Team:TU Delft/9 May 2010 content

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(New page: ==Session 11== First meeting after have chosen our subject. <h4>Planning</h4> Made a preliminary planning: * Today, team division and general discussion on how to approach things * Next ...)
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* 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?
* 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
* Drug efflux pump will create Drug resistance in E.coli (ethical subject!), Pseudomonas & E.coli membranes are pretty similar according to Hugo
 +
 +
<h5>2. Salt tolerance</h5>
 +
'''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?
 +
 +
<h5>3. Emulsifier</h5>
 +
'''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
 +
 +
<h5>4. Modeling & possible products</h5>
 +
'''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?

Revision as of 13:34, 14 July 2010

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!

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?
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