Transcript Document

Computational Investigation of
Chemotaxis and Surface Motility
in Biofilm Monolayer Formation
Xianfeng Song
Lin Wang
Sima Setayeshgar
Modeling Framework: Chemotaxis

Realistic, stochastic description of
chemotaxis network in E. coli (adapted
from StochSim [1])
 Reactions treated as collisions
between biomolecules
 Experimentally-based rates, protein
copy numbers
 Description of flagellar CCW/CW
response (and resulting running/tumbling
motion) in good agreement with
experiments (adapted from AgentCell[2])
 Based on simple CheY-P
thresholding
 We are currently improving upon this
…
[1] C. J. Morton-Firth,
T. S. Shimizu and D. Bray, J. Mol. Biol. (1999).
[2] T. Emonet, et al. Bioinformatics (2005).
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Biofilm Group Meeting
From experiment [2]:
Our results:
Modeling Framework:
Chemoattractant Diffusion
 Diffusion of chemoattractant with cells as sources
r: rate of chemoattractant secretion
(molecules/time)
 Solve using finite difference scheme on
discrete grid
 Distribute cell source term among
neighboring grid points
 Alternate updating cell positions and
chemoattractant field at each time step
Friday May 18, 2007
Biofilm Group Meeting
Modeling Framework:
Surface Motility
 Surface-adhered cells continue to exhibit
chemotactic response in two dimensions
 Currently neglecting rotational Brownian motion
for motion on the surface (this is included for
three dimensional motion!)
 New run direction following tumble randomly
selected (0, 2) (for three-dimensional motion,
new run direction selected within cone about old
run direction, consistent with experiments)
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Biofilm Group Meeting
Preliminary Results
 No attractant
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Preliminary Results (cont’d)
 Chemoattractant secretion by adherent cells (with
surface motility): Dynamics on surface
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Preliminary Results (cont’d)
 Chemoattractant secretion by adherent cells (with
surface motility): Dynamics in bulk
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Preliminary Results (cont’d)
 Single cell trajectory
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Computational limitations to be resolved …
 Increase system size (eliminate boundary
effects)
 Increase cell number (improve statistics)
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Biofilm Group Meeting
Future Systematic Investigations
 Quantify clustering (beyond “eye-balling”) (for
example, using 2D FFT):
 No clusters, small versus large clusters
 Role of governing biophysical parameters
 Rate of chemoattractant secretion (by surface-attached
cells, all cells?)
 Probability of attachment (to surface, to other cells)
 Chemoattractant diffusion constant
 Cell speed on surface, in bulk
 Role of stochastic versus deterministic description
of chemotaxis signal transduction
Friday May 18, 2007
Biofilm Group Meeting