Newcastle University/3 July 2008

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'''Minutes IGEM'''
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Date: 03/04/08
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Place: CT. 601
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Time: 15.30-17.00
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Attendees: 8/9
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Guest: Jan Willem-Venning
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Supervisors:
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Dr Anil Wipat (anil.wipat@newcastle.ac.uk), Dr Jennifer Hallinan (j.s.hallinan@newcastle.ac.uk), Dr Matthew Pocock (matthew.pocock@newcastle.ac.uk), Morgan Taschuk (mtaschuk@gmail.com)
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Team Members:
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Nina Nielsen (nina.nielsen-dzumhur@newcastle.ac.uk), Mark Wappett (mark.wappett@newcastle.ac.uk), Megan Aylward (megan.aylward@newcastle.ac.uk)
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Agenda 1
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Discussing the GA Homework
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Nina describes her Java code on the screen (eclipse).
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Mark describes his Java code on the screen (intelliJ).
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Both only took about 10 seconds to run. Agree that these programmes are much better than BlueJay!
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Run out of time so decide Megan can describe her code later.
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Agenda 2
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Discussing more application ideas. HAVE TO KNOCK ONE OUT TODAY!
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Mark describes another idea based on MRSA
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Based on a potential vaccine developed for Malaria parasite.
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Works by priming the T cells to EDA175 conserved\to parasite.
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As soon as it gets into body should trigger an immune response.
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Presence of proteins on MRSA surface are quite conserved too (Isda and isdb).
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Utilize the same theory. Use Bacillus because harmless, to alter the surface.
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Jan mentions a lot of work has been carried out to use spores of Bacillus as oral vaccines. The spores are easy to probe, harvest and are very stable.
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However Jan also says although this is a good idea and would make a good biobrick, it is already relatively simple to make and you wouldn’t need to implement a GA. Also not sexy enough!?
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Anil asks if Mark has identified a particular protein on MRSA
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Marks mentions there are potentially 4..could use them all?
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But Matt asks if these proteins are specific to MRSA or all SA and it turns out they are not specific to MRSA. This is dangerous as SA exists non-pathogenically on our hands and other places and triggering an immune response to these bacteria wouldn’t be great.
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Group discusses potential of a specific protein expressed extracellularly on MRSA.
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Morgan queries whether there is another way of detecting MRSA?
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Fall back to the problem of detection intracellularly?
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Idea last week didn’t work spatially.
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Nina talks about using two component systems and generating models to inhibit multiple signalling pathways in MRSA.
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To maintain specificity to a type of resistance, the particular HK and RRs can be subjected. For example Vancomycin resistant superbugs with VanR and VanS proteins.
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But a problem with MRSA is that the proteins may not be well conserved.
 +
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Matt mentions a need to find extracellular conserved proteins.
 +
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Megans draws a schematic/flow diagram on the board depicting how a Receptor on a bacillus plasmid, specific to proteins secreted extracellularly by MRSA, can cause a cascade of events in the Bacillus genome, including the expression of GFP (or/and othe fluorescent proteins).
 +
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This would provide a rapid diagnostic, which is missing in the market.
 +
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Jan mentions that some kind of signal amplifier may be necessary to switch on the fluorescence protein effectively.
 +
A possibility of indicating the strength of the MRSA is also possible.
 +
 +
Jen then suggests that the Bacillus (good bug) could maybe be used to detect the presence of many resistant bacteria (bad bugs) by detecting multiple proteins. Could have several colours for several types of “superbugs”.
 +
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Anil suggested the name “Police Bugs”
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Jen mentions that the amplification system links very nicely with an EA
 +
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Jan suggested that the one bug could be 50% MRSA sensitive and 50% another resistant bacteria (such as streptococcus) sensitive, as the interpretation could be easier that way.
 +
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Matt then suggested using combinations of colours so that the resistance is more specified and more types of bacteria can be defined and detected. For example, the presence of MRSA switching a red protein off, green on and yellow on but streptococcus switching red on, green on and yellow off. This would create a profile which would be more accurate too.
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Agenda 3
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Editing Wiki
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• Morgan went through how to add documents and edit the wiki page. A series of buttons that work like a very simple HTML.
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Action Plan.
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• Organize meeting for artificial neural networks for week starting 06/04/08
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• Research and read about specific extracellular proteins secreted from MRSA, possible receptors or RR that could be expressed on Bacillus to receive an input when the MRSA protein is secreted.
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• Put appropriate papers on wiki
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AOB
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• Matt will be talking about EA on Friday 04/04/08
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• Anil is away next week.
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Action Plan
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Next Meeting: 03/04/08 at 15.30 CT 701.

Revision as of 13:38, 11 July 2008

Back to Calendar


Minutes IGEM

Date: 03/04/08 Place: CT. 601 Time: 15.30-17.00

Attendees: 8/9

Guest: Jan Willem-Venning

Supervisors: Dr Anil Wipat (anil.wipat@newcastle.ac.uk), Dr Jennifer Hallinan (j.s.hallinan@newcastle.ac.uk), Dr Matthew Pocock (matthew.pocock@newcastle.ac.uk), Morgan Taschuk (mtaschuk@gmail.com)

Team Members: Nina Nielsen (nina.nielsen-dzumhur@newcastle.ac.uk), Mark Wappett (mark.wappett@newcastle.ac.uk), Megan Aylward (megan.aylward@newcastle.ac.uk)


Agenda 1 Discussing the GA Homework

Nina describes her Java code on the screen (eclipse). Mark describes his Java code on the screen (intelliJ). Both only took about 10 seconds to run. Agree that these programmes are much better than BlueJay! Run out of time so decide Megan can describe her code later.

Agenda 2 Discussing more application ideas. HAVE TO KNOCK ONE OUT TODAY!

Mark describes another idea based on MRSA Based on a potential vaccine developed for Malaria parasite. Works by priming the T cells to EDA175 conserved\to parasite. As soon as it gets into body should trigger an immune response. Presence of proteins on MRSA surface are quite conserved too (Isda and isdb). Utilize the same theory. Use Bacillus because harmless, to alter the surface. Jan mentions a lot of work has been carried out to use spores of Bacillus as oral vaccines. The spores are easy to probe, harvest and are very stable. However Jan also says although this is a good idea and would make a good biobrick, it is already relatively simple to make and you wouldn’t need to implement a GA. Also not sexy enough!? Anil asks if Mark has identified a particular protein on MRSA Marks mentions there are potentially 4..could use them all? But Matt asks if these proteins are specific to MRSA or all SA and it turns out they are not specific to MRSA. This is dangerous as SA exists non-pathogenically on our hands and other places and triggering an immune response to these bacteria wouldn’t be great. Group discusses potential of a specific protein expressed extracellularly on MRSA. Morgan queries whether there is another way of detecting MRSA? Fall back to the problem of detection intracellularly? Idea last week didn’t work spatially.

Nina talks about using two component systems and generating models to inhibit multiple signalling pathways in MRSA. To maintain specificity to a type of resistance, the particular HK and RRs can be subjected. For example Vancomycin resistant superbugs with VanR and VanS proteins. But a problem with MRSA is that the proteins may not be well conserved.

Matt mentions a need to find extracellular conserved proteins.

Megans draws a schematic/flow diagram on the board depicting how a Receptor on a bacillus plasmid, specific to proteins secreted extracellularly by MRSA, can cause a cascade of events in the Bacillus genome, including the expression of GFP (or/and othe fluorescent proteins).

This would provide a rapid diagnostic, which is missing in the market.

Jan mentions that some kind of signal amplifier may be necessary to switch on the fluorescence protein effectively. A possibility of indicating the strength of the MRSA is also possible.

Jen then suggests that the Bacillus (good bug) could maybe be used to detect the presence of many resistant bacteria (bad bugs) by detecting multiple proteins. Could have several colours for several types of “superbugs”.

Anil suggested the name “Police Bugs”

Jen mentions that the amplification system links very nicely with an EA

Jan suggested that the one bug could be 50% MRSA sensitive and 50% another resistant bacteria (such as streptococcus) sensitive, as the interpretation could be easier that way.

Matt then suggested using combinations of colours so that the resistance is more specified and more types of bacteria can be defined and detected. For example, the presence of MRSA switching a red protein off, green on and yellow on but streptococcus switching red on, green on and yellow off. This would create a profile which would be more accurate too.


Agenda 3 Editing Wiki

• Morgan went through how to add documents and edit the wiki page. A series of buttons that work like a very simple HTML.

Action Plan. • Organize meeting for artificial neural networks for week starting 06/04/08 • Research and read about specific extracellular proteins secreted from MRSA, possible receptors or RR that could be expressed on Bacillus to receive an input when the MRSA protein is secreted. • Put appropriate papers on wiki

AOB • Matt will be talking about EA on Friday 04/04/08 • Anil is away next week.



Action Plan

Next Meeting: 03/04/08 at 15.30 CT 701.

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