User:Allancrossman

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Allan Crossman, member of Edinburgh 2011.

Contents

Personal TODO list

  • Plan for zipper system.
  • From Monday meeting:
    • Can GFP on INP be seen?
      • Maybe: there is fluorescence in Vibrio anguillarum in but it is weaker than cytosolic GFP. See [http://www.springerlink.com/content/y454ut81w52h6431/ here]. In E. coli there is extensive proteolysis. See [http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.2009.01724.x/abstract here].
    • What is known about what malS does?
      • "[http://jb.asm.org/cgi/content/full/193/10/2517 recognizes long dextrins and preferentially releases maltohexaose from the nonreducing ends of linear maltodextrins]" - i.e. it works at the end of the chain?
    • What is known about what bglX does?
      • [http://mic.sgmjournals.org/content/142/7/1659.full.pdf+html Can be assayed with ONP-β-D-glucopyranoside]
    • Table of all our stuff, whether it has RBS, start codon, stop codon, etc.
  • Some other sequences arrive on Wednesday.
  • Ought to get new INP with BglII/SpeI sites sequenced.
  • Plan for pIII beads reactor?
  • Can we suppress the hover-over thing for pages with no hard words?
  • Team:Edinburgh/Carotenoids
  • Add hints.

Notes to self

  • We must have a "data page" that explains the system and links to actual data which must be on the Registry.
  • 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.
  • 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
  • [http://partsregistry.org/Part:BBa_K415151:Experience BBa_K415151:Experience] - can this count for anything?

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?

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).

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).


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