Blog from James Meyo (#4)

Hello again,
The semester is almost over and I am busy writing up my assignments to ensure I meet my deadlines. The first section of my thesis is due soon and I am currently writing it in small chunks. This will be a very big step towards completing my thesis and I am getting a little anxious as the deadline approaches. The writing process is quite interesting because it makes me slowly realize how I want to state different concepts. This writing experience is very different from talking about my thesis during conversations where I get to modify my language depending on the level of familiarity of the people I am talking to. I am also really excited about thesis café sessions in the library. Thesis café provides seniors with a quiet space to work on thesis with the advantage of speaking to a peer writing specialist. The chai and cookies provided during thesis café also lighten up the mood and make the whole experience much more enjoyable.
In lab, I have had little luck with the sonication protocol after making numerous modifications to the procedure. After improving the precision of the DNA fragments obtained, I am yet to accurately obtain fragments between 200-500bp on a consistent basis. My most recent attempt involved incubating the DNA sample in SDS lysis buffer for different periods and at a range of temperatures before sonication. The aim of this incubation period was to induce cell lysis pre-sonication, similar to the bead beating technique that is known to be effective but expensive. This modification did not result in the desired product, consequently, I moved onto the next proposed procedural adjustment. I plan on using glass beads during the actual sonication protocol with the expectation that the physical force of the glass beads during sonication will effectively fragment the DNA to the appropriate size. The glass beads are between 212-300 microns in size and are acid washed prior to use. These sonication beads have been used to great effect in various ChIP protocols and should prove to be very useful. Last week I ordered some sonication beads and expect to see the effect of this modification in the coming days.
Well, that’s it for now. Cross your fingers for the sonication beads and I shall keep you posted on progress.