Team:BCCS-Bristol/Calendar-Main/18 June 2008

Meeting: Final Project Presentations

Time: 4:00pm - 5:00pm

Location: BCCS Office

Agenda

• Funding for undergraduates members of the team
• Presentation of project ideas
• Preparation of the meeting with the advisors on 25th June
• AOB

Attendees

Summary

1. Funding currently stands as follows:
   • Ian is being funded directly by BBSRC
   • Maria has secured personal funding
   • Biochemistry department has agreed to fund up to 2 students
   • Biology department has agreed to fund to up 3 students. Obviously there are more than 3 biology students so it will be necessary to consider how this money can be split based on commitment (see actions).
   • We may consider approaching some commercial sponsors to secure possible expenses for lab work. This needs to be agreed first though.
   • Stipend will be for 10-12 weeks and it is envisaged that they will start on or after the 1st July.
2. Project presentations:
   • Radio Receiver (Slides) - Extending the work in a theoretical paper. The physics for the project has not yet been fully thought through meaning it is not yet fully understood the frequency range or power that would be required to cause effect. Initially a wide-band input of varying power could be used but it would be good to single out the major frequencies. To detect a change in conformational state FRET was initially proposed, however, this requires skilled operators which may not be available in Bristol. Instead, a bi-partite GFP was suggested. On order to get a working product, the calcium binding site will need to be randomly mutated and screened to produce a working sequence that can then be used in a more useful way (e.g. signalling cascade). There are some practicalities in getting hold of RF emitters but they should be available from the communications group in engineering.
   • Random Number Generator (Slides) - First method to use inteins/exteins (self-excising proteins). There is very little data on the probability of a protein excising and they are thought to be highly efficient. For this reason the method has been dropped. Second approach was to create an area of DNA that would naturally mutate at a high rate. This again was dropped, however, due to problems is getting a high probability of mutation and the issues in how to use the result for further processes. The final approach was to use 2 reporters on a single plasmid with an RNA polymerase transcription site which could initiate in either direction in the middle of the reporters. This should give a 50/50 chance of either reporter being produced which then will repress the other reporter. This should ensure a single steady state is reached eventually. It would also be possible to chain plasmids to create random outputs of a larger length. The difficulty is in designing the plasmid such that events take similar time to complete such that no bias is present.
   • GRN Interaction (Slides) - This would be a project along similar lines to the Ljubljana team. Research was carried out on possible areas in biology that could be optimised, however, a great deal of area specific knowledge would need to be known to find such cases. Also, many of the diseases present today are due to single point mutations where GRN interaction is probably not the most effective form of cure. Instead, one possible direction is looking at ways that GRNs could be used to replace drugs. They can be made more specific which would hopefully reduce side-effects and allowed for a much more finally controlled process than currently possible. Another possible direction would be an anti-virus tool for cells. Using influences form computer networking where routing nodes slow down there transmission rate when they think they may be infected, a similar principle could be used in cells. A general indicator for inflection would need to be found such that on being sensed, metabolism could be slowed down to give the immune system a greater length of time to find and neutralise the cell. There are many outstanding questions, however, as this would require working with mammalian cells and with complex pathways.
   • Co-operative Movement (Slides) - This would be attempting to use co-operation in a bacterial population to perform a task none could on their own. In this case moving particles larger than a single bacteria. The main aspects of this are the need for switchable chemoattractants and sensors to detect when in contact with item to move and when near other bacteria moving an item. The switchable chemoattractant has already been implemented by the UCSF team with parts available in the library. This means only the sensing a control aspects would need to be investigated further. Some research has been carried out into using G-proteins but it may be better to use sensors naturally occurring in E.coli. This is a fairly large project which would require further testing of existing parts and any sensors created.
   • Bio-film - Unfortunately there was not enough time to talk through this project and although some progress had been made it was not thought to be in a state that could be carried forward this year.

Actions

• (Everyone) Look through the project presentations and order the projects based on your preference.
• (Biology) Discuss the funding situation
• (Tom G) Setup meeting on Friday to make final project selections before presentations to advisors.