Team:Newcastle/Meetings/30 March 2009

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30/03/2009 - iGEM 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)

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

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.

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