Difference between revisions of "Team:Edinburgh UG/Results"

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<h1>Results</h1>
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            <br>
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            <h1 style="font-size: 60px; text-align: center; margin-top: 0; padding-top: 0;"> Results </h1> <br>
  
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<p>Here you can describe the results of your project and your future plans. </p>
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            <h2 class="header-subsection"> Overview </h2>
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            <p> <strong> Material needed </strong></p>
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            <ol type="1" style="list-style-image: none; font-size: 17px;">
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                <li>We cloned Dre, VCre, SCre, and Vika generators into Biobrick format, removing all illegal sites when necessary.</li>
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                <li>We assembled T7-LacO-Cre generator and cloned it into Biobrick format.</li>
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                <li>We successfully assembled 12 out of 15 of measurement constructs to allow users to quantify recombinase activity
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                    in vivo.</li>
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                <li>We assembled 10 target sites for Cre and proved their functionality in vitro. We also assembled the target
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                    sites for Dre, VCre, SCre, and Vika – Rox, VLox, SLox, and Vox respectively. Their functionality is proved
 +
                    in the measurement constructs.</li>
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                <li>We have extensively quantified the recombination efficiency of the five recombinases in E. coli.
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                </li>
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                <li>We have built software and used it to design assembly methods for six logic gates using tyrosine recombinase.</li>
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                <li>We have built deterministic and stochastic modeling to simulate the behavior of site-specific recombinase.
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                    We also devised an algorithm to detect potential recombination sites in a genome.</li>
 +
                <li>We have conducted an investigation into interdisciplinarity. This includes a survey to identify challenges
 +
                    in interdisciplinary work, and a systematic analysis of past iGEM teams, to test correlation between
 +
                    interdisciplinarity and iGEM achievement.</li>
 +
                <li>We have integrated the result from the interdisciplinarity study to improve accessibility of SMORE in four
 +
                    aspects: readability, hardware, user experience and data.</li>
 +
            </ol><br><br>
  
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<h5>What should this page contain?</h5>
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            <h2 class="header-subsection"> Cloning Dre, VCre, SCre, Vika </h2>
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<ul>
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<li> Clearly and objectively describe the results of your work.</li>
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<li> Future plans for the project. </li>
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<li> Considerations for replicating the experiments. </li>
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</ul>
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<h5>You should also describe what your results mean: </h5>
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            <p> Using PCR mutagenesis, we have successfully removed the illegal XbaI site from all four recombinases. </p>
 +
            <p> We then cloned the T7-LacO-regulated recombinases into biobrick format. For SCre, there are two illegal PstI
 +
                sites within the coding sequence (CDS), and for VCre, there is one illegal PstI site within the CDS. We have
 +
                successfully removed all the illegal sites.
 +
            </p>
 +
            <p>
 +
                We submitted all four recombinases as T7-LacO-regulated generator, in pSB1C3 and contain no illegal sites (BBa_K2406081,
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                BBa_K2406082, BBa_K2406083, BBa_K2406084).
 +
            </p>
  
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<ul>
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            <h2 class="header-subsection"> T7-LacO-regulated Cre generator </h2>
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<li> Interpretation of the results obtained during your project. Don't just show a plot/figure/graph/other, tell us what you think the data means. This is an important part of your project that the judges will look for. </li>
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            <p> We have successfully cloned T7-LacO out of pET28b, and used the cloned fragment to perform a five-part MoClo
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<li> Show data, but remember all measurement and characterization data must be on part pages in the Registry. </li>
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                assembly. The assembled T7-LacO-regulated Cre generator was then cloned into biobrick format (BBa_K2406080).
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<li> Consider including an analysis summary section to discuss what your results mean. Judges like to read what you think your data means, beyond all the data you have acquired during your project. </li>
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                </p>
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</ul>
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</div>
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            <h2 class="header-subsection"> Standardized measurement constructs </h2>
 +
            <p>We have created standardized measurement constructs to quantify recombinase activity in vivo. They are essentially
 +
                transcriptional terminator flanked by two recombination target sites, inserted between a constitutive promoter
 +
                and a RFP gene. Of fifteen possible combinations for five recombinases (Cre, Dre, VCre, SCre, Vika), we have
 +
                successfully generated, sequenced, and submitted twelve of them:
  
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<div class="clear"></div>
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            </p>
  
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            <figure style="text-align: center">
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                <img class="same-width" src="https://static.igem.org/mediawiki/2017/6/62/T--Edinburgh_UG--results_page_table.jpg">
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                <br>
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                <figcaption style="padding-top: 20px; font-size: 20px;"> Caption</figcaption>
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            </figure><br><br><br><br>
  
 +
            <h2 class="header-subsection"> Assembling and testing the 14 recombination sites </h2>
 +
            <p> We have successfully cloned the Rox (BBa_K2406000), Vox (BBa_K2406001), VLox (BBa_K2406002), and SLox (BBa_K2406003) in to pSB1C3 biobrick for use. Their functionality is demonstrated in the measurement constructs, described above.
 +
            </p>
 +
            <p>
 +
                We have also cloned ten additional target sites that can be recognized by the Cre recombinase. They are called Lox511 (BBa_K2406008), Lox2272 (BBa_K2406009), Lox5161 (BBa_K2406010), LoxN (BBa_K2406011), M2 (BBa_K2406012), M3 (BBa_K2406013), M7 (BBa_K2406014), M11 (BBa_K2406015), Nuoya (BBa_K2406016), and Zsoka (BBa_K2406017). They are all proved to be functional by in vitro assay using cell lysate containing Cre recombinase.
 +
            </p>
  
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<h5> Project Achievements </h5>
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            <h2 class="header-subsection"> Quantitative measurement of recombinase activity </h2>
  
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<p>You can also include a list of bullet points (and links) of the successes and failures you have had over your summer. It is a quick reference page for the judges to see what you achieved during your summer.</p>
+
            <p>
 +
                We have co-transformed both of our T7-LacO-recombinase generator and our measurement construct into E. coli BL21 (DE3). These strains are then incubated with or without IPTG, on either LB plate over 48 hours, or in LB media in plate reader. We have thoroughly characterized the recombination efficiency of the five recombinases, and determined what combinations are the most orthogonal pairs for future applications.
 +
            </p>
  
−
<ul>
+
            <p>
−
<li>A list of linked bullet points of the successful results during your project</li>
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                We have determined that [probably] Dre/Rox recombinase is the most efficient SSR in E. coli, and that it is orthogonal to the rest of the recombinases. However, [describe what pairs are not orthogonal]. Therefore, we recommend using __ and __ for parallel reactions in E. coli.
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<li>A list of linked bullet points of the unsuccessful results during your project. This is about being scientifically honest. If you worked on an area for a long time with no success, tell us so we know where you put your effort.</li>
+
            </p>
−
</ul>
+
  
−
</div>
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            <h2 class="header-subsection"> Logic gates and software </h2>
 +
            <p>We have designed two-input OR, NOR, AND, NAND, XOR, and XNOR gates using the excision property of two orthogonal tyrosine recombinases: </p>
 +
            <p>As they contain a high degree of repetitiveness, we had difficulty ordering them as single DNA. Therefore, we designed software to ______</p>
 +
           
 +
            <h2 class="header-subsection"> Modeling the behavior of site-specific recombinase </h2>
 +
            <p>We have built deterministic and stochastic models to simulate the behavior of our E. coli strain used for measurement (BL21 (DE3) E. coli carrying T7-LacO-recombinase generator and measurement constructs). The model is able to predict that the leaky expression of recombinase can induce a significant degree of terminator excision, leading to a moderate background expression of RFP.  </p>
 +
            <p>Furthermore, we have developed an algorithm and used it to scan through the genome of E. coli BL21 (DE3) strain, and identified five genomic regions that may potentially be a functional target site for Cre recombinase. </p>
  
 +
            <h2 class="header-subsection"> Human practice: Interdisciplinarity in Synthetic Biology </h2>
 +
            <p>Due to the interdisciplinary nature of SMORE, we investigated interdisciplinarity in biology to understand how people would use it. </p>
 +
            <p>We conducted a skill exchange survey with Team Bulgaria and Israel. The survey identified the use of technical language as pivotal in mutual understanding in interdisciplinary collaboration.  </p>
 +
            <p>We also measured the diversity in discipline of past iGEM teams and analyzed it with iGEM achievements. We found no significant correlation between diversity and achievements. We proposed hypotheses to explain the result. </p>
  
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<div class="column half_size" >
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            <h2 class="header-subsection"> Human practice: Accessibility Improvement of SMORE </h2>
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            <p>From the aforementioned study, we identified challenges in interdisciplinary work and decided an improvement of accessibility is needed to promote interdisciplinary use of SMORE. We improved accessibility in four aspects: </p>
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<h5>Inspiration</h5>
+
            <p>Readability: we wrote highly readable introductory paragraphs for a wide audience. We also provided highly readable protocols for the software and the cell sorter. </p>
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<p>See how other teams presented their results.</p>
+
            <p>Hardware: we devised a microfluidic device with a 3D syringe pump – an alternative to the expensive cell sorter in the market – to use with SMORE’s randomizer strategy. </p>
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<ul>
+
            <p>Software: we wrote an oligonucleotide designer programme to help the inexperienced to design oligos to use with SMORE. </p>
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<li><a href="https://2014.igem.org/Team:TU_Darmstadt/Results/Pathway">2014 TU Darmstadt </a></li>
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            <p>Data: we compiled and experimentally verified recombinase-related sequence data to establish recombination as a convenient and reliable technology. </p>
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<li><a href="https://2014.igem.org/Team:Imperial/Results">2014 Imperial </a></li>
+
        </div>
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<li><a href="https://2014.igem.org/Team:Paris_Bettencourt/Results">2014 Paris Bettencourt </a></li>
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    </div>
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</ul>
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{{:Team:Edinburgh_UG/Templates/Footer}}

Revision as of 18:58, 31 October 2017





Results


Overview

Material needed

  1. We cloned Dre, VCre, SCre, and Vika generators into Biobrick format, removing all illegal sites when necessary.
  2. We assembled T7-LacO-Cre generator and cloned it into Biobrick format.
  3. We successfully assembled 12 out of 15 of measurement constructs to allow users to quantify recombinase activity in vivo.
  4. We assembled 10 target sites for Cre and proved their functionality in vitro. We also assembled the target sites for Dre, VCre, SCre, and Vika – Rox, VLox, SLox, and Vox respectively. Their functionality is proved in the measurement constructs.
  5. We have extensively quantified the recombination efficiency of the five recombinases in E. coli.
  6. We have built software and used it to design assembly methods for six logic gates using tyrosine recombinase.
  7. We have built deterministic and stochastic modeling to simulate the behavior of site-specific recombinase. We also devised an algorithm to detect potential recombination sites in a genome.
  8. We have conducted an investigation into interdisciplinarity. This includes a survey to identify challenges in interdisciplinary work, and a systematic analysis of past iGEM teams, to test correlation between interdisciplinarity and iGEM achievement.
  9. We have integrated the result from the interdisciplinarity study to improve accessibility of SMORE in four aspects: readability, hardware, user experience and data.


Cloning Dre, VCre, SCre, Vika

Using PCR mutagenesis, we have successfully removed the illegal XbaI site from all four recombinases.

We then cloned the T7-LacO-regulated recombinases into biobrick format. For SCre, there are two illegal PstI sites within the coding sequence (CDS), and for VCre, there is one illegal PstI site within the CDS. We have successfully removed all the illegal sites.

We submitted all four recombinases as T7-LacO-regulated generator, in pSB1C3 and contain no illegal sites (BBa_K2406081, BBa_K2406082, BBa_K2406083, BBa_K2406084).

T7-LacO-regulated Cre generator

We have successfully cloned T7-LacO out of pET28b, and used the cloned fragment to perform a five-part MoClo assembly. The assembled T7-LacO-regulated Cre generator was then cloned into biobrick format (BBa_K2406080).

Standardized measurement constructs

We have created standardized measurement constructs to quantify recombinase activity in vivo. They are essentially transcriptional terminator flanked by two recombination target sites, inserted between a constitutive promoter and a RFP gene. Of fifteen possible combinations for five recombinases (Cre, Dre, VCre, SCre, Vika), we have successfully generated, sequenced, and submitted twelve of them:


Caption




Assembling and testing the 14 recombination sites

We have successfully cloned the Rox (BBa_K2406000), Vox (BBa_K2406001), VLox (BBa_K2406002), and SLox (BBa_K2406003) in to pSB1C3 biobrick for use. Their functionality is demonstrated in the measurement constructs, described above.

We have also cloned ten additional target sites that can be recognized by the Cre recombinase. They are called Lox511 (BBa_K2406008), Lox2272 (BBa_K2406009), Lox5161 (BBa_K2406010), LoxN (BBa_K2406011), M2 (BBa_K2406012), M3 (BBa_K2406013), M7 (BBa_K2406014), M11 (BBa_K2406015), Nuoya (BBa_K2406016), and Zsoka (BBa_K2406017). They are all proved to be functional by in vitro assay using cell lysate containing Cre recombinase.

Quantitative measurement of recombinase activity

We have co-transformed both of our T7-LacO-recombinase generator and our measurement construct into E. coli BL21 (DE3). These strains are then incubated with or without IPTG, on either LB plate over 48 hours, or in LB media in plate reader. We have thoroughly characterized the recombination efficiency of the five recombinases, and determined what combinations are the most orthogonal pairs for future applications.

We have determined that [probably] Dre/Rox recombinase is the most efficient SSR in E. coli, and that it is orthogonal to the rest of the recombinases. However, [describe what pairs are not orthogonal]. Therefore, we recommend using __ and __ for parallel reactions in E. coli.

Logic gates and software

We have designed two-input OR, NOR, AND, NAND, XOR, and XNOR gates using the excision property of two orthogonal tyrosine recombinases:

As they contain a high degree of repetitiveness, we had difficulty ordering them as single DNA. Therefore, we designed software to ______

Modeling the behavior of site-specific recombinase

We have built deterministic and stochastic models to simulate the behavior of our E. coli strain used for measurement (BL21 (DE3) E. coli carrying T7-LacO-recombinase generator and measurement constructs). The model is able to predict that the leaky expression of recombinase can induce a significant degree of terminator excision, leading to a moderate background expression of RFP.

Furthermore, we have developed an algorithm and used it to scan through the genome of E. coli BL21 (DE3) strain, and identified five genomic regions that may potentially be a functional target site for Cre recombinase.

Human practice: Interdisciplinarity in Synthetic Biology

Due to the interdisciplinary nature of SMORE, we investigated interdisciplinarity in biology to understand how people would use it.

We conducted a skill exchange survey with Team Bulgaria and Israel. The survey identified the use of technical language as pivotal in mutual understanding in interdisciplinary collaboration.

We also measured the diversity in discipline of past iGEM teams and analyzed it with iGEM achievements. We found no significant correlation between diversity and achievements. We proposed hypotheses to explain the result.

Human practice: Accessibility Improvement of SMORE

From the aforementioned study, we identified challenges in interdisciplinary work and decided an improvement of accessibility is needed to promote interdisciplinary use of SMORE. We improved accessibility in four aspects:

Readability: we wrote highly readable introductory paragraphs for a wide audience. We also provided highly readable protocols for the software and the cell sorter.

Hardware: we devised a microfluidic device with a 3D syringe pump – an alternative to the expensive cell sorter in the market – to use with SMORE’s randomizer strategy.

Software: we wrote an oligonucleotide designer programme to help the inexperienced to design oligos to use with SMORE.

Data: we compiled and experimentally verified recombinase-related sequence data to establish recombination as a convenient and reliable technology.