bioRxiv Subject Collection: Neuroscience's Journal

Distinct patterns of de novo coding variants contribute to Tourette Syndrome etiology
Tourette syndrome (TS) is a highly heritable childhood-onset neuropsychiatric disorder characterized by persistent motor and vocal tics. While both common and rare variants contribute to TS susceptibility, the role of rare de novo mutations (DNMs) remains incompletely characterized. Here, we report findings from the largest TS whole-exome sequencing study to date, analyzing 1,466 TS trios alongside 6,714 autism spectrum disorder (ASD) trios and 5,880 unaffected sibling controls from the Simons Simplex Collection (SSC) and SPARK cohorts. Leveraging a trio-based design across these cohorts enabled calibrated assessment of DNM burden while controlling for background mutation rates. We observed a significant exome-wide enrichment of protein-truncating DNMs in TS probands, particularly within genes intolerant to loss-of-function variation (pLI [≥] 0.9), with little contribution from damaging missense variants. Notably, TS probands did not exhibit enrichment in previously implicated ASD or developmental delay (DD) genes, but elsewhere in the genome, suggesting a distinct rare variant architecture. Using a Bayesian statistical framework that integrates both de novo and rare inherited coding variants, we identified three candidate TS risk genes with FDR [≤] 0.05: PPP5C, EXOC1, and GXYLT1. Literature shows that they have prior links to neurodevelopmental and psychiatric disorders. These findings reveal a rare variant burden in TS that is genetically distinguishable from ASD, underscore the importance of loss-of-function mutations in TS risk, and nominate novel candidate genes for future functional investigation.

Biased inter-columnar communication and short-term plasticity in mouse barrel cortex
The barrel cortex (BC) processes input from whiskers to probe and analyze objects in an environment. This sensory input exhibits a complex phase, direction, and frequency-dependent structure arising from whisking kinematics. Little is known about how BC microcircuits process this information. In particular, it remains unclear how the BC extracts relevant spatiotemporal features by integrating input from multiple whiskers. To investigate communication within and between cortical barrels, we targeted a hybrid voltage sensor (hVOS) to Scnn1a excitatory neurons in BC layer 4 (L4) of male and female mice (mean age 7.8 weeks), and imaged population responses to electrical stimulation. Coronal and sagittal slices presented the laminar structure with barrels aligned along stereotyped whisking directions. Voltage imaging tracked activity along an L4[->]L2/3[->]L4 relay during inter-barrel communication. AMPA receptor blockade demonstrated that this relay depends on excitatory synaptic transmission and revealed intra- and inter-barrel feedforward inhibition. Single-pulse responses were isotropic in amplitude, conduction velocity, and half-width, but latency was longer for communication with dorsal and caudal barrels. Furthermore, paired-pulse depression was weakest and recovery slowest for protraction-related directions, especially between caudally adjacent barrels, suggesting preferential enhancement of repetitive inputs in this direction. These results identify direction-dependent synaptic circuitry in the shaping of inter-barrel communication. Anisotropy in short-term plasticity aligns with whisker motion kinematics, suggesting that BC microcircuits are tuned to preserve temporal fidelity and selectively filter inputs according to whisking phase and direction.

Mapping brain volume changes in the zQ175DN mouse model of Huntington's disease: a longitudinal MRI study
Huntington's disease (HD) is a progressive neurodegenerative disease affecting motor and cognitive abilities, as well as exhibiting psychiatric manifestations. Studies in people with HD (PwHD) consistently report atrophy of the caudate and putamen as an early pathological event and is therefore considered an early biomarker. Investigating whether similar phenotypic features are apparent in rodent HD models is important since it could have translational potential in evaluating the efficacy of novel therapeutic strategies. We used high-resolution anatomical images to longitudinally investigate brain morphology in the zQ175DN heterozygous mouse model (HET) and wildtype littermates (WT) at 3, 6, and 10 months of age (M), which reflect different stages of phenotypic progression. We investigated volumetric alterations using semi-automatic segmentations of HD on relevant regions-of-interest (striatum, cerebellum, corpus callosum, cerebral cortex, ventricles, and total brain volume) and whole brain voxel-wise Tensor Based Morphometry (TBM) analysis. The striatum showed the earliest progressive lower absolute volume in HET mice compared to WT, starting from 3M, followed by lower absolute volume of cortex and corpus callosum concomitantly at 6 and 10M. TBM highlighted lower relative local volume in the rostral-medial striatum at all ages, and in cerebral cortex in HET mice at 6 and 10M. A bigger relative local volume in the cerebellum was observed at all ages in HET mice, and in the globus pallidus, substantia nigra, at 6 and 10M. Overall, this study revealed key structural abnormalities that resemble the natural history of PwHD. Hence, analysis of brain structure through MRI in the zQ175DN heterozygous mouse model holds potential for testing disease-modifying treatments expected to slow down or prevent structural degeneration.

Distinct involvements of the subthalamic nucleus subpopulations in reward-biased decision-making in monkeys
The subthalamic nucleus (STN) is a part of the indirect and hyperdirect pathways in the basal ganglia (BG) and has been implicated in movement control, impulsivity, and decision-making. We recently demonstrated that, for perceptual decisions, the STN includes at least three subpopulations of neurons with different decision-related activity patterns (Branam et al., 2024). Here we show that, for decisions that require both perceptual and reward-based processing, many STN neurons are sensitive to both sensory evidence and reward expectations. Within a drift-diffusion framework, STN subpopulations show different relationships to model components reflecting formation of the decision variable, dynamics of the decision bound, and non-decision-related processes. The subpopulations also differ in their representations of quantities related to decision evaluation, including choice accuracy and reward expectation. These results suggest that the STN plays multiple roles in decision formation and evaluation to guide complex decisions that combine multiple sources of information.

Low rank adaptation of chemical foundation models generate effective odorant representations
Featurizing odorants to enable robust prediction of their properties is difficult due to the complex activation patterns that odorants evoke in the olfactory system. Structurally similar odorants can elicit distinct activation patterns in both the sensory periphery (i.e., at the receptor level) and downstream brain circuits (i.e., at a perceptual level). Despite efforts to design or discover features for odorants to better predict how they activate the olfactory system, we lack a universally accepted way to featurize odorants. In this work, we demonstrate that feature-based approaches that rely on pre-trained foundation models do not significantly outperform classical hand-designed features, but that targeted foundation model fine-turning can increase model performance beyond these limits. To show this, we introduce a new model that creates olfaction-specific representations: LoRA-based Odorant-Receptor Affinity prediction with CROSS-attention (LORAX). We compare existing chemical foundation model representations to hand-designed physicochemical descriptors using feature-based methods and identify large information overlap between these representations, highlighting the necessity of fine-tuning to generate novel and superior odorant representations. We show that LORAX produces a feature space more closely aligned with olfactory neural representation, enabling it to outperform existing models on predictive tasks.

Environmental Noise Alters Neural Regulation Without Behavioral Impairment: A Pilot EEG Study
Environmental factors can profoundly influence cognitive performance and well-being in the workplace. Exposure to environmental noise is a potent stressor that elevates arousal and impairs attention, whereas natural elements are associated with stress reduction and cognitive restoration. In this pilot study, we examined whether natural soundscapes could buffer the neural effects of noise exposure. Eleven healthy adults performed five cognitive tasks, Stroop, N-back, Go/No-Go, Dot-Probe, and Visual Search, under three auditory conditions: Noise (simulated urban traffic), Nature (ambient natural sounds), and Control (silence with earplugs). Continuous electroencephalography (EEG) captured oscillatory activity, and participants provided self-reports of mood, stress, and lifestyle habits. Behavioral accuracy and reaction time did not differ significantly across environments (all p > 0.10), indicating preserved overt performance. However, EEG revealed clear environment-dependent modulation. Relative to Control, the Noise condition produced a marked shift toward beta-dominant activity in midline cortex: mixed-effects models showed higher /{beta} ratios over central (t=3.8, cluster-corrected p<0.01) and centroparietal (t=4.6, p<0.01) regions, reflecting reduced posterior power and a sustained-alertness profile. In contrast, Nature exposure preserved posterior regulation while easing cognitive-load markers, {theta}/ ratios fell in bilateral temporal cortex (t=-3.2, p<0.05), {theta}/{beta} ratios dropped across frontocentral and temporal networks (t=-3.6 to -7.4, p<0.01), and the engagement index rose in the same territories (t=-3.6 to -7.3, p<0.001), consistent with greater intrinsic engagement and lower self-reported stress during the nature soundscape. Although behavioral performance remained stable, EEG data revealed distinct neural costs of noise exposure and a protective effect of natural soundscapes. These findings suggest that traditional task metrics may underestimate cognitive strain, and that biophilic auditory environments could help sustain neural efficiency and resilience in demanding work settings.

Methodological choices strongly modulate the sensitivity and specificity of lesion-symptom mapping analyses
Lesion mapping results can vary substantially as a function of specific analysis parameters, but the extent to which individual methodological choices interact to modulate the sensitivity and specificity of results is not clear. Here, we employed a large-scale simulation approach to inform practical recommendations for lesion symptom mapping studies. Routine clinical imaging from 959 stroke survivors (mean age = 72.5, 49.3% female) was used to conduct 384,780 lesion mapping analyses based on simulated behavioural data. Each simulated analysis used different combinations of plausible sample inclusion criteria, analysis parameters (e.g., correction factors), analysis types (e.g., univariate vs. multivariate), and underlying target correlates. Simulated analysis accuracy (Dice similarity coefficient and percent coverage of target correlates) was compared across designs.Overall, analysis accuracy varied widely and was substantially modulated by the specific design used. Analyses that maximised lesion coverage by including large and diverse samples reliably outperformed analyses using more restricted samples. Analyses using direct total lesion volume controls outperformed analyses using other (or no) volume corrections across all accuracy measures. False discovery rate corrections yielded the best performance in terms of target coverage, while permutation corrections yielded the best Dice coefficients. While multivariate approaches were more accurate than univariate analyses in terms of Dice coefficient, univariate analyses generated higher target hit rates and percent target coverage.These results identify specific analysis designs suitable for studies aiming to maximise their sensitivity and/or specificity to underlying critical correlates, while highlighting the inferential strengths and weaknesses of these complementary approaches.

Mitochondrial bioenergetic signatures differentiate asymptomatic from symptomatic Alzheimer's disease
Asymptomatic Alzheimer's disease (AsymAD) refers to individuals who, despite exhibiting amyloid-b plaques and tau pathology comparable to Alzheimer's disease (AD), maintain cognitive performance similar to cognitively normal individuals. The resilience mechanism in these AsymAD individual remains understudied. We performed a systematic analysis comparing AsymAD and AD across multiple cohorts (ROSMAP, Banner and Mount Sinai), brain regions (BA6, BA9, BA36 and BA37) and neuronal and glial cell types using proteomics and transcriptomics data. AsymAD brains exhibited preserved mitochondrial bioenergetics, characterized by enhanced oxidative phosphorylation (OXPHOS), electron transport chain (ETC) activity, fatty acid and lipid metabolism, and branched-chain amino acid (BCAA) utilization. Pathways regulating mitochondrial complex biogenesis and calcium homeostasis were also upregulated. Key mitochondrial proteins such as MRPL47, CPT2, BCAT2, and IDH2, were consistently upregulated in AsymAD, whereas MACROD1 was downregulated. At the cellular level, excitatory neurons, including superficial, mid-layer, and deep-layer subtypes, exhibited the most preserved mitochondrial function, whereas vulnerable inhibitory subtypes, including PVALB and SST neurons, showed increased cellular abundance and bioenergetic activity. In contrast, microglia and oligodendrocytes proportions were reduced in AsymAD relative to AD. Our findings identify preserved mitochondrial bioenergetics as a defining feature of resilience in AD and suggest that enhancing NADH metabolism via NAD+ precursor-based interventions may potentially help in maintaining cognitive function despite amyloid and tau pathology.

VTA dopamine neuron activity produces spatially organized value representations
How does the activity of midbrain dopamine (DA) neurons reinforce actions? A prominent hypothesis is that the activity of ventral tegmental area (VTA) DA neurons instructs representations of predicted reward, or value, in downstream neurons1. To directly test this model, we performed comprehensive striatal recordings in mice engaged in a trial-and-error probabilistic learning task where they continuously adapted their choices to obtain a reward of optogenetic stimulation of VTA DA neurons (paired with an auditory cue). We then assessed neural representations of action values (estimated from a behavioral model), revealing for the first time that VTA DA stimulation is sufficient to generate downstream neural correlates of action value. Surprisingly, these value correlates were strongest in the intermediate caudoputamen (CP) and weakest in the nucleus accumbens (NAc), despite NAc being the major projection target of VTA DA neurons2,3. This was true not only for the value of each choice, but also for state value (reward expectation) and relative value (the decision variable). However, value representations were differentially organized within the intermediate CP, with ventromedial domains (which receive inputs from orbitofrontal cortex) preferentially encoding state value and dorsolateral domains (which receive inputs from motor cortex) preferentially encoding relative value. A difference in learning rate for the value computation between NAc and CP did not explain the relatively weak value correlates in NAc. Instead, we found that VTA DA stimulation was sufficient to produce learned neural responses to the stimulation-paired auditory cue throughout the striatum, including in the NAc, and that animals work for this cue rather than for VTA DA stimulation itself. Overall, this suggests that VTA DA neurons support trial-and-error learning indirectly, by making stimuli valuable ('conditioned reinforcers'), which in turn support the generation of action value representations in the CP.

Unconscious switching of dorsal and medial pathways for plasticity and stability during NREM and REM sleep
While visual perceptual learning improves during non-REM sleep and stabilizes during REM sleep via excitatory-inhibitory neurotransmitter (E/I) balance in early visual areas (EVA), the role of prefrontal regions remains unclear. Here, we show that contributions of the dorsolateral prefrontal cortex (DLPFC) and medial prefrontal cortex (mPFC) differ by sleep stage in human adults. During non-REM sleep, plasticity increased in DLPFC, indexed by elevated E/I balance measured with magnetic resonance spectroscopy and polysomnography, in correlation with performance gains. During REM sleep, stability increased in mPFC, indexed by reduced E/I balance, in correlation with resilience to retrograde interference from new learning. E/I balance changes and their effects on learning paralleled those in EVA. Connectivity weights between EVA and DLPFC, and between EVA and mPFC, switched with sleep stage. These findings suggest the presence of dorsal and medial pathways that unconsciously alternate between non-REM sleep and REM sleep to improve and stabilize learning.

A switch in arousal circuit architecture shapes sleep across the lifespan
Sleep is a continuous behavior across the lifespan, yet its features and functions evolve markedly with development. In Drosophila melanogaster, as in mammals, early life sleep differs from mature sleep, but it is unknown whether disparate sleep regulatory mechanisms underlie these changes. Here, we identify distinct populations of octopaminergic (OA) neurons that promote arousal in larval and adult flies, thus revealing a developmental switch in sleep-wake circuit architecture. Of eight OA neurons present in the sub-esophageal zone (SEZ) of the nervous system at both life stages, dedicated, non-overlapping subsets drive arousal in larvae versus adults. Morphologic and connectomic analyses show that larval OA arousal neurons project primarily to the ventral nerve cord and lack substantial sensory input, suggesting a circuit logic optimized for internally driven arousal during early development. In contrast, adult OA arousal neurons target higher brain regions involved in cognition and receive rich multimodal sensory input, supporting wakefulness in response to environmental cues. These findings highlight a developmental transition in arousal circuitry that mirrors changing ecological demands, with juvenile systems organized to prioritize growth and feeding, insulated from sensory disturbance, and mature systems supporting sensory-guided behavior. Our results support a model of sleep regulation as a developmentally dynamic process, in which shared neuromodulators like OA operate through distinct cellular substrates tailored to life stage-specific behavioral priorities.

Embodied Navigation: whole-body movement drives path integration in large-scale free-walking virtual reality
Human navigation relies on combining body cues (vestibular and proprioceptive signals) with visual cues such as optic flow. The weighting and integration of these signals during the continuous tracking of walked distances and angles, known as path integration, remain poorly understood. Previous path integration studies have been limited to small spaces (<150 m2) and the influence of complex environments on cue weighting of body and vision cues is still unclear. Here, we conducted the largest-environment free-walking virtual reality navigation study to date in a 45x25 m facility (1,215 m2) using triangle completion tasks in naturalistic environments. We systematically manipulated sensory input across three conditions: natural active walking (full sensory integration), active joystick control (visual cues only), and blindfolded active walking (body cues only). Participants navigated through both sparse fallow land without trees and more complex forest environments with 400 trees. We embedded performance data in a Bayesian cue combination model to analyse the underlying combination mechanism. Our results provide evidence that most participants substantially favour body cues over visual cues in a non-Bayesian combination process, with considerable inter-individual variance in cue dominance strength and side biases. While transitioning from fallow land to forests reduced directional variance, weighting of body and visual information remained constant. These findings advance our understanding of human spatial navigation by demonstrating that body-based cues dominate path integration even in visually rich, large-scale environments, challenging assumptions about optimal Bayesian cue integration in human navigation.

Early Sleep-Dependent Sensory Gating in the Olfactory System
Disconnection from the external world is a defining feature of sleep. Although most models attribute sensory gating to thalamocortical mechanisms, the olfactory system-bypassing the thalamus-offers a unique window into earlier stages of sensory disconnection. Here, we combine chronic and acute recordings in rodents to test whether nasal sensory inputs are internalized during sleep. We show that respiration-locked potentials and gamma activity in the olfactory bulb are strongly modulated by brain state: they diminish during sleep and reappear during wakefulness and cortical activation. This gating occurs independently of respiratory dynamics and arises near the first synapse of the olfactory pathway. Finally, we find that neocortical slow-wave activity correlates with reduced olfactory entrainment, with coupling progressively vanishing as sleep deepens. These findings reveal a sleep-dependent sensory gating mechanism at early stages of a non-thalamic pathway, providing new insights into the neural substrates of sensory disconnection during sleep.

Rhythmic light stimulation elicits multiple concurrent neural responses that separably shape human perception
Rhythmic light stimulation offers solutions to innumerable cognitive and neurological disorders. However, like any neuromodulatory technique, responses to rhythmic light stimulation are highly variable, producing challenges in replicating lab-based studies and translating findings to the clinic. Across three MEG/EEG experiments, we show that this variability can, in part, be attributed to rhythmic light stimulation eliciting multiple, coexisting neural responses which have separable impacts on cognition. Specifically, we find that rhythmic light stimulation produces distinct neural responses at the fundamental (f) and second harmonic (2f) frequencies, and that these responses are differentially shaped by endogenous oscillatory dynamics that vary across participants. Importantly, these responses separably contribute to perception, with harmonic gamma-band responses supporting the representation of stimulus-specific information, and the phase of harmonic alpha-band responses causally contributing to near-threshold visual perception. We reproduce these effects across datasets, paradigms, and oscillatory bands, suggesting that the multiplex oscillatory responses elicited by rhythmic light stimulation are a robust and pervasive phenomenon. We propose that the complexity of neural responses to rhythmic stimulation can explain why there is substantial variability between studies using these techniques, and that understanding these complex responses may help advance neuromodulatory technologies for both fundamental and clinical neuroscience.

Immature olfactory sensory neurons provide complementary input in the healthy olfactory system
Adult neurogenesis of olfactory sensory neurons (OSNs) in the rodent olfactory system provides the unique opportunity to understand how new neurons functionally integrate into existing circuitry and contribute to behaviors. Immature OSNs express odorant receptors (ORs), form dendritic knobs with short cilia, and project their axons into the olfactory bulb (OB) where they form functional synapses. Furthermore, immature OSNs respond selectively to odorants and exhibit graded responses in a higher concentration range than mature OSNs, suggesting that they provide a distinct odor input stream. Finally, in mice that lack mature OSNs, sensory input from immature OSNs is sufficient to mediate odor detection and discrimination behavior. What remains unknown, however, is how these immature OSNs contribute to odor-guided behavior in the healthy, intact olfactory system. Here we show, using male and female mice, that chemogenetically silencing immature OSNs impairs odor detection ability without affecting their odor discrimination ability. Furthermore, immature OSN silencing reduces the amplitude of odor-evoked dendritic calcium responses of OB neurons in vivo. Together, these findings suggest that immature OSNs provide distinct odor input that complements mature OSN input to contribute to odor-guided behaviors in the healthy, intact olfactory system.

Fibrin-containing Hydrogels Regulate Human Astrocyte State and Neuronal Reprogramming
Astrocytes are key components in reactive gliosis after brain injury, yet defined in vitro models dissecting the influence of extracellular matrix (ECM) components enriched after injury, such as fibrin, on human astrocyte behaviour and function are still missing. Here, we use fibrinogen-derived fibrin and fibrin-alginate-RGD (FAR) 3D hydrogel substrates to examine the influence on human iPSC-derived astrocyte behaviour and their direct conversion into neurons. Astrocytes develop complex morphologies in 3D-FAR hydrogels while are more proliferative and migratory in 3D-Fibrin. Interestingly, gene expression profile analysis revealed different reactive states of astrocytes in 3D-Fibrin and 3D-FAR, which persist over time. The highly inflammatory state in 3D-FAR is largely incompatible with direct neuronal reprogramming hampering the direct conversion even at early stages. Conversely, astrocytes in 3D-Fibrin hydrogels can readily convert into neurons, demonstrating a potent influence of how fibrin is presented on eliciting distinct astrocyte states with great relevance for fate conversion.

A system for 3D reconstruction of mouse behaviour
Recent development in machine vision has enabled researchers unprecedented resolution in measuring behaviour in freely moving animals. However, the hardware implementation of a behavioural arena for capturing 3D behaviours remains time consuming and unstandardised. Here we first provide detailed instructions on how to build and calibrate such a system. Secondly, we provide instructions on how to process video data to obtain a 3D reconstruction of mouse behaviour. Finally, we provide results from behavioural tests in which 3D reconstruction enables clear-cut separation of behavioural responses to distinct sensory stimuli.

Eye Movement-Related Eardrum Oscillations (EMREOs) Do Not Have a Direct Impact on Auditory Spatial Discrimination
Eye-movement-related eardrum oscillations (EMREOs) are acoustic signals recorded in the ear that are thought to reflect displacements of the tympanic membrane induced by saccadic eye movements. Speculations hold that their underlying mechanisms play a role in aligning visual and acoustic signals. Yet whether and how the eardrum moves during an EMREO remains unclear. Starting from the assumption that the EMREO signal directly reflects eardrum movements, we probed human sound lateralization performance for sounds presented at different times during a saccade, hence the EMREO. Since the EMREO generation involves the two middle ear muscles, whose tension can alter sound transmission, we expected spatial sound discrimination performance to vary with the state of the ERMEO at the time of sound presentation. We contrasted perceptual sensitivity, bias, and reaction times for targets presented during either positive/negative or during small/large EMREO deflections in two tasks, one relying on free-field sounds and one presenting sounds in-ear. However, no analysis revealed any significant effect. Still, and in line with previous studies, we found that sound localization performance was dependent on the congruency of saccade and acoustic target directions. We conclude that either the eardrum does not move as directly reflected by the EMREO signal, or it does so, but the underlying changes at the tympanic membrane only have minimal perceptual impact. These results call for more refined studies to understand how the eardrum moves during a saccade and whether or how the EMREO impacts auditory or multisensory perception.

The individual brain: mapping variability in hemispheric functional organization across cognitive domains in a representative sample
Several core cognitive networks in the human brain show marked left-right differences in their functional organization. While these asymmetries are well described at the level of individual functions, overarching patterns of variability in hemispheric functional organization across multiple domains have not been mapped in a representative sample. To address this gap, we conducted a large-scale neuroimaging study with 200 participants (100 left-handers and 100 right-handers) to map hemispheric phenotypes across four distinct cognitive domains: language, tool use, spatial attention, and face perception. We challenge the traditional one-size-fits-all view of hemispheric organization by showing that deviations from the typical pattern of functional segregation are more prevalent than generally assumed, in both left- and right-handers. As predicted, variation in asymmetry was more pronounced in the left-handed sample. Critically, we found no evidence that the prototypical, textbook, pattern of brain organization confers any advantage in general cognitive ability or IQ. These results challenge the assumption of a single optimal brain organization and demonstrate that hemispheric functional segregation in humans is much more variable than anticipated.