EMSL Summer School inspires hands-on research opportunity for undergraduate students

The COVID-19 pandemic sent most people home, closing many hands-on scientific laboratory experiences.

As a result, the Environmental Molecular Sciences Laboratory made the decision to switch its normally in-person Summer School to an online experience in 2020.

EMSL Summer School provides PhD students, postdoctoral researchers, and early career scientists with a free opportunity to access hands-on training as it pertains to molecular-level biological and environmental science research.

In 2020, EMSL Summer School participants learned about digital platforms and tools for modeling multiscale microbial dynamics online. This included datasets available through the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS), data analysis for metagenomics, and how to access and use KBase. Funded through the Department of Energy, KBase brings together a variety of data and analysis tools into a central platform, using scalable computing infrastructure to perform sophisticated systems biology analysis.

Through the exploration and use of these online tools at EMSL Summer School, Aditi Sengupta, then a postdoctoral research associate at Pacific Northwest National Laboratory, came up with an idea to use the tools for hands-on research experiences for undergraduate students from home. In fall 2020, she was able to implement this idea as an assistant professor of biology at California Lutheran University.

“Through EMSL Summer School, I developed an understanding of how to use this openly available data, as well as what tools are out there for this data,” Sengupta said. “I figured I could use what I learned to craft learning opportunities for students in the classroom, even from home. All faculty were struggling with ways to engage students for virtual labs during COVID. This sounded like a great opportunity.”

Hands-on science from home

Sengupta developed a curriculum that would expose a cohort of fall 2020 undergraduate biology students at California Lutheran University to several tools and datasets from EMSL Summer School. In groups, the students used openly accessible data from the WHONDRS campaign, formed hypotheses of outcomes for and from the data, and tested them using the bioinformatics pipeline in KBase. Bioinformatics involves the use of computers and software to understand and analyze biological data, providing information such as protein structure, DNA sequences, and other details.

“Because of the available online tools and datasets, we didn’t have to start from scratch by performing our own experiments,” Sengupta said. “The students had narratives in KBase, or analyses in the pipeline, that were already set.”

Each group of students worked on different datasets. One group picked a sediment metagenome dataset. One other group picked a sediment genome dataset from another location, and so forth.

Sengupta said some of the primary objectives of the groups included understanding what was unique about the data in their dataset and determining what types of microbial signatures they were working with. Some others included evaluating what kind of biogeochemical functions they could perform or indicating what temperature ranges their samples derived from and whether that mattered. They also looked at whether their datasets had the same molecular signatures throughout.

“The students were excited to learn that a handful of genes, or an abundance of genes, were the same and found in all sediments of a certain dataset,” she said. “Some sediments also had a unique set of genes.”

Sengupta said the experience seemed to keep students engaged and inquisitive, especially during COVID when everything became a blur. The students confirmed this sentiment through an end-of-semester class survey.

“It kept them motivated to do something together,” she said. “They had a common purpose, so to speak. They really seemed to be excited about learning something new. It helped with the morale of the class.”

Intensive research projects

After the success of the curriculum in her course, Sengupta opened the opportunity to a few students working in her laboratory. She figured it would be great to have students fully analyze datasets they were familiar with stemming from experiments they were readily a part of. The students performed data analyses as part of independent research projects for academic credit, which involved writing thesis papers on their results.

Compared to the fall cohort of students in the classroom setting, the students working in Sengupta’s lab had more time to do a deeper dive into the data. They could run more analyses, problem solve from the errors they ran into as a result of their analyses, and reach out to the developers for KBase about problem solving options.

“The thing about openly available tools like KBase is when students would run into issues and errors, they could send questions to the KBase support team and the team would respond directly to them,” she said. “They felt supported. The team helped them troubleshoot some of the issues they had.”

Two of the students from her lab, Justin Garcia and Joyce Barahona, used the experience as a stepping stone for getting into graduate school. Garcia is now attending medical school, and Barahona is attending nursing school. A third student, Nallely Delara, is also now applying to graduate school. Together, these three students also coauthored a paper with Sengupta about their experience, which was recently published in the Journal of College Science Teaching.

Importance of open access datasets

Sengupta said one thing that surprised her most between the classroom experience and the students working in her lab was that she had students coming back to her later about how they could access additional open databases. This got her thinking about how to identify additional online datasets and tools. These opportunities, she said, stand to open a multitude of opportunities for academic institutions that may not have the funding or resources to support fundamental scientific research. These experiences, she said, also help introduce students to careers such as bioinformatics that they would otherwise never have explored.

“From my experience in interacting with other faculty and students, it is primarily by word of mouth that you find out about these datasets and tools,” she said. “I know about a few of these because I attended EMSL Summer School. There is no central knowledge bank of data repositories. If we all came together, it would be hugely helpful. Imagine the doors that would open for both students and academic institutions.”

Expanding opportunities through EMSL

Sengupta now serves as a project manager at EMSL, supporting the laboratory’s user program. Through the program, researchers can submit proposals to access more than 120 advanced scientific instruments and expertise in the biological, computational, and environmental sciences.

Sengupta said she is excited to have a piece in further sharing datasets and capabilities readily available at EMSL through her role in the user program. Additionally, she is excited for the potential of EMSL’s new Science Central platform that expands access to data from EMSL user projects.

“The fact that we have these tools available to use, and with engaging events like EMSL Summer School, we are helping to spread the word and increase access to these sorts of resources,” she said. “Coming from a minority-serving institution where some students don’t have steady internet at their houses to perform an in-depth analysis, openly accessible data and analysis tools make the world of difference. It will help prepare the next generation of scientists and inform future scientific discovery.”