This week has been devoted to getting ready for the end of the semester, but I did manage to run a couple of gels on my PCR samples from last week in order to verify the results I obtained.
I am glad to report that this latest round of gels showed that DNA amplification did occur in 8 of the 9 bacterial species I tested. This is a slight change from the 9 reported last week, but still an excellent result. The reason for the discrepancy in that one organism? I suspect the original well correlating to that species that showed DNA may have simply had some bleed-over from an adjacent well. This shouldn't happen in a perfect scenario, but in a real-life lab situation, odd things and errors occasionally happen.
At any rate, this result does not yet indicate that amplification is not possible for the species in question, Pseudomonas aeruginosa. Pseudomonas differs slightly from the other organisms I am testing, in that it forms biofilms which can impede DNA extraction from the cell. In fact, during the extraction process that produced the series of samples I tested for this experiment, I did not see visible chromosomal threading during the alcohol precipitation phase of the extraction. While a lack of visible threading does not automatically indicate the absence of DNA, it is a possibility that cannot be ignored. Therefore, I must adjust the extraction protocol for the presence of biofilm, conduct another extraction, and re-run the PCR experiment on Pseudomonas a couple of more times in order to rule out the possibility that my first round of experiments may not have produced any DNA for amplification.
Such additional tests, however, will have to wait until the summer session resumes, as our last week of lab time is upon us.
Until then, have an excellent end of the semester. See you soon!
Image credit: imgbuddy.com
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