Difference between revisions of "Team:Paris Bettencourt/Project/Continuity"
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{{Paris_Bettencourt/header}} | {{Paris_Bettencourt/header}} | ||
{{Paris_Bettencourt/menu}} | {{Paris_Bettencourt/menu}} | ||
− | {{Paris_Bettencourt/banner|page_id= | + | {{Paris_Bettencourt/banner|page_id=continuity|page_name=Continuity}} |
<html> | <html> | ||
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<img src="https://static.igem.org/mediawiki/2015/8/88/PB_growth.png"/> | <img src="https://static.igem.org/mediawiki/2015/8/88/PB_growth.png"/> | ||
− | <p class="caption">Our model for decreasing the fitness burden of our organism during the production phase. The cells do not produce any vitamin during the manufacturing process. The vitamin production is triggered before the distribution.</p> | + | <p class="caption"><b>Our model for decreasing the fitness burden of our organism during the production phase.</b> The cells do not produce any vitamin during the manufacturing process. The vitamin production is triggered before the distribution.</p> |
</div> | </div> | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
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<h2>The ID gene</h2> | <h2>The ID gene</h2> | ||
− | <div class="column-left"> | + | <div class="column-left" style="width:40%"> |
<p>The quality control of our system is possible thanks to an ID gene, which consists in the fluorescent protein mCherry expressed to low levels. We chose this protein because its fluorescence colour is easily distinguishable from the media that will be used for growth, hence a better signal.</p> | <p>The quality control of our system is possible thanks to an ID gene, which consists in the fluorescent protein mCherry expressed to low levels. We chose this protein because its fluorescence colour is easily distinguishable from the media that will be used for growth, hence a better signal.</p> | ||
<p>The aim of this gene is to provide a quick and reliable way to determine whether the strain that will be distributed is the one intended. After growing the micro-organism in a bioreactor, a sample is taken in order to start a new culture from it. We suggest that, while doing so, the sample has to pass a quality check where its fluorescence is measured.</p> | <p>The aim of this gene is to provide a quick and reliable way to determine whether the strain that will be distributed is the one intended. After growing the micro-organism in a bioreactor, a sample is taken in order to start a new culture from it. We suggest that, while doing so, the sample has to pass a quality check where its fluorescence is measured.</p> | ||
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</div> | </div> | ||
− | <div class="column-right"> | + | <div class="column-right" style="width:55%"> |
<a href="https://static.igem.org/mediawiki/2015/f/ff/PB_workflow.png"> | <a href="https://static.igem.org/mediawiki/2015/f/ff/PB_workflow.png"> | ||
− | <img src="https://static.igem.org/mediawiki/2015/f/ff/PB_workflow.png | + | <img src="https://static.igem.org/mediawiki/2015/f/ff/PB_workflow.png"/> |
</a> | </a> | ||
− | <span class="caption">How quality control will be performed. The transfer of the inoculate should be done in sterile conditions in a container that also plays the role of fluorimeter cuvette. This ensures that even low-budget labs will always distribute the right strain to people.</span> | + | <br/> |
+ | <span class="caption"><b>How quality control will be performed.</b> The transfer of the inoculate should be done in sterile conditions in a container that also plays the role of fluorimeter cuvette. This ensures that even low-budget labs will always distribute the right strain to people.</span> | ||
</div> | </div> | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
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<a href="https://static.igem.org/mediawiki/2015/7/75/PB_landingpad.png"><img src="https://static.igem.org/mediawiki/2015/7/75/PB_landingpad.png" style="width:90%"/></a> | <a href="https://static.igem.org/mediawiki/2015/7/75/PB_landingpad.png"><img src="https://static.igem.org/mediawiki/2015/7/75/PB_landingpad.png" style="width:90%"/></a> | ||
<br/> | <br/> | ||
+ | <span class="caption"><b>The proposed process for addition of new operons to the chassis.</b> A standard cassette is integrated in the PhiC31 locus. It then becomes a new possible outcome for the random differentiation, thanks to the addition of a new LoxP site.</span> | ||
</div> | </div> | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
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<img src="https://static.igem.org/mediawiki/2015/6/65/PB_brainbow.png" style="width:100%" align="middle"/> | <img src="https://static.igem.org/mediawiki/2015/6/65/PB_brainbow.png" style="width:100%" align="middle"/> | ||
</a> | </a> | ||
− | <p class="caption"> | + | <p class="caption"> |
+ | <b>Overview of the differentiation process.</b> For a complete organism with four metabolic operons, there are four possible outcomes, each of them leading to the expression of only one operon. In other words, each cell randomly choses one operon to express. | ||
+ | </p> | ||
</div> | </div> | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
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<h3>How to induce the differentiation?</h3> | <h3>How to induce the differentiation?</h3> | ||
There are different ways the CRE recombinase can be induced. | There are different ways the CRE recombinase can be induced. | ||
− | <h4>Chemical</h4> | + | <h4>Chemical induction</h4> |
A chemical would be one of the most predictable, efficient way to differentiate the cells. However, it requires to have access to this chemical, and to open the reactor which can be impractical for community labs with low resources to maintain sterility. It is nevertheless the solution of choice for funded factories. Carbohydrates such as glucose, arabinose or lactose seem to be the best options since they are not toxic. | A chemical would be one of the most predictable, efficient way to differentiate the cells. However, it requires to have access to this chemical, and to open the reactor which can be impractical for community labs with low resources to maintain sterility. It is nevertheless the solution of choice for funded factories. Carbohydrates such as glucose, arabinose or lactose seem to be the best options since they are not toxic. | ||
<h4>Heat</h4> | <h4>Heat</h4> | ||
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<p>In theory, the cells with this cassette integrated in the chromosome are expected to emit a red fluorescence. Upon induction of the CRE-recombinase, they should lose the red fluorescence and start to express either mCerualean (a cyan fluorescent protein) or mVenus (a yellow fluorescent protein). Each cell should express only one of those two proteins at the same time.</p> | <p>In theory, the cells with this cassette integrated in the chromosome are expected to emit a red fluorescence. Upon induction of the CRE-recombinase, they should lose the red fluorescence and start to express either mCerualean (a cyan fluorescent protein) or mVenus (a yellow fluorescent protein). Each cell should express only one of those two proteins at the same time.</p> | ||
− | < | + | <p><img src="https://static.igem.org/mediawiki/2015/8/8f/PB_colibow_sequence.png"/></p> |
+ | <span class="caption"><b>Map of the DNA sequence we constructed.</b> The promoter BBaJ23199 is constitutive. mCherry, mCerulean, mVenus are fluorescent proteins of different colours.</span> | ||
<div class="column-left"> | <div class="column-left"> | ||
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<div class="column-right"> | <div class="column-right"> | ||
<img src="https://static.igem.org/mediawiki/2015/a/a7/PB_colibow_integrated.png" style="width:80%"/> | <img src="https://static.igem.org/mediawiki/2015/a/a7/PB_colibow_integrated.png" style="width:80%"/> | ||
+ | <span class="caption"><b>Gel electrophoresis after PCR for checking the integration.</b> We amplified the junctions between the artificial cassette and <i>E. coli </i>'s chromosome. For every screened clone, the two bands have the expected sizes, which proves that the cassette is integrated in the correct locus.</span> | ||
</div> | </div> | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
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<div class="column-left"> | <div class="column-left"> | ||
<img src="https://static.igem.org/mediawiki/2015/5/5b/PB_colibow_proteins.png" style="width:80%"/> | <img src="https://static.igem.org/mediawiki/2015/5/5b/PB_colibow_proteins.png" style="width:80%"/> | ||
+ | <span class="caption"><b>Gel electrophoresis after PCR for checking the presence of the three fluorescent proteins.</b> For the clone shown here, it means that all three proteins ORFs are present on the chromosome, even though only the first one is actually expressed.</span> | ||
</div> | </div> | ||
<div class="column-right"> | <div class="column-right"> | ||
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<h3>Sequencing of the Lox Array</h3> | <h3>Sequencing of the Lox Array</h3> | ||
− | <p>To investigate whether unexpected recombination occured within the LoxP sites due to homologous recombination, we performed sequencing on the first part of the integrated cassette, where the Lox Array is. This way we could make sure that it was still intact and contained no PCR-induced mutations.</p> | + | <p>To investigate whether unexpected recombination occured within the LoxP sites due to homologous recombination, we performed Sanger sequencing on the first part of the integrated cassette, where the Lox Array is. This way we could make sure that it was still intact and contained no PCR-induced mutations.</p> |
</div> | </div> | ||
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<span class="legend"> | <span class="legend"> | ||
+ | <b>Characterization of the promoter followed by the four LoxP sites.</b><br/> | ||
Using standard biobrick assembly, three plasmids were constructed and transformed into <i>E. coli</i>:</span> | Using standard biobrick assembly, three plasmids were constructed and transformed into <i>E. coli</i>:</span> | ||
<ul style="font-size:13px"> | <ul style="font-size:13px"> | ||
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<img src="https://static.igem.org/mediawiki/2015/b/be/PB_colibow_fluorescence.png"/> | <img src="https://static.igem.org/mediawiki/2015/b/be/PB_colibow_fluorescence.png"/> | ||
<span class="legend"> | <span class="legend"> | ||
+ | <b>Expression of the first protein of the cassette in the chromosome.</b><br/> | ||
A "mother cell" with our differentiation system integrated in the chromosome was grown to exponential phase and its fluorescence was measured when OD<sub>600</sub> reached 0.3. As a negative control, a cell without fluorescent underwent the same treatment. | A "mother cell" with our differentiation system integrated in the chromosome was grown to exponential phase and its fluorescence was measured when OD<sub>600</sub> reached 0.3. As a negative control, a cell without fluorescent underwent the same treatment. | ||
Excitation wavelength: 585 nm. | Excitation wavelength: 585 nm. |
Revision as of 00:22, 19 September 2015