User:Allancrossman

Allan Crossman, member of Edinburgh 2011.

Personal TODO list

• What happened to our primers e.g. for xylA?
• What is density of displayed INP?
• Plan for zipper system.
• Plan for pIII beads reactor?
• Can we suppress the hover-over thing for pages with no hard words?
• Test wiki on IE8 (and 6 if I can find it)
• Add hints.

Notes to self

• We MUST have (somewhere) a team description page, a project abstract, a complete project description, a lab notebook, and a safety page.
• inaZ is [http://www.ncbi.nlm.nih.gov/nuccore/71553748?from=1850733&to=1855854 here], broken by an IS.
• To add hints, edit Team:Edinburgh/tech/Hints and also add <span class="hardword" id="foo">foo</span> in the relevant page.
• Assembly page is here: Team:Edinburgh/AssemblyContent
• The bglX part has a PstI site in it. Once fixed, the official part docs will need to be redone.
• [http://www.lifesci.dundee.ac.uk/groups/tracy_palmer/docs/signals.htm Substrates of TAT pathway in E. coli]
• RBS strengths from Warsaw 2010

Video game concept

You control a humble ribosome. You are powered by sugar. Outside the cell is cellobiose floating around. You can express B-glucosidase on the cell exterior to get more sugar. You can express other stuff. There's cellulose floating around too. You can express cellulases. There's phage. You can express proteases or somesuch?

Recombination avoidance test?

If INP works, and if we have the money, we could test whether our recombination avoidance strategy actually works, by getting a new version of BBa_K265008 synthesised with synonymous codons, and setting up a construct such that some reporter (e.g. LacZ, YFP, or whatever) would only be expressed if recombination occurred:

Promoter - RBS - INP1 - Terminator - Space - INP2 - Reporter

See if there is any difference between this and:

Promoter - RBS - INP1 - Terminator - Space - INP1 - Reporter

...when cloned into a RecA positive E. coli strain.

Lignin degradation

• Requires glucose oxidase to supply H2O2, a cofactor for other enzymes...
  • Lignin peroxidase
  • Manganaese peroxidase
  • Laccase?

Some of these use flavin cofactors but it seems proteins using these can be successfully displayed using INP (Van Bloois et al, 2009).

(Stop - Weak RBS) spoligos

Explanation: CTAG C + stops + random junk + weak RBS (<partinfo>BBa_B0033</partinfo>)

FS: 5'-- ctag c taa taa tgacctacttaa tcacacaggac g      --3'
RL: 3'-- gatc g att att actggatgaatt agtgtgtcctg c ctag --5'
RT: 3'--      g att att actggatgaatt agtgtgtcctg c      --5'

So, converting everything to 5'--3' format we get:

• FS: ctag c taa taa tgacctacttaa tcacacaggac g
• RL: gatc c gtcctgtgtga ttaagtaggtca tta tta gctag
• RT: c gtcctgtgtga ttaagtaggtca tta tta g

References

• Van Bloois E, Winter RT, Janssen DB, Fraaije MW (2009) [http://www.springerlink.com/content/d471504054865565/fulltext.pdf Export of functional Streptomyces coelicolor alditol oxidase to the periplasm or cell surface of Escherichia coli and its application in whole-cell biocatalysis]. Applied Microbiology and Biotechnology 83: 679-687 (doi: 10.1007/s00253-009-1904-0).