Linksvayer Lab week 6- Gels and why I don't like them

Hi my name is Ben Wagner and I've been working in the Linksvayer Lab at Penn. We work on evolutionary biology and collective decision making in ants.

Although I still have 2 weeks left in the lab, I feel like I've already learned what will be my most important lesson from this summer. This lesson is simple: Science takes forever. I'm not saying this is a negative way (necessarily) but more of an important lesson all future exp-ers and scientists should know. I have had multiple hour long incubation and waiting periods, ant feeding periods that took up most of my day, and my project expand until it is 10 times the original size, with 20 times as much work.

But regardless, week 6 was an excellent week, although it started off very badly. The week was a week of PCR and Gel electrophoresis, which shouldn't be bad. PCR is easy, gels are fine, just a lot of waiting time, but that's okay! PCR appeared to be running correctly We had already run a number of gels, and the creation of these gels lead to spills, leaks, and a small TAE buffer explosion in the microwave. But that's okay, nothing serious and its all in the name of science! Probably half our samples had been tested in at least one marker in the gel (so 1/8th what the final sample amount will be). 
Then, A talk with an old lab Post-Doc, Luigi, resulted in my learning that all the PCR i had run so far, and tested on the gels, was completely wrong. It pretty much came down to my strands had been coming out at somewhere around 50 bp, which Riley and I thought was correct. Nope!   They should be around 250-300. So we decided to find the issue. We started single-plexing (one marker instead of multiple), fiddled with the marker amount, changed temperatures in the thermocycler. Then, Dr. Linksvayer gave us the advice to use use 4uL DNA, instead of the 1uL that multiple protocols told us to use. Now we have have successful results on the gel!!! The next step is to see if this will work with multiplexing, because otherwise this project will not be finished anytime soon.

With only 2 weeks left, I'm not so sure this project will be finished, especially because Dr. Linksvayer wants me to help with behavioral things in those weeks. And because we haven't actually submitted anything to sequencing yet, which normally takes about a month, and then after that statistical tests need to be run to make a photogenic tree.... So it won't be done by the time I am. But maybe data collection will be. We'll just have to see. Hope all my fellow exp-ers have had a good summer in their labs, I'll keep you guys posted.