Summer Session-Material Review

Hello! Welcome back to my blog. This week, I spent most of my time learning more about the technology I am using and reviewing various published papers on the nuances of the 16s gene. However, I did manage to get some time in the lab; I ran an experiment to test the effect of a lower agarose gel concentration on visual review of DNA samples under UV light. Thinner gels can increase the speed of particle travel during an electrophoresis, but what I was particularly looking for was a reduction in the "warbling effect" I have been seeing in the sample banding of my 1% gels. So I changed my concentration to 0.7 % and ran an electrophoresis to measure the results. The gel concentration did not make a difference in the banding or migration rate of the samples I tested.

From there, I moved on to running a PCR on my gram positive bacterial species using primer set 4-CAT-f and 4-CAT-r. I just wanted to repeat some earlier data by replicating previous methodology, so I cultured a new set of bacteria, performed an extraction, ran the PCR and gel-tested the results.

From the pics I took post-PCR, it appears that amplification was again successful. This is a good turn of events, as it allows me to proceed with the next phase of my project. Namely, sending my samples out to be sequenced so that I can determine which region of the gene was targeted. More on that in a later blog.

Until next week, live long, and prosper.

Photo: PCR samples; pic shows ladder in well to the left; remaining six wells correspond to gram positive bacteria used in this study.