8th Kavli Futures Symposium: Tool Development for the Brain Activity Map Project

AT THE TURN OF THE LAST CENTURY,  innovative biological stains gave the neuroscientist Santiago Ramón y Cajal the first microscopic glimpses of massively interconnecting webs of tightly packed human brain cells, which he described as “impenetrable jungles where many investigators have lost themselves.”

Over a hundred years later, two dozen cutting-edge neuroscientists, experts in brain activity and nanotechnology specialists gathered December in Arlington, VA to report on how revolutionary advances in their fields could help penetrate those thorny neuronal thickets and improve the current patchy understanding of how the brain works.

This was the latest step toward advancing a massive initiative known as the Brain Activity Map Project (BAM). BAM is envisioned as a large-scale, public interdisciplinary research effort with the ambitious goal of measuring activity in the brain, using that information to come up with ideas on how the brain works, and then testing those ideas. It’s an initiative designed to fill in the vital knowledge gap between the microscale of single cells and macroscale of the entire brain.

Understanding the Middle Ground

From a suite of spectacular tools, scientists can now study single neuron operations down to single molecules and we can observe the entire human brain in action. Yet it is the middle ground that contains the mysterious tangle of circuits that produce higher, complex brain functions ranging from decisions to skilled actions.

The Connectome project is providing an essential wiring diagram of the brain across scales, but there has been only a limited ability to measure the function of large networks of neurons to reveal the unique properties that can emerge at this scale. Only by bridging the nano, micro, middle, and macro scales can science develop and test deep theories of how the human brain works.

Much of BAM would focus on developing revolutionary new tools to measure, to analyze, and to manipulate large numbers of neurons as they operate. These data can inform and spark theories of brain function, with an ultimate goal to understand how the human brain works and what goes wrong in brain disorders. In addition to answering such basic questions as how we recognize faces, make decisions, and remember events, BAM is likely to have practical payoffs in new diagnostics and therapies for disorders of the nervous system and new technologies that can recreate brain functions – “smart tech.” Key goals of BAM are bringing the tools of physical sciences to life science, providing infrastructure to store and to process data, and most importantly to unite experimental and theoretical neuroscientists who will use the new tools to advance our understanding of the brain across scales.

As a next step to furthering BAM, scientists and technologists gathered December for the 8th Kavli Futures Symposium to discuss current bottlenecks in neuroscience, and how nanotechnology, optogenetics and other novel tools emerging from the physical and life sciences could lead to potential breakthroughs in understanding brain function. “We don’t have the tools to sleuth how the brain works at the level of large numbers of neurons to produce functions like consciousness, creativity, or the ability to understand what’s in a scene; consequently, there is a whole sphere of questions that can’t be addressed,” said John Donoghue, Director of the Institute for Brain Science, Brown University and one of the symposium’s organizers. “We’re at a moment when nanotechnologists, with their armory of tools, can make a huge difference in neuroscience research.”

Another organizer, Rafa Yuste, Co-Director of the Kavli Institute for Brain Science, Columbia University added, “We are figuring out the neural code but we are solely looking at individual neurons, as if they were single pixels on a video screen, whereas we need the technology that will help us look at the whole picture in high definition. We will never understand the movie until we have all the pixels. We need new techniques. Every breakthrough in science is always linked to the introduction of new techniques.”

Scaling to the Biological World

As noted in the symposium, eavesdropping on the network of thousands to millions of neurons that underlie specific brain functions is challenging. The most sensitive way to pick up on the electrical chatter of an individual neuron that reveals its activity is to place a microelectrode near it. If placed very close, the tip of the electrode can “hear it talking.” Packing in and powering enough electrodes and wires to monitor the activity of an entire neuronal network is not yet possible, and too many probes might damage the very network we are trying to measure.

But as brought out by the symposium’s participants, that may soon change with emerging sets of tools for neuroscience from nanoengineering, optogenetics, and synthetic biology. Nanotechnologists are making rapid progress in shrinking devices, including electrical sensors and wires, some of which are made from flexible, softer materials that can be more compatible with the brain. “This amazing miniaturization of devices is approaching the complexity and size needed to probe every neuron in a neural circuit,” said Paul McEuen, Director of the Kavli Institute at Cornell for Nanoscale Science. “The technology is within reach to make hundreds of thousands of measurements, which is exciting because we learn something new whenever things change by a factor of 10.” Some of these devices are going wireless, enabling more extensive use in the brain and their translation to neurodevices that provide new ways to treat human brain disorders, like Parkinson’s disease or paralysis.

Optical methods are providing entirely new ways to image the activity of entire neural circuits. These methods use light as a trigger to electrical and chemical activity at the resolution of individual neurons, or as a tool to report that activity at subcellular scales. With these techniques, the activity of thousands of neurons can be detected simultaneously. In addition, this innovative imaging coupled to novel setups, including mini-microscopes the size of a dime attached to animals’ heads, enable researchers to shine light into the brain to see and to measure details of brain activity while an animal is behaving.

Researchers can also image activity deeper in the brain with fiber optic techniques that channel light into more remote areas. These deep brain areas, which have been somewhat terra incognita, are thought to play major roles in a number of common brain disorders – including anxiety and mood disorders, and Parkinson’s disease – but have been out of view for optical recording. Scientists can also genetically engineer experimental animals so light can switch on or off the activity of specific neurons in their living brains allowing them to test the function of each neuron in its community.

Innovative analytic techniques, combined with methods from physics and chemistry, are also expanding the boundaries of what can be clearly imaged. Scientists can now image brain tissue in three dimensions or over large flat surface areas with high resolution. Imaging of the organelles within cells is also now possible and is important because, as Jennifer Lippincott-Schwartz of the National Institute of Child Health and Development noted, “Many organelles dictate the fate and behavior of cells.”

The ability to detect key chemicals that often modulate the brain networks is also literally making headway. Researchers can insert artificial receptors to flag the chemical messengers that stimulate or inhibit brain activity, as well as reveal fine-tuned chemical differences between neurons that otherwise look the same. Protein differences can even be imaged within the branchlike extensions of neurons, called axons and dendrites, as well as within their organelles. “We can create maps showing the spatial arrangements of molecules that reveal intracellular dynamics. This painting of organelles based on specific proteins reveals their functions,” said Lippincott-Schwartz.

There remains further to go – the scale at which interneuronal communication occurs is not yet within our grasp; but each time smaller scales and shorter times have been probed in the brain, new discoveries have been made, noted Anne Andrews, Richard Metzner Endowed Chair in Clinical Neuropharmacology at UCLA.

The new field of synthetic biology also offers the possibility that researchers can modify cells of the immune system so they can deliver activity-sensing nanodevices to individual neurons. “Nature has provided many sophisticated nanostructures (such as polymerases and luciferases), which we can harvest to read and write at single-neuron resolution, at million-fold lower energy and space consumption than current implants” said George Church, Professor of Genetics at Harvard Medical School, and Director of Wyss Institute Synthetic Biology and PersonalGenomes.org. Molecular engineering promises new ways to “tape record” and alter the activity of networks of neurons.

Recent Discoveries

Remarkable recent feats in neuroscience achieved by applying these innovative techniques offer hope that a more complete understanding of the brain of a mammal can be achieved within the next 10 to 20 years if sufficient resources are applied to the task. Here are some of the striking achievements reported at the symposium:

  • Wireless sensors in the region of the monkey brain that governs its movements revealed the real-time brain activity of 100 neurons as the animal moved about naturally.
  • Artificial receptors measured the activity of six different chemical messengers in the brain, including serotonin (which helps govern our emotions) and glutamate (which plays a key role in learning and memory).
  • Light-based tools imaged the filigreed ends of axons and dendrites where the exchange of chemical and electrical signals between brain cells occurs. These exchanges are key to understanding neural networks and the higher functions they fuel. This imaging can be done in live animals over long periods of time, such as weeks.
  • Complete brain electrical activity of the zebrafish was tracked via imaging fluctuations in the calcium concentrations that result from that activity.
  • One thousand neurons and their connections were imaged simultaneously in the mouse. These neurons were part of a network that underlies the animal’s encoding into memory of where it is in space. The imaging was done while the mouse was moving.
  • A human with complete paralysis of her arms and legs used activity from a few dozen neurons in a brain circuit to control a robot arm that allowed her to serve herself coffee for the first time in nearly 15 years.

“An important goal is to understand broad scale functional mechanisms—how brain areas talk to one another,” said Mark Schnitzer, Associate Professor of Biology and Applied Physics, Stanford University.

Collaboration and Innovation

Despite these achievements, progress in making new tools to measure brain activity is impeded by the need for greater collaboration between neuroscientists and nanoscientists, engineering and other researchers with expertise in innovative physical science tools and analytics. As several participants noted, there is a natural tendency for scientists to stay within a limited research field and not be exposed to others due to how many universities and federal funding opportunities are structured.

"Nanoscientists do not usually target their efforts to address a specific goal, like interpreting neural coding patterns or looking at specific diseases,” said Paul Weiss, the Fred Kavli Chair in NanoSystems Sciences at the UCLA. Said Tim Harris, Director of the Applied Physics and Instrumentation Group at the Howard Hughes Medical Institute’s Janelia Farm, “The only way this is going to work is if the people making the tools are holding hands with the biologists that are seeking the data. Unlike the one dimensional data of gene sequence, brain activity varies three dimensionally in space with submicron resolution and submilisecond in time. Biological context is critical for any valid study.” Progress in this regard also depends on training a new generation of interdisciplinary scientists, pointed out Yuste.

Axel Scherer, Co-Director of the Kavli Nanoscience Institute at California Institute of Technology and an organizer of the symposium, also noted that progress in neuroscience is inhibited by the inertia of device companies, which don’t have neuroscience goals at the top of their lists because it isn’t profitable to fabricate the small numbers of devices neuroscientists need for their research. The end result, said Scherer, is that each neuroscience researcher has to cobble together his or her own instrumentation. “We have to figure out commonality and produce electrophysiology probes in large enough numbers to serve the neuroscience community more efficiently.”

Scherer noted that an overarching structure facilitated by BAM could support the development and distribution of innovative tools that could transform neuroscience research. Such an infrastructure would provide economies of scale, he said, and may also lead to profitable business spinoffs with many unexpected new technologies. It was pointed out that similar benefits were reaped from the Human Genome Project (HGP), the publically funded effort to decipher the human genome, which completed its mission quicker than expected because of the synergy of combining the efforts of multiple labs throughout the world.

Most immediately, BAM will move forward identifying needs and benchmarks for what one participant called neuroscience’s “Holy Grail.” As noted by BAM’s proposers in Neuron, “We believe that neuroscience is ready for a large-scale functional mapping of the entire brain circuitry, and that such mapping will directly address the emergent level of function, shining much-needed light into the ‘impenetrable jungles’ of the brain.”

It will also identify the dynamics for conducting research and developing technologies in a way that is interdisciplinary, comprehensive and focused. By identifying and later bolstering these dynamics, the project would influence the cultures of all the participating fields, including the future training of researchers. “We should not underestimate the repercussions that such a project could have for education, …[which could] lead to the training of a new generation of scientists and the opening up of new strategies for evaluating pedagogical effectiveness,” the proposers noted as well in Neuron.

- January 2013