Honors & Awards

  • Berry Postdoctoral Fellow, Stanford University School of Medicine (2009-2012)

Professional Education

  • Doctor of Philosophy, Massachusetts Institute of Technology (2009)

Stanford Advisors


All Publications

  • Structural and molecular interrogation of intact biological systems. Nature Chung, K., Wallace, J., Kim, S., Kalyanasundaram, S., Andalman, A. S., Davidson, T. J., Mirzabekov, J. J., Zalocusky, K. A., Mattis, J., Denisin, A. K., Pak, S., Bernstein, H., Ramakrishnan, C., Grosenick, L., Gradinaru, V., Deisseroth, K. 2013; 497 (7449): 332-337


    Obtaining high-resolution information from a complex system, while maintaining the global perspective needed to understand system function, represents a key challenge in biology. Here we address this challenge with a method (termed CLARITY) for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. Using mouse brains, we show intact-tissue imaging of long-range projections, local circuit wiring, cellular relationships, subcellular structures, protein complexes, nucleic acids and neurotransmitters. CLARITY also enables intact-tissue in situ hybridization, immunohistochemistry with multiple rounds of staining and de-staining in non-sectioned tissue, and antibody labelling throughout the intact adult mouse brain. Finally, we show that CLARITY enables fine structural analysis of clinical samples, including non-sectioned human tissue from a neuropsychiatric-disease setting, establishing a path for the transmutation of human tissue into a stable, intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease.

    View details for DOI 10.1038/nature12107

    View details for PubMedID 23575631

  • Closed-loop optogenetic control of thalamus as a tool for interrupting seizures after cortical injury NATURE NEUROSCIENCE Paz, J. T., Davidson, T. J., Frechette, E. S., Delord, B., Parada, I., Peng, K., Deisseroth, K., Huguenard, J. R. 2013; 16 (1): 64-U98


    Cerebrocortical injuries such as stroke are a major source of disability. Maladaptive consequences can result from post-injury local reorganization of cortical circuits. For example, epilepsy is a common sequela of cortical stroke, but the mechanisms responsible for seizures following cortical injuries remain unknown. In addition to local reorganization, long-range, extra-cortical connections might be critical for seizure maintenance. In rats, we found that the thalamus, a structure that is remote from, but connected to, the injured cortex, was required to maintain cortical seizures. Thalamocortical neurons connected to the injured epileptic cortex underwent changes in HCN channel expression and became hyperexcitable. Targeting these neurons with a closed-loop optogenetic strategy revealed that reducing their activity in real-time was sufficient to immediately interrupt electrographic and behavioral seizures. This approach is of therapeutic interest for intractable epilepsy, as it spares cortical function between seizures, in contrast with existing treatments, such as surgical lesioning or drugs.

    View details for DOI 10.1038/nn.3269

    View details for Web of Science ID 000312633900014

    View details for PubMedID 23143518

  • Recombinase-Driver Rat Lines: Tools, Techniques, and Optogenetic Application to Dopamine-Mediated Reinforcement NEURON Witten, I. B., Steinberg, E. E., Lee, S. Y., Davidson, T. J., Zalocusky, K. A., Brodsky, M., Yizhar, O., Cho, S. L., Gong, S., Ramakrishnan, C., Stuber, G. D., Tye, K. M., Janak, P. H., Deisseroth, K. 2011; 72 (5): 721-733


    Currently there is no general approach for achieving specific optogenetic control of genetically defined cell types in rats, which provide a powerful experimental system for numerous established neurophysiological and behavioral paradigms. To overcome this challenge we have generated genetically restricted recombinase-driver rat lines suitable for driving gene expression in specific cell types, expressing Cre recombinase under the control of large genomic regulatory regions (200-300 kb). Multiple tyrosine hydroxylase (Th)::Cre and choline acetyltransferase (Chat)::Cre lines were produced that exhibited specific opsin expression in targeted cell types. We additionally developed methods for utilizing optogenetic tools in freely moving rats and leveraged these technologies to clarify the causal relationship between dopamine (DA) neuron firing and positive reinforcement, observing that optical stimulation of DA neurons in the ventral tegmental area (VTA) of Th::Cre rats is sufficient to support vigorous intracranial self-stimulation (ICSS). These studies complement existing targeting approaches by extending the generalizability of optogenetics to traditionally non-genetically-tractable but vital animal models.

    View details for DOI 10.1016/j.neuron.2011.10.028

    View details for Web of Science ID 000297971100008

    View details for PubMedID 22153370

  • Neocortical excitation/inhibition balance in information processing and social dysfunction NATURE Yizhar, O., Fenno, L. E., Prigge, M., Schneider, F., Davidson, T. J., O'Shea, D. J., Sohal, V. S., Goshen, I., Finkelstein, J., Paz, J. T., Stehfest, K., Fudim, R., Ramakrishnan, C., Huguenard, J. R., Hegemann, P., Deisseroth, K. 2011; 477 (7363): 171-178


    Severe behavioural deficits in psychiatric diseases such as autism and schizophrenia have been hypothesized to arise from elevations in the cellular balance of excitation and inhibition (E/I balance) within neural microcircuitry. This hypothesis could unify diverse streams of pathophysiological and genetic evidence, but has not been susceptible to direct testing. Here we design and use several novel optogenetic tools to causally investigate the cellular E/I balance hypothesis in freely moving mammals, and explore the associated circuit physiology. Elevation, but not reduction, of cellular E/I balance within the mouse medial prefrontal cortex was found to elicit a profound impairment in cellular information processing, associated with specific behavioural impairments and increased high-frequency power in the 30-80?Hz range, which have both been observed in clinical conditions in humans. Consistent with the E/I balance hypothesis, compensatory elevation of inhibitory cell excitability partially rescued social deficits caused by E/I balance elevation. These results provide support for the elevated cellular E/I balance hypothesis of severe neuropsychiatric disease-related symptoms.

    View details for DOI 10.1038/nature10360

    View details for Web of Science ID 000294603900027

    View details for PubMedID 21796121

  • Optogenetics in Neural Systems NEURON Yizhar, O., Fenno, L. E., Davidson, T. J., Mogri, M., Deisseroth, K. 2011; 71 (1): 9-34


    Both observational and perturbational technologies are essential for advancing the understanding of brain function and dysfunction. But while observational techniques have greatly advanced in the last century, techniques for perturbation that are matched to the speed and heterogeneity of neural systems have lagged behind. The technology of optogenetics represents a step toward addressing this disparity. Reliable and targetable single-component tools (which encompass both light sensation and effector function within a single protein) have enabled versatile new classes of investigation in the study of neural systems. Here we provide a primer on the application of optogenetics in neuroscience, focusing on the single-component tools and highlighting important problems, challenges, and technical considerations.

    View details for DOI 10.1016/j.neuron.2011.06.004

    View details for Web of Science ID 000292806200004

    View details for PubMedID 21745635

  • Hippocampal Replay of Extended Experience NEURON Davidson, T. J., Kloosterman, F., Wilson, M. A. 2009; 63 (4): 497-507


    During pauses in exploration, ensembles of place cells in the rat hippocampus re-express firing sequences corresponding to recent spatial experience. Such "replay" co-occurs with ripple events: short-lasting (approximately 50-120 ms), high-frequency (approximately 200 Hz) oscillations that are associated with increased hippocampal-cortical communication. In previous studies, rats exploring small environments showed replay anchored to the rat's current location and compressed in time into a single ripple event. Here, we show, using a neural decoding approach, that firing sequences corresponding to long runs through a large environment are replayed with high fidelity and that such replay can begin at remote locations on the track. Extended replay proceeds at a characteristic virtual speed of approximately 8 m/s and remains coherent across trains of ripple events. These results suggest that extended replay is composed of chains of shorter subsequences, which may reflect a strategy for the storage and flexible expression of memories of prolonged experience.

    View details for DOI 10.1016/j.neuron.2009.07.027

    View details for Web of Science ID 000269570400009

    View details for PubMedID 19709631

  • Highly efficient small interfering RNA delivery to primary mammalian neurons induces MicroRNA-like effects before mRNA degradation JOURNAL OF NEUROSCIENCE Davidson, T. J., Harel, S., Arboleda, V. A., Prunell, G. F., Shelanski, M. L., Greene, L. A., Troy, C. M. 2004; 24 (45): 10040-10046


    The study of protein function in neurons has been hindered by the lack of highly efficient, nontoxic methods of inducing RNA interference in such cells. Here we show that application of synthetic small interfering RNA (siRNA) linked to the vector peptide Penetratin1 results in rapid, highly efficient uptake of siRNA by entire populations of cultured primary mammalian hippocampal and sympathetic neurons. This treatment leads to specific knock-down of targeted proteins within hours without the toxicity associated with transfection. In contrast to current methods, our technique permits study of protein function across entire populations with minimal disturbance of complex cellular networks. Using this technique, we found that protein knock-down (evident after 6 hr) precedes any decrease in targeted message (evident after 24 hr), suggesting an early, translational repression by perfectly targeted siRNAs.

    View details for DOI 10.1523/JNEUROSCI.3643-04.2004

    View details for Web of Science ID 000225022600002

    View details for PubMedID 15537872

  • Efficient Universal Computing Architectures for Decoding Neural Activity PLOS ONE Rapoport, B. I., Turicchia, L., Wattanapanitch, W., Davidson, T. J., Sarpeshkar, R. 2012; 7 (9)


    The ability to decode neural activity into meaningful control signals for prosthetic devices is critical to the development of clinically useful brain- machine interfaces (BMIs). Such systems require input from tens to hundreds of brain-implanted recording electrodes in order to deliver robust and accurate performance; in serving that primary function they should also minimize power dissipation in order to avoid damaging neural tissue; and they should transmit data wirelessly in order to minimize the risk of infection associated with chronic, transcutaneous implants. Electronic architectures for brain- machine interfaces must therefore minimize size and power consumption, while maximizing the ability to compress data to be transmitted over limited-bandwidth wireless channels. Here we present a system of extremely low computational complexity, designed for real-time decoding of neural signals, and suited for highly scalable implantable systems. Our programmable architecture is an explicit implementation of a universal computing machine emulating the dynamics of a network of integrate-and-fire neurons; it requires no arithmetic operations except for counting, and decodes neural signals using only computationally inexpensive logic operations. The simplicity of this architecture does not compromise its ability to compress raw neural data by factors greater than [Formula: see text]. We describe a set of decoding algorithms based on this computational architecture, one designed to operate within an implanted system, minimizing its power consumption and data transmission bandwidth; and a complementary set of algorithms for learning, programming the decoder, and postprocessing the decoded output, designed to operate in an external, nonimplanted unit. The implementation of the implantable portion is estimated to require fewer than 5000 operations per second. A proof-of-concept, 32-channel field-programmable gate array (FPGA) implementation of this portion is consequently energy efficient. We validate the performance of our overall system by decoding electrophysiologic data from a behaving rodent.

    View details for DOI 10.1371/journal.pone.0042492

    View details for Web of Science ID 000308738500006

    View details for PubMedID 22984404

  • Micro-drive array for chronic in vivo recording: drive fabrication. Journal of visualized experiments : JoVE Kloosterman, F., Davidson, T. J., Gomperts, S. N., Layton, S. P., Hale, G., Nguyen, D. P., Wilson, M. A. 2009


    Chronic recording of large populations of neurons is a valuable technique for studying the function of neuronal circuits in awake behaving rats. Lightweight recording devices carrying a high density array of tetrodes allow for the simultaneous monitoring of the activity of tens to hundreds of individual neurons. Here we describe a protocol for the fabrication of a micro-drive array with twenty one independently movable micro-drives. This device has been used successfully to record from hippocampal and cortical neurons in our lab. We show how to prepare a custom designed, 3-D printed plastic base that will hold the micro-drives. We demonstrate how to construct the individual micro-drives and how to assemble the complete micro-drive array. Further preparation of the drive array for surgical implantation, such as the fabrication of tetrodes, loading of tetrodes into the drive array and gold-plating, is covered in a subsequent video article.

    View details for DOI 10.3791/1094

    View details for PubMedID 19381129

  • Micro-drive array for chronic in vivo recording: tetrode assembly. Journal of visualized experiments : JoVE Nguyen, D. P., Layton, S. P., Hale, G., Gomperts, S. N., Davidson, T. J., Kloosterman, F., Wilson, M. A. 2009


    The tetrode, a bundle of four electrodes, has proven to be a valuable tool for the simultaneous recording of multiple neurons in-vivo. The differential amplitude of action potential signatures over the channels of a tetrode allows for the isolation of single-unit activity from multi-unit signals. The ability to precisely control the stereotaxic location and depth of the tetrode is critical for studying coordinated neural activity across brain regions. In combination with a micro-drive array, it is possible to achieve precise placement and stable control of many tetrodes over the course of days to weeks. In this protocol, we demonstrate how to fabricate and condition tetrodes using basic tools and materials, install the tetrodes into a multi-drive tetrode array for chronic in-vivo recording in the rat, make ground wire connections to the micro-drive array, and attach a protective cone onto the micro-drive array in order to protect the tetrodes from physical contact with the environment.

    View details for DOI 10.3791/1098

    View details for PubMedID 19387422

Stanford Medicine Resources: