New Microbiome Center to Combine MBL, University of Chicago, and Argonne Expertise

UChicago Strategic Collaborative Initiative Seed Grants

Of Whales, Scales, and Microbes: New Program for UChicago Undergraduates at MBL Offers Broad View of Marine Biodiversity

By Diana Kenney

It’s one thing to debate Darwin’s evolutionary theory in the classroom. It’s quite another to do so after vivid encounters with the natural world: mucking through a salt marsh to scoop up microbes; observing a dolphin dissection and seeing how strikingly human it looks inside; gazing into the eyes of a whale that seems eerily aware.

Jutting from the façade of the MBL’s Candle House is a replica of the bow of the Charles W. Morgan, a whaleboat built in 1841 in New Bedford, Mass. After many voyages, it was restored at Mystic Seaport, Conn., where it is open to visitors, including students in the Whale Program last fall.

Jutting from the façade of the MBL’s Candle House is a replica of the bow of the Charles W. Morgan, a whaleboat built in 1841 in New Bedford, Mass. After many voyages, it was restored at Mystic Seaport, Conn., where it is open to visitors, including students in the Whale Program last fall.

That may be why the 10 University of Chicago students who just completed a new quarter-long program, “The Whale: Biology, Culture, and Evolution on Nantucket Sound,” comprised “one of the best classes I’ve had at the undergraduate level,” says Robert Richards, the Morris Fishbein Distinguished Service Professor in the History of Science and Medicine. “These kids were all extremely sharp. We argued to the end, in kindly and good fashion. They wanted to challenge everything! They were the kind of students you think of as ideal at the University.”

Richards has taught Darwinism at UChicago for many years, but last fall it was in the context of the new “Whale Program” held at the University-affiliated Marine Biological Laboratory in Woods Hole, Mass. For three weeks prior to Richards’ course, the students, all non-biology majors, took an intensive laboratory course on “Experimental Biology by the Sea,” led by Karl Matlin, professor of surgery, and Chris Schonbaum, senior lecturer in the Biological Sciences Collegiate Division.

“We introduced them to research on not only whales, but also fish and crabs, sea urchins, frogs, and microbes,” Matlin says. “The whale was a foil for this course in many ways,” he says, one being exposure to marine research experiments at the MBL and in Woods Hole. “We hoped that, by the time they got to Darwin, they would have a better sense of biodiversity and the natural environment, and how evolution might work.”

Kicking off this new study-abroad style program was a course on “Whales, Whaling, and American History,” taught by Michael Rossi, assistant professor of the history of medicine. “How to Observe Alien Animals,” taught by UChicago graduate student Lily Huang, rounded out the quarter in Woods Hole.

A sense of place

Woods Hole whalers took part in the golden era of American whaling in the early 19th century, spearheaded by enormously profitable operations based in Nantucket and New Bedford, Mass. American whalers were especially good at hunting sperm whales and extracting the valuable spermaceti from the head, a waxy substance that was refined for luxury items such as high-quality candles, lamp oil, and perfumes. MBL’s Candle House building was originally a spermaceti candle factory.

University of Chicago students inspect a beluga whale at Mystic Aquarium in Mystic, Conn. The students recorded whale sounds and behaviors for a unit on cetacean bioacoustics and communication. Credit: Michael Rossi

University of Chicago students inspect a beluga whale at Mystic Aquarium in Mystic, Conn. Credit: Michael Rossi

Rossi’s course immersed the students in the intellectual, social, and cultural history of American whaling through readings, discussions, and excursions beyond Woods Hole.

“It’s one thing to read about a harpoon and another thing to see this 12-foot-long piece of wood and iron,” Rossi says of their trip to the New Bedford Whaling Museum. They spent a day exploring Nantucket Island, where they met with Nathaniel Philbrick, author of In the Heart of the Sea: The Tragedy of the Whaleship Essex, recently released as a movie. And they observed whales in the wild during a boat trip out of Provincetown, Mass.

“It’s really neat to study in a place where we learn about what is right around us,” says Greg Ross, a second-year student in the Whale Program.

“Just because it happened in the past doesn’t mean it’s forgotten in Woods Hole,” adds Kelly Peyton, a fourth-year anthropology major. “The alignment of it all was awesome.”

As they moved forward in history, they considered shifting social attitudes toward whales. “We went from thinking of whales as an exploitable natural resource that is more or less insensible and perhaps even malevolent, to an animal that perhaps is a model for other types of mammalian cognition, such as humans,” Rossi says. “How would you know? What happens when you project intelligence onto another creature?”

And they read Moby Dick, which Rossi calls “a deeply weird, strange book. You can read it almost without a plot. It’s all about the risks of confronting the vastness of the unknown—and the rewards.”

The power of observation

Observation was a common theme running through the Whale Program’s courses, Matlin says. Huang’s course, for example, began with the question, “What would be a better strategy for studying the lives of other animals: To assume that their experience is basically assimilable to ours, or utterly alien?” “The course was brimming from the start. There was a lot to say,” Huang says.

UChicago students Luiza Gundim and Alexander Okamoto pipette reagents for DNA extraction in a lab led by MBL scientists Linda Amaral Zettler and Julie Huber. Credit: Tom Kleindinst

UChicago students Luiza Gundim and Alexander Okamoto pipette reagents for DNA extraction in a lab led by MBL scientists Linda Amaral Zettler and Julie Huber. Credit: Tom Kleindinst

“In the lab, observation is critical,” Matlin says of his experimental biology course. The students carried out several classical experiments in sea-urchin embryology, some originally conducted at the MBL, and learned about MBL’s formative role in this field through a lecture by historian Jane Maienschein of Arizona State University. They then moved into a microbial ecology unit, led by MBL scientists Linda Amaral-Zettler and Julie Huber.

“We stomped around the marsh measuring salinity, temperature, oxygen, and taking sediment samples,” Huber says. “By the end of the week, the students had looked at the samples under the microscope, extracted microbial DNA, amplified genes from the DNA, and sequenced the DNA.”

The students then spent several days at another research organization, Woods Hole Oceanographic Institution, where they studied cetacean anatomy, physiology, and coastal strandings and whale communication.

Their varied observations in embryology and animal physiology later proved valuable in Richards’ course. “They had much more evidence, and more kinds of experience to prepare them to talk reasonably about Darwin’s theory,” Richards says.

Darwin, of course, “was a great observer,” Richards says. “A good deal of his argument for evolution by natural selection depended on his observations in biogeography, embryology, artificial selection, the patterns and variety of species and genera in the natural world.

“While each one may not be completely convincing, all together they produced, as Darwin said, ‘one long argument’ for his view.”

Applications Now Accepted for UChicago-MBL Scholarship

Beginning its second year, applications are now being accepted for the University of Chicago – Marine Biological Laboratory Scholarship for undergraduate study.

Each application cycle, the University of Chicago will offer one full-tuition MBL scholarship to a qualified applicant. The scholarship will be renewable for four years as long as the recipient remains in good academic standing and one of their parents is a year-round, minimum 0.5 FTE (20 hours/week) employee of the MBL. This is a great opportunity for MBL families to take advantage of the outstanding education the University of Chicago provides for its students. We ask any families that have students applying to the University of Chicago this year to fill out the following by January 3, 2016: MBL Employment Verification Form.

uchicago.campusTo be awarded the full-time scholarship, the student must be accepted for first-year admission to the University of Chicago and must be among the most qualified applicants from Marine Biological Laboratory families as judged by the admissions committee. First-year applicants are required to complete either the Universal College Application or the Common Application , both available online. Additionally, students will be required to complete the University of Chicago Supplement which is available online or through the Common Application. The deadline for applications to the University of Chicago is November 1, 2015 for Early Action and January 1, 2016 for Regular Decision.

These are merit-based scholarship and do not preclude the possibility of additional need-based financial assistance from the University. The University strives to ensure financial need is not the controlling factor in determining whether a student can attend. To apply for financial aid, the UChicago Financial Aid Worksheet is due November 1, 2015 for early action applicants. The Free Application for Federal Student Aid (FAFSA) must be filed with the appropriate processing agencies by February 1, 2015 for regular notification. For additional information, please visit

If you have questions about the scholarship or would like additional information about admission to the University of Chicago, please contact Emily Benoit, Assistant Director of Admissions, at or (773) 702-7944.

Undergraduates Wrap Up an MBL Summer with Successful Poster Session

By Diana Kenney

Looking ahead to a new academic year starting in late September, several University of Chicago students recently flew home after a summer at the MBL. Before leaving, they shared the knowledge they had gained during their Metcalf Summer Undergraduate Research Fellowships (SURF) at a well-attended poster session in Swope Center.

Each student had spent twelve weeks in the lab of an MBL scientist who provided mentoring on a research project. Several of the students partnered on their research with an REU (Research Experiences for Undergraduates) student from another university.

“Twelve weeks is a long time; we managed to accomplish a lot,” said Associate Scientist Linda Amaral Zettler, who mentored Metcalf SURF student Irene Zhang and REU student Louise Barias of Dartmouth College. “Irene was exposed to all the major analyses in my lab. She has those skills under her belt now, which will really help her if she moves on in the field.”

Below are a few snapshots from the Metcalf SURF poster session, which was organized by Beth Simmons, Assistant Director of Education. Other UChicago Metcalf undergraduates this summer and their MBL mentors were: Clara Kao (Jonathan Gitlin); Eva Kinnebrew (Chris Neill); Hanna Weller (Roger Hanlon); Leonard Shaw (Maureen Conte); Petra Byl (Joe Vallino/Julie Huber); and Jonathan Michelson (Jim Tang).

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UChicago Lab School Students “Get Their Hands in the Water” at MBL

By Rachel Buhler

Taking a break in a lounge in Loeb Laboratory, the two high-school science teachers looked sunburned, tired, but very happy. Daniel Calleri and Sharon Housinger of the University of Chicago Laboratory Schools had spent the prior day with 12 of their students on Naushon Island, off the coast of Woods Hole. Nets in hand, they scouted out and collected marine organisms with the expert help of Dave Remsen, director of the MBL’s Marine Resources Center. After boating back to Woods Hole, the group took their finds into an MBL lab for further study.

“We wanted the students to jump right in and get their hands in the water, to take full advantage of Woods Hole in this short period of time,” said Calleri.

The 12 Lab School sophomores, juniors, and seniors spent a week at the MBL last month with Calleri, Housinger, and Alexzandra Wallace, the Lab School’s Manager of Special Projects and Outreach. The teachers had come to the MBL in 2014 to explore a possible collaboration with MBL Education Director Bill Reznikoff, and this summer’s stay was the successful result.

“This is another example of the MBL’s expanding relationship with the University of Chicago,” said MBL President and Director Hunt Willard. “We were happy to help introduce the Lab School students to the Woods Hole environment and the study of local marine organisms.”

UChicago Lab School students Whitney Thomas and Delnaz Patel observe plankton from the plankton tow, one of their many encounters with microorganisms during their MBL trip. Credit: Beth Simmons

UChicago Lab School students Whitney Thomas and Delnaz Patel observe plankton from the plankton tow, one of their many encounters with microorganisms during their MBL trip.
Credit: Beth Simmons

In their MBL lab, the students observed fertilization of sea squirt (Ciona) eggs and, through the microscope, watched the embryos divide. They also experimented with neural stimulation of squid skin thanks to inspiration from the YouTube hit “Insane in the Chromatophores” by Backyard Brains, which was recorded at the MBL in 2012. In addition, they learned how and why other organisms at the MBL are studied, including frogs, horseshoe crabs, and microscopic animals called rotifers.

After being chosen to visit the MBL through a competitive application process, the Lab School students prepared by taking a quarter-long marine biology course. In Woods Hole, their teachers were thrilled to bring them into the ecosystems they had studied in their textbooks. “It was like instant connection and understanding,” Housinger said. “I was thinking this morning when they were in the lab looking at the embryos, that they probably learned more embryology in two hours than we would have been able to teach in two weeks in the classroom.”

The students also saw at MBL that there are many ways to engage with marine biology, such as through training in physics (leading to microscope development) or chemistry. “For biology, traditionally they are taught, ‘Here’s this list of words, memorize it, and now you know marine biology,’ and it’s no wonder why people don’t go into it,” Calleri said. “It’s never presented as a field that has opportunity for professional growth and development. But at MBL, you get to see that writ large.” The MBL showed students who are starting to form collegiate aspirations several real-life examples of careers in the sciences.

A number of MBL faculty and staff members offered their time to interact with the Lab School students to ensure they had a well-rounded experience. They included Beth Simmons (Education Department); Dave Remsen and Scott Bennett (Marine Resources Center), Shalin Mehta and Hiro Ishii (Bell Center), Kristen Gribble (Bay Paul Center), Ivan Valiela (Ecosystems Center), and Esther Pearl (National Xenopus Resource).

The teachers hope an MBL trip will become part of the annual curriculum at the University of Chicago Laboratory Schools. “The students are seeing the MBL motto of ‘Biological Discovery’ in real-time,” Wallace exclaimed.

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

By Kelsey Calhoun

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:

Caroline Albertin_smCarrie 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?”

5-Katharine-Criswell-of-UChicago-at-MBL-Credit-Tom-Kleindinst_smKate 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_smSamuel 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.

3-Darcy-Ross-UChicago-Credit-DanielCojanu_smDarcy 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.”

Neuroscientists Invited to Apply for a Travel Award to Attend the SPINES Neuroscience Symposium in Chicago

Monday, June 15, 2015, Chicago, IL

Contact: Chinonye Nnakwe, PhD

Event: SPINES Neuroscience Symposium—Scientific Excellence and Lifelong Mentoring to Increase Diversity

Date and Location: October 16, 2015 – Hyatt Regency Chicago, 151 E. Wacker Dr., Chicago IL

Deadline to Apply for a Travel Award: June 30, 2015

The aim of the SPINES Neuroscience Symposium is to deepen our knowledge and understanding of current findings in neuroscience, recruit young and aspiring underrepresented scientists, as defined by the National Institutes of Health, to the field of neuroscience and to enhance retention and success of those already in scientific careers.

The planning committee seeks applicants to apply for a travel award. For further information and an application visit the website:

Applications from pre-doctoral and postdoctoral neuroscientists, and faculty/scientists from academia, industry and non-profit organizations are encouraged. There is a special interest in receiving applications from past and present SPINES students. The deadline to apply for a travel award is June 30, 2015.

About the Symposium
The SPINES Neuroscience Symposium will bring together a large contingent of underrepresented minority neuroscientists from multiple SPINES generations to provide encouragement, support, and networking, in the context of a scientific conference. Planned activities include scientific lectures, professional development workshops, lightning talks, mentoring sessions, and a showcase of the successes of SPINES student and faculty alumni.

About the SPINES Course
SPINES (Summer Program in Neuroscience, Ethics & Survival) is a novel professional development course offered each year at the Marine Biological Laboratory (MBL) to facilitate the careers of underrepresented doctoral and postdoctoral students and early career neuroscientists. It is considered a model for the successful training of early career scientists from underrepresented groups. The SPINES course has been offered for over 20 years and has hundreds of alumni — from those who are beginning their careers to those nearing retirement. The key ingredients for the success of SPINES are career-long mentoring, monitoring, networking, and understanding the current boundaries of neuroscience knowledge. No other experience, except graduate training, has such a profound effect upon a student’s research career, as does a summer course at the MBL. Many describe the effect as magical and transformative.

Additional Symposium Sponsors
Alzheimer’s Association
Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior

MBL–UChicago Exploratory Research Seed Funds Announced

We are pleased to announce grants in support of collaborative research among UChicago and MBL faculty (both visiting and year round) at the MBL. The grants will seed novel research that initiates collaboration between individuals and institutions and can serve as the substrate for future grant proposals. The intent is to provide the basis for collaborative research between UChicago faculty and visiting and/or year-round faculty of the MBL.

These grants are intended to be exploratory funds: budgets are at a maximum of $25,000, proposals are short, target dates are quarterly, and review and funding will be rapid.

Applications are accepted in Fall, Winter, and Spring Quarters. The next round is due April 30, 2015.

Completed applications are due by midnight CST on April 30th.


Winter 2015 MBL – UChicago Exploratory Seed Fund Winners

Melina Hale, Jennifer Morgan
“Behavioral change and neural circuit reorganization during metamorphosis in Xenopus

Understanding of neural circuit development and evolution is limited by the difficulty of establishing neuron homology among organisms and species. How does the startle circuit reconfigure from driving unilateral axial bending to controlling bilateral limb movement during development and evolution? Here we focus on development and will examine the M-cell circuit through the transition from tadpole to frog in Xenopus laevis. This work will provide new insights into how neural circuits develop through major behavioral transitions and will inform examination of startle circuit evolution in tetrapods. Homology of the M-cells to hindbrain neurons of amniotes is unknown; ultimately we aim to trace the evolution of this neuron and its circuit across the water-to-land transition and through tetrapod diversity.

Marine Biological Laboratory Semester in Environmental Science Open to UChicago Students