Endy:Evolutionary stability project

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(Useful Resources)
Current revision (14:43, 24 March 2006) (view source)
(Project Outline)
 
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#Measure mutation rate of counter-selectable marker in long-term culture.
#Measure mutation rate of counter-selectable marker in long-term culture.
#Develop an [[Endy:Algorithm for codon optimization for evolutionary stability|codon optimization algorithm]] for specifying a new DNA seq for the counter-selectable marker
#Develop an [[Endy:Algorithm for codon optimization for evolutionary stability|codon optimization algorithm]] for specifying a new DNA seq for the counter-selectable marker
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#*Background research on the mechanisms by which cell spontaneiously mutate, the start of this can be found [[Endy:Algorithm for codon optimization for evolutionary stability|here]].
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#*[[Endy:Evolutionary stability project/Mutation background|Background research]] on the mechanisms by which cell spontaneiously mutate, the start of this can be found [[Endy:Algorithm for codon optimization for evolutionary stability|here]].
#Synthesize  counter-selectable marker with "stabilized" sequence
#Synthesize  counter-selectable marker with "stabilized" sequence
#Measure the mutation rate of the new marker.
#Measure the mutation rate of the new marker.

Current revision

This page will help coordinate the experimental/computational work being undertaken to improve the evolutionary stability of engineered biological systems. Read here for more background.

Project Outline

  1. Evaluate and select several counter-selectable markers.
  2. Evaluate a method for reliable long-term cell growth in E.Coli. These include:
    • Chemostat
    • Batch dilutions
  3. Measure mutation rate of counter-selectable marker in long-term culture.
  4. Develop an codon optimization algorithm for specifying a new DNA seq for the counter-selectable marker
  5. Synthesize counter-selectable marker with "stabilized" sequence
  6. Measure the mutation rate of the new marker.

Useful Resources

  • E.Coli book chapter 18 (Mutagenesis)
  • Schaaper, R. M. and R. L. Dunn (1991). "Spontaneous mutation in the Escherichia coli lacI gene." Genetics 129(2): 317-26.
    • Jasonk 21:40, 15 March 2006 (EST):Example of a characterization of the "mutation spectra" for a gene.

References

  • Cell density regulation circuit lost function in ~70hrs in a 50ml chemostat culture
  1. You L, Cox RS 3rd, Weiss R, and Arnold FH. . pmid:15064770. PubMed HubMed [coolpmid]
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