oops. Day 3 and Day 4

11/28/11
Well I just noticed that I didn't make a post for my trip to the NYSM over break.  On Monday over break, I headed up to the NYSM and Dr. Kirchman and I quickly got to work. We went to the ancient DNA lab where we got some Taq gold. Taq gold is a high quality solution used in PCR. Now, what is PCR? Well, since the pieces of rail tissue we used were so small, there was not a lot of DNA in them. What PCR does is it splits the chain of DNA in half using heat(I think I am going to try to draw a picture on paint and post it).  DNA is made up of G's, C's, T's, and A's. The PCR adds ends to the DNA, and then since we know that G goes with C and T goes with A, during the PCR, G's C's T's and A's are taken from a 'soup' mixture of monomers and matched accordingly with each half strand of the DNA, forming two separate, yet identical strands of DNA.  The DNA is then cooled again so that the newly added strands can attach to each previous strand. This process the repeats as the DNA is heated again, and the amount of DNA doubles each time. We completed the long PCR with our rail DNA and then made a gel so that we would be able to see the DNA.  The gel is basically what it sounds like.  After mixing a few chemicals whose names escape me and adding a mutagen (I believe it is ethidium bromide) which allows the DNA to be seen under an ultraviolet light. After making the gel and allowing it to harder, we put the results of the PCR in the wells in the gel along with some dye.  We then ran electricity through the gel. Since DNA has a slight negative charge, it moves from the negative side of the gel toward the positive.  The gel works as a sieve, however, allowing smaller sized particles to move through the gel more easily than the larger.  However, when we viewed our rail DNA through the camera on top of an enclosed box that shone ultraviolet on our gel, we didn't see any DNA. It appeared that our rail DNA extraction had been a failure.

12/5/11
The next week, Dr. Kirchman had some exciting news.  He had tried the PCR on the thrush DNA we had extracted our first week and had found that after running the PCR on the thrush DNA, the DNA was not visible under the ultra-violet light.  He had also noticed some 'snowflakey' stuff in the tubes containing the DNA.  This means that the PCR had done something to the extracted DNA or reacted strangely to something in our quick start DNA kit we used to extract the DNA from both the thrushes and the rails. Dr. Kirchman ran the rail DNA through a filter, but the 'snowflakey' stuff remained in the tube. However, the 'snowflakey' stuff may not even be the cause of our problems and some other chemical causing the problems may have been successfully filtered, leaving DNA that would be visible under our ultraviolet light.  We spent today doing PCR with the filtered rail DNA along with other bird DNA simply to test how the PCR affect other bird DNA samples. I even got the chance to make a gel (almost) all by myself :).  While hopefully the filter solved our DNA difficulties, I will not know until next week to see if the new PCR results were successful!