Sortostat/Notebook

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Revision as of 13:03, 17 September 2007 by Jason R. Kelly (Talk | contribs)
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Contents

Experiments

Future Experiments

replace bulb before these experiments

  • check on pH of the media if we are adding AHL, it needs to be <8 for AHL to be stable.
  • Zig-zag run where we vary from 0.4 to 0.6 so that we can get more sampling of the selective pressure.
  • Maintenance of a slower growing variant vs. a faster growing "mutant".
    • Could demonstrate this with a slower growing CFP vs YFP or via something like F2620.
  • Zig-zag experiment with different dilution rate (e.g. different total number of cells).
  • Get the exact size of sorting chamber by cell counting
  • F2620 is in MG1655 whose flagella might cause a problem
    • Need to co-transform with RFP expression plasmid anyway.
  • We already have the zig-zag automated, but should include a "pulse" as well (e.g. /-\_/-\) where it has regions with no selection.

Modeling

  • Sortostat/Model
  • How much faster can we drive it given the timing?
  • Are there more or less cells in a sort vs a screen?
    • No, looked at this before last lab meeting, but should write it up.
  • Do fluctuations in the total cell count correlate with anything?
  • 2/18/06 lab notebook page has some information about the appropriate sorting volume to use in the model, move this to the wiki

Output

  • Sortostat mFiles doc - list of all the mfiles that matter (except the image processing). These are all commented and cleaned up at this point.
  • Sortostat Modeling Probability Distributions doc - description of the modeling of the probability distributions for the number of cells in the sorting chamber and how many are CFP or YFP.
  • Sortostat Modeling Stochastic Sim doc - description of the stochastic simulation of Sortostat performance.

Analytical model

  • put the cleaning period / dilution rate formula derivations on the wiki.
  • write up the chemostat equations as they relate to the SS cell concentration (e.g. limiting substrate? Should we reduce the concentration of glycerol?)
    • 12.5 min between cleaning (doubling time = 0.55)
    • 13.6 min between cleaning (doubling time = 0.60)
    • 14.8 min between cleaning (doubling time = 0.65)
    • 15.9 min between cleaning (doubling time = 0.7)
    • 17min between cleaning (doubling time = 0.75)
    • 18.2min between cleaning (doubling time = 0.8)
    • 19.2min between cleaning (doubling time = 0.85hr)

LabView

  • why do we need to initialize the load paraemters array?

To Do List

  • Figure out the MATLAB memory leak
    • I suspect this is because I'm not closing the image files properly in the MATLAB script that runs, or it could be something more annoying.
    • Does the leak influence the timing of the events, by making the image processing take too long? (e.g. why does the timing graph get noisy after awhile?)
    • Is it the MATLAB thread that blows up or the LabView? it's MATLAB.
  • output the direction of sorting to the output file
  • Clean up the Image Processing MATLAB scripts

Done

  • Why do I see any variability in the timing? Timing between cleaning events is rock solid, the timing between sorts is influenced by the time it takes to process the image.
  • Change the code so that when flipping based on the CFP it is the moving average that is used, rather than a single image.
  • Make the list of experiments to evaluate the device performance limits.
    • Sorting at various dilution rates, followed by a sort to extinction.

References

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