts, each team member kept a detailed record of their daily activities. We have condensed the information from all of these sources so that each entry in this virtual notebook contains the highlights of each day’s work. View the daily progress of our project via the lab Notebook.

Parts

Parts

BioBricks are the foundation of iGEM. We have created more than 40 basic and composite parts that are now available for the entire synthetic biology community to use. Among these parts are 11 new variant lox sites in both forward and reverse versions. Using these variants, we have constructed “modules” consisting of RFP floxed by multiple different combinations. Furthermore, we have assembled new cre recombinase expression cassettes and added them to the RFP modules. View the parts built by our team.

Acknowledgements

Acknowledgements

This project and our participation in iGEM 2010 would not have been possible without help from numerous sources. We have received invaluable assistance from numerous people both at Davidson College and at Missouri Western State University. Furthermore, many organizations have contributed generously to our efforts, and without their help, we could not have come this far. This section is a thank you to our sponsors and all of those who have helped us in any way.

Top