Then and Now: Daniel Colón-Ramos Surveys Synapses

More than a century ago, neuroscientist Santiago Ramón y Cajal used his keen observation skills and a recently developed staining method to describe how synapses mediate communication between neurons. The term synapse did not exist back then—it was coined a few years later by physiologist Charles Sherrington—so Cajal poetically referred to the neural connections as the “protoplasmic kisses that appear to constitute the final ecstasy of an epic love story.”¹

As a Yale University cell biologist and neuroscientist, Daniel Colón-Ramos seeks out the molecular truth in Cajal’s words. “If you could run this story over and over again but eliminate certain components, you can find out which components are absolutely essential for the protoplasmic kiss to form,” Colón-Ramos said. Like the telling of a love story, “we can find out what are the things that happened with each of these cells that ended up in the formation of a particular junction, in a particular time, in a particular place,” he added. All of those details can not only tell neuroscientists how synapses form but also how cells communicate and self-organize to form the nervous system, he said.

For almost two decades, Colón-Ramos and his team have used the transparent nematode Caenorhabditis elegans to dissect Cajal’s protoplasmic kisses. Six years ago, The Scientist featured Colón-Ramos’s work on how synapses are created, endure, and shape an organism’s behavior. Since then, Colón-Ramos’s team has continued this quest and described how energy metabolism influences neuronal function and identity, while also creating tools to further scientists’ understanding of cellular communication.

Neuronal Metabolism Mirrors Neuronal Identity

Back in 2020, Colón-Ramos’s team started to explore how energy metabolism, the biochemical pathways that fuel cell function, work in neurons. Researchers knew that glucose metabolism via glycolysis and oxidative phosphorylation provided the energy the brain needs, but it was not clear how metabolism functioned inside neuronal cells themselves.

To investigate this question, the researchers first had to overcome a technical barrier: While there were tools to examine these pathways biochemically, they did not provide the resolution needed to assess the distribution of the metabolic pathway components inside the cell or how they responded to changes in the cell’s state. “That brought our research in that area to a pause because we were unable to do in vivo biochemistry,” Colón-Ramos said.

With the help of Richard Goodman, who was a biologist and biochemist at the Vollum Institute at the time and is now at Colón-Ramos’ lab, he devised a fluorescent biosensor to track a key rate-limiting metabolite of glycolysis. By combining this tool with genetic manipulations of C. elegans exposed to varied environmental conditions, they found that different neurons have varied glycolytic states that they can dynamically regulate to meet their energy needs. Disrupting the trafficking of mitochondria to synapses also revealed that neurons locally regulate glycolysis at synaptic regions.² “These pathways that we always assumed that were happening everywhere all the time are actually at synapses, compartmentalized,” Colón-Ramos explained. “[That] shapes the ability of the nervous system to perform work, and it puts [these pathways and their localization] in an instructive role to how synapses function.”

More recently, Colón-Ramos and his team have begun to uncover how energy metabolism pathways affect neuronal function by examining cells in C. elegans that show high and low levels of glycolysis. They have shown, for instance, that differences in glycolysis shape the neuron’s electrophysiological properties, revealing that metabolism is tightly linked to the functional identity of each cell.³ “The picture that is emerging is quite fascinating,” Colón-Ramos said. “This puts metabolism at the same category as, for example, other cellular identity features, such as the identity of the neurotransmitter or the morphology of the cell.”

A Tool-Making Guide to Neuronal Communication

Over the years, Colón-Ramos realized that to explore many of the questions he was interested in, he would have to come up with new tools, similarly to what Cajal did over a century ago when he decided to use the recently developed silver nitrate stain to visualize neurons and their features.

Continue reading below...

Article

Expanding What Super-Resolution Microscopy Can Capture

How fluorescence lifetime-based STED increases the quality of super-resolution images

Read More

To systematically map neurotransmitter co-transmission organization, that is, how neurons that produce more than one neurotransmitter are spatially distributed, his team devised SynaptoTagMe, a genetic toolkit that enables researchers to fluorescently label proteins in neurotransmitter vesicles.⁴ Even though co-transmission is a neuronal feature conserved across the animal kingdom, researchers lacked tools to image it live in single neurons. By combining the tagged vesicles with conditional knockout C. elegans strains, in which either the packaging or production of specific neurotransmitters was disrupted, the team discovered that 10 percent of the worm’s neurons are equipped to produce more than one neurotransmitter, suggesting that they may do co-transmission. Colón-Ramos’s team is currently digging deeper into these results to examine how C. elegans sensory neurons use co-transmission to regulate behavior. “It raises fascinating questions about how is the system, in a co-transmitting neuron, deciding if it's going to make a glutamatergic vesicle or a cholinergic vesicle and how the system differentiates between those two vesicles,” he explained.

Colón-Ramos also teamed up with data scientists to create an online, open-source platform dubbed NeuroSC that allows the integration of information about the connectome (the synapses or projections between neurons), the contactome (physical contacts between different neural cells), and neural anatomy from microscopy studies to examine the spatiotemporal neuronal changes that occur during development.⁵ Colón-Ramos noted that while his team initially validated NeuroSC in C. elegans, ongoing collaborations with other research teams are showing the tool can be applied to other model systems, such as zebrafish, as well. “We are excited about how these new approaches can be applied to these new connectomes and how these overarching principles of neurodevelopment might be shared across different systems,” he said.

Looking back, Colón-Ramos emphasized how the scientific training he received over the years prepared him to embrace opportunities outside academia and contribute more directly to society. For instance, he recalled his involvement in a scientific coalition in Puerto Rico that advised the country’s government during the pandemic and helped save thousands of lives. “Science has contributed to my life so much in that aspect of enabling me to teach, to interface with different trainees, to ignite imagination, [and] to serve different communities,” he said. “It's far beyond what I thought I was going to be able to do when I started my training in science.”