Minutes

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[http://2006.igem.org/University_of_Edinburgh_2006 Main page]
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==<font color='red'>Week 9:  14<sup>th</sup> - 18<sup>th</sup> August</font>==
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==Meeting - 15<sup>th</sup> August''==
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'''Wiki'''
 +
 +
* Still need to fix the primers!
 +
 +
 +
'''Cambridge visit'''
 +
 +
* Cambridge are coming from the 22<sup>nd</sup> to 24<sup>th</sup> 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
 +
 +
 +
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==<font color='red'>Week 7:  31<sup>st</sup> July - 4<sup>th</sup> August</font>==
 +
 +
==Meeting  - 2<sup>nd</sup> 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<sup>nd</sup> to 24<sup>th</sup> 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<sup>th</sup> – 16<sup>th</sup> August
 +
* Laszlo: 8<sup>th</sup> – 22<sup>nd</sup> August
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* Sree: 24<sup>th</sup> – 25<sup>th</sup> August
 +
* Jelena: 27<sup>th</sup> August – 9<sup>th</sup> September
 +
* Kim: 8<sup>th</sup> – 28<sup>th</sup> 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!)
 +
 +
 +
==<font color='red'>Week 5:  17<sup>th</sup> - 21<sup>st</sup> July</font>==
==<font color='red'>Week 5:  17<sup>th</sup> - 21<sup>st</sup> July</font>==
==Meeting  - 18<sup>th</sup> July''==
==Meeting  - 18<sup>th</sup> July''==
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'''Labwork on Arsenic Biosensor:'''
'''Labwork on Arsenic Biosensor:'''
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* Meeting on Thursday at 2pm in Honours Room
* Meeting on Thursday at 2pm in Honours Room
* Website development
* Website development
-
* Design a badge if you have a spare five minutes
+
* Design a badge if you have a spare five minutes
* Presentation completed
* Presentation completed
 +
 +
 +
[http://2006.igem.org/University_of_Edinburgh_2006 Main page]
 +
__NOTOC__

Latest revision as of 09:34, 25 October 2006

Main page

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


Main page

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