Zachary F. Mainen

Serotonergic neurons in the dorsal raphe nucleus (DRN) project extensively throughout the forebrain, yet their influence on global network states remains controversial. Serotonin is implicated in regulating slow-oscillations, so-called UP and DOWN states, which occur during sleep and light anesthesia. While optogenetic fMRI suggests that serotonin (5-HT) suppresses brain-wide activity, classical electrical stimulation studies report the induction of cortical UP states. To resolve this discrepancy, we combined optogenetic 5-HT stimulation with large-scale Neuropixel recordings across the forebrain of lightly anesthetized mice. We demonstrate that selective 5-HT release consistently induces DOWN states across the cortex and striatum, while leaving midbrain dynamics largely unaffected. A multi-area computational model constrained by biologically plausible connectivity, indicates that in certain regions the transitions arises from network-level synchronization rather than direct DRN input.

Brain activity controls adaptive behavior but also drives unintentional incidental movements. Such movements could potentially be used to read out internal cognitive variables that are also neurally computed. Establishing this would require ruling out that incidental movements reflect cognition merely because they are coupled with task-related responses through the biomechanics of the body. Here we addressed this issue in a foraging task for mice, where multiple decision variables are simultaneously encoded even if, at any given time, only one of them is used. We found that characteristic features of the face simultaneously encode not only the currently used decision variables but also independent and unexpressed ones, and we show that these features partially originate from neural activity in the secondary motor cortex. Our results suggest that facial movements reflect ongoing computations above and beyond those related to task demands and demonstrate the ability of noninvasive monitoring to expose otherwise latent cognitive states.

The neural representations of prior information about the state of the world are poorly understood¹. Here, to investigate them, we examined brain-wide Neuropixels recordings and widefield calcium imaging collected by the International Brain Laboratory. Mice were trained to indicate the location of a visual grating stimulus, which appeared on the left or right with a prior probability alternating between 0.2 and 0.8 in blocks of variable length. We found that mice estimate this prior probability and thereby improve their decision accuracy. Furthermore, we report that this subjective prior is encoded in at least 20% to 30% of brain regions that, notably, span all levels of processing, from early sensory areas (the lateral geniculate nucleus and primary visual cortex) to motor regions (secondary and primary motor cortex and gigantocellular reticular nucleus) and high-level cortical regions (the dorsal anterior cingulate area and ventrolateral orbitofrontal cortex). This widespread representation of the prior is consistent with a neural model of Bayesian inference involving loops between areas, as opposed to a model in which the prior is incorporated only in decision-making areas. This study offers a brain-wide perspective on prior encoding at cellular resolution, underscoring the importance of using large-scale recordings on a single standardized task.

Serotonin (5-HT) is a central neuromodulator which is implicated in, amongst other functions, cognitive flexibility. 5-HT is released from the dorsal raphe nucleus (DRN) throughout nearly the entire forebrain. Little is known, however, about how serotonin affects downstream populations of neurons and how this modulation might support its cognitive functions. Here, we optogenetically stimulated serotonergic neurons in the DRN while recording large parts of the brain with Neuropixels during quiet wakefulness and performance of a perceptual decision-making task. During quiet wakefulness, 5-HT stimulation induced a rapid switch in internal state, as indicated by dilation of the pupil, suppression of hippocampal sharp wave ripples, and increased exploratory behaviors, such as whisking. To elucidate the brain-wide effect of serotonin release we performed acute Neuropixel recordings in seven target locations, a total of 7,478 neurons were recorded across 17 mice. We found that 5-HT stimulation significantly modulated neural activity in all the recorded brain regions, both during quiet wakefulness and task performance. During task performance, however, we observed no change in behavior when stimulating 5-HT. We found that the 5-HT modulation of high-dimensional neural dynamics is confined to a subspace which is orthogonal relative to the choice axis. These observations describe a possible mechanism for the induction of state-dependent stimulus representations, suggesting a neural basis for neuromodulatory effects on brain-wide circuits to flexible decision-making.

Electrophysiology has proven invaluable to record neural activity, and the development of Neuropixels probes dramatically increased the number of recorded neurons. These probes are often implanted acutely, but acute recordings cannot be performed in freely moving animals and the recorded neurons cannot be tracked across days. To study key behaviors such as navigation, learning, and memory formation, the probes must be implanted chronically. An ideal chronic implant should (1) allow stable recordings of neurons for weeks; (2) allow reuse of the probes after explantation; (3) be light enough for use in mice. Here, we present the ‘Apollo Implant’, an open-source and editable device that meets these criteria and accommodates up to two Neuropixels 1.0 or 2.0 probes. The implant comprises a ‘payload’ module which is attached to the probe and is recoverable, and a ‘docking’ module which is cemented to the skull. The design is adjustable, making it easy to change the distance between probes, the angle of insertion, and the depth of insertion. We tested the implant across eight labs in head-fixed mice, freely moving mice, and freely moving rats. The number of neurons recorded across days was stable, even after repeated implantations of the same probe. The Apollo implant provides an inexpensive, lightweight, and flexible solution for reusable chronic Neuropixels recordings.

Electrophysiology has proven invaluable to record neural activity, and the development of Neuropixels probes dramatically increased the number of recorded neurons. These probes are often implanted acutely, but acute recordings cannot be performed in freely moving animals and the recorded neurons cannot be tracked across days. To study key behaviors such as navigation, learning, and memory formation, the probes must be implanted chronically. An ideal chronic implant should (1) allow stable recordings of neurons for weeks; (2) allow reuse of the probes after explantation; (3) be light enough for use in mice. Here, we present the “Apollo Implant”, an open-source and editable device that meets these criteria and accommodates up to two Neuropixels 1.0 or 2.0 probes. The implant comprises a “payload” module which is attached to the probe and is recoverable, and a “docking” module which is cemented to the skull. The design is adjustable, making it easy to change the distance between probes, the angle of insertion, and the depth of insertion. We tested the implant across eight labs in head-fixed mice, freely moving mice, and freely moving rats. The number of neurons recorded across days was stable, even after repeated implantations of the same probe. The Apollo implant provides an inexpensive, lightweight, and flexible solution for reusable chronic Neuropixels recordings.

Brain activity controls adaptive behavior but also drives unintentional incidental movements. Such movements could thus potentially be used to read out internal cognitive variables also neurally computed. Establishing this, however, would require ruling out that incidental movements reflect cognition only because they are coupled with task-related responses through the biomechanics of the body. We addressed this issue in a foraging task for mice where multiple decision variables are simultaneously encoded even if, at any given time, only one of them is used. We found that characteristic features of the face simultaneously encode not only the currently used decision variables, but also independent and unexpressed ones, and we show that these features partially originate from neural activity in the secondary motor cortex. Our results suggest that the face reflects ongoing computations above and beyond those related to task demands, demonstrating the ability of noninvasive monitoring to expose otherwise latent cognitive states.

The ability to persist toward a desired objective is a fundamental aspect of behavioral control whose impairment is implicated in several behavioral disorders. One of the prominent features of behavioral persistence is that its maturation occurs relatively late in development. This is presumed to echo the developmental time course of a corresponding circuit within late-maturing parts of the brain, such as the prefrontal cortex, but the specific identity of the responsible circuits is unknown. Here, we used a genetic approach to describe the maturation of the projection from layer 5 neurons of the neocortex to the dorsal raphe nucleus in mice. Using optogenetic-assisted circuit mapping, we show that this projection undergoes a dramatic increase in synaptic potency between postnatal weeks 3 and 8, corresponding to the transition from juvenile to adult. We then show that this period corresponds to an increase in the behavioral persistence that mice exhibit in a foraging task. Finally, we used a genetic targeting strategy that primarily affected neurons in the medial prefrontal cortex, to selectively ablate this pathway in adulthood and show that mice revert to a behavioral phenotype similar to juveniles. These results suggest that frontal cortical to dorsal raphe input is a critical anatomical and functional substrate of the development and manifestation of behavioral persistence.