Team:Newcastle/Meetings/30 March 2009

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 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 X-Mind for collaborative ideas (Ongoing)
 * Look up 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

Agenda of the meeting
[[Media:Flowchart_and_BioBricks_for_Bacillus_subtilis.ppt‎]]
 * Show our flowchart/presentation
 * Run through individual research/biobricks

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