Chalkboard of Ideas

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