establishing baseline performance scores for the cagen robust gene response challenge

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Establishing Baseline Performance Scores for the CAGEN Robust Gene Response ChallengeShaunak Sen Caltech CDS Dec 14, 2011CAGEN - Critical Assessment of Genetically Engineered Networks

Systematize the design of genetic networks (address issues of 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 Performance Scorefor Self AssessmentAnd Critical AssessmentPurposeEstablish Baseline PerformanceANNOUNCEMENTSELECTIONPerformance metric to score robustness and speed of designs

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

j = 1, 2, 3, 15(at least 5 traces for 3 temperatures)r(t) is a trace chosen as reference,M is equilibrium amplitude of r(t),T1 is time when r(t) is 10% of M, andT2 is time after which r(t) stays within 10% of M.TimeInputOutputSmallSingle 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 inductionBaseline Performance Score for Self AssessmentPerformance 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 = 1.45S = 1.22Critical assessment will be on a fluidic platform allowing for controlled induction timeGFPPinducibleE. coli30 C32 C34 C???gfpPlacIPTG

Simulation/Eric KlavinsBenefit #1.Exact induction timemeasurement.Benefit #2:Similar decay timemeasurement.

MovieGFPPlacSingle-Cell Dynamics with Controlled Induction Time

S = 2.2912

xPxXPopulation level metric to estimate performance scorePopulation Dynamics/Flow CytometrySingle-Cell Dynamics/ Microscopy

Future WorkFast Linear Amplifier in 3 StepsTimeInputOutputTimeInputOutputSmall3. Linear Response2. Fast Decay1. Fast Increase(this CAGEN Challenge)InputOutputSmall14