Collective dynamics in swimming Escherichia coli bacteria

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Collective dynamics in swimming Escherichia coli
bacteria
Mingming Wu, The School of Chemical and
Biomolecular Engineering, The Sibley School of
Mechanical and Aerospace Engineering, Cornell
University
Photo credit Victor Soujik
This work is supported by the National Science
Foundation (CBET-0619626), the New York State
Office of Science, Technology and Academic
Research (NYSTAR), and the Cornell
Nanobiotechnology Center.
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• Part I Collective responses of receptors in
  bacterial chemotaxis
• Eugene Kalinin, Lili Zhang (Beijing Univ),
  Yuhai Tu (IBM) and Mingming Wu

A multi-scale approach
mm
mm
nm
Receptor cluster
An E.coli bacterium
Swimming E.coli
Kalinin et al., Biophysical Journal,
96,2439(2009).
3
Swimming E.coli bacterium a perfect model
organism for physicists and engineers
1mm
High sensitivity nM Range of sensing 4 decades
Biosensor (receptor cluster)
motor
Propeller(flagella)

Input
Control
Output
Adaptation
Photo credit Keiichi Nimba
Ref. E.Coli in motion, Howard Berg, 2003.
Sourjik, Trends in Microbiology, 2004
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Locomotion of E.coli cells
3D
2D
Run
Tumble
B

B
Wu et al. AEM, 72, 4987(2006). Turner L., JB,
182,1793(2000).
Bacterial tracks
Roberts et al. Expt. In Fluids, 38,461(2005)
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E.Coli bacterial chemotaxis
Behavioral level Bacteria lengthen their runs
when move towards high chemo attractant
concentration (Berg, 1975)
Molecular level The bacterial chemotaxis
signaling transduction pathway has been
constructed along with measurements of many
kinetic constants.
20 minutes movie
Missing link From molecules to cellular
behavior.
L 361 mM
L 139 mM
MeAsp
Kalinin et al., Biophysical Journal,
96,2439(2009).
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Current understanding of molecular pathway for
bacteria chemotaxis
(KEGG database)
Bacteria motion
Berg et al.
Cluzel et al.
Motor kinetics
control
Sensing
Adaptation
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An agarose gel based microfluidic chemotaxis
device a well defined chemical gradient
Diao et al. Lab Chip 6,381(2006). Cheng et al.
Lab Chip, 7, 763 (2007).
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A dynamic equilibrium
(a)
Chemosensitivity CMC- average y positions of all
cells
-- chemotactic drift velocity
Keller-Segel model
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Quantifying the dynamic equilibrium
Both chemical gradient and dynamic processes of
swimming E.coli Reach steady state in 7
minutes.
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Bacterial chemo-sensitivity curve

• Expt
• -- Model.

Tar
Tsr
High sensitivity mM Wide sensing range 4
decades
Kalinin et al., Biophysical Journal,
96,2439(2009).
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Collective responses of receptors through
conformational change
Receptor coorperativity
Classical theory Suppose that receptors do not
interact with each other. Chemosensitivity is
governed by the rate change of the receptor
occupancy.
Predictions
Bacteria will maintain high chemo-sensitivity in
a narrow concentration region near Kd.
(Nature, 393, 85-88, 1998)
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The Monod Wyman Changeus Tu (MWCT) model
MWC model The conformational state of the
regulator protein is determined by thermal
dynamic equilibrium
a 0 1
Activity
Ligand binding
methylation
Energy (Hamiltonian) of the states
Magnetic field
Ising coupling
Spin
The mixed Ising model
Mello et al. Biophys. J. 87, 2004
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Comparison with experiments
WMCT model
a activity of CheA N cluster size L ligand
concentration m adaptation state e free energy
Experiment
Theory
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Bacteria sense chemical concentration at
logarithmic Scale
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Bacterial chemotaxis in dual chemical gradients
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Bacterial chemotaxis in dual gradients receptor
number rules
C
Tar/Tsr
B
A
Chemo preference in dual gradients depends on
Tar/Tsr
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Part II Hydrodynamics in bacterial suspension
Qian Liao, Lindsey Sidrane, Ned Schoenthaler,
Kasyap T Vasudevan (poster, wed), Donald Koch
Hydrodynamic force field of a swimming E.coli
Modified stokes equation
First moment of force distribution Exerted by
bacteria

Liao et al. Physics of fluids, 19, 061701(2007).
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Hydrodynamics in bacterial suspension
Pair velocity correlation
Hydrodynamic flow field around an swimming
E.coli bacterium

Experiment and theory
Liao et al. Physics of fluids, 19, 061701(2007).
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Measured velocity correlation of swimming bacteria
--- experiment theory

Bacterial collective dynamics occurs at 10 mm
length scale.
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Critical concentration for the onset of
collective swimming
Diffusion Coef (mm2/s)

Cell density (/mL)
1 mm fluorescent beads in bacterial suspension
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Coffee stain problem

Nagel et al. American Journal of Physics, 67,
17(1990).
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Bacterial culture stain

1mm
400mm
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Bacterial culture stain

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Role of collective dynamics in mammalian cell
chemotaxis

• Development
• Immune response
• Tissue formation
• Cancer metastasis
• References David Rogers, Vanderbilt University,
  1950 http//www.biochemweb.org/fenteany/research/c
  ell_migration/neutrophil.html
• Serini et al. The EMBO hournal, 22, 1771(2003)

Neutrophil chases a bacterium
ECs form a network
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Dentritic cell chemotaxis in 3D
Increasing chemokine gradient
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The end