Difference between revisions of "Team:Edinburgh OG/Improve"

 
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<h1>Improve</h1>
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<p>For teams seeking to improve upon a previous part or project, you should document all of your work on this page. Please remember to include all part measurement and characterization data on the part page on the Registry. Please include a link to your improved part on this page.</p>
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<h3>Gold Medal Criterion #2</h3>
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<p><b>Standard Tracks:</b> Create a new part that has a functional improvement upon an existing BioBrick part. The sequences of the new and existing parts must be different. You must perform experiments with both parts to demonstrate this improvement.  Document the experimental characterization on the Part's Main Page on the Registry for both the existing and new parts. Both the new and existing Main Page of each Part’s Registry entry must reference each other. Submit a sample of the new part to the Registry.
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The existing part must NOT be from your 2018 part number range and must be different from the part documented in bronze #4.
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  <tr><td  bgColor="#FEE5AD"></td> <td colspan="3" width="975px" bgColor="#FEE5AD" align="center"><h1>Our Best Improved Part ! ! !</h2></td> <td  bgColor="#FEE5AD"></td> </tr>
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<b>Special Tracks:</b> Improve the function of an existing iGEM project (that your current team did not originally create) and display your achievement on your wiki.</p>
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        <th>Registry Number</th>
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        <th>Brief Description</th>
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        <th>Key Details</th>
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        <th>Length</th>
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        <th>Sequence information</th>
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        <td><a href="http://parts.igem.org/Part:BBa_K2739000">BBa_K2739000</a></td>
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        <td>ProR-PhaR </td>
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        <td>The phasin autoregulation system with native promoter</td>
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        <td>658bp</td>
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        <td>Original Sequence obtained from: <a href="https://www.ncbi.nlm.nih.gov/nuccore/AM260479.1/">NCBI(AM260479.1)</a> and <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570403/">Monitoring and kinetic analysis of the molecular interactions by which a repressor protein, PhaR, binds to target DNAs and poly[(R)-3-hydroxybutyrate] (2013) </a>. Sequence is codon optimised for <em>E.coli</em>.</td>
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      <tr><td>Previous Parts </td></tr>
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        <td><a href="http://parts.igem.org/Part:BBa_K108015">BBa_K108015</a></td>
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        <td>PhaR (From previous team)</td>
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        <td>The phasin autoregulation system </td>
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        <td>552bp</td>
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        <td> Source of sequence :<a href="http://mic.microbiologyresearch.org/content/journal/micro/10.1099/00221287-148-8-2413#tab2">Regulation of phasin expression and polyhydroxyalkanoate (PHA) granule formation in Ralstonia eutropha H16 (2002)</a> and NCBI (No further indication). No codon optimisation for <em>E.coli</em>. No result or user experience provided. </td>
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        <td><a href="http://parts.igem.org/Part:BBa_K108014">BBa_K108014</a></td>
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        <td>ProP (From previous team)</td>
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        <td>The native promoter and RBS of phasin autoregulation system </td>
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        <td>234bp</td>
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        <td> Source of sequence :<a href="http://mic.microbiologyresearch.org/content/journal/micro/10.1099/00221287-148-8-2413#tab2">Regulation of phasin expression and polyhydroxyalkanoate (PHA) granule formation in Ralstonia eutropha H16 (2002)</a> and NCBI (No further indication). No codon optimisation for <em>E.coli</em>. No result or user experience provided. </td>
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    <div class="container"><button class="btn btn-warning" type="button" data-toggle="collapse" data-target="#tittle4"><h3><strong> &#32; &nbsp;Sequence Selection and Codon Optimisation  </strong></h3></button>
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<p style="text-align: justify;">The sequence of PhaR promoter in this project is more properly selected in comparison with the previous parts. Previous publication: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570403/">Monitoring and kinetic analysis of the molecular interactions by which a repressor protein, PhaR, binds to target DNAs and poly[(R)-3-hydroxybutyrate] (2013) </a> is served as reference guideline and the selected functional promoter sequence is 134bp shorter than the previous part.</p>
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<p style="text-align: justify;">The template sequence of PhaR in this project is based on <a href="https://www.ncbi.nlm.nih.gov/nuccore/AM260479.1/">NCBI(AM260479.1)</a>, being 4bp difference to the previous part. </p>
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<left><img src="https://static.igem.org/mediawiki/parts/8/88/T--Edinburgh_OG--Improve-image_2.jpeg" height="auto"></left>
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<p style="text-align: justify;">Figure 1. Sequence alignment of NCBI(AM260479.1) and BBa_K108015. The 4bp difference is indicated by red color. </p>
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<p style="text-align: justify;">The sequence is codon optimised to E.coli via IDT. <a href="http://parts.igem.org/Part:BBa_K2739000:Design">(See the Registry design page for the detail alignment) </a></p>
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<div class="container"><button class="btn btn-warning" type="button" data-toggle="collapse" data-target="#tittle3"><h3><strong> &#32; &nbsp;Further Application and Research  </strong></h3></button>
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<p style="text-align: justify;">This composite part has allow us to investigate A)  its relation in PHA production through PHA operon; B) its function on PHA production with Phasin (BBa_K2739005); C) Assess the secretion function of Phasin-HlyA is compatible with phaR and if the improvement of phaR of PHA production is remained in this parts composition (BBa_K2739006);.</p>
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<left><img src="https://static.igem.org/mediawiki/parts/3/3b/T--Edinburgh_OG--Improve-image_1.jpeg" height="auto"></left>
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          <p style="text-align: justify;">Figure 2. Diagram of other PhaR Biobricks development. </p>
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Latest revision as of 23:49, 16 October 2018

PhagED: a molecular toolkit to re-sensitise ESKAPE pathogens

 

 

 

 

 

Our Best Improved Part ! ! !
Registry Number Brief Description Key Details Length Sequence information
BBa_K2739000 ProR-PhaR The phasin autoregulation system with native promoter 658bp Original Sequence obtained from: NCBI(AM260479.1) and Monitoring and kinetic analysis of the molecular interactions by which a repressor protein, PhaR, binds to target DNAs and poly[(R)-3-hydroxybutyrate] (2013) . Sequence is codon optimised for E.coli.
Previous Parts
BBa_K108015 PhaR (From previous team) The phasin autoregulation system 552bp Source of sequence :Regulation of phasin expression and polyhydroxyalkanoate (PHA) granule formation in Ralstonia eutropha H16 (2002) and NCBI (No further indication). No codon optimisation for E.coli. No result or user experience provided.
BBa_K108014 ProP (From previous team) The native promoter and RBS of phasin autoregulation system 234bp Source of sequence :Regulation of phasin expression and polyhydroxyalkanoate (PHA) granule formation in Ralstonia eutropha H16 (2002) and NCBI (No further indication). No codon optimisation for E.coli. No result or user experience provided.

The sequence of PhaR promoter in this project is more properly selected in comparison with the previous parts. Previous publication: Monitoring and kinetic analysis of the molecular interactions by which a repressor protein, PhaR, binds to target DNAs and poly[(R)-3-hydroxybutyrate] (2013) is served as reference guideline and the selected functional promoter sequence is 134bp shorter than the previous part.

The template sequence of PhaR in this project is based on NCBI(AM260479.1), being 4bp difference to the previous part.

Figure 1. Sequence alignment of NCBI(AM260479.1) and BBa_K108015. The 4bp difference is indicated by red color.

The sequence is codon optimised to E.coli via IDT. (See the Registry design page for the detail alignment)

This composite part has allow us to investigate A) its relation in PHA production through PHA operon; B) its function on PHA production with Phasin (BBa_K2739005); C) Assess the secretion function of Phasin-HlyA is compatible with phaR and if the improvement of phaR of PHA production is remained in this parts composition (BBa_K2739006);.

Figure 2. Diagram of other PhaR Biobricks development.