Researcher: Ed Boyden

Ed Boyden wins 2016 Breakthrough Prize in Life Sciences

Anne Trafton |

MIT researchers took home several awards last night at the 2016 Breakthrough Prize ceremony at NASA’s Ames Research Center in Mountain View, California.

Edward Boyden, an associate professor of media arts and sciences, biological engineering, and brain and cognitive sciences, was one of five scientists honored with the Breakthrough Prize in Life Sciences, given for “transformative advances toward understanding living systems and extending human life.” He will receive $3 million for the award.

MIT physicists also contributed to a project that won the Breakthrough Prize in Fundamental Physics. That prize went to five experiments investigating the oscillation of subatomic particles known as neutrinos. More than 1,300 contributing physicists will share in the recognition for their work, according to the award announcement. Those physicists include MIT associate professor of physics Joseph Formaggio and his team, as well as MIT assistant professor of physics Lindley Winslow.

Larry Guth, an MIT professor of mathematics, was honored with the New Horizons in Mathematics Prize, which is given to promising junior researchers who have already produced important work in mathematics. Liang Fu, an assistant professor of physics, was honored with the New Horizons in Physics Prize, which is awarded to promising junior researchers who have already produced important work in fundamental physics.

“By challenging conventional thinking and expanding knowledge over the long term, scientists can solve the biggest problems of our time,” said Mark Zuckerberg, chairman and CEO of Facebook, and one of the prizes’ founders. “The Breakthrough Prize honors achievements in science and math so we can encourage more pioneering research and celebrate scientists as the heroes they truly are.”

Optogenetics

Boyden was honored for the development and implementation of optogenetics, a technique in which scientists can control neurons by shining light on them. Karl Deisseroth, a Stanford University professor who worked with Boyden to pioneer the technique, was also honored with one of the life sciences prizes.

Optogenetics relies on light-sensitive proteins, originally isolated from bacteria and algae. About 10 years ago, Boyden and Deisseroth began engineering neurons to express these proteins, allowing them to selectively stimulate or silence them with pulses of light. More recently, Boyden has developed additional proteins that are even more sensitive to light and can respond to different colors.

Scientists around the world have used optogenetics to reveal the brain circuitry underlying normal neural function as well as neurological disorders such as autism, obsessive-compulsive disorder, and depression.

Boyden is a member of the MIT Media Lab and MIT’s McGovern Institute for Brain Research.

Neutrino oscillations

The Breakthrough Prize in Fundamental Physics was awarded to five research projects investigating the nature of neutrinos: Daya Bay (China); KamLAND (Japan); K2K/T2K (Japan); Sudbury Neutrino Observatory (Canada); and Super-Kamiokande (Japan). Researchers with these experiments were recognized “for the fundamental discovery of neutrino oscillations, revealing a new frontier beyond, and possibly far beyond, the standard model of particle physics.”

Formaggio and his team at MIT have been collaborating on the Sudbury Neutrino Observatory (SNO) project since 2005. Research at the observatory, 2 kilometers underground in a mine near Sudbury, Ontario, demonstrated that neutrinos change their type — or “flavor” — on their way to Earth from the sun.

Winslow has been a collaborator on KamLAND, located in a mine in Japan, since 2001. Using antineutrinos from nuclear reactors, this experiment demonstrated that the change in flavor was energy-dependent. The combination of these results solved the solar neutrino puzzle and proved that neutrinos have mass.

The MIT SNO group has participated heavily on the analysis of neutrino data, particularly during that experiment’s final measurement phase. The MIT KamLAND group is involved with the next phase, KamLAND-Zen, which is searching for a rare nuclear process that if observed, would make neutrinos their own antiparticles.

Reaching new horizons

Guth, who will receive a $100,000 prize, was honored for his “ingenious and surprising solutions to long standing open problems in symplectic geometry, Riemannian geometry, harmonic analysis, and combinatorial geometry.”

Guth’s work at MIT focuses on combinatorics, or the study of discrete structures, and how sets of lines intersect each other in space. He also works in the area of harmonic analysis, studying how sound waves interact with each other.

Guth’s father, MIT physicist Alan Guth, won the inaugural Breakthrough Prize in Fundamental Physics in 2015.

Fu will share a New Horizons in Physics Prize with two other researchers: B. Andrei Bernevig of Princeton University and Xiao-Liang Qi of Stanford University. The physicists were honored for their “outstanding contributions to condensed matter physics, especially involving the use of topology to understand new states of matter.”

Fu works on theories of topological insulators — a new class of materials whose surfaces can freely conduct electrons even though their interiors are electrical insulators — and topological superconductors. Such materials may provide insight into quantum physics and have possible applications in creating transistors based on the spin of particles rather than their charge.

Yesterday’s prize ceremony was hosted by producer/actor/director Seth MacFarlane; awards were presented by the prize sponsors and by celebrities including actors Russell Crowe, Hilary Swank, and Lily Collins. The Breakthrough Prizes were founded by Sergey Brin and Anne Wojcicki, Jack Ma and Cathy Zhang, Yuri and Julia Milner, and Mark Zuckerberg and Priscilla Chan.

“Breakthrough Prize laureates are making fundamental discoveries about the universe, life, and the mind,” Yuri Milner said. “These fields of investigation are advancing at an exponential pace, yet the biggest questions remain to be answered.”

Bold new microscopies for the brain

by Elizabeth Doherty |

McGovern researchers create unexpected new approaches to microscopy that are changing the way scientists look at the brain.

Ask McGovern Investigator Ed Boyden about his ten-year plan and you’ll get an immediate and straight-faced answer: “We would like to understand the brain.”

He means it. Boyden intends to map all of the cells in a brain, all of their connections, and even all of the molecules that form those connections and determine their strengths. He also plans to study how information flows through the brain and to use this to generate a working model. “I’d love to be able to load a map of an entire brain into a computer and see if we can simulate the brain,” he says.

Boyden likens the process to reverse-engineering a computer by opening it up and looking inside. The analogy, though not perfect, provides a sense of the enormity of the task ahead. As complicated as computers are, brains are far more complex, and they are also much harder to visualize, given the need to see features at multiple scales. For example, signals travel from cell to cell through synaptic connections that are measured in nanometers, but the signals are then propagated along nerve fibers that may span several centimeters—a difference of more than a million-fold. Modern microscopes make it possible to study features at one scale or the other, but not both together. Similarly, there are methods for visualizing electrical activity in single neurons or in whole brains, but there is no way to see both at once. So Boyden is building his own tools, and in the process is pushing the limits of imagination. “Our group is often trying to do the opposite of what other people do,” Boyden says.

Boyden’s new methods are part of a broader push to understand the brain’s connectivity, an objective that gained impetus two years ago with the President’s BRAIN Initiative, and with allied efforts such as the NIH-funded Human Connectome Project. Hundreds of researchers have already downloaded Boyden’s recently published protocols, including colleagues at the McGovern Institute who are using them to advance their studies of brain function and disease.

Just add water

Under the microscope, the brain section prepared by Jill Crittenden looks like a tight bundle of threads. The nerve fibers are from a mouse brain, from a region known to degenerate in humans with Parkinson’s disease. The loss of the tiny synaptic connections between these fibers may be the earliest signs of degeneration, so Crittenden, a research scientist who has been studying this disease for several years in the lab of McGovern Investigator Ann Graybiel, wants to be able to see them.

But she can’t. They are far too small— smaller than a wavelength of light, meaning they are beyond the limit for optical microscopy. To bring these structures into view, one of Boyden’s technologies, called expansion microscopy (ExM), simply makes the specimen bigger, allowing it to be viewed on a conventional laboratory microscope.

The idea is at once obvious and fantastical. “Expansion microscopy is the kind of thing scientists daydream about,” says Paul Tillberg, a graduate student in Boyden’s lab. “You either shrink the scientist or expand the specimen.”

Leaving Crittenden’s sample in place, Tillberg adds water. Minutes later, the tissue has expanded and become transparent, a ghostly and larger version of its former self.

Crittenden takes another look through the scope. “It’s like someone has loosened up all the fibers. I can see each one independently, and see them interconnecting,” she says. “ExM will add a lot of power to the tools we’ve developed for visualizing the connections we think are degenerating.”

It took Tillberg and his fellow graduate student Fei Chen several months of brainstorming to find a plausible way to make ExM a reality. They had found inspiration in the work of MIT physicist Toyoichi Tanaka, who in the 1970s had studied smart gels, polymers that rapidly expand in response to a change in environment. One familiar example is the absorbent material in baby diapers, and Boyden’s team turned to this substance for the expansion technique.

The process they devised involves several steps. The tissue is first labeled using fluorescent antibodies that bind to molecules of interest, and then it is impregnated with the gel-forming material. Once the gel has set, the fluorescent markers are anchored to the gel, and the original tissue sample is digested, allowing the gel to stretch evenly in all directions.

When water is added, the gel expands and the fluorescent markers spread out like a picture on a balloon. Remarkably, the 3D shapes of even the finest structures are faithfully preserved during the expansion, making it possible to see them using a conventional microscope. By labeling molecules with different colors, the researchers can even distinguish pre-synaptic from post-synaptic structures. Boyden plans eventually to use hundreds, possibly thousands, of colors, and to increase the expansion factor to 10 times original size, equivalent to a 1000-fold increase in volume.

ExM is not the only way to see fine structures such as synapses; they can also be visualized by electron microcopy, or by recently-developed ‘super-resolution’ optical methods that garnered a 2014 Nobel Prize. These techniques, however, require expensive equipment, and the images are very time-consuming to produce.

“With ExM, because the sample is physically bigger, you can scan it very quickly using just a regular microscope,” says Boyden.

Boyden is already talking to other leading researchers in the field, including Kwanghun Chung at MIT and George Church at Harvard, about ways to further enhance the ExM method. Within the McGovern Institute, among those who expect to benefit from these advances is Guoping Feng, who is developing mouse models of autism, schizophrenia and other disorders by introducing some of the same genetic changes seen in humans with these disorders. Many of the genes associated with autism and schizophrenia play a role in the formation of synapses, but even with the mouse models at his disposal, Feng isn’t sure what goes wrong with them because they are so hard to see. “If we can make parts of the brain bigger, we might be able to see how the assembly of this synaptic machinery changes in different disorders,” he says.

3D Movies Without Special Glasses

Another challenge facing Feng and many other researchers is that many brain functions, and many brain diseases, are not confined to one area, but are widely distributed across the brain. Trying to understand these processes by looking through a small microscopic window has been compared to watching a soccer game by observing just a single square foot of the playing field.

No current technology can capture millisecond-by-millisecond electrical events across the entire living brain, so Boyden and collaborators in Vienna, Austria, decided to develop one. They turned to a method called light field microscopy (LFM) as a way to capture 3D movies of an animal’s thoughts as they flash through the entire nervous system.

The idea is mind-boggling to imagine, but the hardware is quite simple. The instrument records images in depth the same way humans do, using multiple ‘eyes’ to send slightly offset 2D images to a computer that can reconstruct a 3D image of the world. (The idea had been developed in the 1990s by Boyden’s MIT colleague Ted Adelson, and a similar method was used to create Google Street View.) Boyden and his collaborators started with a microscope of standard design, attached a video camera, and inserted between them a six-by-six array of miniature lenses, designed in Austria, that projects a grid of offset images into the camera and the computer.

The rest is math. “We take the multiple, superimposed flat images projected through the lens array and combine them into a volume,” says Young-Gyu Yoon, a graduate student in the Boyden lab who designed and wrote the software.

Another graduate student, Nikita Pak, used the new method to measure neural activity in C. elegans, a tiny worm whose entire nervous system consists of just 302 neurons. By using a worm that had been genetically engineered so that its neurons light up when they become electrically active, Pak was able to make 3D movies of the activity in the entire nervous system. “The setup is just so simple,” he says. “Every time I use it, I think it’s cool.”

The team then tested their method on a larger brain, that of the larval zebra fish. They presented the larvae with a noxious odor, and found that it triggered activity in around 5000 neurons, over a period of about three minutes. Even with this relatively simple example, activity is distributed widely throughout the brain, and would be difficult to detect with previous techniques. Boyden is now working towards recording activity over much longer timespans, and he also envisions scaling it up to image the much more complex brains of mammals.

He hopes to start with the smallest known mammal, the Etruscan shrew. This animal resembles a mouse, but it is ten times smaller, no bigger than a thimble. Its brain is also much smaller, with only a few million neurons, compared to 100 million in a mouse.

Whole brain imaging in this tiny creature could provide an unprecedented view of mammalian brain activity, including its disruption in disease states. Feng cites sensory overload in autism as an example. “If we can see how sensory activity spreads through the brain, we can start to understand how overload starts and how it spills over to other brain areas,” he says.

Visions of Convergence

While Boyden’s microscopy technologies are providing his colleagues with new ways to study brain disorders, Boyden himself hopes to use them to understand the brain as a whole. He plans to use ExM to map connections and identify which molecules are where; 3D whole-brain imaging to trace brain activity as it unfolds in real time, and optogenetics techniques to stimulate the brain and directly record the resulting activity. By combining all three tools together, he hopes to pin stimuli and activity to the molecules and connections on the map and then use that to build a computational model that simulates brain activity.

The plan is grandiose, and the tools aren’t all ready yet, but to make the scheme plausible in the proposed timeframe, Boyden is adhering to a few principles. His methods are fast, capturing information-dense images rapidly rather than scanning over days, and inclusive, imaging whole brains rather than chunks that need to be assembled. They are also accessible, so researchers don’t need to spend large sums to acquire specialized equipment or expertise in-house.

The challenges ahead might appear insurmountable at times, but Boyden is undeterred. He moves forward, his mind open to even the most far-fetched ideas, because they just might work.

MIT team enlarges brain samples, making them easier to image

Anne Trafton |

Beginning with the invention of the first microscope in the late 1500s, scientists have been trying to peer into preserved cells and tissues with ever-greater magnification. The latest generation of so-called “super-resolution” microscopes can see inside cells with resolution better than 250 nanometers.

A team of researchers from MIT has now taken a novel approach to gaining such high-resolution images: Instead of making their microscopes more powerful, they have discovered a method that enlarges tissue samples by embedding them in a polymer that swells when water is added. This allows specimens to be physically magnified, and then imaged at a much higher resolution.

This technique, which uses inexpensive, commercially available chemicals and microscopes commonly found in research labs, should give many more scientists access to super-resolution imaging, the researchers say.

“Instead of acquiring a new microscope to take images with nanoscale resolution, you can take the images on a regular microscope. You physically make the sample bigger, rather than trying to magnify the rays of light that are emitted by the sample,” says Ed Boyden, an associate professor of biological engineering and brain and cognitive sciences at MIT.

Boyden is the senior author of a paper describing the new method in the Jan. 15 online edition of Science. Lead authors of the paper are graduate students Fei Chen and Paul Tillberg.

Physical magnification

Most microscopes work by using lenses to focus light emitted from a sample into a magnified image. However, this approach has a fundamental limit known as the diffraction limit, which means that it can’t be used to visualize objects much smaller than the wavelength of the light being used. For example, if you are using blue-green light with a wavelength of 500 nanometers, you can’t see anything smaller than 250 nanometers.

“Unfortunately, in biology that’s right where things get interesting,” says Boyden, who is a member of MIT’s Media Lab and McGovern Institute for Brain Research. Protein complexes, molecules that transport payloads in and out of cells, and other cellular activities are all organized at the nanoscale.

Scientists have come up with some “really clever tricks” to overcome this limitation, Boyden says. However, these super-resolution techniques work best with small, thin samples, and take a long time to image large samples. “If you want to map the brain, or understand how cancer cells are organized in a metastasizing tumor, or how immune cells are configured in an autoimmune attack, you have to look at a large piece of tissue with nanoscale precision,” he says.

To achieve this, the MIT team focused its attention on the sample rather than the microscope. Their idea was to make specimens easier to image at high resolution by embedding them in an expandable polymer gel made of polyacrylate, a very absorbent material commonly found in diapers.

Before enlarging the tissue, the researchers first label the cell components or proteins that they want to examine, using an antibody that binds to the chosen targets. This antibody is linked to a fluorescent dye, as well as a chemical anchor that can attach the dye to the polyacrylate chain.

Once the tissue is labeled, the researchers add the precursor to the polyacrylate gel and heat it to form the gel. They then digest the proteins that hold the specimen together, allowing it to expand uniformly. The specimen is then washed in salt-free water to induce a 100-fold expansion in volume. Even though the proteins have been broken apart, the original location of each fluorescent label stays the same relative to the overall structure of the tissue because it is anchored to the polyacrylate gel.

“What you’re left with is a three-dimensional, fluorescent cast of the original material. And the cast itself is swollen, unimpeded by the original biological structure,” Tillberg says.

The MIT team imaged this “cast” with commercially available confocal microscopes, commonly used for fluorescent imaging but usually limited to a resolution of hundreds of nanometers. With their enlarged samples, the researchers achieved resolution down to 70 nanometers. “The expansion microscopy process … should be compatible with many existing microscope designs and systems already in laboratories,” Chen adds.

Large tissue samples

Using this technique, the MIT team was able to image a section of brain tissue 500 by 200 by 100 microns with a standard confocal microscope. Imaging such large samples would not be feasible with other super-resolution techniques, which require minutes to image a tissue slice only 1 micron thick and are limited in their ability to image large samples by optical scattering and other aberrations.

“The exciting part is that this approach can acquire data at the same high speed per pixel as conventional microscopy, contrary to most other methods that beat the diffraction limit for microscopy, which can be 1,000 times slower per pixel,” says George Church, a professor of genetics at Harvard Medical School who was not part of the research team.

“The other methods currently have better resolution, but are harder to use, or slower,” Tillberg says. “The benefits of our method are the ease of use and, more importantly, compatibility with large volumes, which is challenging with existing technologies.”

The researchers envision that this technology could be very useful to scientists trying to image brain cells and map how they connect to each other across large regions.

“There are lots of biological questions where you have to understand a large structure,” Boyden says. “Especially for the brain, you have to be able to image a large volume of tissue, but also to see where all the nanoscale components are.”

While Boyden’s team is focused on the brain, other possible applications for this technique include studying tumor metastasis and angiogenesis (growth of blood vessels to nourish a tumor), or visualizing how immune cells attack specific organs during autoimmune disease.

The research was funded by the National Institutes of Health, the New York Stem Cell Foundation, Jeremy and Joyce Wertheimer, the National Science Foundation, and the Fannie and John Hertz Foundation.

Fifteen MIT scientists receive NIH BRAIN Initiative grants

Anne Trafton |

Today, the National Institutes of Health (NIH) announced their first round of BRAIN Initiative award recipients. Six teams and 15 researchers from the Massachusetts Institute of Technology were recipients.

Mriganka Sur, principal investigator at the Picower Institute for Learning and Memory and the Paul E. Newton Professor of Neuroscience in MIT’s Department of Brain and Cognitive Sciences (BCS) leads a team studying cortical circuits and information flow during memory-guided perceptual decisions. Co-principal investigators include Emery Brown, BCS professor of computational neuroscience and the Edward Hood Taplin Professor of Medical Engineering; Kwanghun Chung, Picower Institute principal investigator and assistant professor in the Department of Chemical Engineering and the Institute for Medical Engineering and Science (IMES); and Ian Wickersham, research scientist at the McGovern Institute for Brain Research and head of MIT’s Genetic Neuroengineering Group.

Elly Nedivi, Picower Institute principal investigator and professor in BCS and the Department of Biology, leads a team studying new methods for high-speed monitoring of sensory-driven synaptic activity across all inputs to single living neurons in the context of the intact cerebral cortex. Her co-principal investigator is Peter So, professor of mechanical and biological engineering, and director of the MIT Laser Biomedical Research Center.

Ian Wickersham will lead a team looking at novel technologies for nontoxic transsynaptic tracing. His co-principal investigators include Robert Desimone, director of the McGovern Institute and the Doris and Don Berkey Professor of Neuroscience in BCS; Li-Huei Tsai, director of the Picower Institute and the Picower Professor of Neuroscience in BCS; and Kay Tye, Picower Institute principal investigator and assistant professor of neuroscience in BCS.

Robert Desimone will lead a team studying vascular interfaces for brain imaging and stimulation. Co-principal investigators include Ed Boyden, associate professor at the MIT Media Lab, McGovern Institute, and departments of BCS and Biological Engineering; head of MIT’s Synthetic Neurobiology Group, and co-director of MIT’s Center for Neurobiological Engineering; and Elazer Edelman, the Thomas D. and Virginia W. Cabot Professor of Health Sciences and Technology in IMES and director of the Harvard-MIT Biomedical Engineering Center. Collaborators on this project include: Rodolfo Llinas (New York University), George Church (Harvard University), Jan Rabaey (University of California at Berkeley), Pablo Blinder (Tel Aviv University), Eric Leuthardt (Washington University/St. Louis), Michel Maharbiz (Berkeley), Jose Carmena (Berkeley), Elad Alon (Berkeley), Colin Derdeyn (Washington University in St. Louis), Lowell Wood (Bill and Melinda Gates Foundation), Xue Han (Boston University), and Adam Marblestone (MIT).

Ed Boyden will be co-principal investigator with Mark Bathe, associate professor of biological engineering, and Peng Yin of Harvard on a project to study ultra-multiplexed nanoscale in situ proteomics for understanding synapse types.

Alan Jasanoff, associate professor of biological engineering and director of the MIT Center for Neurobiological Engineering, will lead a team looking at calcium sensors for molecular fMRI. Stephen Lippard, the Arthur Amos Noyes Professor of Chemistry, is co-principal investigator.

In addition, Sur and Wickersham also received BRAIN Early Concept Grants for Exploratory Research (EAGER) from the National Science Foundation (NSF). Sur will focus on massive-scale multi-area single neuron recordings to reveal circuits underlying short-term memory. Wickersham, in collaboration with Li-Huei Tsai, Kay Tye, and Robert Desimone, will develop cell-type specific optogenetics in wild-type animals. Additional information about NSF support of the BRAIN initiative can be found at NSF.gov/brain.

The BRAIN Initiative, spearheaded by President Obama in April 2013, challenges the nation’s leading scientists to advance our sophisticated understanding of the human mind and discover new ways to treat, prevent, and cure neurological disorders like Alzheimer’s, schizophrenia, autism, and traumatic brain injury. The scientific community is charged with accelerating the invention of cutting-edge technologies that can produce dynamic images of complex neural circuits and illuminate the interaction of lightning-fast brain cells. The new capabilities are expected to provide greater insights into how brain functionality is linked to behavior, learning, memory, and the underlying mechanisms of debilitating disease. BRAIN was launched with approximately $100 million in initial investments from the NIH, the National Science Foundation, and the Defense Advanced Research Projects Agency (DARPA).

BRAIN Initiative scientists are engaged in a challenging and transformative endeavor to explore how our minds instantaneously processes, store, and retrieve vast quantities of information. Their discoveries will unlock many of the remaining mysteries inherent in the brain’s billions of neurons and trillions of connections, leading to a deeper understanding of the underlying causes of many neurological and psychiatric conditions. Their findings will enable scientists and doctors to develop the groundbreaking arsenal of tools and technologies required to more effectively treat those suffering from these devastating disorders.

Noninvasive brain control

Anne Trafton |

Optogenetics, a technology that allows scientists to control brain activity by shining light on neurons, relies on light-sensitive proteins that can suppress or stimulate electrical signals within cells. This technique requires a light source to be implanted in the brain, where it can reach the cells to be controlled.

MIT engineers have now developed the first light-sensitive molecule that enables neurons to be silenced noninvasively, using a light source outside the skull. This makes it possible to do long-term studies without an implanted light source. The protein, known as Jaws, also allows a larger volume of tissue to be influenced at once.

This noninvasive approach could pave the way to using optogenetics in human patients to treat epilepsy and other neurological disorders, the researchers say, although much more testing and development is needed. Led by Ed Boyden, an associate professor of biological engineering and brain and cognitive sciences at MIT, the researchers described the protein in the June 29 issue of Nature Neuroscience.

Optogenetics, a technique developed over the past 15 years, has become a common laboratory tool for shutting off or stimulating specific types of neurons in the brain, allowing neuroscientists to learn much more about their functions.
The neurons to be studied must be genetically engineered to produce light-sensitive proteins known as opsins, which are channels or pumps that influence electrical activity by controlling the flow of ions in or out of cells. Researchers then insert a light source, such as an optical fiber, into the brain to control the selected neurons.

Such implants can be difficult to insert, however, and can be incompatible with many kinds of experiments, such as studies of development, during which the brain changes size, or of neurodegenerative disorders, during which the implant can interact with brain physiology. In addition, it is difficult to perform long-term studies of chronic diseases with these implants.

Mining nature’s diversity

To find a better alternative, Boyden, graduate student Amy Chuong, and colleagues turned to the natural world. Many microbes and other organisms use opsins to detect light and react to their environment. Most of the natural opsins now used for optogenetics respond best to blue or green light.

Boyden’s team had previously identified two light-sensitive chloride ion pumps that respond to red light, which can penetrate deeper into living tissue. However, these molecules, found in the bacteria Haloarcula marismortui and Haloarcula vallismortis, did not induce a strong enough photocurrent — an electric current in response to light — to be useful in controlling neuron activity.

Chuong set out to improve the photocurrent by looking for relatives of these proteins and testing their electrical activity. She then engineered one of these relatives by making many different mutants. The result of this screen, Jaws, retained its red-light sensitivity but had a much stronger photocurrent — enough to shut down neural activity.

“This exemplifies how the genomic diversity of the natural world can yield powerful reagents that can be of use in biology and neuroscience,” says Boyden, who is a member of MIT’s Media Lab and the McGovern Institute for Brain Research.

Using this opsin, the researchers were able to shut down neuronal activity in the mouse brain with a light source outside the animal’s head. The suppression occurred as deep as 3 millimeters in the brain, and was just as effective as that of existing silencers that rely on other colors of light delivered via conventional invasive illumination.

A key advantage to this opsin is that it could enable optogenetic studies of animals with larger brains, says Garret Stuber, an assistant professor of psychiatry and cell biology and physiology at the University of North Carolina at Chapel Hill.
“In animals with larger brains, people have had difficulty getting behavior effects with optogenetics, and one possible reason is that not enough of the tissue is being inhibited,” he says. “This could potentially alleviate that.”

Restoring vision

Working with researchers at the Friedrich Miescher Institute for Biomedical Research in Switzerland, the MIT team also tested Jaws’s ability to restore the light sensitivity of retinal cells called cones. In people with a disease called retinitis pigmentosa, cones slowly atrophy, eventually causing blindness.

Friedrich Miescher Institute scientists Botond Roska and Volker Busskamp have previously shown that some vision can be restored in mice by engineering those cone cells to express light-sensitive proteins. In the new paper, Roska and Busskamp tested the Jaws protein in the mouse retina and found that it more closely resembled the eye’s natural opsins and offered a greater range of light sensitivity, making it potentially more useful for treating retinitis pigmentosa.

This type of noninvasive approach to optogenetics could also represent a step toward developing optogenetic treatments for diseases such as epilepsy, which could be controlled by shutting off misfiring neurons that cause seizures, Boyden says. “Since these molecules come from species other than humans, many studies must be done to evaluate their safety and efficacy in the context of treatment,” he says.

Boyden’s lab is working with many other research groups to further test the Jaws opsin for other applications. The team is also seeking new light-sensitive proteins and is working on high-throughput screening approaches that could speed up the development of such proteins.

The research at MIT was funded by Jerry and Marge Burnett, the Defense Advanced Research Projects Agency, the Human Frontiers Science Program, the IET A. F. Harvey Prize, the Janet and Sheldon Razin ’59 Fellowship of the MIT McGovern Institute, the New York Stem Cell Foundation-Robertson Investigator Award, the National Institutes of Health, the National Science Foundation, and the Wallace H. Coulter Foundation.

Illuminating neuron activity in 3-D

Anne Trafton |

Researchers at MIT and the University of Vienna have created an imaging system that reveals neural activity throughout the brains of living animals. This technique, the first that can generate 3-D movies of entire brains at the millisecond timescale, could help scientists discover how neuronal networks process sensory information and generate behavior.

The team used the new system to simultaneously image the activity of every neuron in the worm Caenorhabditis elegans, as well as the entire brain of a zebrafish larva, offering a more complete picture of nervous system activity than has been previously possible.

“Looking at the activity of just one neuron in the brain doesn’t tell you how that information is being computed; for that, you need to know what upstream neurons are doing. And to understand what the activity of a given neuron means, you have to be able to see what downstream neurons are doing,” says Ed Boyden, an associate professor of biological engineering and brain and cognitive sciences at MIT and one of the leaders of the research team. “In short, if you want to understand how information is being integrated from sensation all the way to action, you have to see the entire brain.”

The new approach, described May 18 in Nature Methods, could also help neuroscientists learn more about the biological basis of brain disorders. “We don’t really know, for any brain disorder, the exact set of cells involved,” Boyden says. “The ability to survey activity throughout a nervous system may help pinpoint the cells or networks that are involved with a brain disorder, leading to new ideas for therapies.”

Boyden’s team developed the brain-mapping method with researchers in the lab of Alipasha Vaziri of the University of Vienna and the Research Institute of Molecular Pathology in Vienna. The paper’s lead authors are Young-Gyu Yoon, a graduate student at MIT, and Robert Prevedel, a postdoc at the University of Vienna.

High-speed 3-D imaging

Neurons encode information — sensory data, motor plans, emotional states, and thoughts — using electrical impulses called action potentials, which provoke calcium ions to stream into each cell as it fires. By engineering fluorescent proteins to glow when they bind calcium, scientists can visualize this electrical firing of neurons. However, until now there has been no way to image this neural activity over a large volume, in three dimensions, and at high speed.

Scanning the brain with a laser beam can produce 3-D images of neural activity, but it takes a long time to capture an image because each point must be scanned individually. The MIT team wanted to achieve similar 3-D imaging but accelerate the process so they could see neuronal firing, which takes only milliseconds, as it occurs.

The new method is based on a widely used technology known as light-field imaging, which creates 3-D images by measuring the angles of incoming rays of light. Ramesh Raskar, an associate professor of media arts and sciences at MIT and an author of this paper, has worked extensively on developing this type of 3-D imaging. Microscopes that perform light-field imaging have been developed previously by multiple groups. In the new paper, the MIT and Austrian researchers optimized the light-field microscope, and applied it, for the first time, to imaging neural activity.

With this kind of microscope, the light emitted by the sample being imaged is sent through an array of lenses that refracts the light in different directions. Each point of the sample generates about 400 different points of light, which can then be recombined using a computer algorithm to recreate the 3-D structure.

“If you have one light-emitting molecule in your sample, rather than just refocusing it into a single point on the camera the way regular microscopes do, these tiny lenses will project its light onto many points. From that, you can infer the three-dimensional position of where the molecule was,” says Boyden, who is a member of MIT’s Media Lab and McGovern Institute for Brain Research.

Prevedel built the microscope, and Yoon devised the computational strategies that reconstruct the 3-D images.

Aravinthan Samuel, a professor of physics at Harvard University, says this approach seems to be an “extremely promising” way to speed up 3-D imaging of living, moving animals, and to correlate their neuronal activity with their behavior. “What’s very impressive about it is that it is such an elegantly simple implementation,” says Samuel, who was not part of the research team. “I could imagine many labs adopting this.”

Neurons in action

The researchers used this technique to image neural activity in the worm C. elegans, the only organism for which the entire neural wiring diagram is known. This 1-millimeter worm has 302 neurons, each of which the researchers imaged as the worm performed natural behaviors, such as crawling. They also observed the neuronal response to sensory stimuli, such as smells.

The downside to light field microscopy, Boyden says, is that the resolution is not as good as that of techniques that slowly scan a sample. The current resolution is high enough to see activity of individual neurons, but the researchers are now working on improving it so the microscope could also be used to image parts of neurons, such as the long dendrites that branch out from neurons’ main bodies. They also hope to speed up the computing process, which currently takes a few minutes to analyze one second of imaging data.

The researchers also plan to combine this technique with optogenetics, which enables neuronal firing to be controlled by shining light on cells engineered to express light-sensitive proteins. By stimulating a neuron with light and observing the results elsewhere in the brain, scientists could determine which neurons are participating in particular tasks.

Other co-authors at MIT include Nikita Pak, a PhD student in mechanical engineering, and Gordon Wetzstein, a research scientist at the Media Lab. The work at MIT was funded by the Allen Institute for Brain Science; the National Institutes of Health; the MIT Synthetic Intelligence Project; the IET Harvey Prize; the National Science Foundation (NSF); the New York Stem Cell Foundation-Robertson Award; Google; the NSF Center for Brains, Minds, and Machines at MIT; and Jeremy and Joyce Wertheimer.

Optogenetic toolkit goes multicolor

Anne Trafton |

Optogenetics is a technique that allows scientists to control neurons’ electrical activity with light by engineering them to express light-sensitive proteins. Within the past decade, it has become a very powerful tool for discovering the functions of different types of cells in the brain.

Most of these light-sensitive proteins, known as opsins, respond to light in the blue-green range. Now, a team led by MIT has discovered an opsin that is sensitive to red light, which allows researchers to independently control the activity of two populations of neurons at once, enabling much more complex studies of brain function.

“If you want to see how two different sets of cells interact, or how two populations of the same cell compete against each other, you need to be able to activate those populations independently,” says Ed Boyden, a member of the McGovern Institute for Brain Research at MIT and a senior author of the new study.

The new opsin is one of about 60 light-sensitive proteins found in a screen of 120 species of algae. The study, which appears in the Feb. 9 online edition of Nature Methods, also yielded the fastest opsin, enabling researchers to study neuron activity patterns with millisecond timescale precision.

Boyden and Gane Ka-Shu Wong, a professor of medicine and biological sciences at the University of Alberta, are the paper’s senior authors, and the lead author is MIT postdoc Nathan Klapoetke. Researchers from the Howard Hughes Medical Institute’s Janelia Farm Research Campus, the University of Pennsylvania, the University of Cologne, and the Beijing Genomics Institute also contributed to the study.

In living color

Opsins occur naturally in many algae and bacteria, which use the light-sensitive proteins to help them respond to their environment and generate energy.

To achieve optical control of neurons, scientists engineer brain cells to express the gene for an opsin, which transports ions across the cell’s membrane to alter its voltage. Depending on the opsin used, shining light on the cell either lowers the voltage and silences neuron firing, or boosts voltage and provokes the cell to generate an electrical impulse. This effect is nearly instantaneous and easily reversible.

Using this approach, researchers can selectively turn a population of cells on or off and observe what happens in the brain. However, until now, they could activate only one population at a time, because the only opsins that responded to red light also responded to blue light, so they couldn’t be paired with other opsins to control two different cell populations.

To seek additional useful opsins, the MIT researchers worked with Wong’s team at the University of Alberta, which is sequencing the transcriptomes of 1,000 plants, including some algae. (The transcriptome is similar to the genome but includes only the genes that are expressed by a cell, not the entirety of its genetic material.)

Once the team obtained genetic sequences that appeared to code for opsins, Klapoetke tested their light-responsiveness in mammalian brain tissue, working with Martha Constantine-Paton, a professor of brain and cognitive sciences and of biology, a member of the McGovern Institute for Brain Research at MIT, and also an author of the paper. The red-light-sensitive opsin, which the researchers named Chrimson, can mediate neural activity in response to light with a 735-nanometer
wavelength.

The researchers also discovered a blue-light-driven opsin that has two highly desirable traits: It operates at high speed, and it is sensitive to very dim light. This opsin, called Chronos, can be stimulated with levels of blue light that are too weak to activate Chrimson.

“You can use short pulses of dim blue light to drive the blue one, and you can use strong red light to drive Chrimson, and that allows you to do true two-color, zero-cross-talk activation in intact brain tissue,” says Boyden, who is a member of MIT’s Media Lab and an associate professor of biological engineering and brain and cognitive sciences at MIT.

Researchers had previously tried to modify naturally occurring opsins to make them respond faster and react to dimmer light, but trying to optimize one feature often made other features worse.

“It was apparent that when trying to engineer traits like color, light sensitivity, and kinetics, there are always tradeoffs,” Klapoetke says. “We’re very lucky that something natural actually was more than several times faster and also five or six times more light-sensitive than anything else.”

Selective control

These new opsins lend themselves to several types of studies that were not possible before, Boyden says. For one, scientists could not only manipulate activity of a cell population of interest, but also control upstream cells that influence the target population by secreting neurotransmitters.

Pairing Chrimson and Chronos could also allow scientists to study the functions of different types of cells in the same microcircuit within the brain. Such cells are usually located very close together, but with the new opsins they can be controlled independently with two different colors of light.

“I think the tools described in this excellent paper represent a major advance for both basic and translational neuroscience,” says Botond Roska, a senior group leader at the Friedrich Miescher Institute for Biomedical Research in Switzerland, who was not part of the research team. “Optogenetic tools that are shifted towards the infrared range, such as Chrimson described in this paper, are much better than the more blue-shifted variants since these are less toxic, activate less the pupillary reflex, and activate less the remaining photoreceptors of patients.”

Most optogenetic studies thus far have been done in mice, but Chrimson could be used for optogenetic studies of fruit flies, a commonly used experimental organism. Researchers have had trouble using blue-light-sensitive opsins in fruit flies because the light can get into the flies’ eyes and startle them, interfering with the behavior being studied.

Vivek Jayaraman, a research group leader at Janelia Farms and an author of the paper, was able to show that this startle response does not occur when red light is used to stimulate Chrimson in fruit flies.

Because red light is less damaging to tissue than blue light, Chrimson also holds potential for eventual therapeutic use in humans, Boyden says. Animal studies with other opsins have shown promise in helping to restore vision after the loss of photoreceptor cells in the retina.

The researchers are now trying to modify Chrimson to respond to light in the infrared range. They are also working on making both Chrimson and Chronos faster and more light sensitive.

MIT’s portion of the project was funded by the National Institutes of Health, the MIT Media Lab, the National Science Foundation, the Wallace H. Coulter Foundation, the Alfred P. Sloan Foundation, a NARSAD Young Investigator Grant, the Human Frontiers Science Program, an NYSCF Robertson Neuroscience Investigator Award, the IET A.F. Harvey Prize, Janet and Sheldon Razin ’59, and the Skolkovo Institute of Science and Technology.

MIT researchers join Obama for brain announcement

Anne Trafton |

Four MIT neuroscientists were among those invited to the White House on Tuesday, April 2, when President Barack Obama announced a new initiative to understand the human brain.

Professors Ed Boyden, Emery Brown, Robert Desimone and Sebastian Seung were among a group of leading researchers who joined Obama for the announcement, along with Francis Collins, director of the National Institutes of Health, and representatives of federal and private funders of neuroscience research.

In unveiling the BRAIN (Brain Research through Advancing Innovative Neurotechnologies) Initiative, Obama highlighted brain research as one of his administration’s “grand challenges” — ambitious yet achievable goals that demand new innovations and breakthroughs in science and technology.

A key goal of the BRAIN Initiative will be to accelerate the development of new technologies to visualize brain activity and to understand how this activity is linked to behavior and to brain disorders.

“There is this enormous mystery waiting to be unlocked,” Obama said, “and the BRAIN Initiative will change that by giving scientists the tools they need to get a dynamic picture of the brain in action and better understand how we think and how we learn and how we remember. And that knowledge could be — will be — transformative.”

To jump-start the initiative, the NIH, the Defense Advanced Research Projects Agency, and the National Science Foundation will invest some $100 million in research support beginning in the next fiscal year. Planning will be overseen by a working group co-chaired by Cornelia Bargmann PhD ’87, now at Rockefeller University, and William Newsome of Stanford University. Brown, an MIT professor of computational neuroscience and of health sciences and technology, will serve as a member of the working group.

Boyden, the Benesse Career Development Associate Professor of Research in Engineering, has pioneered the development of new technologies for studying brain activity. Desimone, the Doris and Don Berkey Professor of Neuroscience, is director of MIT’s McGovern Institute for Brain Research, which conducts research in many areas relevant to the new initiative. Seung, a professor of computational neuroscience and physics, is a leader in the field of “connectomics,” the effort to describe the wiring diagram of the brain.

 

Ed Boyden to share prestigious brain prize

Anne Trafton |

Ed Boyden, a faculty member in the MIT Media Lab and the McGovern Institute for Brain Research, was today named a recipient of the 2013 Grete Lundbeck European Brain Research Prize. The 1 million Euro prize is awarded for the development of optogenetics, a technology that makes it possible to control brain activity using light.

The Brain Prize is awarded annually by the Denmark-based Lundbeck Foundation for outstanding contributions to European neuroscience. Boyden is recognized for work done in collaboration with Karl Deisseroth at Stanford University, which builds on earlier discoveries by four European researchers: Ernst Bamberg, Georg Nagel and Peter Hegemann in Germany, and Gero Miesenböck, now in Oxford, U.K. The prize will be shared equally between all six researchers.

The idea of using light to control brain activity was suggested by Francis Crick in 1999, and Miesenbock performed a proof of concept demonstration in 2002, showing that light-sensitive proteins obtained from the eyes of fruit-flies could be used to activate mammalian neurons. A further breakthrough was enabled by the discovery of channelrhodopsin-2 (ChR2), a light-activated ion channel from a common pond algal species that had been characterized by Hegemann in Martinsried and by Nagel and Bamberg in Frankfurt.

The application of ChR2 to neuroscience was pioneered by Boyden and Deisseroth at Stanford University, where Deisseroth is now a faculty member. In a collaboration that began when Boyden was a graduate student and Deisseroth a postdoctoral fellow, they obtained the ChR2 gene from Nagel and Bamberg, expressed it in cultured neurons, and pulsed the dish with blue light to see whether it could trigger neural activity. The first experiment was performed in August 2004, and it worked first time; as Boyden recounted in a recent historical article, “serendipity had struck — the molecule was good enough in its wild-type form to be used in neurons right away.”

They reported this result in 2005, in a landmark paper in Nature Neuroscience that has now been cited more than 600 times. Their method, later dubbed “optogenetics,” is now used by hundreds of labs worldwide and is also being explored for a wide range of potential therapeutic applications. In announcing the Brain Prize, the chairman of the selection committee, Professor Colin Blakemore, described optogenetics as “arguably the most important technical advance in neuroscience in the past 40 years.”

Boyden joined the MIT faculty in 2006, where he is now the Benesse Career Development Professor in the Media Lab, with joint appointments at the McGovern Institute for Brain Research and in the Departments of Biological Engineering and Brain and Cognitive Sciences. His contributions have been recognized by numerous awards and honors, including the inaugural AF Harvey Prize and the 2011 Perl/UNC prize (shared with Karl Deisseroth and with Feng Zhang, also at MIT). He continues to develop novel optogenetic tools, along with many other technologies for understanding and manipulating neural circuits within the living brain.

Boyden’s work was supported by the Fannie and John Hertz Foundation, the Helen Hay Whitney Foundation, the McKnight Foundation, Jerry and Marge Burnett, DARPA and the Department of Defense, Google, Harvard/MIT Joint Grants Program in Basic Neuroscience, Human Frontiers Science Program, IET A. F. Harvey Prize, MIT McGovern Institute and MIT Media Lab, NARSAD, New York Stem Cell Foundation-Robertson Investigator Award, NIH, NSF, Paul Allen Distinguished Investigator in Neuroscience Award, Shelly Razin, SkTech, Alfred P. Sloan Foundation, the Society for Neuroscience Research Award for Innovation in Neuroscience (RAIN), and the Wallace H. Coulter Foundation.

Precisely engineering 3-D brain tissues

Anne Trafton |

Borrowing from microfabrication techniques used in the semiconductor industry, MIT and Harvard Medical School (HMS) engineers have developed a simple and inexpensive way to create three-dimensional brain tissues in a lab dish.

The new technique yields tissue constructs that closely mimic the cellular composition of those in the living brain, allowing scientists to study how neurons form connections and to predict how cells from individual patients might respond to different drugs. The work also paves the way for developing bioengineered implants to replace damaged tissue for organ systems, according to the researchers.

“We think that by bringing this kind of control and manipulation into neurobiology, we can investigate many different directions,” says Utkan Demirci, an assistant professor in the Harvard-MIT Division of Health Sciences and Technology (HST).

Demirci and Ed Boyden, associate professor of biological engineering and brain and cognitive sciences at MIT’s Media Lab and McGovern Institute,  are senior authors of a paper describing the new technique, which appears in the Nov. 27 online edition of the journal Advanced Materials. The paper’s lead author is Umut Gurkan, a postdoc at HST, Harvard Medical School and Brigham and Women’s Hospital.

‘Unique challenges’

Although researchers have had some success growing artificial tissues such as liver or kidney, “the brain presents some unique challenges,” Boyden says. “One of the challenges is the incredible spatial heterogeneity. There are so many kinds of cells, and they have such intricate wiring.”

Brain tissue includes many types of neurons, including inhibitory and excitatory neurons, as well as supportive cells such as glial cells. All of these cells occur at specific ratios and in specific locations.

To mimic this architectural complexity in their engineered tissues, the researchers embedded a mixture of brain cells taken from the primary cortex of rats into sheets of hydrogel. They also included components of the extracellular matrix, which provides structural support and helps regulate cell behavior.

Those sheets were then stacked in layers, which can be sealed together using light to crosslink hydrogels. By covering layers of gels with plastic photomasks of varying shapes, the researchers could control how much of the gel was exposed to light, thus controlling the 3-D shape of the multilayer tissue construct.

This type of photolithography is also used to build integrated circuits onto semiconductors — a process that requires a photomask aligner machine, which costs tens of thousands of dollars. However, the team developed a much less expensive way to assemble tissues using masks made from sheets of plastic, similar to overhead transparencies, held in place with alignment pins.

The tissue cubes can be made with a precision of 10 microns, comparable to the size of a single cell body. At the other end of the spectrum, the researchers are aiming to create a cubic millimeter of brain tissue with 100,000 cells and 900 million connections.

The new system is the first that includes all of the necessary features for building useful 3-D tissues: It is inexpensive, precise, and allows complex patterns to be generated, says Metin Sitti, a professor of mechanical engineering at Carnegie Mellon University. “Many people could easily use this method for creating heterogeneous, complex gel structures,” says Sitti, who was not part of the research team.

Answering fundamental questions

Because the tissues include a diverse repertoire of brain cells, occurring in the same ratios as they do in natural brain tissue, they could be used to study how neurons form the connections that allow them to communicate with each other.

“In the short term, there’s a lot of fundamental questions you can answer about how cells interact with each other and respond to environmental cues,” Boyden says.

As a first step, the researchers used these tissue constructs to study how a neuron’s environment might constrain its growth. To do this, they placed single neurons in gel cubes of different sizes, then measured the cells’ neurites, long extensions that neurons use to communicate with other cells. It turns out that under these conditions, neurons get “claustrophobic,” Demirci says. “In small gels, they don’t necessarily send out as long neurites as they would in a five-times-larger gel.”

In the long term, the researchers hope to gain a better understanding of how to design tissue implants that could be used to replace damaged tissue in patients. Much research has been done in this area, but it has been difficult to figure out whether the new tissues are correctly wiring up with existing tissue and exchanging the right kinds of information.

Another long-term goal is using the tissues for personalized medicine. One day, doctors may be able to take cells from a patient with a neurological disorder and transform them into induced pluripotent stem cells, then induce these constructs to grow into neurons in a lab dish. By exposing these tissues to many possible drugs, “you might be able to figure out if a drug would benefit that person without having to spend years giving them lots of different drugs,” Boyden says.

Other authors of the paper are Yantao Fan, a visiting graduate student at HMS and HST; Feng Xu and Emel Sokullu Urkac, postdocs at HMS and HST; Gunes Parlakgul, a visiting medical student at HMS and HST; MIT graduate students Jacob Bernstein and Burcu Erkmen; and Wangli Xing, a professor at Tsinghua University.

The research was funded by the National Science Foundation, the Paul Allen Family Foundation, the New York Stem Cell Foundation, the National Institutes of Health, the Institute of Engineering and Technology A.F. Harvey Prize, and MIT Lincoln Laboratory.