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| - | {{:Team:BCCS-Bristol/Header}}
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| - | ==6th August 2009==
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| - | The introduction of elliptical bacteria essentially compelled us to use a rigid-body physics engine to avoid hacking things on to the current (particle-based) physics engine. However, we have decided that the effort required in switching is not enough to justify the benefits of having shapely bacteria in what is essentially a package focused on statistics, not mechanics. Thus we have resolved to roll back changes regarding the elliptical bacteria and instead focus on converting the existing particle based engine to 3D. [https://static.igem.org/mediawiki/2009/2/27/BCCS-Bristol_Modelling_update.ppt Slides here].
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| - | ==30th July 2009==
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| - | The focus of this meeting was to finalize the project proposal, now found at [[Team:BCCS-Bristol/Project]]. On the modelling side, we delegated GRNs to Petros/Antos, vesicles to Steve, magnetotaxis to Emily and performance/population dynamics to Mattia. Lab work progresses.
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| - | ==3rd July 2009==
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| - | The project has gained a direction and a lot of work has been done in both modelling and wet-lab aspects. A review of the project and its goals was given to all advisors and views about further work.
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| - | We are improving BSim to have a more "real-life" feeling. Current progress includes the shape of bacteria and population dynamics.
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| - | A copy of the presentation can be found [https://static.igem.org/mediawiki/2009/a/ad/BCCS_iGEM_meeting_23Jul.pdf here].
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| - | The tangible progress in the wetlab is expanded in this presentation found [https://static.igem.org/mediawiki/2009/7/7f/BCCS_Labwork_Presentation_17to23_Jul.pdf here].
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| - | ==16th July 2009==
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| - | Discussed the progress of the project. We are currently focused on the vesicle formation part of the project although some steps have been taken in trying to develop magnetotaxis ''ex vivo''.
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| - | The relevant presentation can be found [https://static.igem.org/mediawiki/2009/7/7e/BCCS_igem_meeting_16_Jul.pdf here].
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| - | ==9th July 2009==
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| - | ===Vesicles with a twist...part II===
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| - | After a week's worth of digging through the literature we have managed to find possible '' non-toxic '' candidate proteins that pack within outer membrane vesicles produced by E.coli. Thus we have settled into implementing directed communication and delivery of proteins of interest between different cells/populations. This will possibly form the bigger part of the project and if time permits we will combine this with our ''magnetotaxis'' idea.
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| - | With respect to [https://2009.igem.org/Team:BCCS-Bristol/Modeling modelling ] we are interested in developing a useful tool for the community and research by possibly expanding the existing BSim software. For further information visit the [https://2009.igem.org/Team:BCCS-Bristol/Modeling modelling ] page of the wiki.
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| - | With respect to the lab we will pursuit the building of biobricks that will allow the implementation of proteins of interest into OMVs (outer membrane vesicles) as a first part to the project. Upon the succesful completion of this first task we want to implement some GRN for the control of responses of both production and/or message acceptance.
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| - | A copy of the presentation of this meeting can be found [https://static.igem.org/mediawiki/2009/e/e1/BCCS_meeting09Jul09.pdf here].
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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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| - | Presentation of initial ideas at MCB2009.
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