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Establishing Baseline Performance Scores for the CAGEN Robust Gene Response ChallengeShaunak Sen Caltech CMS Oct 11, 2011CAGEN - Critical Assessment of Genetically Engineered Networks

Systematize the design of genetic networks (robustness, connectability)

- Facilitate applications, for ex. in agriculture, medicineCAGEN Challenge #1 : Robust Gene ResponseDetectable: >10 fold inductionRobust: Low variability across cells & temperaturesFast: Quick responseTimeIPTG AdditionYFP induction1 X0>10 X0SpeedLow VariabilityINPUTOUTPUTInduce OUTPUT (YFP) in response to INPUT (IPTG), so that,Critical Assessment of Selected DesignsChallenge SpecificationsSelf Assessment by ParticipantsPurpose: Establish Baseline PerformancePurposeEstablish Baseline PerformanceANNOUNCEMENTSELECTIONPerformance metric to score robustness and speed of designs

Worst CaseTime integral of square errorNormalizing factor(equilibrium amplitude of reference trace)

Time (hours)Protein Levels (nM)simulationr(t)yj(t)j=215xPxXSingle cell dynamics are measured for a simple reference design, for different temperaturesYFPPinducibleE. coli30 C32 C34 C#1???#2???yfpPlacIPTG#1cI-yfpPlacIPTG#2MoviesYFPPinducible

Reference trace exhibits > 10x inductionTime (minutes)Mean Fluorescence (a.u.)No inductionCamera Bgd.Cell division10x inductionPerformance scores for inducible protein expression circuits

Time (minutes)Mean Fluorescence (a.u.)yfpPlacIPTG#1Reference trace (32 C)Traces at 32 CTraces at 34 CTraces at 30 C

Time (minutes)Mean Fluorescence (a.u.)cI-yfpPlacIPTG#2Reference trace (34 C)Traces at 34 CTraces at 30 CS = 0.27S = 0.29Population level metric to estimate performance score

Time (minutes)Protein Levels (nM)Count

Population Dynamics/Flow Cytometry

Time (hours)Protein Levels (nM)simulationr(t)yj(t)j=215Single-Cell Dynamics/ Microscopy

Future WorkRefined single-cell measurements using fluidics

Simulation/Eric KlavinsCritical Assessment of Selected DesignsChallenge SpecificationsSelf Assessment by ParticipantsBaseline for Critical AssessmentBenefit #1.Exact induction timemeasurement.Benefit #2:Similar decay timemeasurement.