Minutes

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Week 9: 14^th - 18^th August

Meeting - 15^th August

Wiki

• Still need to fix the primers!

Cambridge visit

• Cambridge are coming from the 22^nd to 24^th August
• Meal and drinks on Tuesday 22nd August followed by a ghost tour or a show
• ICL aren’t coming

Presentation

• Need to make up a presentation – what’s been achieved since Cambridge visit
• Make it about half an hour long

• Characterisation experiments – Kim & Jen
• Lab (AM) – Farid & Jude
• Model – Patrick & Bryony

• Send slides to Jen on Friday 18th August

pH Turtle

• Bryony will try & get a laptop as Chris’ other one didn’t work

Modelling

• Worked up from a molecular to a concentration basis
• Want to correlate LacZ output with pH measured – need to add on reactions
• Is it possible to model other components present in the media e.g. amino acids?
• Have joined all three operons in the model
• Have some results - see discussion board
• pH shown to get very high when urease is switched on
• Going to do parameter sensitivity analysis
• Chris asked if it is possible to check model with any papers...

Biobricks

• ArsR with LacZ tests have been carried out
• Arsenic doesn’t affect pH response – maybe LacZ is constantly on/problem with arsenic promoter?
• Need to sequence – first must get preparation protocol from Jen or Chris
• Plan was to combine LacZ and Lambda CI with arsenic promoter but not much point until we have a working arsenic promoter. Apparently the one we have used so far gives a very weak signal.

• Chris has bacillus arsenic promoter bio-bricked. Farid is putting it into our e-coli.

• Have urease to use with calcium phosphate. Is it biobricked?
• Sree is going to design experiments and carry these out, probably in September

Practical construction of working device

• Make up 0.1M KCl buffer solution
• Make up Buffer Z for ONTG LacZ assay

• Come up with solid concept for device and then email Andrew Meharg (author of Venomous Earth) to ask his advice

Website

• Add other photos to gallery
• Put up some significant results
• Need to design Macteria mascot – have attempted this but it's awful!

Visas

• Sree, Patrick and Farid must get visas to go to USA. Involves making an appointment at the US embassy in either Belfast or London, getting a 9 day business visa which only allows visit to MIT and costs about £100.

• Need to check requirements for UK citizen entry to USA.

• Bryony might not be coming to MIT, depends on her PHD work.

Miscellaneous

• Bryony is aiming to finish by the end of this week
• Sree can work September and October
• Kim can work October

Week 7: 31^st July - 4^th August

Meeting - 2^nd August

Wiki

• Update Wiki re. primers for biobricks

Tamara’s visit

• Team meeting at 10am in Hons room on Tuesday 8th August
• Construct an agenda for meeting
• Show her round the labs
• Attend a Fringe Festival show in the evening

Cambridge visit

• Best dates are 22^nd to 24^th August
• Failing this, the start of September is okay
• Jude currently has 3 spare rooms (possibly 4) from 22nd to 24th August
• Invite ICL as well

Holidays

• Jude: 8^th – 16^th August
• Laszlo: 8^th – 22^nd August
• Sree: 24^th – 25^th August
• Jelena: 27^th August – 9^th September
• Kim: 8^th – 28^th September
• Farid: ??? September
• Bryony: ??? September

pH Turtle

• Currently not working. Chris suggests deleting mouse software from laptop. Will try this.

Modelling

• Meeting on Friday 4th August with Hong Wu

Practical construction of working device

• Kim has come up with lots of characterization experiments to be done in the lab next week once we have the arsenic-sensing device

• Device might be ready on Friday 4th August

• Email Andrew Meharg (author of Venomous Earth) to ask his advice on arsenic biosensing device

Website

• Do we need a disclaimer?

• Need to design Macteria mascot – possibly ask the guy who did the cartoon for Drew and Endy (Nature website)!

Biobricks

• These can be added to the registry when they are ready (well done Jude who has done this before the minutes have been typed!)

Week 5: 17^th - 21^st July

Meeting - 18^th July

Labwork on Arsenic Biosensor:

Biobricks

• PCR on arsenic and LacZ parts
• 4 bands on gel from LacZ so need to find out which one is the correct one
• Create sticky ends
• Working towards arsenic device – may be ready in about 2 weeks

pH Experiments

• Want to measure population density at the point at which pH of blue and white E-Coli diverges
• Difference between stationary and growth phase response is possibly due to the fact that the bacteria ‘want’ to use up the lactose when they’re in the growth phase
• Ideal conditions for growth in LB have been established
• Want to carry out experiments using different growth media

Model

• Plenty of info on Lac operon
• Paper found regarding ArsR relation to arsenic concentration
• Autoregulation – ArsR represses itself
• Background noise may be caused due to degradation of ArsR repressor
• Might be possible to reduce this background noise by separating the promoter from the ArsR gene
• Need to calculate what pH from urea breakdown will be for different concentrations
• It is thought to be necessary to have the two-part promoter (with activator and repressor binding sites) in order to prevent a build up of alkalinity which could harm the bacteria

Wiki

• Update biobricks

Cambridge trip

• Train leaves Edinburgh Waverley at 9.30am so try to be there by about 9am
• Need to prepare a presentation (half an hour long)
• Update animation of arsenic biosensor
• Focus is arsenic project
• Mention 3D structure builder briefly

• Presentation layout
  • Background – Jelena
  • Building biobricks – Jude
  • pH experiment/animation – Kim
  • Modelling – Patrick

Idea 6/11 – 3D structure builder

• Primer design for urease
• LacI biobrick – is it ok?

To do

• Moving all experiments to Andrew Miller’s lab
• Meeting on Thursday at 2pm in Honours Room
• Website development
• Design a badge if you have a spare five minutes
• Presentation completed

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