Team:Newcastle/Meetings/9 April 2009

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Contents 1 Instructor Meeting 9th April 2009 2 Actions 3 Notes 4 BioBrick Parts 5 Other Business

Instructor Meeting 9th April 2009

Students: Jess, James, Matt, Craig, Hanny, Goxsel Instructors: Jen, Matthew, Neil

Apologies: Dan, Morgan, Jane, Arun

Actions

Neil - sin operon info to students, and BioBrick tutorial

Jen - circulate drawing of stochastic switch / slider

Students - email Neil about tutorial [done]

- consider the comments / notes and produce a priority plan of the way forward

- once finished send flow chart to Nigel Robinson for verification

- E-mail Colin Harwood to ask if there is an invertible sequence of Bacillus DNA

- Make a list of all the promoters that can be used in Bacillus so we have a list to pick from

- High priority:

1. update flow dia. and gene on / off table.

2. concentrate on some modelling priorities

3. Need to do a table of inputs (metal combos) and ouptputs (on / off - gate type)

4. Need to understand sporulation stages, genes etc... (see notes for more details)

Notes

Comments on presentation of flow diagram.

- Sigma factors that regulate cadA?

- Include concept of metabolic loading ie switch on metallotionein in the cells that become metal-mops ans sporulate.

- Switch on cadA (yvgW) when a threshold Cd conc is reached ie we need to sense the level. Cell is probably doing this anyway need to model to see how high we should put it.

- Beware again of expressing things (eg gfp) in cells you want to be fit - metabolic loading concept

- DNA re-arrangement: fimE switch ok but look for one in Bacillus. Could we use a cascade of switches like this to show hi, medium and lo Cd exposure in the bio-mem?

- Need to understand sig factors and generic repressors better

- There are limited set of factors (eg sig) in spore that can be used ie need to CHECK THIS

- Can we (and should we) express DNAase in late stage of sporulation so it commits suicide ie no chance of germination, this would be downstream of one of the flip switches for the metal-mopper set.

- Should we develope debugger bricks with generic splicing point, promoters and reporters?

BioBrick Parts

Metal Sensor

- ! Need to do a table of inputs (metal combos) and ouptputs (on / off - gate type) !

- is arsR a epressor or activator ?

- re-do brick for sensor, promoters and correct order

Stochastic Switch or Slider

- control over sinR or sinI should give us a stochastic sliding effect like a fader on your hi fi - nice looking biobrick too!

- issues with complexity of the system oligermerization etc... model needed maybe Jane and Goxsel lead on this (Neil)?

- Jen will send round a re-drawm circuit

- ! Need complete flow diagram and pictures of sporulation cell cycle inc genes, factors, promoters, activators, repressors and everything else !Check it with Geoff Herrington.

- Protease tags in switch proteins ? Not sure what this means: was it so they get broken down quickly once they do the job?

Metallothionein = Metal Mops

http://en.wikipedia.org/wiki/Metallothionein

- Getting into spore using tags - what is the consensus seq of these tags?

- Issues about when to switch on and off

-

Other Business

- Email Neil about BioBrick tutorial 30th April[done]

- Mike Cooley signed up as instructor

- SGM (Soc. General Microbiology) has donated funding

- Neil can send us some info on sin operon he has

- Neil and Alister (Edinburgh Uni.) discussed a UK get together in July

- Can we do something with small spore proteins to make them tougher?

Matt will be absent from the next meeting.