Team:Newcastle/Meetings/2 July 2009

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Contents 1 IGEM Meeting 2 July 2009 1.1 Agenda 1.2 Action points 1.3 BioBrick Model 1.4 Modelling Questions 1.5 Labwork 1.6 MatLab 1.7 Sequentia Tutorial

IGEM Meeting 2 July 2009

• Chair: Hanny
• Students present: James, Goksel, Matt, Jess, Jane
• Instructors present: Neil, Jen, Daniel

Agenda

• Run through action points
• Go through Biobrick model (Matt)
• Go through Stochastic switch(Goksel, Jess)
• Ask questions about the model (James , Jane)
• Talk about the lab work
• Ask about MatLab
• Ask about Sequentia tutorial
• Ask about uploading information onto external wiki

Action points

• Model of Metal Intake
  • James has done some of the work but needs more help from biologists!
  • It was discussed that we first of all need to model cadmium only and THEN we can consider other metals - start from the basics.
  • Need to find out how much cadmium binds to the promoter/protein per second
  • Need to measure how much protein is expressed by promoter activation
  • Using this data, work out how much cadmium is taken in by the metallothionein
  • It was decided that the whole team (students) should meet up after lab sessions to work together on getting relevant data and get this model working.
  • We need TWO models - 1) A model for Bacillus subtilis response to cadmium in different scenarios and 2) A model for cadmium influx in B. subtilis
• Model sinI operon
  • Goksel has made model based on a paper on stochastic switches without changing parameters.
  • Question: Should we leave the model sequence as it is?
• Model comK sequence
  • Jane has done model based on given equations on paper
  • Not quite sure on the layout of the model (in diagram structure)
  • Can now study CellML
• Promoter Library
  • Program and task carried out by Jen
• Prioritise BioBricks
  • Ongoing process
  • Meeting up outside of lab hours to 'map' out project, decide on the BioBricks and design them (along with DNA sequences)
  • Need tutorial on Sequentia
• Coding in J-Sim
  • Ongoing
• Write up about Cadmium and the Environment
  • Information has been researched and written into paragraphs
  • Information could be re-written and tidied
• Decide on Awards
  • Gold Award!
  • Our project fits into the Environmental project strand
  • Wiki, Presentation, Poster
• Lab Space (Rotas)
  • Decided in meeting that because there is currently six of us, 2 groups of three will start off
  • These groups of three consist of one biologist and two non-biologists
  • Once others come back, may go into pairs
• External Wiki photos to be uploaded
  • Goksel has uploaded some photographs of Newcastle onto other website
• CCS template issues on Firefox/Safari/Some versions of IE, etc
  • James has sorted the problem - it turned out to be more than a CSS issue. James changed the links from 'Wiki' links to HTML links and that has resolved the issue.
• Do a new version of the timetable
  • Has been updated
• Plan for a week off before coming back for next teaching year (September-ish), to relax before even more work
  • Didn't discuss
• Phil to be added to the mailing list
  • An administrator of the mailing list needs to do this if not done already

• Thoughts and ideas from iGem UK get-together
  • Need to write up about ethics and social implications of project and synthetic biology
    • Awaiting e-mail from Edinburgh University regarding ideas and thoughts generated from the discussion activity
  • Need to write up a report of the Edinburgh trip
    • James has written a few paragraphs which has been posted onto the internal wiki
  • Add photos and presentation to the wiki
    • Ongoing
• Ask Arun about his backing time(done)
  • Arun probabliy back to team next week
• Jane suggest to add side bar or hyperlink for biology item we used in wiki

BioBrick Model

Attempted to go though our proposed designs. However there was a lack of clarity on how and where the biobricks fitted into the system. As a new action point, it was suggested that we place on the wiki a clear description and diagram showing all of the components of the project linked up in the correct way.

Modelling Questions

Question: In the metal intake model, should we consider the manganese ions (cadmium sneaks through the membranes of Bacillus subtilis through the manganese transport system)? Answer: Yes - Mn should be considered in the model eventually. For now, we need to concentrate on cadmium alone.

Question: What about the invertable sequence for the second stochastic switch? Answer: Look to see whether part is in repository. If it can be found there, use the part and characterise it/make it better.

Labwork

So far in labs, the team has made competent cells. Attempts to transform these E.coli with plasmids containing the ampicillin resistance gene will be made tomorrow. There will also be 'controls' carried out including media with/without ampicillin. One half of the team will take part in these transformations; the other half will do transformations of Monday but with BioBricks sent to us from iGem.

In the meantime, the advisors have asked the team to research the parts repository for a plasmid backbone to use for the project.

MatLab

In the meeting, the issues surrounding MatLab were discussed. Apparently, we need the Syn Biology toolbox. Jen says she has not yet done it but will be able to do it soon.

Sequentia Tutorial

Neil would be able to give us a tutorial except the key server on which Sequentia works is currently not working. However, Neil has advised that we download the PC trail version of Sequentia onto our computers and learn through the tutorials online.