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Contents

Week 9: 14th - 18th August

Meeting - 15th August

Wiki

  • Still need to fix the primers!


Cambridge visit

  • Cambridge are coming from the 22nd to 24th 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: 31st July - 4th August

Meeting - 2nd 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 22nd to 24th 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: 8th – 16th August
  • Laszlo: 8th – 22nd August
  • Sree: 24th – 25th August
  • Jelena: 27th August – 9th September
  • Kim: 8th – 28th 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: 17th - 21st July

Meeting - 18th 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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