Team:Newcastle/Meetings/23 March 2009

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.
 * 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