Team:Calgary/Project/DataPage

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<h1>Data Page</h1>
<h1>Data Page</h1>
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<h2>Characterization of new parts submitted to the Registry</h2>
 
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<p> This year we submitted two new reporters to the registry, <b>Beta-lactamase</b> (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189008">Bba_ K118908</a>) and <b>Recombinant Human Ferritin</b> (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189008">Bba_ K118918</a>). We built the parts, expressed, and purified these proteins < show here>. </p>
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<figure>
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<img src="https://static.igem.org/mediawiki/2013/2/28/2013igemcalgaryoverviewabstractimage.png" width="819"><figcaption>Figure 1: Summarizing parts that we built for each of the components of our system. For our detector, indicated in green, we built different TALE proteins that we characterized using nitrocellulose and immuno based assays. To find out more about our detector click <a href="https://2013.igem.org/Team:Calgary/Project/OurSensor/Detector">here</a>. We submitted two new reporters-- <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189018">ferritin</a> and <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189008">&beta;-lactamase</a> and characterized these proteins individually. To bring the detector and the reporter together we used a <a href="http://https://2013.igem.org/Team:Calgary/Project/OurSensor/Linker">linker</a> by using E coil and K coil. </figcaption></figure>
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<p>We characterized ferritin as a reporter. Firstly, we converted ferritin into Prussian blue ferritin, which has high catalytic activity. In addition, this is a very attractive reporter because it is quite stable in a large range of temperature and pH conditions. Prussian blue ferritin uses conventional horseradish peroxidase substrates, ABTS and TMB. We did a Michelis-Menten kinetic analysis with Prussian blue ferritin and characterized it under ranging temperature and pH conditions. We also showed that Prussian blue ferritin is a good reporter by doing dot-blots on nitrocellulose and our model prototype (see below) with its substrates to give us a quantitative and qualitative output, respectively. In addition, we showed that ferritin, a protein with 24 subunits is expressed and functional in our system. We have also converted this ferritin into Prussian blue ferritin on which we have done intial characterization on nitrocellulose. <LINK TO DATA PLEASE></p>
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<h2>Characterization of New Parts Submitted to the Registry</h2>
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<p> We have bulit and expressed beta lactamse in our bacterial cells which we have characterized using an ampicillin <a href="https://2013.igem.org/Team:Calgary/Project/OurSensor/Reporter/BetaLactamase">survival assays</a>. We have also built the TALE A linked to beta lactmase, representing the alternative mobile unit in our sensor, which we have expressed and purified. This fusion protein has also been characterized with variations in the ampicillin assay. We have also done initial characterizations of the beta lactamse as a reporter by using benzylpenicillin as a substrate which gives a pH output. When combined with phenol red as a pH indicator, we have shown a colourimetric output which correlates to changing amounts of beta lactamase.  <link>.
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<ul>
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<li>Submitted two new reporters to the registry: Beta-lactamase (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189008">Bba_ K1189008</span></a>) and Recombinant Human Ferritin  (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189021">Bba_ K1189008</span></a>). We submitted these parts alone, with 6-his tags and lacI inducible promoters and fused to TALE-A (Slovenia 2012). In addition, we submitted Recombinant Human Ferritin with E coil dimerization domains in order to be used as a modular scaffold (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189018">Bba_K1189018</span></a>).  </li>
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<h2>Further characterization and improvement of parts already present within the registry</h2>
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<li>Expressed Ferritin (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189021">Bba_ K1189008</span></a>), which possesses 24 subunits, and showed successful chemical conversion of our expressed protein into Prussian Blue ferritin. We also showed that this part could feasibly be used as a reporter in a nitrocellulose test-strip system as well as in solution.</li>
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<li>Expressed and purified beta-lactamase both with and without TALE-A (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189007">Bba_ K1189007</b></span></a>) and (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189031">Bba_ K1189031</b></span></a>) and characterized the functionality of these Biobricks as a reporter using both pH and ampicillin resistance <a href="https://2013.igem.org/Team:Calgary/Project/OurSensor/Reporter/BetaLactamase">assays</span></a>. </li></ul>
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<li> The kozak sequence on TALE A (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K782004"> Part:BBa_K782004</a>) and TALE B ( <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K782006"> Part:BBa_K782006</a>) were removed, and an IPTG inducible promoter with RBS (<a href="http://parts.igem.org/Part:BBa_J04500"> Part:BBa_J04500</a>) was constructed upstream of the genes, so that the part could be expressed in <i>E.coli</li>.
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<h2>Further Characterization and Improvement of Parts Already in the Registry</h2>
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<p> We made further improvement to  TALE A (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K782004"> Part:BBa_K782004</a>) and TALE B (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K782006"> Part:BBa_K782006</a>) in our bigger constructs including J04500+His+TALEA+link+Kcoil (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189029"> BBa_K1189029</a>), J04500+His+TALB+link+Kcoil (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189030"> BBa_K1189030</a>), J04500+His+TALA+Link+Blac (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189031"> BBa_K1189031</a>),  and J04500+His+TALA+hFTN+lFTN (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189021"> BBa_K1189021</a>):</p>
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<li>They were codon optimized for <i>E.coli</i> to increase the expression level in a chassis used by most of the iGEM community.</li>
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<li>the Nuclear Localization Sequence (NLS) at the C-teminus of the TALEs were removed, as <i>E.coli</i> does not have a nucleus.</li>
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<li> a KasI restriction cut site was added after the C-terminus of the TALE, in order to create a plug-and-play system. If a future iGEM team requires to use one of our parts in the future, they can easily swap TALE A and TALE B with their own engineered TALE. </li>
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<h4> we were also able to show that we can successfully express and purify most of these constructs. </h4)
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<p><a href="https://2012.igem.org/Team:Slovenia/TheSwitchDesignedTALregulators">Slovenia 2012 iGEM team</a> did a great characterization of TALE A (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K782004"> Part:BBa_K782004</a>) and TALE B ( <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K782006"> Part:BBa_K782006</a>). We used these parts as a proof of concept of our system. Along the way we made some changes to these parts to make them more useful to us and the parts registry. <a href="https://2012.igem.org/Team:Slovenia/TheSwitchDesignedTALregulators">Slovenia 2012 iGEM team</a> used these parts in eukaryotic cells. Therefore, these parts had a kozak sequence before the start of the gene.
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<p> In 2012, the Wagenigen team worked with and did initial characterized a coiled coil system known as the E and K coils for their project. However, they did not submit the physical DNA for the coils. These coiled coils are very useful for <i> in vitro </i> assembly of different proteins and their ability to scaffold proteins together when fusion does not work, making an attractive addition to the registry. We submitted these parts <b> K coil</b>(Bba_K1189027) and <b> E coil </b> (Bba_K1189011). We also added these parts with a his-6 tag such that fusion proteins with K or E coil can be purified out using affinity chromatography. These four parts have been submitted in the Freiburg fusion biobrick backbone to allow easier construction of fusion protein for future teams. We have done initial characterization demonstrating that the coils allow <i> in vitro </i> assembly by doing a dot blot assay with our mobile TALE detector and Prussian blue reporter, both of which we have built, expressed, and purified with the coiled coils. <LINK HERE>  </p>
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<p>We have also mutated, optimized, and repurposed Slovenia’s TALE proteins from 2012 to work in <i>E. coli </i>. The TALE that Slovenia submitted had mutations, as it is difficult to sequence RVDs in TALEs. We amended the TALE to fit the correct binding sequence. This was not optimized to work in <i>E. coli</i>, it had a eukaryotic ribosomal binding site called a Kozak sequence. In the presence ok Kozak sequence the TALEs are not expressed in <i> E. coli</i> <link here>. We removed the Kozak sequence and codon optimized the TALEs for expression in <i>E. coli</i>. Further, we characterized the TALEs and showed that they bind to the correct nucleotide sequences.</p>
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<p> Something about the kas1 site that ALi put in </p>
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<ul><li> Submitted optimized parts of TALE-A (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189022">Bba_ K1189022</span></a>) and TALE-B (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189023">Bba_ K1189023</span></a>) (Slovenia 2012) for use in <i>E. coli </i> by removing the eukaryotic Kozak sequence and nuclear localization signal, codon optimizing it for expression in <i>E. coli </i> and finally adding a KasI restriction site in the composite part such that future teams can essentially plasmid switch their own custom TALEs into our system. We also fixed a mutation in the binding region of TALE-B.</li>
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<h2> Modelleing </h>
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<li> Showed that the improved TALES were able to be expressed in <I>E. coli</i>.</li>
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<p> Quantitative and qualitative <p>
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<li>Submitted multiple composite parts of TALE-A and TALE-B with his-6 tags for easy purification, as well as with linkers and our two reporters: Beta-lactamase and ferritin.</li>  
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<h2> Collaboration </h>
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<li>Expressed and successfully purified various TALE constructs: TALE-A (<a href="http://parts.igem.org/Part:BBa_K1189000">BBa_K1189000</a>); TALE-B (<a href="http://parts.igem.org/Part:BBa_K1189001">BBa_K1189001</a>); TALE-A with a K coil (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189029">BBa_K1189029</a>);  TALE-A linked to beta-lactamase  (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189031">BBa_K1189031</a>); TALE-A fused to ferritin (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189021">BBa_K1189021</a>). </li>
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<li>Submitted the K coil (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189010">BBa_K1189010</span></a>) and E coil (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189011">BBa_K1189011</a></span>), previously in the registry, however lacking DNA. These coiled coils are very useful for <i> in vitro </i> assembly of different proteins and their ability to scaffold proteins together when fusion does not work, making an attractive addition to the registry. We also added a his-6 tag to these coils K coil with His-6 tag (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189012">Bba_K1189012</a></span>) and E coil with a His-6 tag (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189013">Bba_K1189013</a></span>). We submitted these coils in the <a href="http://parts.igem.org/Assembly_standard_25">Freiburg backbone</span></a> for easy fusion of proteins. </li>
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<li>Characterized the binding of these coils, demonstrating that the coils allow <i> in vitro </i> assembly by doing a dot blot assay with our mobile TALE detector and Prussian blue reporter, both of which we have built, expressed, and purified with the coiled coils. These results can be found (<a href="https://2013.igem.org/Team:Calgary/Project/OurSensor/Linker
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" >here</a>).</li>
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<li>Demonstrated that TALE-A with a K coil (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189029">BBa_K1189029</a>) binds specifically to its target DNA. These results can be found (<a href="https://2013.igem.org/Team:Calgary/Project/OurSensor/Detector
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" >here</a>).</li>
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<li>We were able to calculate the <a href="https://2013.igem.org/Team:Calgary/Project/OurSensor/Detector
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" >dissociation constant</a> of TALE-A (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189029">BBa_K1189029</a>) and TALE-B with coils in the FerriTALE complex.</li>
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</ul>
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<h2> Modelling </h2>
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<ul><li>Built an <a href="https://2013.igem.org/Team:Calgary/Project/OurSensor">animation in Maya</span></a> in order to communicate more visually how our sensor system functions from start to finish. </li>
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<li> Built a <a href="https://2013.igem.org/wiki/index.php?title=Team:Calgary/Project/OurSensor/Modelling/SpatialModelling">spatial model in Maya</span></a> to show how the potential mechanism of DNA-TALE binding to nitrocellulose in our prototype could result in reduction of the TALEs sensitivity. This directly influenced the way we designed our system, encouraging us to add in linkers/scaffolds.</li>
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<li>Constructed a quantitative <a href="https://2013.igem.org/Team:Calgary/Project/OurSensor/Modelling/QuantitativeModelling">Mathematica model</span></a> to test how amounts of target DNA versus detector proteins could influence sensitivity of the prototype.</li>
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<li> Built a Mathematica model to <a href="https://2013.igem.org/Team:Calgary/Project/OurSensor/Modelling/QuantitativeModelling">analyze kinetics of several common reporter enzymes</span></a> found in the registry, which culminated in the selection of our reporters.</li>
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<li> Built a Scilab model of <a href="https://2013.igem.org/Team:Calgary/Project/OurSensor/Modelling/QuantitativeModelling">differential equations</span></a> to show how fast we can get a detectable result from our system. This model used constants from our own experiments to make this prediction.</li>
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</ul>
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<h2> Human Practices</h2>
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<ul>
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<li><a href="https://2013.igem.org/Team:Calgary/Project/HumanPractices/InformedDesign">Consulted</a> with three key stakeholders in the beef-cattle industry and implemented their suggestions into our design in terms of where we would implement our test in the meat processing chain, the time requirements for our test as well as the need for ease of use and robustness in our final system </li>
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<li> Built upon previous outreach activities as well as took on a few new initiatives in order to engage more people in our community about our project</li>
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</ul>
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<h2> Collaboration</h2>
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<ul><li> Collaborated with Paris Bettencourt to create  <a href="https://2013.igem.org/Team:Calgary/Project/Collaboration/BiosensorDatabase">SensiGEM</span></a>, a searchable database of biosensors. Here we identified all the different biosensors in the registry over the years and categorized them by their inputs and outputs in order to guide future teams in the selection of their biosensors.</li>
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<li> Helped establish the first Consort High School iGEM team in collaboration with the <a href="https://2013.igem.org/Team:Calgary_Entrepreneurial">Calgary Entrepreneurial</span></a> team. Consort performed amazingly well winning the Best Human Practices at the iGEM High School Jamboree!</li>
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</ul>
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<p> Sensigem </p>
 
<h2>Additional Work and Characterization</h2>
<h2>Additional Work and Characterization</h2>
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<p>We characterized a portable prototype showing that this final system is feasible. We used a homestyle pregnancy kit to show that this is possible LINK HERE. We showed that it is possible to flow DNA through the strip, add protein on the strip and get a colour output using ferritin.</p>
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<ul><li>Characterized a portable prototype showing that this final system is feasible. We used a homestyle pregnancy kit to show that this is possible <a href="https://2013.igem.org/Team:Calgary/Project/OurSensor/Prototype">here</span></a>. We showed that it is possible to flow DNA through the strip, add protein on the strip and get a colour output using our ferritin reporter. </li>
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</p>
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</ul>
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<h2> Human practices </h2>
 
</section>
</section>
</html>
</html>

Latest revision as of 03:59, 29 October 2013

Data Page

Figure 1: Summarizing parts that we built for each of the components of our system. For our detector, indicated in green, we built different TALE proteins that we characterized using nitrocellulose and immuno based assays. To find out more about our detector click here. We submitted two new reporters-- ferritin and β-lactamase and characterized these proteins individually. To bring the detector and the reporter together we used a linker by using E coil and K coil.

Characterization of New Parts Submitted to the Registry

  • Submitted two new reporters to the registry: Beta-lactamase (Bba_ K1189008) and Recombinant Human Ferritin (Bba_ K1189008). We submitted these parts alone, with 6-his tags and lacI inducible promoters and fused to TALE-A (Slovenia 2012). In addition, we submitted Recombinant Human Ferritin with E coil dimerization domains in order to be used as a modular scaffold (Bba_K1189018).
  • Expressed Ferritin (Bba_ K1189008), which possesses 24 subunits, and showed successful chemical conversion of our expressed protein into Prussian Blue ferritin. We also showed that this part could feasibly be used as a reporter in a nitrocellulose test-strip system as well as in solution.
  • Expressed and purified beta-lactamase both with and without TALE-A (Bba_ K1189007) and (Bba_ K1189031) and characterized the functionality of these Biobricks as a reporter using both pH and ampicillin resistance assays.

Further Characterization and Improvement of Parts Already in the Registry

  • Submitted optimized parts of TALE-A (Bba_ K1189022) and TALE-B (Bba_ K1189023) (Slovenia 2012) for use in E. coli by removing the eukaryotic Kozak sequence and nuclear localization signal, codon optimizing it for expression in E. coli and finally adding a KasI restriction site in the composite part such that future teams can essentially plasmid switch their own custom TALEs into our system. We also fixed a mutation in the binding region of TALE-B.
  • Showed that the improved TALES were able to be expressed in E. coli.
  • Submitted multiple composite parts of TALE-A and TALE-B with his-6 tags for easy purification, as well as with linkers and our two reporters: Beta-lactamase and ferritin.
  • Expressed and successfully purified various TALE constructs: TALE-A (BBa_K1189000); TALE-B (BBa_K1189001); TALE-A with a K coil (BBa_K1189029); TALE-A linked to beta-lactamase (BBa_K1189031); TALE-A fused to ferritin (BBa_K1189021).
  • Submitted the K coil (BBa_K1189010) and E coil (BBa_K1189011), previously in the registry, however lacking DNA. These coiled coils are very useful for in vitro assembly of different proteins and their ability to scaffold proteins together when fusion does not work, making an attractive addition to the registry. We also added a his-6 tag to these coils K coil with His-6 tag (Bba_K1189012) and E coil with a His-6 tag (Bba_K1189013). We submitted these coils in the Freiburg backbone for easy fusion of proteins.
  • Characterized the binding of these coils, demonstrating that the coils allow in vitro assembly by doing a dot blot assay with our mobile TALE detector and Prussian blue reporter, both of which we have built, expressed, and purified with the coiled coils. These results can be found (here).
  • Demonstrated that TALE-A with a K coil (BBa_K1189029) binds specifically to its target DNA. These results can be found (here).
  • We were able to calculate the dissociation constant of TALE-A (BBa_K1189029) and TALE-B with coils in the FerriTALE complex.

Modelling

  • Built an animation in Maya in order to communicate more visually how our sensor system functions from start to finish.
  • Built a spatial model in Maya to show how the potential mechanism of DNA-TALE binding to nitrocellulose in our prototype could result in reduction of the TALEs sensitivity. This directly influenced the way we designed our system, encouraging us to add in linkers/scaffolds.
  • Constructed a quantitative Mathematica model to test how amounts of target DNA versus detector proteins could influence sensitivity of the prototype.
  • Built a Mathematica model to analyze kinetics of several common reporter enzymes found in the registry, which culminated in the selection of our reporters.
  • Built a Scilab model of differential equations to show how fast we can get a detectable result from our system. This model used constants from our own experiments to make this prediction.

Human Practices

  • Consulted with three key stakeholders in the beef-cattle industry and implemented their suggestions into our design in terms of where we would implement our test in the meat processing chain, the time requirements for our test as well as the need for ease of use and robustness in our final system
  • Built upon previous outreach activities as well as took on a few new initiatives in order to engage more people in our community about our project

Collaboration

  • Collaborated with Paris Bettencourt to create SensiGEM, a searchable database of biosensors. Here we identified all the different biosensors in the registry over the years and categorized them by their inputs and outputs in order to guide future teams in the selection of their biosensors.
  • Helped establish the first Consort High School iGEM team in collaboration with the Calgary Entrepreneurial team. Consort performed amazingly well winning the Best Human Practices at the iGEM High School Jamboree!

Additional Work and Characterization

  • Characterized a portable prototype showing that this final system is feasible. We used a homestyle pregnancy kit to show that this is possible here. We showed that it is possible to flow DNA through the strip, add protein on the strip and get a colour output using our ferritin reporter.