Confusing Computers

2/27/12
Today Dr. Kirchman did not work in the lab, but on his computer. The DNA we had sent off was back and sequenced so we spent the day cleaning up the data. To sequence DNA, a fluorescent dye is given to each nucleotide. A computer measures the wavelength each nucleotide produces, and using these wavelengths, can determine the nucleotide that goes with the corresponding color. Primers run in opposite directions that read the DNA sequence. Two primers are used because it takes a little while for a primer to get going so the wavelengths of the nucleotides are really unclear in the beginning. Therefore, if you have two primers that are unclear in the beginning, but are clear at the end and they run in opposite directions, you will hopefully be able to get a clear idea of what the nucleotides are.  However, since our DNA samples of the rail birds were so small, the quality of our DNA wasn't too great, leading to the wavelengths of the nucleotides looking a bit like this:

when in a perfect world, they should look like this:

Basically, what I did today was edit the base pairs. When the computer cannot recognize whether the wavelength is a C or a G, there are other letters (for example R, K, and W) that represent a nucleotide that can be a C or a G or an A or a G. I went through the DNA and tried to make my best guess about what nucleotide matched the wavelength based on the prettier looking primer. Sometimes both wavelengths were messy and had double peaks really close to one another in which case, I would use one of the letters that represented that the exact nucleotide was unclear.
After going through all the base pairs, I then had to cut off the primers at the ends of the section of DNA. I did this by taking the sequenced primers and having the computer match them up at the ends of the sequence. I then simply removed the bases that overlapped with the primer. Lucky for me, the four DNA sequences I did were relatively clean and the section of DNA that Dr. Kirchman and I are using to examine the rail birds is relatively small. I am not going through the entire rail genome (which would take forever to do), but simply a small section of the DNA. Thankfully, I also did an okay job of my DNA cleaning up skills because when Dr. Kirchman and I quickly looked at the sequences, the nucleotides from the rail birds all pretty much matched up. Next week I will not be seeing Dr. Kirchman since it will be spring break, but he hopes to take a closer look at the rail DNA while I am gone and start analyzing it.

Presidents Day!

Did not meet :(

deceased downy ducks

2/13/12
Today, Dr. Kirchman and I spent a fun day in the range (where they keep the stuffed animals and skeletons... and where my emu friend is located) rather than the lab. Dr. Kirchman was going to lecture for a group of ornithology students from Bard College and show them some bird species requested by their professor. Dr. Kirchman took me to the range and showed me where they kept the birds for teaching lessons. Faced with 5 massive metal cabinets, a stepstool, and a piece of paper with about 25 different birds on it, I was off to the races as Dr. Kirchman went to go get passes for when the students came.
All I can say is thank goodness the cabinets were labeled! I slowly made my way down the list, straining to read little tags on the birds' feet and then trying to find the common name to match the one on the sheet rather than the scientific name. Luckily, some common sense came in handy while faced with a giant row of stuffed birds with an overwhelming number of tags in small print. Using my deductive reasoning skills, I was able to determine that when I was looking for a 'purple finch' I should look for a purple bird. I am proud to say that when Dr. Kirchman came back, I had found all the birds on the list but two, one of which was not in the collection, and the other, the ruddy duck, had been mounted on a platform right across from where I was working and had literally been staring me in the face. After moving my emu friend onto a table to create a little more space in the range, Dr. Kirchman showed me a hummingbird skeleton. It was amazing to see how tiny the bones were, and the only larger bones were the skull and the sternum. 
While waiting for the students to arrive, Dr. Kirchman gave me two articles to read. I found one really interesting on climate change and how species were forced to adapt much more quickly, but the other article went over my head and before I could finish, the Bard students arrived. I was introduced to the professor, but while we were waiting in the lobby for some lollygagging students, I ran out of time and had to leave before I could hear Dr. Kirchman's lecture.
Next week is Presidents Day, so Dr. Kirchman and I will not meet, but Dr. Kirchman is going to send our rail DNA to be sequenced and I will have some computer work when I next see Dr. Kirchman as we approach our moment of truth in the rail project.

Reading post!

I was given this reading over Thanksgiving break, so I'm not quite sure what to put as the date (sorry Mr. Calos!)
Anyway, when I went to NYSM over Thanksgiving break, Dr. Kirchman gave me an article that he and some of his peers had written about the North American ivory-billed woodpeckers.
I'm not quite sure how to get the reading on here, but here is a link: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1686174/
Though I admit that some of  the vocabulary went over my head, I found the article to be interesting as well as informative overall. Basically Dr. Kirchman and his colleagues used mitochondrial DNA to compare the ivory-billed woodpeckers and Cuban woodpeckers which are very similar to the ivory-billed.  When Dr. Kirchman decoded the DNA, however, it was found that the two species of woodpecker had split off in the Mid-Pleistocene (more than one million years ago). The North American ivory-billed woodpecker was thought to be extinct until there were reported sightings of the bird in 2005, and by decoding the DNA in this experiment, Dr. Kirchman hoped to create a foundation that could test whether the sighted bird was really an ivory-billed woodpecker by comparing the DNA of a dropped feather or feces sample to his DNA sequence. There were no conclusive conformations of the ivory-billed woodpecker sighting, though, and no feces samples or feather were ever found to confirm a positive match.

<-- woodpecker :)

Gels and pipet tips and sunburns (oh my!)

2/6/12
Today I had a lot of fun in the lab. Dr. Kirchman started off by telling me about another PCR he had run. In order to sequence the DNA, we are sending only the section of the DNA that we need to be sequenced rather than the whole thing. However, we need to make sure that this section of DNA is in good enough quality to be sequenced. Dr. Kirchman tested some of the PCR product and while there was some DNA there, it was very faint and not a bright band of good quality DNA. Today, we ran a larger amount of the PCR product (20 microliters) through a gel in order to hopefully get better quality DNA. This was no ordinary gel though. This was a gel that my own two hands created without Dr. Kirchman even in the lab with me :D I even avoided microwave explosions and air bubbles in my gel, and was deemed worthy of a thumbs up by Dr. Kirchman thanks to my nice work. While Dr. Kirchman quickly loaded some DNA samples from our latest three PCRs (choosing the samples with the highest quality DNA), I restocked the boxes that held pipet tips, improving my hand eye coordination in the process (I've noticed a trend where everything that has to do with DNA is usually tiny).
Then came the really fun part. After running the DNA through my gel, Dr. Kirchman and I used the big machine that produced ultraviolet light (that's where I got the pictures of the previous PCR's a couple posts below) to cut out the DNA from the gel. While I didn't quite have the hand eye coordination to participate (as I told Dr. Kirchman, I was never good at the game Operation as a kid) I donned a pair of protective goggles and stared captivated at the glowing strips of DNA along with how easy Dr. Kirchman made it seem to cut out minuscule blocks of DNA. Dr. Kirchman had to be very careful while cutting out the DNA, however, and make sure his sleeves and gloves were covering his skin, because it is possible for the UV rays to give you a sunburn.
After cutting out the DNA strips, Dr. Kirchman and I used a kit to clean up the DNA, or at least started to use the kit until we ran out of time. We first had to incubate the blocks of DNA and a mixture from the kit in order to melt down the gel.  The blocks of DNA were put in test tubes with 150 microliters of the mixture and then put in a little boat-type tray that would float in a machine that would keep the water at 50 degrees celcius. Special tubes that come with the kit contain filters that contain things that will cause the DNA to bind  to them, but allow the other stuff to filter through. Hopefully, when we are done with the kit, we will be left with some good quality DNA ready to be sequenced.

Long weekend!

1/30/12
Today was a long weekend and I did not go to NYSM :(