Week 2-The Lovely World of Evolutionary Genetics
Hi guys! My second week in the lab is finished :) The week was definitely challenging, but I learned a LOT. A bit more about my project: I am using Daphnia melanica, which is a strain of Daphnia found in Washington state. The postdoc I work for, Brooks, did previous research on this strain. Based on his results, I am looking to see if there is a difference in transcription for an enzyme thought to be responsible for repairing UV-damaged DNA between Daphnia in low and high-UV ponds. Below is a photograph of Daphnia melanica taken by Lindsay Schaffner.
I couldn't just jump into my project because there is a whole bunch of prep work required before dealing with molecular genetics. Luckily, the genome for Daphnia melanica is known – we could therefore choose primers that would target specific regions. Since we also know many base pairs each of those regions should be, we were able to easily compare our results to the expected values. While we had 10 primers to work with that should all hypothetically work on the DNA, usually only one or a few do. This is why I had to test all of the primers to see which one(s) worked best.
I started my research project this week by preparing and testing out primers, extracting RNA from Daphnia, using reverse transcriptase to convert the RNA to DNA, using polymerase chain reaction (PCR), making and running gels for electrophoresis, and analyzing my results. Those steps alone took 5 days! Molecular work can require a great deal of patience, but it is very rewarding. Fun fact: AIDS/HIV use reverse transcriptase to convert RNA to DNA. Normal viruses convert DNA to RNA. I found the connection between the procedure I am implementing and the mechanism of AIDS to be really interesting. However, the reverse transcriptase I am performing is not problematic or deadly; it is used to isolate the region ACTUALLY transcribed rather than the region that is coded in the DNA.
In genetics lab, students were only responsible for portions of the PCR procedure. For this reason, I was very excited to perform the entire extraction/reverse transcriptase/PCR/electrophoresis experiment from start to finish. This was the first time that I was able to extract the DNA from an organism and work with its RNA. The whole thing was a very cautious procedure; every time I worked with the RNA, I had to take extra measures such as repeatedly changing my gloves and spraying down the work space/instruments with "RNaseZap." Fortunately, the hard work paid off! One of our primers is a possible strong match for the experiment, so next week we will run more tests on it.
My pre-PCR workspace!! I use the nanodropper and gel analyzer in a different lab. My post-PCR workspace is also in a different room. Because I am using PCR (which amplifies DNA greatly), I have to be careful to keep my post and pre-PCR materials completely separate. Otherwise, I'd risk contamination.
It can be pretty nerve-racking, pipetting fractions of microliters and trying not to contaminate anything! To make sure all of the pipettes were as accurate as possible, I personally checked the displayed volume against the actual volume for every device I intended to use. That is how important accuracy is with these types of experiments!
Both my lab and the Biology Research Fellowship Program make sure to schedule in occasional breaks and fun social activities. This Wednesday, the Summer Institute for Life Sciences here at Cornell hosted an ice cream social for everyone on campus who was interested in biological research. The students were given Purity ice cream (if you haven't tried it, you have to) and split up into groups according to research interests. This was a great opportunity to meet other students staying here this summer and to learn about their projects.
These are some of the main people who I work with in the lab. Chris (far left, Class of '14) started working in the lab with me last summer, and he continued working on the chemostat project with me during the school year. Brooks Miner (second from far left) is the postdoc I work with. Lindsay (next to Brooks), the Research Support Specialist, works with Ellie (on microscope), who is a visiting student from Hobart. They study Daphnia. Special activities in this lab this week included celebrating our new graduate student's birthday (her name is Katie) and getting ice cream at Trillium. Katie also made these really tasty peanut butter bars. Our lab really loves food :D
Well, it's time for me to try to find some easy recipes for tomorrow's "family brunch." I cannot cook at all, so this might actually end up being quite challenging. A piece of advice for anyone who will be spending a lot of time away from their home: try to make a weekly meal tradition with friends so that you feel more at home and have a guaranteed home-cooked meal. It really helps :) Then go get "Yogurt Crazy" in Collegetown for dessert because it is awesome (and it can be healthy too!).
Have a great week everyone! :)