Team:BCCS-Bristol

From 2010.igem.org

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{{:Team:BCCS-Bristol/Header}}
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__NOTOC__
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<img src="https://static.igem.org/mediawiki/2010/b/bc/AgrEcoli_alt_logo.png" width="100%"/>
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{| class="panel" align="center" width="90%" 
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|width="33%" padding="3px"| <html><center><a href="https://2009.igem.org/Team:BCCS-Bristol/Project">
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<img src="https://static.igem.org/mediawiki/2009/5/56/BCCS_Project_button.jpg" border="0">
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|width="33%" padding="3px"| <html><center><a href="https://2009.igem.org/Team:BCCS-Bristol/BSim">
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<img src="https://static.igem.org/mediawiki/2009/e/e9/BCCS_BSim_button.jpg" border="0">
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|width="33%"  padding="3px"| <html><center><a href="https://2009.igem.org/Team:BCCS-Bristol/Bioscaffold"><img src="https://static.igem.org/mediawiki/2010/3/37/BCCS_Beakers.jpg"></a></center></html>
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|width="33%"  padding="3px"| <html><center><a href="https://2009.igem.org/Team:BCCS-Bristol/Team"><img src="http://www.sport-schiestl.at/team-niemand.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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|<center>[[Team:BCCS-Bristol/Modelling|'''MODELLING''']]</center>
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|<center>[[Team:BCCS-Bristol/Team|'''TEAM''']]</center>
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|We aim to produce a system for directed delivery of proteins in outer membrane vesicles (OMVs). This work is supported through agent-based simulation of OMV communication.
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|To assess the effectiveness of an OMV-based communication solution, we have developed a new version of BSim, our stochastic agent based modelling framework.
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|In-frame fusion of arbitrary bio-bricks leaving behind a scarless, joining region
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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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</center>
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===Wetlab===
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{|
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|
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<!---== This is a header ==
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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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|}
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{|
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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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<!--- The Mission, Experiments --->
 
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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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!align="center"|[[Team:BCCS-Bristol|Home]]
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===Modelling===
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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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*'''BSim Environmental Interactions'''
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<!--You <strong>MUST</strong> have a team description page, a project abstract, a complete project description, a lab notebook, and a safety page.  PLEASE keep all of your pages within your teams namespace. -->
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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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<!-- *** End of the alert box *** -->
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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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{|align="justify"
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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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|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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{|
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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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===Human Practices===
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|[[Image:BCCS-Bristol_team.png|right|frame|Your team picture]]
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*'''Publicising agrEcoli'''
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|align="center"|[[Team:BCCS-Bristol | Team Example]]
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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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: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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|[[Image:BCCS-Bristol-ClevedonVisit-03.jpg|thumbnail|400px|right|Public Engagement- Clevedon School Visit]]
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<center>
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==Sponsors==
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[[Image:BCCS_Sponsors_Logo_Banner.png|upright= 3.3|frameless|center]]
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</center>

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"