Team:Edinburgh/Modelling

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Revision as of 13:04, 1 July 2011

Possible models...

Synergy vs. non-synergy

Does the whole theory behind our projects - synergy - even work?

Evolutionary analysis of cell-display vs. secretion?

This idea is broadly suggested by [http://www.springerlink.com/content/4l4m28lp06120253/ Van Zyl et al (2007)].

One potential benefit of attaching enzymes to the cell surface rather than secreting them into the media is that any mutations that increase enzyme efficiency will specifically benefit the cell with the mutation, as the increased sugar yield will be physically present at the cell. The mutation will thus confer a fitness advantage, potentially allowing it to take over the culture.

By contrast, if a cell produces a secreted protein that is of higher efficiency, it will disperse and benefit random cells in the culture.

Synonymous codon usage to avoid recombination

Our projects involve having multiple fusion proteins expressed, each of which uses a genetically identical carrier protein (e.g. ice-nucleation protein or the M13 pVIII gene). The presence of repeated sequences in DNA (i.e. the same sequence in multiple locations) can lead to genetic instability.

To combat this, it ought to be possible to design different versions of the genes that code for the same amino acids but use different codons and so are as distinct as possible. This could be investigated by computer.

References

Van Zyl WH, Lynd LR, Den Haan R, McBride EJ (2007) [http://www.springerlink.com/content/4l4m28lp06120253/ Consolidated bioprocessing for bioethanol production using Saccharomyces cerevisiae]. Advances in Biochemical Engineering/Biotechnology 108: 205-235 (doi: 10.1007/10_2007_061).

This was the old Navbox for Edinburgh; now it's obsolete...

Edinburgh 2011

Project documentation: Project - BioSandwich - Parts - Modeling - Lab Notebook - Safety - Team - Attributions

Pages for members: Wiki Watch - Useful Links - Sequences - Primers - Practices - Official Profile (has email addresses)

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 This idea is broadly suggested by [http://www.springerlink.com/content/4l4m28lp06120253/ Van Zyl ''et al'' (2007)].
-One potential benefit of attaching enzymes to the cell surface rather than secreting them into the ether is that any mutations that increase enzyme efficiency will specifically benefit the cell with the mutation, as the increased sugar yield will be physically present at the cell. The mutation will thus confer a fitness advantage, potentially allowing it to take over the culture.
+One potential benefit of attaching enzymes to the cell surface rather than secreting them into the media is that any mutations that increase enzyme efficiency will specifically benefit the cell with the mutation, as the increased sugar yield will be physically present at the cell. The mutation will thus confer a fitness advantage, potentially allowing it to take over the culture.
 By contrast, if a cell produces a ''secreted'' protein that is of higher efficiency, it will disperse and benefit random cells in the culture.