View from the inside of a nerve cell. The synapse and the muscle cell are not pictured, but would be below the nerve cell’s cell membrane, at the bottom. In the frog NMJ (A), neurotransmitter-containing packets (vesicles) waiting to be dumped into the synapse are arranged in two rows. (Vesicles are in red, calcium channels below the vesicles are small red dots, and the calcium ions diffusing in the nerve terminal are represented as small blue or yellow dots.) In the mouse (B), the vesicles are organized in clusters that each contain two vesicles. Simulations on Bridges showed that the frog system, when rearranged in clusters like the mouse, began to behave like the mouse NMJ.

Function Follows Form

Simulations on XSEDE Resource plus Lab Work on Frog Neuromuscular Junction Sheds Light on Human Diseases

When a nerve cell passes a message to its neighbors, it must do so via chemicals sent across the synapse—a small space between the cells. Early researchers studied a synapse called the frog neuromuscular junction (NMJ) because it is large and easy to work with. But its different organization and behavior compared to mammalian synapses led many scientists to dismiss it as not relevant to human biology. A team of University of Pittsburgh and XSEDE Extended Collaborative Support Service (ECSS) scientists performed simulations on the XSEDE-allocated Bridges supercomputer at the Pittsburgh Supercomputing Center (PSC) and parallel lab experiments on the frog and mouse NMJ. They showed that, when reorganized into the same geometric pattern as in the mouse, the components of the frog NMJ act like those in the mouse. Lessons from the work are already being used to design candidate drugs to treat human neuromuscular diseases.

Why It’s Important:

The synapse—the small space between a nerve cell and its neighbor—is where the rubber meets the road in just about everything our brains, senses and muscles do. Whenever a nerve cell fires, whether to tell a muscle to twitch, convey the smell of strawberries, or trigger a hallucination in someone with schizophrenia, it must pass the message along with a burst of neurotransmitter chemicals released into the synapse. Whether we’re trying to restore use of the legs to someone with spinal cord damage, treat a psychiatric condition, or protect nerve cells from a degenerative neuromuscular disease, synapses are likely to play an important role.

“It’s worth saying that neurotransmitter release underlies everything in the brain. We still don’t know how that works … and it’s a basic process in the nervous system.”—Anne Homan, University of Pittsburgh

But for all the synapse’s importance, scientists still face challenges in understanding exactly how it works. The mouse neuromuscular junction (NMJ)—the synapse between a nerve cell that makes a mouse’s muscle move and a muscle cell—is similar to many synapses in humans. It’s also proven a good stand-in for scientists studying human neuromuscular diseases. Historically, some of the first studies of how cells communicate with one another in the nervous system began with the frog NMJ. That’s because it’s large enough to easily see in a microscope. It also allows variety of experimental manipulations. But because frogs are amphibians and not mammals, scientists have disagreed about the relevance of the frog NMJ to human biology.

“The frog neuromuscular junction is easy to get to and hundreds of microns in length. It’s a simple model in which you have a monster synapse … with chemical release sites arranged in a regular pattern like ties on a railroad track. It’s easy to manipulate, characterize and study.”—Stephen Meriney, University of Pittsburgh

Both the organization of the frog and mouse NMJs and their behavior differ. But the chemical actors—proteins, neurotransmitters and other components—are identical in the frog and mouse NMJ. This fact led the team of Stephen Meriney of the University of Pittsburgh; his graduate student Anne Homan; Rozita Laghaei, an XSEDE ECSS expert at PSC; and colleagues at PSC and Pitt to use these systems as models to determine how structure influences function.

How XSEDE and PSC Helped:

Homan carried out a series of lab experiments on frog and mouse NMJs. Meanwhile, Laghaei used the MCell software to create a virtual nerve cell/muscle cell pair running on PSC’s Bridges supercomputer. MCell was developed by the National Center for Multiscale Modeling of Biomedical Systems, made up of PSC, Pitt, the Salk Institute and Carnegie Mellon University. The task was challenging, since MCell must carry out complex calculations that depend on each other’s results to proceed. So the common supercomputing strategy of splitting the problem into many small parts that can be performed independently at the same time wasn’t possible. Laghaei had to run the same simulation tens of thousands of times, each differing by random changes. This approach built up a representative sample of the behavior of neurotransmitter release by the nerve cell, bit by bit. The method, called Monte Carlo simulation, required massive computer memory. Bridges’ unique large-memory nodes made the computation manageable.

“The MCell part of the study was to model as close as possible what the experimentalists see … It involved lots of computations. We ran several simulations exactly the same except for sequences of random numbers that we use to model … transmitter release at neuromuscular junctions (which is a stochastic process) and did that experiment ten thousand times … It required huge memory; the output of the simulation kept track of every particle.”—Rozita Laghaei, PSC

The comparison of the lab and computer experiments shed a lot of light on the scientists’ questions. In the computer model, Laghaei reorganized the components of a frog NMJ so that they were laid out in the same geometric pattern as in a mouse NMJ. She found that the behavior of the new system was identical to what Homan saw in the real mouse. The difference between the two species lay entirely in how the NMJ components were organized, and not in a more fundamental difference. This result shows that the frog system is relevant to human synapses after all. Later simulations showed that the scientists could tune the behavior of the NMJ at will by changing the geometry of the components. The group reported their results in two papers in the Journal of Neurophysiology in November and December 2017. The work is a vital first step in understanding the NMJ and other synapses. Colleagues in Pitt’s Department of Chemistry are now using the lessons learned to understand the fundamental changes that occur in diseases of synapses. They aim to design new drug candidates to treat neuromuscular diseases in humans.