Big birds and bitty bones

4/23/12

Today Dr. Kirchman and I had another fun day in the lab. We decided that a few more bird skeletons were ready to emerge from the ammonia solution and be boxed and labeled. However, this time, I would have to do a little bit more of the work by myself. While one jar containing a bird skeleton was rinsing in the sink to wash out all of the stinky ammonia solution, Dr. Kirchman had me label some boxes and place bird skeletons we had done the previous week inside of them. While I was very nervous about the quality of my handwriting (which ironically gets much worse whenever I'm worried it is going to look messy) I successfully completed two boxes. Then we picked through the bird in the sink, making sure none of the bones were missing. Then we had to remove any remaining tissue or tendons from the bird. This, luckily, was not too difficult with the two smaller birds we did. However, after cleaning up those two birds and leaving them to dry on the blotting paper, Dr. Kirchman and I were only left with two humongous birds. I reluctantly dragged a giant bird skeleton into the sink, uncertain about the arduous task ahead and began to rinse it out. While the big bird :) was rinsingDr. Kirchman asked me to label the bones of the three smaller birds we had just put in the boxes. Each bird has an identification number and that identification number needs to be labeled on as many bones as possible so that in case the bones were dropped, one would still be able to identify which bones went with which bird. The problem: all three of the birds I worked on were minuscule.

The bone I am holding which is the skull was one of the largest bones I had to write on. I think I wrote some of the tiniest numbers I ever had in my life, and luckily I wrote those numbers successfully. Dr. Kirchman even jokingly suggested that if I ever dropped out of school, I could get a job labeling bones :). I truly did not know that my handwriting could successfully be that small. After labeling all three skeletons, the big bird was finally all rinsed off. Dr. Kirchman and I cleaned up the skeleton which was much harder to clean that the smaller bird skeletons. We even needed scissors to cut the tendons and even then it was difficult. Dr. Kirchman and I removed as much of the tissue and tendons as we could and then put it back in the jar and added some fresh ammonia solution so that it could soak for a little longer. All over all, it was a pretty fun day in the lab.

Perfecting PCRs

4/16/12
Today Dr. Kirchman and I got to do some lab work (luckily, I had even remembered to bring along a pair of closed-toe shoes to replace my flip-flops). Dr. Kirchman is also working on a project with spruce grouse so today I helped him run a gel. A previous PCR on the gel hadn't turned out so well so Dr. Kirchman decided to try and run a longer strand of the mitochondrial gene of the spruce grouse. To do this, we first needed to collect a bunch of primers so that they would be able to sequence the strip all the way from one section to the next. After going on a primer search through the freezers in the lab, we finally had enough and I started to make a gel. There were a lot of leftover gels from previous uses so I carefully (no explosions this time) melted down the gels in the microwave and then added the mutagen. Since we had 16 different DNA samples, I used two different combs for the same gel so that we would have enough slots to run all 16 samples at once. After the gel turned opaque and congealed, I was able to mix the ultraviolet sensitive dye with all 16 samples and squirt them into the gel with no mistakes and no desperate cry for assistance. I believe I am now worthy of the title of pipet master-in-training. When Dr. Kirchman and I went to run the gel however, there were some difficulties. The machine did not seem to want to send any electricity through the gel! However, after some fiddling around, we finally added more buffer which did the trick and the machine began to conduct electricity through the gel.
Since it takes 40 minutes for a gel to be successfully run, Dr. Kirchman and I went to the prep lab and after giving Joe a quick hello, I started cleaning my skeletons and putting them into boxes. Fist we put the skeletons on a metal container with holes in the bottom that let the ammonia fall through, but keep the bones from going down the drain of the sink. Next we put the bones on blotting paper and let them dry, sorting through the bones and extracting any remaining tissue or tendons from the skeleton. Once the skeleton was dry, it was put in a box corresponding with its size and then properly labeled with its scientific name, where it was found, when it was found, and other important details of the like.

Hello Joe!

When Dr. Kirchman and I went back to the lab to check on our PCR, it worked very well to our surprise. Every single one of our DNA samples was showing up and all of our negative controls were not showing anything. After marveling at our perfect PCR for a couple seconds, my time was up and Dr. Kirchman and I had to clean up. All over all it was a pretty good day in the lab with a minimum of technical difficulties and an abundance of success.

Long weekend

4/9/12
Today was long weekend so I did not meet with Dr. Kirchman :(

Charming Charts

4/2/12
Today Dr. Kirchman and I spent another day working on graphs for the rail project. These were no mere data tables however, but complicated logarithm and other confusing number graphs. First, I'll show you the graphs just to give you an idea of what they look like:

Unlike the data table I made last week, these graphs add a helpful visual component to seeing trends. Before I went to NYSM, Dr. Kirchman had already arranged the data I had put in my data table last week through some complicated mathematical process that was beyond me that basically summed up all the data and measurements we had for an individual bird into one number so that the data would be in the correct form to use a program. Then, we would try and use different measurements to show a trend in the graph. For example, in PC1 vs PC2 (physical characteristic one versus physical characteristic two), Dr. Kirchman and I successfully depicted a trend in flight that is easy on the eyes. As I talked about last week, one can often conclude that a bird is flightless if it has very long leg bones and a small sternum and arm bones. Therefore, for the first graph, the x axis (PC1) deals with the length of leg bones along with other measurements and the y axis (PC2) dealt with measurements of bones dealing with flight such as the sternum, radius etc. Therefore, G. philippensis can most likely fly (which Dr. Kirchman confirmed) and G. australis is most likely flightless (which Dr. Kirchman also confirmed, therefore our graphs were accurate and good to go). The second graph PC2 vs PC3 was also focused on size and the flying capabilities of birds, but since we could not get a distinct trend (since all of the groups are so close together and overlapping) the graph is rather unclear and we decided to move on.  While the graphs may look simple, they actually took up most of my time during my internship, but I am quickly becoming an expert of graphing computer programs.

For the last couple minutes of my Monday morning at NYSM, Dr. Kirchman and I went to see how the skeletons we had placed in the diluted ammonia solution last week were coming along. Since the skeletons looked pretty clean, Dr. Kirchman began to show me how to pick the skeleton clean, removing any lingering traces of tissue or ligaments along with the talon sheaths that covered the bird's toes. Before I could have a chance to try it out, though, we ran out of time :(. Hopefully we will continue the rail project next week and I will be able to finish my skeletons.