User:Allancrossman

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Allan Crossman

Allan Crossman, member of Edinburgh 2011.

Contents

Personal TODO list

  • Get INP-YFP localisation info from Sylvia.
  • Get those pics from Eugene.
  • Work out complete sequence of the PlacLacZ-INP we have and prepare for Gibson using it.
  • RFC for BioSandwich
  • Table of all our stuff, whether it has RBS, start codon, stop codon, etc.
  • Add hints.

Notes to self

  • [http://mic.sgmjournals.org/content/142/7/1659.full.pdf+html bglX info]
  • 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.
  • User:Allancrossman/Gibson and User:Allancrossman/Gibson2
  • inaZ is [http://www.ncbi.nlm.nih.gov/nuccore/71553748?from=1850733&to=1855854 here], broken by an IS.
  • [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://www.ncbi.nlm.nih.gov/nuccore/AF130864.1 pG8SAET]
  • Contributions: Yassen
  • Contributions: Lukasz

Large display of small GIF

Non-synergistic versus synergistic systems. Dark regions are places where the cellulose has been degraded down to free glucose molecules.

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).

Gold medal criteria

  • Our wiki watch page is clearly a type of collaboration.
  • Cooperation with Trieste re: C. fimi BGlu sequence.
  • Cooperation with Trieste re: C. fimi BGlu assay.
  • Registry update for K415151.
  • Registry update for K392008.
  • Registry update for K265008.
  • All our human practices stuff.

Tables for Yassen

Equipment Size (m3) Cost constant (£) Index Purchase cost (£) Number required Total cost (£)
Boiler 8 70 0.8 13,218.33 4 52,873.31
Reactor 1 4 18,5000 0.45 47,158.74 1 47,158.74
Reactor 2 4 18,500 0.45 34,522.22 1 34,522.22
Reactor 3 4 18,500 0.45 34,522.22 1 34,522.22
Reactor 4 4 18,500 0.45 34,522.22 1 34,522.22
Reactor 5 4 18,500 0.45 34,522.22 1 34,522.22
Reactor 6 4 18,500 0.45 34,522.22 1 34,522.22
Tank 100-102 3.3 1,400 0.55 2,699.67 3 8099.01
Tank 103 93.2 1,400 0.55 16,955.35 1 16,955.35
Tank 104 40 1,400 0.55 10,647.83 1 10,647.83
Tank 105 147 1,400 0.55 21,784.75 1 21,784.75
Tank 106 17 1,400 0.55 6,650.82 1 6,650.82

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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