Mentored by MBL Scientists, UChicago Metcalf Students Forge Ahead with Research

Mentored by MBL Scientists, UChicago Metcalf Students Forge Ahead with Research

By Diana Kenney

As the seriousness of the Covid-19 pandemic hit home last March, the MBL began the nearly surreal process of adapting or canceling the multitude of courses, programs and events that, in a typical year, immerse the campus in a joyful whirlwind of scientific activity.

More than 1,500 students, faculty and scientists from around the world were looking forward to convening at MBL in the coming months. So very quickly, MBL leadership, staff, and course directors found numerous solutions, including the MVP webinars, to keep this essential community engaged and learning, while respecting the need to cancel in-person research and training.

One such program that adapted with agility is the University of Chicago’s Jeff Metcalf Summer for Undergraduate Research Fellows (SURF) initiative. Typically, the students selected for this program spend the summer in Woods Hole, working closely with an MBL scientist on a research project that aligns with their interests. This year, the student-mentor matches had been made and the projects were already planned when it became clear that the program had to cancel or change course.

MBL scientist Duygu Ozpolat adapted her SURF project to focus on image analysis, which can occur remotely. The project is part of her lab’s initiative to study regeneration in an annelid worm.

“So I reached out to the faculty mentors and asked if they could take on their Metcalf fellows remotely,” said Jean Enright of MBL Education. While some projects were impossible to carry out online, others were adaptable. And MBL scientists designed new projects for the students that were digitally native. In the end, “eight brave students agreed to take on a remote project,” said Bill Green, a professor at University of Chicago and SURF program advisor, at the students’ culminating and successful Zoom poster session on August 18.

Jack Riley (UChicago ‘23), for example, was initially disappointed that he couldn’t come to MBL for his SURF fellowship. Two years ago, Riley had spent a week at MBL through the High School Science Discovery Program, “an important experience for me that played a role in my decision to apply to University of Chicago and my plan to study biology,” he says. “Naturally, when I saw the chance to spend a summer in Woods Hole through the SURF program, I sprung for it immediately.” His planned project could not translate to digital, but fortunately MBL scientist Emil Ruff volunteered to develop new projects for Riley and another accepted SURF student, Alex Ellerstein (UChicago ‘23).

Metcalf fellow Jack Riley presents his research at the program’s virtual poster session.

“Jack and Alex were both very enthusiastic about their project from the beginning, although it was well beyond their comfort zone,” Ruff said. Using online databases and metagenomics, the students investigated genomes of uncultured microbes in the roots of cordgrass (Spartina alterniflora), a plant that populates salt marshes from the East Coast to South America.

“Both of them had very little experience with DNA sequence analyses and bioinformatics, but they very quickly learned to use the tools,” Ruff said. “Halfway through the summer, they were already able to work independently on their project using their own computational workflows they had prepared.” Both students also joined regular meetings with other scientists at MBL, as their work was part of a larger project led by MBL scientist Zoe Cardon, Ruff and colleagues and funded by the Symbiosis in Aquatic Systems Initiative of the Betty and Gordon Moore Foundation

“My mentors, Drs. Ruff, Sherlynette Perez Castro, and Elena Lopez Peredo, were incredible teachers and guides who led me through the new experience (for me) of doing biological research entirely on a computer,” Riley said. “I learned a ton about topics I’d known little about before. This was certainly a rewarding summer in spite of the change of location, and I hope I get the chance to come back to MBL in person soon!”

Metcalf fellow Cicily Padaam zooms in on her poster to explain future directions of the research.

MBL scientist Hilary Morrison had also accepted two Metcalf fellows for bioinformatics projects. She had weekly Zoom calls with her students, Cicily Padaam (UChicago ’23) and Cynthia Smith (UChicago ‘21), training them in techniques such a protein analysis, DNA sequence analysis and constructing microbial “family trees.”

“The Zoom meetings were a blessing,” Padaam said. “Dr. Morrison taught me how to use many tools I had not previously been exposed to and valuable skills, like navigating National Center for Biotechnology Information (NCBI) databases. Dr. Morrison was very encouraging, approachable and supportive through the whole process, and I learned a lot from her about microbial ecology.”

While this year’s Metcalf fellows missed the camaraderie of being together in Woods Hole and live exposure to all the people, organisms and resources that make the MBL so special, some of them did find ways to network.

“Though I was not able to work in a laboratory – I did most of my work sitting in my bedroom at home – I was pretty starstruck to be able to join Zoom meetings with the scientists Dr. Morrison is working with on an NSF-funded study called “The Macroalgal Microbiome in Space and Time,” Padaam says. “I am so grateful and proud that I was able to contribute in some way to this study.”

Padaam also took advantage of digital seminars offered by the MBL, including the Whitman Center’s Brown Bag Lunch series and the Friday Evening Lectures. She also attended an online seminar series, “Microbial ‘Omics for Beginners,” organized by MBL Fellow A. Murat Eren, assistant professor at the University of Chicago.

Metcalf fellow Bianca Campagnari analyzed a protein family found in cephalopods, working with MBL scientist Carrie Albertin.

“While I didn’t have the chance to be at MBL physically, I still felt welcomed into the community,” she says. “This opportunity has made me all the more excited to (hopefully) go to Woods Hole in the future!”

Other MBL scientists redesigned their SURF projects to focus on image analysis, which can be mentored remotely, including Duygu Özpolat and Roger Hanlon.

MBL Education Director Linda Hyman warmly congratulated the Metcalf fellows in introducing their well-attended final poster session. “This has been such a challenging summer for everyone,” she said. “But, at the end of the day, we are here to celebrate the work you did despite all of these challenges. From looking over your abstracts and talking to your mentors, I know it’s been incredibly productive and satisfying. It’s been an experiment – and we’ll call it a successful one!”

The 2020 Metcalf SURF Fellows and their projects/MBL mentors are listed below:

Adrian Kwiatkowski: “Investigating the Effects of Electroporation with Morpholinos on Platynereis  dumerilli Regeneration using Image Analysis”
Mentor: Duygu Özpolat, MBL Hibbitt Fellow

Bianca Campagnari: “Suckerins: A New Decapodiform Protein Family”
Mentor: Carrie Albertin, PhD, MBL Hibbitt Fellow

Aster Taylor: “Quantifications of Cephalopod Camouflage in Color and Spatial Scale”
Mentor:  Roger Hanlon, MBL Senior Scientist

Cicily Paadam: “ A Reference Database for Improved Taxonomy Annotation of Marine Microbiome 16S rRNA Gene Sequences”
Mentor:  Hilary Morrison, MBL Senior Scientist

Cynthia Smith: “Arachnula Protein Analysis”
Mentor:  Hilary Morrison, MBL Senior Scientist

Jack Riley: “Searching for Methanotrophs in Spartina alterniflora Rhizospheres”
Mentor:  Emil Ruff, MBL Assistant Scientist

Alex Ellerstein: “Investigating Sulfide Oxidizers in Spartina alterniflora Root Samples”
Mentor:  Emil Ruff, MBL Assistant Scientist

Jonathan Tang: “Metapangenomic Analysis of Two Oral Genera”
Mentor:  Jessica Mark Welch, MBL Associate Scientist