University of Chicago Undergraduates Gain Professional Research Experience at MBL

By Raleigh McElvery

Isa Alvarez received the 2016 McCarter Family Metcalf Fellow Award, which is presented to a high-achieving University of Chicago student to help defray the costs associated with his or her research internship.

Isa Alvarez received the 2016 McCarter Family Metcalf Fellow Award, which is presented to a high-achieving University of Chicago student to help defray the costs associated with his or her research internship. Her mentor at MBL is David Mark Welch of the Bay Paul Center.

Ten undergraduates from the University of Chicago are gaining substantive, project-based, and professional research experience at the MBL this summer through the MBL/Jeff Metcalf Summer for Undergraduate Research Fellows (SURF) Program.

The goal of this 12-week program is to immerse undergraduates in scientific research by training with leading scientists who are at the MBL during the summer.

“The Metcalf SURF Program is an outstanding example of the MBL/UChicago partnership, which promotes opportunities for research and educational advancement,” says Rae Nishi, Director of Education at the MBL.

Students begin by proposing a project, and are paired with an MBL scientist whose expertise parallels their own curiosities and career goals. In an effort to create a comprehensive research experience, MBL mentors guide students toward successful project completion, providing hands-on training either in the field or at the lab bench.

The Program is enriched by weekly brown-bag lunches with summer MBL scientists, networking opportunities with other undergraduates on campus, and evening seminars, as well as a variety of cultural and social activities. Additional workshops are also offered to assist in professional development. The summer culminates in a symposium, allowing students to present their projects to peers and the MBL community, prior to submission of a final paper.

This year’s Metcalf SURF students are interested in a variety of research areas, including microbiology, neurodegeneration, oceanography, ecology, and more. The 2016 participants are:

UChicago undergraduate Michael Sloyan, left, with his Metcalf SURF mentor, MBL Whitman Center scientist John Oakey of University of Wyoming.

UChicago undergraduate Michael Sloyan, left, with his Metcalf SURF mentor, MBL Whitman Center scientist John Oakey of University of Wyoming.

Alexandra Sjaarda

“Species Analysis of Micron-Scale Biogeography of the Human Oral Microbiome”

Mentor: Jessica Mark Welch, Bay Paul Center

Isa Alvarez

“Sea Star Associated Densovirus (SSaDV) and the Microbiome”

Mentor: David Mark Welch, Bay Paul Center

Molly Bennett

“Visualizing and Interpreting the Spatial Organization of Subgingival Plaque through Spectral Imaging Fluorescence In Situ Hybridization (FISH)”

Mentor: Jessica Mark Welch, Bay Paul Center

Nikita Mehta

“Investigating the Effects of Amyloid Beta (AB) on Mitochondrial Function and Long Term Potentiation in Hippocampal Neurons and Mouse Models of Alzheimer’s Disease”

Mentor: Elizabeth Jonas, Whitman Center

Tynan Bowyer

“Changing Marsh Landscape over Decades of Rising Sea Level”

Mentor: Ivan Valiela, Ecosystems Center

David Vishny

“Marine Microbial Ecology and the “Plastisphere”:  Community Assembly, Competition and Growth”

Mentor: Linda Amaral Zettler, Bay Paul Center

Michael Sloyan

“Artificial Microfluidic Droplet Interfaces as Functional Mimics of the Cytoskeletal Cortex”

Mentor: John Oakey, Whitman Center

Olivia Cattau

“Analyzing the Metrics of Rapid Neural Polyphenism in Cephalopod Molluscs”

Mentor: Roger Hanlon, Bell Center

Vishok Srikanth

“In Vitro Studies of Eukaryotic Ribozyme-Associated Mobile Genetic Elements”

Mentor: Irina Arkhipova, Bay Paul Center

Petry Byl

“Assessing Microbial Coordination over Time and Space in Siders Pond: Insights into Microbial Metabolic Networks that Drive Earth’s Biogeochemical Cycles”

Mentors: Julie Huber, Bay Paul Center / Joe Vallino, Ecosystems Center

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

UChicago Strategic Collaborative Initiative Seed Grants

“What Happens at the MBL Doesn’t Stay at the MBL”: Postscript to the UChicago Lab Schools Visit

Junior Owen Lasko at Sippewissett, a salt marsh and research site near the MBL. Credit: Beth Simmons

Junior Owen Lasko at Sippewissett, a salt marsh and research site near the MBL. Credit: Beth Simmons

Inspired by a week spent at the MBL last summer, several high schoolers are pursuing independent marine science projects at the University of Chicago Laboratory Schools. As recounted in the schools’ magazine, LabLife, two students built a saltwater tank once they got back to Chicago so they could continue studying marine organisms. One student had been intrigued by instrumentation development at MBL, “so we set him loose with some old microscopes, and he’s taken them apart and rewired them,” reports Lab Schools teacher Sharon Housinger, who set up a blog about the MBL visit. And three students set up experiments to study rotifers, the microscopic animals they met via MBL scientist Kristin Gribble, who uses them as a model system to study aging processes.

“We all learned so much and we had a great group dynamic … it just really worked on every level,” said Lab Schools junior Owen Lasko of their MBL trip. Read the article here.

 

Data Science Specialist Michael Franklin to Lead Computer Science at UChicago

Michael Franklin UChicagoThe University of Chicago announced today that prominent data science scholar Michael Franklin will chair its Department of Computer Science and serve as senior advisor to the provost on computation and data science.

Franklin will provide leadership for a major expansion in faculty, education programs, and scientific directions of the computer science department, building upon ongoing UChicago data science projects, and the expanding research area of data science among the University’s affiliated institutions, including the MBL.

Research at the MBL depends increasingly on the generation of large amounts of data of many different types, ranging from to imaging, to genome sequences, to longitudinal environmental surveys.  As such, one of the key areas of strategic focus at the MBL is the use of cutting-edge imaging and computation to illuminate cellular function and previously unknown biology.

“We are delighted with the appointment of Professor Franklin and look forward to engaging him fully in the work of the MBL,” said Jonathan Gitlin, Director of the Division of Research at the MBL. “His appointment will greatly enrich our ongoing partnerships in computational sciences with UChicago and Argonne National Laboratory that are vital to our collective research vision.”

Read UChicago announcement

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.”

Julie Huber Presents “Planet Microbe” at UChicago 125th Anniversary Event

Leadership and scientists from the University of Chicago and its three affiliated laboratories — MBL, Argonne National Laboratory, and Fermi National Accelerator Laboratory – gathered in Chicago last month to celebrate the past, present, and future of these collaborative partnerships, as well as the University’s 125th anniversary year. (Please see University of Chicago news story about the event here.)

Julie Huber speaks at the William Eckhardt Research Center last month at the University of Chicago. Credit: Rob Hart

Julie Huber speaks at the William Eckhardt Research Center last month at the University of Chicago. Credit: Rob Hart

As part of the celebration, Julie Huber, associate scientist and associate director of the MBL’s Josephine Bay Paul Center, gave one of four “Short Talks on Groundbreaking Research” (see video here). Huber and her colleagues are interested in large, cross-disciplinary questions, such as “How does life spread across the planet?” and “How do life and its environment co-evolve?” In that context, her lab is focused on the smallest and most abundant life form on Earth, the microbes.

Huber described the “stunning diversification” of microbial forms, which inhabit almost every niche on the planet. “What we do very well in Woods Hole is study the ocean,” she said, and her lab is exploring the mostly unknown realm of microbes living in deep-sea volcanic systems and beneath the seafloor. In these extreme, high-pressure environments, microbes have evolved novel strategies to survive, such as harvesting energy not from the sun but from the chemical energy of water-rock reactions.

Describing extreme marine microbes “may seem like very strange science, but the implications and applications are wide-ranging,” Huber said, including for research on how life began, the search for extraterrestrial life, and for discovery and development of new natural products ranging from anti-cancer drugs to biofuels.

“We have a lot left of our Planet Microbe to explore,” she said.

UChicago-MBL Undergraduate Scholarship is Awarded to Daniel Morrison

Daniel G. Morrison, a graduate of Falmouth High School, is the first recipient of the UChicago-MBL Scholarship for undergraduate study. Daniel received a full-tuition scholarship to UChicago and enrolled in September as a first-year student.

Daniel is the son of Hilary Morrison, senior research scientist in the Bay Paul Center. Children of year-round MBL employees (minimum 20 hours/week) who are accepted to the University of Chicago are eligible for consideration for this scholarship.

Daniel reports that “UChicago has been great so far; it’s a very challenging experience but also extremely rewarding.” He is considering majoring in either math or computer science. “Outside of class, I’m really enjoying singing in the Rockefeller Chapel Choir,” he says. “We’ll be performing Handel’s Messiah before winter break starts.”

The deadline to apply to the University of Chicago for the 2016-2017 academic year is January 1 (regular decision candidates).

Dan Morrison

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 https://collegeadmissions.uchicago.edu/costs.

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 ebenoit@uchicago.edu 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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