Revision as of 23:59, 31 October 2017

Design

Overview

On this page we explain the design principles we defined for our project and how we followed them. We structured our work in phases and tried to proceed through them. The phases apply to theoretical work (models) as well as to the practical (experiments). In first phase, we learned to handle the subjects and get familiar with the theory and literature. We designed, ordered and built constructs for tests of the experimental procedure and for further optimization. In the second phase, we tested predictions of the models and delivered parameters for new models with experiments. We optimized single parts to work in a regime where the model predicted the circuit to be functional.

We designed the project in a hierarchical bottom-up engineering approach: We divided the circuit into its different functions (F_a-F_e) and engineered them until they met our criteria.

Circuit Functions:

The individual constructs were assembled with molecular cloning and the functions were tested with reporter genes such as gfp and mcherry. Only if they behaved according to our requirements, we combined functions together. In parallel, we ordered the full genetic circuit of CATE with restriction sites along the critical loci in order to rapidly exchange promotors ribosome binding sites or coding sequences after we experimentally optimized the parts.

We worked in parallel on the functions of CATE, thats why every function goes through the phases independently.

Phase I

In Phase I we decided for specific DNA parts by reading up literature and planned the assembly of the parts into test devices. The test devices were then used to develop working assays.

Plasmid Creation during the CATE project

Phase II

In this phase the assays work and show us if the function behaves as expected. We could therefore start to tune the functions by changing the expression level of proteins with RBS libraries or different designs of a promotor. Because of time restrictions we did not go into protein engineering. We created reduced libraries (Red Libs) to create variants with an expression level that fits the needs of the circuit. As soon as the parts met our requirements, we proceeded to combine them to more complex circuits in phase III.

Phase III

If two functions were ready to be combined, phase III experiments were initiated. The assays were kept the same as in phase II.

Phase IV - proof of concept

This is the final phase and important features of CATE are shown to work in phase IV experiments.

Experiments Plan

Here you find the overview of the phases of our project and which parts were used at which time.

@@ Line 13: / Line 13: @@
 <section class="first">
      <h1>Overview</h1>
-     <p>On this page we explain the design principles we defined for our project and how we followed them. We structured our work in phases and tried to proceed through them. The phases apply to theoretical work (models) as well as to the practical (experiments). In the early phases, we learned to handle the subjects and get familiar with the theory and literature. We designed, ordered and built constructs for tests of the experimental procedure and for further optimization. In later phases, we tested predictions of the models and delivered parameters for new models. We engineered single parts to behave as our circuit requires by implementing predictions of the models. We combined functions if possible and showed that we can build more complex circuits with them.
+     <p>On this page we explain the design principles we defined for our project and how we followed them. We structured our work in phases and tried to proceed through them. The phases apply to theoretical work (models) as well as to the practical (experiments). In first phase, we learned to handle the subjects and get familiar with the theory and literature. We designed, ordered and built constructs for tests of the experimental procedure and for further optimization. In the second phase, we tested predictions of the models and delivered parameters for new models with experiments. We optimized single parts to work in a regime where the model predicted the circuit to be functional.
 </p>
 <p>
-We designed the project in a hierarchical bottom-up engineering approach: We divided the circuit into its different functions (F<sub>a</sub>-F<sub>e</sub>) and engineered them until they met our criteria:</p>
+We designed the project in a hierarchical bottom-up engineering approach: We divided the circuit into its different functions (F<sub>a</sub>-F<sub>e</sub>) and engineered them until they met our criteria.</p>
+<p><b>Circuit Functions:</b></p>
 <ul>
          <li><a href="https://2017.igem.org/Team:ETH_Zurich/Circuit/Fa_Tumor_Sensor">Tumor Sensor</a></li>

Difference between revisions of "Team:ETH Zurich/Design"