Team:Newcastle/Meetings/23 March 2009

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Contents 1 23/03/2009 - iGEM Meeting 1.1 Agenda of the Meeting 1.2 Minutes of the Meeting 1.3 Agenda of the Meeting (26/03/09) 1.4 Action Points of the Meeting (26/03/09) 1.5 Minutes of the Meeting (26/03/09) 1.6 Action Points of the Meeting

23/03/2009 - iGEM Meeting

Agenda of the Meeting

• Review our project in mind (on the 18/03/09 meeting, question was posted on the objective of 3rd idea to be used together with the 1st idea).
• Decide on our project's title.
• Post our idea on the external wiki.
• Need to list all the BioBricks needed for modelling.
• Develop software systems which stimulates the system.

Minutes of the Meeting

• Discussed names, began thinking of 'sponges', but then decided on a parody of the Atari videogame character "Pac Mac", "Bac Man", as suggested by Goksel initially and extended by Craig, to an Eco-warrior called Sir Bac-man..
• We reviewed the opening paragraph, and welcome blurb for the iGem wiki; Craig volenteered to write a draft.
• Discussed various scenerios for Biobrick design, splitting the project into its parts.

1. Sense metals for Memory.
2. Getting Cd into cell.
3. Keep it in the cell.
4. Pump it into the spore (while forming).
5. Sense environment and sporulate.
6. Stochastic switch.

• Created various diagrams for these ideas.
• From these scenerios, we decided to assign each person some reading:
  • Matt - sensing cadmium (CzrA, CueR, ArsR).
  • Craig - cadA efflux system.
  • Hanny - smta.
  • Jane - how to trigger sporulation.
  • Goksel - stochastic switches.
  • Arun - DNA re-arrangement.
  • James - how to keep Cd in the cell.
  • Jess - how to pump Cd to spore.
  • All - how to use Zinc as a backup.
• Wednesday 25 March 13:00 CLT601 - Discussed research and decided to email questions.
• Next iGem formal meeting - Thursday 26 March 16:00 CLT922.

Agenda of the Meeting (26/03/09)

• present the paragraph summary for the external wiki
• students to present parts they researched on
• overview of the process
• present Biobricks and development

Action Points of the Meeting (26/03/09)

• 10% sporulate or 10% continue as vegetative cells
• set a date for BioBrick tutorial

Minutes of the Meeting (26/03/09)

• Advisors present: Neil, Dan, Morgan, Nigel
• Students absent: Arun
• Jane was chairing the meeting, and discussed the Action Points from the last meeting.

• We reviewed Craig’s introduction for the iGem website. There is only one minor correction to be made; software modeller to software engineer. Advisors liked the Bac-Man idea.
• 90/10% is for modelling to decide. Second Stochastic switch is to be used during pre-spore.
• Individual research
  • Jess
    • Cerevicie (sp?), Crs5 – zinc, cadmium.
    • How they are regulated CupA/smtA (preferred).
    • How much metal? (Dan) - 7 (4/3) human (Nigel), 4 on smtA, 54 amino acids.
    • Spore wall – advisors have same concern.
    • Timing may be a solution, using an early sigma factor, metallothiane linked to early sf.
    • Yugx/yugw operon not cadA (Nigel’s 2006 paper).
    • Look for y knocked out mutations.
  • Health and Safety concerns of using Cadmium, ask University’s permission.
  • Goskel
    • How to tune balance of SinI – different strength promoters – weak before P3
    • Could use Jen’s model for this, or use Equations to create a model.
    • DNA Salmonella phase
    • Drain/thrive population – model
    • Enhance population where there is Cadmium?
  • Hanny
    • SmtA instead of CupA
    • (Nigel) BNA has made cd for SmtA/B
    • 12 m molar to 2 m molar
    • Microbe TB hidden in genome
    • Not in Database yet - MyaT
  • Matt – Sensing
    • Metallothianine production after first stochastic switch.
    • Fur targets just (cobalt?)
    • Ditch cueR, just use two.
    • Use Zinc as backup?
    • AND gate may be in repository
    • Cadmium specific Zur
    • DNA rearrange – biobrick? - smtA, ArsR, CzrA
    • sigA promote 2 binding sites, neuclotide
    • AP swich off CadA intro into prowel trigger sporlation.
    • Replace CadA?
    • 7 Cd, 64 amino acids
    • CzcD not for Bacillus Subtillus (CadA)
  • How does Cd get into the cell?
    • No normal Cd uptake
    • mntH manages unspc
    • Sneaks through
    • Mutate?
    • Cry - Bacillus Thongenese - Spore crystal protein - Insects do not eat

Action Points of the Meeting

• Create a Flowchart (big with genes)
• Develop software systems which stimulates the system
  • 10% sporulate or 10% continue as vegetative cells - Modelling
• Familiarise self with BioBricks, website to go: www.partsregistry.org - ALL
  • List all the BioBricks needed
  • Organise a Biobrick tutorial with Anil for a week on Thursday?
• Use software such as X-Mind for collaborative ideas
• Post paragraph, and maybe wiki-design on main wiki