Unzipping Genes
by Jim Hellegaard | Wednesday, Nov 04, 2020
Students in Florida Atlantic University’s first course-based undergraduate research experience (CURE) recently explored unlocking the genetic puzzles of one of nature’s unique creatures: Mexican cavefish.
These cavefish sleep very little, don’t become stressed and tend to binge eat. Their evolved distinctive traits are linked to diseases such as obesity, diabetes and insomnia.
The ultimate goal in this first-of-its-kind course is to identify the candidate genes that play an important role in the cavefish’s evolution.
The advanced course at the new STEM Training Hub at FAU’s John D. MacArthur Campus in Jupiter is led by Bethany Stanhope, Ph.D., the executive director for academic operations of FAU’s Jupiter Campus, and Johanna Kowalko, Ph.D., an assistant professor of biology in FAU’s Harriet L. Wilkes Honors College.
Stanhope and Kowalko are part of a team of researchers at FAU who have studied this single species of fish that has become an important model for understanding the genetic basis of trait evolution, Stanhope said.
Students are trained in the latest gene-editing technologies, known as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), in order to generate original scientific data for publication. They explore bioinformatics databases to select and test genes related to eyes, pigmentation and taste bud development with an ultimate goal of using CRISPR tools to generate mutant fish for analysis.
“You can compare cavefish and the surface fish and then you can map regions of the genome that are associated with particular traits such as loss of pigmentation or eye loss,” Stanhope explained. “So, one of the goals in the class was to take some of the mapping studies and look at those regions of the genome that are associated with these different traits. The students then identify candidate genes that fall under those QTL (quantitative trait loci) and actually functionally test those genes and see, if they mutated them, if they would potentially replicate and make cave-like traits.”
The course was developed in part as the result of a National Science Foundation (NSF) grant awarded to Kowalko, Suzanne McGaugh, Ph.D., University of Minnesota, and Nicolas Rohner, Ph.D., Stowers Institute for Medical Research in Missouri. McGaugh and Rohner joined the course as guest expert instructors, adding to the students’ experience.
In addition, the creation of the course is also part of several joint NSF cavefish grants awarded to Kowalko, Erik Duboué, Ph.D., an assistant professor of biology in FAU’s Harriet L. Wilkes Honors College, and Alex Keene, Ph.D., an associate professor of biological sciences in FAU’s Charles E. Schmidt College of Science, to expand undergraduate training and outreach.
“Watching the students learn the process of scientific discovery — starting with an idea, designing experiments, sometimes struggling, but ultimately triumphing by generating original data and results — is quite amazing,” Stanhope said.
Restrictions from COVID-19 concerns caused the State University System of Florida to order all of its institutions to transition to online education in March. Unfortunately, this meant Stanhope and Kowalko were unable to functionally test the genes the students had chosen to target.
The researchers made a number of adjustments, including providing students with images to analyze from research previously performed by Stanhope and Kowalko. The students continued to analyze data and presented their final projects, said Stanhope, adding students will finish experiments when the labs reopen.
“The students still got to implement their proposed protocols, with some adjustments made, analyze data and evaluate the results,” Kowalko said. “All of which was really important to us and allowed us to stay true to the learning goals of the (new) course, even in a remote setting."