Difference between revisions of "Team:Exeter/Parts"
| (4 intermediate revisions by 2 users not shown) | |||
| Line 118: | Line 118: | ||
| − | <div class='container'> | + | <div class='container' id="toeholds"> |
<!-- Put your content below this --> | <!-- Put your content below this --> | ||
| Line 124: | Line 124: | ||
<h1>Parts</h1> | <h1>Parts</h1> | ||
| − | <h2 | + | <h2>Toeholds</h2> |
For our project, four biobricks were submitted to the registry, all of which are added as basic parts. Although two of the parts contain multiple parts from the iGEM registry, these have not been entered as composite parts. The main reason for this is that the inclusion of biobrick assembly scars in certain parts of the toehold structure could mess with the structure and function of the toehold, and would impose additional constraints upon the toehold design. Given this, we believe that it would be most useful to the synthetic biology community if this was characterised as a basic part which can be swapped between plasmid vectors as required, and the target changed using Q5 site-directed mutagenesis. | For our project, four biobricks were submitted to the registry, all of which are added as basic parts. Although two of the parts contain multiple parts from the iGEM registry, these have not been entered as composite parts. The main reason for this is that the inclusion of biobrick assembly scars in certain parts of the toehold structure could mess with the structure and function of the toehold, and would impose additional constraints upon the toehold design. Given this, we believe that it would be most useful to the synthetic biology community if this was characterised as a basic part which can be swapped between plasmid vectors as required, and the target changed using Q5 site-directed mutagenesis. | ||
| Line 135: | Line 135: | ||
| − | <h4 id="K1586000"><a href="http://parts.igem.org/Part:BBa_K1586000">BBa_K1586000: Synthetic toehold riboswitch J23100 (GreenFET1J)</a> | + | <h4 id="K1586000"><a href="http://parts.igem.org/Part:BBa_K1586000">BBa_K1586000: Synthetic toehold riboswitch J23100 (GreenFET1J)</a></h4> |
<div class="containerSlider500" style="float:right"> | <div class="containerSlider500" style="float:right"> | ||
| Line 193: | Line 193: | ||
| − | <h4 id="K1586003"><a href="http://parts.igem.org/Part:BBa_K1586003">BBa_K1586003: EsxB toehold riboswitch J23100 (ZeusJ)</a> | + | <h4 id="K1586003"><a href="http://parts.igem.org/Part:BBa_K1586003">BBa_K1586003: EsxB toehold riboswitch J23100 (ZeusJ)</a> </h4> |
<div class="containerSlider500" style="float:right"> | <div class="containerSlider500" style="float:right"> | ||
<div class="sliderstatic500"> | <div class="sliderstatic500"> | ||
| − | <div class="slide"><a href="http://parts.igem.org/Part:BBa_K1586003"><img src="https://static.igem.org/mediawiki/2015/ | + | <div class="slide"><a href="http://parts.igem.org/Part:BBa_K1586003"><img src="https://static.igem.org/mediawiki/2015/0/0e/Exeter_K1586003_features.png" title="Figure 3: Features of K1586003."></a></div> |
</div> | </div> | ||
</div> | </div> | ||
| − | + | <p id="reporters"> | |
Part BBa_K1586003 was a toehold designed with the aim of being used in diagnosis, but as with all toehold switches designed it can be applied in many different scenarios. As our project was concerned with showing the potential of toehold switches in aiding <em>M.bovis</em> diagnosis, the switch is designed to detect and become activated by EsxB mRNA. EsxB is a gene found in <em>M.bovis</em>, but not the BCG vaccine, and encodes for Esat6, which is involved in its pathogenicity. This toehold has been tested <em>in silico</em>, and will be further characterised at the University of Exeter after the competition has ended. To see data for this toehold, visit either the <a href="http://parts.igem.org/Part:BBa_K1586003">registry page</a>, or the <a href="https://2015.igem.org/Team:Exeter/Results">results page</a>. Figure 3 shows annotated features for this part. | Part BBa_K1586003 was a toehold designed with the aim of being used in diagnosis, but as with all toehold switches designed it can be applied in many different scenarios. As our project was concerned with showing the potential of toehold switches in aiding <em>M.bovis</em> diagnosis, the switch is designed to detect and become activated by EsxB mRNA. EsxB is a gene found in <em>M.bovis</em>, but not the BCG vaccine, and encodes for Esat6, which is involved in its pathogenicity. This toehold has been tested <em>in silico</em>, and will be further characterised at the University of Exeter after the competition has ended. To see data for this toehold, visit either the <a href="http://parts.igem.org/Part:BBa_K1586003">registry page</a>, or the <a href="https://2015.igem.org/Team:Exeter/Results">results page</a>. Figure 3 shows annotated features for this part. | ||
| + | </p> | ||
| + | |||
| + | |||
| + | <h3>Reporter characterisation: chromoproteins</h3> | ||
| + | |||
| + | <p> | ||
| + | Ideally, our diagnostic test would be carried out in the field with little technical equipment/training, therefore visualisation of the result must be simple. In order to do this, we decided that a colour change would be best, and that the expression of chromoproteins on activation of the toehold would be a good way to achieve this. In order to better inform ourselves and the model, and also to generate data which would be useful for testing toeholds with chromoproteins as the protein coding regions, we decided to further characterise some of the chromoproteins in the iGEM registry; <a href="http://parts.igem.org/Part:BBa_K1431814">amajLime</a>, <a href="http://parts.igem.org/Part:BBa_K1073020">aeBlue</a>, and <a href="http://parts.igem.org/Part:BBa_K1073022">eforRed</a>. These parts were characterised by; recording each protein's individual absorbance spectrum to find their peak maxima, constructing a standard curve of protein concentration vs. OD at peak maxima for each chromoprotein, and determination of each chromoprotein' visual limit (i.e. the concentration at which the colour change is obvious). To see the rationale and results of this characterisation, visit the <a href="https://2015.igem.org/Team:Exeter/Experiments#further_characterisation">experiment's page</a>. | ||
| + | |||
| + | </p> | ||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| − | |||
<!-- End of your content --> | <!-- End of your content --> | ||
Latest revision as of 22:58, 18 September 2015
Parts
Toeholds
For our project, four biobricks were submitted to the registry, all of which are added as basic parts. Although two of the parts contain multiple parts from the iGEM registry, these have not been entered as composite parts. The main reason for this is that the inclusion of biobrick assembly scars in certain parts of the toehold structure could mess with the structure and function of the toehold, and would impose additional constraints upon the toehold design. Given this, we believe that it would be most useful to the synthetic biology community if this was characterised as a basic part which can be swapped between plasmid vectors as required, and the target changed using Q5 site-directed mutagenesis.BBa_K1586000: Synthetic toehold riboswitch J23100 (GreenFET1J)
BBa_K1586001: Synthetic toehold riboswitch T7 (GreenFET1T7)
BBa_K1586002: EsxB toehold riboswitch J23100 STOP (ZeusJSTOP)
BBa_K1586003: EsxB toehold riboswitch J23100 (ZeusJ)
Part BBa_K1586003 was a toehold designed with the aim of being used in diagnosis, but as with all toehold switches designed it can be applied in many different scenarios. As our project was concerned with showing the potential of toehold switches in aiding M.bovis diagnosis, the switch is designed to detect and become activated by EsxB mRNA. EsxB is a gene found in M.bovis, but not the BCG vaccine, and encodes for Esat6, which is involved in its pathogenicity. This toehold has been tested in silico, and will be further characterised at the University of Exeter after the competition has ended. To see data for this toehold, visit either the registry page, or the results page. Figure 3 shows annotated features for this part.
Reporter characterisation: chromoproteins
Ideally, our diagnostic test would be carried out in the field with little technical equipment/training, therefore visualisation of the result must be simple. In order to do this, we decided that a colour change would be best, and that the expression of chromoproteins on activation of the toehold would be a good way to achieve this. In order to better inform ourselves and the model, and also to generate data which would be useful for testing toeholds with chromoproteins as the protein coding regions, we decided to further characterise some of the chromoproteins in the iGEM registry; amajLime, aeBlue, and eforRed. These parts were characterised by; recording each protein's individual absorbance spectrum to find their peak maxima, constructing a standard curve of protein concentration vs. OD at peak maxima for each chromoprotein, and determination of each chromoprotein' visual limit (i.e. the concentration at which the colour change is obvious). To see the rationale and results of this characterisation, visit the experiment's page.