Team:BCCS-Bristol

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{{:Team:BCCS-Bristol/Header}}
{{:Team:BCCS-Bristol/Header}}
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== Background ==
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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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</a></center></html>
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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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</a></center></html>
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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/2009/4/49/BCCS_Bioscaffold_logo.jpg"></a></center></html>
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|<center>[[Team:BCCS-Bristol/Project|The Project]]</center>
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|<center>[[Team:BCCS-Bristol/BSim|Modelling]]</center>
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|<center>[[Team:BCCS-Bristol/Bioscaffold|The Bioscaffold]]</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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|}
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== VESECURE - discrete targeted communication with Outer Membrane Vesicles ==
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Directed delivery of specific proteins into cells would have dramatic consequences for drug delivery and expand the horizons of synthetic biology into the multicellular domain via discrete, targeted communication.
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Gram-negative bacteria naturally produce outer member vesicles (OMVs): spherical, bilayered proteolipids from 20-200nm in diameter. OMVs carry outer membrane, periplasmic and cytoplasmic proteins, DNA, RNA and other biological molecules. They protect their cargo from the extracellular environment and deliver it to a multitude of target cells via membrane fusion.
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We investigate the possibility of allowing the secretion of any protein in OMVs via fusion with novel, non-toxic partners enhanced in OMVs, using a novel Bioscaffold compatible with the current assembly standard. A new version of the award winning BSim software has been developed to study applications at the population level such as communication. The ultimate goal is to create a safe and standardised system for directed delivery of proteins into cells.
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== Team background ==
The [http://bccs.bris.ac.uk/ Bristol Centre for Complexity Sciences (BCCS)] is a new highly interdisciplinary centre for training and research funded by the UK Engineering and Physical Science Research Council (EPSRC). It is a major collaboration across 4 faculties within the [http://www.bris.ac.uk/ University of Bristol].
The [http://bccs.bris.ac.uk/ Bristol Centre for Complexity Sciences (BCCS)] is a new highly interdisciplinary centre for training and research funded by the UK Engineering and Physical Science Research Council (EPSRC). It is a major collaboration across 4 faculties within the [http://www.bris.ac.uk/ University of Bristol].
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* Attempt to apply, where appropriate, techniques from the field of Complexity Science.
* Attempt to apply, where appropriate, techniques from the field of Complexity Science.
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== Meetings ==
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== Acknowledgments ==
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[[Team:BCCS-Bristol/Modeling_To_Do_List]]
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=== 2nd July 2009 ===
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====Vesicles with a twist====
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We seem to have settled down to the idea that implementing magnetotaxis ''in vivo'' in E.coli will be infeasible within the given time-frame. Instead we have decided to move in the direction where we will try implementing the usage of vesicles in our project.
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We are still thinking of perhaps implementing magnetotaxis combined with bacteria in an ''in vitro'' manner.
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=== 26th June 2009 ===
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==== Bacterial diagnosis ====
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Ollie and Thanasis spent some time this week looking into whether we could use bacteria to detect and report on the state of an organism. It now seems we have now dropped the idea on the grounds it is too similar to projects attempted in previous years (NYMU, KULeuven) and would require licensing. However there was a suggestion that this idea could be taken in the direction of sequence based toggle switches to carry out a (more complicated) decision tree based diagnosis.
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==== Magnetic bacteria ====
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Petros prepared some slides on the biological feasibility of engineering E.coli to synthesize magnetosome [https://static.igem.org/mediawiki/2009/0/09/BCCS_magnetoiGEM2009.pdf (Copy of the presentation found here)]
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Links to the papers cited in the presentation can be found here:
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*[http://www.nature.com/nrmicro/journal/v2/n3/full/nrmicro842.html Magnetosome formation in prokaryotes]
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*[http://pubs.acs.org/doi/abs/10.1021/cr078258w Magnetotactic bacteria and magnetosomes]
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*[http://www.jbc.org/cgi/content/full/M106408200 A Magnetosome-specific GTPase from the Magnetic Bacterium Magnetospirillum magneticum AMB-1]
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*[http://aem.asm.org/cgi/content/abstract/67/10/4573 A large gene cluster encoding several magnetosome proteins is conserved in different species of magnetotactic bacteria]
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*[http://www.jbc.org/cgi/content/abstract/277/37/33559 The Escherichia coli Cytochrome c Maturation (Ccm) System Does Not Detectably Attach Heme to Single Cysteine Variants of an Apocytochrome c]
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*[http://aem.asm.org/cgi/content/abstract/75/12/3972 Toward Cloning of the Magnetotactic Metagenome: Identification of Magnetosome Island Gene Clusters in Uncultivated Magnetotactic Bacteria from Different Aquatic  sediments]
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*[http://www.ncbi.nlm.nih.gov/pubmed/18537832 Genetics and cell biology of magnetosome formation in magnetotactic bacteria]
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*[http://www.ncbi.nlm.nih.gov/pubmed/16303747 Complete Genome Sequence of the Facultative Anaerobic Magnetotactic Bacterium Magnetospirillum sp. strain AMB-1]
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Steve and Emily looked into possible applications of magnetotaxis. These papers seem particularly interesting:
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* [http://link.aip.org/link/?APPLAB/89/233904/1 Controlled manipulation and actuation of micro-objects with magnetotactic bacteria]
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* [http://wiki.polymtl.ca/nano/images/0/00/C-2006-MTB-IARP-Sylvain.pdf Towards Autonomous Bacterial Microrobots]
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* [http://www.polymtl.ca/recherche/rc/en/professeurs/details.php?NoProf=122&showtab=PUB Other publications by Sylvain Martel]
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==== Vesicles ====
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Tom gave a [https://static.igem.org/mediawiki/2009/a/a0/BCCS_Vesicles_iGEM_2009.pdf presentation developing the idea of communication and self-assembly using vesicles].
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=== 18th June 2009 ===
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The shortlist was down to 7 projects and 3 of those made it to the next round as voted by the present audience. These are as follows (project title, (votes received)):
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* Magnetic Bacteria (10)
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* Bacterial Vesicles (6)
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* Non-Invasive Reporting/Switches & Sensors (6)
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* Genome Updates & version control (5)
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* Host/Parasite Symbiosis (3)
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* Bacterial Computation
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* RNA Editing
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Thus the top three were chosen to review the literature further and assess the possibility of carrying each out in 3 months.
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=== 11th June 2009 ===
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Kick off meeting. Narrowed down ideas from ~15 to 7. See [[Team:BCCS-Bristol/Brainstorming]].
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=== 2nd June 2009 ===
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We would like to thank the following people, companies and organisations for providing help and resources to the BCCS Bristol iGEM 2009 team:
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Presentation of initial ideas at MCB2009.
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<br><br>
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== Calendar ==
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{| align="center" width="90%"
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<html>
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<iframe src="http://www.google.com/calendar/embed?src=6880fi17dr2g5ubtalfh4jfpno%40group.calendar.google.com&ctz=Europe/London" style="border: 0" width="800" height="600" frameborder="0" scrolling="no"></iframe>
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| width="20%"|<center>[[Image:BCCS_GeneART_logo.gif]]</center> <br>  <center>[[Image:BCCS_MrGENE_logo.gif]]</center> || [http://www.geneart.com/ '''GeneART'''] and [http://www.mrgene.com '''Mr.Gene'''] synthesized DNA sequences to order at a discounted cost and were of great help regarding DNA synthesis procedures.
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</html>
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|}<br>

Latest revision as of 21:49, 21 October 2009

BCCS-Bristol
iGEM 2009

The Project
Modelling
The Bioscaffold
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. To assess the effectiveness of an OMV-based communication solution, we have developed a new version of BSim, our stochastic agent based modelling framework. In-frame fusion of arbitrary bio-bricks leaving behind a scarless, joining region


VESECURE - discrete targeted communication with Outer Membrane Vesicles

Directed delivery of specific proteins into cells would have dramatic consequences for drug delivery and expand the horizons of synthetic biology into the multicellular domain via discrete, targeted communication.

Gram-negative bacteria naturally produce outer member vesicles (OMVs): spherical, bilayered proteolipids from 20-200nm in diameter. OMVs carry outer membrane, periplasmic and cytoplasmic proteins, DNA, RNA and other biological molecules. They protect their cargo from the extracellular environment and deliver it to a multitude of target cells via membrane fusion.

We investigate the possibility of allowing the secretion of any protein in OMVs via fusion with novel, non-toxic partners enhanced in OMVs, using a novel Bioscaffold compatible with the current assembly standard. A new version of the award winning BSim software has been developed to study applications at the population level such as communication. The ultimate goal is to create a safe and standardised system for directed delivery of proteins into cells.

Team background

The Bristol Centre for Complexity Sciences (BCCS) is a new highly interdisciplinary centre for training and research funded by the UK Engineering and Physical Science Research Council (EPSRC). It is a major collaboration across 4 faculties within the University of Bristol.

Both the BCCS and iGEM share an interdisciplinary approach to problem solving and a culture of communication between previously disparate scientific fields. Furthermore, the BCCS aims to nurture the next generation of scientists in complexity, fitting with iGEM's ethos of introducing undergraduates to cutting edge science. This year the team is made up of advisors and students from the BCCS, Engineering Mathematics, Biology, Biochemistry and Chemistry.

By taking part in iGEM the BCCS and Bristol University hopes to:

  • Build links between departments and people within and outside the university,
  • Demonstrate the effectiveness of such collaborations,
  • Attempt to apply, where appropriate, techniques from the field of Complexity Science.

Acknowledgments

We would like to thank the following people, companies and organisations for providing help and resources to the BCCS Bristol iGEM 2009 team:

BCCS GeneART logo.gif

BCCS MrGENE logo.gif
GeneART and Mr.Gene synthesized DNA sequences to order at a discounted cost and were of great help regarding DNA synthesis procedures.