GREAT program creates new opportunities for students to participate in research

In the UC Santa Cruz Paleogenomics Lab, NSF postdoctoral fellow Andrew Sharo is using DNA from 100-year-old samples of steelhead trout to study how their populations have changed over time. It is important work — in California, local steelhead populations are endangered or threatened, and the answers Sharo finds in their genomes could help us figure out how this species has been impacted by habitat loss, introduced species, and climate change.

As the effects of climate change continue to intensify, studying the natural environment will only become more vital, and Sharo believes that the only way we can get the brightest minds working on these problems is through mentoring new generations of scientists.

“Mentoring students is really important,” Sharo said. “I want the field to be a place that is welcoming and exciting for people so we get really smart interested folks into ecology and evolutionary biology. That doesn’t happen if you don’t put some effort into training them.”

This summer, Sharo signed up to be a mentor in a new NHGRI-funded program, “Genome Research Experiences to Attract Talented Undergraduates into the Genomics Field to Enhance Diversity” (GREAT), which welcomed six students from California State University Monterey Bay (CSUMB) to an intensive eight-week research program at UC Santa Cruz. The GREAT program aims to provide students from diverse backgrounds with opportunities to conduct genomics-based research and receive career training from research-intensive universities such as UC Santa Cruz.

“The GREAT scholars are not the only beneficiaries of this partnership,” said Zia Isola, director of the UCSC Genomics Institute Office of Diversity. “Building a diverse and skilled labor force is vital to support the ever-increasing demand for researchers and faculty in the field of computational genomics, and is a top priority at the state and national level.”

Mentees in the inaugural GREAT cohort lived on the UCSC main campus this summer and spent around 40 hours a week attending workshops on career development and working on individual research projects guided by UCSC mentors. The idea was to give them a taste of what it is like to be a research scientist and encourage them to consider careers in genomics and bioinformatics. 

“It is a really ambitious program, and I mean that in a good way,” Sharo said. “It is challenging for the mentors and the students because you only have eight weeks to come up with a project, do the analysis, make the poster, and submit an abstract to a national undergraduate research conference. But I think it is good that they are pushing the students to do so much in such a short time.”

Andrew Sharo’s two mentees, Ezra Collins and Delight Lee, both came from CSUMB but had different majors that gave them complementary strengths when tackling a project on trout genetics. 

Collins, who uses gender-neutral pronouns, is a biology major and already knew quite a bit about trout specifically from working on a high-school research project at a hatchery. They loved doing field work, but did not know a lot about DNA or bioinformatics. Their project in the Paleogenomics lab involved looking at genetic markers that influence migration timing, and differences in these markers between samples from current populations of steelhead trout and older samples that had been preserved for over 100 years. 

Collins’ analyses found a very slight trend toward premature migrating in current trout populations compared with the ancient samples. Carrying out this research required learning to run computational analysis on the trout’s genomes, which is not an easy feat considering the genome contains more than 46,000 known protein coding genes and huge chunks of nearly identical sequence. They said the experience gave them a new tool they can use in their studies, and made them want to learn more about programming.

“I’ve been doing a lot more programming than I ever have,” Collins explained. “I still have a lot to learn, but I think I have gotten better at it. It is making me want to go and pursue this more and learn more about programing designs.”

Delight Lee, Sharo’s other mentee, is a computer science major and so was more familiar with programming, but didn’t know much about biology or how computer science could be used to analyze data for conservation efforts. 

“I knew there were computer science students going into bioinformatics, but I didn’t know too much about it. I just knew there were vast amounts of genomics data that needed a lot of computer majors. I definitely gained a lot more knowledge about [the field] through this program,” she said. 

Coming into the program, Lee had been thinking about pursuing graduate school, but wasn’t sure if she was ready. She worked on a project similar to Collins’s project, but focused on changes in the age at which the trout matured over time, rather than changes in when they spawn. While Collins struggled most with learning programming during the program, Lee struggled more with learning biology terms, particularly since English is her second language. She credits the program with helping her to learn how to handle stress, and also giving her the confidence to know that she can handle a fast-paced research environment. 

“Now I know I do want to go to grad school –- it gave me a good idea of what to expect,” she said. 

“Partnering with UCSC on this program has been an incredible opportunity for our students,” said Nathaniel Jue, associate professor of biology and chemistry at CSUMB and one of the program creators. “The world class research projects in which our students have been able to participate have been truly impactful to their development as future scientists and will have real impact on their career paths in the future.” 

The program wrapped up with a presentation on August 16 at which all the mentees presented the projects and got a chance to show off all they had accomplished in just eight weeks. 

“After seeing their research presentations at the end of the summer, you could see real growth in their confidence and capacities as scientists,” Jue said. “The UCSC Genomics Institute has been an incredibly supportive partner in this program and we are looking forward to providing more students with this unique opportunity.”