Research Area: Neurobiology

‘What Were you Thinking?’

How brain circuits integrate many sources of context to flexibly guide behavior

Picower Institute
September 29, 2021

Mating is instinctual for a mouse but sometimes, for instance when his potential partner smells sick, a male mouse will keep away. When Mark Hyman Jr. Career Development Associate Professor Gloria Choi and colleagues published a study in Nature in April revealing how this primal form of social distancing occurs, they provided an exquisite (and timely) example of how brain circuits factor context into behaviors, making them adaptive and appropriate even when they are innate, or “hardwired.” 

When the odor of illness enters the mouse’s nose, that stimulates neurons in its vomeronasal organ to send an electrical signal through a nerve to the brain’s olfactory bulb. Cells there, Choi’s team discovered, relay the signal on to neurons in a region called the cortical amygdala that govern the mating instinct. Finally, completing the health-preserving circuit that will inhibit the mating instinct, those neurons pass on the message to brethren in the neighboring medial amygdalar nucleus. In so doing, this sequence feeds a sensory context, the female’s ill odor, into a circuit to override the default context of an internal state, the instinct to mate. The researchers even showed that by artificially stimulating cortical amygdala neurons they could prevent a mouse from mating with a healthy partner and by artificially silencing those same cells they could make a mouse mate with an ill-smelling one.

As you can learn below, the brain has much greater flexibility in how it operates than the electrical circuits that power your house or even the chips that drive your cell phone. But fundamentally it is the routing of electrical signals from neuron to neuron that forms the basis not only for how we behave, but also how we match behavior appropriately to the circumstances we encounter, Choi said.

“The closest component to behaviors and internal states, and changes in those, are still believed to be neurons and circuits,” she said.

Understanding how brain circuits produce behavior is an exciting area of neuroscience research, including in many Picower Institute labs. Their studies are helping to elucidate how the brain’s anatomy is arranged to process information, and how the many dimensions of flexibility that the central nervous system overlays upon that infrastructure can integrate context to guide appropriate behavior. Context, after all, comes from many sources in many forms—from the senses, like scents and sounds and sights; from internal states, like mating drive or hunger or sleepiness; and even from time and place and from what we’ve learned and remember.

So what were you thinking when you did “this” instead of “that”? You were thinking about the context and relying on your brain’s ability to account for it.

Chemical control

The popular “circuit” metaphor makes it easy to think of neurons as merely switches and wires that pass electrical transmissions from one point to another. And indeed they do that, although instead of being screwed and soldered to metal contacts, they use molecules called neurotransmitters to send signals across tiny junctions called synapses. But if that were all that was going on, the brain would be pretty static and it is anything but. Many members of the Institute’s faculty study how learning occurs and memories are formed when the brain changes its synapses to create or edit circuit connections, but none of that is strictly necessary for existing circuits to flexibly control behaviors that we’ve already learned or that are innate. The brain has other ways to flexibly change how it operates. Choi’s team, for instance, found that the behavioral change of inhibiting mating could not occur without the cortical amygdala neurons also sending a chemical, thyrotrophin releasing hormone (TRH), to the medial amygdalar nucleus neurons. 

In the lab of Lister Brothers Associate Professor Steven Flavell, researchers study how internal states and behaviors emerge and change using a worm so simple that its complete, invariant “wiring diagram” has been completely mapped out for decades. Yet even in C. elegans, with its exact total of 302 neurons, scientists are still discovering how the animal adapts its actions to survive and thrive in a world of ever-changing contexts.

“Since 1986, that wiring diagram has been staring at researchers,” Flavell quipped. “Many of the small circuits embedded in the wiring diagram have been closely studied, while others haven’t. But a key question that we are trying to answer is how does the whole system work. How are these circuits coupled together to give rise to so-called ‘brain states’?”

In several studies Flavell has shown how a small number of neurons encode contexts and then signal that those circumstances are afoot by releasing chemicals called “neuromodulators” to many other neurons, giving rise to a brain state. Just as TRH may be doing in the circuit Choi uncovered, neuromodulators such as serotonin and dopamine, which are also ubiquitous in humans, add an extra dimension of tuning that can change, or “modulate,” how hardwired circuits process information and output behaviors, Flavell said. Neuromodulators can make neurons more or less electrically excitable given the same degree of input, Flavell explained. They can also make transmission at individual synapses more or less effective.

“The physical connections are like a roadmap, but the way that traffic is actually flowing on the road, the way that neurons are coupled to each other, is dynamic and changes with the animal’s context,” Flavell said. Neuromodulators are one way to make that happen.

For instance, in a 2019 paper in Cell, Flavell’s lab showed how a hungry worm knows to slow down and savor a patch of yummy bacteria when it finds one. A single neuron called NSM extends a little tendril called a neurite into the worm’s pharynx. Equipped with bacterial sensors (that turn out to also be present in the human intestine), the neurite detects when the worm has started to ingest and mash up its food. NSM releases serotonin, which finds its way to many of the neurons in worm’s brain that control locomotion. Upon sensing the serotonin, they hit the brakes.

In a more recent study in bioRxiv, the lab takes their investigation of neuromodulators even further. The study characterizes exactly how serotonin release from NSM modulates that activity of specific neurons in the C. elegans brain. In addition, Flavell’s group found that a neuron called AIA integrates information from sensory neurons about the smell of food. NSM can help determine what it does with that information, depending on whether it detects that the worm is eating or not. If it is, the smell of food (detected by AIA) reinforces that it should stick around to continue dining, a state maintained with serotonin. If the worm isn’t eating, the food smells signal that the animal should go exploring to find the source of that enticing odor. AIA, in that case, can instead trigger neurons that produce a different neuromodulator, called PDF, that cause the worm to start roaming (toward the food odor). Even in the simple circuitry of C. elegans, context changes how neurons interact, giving the animal flexibility to process sensory information.

That neurons capable of emitting neuromodulators can exert far-flung influence over behavior is illustrated by research in Newton Professor Mriganka Sur’s lab, too. There Sur’s team has a focus on a deeply situated, tiny brain region called the locus coeruleus (LC) that happens to supply most of the brain’s norepinephrine. Classically, neuroscientists have regarded norepinephrine from the LC as increasing the brain’s internal state of general arousal, but recent research in the Sur lab suggests it has profound, context-dependent effects on learning and behavior.

For instance, members of the lab have trained mice to expect a reward if they push a lever after hearing a high-pitched tone; the mice also receive an unexpected and irritating puff of air if they mistakenly press the lever after a low-pitched tone. By varying the loudness of the tones, the researchers can also vary the certainty the mice have about what tone they heard. Sur’s lab has found that the louder a high-pitched tone, the more norepinephrine a mouse will send to the motor cortex, which plans movement, before pushing the lever – as if greater certainty prompts it more strongly to push the lever. 

Once the lever has been pushed and the mouse gets its feedback of reward or air puff, LC neurons producing norepinephrine then act to fine-tune learning by calling attention to any surprising feedback, Sur’s team has seen. For instance, if the tone was high pitched and faint, but the mouse took the risk to push the lever, the neurons will send a burst of norepinephrine to the prefrontal cortex to note that pleasant surprise. The biggest post-push surge of the neuromodulator, however, occurs when the mouse guesses wrong: that norepinephrine release to the prefrontal cortex appears to signal that the adverse result must be noted. Sure enough, Sur said, the team has seen that the mouse’s performance typically improves after making an error. The LC’s neuromodulatory actions may contribute to that behavioral improvement, though more research is needed to prove it.

Sur’s is not the only research in The Picower Institute showing that the LC communicates with the prefrontal cortex to improve task performance, though. Last November in the Proceedings of the National Academy of Sciences, Picower Professor Susumu Tonegawa’s lab showed that LC norepinephrine neurons connect via distinct circuits to two different parts of the prefrontal cortex to endow mice with both the ability to curb impulses (i.e. to not “jump the gun” when waiting to perform tasks) and to ignore distractions, such as false cues. 

Rhythms among regions

Much as the Sur and Tonegawa labs have been investigating the LC, Fairchild Professor Matt Wilson’s lab studies how a different region appears to be a key hub for integrating contexts such as location, motion and memories of reward into behaviors such as navigation: the lateral septum (LS). As rats learn to find and return to the location of a reward in a maze, the lab’s extensive measurements of electrical activity among neurons in the LS shows that those cells are taking in and processing crucial contextual input from many other regions. The LS then appears to package that context to help direct the rat’s navigational plans and actions.

Over the past two years, Wilson and former graduate student Hannah Wirtshafter have published papers in Current Biology and in eLife showing that populations of LS neurons distinctively encode place information coming from the hippocampus, reward information coming from the ventral tegmental area and speed and acceleration information coming from the brainstem. The encoding is apparent in changes in the timing and rate at which the neurons “fire,” or electrically activate, in these different contexts. Some LS neurons, for example, become especially active specifically when the rat nears the reward location. In a new article published in Neuroscience and Biobehavioral Reviews in July, Wilson and Wirtshafter combined their observations with those of other labs to propose that the lateral septum packages all this contextual information into an “integrated movement value signal.”

“The lateral septum has a ton of different inputs,” Wirtshafter said. “What could the animal be doing with place-related firing that’s reward modulated and then velocity and acceleration? The answer, we think, based on where the LS outputs to, is that it is sending a signal about the context and whatever reward is part of that context. It includes what movement needs to be done and whether that movement is worth it in that context.”

While there are ample signs in the research that neuromodulators such as dopamine help the LS communicate about contexts like the feeling of reward, the studies also highlight the key role of another mechanism of flexibility: brain rhythms. Also known as brain waves or oscillations, these rhythms arise from the coordinated fluctuation of electrical activity among neurons that are working in concert. They allow neurons in brain regions to broadcast information and neurons in other regions to tune into those broadcasts, so that they can work together to perform a function, Wilson said.  

“These brain dynamics ensure that whoever is sending the information and whoever is receiving the information are doing it at the same time,” Wilson said.

In fact, Picower Professor Earl Miller, who has published numerous studies on how brain rhythms guide the flow of information across the many regions of the brain’s cortex, uses much the same kind of traffic analogy in talking about the function of rhythms that Flavell uses when talking about neuromodulators. Much as those chemicals can, oscillations also flexibly direct the flow of information on the network of “roads” that physical circuit connections create. The traffic metaphor perhaps combines well with the broadcasting one: Just like drivers who tune into a radio traffic report can decide to take an alternate route when they hear about an accident ahead, neurons in a brain region may act differently when they tune into new contextual information coming in from another brain region.

Wilson and Wirtshafter’s research, for example, demonstrates that lateral septum neurons tune into the hippocampus’s broadcast of location information via a specific “theta” frequency of brain waves. In particular, movement through a place is represented by the phase (peak or trough) of the theta waves with which neurons spike. 

“In the hippocampus, the phase at which a cell fires during theta can communicate information about the current, prospective, or retrospective spatial location,” Wilson and Wirtshafter wrote in their article. “For instance, …firing of individual hippocampus place cells begins on a particular phase of theta rhythm and progressively shifts forward as the animal moves through the place field.”

So maybe you are not a mouse deciding whether to mate or a rat rooting through a maze for a treat, but you are a person who has stayed out late at a friend’s house. Your internal state is that you are tired. You could head out on long drive home to the reward of your clean, warm bed, or you could sleep on your friend’s notably mustier couch and explain it your spouse the next morning. Then you remember from the drive to your friend’s place earlier, that there was an all-night rest stop along the highway where you could get coffee. Whether you decide to take the wheel or your friend’s offer of the couch will come from how a combination of neuromodulators and rhythms route information along circuits through key brain regions to integrate all this context—your internal state of tiredness, the memory of where that rest stop was, and the reward of your bed (or the punishment of an angry spouse who might ask “What were you thinking?”). Your brain gives you all the flexibility you need.

Sara Prescott

Education

  • PhD, 2016, Stanford University School of Medicine
  • BA, 2008, Molecular Biology, Princeton University

Research Summary

Our bodies are tuned to detect and respond to cues from the outside world and from within through exquisite collaborations between cells. For example, the cells lining our airways communicate with sensory neurons in response to chemical and mechanical signals, and evoke key reflexes such as coughing. This cellular collaboration protects our airways from damage and stabilizes breathing, but can become dysregulated in disease. Despite their vital importance to human health, fundamental questions about how sensory transduction is accomplished at these sites remain unsolved. We use the mammalian airways as a model system to investigate how physiological insults are detected, encoded, and addressed at essential barrier tissues — with the ultimate goal of providing new ways to treat autonomic dysfunction.

Awards

  • Warren Alpert Distinguished Scholars Award, 2021
  • Life Sciences Research Foundation Fellowship, 2018
A pivot from accounting to neuroscience

Through a summer research program at MIT, Patricia Pujols explored the neuromuscular junction, and a future in science.

Alison Gold | School of Science
August 26, 2021

Patricia Pujols grew up in the city of Ponce, Puerto Rico, fascinated by documentaries she had seen about human behavior and psychology. She wanted to learn the molecular roots of things like memory, love, hate, happiness, and anger. Despite her early curiosity, becoming a scientist and studying these phenomena didn’t seem like a possibility.

“Where I grew up, people didn’t really encourage me to study science,” she says. Instead, she initially pursued a career in accounting. “Later on, after the death of my father, I realized life is short. I prefer to do the thing that I love and am passionate about. And for me, that is teaching and learning science.”

With a strong network of mentors to inspire and push her, Pujols is now well on her way to becoming a scientist. She has a semester left in her undergraduate degree at Universidad Central de Bayamón in Puerto Rico, where she is pursuing a major in neuroscience and a minor in psychology. After she graduates, she plans to earn a PhD. This summer, she was part of the MIT Summer Research Program in Biology (MSRP-Bio), which invites non-MIT undergraduate science majors to the Institute for 10 weeks of summer research.

“MSRP-Bio is designed for students like Patricia, who are driven and passionate about science, with limited access to research at their own institution and ready for a challenging and rigorous research experience at MIT that will prepare them for graduate school and open a lot of doors,” says Mandana Sassanfar, the Department of Biology’s director of outreach. “In addition, the program greatly facilitates access to MIT faculty and graduate students and provides a strong community-building component to give students a sense of belonging.”

Pujols arrived at MIT through the guidance of one of her undergraduate professors, molecular neuroscientist Ramon Jorquera. Jorquera worked with Pujols back in Puerto Rico, and is now at the Universidad Andrés Bello in Santiago, Chile.

“He was the first person to invite me to a research lab,” Pujols says. “He has helped me a lot with everything, with gaining confidence, with my English language skills, and with seeing that I can really do this.”

Years ago, Jorquera worked as a fellow in the lab of Troy Littleton, the Menicon Professor of Biology at MIT and the Picower Institute for Learning and Memory. It was Jorquera who encouraged Pujols to apply to a research program at the University of North Carolina at Charlotte several summers ago, and then to apply to MSRP-Bio. Now, just like her mentor, Pujols is working in the Littleton lab to answer crucial questions about human behavior.

Every summer, the Littleton lab welcomes MSRP students.

“This year, while pairing candidates, Patricia was sort of an obvious match for us in terms of her prior research and interests,” Littleton says. “The major interest of my lab is to really understand how neurons talk to each other within the nervous system. The ability of neurons to rapidly communicate drives our behavior, ability to learn, and to remember. That biology all occurs at specific sites known as synapses, where neurons connect with each other.”

Problems in synapse formation or function contribute to the progression of brain disorders and diseases including Alzheimer’s, Parkinson’s, schizophrenia, and many others.

At each of the billions of synapses in the human nervous system, one neuron sends a chemical message and the next receives it –– just like two friends texting. The sender is known as the presynaptic neuron, and the receiver is called the postsynaptic neuron. To allow for seamless, rapid transit of information, the sites where the chemicals are released from on the presynaptic neuron must perfectly align with the receptors on the postsynaptic neuron.

“All of our work is built around genetics,” Littleton says. “We do manipulations where you take out a gene or alter its coding a bit and see how things change. This allows us to piece together how the individual proteins at synapses work to allow neurons to effectively talk to each other.”

To conduct their work, the Littleton lab uses Drosophila melanogaster, the common fruit fly whose genome is well-characterized and is widely used as a genetic model system. After removing a piece of genetic code, they can image the fly’s synapses to see if there was a change in the alignment of the synaptic chemical receptors. They also test if the synapses’ ability to actually transmit and receive chemical messages has changed.

This summer, Pujols is studying the neuromuscular junction, a particular type of synapse where a motor neuron communicates with a muscle cell. This communication enables movement.

In mammals, the motor neuron (the sender, in this case), secretes a protein called agrin that helps to align the key components of the synapse. Agrin is important for organizing acetylcholine receptors in the synapse. Acetylcholine is a neurotransmitter released from motor neurons that is essential for movement. Mutations in agrin in humans can therefore cause muscular dystrophies and various autoimmune disorders.

In Drosophila, it is a neurotransmitter called glutamate, not acetylcholine, that operates at the neuromuscular junction. Researchers want to know if the way that agrin organizes acetylcholine receptors in the mammalian neuromuscular junction is similar to the way that a protein called perlecan organizes the neuromuscular junctions in Drosophila.

To address this question, Pujols has spent her summer removing perlecan from either the sending motor neuron or the receiving muscle cell in Drosophila, and examining how synapse formation and clustering of glutamate receptors is altered. Pujols is working closely with PhD candidate Ellen Guss in a partnership she calls “the best experience ever.”

Both Littleton and Pujols stress the importance of mentorship in the journey to becoming a scientist. When he was an undergraduate at Louisiana State University, Littleton spent a summer at the University of Florida, working with a scientist whose guidance shaped him. That summer was one of his most influential experiences as a scientist, he says.

At MIT, Pujols says, “I stepped out of my comfort zone and strengthened my skills. MSRP gave me all the tools I needed to have an enriching experience in science, as well as the opportunity to meet colleagues that I will remember for the rest of my life.”

To other students thinking of pursuing a career as a scientist, Pujols says, “don’t be afraid.”

“You will get a lot of opinions about what to do, that it’s too difficult, or you don’t have the potential, or some other negative thing,” Pujols says. “I think the most important thing is that you do what you love, even though maybe you are going against the current. You don’t want to have regrets.”

Mapping the cellular circuits behind spitting

Roundworms change the flow of material in and out of their mouths in response to bright light, revealing a new way for neurons to control muscle cells.

Raleigh McElvery
July 23, 2021

For over a decade, researchers have known that the roundworm Caenorhabditis elegans can detect and avoid short-wavelength light, despite lacking eyes and the light-absorbing molecules required for sight. As a graduate student in the Horvitz lab, Nikhil Bhatla proposed an explanation for this ability. He observed that light exposure not only made the worms wriggle away, but it also prompted them to stop eating. This clue led him to a series of studies that suggested that his squirming subjects weren’t seeing the light at all — they were detecting the noxious chemicals it produced, such as hydrogen peroxide. Soon after, the Horvitz lab realized that worms not only taste the nasty chemicals light generates, they also spit them out.

Now, in a study recently published in eLife, a team led by former graduate student Steve Sando reports the mechanism that underlies spitting in C. elegans. Individual muscle cells are generally regarded as the smallest units that neurons can independently control, but the researchers’ findings question this assumption. In the case of spitting, they determined that neurons can direct specialized subregions of a single muscle cell to generate multiple motions — expanding our understanding of how neurons control muscle cells to shape behavior.

“Steve made the remarkable discovery that the contraction of a small region of a particular muscle cell can be uncoupled from the contraction of the rest of the same cell,” says H. Robert Horvitz, the David H. Koch Professor of Biology at MIT, a member of the McGovern Institute for Brain Research and the Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute Investigator, and senior author of the study. “Furthermore, Steve found that such subcellular muscle compartments can be controlled by neurons to dramatically alter behavior.”

A roundworm spits after it is exposed to the nasty-tasting hydrogen peroxide produced by bright light. Video by Steve Sando.

Roundworms are like vacuum cleaners that wiggle around hoovering up bacteria. The worm’s mouth, also known as the pharynx, is a muscular tube that traps the food, chews it, and then transfers it to the intestines through a series of “pumping” contractions.

Researchers have known for over a decade that worms flee from UV, violet, or blue light. But Bhatla discovered that this light also interrupts the constant pumping of the pharynx, because the taste produced by the light is so nasty that the worms pause feeding. As he looked closer, Bhatla noticed the worms’ response was actually quite nuanced. After an initial pause, the pharynx briefly starts pumping again in short bursts before fully stopping — almost like the worm was chewing for a bit even after tasting the unsavory light. Sometimes, a bubble would escape from the mouth, like a burp.

After he joined the project, Sando discovered that the worms were neither burping nor continuing to munch. Instead, the “burst pumps” were driving material in the opposite direction, out of the mouth into the local environment, rather than further back into the pharynx and intestine. In other words, the bad-tasting light caused worms to spit. Sando then spent years chasing his subjects around the microscope with a bright light and recording their actions in slow motion, in order to pinpoint the neural circuitry and muscle motions required for this behavior.

“The discovery that the worms were spitting was quite surprising to us, because the mouth seemed to be moving just like it does when it’s chewing,” Sando says. “It turns out that you really needed to zoom in and slow things down to see what’s going on, because the animals are so small and the behavior is happening so quickly.”

To analyze what’s happening in the pharynx to produce this spitting motion, the researchers used a tiny laser beam to surgically remove individual nerve and muscle cells from the mouth and discern how that affected the worm’s behavior. They also monitored the activity of the cells in the mouth by tagging them with specially-engineered fluorescent “reporter” proteins.

They saw that while the worm is eating, three muscle cells towards the front of the pharynx called pm3s contract and relax together in synchronous pulses. But as soon as the worm tastes light, the subregions of these individual cells closest to the front of the mouth become locked in a state of contraction, opening the front of the mouth and allowing material to be propelled out. This reverses the direction of the flow of the ingested material and converts feeding into spitting.

The team determined that this “uncoupling” phenomenon is controlled by a single neuron at the back of the worm’s mouth. Called M1, this nerve cell spurs a localized influx of calcium at the front end of the pm3 muscle likely responsible for triggering the subcellular contractions.

M1 relays important information like a switchboard. It receives incoming signals from many different neurons, and transmits that information to the muscles involved in spitting. Sando and his team suspect that the strength of the incoming signal can tune the worm’s behavior in response to tasting light. For instance, their findings suggest that a revolting taste elicits a vigorous rinsing of the mouth, while a mildly unpleasant sensation causes the worm spit more gently, just enough to eject the contents.

In the future, Sando thinks the worm could be used as a model to study how neurons trigger subregions of muscle cells to constrict and shape behavior — a phenomenon they suspect occurs in other animals, possibly including humans.

“We’ve essentially found a new way for a neuron to move a muscle,” Sando says. “Neurons orchestrate the motions of muscles, and this could be a new tool that allows them to exert a sophisticated kind of control. That’s pretty exciting.”

Former Horvitz lab graduate student Steve Sando studies the neurons that allow roundworms to taste the chemicals produced by light — and then spit them out.

Citation:
“An hourglass circuit motif transforms a motor program via subcellularly localized muscle calcium signaling and contraction”
eLife, online July 2, 2021, DOI: 10.7554/eLife.59341
Steven R Sando, Nikhil Bhatla, Eugene L Q Lee, and H. Robert Horvitz

Siniša Hrvatin

Education

  • PhD, 2013, Harvard University
  • A.B., 2007, Biochemical Sciences, Harvard University

Research Summary

To survive extreme environments, many animals have evolved the ability to profoundly decrease metabolic rate and body temperature and enter states of dormancy, such as torpor and hibernation. Our laboratory studies the mysteries of how animals and their cells initiate, regulate, and survive these adaptations. Specifically, we focus on investigating: 1) how the brain regulates torpor and hibernation, 2) how cells adapt to these states, and 3) whether inducing these states can slow down tissue damage, disease progression, and even aging. Our long-term goal is to explore potential applications of inducing similar states of “suspended animation” in humans.

Awards

  • Warren Alpert Distinguished Scholar, Warren Albert Foundation, 2019
  • NIH Director’s New Innovator Award, 2022
  • Searle Scholar, 2023
  • Pew Scholar, 2023
  • McKnight Scholar, 2024
Study of synapse strength focuses on ‘active zones’

With new NIH grant, team will learn how neurons build key sites that release neurotransmitters a lot, or a little, to drive nervous system communication

Picower Institute
March 16, 2021

Job descriptions for the thousands of types of neurons in the brain typically include a common function: release chemicals called neurotransmitters to communicate across circuit connections called synapses. In a new study funded by the National Institutes of Health, the lab of MIT Professor Troy Littleton will seek to understand how neurons construct synapses of different strengths, a variety that may be key to the diversity of neural communication.

Littleton, Menicon Professor of Neuroscience in The Picower Institute for Learning and Memory and the Departments of Biology and Brain and Cognitive Sciences at MIT, said the findings could increase scientists’ understanding of how neural circuits develop and change to reflect learning and experience – a phenomenon called plasticity – and might also suggest ways to adjust synaptic strength when it is atypical in disorders such as autism or intellectual disability.

Video from a 2018 Littleton Lab study shows calcium flux (green) indicating the release of glutamate at synapses tagged by the presence of a glutamate receptor (red).

Using neurons that control muscles in the Drosophila fruit fly, the study will focus on “active zones” (AZs), which are tiny neural structures that enable the release of neurotransmitters across each synapse. The flies provide a simple model, Littleton said, that can help elucidate many basic factors affecting AZ strength that are also at play in the neurons of other animals, including mammals.

“Understanding the rules in a simple model like Drosophila that help to define when a synapse is strong or weak allows us to view these principles as fundamental elements of how neurons control synaptic growth and development,” he said. “Depending on which of these factors a neuron modifies or plays around with, it is likely to be able to make synapses stronger or weaker in very different patterns.”

During larval development the neurons build hundreds of AZs. In a 2018 study, Littleton’s lab found that AZs vary widely in their strength: About 10 percent release neurotransmitters as much as 50 times more often than the majority of weaker synapses. The researchers also found that the strongest AZs were typically the ones that had the most time to develop and accumulate their many protein building blocks.

In the new study, which will provide nearly $1.9 million over five years, the team will learn how those active zones get built step by step out of more than a dozen different proteins that arrive at different stages of development. Because some AZs apparently build up bigger and stronger than others, Littleton likens the process to the construction of a variety of houses in a neighborhood—from big four-bedroom homes to little townhomes. The new study, including preliminary work the team has done with the support of the Picower Institute Innovation Fund, will help explain how each kind of structure emerges, in their relative abundance, in the same cell.

In one set of experiments, for instance, his team will study whether the supply of building materials – the various proteins – is a limitation on how many AZs can mature to full strength before development ceases (i.e. maybe they don’t all get enough lumber or nails to fully frame the house in time). The scientists will test that, for instance, with genetic manipulations that change the amount of key proteins produced. By imaging the proteins as they accumulate and by looking in on the same AZs day after day, a technique the lab uses called “intravital imaging,” they can see how changing protein availability changes the construction of AZs in a neuron.

With a house blueprint background a cartoon shows two frames: a few lines and circles arranged over a horizontal bar and then a larger array of lines over the bar with the overall appearance of an erupting fountain or a sprouting plant
A model of active zone construction: Numerous proteins arrive over time during development to ultimately build a structure for releasing neurotransmitters.

In another set of experiments, the team will test whether some AZs are better than others at acquiring the available material supply and putting it to use (i.e. some may have more carpenters than others to make the best use of the available nails and lumber). And to better understand how the construction process might work in longer-lived animals like mammals, where protein materials not only need to be gathered but also maintained and replaced, they will artificially prolong the flies’ larval stage.

In a third set of tests they will examine the case of two types of neurons that each connect to the same fly muscles but exert control in different ways. Though each type works by releasing the same neurotransmitter, called glutamate, “tonic” neurons feature small but constant glutamate release, while the “phasic” cells release stronger, but more occasional, bursts. The study will examine how AZ development differs, for instance, due to differences in gene expression to promote the different function of these otherwise similar cells.

In all, their goal will be to determine how neurons build their different capacities and styles of connection and communication.

In addition to Littleton the research team includes research scientists Yulia Akbergenova and Suresh Jetti, and graduate students Karen Leopold Cunningham and Andrés Crane.

Our gut-brain connection

“Organs-on-a-chip” system sheds light on how bacteria in the human digestive tract may influence neurological diseases.

Anne Trafton | MIT News Office
January 29, 2021

In many ways, our brain and our digestive tract are deeply connected. Feeling nervous may lead to physical pain in the stomach, while hunger signals from the gut make us feel irritable. Recent studies have even suggested that the bacteria living in our gut can influence some neurological diseases.

Modeling these complex interactions in animals such as mice is difficult to do, because their physiology is very different from humans’. To help researchers better understa nd the gut-brain axis, MIT researchers have developed an “organs-on-a-chip” system that replicates interactions between the brain, liver, and colon.

Using that system, the researchers were able to model the influence that microbes living in the gut have on both healthy brain tissue and tissue samples derived from patients with Parkinson’s disease. They found that short-chain fatty acids, which are produced by microbes in the gut and are transported to the brain, can have very different effects on healthy and diseased brain cells.

“While short-chain fatty acids are largely beneficial to human health, we observed that under certain conditions they can further exacerbate certain brain pathologies, such as protein misfolding and neuronal death, related to Parkinson’s disease,” says Martin Trapecar, an MIT postdoc and the lead author of the study.

Linda Griffith, the School of Engineering Professor of Teaching Innovation and a professor of biological engineering and mechanical engineering, and Rudolf Jaenisch, an MIT professor of biology and a member of MIT’s Whitehead Institute for Medical Research, are the senior authors of the paper, which appears today in Science Advances.

The gut-brain connection

For several years, Griffith’s lab has been developing microphysiological systems — small devices that can be used to grow engineered tissue models of different organs, connected by microfluidic channels. In some cases, these models can offer more accurate information on human disease than animal models can, Griffith says.

In a paper published last year, Griffith and Trapecar used a microphysiological system to model interactions between the liver and the colon. In that study, they found that short-chain fatty acids (SCFAs), molecules produced by microbes in the gut, can worsen autoimmune inflammation associated with ulcerative colitis under certain conditions. SCFAs, which include butyrate, propionate, and acetate, can also have beneficial effects on tissues, including increased immune tolerance, and they account for about 10 percent of the energy that we get from food.

In the new study, the MIT team decided to add the brain and circulating immune cells to their multiorgan system. The brain has many interactions with the digestive tract, which can occur via the enteric nervous system or through the circulation of immune cells, nutrients, and hormones between organs.

Several years ago, Sarkis Mazmanian, a professor of microbiology at Caltech, discovered a connection between SCFAs and Parkinson’s disease in mice. He showed that SCFAs, which are produced by bacteria as they consume undigested fiber in the gut, sped up the progression of the disease, while mice raised in a germ-free environment were slower to develop the disease.

Griffith and Trapecar decided to further explore Mazmanian’s findings, using their microphysiological model. To do that, they teamed up with Jaenisch’s lab at the Whitehead Institute. Jaenisch had previously developed a way to transform fibroblast cells from Parkinson’s patients into pluripotent stem cells, which can then be induced to differentiate into different types of brain cells — neurons, astrocytes, and microglia.

More than 80 percent of Parkinson’s cases cannot be linked to a specific gene mutation, but the rest do have a genetic cause. The cells that the MIT researchers used for their Parkinson’s model carry a mutation that causes accumulation of a protein called alpha synuclein, which damages neurons and causes inflammation in brain cells. Jaenisch’s lab has also generated brain cells that have this mutation corrected but are otherwise genetically identical and from the same patient as the diseased cells.

Griffith and Trapecar first studied these two sets of brain cells in microphysiological systems that were not connected to any other tissues, and found that the Parkinson’s cells showed more inflammation than the healthy, corrected cells. The Parkinson’s cells also had impairments in their ability to metabolize lipids and cholesterol.

Opposite effects

The researchers then connected the brain cells to tissue models of the colon and liver, using channels that allow immune cells and nutrients, including SCFAs, to flow between them. They found that for healthy brain cells, being exposed to SCFAs is beneficial, and helps them to mature. However, when brain cells derived from Parkinson’s patients were exposed to SCFAs, the beneficial effects disappeared. Instead, the cells experienced higher levels of protein misfolding and cell death.

These effects were seen even when immune cells were removed from the system, leading the researchers to hypothesize that the effects are mediated by changes to lipid metabolism.

“It seems that short-chain fatty acids can be linked to neurodegenerative diseases by affecting lipid metabolism rather than directly affecting a certain immune cell population,” Trapecar says. “Now the goal for us is to try to understand this.”

The researchers also plan to model other types of neurological diseases that may be influenced by the gut microbiome. The findings offer support for the idea that human tissue models could yield information that animal models cannot, Griffith says. She is now working on a new version of the model that will include micro blood vessels connecting different tissue types, allowing researchers to study how blood flow between tissues influences them.

“We should be really pushing development of these, because it is important to start bringing more human features into our models,” Griffith says. “We have been able to start getting insights into the human condition that are hard to get from mice.”

The research was funded by DARPA, the National Institutes of Health, the National Institute of Biomedical Imaging and Bioengineering, the National Institute of Environmental Health Sciences, the Koch Institute Support (core) Grant from the National Cancer Institute, and the Army Research Office Institute for Collaborative Biotechnologies.

Playing chess, not checkers

Neurons dynamically control their myelin patterns.

Picower Institute
January 1, 2021

Harvard and MIT researchers have discovered a new way that the brain responds to stimuli, with different types of neurons using myelin in different ways. By dynamically controlling myelin, the insulating coating around their long axon projections that helps with signal conduction, neurons have more ways to adapt to changes. Published in the journal Science, the study in mice advances scientists’ understanding of how the brain works and opens avenues for exploring new disease mechanisms.

“The brain requires a diversity of mechanisms at its disposal in order to adapt to stimuli. We know that neurons have different properties, and we demonstrated several years ago that neurons have different patterns of myelination. Now, we have found an additional layer of complexity: neurons actively use their myelin in dynamic and different ways,” said co-senior author Paola Arlotta, the Golub Family Professor of Stem Cell and Regenerative Biology at Harvard University.

In biology textbooks, the prototypical image of a neuron depicts the axon with a series of equally sized, evenly spaced pieces of myelin. However, the Arlotta lab showed in 2014 that the picture is more complicated: different types of neurons show different patterns of myelination, with varying lengths of myelin or no myelination on some segments. In the current study, the researchers delved deeper into the phenomenon of how myelination patterns might change over time.

A video showing a 3D block of red and green neurons with myelin
Researchers used a live imaging system to capture both neurons (red) and their surrounding myelin (green) at the same time. Credit: Arlotta Laboratory, Harvard University.

To investigate myelin plasticity, the researchers used mouse models where specific neuron types were fluorescently labeled. They changed the animals’ sensory input by closing one eye, then tracked how the brain responded using a custom-built in vivo imaging system in the lab of collaborator and co-senior author Elly Nedivi.

“Our multicolor method enables the simultaneous visualization of both the myelin and the axons it was wrapping. This allowed us to closely track how myelin was changing over time as mice reconfigured the visual cortex as sight became deprived in one eye,” said Nedivi, who is the William R. (1964) & Linda R. Young Professor of Neuroscience at MIT, and a member of The Picower Institute for Learning and Memory and the Departments of Biology and Brain and Cognitive Sciences.

The researchers found that even though they tracked neurons that were next to each other and part of the same network, different cell types had different responses — specifically, inhibitory neurons remodeled their myelin more than excitatory neurons.

“In the inhibitory neurons, we saw a two-times increase in the number of myelin changes. Those changes can be any way you can imagine: they can be myelin segments shortening or elongating, the addition of new myelin, and also the elimination of an entire piece of myelin,” said Sung Min Yang, lead author and postdoctoral fellow in the Arlotta lab.

The unique capacity to change their myelin opens up possibilities for the neurons, Yang said: “It turns out that neurons do not move myelin around in a consistent way, as in a game of checkers where every game piece has the same move. Instead, the brain is playing chess, where different neurons — or pieces — can move in different ways. This gives the brain more choice in how to use myelin, which is a limited resource.”

The researchers also found that neurons did not necessarily have to produce new myelin, but could reuse and reshape what they already had in order to respond.

“We have discovered a fundamental property of the brain that opens the window to conceptualizing how the organ maximizes its power and optimizes its function. The dynamic distribution of myelin is yet another level of mechanism that the brain uses to diversify its response to a given stimulus — the endless combinations can enable a more complex, even surprising outcome,” Arlotta said.

Based on the findings, the researchers can now investigate how myelin plasticity plays a role in other contexts, including disease.

“We hope to be able to investigate myelin pathology in human brain organoid models, which can be generated from patients or engineered to contain specific mutations associated with myelin abnormalities, in order to better understand the disease mechanisms,” Arlotta said.

This research was supported by the Stanley Center for Psychiatric Research at the Broad Institute of MIT and Harvard, the National Institute of Mental Health, the National Institutes of Health, and the JPB Foundation.

Neuroscientists identify brain circuit that encodes timing of events

Findings suggest this hippocampal circuit helps us to maintain our timeline of memories.

Anne Trafton | MIT News Office
January 12, 2021

When we experience a new event, our brain records a memory of not only what happened, but also the context, including the time and location of the event. A new study from MIT neuroscientists sheds light on how the timing of a memory is encoded in the hippocampus, and suggests that time and space are encoded separately.

In a study of mice, the researchers identified a hippocampal circuit that the animals used to store information about the timing of when they should turn left or right in a maze. When this circuit was blocked, the mice were unable to remember which way they were supposed to turn next. However, disrupting the circuit did not appear to impair their memory of where they were in space.

The findings add to a growing body of evidence suggesting that when we form new memories, different populations of neurons in the brain encode time and place information, the researchers say.

“There is an emerging view that ‘place cells’ and ‘time cells’ organize memories by mapping information onto the hippocampus. This spatial and temporal context serves as a scaffold that allows us to build our own personal timeline of memories,” says Chris MacDonald, a research scientist at MIT’s Picower Institute for Learning and Memory and the lead author of the study.

Susumu Tonegawa, the Picower Professor of Biology and Neuroscience at the RIKEN-MIT Laboratory of Neural Circuit Genetics at the Picower Institute, is the senior author of the study, which appears this week in the Proceedings of the National Academy of Sciences.

Time and place

About 50 years ago, neuroscientists discovered that the brain’s hippocampus contains neurons that encode memories of specific locations. These cells, known as place cells, store information that becomes part of the context of a particular memory.

The other critical piece of context for any given memory is the timing. In 2011, MacDonald and the late Howard Eichenbaum, a professor of psychological and brain sciences at Boston University, discovered cells that keep track of time, in a part of the hippocampus called CA1.

In that study, MacDonald, who was then a postdoc at Boston University, found that these cells showed specific timing-related firing patterns when mice were trained to associate two stimuli — an object and an odor — that were presented with a 10-second delay between them. When the delay was extended to 20 seconds, the cells reorganized their firing patterns to last 20 seconds instead of 10.

“It’s almost like they’re forming a new representation of a temporal context, much like a spatial context,” MacDonald says. “The emerging view seems to be that both place and time cells organize memory by mapping experience to a representation of context that is defined by time and space.”

In the new study, the researchers wanted to investigate which other parts of the brain might be feeding CA1 timing information. Some previous studies had suggested that a nearby part of the hippocampus called CA2 might be involved in keeping track of time. CA2 is a very small region of the hippocampus that has not been extensively studied, but it has been shown to have strong connections to CA1.

To study the links between CA2 and CA1, the researchers used an engineered mouse model in which they could use light to control the activity of neurons in the CA2 region. They trained the mice to run a figure-eight maze in which they would earn a reward if they alternated turning left and right each time they ran the maze. Between each trial, they ran on a treadmill for 10 seconds, and during this time, they had to remember which direction they had turned on the previous trial, so they could do the opposite on the upcoming trial.

When the researchers turned off CA2 activity while the mice were on the treadmill, they found that the mice performed very poorly at the task, suggesting that they could no longer remember which direction they had turned in the previous trial.

“When the animals are performing normally, there is a sequence of cells in CA1 that ticks off during this temporal coding phase,” MacDonald says. “When you inhibit the CA2, what you see is the temporal coding in CA1 becomes less precise and more smeared out in time. It becomes destabilized, and that seems to correlate with them also performing poorly on that task.”

Memory circuits

When the researchers used light to inhibit CA2 neurons while the mice were running the maze, they found little effect on the CA1 “place cells” that allow the mice to remember where they are. The findings suggest that spatial and timing information are encoded preferentially by different parts of the hippocampus, MacDonald says.

“One thing that’s exciting about this work is this idea that spatial and temporal information can operate in parallel and might merge or separate at different points in the circuit, depending on what you need to accomplish from a memory standpoint,” he says.

MacDonald is now planning additional studies of time perception, including how we perceive time under different circumstances, and how our perception of time influences our behavior. Another question he hopes to pursue is whether the brain has different mechanisms for keeping track of events that are separated by seconds and events that are separated by much longer periods of time.

“Somehow the information that we store in memory preserves the sequential order of events across very different timescales, and I’m very interested in how it is that we’re able to do that,” he says.

The research was funded by the RIKEN Center for Brain Science, the Howard Hughes Medical Institute, and the JPB Foundation.

Aspiring physician explores the many levels of human health

During her time at MIT, senior Ayesha Ng’s interests have expanded from cellular biology to the social systems that shape public health.

Alison Gold | School of Science
November 9, 2020

It was her childhood peanut allergy that first sparked senior Ayesha Ng’s fascination with the human body. “To see this severe reaction happen to my body and not know what was happening — that made me a lot more curious about biology and living systems,” Ng says.

She didn’t exactly plan it this way. But in her three and a half years at MIT, Ng, a biology and cognitive and brain sciences double major from the Los Angeles, California area, has conducted research and taken classes examining just about every level of human health — from cellular to societal.

Most recently, her passion for medicine and health equity led her to the National Foundation for the Centers for Disease Control and Prevention (CDC), where, this summer, she worked to develop guidelines for addressing health disparities on state and local health jurisdictions’ Covid-19 data dashboards. Now, as an aspiring physician amidst the medical school application process, Ng has a sense of how microbiological, physiological, and social systems interact to affect a person’s health.

Starting small

Throughout her entire first year at MIT, Ng studied the biology of health at a cellular level. Specifically, she researched the effects of fasting and aging on regeneration of intestinal stem cells, which are located in the human intestinal crypts and continuously self-divide and reproduce. Understanding these metabolic mechanisms is crucial, as their deregulation can lead to age-associated diseases such as cancer.

“That experience allowed me to broaden my technical skills, just getting used to so many different types of molecular biological techniques right away, which I really appreciated,” Ng says of her time at the Whitehead Institute for Biomedical Research in Professor David Sabatini’s lab.

“After some time, I realized that I also wanted to also study sciences at a broader, more macro level, instead of only the microbiology and molecular biology that we were studying in Course 7,” Ng says of her biology major.

In addition to studying the biology of cancer, Ng had developed a curiosity about the human brain and how it functions. “I was really interested in that, because my grandpa has dementia,” Ng says.

Seeing her grandfather’s cognitive decline, she was inspired to become involved in MIT BrainTrust, a student organization that offers a social support network for individuals from around the Boston, Massachusetts area who have brain injuries. “We have these meetings, in which I serve as one of only one or two students there to facilitate a safe space where we can have all these individuals with brain injury gather,” Ng says of the peer-support aspect of the program. “They can really share their mutual challenges and experiences.”

Investigating the brain

To pursue her interest in brain research and the societal impact of brain injuries, Ng traveled to the University of Hong Kong the summer after her first year as an MIT International Science and Technology Initiatives (MISTI) China Fung Scholar. Working with Professor Raymond Chang, she began to examine neurodegenerative disease and used tissue-clearing techniques to visualize 3D mouse brain structures at cellular resolution. “That was personally meaningful for me, to research about that and learn more about dementia,” Ng says.

Returning to MIT her sophomore year, Ng was certain that she wanted to continue studying the brain. She began working on Alzheimer’s research at the MIT Picower Institute for Learning and Memory in the lab of Professor Li-Huei Tsai, the Picower Professor of Neuroscience at MIT. Much existing research into Alzheimer’s disease has been at the bulk-tissue level, focusing on the neurons’ role in neurodegeneration associated with aging.

Ng’s work with Tsai considers the complexity of alterations across genes and less-abundant cell types, such as microglia, astrocytes, and other supporting glial cells that become dysregulated in the brains of patients with Alzheimer’s. Considering the interplay between and within cell types during neurodegeneration is most intriguing to her. While some molecular processes are protective, other damaging ones simultaneously occur and can exist even within the same cell type. This intricacy has made the mechanistic basis behind Alzheimer’s progression elusive and the research that much more crucial.

“It’s really interesting to see how heterogeneous and complex the responses are in Alzheimer’s brains,” Ng says of the research program with Tsai, a founding director of MIT’s Aging Brain Initiative. “I really think about these potential new drug targets to improve treatment for Alzheimer’s in the future because I have seen, with my grandpa especially, how treatment is really lacking in the neurodegeneration field. There’s no treatment that’s been able to stop or even slow the progression of Alzheimer’s disease.”

Her research project in the Tsai Lab relies on a technology called single-nucleus RNA sequencing (snRNA-seq), which extracts the genomic information contained in individual cells. This is followed by computational dimension reduction and clustering algorithms to examine how Alzheimer’s disease differentially affects genes and specific cell types.

“With that project, we’ve been able to use single-nucleus RNA sequencing to really look at the brains of human Alzheimer’s patients,” Ng says. “And with the single-cell technology, we’re able to look at brain tissue at a much higher resolution, allowing us to see that there’s so much heterogeneity within the brain.”

After conducting more than a year of Alzheimer’s research and then taking a human physiology class in her third year, Ng decided to add a second major in brain and cognitive sciences to gain deeper insight specifically into how the nervous system within the body functions.

“That class really allowed me to realize that I really love organ systems and wanted to study by looking at more physiological mechanisms,” Ng says. “It has been really great to, at the end of my college career, really delve more into a very specific system.”

Medicine and society

Having gained perspective on cellular and microbiology, and human organ systems, Ng decided to zoom out further, interning this past summer at the National Foundation for the CDC. She found the opportunity through MIT’s PKG Center, applied as one of 60 candidates, and was selected for a team of four. There, as a member of the CDC Foundation’s Health Equity Strike Team, she examined how to increase transparency of publicly available Covid-19 data on health disparities and how the narrative tied to health equity can be modified in public health messages. This involved harnessing data about the demographics of those most affected during Covid-19 — including how infection and mortality rates differ starkly based on social factors including housing conditions, socioeconomic status, race, and ethnicity.

“Thinking about all these factors, we compiled a set of best practices for how to present data about Covid-19, what data should be collected, and tried to push those out to help jurisdictions as best-practice recommendations,” Ng says. “That did really increase my interest in health equity and made me realize how important public health is as well.”

Amidst the Covid-19 pandemic, Ng is spending the first semester of her senior year at home with her family in the Los Angeles area. “I really miss the people and not being able to interact with not only other students and peers, but also faculty as well,” she says. “I really wanted to enjoy time with friends, and just explore more of MIT, too, which I didn’t always get the chance to do over the past few years.”

Still, she continues to participate in both BrainTrust and MIT’s Asian Dance team, remotely, through weekly practices on Zoom.

“I think dance is one of the biggest de-stressors for me; I had never done dance before going to college. Getting to meet this team and join this community allowed me not only to connect to my Asian cultural roots, but also just expose myself to this new art form where I could really learn how to express myself on stage,” Ng says. “And that really has been the source of relief for me to just liberate any worries that I have, and has increased my sense of self-awareness and self-confidence.”

Armed with the many experiences she has enjoyed at MIT, both in and out of the classroom, Ng plans to continue studying both medicine and public health. She’s excited to explore different potential specialties and is currently most intrigued by surgery. Whichever specialty she may choose, she is determined to include health equity and cultural sensitivity in her practice.

“Seeing surgeons, I personally think that being able to physically heal a patient with my own hands, that would be the most rewarding feeling,” Ng says. “I will strive to, as a physician, use whatever platform that I have to advocate for patients and really drive health-care systems to overcome disparities.”