Innovative Approaches to Bioengineering: iGEM Imperial Week 1 Insights
In the first week of iGEM at Imperial, we brainstormed and evaluated three groundbreaking ideas: 1) Bio-Clock - a system using AHL for time-based cell fluorescence; 2) Bio-Memory - data storage in bacteria with high compression; and 3) Oscillator - a stable, tunable AHL oscillation model for predator-prey dynamics. We aim to model and investigate these concepts in weeks to come, deciding to pursue the Oscillator as our main project. This journal entry outlines our strategic approach and early results in bioengineering research.
Innovative Approaches to Bioengineering: iGEM Imperial Week 1 Insights
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Presentation Transcript
Week 1 Engineering/Biology Introduction Lectures Journal Club Wiki Brainstorming 3 ideas Starting off: Week 1
Bio-Clock (Re-defining Time) • Pulse of AHL moves along a gutter of medium • Cells fluoresce when activated • Refractory period • The time period is controlled by • the radius • gutter width • cell density
Bio-Memory 1010100000000011111000010101011111100000000111111111000001010100010100001000010100101001010000001001010101001010101001101010101001010 • Data stored in bacteria written using a green laser • Data read using a UV laser + fluorimeter • Cells either 1 (RFP) or 0 (no RFP) • Data stored in switch Very High Compression due to small size of bacteria
The Oscillator • Culture Wide oscillations of AHL • Frequency must be tuned easily • Oscillations must be stable Changing Concentration of AHL
Week 2 Investigation of all 3 ideas Modelling Evaluating risks Start work in the Wet lab Decision on the Oscillator as main project;can use other ideas as further developments Week 3 Further research Modelling Assembly of parts Protocols for testing parts Setting up OWW
Predator Prey Dynamics Simply Make a Bio-chemical system that can do this. Lotka-Voltarra Model output
A A B B Design • Positive Feedback of A • AB Induces production of more B • Both A and B are used to make AB
A B Two Cell System • Two independent populations of Cells • These cells do not kill each other • Altering the initial ratios of these cells will alter the frequency of oscillations
A A A A Design Cell1 (Prey) • Prey cell must produce molecule A exponentially Lux R is produced which detects molecule A Pc Lux R Then initiates transcription at Plux Pc is always on Lux I Plux Which Produces More A
Design The Predator Cell The role of a predator is to reduce the prey numbers as a function of the predator population numbers. Predator Detect Prey Population Size Reduce Prey Population Size
Lux R aiiA Plux Design The Predator Cell Detects Prey Population Size Reduces Prey Population Size
Design The Predator Cell A LuxR A A LuxR aiiA Lux R aiiA Plux
Pc Lux R Lux I Plux A A A Design (Entire System) Diffusion Extra cellular pool of A (HSL) (this should oscillate) The Prey Cell The Predator Cell LuxR A A LuxR aiiA Lux R aiiA Plux
Modelling • Tom’s Monster
A shocking discovery: at first sight... • After finishing our oscillator design... • MIT Project 2004: • Cell-Cell synchronized Oscillator Design • Similar approach using concepts of quorum sensing • BUT: This system does not use predator-prey dynamics and is implemented in a single cell (ours is multicellular MIT Oscillator Design http://web.mit.edu/~cbatten/www/work/ssbc04/system-spec-ssbc04.pdf
Communication: The Wiki • Wiki-Newspaper • Documentation for future references • Communication • Within the team • With other teams • Monitoring progress (Gantt Chart) • Present ourselves & our project
Outline • Further modelling & testing of parts • Parts assembly • Phase 2 • Coupling the oscillator to a biological to electrical interface • Synchronizing oscillations 2 petri dishes
