Team:Newcastle/Meetings/30 March 2009

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Contents 1 30/03/2009 - iGEM Meeting 1.1 Action points from the last meeting 1.2 Agenda of the Meeting 1.3 Minutes 2 Meeting 02/04/2009 2.1 Agenda of the meeting 2.2 Minutes of the meeting 2.3 Action Points

30/03/2009 - iGEM Meeting

• 14:00 start CLT601
• Team members absent: Craig, Arun

Action points from the last meeting

• Develop software systems which stimulates the system (Ongoing)
  • 10% sporulate or 10% continue as vegetative cells - Modelling
• Familiarise self with [http://www.partsregistry.org BioBricks] - ALL
  • List all the BioBricks needed (Current job)
  • Create big flowchart (with gene names) (Current job)
  • Organise a Biobrick tutorial with Anil for a week on Thursday?
• Use software such as [http://share.xmind.net/ X-Mind] for collaborative ideas (Ongoing)
• Look up [http://www.safety.ncl.ac.uk safety regulations] (Ongoing - Advisors)

Agenda of the Meeting

• Post paragraph, and maybe wiki-design on main wiki (DONE, No formatting)
• Create a Flowchart (big with genes) (Done on whiteboard, to create electronically)

Minutes

• Hand out work for preparation before meeting on Wednesday (11:00am CLT.601)
  • Arun - DNA rearrangement + germination gene regulation
  • Jess – SmtA BB + triggering
  • James – CadA system biobrick
  • Matt – Czr+ArsR+BS
  • Goksel – SinI, SinR SS
  • Hanny – Mnth BB (+Sporulation?)
  • Jane – Triggering Spoulation
• Looked at other teams wikis (Not many with ideas up)
• Formal meeting on Thursday 4pm

Meeting 02/04/2009

Agenda of the meeting

• Show our flowchart/presentation
• Run through individual research/biobricks

Media:Flowchart_and_BioBricks_for_Bacillus_subtilis.ppt‎

Minutes of the meeting

• Members present - James, Matt, Jess, Hanny, Goksel
• Advisors present - Morgan, Matt
• Bacillus subtilis should always be written as italic. Gene names should start with lowercase whereas protein name should start with uppercase.
• Do not use green and red colous on presentations.
• When a protein sequence is known, to find similar proteins do a blast search.
• To control cadA system directly by ArsR and CzrR, we can insert the binding sites of these proteins into the binding site of CadA.
• Cd uptake in bacteria is preferred to other metals like Zinc.

Action Points

• Watch out for other team's wikis. Every week give a review for 5 minutes for other wikis
• Combine the first two boxes on the presentation.
• The diagram shouls also include the system that pumps out Cd
• The first stochastic switch should be wired to Cd sensing system directly whereas the second one should be influenced by the system.
• We should also model the state when there is no metal
• Always use DNa rearrangement upon Cd exposure.
• While doing a presentation, create a table and display which genes are ON and OFF for each step
• Model Cd uptake using a CellML model
• Display the spore timeline while presenting the required actions step by step
• Do not use GFP inside biobricks. In this way they are not modular.
• List the names of genes that need to be knocked out. E.g mntH.
• For each gene, specify whether the gene exits in B. subtilis or it is taken from another organism.
• Investigate if arsR has another name in literature.
• Investigate the operator site of arsR
• Investigate how cadA is regulated. We can use sigma factors to regulate cadA system or we can expres a repressor to deactivate the system.
• Model the following sub systems
  • Cd pumps. we can then decide how many of them we need
  • AND gate for metal sensing
  • Stochastic swicthes
  • DNA rearrangement
  • Population of cells
  • Smta - sponge system
  • Number of metals that a spore can store