bioRxiv Subject Collection: Neuroscience's Journal

LoCS-Net: Localizing Convolutional Spiking Neural Network for Fast Visual Place Recognition
Visual place recognition (VPR) is the ability to recognize locations in a physical environment based only on visual inputs. It is a challenging task due to perceptual aliasing, viewpoint and appearance variations and complexity of dynamic scenes. Despite promising demonstrations, many state-of-the-art VPR approaches based on artificial neural networks (ANNs) suffer from computational inefficiency. Spiking neural networks (SNNs), on the other hand, implemented on neuromorphic hardware, are reported to have remarkable potential towards more efficient solutions computationally, compared to ANNs. However, the training of the state-of-the-art (SOTA) SNNs for the VPR task is often intractable on large and diverse datasets. To address this, we develop an end-to-end convolutional SNN model for VPR, that leverages back-propagation for tractable training. Rate-based approximations of leaky integrate-and-fire (LIF) neurons are employed during training to enable back-propagation, and the approximation units are replaced with spiking LIF neurons during inference. The proposed method outperforms the SOTA ANNs and SNNs by achieving 78.2% precision at 100% recall on the challenging Nordland dataset, compared with 53% SOTA performance, and exhibits competitive performance on the Oxford RobotCar dataset while being easier to train and faster in both training and inference when compared to other ANN and SNN-based methods.

Neural correlates in the time course of inferences: costs and benefits for less-skilled readers at university level.
Inferences are an indicator of a greater reading comprehension, as they imply a combination of implicit and explicit information that usually combines a textual representation with background knowledge of the reader. The aim of this study is to explore the costs and benefits of the time course of inferences in university students with reading comprehension difficulties at 3 stages during a narration. The method used was the event-related potential (ERP) technique in order to register the brain activity of 63 teaching program students while they read familiar, less-familiar and neutral stories. Results show a slow negativity potential component with greater negativity in words coming from familiar contexts when compared to less familiar and neutral ones in the first locus; an N400 component and a Post-N400 component in the second locus, reflecting greater negativity in familiar contexts when compared to less-familiar ones; and, lastly, through the use of a lexical decision task, FN400 and N400 components were found in the third locus, especially for pseudowords. These results are interpreted as a preferably bottom-up processing, which is characterized by lexical access difficulties in less-skilled readers.

Septo-hypothalamic regulation of binge-like alcohol consumption by the nociceptin system.
High intensity alcohol drinking during binge episodes overwhelmingly contributes to the socioeconomic burden created by Alcohol Use Disorders (AUD). Novel interventions are needed to add to the current therapeutic toolkit and nociceptin receptor (NOP) antagonists have shown promise in reducing heavy drinking days in patients with an AUD. However, an endogenous locus of nociceptin peptide and discrete sites of NOP action underlying this effect remains understudied. Here we show that the lateral septum (LS), a region contributing to binge drinking, is enriched in neurons expressing mRNA coding for the nociceptin peptide (Pnoc). Pnoc-expressing neurons of the LS (LSPnoc) are tuned to stimuli associated with negative valence and display increased excitability during withdrawal from binge-like alcohol drinking. LSPnoc activation was found to have aversive qualities and also potentiates binge-like drinking behavior, suggesting a convergence of circuitry that promotes aversion and drives alcohol consumption. Viral mediated tracing and functional assessment of LSPnoc projection fields revealed GABAergic synapses locally within the LS, and downstream within the lateral hypothalamus (LH) and supramammillary nucleus (SuM). Genetic deletion of NOP from the LS attenuated binge-like alcohol intake in male mice while NOP deletion from the LH and SuM decrease alcohol intake in females. Together, these findings are the first to demonstrate an endogenous population of nociceptin expressing neurons that contributes to alcohol consumption and identifies sex-dependent modulation of alcohol drinking by NOP.

Microglia contact cerebral vasculature through gaps between astrocyte endfeet
The close spatial relationship between microglia and cerebral blood vessels implicates microglia in vascular development, homeostasis and disease. In this study we used the publicly available Cortical MM^3 electron microscopy dataset to systematically investigate microglial interactions with the vasculature. Our analysis revealed that approximately 20% of microglia formed direct contacts with blood vessels through gaps between adjacent astrocyte endfeet. We termed these contact points "plugs". Plug-forming microglia exhibited closer proximity to blood vessels than non-plug forming microglia and formed multiple plugs, predominantly near the soma, ranging in surface area from ~0.01 um2 to ~15 um2. Plugs were enriched at the venule end of the vascular tree and displayed a preference for contacting endothelial cells over pericytes at a ratio of 3:1. In summary, we provide novel insights into the ultrastructural relationship between microglia and the vasculature, laying a foundation for understanding how these contacts contribute to the functional cross-talk between microglia and cells of the vasculature in health and disease.

Molecular dissection of HERV-W dependent microglial- and astroglial cell polarization
The endogenous retrovirus type W (HERV-W) is a human-specific entity, which was initially discovered in multiple sclerosis (MS) patient derived cells. We initially found that the HERV-W envelope (ENV) protein negatively affects oligodendrogenesis and controls microglial cell polarization towards a myelinated axon associated and damaging phenotype. Such first functional assessments were conducted ex vivo, given the human-specific origin of HERV-W. Recent experimental evidence gathered on a novel transgenic mouse model, mimicking activation and expression of the HERV-W ENV protein, revealed that all glial cell types are impacted and that cellular fates, differentiation, and functions were changed. In order to identify HERV-W-specific signatures in glial cells, the current study analyzed the transcriptome of ENV protein stimulated microglial- and astroglial cells and compared the transcriptomic signatures to lipopolysaccharide (LPS) stimulated cells, owing to the fact that both ligands can activate toll-like receptor-4 (TLR-4). Additionally, a comparison between published disease associated glial signatures and the transcriptome of HERV-W ENV stimulated glial cells was conducted. We, therefore, provide here for the first time a detailed molecular description of specific HERV-W ENV evoked effects on those glial cell populations that are involved in smoldering neuroinflammatory processes relevant for progression of neurodegenerative diseases.

Correspondence of fentanyl brain pharmacokinetics and behavior measured via engineering opioids biosensors and computational ethology
Despite the ongoing epidemic of opioid use disorder and death by fentanyl overdose, opioids remain the gold standard for analgesics. Pharmacokinetics (PK) dictates the individual's experience and utility of drugs; however, PK and behavioral outcomes have been conventionally studied in separate groups, even in preclinical models. To bridge this gap, we developed the first class of sensitive, selective, and genetically encodable fluorescent opioid biosensors, iOpioidSnFRs, including the fentanyl sensor, iFentanylSnFR. We expressed iFentanylSnFR in the ventral tegmental area of mice and recorded [fentanyl] alongside videos of behaviors before and after administration. We developed a machine vision routine to quantify the effects of the behavior on locomotor activity. We found that mice receiving fentanyl exhibited a repetitive locomotor pattern that paralleled the [fentanyl] time course. In a separate experiment, mice navigating a complex maze for water showed a dosedependent impairment in navigation, in which animals repeated incorrect paths to the exclusion of most of the unexplored maze for the duration of the average fentanyl time course. This approach complements classical operant conditioning experiments and introduces a key feature of human addiction, the ability to carry out an ethologically relevant survival task, only now quantified in rodents. Finally, we demonstrate the utility of iFentanylSnFR in detecting fentanyl spiked into human biofluids and the generalizability of engineering methods to evolve selective biosensors of other opioids, such as tapentadol and levorphanol. These results encourage diagnostic and continuous monitoring approaches to personalizing opioid regimens for humans.

Even Small Visual Latencies Can Profoundly Impair Implicit Sensorimotor Learning
Short sub-100ms visual feedback latencies are common in many types of human-computer interactions yet are known to markedly reduce performance in a wide variety of motor tasks from simple pointing to operating surgical robotics. These latencies are also present in the computer-based experiments used to study the sensorimotor learning that underlies the acquisition of motor performance. Inspired by neurophysiological findings showing that cerebellar LTD and cortical LTP would both be disrupted by sub-100ms latencies, we hypothesized that implicit sensorimotor learning may be particularly sensitive to these short latencies. Remarkably, we find that improving latency by just 60ms, from 85 to 25ms in latency-optimized experiments, increases implicit learning by 50% and proportionally decreases explicit learning, resulting in a dramatic reorganization of sensorimotor memory. We go on to show that implicit sensorimotor learning is considerably more sensitive to latencies in the sub-100ms range than at higher latencies, in line with the latency-specific neural plasticity that has been observed. This suggests a clear benefit for latency reduction in computer-based training that involves implicit sensorimotor learning and that across-study differences in implicit motor learning might often be explained by disparities in feedback latency.

Mitochondrial dysfunction drives a neuronal exhaustion phenotype in methylmalonic aciduria
Methylmalonic aciduria (MMA) is an inborn error of metabolism resulting in loss of function of the enzyme methylmalonyl-CoA mutase (MMUT). Despite acute and persistent neurological symptoms, the pathogenesis of MMA in the central nervous system is poorly understood, which has contributed to a dearth of effective brain specific treatments. Here we utilised patient-derived induced pluripotent stem cells and in vitro differentiation to generate a novel human neuronal model of MMA. We reveal strong evidence of mitochondrial dysfunction caused by deficiency of MMUT in patient neurons. By employing patch-clamp electrophysiology, targeted metabolomics, and bulk transcriptomics, we further expose an altered state of excitability, which we suggest may be connected to metabolic rewiring which is exacerbated by application of 2-dimethyloxoglutrate. Our work provides first evidence of mitochondrial driven neuronal dysfunction in MMA, which through our comprehensive characterisation of this paradigmatic model, enables first steps to identifying effective therapies.

Contradictory behavioral effects of neuronal perturbations on behavioral responses to linearly polarized light in freely walking Drosophila
Many insects can use the polarization of the skylight as a navigational cue. As shown previously, freely walking Drosophila orient along the e-vector of linearly polarized UV light presented both dorsally and ventrally. We are interested in the neuronal mechanisms leading to this behavior, and specifically how the central complex and its inputs are involved. We investigated the behavior of flies exposed to linearly polarized near-UV light (400 nm) presented dorsally. Flies walked freely in a circular, flat arena surrounded by a heat barrier. Using the GAL4-UAS genetic system, we drove the expression of the potassium inward rectifier KIR2.1 to perturb each of several different neuron types of the polarization vision pathway. Perturbing EPG compass neurons in the central complex slightly weakened average alignment and increased its variability. On the other hand, when two different GAL4 lines driving expression in the ER4m ring neurons, identified by connectomics as the major polarization inputs to the fly central complex, were perturbed, the alignment strength increased. A similar effect was observed when the inputs to ER4m, the TuBua neurons, were perturbed. We did not predict EPG and ER4m perturbations to cause opposite effects. Further investigation would be required to understand the physiological mechanisms of these contradictory behavioral effects.

Cell-type specialization of layer 5 excitatory neurons in tactile behavior
Layer 5 is the canonical output layer of sensory cortex. The two most numerous neural constituents of Layer 5 are pyramidal tract (PT) and intratelencephalic (IT) neurons. These output cell classes combine diverse sets of inputs and project to distinct locations across the brain, suggesting differing roles in sensory information processing. Here, we investigated the representation of touch and whisker motion in these two cell types within primary somatosensory cortex (S1) using optogenetically targeted single unit electrophysiology during whisker-guided object localization. PT neurons (N = 32) had much higher spike rates than IT (N=26) during behavior. Individual members of both were modulated by, but average population firing rates were stable between quiet and whisking periods. PT neurons showed greater absolute spike rate changes, but less relative modulation than IT neurons to whisking kinematic features. Touch-excited PT (N = 18) and IT neurons (N = 8) rapidly adapted to active touch. Both populations encoded the azimuthal position of touched objects, with IT neurons more sharply tuned to position. However, position was more precisely decodable from PT population activity, due to greater evoked spikes per touch. A consequence of these characteristics is that PT neurons, with their higher firing rates, may be more effective participants in rate-based neural codes, while IT neurons, with their sharp modulation, may be more effective in timing or synchrony-based codes.

Neuronal activity promotes axonal node-like clustering prior to myelination and remyelination in the central nervous system.
Nodes of Ranvier ensure the fast saltatory conduction along myelinated axons, through their enrichment in voltage-gated sodium and potassium channels. We and others have shown that node-like cluster assembly can occur before myelination. In multiple sclerosis, demyelination is associated with node of Ranvier disassembly, but node-like reassembly can occur prior to remyelination. Given the crucial role of neuronal activity in inducing (re)myelination, we asked whether neuronal activity could regulate node-like clustering. We show that node-like clustering is promoted by neuronal activity and decreased when excitatory glutamatergic receptors are inhibited. Altering glutamatergic neurotransmission leads to the downregulation of Nav1.1 expression, which we show to be critical for node-like clustering. Neuronal activity also promotes node-like clustering in remyelination. As node-like clusters modulate conduction velocity and myelination initiation along axons, we propose that activity-dependent node-like clustering could modulate neuronal network establishment, as well as myelination regulation and patterning during development, plasticity and repair.

A feedback-driven IoT microfluidic, electrophysiology, and imaging platform for brain organoid studies
The analysis of tissue cultures, particularly brain organoids, takes a high degree of coordination, measurement, and monitoring. We have developed an automated research platform enabling independent devices to achieve collaborative objectives for feedback-driven cell culture studies. Unified by an Internet of Things (IoT) architecture, our approach enables continuous, communicative interactions among various sensing and actuation devices, achieving precisely timed control of in vitro biological experiments. The framework integrates microfluidics, electrophysiology, and imaging devices to maintain cerebral cortex organoids and monitor their neuronal activity. The organoids are cultured in custom, 3D-printed chambers attached to commercial microelectrode arrays for electrophysiology monitoring. Periodic feeding is achieved using programmable microfluidic pumps. We developed computer vision fluid volume estimations of aspirated media, achieving high accuracy, and used feedback to rectify deviations in microfluidic perfusion during media feeding/aspiration cycles. We validated the system with a 7-day study of mouse cerebral cortex organoids, comparing manual and automated protocols. The automated experimental samples maintained robust neural activity throughout the experiment, comparable with the control samples. The automated system enabled hourly electrophysiology recordings that revealed dramatic temporal changes in neuron firing rates not observed in once-a-day recordings.

Dorsomedial Striatal Glutamatergic Transmission Inhibits Binge Drinking in Selectively Bred Crossed High Alcohol Preferring Mice
Crossed high alcohol preferring (cHAP) mice have been selectively bred to consume considerable amounts of alcohol resulting in binge drinking. The dorsal striatum (DS) is a brain region involved in action selection where the dorsomedial striatum (DMS) is involved in goal-directed action selection and dorsolateral striatum (DLS) is involved in habitual action selection. Alcohol use disorder (AUD) may involve a disruption in the balance between the DMS and DLS. While the DLS is involved in binge drinking, the reliance on the DMS and DLS in binge drinking has not been investigated in cHAP mice. We have previously demonstrated that glutamatergic activity in the DLS is necessary for binge-like alcohol drinking in C57BL/6J mice, another high drinking mouse. Because of this, we hypothesized that DLS glutamatergic activity would gate binge-like alcohol drinking in cHAP mice. cHAP mice underwent bilateral cannulation into the DMS or DLS and were allowed free-access to 20% alcohol for two-hours each day for 11 days. Mice were microinjected with the AMPA receptor (AMPAR) antagonist, NBQX, into the DMS or DLS immediately prior to alcohol access. AMPAR protein expression was also assessed in a separate group of animals in DS subregions following an 11-day drinking history. We found that intra-DMS (but not intra-DLS) NBQX, alters binge alcohol drinking, with intra-DMS NBQX increasing alcohol consumption. We also found that the ratio of GluA1 to GluA2 differs across DS subregions. Together, these findings suggest that glutamatergic activity in the DMS may serve to limit binge drinking in cHAP mice.

Low-grade systemic inflammation stimulates microglial turnover and accelerates the onset of Alzheimer's-like pathology
Several in vivo studies have shown that systemic inflammation, mimicked by LPS, triggers an inflammatory response in the CNS, driven by microglia, characterised by an increase in inflammatory cytokines and associated sickness behaviour. However, most studies induce relatively high systemic inflammation, not directly compared with the more common low grade inflammatory events experienced in humans during the life course. Using mice, we investigated the effects of low-grade systemic inflammation during an otherwise healthy early life, and how this may pre-condition the onset and severity of Alzheimer's disease (AD)-like pathology. Our results indicate that low grade systemic inflammation induces sub-threshold brain inflammation and promotes microglial proliferation driven by the CSF1R pathway, contrary to the effects caused by high systemic inflammation. In addition, repeated systemic challenges with low grade LPS induce disease-associated microglia. Finally, using an inducible model of AD-like pathology (Line 102 mice), we observed that pre-conditioning with repeated doses of low-grade systemic inflammation, prior to APP induction, promotes a detrimental effect later in life, leading to an increase in Abeta accumulation and disease-associated microglia. These results support the notion that episodic low grade systemic inflammation has the potential to influence the onset and severity of age-related neurological disorders, such as Alzheimer's disease.

Rat primary cortical cell tri-culture to study effects of amyloid-beta on microglia function
INTRODUCTION: The etiology and progression of sporadic Alzheimer's Disease (AD) have been studied for decades. One proposed mechanism is that amyloid-beta (A{beta}) proteins induce neuroinflammation, synapse loss, and neuronal cell death. Microglia play an especially important role in A{beta} clearance, and alterations in microglial function due to aging or disease may result in A{beta} accumulation and deleterious effects on neuronal function. However, studying these complex factors in vivo, where numerous confounding processes exist, is challenging, and until recently, in vitro models have not allowed sustained culture of microglia, astrocytes and neurons in the same culture. Here, we employ a tri-culture model of rat primary neurons, astrocytes, and microglia and compare it to co-culture (neurons and astrocytes) and mono-culture enriched for microglia to study microglial function (i.e., motility and A{beta} clearance) and proteomic response to exogenous A{beta}. METHODS: We established cortical co-culture (neurons and astrocytes), tri-culture (neurons, astrocytes, and microglia), and mono-culture (microglia) from perinatal rat pups. On days in vitro (DIV) 7 - 14, the cultures were exposed to fluorescently-labeled A{beta} (FITC-A{beta}) particles for varying durations. Images were analyzed to determine the number of FITC-A{beta} particles after specific lengths of exposure. A group of cells were stained for {beta}III-tubulin, GFAP, and Iba1 for morphological analysis via quantitative fluorescence microscopy. Cytokine profiles from conditioned media were obtained. Live-cell imaging with images acquired every 5 minutes for 4 hours was employed to extract microglia motility parameters (e.g., Euclidean distance, migration speed, directionality ratio). RESULTS & DISCUSSION: FITC-A{beta} particles were more effectively cleared in the tri-culture compared to the co-culture. This was attributed to microglia engulfing FITC-A{beta} particles, as confirmed via epifluorescence and confocal microscopy. Adding FITC-A{beta} significantly increased the size of microglia, but had no significant effect on neuronal surface coverage or astrocyte size. Analysis of the cytokine profile upon FITC-A{beta} addition revealed a significant increase in proinflammatory cytokines (TNF-, IL-1, IL-1{beta}, IL-6) in tri-culture, but not co-culture. In addition, A{beta} addition altered microglia motility marked by swarming-like motion with decreased Euclidean distance yet unaltered speed. These results highlight the importance of cell-cell communication in microglia function (e.g., motility and A{beta} clearance) and the utility of the tri-culture model to further investigate microglia dysfunction in AD.

Human cortical neurons rapidly generated by direct ES cell programming integrate into stroke-injured rat cortex
Stroke is a major cause of long-term disability in adult humans, the neuronal loss leading to motor, sensory, and cognitive impairments. Replacement of dead neurons by intracerebral transplantation of stem cell-derived neurons for reconstruction of injured neuronal networks has potential to become a novel therapeutic strategy to promote functional recovery after stroke. Here we describe a rapid and efficient protocol for the generation of cortical neurons via direct programming of human embryonic stem (hES) cells. Our results show that 7 days overexpression of the transcription factor neurogenin 2 (NGN2) in vitro was enough to generate hES-induced cells with cortical phenotype, as revealed by immunocytochemistry and RT-qPCR, and electrophysiological properties of neurons in an intermediate stage of maturity. At 3 months after translantation into the stroke-injured rat cortex, the hES-induced neurons (hES-iNs) showed immunocytochemical markers of mature layer-specific cortical neurons and sent widespread axonal projections to several areas in both hemispheres of the host brain. Their axons became myelinated and formed synaptic contacts with host neurons, as shown by immunoelectron microscopy. Our findings demonstrate for the first time that direct transcription factor programming of hES cells can efficiently and rapidly produce cortical neurons with capacity to integrate into the stroke-injured brain.

Cycle-frequency content EEG analysis improves the assessment of respiratory-related cortical activity
Time-Frequency (T-F) analysis of EEG is a common technique to characterise spectral changes in neural activity. This study explores the limitations of utilizing conventional spectral techniques in examining cyclic event-related cortical activities due to challenges, including high inter-trial variability. Introducing the Cycle-Frequency (C-F) analysis, we aim to enhance the evaluation of cycle-locked respiratory events. For synthetic EEG that mimicked cycle-locked pre-motor activity, C-F had better frequency and time precision compared to conventional T-F analysis, even when the number of trials was reduced from 50 to 20. Preliminary validations using EEG data during both unloaded breathing and loaded breathing (that evokes pre-motor activity) suggest potential benefits of using the C-F method, particularly in normalizing time units to cyclic activity phases and refining baseline placement and duration. The proposed approach could provide new insights for the study of rhythmic neural activities, complementing T-F analysis.

Redox-dependent synaptic clustering of gephyrin
Reactive oxygen species (ROS) play a central role in enhancing inhibitory signal transmission, thus extending their role beyond oxidative stress in disease and aging. However, the underlying molecular mechanisms mediating these functions have remained elusive. At inhibitory synapses, the scaffolding protein gephyrin clusters glycine and GABA type A receptors. Since gephyrin harbors multiple surface-exposed cysteines, we investigated the regulatory influence of ROS on gephyrin. We show that H2O2-induced oxidation of gephyrin cysteines triggered reversible, synaptic multimerization through disulfide bridge formation, which provided more receptor binding sites, lead to proteolytic protection and enhanced liquid-liquid phase separation. We identified mitochondria-derived ROS as a physiological source and observed oxidized gephyrin multimers in vivo, indicating that gephyrin can be regulated by the redox environment. Collectively, our findings suggest that cysteines in gephyrin modulate synaptic localization and clustering as regulatory redox-switches thereby establishing a link between neuronal and mitochondrial activity.

Atypical retinal function in a mouse model of Fragile X syndrome
Altered function of peripheral sensory neurons is an emerging mechanism for symptoms of autism spectrum disorders. Visual sensitivities are common in autism, but whether differences in the retina might underlie these sensitivities is not well-understood. We explored retinal function in the Fmr1 knockout model of Fragile X syndrome, focusing on a specific type of retinal neuron, the "sustained On alpha" retinal ganglion cell. We found that these cells exhibit changes in dendritic structure and dampened responses to light in the Fmr1 knockout. We show that decreased light sensitivity is due to increased inhibitory input and reduced E-I balance. The change in E-I balance supports maintenance of circuit excitability similar to what has been observed in cortex. These results show that loss of Fmr1 in the mouse retina affects sensory function of one retinal neuron type. Our findings suggest that the retina may be relevant for understanding visual function in Fragile X syndrome.

Social state gates vision using three circuit mechanisms in Drosophila
Animals are often bombarded with visual information and must prioritize specific visual features based on their current needs. The neuronal circuits that detect and relay visual features have been well-studied. Yet, much less is known about how an animal adjusts its visual attention as its goals or environmental conditions change. During social behaviors, flies need to focus on nearby flies. Here, we study how the flow of visual information is altered when female Drosophila enter an aggressive state. From the connectome, we identified three state-dependent circuit motifs poised to selectively amplify the response of an aggressive female to fly-sized visual objects: convergence of excitatory inputs from neurons conveying select visual features and internal state; dendritic disinhibition of select visual feature detectors; and a switch that toggles between two visual feature detectors. Using cell-type-specific genetic tools, together with behavioral and neurophysiological analyses, we show that each of these circuit motifs function during female aggression. We reveal that features of this same switch operate in males during courtship pursuit, suggesting that disparate social behaviors may share circuit mechanisms. Our work provides a compelling example of using the connectome to infer circuit mechanisms that underlie dynamic processing of sensory signals.

Transcriptional modulation unique to vulnerable motor neurons predict ALS across species and SOD gene mutations
Amyotrophic lateral sclerosis (ALS) is characterized by the progressive loss of somatic motor neurons (MNs), which innervate skeletal muscles. However, certain MN groups including ocular MNs that regulate eye movement are relatively resilient to ALS. To reveal mechanisms of differential MN vulnerability, we investigate the transcriptional dynamics of two vulnerable and two resilient MN populations in SOD1G93A ALS mice. Differential gene expression analysis shows that each neuron type displays a largely unique spatial and temporal response to ALS. Resilient MNs regulate few genes in response to disease, but show clear divergence in baseline gene expression compared to vulnerable MNs, which in combination may hold the key to their resilience. EASE, fGSEA and ANUBIX enrichment analysis demonstrate that vulnerable MN groups share pathway activation, including regulation of neuronal death, inflammatory response, ERK and MAPK cascades, cell adhesion and synaptic signaling. These pathways are largely driven by 11 upregulated genes, including Atf3, Cd44, Gadd45a, Ngfr, Ccl2, Ccl7, Gal, Timp1, Nupr1, Serpinb1a and Chl1, and indicate that cell death occurs through similar mechanisms across vulnerable MNs albeit with distinct timing. Machine learning using DEGs upregulated in our SOD1G93A spinal MNs predict disease in human stem cell-derived MNs harboring the SOD1E100G mutation, and show that dysregulation of VGF, PENK, INA and NTS are strong disease-predictors across SOD1 mutations and species. Meta-analysis across mouse SOD1 transcriptome datasets identified a shared transcriptional vulnerability code of 32 genes including e.g Sprr1a, Atf3, Fgf21, C1qb, Nupr1, Gap43, Adcyap1, Vgf, Ina and Mt1. In conclusion our study reveals vulnerability-specific gene regulation that may act to preserve neurons and can be used to predict disease.

Spatial contextual information modulates affordance processing and early electrophysiological markers of scene perception
Scene perception allows humans to extract information from their environment and plan navigation efficiently. The automatic extraction of potential paths in a scene, also referred to as navigational affordances is supported by scene-selective regions (SSRs) that enable efficient human navigation. Recent evidence suggests that the activity of these SSRs can be influenced by information from adjacent spatial memory areas. However, it remains unexplored how these contextual information could influence the extraction of bottom-up information, such as navigational affordances, from a scene and the underlying neural dynamics. Therefore, we analyzed event-related potentials (ERPs) in 26 young adults performing scene and spatial memory tasks in artificially generated rooms with varying numbers and locations of available doorways. We found that increasing the number of navigational affordances only impaired performance in the spatial memory task. ERP results showed a similar pattern of activity for both tasks, but with increased P2 amplitude in the spatial memory task compared to the scene memory. Finally, we reported no modulation of the P2 component by the number of affordances in either task. This modulation of early markers of visual processing suggests that the dynamics of SSR activity are influenced by a priori knowledge, with increased amplitude when participants have more contextual information about the perceived scene. Overall, our results suggest that prior spatial knowledge about the scene, such as the location of a goal, modulates early cortical activity associated with scene-selective regions, and that this information may interact with bottom-up processing of scene content, such as navigational affordances.

Widespread innervation of motoneurons by spinal V3 neurons globally amplifies locomotor output in mice.
While considerable progress has been made in understanding the neuronal circuits that underlie the patterning of locomotor behaviours such as walking, less is known about the circuits that amplify motoneuron output to enable adaptable increases in muscle force across different locomotor intensities. Here, we demonstrate that an excitatory propriospinal neuron population (V3 neurons, Sim1+) forms a large part of the total excitatory interneuron input to motoneurons (~20%) across all hindlimb muscles. Additionally, V3 neurons make extensive connections among themselves and with other excitatory premotor neurons (such as V2a neurons). These circuits allow local activation of V3 neurons at just one segment (via optogenetics) to rapidly depolarize and amplify locomotor-related motoneuron output at all lumbar segments in both the in vitro spinal cord and the awake adult mouse. Interestingly, despite similar innervation from V3 neurons to flexor and extensor motoneuron pools, functionally, V3 neurons exhibit a pronounced bias towards activating extensor muscles. Furthermore, the V3 neurons appear essential to extensor activity during locomotion because genetically silencing them leads to slower and weaker mice with a poor ability to increase force with locomotor intensity, without much change in the timing of locomotion. Overall, V3 neurons increase the excitability of motoneurons and premotor neurons, thereby serving as global command neurons that amplify the locomotion intensity.

Lesion-remote astrocytes govern microglia-mediated white matter repair
Spared regions of the damaged central nervous system undergo dynamic remodeling and exhibit a remarkable potential for therapeutic exploitation. Here, lesion-remote astrocytes (LRAs), which interact with viable neurons, glia and neural circuitry, undergo reactive transformations whose molecular and functional properties are poorly understood. Using multiple transcriptional profiling methods, we interrogated LRAs from spared regions of mouse spinal cord following traumatic spinal cord injury (SCI). We show that LRAs acquire a spectrum of molecularly distinct, neuroanatomically restricted reactivity states that evolve after SCI. We identify transcriptionally unique reactive LRAs in degenerating white matter that direct the specification and function of local microglia that clear lipid-rich myelin debris to promote tissue repair. Fueling this LRA functional adaptation is Ccn1, which encodes for a secreted matricellular protein. Loss of astrocyte CCN1 leads to excessive, aberrant activation of local microglia with (i) abnormal molecular specification, (ii) dysfunctional myelin debris processing, and (iii) impaired lipid metabolism, culminating in blunted debris clearance and attenuated neurological recovery from SCI. Ccn1-expressing white matter astrocytes are specifically induced by local myelin damage and generated in diverse demyelinating disorders in mouse and human, pointing to their fundamental, evolutionarily conserved role in white matter repair. Our findings show that LRAs assume regionally divergent reactivity states with functional adaptations that are induced by local context-specific triggers and influence disorder outcome.

Efficiency and reliability in biological neural network architectures
Neurons in a neural circuit have been demonstrated to have astonishing diversity in terms of numbers and targets of their synaptic connectivity and the statistics of their spiking activity. We hypothesize that this is the result of an underlying struggle between reliability, robustness and efficiency of the information represented by their spike trains. Specifically, certain architectures of connectivity foster highly uncorrelated and thus efficient activity, others foster the opposite trends, i.e., robust activity. Both coexists in a neural circuit, leading to the observed long-tailed and highly diverse distributions of connectivity and activity metrics, and allowing the robust subpopulations to promote the reliability of the network as a whole. To test the hypothesis and characterize these architectures, we analyzed several openly available connectomes and found that all of them contained groups of neurons with very different levels of complexity of their connectivity. Using co-registered functional data and simulations of a morphologically detailed network model, we found that low complexity groups were indeed characterized by efficient spiking activity and high complexity groups by reliable but inefficient activity. Moreover, for neurons in cortical input layers, the focus was increasing reliability; for output layers, it was increasing efficiency. To test the effect of the complex subpopulations on the reliability of the network as a whole, we manipulated the connectivity in the model to increase or decrease complexity and confirmed that it affected activity in the expected ways. Our results impact our understanding of the neural code, demonstrating that it is as diverse as neuronal connectivity and activity, and must be understood in the context of the efficiency/reliability struggle.

Cholinergic Transmission in an Inducible Transgenic Mouse Model of Paroxysmal Dystonia
Altered interaction between striatonigral dopaminergic (DA) inputs and local acetylcholine (ACh) in striatum has long been hypothesized to play a central role in dystonia pathophysiology. Indeed, previous research across various genetic mouse models of human isolated dystonia has identified as a shared endophenotype with paradoxical excitation of striatal cholinergic interneurons (ChIs) activity in response to activation of dopamine D2 receptor (D2R). These mouse models lack a dystonic motor phenotype, which leaves a critical gap in comprehending the role of ACh transmission in the manifestation of dystonia. To tackle this question, we used a combination of ex vivo slice physiology and in vivo monitoring of striatal ACh dynamics in the inducible, phenotypically penetrant, transgenic mouse model of paroxysmal non-kinesigenic dyskinesia (PNKD). We found that, similarly to other genetic models, the PNKD mouse displays D2R-induced paradoxical excitation of ChI firing in ex vivo striatal brain slices. In vivo, caffeine triggers dystonic symptoms while reversing the D2R-mediated excitation of ChIs and desynchronizing the striatal cholinergic network. In WT littermate controls, caffeine stimulates spontaneous locomotion through a similar but reversed mechanism involving an excitatory switch of the D2R control of ChI activity, associated with enhanced cholinergic network synchronization. Together these observations suggest that D2Rs may play an important role in synchronizing the ChI network during heightened movement states. The 'paradoxical excitation' described in dystonia models could represent a compensatory or protective mechanism that prevents manifestation of movement abnormalities and allows for phenotypic dystonia when lost.

Synchrony between midbrain gene transcription and dopamine terminal regulation is modulated by chronic alcohol drinking
Alcohol use disorder is marked by disrupted behavioral and emotional states which persist into abstinence. The enduring synaptic alterations that remain despite the absence of alcohol are of interest for interventions to prevent relapse. Here, 28 male rhesus macaques underwent over 20 months of alcohol drinking interspersed with three 30-day forced abstinence periods. After the last abstinence period, we paired direct sub-second dopamine monitoring via ex vivo voltammetry in nucleus accumbens slices with RNA-sequencing of the ventral tegmental area. We found persistent augmentation of dopamine transporter function, kappa opioid receptor sensitivity, and dynorphin release -- all inhibitory regulators which act to decrease extracellular dopamine. Surprisingly, though transcript expression was not altered, the relationship between gene expression and functional readouts of these encoded proteins was highly dynamic and altered by drinking history. These results outline the long-lasting synaptic impact of alcohol use and suggest that assessment of transcript-function relationships is critical for the rational design of precision therapeutics.

FABEL: Forecasting Animal Behavioral Events with Deep Learning-Based Computer Vision
Behavioral neuroscience aims to provide a connection between neural phenomena and emergent organism-level behaviors. This requires perturbing the nervous system and observing behavioral outcomes, and comparing observed post-perturbation behavior with predicted counterfactual behavior and therefore accurate behavioral forecasts. In this study we present FABEL, a deep learning method for forecasting future animal behaviors and locomotion trajectories from historical locomotion alone. We train an offline pose estimation network to predict animal body-part locations in behavioral video; then sequences of pose vectors are input to deep learning time-series forecasting models. Specifically, we train an LSTM network that predicts a future food interaction event in a specified time window, and a Temporal Fusion Transformer that predicts future trajectories of animal body-parts, which are then converted into probabilistic label forecasts. Importantly, accurate prediction of food interaction provides a basis for neurobehavioral intervention in the context of compulsive eating. We show promising results on forecasting tasks between 100 milliseconds and 5 seconds timescales. Because the model takes only behavioral video as input, it can be adapted to any behavioral task and does not require specific physiological readouts. Simultaneously, these deep learning models may serve as extensible modules that can accommodate diverse signals, such as in-vivo fluorescence imaging and electrophysiology, which may improve behavior forecasts and elucidate invervention targets for desired behavioral change.

Putaminal dopamine modulates movement motivation in Parkinson's disease
The relative inability to produce effortful movements (akinesia) is the most specific motor sign of Parkinson's disease. The motor motivation hypothesis suggests that akinesia may not reflect a deficiency in motor control per se, but a deficiency in cost-benefit considerations for motor effort. For the first time, we investigated the quantitative effect of dopamine depletion on the motivation of motor effort in Parkinson's disease. A total of 21 patients with Parkinson's disease and 26 healthy controls were included. An incentivized force task was used to capture the amount of effort participants were willing to invest for different monetary incentive levels and dopamine transporter depletion in the bilateral putamen was assessed. Our results demonstrate that patients with Parkinson's disease applied significantly less grip force than healthy controls, especially for low incentive levels. Congruously, decrease of motor effort with greater loss of putaminal dopaminergic terminals was most pronounced for low incentive levels. This signifies that putaminal dopamine is most critical to motor effort when the trade-off with the benefit is poor. Taken together, we provide direct evidence that the reduction of effortful movements in Parkinson's disease depends on motivation and that this effect is associated with putaminal dopaminergic degeneration.

Internal monitoring of whisking and locomotion in the superior colliculus
To localize objects using active touch, our brain must merge its map of the body surface with an ongoing representation of self-motion. While such computations are often ascribed to the cerebral cortex, we examined the midbrain superior colliculus (SC), due to its close relationship with the sensory periphery as well as higher, motor-related brain regions. We discovered that active whisking kinematics and locomotion speed accurately predict the firing rate of mouse SC neurons. Kinematic features occurring either in the past, present, or future best predicted spiking, indicating that the SC population continuously estimates the trajectory of self-motion. Half of all self-motion encoding neurons displayed a touch response as an object entered the active whisking field. Trial-to-trial variation in the size of this response was explained by the position of the whisker upon touch. Taken together, these data indicate that SC neurons linearly combine an internal estimate of self-motion with external stimulation to enable active tactile localization.

Naturalistic Object Representations Depend on Distance and Size Cues
Egocentric distance and real-world size are important cues for object perception and action. Nevertheless, most studies of human vision rely on two-dimensional pictorial stimuli that convey ambiguous distance and size information. Here, we use fMRI to test whether pictures are represented differently in the human brain from real, tangible objects that convey unambiguous distance and size cues. Participants directly viewed stimuli in two display formats (real objects and matched printed pictures of those objects) presented at different egocentric distances (near and far). We measured the effects of format and distance on fMRI response amplitudes and response patterns. We found that fMRI response amplitudes in the lateral occipital and posterior parietal cortices were stronger overall for real objects than for pictures. In these areas and many others, including regions involved in action guidance, responses to real objects were stronger for near vs. far stimuli, whereas distance had little effect on responses to pictures--suggesting that distance determines relevance to action for real objects, but not for pictures. Although stimulus distance especially influenced response patterns in dorsal areas that operate in the service of visually guided action, distance also modulated representations in ventral cortex, where object responses are thought to remain invariant across contextual changes. We observed object size representations for both stimulus formats in ventral cortex but predominantly only for real objects in dorsal cortex. Together, these results demonstrate that whether brain responses reflect physical object characteristics depends on whether the experimental stimuli convey unambiguous information about those characteristics.

Neurodevelopmental Subtypes of Functional Brain Organization in the ABCD Study Using a Rigorous Analytic Framework
The current study demonstrates that an individual's resting-state functional connectivity (RSFC) is a dependable biomarker for identifying differential patterns of cognitive and emotional functioning during late childhood. Using baseline RSFC data from the Adolescent Brain Cognitive Development (ABCD) study, which includes children aged 9-11, we identified four distinct RSFC subtypes We introduce an integrated methodological pipeline for testing the reliability and importance of these subtypes. In the Identification phase, Leiden Community Detection defined RSFC subtypes, with their reproducibility confirmed through a split-sample technique in the Validation stage. The Evaluation phase showed that distinct cognitive and mental health profiles are associated with each subtype, with the Predictive phase indicating that subtypes better predict various cognitive and mental health characteristics than individual RSFC connections. The Replication stage employed bootstrapping and down-sampling methods to substantiate the reproducibility of these subtypes further. This work allows future explorations of developmental trajectories of these RSFC subtypes.

An arrayed CRISPR/Cas9 screen identifies mTORC1 as a regulator of lipid droplet accumulation in APOE E3 and APOE KO iPSC-derived microglia
Variants of the Apolipoprotein E (APOE) gene, particularly the E4 allele, are significantly associated with an increased risk of Alzheimer's Disease and have been implicated in neuroinflammatory processes due to disrupted lipid metabolism. Lipid alterations can manifest in glial cells as an excessive buildup of lipids, potentially contributing to neuroinflammation. In this study, we observed a heightened lipid load in APOE-deficient human induced pluripotent stem cell (iPSC)-derived microglia relative to cells with other APOE isoforms. To explore the mechanisms governing lipid handling within microglia, we established a technique for the nucleofection of CRISPR/Cas9 ribonucleoprotein complexes into iPSC-derived myeloid cells. Utilizing this method, we performed a targeted screen to identify key upstream modifiers in lipid droplet formation. Our findings highlight the mammalian target of rapamycin complex 1 (mTORC1) signaling pathway as a pivotal influence on lipid storage in microglia with both APOE3 and APOE knockout genotypes, underscoring its role in lipid dysregulation associated with Alzheimer's Disease and neuroinflammation.

Spectral waveform analysis dissociates human cortical alpha rhythms
The non-sinusoidal waveform of neuronal oscillations reflects the physiological properties of underlying circuit interactions and may serve as an informative biomarker of healthy and diseased human brain function. However, little is known about which brain rhythms can be dissociated based on their waveform and methods to comprehensively characterize waveforms are missing. Here, we introduce a novel spectral waveform analysis (SWA) that provides a complete waveform description, is noise-resistant, and allows to reconstruct time-domain waveforms. We applied this framework to human magnetoencephalography (MEG) recordings during rest and identified several distinct and previously unknown cortical alpha waveforms that were temporally stable and specific for individual subjects. Our findings suggest at least four distinct alpha rhythms in human sensorimotor, occipital, temporal, and parietal cortex. SWA provides a powerful new framework to characterize the waveform of neural oscillations in the healthy and diseased human brain.

Neurosphere culture derived from aged hippocampal dentate gyrus
The neurosphere assay is the gold standard for determining proliferative and differentiation potential of neural progenitor cells (NPCs) in neurogenesis studies. While several in vitro assays have been developed to model the process of neurogenesis, they have predominantly used embryonic and early postnatal NPCs derived from the dentate gyrus (DG). A limitation of these approaches is that they do not provide insight into adult-born NPCs, which are modeled to affect hippocampal function and diseases later in life. Here, we show a novel free-floating neurosphere culture system using NPCs isolated from the DG of mature adult and aged mice. The protocol outlines detailed steps on the isolation, propagation, and maintenance of neurospheres from adult and aged (>12 months old) mouse brain and how to differentiate cultured neurospheres into neurons and astrocytes. Culturing adult and aged NPCs provides an important in vitro model to (1) investigate cellular and molecular properties of this unique cell population and (2) expand the understanding of plasticity in the adult and aging brain. This protocol requires ~2 hours to complete dissection, dissociation and culture plating, while differentiation to neuronal and astrocytic lineages takes 9 days. By focusing on neurospheres obtained from animals at later ages this model facilitates investigation of important biological questions related to development and differentiation of hippocampal neurons generated throughout adult life.

Endopiriform neurons projecting to ventral CA1 are a critical node for recognition memory
The claustrum complex is viewed as fundamental for higher order cognition; however, the circuit organization and function of its ventral subregion, the endopiriform (EN), are not well understood. Using circuit analyses in mice, we show that EN neurons defined by their projection to ventral CA1 (ENvCA1-proj. neurons) were a major source of afferents to ventral CA1 (vCA1), with diverging collaterals to the olfactory-limbic system, and formed recurrent circuits within EN and with the piriform cortex. In vCA1, these axons exclusively targeted the distal subregion triggering potent feedforward inhibition of pyramidal neurons. By combining in vivo neuronal activity monitoring, circuit manipulations, and behavior analysis, we found that, during all phases of recognition memory test, the ENvCA1-proj. activity correlated with the time mice spent in particular arena locations. The ENvCA1-proj. activity was biased around social or non-social stimuli when they were present, especially when they were novel, a pattern consistent with salience detection and attention. Inhibition of EN vCA1-proj. neurons disrupted mice's memory-guided response to novel relative to familiar stimuli, without affecting innate bias for novel stimuli. These findings suggest EN as an essential node for social and object recognition memory, most likely by responding to salient environmental stimuli and by coordinating this response with downstream limbic system.

Whole-body connectome of a segmented annelid larva
Nervous systems coordinate effectors across the body during movements. We know little about the cellular-level structure of synaptic circuits for such body-wide control. Here we describe the whole-body synaptic connectome of a segmented larva of the marine annelid Platynereis dumerilii. We reconstructed and annotated over 9,000 neuronal and non-neuronal cells in a whole-body serial electron microscopy dataset. Differentiated cells were classified into 202 neuronal and 92 non-neuronal cell types. We analyse modularity, multisensory integration, left-right and intersegmental connectivity and motor circuits for ciliated cells, glands, pigment cells and muscles. We identify several segment-specific cell types, demonstrating the heteromery of the annelid larval trunk. At the same time, segmentally repeated cell types across the head, the trunk segments and the pygidium suggest the serial homology of all segmental body regions. We also report descending and ascending pathways, peptidergic circuits and a multi-modal mechanosensory girdle. Our work provides the basis for understanding whole-body coordination in an entire segmented animal.

Dynamic role of GlyT1 as glycine sink or source: pharmacological implications for the gain control of NMDA receptors
Glycine transporter 1 (GlyT1) mediates termination of inhibitory glycinergic receptors signaling in the spinal cord and brainstem, and is also diffusely present in the forebrain. Here, it regulates the ambient glycine concentration influencing the "glycine"-site occupancy of N-methyl-D-aspartate (NMDARs). GlyT1 is a reversible transporter with a substantial, but not excessive, sodium-motive force for uphill transport. This study examines its potential role as a glycine source, either by reversed-uptake or by heteroexchange. I explored how glycine accumulation triggers its release, facilitating the activation of NMDARs by glutamate applied alone. Indeed, glutamate evokes no current in "naive" oocytes coexpressing GluN1/GluN2A and GlyT1, a previously characterized cellular model, but now using GlyT1 as the only potential source of coagonist for NMDAR activation. After glycine uptake, however, glutamate evokes large currents, blocked by ALX-5407 and potentiated by sarcosine, a specific inhibitor and substrate of GlyT1, respectively. These results suggest higher occupancy of the co-agonist site when GlyT1 functions as a glycine source either by reversed-uptake or by heteroexchange. A difference between these two glycine-release mechanisms occurs at hyperpolarized potentials, which induce an apparent voltage-dependent block of NMDAR currents, whereas heteroexchange preserves NMDAR activation at these potentials. Together, these results confirm GlyT1-mediated efflux as a positive regulator of NMDAR co-agonist site occupancy, and demonstrate sarcosine heteroexchange effectiveness in enhancing coagonist site occupancy. Depending on its actual mode of transport, GlyT1-inhibitors and sarcosine may have distinct effects on ambient glycine and NMDAR facilitation, and be a source of variation in reversing NMDAR hypofunction in schizophrenia.