BCCS-Bristol Project: agrEcoli Team Neeraj Oak BCCS Katharine - - PowerPoint PPT Presentation

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BCCS-Bristol Project: agrEcoli Team Neeraj Oak BCCS Katharine - - PowerPoint PPT Presentation

Mar 16, 2023 210 likes •634 views

BCCS-Bristol Project: agrEcoli Team Neeraj Oak BCCS Katharine Coyte Biology Thomas Todd BCCS Roz Sandwell Engineering Maths Thomas Layland Biochemistry Antoni Matyjaszkiewicz Engineering Maths Kira Kowalska Engineering Maths Track-

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Team

Neeraj Oak BCCS Katharine Coyte Biology Thomas Todd BCCS Roz Sandwell Engineering Maths Thomas Layland Biochemistry Antoni Matyjaszkiewicz Engineering Maths Kira Kowalska Engineering Maths

BCCS-Bristol Project: agrEcoli

Track- Food & Energy

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What is agrEcoli? Part design and construction Modelling Publicising agrEcoli

Contents

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Precision Farming

 Aimed at arable farmers  Fertilise only where needed  Saves money  Saves fertiliser

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Environmental Costs

 7 Tonnes of CO2

Equivalent → 1 tonne

  • f fertiliser

 Causes eutrophication

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Soil Cross-Section

Deep Soil Top Soil

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Location Nutrients

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What is agrEcoli? Part design and construction Modelling Publicising agrEcoli

Contents

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RBS T T T T GFP PyeaR

Part Design

Nitrate sensitive promoter Why PyeaR?

 Proteins involved native to E. coli  Independent of metabolic state

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RBS GFP

PyeaR Nitrates

How does PyeaR work?

NsrR

Nitrate breakdown products

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RBS GFP

PyeaR

How does PyeaR work?

NsrR

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PyeaR

How does PyeaR work?

Why GFP?

 Detectable  Quantifiable  No substrate required

RBS T T T T GFP PyeaR

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Results and Initial Characterization

 Tested transformants in

solution containing varying levels of potassium nitrate

 It works! 

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Detecting Signal in Soil

 Signal needs to be detectable in

soil

 Performed several experiments

looking at behaviour of E. coli constitutively expressing GFP in soil

 Raised two major problems:

 Hard to detect  Many weakly fluorescing

bacteria or a few strong ones?

 Need to know the number of cells

to map from fluorescence magnitude to concentration of nitrate

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Using a Ratio

 Created E. coli constitutively

expressing RFP

 Measure the ratio of red to

green

 Compare this against some

scale to indicate soil nitrate levels

 How to solve the problem of

colony size difference?

 The Ratio

RFP GFP

MG1655

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Using a Ratio

 Consulted with farmers

about typical soil nitrate levels

 Tested the transformants

further within this range: 0 – 2mM potassium nitrate

 Used this data to calculate a

relationship between signal ratio and nitrate level

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Beads

 How to solve the problem

  • f signal detection?

 A higher concentration of

agrEcoli

 Better access to nitrate

 Cell encapsulation in gel

facilitates this

 Gellan gel

Make mixture, heat Cool, mix with dense agrEcoli slurry Pipette drops into ionic solution to initiate gellation Agitate and store in broth

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What is agrEcoli? Part design and construction Modelling Publicising agrEcoli

Contents

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BSim through the ages

BSim 2008 – stochastic agent based simulation in a fluid environment BSim 2009 – robust modular components, well parameterised BSim 2010 – Full graphical user interface, micro- environmental interactions

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BSim through the ages

BSim 2008 – stochastic agent based simulation in a fluid environment BSim 2009 – robust modular components, well parameterised BSim 2010 – Full graphical user interface, micro- environmental interactions

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BSim through the ages

BSim 2008 – stochastic agent based simulation in a fluid environment BSim 2009 – robust modular components, well parameterised BSim 2010 – Full graphical user interface, micro- environmental interactions

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BSim through the ages

BSim 2008 – stochastic agent based simulation in a fluid environment BSim 2009 – robust modular components, well parameterised BSim 2010 – Full graphical user interface, micro- environmental interactions

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BSim through the ages…

BSim 2008 – stochastic agent based simulation in a fluid environment BSim 2009 – robust modular components, well parameterised BSim 2010 – Full graphical user interface, micro- environmental interactions

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Modelling Environmental Interactions

 Cell encapsulation  Micro fluidics  Bio-films

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New Modelling Capabilities

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New Modelling Capabilities

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Modelling the Beads

Confocal scan of bead Create mesh Model in BSim

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BSim Feature Comparison Feature

GUI Intracellular Dynamics Multicellular Dynamics Environmental Interaction

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What is agrEcoli? Part design and construction Modelling Publicising agrEcoli

Contents

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Wider context of our research

 Functional prototype  Engaging the public in

synthetic biology

 Our project as a hypothetical

product

 Building on previous teams’

work

 Our new idea: a publicity

campaign

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Public perception

 More public information

required

 Scientific community input  Safety and security  Opinions forming on

synthetic biology

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Product Information Flyer

product description environmental motivation safety features

  • E. coli & legislation information
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What can we do with this campaign?

 Bringing real beads to market

 Legalities of releasing GMOs  Explore patenting and protection  Acquire endorsements from trusted organisations

 For next year’s competition

 Collaboration: many team leaflets advertising their products  Science fairs and public discussion

 Publicity approach promotes our research and its potential

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Summary

 Well characterised working prototype  Novel delivery method  Extended our modelling framework, BSim, and used it to

analyse behaviour in beads

 New approach to human practices through publicising

agrEcoli

 See wiki for more- 2010.igem.org/Team:BCCS-Bristol

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Sponsors

Supervisors

Nigel Savery Biochemistry Claire Grierson Biology Mario di Bernardo Engineering Maths Krasimira Tsaneva-Atanasova Engineering Maths Caroline Colijn Engineering Maths John Hogan BCCS Paul Verkade Biochemistry