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Neurotechnology: A Look Back at President Obama’s BRAIN Initiative

Progress in science depends on new techniques, new discoveries, and new ideas, probably in that order. – Sydney Brenner

In 2012, my former research mentor and principal investigator Rafael Yuste published a paper with his colleagues proposing the Brain Activity Map (BAM) Project. Little did we know that this project would be taken up by the Obama Administration in 2013 and transformed into the Brain Research Advancing through Innovative Neurotechnologies (BRAIN) Initiative. The basic principle of the BAM Project is to understand how the coordinated activity of large numbers of neurons leads to complex behaviors, we must first characterize all these neurons and reconstruct a full record of their neural activity. In order to do so, Professor Yuste and his colleagues believed large-scale, international collaboration was necessary. Their idea caught on and received extensive press coverage. As an undergraduate student in the lab, I recall newscasters from nearly every network coming in everyday to interview Professor Yuste. Seeing all this excitement about neuroscience at an early stage in my career inspired me to move forward in this field.

Since President Obama’s announcement of the BRAIN Initiative in 2013, many leading technology firms, academic institutions, and scientists have made significant contributions to the initiative. The BRAIN Initiative reflects a government strategy to focus on investment of tool development for neuroscience. Although some may argue that science is primarily shaped by ideas, tools are critical to advancement in science. Moreover, tools and ideas work in synergy. New tools can generate new findings that challenge old ideas. These new ideas can then, in turn, generate new questions that will require new tools. As a researcher in neuroscience, I have seen how advances in imaging techniques have transformed the field. In this post, I will discuss two methods sponsored by the BRAIN Initiative that have shaped the way we study the brain. These methods are optogenetics and super resolution microscopy. I will conclude by discussing how new ideas are critical to interpret the data acquired from these tools and ultimately unravel the mysteries of the brain.


In 2015, Nature Neuroscience celebrated the 10th anniversary of optogenetics and features articles by the first and senior authors of the original paper. Optogenetics has also captivated the public’s attention through this famous photo:

Optogenetics in Action: An optic fiber feeds flashes of light into the brain of a genetically modified mouse. Digital image courtesy of Getty’s Open Content Program (John B. Carnett / Getty Images)
Optogenetics in Action: An optic fiber feeds flashes of light into the brain of a genetically modified mouse. Digital image courtesy of Getty’s Open Content Program (John B. Carnett / Getty Images)

Optogenetics is a technique that uses light to artificially activate cells, tissues, and even organisms. More specifically, the light-sensitive target is introduced genetically. Neurons in freely moving mammals can be controlled for rapid excitation or inhibition. With this technique, we can manipulate activity in live neurons with molecular specificity and millisecond precision. Light delivery is also non-invasive, enabling remote control of neural activity. Proteins activated by light stimulation are known as caged compounds. To excite neurons, light-induced inward cation currents can be used to depolarize neurons and initiate action potentials. Conversely, light-induced inward anion currents of chloride ions can be used to hyperpolarize neurons and stop firing patterns. Optogenetics has been implemented in a diverse array of model organisms including flies, rats, and primates.

The BRAIN Initiative has focused on the development of optogenetic tools based on light-activated channels and ion pumps. With the rapid activation and genetic delivery of light-sensitive channels to specific cell types and brain regions, scientists can reliably generate hypotheses and results regarding brain function. Researchers also hope to manipulate neural activity in vivo, which would use optogenetics to label a single cell rather than a cell type in a behaving animal.

Super Resolution Microscopy

Although optogenetics enables neuroscientists to study the brain at the cellular level, much of what happens in the brain occurs at a sub-cellular level. For instance, synapses at the nano-scale are structures that permit neurons to pass electrical or chemical signals to other neurons. To image synapses, neuroscientists often use super-resolution microscopy. In 2014, Eric Betzig, Stefan Hell, and William Moerner, were awarded the Nobel Prize in Chemistry for their work on super resolution microscopy. This technique bypassed the diffraction barrier of fluorescence microscopy. Eric Betzig’s contribution to this achievement was the invention of Photoactivated Localization Microscopy (PALM) alongside his colleague Harold HessThe basic principle of PALM is that a low-power activating laser beam will activate fluorophores. These fluorophores are activated by light and are left at an “on” state. The molecules that are left “on” are then imaged by a high-power laser beam that converts them back to their “off” state. This process of activation and inactivation is repeated over thousands of frames until all the molecules have been imaged. The final results of super-resolution microscopy are breathtaking.

The BRAIN Initiative has expanded the use of super-resolution microscopy by focusing on obtaining images for a large number of target species. Ed Boyden at the Massachusetts Institute of Technology directed a project to develop tools capable of resolving the protein composition of synapse types in cultured neurons and intact brain tissues. Their super-resolution imaging method is known as DNA-PAINT (Points Accumulation for Imaging in Nanoscale Topography). With DNA-PAINT, scientists can identify the structural organization of synapse proteins. Since many neurological and psychiatric diseases, including Alzheimer’s disease, are associated with dysregulated synapses, it is important to identify synapse proteins for understanding proper neuronal function and related pathogenesis.


With the BRAIN Initiative led by the Obama administration, the development of imaging techniques has been exceptionally productive these past few years. Optogenetics and super resolution microscopy have allowed neuroscientists to probe neurons by light, see cellular properties in live animals, and examine sub-cellular structures at the nanoscale. As these tools progress, I believe we will see combinations of techniques such as fluorescence-labeling with super-resolution microscopy. Ultimately, as our toolbox grows, our opportunities in science grow as well.


  1. Fenno, L., Yizhar, O., & Deisseroth, K. (2011). The development and application of optogenetics. Neuroscience, 34(1), 389.
  2. Grote, M., Engelhard, M., & Hegemann, P. (2014). Of ion pumps, sensors and channels—perspectives on microbial rhodopsins between science and history. Biochimica et Biophysica Acta (BBA)-Bioenergetics, 1837(5), 533-545.
  3. Lakadamyali, M., Babcock, H., Bates, M., Zhuang, X., & Lichtman, J. (2012). 3D multicolor super-resolution imaging offers improved accuracy in neuron tracing. PloS one, 7(1), e30826.
  4. Szobota, S., & Isacoff, E. Y. (2010). Optical control of neuronal activity.Annual review of biophysics, 39, 329-348.
  5. Wilt, B. A., Burns, L. D., Ho, E. T. W., Ghosh, K. K., Mukamel, E. A., & Schnitzer, M. J. (2009). Advances in light microscopy for neuroscience.Annual review of neuroscience, 32, 435.
  6. Van Spronsen, M., & Hoogenraad, C. C. (2010). Synapse pathology in psychiatric and neurologic disease. Current neurology and neuroscience reports, 10(3), 207-214.

Featured Image: Super-Resolution Microscopy Figure in PLOS ONE paper licensed under a Creative Commons Attribution-Noncommercial 2.0 License.


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