Weekly Discussions

19 January 2010

Why make something noisy?

• The benefit of sampling
• or maybe trying every ombination along a spectrum
• a maze
• Minesweeper? - except a wrong turn can't be completely detrimental to the whole system .... maybe though - aging / death discussion

Positive feedback loops --> bistable, bimodal phenotype

• ex. S. cerevisiae with galactose (Acar paper) - have 2 positive, 1 negative - negative allows switching between states
• perhaps the two states can be complementary to each other
• random on/off transition
• barcodes? decoding, decrypting - combination lock-ish - bacteria as a random number generator - stops when it fits the "slot"

Meeting with Dr. Campbell

• went through papers - paper simulating how noise can continue an oscillatory system
• positive feedback loops are important
• Minesweeper --> maybe Battleship
• the aging papers Dr. C sent - thinking can somehow randomly switch something on, if beneficial to survival @ that time, will select for those and kill the others
• maybe some cell differentiation using +/- feedback
• maybe some antenna-ish like sampling - a Biosensor - cell has lots of sensors, randomly sample for something, if detect something with one of the sensors then report...do something else while other cells can keep sensing

25 January 2010

I still like the oscillatory idea - noise driving oscillation --> What is oscillation good for? Combining oscillation and quorum sensing - synchronize system

Biosensors = about the promoter - want sensor up/down (on/off, like an antenna) from cell to cell to sense environment --> can maybe start positive feedback loop to amplify report / signal

Possible design: sensor promoters that are repressed by LexA, like a cap. Have RecA (protease) that cleaves off LexA from some of the sensor promoters and not others, noisily. Or perhaps hin/hix system can randomly flip some promoters on (correct direction), some off (incorrect direction).

Perhaps use quorum sensing to get coordinated response from cell population - if one cell senses, Lux operon activated - tell other cells to... do something Maybe turn off one of their sensors/reporters?

One of the problems with fluorescent proteins according to the biosensor articles is the detection level - need a lot of it. Perhaps some positive feedback loop here could induce differentiation by noise level? (bistable noise threshold)

Report sensing by inhibition / loss of signal - could have sensor promoter transcribe a protein to degrade reporter - if after a certain time, protein not degraded, then the degrader is degraded (kind of like the noise aspect of the bacteriophage lambda system)

Could have biosensors to mark bacterial communication or movement?

In meeting: Dr. C - what would be the purpose of making this a noise-based system versus always having all sensors on? Don't know.

10 February 2010

I read the aging articles this week, and I thought particularly the Nystrom review was helpful/ thought-provoking. I thought perhaps it would be interesting and useful to create a system that could be applied to a number of different synthetic devices in order to control the noise threshold, and any cells running the device outside of that noise threshold would die, based on the error catastrophe theory.

We talked about this and ppGpp in meeting. Sigma factor competitive binding could have a strong and useful noise component. Random number generator is also a viable idea. Perhaps using sigma factors with this idea, having competitive binding between two reporters as a binary system. Dr. C suggested in a binary number system, cells could be run through a flow cytometer.

One of the oscillatory system articles I read mentioned superconducting junctions - which on the surface sounds interesting and perhaps something cells could do. I'll look into it.

17 February 2010

I read more about the error catastrophe theory and ppGpp this week. (p)ppGpp is very important to the cell, in many species - which means it can be very useful, or very detrimental to mess around with and very tightly regulated, which to me does not lend itself nicely to a noise study. It's still classified as a potential useful part on the chalkboard page.

We began the meeting talking about ppGpp. Dr. Campbell agrees it is still a potentially useful result, and since it has a cofactor DksA, perhaps even though induction of ppGpp is a stringent response, there is a noise factor in the expression/availability of DksA. We should look more into the regulation of DksA and the synthesizers SpoT and RelA. We discussed cells "flipping" into senescence vs. growth and division cycle:

• What if we introduced a toxin that could kill all rapidly dividing or growing cells --> selecting for cells that have randomly flipped into senescence
• Perhaps could synchronize the cultures - would involve getting them all to the same Time 0 point in the cell cycle (I'm pretty sure I've read a yeast paper like that, or there's also something like that in the Genomics textbook, probably around the topic oscillation - will look up)
• Can we select cells based on their flip rate (senescence / growth)? Purpose?
• Make Baby Boomer Bacteria - cells that we somehow stop at a certain point in cell cycle so that they never divide --> get really old cells - perhaps use some sort of negative feedback loop?
• There is a drug that causes cells to keep elongating without dividing (get from Dr. C or look up)

Could we do something that involves elongation, the separation of some plasmid & transcription factor randomly into dividing cells - those that have both... Or conjugation - when cells elongate or move around and make contact with another cell something happens...

Some ideas of Dr. Campbell's on the way home....

1) What if we utilized transposons for random events? Perhaps placing Tet resistance downstream of random genomic loci?

See this link http://www.bio.davidson.edu/Courses/Molbio/MolStudents/spring2010/DesPain/Transposase.html

2) What if we had 20 strains of knockout E. coli and each one could not make one amino acid or nucleotide? Then as the cells got near each other, they might be able to absorb the missing metabolite and grow faster than normal due to limited nutrient agar? As cells congregated, they would make more of each others missing metabolite and the largest, most diverse mass of cells would grow the quickest?