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.

Linksvayer Lab: mid Week 5

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.

At the middle of week 5 I am still working on the microsatellites project, still with hope that I'll be able to get onto an animal behavior in the coming weeks. To remind you what my current project is... I have been taking 15 ants from a large number of colonies, and individually crushing, adding buffers, centrifuging, letting incubate, and finally perform PCR on these samples. There are also steps of Nano Dropping, where I use a Nano Drop machine to test light refraction at certain wave lengths, telling me how much DNA in is the sample, and running gel electrophoresis after PCR, in order to see the size of my samples. We are looking for microsatellites, also known as Short Tandem Repeats (STRs), in order to tell the difference between the genetic codes of the different colonies. Due to the caste systems Pharaoh (and other) ants use, the genetic code of a single colony is very identical, and two sister worker ants are more related than any human is to another human on average, except for identical twins. We are not trying to sequence the entire genome because that takes a long time and is very expensive. Instead we are looking fro Micro Satellites, which we expect could be different between colonies. As an example,we might be looking for a code that says to make a little extra of a certain protein in one colony when compared to another, as opposed to the code that says grow legs, or something all ants do.

Unfortunately I am currently in an awkward spot in time, as we have run out of the Taq MasterMix Polymerase needed to run PCR, as well as multiple of the markers needed to do multiplexing, which is marking the genetic sequence. So for the next few days I am starting up on new colonies, and preparing them for PCR. This means the project is likely to continue even longer, since we had not originally planned on doing more colonies (past the amount from my last post), and because we need to wait for delivery.

Hopefully things will become more exciting here in the near future, but for now its back to crushing ants!

Linksvayer Lab: end of Week 3

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.

My second and third weeks in the lab turned out to be very similar to the first. I'm still working on the genetics project, where we are finding differences in micro-satellites in the Pharaoh Ant colonies in the lab. This information is important for the future of the lab, because it will allow us to compare colonies genetically as well as behaviorally, and determine if certain actions/activities, such as one colony having twice as many queens although still being the same size as another (Pharaoh Ants are polygynous which means they have multiple queens); we then compare this to the genetic difference between the two or more colonies. My P.I. left this week to go to some conferences in Europe, where he'll be learning ant stinger dissection techniques, and talking with the top ant experts on the continent! But before he left he gave me new directions with my project, by which I mean he expanded it. I'm now doing about a dozen more colonies than my previously reported amount, as well as running gel electrophoresis in multiple samples from each colony to test if the PCR worked before submitting them for sequencing.

In total the lab week has been pretty slow. Most of the projects in the lab are coming to a close, so most of my fellow researchers are anxious to finish and start new projects. Although I know my project will not be finished anytime soon, I'll hopefully begin working on more behavioral based work, just to mix things up. Because of many projects almost being finished, everyone has had a little more time to hang out, so I got to know everyone in the lab a lot better, and we even went out for fro-yo after work one day. Unfortunately, we had to say good-bye to our lab tech Katie, who is leaving to go to grad school. But we're excited for our new lab tech Michael to be in charge because he's a really fun guy.

I haven't gotten a chance to return to the Berger lab yet, mainly because every time Riley's been there its been rather serious business. To remind you, Riley, my grad student, works in both Dr. Linksvayer evolutionary biology ant lab and Dr. Berger's epigentics in ants lab. So he's been over there trying to talk to Dr. Berger about his next steps not only in his project but in his future at the lab. This means I've had a lot more unsupervised lab work, to the point of Riley calling me "99%, if not completly, autonomous". I've also taken it upon myself to sign up for ant feeding, which as a temporary volunteer I'm not required to do, but I wanted to do my part. Its a rather long process, due to the hundred or so colonies of Pharaoh Ants and another 300-400 colonies of another type (which I can't remember because I don't use them). For both we need to give them new food and water, which is always interesting because they usually start making nests and climbing all over the test tubes they get water from.

I'm not expecting too much of a change this week, this Riley's going to be at an "ant meeting" all Monday and Tuesday, and with July being off... there will be mostly more of the same. But I am excited for the Penn/CHOP exp lunch Tuesday!

Week 1 (and a half): The Art of Crushing Ants

This summer I'm working at Penn in the Linksvayer Lab, which is focused on evolutionary biology through animal behavior and genetics in ants. At first my work was set back a week by a full safety class. But on June 10th I took the safety class, and after long commute by car, then train, then walking, (about 100 minutes in total, half train, and split evenly between car and walking) I started Tuesday June 11th. Although the lab focuses on animal behavior, because of my past experience in performing PCR (thank you Dr. Peretz and BioTech class!), I am starting off by comparing micro-satellites (points on the genome which we expect to change) in the different colonies of Monomorium pharaonis, called Pharaoh Ants. To do this, we (Me and Riley, the grad-student working with me), are taking 15 ants per colony, for about 15 total colonies, and going through the process of separating each ant, crushing them using a pestle and liquid nitrogen, applying many buffers and Elution, and going through tons of centrifuging. This is what I have been doing for the past week. Starting this afternoon I will begin applying 4 different marker sets to identify the ants, performing PCR, and getting each ant sequenced. For those of you doing the math: its 15 ants x 15 colonies x 4 marker sets = about 900 ants micro-satellite sequences!!!

The most amazing thing about the my experience so far is that this project is MY project! Riley has some of his own stuff, and works with me often, but the project is mine to do and complete, and the info is going to be used for future projects. I should be done this by the end of next week, and then I really start working with everyone on a BIG animal behavior project (which I'll keep a secret for now!). But once that project is finished, I'll be able to compare my results from the micro-satellite to make a final determination about the results from that project, tying in most of the work I'll be doing during my 8 weeks.

There is one more EXTREMELY awesome thing about my experience here. While Dr. Linksvayer's lab is amazing, and I'm becoming friends with the other 8 or so people working here, I have the added bonus of working with another lab! Riley has until the end of the summer to decide between Dr. Linksvayer's and Dr. Berger's lab, so in the mean time we work in both. Dr. Shelley Berger focuses still on ants, but specifically epigenetics. Dr. Berger has a lab of about 35 people, and works in the very high tech Smilow research center, still at Penn. Riley is working on completely different projects at Dr. Berger's lab, and I've gotten to help him over there when we have some time in the afternoon. There I've been able to use really high tech machines, like a Sonic Crusher, which they use to crush ant samples WITH SOUND instead of using a pestle. I've also been able to attend lab meetings, talks by visiting experts, and hopefully next week I'll be doing an ant brain dissection, which has absolutely nothing to do with my work, but everything to do with Riley's.

Not only am I getting great lab experience through my work, but I'm getting to see the work of dozens of other researchers, who are glad to tell me (and brag) about their research. I also get to compare the feeling of a huge and older high tech with a small and newer lab. I can't wait to continue my work and eventually move onto animal behavior, and I'll keep everyone posted with how it goes!