Difference between revisions of "Team:Cologne-Duesseldorf/Test"

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<h3 id="one">Heading one</h3>
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<h3>Designing a Customizable Synthetic Cell Compartment Toolbox</h3>
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<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aenean faucibus pharetra mollis. Quisque a nisi felis. Curabitur gravida orci a enim sodales convallis. Duis magna quam, finibus id nulla id, eleifend imperdiet ex. Maecenas lacinia fermentum nisl, sollicitudin interdum turpis imperdiet tincidunt. Sed ultricies sagittis orci pharetra vulputate. Nunc ac ipsum augue. Suspendisse dapibus quam a rutrum congue. Pellentesque nec mauris et purus interdum tristique id semper odio. Fusce in est maximus, sollicitudin augue non, iaculis leo. Integer vitae metus id felis volutpat imperdiet. Cras elit est, egestas sit amet orci condimentum, aliquet rhoncus purus. Duis sed lectus interdum, vestibulum orci et, aliquam elit. Aliquam eleifend purus nec lorem accumsan, a tincidunt nibh vehicula. Etiam lobortis volutpat lorem, ac dictum libero egestas efficitur. Fusce condimentum tempor ipsum ut condimentum.</p>
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<h3 id="two">Bioreactor simulation</h3>
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<!-- Plot p450 Bioreactor -->
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Synthetic organisms provide a wide range of applications with the potential to tackle
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<img src="https://static.igem.org/mediawiki/2017/f/f7/T--Cologne-Duesseldorf--Nootkatone-p450-Model-Bioreactor.svg">
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the biggest challenges humanity faces. Their creation is therefore one of the major
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<p>The yield of $154.9 \ \frac{\text{mg}}{\text{L}}$ Nootkatol was lower than the published results of Wriessnegger 2014. Our first guess was that the assumption of all enzymes being equally concentrated was probably false. We therefore varied the enzyme concentrations and found that overexpression of valencene synthase increased the yield dramatically by converting way more FPP than before, while overexpressing the other enzymes had little to no effect at all:</p>
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goals in synthetic biology. Many breakthroughs have been achieved in the last
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<!-- Plot Expression analysis -->
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decade, however, the <strong>creation of a fully synthetic cell is yet a milestone to reach for.</strong>
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<img src="https://static.igem.org/mediawiki/2017/8/8a/T--Cologne-Duesseldorf--Nootkatone-Expression-3D.svg">
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<br>
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<p>What can be seen in the plot above is that the system is mostly influenced by concentration changes of valencene synthase. Since the Nootkatone production did not seem to increase further after increasing the valencene synthase concentration by 20-fold, we stuck to that number and simulated our model under the changed conditions.</p>
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A common approach tries to build up artificial cells from scratch, whereas we want to
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<h3 id="accordion">Accordion</h3>
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start by engineering artificial compartments through orthogonalization. For designing
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<button class="accordion">Section 1</button>
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these new compartments we plan to establish an open source toolbox accessible to
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<div class="panel">
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the community at large. This will make it possible to boot up a compartment perfectly
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<p>Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.</p>
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tailored for a specific application, which will enable cheaper and more efficient
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production of biofuels, pharmaceuticals, or high value chemicals.  
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<br>
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By integrating enzymes or biosynthetic pathways into semi-permeable organelles we
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gain higher concentrations of enzymes and metabolites and provide a basis for the
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ideal operation of specialized enzymes. Furthermore, toxic or unstable intermediates
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can be sustained and naturally incompatible reactions can take place
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simultaneously.
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<p>Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.</p>
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We have chosen <span class="label">yeast peroxisomes</span> as our chassis for designing this synthetic organelle, which are very resistant, have a useful import mechanism and are expendable under optimal conditions. <abbr title="Giannopoulou, Evdokia-Anastasia et al. “Towards the Molecular Mechanism of the Integration of Peroxisomal Membrane Proteins.” Biochimica et Biophysica Acta 1863.5 (2016): 863–869. PMC. Web. 20 May 2017.">(Giannopoulou et al, 2017)</abbr>
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<h3 id="tables">Responsive tables</h3>
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<th>Parameter</th>
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<th>Value</th>
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<th>Source</th>
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<p>Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.</p>
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<td>$c_{\text{FPP, Wildtype}}$</td>
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<td>$2.5 \  \frac{\text{nmol}}{\text{OD}}$</td>
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<td><abbr title="2017, Sebastián Rubat - Increasing the intracellular isoprenoid pool in Saccharomyces cerevisiae by structural fine-tuning of a bifunctional farnesyl diphosphate synthase">Rubat 2017</abbr></td>
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<td>$N_{\text{cells per OD}}$</td>
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<p>Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.</p>
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<td>$3E+7 \  \frac{\text{cells}}{\text{OD}}$</td>
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<td><a href="http://bionumbers.hms.harvard.edu/bionumber.aspx?id=100986&ver=3">Bionumbers</a></td>
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<td>$V_{\text{Yeast}}$</td>
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<td>$6E-14 \ \text{L}$</td>
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<td><abbr title="2012, Rob Phillips - Physical Biology of the Cell">Philips 2012</abbr></td>
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<td>$c_{\text{Max FPP}}$</td>
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<td>$1.39E-3  \frac{\text{mol}}{\text{L}}$</td>
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<td>$\frac{c_{\text{FPP, Wildtype}}}{N_{\text{cells per OD}} \cdot V_{\text{Yeast}}}$</td>
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<td>$\mu_{FPP}$</td>
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<td>$1E-6 \frac{1}{\text{s}}$</td>
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<td>Assumption</td>
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<td>$\text{kM}_{\text{Valencene Synthase}}$</td>
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<td>$1.04 \text{µM}$</td>
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<td><a href="http://www.brenda-enzymes.org/enzyme.php?ecno=4.2.3.73">Brenda</a></td>
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<td>$\text{kM}_{\text{p450 BM3}}$</td>
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<td>$126 \text{µM}$</td>
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<td><a href="http://www.brenda-enzymes.de/enzyme.php?ecno=1.14.14.1">Brenda</a></td>
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<td>$\text{kM}_{\text{ADH-21}}$</td>
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<td>$161 \text{µM}$</td>
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<td><abbr title="2017, Sebastián Rubat - Increasing the intracellular isoprenoid pool in Saccharomyces cerevisiae by structural fine-tuning of a bifunctional farnesyl diphosphate synthase">Rubat 2017</abbr></td>
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<td>$\text{kcat}_{\text{Valencene Synthase}}$</td>
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<td>$0.0032 \frac{1}{\text{s}}$</td>
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<td><a href="http://www.brenda-enzymes.org/enzyme.php?ecno=4.2.3.73">Brenda</a></td>
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<td>$\text{kcat}_{\text{p450 BM3}}$</td>
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<td>$2.619 \frac{1}{\text{s}}$</td>
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<td><a href="http://www.brenda-enzymes.de/enzyme.php?ecno=1.14.14.1">Brenda</a></td>
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<td>$\text{kcat}_{\text{ADH-21 forward}}$</td>
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<td>$6 \frac{1}{\text{s}}$</td>
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<td><a href="http://onlinelibrary.wiley.com/doi/10.1002/cctc.201402952/full">Schulz 2015</a></td>
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<td>$\text{kcat}_{\text{ADH-21 backward}}$</td>
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<td>$1.2 \frac{1}{\text{s}}$</td>
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<td>$\frac{\text{kcat}_{\text{ADH-21 forward}}}{5}$</td>
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<td>$c_{\text{Enzyme}}$</td>
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<td>$1 \text{µM}$</td>
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<td>Assumption</td>
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Revision as of 10:11, 23 September 2017

Heading

Heading one

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Bioreactor simulation

The yield of $154.9 \ \frac{\text{mg}}{\text{L}}$ Nootkatol was lower than the published results of Wriessnegger 2014. Our first guess was that the assumption of all enzymes being equally concentrated was probably false. We therefore varied the enzyme concentrations and found that overexpression of valencene synthase increased the yield dramatically by converting way more FPP than before, while overexpressing the other enzymes had little to no effect at all:

What can be seen in the plot above is that the system is mostly influenced by concentration changes of valencene synthase. Since the Nootkatone production did not seem to increase further after increasing the valencene synthase concentration by 20-fold, we stuck to that number and simulated our model under the changed conditions.

Accordion

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Callout

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Responsive tables

Parameter Value Source
$c_{\text{FPP, Wildtype}}$ $2.5 \ \frac{\text{nmol}}{\text{OD}}$ Rubat 2017
$N_{\text{cells per OD}}$ $3E+7 \ \frac{\text{cells}}{\text{OD}}$ Bionumbers
$V_{\text{Yeast}}$ $6E-14 \ \text{L}$ Philips 2012
$c_{\text{Max FPP}}$ $1.39E-3 \frac{\text{mol}}{\text{L}}$ $\frac{c_{\text{FPP, Wildtype}}}{N_{\text{cells per OD}} \cdot V_{\text{Yeast}}}$
$\mu_{FPP}$ $1E-6 \frac{1}{\text{s}}$ Assumption
$\text{kM}_{\text{Valencene Synthase}}$ $1.04 \text{µM}$ Brenda
$\text{kM}_{\text{p450 BM3}}$ $126 \text{µM}$ Brenda
$\text{kM}_{\text{ADH-21}}$ $161 \text{µM}$ Rubat 2017
$\text{kcat}_{\text{Valencene Synthase}}$ $0.0032 \frac{1}{\text{s}}$ Brenda
$\text{kcat}_{\text{p450 BM3}}$ $2.619 \frac{1}{\text{s}}$ Brenda
$\text{kcat}_{\text{ADH-21 forward}}$ $6 \frac{1}{\text{s}}$ Schulz 2015
$\text{kcat}_{\text{ADH-21 backward}}$ $1.2 \frac{1}{\text{s}}$ $\frac{\text{kcat}_{\text{ADH-21 forward}}}{5}$
$c_{\text{Enzyme}}$ $1 \text{µM}$ Assumption

Mega menu

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Aikaterini Karapantsaiou
Anna Sappler
Bastiaan Tjeng
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Aikaterini Karapantsiou

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