Team:Calgary/Project/Achievements

From 2014.igem.org

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<h1>Achievements</h1>
<h1>Achievements</h1>
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<p>Enter Text Here</p>
+
 
 +
<h2>Policies and Practices:</h2>
 +
 
 +
<ul>
 +
<li>Thoroughly researched our <span class="Orange"><b>target markets</b></span> and <span class="Orange"><b>differing legislations</b></span> that could affect our system</li>
 +
 
 +
<li>Connected with many different experts in the fields of infectious diseases, anti-malarial medications and public health to truly understand the needs and <span class="Orange"><b>feasibility</b></span> of the project</li>
 +
 
 +
<li>Connected with the foremost authority in low cost diagnostics, Foundation for Innovative New Diagnostics (FIND), to discuss the <span class="Orange"><b>viability</b></span> of our design and concept</li>
 +
 
 +
<li>Connected with a small village clinic in rural Uganda, which gave an opportunity to see the facility as well as discuss the topic with <span class="Orange"><b>local physicians</b></span></li>
 +
<li>Featured iGEM and our project on a global stage at the United Nations, in Geneva, and created discussion regarding the <span class="Orange"><b>advancement</b></span> of synthetic biology</li>
 +
</ul>
 +
 
 +
<h2>Modelling:</h2>
 +
 
 +
<ul>
 +
<li>Designed and manufactured a <span class="Blue"><b>prototype</b></span> of informed design based on our biological system</li>
 +
<li><span class="Blue"><b>Cost analysis</b></span> of our prototype and system to ensure that this project is feasible in developing nations</li>
 +
<li><span class="Blue"><b>Quantified</b></span> the visible threshold of detection for several reporters using time-lapsed cell count and absorbance readings, as well as a programmed colour sensor</li>
 +
<li><span class="Blue"><b>Programmed</b></span> an Arduino UNO microcontroller, colour sensor, and LCD screen to detect colour change among detection chambers, allowing for quantification of the colour</li>
 +
<li>Applied circuitry of a heating pad/temperature considerations for <span class="Blue"><b>ideal</b></span> isothermal PCR conditions</li>
 +
<li>Used Autodesk Maya Software to <span class="Blue"><b>visually model</b></span> and represent our system</li>
 +
<li>Used Solid-works Software to <span class="Blue"><b>model</b></span> fluid flow analysis for different prototype designs</li>
 +
</ul>
 +
 
 +
 
 +
<h2>Transformation:</h2>
 +
 
 +
<ul>
 +
<li><span class="Orange"><b>Transformed</b></span> <i>B. subtilis</i> with a primer product containing 125 bp of
 +
homologous sequence flanking our gene of interest</li>
 +
 
 +
<li>Modified and optimized general transformation: <span class="Orange"><b>characterized</b></span> effect of
 +
changing xylose concentrations, temperature, and shaking</li>
 +
<li><span class="Orange"><b>Optimization</b></span> of transformation in small, liquid volume</li>
 +
<li><span class="Orange"><b>Sporulated</b></span> <i>B. subtilis</i></li>
 +
 
 +
<li><span class="Orange"><b>Activated</b></span> <i>B. subtilis</i> spores back to vegetative state</li>
 +
        <li>Isolated the master regular for competency, <span class="Orange"><i><b>comK</b></i></span> from the genome of <i>B. subtilis</i> using PCR and inserted it into a <span class="Orange"><b>Biobrick</b></span> vector for future application as an iGEM standard part.
 +
</ul>
 +
 
 +
 
 +
<h2>Sample Preparation:</h2>
 +
 
 +
<ul>
 +
<li>Demonstrated efficacy of <span class="Blue"><b>isothermal PCR</b></span> to amplify DNA sequences
 +
without the need of a thermocycler, using freeze-dried components</li>
 +
<li>Demonstrated ability to amplify target DNA sequence from whole
 +
<i>E. coli</i> cells in a <span class="Blue"><b>blood mixture</b></span></li>
 +
<li>Obtained <span class="Blue"><b>specificity</b></span> in target sequence primers - specific to numerous strains of
 +
<i>N. meningititis</i> but not other pathogens including a commensal strain of <i>N. meningititis</i>
 +
 
 +
</ul>
 +
 
 +
 
 +
<h2>Detection/Genetic circuit</h2>
 +
 
 +
<ul>
 +
<li>Designed composite <span class="Orange"><b>regulatory promoter sequences</b></span> - used to allow repression of a downstream reporter with a specific repressor. Includes 5 variants of repressible promoters in either single or
 +
triplicate repeats for variation in strength of repression</li>
 +
<li>Demonstrated <span class="Orange"><b>interaction</b></span> (i.e. repression) between the reporter gene and repressor gene in <i>E. coli</i></li>
 +
<li>Demonstrated the efficacy of <span class="Orange"><b>homologous recombination</b></span> in <i>B. subtilis</i> and showed the minimum length of flanking sequences</li>
 +
<li><span class="Orange"><b>Biobricked</b></span> and submitted the full-length <span class="Orange"><i><b>lacZ</b></i></span> gene, previously non-existent in the latest
 +
distribution plates</li>
 +
<li>Constructed a <span class="Orange"><b>reporter operon</b></span> consisting of a constitutive promoter (<i>Pveg</i>), ribosome binding site, operator (C1434) and reporter (<i>lacZ/RFP</i>).</li>
 +
<li>Constructed a <span class="Orange"><b>complementary repressor operon</b></span> consisting of a constitutive promoter (<i>Pveg</i>), ribosome binding site, and repressor pertaining to the operator. Repressor was also flanked with regions homologous to certain sequences within our pathogens of interest.</li>
 +
</ul>
 +
 
 +
 
 +
 
</section>
</section>
</html>
</html>

Latest revision as of 03:12, 18 October 2014

Achievements

Policies and Practices:

  • Thoroughly researched our target markets and differing legislations that could affect our system
  • Connected with many different experts in the fields of infectious diseases, anti-malarial medications and public health to truly understand the needs and feasibility of the project
  • Connected with the foremost authority in low cost diagnostics, Foundation for Innovative New Diagnostics (FIND), to discuss the viability of our design and concept
  • Connected with a small village clinic in rural Uganda, which gave an opportunity to see the facility as well as discuss the topic with local physicians
  • Featured iGEM and our project on a global stage at the United Nations, in Geneva, and created discussion regarding the advancement of synthetic biology

Modelling:

  • Designed and manufactured a prototype of informed design based on our biological system
  • Cost analysis of our prototype and system to ensure that this project is feasible in developing nations
  • Quantified the visible threshold of detection for several reporters using time-lapsed cell count and absorbance readings, as well as a programmed colour sensor
  • Programmed an Arduino UNO microcontroller, colour sensor, and LCD screen to detect colour change among detection chambers, allowing for quantification of the colour
  • Applied circuitry of a heating pad/temperature considerations for ideal isothermal PCR conditions
  • Used Autodesk Maya Software to visually model and represent our system
  • Used Solid-works Software to model fluid flow analysis for different prototype designs

Transformation:

  • Transformed B. subtilis with a primer product containing 125 bp of homologous sequence flanking our gene of interest
  • Modified and optimized general transformation: characterized effect of changing xylose concentrations, temperature, and shaking
  • Optimization of transformation in small, liquid volume
  • Sporulated B. subtilis
  • Activated B. subtilis spores back to vegetative state
  • Isolated the master regular for competency, comK from the genome of B. subtilis using PCR and inserted it into a Biobrick vector for future application as an iGEM standard part.

Sample Preparation:

  • Demonstrated efficacy of isothermal PCR to amplify DNA sequences without the need of a thermocycler, using freeze-dried components
  • Demonstrated ability to amplify target DNA sequence from whole E. coli cells in a blood mixture
  • Obtained specificity in target sequence primers - specific to numerous strains of N. meningititis but not other pathogens including a commensal strain of N. meningititis

Detection/Genetic circuit

  • Designed composite regulatory promoter sequences - used to allow repression of a downstream reporter with a specific repressor. Includes 5 variants of repressible promoters in either single or triplicate repeats for variation in strength of repression
  • Demonstrated interaction (i.e. repression) between the reporter gene and repressor gene in E. coli
  • Demonstrated the efficacy of homologous recombination in B. subtilis and showed the minimum length of flanking sequences
  • Biobricked and submitted the full-length lacZ gene, previously non-existent in the latest distribution plates
  • Constructed a reporter operon consisting of a constitutive promoter (Pveg), ribosome binding site, operator (C1434) and reporter (lacZ/RFP).
  • Constructed a complementary repressor operon consisting of a constitutive promoter (Pveg), ribosome binding site, and repressor pertaining to the operator. Repressor was also flanked with regions homologous to certain sequences within our pathogens of interest.