All Publications

  • Three-dimensional intact-tissue sequencing of single-cell transcriptional states SCIENCE Wang, X., Allen, W. E., Wright, M. A., Sylwestrak, E. L., Samusik, N., Vesuna, S., Evans, K., Liu, C., Ramakrishnan, C., Liu, J., Nolan, G. P., Bava, F., Deisseroth, K. 2018; 361 (6400): 380-+
  • Ancestral Circuits for the Coordinated Modulation of Brain State. Cell Lovett-Barron, M., Andalman, A. S., Allen, W. E., Vesuna, S., Kauvar, I., Burns, V. M., Deisseroth, K. 2017; 171 (6): 1411–23.e17


    Internal states of the brain profoundly influence behavior. Fluctuating states such as alertness can be governed by neuromodulation, but the underlying mechanisms and cell types involved are not fully understood. We developed a method to globally screen for cell types involved in behavior by integrating brain-wide activity imaging with high-content molecular phenotyping and volume registration at cellular resolution. We used this method (MultiMAP) to record from 22 neuromodulatory cell types in behaving zebrafish during a reaction-time task that reports alertness. We identified multiple monoaminergic, cholinergic, and peptidergic cell types linked to alertness and found that activity in these cell types was mutually correlated during heightened alertness. We next recorded from and controlled homologous neuromodulatory cells in mice; alertness-related cell-type dynamics exhibited striking evolutionary conservation and modulated behavior similarly. These experiments establish a method for unbiased discovery of cellular elements underlying behavior and reveal an evolutionarily conserved set of diverse neuromodulatory systems that collectively govern internal state.

    View details for PubMedID 29103613

  • In Vivo Interrogation of Spinal Mechanosensory Circuits. Cell reports Christensen, A. J., Iyer, S. M., François, A., Vyas, S., Ramakrishnan, C., Vesuna, S., Deisseroth, K., Scherrer, G., Delp, S. L. 2016; 17 (6): 1699-1710


    Spinal dorsal horn circuits receive, process, and transmit somatosensory information. To understand how specific components of these circuits contribute to behavior, it is critical to be able to directly modulate their activity in unanesthetized in vivo conditions. Here, we develop experimental tools that enable optogenetic control of spinal circuitry in freely moving mice using commonly available materials. We use these tools to examine mechanosensory processing in the spinal cord and observe that optogenetic activation of somatostatin-positive interneurons facilitates both mechanosensory and itch-related behavior, while reversible chemogenetic inhibition of these neurons suppresses mechanosensation. These results extend recent findings regarding the processing of mechanosensory information in the spinal cord and indicate the potential for activity-induced release of the somatostatin neuropeptide to affect processing of itch. The spinal implant approach we describe here is likely to enable a wide range of studies to elucidate spinal circuits underlying pain, touch, itch, and movement.

    View details for DOI 10.1016/j.celrep.2016.10.010

    View details for PubMedID 27806306

  • Optogenetic and chemogenetic strategies for sustained inhibition of pain. Scientific reports Iyer, S. M., Vesuna, S., Ramakrishnan, C., Huynh, K., Young, S., Berndt, A., Lee, S. Y., Gorini, C. J., Deisseroth, K., Delp, S. L. 2016; 6: 30570-?


    Spatially targeted, genetically-specific strategies for sustained inhibition of nociceptors may help transform pain science and clinical management. Previous optogenetic strategies to inhibit pain have required constant illumination, and chemogenetic approaches in the periphery have not been shown to inhibit pain. Here, we show that the step-function inhibitory channelrhodopsin, SwiChR, can be used to persistently inhibit pain for long periods of time through infrequent transdermally delivered light pulses, reducing required light exposure by >98% and resolving a long-standing limitation in optogenetic inhibition. We demonstrate that the viral expression of the hM4D receptor in small-diameter primary afferent nociceptor enables chemogenetic inhibition of mechanical and thermal nociception thresholds. Finally, we develop optoPAIN, an optogenetic platform to non-invasively assess changes in pain sensitivity, and use this technique to examine pharmacological and chemogenetic inhibition of pain.

    View details for DOI 10.1038/srep30570

    View details for PubMedID 27484850

    View details for PubMedCentralID PMC4971509

  • The use of optical clearing and multiphoton microscopy for investigation of three-dimensional tissue-engineered constructs. Tissue engineering. Part C, Methods Calle, E. A., Vesuna, S., Dimitrievska, S., Zhou, K., Huang, A., Zhao, L., Niklason, L. E., Levene, M. J. 2014; 20 (7): 570–77


    Recent advances in three-dimensional (3D) tissue engineering have concomitantly generated a need for new methods to visualize and assess the tissue. In particular, methods for imaging intact volumes of whole tissue, rather than a single plane, are required. Herein, we describe the use of multiphoton microscopy, combined with optical clearing, to noninvasively probe decellularized lung extracellular matrix scaffolds and decellularized, tissue-engineered blood vessels. We also evaluate recellularized lung tissue scaffolds. In addition to nondestructive imaging of tissue volumes greater than 4 mm(3), the lung tissue can be visualized using three distinct signals, combined or singly, that allow for simple separation of cells and different components of the extracellular matrix. Because the 3D volumes are not reconstructions, they do not require registration algorithms to generate digital volumes, and maintenance of isotropic resolution is not required when acquiring stacks of images. Once a virtual volume of tissue is generated, structures that have innate 3D features, such as the lumens of vessels and airways, are easily animated and explored in all dimensions. In blood vessels, individual collagen fibers can be visualized at the micron scale and their alignment assessed at various depths through the tissue, potentially providing some nondestructive measure of vessel integrity and mechanics. Finally, both the lungs and vessels assayed here were optically cleared, imaged, and visualized in a matter of hours, such that the added benefits of these techniques can be achieved with little more hassle or processing time than that associated with traditional histological methods.

    View details for DOI 10.1089/ten.TEC.2013.0538

    View details for PubMedID 24251630

    View details for PubMedCentralID PMC4074743

  • Multiphoton fluorescence, second harmonic generation, and fluorescence lifetime imaging of whole cleared mouse organs JOURNAL OF BIOMEDICAL OPTICS Vesuna, S., Torres, R., Levene, M. J. 2011; 16 (10)


    Multiphoton microscopy of cleared tissue has previously been demonstrated to generate large three-dimensional (3D) volumetric image data on entire intact mouse organs using intrinsic tissue fluorescence. This technique holds great promise for performing 3D virtual biopsies, providing unique information on tissue morphology, and guidance for subsequent traditional slicing and staining. Here, we demonstrate the use of fluorescence lifetime imaging in cleared organs for achieving molecular contrast that can reveal morphologically distinct structures, even in the absence of knowledge of the underlying molecular source. In addition, we demonstrate the power of multimodal imaging, combining multiphoton fluorescence, second harmonic generation, and lifetime imaging to reveal exceptional morphological detail in an optically cleared mouse knee.

    View details for DOI 10.1117/1.3641992

    View details for Web of Science ID 000297465200016

    View details for PubMedID 22029356