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Environmental Genomics Training Informs Work on Organisms’ Response to Pollution

Tess Leuthner, a doctoral student in the Integrated Toxicology and Environmental Health Program at the Nicholas School of the Environment, received a grant to attend the 2016 Environmental Genomics training program at the renowned Mount Desert Island Biological Laboratory.

She was among 19 Duke students who received Graduate Student Training Enhancement Grants (GSTEG) in 2016-17 for training beyond their core disciplines. In brief, here’s what she learned:

This was a unique course, in that we learned how to make cDNA libraries in the lab at the research station with our own samples in our own hands. These were then sequenced at a nearby facility overnight, so that we had our own sequence data to analyze.

The samples that I worked with were isolated from the ubiquitous freshwater crustacean, Daphnia. There were two populations of Daphnia that we investigated: one that is adapted to cadmium from mine smelting runoff, and a reference population from a clean lake that did not receive any runoff. We looked at the change in gene expression of these two populations after they were exposed to cadmium in order to investigate how the different populations respond to a stressor.

For example, as you can see in the heatmap below that I created during the course in the program R, there is variation in gene expression as a response to cadmium based on whether or not the Daphnia are adapted to cadmium.

A data visualization

This course and these data continue to contribute to questions relevant to my thesis work, and I am currently using these same data for a Computational Biology course to dive deeper and answer more questions about how organisms are adapting and responding to pollution. I hope to use these data to create a model to better understand and predict how populations respond to anthropogenic stressors on the genomic level.

I gained the knowledge to create, manage and analyze genomics datasets, but I also met new colleagues and collaborators. I continue to communicate and collaborate with scientists and peers that I met during this course.

This internal funding mechanism from the Office of the Vice Provost for Interdisciplinary Studies encourages graduate students to step away from their core research and training to acquire additional skills, knowledge or co-curricular experiences that will give them new perspectives on their research agendas. Graduate Student Training Enhancement Grants are intended to deepen preparation for academic positions and other career trajectories.

See who received these grants for 2017-18, and read about other 2016-17 recipients’ experiences:

Images: Tess Leuthner (seated at far right) and her fellow participants in Environmental Genomics 2016; Leuthner’s heatmap showing variation in gene expression as a response to cadmium