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iGEM @ Imperial. Week 1 Engineering/Biology Introduction Lectures Journal Club Wiki Brainstorming 3 ideas. Starting off: Week 1. Only three ideas made the cut. Bio-Clock (Re-defining Time). Pulse of AHL moves along a gutter of medium Cells fluoresce when activated Refractory period - PowerPoint PPT Presentation

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  • iGEM @ Imperial

  • Starting off: Week 1Week 1

    Engineering/Biology Introduction LecturesJournal ClubWikiBrainstorming

    3 ideas

  • Only three ideas made the cut.

  • Bio-Clock (Re-defining Time) Pulse of AHL moves along a gutter of medium Cells fluoresce when activatedRefractory periodThe time period is controlled by the radiusgutter width cell density

  • Bio-Memory1010100000000011111000010101011111100000000111111111000001010100010100001000010100101001010000001001010101001010101001101010101001010Data stored in bacteria written using a green laserData read using a UV laser + fluorimeterCells either 1 (RFP) or 0 (no RFP)Data stored in switch

    Very High Compression due to small size of bacteria

  • The OscillatorCulture Wide oscillations of AHLFrequency must be tuned easilyOscillations must be stableChanging Concentration of AHL

  • Week 2

    Investigation of all 3 ideasModellingEvaluating risksStart work in the Wet labDecision on the Oscillator as main project; can use other ideas as further developments

    Week 3

    Further researchModellingAssembly of partsProtocols for testing partsSetting up OWW

  • Predator Prey DynamicsLotka-Voltarra Model outputSimply Make a Bio-chemical system that can do this.

  • Predator-Prey Interaction

    Stable interactions assuming:

    Predator and prey distributions are random.The only cause of death to the prey species is through predationThe growth rate of the predator species is solely dependent on predation of the prey.The Prey species shows exponential growth in the absence of predation with no carrying capacityThe Parameters are constant over time

  • Design Positive Feedback of A AB Induces production of more B Both A and B are used to make AB

  • Two Cell SystemTwo independent populations of CellsThese cells do not kill each otherAltering the initial ratios of these cells will alter the frequency of oscillations

  • Design Cell1 (Prey)Prey cell must produce molecule A exponentiallyPcPluxLux RLux IPc is always onLux R is produced which detects molecule AThen initiates transcription at PluxWhich Produces More A

  • DesignThe Predator CellThe role of a predator is to reduce the prey numbers as a function of the predator population numbers.

    PredatorDetect Prey Population SizeReduce Prey Population Size

  • DesignThe Predator CellDetects Prey Population SizeReduces Prey Population Size

  • DesignPluxLux RaiiAThe Predator CellAALuxRLuxRAaiiA

  • Design (Entire System)Extra cellular pool of A (HSL) (this should oscillate)DiffusionPluxLux RaiiAThe Predator CellALuxRLuxRAaiiAThe Prey Cell

  • ModellingToms Monster

  • Modelling

  • Testing parts: T9002

  • A shocking discovery: at first sight...After finishing our oscillator design...MIT Project 2004:Cell-Cell synchronized Oscillator DesignSimilar approach using concepts of quorum sensingBUT: 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 WikiWiki-NewspaperDocumentation for future referencesCommunicationWithin the teamWith other teamsMonitoring progress (Gantt Chart)Present ourselves & our project

  • OutlineFurther modelling & testing of partsParts assembly

    Phase 2Coupling the oscillator to a biological to electrical interface Synchronizing oscillations 2 petri dishes

  • Thank you