Difference between revisions of "Chalkboard of Ideas"
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* Quorum sensing | * Quorum sensing | ||
* Aging / Death (selective advantage of noisy system?) | * Aging / Death (selective advantage of noisy system?) | ||
| − | + | * Cell to cell conjugation | |
| − | + | * Cell elongation | |
| + | * Senescence | ||
| + | * Flagella - movement | ||
== Possible Applications of Noise == | == Possible Applications of Noise == | ||
| + | * [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Noise_Tuner_Proposal.pdf Noise threshold] - if noise level above measure wanted, amplify it causing death to all those cells --> tight controlled system | ||
| + | # 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 | * 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 | * Combination lock - random generation of lock, random opening of lock - survey possibilities until something clicks | ||
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* Biosensor | * Biosensor | ||
* Random number generator (perhaps binary - 0,1 = two reporters) | * Random number generator (perhaps binary - 0,1 = two reporters) | ||
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== Mechanisms to Use to Create Noise == | == Mechanisms to Use to Create Noise == | ||
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== Usable Parts == | == Usable Parts == | ||
| + | * [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000307 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 | * '''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 | *''' 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 | *''' Lux operon''' - quorum sensing - synchronized behaviour | ||
Latest revision as of 02:31, 16 March 2010
Contents
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
- 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
