HomeResearchOptical Deconstruction of Intact Biological Systems

Our Scientists

Optical Deconstruction of Intact Biological Systems

Research Summary

Karl Deisseroth develops optical methods for high-resolution investigation of intact biological systems. His group has pioneered optogenetics, a technology that uses light to control millisecond-precision activity patterns in defined cell types in the brains of freely moving mammals, and CLARITY, a chemical engineering technology that enables high-resolution structural and molecular access to intact brains. A practicing psychiatrist, Deisseroth has also applied his technologies to study anxiety, depression, and social dysfunction.

Our research group builds optical tools for precise, high-resolution investigation of intact biological systems, with a focus on the vertebrate central nervous system; in particular, over the past decade my laboratory has developed the technologies we term optogenetics and CLARITY and applied these tools to study the neural circuit underpinnings of adaptive and maladaptive behavior. We also make teaching and dissemination of these tools a high priority, a process that includes worldwide distribution of reagents, up-to-date and detailed support on our portals (optogenetics.org and clarityresourcecenter.org), and free educational courses in our laboratory, which researchers from around the world visit for hands-on training; these visiting scientists can then return home and help other scientists advance diverse fields of investigation.

Optogenetics is a technology we developed for precisely controlling millisecond-scale activity patterns in specific cell types, even within freely behaving animals, for which we use microbial opsin genes and fiberoptic-based neural interfaces. To not only discover the principles but also make this approach broadly useful, we have developed diverse strategies for targeting microbial opsin genes and light itself to meet the challenging constraints of the freely behaving mammal, engineered a broad panel of microbial opsin genes covering a range of optical and kinetic properties, and built high-speed behavioral and neural activity readout tools compatible with real-time optogenetic control.

Figure 1: Optogenetics, a technology that uses light to control millisecond-precision activity patterns in defined cell types in the nervous system of freely moving animals. Image: Inbal Goshen and Karl Deisseroth.

Beyond development and distribution, we also have broadly employed optogenetics in the lab. I am a psychiatrist, and in my research group we take a particular interest in the neural circuit underpinnings of depression, anxiety, reward, and motivation. For example, we have used these tools to determine the precise causal role of defined activity patterns in dopamine neurons for motivated behavior and reward learning; these behaviors are relevant to hedonic symptoms involved in depression and substance abuse, as well as in physiological reward processes. Along with our collaborators, we also have used optogenetics to define a causal role for cortical inhibitory parvalbumin neurons in specific kinds of brain rhythmicity relevant to schizophrenia and autism and to implicate excitation/inhibition dynamics in social behavior and in the flow of quantifiable information within neocortical microcircuits. In a final example, we have used optogenetic approaches to target deep brain structures such as the subthalamic nucleus in animal models, to determine the circuit and cellular mechanisms of deep brain stimulation as used in Parkinson's and other neuropsychiatric diseases.

In our ongoing optogenetics work, we are further developing technology in the areas of genomics, molecular engineering, and optics. Via genomic screening we will continue our identification of families of new optogenetic effectors, to identify and engineer novel properties such as altered action spectrum and ion flux characteristics. Already significant advances have come from structural modeling, mutagenesis, and chimeras; for example, in 2008 our genomic strategies led to identification of a red-shifted channelrhodopsin from Volvox carteri, which with additional engineering based on molecular modeling with our collaborators led to the creation of the C1V1 channelrhodopsin, which enabled combinatorial excitation in living mammals (and incidentally, as we recently found, also turned out to be important for two-photon optogenetics). This illustrates the synergy among opsin discovery, modeling, engineering, and application—but represents only the tip of the iceberg of opportunity, thanks in part to recent elucidation of the channelrhodopsin crystal structure together with our collaborators. These advances will spark further development for optical compatibility with genetically encoded Ca2+ indicators and with three-dimensional microscopies that we have found can enable volumetric optical control and imaging in mammalian tissues. Together, these optogenetics efforts will enhance complex, fast, and specific play-in and readout of activity for probing circuit function in health and disease.

Separate from optogenetics, to further meet the challenge of understanding how animal behaviors arise from neural circuitry, we have developed new technology to optically resolve high-resolution structural detail in intact nervous systems. Our CLARITY approach can be used to transform intact biological tissue into a hybrid form in which tissue components are removed and replaced with exogenous elements, resulting in a transparent tissue hydrogel that both preserves and makes accessible struc­tural and molecular information for visualization and analysis. With CLARITY, we have now immunostained and imaged whole mouse brains completely intact, and we have used molecular markers to identify individual structures and projections in human brain tissue. CLARITY can in this way help unlock rich sources of information for probing disease mechanisms as well as the native structure and complexity of the nervous system.

Figure 2: CLARITY, a technology that allows fine structural-visualization and macromolecular-labeling of detailed properties within intact, unsectioned biological tissues such as this mouse brain (hippocampus shown with multicolor molecular labels for different cell types). Image: Kwanghun Chung and Karl Deisseroth.

Going forward, we will further develop advanced microscopies for CLARITY. For imaging large samples at high resolution and high data-acquisition rates, light sheet illumination or two-photon line-scan microscopy may be methods of choice. Clarified tissue appears to be com­patible with diverse imaging readout modalities; moreover, the multiround molecular phenotyping capacity of CLARITY may be suitable for provid­ing enriched detail on the composition and relationships of subcellular structures such as synapses and for globally mapping synaptically connected and acti­vated populations. CLARITY can be seen as a general approach for building new structures and installing new functions from within biological systems—an approach that may find other applications as the technology is developed and other components introduced. And beyond neuroscience, CLARITY is currently being explored for the evaluation, diagnosis, and prognosis of patho­logical states such as cancer, infection, and autoimmune disease, as well as for the study of normal tissue development and function.

In the lab, we use this expanding panel of interdisciplinary tools for precise interrogation of circuits in behaving animals as well as in isolated brain tissues. My clinical focus has led to the implementation in our laboratory of well-validated animal models of neuropsychiatric symptomatology. We explore and test which structurally defined cellular dynamics features are necessary and sufficient for circuit and animal behavior relevant to normal function, major disease symptoms, and disease symptom treatment. Our in vivo behavioral experiments are linked to quantitative electrophysiology and activity imaging, to probe not only behavior but also circuit manifestations. We hope that this approach will help in the understanding of nervous system function in health and disease and more generally help advance the study of intact biological systems.

The National Institute of Mental Health, the National Institute on Drug Abuse, and the National Science Foundation have provided support for these projects, along with the Brain and Behavior Research Foundation, and the McKnight, Keck, Gatsby, Klingenstein, and Coulter foundations.

Last updated July 17, 2013

Scientist Profile

Stanford University
Neuroscience, Physiology