From 2010.igem.org

Revision as of 14:18, 27 October 2010

Achievements Overview

Short movie of an E. coli cell switching between the tumbling and the straight swimming modes..

The E. lemming

Watch the smallest remotely controlled robot in action at ETH Zurich! (Includes recorded video of live images of the light controlled E. coli - The E. lemming is alive!)

BioBrick Toolbox

Get a glimpse of our collection of BioBricks that showcases the proteins we made not only for E. lemming's chemotaxis signaling network and cellular anchoring, but also for its light sensing & fluorescence reporting pathway, including our favorites: the light-sensitive couple PhyB-Pif3 and the Archeal light receptor-an intra-species fusion protein! You also find here the characterization of our parts.

MATLAB Toolbox (Lemming Toolbox)

MATLAB Toolbox Screenshot of the Simulink blocks available in the toolbox. Please note that these blocks can be visually assembled with the Simulink blocks of other Toolboxes (e.g. blocks for nearly any mathematical function), and that the algorithms we developed can be accessed directly through Matlab code, too.

We managed to develop all our computer based tools & algorithms as re-usable, publicly available modules and we assembled the entire in silico setup of the E. Lemming into a MATLAB Toolbox! Our Toolbox includes 18 Simulink blocks encapsulating the algorithms we developed/implemented. We want to share our work with the iGEM community and interested persons and made it freely available for [http://sourceforge.net/projects/ethzigem10/files/LemmingToolbox_Setup.zip/download downloading].

New Technical Standard

After weeks of applying the cloning strategy [http://dspace.mit.edu/handle/1721.1/46721 BBF RFC28], we came up with our own strategy on how BFF RFC28 could be made compatible with Tom Knight`s original assembly standard.

Model of light-inducible chemotaxis pathway

We worked out a model to control chemotaxis by light. The idea was to instrumentalize light sensitive proteins (LSPs) in order to manipulate the concentrations of the chemotaxis proteins (eg CheY), through an intracellular anchoring reaction. As a consequence, we can take control on this pathway-and direct the E.lemming's movement!

Movement Model

We made a stochastic model to realistically simulate the chemotaxis motion of the cell in silico, which responds to the light input that is converted into changes in the chemotaxis pathway, that influence the motion of the E. lemming.

μPlateImager - software for the microscope

We developed μPlateImager, a platform independent software which enables the parallel acquisition of images and the remote control of light input signals. As a result, we achieved to control our E. lemmings with light, LIVE, while having them under the lens! Watch our short movie on this page!

E. lemming 2D - The Game

We invented a synthetic biology shooting game featuring our very own E. lemming! Give it a try and play with our E. lemming!

Controller

We developed five novel controllers for directing the E. lemming to the desired target. As stimuli for altering the bacterial movement, we use light inputs.

Systems Design

See how we managed to use our models to support the wetlab and vice versa when we designed the system.

Systems Implementation

Have a look at how we simulated the entire setup in silico.