AHHH overwhelmingness in the lab :)

1/23/12
I still keep forgetting that it is 2012 :) Anyway, there were luckily no transportation mishaps for me today and the shuttle ride to and from the internship went smoothly (hurrah!). When I got to NYSM, Dr. Kirchman and I quickly jumped into the lab and I got to make another gel for another gel for a PCR. Sadly, me being a newbie, something had to go wrong. I'm sorry I can never remember the names of anything, but the powder that mix with water which you heat up in the microwave that cools (after you throw in a mutagen) and forms the gel... well there was a microwave incident. When you heat up the powder water mixture in the microwave to get it to dissolve, it gets VERY bubbly VERY quickly. I was struggling trying to see through the microwave door and well, I allowed a little volcano to form in the microwave. After cleaning up the bubbly over spill Dr. Kirchman had me pop in a strip or two of some gel from old PCRs into the flask containing what was left of our water powder mixture. You can melt down strips like these and make an entire recycled gel if you have enough, but we just melted a couple in what was left of our mixture to create what was fairly close to the original amount. After putting a little too much of the buffer (the buffer is just water, but the really clean sciency water :D) in the gel holding device (I really couldn't tell you... i think the brand is called owl maybe?) I poured my melted water powder mixture into the container and put in a comb to make the wells in which we would put the DNA.
Since we had to wait for the gel to set, Dr. Kirchman took me to the range (where they keep all the skeletons and stuffed animals) to help him find some specimens he would be showing to a class later that day to illustrate the evolution of limbs. For example, Dr. Kirchman's friend, Joe, who also works at NYSM showed us a mole humerus. The mole's arms had adapted so that they were perfect for shoveling dirt and the humerus was at an angle so it would be easier for the mole to scoop (http://www.mnh.si.edu/mna/full_image.cfm?image_id=834 <-- mole arm :D).
After freeing an emu from a crate (with the help of a screwdriver, scissors, and wire cutters), we went back to the lab to see that our gel had turned opaque and was ready for us to place the DNA in the wells. Putting the DNA in the wells, however, takes quite a steady hand. My hands are not that steady. However, I was doing pretty well until Dr. Kirchman commented on how well I was doing. With my chest puffed out as I began to put the 7th sample of DNA in a well..... I pushed the pipet down into the bottom of the well too hard which meant the DNA couldn't come out of the pipet and when i removed the pipet the DNA splooshed everywhere but inside the gel. Whoops. Dr. Kirchman quickly whipped up another sample of that same DNA, fixed my mistake, and I finished the last two wells successfully. Overall it was a good day in the lab, mistakes and all, because practice makes perfect :). Hopefully it will just be a little more perfect next time.

PCR pictures :D

This is PCR 169 and it is the first PCR where we were actually able to see some nice rail DNA without the scary wiggly streaky things (possibly caused by the snow-flaky substance in the DNA). After Dr. Kirchman cleaned up the DNA removing any proteins our other materials that could have contaminated it during extraction, we were able to see the DNA even though it wasn't very pretty. The first test tube with the nicer looking DNA is a control that contains a DNA sample that we know will work to make sure that if the DNA had not shown up, it would not have been a technical error.

This is the cleaned up DNA from PCR 169. Dr. Kirchman cut out the DNA from PCR 169 from the gel and cleaned it up one last time. As you can see, it worked and the DNA is much... prettier :). The first tube is a control that is supposed to work every time, and it did. The test tubes with the very bright DNA are the tubes with the better-quality DNA.  The tube on the end separated from the others is a sample of DNA in a different gel so that we can make sure that there is not a problem with the gel that would cause a problem with the DNA.

Back from Break

1/16/12
I am finally back from break, so we spent the day in the lab catching up and refreshing. Dr. Kirchman had a set of books on birds and I was able to learn a bit more about rails. Rails are literally found ALL over the world, but we are focusing on the rails on the Solomon Islands. Even on these small islands, the range of diversity in these birds is amazing. The birds we are studying are categorized in the species Roviana. On the evolutionary tree of life (more scientifically known as a phylogenetic tree) Gallirallus rovianae is a decedent of the buff-banded rails or Gallirallus philippensis. Here it gets a little more tricky. A scientist (whose name I cannot recall) traveled to the Solomon Islands. A native had caught a Roviana rail, but had eaten it. However, he skinned the bird and salted it and then presented it to the scientist. The scientist recognized this to be a new species of rails, but also realized that not all of the rail's feathers had not grown in and it was therefore not an adult. Baby rail's molt patterns change from when they are young to when they grow up, the same way a duckling is yellow and fuzzy, but has different coloring as an adult.
The Roviana rail had similar coloring to the buff-banded rail and was therefore placed as a decedent of the buff-banded rail in the rail phylogenetic tree. However, since the Roviana rail is not mature, the similar coloring to the buff-breasted rail cannot be relied upon. The Roviana rail also has many similarities to a rail called Nesoclopeus woodfordi. By processing the DNA we have now collected from our Roviana rail, we will be able to determine where the G. rovianae belongs on the phylogenetic tree (I hope I'm not saying anything wrong here :O).
Our next step in our rail project is sending the DNA off to be processed and sent back to us with a nice long list of Cs, Ts, Gs, and As. However, it is cheaper for us to send a case of 96 DNA samples than it would be to have to send the 24 individual samples we currently have, but that just means I will get to spend more time in the lab! We currently have mitochondrial DNA from our Roviana rail. Mitochondrial DNA, though, is the DNA you received from your mother, and therefore only contains half of your genetic makeup (since it does not include the father's DNA). We are going to extract nucleic DNA that contains the rail's entire genetic makeup and fill up the rest of the case. I also have some exciting pictures of the results of our PCR under the ultraviolet light which I will explain above :D