Wiki/Team:Imperial College London/Notebook/July 6

From 2011.igem.org

Action points for the day:
-bios on the wiki
-sci-fi meeting
-characterisation talk
-come up with more ideas
-do more research on anti-venom and prodigiosin

We started the day off by brainstorming several idea and selecting the ones we thought were viable enough to be presented to the professors on Friday.

Brainstorming:
Venom and BAS ideas to be presented on Friday!
-desertification (overdone already)
-thermophiles (make them express melanin so they can be heated up by the sun, saving energy)
-cell-cell signal transduction (can be used as inhibition or activation)
-desalination (commercial membranes are probably more efficient)
-data storage in bacteria (use DNA to encode information has already been done but it might be useful to come up with a new way of retrieving the information. Storing data in RNA might be more efficient)
-ocean metals (retrieving valuable materials from sea water, main problem: materials are only present at really low concentration and might be hard to retrieve) -cross-linking of hair to something useful
-dictostylium
-using melanin for heat production from sound in bacteria. The heat could then be converted into an output, producing sound sensitive bacteria. Is melanin really able to detect sound??
-modifying silk worms?
-radiotrophic fungi (fungi that use gamma radiation to produce ATP - the pathway could be used in E. coli to absorb radioactivity but the exact pathway does not seem to be known (Wikipedia))
-serum bile acid as a biomarker of liver problems in pregnancy

After the brain-storming session we had a talk from Chris about characterisation giving me a glimpse into what I would be expecting in the weeks after the project has been pinned down on a single idea.

Characterization presentation by Chris:
in vivo presentation
-Timer vs. switch. need to know characteristics of parts.
-How to characterise: Look at individual parts. What goes in, what goes out. What function is carried out.
-What specifically do you want to characterise? Terminator, core-promoter, RBS, reporter, coding region.
-Terminator requires several different characterizations.
-Place promoter, coding region into an expression circuit with a reporter.
-Standards are only existant for promoters. How strong promoters are.
-Canton paper 2008: Base characteristics that you need to know about an inducible promoter.
-How responsive (transfer function of response), dynamic? (output) All relative to J23101.
-Synthesis rate, number of cells and divide your promoter output with standard which gives you a value relative to J23101. RPU (relative promoter unit)
-RBS calculator gives you a value to how strong it is. Need to debug yourself.
-Hard to characterise until we know what we want to do.
-Plate readers look at OD, fluorescene, luminescence.
-Individual cells analyzed for GFP and RFP.
Chris works on methods to make it more high-throughput (automates to make faster). Won't consider optimizing something unless it worked twice on the assays. Fluorescence doesn't give use pinpoint accuracy. Can't be measured really well, only bulk events and not specific events. Enzymatic activity more done in vitro. You're working with factories that work depending on what they're in.
Can find Chris though James at any time.
Make sure positive and negative control will work.
We currently have two running ideas; the anti-venom and a bile acid sensor. We have split off into two teams and each is working hard in order to build a system that the professors might agree to this Friday at 3:30pm. The deadline is approaching and we still require 2 more possible projects to present to the professors.

(Text by Rebekka and Chris)