Team:TU Delft/9 May 2010 content

From 2010.igem.org

Contents

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!
Meeting at Aljosha's place

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! The pictures were added to the iJAM album on Facebook