University of Chicago Pilots Undergraduate “September Courses” at MBL

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Sampling at Wood Neck Beach for the “Marine Invertebrates of Woods Hole” course. L-R: Lavina Li, a 4th-year Anthropology/Chemistry major, and course teaching assistant Brooke Weigel, a PhD student in Evolutionary Biology. Credit: Megan Costello

Sampling at Wood Neck Beach for the “Marine Invertebrates of Woods Hole” course. L-R: Lavina Li, a 4th-year Anthropology/Chemistry major, and course teaching assistant Brooke Weigel, a PhD student in Evolutionary Biology. Credit: Megan Costello

“It’s intense—and enjoyable,” University of Chicago undergraduate Savy Johnson says of the new course that has landed her on the MBL’s Woods Hole campus for three weeks this September.

Johnson is taking “Observing Proteins in Action: How to Design and Build Your Own Instruments,” one of three new courses at MBL offered to UChicago undergraduates in any major. Thirty-five students signed up for one of these pilot “MBL September Courses,” which take place before UChicago’s fall-quarter classes begin.

“These courses are part of our regular fall term. The students will take the remaining three courses of the quarter when they get back to Chicago,” says Jocelyn Malamy, associate professor of Molecular Genetics and Cell Biology at UChicago and an MBL Whitman Center scientist.

“We are taking our first steps forward to really integrate course opportunities at the MBL into our mainstream curriculum,” says Malamy, who spearheaded these courses in her role as Master, Biological Sciences Collegiate Division at the University.

The enrolled students’ majors are diverse – from Biology to Geophysical Sciences to Economics to Theater. All University of Chicago students must take two quarters of biology, and these MBL courses count toward that requirement.

Faculty from both the University and MBL are teaching the courses, which explicitly “take advantage of the wonderful scientific and ecological resources of the MBL location,” Malamy says.

And the course faculty have elected to adopt the model the MBL has developed for its immersive Advanced Research Training Courses: lectures in the morning, lab and field work in the afternoon, and the opportunity for students to develop independent research projects.

“Three weeks is a tight time frame, but nevertheless, the University of Chicago kids are amazing. I think they’ll be able to do some really great [projects],” Malamy says.

Gaibo Zhang , a 4th-year Economics/Computer Science major, measures a transect of Little Sippewissestt Marsh, Falmouth, for the “Microbiomes Across Environments” course. Credit: David Mark Welch

Gaibo Zhang , a 4th-year Economics/Computer Science major, measures a transect of Little Sippewissestt Marsh, Falmouth, for the “Microbiomes Across Environments” course. Credit: David Mark Welch

A Dazzling Diversity

Indeed, after five days, the 12 undergraduates in the “Microbiomes Across Environments” course had come up with 12 different research projects, “and a lot of them had done their sampling or analysis or set up their experiments. I was just blown away by how hands-on they became, so quickly,” says Jack Gilbert, faculty director of the Microbiome Center at the University of Chicago and co-director of the MBL course with David Mark Welch, director of the MBL Division of Research.

Gilbert and Mark Welch are teaching the students how to analyze the (immense) microbial diversity in any kind of niche – from the human body to a coastal salt marsh. Some students have chosen to focus on the microbiome in samples of water, soil, plants, or animals they collected from field sites near Woods Hole; others sampled from fish, skates, and other organisms in the MBL’s Marine Resources Center; and still others took microbiome samples from their own bodies.

They are asking questions about microbiome changes across tidal gradients or landscape variations, as marine embryos develop, or in the mouth after different foods are eaten.

Even though some of the students have no experience with biological research, they are learning the most up-to-date methods of metagenomics: how to extract DNA from their samples and prepare it for next-generation sequencing at the MBL’s Keck Facility; and bioinformatics strategies to make sense of the hundreds of thousands of DNA sequences (and microbes) their samples contain.

“The goal is that they will carry out an actual microbiome experiment,” says Mark Welch, who also directs the MBL’s Bay Paul Center, where scientists have been pioneering metagenomic strategies since the 1990s.

Invertebrates Everywhere

A crash course in biodiversity is also rolling out for the 14 students in “Marine Invertebrates of Woods Hole: Ecology, Diversity, and Function.”

“It’s super interesting. It’s an immersion course in marine biology, which is the best way to learn,” says Jennifer Teng, a 4th year Biology major.

Drawings of marine organisms and notes on their anatomy by Jennifer Teng, a 4th-year Biology major and student in the Marine Invertebrates course. Credit: Megan Costello

Drawings of marine organisms and notes on their anatomy by Jennifer Teng, a 4th-year Biology major and student in the Marine Invertebrates course. Credit: Megan Costello

The course director is Michael LaBarbera, professor emeritus of Organismal Biology and Anatomy at UChicago.

“We are introducing the students to the biology of the major invertebrate groups and to their diversity in the Woods Hole environment,” he says. “On the first day we went to Nobska Point and collected and identified 30 to 40 different species. On the first day!”

The students have since sampled at several other sites and gathered their “finds” in a tank room in Loeb Laboratory. Using the manual “Keys to Marine Invertebrates of the Woods Hole Region,” they are identifying the species they find by anatomical and taxonomic cues. The manual was first drawn up in 1964 at the MBL and LaBarbera began updating it last fall.

“The Woods Hole Keys is an important resource that we can build upon,” LaBarbera says. One student found a crab (Hemigrapsus) that wasn’t listed at all in the original manual; it’s a West Coast species that appeared in New Jersey in 1990 and moved up the coast. “It’s now the second-most common crab we are finding,” LaBarbera says. “We are in a world of flux: sea temperatures, sea levels are up since 1964.”

The students are following their own interests. On a recent afternoon in the lab, some were clustered around two jellyfish tanks brought by course faculty member Jack Costello, an MBL Whitman Center scientist from Providence College. One group was learning how to use Costello’s high-speed camera to quantify the animals’ locomotion; another group watched the sinuous creatures capture and eat prey. Other students were anticipating interactions with MBL Senior Scientist Roger Hanlon, the third course faculty member. Hanlon will introduce them to the study of the most behaviorally sophisticated invertebrates, the cephalopods (squid, octopus, and cuttlefish).

“We don’t give the students exercises. We say, ‘Watch the animal, come up with a question, and see if you can address the question with the equipment we have,’” LaBarbera says. “By the end of the course they will all be doing projects.”

If You Can Build It, You Understand It

The “Proteins in Action” course adopts another common feature of MBL’s Advanced Research Courses: The students learn how to build customized scientific instruments.

“Once the course is over and the students can digest the material – and it’s an enormous amount, it’s a fire hose of new data – they will be able to design devices for their own experiments,” says faculty member Eduardo Perozo, professor of Biochemistry and Molecular Biology at the University of Chicago.

Building a circuit for a voltage clamp in the “Observing Proteins in Action” course. L-R: Savy Johnson, 2nd-year Biology/Economics major and Matthew Lawson, 2nd-year Neuroscience/Psychology major. Photo by Tom Kleindinst

Building a circuit for a voltage clamp in the “Observing Proteins in Action” course. L-R: Savy Johnson, 2nd-year Biology/Economics major and Matthew Lawson, 2nd-year Neuroscience/Psychology major. Photo by Tom Kleindinst

“We start with the properties of simple electrical components,” says course director Eric Schwartz, professor of Pharmacological and Physiological Sciences at the University. “The students build simple analog circuits and then build them into more complicated circuits, like a voltage clamp” (a neuroscience tool used to measure electrical current across the cell membrane of neurons and other cells).

Then Perozo will teach them how to isolate a protein — in this case a membrane channel protein from a bacterium. They will incorporate the proteins into live egg cells or bilayers, guided by course faculty member Ana Correa of University of Chicago.

Next – like many at MBL before them — the students will build a fluorescence microscope from parts. This scope will allow them to simultaneously study the electrical and optical properties of the proteins, such as the conformational changes that accompany electrical changes. Schwartz and Francisco Bezanilla, professor of Biochemistry and Molecular Biology at the University, will lead this section.

“We want for them to understand how we discover new ideas,” says Schwartz. For a final project, the students will design devices to record action potentials in Venus flytrap plants.

Like the other two courses, this one did not previously exist in the University of Chicago curriculum. “When I was an undergrad, I would have done anything I could to get into this course!” says Perozo. “This is an amazing experience, both for the faculty and for the students.”