Monday, August 21, 2006

RNA becometh DNA day

Today I destroy some DNA and make some more (ie. DNase treat my RNA samples and then reverse transcribe them). I can then do the real time pcr tomorrow, and then western blots to measure Sxy levels during the rest of the week. I am very eager to get this sxy manuscript together, so I will bust my ass to get the results we need before the long weekend. At the same time, I'm going to work more on writting the manuscript - it's hard in the absence of the key experiments I'm doing now, but I will try write outlines to address the possible outcomes and begin to flesh out the discussion. I look forward to writing the discussion because it will require delving into some good ol' RNA regulation work from the microbiology community.

Also, if my real time pcr shows that hypercompetent mutants have higher levels of full-length sxy transcripts, I want to draft up an experiment to test whether WT cells generate just as much 5' UTR RNA, which would suggest that the the hypercompetence mutations allow for full transcript reads, while in WT the transcript is prematurely terminated by formation of the loop. The outcomes of this experiment could be complicated by many things (ie. rapid degradation of 5' ends when they are not followed by a full transcript), so I hope to mine the trp attenuation literature to see how that model was established. A full discussion of attenuation will also be necesarry for the discussion of the paper as we work to solve how sxy is regulated.


At 7:56 PM, Blogger Heather Maughan said...

Is that the working model...that sxy transcription is terminated due to the formation of the loop structure? What about for genes where loops increase their expression?

At 9:57 AM, Blogger Okapia Johnstoni said...

remind me to give you that riboswitch paper on how they tested the lengths of transcripts produced in the presence or (and) absence of specific ligand). I think that this would be a good way to check if there is more then one type of sxy transcript.


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