840:153g:Projects/project2/2008/10/30

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Not doing very good

So today what we did is set up a digestion reaction that will take our wintergreen part (Bba_J45120) and cut it with restriction enzymes that will make it biobrick compatible. Upon cutting the part with the enzymes we will then run a gel and cut the bands out of the gel inorder to purify the part from all the PCR and restriction enzyme products. Also today Diveena and Surabhi went around and began asking people to smell the samples of E.coli that we had grown in Salicylic Acid to begin to characterize the part. We want to know at what concentration of salisylic acid the strongs smell of wintergreen is produced. We got interesting data that is hard to describe right now. What I think we need to do is ask more people and see if a diffinative trend appears. Right now I think we have to small of a sample size.

The gel that was ran. Did not look like it was suppose to. I got a text late in the afternoon saying that the gel did not turn out like we had hoped. What does that mean? I do not know because I have not seen the gel and I did not get a chance to talk anything over with my group about what we should do next.

-Corey-

As mentioned by Corey, the gel did not turn out as expected as the band size observed for part 5001 is bigger than what we should be getting, it is possible that the part in the plasmid is not the biobrick that we are interested in. After discussion with Axel,we discovered that even with the correct UV promoter part 5001, the complete composite biobrick with the promoter and the wintergreen odor generator would not be biobrick compatible as it would not contain all the standard prefix and suffix needed as the primers that was initially designed did not contain both prefixes and suffixes (Xbal and EcoR1 on the left and Pst1 and Spe 1 on the right) We are faced yet with another challenge if the UV promoter is not present in the plasmid sent by iGEM. The results that is being obtained with the UV promoter amplification could be a results of the primer amplifying a region on the genomic DNA from E.coli that was carried over during the plasmid extraction step. Therefore, another plasmid extraction needs to be done to make sure that the amplification is not a contamination of genomic DNA that is being amplified. If it does not work,we would have to resort to another promoter as well as work on possibly sequencing the pcr product of part 5001 (UV promoter)to determine if the sequence we are interested in is actually present in there. The bands on the gel was cut out and the pieces was frozen away.

-Diveena-