From Octopus Development to Arctic Change: UChicago Graduate Students Pursue Research Questions at the MBL

From octopus embryology to the proteins active in Arctic soil, University of Chicago graduate students are exploring a range of questions at the MBL this summer as recipients of a University of Chicago Graduate Student Research Award. Now in its second year, this program enables selected UChicago students to enroll in an MBL course or collaborate with an MBL research mentor. This year’s awardees are:

Carrie Albertin spent several weeks at the MBL investigating octopus development, as a follow-up to her recent work on octopus genomics. Albertin is first author of the cover story in Nature this week, which provides the first whole-genome analysis of an octopus (O. bimaculoides). This also represents the first complete sequencing of a cephalopod, a class of predatory molluscs that includes octopus, squid, cuttlefish, and nautilus. A sixth-year graduate student in Cliff Ragsdale’s lab in the Department of Organismal Biology and Anatomy at the University of Chicago, Albertin plans to defend her thesis soon after incorporating this summer's work. Her MBL research was sponsored by Senior Scientist Roger Hanlon; she also worked closely with Research Associate Stephen Senft.

Albertin is interested in the unusual body plans of the cephalopods. The octopus, with its large brain and eight arms capable of grasping objects, is constructed very differently than most other animals, even other molluscs. “By sequencing the genome, you get access to the whole [genetic] toolkit the animal has” to develop its body plan, says Albertin. Genomic analysis also allowed her to “get a broad look of how to build a cephalopod,” she says, and uncovered quite a few surprises. Read more here "Octopus genome sequenced," UChicago Medicine & Biological Sciences.

Albertin’s octopus developmental studies at the MBL this summer complement her genomic research. “These are two different snapshots of the same species,” she says. She took advantage of healthy specimens in the MBL’s Marine Resources Center and a powerful scanning electron microscope (SEM), which gives “a very different view [of structure] compared to a light microscope or even a confocal microscope,” she says. “You see all kinds of surface detail that you wouldn’t normally get.” Albertin used the SEM to look at various octopus body tissues and a technique called in situ hybridization to determine which genes are expressed as those tissues develop. The SEM data will add another dimension to the broader question that interests Albertin: “How do you get from a single cell to an eye, a brain, an arm?”

Kate Criswell attended the 2014 Embryology course as a recipient of a UChicago Graduate Research Award and came back to the MBL this summer, using part of her original award. Criswell returned to study the development of skates: flat, cartilaginous fish that resemble stingrays. Using a technique called fate mapping, Criswell is tracking how skate embryos grow and investigating what undeveloped tissues will become in the mature skate. She’s particularly interested in how the spine and the vertebrae form.

Not many scientists study skates, but for Criswell’s research questions, it’s one of the best experimental systems. As a fourth year-graduate student with Michael Coates, Professor of Organismal Biology and Anatomy at UChicago, Criswell sometimes has skates flown into the lab from a faraway ocean. However, she’s found it’s difficult to keep them healthy in the lab’s artificial seawater. In terms of experiments, “everything goes much more smoothly at the MBL,” Criswell says. She’s been able to collect a large amount of data with her MBL mentor, Whitman Center Investigator Andy Gillis of Dalhousie University, and she’ll analyze it over the winter.

This Chicago winter may be Criswell’s last, as she is about to graduate, but she hopes her work with skates—and her pilgrimages to the MBL—will continue. “The MBL has such a great, inspiring, positive, and creative atmosphere,” she says. Wherever Criswell goes after graduation, the MBL will likely be part of the plan.

Samuel Miller, a fifth-year graduate student in Albert Colman’s lab in UChicago’s Department of the Geophysical Sciences, came to the MBL for its expertise in Arctic ecology. Miller studies frozen Arctic soils (permafrost) using proteomics, a method that investigates all the proteins present in a particular tissue, organism, or environmental sample. He’s interested in how permafrost soil microbes are responding to global warming. As the permafrost warms, proteins produced by microbes degrade frozen organic matter in the soil, which releases greenhouse gases, such as carbon dioxide. Understanding the types of soil proteins present will shed light on the response of the Arctic carbon cycle to a rapidly changing climate.

Miller is also identifying the microbial genes that encode Arctic soil proteins. This metagenomic approach is an essential complement to proteomics, since the DNA in a soil sample indicates the range of proteins that can potentially be expressed. His Graduate Research Award is supporting metagenomic analysis at UChicago, as well as a week at the MBL working with Senior Scientists Anne Giblin and Gus Shaver, both MBL Arctic researchers. Giblin and Shaver have long experience conducting research at Toolik Field Station in Alaska, where Miller collected soil cores last year.

Darcy Ross also attended the Embryology course in 2014 and has returned to the MBL to continue her research. She is interested in the development of snail shells, specifically in the slipper snail (Crepidula fornicata). She wants to know how the shells form and what shell building involves, but the larger question behind her investigation concerns how shells have evolved.

The experiments Ross has designed can be conducted at UChicago, where Ross is a third-year graduate student with Neil Shubin, Bensley Professor of Organismal Biology and Anatomy. But the snails stay healthier in natural seawater at MBL, so Ross is working out of Shubin’s lab in the MBL’s Whitman Center this summer. Ross also has expert advice here. “One of the Embryology course faculty members, Jonathan Henry of the University of Illinois, is the snail guy,” Ross says. Henry, who is co-mentoring Ross’s MBL research, has developed techniques and protocols to explore these very small experimental subjects. Ross is using UV light and various drugs to determine which genes play a role in shell coiling, and she wants to know whether different species’ shells are built by disparate methods. “It’s time to start looking at the inside of the shell” and the story behind it, Ross says, “as well as the outside.”