Team:LCG-UNAM-Mexico/Notebook/2008-May

Preliminary Projects Group Presentation (2nd Round)
Discussion of Papers & Ideas
Sprinzak & Elowitz, 2005.

Combinatorial experiment.
Three TF and 5 binding sites.
Combinatorial and phenotypes analysis.
With a few well characterized elements much can be done.

Experimental Technique: Promoters recombination.
Suggestion: PCR to avoid direct recombination.

It is not enough to have the network topology, the context also influences the outcome.
We need to check whether the module works in the desired conditions. Two modules working separately doesn't mean that they will work when joined together.

Next steps, future models:
-Protein level phosphorylation (example: Phytocrome found in cyanobacteria that get phosphorylated when activated with a specific wavelength and eventually trigger the activation of TF.
-miRNA (only in eukaryotes, not found in yeast)

Sequence-specific Ribosomes. (few well characterized)

Repressilator: Three genes that are repressed among them.

Signaling cascades not exploited yet. Response time delay. It is mentioned as the simplest system. The noise is accumulated in these systems.
Design a signaling cascade and see how noise affects and speads throughout the system. Compare the noise of a two element cascade with the one of a three-element cascade.
Evidence that a noisy system, to reduce noise introduces noise into the noise, and as a result the system become ordered. Increase copies of the elements and see how does the noise is affected. Theory says that noise should decrease, see if this system converges to a deterministic system.

Compare strains with different protein production ratios. EXPLOIT MORE THIS POINT. See if it is easy to do. However in this system it is very unlikely to find multi-stationary states.

Measuring noise is a potential problem, Do we have access to technology to measure it?

Investigate the difficulty to study the competition between the two enzymes for same metabolite in a metabolic pathway.

In positive circuits it is possible to see multiple states.

Ideas:
-Counting in module 2 (even and odd) 2nd option
-Mosaic rejected
-Singing bacteria. Researching
-Pong Researching
-Balance between populations 2nd Option
-Counting days rejected
^sign-sensitive delay

Pong- Research
Possibilities
* Bacteria motility.
The cell motility trigger a repellent in the closer cell population, along with a reporter, then it would move to the second cell population, which will share the roles.

Repellent -> weak organic acids such as formic, acetic acid, benzoic, and salicylic [works by decreasing intracellular pH]. Amino acids as leucine and valine, indol. Also alcohols, polyols, and heavy cations (Co and Ni).

The stimulus is detected by a membrane receptor (MCP methyl accepting chemotaxis proteins) TSR, Tar, Trg, Tap [These 4 described in E.coli].

The cascade of signaling is initialized when there is a conformational change induced by ligand, in the cytoplasmic side of the protein. This change is recognized by a complex formed by CheA-CheW. CheA is a kinase that is inhibited when ligand recognizes attractors and is activated when repellent is present. CheA donates its phosphate to CheY and CheB, CheY-P interacts with a complex that has a switch function at the flagelar base engine, this switch is responsible for the change between CW [clockwise] and CCW [counterclockwise]. Studied in S. thypimurium and E. coli.
We still face the problem of degrading the repellent [activator], and the noise accumulation.

May 12th(summary)- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---- ----- --- --- ----- ---- ----- ------ ---- -- -- --- ------- - ----- --- ---- --- --- -- - ------ -- ---- --- --- --- -- -- ----- ---, --- - - --- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---- ----- --- --- ----- ---- ----- ------ ---- -- -- --- ------- - ----- --- ----.

May 21st(summary)- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---- ----- --- --- ----- ---- ----- ------ ---- -- -- --- ------- - ----- --- ---- --- --- -- - ------ -- ---- --- --- --- -- -- ----- ---, --- - - --- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---- ----- --- --- ----- ---- ----- ------ ---- -- -- --- ------- - ----- --- ----.

May 28th(summary)- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---- ----- --- --- ----- ---- ----- ------ ---- -- -- --- ------- - ----- --- ---- --- --- -- - ------ -- ---- --- --- --- -- -- ----- ---, --- - - --- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---- ----- --- --- ----- ---- ----- ------ ---- -- -- --- ------- - ----- --- ----.