Modeling a Simple Gene Regulatory System The Lactose Operon - PowerPoint PPT Presentation

Modeling a Simple Gene Regulatory System The Lactose Operon Christian Jacob Evolutionary and Swarm Design Group Artificial Intelligence Lab Department of Computer Science University of Calgary Evolutionary Swarm Christian Jacob, University of Calgary Design

E. Coli and Lactose Evolutionary Swarm Christian Jacob, University of Calgary Design

How the Lac Operon Works … Evolutionary Swarm Christian Jacob, University of Calgary Design

Lactose Operon—Schematic (1) The Lac Operon and its Consituents Evolutionary Swarm Christian Jacob, University of Calgary Design

Lactose Operon—Schematic (2) Turning off the Lac Operon Evolutionary Swarm Christian Jacob, University of Calgary Design

Lactose Operon—Schematic (3) Repressor Inhibition turns the Lac Operon on . Evolutionary Swarm Christian Jacob, University of Calgary Design

: i + o + z + TetramerBindLactose mutation state Lactose Operon Model Lactose Repressor Glucose Glucose Lactose Bgal Lactose Symbolic & Rule-based Glucose Glucose Bgal Glucose Glucose Glucose Glucose LactosePermease RNAPolymerase CAPcAMP Promoter LacI CAP Promoter Operator LacZ LacY Evolutionary Swarm Christian Jacob, University of Calgary Design

Symbolic, Rule-based Lac Operon Model • Cytoplasm = { Operon[Promoter[], LacI[]], Operon[Promoter[], Operator[], LacZ[], LacY[]], RNAPolymerase[], Lactose, Glucose, LactosePermease[], Bgal[], RepressorTetramer[ S1[],S2[],S3[],S4[]] } Evolutionary Swarm Christian Jacob, University of Calgary Design

Symbolic, Rule-based Lac Operon Model Evolutionary Swarm Christian Jacob, University of Calgary Design

Symbolic Lac Model: Graphical Output : i + o + z + TetramerBindLactose mutation state Lactose Repressor Glucose Glucose Lactose Bgal Lactose Glucose Glucose Bgal Glucose Glucose Glucose Glucose LactosePermease RNAPolymerase CAPcAMP Promoter LacI CAP Promoter Operator LacZ LacY Evolutionary Swarm Christian Jacob, University of Calgary Design

Lactose Operon Model in Mathematica Evolutionary Swarm Christian Jacob, University of Calgary Design

Lactose Operon Model Spatial & Agent-based Evolutionary Swarm Christian Jacob, University of Calgary Design

Lactose Operon 3D—Step by Step … Repressor β -gal (1) Circular DNA, Coding Regions, and RNA Polymerase Evolutionary Swarm Christian Jacob, University of Calgary Design

Lactose Operon 3D—Step by Step (2) … RNA polymerase (2) RNA Polymerase docking to DNA Evolutionary Swarm Christian Jacob, University of Calgary Design

Lactose Operon 3D—Step by Step (3) … (3) RNA Polymerase (with mRNA) transcribing the lacI gene Evolutionary Swarm Christian Jacob, University of Calgary Design

Lactose Operon 3D—Step by Step (4) … RNA polymerase Ribosome (4) Ribosome attaching to mRNA, producing amino acid chain Evolutionary Swarm Christian Jacob, University of Calgary Design

Lactose Operon 3D—Step by Step (6) … (6) Ribosome attaching to mRNA, producing amino acid chain (cont.) Evolutionary Swarm Christian Jacob, University of Calgary Design

Lactose Operon 3D—Step by Step (7) … (7) Repressor Synthesis Evolutionary Swarm Christian Jacob, University of Calgary Design

Lactose Operon 3D—Step by Step (8) … Repressor RNA polymerase Repressor Ribosome (8) Repressor binding to Operator Site Evolutionary Swarm Christian Jacob, University of Calgary Design

Lactose Operon 3D—Step by Step (9) … Ribosome Repressors RNA polymerase β -Galactosidase (9) β -Galactosidase Synthesis Evolutionary Swarm Christian Jacob, University of Calgary Design

Lactose Operon 3D in Action Julie Andreotti, Ian Burleigh, Garret Suen Evolutionary Swarm Christian Jacob, University of Calgary Design

Lactose Operon in the CAVE Evolutionary Swarm Christian Jacob, University of Calgary Design

Lactose Operon Simulation in the CAVE Evolutionary Swarm Christian Jacob, University of Calgary Design

References • Garret Suen and Christian Jacob A Symbolic and Graphical Gene Regulation Model of the lac Operon IMS 2003, 5th International Mathematica Symposium. In: P. Mitic et al. (ed), Challenging the Boundaries of Symbolic Computation, Imperial College Press, 2003, pp. 73-80. • Ian Burleigh, Garret Suen, and Christian Jacob DNA in Action! A 3D Swarm-based Model of a Gene Regulatory System ACAL 2003, 1st Australian Conference in Artificial Life, Canberra, 2003. Evolutionary Swarm Christian Jacob, University of Calgary Design