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From 2010.igem.org

Contents 1 Session 11 1.1 Planning 1.2 Team Division 1.2.1 1. Hydrocarbon degradation 1.2.2 2. Salt tolerance 1.2.3 3. Emulsifier 1.2.4 4. Modeling & possible products 2 iJAM session 1

Session 11

First meeting after have chosen our subject.

Planning

Made a preliminary planning:

• Today, team division and general discussion on how to approach things
• Next meeting: Preliminary plan on general approach per group, possible questions for the whole group, and a general discussion. When making the lab-plans, also incorporate deadlines at which goals must be reached.
• Following, weekly meetings to keep everyone up to date?
• End of May: Meeting with the professors / staff of kluyver etc in which each group’s plan will be presented, and we will ask the people attending to give advise / comments / remarks
• June: Lab work!

Team Division

As already mentioned, our subject can be divided into 4 subparts, but each subpart will need team members as well as an initial plan of action.

1. Hydrocarbon degradation

Team members: Hugo, Mathias & Kira

• Focus on alkenes
• Paper by Rojo: 3 main enzymes, Make different strains for each type of alkene degradation (different enzymes for different lengths), Gene’s are in a cluster, so design a primer for this cluster,
• Using GC for measuring the alkenes?
• Hydrocarbon Resistance: Paper by Lazaroaie => This is phase 2! First start with a “normal” strain under mild conditions – check how high the normal resistance is?
• Drug efflux pump will create Drug resistance in E.coli (ethical subject!), Pseudomonas & E.coli membranes are pretty similar according to Hugo

2. Salt tolerance

Team members: Nadine, Mia

• Salt in the solution: test with sodium chloride
• Conductivity or polarity measurements?
• Paper with salt tolerancein E.coli: Kapardra
• Biobrick: not well characterized? Check presentation? If not: Characterize it?
• Ecotin? (osmoprotectant)
• Regulation system? Sensor? Existing biobrick?

3. Emulsifier

Team members: Pieter, Eva

• First look at hydrocarbon degrading organisms first, and what kind of emulsifier they excrete and see if we can use this (see nature review on huddle for further reference)
• Designing our own peptide? (but this would be a bit more difficult, but possible, no more than 16 aa!)
• Export would be the main problem? (Self-destroying population?)
• Start by choosing the emulsifier

4. Modeling & possible products

Team members: Jelmer, Luke

• MFA (3 days?) Alkene degradation: look at SB assignment…
• Thermodynamics?
• Prediction of growthrate (Heijnen hypothesis?)
• Prediction of emulsion capacity
• Molecular dynamics simulation
• Towards the end of the project model if we could put everything together?
• Regulation strategy for salt tolerance?
• PHB, butanol or ethanol?

iJAM session 1

Our first iJAM session!