E.Coli e.Coli is a very bad disease and you need to try to avoid it.
A synthetic E - Amazon S3 · PDF fileA synthetic E.coli predator-prey ecosystem FK...
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A synthetic E.coli predator-prey ecosystem
FK Balagaddé, H Song, J Ozaki, CH Collins, M Barnet, FH Arnold, SR Quake, L YouMolecular Systems Biology 4:187 (2008)
Presented by Kelly Drinkwater20.385 Week 13May 5, 2010
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Predator-prey oscillation
Frank Hoppensteadt. “Prey-Predator Cycles”. <http://www.scholarpedia.org/article/Predator-prey_model>
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Translating into E.coliusing AHL signals
Note IPTG induction of cooperationat Plac/ara-1
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Microchemostats
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It oscillates!
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First round of assumptions
• Logistic cell growth• First-order decay • Constant synthesis of AHLs• Simplified kinetics• No basal promoter activity• Ignore diffusion in medium• No crosstalk AHL1/AHL2
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Quasi-steady-state assumptions
• mRNA, LuxR, LasR, and ccdB are steady
• QSSA really means “changes fast compared to gene regulation & cell growth”
• Further QSSAs changed qualitative behavior, killed oscillation completely.
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Final simplifieddiffEQ model
Noise terms
c1 = predatorsc2 = preyAe1 = predator signalAe2 = prey signaldci = cell death rate constK1 = regulator synthesisβ = cooperativityD = dilution ratekAi = signal synthesisdAei = signal decay
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Recall...
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IPTG changes system behavior
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Modeling effect of IPTG(Predator, Prey)
Oscillation
No oscillation Hopf bifurcation:system eigenvaluecrosses imaginary axis,qualitative behaviorchange
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System is not stable in cells
• Hard to avoid: ccdB exerts strong evolutonary pressure
• Makes time-courses short and messy due to microchemostat
• Lesson: Kill-switch design is hard
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Contributions
• Constructed working predator-prey system
• Pioneered use of microchemostat
• Modeled system behavior under different conditions
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Synthetic cooperation in engineered yeast populationsW Shou, S Ram, JMG VilarPNAS 104:6 (2007)
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CoSMO• Big contribution:
STABILITY
• Auxotrophy-based codependence (recommended to my 20.20 group)
• Useful basis for many kinds of cooperative systems
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Problem: nutrients release w/ cell death
Why not export metabolites??
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But it still seems to work
+ overproductionof Ade/Lys
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Viability depends on initial conditions
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Population ratio stabilizes near 1:1
Range:~1:5 - 5:1
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Increased robustness over long term
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Round-0
Round-1
0
How? Evolved better metabolite sharing?
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Contributions
• Built symmetrically cooperating yeast system
• Stable over the long term
• Derived constraints on viable initial conditions
• Demonstrated convergence to a small population ratio
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Considerations for biofuels project
• Use auxotrophy-based codependence instead of inducer-based (evolutionarily stable)
• Tune final population ratio for best nutrient recycling
• Take care with initial conditions, possibly supplement cultures at first
• Self-regulation strictly necessary? (Probably still a good idea)