From 2006.igem.org

Revision as of 19:19, 20 April 2006

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

Meeting on April 20th-

1. We first just went over what "bricks" are. So they are bascially promoters, genes, regulatory seqeunces that are going to be ordered from MIT.

2. We then started talking about how bacteria can be made sensitive to voltage changes in accordance with the idea presented last week concerning the conversion of sound to voltage. One of the proposed ideas was the use of voltage gated channels in response to a certain threshold voltage. The advantage of this is that the voltage gated channels open quickly and can potentially result in a continuum of current. However, how can an influz of cations translate into something visible? The possibility of proteins sensitive to ions was discussed however there aren't many of these proteins. In addition, the possibility that a cation influx could result in the tranlation of proteins was also introduced yet the problem with this idea is that transcription/translation of proteins is too slow a process for our needs.

3. Two voltage gated channels that Prof. Nadeau has in the lab are MSCL which is sensitive to pressure changes, and NACHBac which is sensitive to voltage changes.

4. The idea of using bacteria to produce a picture was reintroduced. One of the past projects had taken advantage of light sensitive bacteria to produce a picture, and therefore, for us to explore this idea the bacteria has to be sensitive to something other than light when producing the picture. Some sugars like lactose and arabinose as chemical triggers in the production of color in bacteria was suggested. However, diffusion of the chemical triggers and the secreted color would be too fast to obtain a clear image.

5. The idea of putting a catylase into e-coli resulting in the production of oxygen and water was also discussed.

6. There will not be a meeting next Thursday, April 27th. The first day of the Biomedical Engineering 506 class will be on May 2nd and we will meet in room 321 in the Duff building. The class starts at 10 and ends at 1 on MTWR. Prof. Nadeau is trying to get the fees for the summer course waived for iGEM participants by negotiating with certain science departments. So please email Prof Nadeau the department that you are part of as well as the contact information for the head of your department in order to waive the summer fee.

7. The articles "Reconstruction of Genetic Circuits" by David Sprinzak and Michael B. Elowitz, from Nature (November 24 2005,Vol 438) as well as the article "Combinatorial Synthesis of Genetic Networks" by Calin C Guet, Michael B Elowitz, Weihong Hsing and Stanislas Leibler from Science (May 24 2002, Vol 296) were handed out to read.

-Ashwini