Imperial College/21 July 2008

= 21 July 2008 =

Briefing

 * 3 Subgroups to research on their specific areas: Alternative photoreceptors to YtvA-σB activation pathway, Biomaterial synthesis and B.Subtilis protocols/promoters/rbs etc.

Debriefing

 * Each Group gave a summary of their sections, followed by a discussion on any potential problems:

B.subtilis

 * The knock out of espE is in a wild-type strain as opposed to lab based stains. Group was unclear on what a lab stain actually was and the problems of not using them.
 * Wild type strains have differing motility from lab strains.
 * Look at degradation tags to add to the EspE, this could help tune our design after the initial testing and the modeling.
 * Need to identify promoters including - inducible, constitutive and possibly repressible.
 * Need to identify sequences for integration.
 * Use of integration method to introduce BioBricks into B.Subtilis, a.k.a. Integrated BioBricks
 * Plasmids will be grown in E.Coli so as to facilitate genetic manipulation and maintainance before transferring any genetic material into B.Subtilis.
 * LacZ, IPTG inducible promoters are most commonly used in B.Subtilis.

Light Induction

 * Pursue the possibility of synthesising two constructs,
 * 1) The natural YtvA can be used, all we have to do is to use a σB promoter that can be put upstream of our constructs.
 * 2) Investigate an heterogeneous pathway in B.subtilis. One suggestion has been to investigate the use of a previously engineered part from iGEM competition were EnvZ-OmpR was made photosensitive.
 * 3) Rhodopsin is membrane bound, might not work on Gram positive bacteria.
 * Need to find out any parameters such as time dependence, threshold of response.
 * Check on the wavelength of light which affects B.Subtilis.
 * Find out what kind of data can be collected on bacteria motility. Should try to look at the motility of E.Coli first, then swap over to B.Subtilis.

Biomaterials
Focus on three main points:
 * Need to firstly identify a list of biomaterials with relevant features, i.e. concentration dependence of assembly, no. of subunits.
 * Need to investigate the types of secretion we can pursue, what sequence do we need and what machinery do we need.
 * Self Assembly, might want to look at amyloid peptides,
 * Conc dependence,
 * One or multiple subunits needed,
 * More details are required on the in-vitro properties of biomaterials.
 * Find out the protein coating on spores.

Summary

 * Need to get into construct, part design. Draw out design diagrams, Bioengineers to help with conceptual framework and modelling i.e. responsiveness of signal to clutch and other parameters.
 * Look at websites for culturing B.Subtilis.
 * Identify other companies which do DNA sequencing, should not rely entirely on GeneArt.
 * Need for timetable and project management, milestones on design, modelling, protocols etc.
 * Next Monday and Wednesday, demonstration on lab use.
 * 1 August - Team project descriptions due (Late summer teams)!