Researcher of the Month
Anthropology, Biology (specialization in Ecology & Evolution) majors, class of 2015
Research Mentor: Dr. Brenna Henn, Ecology & Evolution
“I’ve learned so much in these last few months that I couldn’t have learned just sitting
in a classroom,”
explains Angela Taravella, a double major in Anthropology and Biology (class of 2015).
This past spring, Angela participated in the Turkana Basin Institute (TBI) field school where she surveyed archaeological sites, and studied modules on Kenyan geology, paleontology, ecology, archaeology, and human evolution. In addition, she did several independent research projects at TBI, including one on the survival rate of the Anopheles mosquito under different environmental and demographic conditions.
Angela pursued her interest in understanding human immunity to malaria by contacting Dr. Brenna Henn of the Department of Ecology & Evolution, and arranging to do a computational research project on the “ Migration patterns and evolutionary history of the Duffy blood group expression in African populations ” for summer 2014. As a new member to the lab, she spent some time learning more about bioinformatics and statistical programming. Angela’s research for summer 2014 was funded by a URECA-UG Bio Alumni award—one of 6 such awards given this year.
Angela is a first generation college student and a graduate of William Floyd High School. Her hobbies include drawing, running and hiking – and generally being outdoors. At Stony Brook, Angela is a Resident Assistant, and an e-board member of the Undergraduate Anthropology Society. Angela hopes to return to TBI as a TA, and plans to pursue a PhD in biological anthropology. Below are excerpts of her interview with Karen Kernan, URECA Director.
Photo (top, right): courtesy of John Griffin, Office of Communications; (left) courtesy of Kate Sherwood
Karen: Tell me about your research.
Angela. Here’s a little background as to why I got interested in this project. This past spring, I participated in the Turkana Basin Institute / TBI field school program. It was an amazing experience! And in the ecology module, we learned a lot about malaria – how it is transmitted, the details of the disease, and how certain P lasmodium species can affect humans and other animals. I did a research project on the survival rate of the Anopheles mosquito (the vector for malaria) in different environmental conditions. And I became interested in furthering my knowledge as to how different malaria preventing alleles are spread across the continent. So I did a little more looking around and found Dr. Brenna Henn’s lab website, and contacted her. I told her I was very interested in the kind of work she does, that I would love to do a project in her lab or to get some hands on experience. And we had conversations back and forth via email and found a project that correlates with my interests and the interests of the lab. She suggested that the Duffy blood group was something that I could look at in more depth—that there’s a mutation in one of the alleles that causes resistance to Plasmodium vivax which is one of the species that affects humans with malaria. So from there we worked out a project to see the migration pattern and the evolutionary history of this allele …
How do you collect data for this project?
Right now, the Henn lab already has generated and sequenced genomic data of Khoesan individuals and data of individuals from various populations from the Human Genome and Diversity Project (Stanford University). I have the SNP (single nucleotide polymorphism) id of where the Duffy locus mutational point is, so I’m pulling out a 5kb region around the Duffy locus from exome and SNP data that I have merged and phased . Phasing this data will allow me to align the maternal and paternal sides of the chromosome and enable me to determine the Duffy haplotype of each individual. …Then from there I can put this data into a program called Network, which will create a phylogenetic network where you can see if Duffy is grouping with each other, or if it’s scattered….and we can try to figure out what’s going on; when did this mutation evolve? Was the Duffy negative allele ancestral or derived in the common ancestral population for all humans? Did Duffy negative evolve only once, or multiple times?
Sounds like a great supplement to the work you did at Turkana.
With the Turkana Basin Institute program for every module you had to do some research project on your own, plus my current summer research in Dr. Henn’s lab-- I’ve learned so much in these last few months that I couldn’t have learned sitting in a classroom.
What are your future plans?
I’m hoping after I graduate to go back to TBI as a TA – I would love that. And eventually, I would like to get into a PhD program- possibly in anthropology or biology. I really love anthropology, especially the biological and evolutionary aspect of anthropology. We know a lot about humans (written history) but there’s this prehistory that we have to interpret. Using genetics and our DNA is also a way to look into our human past and see who was moving around, what was going on – instead of solely relying just on the archaeological record.
What’s the biggest challenge of the work you do?
I would say the biggest challenge would be looking at such large data sets. Just the size of the data sets-and the format it’s in, was something I had never used before. (I’ve been using PuTTY –which is a type of UNIX and the data can be in various formats such as PLINK and VCF) Learning how to navigate and manipulate the data to get it into a format that I can look at and decipher what’s going on—that’s been a lot of what I’ve been learning over the summer.
There is a bioinformatist, Dean, that works in the lab. He guided me throughout the initial few works and he still helps me when I have a problem doing something or am confused about something. There are also masters and PhD students in the lab that are more than willing to help me. When I first came into the lab, one of the PhD students, Shyamie, helped me a lot with using R- a program that I hadn’t used before. I had to do something simple like make a histogram. She took the time to sit with me and really showed me how to do everything; she showed me how to take notes as I go along so I could go back and look at it and be more independent the next time. Brenna also gave me a lot of readings to help me out as well.
I’ve been using a lot of different programs in this lab. But now I have this computer experience that I can grow from and develop more over time which I would hope to do. I really like doing the bioinformatics and computer work. You can see and interpret a lot from this data, not just the Duffy allele but with other alleles/mutations in populations.
Tell me about your mentor.
Brenna Henn is a really great mentor. We meet every week and she always makes sure that I know what I’m doing. Whatever questions I have –I go to her and she helps me out. She explains everything to me-so if she uses a new term, she’ll explain it to me or she’ll refer me to a reading that could help me understand it. She’s very clear and concise. Going into a lab where I didn’t have the prior experience, I need to do as much background research and reading as possible to understand the jargon and terminology that they use. When we have lab meetings, she always makes sure that whoever is presenting explains what they’re doing at the smallest level so that everyone can understand what’s going on, what the meaning is.
What’s your favorite part of doing research?
My favorite part is finding things out that weren’t known before, and trying new things. As silly as it sounds, what I like is getting into problems and solving the problems. It’s just the whole learning experience behind it. I was trying to merge data sets and I ran into problems –but now I’m problem solving. In the end, I feel like I’m going to have a project that I can tell a story and people are going to be able to understand it. The end result should be answering the questions that I initially had for my project.
What was the most surprising aspect of the work you’ve done so far?
I didn’t realize, when I was starting out, that you can look at the individual chromosomes and individual areas on the chromosomes. With the data from the Henn lab, I was able to look at the first chromosome in the Duffy region and see what the specific ancestry in that region on the chromosome. I didn’t know you could look at ancestry that deep into things--that you can actually look on the chromosome and see an individual’s ancestry part by part which was very interesting.
Do you have any advice for students?
Don’t be afraid to reach out to professors or possible mentors and say, “Hey, I’m interested in what you’re doing. Can I work in your lab or do a project.” That’s basically what I did, and it’s been an amazing experience.
Have you always been interested in anthropology and biology?
Even growing up, I did a lot of drawing and loved being outside (hiking, running)– I love observing and seeing nature in real life. Observing and drawing nature and the world around me has been a long time passion of mine.
Did you do a lot of sketching at TBI?
I didn’t have my drawing materials with me. You have to travel very light! But we did have a part where we got to study mosquitoes- we put them on a light microscope and looked at every stage- larvae, then pupae and the mosquito – and we drew each stage. That was really fun for me because I like drawing, and I was interesting to observe the structure of the organism and see its development.
How did you first come to find out about Stony Brook?
I went to William Floyd High School and my AP bio teacher, Mr. Flynn, was someone who shaped and created my interest for biology. He was a very good teacher; he made the classes very interactive and enjoyable and we actually came to Stony Brook and did a lab here. It was a long time ago-11th grade –and it was all new to me at that point. I had never visited a college campus before. And when I came here, I really liked it.
My chemistry teacher went here as well. And that was a big influence as to why I chose to come to Stony Brook because I knew a lot of my teachers had a good experience here.
I originally came in to Stony Brook as a bio major – and then I decided that I really love anthropology as well. I really like Ecology, Human Evolution, Human Diversity, and Population Genetics. Combining the two majors was the best step for me for undergrad. With the Anthropology major, my specialization is physical anthropology. And with Biology, my specialization is ecology and evolution.
What for you has been valuable about doing a summer research program?
Being there every day, you have your problems that you have to figure out and deal with. You can get a lot done. I keep hitting a lot of hiccoughs but I’m learning a lot, doing a lot of reading. I’m really glad that I decided to do this research over the summer. If I were to start this research in the fall- just figuring out how to use the computer and how to look at the data and analyze the data would have taken me so long. But now, once I finish this project and start another project I’ll be able to jump right into it and I won’t need to do so much extra background learning/reading… I’m doing all of that now, this summer, when I have the time to do the reading, figuring out how the lab works and the computer and everything.
You can only learn so much in a classroom. You can learn the theories. And you can learn the vocab and the lingo and the jargon. But going into a lab, you are actually applying what you’ve learned in class into your project.