Thesis: Ph. D., Massachusetts Institute of Technology, Department of Brain and Cognitive Sciences, 2016.Cataloged from PDF version of thesis.Includes bibliographical references.Incoming sensory information from all modalities, with the exception of olfaction, synapses in the thalamus on the way to neocortex. This sensory relay is uniquely positioned to act as a gate, to determine which inputs from the periphery are processed by the neocortex. A key 'guardian' of the gate may be the thalamic reticular nucleus (TRN). The TRN is a primary source of GABAergic input to thalamic relay nuclei. The TRN projects directly to the rest of thalamus, generating feedforward and feedback inhibition. It is therefore positioned to mediate forebrain function, and specifically the computations of the neocortex-thalamic loop. Accordingly, failures of the normal dynamics of the TRN are prominent in disease Thalamocortical and corticothalamic projections synapse within this nucleus, and it is subject to a variety of neuromodulatory influences. Depolarization of TRN neurons, and their subsequent firing, is driven by a variety of sources on a range of time scales. The TRN receives excitatory inputs ranging from single spikes to sustained tonic firing to bursting in thalamic relay neurons or layer 6 of neocortex. The temporal dynamics of these inputs, and their spatial organization, can drive different types of firing behavior in TRN. Layer 6 cells form strong synapses in the TRN and even sparse activity in this layer would be predicted to drive substantial inhibition in vivo. Primary thalamocortical relay projections branch into the TRN on their way to sensory cortices, and the nature of this excitatory input reflects the functional modes of the relay nuclei. Inputs include tonic firing that reflects high fidelity to peripheral input, as well as extended bouts of bursting, similar to that seen in TRN itself. In sum, a variety of inputs can excite TRN neurons on different time scales. Understanding how these different patterns may regulate excitability in general, and burst activity specifically, is key to understanding thalamocortical function. The Moore laboratory previously showed that TRN activation could modulate firing and bursting in relay neurons, and induce spindles in the neocortex. In these experiments, the activity of TRN cells during stimulation could only be inferred from downstream effects on spiking and spindle rhythms. Characterizing responses within TRN using a similar stimulation protocol provided a more complete view of the circuit activity underlying this evoked behavior. In Chapter 2 I provided optogenetic input while characterizing multi-unit responses in the TRN and well-sorted single units. I found that longer duration activation drove enhanced bursting and decreased latency to bursting. I also discovered two new -types of cell responses, a more sensitive 'non-linear' cell type that was prone to sustained responses and to bursting, and a more 'linearly' responsive cell class that fired in direct proportion to the duration of stimulation. These findings provide direct predictions as to the behavior of TRN neurons in response to a range of natural depolarizing inputs, and a guide for the optical control of this key structure in studies of network function and behavior. As indicated by the availability of neuromodulatory inputs to TRN, and its apparent role in basic state changes such as sleep and wakefulness, long-term shifts in its depolarization are also likely essential to normal brain function. Optogenetics has rapidly become a standard technique in systems neuroscience, and its genetic specificity and rapid development of new compounds has revolutionized our ability to causally manipulate neural circuits. While the use of light to drive cellular reactions brings a number of advantages when compared to electrical stimulation, there are still many limitations, especially in vivo. Light delivery through tissue is problematic in the intact brain, so targeting deep structures relies on implanted fiber optics and/or LEDs. These methods are not ideal for illuminating large or irregularly-shaped regions without using high light intensity or large arrays of invasive devices. I have been key in inventing a new approach using bioluminescent light to drive optogenetic responses ('BL-OG'). This approach leverages the variety of light sensitive molecules and bioluminescent emitters while providing a means of chemical control. BL-OG combines the cell-type specificity of conventional optogenetics with the potential for noninvasive, system-wide activation. In Chapter 3, I review both this new method and some of my contributions to its realization, specifically demonstrating its functionality in the TRN in vitro and in vivo.by Bryan T. Higashikubo.Ph. D.