A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality

Regulation of perisomatic synapses from cholecystokinin basket interneurons through NrCAM and Ankyrin B

The perisomatic region of cortical pyramidal neurons (PNs) integrates local and long-range inputs and regulates firing. This domain receives GABAergic inputs from cholecystokinin (CCK)- and Parvalbumin (PV)-expressing basket cells (BCs) but how synaptic contacts are established is unclear. Neuron-glial related cell adhesion molecule (NrCAM) is a homophilic transmembrane protein that binds the scaffold protein Ankyrin B. Here we show that NrCAM and Ankyrin B mediate perisomatic synaptic contact between CCK-BCs and PNs in mouse medial prefrontal cortex (mPFC). Immunolabeling of CCK-BC terminals for vesicular glutamate transporter-3 (VGLUT3) or vesicular GABA transporter (VGAT) revealed a significant decrease in CCK-BC synaptic puncta on PN soma in NrCAM-null mice, however no decrease in PV-BC puncta or cell loss. VGLUT3+ CCK-BC puncta were also decreased by Ankyrin B deletion from PNs in Nex1Cre-ERT2:Ank2flox/flox:EGFP mice. A novel CCK-BC reporter mouse expressing tdTomato (tdT) at the Synuclein-γ (Sncg) locus showed NrCAM localized to Sncg + CCK-BCs, and to postsynaptic PN soma in Nex1Cre-ERT2:Ank2+/+:EGFP mice. Results suggest that NrCAM and Ankyrin B contribute to the establishment of connectivity between CCK-BCs and excitatory neurons of the mPFC.

A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types

The mammalian cortex is comprised of cells classified into types according to shared properties. Defining the contribution of each cell type to the processes guided by the cortex is essential for understanding its function in health and disease. We use transcriptomic and epigenomic cortical cell-type taxonomies from mouse and human to define marker genes and putative enhancers and create a large toolkit of transgenic lines and enhancer adeno-associated viruses (AAVs) for selective targeting of cortical cell populations. We report creation and evaluation of fifteen transgenic driver lines, two reporter lines, and >1,000 different enhancer AAV vectors covering most subclasses of cortical cells. The tools reported here have been made publicly available, and along with the scaled process of tool creation, evaluation, and modification, they will enable diverse experimental strategies toward understanding mammalian cortex and brain function.

Key Connectomes and Synaptic-Compartment-Specific Risk Genes Drive Pathological α-Synuclein Spreading

Previous studies have suggested that pathological α-synuclein (α-Syn) mainly transmits along the neuronal network, but several key questions remain unanswered: 1) How many and which connections in the connectome are necessary for predicting the progression of pathological α-Syn? 2) How to identify risk genes that affect pathology spreading functioning at presynaptic or postsynaptic regions, and are these genes enriched in different cell types? Here, these questions are addressed with novel mathematical models. Strikingly, the spreading of pathological α-Syn is predominantly determined by the key subnetworks composed of only 2% of the strongest connections in the connectome. Genes associated with the selective vulnerability of brain regions to pathological α-Syn transmission are further analyzed to distinguish those functioning at presynaptic versus postsynaptic regions. Those risk genes are significantly enriched in microglial cells of presynaptic regions and neurons of postsynaptic regions. Gene regulatory network analyses are then conducted to identify "key drivers" of genes responsible for selective vulnerability and overlapping with Parkinson's disease risk genes. By identifying and discriminating between key gene mediators of transmission operating at presynaptic and postsynaptic regions, this study has demonstrated for the first time that these are functionally distinct processes.

Using DeepLabCut-Live to probe state dependent neural circuits of behavior with closed-loop optogenetic stimulation

BACKGROUND

Closed-loop behavior paradigms allow for real-time investigation of state-dependent neural circuits underlying behavior. However, studying context-dependent locomotor perturbations is challenging due to limitations in molecular tools and techniques for real-time manipulation of spinal circuits.

NEW METHOD

We developed a novel closed-loop optogenetic stimulation paradigm that leverages DeepLabCut-Live pose estimation to manipulate primary sensory afferent activity at specific phases of the locomotor cycle in mice. A compact DeepLabCut model was trained to track hindlimb kinematics in real-time and integrated into the Bonsai visual programming framework. This system enabled LED triggered photo-stimulation of sensory neurons expressing channelrhodopsin based on user-defined pose-based criteria, such as stance or swing phase.

RESULTS

Optogenetic activation of nociceptive TRPV1+ sensory neurons during treadmill locomotion reliably evoked paw withdrawal responses. Stimulation during the stance phase generated a brief withdrawal and impacted the duration of the following swing phase. Stimulation during the swing phase increased the height of paw withdrawal during swing and reduced the duration of the following stance phase.

COMPARISON WITH EXISTING METHODS

This method allows for high spatiotemporal precision in manipulating spinal circuits based on locomotor phase. Unlike previous approaches, this closed-loop system accounts for state-dependent nature of sensorimotor responses, enabling controlled, real-time modulation of locomotion.

CONCLUSIONS

Integrating DeepLabCut-Live with optogenetics provides a powerful tool for dissecting the context-dependent role of sensory feedback and spinal interneurons in locomotion. This technique opens new avenues for uncovering the neural substrates of state-dependent behaviors and has broad applicability for studies of real-time closed-loop manipulation based on pose estimation.

Enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits

We present an enhancer-AAV toolbox for accessing and perturbing striatal cell types and circuits. Best-in-class vectors were curated for accessing major striatal neuron populations including medium spiny neurons (MSNs), direct- and indirect-pathway MSNs, Sst-Chodl, Pvalb-Pthlh, and cholinergic interneurons. Specificity was evaluated by multiple modes of molecular validation, by three different routes of virus delivery, and with diverse transgene cargos. Importantly, we provide detailed information necessary to achieve reliable cell-type-specific labeling under different experimental contexts. We demonstrate direct pathway circuit-selective optogenetic perturbation of behavior and multiplex labeling of striatal interneuron types for targeted analysis of cellular features. Lastly, we show conserved in vivo activity for exemplary MSN enhancers in rats and macaques. This collection of striatal enhancer AAVs offers greater versatility compared to available transgenic lines and can readily be applied for cell type and circuit studies in diverse mammalian species beyond the mouse model.

Enhancer AAVs for targeting spinal motor neurons and descending motor pathways in rodents and macaque

Experimental access to cell types within the mammalian spinal cord is severely limited by the availability of genetic tools. To enable access to spinal motor neurons (SMNs) and SMN subtypes, we generated single-cell multiome datasets from mouse and macaque spinal cords and discovered putative enhancers for each neuronal population. We cloned these enhancers into adeno-associated viral vectors driving a reporter fluorophore and functionally screened them in the mouse. We extensively characterized the most promising candidate enhancers in rat and macaque and developed an optimized pan-SMN enhancer virus. Additionally, we generated derivative viruses expressing iCre297T recombinase or ChR2-EYFP for labeling and functional studies, and we created a single vector with combined enhancer elements to achieve simultaneous labeling of layer 5 extratelencephalic projecting neurons and SMNs. This unprecedented SMN toolkit will enable future investigations of cell type function across species and potential therapeutic interventions for human neurodegenerative diseases.

Endogenously generated patterns of neural activity sculpt axon connectivity

Neural activity is crucial in establishing functional circuit connectivity in the central nervous system. Prior to the onset of sensory experience, sensory organs spontaneously generate patterned neural activity, which is essential for sculpting and refining immature circuit connectivity coordinating functional and physiological responses to the external world in advance. How these endogenous patterns of neural activity drive circuit refinement is a major long-standing question; however, it has been impeded, at least partly, by technical difficulties in visualizing circuit refinement and patterned spontaneous activity in living animals. In this review, I discuss recent progress in visualizing circuit refinement processes and patterned spontaneous activity at the single-axon level in the mammalian visual system and consider how endogenous patterns of spontaneous activity drive fine-scale axon refinement during development.

Inhibitory and disinhibitory VIP IN-mediated circuits in neocortex

Cortical GABAergic interneurons (INs) expressing the neuropeptide vasoactive-intestinal peptide (VIP) predominantly function by inhibiting dendritic-targeting somato-statin (SST) expressing INs, thereby disinhibiting pyramidal cells (PCs) and facilitating cortical circuit plasticity. VIP INs are a molecularly heterogeneous group, but the physiological significance of this diversity is unclear at present. Here, we have characterized the functional diversity of VIP INs in the primary somatosensory cortex (vS1) using intersectional genetic approaches. We found that VIP INs are comprised of four primary populations that exhibit different laminar distributions, axonal and dendritic arbors, intrinsic electrophysiological properties, and efferent connectivity. Furthermore, we observe that these populations are differentially activated by long-range inputs, and display distinct responses to neuromodulation by endocannabinoids, acetylcholine and noradrenaline. Stimulation of VIP IN subpopulations in vivo results in differential effects on the cortical network, thus providing evidence for specialized modes of VIP IN-mediated regulation of PC activity during cortical information processing.

Channel synapse mediates neurotransmission of airway protective chemoreflexes

Neural reflexes to chemicals in the throat protect the airway from aspiration and infection. Mechanistic understanding of these reflexes remains premature, exemplified by chronic cough-a sensitized cough reflex-being a prevalent unmet clinical need. Here, in mice, a whole-body search for channel synapses-featuring CALHM1/3 channel-mediated neurotransmitter release-and single-cell transcriptomics uncovered subclasses of the Pou2f3+ chemosensory cell family in the throat communicating with vagal neurons via this synapse. They express G protein-coupled receptors (GPCRs) for noxious chemicals, T2Rs, which upon stimulation trigger swallow and cough-like expulsive reflexes in the hypopharynx and larynx, respectively. These reflexes were abolished by Calhm3 and Pou2f3 knockout and could be triggered by targeted optogenetic stimulation. Furthermore, aeroallergen exposure augmented CALHM3-dependent expulsive reflex. This study identifies Pou2f3+ epithelial cells with channel synapses as chemosensory end organs of airway protective reflexes and sites of their hyperresponsiveness, advancing mechanistic understanding of airway defense programs with distinct therapeutic potential.

GRIN lens implantation strategies for in vivo calcium imaging using miniature microscopy

Miniature microscopy (Miniscope) has become one of the most popular and valuable neuroscience tools in the last decade. Miniscope in vivo calcium imaging during freely moving behavior has led to a number of transformative discoveries about neural coding across a large range of behaviors. The UCLA Miniscope Project is an open-source miniaturized microscopy platform that has greatly benefited the neuroscience community and led to the release of a number of different miniaturized microscopes with extended capabilities. While researchers can record from essentially any brain region through a cranial window or a gradient index of refraction (GRIN) lens, there is still a need for comprehensive protocols which describe detailed surgical procedures for successful miniaturized microscopy applications across different brain regions. Here, we provide step-by-step surgical procedures for implantation of GRIN lenses to record from a number of different brain regions including subregions in the medial prefrontal cortex (PrL, IL, DP), subregions in the hippocampus (dCA1, CA2 and vCA1), and the ventral striatum (nucleus accumbens, NAc). Moreover, we also provide surgical methods of new multi-brain regions imaging techniques developed by our group to record bilateral medial prefrontal cortex (mPFCs) or simultaneously record mPFC and NAc. Taken together, this protocol details easy and reproducible techniques for GRIN lens implantation and miniaturized microscopy in multiple structures.

A transgenic mouse line for rabies virus-mediated trans-synaptic tracing in the postnatal developing brain

Neural circuits are composed of numerous neurons that perform diverse functions. Understanding the mechanisms of neural processing requires elucidating the connections among individual neurons. Rabies virus (RV)-mediated trans-synaptic tracing enables the visualization of direct presynaptic neurons of a defined neural population, facilitating the precise mapping of neural circuits across various brain regions. This method relies on RV mutants that require the expression of the TVA receptor and rabies glycoprotein to infect and spread to presynaptic neurons. Traditionally, adeno-associated virus (AAV) has been used to express these proteins. However, because AAV requires several weeks to achieve sufficient gene expression, it is challenging to use this approach for studying neural connections during postnatal development. To address this limitation, we generated a transgenic mouse line, termed Ai162-nCTG, which expresses nuclear-localized mCherry, the TVA receptor, and rabies glycoprotein in a Cre-dependent manner. As a proof-of-principle, we crossed the Ai162-nCTG line with the vasopressin-Cre line. In the paraventricular hypothalamic nucleus, where a major cluster of vasopressin neurons exists, mCherry expression was highly specific to vasopressin neurons, although not all vasopressin neurons co-expressed mCherry. We injected RV into the paraventricular hypothalamic nucleus and compared the labeling patterns with those of the conventional AAV-based approach. Although both methods labeled input cells in similar brain regions, the AAV-based approach was superior in terms of labeling efficiency. We also demonstrated that the Ai162-nCTG-based method enables rabies virus-mediated trans-synaptic tracing in mice at postnatal day 7 and 30. The distribution of presynaptic neurons was largely similar in the juvenile and adult stages, suggesting that paraventricular vasopressin neurons do not significantly change their presynaptic inputs during post-weaning development. Taken together, these findings suggest that the Ai162-nCTG line can be used for rabies virus-mediated trans-synaptic tracing when AAV administration is challenging. We also acknowledge and discuss the technical constraints associated with this mouse line.

Sainsc: A Computational Tool for Segmentation-Free Analysis of In Situ Capture Data

Spatially resolved transcriptomics (SRT) has become the method of choice for characterising the complexity of biomedical tissue samples. Until recently, scientists were restricted to SRT methods that can profile a limited set of target genes at high spatial resolution or transcriptome-wide but at a low spatial resolution. Through recent developments, there are now methods that offer both subcellular spatial resolution and full transcriptome coverage. However, utilising these new methods' high spatial resolution and gene resolution remains elusive due to several factors, including low detection efficiency and high computational costs. Here, we present Sainsc (Segmentation-free analysis of in situ capture data), which combines a cell-segmentation-free approach with efficient data processing of transcriptome-wide nanometre-resolution spatial data. Sainsc can generate cell-type maps with accurate cell-type assignment at the nanometre scale, together with corresponding maps of the assignment scores that facilitate interpretation of the local confidence of cell-type assignment. We demonstrate its utility and accuracy for different tissues and technologies. Compared to other methods, Sainsc requires lower computational resources and has scalable performance, enabling interactive data exploration. Sainsc is compatible with common data analysis frameworks and is available as open-source software in multiple programming languages.

ATLAS: a rationally designed anterograde transsynaptic tracer

Genetically modified rabies virus can map neural circuits retrogradely from genetically determined cells. However, similar tools for anterograde tracing are not available. Here, we describe a method for anterograde transsynaptic tracing from genetically determined neurons based on a rationally designed protein, ATLAS. Expression of ATLAS in neurons causes presynaptic release of a payload composed of an antibody-like protein, AMPA.FingR, which binds to the N terminus of GluA1, and a recombinase. In the synaptic cleft, AMPA.FingR binds to GluA1, causing the payload to be endocytosed into postsynaptic cells and delivered to the nucleus, where it triggers expression of a recombinase-dependent reporter. In mice, ATLAS mediates monosynaptic transneuronal tracing from random or genetically determined cells that is strictly anterograde, synaptic and nontoxic. Moreover, ATLAS-mediated tracing shows activity dependence, suggesting that it can label active circuits underlying specific behaviors. Finally, ATLAS is composed of modular components that can be independently replaced or modified.

Multimodal identification of the mouse brain using simultaneous Ca2+ imaging and fMRI

Individual differences in neuroimaging are of interest to clinical and cognitive neuroscientists based on their potential for guiding the personalized treatment of various heterogeneous neurological conditions and diseases. Despite many advantages, the prevailing modality in this field-blood-oxygen-level-dependent (BOLD) functional magnetic resonance imaging (fMRI)-suffers from low spatiotemporal resolution and specificity as well as a propensity for noise and spurious signal corruption. To better understand individual differences in BOLD-fMRI data, we can use animal models where fMRI, alongside complementary but more invasive contrasts, can be accessed. Here, we apply simultaneous wide-field fluorescence calcium imaging and BOLD-fMRI in mice to interrogate individual differences using a connectome-based identification framework adopted from the human fMRI literature. This approach yields high spatiotemporal resolution cell-type specific signals (here, from glia, excitatory, as well as inhibitory interneurons) from the whole cortex. We found mouse multimodal connectome-based identification to be successful and explored various features of these data.

The dorsal column nuclei scale mechanical sensitivity in naive and neuropathic pain states

During pathological conditions, tactile stimuli can aberrantly engage nociceptive pathways leading to the perception of touch as pain, known as mechanical allodynia. The brain stem dorsal column nuclei integrate tactile inputs, yet their role in mediating tactile sensitivity and allodynia remains understudied. We found that gracile nucleus (Gr) inhibitory interneurons and thalamus-projecting neurons are differentially innervated by primary afferents and spinal inputs. Functional manipulations of these distinct Gr neuronal populations bidirectionally shifted tactile sensitivity but did not affect noxious mechanical or thermal sensitivity. During neuropathic pain, Gr neurons exhibited increased sensory-evoked activity and asynchronous excitatory drive from primary afferents. Silencing Gr projection neurons or activating Gr inhibitory neurons in neuropathic mice reduced tactile hypersensitivity, and enhancing inhibition ameliorated paw-withdrawal signatures of neuropathic pain and induced conditioned place preference. These results suggest that Gr activity contributes to tactile sensitivity and affective, pain-associated phenotypes of mechanical allodynia.

Development and characterization of an Sf-1-Flp mouse model

The use of genetically engineered tools, including combinations of Cre-LoxP and Flp-FRT systems, enables the interrogation of complex biology. Steroidogenic factor-1 (SF-1) is expressed in the ventromedial hypothalamic nucleus (VMH). Development of genetic tools, such as mice expressing Flp recombinase (Flp) in SF-1 neurons (Sf-1-Flp), will be useful for future studies that unravel the complex physiology regulated by the VMH. Here, we developed and characterized Sf-1-Flp mice and demonstrated their utility. The Flp sequence was inserted into the Sf-1 locus with P2A. This insertion did not affect Sf-1 mRNA expression levels and Sf-1-Flp mice do not have any visible phenotypes. They are fertile and metabolically comparable to wild-type littermate mice. Optogenetic stimulation using adeno-associated virus (AAV) carrying Flp-dependent channelrhodopsin-2 (ChR2) increased blood glucose and skeletal muscle PGC-1α in Sf-1-Flp mice. This was similar to SF-1 neuronal activation using Sf-1-BAC-Cre and AAV carrying Cre-dependent ChR2. Finally, we generated Sf-1-Flp mice that lack β2-adrenergic receptors (Adrb2) only in skeletal muscle with a combination of Cre/LoxP technology (Sf-1-Flp:SKMΔAdrb2). Optogenetic stimulation of SF-1 neurons failed to increase skeletal muscle PGC-1α in Sf-1-Flp:SKMΔAdrb2 mice, suggesting that Adrb2 in skeletal muscle is required for augmented skeletal muscle PGC-1α by SF-1 neuronal activation. Our data demonstrate that Sf-1-Flp mice are useful for interrogating complex physiology.

Hypothalamic PNOC/NPY neurons constitute mediators of leptin-controlled energy homeostasis

Leptin acts in the brain to suppress appetite, yet the responsible neurocircuitries underlying leptin's anorectic effect are incompletely defined. Prepronociceptin (PNOC)-expressing neurons mediate diet-induced hyperphagia and weight gain in mice. Here, we show that leptin regulates appetite and body weight via PNOC neurons, and that loss of leptin receptor (Lepr) expression in PNOC-expressing neurons in the arcuate nucleus of the hypothalamus (ARC) causes hyperphagia and obesity. Restoring Lepr expression in PNOC neurons on a Lepr-null obese background substantially reduces body weight. Lepr inactivation in PNOC neurons increases neuropeptide Y (Npy) expression in a subset of hypothalamic PNOC neurons that do not express agouti-related peptide (Agrp). Selective chemogenetic activation of PNOC/NPY neurons promotes feeding to the same extent as activating all PNOCARC neurons, and overexpression of Npy in PNOCARC neurons promotes hyperphagia and obesity. Thus, we introduce PNOC/NPYARC neurons as an additional critical mediator of leptin action and as a promising target for obesity therapeutics.

Fate plasticity of interneuron specification

Neuronal subtype generation in the mammalian central nervous system is governed by competing genetic programs. The medial ganglionic eminence (MGE) produces two major cortical interneuron (IN) populations, somatostatin (Sst) and parvalbumin (Pvalb), which develop on different timelines. The extent to which external signals influence these identities remains unclear. Pvalb-positive INs are crucial for cortical circuit regulation but challenging to model in vitro. We grafted mouse MGE progenitors into diverse 2D and 3D co-culture systems, including mouse and human cortical, MGE, and thalamic models. Strikingly, only 3D human corticogenesis models promoted efficient, non-autonomous Pvalb differentiation, characterized by upregulation of Pvalb maturation markers, downregulation of Sst-specific markers, and the formation of perineuronal nets. Additionally, lineage-traced postmitotic Sst-positive INs upregulated Pvalb when grafted onto human cortical models. These findings reveal unexpected fate plasticity in MGE-derived INs, suggesting that their identities can be dynamically shaped by the environment.

A deep learning strategy to identify cell types across species from high-density extracellular recordings

High-density probes allow electrophysiological recordings from many neurons simultaneously across entire brain circuits but fail to reveal cell type. Here, we develop a strategy to identify cell types from extracellular recordings in awake animals and reveal the computational roles of neurons with distinct functional, molecular, and anatomical properties. We combine optogenetics and pharmacology using the cerebellum as a testbed to generate a curated ground-truth library of electrophysiological properties for Purkinje cells, molecular layer interneurons, Golgi cells, and mossy fibers. We train a semi-supervised deep learning classifier that predicts cell types with greater than 95% accuracy based on the waveform, discharge statistics, and layer of the recorded neuron. The classifier's predictions agree with expert classification on recordings using different probes, in different laboratories, from functionally distinct cerebellar regions, and across species. Our classifier extends the power of modern dynamical systems analyses by revealing the unique contributions of simultaneously recorded cell types during behavior.

Interpretable deep learning for deconvolutional analysis of neural signals

The widespread adoption of deep learning to model neural activity often relies on "black-box" approaches that lack an interpretable connection between neural activity and network parameters. Here, we propose using algorithm unrolling, a method for interpretable deep learning, to design the architecture of sparse deconvolutional neural networks and obtain a direct interpretation of network weights in relation to stimulus-driven single-neuron activity through a generative model. We introduce our method, deconvolutional unrolled neural learning (DUNL), and demonstrate its versatility by applying it to deconvolve single-trial local signals across multiple brain areas and recording modalities. We uncover multiplexed salience and reward prediction error signals from midbrain dopamine neurons, perform simultaneous event detection and characterization in somatosensory thalamus recordings, and characterize the heterogeneity of neural responses in the piriform cortex and across striatum during unstructured, naturalistic experiments. Our work leverages advances in interpretable deep learning to provide a mechanistic understanding of neural activity.

Enteric glutamatergic interneurons regulate intestinal motility

The enteric nervous system (ENS) controls digestion autonomously via a complex neural network within the gut wall. Enteric neurons expressing glutamate have been identified by transcriptomic studies as a distinct subpopulation, and glutamate can affect intestinal motility by modulating enteric neuron activity. However, the nature of glutamatergic neurons, their position within the ENS circuit, and their function in regulating gut motility are unknown. We identify glutamatergic neurons as longitudinally projecting descending interneurons in the small intestine and colon and as a novel class of circumferential neurons only in the colon. Both populations make synaptic contact with diverse neuronal subtypes and signal with multiple neurotransmitters and neuropeptides in addition to glutamate, including acetylcholine and enkephalin. Knocking out the glutamate transporter VGLUT2 from enkephalin neurons disrupts gastrointestinal transit, while ex vivo optogenetic stimulation of glutamatergic neurons initiates colonic propulsive motility. Our results posit glutamatergic neurons as key interneurons that regulate intestinal motility.

Dietary availability acutely influences puberty onset via a hypothalamic neural circuit

Reproduction poses a substantial burden, especially for mammalian females. Puberty onset serves as a vital checkpoint, regulated based on the body's energy state, to prevent inappropriate reproductive activity under malnutrition. However, the neural basis of this puberty checkpoint remains poorly understood. Here, we demonstrate that peripubertal malnutrition in female mice reduces the synchronous activity episodes of arcuate kisspeptin neurons, which are critical regulators of the gonadotropin axis. Improved dietary availability increased the frequency of this pulsatile activity, facilitating puberty onset. Using a viral-genetic approach, we show that the activity of agouti-related protein neurons in the arcuate nucleus, a hunger center, can bidirectionally regulate the pulsatile activity of kisspeptin neurons and follicular maturation in the ovaries. Collectively, a neural circuit connecting feeding to reproductive centers acts as an adjuster of the frequency of pulsatile kisspeptin neuron activity based on dietary availability, contributing to the neural basis of the puberty checkpoint.

Profiling translation in the nervous system

Regulation at the level of translation is critical in the nervous system, such as for the formation of cell-type-specific proteomes or plastic changes in neural circuits. Whilst current knowledge of the translatome is relatively limited compared to transcriptome, a growing array of tools to analyse translation is becoming available. In this review, we discuss techniques for profiling translation on a genome-wide scale with a special emphasis on cell-type-specific analyses in the nervous system. This includes polysome-profiling-seq, Translating Ribosome Affinity Purification (TRAP)-seq and ribosome profiling (Ribo-seq). We review recent advances to achieve spatial resolution of translatome analysis, such as genetic labelling of the targeted cells and cell sorting, and discuss the biological implications of translational regulation in the brain and potential future extensions.

The MICrONS Consortium, Bae JA, Baptiste M, Baptiste MR, Bishop CA, Bodor AL, Brittain D, Brooks V, Buchanan J, Bumbarger DJ, Castro MA, Celii B, Cobos E, Collman F, da Costa NM, Danskin B, Dorkenwald S, Elabbady L, Fahey PG, Fliss T, Froudarakis E, Gager J, Gamlin C, Gray-Roncal W, Halageri A, Hebditch J, Jia Z, Joyce E, Ellis-Joyce J, Jordan C, Kapner D, Kemnitz N, Kinn S, Kitchell LM, Koolman S, Kuehner K, Lee K, Li K, Lu R, Macrina T, Mahalingam G, Matelsky J, McReynolds S, Miranda E, Mitchell E, Mondal SS, Moore M, Mu S, Muhammad T, Nehoran B, Neace E, Ogedengbe O, Papadopoulos C, Papadopoulos S, Patel S, Vega GJYP, Pitkow X, Popovych S, Ramos A, Reid RC, Reimer J, Rivlin PK, Rose V, Sauter ZM, Schneider-Mizell CM, Seung HS, Silverman B, Silversmith W, Sterling A, Sinz FH, Smith CL, Swanstrom R, Suckow S, Takeno M, Tan ZH, Tolias AS, Torres R, Turner NL, Walker EY, Wang T, Wanner A, Wester BA, Williams G, Williams S, Willie K, Willie R, Wong W, Wu J, Xu C, Yang R, Yatsenko D, Ye F, Yin W, Young R, Yu SC, Xenes D, Zhang C. Functional connectomics spanning multiple areas of mouse visual cortex

Understanding the brain requires understanding neurons' functional responses to the circuit architecture shaping them. Here we introduce the MICrONS functional connectomics dataset with dense calcium imaging of around 75,000 neurons in primary visual cortex (VISp) and higher visual areas (VISrl, VISal and VISlm) in an awake mouse that is viewing natural and synthetic stimuli. These data are co-registered with an electron microscopy reconstruction containing more than 200,000 cells and 0.5 billion synapses. Proofreading of a subset of neurons yielded reconstructions that include complete dendritic trees as well the local and inter-areal axonal projections that map up to thousands of cell-to-cell connections per neuron. Released as an open-access resource, this dataset includes the tools for data retrieval and analysis1,2. Accompanying studies describe its use for comprehensive characterization of cell types3-6, a synaptic level connectivity diagram of a cortical column4, and uncovering cell-type-specific inhibitory connectivity that can be linked to gene expression data4,7. Functionally, we identify new computational principles of how information is integrated across visual space8, characterize novel types of neuronal invariances9 and bring structure and function together to uncover a general principle for connectivity between excitatory neurons within and across areas10,11.

Developmental molecular signatures define de novo cortico-brainstem circuit for skilled forelimb movement

Skilled movement relies on descending cortical projections to the brainstem and spinal cord. While corticospinal neurons (CSN) have long been recognized for their role in fine motor control, the contribution of cortical projections to the brainstem remains poorly understood. Here, we identify a previously unrecognized direct cortico-brainstem circuit that emerges early in development and persists into adulthood. A subset of subcerebral projection neurons (SCPN) limit their projections to the brainstem from the earliest stages of axon extension without ever extending to the spinal cord. Using FACS purification and single-cell RNA sequencing, we show that these cortico-brainstem neurons (CBN) can be prospectively identified by the expression of Neuropeptide Y (Npy) in development. Functional silencing of Npy+ CBN in adulthood leads to impaired skilled forelimb reaching, demonstrating their essential role in adult motor control. Npy+ CBN project preferentially to rostral brainstem regions, including the midbrain reticular formation. These findings reveal developmental molecular signatures that define cortico-brainstem pathways for adult skilled movement. Our work provides new insights into the developmental logic that establishes descending cortical circuits and opens avenues for targeted investigation of their roles in motor function and recovery after injury.

Enhancer AAVs for targeting spinal motor neurons and descending motor pathways in rodents and macaque

Experimental access to cell types within the mammalian spinal cord is severely limited by the availability of genetic tools. To enable access to lower motor neurons (LMNs) and LMN subtypes, we generated single cell multiome datasets from mouse and macaque spinal cords and discovered putative enhancers for each neuronal population. We cloned these enhancers into adeno-associated viral vectors (AAVs) driving a reporter fluorophore and functionally screened them in mouse. We extensively characterized the most promising candidate enhancers in rat and macaque and developed an optimized pan LMN enhancer virus. Additionally, we generated derivative viruses expressing iCre297T recombinase or ChR2-EYFP for labeling and functional studies, and we created a single vector with combined enhancer elements to achieve simultaneous labeling of layer 5 extratelencephalic projecting (ET) neurons and LMNs. This unprecedented LMN toolkit will enable future investigations of cell type function across species and potential therapeutic interventions for human neurodegenerative diseases.

Divergent opioid-mediated suppression of inhibition between hippocampus and neocortex across species and development

Within adult rodent hippocampus (HPC), opioids suppress inhibitory parvalbumin-expressing interneurons (PV-INs), disinhibiting local microcircuits. However, it is unknown whether this disinhibitory motif is conserved across cortical regions, species, or development. We observed that PV-IN-mediated inhibition is robustly suppressed by opioids in HPC proper but not primary neocortex in mice and non-human primates, with spontaneous inhibitory tone in resected human tissue also following a consistent dichotomy. This hippocampal disinhibitory motif is established in early development when PV-INs and opioids regulate early population activity. Morphine pretreatment partially occludes this acute opioid-mediated suppression, with implications for the effects of opioids on hippocampal network activity important for learning and memory. Our findings demonstrate that PV-INs exhibit divergent opioid sensitivity across brain regions, which is remarkably conserved over evolution, and highlight the underappreciated role of opioids acting through immature PV-INs in shaping hippocampal development.

Binocular processing facilitates escape behavior through multiple pathways to the superior colliculus

The superior colliculus (SC) is the main brain region regulating defensive behaviors to visual threats. Yet, how the SC integrates binocular visual information and to what extent binocular vision drives defensive behaviors remains unknown. Here, we show that SC neurons respond to binocular visual input with diverse synaptic and spiking responses, summating visual inputs largely sublinearly. Using pathway-specific optogenetic silencing, we find that contralateral and ipsilateral visual information is carried to binocular SC neurons through retinal, interhemispheric, and corticotectal pathways. These pathways carry binocular visual input to the SC in a layer-specific manner, with superficial layers receiving visual information through retinal input, whereas intermediate and deep layers rely on interhemispheric and corticotectal pathways. We further show that binocular vision facilitates visually evoked escape behavior. Together, our data shed light on the cellular and circuit mechanisms underlying binocular visual processing in the SC and its role in defensive behaviors to visual threats.

Early and widespread cerebellar engagement during hippocampal seizures and interictal discharges

Despite research illustrating the cerebellum may be a critical circuit element in processes beyond motor control, and growing evidence for a role of the cerebellum in a range of neurological disorders, including the epilepsies, remarkably little is known about cerebellar engagement during seizures. We therefore implemented a novel method for repeated widefield calcium imaging of the cerebellum in awake, chronically epileptic mice. We found widespread changes in cerebellar Purkinje cell activity during temporal lobe seizures. Changes were noted in the anterior and posterior cerebellum (lobules IV-VII), along the midline (vermis), and both ipsilaterally and contralaterally (in the simplex and Crus I) to the seizure focus. This was true for both overtly behavioral seizures and for hippocampal seizures that remained electrographic only -- arguing against cerebellar modulation simply reflecting motor components. Moreover, even brief interictal spikes produced widespread alterations in cerebellar activity. Perhaps most remarkably, changes in the cerebellum also occurred prior to any noticeable change in the hippocampal electrographic recordings. Together these results underscore the relevance of the cerebellum with respect to seizure networks, warranting a more consistent consideration of the cerebellum in epilepsy.

A Comprehensive Atlas of Cell Type Density Patterns and Their Role in Brain Organization

Cell-type composition across brain regions is a critical structural factor shaping both local and long-range brain circuits. Here, we employed single-cell resolution imaging of the mouse brain, combined with computational analyses, to map the distribution of 30 cell classes and types defined by gene marker expression in Cre recombinase-based genetic mouse models. This approach generated a comprehensive atlas of cell type-specific densities across the male and female brain, revealing (1) surprisingly broad sex differences in cells tagged by developmental cell-type markers, (2) shared cell type composition signatures among functionally related brain structures, and (3) close associations not only between specific cell types but also discrete cell type densities and anatomical regions and subregions. In summary, despite the relatively broad cell type classification enabled by the Cre mouse models, our findings highlight intricate relationships between brain cell type distribution and anatomical organization, associating distinct local cell densities with region-specific brain functions.

Enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits

We present an enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits. Best-in-class vectors were curated for accessing major striatal neuron populations including medium spiny neurons (MSNs), direct and indirect pathway MSNs, as well as Sst-Chodl, Pvalb-Pthlh, and cholinergic interneurons. Specificity was evaluated by multiple modes of molecular validation, three different routes of virus delivery, and with diverse transgene cargos. Importantly, we provide detailed information necessary to achieve reliable cell type specific labeling under different experimental contexts. We demonstrate direct pathway circuit-selective optogenetic perturbation of behavior and multiplex labeling of striatal interneuron types for targeted analysis of cellular features. Lastly, we show conserved in vivo activity for exemplary MSN enhancers in rat and macaque. This collection of striatal enhancer AAVs offers greater versatility compared to available transgenic lines and can readily be applied for cell type and circuit studies in diverse mammalian species beyond the mouse model.

Slow cortical dynamics generate context processing and novelty detection

The cortex amplifies responses to novel stimuli while suppressing redundant ones. Novelty detection is necessary to efficiently process sensory information and build predictive models of the environment, and it is also altered in schizophrenia. To investigate the circuit mechanisms underlying novelty detection, we used an auditory "oddball" paradigm and two-photon calcium imaging to measure responses to simple and complex stimuli across mouse auditory cortex. Stimulus statistics and complexity generated specific responses across auditory areas. Neuronal ensembles reliably encoded auditory features and temporal context. Interestingly, stimulus-evoked population responses were particularly long lasting, reflecting stimulus history and affecting future responses. These slow cortical dynamics encoded stimulus temporal context and generated stronger responses to novel stimuli. Recurrent neural network models trained on the oddball task also exhibited slow network dynamics and recapitulated the biological data. We conclude that the slow dynamics of recurrent cortical networks underlie processing and novelty detection.

Prospective contingency explains behavior and dopamine signals during associative learning

Associative learning depends on contingency, the degree to which a stimulus predicts an outcome. Despite its importance, the neural mechanisms linking contingency to behavior remain elusive. In the present study, we examined the dopamine activity in the ventral striatum-a signal implicated in associative learning-in a Pavlovian contingency degradation task in mice. We show that both anticipatory licking and dopamine responses to a conditioned stimulus decreased when additional rewards were delivered uncued, but remained unchanged if additional rewards were cued. These results conflict with contingency-based accounts using a traditional definition of contingency or a new causal learning model (ANCCR), but can be explained by temporal difference (TD) learning models equipped with an appropriate intertrial interval state representation. Recurrent neural networks trained within a TD framework develop state representations akin to our best 'handcrafted' model. Our findings suggest that the TD error can be a measure that describes both contingency and dopaminergic activity.

Distinguish risk genes functioning at presynaptic or postsynaptic regions and key connectomes associated with pathological α-synuclein spreading

Previous studies have suggested that pathological α-synuclein (α-Syn) mainly transmits along the neuronal network, but several key questions remain unanswered: (1) How many and which connections in the connectome are necessary for predicting the progression of pathological α-Syn? (2) How to identify risk gene that affects pathology spreading functioning at presynaptic or postsynaptic regions, and are these genes enriched in different cell types? Here, we addressed these key questions with novel mathematical models. Strikingly, the spreading of pathological α-Syn is predominantly determined by the key subnetworks composed of only 2% of the strongest connections in the connectome. We further explored the genes that are responsible for the selective vulnerability of different brain regions to transmission to distinguish the genes that play roles in presynaptic from those in postsynaptic regions. Those risk genes were significantly enriched in microglial cells of presynaptic regions and neurons of postsynaptic regions. Gene regulatory network analyses were then conducted to identify 'key drivers' of genes responsible for selective vulnerability and overlapping with Parkinson's disease risk genes. By identifying and discriminating between key gene mediators of transmission operating at presynaptic and postsynaptic regions, our study has demonstrated for the first time that these are functionally distinct processes.

Regulation of Perisomatic Synapses from Cholecystokinin Basket Interneurons through NrCAM and Ankyrin B

The perisomatic region of cortical pyramidal neurons (PNs) integrates local and long-range inputs and regulates firing. This domain receives GABAergic inputs from cholecystokinin (CCK)- and Parvalbumin (PV)-expressing basket cells (BCs) but how synaptic contacts are established is unclear. Neuron-glial related cell adhesion molecule (NrCAM) is a homophilic transmembrane protein that binds the scaffold protein Ankyrin B. Here we show that NrCAM and Ankyrin B mediate perisomatic synaptic contact between CCK-BCs and PNs in mouse medial prefrontal cortex (mPFC). Immunolabeling of CCK-BC terminals for vesicular glutamate transporter-3 (VGLUT3) or vesicular GABA transporter (VGAT) revealed a significant decrease in CCK-BC synaptic puncta on PN soma in NrCAM-null mice, however no decrease in PV-BC puncta or cell loss. VGLUT3+ CCK-BC puncta were also decreased by Ankyrin B deletion from PNs in Nex1Cre-ERT2:Ank2 flox/flox :EGFP mice. A novel CCK-BC reporter mouse expressing tdTomato (tdT) at the Synuclein-γ ( Sncg ) locus showed NrCAM localized to Sncg+ CCK-BCs, and to postsynaptic PN soma in Nex1Cre-ERT2:Ank2 +/+ :EGFP mice. Results suggest that NrCAM and Ankyrin B contribute to the establishment of connectivity between CCK-BCs and excitatory neurons of the mPFC.

Heterogeneous monotonic and non-monotonic responses to odor in mitral/tufted glomeruli of the mouse olfactory bulb

Current models of olfactory sensory processing in the olfactory bulb (OB) posit that both intra- and interglomerular inhibitory circuits are involved in transforming sensory input. However, the impact of these circuits on different olfactory receptor neuron (ORNs) inputs remains poorly understood. We generated a model of the OB input-output transformation in which the output of each glomerulus is a function of its ORN input, local feed-forward intraglomerular inhibition and interglomerular normalization in which activity of each glomerulus is divided by the population response. The output of the model included linear and non-linear concentration-response relationships that depended on the input ORN Hill coefficient and half-activation value. The concentration-response relationships could be broadly categorized into four groups based on how the output response was influenced by increasing the concentration. Increasing concentration evoked monotonic increases (I) or decreases (D) in some glomeruli. Other glomeruli responded with non-monotonic decreases then increases (DI) or increased then decreased (ID). The non-monotonic ID glomeruli required interglomerular inhibition in our model, were most common in glomeruli with higher affinity ORN input and were heterogeneous in the magnitude of their drop. In vivo 2-photon Ca2+ imaging from MTC glomeruli in awake mice revealed qualitatively similar response types. Increasing levels of excitation drove higher levels of suppression in subsets of glomeruli, and nearly half of the recorded MTC glomeruli could be classified as ID. Additionally, the sensitivity of individual glomeruli was significantly correlated with the degree to which it was non-monotonic. Our results demonstrate that nonlinear responses of MTC to changes in odor concentration are not unusual, but indeed are typical, and that they can be explained by intra- and interglomerular inhibition.

Acute and circadian feedforward regulation of agouti-related peptide hunger neurons

When food is freely available, eating occurs without energy deficit. While agouti-related peptide (AgRP) neurons are likely involved, their activation is thought to require negative energy balance. To investigate this, we implemented long-term, continuous in vivo fiber-photometry recordings in mice. We discovered new forms of AgRP neuron regulation, including fast pre-ingestive decreases in activity and unexpectedly rapid activation by fasting. Furthermore, AgRP neuron activity has a circadian rhythm that peaks concurrent with the daily feeding onset. Importantly, this rhythm persists when nutrition is provided via constant-rate gastric infusions. Hence, it is not secondary to a circadian feeding rhythm. The AgRP neuron rhythm is driven by the circadian clock, the suprachiasmatic nucleus (SCN), as SCN ablation abolishes the circadian rhythm in AgRP neuron activity and feeding. The SCN activates AgRP neurons via excitatory afferents from thyrotrophin-releasing hormone-expressing neurons in the dorsomedial hypothalamus (DMHTrh neurons) to drive daily feeding rhythms.

Development and Characterization of a Sf-1-Flp Mouse Model

The use of genetically engineered tools, including combinations of Cre-LoxP and Flp-FRT systems, enable the interrogation of complex biology. Steroidogenic factor-1 (SF-1) is expressed in the ventromedial hypothalamic nucleus (VMH). Development of genetic tools, such as mice expressing Flp recombinase (Flp) in SF-1 neurons (Sf-1-Flp), will be useful for future studies that unravel the complex physiology regulated by the VMH. Here, we developed and characterized Sf-1-Flp mice and demonstrated its utility. Flp sequence was inserted into Sf-1 locus with P2A. This insertion did not affect Sf-1 mRNA expression levels and Sf-1-Flp mice do not have any visible phenotypes. They are fertile and metabolically comparable to wild-type littermate mice. Optogenetic stimulation using adeno-associated virus (AAV)-bearing Flp-dependent channelrhodopsin-2 (ChR2) increased blood glucose and skeletal muscle PGC-1α in Sf-1-Flp mice. This was similar to SF-1 neuronal activation using Sf-1-BAC-Cre and AAV-bearing Cre-dependent ChR2. Finally, we generated Sf-1-Flp mice that lack β2-adrenergic receptors (Adrβ2) only in skeletal muscle with a combination of Cre/LoxP technology (Sf-1-Flp::SKMΔAdrβ2). Optogenetic stimulation of SF-1 neurons failed to increase skeletal muscle PGC-1α in Sf-1-Flp::SKMΔAdrβ2 mice, suggesting that Adrβ2 in skeletal muscle is required for augmented skeletal muscle PGC-1α by SF-1 neuronal activation. Our data demonstrate that Sf-1-Flp mice are useful for interrogating complex physiology.

Cerebellar output neurons can impair non-motor behaviors by altering development of extracerebellar connectivity

The capacity of the brain to compensate for insults during development depends on the type of cell loss, whereas the consequences of genetic mutations in the same neurons are difficult to predict. We reveal powerful compensation from outside the mouse cerebellum when the excitatory cerebellar output neurons are ablated embryonically and demonstrate that the main requirement for these neurons is for motor coordination and not basic learning and social behaviors. In contrast, loss of the homeobox transcription factors Engrailed1/2 (EN1/2) in the cerebellar excitatory lineage leads to additional deficits in adult learning and spatial working memory, despite half of the excitatory output neurons being intact. Diffusion MRI indicates increased thalamo-cortico-striatal connectivity in En1/2 mutants, showing that the remaining excitatory neurons lacking En1/2 exert adverse effects on extracerebellar circuits regulating motor learning and select non-motor behaviors. Thus, an absence of cerebellar output neurons is less disruptive than having cerebellar genetic mutations.

Multimodal identification of the mouse brain using simultaneous Ca 2+ imaging and fMRI

Individual differences in neuroimaging are of interest to clinical and cognitive neuroscientists based on their potential for guiding the personalized treatment of various heterogeneous neurological conditions and diseases. Despite many advantages, the workhorse in this arena, BOLD (blood-oxygen-level-dependent) functional magnetic resonance imaging (fMRI) suffers from low spatiotemporal resolution and specificity as well as a propensity for noise and spurious signal corruption. To better understand individual differences in BOLD-fMRI data, we can use animal models where fMRI, alongside complementary but more invasive contrasts, can be accessed. Here, we apply simultaneous wide-field fluorescence calcium imaging and BOLD-fMRI in mice to interrogate individual differences using a connectome-based identification framework adopted from the human fMRI literature. This approach yields high spatiotemporal resolution cell-type specific signals (here, from glia, excitatory, as well as inhibitory interneurons) from the whole cortex. We found mouse multimodal connectome-based identification to be successful and explored various features of these data.

Targeting spinal mechanistic target of rapamycin complex 2 alleviates inflammatory and neuropathic pain

The development and maintenance of chronic pain involve the reorganization of spinal nocioceptive circuits. The mechanistic target of rapamycin complex 2 (mTORC2), a central signalling hub that modulates both actin-dependent structural changes and mechanistic target of rapamycin complex 1 (mTORC1)-dependent mRNA translation, plays key roles in hippocampal synaptic plasticity and memory formation. However, its function in spinal plasticity and chronic pain is poorly understood. Here, we show that pharmacological activation of spinal mTORC2 induces pain hypersensitivity, whereas its inhibition, using downregulation of the mTORC2-defining component Rictor, alleviates both inflammatory and neuropathic pain. Cell type-specific deletion of Rictor showed that the selective inhibition of mTORC2 in a subset of excitatory neurons impairs spinal synaptic potentiation and alleviates inflammation-induced mechanical and thermal hypersensitivity and nerve injury-induced heat hyperalgesia. The ablation of mTORC2 in inhibitory interneurons strongly alleviated nerve injury-induced mechanical hypersensitivity. Our findings reveal the role of mTORC2 in chronic pain and highlight its cell type-specific functions in mediating pain hypersensitivity in response to peripheral inflammation and nerve injury.

Brain-wide cell-type-specific transcriptomic signatures of healthy ageing in mice

Biological ageing can be defined as a gradual loss of homeostasis across various aspects of molecular and cellular function1,2. Mammalian brains consist of thousands of cell types3, which may be differentially susceptible or resilient to ageing. Here we present a comprehensive single-cell RNA sequencing dataset containing roughly 1.2 million high-quality single-cell transcriptomes of brain cells from young adult and aged mice of both sexes, from regions spanning the forebrain, midbrain and hindbrain. High-resolution clustering of all cells results in 847 cell clusters and reveals at least 14 age-biased clusters that are mostly glial types. At the broader cell subclass and supertype levels, we find age-associated gene expression signatures and provide a list of 2,449 unique differentially expressed genes (age-DE genes) for many neuronal and non-neuronal cell types. Whereas most age-DE genes are unique to specific cell types, we observe common signatures with ageing across cell types, including a decrease in expression of genes related to neuronal structure and function in many neuron types, major astrocyte types and mature oligodendrocytes, and an increase in expression of genes related to immune function, antigen presentation, inflammation, and cell motility in immune cell types and some vascular cell types. Finally, we observe that some of the cell types that demonstrate the greatest sensitivity to ageing are concentrated around the third ventricle in the hypothalamus, including tanycytes, ependymal cells, and certain neuron types in the arcuate nucleus, dorsomedial nucleus and paraventricular nucleus that express genes canonically related to energy homeostasis. Many of these types demonstrate both a decrease in neuronal function and an increase in immune response. These findings suggest that the third ventricle in the hypothalamus may be a hub for ageing in the mouse brain. Overall, this study systematically delineates a dynamic landscape of cell-type-specific transcriptomic changes in the brain associated with normal ageing that will serve as a foundation for the investigation of functional changes in ageing and the interaction of ageing and disease.

Divergent opioid-mediated suppression of inhibition between hippocampus and neocortex across species and development

Within the adult rodent hippocampus, opioids suppress inhibitory parvalbumin-expressing interneurons (PV-INs), thus disinhibiting local micro-circuits. However, it is unknown if this disinhibitory motif is conserved in other cortical regions, species, or across development. We observed that PV-IN mediated inhibition is robustly suppressed by opioids in hippocampus proper but not primary neocortex in mice and nonhuman primates, with spontaneous inhibitory tone in resected human tissue also following a consistent dichotomy. This hippocampal disinhibitory motif was established in early development when PV-INs and opioids were found to regulate early population activity. Acute opioid-mediated modulation was partially occluded with morphine pretreatment, with implications for the effects of opioids on hippocampal network activity important for learning and memory. Together, these findings demonstrate that PV-INs exhibit a divergence in opioid sensitivity across brain regions that is remarkably conserved across evolution and highlights the underappreciated role of opioids acting through immature PV-INs in shaping hippocampal development.

Recent odor experience selectively modulates olfactory sensitivity across the glomerular output in the mouse olfactory bulb

Although animals can reliably locate and recognize odorants embedded in complex environments, the neural circuits for accomplishing these tasks remain incompletely understood. Adaptation is likely to be important as it could allow neurons in a brain area to adjust to the broader sensory environment. Adaptive processes must be flexible enough to allow the brain to make dynamic adjustments, while maintaining sufficient stability so that organisms do not forget important olfactory associations. Processing within the mouse olfactory bulb is likely involved in generating adaptation, although there are conflicting models of how it transforms the glomerular output of the mouse olfactory bulb. Here we performed 2-photon Ca2+ imaging from mitral/tufted glomeruli in awake mice to determine the time course of recovery from adaptation, and whether it acts broadly or selectively across the glomerular population. Individual glomerular responses, as well as the overall population odor representation were similar across imaging sessions. However, odor-concentration pairings presented with interstimulus intervals upwards of 30-s evoked heterogeneous adaptation that was concentration-dependent. We demonstrate that this form of adaptation is unrelated to variations in respiration, and olfactory receptor neuron glomerular measurements indicate that it is unlikely to be inherited from the periphery. Our results indicate that the olfactory bulb output can reliably transmit stable odor representations, but recent odor experiences can selectively shape neural responsiveness for upwards of 30 seconds. We propose that neural circuits that allow for non-uniform adaptation across mitral/tufted glomeruli could be important for making dynamic adjustments in complex odor environments.

Shifting GnRH Neuron Ensembles Underlie Successive Preovulatory Luteinizing Hormone Surges

The gonadotropin-releasing hormone (GnRH) neurons operate as a neuronal ensemble exhibiting coordinated activity once every reproductive cycle to generate the preovulatory GnRH surge. Using GCaMP fiber photometry at the GnRH neuron distal dendrons to measure the output of this widely scattered population in female mice, we find that the onset, amplitude, and profile of GnRH neuron surge activity exhibits substantial variability from cycle to cycle both between and within individual mice. This was also evident when measuring successive proestrous luteinizing hormone surges. Studies combining short (c-Fos and c-Jun) and long (genetic robust activity marking) term indices of immediate early gene activation revealed that, while ∼50% of GnRH neurons were activated at the time of each surge, only half of these neurons had been active during the previous proestrous surge. These observations reveal marked inter- and intra-individual variability in the GnRH surge mechanism. Remarkably, different subpopulations of overlapping GnRH neurons are recruited to the ensemble each estrous cycle to generate the GnRH surge. While engendering variability in the surge mechanism itself, this likely provides substantial robustness to a key event underlying mammalian reproduction.

Window into the Brain: In Vivo Multiphoton Imaging

Decoding the principles underlying neuronal information processing necessitates the emergence of techniques and methodologies to monitor multiscale brain networks in behaving animals over long periods of time. Novel advances in biophotonics, specifically progress in multiphoton microscopy, combined with the development of optical indicators for neuronal activity have provided the possibility to concurrently track brain functions at scales ranging from individual neurons to thousands of neurons across connected brain regions. This Review presents state-of-the-art multiphoton imaging modalities and optical indicators for in vivo brain imaging, highlighting recent advancements and current challenges in the field.

Deep imaging of LepR+ stromal cells in optically cleared murine bone hemisections

Tissue clearing combined with high-resolution confocal imaging is a cutting-edge approach for dissecting the three-dimensional (3D) architecture of tissues and deciphering cellular spatial interactions under physiological and pathological conditions. Deciphering the spatial interaction of leptin receptor-expressing (LepR+) stromal cells with other compartments in the bone marrow is crucial for a deeper understanding of the stem cell niche and the skeletal tissue. In this study, we introduce an optimized protocol for the 3D analysis of skeletal tissues, enabling the visualization of hematopoietic and stromal cells, especially LepR+ stromal cells, within optically cleared bone hemisections. Our method preserves the 3D tissue architecture and is extendable to other hematopoietic sites such as calvaria and vertebrae. The protocol entails tissue fixation, decalcification, and cryosectioning to reveal the marrow cavity. Completed within approximately 12 days, this process yields highly transparent tissues that maintain genetically encoded or antibody-stained fluorescent signals. The bone hemisections are compatible with diverse antibody labeling strategies. Confocal microscopy of these transparent samples allows for qualitative and quantitative image analysis using Aivia or Bitplane Imaris software, assessing a spectrum of parameters. With proper storage, the fluorescent signal in the stained and cleared bone hemisections remains intact for at least 2-3 months. This protocol is robust, straightforward to implement, and highly reproducible, offering a valuable tool for tissue architecture and cellular interaction studies.

Molecular logic for cellular specializations that initiate the auditory parallel processing pathways

The cochlear nuclear complex (CN), the starting point for all central auditory processing, encompasses a suite of neuronal cell types highly specialized for neural coding of acoustic signals. However, the molecular logic governing these specializations remains unknown. By combining single-nucleus RNA sequencing and Patch-seq analysis, we reveal a set of transcriptionally distinct cell populations encompassing all previously observed types and discover multiple hitherto unknown subtypes with anatomical and physiological identity. The resulting comprehensive cell-type taxonomy reconciles anatomical position, morphological, physiological, and molecular criteria, enabling the determination of the molecular basis of the specialized cellular phenotypes in the CN. In particular, CN cell-type identity is encoded in a transcriptional architecture that orchestrates functionally congruent expression across a small set of gene families to customize projection patterns, input-output synaptic communication, and biophysical features required for encoding distinct aspects of acoustic signals. This high-resolution account of cellular heterogeneity from the molecular to the circuit level reveals the molecular logic driving cellular specializations, thus enabling the genetic dissection of auditory processing and hearing disorders with a high specificity.

Multi-dimensional oscillatory activity of mouse GnRH neurons in vivo

The gonadotropin-releasing hormone (GnRH) neurons represent the key output cells of the neural network controlling mammalian fertility. We used GCaMP fiber photometry to record the population activity of the GnRH neuron distal projections in the ventral arcuate nucleus where they merge before entering the median eminence to release GnRH into the portal vasculature. Recordings in freely behaving intact male and female mice revealed abrupt ~8 min duration increases in activity that correlated perfectly with the appearance of a subsequent pulse of luteinizing hormone (LH). The GnRH neuron dendrons also exhibited a low level of unchanging clustered, rapidly fluctuating baseline activity in males and throughout the estrous cycle in females. In female mice, a gradual increase in basal activity that exhibited ~80 min oscillations began in the afternoon of proestrus and lasted for 12 hr. This was associated with the onset of the LH surge that ended several hours before the fall in the GCaMP signal. Abrupt 8 min duration episodes of GCaMP activity continued to occur on top of the rising surge baseline before ceasing in estrus. These observations provide the first description of GnRH neuron activity in freely behaving animals. They demonstrate that three distinct patterns of oscillatory activity occur in GnRH neurons. These are comprised of low-level rapid baseline activity, abrupt 8 min duration oscillations that drive pulsatile gonadotropin secretion, and, in females, a gradual and very prolonged oscillating increase in activity responsible for the preovulatory LH surge.

Satellite Glial Cells: No Longer the Most Overlooked Glia

Many glial biologists consider glia the neglected cells of the nervous system. Among all the glia of the central and peripheral nervous system, satellite glia may be the most often overlooked. Satellite glial cells (SGCs) are located in ganglia of the cranial nerves and the peripheral nervous system. These small cells surround the cell bodies of neurons in the trigeminal ganglia (TG), spiral ganglia, nodose and petrosal ganglia, sympathetic ganglia, and dorsal root ganglia (DRG). Essential SGC features include their intimate connections with the associated neurons, their small size, and their derivation from neural crest cells. Yet SGCs also exhibit tissue-specific properties and can change rapidly, particularly in response to injury. To illustrate the range of SGC functions, we will focus on three types: those of the spiral, sympathetic, and DRG, and consider both their shared features and those that differ based on location.