Chalkboard of Ideas

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Characteristics to Utilize with Noise

  • Differentiation (bimodal populations)
  • Oscillatory circuit
  • Quorum sensing
  • Aging / Death (selective advantage of noisy system?)
  • Cell to cell conjugation
  • Cell elongation
  • Senescence
  • Flagella - movement

Possible Applications of Noise

  • Noise threshold - if noise level above measure wanted, amplify it causing death to all those cells --> tight controlled system
  1. Maybe tie system to Tet resistance or something similar? - die if too low or too high of output (but tunable by protein threshold, not user)
  • Battleship - randomly survey area until get a hit, spread out from that point
  • Combination lock - random generation of lock, random opening of lock - survey possibilities until something clicks
  • Maze
  • Biosensor
  • Random number generator (perhaps binary - 0,1 = two reporters)

Mechanisms to Use to Create Noise

  • Positive feedback loops
  • Long cascades
  • Transcriptional bursting? (promoter manipulation)
  • Translational bursting? (codon usage, ribosome binding affinity?)
  • Carbonylation of proteins - causes rapid degradation - could be useful in stochasticity in degradation rate

Usable Parts

  • Freed collection of high-noise promoters
  • ppGpp (Guanosine tetraphosphate) - an alarmone nucleotide produced by two synthetases that controls the activity of sigma transcription factors in survival and senescence/cross-protection pathways (competitive sigma factor binding) Con = ppGpp is necessary in many amino acid synthesis pathways, which might be a problem if manipulating ppGpp levels - or might not be
  • RecA / LexA - protease / repressor (could be used as a way to randomly quiet and turn on genes. Con = RecA involved in stress response - impt in wt cells, could be detrimental to manipulate
  • Lux operon - quorum sensing - synchronized behaviour