Difference between revisions of "Template:Team:Utrecht/MainBody"

Latest revision as of 00:24, 15 December 2017

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Cas9 & Cpf1 secretion
and activity

Comparison of endonuclease activity for Cas9 and Cpf1 that has been produced in, and excreted by, HEK293 cells.

MESA two-component system replication

Details on the MESA two-component system, explanation of its relation to our design and the results of its reproduction.

OUTCASST system production

Detailed explanation of the OUTCASST mechanism, experimental progress and technical prospects.

Modeling and
mathematics

Ordinary differential equations, cellular automaton and an object based model for optimal linker-length estimation.

InterLab study participation

Results and details of our measurements for the iGEM 2017 InterLab Study.

Stakeholders & opinions

Interviews and dialogues with stakeholders, potential users, third parties and experts relating to pathogen detection or DNA-based diagnostics.

Risks & safety-issues

Implications and design considerations relating to safety in the usage and implementation of OUTCASST as a diagnostics tool.

Design & integration

OUTCASST toolkit and product design with factors such as bio-safety and user-friendliness taken into account.

Outreach

Videos we made for the dutch public, together with 'de Kennis van Nu'.

Meet our team

About us, our interests and roles in the team and our supervisors.

Sponsors

A listing of our sponsors, how they assisted us and our gratitude for their assistance.

Collaborations

Read about our exchanges with other iGEM teams and government agencies.

Achievements

A short description of all that we have achieved during our participation in the iGEM.

Attributions

A thank-you for everyone that assited us, both in and outside the lab.

@@ Line 762: / Line 762: @@
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+<div style="position: absolute;top: 0;right: -250px;width: 200px;text-align: center;border: 1px solid gold;padding: 10px;border-radius: 10px;box-sizing: border-box;background: #ffedb8;">
+<div style="
+    font-weight: bold;
+    font-size: 20px;
+    color: #c48b00;
+    border-bottom: 1px solid #ffd700;
+	padding-bottom: 15px;
+    margin-bottom: 15px;
+">Awards</div>
+<img width="100" src="https://static.igem.org/mediawiki/2017/thumb/a/a2/UU_gold_medal.png/240px-UU_gold_medal.png"><br><div style="font-size: 15px;color: #c48b00; border-bottom: 1px solid #ffd700; padding-bottom: 15px; margin-top: 5px;">Gold medal</div>
+<div style="margin-top: 15px; margin-bottom: 10px; font-size: 15px;color: #c48b00;"><b>Nominated</b><br />Best integrated human practices</div>
+</div>
 		<div class="page-heading">The OUTCASST two-component system</div>
 	This year is the debut year for the Utrecht University iGEM team. Our team has developed an easy to use and cheap DNA detection kit for disease diagnosis in areas of the world where advanced diagnostic technologies are not available. We call our system ‘OUTCASST’, which stands for ‘Out-of-cell Crispr-Activated Sequence-specific Signal Transducer’.
@@ Line 838: / Line 851: @@
 	A final product would include the use of so-called anhydrobiotic insect <i>Polypedilum vanderplanki</i> cells, which can be air-dried, allowing them to be stored for prolonged periods of time at room temperature. The OUTCASST system is cheap to produce, store and ship, and requires nothing more then a simple microscope as a readout.
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@@ Line 1,046: / Line 1,073: @@
 <br><br>
 Additionally, together with team Wageningen_UR a final experiment was done to verify that the protein in the medium was indeed secreted instead of due to involuntary cell lysis (see <a onclick="return change_page('collaborations', 1)" href="collaborations">Collaborations</a>).
-This experiment was done in duplo, by members from both team Wageningen_UR and team Utrecht, individually, to provide independent verification of the result. This final experiment was done according to a collaboration protocol that was shared with the Wageningen_UR team [Experimental\Protocols\Wiki ready\Experimental\Protocols\Wiki ready.pdf].
+This experiment was done in duplo, by members from both team Wageningen_UR and team Utrecht, individually, to provide independent verification of the result. This final experiment was done according to a collaboration protocol that was shared with the Wageningen_UR team <a target=_BLANK href="https://static.igem.org/mediawiki/2017/4/40/UuProtocolCollaborationWageningen.pdf" class="pdf pdf-inline"></a>.
 <br><br>
 <b>Endonuclease activity assay</b>
@@ Line 1,545: / Line 1,572: @@
 We could then substitute these three concentrations for their expressions in the expression of the target chain concentration. Making further quasi steady state assumptions on the formation of the pre-cleavage and post-cleavage complexes reduces the expression by two more dependencies. This was done in mathematica notebook, found <a target=_BLANK href="https://static.igem.org/mediawiki/2017/2/21/UuModelingQSSAWorkouts.txt" class="url_external">here</a>.
 <br><br>
-[INSERT WILL FOLLOW]
+The resulting expression shows that the concentration of target chain depends on: 1) The concentrations of its production relative to the production of the protease chain. 2) The concentration of protease chain. 3) The concentration of substrate. 4) How much cleaved target chain is available to trap said substrate.
+<br><br>
+The fraction of the total target chain that is cleaved is a saturation function that depends on substrate and protease chain concentrations with respect to how quickly the function's saturation point is attained. We can minimize the cleaved target chain fraction, and the occurrence of substrate trapping with it, by simply having a target chain amount that is much larger than that of the substrate.
+<br><br>
+In short, the more substrate there is available per target chain, the less signal per substrate molecule we can get as ineffectual target chain concentration increases.
+<br><br>
+The equations suggest that there is a theoretical optimum for the production rates of both chains, relative to the substrate concentration in the system. Due to time constraints, the expression for this optimum could not be given. The methods given in the mathematica script provided here should be able to reach this solution, given enough time. The meaning of such an optimum, however, is questionable. As the substrate concentrations in our toolkit may differ greatly depending on severity of infection and chance, optimization through growth-rates would need to be different per sample. In conclusion, the only effective optimization of protein productions is to make sure that the protein concentrations greatly exceed the sample concentration of DNA sequence we wish to detect.
 <br><br>
@@ Line 1,677: / Line 1,711: @@
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+	<figure class="js-item column shuffle-item shuffle-item--visible" onclick="jQuery('html, body').animate({scrollTop: jQuery('#item-parasitology').offset().top - 150}, 500);" style="cursor: pointer; position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(225px, 129px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
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+	<figure class="js-item column col-span shuffle-item shuffle-item--visible" onclick="jQuery('html, body').animate({scrollTop: jQuery('#item-genomediagnostics').offset().top - 150}, 500);" style="cursor: pointer; position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(0px, 389px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
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 <div class="page-heading">Achievements</div>
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