The wonders of Molecular biology

Monday was an interesting day. First was a lecture about 16srRNA and why it is used as the main way to determine if organisms are different species. I found out that 16s is around 1500 nts long. We were shown were on the sequence some of the more common primers would go and in which way they would amplify the sequence during PCR. Upon returning to the lab some of us began spotting the remaining 10kGy gamma radiation treatment along with its unirradiated control. Others began preparing to run out their recently isolated DNA from their serial dilution isolates. Upon completion of my groups gel there were some isolations that worked fine and others that appear to not have worked this was observed by the presence or absence of a band in the image. We can not completely say they did not work until after the PCR is checked since we could have just isolated too little DNA to show on the gel. I have to go back and check but there were some isolates that were really difficult to remove from the agar and I believe that those might be the ones that possibly did not work. I did not get to it during class but we were also given the task of taking all the available DNA sequences for our group’s main 26 isolates and putting them into EZtaxon and BLAST to see what organisms they were most related too. The biggest difference between EZtaxon and BLAST is that EZtaxon compares against type strain sequences only and BLAST compares the sequence to any sequence in the data base. My results show that of the 10 isolates that we do have sequences for at this time 9 are of the Genus Blastococcus and 1 is of the Genus Modestobacter.
Wednesday we had a lecture about PCR. During the lecture we had a brief overview of PCR and were given the amounts of the constituents of a 50μl PCR reaction. The constituents for this PCR reaction are Buffer which already contains the MgCl, dNTPs, diH2O, Primers, Taq, and DNA. When making a master mix always make 2 extra then the amount of DNA sample you have. One of these extra reactions will be your negative control the other is for mishaps when pipetting. Along with the set up of the PCR we also streaked stock plates for our continuing experiments along with an extra 2 plates that are Isolates to be used during Microscopy on Monday My groups Isolates were ones that had come up during the EZtaxon search as Blastococcus aggregatus and Modestobacter versicolor.
On Thursday afternoon was the awards ceremony were I officially received my award.