Optogenetics publications

In mammals, slow-wave sleep is characterized by synchronized neuronal activity that alternates between on and off periods. Slow-wave activity (SWA) and synchrony reflect sleep need, are correlated with synaptic strength in cortical circuits and promote synaptic downselection and memory consolidation. Here we assessed whether these core benefits of sleep can be obtained during waking. We locally induced alternating on/off periods during wakefulness using optogenetics in mice. This led to a local ipsilateral reduction in SWA and synchrony during subsequent sleep, and to reduced markers of synaptic strength. Moreover, bilateral induction of off periods over sensorimotor cortex during sleep deprivation restored memory consolidation. Thus, inducing on/off activity during wakefulness is sufficient to reduce local sleep need and fulfill core functions of sleep.

Preparing and initiating movements at the right time is critical for goal-directed behavior. Before movement execution, motor cortical areas exhibit preparatory activity, which decreases from premotor to primary motor areas. During the shift from preparation to execution activity in neural state space transitions from movement-null to movement-potent dimensions. However, the circuit-level mechanisms underlying this shift remain unresolved. Here, we demonstrate that projections from the rat premotor cortex (rostral forelimb area [RFA]) to the primary motor cortex (caudal forelimb area [CFA]) encode primarily pre-movement activity. Optogenetic inhibition of these projections has behavioral effects comparable to inhibiting either RFA or CFA alone. During preparation, RFA projections enhance and suppress CFA neurons similarly, affecting activity along CFA's preparatory dimension. During movement, RFA's influence shifts predominantly to excitatory, aligning with CFA's movement-potent dimension. These results establish a mechanistic link between neural state space concepts and underlying circuit mechanisms, providing an intuitive model for movement control.

Across sensory modalities, peripheral deafferentation can induce maladaptive central plasticity that amplifies sensory responses while distorting affective processing, rendering innocuous stimuli unpleasant, intrusive, or even painful. Here, we examined the affective dimension of compensatory plasticity in a mouse model of hyperacusis by introducing noise-induced focal cochlear lesions and tracking maladaptive plasticity in the lateral amygdala (LA), a key limbic hub for sensory-affective valuation. Whereas control mice habituated to neutral sounds, mice with noise-induced hearing loss (NIHL) showed sustained LA hyperresponsivity and abnormally strong temporal coupling between calcium transients and pupil dilations, an autonomic index of arousal. NIHL also disrupted discriminative auditory threat learning, producing poorly selective, non-extinguishing enhancement of LA responses and freezing to both threatening and non-threatening sounds. We posited that potentiating inhibition in the higher-order auditory cortex (HO-AC), a prominent source of auditory sensory input to the LA, could reinstate normal affective sound processing after NIHL. Brief bouts of 40-Hz optogenetic activation of HO-AC parvalbumin-expressing inhibitory neurons (PVNs) durably reversed LA sensitization, normalized pupil-indexed arousal dynamics, and reinstated discriminative auditory threat memory. These findings identify cortical inhibitory potentiation as a strategy for reversing neural, autonomic, and behavioral signatures of distorted affective sound processing after peripheral sensory injury.

Parvalbumin-expressing inhibitory neurons (PVNs) stabilize cortical network activity, generate gamma rhythms, and regulate experience-dependent plasticity. We found that PVNs act like a volume knob in the mouse auditory cortex (ACtx), bi-directionally adjusting neural and perceptual sensitivity to sound level over a 20 dB range. PVN-based gain adjustments were "sticky," such that a single bout of PVN activation at 40 Hz-but not at 1 or 70 Hz-sustainably dampened ACtx sound responsiveness, enhanced feedforward inhibition, and behaviorally desensitized mice to loudness. We then developed a mouse model of adult-onset hyperacusis by demonstrating ACtx hyperactivity, PVN hypofunction, and loudness hypersensitivity following a restricted noise-induced cochlear lesion. We found that several minutes of 40-Hz PVN stimulation in noise-exposed mice sustainably dampened ACtx hyperactivity and restored normal loudness sensitivity for 1 week. These findings demonstrate that sensory disorders caused by permanent peripheral injuries can be reversed by patterned stimulation of cortical circuits that directly regulate perception.

Basal forebrain cholinergic neurons (BFCNs) densely innervate auditory cortex (ACtx), conveying signals linked to internal brain states and external sensory cues. Acetylcholine (ACh) is known to rapidly modulate cortical circuits through nicotinic ACh receptor (nAChR)-mediated activation of layer 1 inhibitory neurons (L1-INs). However, BFCN terminals are also abundant in deeper layers, where their functional impact has received less attention. Using multi-plex in situ labeling across cortical layers and cell types, we found that layer 6 pyramidal neurons (L6-PNs) are highly enriched in diverse transcripts for nAChR subunits and muscarinic ACh receptors (mAChRs). In vivo optogenetic activation of BFCN axons revealed persistent modulation of regular spiking units in L2-6 but a rapid phasic activation only in L6. In acute slices, optogenetic activation of BFCN axons elicited fast nAChR-mediated excitatory post-synaptic potentials in L6-PNs, comparable to responses in L1-INs, and slower mAChR-mediated inhibitory responses. These findings identify L1-INs and excitatory L6-PNs as two major hubs for BFCN modulation of cortical circuits. By recruiting distinct receptor mechanisms and circuit motifs in L1 and L6, BFCNs may engage parallel pathways of cholinergic control that couple fast, transient modulation with slower, sustained regulation to shape cortical perception and plasticity.

The hypothalamus is critical for regulating behaviors essential for survival and locomotion, but how it integrates internal needs and transmits locomotion commands to the spinal cord (SC) remains unclear. We found that glutamatergic neurons in lateral hypothalamic area (LHA) are essential for regulating motivated locomotor activity. Using single-neuron projectome analysis, trans-synaptic tracing, and optogenetic manipulation, we showed that LHA facilitates motivated locomotion during food seeking via pontine reticular nucleus, oral part (PnO) projection neurons, rather than direct SC projections or indirect stress signaling via medial septum and diagonal band. Activating PnO-SC projection neurons also initiated locomotion. Importantly, LHA-PnO projection neurons were crucial for regulating locomotor recovery following mouse spinal cord injury (SCI). Motor cortex signals gated LHA deep brain stimulation treatment markedly promoted long-term restoration of hindlimb motor functions after severe SCI. Thus, we have identified a hypothalamic-pontine-spinal pathway and the stimulation paradigm for potential therapeutic intervention after SCI.

Memory consolidation enables animals to draw on past experiences to guide future behavior. This process involves system- and synaptic-level changes and predominantly occurs during sleep. While hippocampal-cortical circuits are well studied in this context, the contributions of other systems, including dopaminergic circuits—key players in learning-related processes—remain poorly understood. Ventral tegmental area dopaminergic (VTA DA ) neurons are active during sleep and suggested to participate in memory consolidation processes; however, causal evidence for this is lacking. Using calcium-dependent fiber photometry, electrophysiology, and chemogenetic and optogenetic manipulations across learning paradigms, we explore the functions of VTA DA neuronal activity during sleep. We show that VTA DA activity during nonrapid eye movement sleep is experience dependent, is enhanced by motor skill and associative learning, facilitates motor skill memory consolidation, and exhibits a motor learning–dependent increase in temporal coordination with cortical spindle oscillations. Our findings uncover a previously unidentified function for VTA DA neurons in consolidating memories during sleep, advancing understanding of this central neuromodulator’s functions in regulating fundamental biological processes.

Cerebral cortex and cerebellum are essential for sensorimotor control, but the dynamics of their interactions remain unclear. Here, we investigated which pathways prevail during preparation and execution of spontaneous whisker movements in mice. During preparation, neuronal activity of primary motor (M1) and somatosensory (S1) cortex precede that of cerebellar crus regions, with a lead that is consistent with relaying a copy of motor commands. After movement onset, the phase of the signal inverts, indicating a dominant vector signaling from cerebellum to cerebrum. At this stage, Purkinje cell activity correlates more with S1 than M1, generating a prediction of sensory consequences during motor actions. A computational cerebello-cortical model could replicate the changes in dynamics and directionality. Optogenetic manipulations of pons and thalamus confirm the modeled predictions on stage-dependent dynamics. Together our data point towards a swap in direction of information flow between cerebrum and cerebellum when motor preparation switches to execution.

The locus coeruleus–norepinephrine (LC-NE) system regulates arousal and awakening; however, it remains unclear whether the LC does this in a global or circuit-specific manner. We hypothesized that sensory-evoked awakenings are predominantly regulated by specific LC-NE efferent pathways. Anatomical, physiological, and functional modularities of LC-NE pathways involving the mouse basal forebrain (BF) and pontine reticular nucleus (PRN) were tested. We found partial anatomical segregation between the LC → PRN and LC → BF circuits. Extracellular NE dynamics in BF and PRN exhibited distinct sound-evoked activation during sleep, including a fast sound-evoked NE peak specific to PRN. Causal optogenetic interrogation of LC efferent pathways, by retro-channelrhodopsin (ChR2) activation or Platynereis dumerilii ciliary opsin (PdCO) silencing of synapses in target regions, revealed a role for early LC → PRN activity in driving arousal and sound-evoked awakenings. Together, our results uncover a role for early LC-NE PRN activity in connecting sensory and arousal pathways and establish LC heterogeneity in regulating arousal.

The central nervous system controls movement by combining neuromotor modules, known as muscle synergies. Previous studies suggest that spinal premotor interneurons (PreM‐INs) contribute to the encoding of stable muscle synergies for voluntary movement. But descending and sensory inputs also influence motor outputs through the spinal interneuronal network, which may be configured by its inputs to encode different sets of muscle synergies depending on the network state, thereby recruiting different selections of synergies. Here we tested this possibility of state‐dependent synergy encoding by examining the muscle synergies represented by the same upstream spinal interneurons under different activity states induced by various optogenetic stimulation patterns. Lumbosacral spinal units and electromyographic (EMG) activities of hindlimb muscles were simultaneously recorded from anaesthetized Thy1‐ChR2 mice as the spinal cord was stimulated by one or two optic fibres at different intensities. The synergy encoded by each unit was revealed as a ‘muscle field’ derived from spike‐triggered averages of EMG, whereas the entire muscle synergy set was factorized from the EMG. We found that although the muscle synergy set remained stable across stimulation conditions, the muscle fields of the same units were matched to different synergies within the set in different states. Thus the interneurons may flexibly adjust their connectivity with the motoneurons of the muscles as descending and sensory afferents impose different states on the spinal network. State‐dependent encoding of muscle synergies may allow different synergies to be selected for producing stable movement in an ever‐changing workspace environment. image Key points Muscle synergies for locomotion can be represented by spinal interneurons, as revealed by the interneurons’ muscle fields derived from spike‐triggered averages of EMG. The muscle field of a single spinal interneuron may vary under different stimulation conditions, as demonstrated by optogenetic stimulation. Encoding of muscle synergies is dependent on the state of spinal activities, thus facilitating the selection of appropriate synergies in different dynamic environments.

The mediodorsal thalamic nucleus (MD) forms neural circuits with various brain regions, including the prefrontal cortex (PFC), the reticular thalamic nucleus (TRN), and the midbrain reticular nucleus (MRN). However, the specific roles and underlying mechanisms in auditory information processing remain unclear. Here, we perform multi-channel electrophysiological recordings in awake mice to investigate the response patterns of the MD to auditory stimuli, as well as the regulatory effects of PFC, MRN, and TRN inputs. We identify two distinct types of sound-evoked responses. The Phasic-response features a transient burst firing to the stimulus with short latency, rapidly adapting to baseline and corresponding to the onset fluctuation of the local field potential. The Sustained-response is marked by prolonged firing with longer latency and is accompanied by persistent enhancement of oscillatory power following stimulus offset. The response patterns of MD neurons remain consistent across different types of auditory stimuli. Optogenetic inactivation of the MRN suppresses both response types in the MD. The Sustained-response is attenuated by PFC inactivation but enhanced by TRN inactivation, while the Phasic-response remains unaffected by inactivation of either the PFC or TRN. Our findings expand the understanding of the MD's role in sound information integration and auditory cognitive regulation.

Extracellular recordings in freely moving mice, especially those with movable electrodes (microdrives), are crucial for understanding brain function. However, existing microdrives are often heavy, expensive, fragile, and unsuited for long-term studies with multichannel recordings. The OptoDrive is a new, lightweight (3.2 g), low-cost system for chronic neural recordings and optogenetic manipulation in mice. It features a detachable, 16-channel tungsten-wire electrode assembly with a 3 mm stroke (15 μm step displacement) and an integrated optical fiber. This system enables repeated implantation and explantation without surgery, requiring only gas anesthesia. The OptoDrive has demonstrated stable recordings from the lateral hypothalamus of freely behaving mice for nearly 1 month and successful optogenetic silencing of neuronal activity. In conclusion, OptoDrive offers a cost-effective, compact solution for long-term electrophysiology and optogenetics in freely moving mice.

Closed-loop neural control is a powerful tool for both the scientific exploration of neural function and for mitigating deficiencies found in open-loop deep brain stimulation (DBS). Here, we present a protocol for artificial intelligence-guided neural control in rats using deep reinforcement learning (RL) and infrared neural stimulation (INS). We describe steps for integrating RL closed-loop control into neuroscience and neuromodulation studies. We then detail procedures for using and deploying infrared INS in chronic DBS applications. For complete details on the use and execution of this protocol, please refer to Coventry et al.1 and Coventry and Bartlett.2.

The cerebellum is critical for coordinating movements related to eating, drinking and swallowing, all of which require proper control of the tongue. Cerebellar Purkinje cells can encode tongue movements, but it is unclear how their simple spikes and complex spikes induce changes in the shape of the tongue that contribute to goal‐directed movements. To study these relations, we recorded and stimulated Purkinje cells in the vermis and hemispheres of mice during spontaneous licking from a stationary or moving water spout. We found that Purkinje cells can encode rhythmic licking with both their simple spikes and complex spikes. Increased simple spike firing during tongue protrusion induces ipsiversive bending of the tongue. Unexpected changes in the target location trigger complex spikes that alter simple spike firing during subsequent licks, adjusting the tongue trajectory. Furthermore, we observed increased complex spike firing during behavioural state changes at both the start and the end of licking bouts. Using machine learning, we confirmed that alterations in Purkinje cell activity accompany licking, with different Purkinje cells often exerting heterogeneous encoding schemes. Our data highlight that directional movement control is paramount in cerebellar function and that modulation of the complex spikes and that of the simple spikes are complementary during acquisition and execution of sensorimotor coordination. These results bring us closer to understanding the clinical implications of cerebellar disorders during eating, drinking and swallowing. image Key points When drinking, mice make rhythmic tongue movements directed towards the water source. Cerebellar Purkinje cells can fire rhythmically in tune with the tongue movements. Purkinje cells encode changes in the position of the water source with complex spikes. Purkinje cell simple spike firing affects the direction of tongue movements. Purkinje cells that report changes in the position of the target can also adjust movements in the right direction.

Brain stimulation holds promise for treating brain disorders, but personalizing therapy remains challenging. Effective treatment requires establishing a functional link between stimulation parameters and brain response, yet traditional methods like random sampling (RS) are inefficient and costly. To overcome this, we developed an active learning (AL) framework that identifies optimal relationships between stimulation parameters and brain response with fewer experiments. We validated this framework through three experiments: (1) in silico modeling with synthetic data from a Parkinson’s disease model, (2) in silico modeling with real data from a non-human primate, and (3) in vivo modeling with a real-time rat optogenetic stimulation experiment. In each experiment, we compared AL models to RS models, using various query strategies and stimulation parameters (amplitude, frequency, pulse width). AL models consistently outperformed RS models, achieving lower error on unseen test data in silico ( p <0.0056, N =1,000) and in vivo ( p =0.0036, N =20). This approach represents a significant advancement in brain stimulation, potentially improving both research and clinical applications by making them more efficient and effective. Our findings suggest that AL can substantially reduce the cost and time required for developing personalized brain stimulation therapies, paving the way for more effective and accessible treatments for brain disorders.

A major challenge in neuroscience is to understand how neural representations of sensory information are transformed by the network of ascending and descending connections in each sensory system. By recording from neurons at several levels of the auditory pathway, we show that much of the nonlinear encoding of complex sounds in auditory cortex can be explained by transformations in the midbrain and thalamus. Modeling cortical neurons in terms of their inputs across these subcortical populations enables their responses to be predicted with unprecedented accuracy. By contrast, subcortical responses cannot be predicted from descending cortical inputs, indicating that ascending transformations are irreversible, resulting in increasingly lossy, higher-order representations across the auditory pathway. Rather, auditory cortex selectively modulates the nonlinear aspects of thalamic auditory responses and the functional coupling between subcortical neurons without affecting the linear encoding of sound. These findings reveal the fundamental role of subcortical transformations in shaping cortical responses.

Homeostatic plasticity represents a set of mechanisms that are thought to recover some aspect of neural function. One such mechanism called AMPAergic scaling was thought to be a likely candidate to homeostatically control spiking activity. However, recent findings have forced us to reconsider this idea as several studies suggest AMPAergic scaling is not directly triggered by changes in spiking. Moreover, studies examining homeostatic perturbations in vivo have suggested that GABAergic synapses may be more critical in terms of spiking homeostasis. Here, we show results that GABAergic scaling can act to homeostatically control spiking levels. We found that perturbations which increased or decreased spiking in cortical cultures triggered multiplicative GABAergic upscaling and downscaling, respectively. In contrast, we found that changes in AMPA receptor (AMPAR) or GABAR transmission only influence GABAergic scaling through their indirect effect on spiking. We propose that GABAergic scaling represents a stronger candidate for spike rate homeostat than AMPAergic scaling.

Numerous studies have shown that neuronal representations in sensory pathways are far from static but are instead strongly shaped by the complex properties of the sensory inputs they receive. Adaptation dynamically shapes the neural signaling that underlies our perception of the world yet remains poorly understood. We investigated rapid adaptation across timescales from hundreds of milliseconds to seconds through simultaneous multi-electrode recordings from the ventro-posteromedial nucleus of the thalamus (VPm) and layer 4 of the primary somatosensory cortex (S1) in male and female anesthetized mice in response to controlled, persistent whisker stimulation. Observations in VPm and S1 reveal a degree of adaptation that progresses through the pathway. Signatures of two distinct timescales of rapid adaptation in the firing rates of both thalamic and cortical neuronal populations were revealed, also reflected in the synchrony of the thalamic population and in the thalamocortical synaptic efficacy that was measured in putatively monosynaptically connected thalamocortical pairs. Controlled optogenetic activation of VPm further demonstrated that the longer timescale adaptation observed in S1 is likely inherited from slow decreases in thalamic firing rate and synchrony. Despite the degraded sensory responses, adaptation resulted in a shift in coding strategy that favors theoretical discrimination over detection across the observed timescales of adaptation. Overall, although multiple mechanisms contribute to rapid adaptation at distinct timescales, they support a unifying framework on the role of adaptation in sensory processing.

The cerebral cortex is widely considered part of the neural substrate of consciousness, but direct causal evidence is missing. Here, we tested in mice whether optogenetic activation of cortical neurons in posterior parietal cortex (PtA) or medial prefrontal cortex (mPFC) is sufficient for arousal from three behavioral states characterized by progressively deeper unresponsiveness: sleep, a coma-like state induced by muscimol injection in the midbrain, and deep sevoflurane-dexmedetomidine anesthesia. We find that cortical stimulation always awakens the mice from both NREM sleep and REM sleep, with PtA requiring weaker/shorter light pulses than mPFC. Moreover, in most cases light pulses produce both cortical activation (decrease in low frequencies) and behavioral arousal (recovery of the righting reflex) from brainstem coma, as well as cortical activation from anesthesia. These findings provide evidence that direct activation of cortical neurons is sufficient for behavioral and/or cortical arousal from sleep, brainstem coma, and anesthesia.

Objective . Therapeutic brain stimulation is conventionally delivered using constant-frequency stimulation pulses. Several recent clinical studies have explored how unconventional and irregular temporal stimulation patterns could enable better therapy. However, it is challenging to understand which irregular patterns are most effective for different therapeutic applications given the massively high-dimensional parameter space. Approach . Here we applied many irregular stimulation patterns in a single neural circuit to demonstrate how they can enable new dimensions of neural control compared to conventional stimulation, to guide future exploration of novel stimulation patterns in translational settings. We optogenetically excited the septohippocampal circuit with constant-frequency, nested pulse, sinusoidal, and randomized stimulation waveforms, systematically varying their amplitude and frequency parameters. Main results. We first found equal entrainment of hippocampal oscillations: all waveforms provided similar gamma-power increase, whereas no parameters increased theta-band power above baseline (despite the mechanistic role of the medial septum in driving hippocampal theta oscillations). We then compared each of the effects of each waveform on high-dimensional multi-band activity states using dimensionality reduction methods. Strikingly, we found that conventional stimulation drove predominantly ‘artificial’ (different from behavioral activity) effects, whereas all irregular waveforms induced activity patterns that more closely resembled behavioral activity. Significance . Our findings suggest that irregular stimulation patterns are not useful when the desired mechanism is to suppress or enhance a single frequency band. However, novel stimulation patterns may provide the greatest benefit for neural control applications where entraining a particular mixture of bands (e.g. if they are associated with different symptoms) or behaviorally-relevant activity is desired.