Discovery, discussion, collaboration, and friendship amid experiments in the Yatsunyk lab.

In this next installment of profiles in summer research with undergraduates, CURChem is featuring Dr. Liliya Yatsunyk of Swarthmore College. She shares about the real life discoveries, discussions, collaborations and friendships happening  alongside the experiments this summer…


Deondre and Barrett with our collaborators Prof. J. Trent and Prof. B. Chaires in Prague during the International Meeting on Quadruplex Nucleic Acids, June 2017

The start of this summer was very unusual for my lab – all of us were away in different countries, and on different continents: I was in Asia co-teaching an environmental studies course (which is unrelated to my research), Deondre and Barrett were in Prague, Czech Republic, at the 6th International Meeting on Quadruplex Nucleic Acids (a key biannual conference in my field. You may wonder, why I was not there? That story is far too long for this blog), and Allan and Linda were in Hershey, PA at the 45th Middle Atlantic Regional Meeting of the ACS. This is how the summer started for us, but let me first introduce my lab.

My name is Liliya Yatsunyk and I am an associate professor of Chemistry at Swarthmore College, PA. This is my tenth year at Swarthmore. I received my undergraduate degree in Ukraine, my PhD at the University of Arizona (with Prof. Ann Walker) and did postdoctoral training at Northwestern University (with Prof. Amy Rosenzweig). I teach Inorganic Chemistry and research non-canonical DNA structures linked to cancer and other human diseases. I love teaching and, at the same time, I love summers when I devote all my time to working with students pushing forward frontiers of science. The main challenge in research for me is to stay on top of my field and generate ideas that are both useful and interesting to pursue.

I love teaching and, at the same time, I love summers when I devote all my time to working with students pushing forward frontiers of science.

Deondre ready to work

This summer my research group is particularly strong and consists of Deondre Jordan, Barrett Powell, Linda Lin and Allan Gao, who were awarded college funding (most of which came from private donors) for summer research. Barrett is a rising senior, Deondre and Allan are rising juniors, and Linda is a rising sophomore; two of the students are from groups underrepresented in the sciences; and all four are amazing! Recently, I received an NIH grant and we are currently looking for a Research Assistant. I have scheduled three interviews so far and have high hopes to bring on board a talented and driven person.

Swarthmore is an undergraduate only liberal arts institution located south of Philadelphia, which grants BA and BS degrees. At Swarthmore, Chemistry majors take only nine chemistry courses; research is not required but many students sign up for it and fall in love with it.

The curious thing about undergraduate researchers is that they do not get discouraged by the experiments that fail.

The students’ summer started on Monday June 5th. Mine has yet to begin. I am writing this blog on an airplane flying from Tokyo to Toronto. Summer is the time for all of us to focus on one thing and one thing only – our research projects. We work hard, think smart, and collaborate.

The main challenge in research for me is to stay on top of my field and generate ideas that are both useful and interesting to pursue.

The curious thing about undergraduate researchers is that they do not get discouraged by the experiments that fail. I learn from them to stay positive at all times and have fun. In addition to research, we actively work on regaining balance in our lives after intense and often crazy semesters. At group meetings we report the steps taken toward this goal: some of us learn how to cook, others take walks, read, or restart sports.

The Goals and the Plan

Deondre, Barrett, and I are working on a project new to my lab – a collaboration with the lab of Eric Brown at the University of Pennsylvania. Both students started working in my laboratory over a year ago and now they are as much of experts on the topic as I am. They are no longer my students, but my collaborators. I am amazed at how far hard work and 12 months of time can carry students along their research trajectory. Barrett is an expert on crystallization and gel electrophoresis (all his gels come out perfect!!!).

They are no longer my students, but my collaborators.

Deondre is an expert on biophysical methods (UV-vis and Circular Dichroism, the latter is a work horse of our laboratory) and on how to analyze a large number of DNA constructs in a short amount of time and keep all numbers in order (I usually help him with the latter task). Barrett is close to getting a good X-ray data set for one of his constructs and we are optimistic about solving the structure by the end of the summer. We also hope to crystallize the DNA in the presence of heavy atoms for phasing purposes – this part is yet more tricky and challenging. Deondre’s goal is to tie loose ends on many parallel projects, i.e. to repeat trials on an endless number of our DNA mutants. Nobody likes to repeat experiments as the excitement of a new discovery is not there, yet as a good scientist one needs to confirm and reproduce the results.

Nobody likes to repeat experiments as the excitement of a new discovery is not there, yet as a good scientist one needs to confirm and reproduce the results.

My goal for this summer is to write the first paper for the project. It seems like a manageable task. This project has too many pieces – we need to write before everything tangles together into an unmanageable mess. We also need to write so that we can crystallize our thoughts and ask better questions in the future. Both Barrett and Deondre have writing tasks of their own – to produce parts of their Honors theses. You might think it is an early start, especially for Deondre who still has two years ahead of him. Yes, it is. I want to help students better manage their senior spring when thesis writing turns into an overwhelming task leading to either poor theses or poor health. I want my students to avoid both. I will also use their writing in the paper I work on. Thus, everybody wins.

Our lab in summer 2017. Allan Gao, Barrett Powell, Prof. Liliya Yatsunyk, Deondre Jordan, and Linda Lin.

Allan Gao started in my laboratory last fall and got minimal supervision from me due to my high teaching load, managed to learn on his own, but had a slow start. His project is beautifully simple. Allan analyzes the concentration-dependent dimerization of our lab’s favorite ligand, NMM (not like my French collaborators call it — M&M). Because we use this ligand widely, we need to understand every detail of its behavior. Analysis of simple systems is usually complex, as Allan has quickly learned. The project has kept him busy for two semesters, dramatically enhanced his creativity, developed his persistence, and provided results for his poster presentation. For this summer, Allan’s task is to finish the project (and, with my help, write a short article about it) and to join the lab-wide crystallization effort focused on complexes between non-canonical DNA and small molecule ligands (e.g. NMM, etc). This project is funded by NIH starting June 1st and is currently a priority in my laboratory.

 

Linda’s pink crystals, which were taken to the synchrotron and diffracted to about 3 A

Linda is a newest member of my lab. She was planning to start working this summer, but during spring semester, an opportunity presented itself, giving Linda the chance to attend a conference where she could present a poster. Linda immediately joined the lab and worked tirelessly during the last weeks of classes and between exams. She got beautiful biophysical data on her DNA-NMM system (as I said earlier, everyone loves NMM) and grew some impressive pink crystals (who does not dream about pink crystals?). Barrett took the crystals to a synchrotron facility and they diffracted!!! The lab was overjoyed!!! For Linda, the summer goal is to complete the lab training, improve the quality of her crystals, and work on solving their structure.

Linda presenting poster at the 45th Middle Atlantic Regional Meeting of the ACS, June 2017

 

This is what the start of our summer looks like. The students have worked without me for a week. I missed their faces, their curiosity, and their presence. I am eager to learn about their conference experiences, and the data they collected without me. I want to be a part of my lab and my summer is starting tomorrow with nine more weeks of discoveries, discussion, experiments, collaborations, and friendships.

 

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