Team:BCCS-Bristol

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<img src="https://static.igem.org/mediawiki/2010/b/bc/AgrEcoli_alt_logo.png" width="100%"/>
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'''agrEcoli is a device based on modified''' '''''E.coli''''' '''bacteria that detects and signals the presence of nitrates. This allows farmers to map the nutrient content of their fields and optimize their fertiliser use. For more information, see our [https://2010.igem.org/Team:BCCS-Bristol/Project Project Abstract]'''
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==Achievements==
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===Wetlab===
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<h1>Nitrogen indicator</h1>
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Nitrogen circulates through Earth’s environment in several forms. Nitrogen is essential to life on Earth. Seventy-eight percent (78%) of the Earth’s atmosphere is nitrogen gas. But most of this nitrogen is not usable by life on Earth. Microscopic organisms called microbes transform nitrogen into a form usable by plants. The plants, in turn, supply nitrogen for animals.
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* '''A Well Characterised New BioBrick'''
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:Our new BioBrick ([http://partsregistry.org/Part:BBa_K381001 BBa_K381001]) causes GFP expression in the presence of nitrates.
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* '''Elegant Solution to Signal Calibration'''
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:By using constitutive RFP expression as a baseline, we have found a reliable and accurate way of quantifying nitrate levels in soil.
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* '''Novel Use of Cell Encapsulation'''
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:By encapsulating our bacteria in gellan beads, we can keep our bacteria contained and concentrated. This improves visibility on soil, and enhances the environmental safety of our device.
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* '''Characterising a Pre-Existing BioBrick'''
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:To better inform our own work, and to add knowledge to the BioBrick Registry, we have characterised Edinburgh 2009’s PyeaR BioBrick ([http://partsregistry.org/Part:BBa_K216009 BBa_ K216009]).
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|[[Image:Beads.png|thumbnail|400px|right|Our new beads]]
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|[[Image:GUI preview sample.JPG|thumbnail|400px|left|BSim screenshot]]
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[[Image:Depth0.png|thumbnail|400px|left|Gel strand rendered in BSim]]
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|width="33%" padding="3px"| <html><center><a href="https://2010.igem.org/Team:BCCS-Bristol/Project">
 
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<img src="https://static.igem.org/mediawiki/2010/e/ea/BCCS_Project_button3.JPG" border="0" <!--height="65px"-->>
 
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|width="33%" padding="3px"| <html><center><a href="https://2010.igem.org/Team:BCCS-Bristol/Wetlab">
 
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<img src="https://static.igem.org/mediawiki/2010/e/e6/BCCS_Beakers3.JPG" border="0" <!--height="65px"-->>
 
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|width="33%"  padding="3px"| <html><center><a href="https://2010.igem.org/Team:BCCS-Bristol/Modelling"><img src="https://static.igem.org/mediawiki/2010/7/77/BCCS_BSim_button3.JPG" <!--height="65px"-->></a></center></html>
 
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|width="33%"  padding="3px"| <html><center><a href="https://2010.igem.org/Team:BCCS-Bristol/Team"><img src="https://static.igem.org/mediawiki/2010/6/60/BCCS_Team3.JPG"></a></center></html>
 
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<!-- |<center>[[Team:BCCS-Bristol/Project|'''PROJECT''']]</center>
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|<center>[[Team:BCCS-Bristol/Wet_lab|'''WET LAB''']]</center>         
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===Modelling===
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|<center>[[Team:BCCS-Bristol/Modelling|'''MODELLING''']]</center> -->
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*'''BSim Environmental Interactions'''
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|Find out about our exciting project!
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|See what we did in the lab!
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|View our interactive BSim model!
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|Meet our team members and supervisors!
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:We have extended BSim, our agent-based modelling framework, to model interactions between bacteria and their environment. We have added 3-Dimensional mesh structures to our simulations, and added an adaptive chemical field routine that can solve partial differential equations in an arbitrary 3-D space without any risk of numerical instability.
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*'''BSim Graphical User Interface (GUI)'''
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:We have made BSim more widely accessible by creating a user-friendly and intuitive graphical user interface. This makes BSim accessible to the entire synthetic biology community, rather than just those with JAVA programming knowledge.
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*'''Gene Regulatory Network Modelling'''
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:We have investigated the behaviour of our bacteria by creating a mathematical model of their behaviour. This model could then be analysed using numerical and analytic methods.
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*'''Collaboration'''
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:Our modelling team have helped to simulate the UCL 2010 team’s new system. Working with another team has also helped to inform the design of the BSim GUI.
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*'''agrEcoli Cost estimates'''
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:In support of our human practices work, our modelling team have looked into the cost to farmers of using agrEcoli, and how much money and fertiliser they can expect to save.
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{|
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===Human Practices===
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*'''Publicising agrEcoli'''
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:Our new approach to human practices, building on previous work by iGEM teams, is a publicity campaign. By presenting our prototype as a functioning and marketable product, we've framed a hypothetical situation in which our project could be released.
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*'''Public Engagement'''
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- The Mission, Experiments -
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:Our team has visited a school and spoken on two radio shows in order to communicate our ideas with the general public.
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
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|[[Image:BCCS-Bristol-ClevedonVisit-03.jpg|thumbnail|400px|right|Public Engagement- Clevedon School Visit]]
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!align="center"|[[Team:BCCS-Bristol|Home]]
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!align="center"|[[Team:BCCS-Bristol/Team|Team]]
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!align="center"|[https://igem.org/Team.cgi?year=2010&team_name=BCCS-Bristol Official Team Profile]
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!align="center"|[[Team:BCCS-Bristol/Project|Project]]
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!align="center"|[[Team:BCCS-Bristol/Parts|Parts Submitted to the Registry]]
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!align="center"|[[Team:BCCS-Bristol/Modeling|Modeling]]
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!align="center"|[[Team:BCCS-Bristol/Notebook|Notebook]]
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!align="center"|[[Team:BCCS-Bristol/Safety|Safety]]
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!align="center"|[[Team:BCCS-Bristol/calendar|Calendar]]
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==Sponsors==
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[[Image:BCCS_Sponsors_Logo_Banner.png|upright= 3.3|frameless|center]]
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|You can write a background of your team here.  Give us a background of your team, the members, etc.  Or tell us more about something of your choosing.
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|[[Image:BCCS-Bristol_logo.png|200px|right|frame]]
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''Tell us more about your project. Give us background.  Use this as the abstract of your project.  Be descriptive but concise (1-2 paragraphs)''
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|[[Image:BCCS-Bristol_team.png|right|frame|Your team picture]]
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|align="center"|[[Team:BCCS-Bristol | Team Example]]
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Latest revision as of 00:55, 28 October 2010

agrEcoli is a device based on modified E.coli bacteria that detects and signals the presence of nitrates. This allows farmers to map the nutrient content of their fields and optimize their fertiliser use. For more information, see our Project Abstract

Achievements

Wetlab

  • A Well Characterised New BioBrick
Our new BioBrick ([http://partsregistry.org/Part:BBa_K381001 BBa_K381001]) causes GFP expression in the presence of nitrates.
  • Elegant Solution to Signal Calibration
By using constitutive RFP expression as a baseline, we have found a reliable and accurate way of quantifying nitrate levels in soil.
  • Novel Use of Cell Encapsulation
By encapsulating our bacteria in gellan beads, we can keep our bacteria contained and concentrated. This improves visibility on soil, and enhances the environmental safety of our device.
  • Characterising a Pre-Existing BioBrick
To better inform our own work, and to add knowledge to the BioBrick Registry, we have characterised Edinburgh 2009’s PyeaR BioBrick ([http://partsregistry.org/Part:BBa_K216009 BBa_ K216009]).
Our new beads
BSim screenshot
Gel strand rendered in BSim

Modelling

  • BSim Environmental Interactions
We have extended BSim, our agent-based modelling framework, to model interactions between bacteria and their environment. We have added 3-Dimensional mesh structures to our simulations, and added an adaptive chemical field routine that can solve partial differential equations in an arbitrary 3-D space without any risk of numerical instability.
  • BSim Graphical User Interface (GUI)
We have made BSim more widely accessible by creating a user-friendly and intuitive graphical user interface. This makes BSim accessible to the entire synthetic biology community, rather than just those with JAVA programming knowledge.
  • Gene Regulatory Network Modelling
We have investigated the behaviour of our bacteria by creating a mathematical model of their behaviour. This model could then be analysed using numerical and analytic methods.
  • Collaboration
Our modelling team have helped to simulate the UCL 2010 team’s new system. Working with another team has also helped to inform the design of the BSim GUI.
  • agrEcoli Cost estimates
In support of our human practices work, our modelling team have looked into the cost to farmers of using agrEcoli, and how much money and fertiliser they can expect to save.

Human Practices

  • Publicising agrEcoli
Our new approach to human practices, building on previous work by iGEM teams, is a publicity campaign. By presenting our prototype as a functioning and marketable product, we've framed a hypothetical situation in which our project could be released.
  • Public Engagement
Our team has visited a school and spoken on two radio shows in order to communicate our ideas with the general public.
Public Engagement- Clevedon School Visit


Sponsors

BCCS Sponsors Logo Banner.png
Retrieved from "http://2010.igem.org/Team:BCCS-Bristol"