Spotlight on Undergraduate Research – Genes to Genomes

Holly (Martha) Elmore Spotlight on Undergraduate Research

Editorial Staff — Mon, 01 Feb 2016 14:00:24 +0000

Publishing research in one of the GSA Journals as an undergraduate is a significant and valuable authorship experience and we want to hear your story (even if it was published years ago!). GSA’s Spotlight on Undergraduate Research showcases GENETICS and G3: Genes|Genomes|Genetics authors who were undergraduates when contributing to their paper.

Holly (Martha) Elmore
PhD Candidate, Harvard University
Undergraduate Institution: Vanderbilt University
Research Advisor: Dr. Antonis Rokas

How did you become involved in research?

By the time I began my sophomore year of college, I knew I wanted to work on genomes and evolution. Dr. Rokas was my Evolution professor that year, and when he mentioned he worked on fungal genomes, I set my sights on working in his lab. I have always been fond of fungi, and turns out their genomes are fascinating! I started working as an undergraduate researcher in the Rokas lab the next semester. I was paired with a graduate student, John Gibbons (now faculty at Clark University), who was studying repetitive regions of the genome, because I shared his fascination with non-coding DNA.

What was it like authoring and contributing to this paper?

Even though I was mostly doing grunt work at first– running six plates of PCR in the morning and running it all out on a gel in the evening– it was already the most exciting project I had ever worked on. At that stage of my career, all the techniques were new and awe-inspiring to me. *I* could copy DNA, literally see it on a gel, and then sequence it. It felt like such a privilege to take part in the research process. When the time finally came for analysis and writing, and I had read so much and I knew the data so closely that I was just bursting with ideas. It was amazing to do such creative work, all the while knowing that, if I did it right, I would find out something real about the hidden world of the genome.

What was the most interesting (or fun!) aspect of your time working on this project?

It was such an incredible feeling when the sequencing data came back. When you’re working with small amount of invisible liquid all day, it can be hard to grasp that there is really something in there. Seeing the sequences (well, to be strictly accurate, fluorescent genotyping) made it all so real. There were plenty of interesting and fun moments, but this one stands out as the most immediate gratification.

How did working on this project influence what you’re doing now (if at all)?

I learned so many specific skills from this project that I have used ever since– PCR, electrophoresis, UNIX command line, etc.– but, most importantly, this project taught me how to do research. How to do research is a skill I will be refining for the rest of my life, but this project gave me a great head start with identifying tractable and interesting questions, planning a project, collaborating with others, managing my expectations, and disseminating my findings. Working in the Rokas Lab cemented my love of fungi and genomics, which I plan to continue studying.

CITATION

Elmore MH, Gibbons JG, Rokas AR. (2012) Assessing the Genome-Wide Effect of Promoter Region Tandem Repeat Natural Variation on Gene Expression. G3: Genes|Genomes|Genomics 2(12): 1643-1649

Adriana Calderon: An optimistic outlook thanks to undergraduate research

Editorial Staff — Mon, 04 Jan 2016 14:00:50 +0000

Adriana Calderon
Undergraduate Senior, Whitworth University
Research Advisor: Dr. Aaron Putzke

How did you become involved in research?

Just over a year ago, near the end of the 2013-14 school year, I was beginning to ask about research positions. When I spoke to my adviser, he informed me about a new teacher coming in who would potentially be needing hands for his lab. As the new year approached, I waited, and in the first week of classes I sent the email which began the whole thing. Dr. P invited me for a small interview, and I was surprised at how quickly he had me dive into reading articles and learning his work. Since then, I’ve been part of the team.

What was it like authoring and contributing to this paper?

It is such an honor and a privilege. It’s really a dream come true. I remember how excited I was when I got the email saying we had been accepted, and I still am. I don’t know that Dr. P understands how incredibly thankful I am to him for letting me be part of this opportunity.

What was the most interesting (or fun!) aspect of your time working on this project?

I would say that synchronizing C. elegans embryos was one of the more interesting things I did. I spent several nights at the lab, peering through a microscope and picking gravid worms away from the rest of the culture and suspending them in liquid to harvest the embryos with an aspirator. As far as the most fun, I would have to say that the company beats it all.

How did working on this project influence what you’re doing now (if at all)?

I think that working in research has not only given me confidence in lab skills, but has also given me a greater appreciation for research in general. I’ve practiced reading primary journal articles, which helps me in my day-to-day school, and it’s given me an optimism with respect to medical school or future research opportunities.

CITATION

Asymmetric Wnt Pathway Signaling Facilitates Stem Cell-Like Divisions via the Nonreceptor Tyrosine Kinase FRK-1 in Caenorhabditis elegans. Danielle Mila, Adriana Calderon, Austin T. Baldwin, Kelsey M. Moore, McLane Watson, Bryan T. Phillips, and Aaron P. Putzke. Genetics. November 2015 201:1047-1060.

More than just a student: Kelsey Moore’s undergraduate research experience

Editorial Staff — Mon, 04 Jan 2016 14:00:14 +0000

Kelsey Moore
Graduate Student, University of Minnesota
Undergraduate Institution: Hope College
Research Advisor: Dr. Aaron Putzke

How did you become involved in research?

I attended Hope College because of its reputation for excellence in undergraduate science training and research opportunities. After settling into my biology major my first year, I was looking to join a research lab to further develop and expand the skill set I was acquiring through my course work. Prior to the beginning of my sophomore year, I met with Dr. Aaron Putzke, a recent hire at the institution, to see if I could work in his lab. Not only were the research and techniques interesting and outside of what I would gain through lab classes, but also his eagerness and enthusiasm for the science was infectious. I began work that fall and continued to work in the lab until my graduation in 2012.

What was it like authoring and contributing to this paper?

I was very happy to be included in the final publication of the project that I had worked on throughout my undergraduate career. Although I had presented several posters and written a capstone thesis on the data I had collected, it was very gratifying to see how the project had expanded since I graduated, and how all of the data collected was able to come together into a cohesive story.

What was the most interesting (or fun!) aspect of your time working on this project?

Although there were lots of enjoyable aspects of working on this project, probably my favorite was being able to be not just a student, but also a colleague, of Dr. Putzke’s. It is a really neat experience to feel like someone you respect and look up to both as a scientist and a person actually values your opinions and ideas.

How did working on this project influence what you’re doing now (if at all)?

Through independent research with Dr. Putzke, I not only gained a variety of laboratory skills and experience within an active research lab that I would have not been able to cultivate within normal lab classes, but I was able to gain experience in proposal writing to fund summer research, in which I received a HHMI undergraduate scholarship, as well as presenting skills through presenting posters both at within college events as well as outside of the college (Midstate’s consortium, international C. elegans meeting). These experiences were paramount in demonstrating to graduate schools I was serious about continuing my research career and is a testament to the experiences that an undergraduate can have at a small liberal arts college where students are enabled and encouraged to perform high-quality science research. I believe due to the outstanding training I received at Hope College as well as through my undergraduate work with Dr. Putzke, I was thoroughly prepared to enter graduate school with many great experiences that my peers were not afforded during their times at larger universities.

CITATION

Jessalyn Tackett: The eye-opening effect of undergraduate research

Editorial Staff — Wed, 30 Dec 2015 14:00:41 +0000

Jessalyn Tackett
Undergraduate Senior, Hendrix College
Research Advisor: Dr. Andrea Duina

How did you become involved in research?

Interest meetings were held at Hendrix College for those interested in research opportunities, and upon hearing Dr. Duina present the research projects in his lab, I applied, and thankfully, I was accepted to work in the lab.

What was it like authoring and contributing to this paper?

The research opportunity was the experience I enjoyed most during my undergraduate career. There were several of us involved in this project, and we each contributed to different parts of the project. A great amount of effort and time was put into each part of the project, and it was an honor to work as a part of this team. Everyone worked hard, and seeing all of the pieces come together was beautifully rewarding. It brought new understanding to material I had learned in my undergraduate classes.

What was the most interesting (or fun!) aspect of your time working on this project?

There was always an opportunity to learn something new, and being able to work on one part of the project, and then contribute to other parts of the project was very enjoyable. Watching genetics take place right in front of your eyes is incredibly beautiful. I loved being able to perform crosses, and then verify that we had the crosses we needed through phenotypic tests and DNA sequencing. Simply observing these genetic events unfold in the lives of S. cerevisiae organisms was a beautiful experience.

How did working on this project influence what you’re doing now (if at all)?

Working on this project helped me realize that there were different career paths one could take in the field of science. Many students around me were applying to medical school, and there was a large push for medical school, but working in the lab gave me the opportunity to meet other people and realize that together we all contribute to science. It gave me a deep appreciation for research itself, as well as undergraduate professors who not only conduct this research, but take the time to educate undergraduate students in this hands-on approach. This experience also gave me a desire to keep up with research, and it gave me the tools to do so.

CITATION

A Systematic Mutational Analysis of a Histone H3 Residue in Budding Yeast Provides Insights into Chromatin Dynamics
Paige Johnson, Virginia Mitchell, Kelsi McClure, Martha Kellems, Sarah Marshall, Mary K. Allison, Harrison Lindley, Hoai-Trang T. Nguyen, Jessalyn E. Tackett, and Andrea A. Duina. G3: Genes|Genomes|Genetics. May 2015. 741-749

Collaboration is key: Faiz Kabbinavar’s undergraduate research experience

Editorial Staff — Mon, 14 Dec 2015 14:00:16 +0000

Faiz Kabbinavar
Undergraduate Institution: University of Pittsburgh Cancer Institute
Research Advisor: Dr.Kara Bernstein

How did you become involved in research?

I became involved in this research when I joined Dr. Kara Bernstein’s lab at the University of Pittsburgh Medical Center in October 2011. I began research in my freshman year and continued through graduation, including summers where, in summer 2013, I was awarded the Dietrich School of Arts and Sciences Summer Undergraduate Research Award Fellowship. This fellowship allowed me to do much of the research that went into this paper in Genetics.

What was it like authoring and contributing to this paper?

Contributing to this paper was an extremely exciting experience. I loved the work that I was doing and working with my other lab mates. Working together and collaborating with another University of Pittsburgh laboratory, we were able to learn much more, which made this paper all the more fun and intriguing.

What was the most interesting (or fun!) aspect of your time working on this project?

The most interesting aspect of this paper was working with my fellow lab members, trying out new types of experiments. For instance, working on meiosis was something fairly new to my lab, so Stephen Godin and I worked together to characterize our proteins of interest. Moreover, it was also interesting to see the more intricate evolutionary data from Dr. Nathan Clark’s lab.

CITATION

Evolutionary and Functional Analysis of the Invariant SWIM Domain in the Conserved Shu2/SWS1 Protein Family from Saccharomyces cerevisiae to Homo sapiens Stephen K. Godin, Camille Meslin, Faiz Kabbinavar, Dominique S. Bratton-Palmer, Christina Hornack, Michael J. Mihalevic, Kyle Yoshida, Meghan Sullivan, Nathan L. Clark, and Kara A. Bernstein. Genetics. April 2015 199:1023–1033

The impact of Sarah Radford’s undergraduate research

Beth Ruedi — Wed, 28 Oct 2015 14:00:48 +0000

Sarah Radford
Postdoctoral Associate, Rutgers University
Undergraduate Research Advisor: Jill B. Keeney
Undergraduate Research Institution: Juniata College

How did you become involved in research?

The professor of my sophomore genetics course, Dr. Gooch, recognized that I was interested in the topic and suggested that I do research. At the time, I had no idea how research worked and had never heard of graduate school, but Dr. Gooch introduced me to Dr. Keeney, and that started my research career.

What was it like authoring and contributing to this paper?

Because I was in a lab at a small liberal arts college, research did not progress quickly. I happened to be working in the lab at the time when the important discovery for this project was made, but many other undergraduates before me contributed, which is why the author list is long. Although we published after I left for graduate school, I wrote a large part of the introduction – it was from the introduction to my undergraduate thesis – so I ended up snagging the first author position.

What was the most interesting (or fun!) aspect of your time working on this project?

I loved working in the lab from the first day. I liked the experiments and the puzzle-solving aspect. The best part for me was the amount of independence I had, despite being in a small undergraduate-driven lab. This has really influenced the way that I work with undergraduates in lab now.

How did working on this project influence what you’re doing now (if at all)?

I have recently been using my undergraduate experience to do some yeast two-hybrid screening. I even pulled out my old “Keeney Laboratory Manual” for reference! But more than just laboratory experience, working on this project is the reason why I chose a career in research.

When this paper was ready for publication, I was already in graduate school. I asked my advisor, Dr. Jeff Sekelsky, what journal he thought we should submit to. He immediately suggested GENETICS, so I suggested that to Dr. Keeney. Since then, the largest part of my publication list consists of papers in GENETICS!

CITATION

Radford, S. J., Boyle, M.L., Sheely, C.J., Graham, J., Haeusser, D.P., Zimmerman, & L., Keeney, J.B. (2004) Increase in Ty1 cDNA recombination in yeast sir4 mutant strains at high temperature. GENETICS 168 (1):89-101. doi: 10.1534/genetics.102.012708