Team:Imperial College/Motility

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Revision as of 08:49, 17 October 2008

Motility Analysis

As part of our chasis characterisation process, we have decided to model B. subtilis motility. In order to do this, the approach illustrated below was taken. The first phase of modelling involved data collection using microscopy techniques and cell tracking. Collected data was then analysed using algorithms which enabled us to extract distributions of parameters as defined in our model.

Materials

We used the Zeiss Axiovert 200 inverted microscope and Improvision Volocity acquisition software. This system offers a full incubation chamber with temperature control and a highly sensitive 1300x1000 pixel camera for fast low-light imaging. Video images are captured into memory by the system at a basal video frame rate of 16.3Hz. This can be further increased to 27.9Hz by performing x4 binning.

Method

We used manual tracking to track B. subtilis, obtaining two-dimensional coordinate data points which describes by the trajectory of the cells.

Data Extraction

We input the coordinate data into algorithms to model cell trajectory and motility.

Motility Model

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 === Motility Analysis ===
 {{Imperial/Box2||
-[[Image:Approach.jpg|450px|center]]
 <br><br>
-The motility of ''B. subtilis'' is hypothesised to be affected by various levels of EpsE expression. In order to model motility as a function of EpsE production, we have decided to use video microscopy techniques to analyse the motility of ''B. subtilis''. We hope to obtain a transfer function model relating EpsE expression to bacterial motility characteristics such as run velocity, run duration, tumbling angle and tumbling duration. This modelling process is shown on the right and has been divided into 3 main sections:
+As part of our chasis characterisation process, we have decided to model ''B. subtilis'' motility. In order to do this, the approach illustrated below was taken. The first phase of modelling involved data collection using microscopy techniques and cell tracking. Collected data was then analysed using algorithms which enabled us to extract distributions of parameters as defined in our model.
+[[Image:Approach.jpg|450px|center]]
+===== Materials =====
+We used the Zeiss Axiovert 200 inverted microscope and Improvision Volocity acquisition software. This system offers a full incubation chamber with temperature control and a highly sensitive 1300x1000 pixel camera for fast low-light imaging. Video images are captured into memory by the system at a basal video frame rate of 16.3Hz. This can be further increased to 27.9Hz by performing x4 binning.
+===== Method =====
+We used manual tracking to track ''B. subtilis'', obtaining two-dimensional coordinate data points which describes by the trajectory of the cells.
+===== Data Extraction =====
+We input the coordinate data into algorithms to model cell trajectory and motility.
+=== Motility Model ===
-#'''[[/Validation | Validation of Tracking Software ]]'''
-#*In order to assess the error associated with tracking algorithms applied to a digitised images sequence, a series of steps were taken to '''[[IGEM:IMPERIAL/2008/Prototype/Drylab/Validation |validate]]''' the tracking software.
-#'''[[/Motility_data_collection|Motility Data Acquisition]]'''
-#*Data on run velocity, run duration, tumbling angle and tumbling duration were extracted from coordinate data output provided by the tracking software as part of the process of gathering data.
-#'''[[/Model_Fitting|Model Fitting]]'''
-#*Several alternative models were created for the purpose of model fitting. The motility data obtained is then analysed and fitted to alternative models. Preferences will then be assigned to fitted models using probabilistic methods such as Bayesian Analysis.
 }}
 {{Imperial/EndPage|Genetic Circuit|Appendices}}