Synapses, the links between neurons that allow them to pass information to one another, are believed to be where memories are stored, yet researchers have little understanding of how they change when memories are made.

New insights into the role of synapses in memory, learning and forgetting — or how sleep, drugs and other stimuli affect them — would revolutionize scientific understanding of the entire brain. But researchers can’t image the entire brain at a high enough resolution to see synapses — tiny structures only a hundredth the diameter of a human hair. That’s partly because scientists have yet to build the technology needed to selectively label, image and analyze these key but miniscule structures. MRI, EEGs and even implanted electrodes can offer only crude data on the brain’s workings.

Scott Fraser, Don Arnold and Carl Kesselman, a multidisciplinary team of distinguished USC researchers, aim to change that.

A new map

The trio has received a highly competitive five-year, $9.7-million Transformative Research Grant from the National Institutes of Health to perform the first direct study of living synapses in the intact brain, allowing researchers to analyze synaptic changes in zebrafish as a memory is made.

The USC researchers chose zebrafish because their transparent brains make them easier to image. They are also large enough to show the same complexities, mechanisms and diseases as the human brain, including mental illness, making the results relevant to neuroscientists and other health researchers.

We want to create a new way of observing how the brain functions in a way that nobody has ever done before. Carl Kesselman

“We want to create a new way of observing how the brain functions in a way that nobody has ever done before,” Kesselman said. “Our approach will offer an overall map of the brain’s synaptic changes, creating an entire circuitry diagram compared to just a view of a single wire.”

Such a comprehensive picture of the brain’s synapses could one day lead to a better understanding of and treatments for post-traumatic stress disorder and other neurological conditions in humans, he added.

Zebrafish experiments

The zebrafish experiments will use a new class of genetically embedded probes developed by Arnold of the USC Dornsife College of Letters, Arts and Sciences. Arnold, who holds a Ph.D. in biomedical engineering from the Johns Hopkins University, and his team have developed a powerful new approach: the zebrafish itself makes a protein that has been engineered to “label” its own synapses with a fluorescent protein that can be seen with the right microscope.

Fraser, with appointments in the USC Viterbi School of Engineering, USC Dornsife and the Keck School of Medicine of USC, is working with an interdisciplinary team to build a powerful light sheet microscope optimized to image the synapses that Arnold’s team will label. The microscope is so fast and sensitive that it can capture a comprehensive image of a zebrafish’s synapses before, during and after a memory is made. This would allow researchers to watch the brain in action as the animal responds to various stimuli.

We pride ourselves on building microscopes that redefine the impossible. Scott Fraser

“We pride ourselves on building microscopes that redefine the impossible,” said Fraser, one of the world’s foremost imaging experts. “This new microscope opens a new doorway in microscopy, perhaps the only tool that is adequate to fully exploit the advantages of the labels Professor Arnold has developed.”

Kesselman — a computer scientist with joint appointments in the Daniel J. Epstein Department of Industrial and Systems Engineering at USC Viterbi and the Department of Preventive Medicine at the Keck School of Medicine and who also serves as director of the Informatics Division at the USC Information Sciences Institute (ISI) — has designed algorithms that will identify, sort and store zebrafish synapses, a challenging proposition given their small size, large number and size of the data. These huge databases of information “will be accessible to researchers using the ‘big data’ tools the USC researchers are developing,” Kesselman said.

Making a memory

To measure synaptic changes when a zebrafish makes a memory, the scientists will exploit some of the classical tools used by psychologists to measure learning and memory. For example, they will pair a flashing light with an electric shock until the fish associates the light with discomfort.

By imaging the fish’s synapses before, during and after the learning experience, the team will create a map of brain changes with learning.

Similarly, the USC trio will chart synaptic changes caused from the loss of a memory — flashing the light several times but no longer following it with a shock — so that the fish no longer remembers the connection between light and discomfort.

Eventually, researchers will have several highly detailed pictures of synaptic changes resulting from different stimuli, which, in turn, should provide insights into fundamental processes underlying learning and memory.

“People have wanted to see this [synaptic changes] for the last 100 years, but the technology wasn’t there,” Arnold said. “Until now.”

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