Team:Cambridge/Notebook/Week1

Monday

We spent the morning compiling a large set of ideas, each on its own post-it-note. We categorised them and excluded those that were clearly unfeasible. If you like, you can see the long list.

In the morning we narrowed them down to a a shortlist of projects.

Tuesday

We spent the morning researching the shortlisted project and seeing a demonstration of the *Techne PCR machine* by Bibi scientific.

In the afternoon we worked on a practical with Qiagen equipment, helped by Simon Morgan. We miniprepped DNA, and then ran it on a gel.

Wednesday

Morning:

• Looked over other projects and compiled characteristics of successful projects
• Presented our projects:
  • Paul: Production - finding something novel for implementation
  • Emily: Degradation
    • There are quite a lot of things to degrade! Even within plastics
      • Genes found to degrade certain plastics: PVA (Poly Vinyl Alcohol), gene produced to degrade it

Bill wore a Honey bear t-shirt

Afternoon

• We selected 4 projects to further work on, each then researching those we did not come up with:
  • Turing Patterns
  • Bioluminescence
  • Quiescence
  • HIV Diagnosis

Thursday

Discussion of Quiescence:

Problems:

• IP Problem, should ask David Summers about the use of his patented idea. Should we instead try to be more original for the project?
• Biobricking is the ultimate aim, but there is not enough for the while project.
• Altering the RNA structure - might it be too complex for iGEM?

Bio-Luminescence and Quiescence joint project -

Proposed breakdown of project:

• Module 1 - Production of Luciferin, Luciferase and Luciferin Recovery enzyme (LRE) - these are all firefly
• Module 2 - Biosynthetic pathway for luciferin
• Module 3 - Biobricking quiescence - require a very good control system to prevent false activation, could add a conformational change to the molecule.

If could not get quiescence to work, would the light producing bacteria be enough of a project? Know we have a "super" luciferase with 12x the affinity for the substrate and not for the product. The firefly systems are all eukaryotic, so suggest that we could perhaps do this in yeast. Control of quiescence could also occur via cyclin control in yeast again.

Bill wore the TV Bear tshirt

Friday

Bill wore Ni tshirt Paul wore I love DNA t-shirt - he was the winner today

Decided to drop HIV project, continuing research on Bio-Luminescence idea.

Started using Flickr account - http://www.flickr.com/photos/52129837@N08/

Bill and Will attempted to estimate the luminosity of a bacterial colony, and compare this to the lower threshold of the human eye during scotopic vision. Used the estimate for the eye sensitivity using http://www.telescope-optics.net/eye_spectral_response.htm .

Theo predicted the structure of Rcd using mfold, but got a different conformation to the one shown in the paper, perhaps the algorithms used on the program have changed between now and when the paper was written.

We listened to Fireflies the song and concluded the lyrics make no sense.

Saturday

Peter made a model of the X RNA to visualise the structure

Sunday