Talk:Team:KULeuven/Concreties

=Oude ideeën=

Andere mogelijkheden

 * There is a BioBrick (BBa_I765001) that is induced by UV-light. This would be perfect: only UV light could than trigger our system. This BioBrick is not confirmed to work, and there is very little information availabla about it. I doubt its proper working, however.


 * Harvard 2005 also did something with UV. It involved the lambda cI repressor, and resulted in UV light switching something on. I do not (yet) understand how it works. See http://openwetware.org/images/8/86/Doucette_et_al._2006.pdf.

Idea 1


This is what I found (up to now).
 * In the paper of Shen-Orr, the example of the feedforward loop with AND-gate is the well-studied Ara-operon (This can occur when X and Y act in an ‘AND-gate’−like manner to control operon Z, as is the case in the araBAD operon in the arabinose feedforward loop)
 * Is dit het enige voorbeeld dat ze aanhalen in shen-orr? misschien is dit systeem nogal moeilijk omvormbaar naar een specifieke filter vermits cAMP nogal een belangrijke rol speelt in de cel – het idee was dan ook om de input van X te veranderen in een induceerbare promoter naar keuze, bijv een OmpR afhankelijke als we het systeen van levskaya met de lichtpuls gebruiken -- IT
 * The input signal is of course arabinose. We will need AraF(GH?) to transport it efficiently from the medium into the cell.
 * What is depicted (see figure) as X, is cAMP (+ CAP)
 * Y is AraC
 * The AND gate is the “unlooping” of the DNA strand in de Ara operon. This happens only in the presence of both AraC bound to arabinose, and CAP-cAMP
 * Product Z are in a WT Ara operon the AraBAD proteïns, but can of course be changed to eg. lactonase. The araBAD genes are located downstream the pBAD promoter, which is activated by the “DNA unlooping”.
 * Kan Z ook een tussenproduct zijn dat enerzijds de inverter ingaat richting HSL productie en anderzijds, na het ribolock-key systeem, lactonase productie aanstuurt -- IT

Note that Y is also to be stimulated by arabinose, so the scheme is actually a bit more complex than the easy scheme depicted in the Shen-Orr paper

Some problems

 * I cannot find literature about the dotted purple arrow: is it überhaupt existing? The article of Shen-Orr suggests it does.
 * cAMP concentration is depressed by glucose, so maybe the purple arrow means that the concentration of glucose is negligible compared to arabinose. This might however not be good enough.
 * What could be done, is making sure that not only AraBAD is made upon (eg) flashing with a light (Austin iGEM 2004), but also making a repressor for the phosphotransferase system of glucose transport. However, then, the pink purple arrow should be the full (non-dotted) pink one.
 * I did not (yet) find the BioBricks of the Austin 2004 team for the input signal.
 * I believe they can be found here: http://partsregistry.org/Featured_Parts:Light_Sensor -- IT
 * Adenylate cyclase inhibition is coupled to the flux of glucose through the glucose PEP:phosphotransferase system . This means that external glucose concentration regulates cAMP production. This is I think a major problem: how do we arrange the system so that it becomes dependent on cytoplasmatic factors?
 * Vandaar dat ik hoop dat er nog een ander systeem in E.coli gekend is dat dit netwerkmotief heeft, daar waren we een beetje vanuit gegaan... -- IT
 * Ik denk dat het systeem zoals hierboven uitgelegd moet lukken. Prof. Winderickx vertelde dat cAMP zowel afhankelijk is van intra- als extracellulaire glucose-concentratie. Dat lost het probleem hier geformuleerd op. Daarenboven klinkt de paper die hieronder geciteerd staat zeer veelbelovend, zij hebben immers al uitvoerig het ara-operon in min of meer hetzelfde perspectief als hier beschreven bestudeerd. Bmoeyaert
 * If cAMP is not degraded fast enough, could cyclic nucleotide phosphodiesterases catalyse this process of degradation?

Interesting reads

 * http://www.weizmann.ac.il/mcb/UriAlon/Papers/The%20Coherent%20Feedforward%20Loop%20Serves%20as%20a%20Sign-sensitive%20Delay%20Element%20in%20Transcription%20Networks.pdf

Idea 2

 * schema filter 1
 * Is probably not working, because the T7 polymerase (even with tag) is much more stable than the RNA Bmoeyaert