Cell Density Detection

From FreeBio

I just noticed us 3 have the shortest names on the team. Hip hip hurray! (no longer true)

Contents

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Ideas

  • One view:
    To have two types of cells, a emitter and a reporter(flourescence).
  • Another view:
    All reporters, but they emit with a different thresholds.
  • All of these require look at bullseyes.
  • Uniform density, high density versus low density. Topographical map.
  • 3 cells versus 1 cell. 3 different density levels.
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Open questions

  • What is the natural aggregration of e coli?
  • How do bacteria respond to each other?
  • e. coli versus yeast.
  • Speed of detector.
  • How feasible is doing this in e. coli? (good)
  • Quorum sensing and signaling.
  • Thresholds.
  • How to do chemotaxis. Emitting things.
  • Clustering algorithm, different metrics based on chemical released.
  • Different densities release a different output.
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Modeling

We can model the diffusion, through either a diff eq method or by a stochastic cellular automata. Interesting idea-> use kernel based methods from AI, to model the patterns formed by acetate.

Both papers give a rather straightforward and apparently accurate way to model this system.

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Jobs

  1. Orr - Schematic Diagram.
  2. Sasha - Math behind, the models.
  3. Yin - Extensions to make awesome.
  4. Hing - Describe the article that is there.
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Papers

  • (CHEMOTAXIS) http://www.princeton.edu/~wbialek/PHY562/chemotaxis/chemotaxis_refs.pdf
    {Note: A list of references on bacterial chemotaxis.} --dna1112 19:20, 4 Jun 2005 (EDT)
  • (QUORUM-SENSING) Design of artificial cell-cell communication using gene and metabolic networks. Bulter T, Lee SG, Wong WW, Fung E, Connor MR, Liao JC. [1]
    {Note: Uses acetatic acid as diffusible signaling molecule.} --dna1112 19:19, 4 Jun 2005 (EDT)
  • (QUORUM-SENSNG) Programmed population control by cell-cell communication and regulated killing. You L, Cox RS 3rd, Weiss R, Arnold FH. Nature. 2004 Apr 22;428(6985):868-71. [2]
    {Note: Uses AHL, a chemical used by another species of bacteria for QS, as signalling molecule.} --dna1112 19:19, 4 Jun 2005 (EDT)
  • (QUORUM-SENSNG) Regulation of gene expression by cell-to-cell communication: acyl-homoserine lactone quorum sensing. Fuqua C, Parsek MR, Greenberg EP. Annu Rev Genet. 2001;35:439-68.{Note: A general review article on how AHL quorum sensing works.} --Orr 23:03, 5 Jun 2005 (EDT)
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