Stanford Advisors

All Publications

  • OPTOGENETICS. Expanding the optogenetics toolkit. Science Berndt, A., Deisseroth, K. 2015; 349 (6248): 590-591

    View details for DOI 10.1126/science.aac7889

    View details for PubMedID 26250674

  • Targeting cells with single vectors using multiple-feature Boolean logic NATURE METHODS Fenno, L. E., Mattis, J., Ramakrishnan, C., Hyun, M., Lee, S. Y., He, M., Tucciarone, J., Selimbeyoglu, A., Berndt, A., Grosenick, L., Zalocusky, K. A., Bernstein, H., Swanson, H., Perry, C., Diester, I., Boyce, F. M., Bass, C. E., Neve, R., Huang, Z. J., Deisseroth, K. 2014; 11 (7): 763-U116

    View details for DOI 10.1038/NMETH.2996

    View details for Web of Science ID 000338321400022

  • Targeting cells with single vectors using multiple-feature Boolean logic. Nature methods Fenno, L. E., Mattis, J., Ramakrishnan, C., Hyun, M., Lee, S. Y., He, M., Tucciarone, J., Selimbeyoglu, A., Berndt, A., Grosenick, L., Zalocusky, K. A., Bernstein, H., Swanson, H., Perry, C., Diester, I., Boyce, F. M., Bass, C. E., Neve, R., Huang, Z. J., Deisseroth, K. 2014; 11 (7): 763-772


    Precisely defining the roles of specific cell types is an intriguing frontier in the study of intact biological systems and has stimulated the rapid development of genetically encoded tools for observation and control. However, targeting these tools with adequate specificity remains challenging: most cell types are best defined by the intersection of two or more features such as active promoter elements, location and connectivity. Here we have combined engineered introns with specific recombinases to achieve expression of genetically encoded tools that is conditional upon multiple cell-type features, using Boolean logical operations all governed by a single versatile vector. We used this approach to target intersectionally specified populations of inhibitory interneurons in mammalian hippocampus and neurons of the ventral tegmental area defined by both genetic and wiring properties. This flexible and modular approach may expand the application of genetically encoded interventional and observational tools for intact-systems biology.

    View details for DOI 10.1038/nmeth.2996

    View details for PubMedID 24908100

  • Structure-Guided Transformation of Channelrhodopsin into a Light-Activated Chloride Channel SCIENCE Berndt, A., Lee, S. Y., Ramakrishnan, C., Deisseroth, K. 2014; 344 (6182): 420-424


    Using light to silence electrical activity in targeted cells is a major goal of optogenetics. Available optogenetic proteins that directly move ions to achieve silencing are inefficient, pumping only a single ion per photon across the cell membrane rather than allowing many ions per photon to flow through a channel pore. Building on high-resolution crystal-structure analysis, pore vestibule modeling, and structure-guided protein engineering, we designed and characterized a class of channelrhodopsins (originally cation-conducting) converted into chloride-conducting anion channels. These tools enable fast optical inhibition of action potentials and can be engineered to display step-function kinetics for stable inhibition, outlasting light pulses and for orders-of-magnitude-greater light sensitivity of inhibited cells. The resulting family of proteins defines an approach to more physiological, efficient, and sensitive optogenetic inhibition.

    View details for DOI 10.1126/science.1252367

    View details for Web of Science ID 000334867800043

  • Prolonged, brain-wide expression of nuclear-localized GCaMP3 for functional circuit mapping. Frontiers in neural circuits Kim, C. K., Miri, A., Leung, L. C., Berndt, A., Mourrain, P., Tank, D. W., Burdine, R. D. 2014; 8: 138-?


    Larval zebrafish offer the potential for large-scale optical imaging of neural activity throughout the central nervous system; however, several barriers challenge their utility. First, ~panneuronal probe expression has to date only been demonstrated at early larval stages up to 7 days post-fertilization (dpf), precluding imaging at later time points when circuits are more mature. Second, nuclear exclusion of genetically-encoded calcium indicators (GECIs) limits the resolution of functional fluorescence signals collected during imaging. Here, we report the creation of transgenic zebrafish strains exhibiting robust, nuclearly targeted expression of GCaMP3 across the brain up to at least 14 dpf utilizing a previously described optimized Gal4-UAS system. We confirmed both nuclear targeting and functionality of the modified probe in vitro and measured its kinetics in response to action potentials (APs). We then demonstrated in vivo functionality of nuclear-localized GCaMP3 in transgenic zebrafish strains by identifying eye position-sensitive fluorescence fluctuations in caudal hindbrain neurons during spontaneous eye movements. Our methodological approach will facilitate studies of larval zebrafish circuitry by both improving resolution of functional Ca(2+) signals and by allowing brain-wide expression of improved GECIs, or potentially any probe, further into development.

    View details for DOI 10.3389/fncir.2014.00138

    View details for PubMedID 25505384

  • The Microbial Opsin Family of Optogenetic Tools CELL Zhang, F., Vierock, J., Yizhar, O., Fenno, L. E., Tsunoda, S., Kianianmomeni, A., Prigge, M., Berndt, A., Cushman, J., Polle, J., Magnuson, J., Hegemann, P., Deisseroth, K. 2011; 147 (7): 1446-1457


    The capture and utilization of light is an exquisitely evolved process. The single-component microbial opsins, although more limited than multicomponent cascades in processing, display unparalleled compactness and speed. Recent advances in understanding microbial opsins have been driven by molecular engineering for optogenetics and by comparative genomics. Here we provide a Primer on these light-activated ion channels and pumps, describe a group of opsins bridging prior categories, and explore the convergence of molecular engineering and genomic discovery for the utilization and understanding of these remarkable molecular machines.

    View details for DOI 10.1016/j.cell.2011.12.004

    View details for Web of Science ID 000298403400011

    View details for PubMedID 22196724

  • High-efficiency channelrhodopsins for fast neuronal stimulation at low light levels PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Berndt, A., Schoenenberger, P., Mattis, J., Tye, K. M., Deisseroth, K., Hegemann, P., Oertner, T. G. 2011; 108 (18): 7595-7600


    Channelrhodopsin-2 (ChR2) has become an indispensable tool in neuroscience, allowing precise induction of action potentials with short light pulses. A limiting factor for many optophysiological experiments is the relatively small photocurrent induced by ChR2. We screened a large number of ChR2 point mutants and discovered a dramatic increase in photocurrent amplitude after threonine-to-cysteine substitution at position 159. When we tested the T159C mutant in hippocampal pyramidal neurons, action potentials could be induced at very low light intensities, where currently available channelrhodopsins were unable to drive spiking. Biophysical characterization revealed that the kinetics of most ChR2 variants slows down considerably at depolarized membrane potentials. We show that the recently published E123T substitution abolishes this voltage sensitivity and speeds up channel kinetics. When we combined T159C with E123T, the resulting double mutant delivered fast photocurrents with large amplitudes and increased the precision of single action potential induction over a broad range of frequencies, suggesting it may become the standard for light-controlled activation of neurons.

    View details for DOI 10.1073/pnas.1017210108

    View details for Web of Science ID 000290203100063

    View details for PubMedID 21504945

  • Ultrafast optogenetic control NATURE NEUROSCIENCE Gunaydin, L. A., Yizhar, O., Berndt, A., Sohal, V. S., Deisseroth, K., Hegemann, P. 2010; 13 (3): 387-U27


    Channelrhodopsins such as channelrhodopsin-2 (ChR2) can drive spiking with millisecond precision in a wide variety of cells, tissues and animal species. However, several properties of this protein have limited the precision of optogenetic control. First, when ChR2 is expressed at high levels, extra spikes (for example, doublets) can occur in response to a single light pulse, with potential implications as doublets may be important for neural coding. Second, many cells cannot follow ChR2-driven spiking above the gamma (approximately 40 Hz) range in sustained trains, preventing temporally stationary optogenetic access to a broad and important neural signaling band. Finally, rapid optically driven spike trains can result in plateau potentials of 10 mV or more, causing incidental upstates with information-processing implications. We designed and validated an engineered opsin gene (ChETA) that addresses all of these limitations (profoundly reducing extra spikes, eliminating plateau potentials and allowing temporally stationary, sustained spike trains up to at least 200 Hz).

    View details for DOI 10.1038/nn.2495

    View details for Web of Science ID 000274860100022

    View details for PubMedID 20081849

  • Bi-stable neural state switches NATURE NEUROSCIENCE Berndt, A., Yizhar, O., Gunaydin, L. A., Hegemann, P., Deisseroth, K. 2009; 12 (2): 229-234


    Here we describe bi-stable channelrhodopsins that convert a brief pulse of light into a stable step in membrane potential. These molecularly engineered probes nevertheless retain millisecond-scale temporal precision. Photocurrents can be precisely initiated and terminated with different colors of light, but operate at vastly longer time scales than conventional channelrhodopsins as a result of modification at the C128 position that extends the lifetime of the open state. Because of their enhanced kinetic stability, these step-function tools are also effectively responsive to light at orders of magnitude lower intensity than wild-type channelrhodopsins. These molecules therefore offer important new capabilities for a broad range of in vivo applications.

    View details for DOI 10.1038/nn.2247

    View details for Web of Science ID 000263182000024

    View details for PubMedID 19079251