Summer Research

Ever wonder what it takes to keep MBL scientists working away? Here’s a clue, in the form of a time-lapse video of the daily upkeep required for the many zebrafish being studied at the MBL this summer. University of Chicago undergraduates Melissa Li and Clara Kao pressed “go” on a video camera and then went about their daily routine of feeding, cleaning, and generally caring for all the fish in the Zebrafish Facility. “We basically make sure everyone is happy and healthy,” Kao says. The 24-second video went up on a blog they’re keeping on their summer of research at the MBL: Summer People, Some Are Not (tagline: Some Are Zebrafish).

These two rising juniors are working in Jonathan Gitlin’s lab this summer, a change from the labs they work in back in Chicago. “When you switch labs for the summer, you get a different sort of snippet of the scientific world,” Li says. Both are interested in coming back to the MBL after the summer is over- Kao is in fact here for her second summer, and is interested in coming back for the Physiology course. With any luck, the blog and video collection will get a chance to expand.

By Kelsey Calhoun

The most exciting phrase to hear in science, the one that heralds new discoveries, is not “Eureka” but “That’s funny…”
—Isaac Asimov (1920–1992)

The process of science is rarely predictable: there are some 180s, some hard left turns, and quite a few long and winding roads. Graduate student Drew Friedmann can attest to this fact: a year and a half ago he was pursuing a completely different research topic and getting nowhere. But it was at the end of some long and frustrating months that he uttered some of the most exciting words you can hear from a scientist: “That’s funny,” or more specifically in this case, “Zebrafish don’t see with their tails.”

Primary motor neurons fluorescing in the young zebrafish, home to the unexpected VALopA Photo cred: D. Friedmann & Isacoff Lab

Primary motor neurons fluorescing in the young zebrafish, home to the unexpected VALopA. Photo credit: D. Friedmann & Isacoff Lab

Friedmann, a 2015 Grass Fellow at the MBL, had originally set out to study what controls the movement of zebrafish. These two-inch-long fish are widely studied, partly because they are transparent when young, making it easy to track their development. Ehud Isacoff’s lab at University of California-Berkeley, where Friedmann is a graduate student, has mapped the flow of calcium—a proxy for neuronal activity—in the nerve cells of developing zebrafish as they move.

Taking this further, Friedmann hoped to focus on how these young fish manage to move by looking at their gap junctions, the direct connections between cells which help them talk to one other. But there are over 30 different types of building blocks, called connexins, that make up these gap junctions, and few clues as to which ones help control movement as the zebrafish develop. Friedmann spent a long, frustrating year tackling this question with different tools and methods, without getting many interesting results.


One day, he tried genetics. Analyzing only the neurons controlling movement in zebrafish tails—the most motile part of the fish—yielded a long list of active genes. One gene on the list, VALopA, caught Friedmann’s eye, because it codes for an opsin, a light-sensitive protein usually only found in eyes. “I went, what is that doing here?” Friedmann remembered. “There are no eyes in the sample!”

The “that’s funny” moment seemed odd enough to merit a little digging. “I’ll just flash some lights and see what happens,” Friedmann thought. The Isacoff lab uses a plethora of microscopes to track the flow of calcium around zebrafish, including a bright green laser. “I was expecting to flash the laser and see a calcium event,” Friedmann explained. But no such luck—light was not stimulating the neurons, embedded with light-sensitive proteins, to fire. Frustrated, Friedmann tried for a while longer, and finally noticed something else odd. If these neurons really didn’t respond to light at all, there should have been a random calcium spike or two right after a light flash, but there wasn’t. There was never a spike after a light flash; instead, the light was actually inhibiting the neurons from firing.

Motor neurons innervating the zebrafish tail Photo credit: D. Friedmann & Isacoff Lab

Motor neurons innervating the zebrafish tail
Photo credit: D. Friedmann & Isacoff Lab

This presents a whole new unexpected puzzle: Why are light-sensitive, movement-controlling neurons inhibited by light? “This opens up two, maybe three big questions,” Friedmann says. “One is how, one is why, and one is how common is this?” Zebrafish always lay their eggs at sunrise, so their development may be affected by light and movement, making it evolutionarily advantageous for the two to be linked. Friedmann’s goal this summer at MBL is to figure out what other cells and systems these light-sensitive neurons are connected to, and trace the full circuit involved in light response. He’s supported at the MBL by a Grass Foundation fellowship, which are given to early-career scientists to carry out independent, investigator-designed projects. The Grass Lab at MBL provides space, cutting-edge equipment, supplies, and housing, so young scientists can spend a summer dedicated to experimentation.

The ability to detect light evolved before eyes, Friedmann explains, and when eyes did evolve, there was no reason to get rid of the old way of sensing light, especially for transparent creatures like zebrafish. These light-sensitive neurons may be heavily involved in healthy zebrafish development and behavior, paving Friedmann’s winding road with all sorts of interesting questions.

By Laurel Hamers

Our arms and legs normally work so fluidly that we may forget that their size and location were determined by complex genetic control during early development.

Keys to the precise regulatory ballet that makes our limbs look the way they do may be found in a seemingly dissimilar group of organisms: sharks and skates.


Skates in the MBL’s Marine Resources Center. Photo credit: Laurel Hamers

Cartilaginous fish like sharks and skates are the oldest fish to have pectoral fins:  paired appendages that are the evolutionary predecessor of our arms. Tetsuya Nakamura, a postdoctoral researcher at the University of Chicago, is spending the summer at the MBL investigating these cartilaginous fish. He hopes to elucidate the molecular mechanisms responsible for the diversity of fin shapes in this single group of fish and, on a broader scale, the evolution of appendage shapes across species.

“The best way to understand the diversity of fin types is to study an extremely strange fish, like the skate,” says Nakamura. “The pectoral fins of skate are very wide—they’re totally different from other animals.”

Nakamura is focusing on Hox genes, which control body patterning during embryonic development; they are responsible, for example, for making sure your arms attach below your shoulders and not out the top of your head. Researchers can manipulate individual Hox genes and readily see structural differences in the body parts influenced by that gene.

By comparing expression patterns of Hox genes in the fins of skates and closely related sharks, Nakamura is identifying specific genes that may be responsible for the skate’s elongated pectoral fins compared to the shark’s narrower ones. He will then manipulate the expression of these genes in an attempt to alter fin shape.

The blue lines show the cartilage structure in the fins of two fish. Note the shark's narrow fins compared to the skate's wide, fan-like ones. Photo credit: Tetsuya Nakamura, composite image by Laurel Hamers

The blue lines show the cartilage structure in the fins of two fish. Note the shark’s narrow fins compared to the skate’s wide, fan-like ones. Photo credit: Tetsuya Nakamura, composite image by Laurel Hamers

“My opinion is that fin width is very important in deciding fin shape,” he says. “If I can control fin width, for example, to make narrower fin bases in skate, I think their fin shape would be like a shark’s.”

Nakamura, who is spending his first summer at MBL, is a member of Neil Shubin’s lab in the Department of Organismal Biology and Anatomy at UChicago.

A closeup of an Aedes aegypti mosquito biting its host. Photo credit: Alex Wild,

The yellow fever mosquito,  Aedes aegypti, biting its prey. Photo credit: Alex Wild,

By Laurel Hamers

It’s a question asked by many a summer stargazer: How do mosquitoes home in on their human prey, turning a relaxing evening into an itchy disaster?

Meg Younger, an MBL Grass Fellow and a postdoctoral scientist at Rockefeller University, is trying to find out by looking at mosquitoes’ neural responses to different combinations of odors.

Behavioral studies have identified several cues that are mildly attractive to mosquitoes: carbon dioxide, heat, and lactic acid, a component of sweat. Presented alone, none of these cues is particularly powerful; when paired together, however, their effects multiply.

“What we don’t know yet is how these stimuli that are ignored or only mildly attractive are transformed into very attractive stimuli in the brain when presented simultaneously,” Younger says.

Younger is using electrophysiology and calcium imaging to monitor olfactory neurons, looking for differences in brain activity when mosquitoes are presented with certain stimuli alone or in different combinations.

She is carrying out her research in the yellow fever mosquito, Aedes aegypti, which is found in tropical and subtropical areas and is the also the major vector for dengue fever and chikungunya.

“The more we know about how mosquitoes process different stimuli to find humans, the more potential we have to come up with creative ways to stop them from biting people and spreading diseases,” Younger says.

By Amanda Rose Martinez

Venture into the Grass Lab this summer on the second floor of Rowe and you’re liable to hear the amorous calls of singing fish.

This week, Liz Whitchurch, a 2011 Grass Fellow who hails from the University of Washington, was busy building the fictitious nests she’ll use to study the auditory behavior of plainfin midshipman, a type of fish that sings to attract its mates.

Grass Fellow Liz Whitchurch is building fictitious nests for her study species, the plainfin midshipman. Photo by Amanda R. Martinez

Whitchurch sets the scene. On spring nights all along the West Coast, randy, male midshipman flood the intertidal zone. They rapidly contract a muscle on their swim bladder, which results in a low, resonant hum that lady midshipman find irresistible.

“They’re calling to the females: ‘Come lay your eggs in my nest,’ ” says Whitchurch. “And the females, out there somewhere in the water, then have the task of localizing that call.” They zero in on the male whose call is most alluring and lay their eggs in his nest. The male then cares for the eggs for the rest of the summer. All told, not a bad deal.

Whitchurch will use a micro-electrode as thin as a strand of hair to measure the midshipman's response to mating calls. Photo by Amanda R. Martinez

“These fish are really interesting because they rely entirely on their auditory sense to reproduce,” Whitchurch explains. But while scientists have observed how the midshipman’s brain encodes sound underwater, to date, studies have only looked at immobilized fish.

“The whole idea is to understand how auditory cues are encoded in the brain while these fish are actually swimming around,” says Whitchurch, who plans to measure the phenomenon for the first time by monitoring midshipman in a six-foot-diameter tank in the MBL’s Marine Resources Center. “If you understand how fish navigate using sound, you can imagine building machines that navigate in the same way,” she says.

In a lab upstairs, Grass Fellow Raquel Vasconcelos, from the University of Lisbon, is investigating the behavior of a different singing fish—the toadfish. Emitting sounds that conjure a boat horn, male toadfish also depend on vocalizations to woo their would-be mates.

Raquel Vasconcelos prepares an electrode to measure the response of a Lusitanian toadfish to minute sound vibrations. Photo by Amanda R. Martinez

Hunched over a machine designed to mimic minute sound vibrations that occur in the ocean, Vasconcelos prepares to insert an electrode into the nerve of an anesthetized toadfish, staged on the machine’s surface. Richard Fay, an expert on fish hearing and a summer fixture at MBL since 1993, lends a hand.

“We think that the fish ear is stimulated not by sound pressure, as in human hearing, but by the motion of sound particles,” explains Fay. In the natural environment, when sound passes through the fish, it moves in the direction of that sound.

Richard Fay of Loyola University Chicago adjusts the accelerometer of a machine designed to mimic nanoscale sound vibrations that occur in the ocean. Photo by Amanda R. Martinez

In studying how toadfish nerves respond to sound vibrations, Vasconcelos hopes to better understand how the fish ear processes auditory feedback or background noise in the water, and how such feedback may affect the toadfish’s vocal, and thus, mating behavior. “There’ve been a lot of studies about auditory feedback in birds,” Vasconcelos said, “but as far as I know this would be the first that looked at fish.”

“Firsts” and other research innovations are an enduring theme at the Grass Lab, which for 14 weeks every summer since 1952 has served as an oasis for burgeoning leaders in the field of neuroscience. It’s an oasis in the sense that it affords its fellows the chance to fiercely pursue their research goals, while in the company of distinguished peers, using state-of-the-art equipment, and with little threat of distraction.

Felix Schweizer shows the Grass Lab's original door, a relic saved from the lab's former location in Lillie. Photo by Amanda R. Martinez

“What distinguishes it from their home labs,” says Felix Schweizer, a ‘94 Grass Fellow who currently serves as the Lab’s co-director, “is that the preparations they’re working on are all very different, which is exciting, right? Most of these preparations are things that we’ve heard about, like the toadfish. But in my lab, for instance, you would never see a toadfish. And then you come here and you see all of these classic things going on—people who do molecular work or maybe more biophysical work. And then suddenly they’ll hear something about animal behavior that they never really thought about.”

It’s this exposure to diverse disciplines that can profoundly impact the way that Grass Fellows think about their work. The result is often original perspectives and novel research methods that have bequeathed the Grass Lab its reputation for creativity. “It’s a very unique environment to do science in,” Schweizer says.

To apply for a Grass Fellowship, please visit: Application deadline is December 5th.

Felix Schweizer expresses the Grass Lab's vibrant legacy. In the background, a portrait shows electrical engineer Albert Grass, who, along with his wife, Ellen, established the Grass Foundation in 1955. Photo by Amanda R. Martinez

Yat Fai (Michael) Yuen, a PhD student from Hong Kong, walked out of Swope one July evening and was intrigued by the sight of Eel Pond hidden in mist. “I went back to my room and got my camera. When I got back the mist had gone — it became suddenly so clear. And I took the picture,” he says. Yuen worked this summer in Rowe Laboratory with Prof. Andrew Miller of Hong Kong University of Science and Technology. Miller directs the Joint Universities Summer Teaching Laboratory (JUSTL), a program that brings promising young Hong Kong scientists to the MBL for summer research.

Eel Pond. Photo by Yat Fai Yuen

Eel Pond. Photo by Yat Fai Yuen

One of the coolest machines in an MBL course this summer—and the courses are famous for having absolutely the best laboratory instrumentation you can get—is a high-pressure freezer, on loan from Leica, in the Physiology course. With an impressive burst of steam, it instantly turns a tissue sample into a flash-frozen slab. Then, the sample can be sliced and observed in an electron microscope, its biological activity freeze-framed at that instant of time.

But what’s really cool is this machine is an offshoot of the “freeze slammer” that MBL Neurobiology course faculty Tom Reese and John Heuser built in the late 1970s. “We pioneered a different kind of freezing, called slam freezing, with the idea of stopping tissue action. We used a copper plate cooled with liquid helium, and we slammed a piece of tissue against it,” says Reese, a researcher at the National Institutes of Health who is now in his 35th year of teaching in the MBL Neurobiology course. Reese and Heuser were able to release synaptic vesicles from frog neurons and capture the event using the slam freezer. “No one had ever observed structure on a millisecond time scale before (this),” Reese says.

“It was a classic experiment,” says Erik Jorgensen of HHMI/University of Utah, a neurobiologist who is “frequently found at the MBL in the summer trying to pull off experiments that cannot be done anywhere else,” he says. Jorgensen has modified the Leica freezer to perform like the freeze slammer, so he can observe instantaneous synaptic events, as Reese and Heuser did. Jorgensen remembers seeing the old Reese-Heuser freeze slammer in the basement of Loeb Laboratory. “These old machines, you had to be an engineer to run them,” Reese remembers. “The new ones are so easy to use, you find it sitting there in the Physiology course for the students to try out!”

MBL visiting investigator Erik Jorgensen demonstrates the high-pressure freezer on loan to the Physiology course this year, which takes a cue from the freeze slammer invented by Neurobiology faculty Tom Reese and

Visiting investigator Erik Jorgensen demonstrates the high-pressure freezer in the Physiology course, which takes a cue from the freeze slammer invented by Neurobiology faculty Tom Reese and John Heuser in the late 1970s. Photo by Tom Kleindinst