Tool to view an unprecedented view of brain cell activity

First-ever seeing brain activity on such a massive scale.


How learning and memory occur is still a mystery.

Now, to resolve this mystery, Johns Hopkins Medicine scientists have created a system to track millions of connections among brain cells in mice. They track it simultaneously and when the animals’ whiskers are tweaked which is an indicator for learning.

Researchers say the new tool gives an unprecedented view of brain cell activity in a synapse. Synapse is a tiny space between two brain cells, where molecules and chemicals are passed back and forth.

“It was science fiction to be able to image nearly every synapse in the brain and watch a change in behavior,” says Richard Huganir, Ph.D., Bloomberg Distinguished Professor of Neuroscience and Psychological and Brain Sciences at The Johns Hopkins University and director of the Department of Neuroscience at the Johns Hopkins University School of Medicine.

A summary of the research was published online first Oct. 18 and in its final form on Nov. 25 in the journal eLife.

The researchers never thought they’d be able to see brain activity on such a massive scale. Before developing the tool, they said that their ability to see brain cell activity was like looking up in the night sky with bare eyes and witnessing billions of stars. “It’s like we can see and track each of the stars at the same time” now, says Austin Graves, Ph.D. instructor of neuroscience at the Johns Hopkin University School of Medicine.

The space between brain cells, or neurons, is incredibly tiny. It’s less than a micron, almost about a tenth of the width of a human hair. Within these junctions between neurons is a highway of passing molecules and proteins — mainly sodium and calcium and transferring from one neuron to another.

When neurotransmitters pass across a synapse and land on a neuron, they activate an AMPA glutamate receptor. AMPA-type glutamate receptors (AMPARs) are crucial molecules to study to understand the function and dynamics of the nervous system. AMPARs mediate the majority of fast excitatory synaptic transmission in the mammalian brain. Their regulation is regarded as a key mechanism underlying long-lasting changes in synaptic efficacy that give rise to learning and memory.

“These receptors are the functional machinery of language between neurons,” says Graves.

Huganir and other scientists have shown that synapses and their receptors are key locations for learning in the brain. It’s where memories are encoded, they say.

To study how synapses operate, scientists customarily culture samples of brain cells in the laboratory to screen for increases or decreases in proteins made by the cells. They also examine subsets of neurons in various brain regions. Still, scientists had not previously imagined synapses in the entire brain on this scale, say the researchers.

For the research, the scientists genetically engineered mice by inserting the GRIA1 gene into the DNA, producing a glowing green tag on all AMPA glutamate proteins. When neurons amp up their signaling, they have more AMPA glutamate proteins, and the green signal gets brighter.

Since AMPA glutamate receptors are prevalent, the researchers pinpoint nearly all excitatory neurons in the mouse brain, which are more likely to send signals to other neurons instead of blocking them.

Then, the researchers tweaked a whisker on each mouse and used high-powered microscopes to track which synapses glowed green and the brightness of the signal. They found about 600,000 glowing synapses and indications that the brightness of the green signal corresponded to the strength of the AMPA glutamate receptor’s response.

Huganir says the new system generates mind-boggling amounts of data. So, the researchers worked with computational scientists in the Johns Hopkins Department of Biomedical Engineering to develop artificial intelligence and machine learning techniques to train and validate algorithms that automatically detect all of the glowing synapses and how they change over time with experience and learning.

Their current work is a proof-of-principle study that shows the capabilities of this synaptic imaging tool, say the researchers. Other scientists have asked to use genetically engineered mice in their studies.

Every green glowing area is one synapse in a living mouse’s brain. The image shows dense constellations of millions of synapses throughout the mouse cortex. Credit: Austin Graves, Johns Hopkins Medicine

The researchers also plan to use the tool to study other mouse behaviors, learning, and memory and examine how synapses change under certain conditions, such as aging, Alzheimer’s Disease, and autism.

The research was supported by the National Institutes of Health’s National Institute on Aging and National Institute of Mental Health (R21 AG063193, R01 MH123212, K99 MH124920) and a Schmidt Science Nascent Innovation Grant.

Journal Reference

  1. Elena Lopez-Ortega, Alexei M Bygrave, Qianwen Zhu, Han L Tan, Richard H Roth, Austin R Graves, Ingie Hong, Alina C Spiegel, Richard C Johnson, Joshua T Vogelstein, Daniel J Tward, Michael I Miller, Richard L Huganir. Visualizing synaptic plasticity in vivo by large-scale imaging of endogenous AMPA receptors. eLife, 2021; 10:e66809 DOI: 10.7554/eLife.66809
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