Author: Anne Trafton

A radiation-free approach to imaging molecules in the brain

Anne Trafton |

Scientists hoping to get a glimpse of molecules that control brain activity have devised a new probe that allows them to image these molecules without using any chemical or radioactive labels.

Currently the gold standard approach to imaging molecules in the brain is to tag them with radioactive probes. However, these probes offer low resolution and they can’t easily be used to watch dynamic events, says Alan Jasanoff, an MIT professor of biological engineering.

Jasanoff and his colleagues have developed new sensors consisting of proteins designed to detect a particular target, which causes them to dilate blood vessels in the immediate area. This produces a change in blood flow that can be imaged with magnetic resonance imaging (MRI) or other imaging techniques.

“This is an idea that enables us to detect molecules that are in the brain at biologically low levels, and to do that with these imaging agents or contrast agents that can ultimately be used in humans,” Jasanoff says. “We can also turn them on and off, and that’s really key to trying to detect dynamic processes in the brain.”

In a paper appearing in the Dec. 2 issue of Nature Communications, Jasanoff and his colleagues used these probes to detect enzymes called proteases, but their ultimate goal is to use them to monitor the activity of neurotransmitters, which act as chemical messengers between brain cells.

The paper’s lead authors are postdoc Mitul Desai and former MIT graduate student Adrian Slusarczyk. Recent MIT graduate Ashley Chapin and postdoc Mariya Barch are also authors of the paper.

Indirect imaging

To make their probes, the researchers modified a naturally occurring peptide called calcitonin gene-related peptide (CGRP), which is active primarily during migraines or inflammation. The researchers engineered the peptides so that they are trapped within a protein cage that keeps them from interacting with blood vessels. When the peptides encounter proteases in the brain, the proteases cut the cages open and the CGRP causes nearby blood vessels to dilate. Imaging this dilation with MRI allows the researchers to determine where the proteases were detected.

“These are molecules that aren’t visualized directly, but instead produce changes in the body that can then be visualized very effectively by imaging,” Jasanoff says.

Proteases are sometimes used as biomarkers to diagnose diseases such as cancer and Alzheimer’s disease. However, Jasanoff’s lab used them in this study mainly to demonstrate the validity their approach. Now, they are working on adapting these imaging agents to monitor neurotransmitters, such as dopamine and serotonin, that are critical to cognition and processing emotions.

To do that, the researchers plan to modify the cages surrounding the CGRP so that they can be removed by interaction with a particular neurotransmitter.

“What we want to be able to do is detect levels of neurotransmitter that are 100-fold lower than what we’ve seen so far. We also want to be able to use far less of these molecular imaging agents in organisms. That’s one of the key hurdles to trying to bring this approach into people,” Jasanoff says.

Jeff Bulte, a professor of radiology and radiological science at the Johns Hopkins School of Medicine, described the technique as “original and innovative,” while adding that its safety and long-term physiological effects will require more study.

“It’s interesting that they have designed a reporter without using any kind of metal probe or contrast agent,” says Bulte, who was not involved in the research. “An MRI reporter that works really well is the holy grail in the field of molecular and cellular imaging.”

Tracking genes

Another possible application for this type of imaging is to engineer cells so that the gene for CGRP is turned on at the same time that a gene of interest is turned on. That way, scientists could use the CGRP-induced changes in blood flow to track which cells are expressing the target gene, which could help them determine the roles of those cells and genes in different behaviors. Jasanoff’s team demonstrated the feasibility of this approach by showing that implanted cells expressing CGRP could be recognized by imaging.

“Many behaviors involve turning on genes, and you could use this kind of approach to measure where and when the genes are turned on in different parts of the brain,” Jasanoff says.

His lab is also working on ways to deliver the peptides without injecting them, which would require finding a way to get them to pass through the blood-brain barrier. This barrier separates the brain from circulating blood and prevents large molecules from entering the brain.

The research was funded by the National Institutes of Health BRAIN Initiative, the MIT Simons Center for the Social Brain, and fellowships from the Boehringer Ingelheim Fonds and the Friends of the McGovern Institute.

Researchers create synthetic cells to isolate genetic circuits

Anne Trafton |

Synthetic biology allows scientists to design genetic circuits that can be placed in cells, giving them new functions such as producing drugs or other useful molecules. However, as these circuits become more complex, the genetic components can interfere with each other, making it difficult to achieve more complicated functions.

MIT researchers have now demonstrated that these circuits can be isolated within individual synthetic “cells,” preventing them from disrupting each other. The researchers can also control communication between these cells, allowing for circuits or their products to be combined at specific times.

“It’s a way of having the power of multicomponent genetic cascades, along with the ability to build walls between them so they won’t have cross-talk. They won’t interfere with each other in the way they would if they were all put into a single cell or into a beaker,” says Edward Boyden, an associate professor of biological engineering and brain and cognitive sciences at MIT. Boyden is also a member of MIT’s Media Lab and McGovern Institute for Brain Research, and an HHMI-Simons Faculty Scholar.

This approach could allow researchers to design circuits that manufacture complex products or act as sensors that respond to changes in their environment, among other applications.

Boyden is the senior author of a paper describing this technique in the Nov. 14 issue of Nature Chemistry. The paper’s lead authors are former MIT postdoc Kate Adamala, who is now an assistant professor at the University of Minnesota, and former MIT grad student Daniel Martin-Alarcon. Katriona Guthrie-Honea, a former MIT research assistant, is also an author of the paper.

Circuit control

The MIT team encapsulated their genetic circuits in droplets known as liposomes, which have a fatty membrane similar to cell membranes. These synthetic cells are not alive but are equipped with much of the cellular machinery necessary to read DNA and manufacture proteins.

By segregating circuits within their own liposomes, the researchers are able to create separate circuit subroutines that could not run in the same container at the same time, but can run in parallel to each other, communicating in controlled ways. This approach also allows scientists to repurpose the same genetic tools, including genes and transcription factors (proteins that turn genes on or off), to do different tasks within a network.

“If you separate circuits into two different liposomes, you could have one tool doing one job in one liposome, and the same tool doing a different job in the other liposome,” Martin-Alarcon says. “It expands the number of things that you can do with the same building blocks.”

This approach also enables communication between circuits from different types of organisms, such as bacteria and mammals.

As a demonstration, the researchers created a circuit that uses bacterial genetic parts to respond to a molecule known as theophylline, a drug similar to caffeine. When this molecule is present, it triggers another molecule known as doxycycline to leave the liposome and enter another set of liposomes containing a mammalian genetic circuit. In those liposomes, doxycycline activates a genetic cascade that produces luciferase, a protein that generates light.

Using a modified version of this approach, scientists could create circuits that work together to produce biological therapeutics such as antibodies, after sensing a particular molecule emitted by a brain cell or other cell.

“If you think of the bacterial circuit as encoding a computer program, and the mammalian circuit is encoding the factory, you could combine the computer code of the bacterial circuit and the factory of the mammalian circuit into a unique hybrid system,” Boyden says.

The researchers also designed liposomes that can fuse with each other in a controlled way. To do that, they programmed the cells with proteins called SNAREs, which insert themselves into the cell membrane. There, they bind to corresponding SNAREs found on surfaces of other liposomes, causing the synthetic cells to fuse. The timing of this fusion can be controlled to bring together liposomes that produce different molecules. When the cells fuse, these molecules are combined to generate a final product.

More modularity

The researchers believe this approach could be used for nearly any application that synthetic biologists are already working on. It could also allow scientists to pursue potentially useful applications that have been tried before but abandoned because the genetic circuits interfered with each other too much.

“The way that we wrote this paper was not oriented toward just one application,” Boyden says. “The basic question is: Can you make these circuits more modular? If you have everything mishmashed together in the cell, but you find out that the circuits are incompatible or toxic, then putting walls between those reactions and giving them the ability to communicate with each other could be very useful.”

Vincent Noireaux, an associate professor of physics at the University of Minnesota, described the MIT approach as “a rather novel method to learn how biological systems work.”

“Using cell-free expression has several advantages: Technically the work is reduced to cloning (nowadays fast and easy), we can link information processing to biological function like living cells do, and we work in isolation with no other gene expression occurring in the background,” says Noireaux, who was not involved in the research.

Another possible application for this approach is to help scientists explore how the earliest cells may have evolved billions of years ago. By engineering simple circuits into liposomes, researchers could study how cells might have evolved the ability to sense their environment, respond to stimuli, and reproduce.

“This system can be used to model the behavior and properties of the earliest organisms on Earth, as well as help establish the physical boundaries of Earth-type life for the search of life elsewhere in the solar system and beyond,” Adamala says.

A new player in appetite control

Anne Trafton |

MIT neuroscientists have discovered that brain cells called glial cells play a critical role in controlling appetite and feeding behavior. In a study of mice, the researchers found that activating these cells stimulates overeating, and that when the cells are suppressed, appetite is also suppressed.

The findings could offer scientists a new target for developing drugs against obesity and other appetite-related disorders, the researchers say. The study is also the latest in recent years to implicate glial cells in important brain functions. Until about 10 years ago, glial cells were believed to play more of a supporting role for neurons.

“In the last few years, abnormal glial cell activities have been strongly implicated in neurodegenerative disorders. There is more and more evidence to point to the importance of glial cells in modulating neuronal function and in mediating brain disorders,” says Guoping Feng, the James W. and Patricia Poitras Professor of Neuroscience. Feng is also a member of MIT’s McGovern Institute for Brain Research and the Stanley Center for Psychiatric Research at the Broad Institute.

Feng is one of the senior authors of the study, which appears in the Oct. 18 edition of the journal eLife. The other senior author is Weiping Han, head of the Laboratory of Metabolic Medicine at the Singapore Bioimaging Consortium in Singapore. Naiyan Chen, a postdoc at the Singapore Bioimaging Consortium and the McGovern Institute, is the lead author.

Turning on appetite

It has long been known that the hypothalamus, an almond-sized structure located deep within the brain, controls appetite as well as energy expenditure, body temperature, and circadian rhythms including sleep cycles. While performing studies on glial cells in other parts of the brain, Chen noticed that the hypothalamus also appeared to have a lot of glial cell activity.

“I was very curious at that point what glial cells would be doing in the hypothalamus, since glial cells have been shown in other brain areas to have an influence on regulation of neuronal function,” she says.

Within the hypothalamus, scientists have identified two key groups of neurons that regulate appetite, known as AgRP neurons and POMC neurons. AgRP neurons stimulate feeding, while POMC neurons suppress appetite.

Until recently it has been difficult to study the role of glial cells in controlling appetite or any other brain function, because scientists haven’t developed many techniques for silencing or stimulating these cells, as they have for neurons. Glial cells, which make up about half of the cells in the brain, have many supporting roles, including cushioning neurons and helping them form connections with one another.

In this study, the research team used a new technique developed at the University of North Carolina to study a type of glial cell known as an astrocyte. Using this strategy, researchers can engineer specific cells to produce a surface receptor that binds to a chemical compound known as CNO, a derivative of clozapine. Then, when CNO is given, it activates the glial cells.

The MIT team found that turning on astrocyte activity with just a single dose of CNO had a significant effect on feeding behavior.

“When we gave the compound that specifically activated the receptors, we saw a robust increase in feeding,” Chen says. “Mice are not known to eat very much in the daytime, but when we gave drugs to these animals that express a particular receptor, they were eating a lot.”

The researchers also found that in the short term (three days), the mice did not gain extra weight, even though they were eating more.

“This raises the possibility that glial cells may also be modulating neurons that control energy expenditures, to compensate for the increased food intake,” Chen says. “They might have multiple neuronal partners and modulate multiple energy homeostasis functions all at the same time.”

When the researchers silenced activity in the astrocytes, they found that the mice ate less than normal.

Suzanne Dickson, a professor of neuroendocrinology at the University of Gothenburg in Sweden described the study as part of a “paradigm shift” toward the idea that glial cells have a less passive role than previously believed.

“We tend to think of glial cells as providing a support network for neuronal processes and that their activation is also important in certain forms of brain trauma or inflammation,” says Dickson, who was not involved in the research. “This study adds to the emerging evidence base that glial cells may also exert specific effects to control nerve cell function in normal physiology.”

Unknown interactions

Still unknown is how the astrocytes exert their effects on neurons. Some recent studies have suggested that glial cells can secrete chemical messengers such as glutamate and ATP; if so, these “gliotransmitters” could influence neuron activity.

Another hypothesis is that instead of secreting chemicals, astrocytes exert their effects by controlling the uptake of neurotransmitters from the space surrounding neurons, thereby affecting neuron activity indirectly.

Feng now plans to develop new research tools that could help scientists learn more about astrocyte-neuron interactions and how astrocytes contribute to modulation of appetite and feeding. He also hopes to learn more about whether there are different types of astrocytes that may contribute differently to feeding behavior, especially abnormal behavior.

“We really know very little about how astrocytes contribute to the modulation of appetite, eating, and metabolism,” he says. “In the future, dissecting out these functional difference will be critical for our understanding of these disorders.”

Pinpointing a brain circuit that can keep fears at bay

Anne Trafton |

People who are too frightened of flying to board an airplane, or too scared of spiders to venture into the basement, can seek a kind of treatment called exposure therapy. In a safe environment, they repeatedly face cues such as photos of planes or black widows, as a way to stamp out their fearful response — a process known as extinction.

Unfortunately, the effects of exposure therapy are not permanent, and many people experience a relapse. MIT scientists have now identified a way to enhance the long-term benefit of extinction in rats, offering a way to improve the therapy in people suffering from phobias and more complicated conditions such as post-traumatic stress disorder (PTSD).

Work conducted in the laboratory of Ki Goosens, a research affiliate of the McGovern Institute for Brain Research, has pinpointed a neural circuit that becomes active during exposure therapy in the rats. In a study published Sept. 27 in eLife, the researchers showed that they could stretch the therapy’s benefits for at least two months by boosting the circuit’s activity during treatment.

“When you give extinction training to humans or rats, and you wait long enough, you observe a phenomenon called spontaneous recovery, in which the fear that was originally learned comes back,” Goosens explains. “It’s one of the barriers to this type of therapy. You spend all this time going through it, but then it’s not a permanent fix for your problem.”

According to statistics from the National Institute of Mental Health, 18 percent of U.S. adults are diagnosed with a fear or anxiety disorder each year, with 22 percent of those patients experiencing severe symptoms.

How to quench a fear

The neural circuit identified by the scientists connects a part of the brain involved in fear memory, called the basolateral amygdala (BLA), with another region called the nucleus accumbens (NAc), that helps the brain process rewarding events. Goosens and her colleagues call it the BLA-NAc circuit.

Researchers have been considering a link between fear and reward for some time, Goosens says. “The amygdala is a part of the brain that is tightly linked with fear memory but it’s also been linked to positive reward learning as well, and the accumbens is a key reward area in the brain,” she explains. “What we’ve been thinking about is whether extinction is rewarding. When you’re expecting something bad and you don’t get it, does your brain treat that like it’s a good thing?”

To find out if there was a specific brain circuit involved, the researchers first trained rats to fear a certain noise by pairing it with foot shock. They later gave the rats extinction training, during which the noise was presented in the absence of foot shock, and they looked at markers of neural activity in the brain. The results revealed the BLA-NAc reward circuit was recruited by the brain during exposure therapy, as the rats gave up their fear of the bad noise.

Once Goosens and her colleagues had identified the circuit, they looked for ways to boost its activity. First, they paired a sugary drink with the fear-related sound during extinction training, hoping to associate the sound with a reward. This type of training, called counterconditioning, associates fear-eliciting cues with rewarding events or memories, instead of with neutral events as in most extinction training.

Rats that received the counterconditioning were significantly less likely to spontaneously revert to their fearful states, compared to those that received regular extinction training for up to 55 days later, the scientists found.

They also found that the benefits of extinction could be prolonged with optogenetic stimulation, in which the circuit was genetically modified so that it could be stimulated directly with tiny bursts of light from an optical fiber.

The ongoing benefit that came from stimulating the circuit was one of the most surprising — and welcome — findings from the study, Goosens says. “The effect that we saw was one that really emerged months later, and we want to know what’s happening over those two months. What is the circuit doing to suppress the recovery of fear over that period of time? We still don’t understand what that is.”

Another interesting finding from the study was that the circuit was active during both fear learning and fear extinction, says lead author Susana Correia, a former research scientist in the Goosens lab who is now a scientist at Ironwood Pharmaceuticals. “Understanding if these are molecularly different subcircuits within this projection could allow the development of a pharmaceutical approach to target the fear extinction pathway and to improve cognitive therapy,” Correia says.

Immediate and future impacts on therapy

Some therapists are already using counterconditioning in treating PTSD, and Goosens suggests that the rat study might encourage further exploration of this technique in human therapy.

And while it isn’t likely that humans will receive direct optogenetic therapy any time soon, Goosens says there is a benefit to knowing exactly which circuits are involved in extinction.

In neurofeedback studies, for instance, brain scan technologies such as fMRI or EEG could be used to help a patient learn to activate specific parts of their brain, including the BLA-NAc reward circuit, during exposure therapy.

Studies like this one, Goosens says, offer a “target for a personalized medicine approach where feedback is used during therapy to enhance the effectiveness of that therapy.”

Other MIT authors on the paper include technical assistant Anna McGrath, undergraduate Allison Lee, and McGovern principal investigator and Institute Professor Ann Graybiel.

The study was funded by the U.S. Army Research Office, the Defense Advanced Research Projects Agency (DARPA), and the National Institute of Mental Health.

Newly discovered neural connections may be linked to emotional decision-making

Anne Trafton |

MIT neuroscientists have discovered connections deep within the brain that appear to form a communication pathway between areas that control emotion, decision-making, and movement. The researchers suspect that these connections, which they call striosome-dendron bouquets, may be involved in controlling how the brain makes decisions that are influenced by emotion or anxiety.

This circuit may also be one of the targets of the neural degeneration seen in Parkinson’s disease, says Ann Graybiel, an Institute Professor at MIT, member of the McGovern Institute for Brain Research, and the senior author of the study.

Graybiel and her colleagues were able to find these connections using a technique developed at MIT known as expansion microscopy, which enables scientists to expand brain tissue before imaging it. This produces much higher-resolution images than would otherwise be possible with conventional microscopes.

That technique was developed in the lab of Edward Boyden, an associate professor of biological engineering and brain and cognitive sciences at the MIT Media Lab, who is also an author of this study. Jill Crittenden, a research scientist at the McGovern Institute, is the lead author of the paper, which appears in the Proceedings of the National Academy of Sciences the week of Sept. 19.

Tracing a circuit

In this study, the researchers focused on a small region of the brain known as the striatum, which is part of the basal ganglia — a cluster of brain centers associated with habit formation, control of voluntary movement, emotion, and addiction. Malfunctions of the basal ganglia have been associated with Parkinson’s and Huntington’s diseases, as well as autism, obsessive-compulsive disorder, and Tourette’s syndrome.

Much of the striatum is uncharted territory, but Graybiel’s lab has previously identified clusters of cells there known as striosomes. She also found that these clusters receive very specific input from parts of the brain’s prefrontal cortex involved in processing emotions, and showed that this communication pathway is necessary for making decisions that require an anxiety-provoking cost-benefit analysis, such as choosing whether to take a job that pays more but forces a move away from family and friends.

Her studies also suggested that striosomes relay information to cells within a region called the substantia nigra, one of the brain’s main dopamine-producing centers. Dopamine has many functions in the brain, including roles in initiating movement and regulating mood.

To figure out how these regions might be communicating, Graybiel, Crittenden, and their colleagues used expansion microscopy to image the striosomes and discovered extensive connections between those clusters of cells and dopamine-producing cells of the substantia nigra. The dopamine-producing cells send down many tiny extensions known as dendrites that become entwined with axons that come up to meet them from the striosomes, forming a bouquet-like structure.

“With expansion microscopy, we could finally see direct connections between these cells by unraveling their unusual rope-like bundles of axons and dendrites,” Crittenden says. “What’s really exciting to us is we can see that it’s small discrete clusters of dopamine cells with bundles that are being targeted.”

Hard decisions

This finding expands the known decision-making circuit so that it encompasses the prefrontal cortex, striosomes, and a subset of dopamine-producing cells. Together, the striosomes may be acting as a gatekeeper that absorbs sensory and emotional information coming from the cortex and integrates it to produce a decision on how to react, which is initiated by the dopamine-producing cells, the researchers say.

To explore that possibility, the researchers plan to study mice in which they can selectively activate or shut down the striosome-dendron bouquet as the mice are prompted to make decisions requiring a cost-benefit analysis.

The researchers also plan to investigate whether these connections are disrupted in mouse models of Parkinson’s disease. MRI studies and postmortem analysis of brains of Parkinson’s patients have shown that death of dopamine cells in the substantia nigra is strongly correlated with the disease, but more work is needed to determine if this subset overlaps with the dopamine cells that form the striosome-dendron bouquets.

How the brain builds panoramic memory

Anne Trafton |

When asked to visualize your childhood home, you can probably picture not only the house you lived in, but also the buildings next door and across the street. MIT neuroscientists have now identified two brain regions that are involved in creating these panoramic memories.

These brain regions help us to merge fleeting views of our surroundings into a seamless, 360-degree panorama, the researchers say.

“Our understanding of our environment is largely shaped by our memory for what’s currently out of sight,” says Caroline Robertson, a postdoc at MIT’s McGovern Institute for Brain Research and a junior fellow of the Harvard Society of Fellows. “What we were looking for are hubs in the brain where your memories for the panoramic environment are integrated with your current field of view.”

Robertson is the lead author of the study, which appears in the Sept. 8 issue of the journal Current Biology. Nancy Kanwisher, the Walter A. Rosenblith Professor of Brain and Cognitive Sciences and a member of the McGovern Institute, is the paper’s lead author.

Building memories

As we look at a scene, visual information flows from our retinas into the brain, which has regions that are responsible for processing different elements of what we see, such as faces or objects. The MIT team suspected that areas involved in processing scenes — the occipital place area (OPA), the retrosplenial complex (RSC), and parahippocampal place area (PPA) — might also be involved in generating panoramic memories of a place such as a street corner.

If this were true, when you saw two images of houses that you knew were across the street from each other, they would evoke similar patterns of activity in these specialized brain regions. Two houses from different streets would not induce similar patterns.

“Our hypothesis was that as we begin to build memory of the environment around us, there would be certain regions of the brain where the representation of a single image would start to overlap with representations of other views from the same scene,” Robertson says.

The researchers explored this hypothesis using immersive virtual reality headsets, which allowed them to show people many different panoramic scenes. In this study, the researchers showed participants images from 40 street corners in Boston’s Beacon Hill neighborhood. The images were presented in two ways: Half the time, participants saw a 100-degree stretch of a 360-degree scene, but the other half of the time, they saw two noncontinuous stretches of a 360-degree scene.

After showing participants these panoramic environments, the researchers then showed them 40 pairs of images and asked if they came from the same street corner. Participants were much better able to determine if pairs came from the same corner if they had seen the two scenes linked in the 100-degree image than if they had seen them unlinked.

Brain scans revealed that when participants saw two images that they knew were linked, the response patterns in the RSC and OPA regions were similar. However, this was not the case for image pairs that the participants had not seen as linked. This suggests that the RSC and OPA, but not the PPA, are involved in building panoramic memories of our surroundings, the researchers say.

Priming the brain

In another experiment, the researchers tested whether one image could “prime” the brain to recall an image from the same panoramic scene. To do this, they showed participants a scene and asked them whether it had been on their left or right when they first saw it. Before that, they showed them either another image from the same street corner or an unrelated image. Participants performed much better when primed with the related image.

“After you have seen a series of views of a panoramic environment, you have explicitly linked them in memory to a known place,” Robertson says. “They also evoke overlapping visual representations in certain regions of the brain, which is implicitly guiding your upcoming perceptual experience.”

The research was funded by the National Science Foundation Science and Technology Center for Brains, Minds, and Machines; and the Harvard Milton Fund.

Study finds brain connections key to learning

Anne Trafton |

A new study from MIT reveals that a brain region dedicated to reading has connections for that skill even before children learn to read.

By scanning the brains of children before and after they learned to read, the researchers found that they could predict the precise location where each child’s visual word form area (VWFA) would develop, based on the connections of that region to other parts of the brain.

Neuroscientists have long wondered why the brain has a region exclusively dedicated to reading — a skill that is unique to humans and only developed about 5,400 years ago, which is not enough time for evolution to have reshaped the brain for that specific task. The new study suggests that the VWFA, located in an area that receives visual input, has pre-existing connections to brain regions associated with language processing, making it ideally suited to become devoted to reading.

“Long-range connections that allow this region to talk to other areas of the brain seem to drive function,” says Zeynep Saygin, a postdoc at MIT’s McGovern Institute for Brain Research. “As far as we can tell, within this larger fusiform region of the brain, only the reading area has these particular sets of connections, and that’s how it’s distinguished from adjacent cortex.”

Saygin is the lead author of the study, which appears in the Aug. 8 issue of Nature Neuroscience. Nancy Kanwisher, the Walter A. Rosenblith Professor of Brain and Cognitive Sciences and a member of the McGovern Institute, is the paper’s senior author.

Specialized for reading

The brain’s cortex, where most cognitive functions occur, has areas specialized for reading as well as face recognition, language comprehension, and many other tasks. Neuroscientists have hypothesized that the locations of these functions may be determined by prewired connections to other parts of the brain, but they have had few good opportunities to test this hypothesis.

Reading presents a unique opportunity to study this question because it is not learned right away, giving scientists a chance to examine the brain region that will become the VWFA before children know how to read. This region, located in the fusiform gyrus, at the base of the brain, is responsible for recognizing strings of letters.

Children participating in the study were scanned twice — at 5 years of age, before learning to read, and at 8 years, after they learned to read. In the scans at age 8, the researchers precisely defined the VWFA for each child by using functional magnetic resonance imaging (fMRI) to measure brain activity as the children read. They also used a technique called diffusion-weighted imaging to trace the connections between the VWFA and other parts of the brain.

The researchers saw no indication from fMRI scans that the VWFA was responding to words at age 5. However, the region that would become the VWFA was already different from adjacent cortex in its connectivity patterns. These patterns were so distinctive that they could be used to accurately predict the precise location where each child’s VWFA would later develop.

Although the area that will become the VWFA does not respond preferentially to letters at age 5, Saygin says it is likely that the region is involved in some kind of high-level object recognition before it gets taken over for word recognition as a child learns to read. Still unknown is how and why the brain forms those connections early in life.

Pre-existing connections

Kanwisher and Saygin have found that the VWFA is connected to language regions of the brain in adults, but the new findings in children offer strong evidence that those connections exist before reading is learned, and are not the result of learning to read, according to Stanislas Dehaene, a professor and the chair of experimental cognitive psychology at the College de France, who wrote a commentary on the paper for Nature Neuroscience.

“To genuinely test the hypothesis that the VWFA owes its specialization to a pre-existing connectivity pattern, it was necessary to measure brain connectivity in children before they learned to read,” wrote Dehaene, who was not involved in the study. “Although many children, at the age of 5, did not have a VWFA yet, the connections that were already in place could be used to anticipate where the VWFA would appear once they learned to read.”

The MIT team now plans to study whether this kind of brain imaging could help identify children who are at risk of developing dyslexia and other reading difficulties.

“It’s really powerful to be able to predict functional development three years ahead of time,” Saygin says. “This could be a way to use neuroimaging to try to actually help individuals even before any problems occur.”

Seeing RNA at the nanoscale

Anne Trafton |

Cells contain thousands of messenger RNA molecules, which carry copies of DNA’s genetic instructions to the rest of the cell. MIT engineers have now developed a way to visualize these molecules in higher resolution than previously possible in intact tissues, allowing researchers to precisely map the location of RNA throughout cells.

Key to the new technique is expanding the tissue before imaging it. By making the sample physically larger, it can be imaged with very high resolution using ordinary microscopes commonly found in research labs.

“Now we can image RNA with great spatial precision, thanks to the expansion process, and we also can do it more easily in large intact tissues,” says Ed Boyden, an associate professor of biological engineering and brain and cognitive sciences at MIT, a member of MIT’s Media Lab and McGovern Institute for Brain Research, and the senior author of a paper describing the technique in the July 4 issue of Nature Methods.

Studying the distribution of RNA inside cells could help scientists learn more about how cells control their gene expression and could also allow them to investigate diseases thought to be caused by failure of RNA to move to the correct location.

Boyden and colleagues first described the underlying technique, known as expansion microscopy (ExM), last year, when they used it to image proteins inside large samples of brain tissue. In a paper appearing in Nature Biotechnology on July 4, the MIT team has now presented a new version of the technology that employs off-the-shelf chemicals, making it easier for researchers to use.

MIT graduate students Fei Chen and Asmamaw Wassie are the lead authors of the Nature Methods paper, and Chen and graduate student Paul Tillberg are the lead authors of the Nature Biotechnology paper.

A simpler process

The original expansion microscopy technique is based on embedding tissue samples in a polymer that swells when water is added. This tissue enlargement allows researchers to obtain images with a resolution of around 70 nanometers, which was previously possible only with very specialized and expensive microscopes.

However, that method posed some challenges because it requires generating a complicated chemical tag consisting of an antibody that targets a specific protein, linked to both a fluorescent dye and a chemical anchor that attaches the whole complex to a highly absorbent polymer known as polyacrylate. Once the targets are labeled, the researchers break down the proteins that hold the tissue sample together, allowing it to expand uniformly as the polyacrylate gel swells.

In their new studies, to eliminate the need for custom-designed labels, the researchers used a different molecule to anchor the targets to the gel before digestion. This molecule, which the researchers dubbed AcX, is commercially available and therefore makes the process much simpler.

AcX can be modified to anchor either proteins or RNA to the gel. In the Nature Biotechnology study, the researchers used it to anchor proteins, and they also showed that the technique works on tissue that has been previously labeled with either fluorescent antibodies or proteins such as green fluorescent protein (GFP).

“This lets you use completely off-the-shelf parts, which means that it can integrate very easily into existing workflows,” Tillberg says. “We think that it’s going to lower the barrier significantly for people to use the technique compared to the original ExM.”

Using this approach, it takes about an hour to scan a piece of tissue 500 by 500 by 200 microns, using a light sheet fluorescence microscope. The researchers showed that this technique works for many types of tissues, including brain, pancreas, lung, and spleen.

Imaging RNA

In the Nature Methods paper, the researchers used the same kind of anchoring molecule but modified it to target RNA instead. All of the RNAs in the sample are anchored to the gel, so they stay in their original locations throughout the digestion and expansion process.

After the tissue is expanded, the researchers label specific RNA molecules using a process known as fluorescence in situ hybridization (FISH), which was originally developed in the early 1980s and is widely used. This allows researchers to visualize the location of specific RNA molecules at high resolution, in three dimensions, in large tissue samples.

This enhanced spatial precision could allow scientists to explore many questions about how RNA contributes to cellular function. For example, a longstanding question in neuroscience is how neurons rapidly change the strength of their connections to store new memories or skills. One hypothesis is that RNA molecules encoding proteins necessary for plasticity are stored in cell compartments close to the synapses, poised to be translated into proteins when needed.

With the new system, it should be possible to determine exactly which RNA molecules are located near the synapses, waiting to be translated.
“People have found hundreds of these locally translated RNAs, but it’s hard to know where exactly they are and what they’re doing,” Chen says. “This technique would be useful to study that.”

Boyden’s lab is also interested in using this technology to trace the connections between neurons and to classify different subtypes of neurons based on which genes they are expressing.

The research was funded by the Open Philanthropy Project, the New York Stem Cell Foundation Robertson Award, the National Institutes of Health, the National Science Foundation, and Jeremy and Joyce Wertheimer.

MIT marks 100 years in Cambridge with “Crossing the Charles” competition

Anne Trafton |

They arrived via water and over land, by raft and hydrofoil, on foot and in experimental vehicles. Some paddled. Some danced. Some walked alongside robots. In all, hundreds of members of the MIT community on Saturday celebrated the 100th anniversary of the Institute’s move from Boston into Cambridge, Massachusetts with a unique procession across the Charles River, fueled by humor and creativity.

The “Crossing the Charles” parade and competition, the centerpiece of MIT’s May 7 Moving Day celebrations, took place simultaneously in the water and on the bridge that carries Massachusetts Avenue over the river.

In the river, a festive flotilla of watercraft journeyed across, including an electric hydrofoil craft, a motorized swarm of kayaks, a bamboo raft, and a pedal-powered floating platform in the shape of the dome from MIT’s main building.

Simultaneously, a colorful parade of students, faculty, staff, and alumni — plus a robotic cheetah — marched across the bridge, some with large floats in tow. Neuroscientists transported an 8-foot-high brain model, made out of plywood and set on wheels; MIT Libraries staff carried a fabric “river on sticks,” adorned with books and a laptop; undergraduates guided a “StrandBeaver,” a massive kinetic sculpture; and MIT’s Casino Rueda salsa dancers, a student club, stopped to perform. Hundreds of alumni marched across at the end of the parade.

“The diversity of the MIT community was on full display,” said John Ochsendorf, professor of civil and environmental engineering and architecture, and a faculty co-chair of the event. “You saw it all, from the brain to the bamboo.”

At an award ceremony following the crossing, MIT President L. Rafael Reif said he wanted to “thank the city of Cambridge for their generosity for 100 years” and joked that the city resembled a tolerant host enduring the visit of a long-running house guest.

“We are glad you stayed,” responded Cambridge Mayor Denise Simmons, in remarks following Reif’s comments.

Simmons also called MIT “a blessing and not a burden” and, in the spirit of the day, noted how useful it was to “keep a sense of humor” intact. Nearby, a 30-foot-high replica of a stone megalith bobbed in the river while a mechanical goose sauntered across Memorial Drive.

A noodle raft, a cheetah, and Oliver Smoot, of course

Moving Day, and the parade across the Charles River, was created in homage to MIT’s ceremonial 1916 crossing of the river, when the Institute’s charter was transported across on a barge, the Bucentaur. The 2016 celebration continued into the evening, with a multimedia extravaganza in Killian Court, followed by dance parties around campus whose themes traced 100 years of music and culture.

Moving Day is part of the series of “MIT 2016” celebrations that have been ongoing this year, commemorating MIT’s first century in Cambridge and launching the Institute’s next century of engagement with the world. MIT was founded in 1861, in Boston, before relocating to the Kendall Square area of Cambridge.

The idea behind the river-crossing event was to “let people do whatever they want and express their technical creativity,” said Annette Hosoi, a professor of mechanical engineering, and the other faculty co-chair of the event. “And people responded — really the whole community.”

Indeed, the parade and competition consisted of 26 entries on the water and 28 groups crossing the bridge. The more conventional water entries included boats from the MIT varsity sailing team and star rower Veronica Toro ’16, an Olympic hopeful. There were also folding kayaks, a “noodle raft” lashed together from pool noodles and kickboards, and a jet-powered boat from MIT’s International Design Center.

“All the watercraft stayed afloat,” Ochsendorf noted approvingly.

(For the record: Participants wore lifejackets and safety personnel were on hand.)

Up on the bridge, members of MIT’s Emergency Medical Services drove an ambulance that is dedicated to the memory of MIT police officer Sean Collier, while experimental vehicles of all kinds dotted the parade. MIT students and alumni demonstrated an aluminum-powered car, cutting-edge wheelchair designs, and a bamboo bicycle, among other entries.

Meanwhile MIT’s robotic cheetah, which can run at over 13 miles per hour, strolled across at a leisurely pace.

The parade’s grand marshal was Oliver Smoot ’62, a familiar name in local lore. As multitudes of area runners and walkers have noticed, the sidewalk over the bridge is marked in increments of “Smoots” — after a 1958 MIT prank in which Smoot’s friends got him to lie down, repeatedly, until they had crossed the entire bridge. For the record, Smoot is 5 feet 7 inches tall, and the bridge is 364.4 Smoots long.

Before the parade, Smoot reenacted lying down on the bridge’s sidewalk but noted that it had been easier for him to do so as an undergraduate. “We were faster and lighter then,” he joked.

Awards gala

A panel of six members of the MIT administration serving as judges gave out four awards to the participants, after what MIT Provost Martin A. Schmidt termed “careful deliberation.”

Brain researchers from three different MIT institutes and departments won the soon-to-be-prestigious Da Vinci Award, given for “creativity and wonder,” for their supersized brain model. Students from Course 4.032 (Design Studio: Information and Visualization) took home the Bosworth Award for “beauty and elegant design,” for their large zooplankton-motif structure, “Time Spirit and the Masquerade of Power,” which also featured printed images from MIT’s campus and history.

Researchers from MIT’s Pappalardo Lab won the Tech Pioneer Award for the “most innovative” craft in the flotilla; they transformed an obstacle course for robots from Course 2.007 (Design and Manufacturing) into a floating vessel. And the MIT Libraries team won the Beaver Spirit Award for the entry best exemplifying school spirit.

The brain researchers’ team, led by Julie Pryor of the McGovern Institute for Brain Research, built their float over two months, with 50 people participating. The plywood vehicle, called “A Beautiful Mind,” consists of 22 coronal “slices” of the brain, based on the personal data of team member Rosa Lafer-Sousa, a researcher in the Department of Brain and Cognitive Sciences (BCS).

Ben Bartelle, also of BCS, personally cut the plywood slices at MIT’s hobby shop.

“We’re MRI people,” Bartelle told MIT News. “We see slices like that all the time.”

So what is it like to see a giant plywood replica of one’s brain, on wheels, crossing the bridge over the Charles River?

“It’s pretty special,” Lafer-Sousa acknowledged. “I couldn’t sleep last night. It felt a little like Christmas.”

Mens, manus, cor: A spectacle on Killian Court

As dusk later fell over the Institute, several thousand students, faculty, staff, and friends filed into MIT’s Killian Court to witness a spectacular pageant of singing, dancing, computer art, and the embodiment of the MIT spirit.

With an illuminated MIT dome serving as a beacon for anyone within eyeshot, the event began with a procession of students bearing oars, a symbol of the 1916 river-crossing, and a parade of drummers welcoming onlookers to the fête.

Over the next hour, characters representing the living spirits of MIT’s motto, “mens et manus” (“mind and hand”) — and the two individuals on the MIT seal — guided the audience through the story of MIT from its humble beginnings in Boston through the Institute’s move to Cambridge a century ago and into the present. “Mens,” representing the theoretical, scientific, humanistic elements of MIT life, and “Manus,” representing the practical applications of these disciplines, spatted over what they thought was the most important aspect of life at MIT: theory or practice.

The two took turns making their case, bringing out, for example, human-sized bobbleheads featuring some of the most noted MIT faculty and alumni from each “side” of the mind-or-hand debate and recounting successes over the previous century — from the 19th-century application of chemical engineering to the new science of home economics by Ellen Swallow Richards to the 2015 detection of gravitational waves led by MIT Professor Emeritus Rainer Weiss. Guided by a robot voiced by MIT alumnus and “Car Talk” host Ray Magliozzi, the duo eventually realized that only with both mind and hand working in unison — and with the addition of “cor,” or “heart” — could MIT have developed into the thriving institution it is today.

Appropriately for the day’s weather — which had a distinctly wintry feel, with chilly temperatures, a brisk wind, and some rain — the event’s finale featured an undulating umbrella dance, which led, finally, into an impressive fireworks display over the Charles River. When it was all over, a roar of applause and hooting filled Killian Court, as attendees grabbed their own umbrellas and made their way to various dance parties hosted across the Institute to cap the day’s festivities.

Oliver Smoot, who has retired to Southern California, noted that he, for one, wasn’t bothered by the elements. “It’s all been great,” he said. And his friend Peter Miller ’62, who rode with Smoot in the grand marshal’s car during the afternoon parade, explained how he had ignored the cold: “From the warmth of all the people waving, and watching, and jumping up and down.”

Maia Weinstock contributed to this story.

Controlling RNA in living cells

Anne Trafton |

MIT researchers have devised a new set of proteins that can be customized to bind arbitrary RNA sequences, making it possible to image RNA inside living cells, monitor what a particular RNA strand is doing, and even control RNA activity.

The new strategy is based on human RNA-binding proteins that normally help guide embryonic development. The research team adapted the proteins so that they can be easily targeted to desired RNA sequences.

“You could use these proteins to do measurements of RNA generation, for example, or of the translation of RNA to proteins,” says Edward Boyden, an associate professor of biological engineering and brain and cognitive sciences at the MIT Media Lab. “This could have broad utility throughout biology and bioengineering.”

Unlike previous efforts to control RNA with proteins, the new MIT system consists of modular components, which the researchers believe will make it easier to perform a wide variety of RNA manipulations.

“Modularity is one of the core design principles of engineering. If you can make things out of repeatable parts, you don’t have to agonize over the design. You simply build things out of predictable, linkable units,” says Boyden, who is also a member of MIT’s McGovern Institute for Brain Research.

Boyden is the senior author of a paper describing the new system in the Proceedings of the National Academy of Sciences. The paper’s lead authors are postdoc Katarzyna Adamala and grad student Daniel Martin-Alarcon.

Modular code

Living cells contain many types of RNA that perform different roles. One of the best known varieties is messenger RNA (mRNA), which is copied from DNA and carries protein-coding information to cell structures called ribosomes, where mRNA directs protein assembly in a process called translation. Monitoring mRNA could tell scientists a great deal about which genes are being expressed in a cell, and tweaking the translation of mRNA would allow them to alter gene expression without having to modify the cell’s DNA.

To achieve this, the MIT team set out to adapt naturally occurring proteins called Pumilio homology domains. These RNA-binding proteins include sequences of amino acids that bind to one of the ribonucleotide bases or “letters” that make up RNA sequences — adenine (A), thymine (T), uracil (U), and guanine (G).

In recent years, scientists have been working on developing these proteins for experimental use, but until now it was more of a trial-and-error process to create proteins that would bind to a particular RNA sequence.

“It was not a truly modular code,” Boyden says, referring to the protein’s amino acid sequences. “You still had to tweak it on a case-by-case basis. Whereas now, given an RNA sequence, you can specify on paper a protein to target it.”

To create their code, the researchers tested out many amino acid combinations and found a particular set of amino acids that will bind each of the four bases at any position in the target sequence. Using this system, which they call Pumby (for Pumilio-based assembly), the researchers effectively targeted RNA sequences varying in length from six to 18 bases.

“I think it’s a breakthrough technology that they’ve developed here,” says Robert Singer, a professor of anatomy and structural biology, cell biology, and neuroscience at Albert Einstein College of Medicine, who was not involved in the research. “Everything that’s been done to target RNA so far requires modifying the RNA you want to target by attaching a sequence that binds to a specific protein. With this technique you just design the protein alone, so there’s no need to modify the RNA, which means you could target any RNA in any cell.”

RNA manipulation

In experiments in human cells grown in a lab dish, the researchers showed that they could accurately label mRNA molecules and determine how frequently they are being translated. First, they designed two Pumby proteins that would bind to adjacent RNA sequences. Each protein is also attached to half of a green fluorescent protein (GFP) molecule. When both proteins find their target sequence, the GFP molecules join and become fluorescent — a signal to the researchers that the target RNA is present.

Furthermore, the team discovered that each time an mRNA molecule is translated, the GFP gets knocked off, and when translation is finished, another GFP binds to it, enhancing the overall fluorescent signal. This allows the researchers to calculate how often the mRNA is being read.

This system can also be used to stimulate translation of a target mRNA. To achieve that, the researchers attached a protein called a translation initiator to the Pumby protein. This allowed them to dramatically increase translation of an mRNA molecule that normally wouldn’t be read frequently.

“We can turn up the translation of arbitrary genes in the cell without having to modify the genome at all,” Martin-Alarcon says.

The researchers are now working toward using this system to label different mRNA molecules inside neurons, allowing them to test the idea that mRNAs for different genes are stored in different parts of the neuron, helping the cell to remain poised to perform functions such as storing new memories. “Until now it’s been very difficult to watch what’s happening with those mRNAs, or to control them,” Boyden says.

These RNA-binding proteins could also be used to build molecular assembly lines that would bring together enzymes needed to perform a series of reactions that produce a drug or another molecule of interest.