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

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

Dec 18, 2023 261 likes •514 views

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

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SLIDE 1

Christian Jacob, University of Calgary

Evolutionary

Design Swarm

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

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SLIDE 2

Christian Jacob, University of Calgary

Evolutionary

Design Swarm

  • E. Coli and Lactose
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SLIDE 3

Christian Jacob, University of Calgary

Evolutionary

Design Swarm

How the Lac Operon Works …

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Christian Jacob, University of Calgary

Evolutionary

Design Swarm

Lactose Operon—Schematic (1)

The Lac Operon and its Consituents

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Christian Jacob, University of Calgary

Evolutionary

Design Swarm

Lactose Operon—Schematic (2)

Turning off the Lac Operon

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SLIDE 6

Christian Jacob, University of Calgary

Evolutionary

Design Swarm

Lactose Operon—Schematic (3)

Repressor Inhibition turns the Lac Operon on.

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Christian Jacob, University of Calgary

Evolutionary

Design Swarm

Promoter LacI RNAPolymerase CAP CAPcAMP Promoter Operator LacZ LacY Repressor Glucose Glucose Glucose Glucose Glucose Glucose LactosePermease Lactose Lactose Lactose Bgal Glucose Bgal Glucose mutation state : i+ o+ z+ TetramerBindLactose

Lactose Operon Model

Symbolic & Rule-based

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SLIDE 8

Christian Jacob, University of Calgary

Evolutionary

Design Swarm

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[]] }

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Christian Jacob, University of Calgary

Evolutionary

Design Swarm

Symbolic, Rule-based Lac Operon Model

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Christian Jacob, University of Calgary

Evolutionary

Design Swarm

Symbolic Lac Model: Graphical Output

Promoter LacI RNAPolymerase CAP CAPcAMP Promoter Operator LacZ LacY Repressor Glucose Glucose Glucose Glucose Glucose Glucose LactosePermease Lactose Lactose Lactose Bgal Glucose Bgal Glucose mutation state : i+ o+ z+ TetramerBindLactose

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Christian Jacob, University of Calgary

Evolutionary

Design Swarm

Lactose Operon Model in Mathematica

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Christian Jacob, University of Calgary

Evolutionary

Design Swarm

Lactose Operon Model

Spatial & Agent-based

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Christian Jacob, University of Calgary

Evolutionary

Design Swarm

Lactose Operon 3D—Step by Step …

(1) Circular DNA, Coding Regions, and RNA Polymerase

β-gal

Repressor

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SLIDE 14

Christian Jacob, University of Calgary

Evolutionary

Design Swarm

Lactose Operon 3D—Step by Step (2) …

(2) RNA Polymerase docking to DNA

RNA polymerase

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Christian Jacob, University of Calgary

Evolutionary

Design Swarm

Lactose Operon 3D—Step by Step (3) …

(3) RNA Polymerase (with mRNA) transcribing the lacI gene

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Christian Jacob, University of Calgary

Evolutionary

Design Swarm

Lactose Operon 3D—Step by Step (4) …

(4) Ribosome attaching to mRNA, producing amino acid chain

RNA polymerase Ribosome

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Christian Jacob, University of Calgary

Evolutionary

Design Swarm

Lactose Operon 3D—Step by Step (6) …

(6) Ribosome attaching to mRNA, producing amino acid chain (cont.)

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Christian Jacob, University of Calgary

Evolutionary

Design Swarm

Lactose Operon 3D—Step by Step (7) …

(7) Repressor Synthesis

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Christian Jacob, University of Calgary

Evolutionary

Design Swarm

Lactose Operon 3D—Step by Step (8) …

(8) Repressor binding to Operator Site

RNA polymerase Ribosome Repressor Repressor

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SLIDE 20

Christian Jacob, University of Calgary

Evolutionary

Design Swarm

Lactose Operon 3D—Step by Step (9) …

(9) β-Galactosidase Synthesis

RNA polymerase Ribosome Repressors β-Galactosidase

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Christian Jacob, University of Calgary

Evolutionary

Design Swarm

Julie Andreotti, Ian Burleigh, Garret Suen

Lactose Operon 3D in Action

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Christian Jacob, University of Calgary

Evolutionary

Design Swarm

Lactose Operon in the CAVE

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Christian Jacob, University of Calgary

Evolutionary

Design Swarm

Lactose Operon Simulation in the CAVE

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Christian Jacob, University of Calgary

Evolutionary

Design Swarm

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.