My practicum site was in Dr. Karen Osborn’s lab in the Smithsonian NMNH. I took on two projects over the course of the Summer. The first centered around genetics, with the goal of building phylogenetic trees for hyperriids (amphipods). I started by gathering sequences, importing them into Geneious, fixing them up, then using the FastTree feature to build the tree. My favorite tree is for Cystisoma. We had a very limited number of Cystisoma sequences, but I was able to make a super clean tree showing the correct relations between the Cystisoma species. Some sequences were mislabeled, meaning the name says one thing, but the tree says something completely different. Analyzing genetic distances and comparing them to other sequences helped me place them correctly.
A major part of the project was categorizing hyperiid specimens in Excel. Most NMNH species in the National Library of Medicine were already in existing spreadsheets. However, not all were present, so I had to copy the identification info from the NLM. This included the ID number, location, the collector (which was usually Dr. Osborn), and how the specimen was preserved so we could know if it was possible to get a second sequence. All of that data had to be organized in new spreadsheets, especially if I was building trees focusing on singular species. I also had to keep track of any failed sequencing and send them over to the support scientists for future resequencing.
My second project consisted of creating a 3D scan/model of a polychaete worm using Dragonfly segmenting software. The learning curve for Dragonfly was a lot steeper. The supervising researcher provided written instructions, but since I had no segmenting experience, they were difficult to understand. The scan was easily the most time-consuming and challenging part of the summer. I faced multiple technical hiccups, like the pen not working properly and slow computers. I had to start over multiple times and the single scan took me over 150 hours. I was purposefully being slow trying to accurately outline the worm with the pen. Then, I filled in the inner areas. Depending on where I was in the scan, I could skip anywhere from 5 to 15 slices. It took the computer anywhere from a few seconds to 30 minutes to interpolate between slices. That’s pretty much all I did. Outline, fill inner areas, skip slices, outline, fill inner areas, interpolate, then clean up slices in between by erasing or adding to the ROI.
This got much harder after I passed the halfway mark because the worm had some very annoying, but very beautiful scales. The scales didn’t always connect to the body, so I spent a lot of time being extra careful not to connect some parts of the ROI because when I hit “fill inner areas” later, it would fill in the space that was supposed to be empty. The general body was also broken up really weirdly in the middle. There was probably some damage or issues scanning the worm, so I had to guestimate where certain body parts would be.
I learned a lot about the science aspect behind phylogenetic trees. In order to use Geneious, I had to learn about DNA structure, amino acid translation, reading frames, genetic codes, etc. I also had to read scientific papers about current hyperrid research in new species identification. Beyond the scientific aspect, I gained invaluable lessons in patience and persistence. There were many times I wanted to give up, but I had to keep growing and adapting as I encountered obstacles. I’m grateful for this experience because it solidified my passion for wanting to pursue a career in research. I don’t think I’ll be exploring specimen collection or segmenting. However, I will be carrying the curiosity that academia requires into my future career.
I found this site through a SGC alumni, Maiya Yen. She’s worked with Karen for a few years and presented her work during one of our colloquiums. I reached out to Karen through email and we were able to get the ball rolling relatively quickly. The advice I would give to future scholars in identifying a site is to start early, especially if you want to get it done during the summer. Also, looking at what SGC alumni did as practicums is very helpful! Just make sure to reach out to potential supervisors as soon as possible, and have multiple options in case something falls through.