From 2006.igem.org

Discussion

Hi eveyone! Since we're not going to have a meeting for a while, I thought it would be a good idea to post our ideas here. - Horia

Alright, it's 1:39am...and I've come up with some random idea as I was studying for my bio exam. During the last meeting, we talked about pH and voltages to control protein regulation. Would it be possible to connect those two ideas (pH and voltages)? I am pretty sure the intracellular function changes as pH changes (like in plants, certain enzymes get activated as pH drops after hydrolysis done by certain hormones) and this might have some effects on the voltage gated channels on E.coli and allowing different influx/eflux of ions that would manipulate activation of protein synthesis. I haven't looked up on the web to see what exactly E.coli do in different situations yet..but, I wasn't really too keen about using wire to generate voltage on that little E.coli...the voltage idea itself is brilliant, and I thought this can be incorporated into pH with the use of voltage gated channel...OR, pH(input) can regulate the voltage difference (output)to create different musical notes (referring back to the last meeting)..Alright, back to studying. - Jieun

Hum, 1:54 am, so it would either be " Note -> Voltage -> pH -> Function" or " Function -> pH -> Voltage -> Note". I guess the question is how to transform voltage into pH or vice versa. Also which ion channels would open in response to a change in pH and how that would affect function. I remember Belinda (correct me if i'm wrong) saying something about using a vesicle filled with a chemotactic agent whose pores would open in response to applied voltage. Maybe if we filled them with carbonic acid or something that would do the trick. I read something similar here (with glucose): http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=6261800&dopt=Abstract Josh talked about using a keyboard and i thought that if we somehow drew a small musical staff on the bottom of the petri dish, we could have the bacteria cluster at different points on the staff depending on which notes we played. Thus we'd write out the music! We could have an electric grid or just individual electrodes that would determine every possible point, and these would trigger the release from (anchored) vesicles of an aggregating agent ( Sodium Fumarate?: http://web.mit.edu/biophysics/papers/PNAS2003b.pdf). To have the cells cluster at the right spots we could have small wells for each horizontal bar on the staff, so that the next note won't influence the previous cluster (i'll try to draw a picture tomorrow). I don't know how big the clusters get so I don't know if this whole thing is feasable... We also talked about using an oscillator (between two colours?) to do a sort of light show. I guess I'll have to read more about those.. It wasn't in any bio class that I took, that's for sure :P - Horia

Hi- I was just searching the internet for genes in e-coli that are senstitive to pH changes and I happened to read about the yfid gene. The article basically said that expression of this gene (which was attached to a reporter gene) was upregulated 3-5 fold when placed in an acidic environment during anaerobic conditions. For example, when the pH of the cytoplasm reached 4.4 the expression of the gene was strongly induced. So therefore, I was thinking that perhaps attaching a GFP gene or some other flourescent gene to the yfid gene could help us visualize pH changes. The link to the article is http://mic.sgmjournals.org/cgi/content/full/148/4/1015 -Ashwini

That's pretty cool. I guess it would help in the pH->function part if we're going to do anything along those lines. Also, I was wandering if anyone was going to go to the meeting tomorrow. If so, could someone post what was said for those of us that can't make it? That would be really appreciated, thanks! -Horia