bioRxiv Subject Collection: Neuroscience's Journal

Neutrophil stalling does not mediate the increase in tau phosphorylation and the cognitive impairment associated with high salt diet
High dietary salt intake has powerful effects on cerebral blood vessels and has emerged as a risk factor for stroke and cognitive impairment. In mice, high salt diet (HSD) leads to reduced cerebral blood flow (CBF), tau hyperphosphorylation and cognitive dysfunction. However, it is still unclear whether the reduced CBF is responsible for the effects of HSD on tau and cognition. Capillary stalling has emerged as a cause of CBF reduction and cognitive impairment in models of Alzheimers disease and diabetes. Therefore, we tested the hypothesis that capillary stalling also contributes to the CBF reduction and cognitive impairment in HSD. Using two-photon imaging, we found that HSD increased stalling of neutrophils in brain capillaries and decreased CBF. Neutrophil depletion reduced the number of stalled capillaries and restored resting CBF but did not prevent tau phosphorylation or cognitive impairment. These novel findings show that, capillary stalling contribute to CBF reduction in HSD, but not to tau phosphorylation and cognitive deficits. Therefore, the hypoperfusion caused by capillary stalling is not the main driver of the tau phosphorylation and cognitive impairment.

When non-canonical olfaction is optimal
The early olfactory system is canonically described by a "one-receptor-to-one-neuron" model: each olfactory sensory neuron (OSN) expresses a single type of olfactory receptor. Although the olfactory systems of classic model organisms approximately follow this canonical organization, many exceptions are known. In particular, Aedes aegypti mosquitoes co-express multiple types of olfactory receptors in many OSNs. Why do some olfactory systems follow the canonical organization while others violate it? We approach this question from the normative perspective of efficient coding. We find that the canonical and non-canonical organizations optimally encode odor signals in different types of olfactory environment. Non-canonical olfaction is beneficial when relevant sources emit correlated odorants and the environment contains odorants from ethologically irrelevant odor sources. Our theory explains previous observations of receptor co-expression and provides a framework from which to understand the structure of early olfactory systems.

Precisely phase-locked acoustic stimuli globally enhance slow oscillations, but depress fast spindles
Introduction: Several studies have shown manipulation of slow oscillations (SO) and sigma power through auditory stimulation during sleep. Most of the evidence, however, regards effects immediately following stimulation rather than enduring effects. Moreover, effects on discrete fast and slow spindles have as yet not been assessed. Materials and Methods: Here we use a modeling-based approach to predict upcoming oscillatory activity in the EEG and precisely phase-lock subtle acoustic stimuli to the start of the SO positive deflection. We assess the effects of stimulation on discrete slow oscillations, fast and slow spindles in the seconds after stimulation and on the longer term. We relate our findings to observations at the level of spectral measures and stimulus evoked responses. Results: Our observations show that slow wave measures were consistently increased, as apparent in measures of discrete SO's, SO and delta power and deflections in the ERP. On the other hand, fast spindle measures showed a temporally localized increase during a stimulus-induced SO positive deflection around 1 second after stimulation, but were globally decreased, both on the short and long term. The latter was apparent in measures of discrete fast spindles and PSD across longer periods of sleep. Conclusions: Acoustic stimuli, precisely phase locked to the SO onset, increase SO's and delta power globally, therewith deepening sleep. On the other hand, fast sleep spindles are globally depressed. This appears to be due, in part, to interruption of ongoing spindles by the stimulus and may furthermore reflect a depressing influence of slow oscillations on fast spindle dynamics. Future studies could evaluate the therapeutic potential of sleep deepening with acoustic stimulation in clinical populations who suffer from reduced deep sleep, such as in insomnia or post-traumatic stress disorder.

Restoration of excitation/inhibition balance enhances neuronal signal-to-noise ratio and rescues social deficits in autism-associated Scn2a-deficiency
Social behavior is critical for survival and adaptation, which is profoundly disrupted in autism spectrum disorders (ASD). Social withdrawal due to information overload was often described in ASD, and it was suspected that increased basal noise, i.e., excessive background neuronal activities in the brain could be a disease mechanism. However, experimental test of this hypothesis is limited. Loss-of-function mutations (deficiency) in SCN2A, which encodes the voltage-gated sodium channel NaV1.2, have been revealed as a leading monogenic cause of profound ASD. Here, we revealed that Scn2a deficiency results in robust and multifaceted social impairments in mice. Scn2a-deficient neurons displayed an increased excitation-inhibition (E/I) ratio, contributing to elevated basal neuronal noise and diminished signal-to-noise ratio (SNR) during social interactions. Notably, the restoration of Scn2a expression in adulthood is able to rescue both SNR and social deficits. By balancing the E/I ratio and reducing basal neuronal firing, an FDA-approved GABAA receptor-positive allosteric modulator improves sociability in Scn2a-deficient mice and normalizes neuronal activities in translationally relevant human brain organoids carrying autism-associated SCN2A nonsense mutation. Collectively, our findings revealed a critical role of the NaV1.2 channel in the regulation of social behaviors, and identified molecular, cellular, and circuitry mechanisms underlying SCN2A-associated disorders.

Exploring brain dynamics within the Approach-Avoidance Bias
Approach-avoidance behaviors (AAB) are fundamental mechanisms that guide interactions with the environment based on the emotional valence of stimuli. While previous research has extensively explored behavioral aspects of the AAB, the neural dynamics underlying these processes remain insufficiently understood. The present study employs electroencephalography (EEG) to systematically investigate the neural correlates of AAB in a non-clinical population, focusing on stimulus- and response-locked event-related potentials (ERPs). Forty-three participants performed a classic Approach-Avoidance Task (AAT) while EEG activity was recorded. Behavioral results confirmed the AAB effect, with faster reaction times in congruent compared to incongruent trials, as well for positive versus negative trials. ERP analyses revealed significant differences in the Valence factor, with early effects for stimulus-locked trials and late differences at the parietal-occipital region for response-locked trials. However, no significant effects were found for the Condition factor, suggesting that the neural mechanisms differentiating congruent and incongruent responses might not be optimally captured through EEG. Additionally, frontal alpha asymmetry (FAA) analyses showed no significant differences between conditions, aligning with the literature. These findings provide novel insights into the temporal and spatial characteristics of AAB-related neural activity, emphasizing the role of early visual processing and motor preparation in affect-driven decision-making. Future research should incorporate methodological approaches for assessing AAB in ecologically valid settings.

Learning reorganizes dendritic and stabilizes axonal initial segment inhibitory synapses in CA1 pyramidal neurons
Structural synaptic plasticity underlies the changes in brain connectivity required for learning and memory. Inhibitory synapses (INS) target all subcellular domains of excitatory pyramidal neurons (PNs), including dendrites, somata and axon initial segments (AIS). These subcellular domains have distinct molecular, structural and physiological profiles which underlie their functions. How structural plasticity of INS supports these functions as well as emerging properties such as memory is largely unknown. To tackle these questions we tracked INS on dendrites, somata and AIS of PNs in the dorsal hippocampal CA1 area of mice over two weeks. Size and temporal dynamics of INS showed a strong compartmentalization and dendritic INS were less dynamic than dendritic spines. Trace fear conditioning led to reorganization of dendritic INS and to stabilization of AIS INS but had a minimal effect on dendritic spines. Finally, mathematical modelling allowed us to probe the mechanisms underlying stabilization of INS upon learning.

Growing Minds, Integrating Senses: Neural and Computational Insights into Age-related Changes in Audio-Visual and Tactile-Visual Learning in Children
Multisensory processing and learning shape cognitive and language development, influencing how we perceive and interact with the world from an early age. While multisensory processes mature into adolescence, it remains poorly understood how age influences multisensory associative learning. This study investigated age-related effects on multisensory processing and learning during audio-visual and tactile-visual learning in 67 children (5.7-13 years) by integrating behavioural and neuroimaging data with computational methods. A reward-learning drift diffusion model revealed that older children processed information faster and made more efficient decisions on multisensory associations. These age-related increases coincided with higher activity in brain regions associated with cognitive control, multisensory integration, and memory retrieval, specifically during audio-visual learning. Notably, the anterior insula exhibited heightened activation in response to lower reward prediction errors, indicative of increased sensitivity to negative feedback with development. Finally, reward prediction errors and values modulated activation in reward processing and cognitive control regions, with this modulation remaining modality-independent and largely stable across age. In conclusion, while children employ similar learning strategies, older children make decisions more efficiently and engage neural resources more strongly. Our findings reflect ongoing maturation of neural networks supporting multisensory learning in middle childhood, enabling more adaptive learning in later childhood.

Functional stability and recurrent STDP in rhythmogenesis
Synapses in the nervous system show considerable volatility, raising the question of how the brain maintains functional stability despite continuous synaptic motility. Previous studies have suggested that functionality may be maintained by an ongoing process of activity-dependent plasticity. Here, we address this question in the context of rhythmogenesis. Specifically, we investigated the hypothesis that rhythmic activity in the brain can develop and be stabilized via activity-dependent plasticity in the form of spike-timing-dependent-plasticity (STDP), extending our previous work that demonstrated rhythmogenesis in a toy model of two effective neurons. We examined STDP dynamics in large recurrent networks in two stages. We first derived the effective dynamics of the order parameters of the synaptic connectivity. Then, a perturbative approach was applied to investigate stability. We show that for a wide range of parameters STDP can induce rhythmogenesis. Moreover, STDP can suppress synaptic fluctuations that disrupt functionality. Interestingly, STDP can channel fluctuations in the synaptic weights into a manifold on which the network activity is not affected, thus, maintaining functionality while allowing a subspace in which synaptic weights can be widely distributed.

Alpha and beta cortico-motor synchronization shape visuomotor control on a single-trial basis
A central question in sensorimotor neuroscience is how sensory inputs are mapped onto motor outputs to enable swift and accurate responses, even in the face of unexpected environmental changes. In this study, we leverage cortico-motor phase synchronization as a window into the dynamics of sensorimotor loops and explore how it relates to online visuomotor control. We recorded brain activity using electroencephalography (EEG) while participants performed an isometric tracking task that involved transient, unpredictable visual perturbations. Our results show that synchronization between cortical activity and motor output (force) in the alpha band (8-13 Hz) is associated with faster motor responses, while beta-band synchronization (18-30 Hz) promotes more accurate control, which is in turn linked to a higher likelihood of obtaining rewards. Both effects are most pronounced immediately before perturbation onset, underscoring the predictive value of cortico-motor phase synchronization for sensorimotor performance. Single-trial analyses further reveal that deviations from the preferred cortico-motor phase relationship are associated with longer reaction times and larger errors, and these phase effects are independent of power effects. Thus, beta-band synchronization may reflect a cautious, reward-oriented control strategy, while alpha-band synchronization enables quicker, though not necessarily efficient, motor responses, indicating a complementary, more reactive control mode. These results highlight the finely tuned nature of sensorimotor control, where different aspects of sensory-to-motor transformations are governed by frequency-specific neural synchronization on a moment-to-moment basis. By linking neural dynamics to motor output, this study sheds light on the spectrotemporal organization of sensorimotor networks and their distinct contribution to goal-directed behavior.

Distinct molecular mechanisms of stress habituation in the mouse hippocampus
Chronic stress is a risk factor for neuropsychiatric disorders, making the ability to adapt to repeated stress a crucial determinant of mental health. On a molecular level, it remains unclear whether repeated exposure to stress is characterized by habituation - a decreased responsiveness to the same stimulus - or by the emergence of new, adaptive responses. Here, we explore how the tightly regulated molecular response triggered by acute restraint stress becomes altered after repeated restraint exposure. Transcriptomic sampling of the mouse hippocampus at multiple time points revealed that repeated stress leads to widespread habituation, damping stress-induced gene expression of all stress-responsive genes. However, we find no evidence for the emergence of new response profiles or alterations in baseline gene expression. Using single-cell multi-omics, we show that these findings hold true across cell types, and we reveal cell type specific patterns of habituation. Transcriptomic and chromatin accessibility profiles identify two distinct mechanisms that contribute to the observed habituation patterns: an early cAMP-associated mechanism that is related to blunted transcription after chronic stress, and a late corticosterone-dependent mechanism that is linked to a shortened transcriptional response. These extensive data are integrated, along with our previous work, into an interactive app, providing a uniquely detailed molecular resource that characterizes the acute stress response and the process of habituation across the genome.

Biological subtyping of autism via cross-species fMRI
It is frequently assumed that the phenotypic heterogeneity in autism spectrum disorder reflects underlying pathobiological variation. However, direct evidence in support of this hypothesis is lacking. Here, we leverage cross-species functional neuroimaging to examine whether variability in brain functional connectivity reflects distinct biological mechanisms. We find that fMRI connectivity alterations in 20 distinct mouse models of autism (n=549 individual mice) can be clustered into two prominent hypo- and hyperconnectivity subtypes. We show that these connectivity profiles are linked to distinct signaling pathways, with hypoconnectivity being associated with synaptic dysfunction, and hyperconnectivity reflecting transcriptional and immune-related alterations. Extending these findings to humans, we identify analogous hypo- and hyperconnectivity subtypes in a large, multicenter resting state fMRI dataset of n=940 autistic and n=1036 neurotypical individuals. Remarkably, hypo- and hyperconnectivity autism subtypes are replicable across independent cohorts (accounting for 25.1% of all autism data), exhibit distinct functional network architecture, are behaviorally dissociable, and recapitulate synaptic and immune mechanisms identified in corresponding mouse subtypes. Our cross-species investigation, thus, decodes the heterogeneity of fMRI connectivity in autism into distinct pathway-specific etiologies, offering a new empirical framework for targeted subtyping of autism.

mTORC1 activation drives astrocyte reactivity in cortical tubers and brain organoid models of TSC
Tuberous Sclerosis Complex (TSC) is a genetic neurodevelopmental disorder associated with early onset epilepsy, intellectual disability and neuropsychiatric disorders. A hallmark of the disorder is cortical tubers, which are focal malformations of brain development that contain dysplastic cells with hyperactive mTORC1 signaling. One barrier to developing therapeutic approaches and understanding the origins of tuber cells is the lack of a model system that recapitulates this pathology. To address this, we established a genetically mosaic cortical organoid system that models a somatic second-hit mutation, which is thought to drive the formation of tubers in TSC. With this model, we find that loss of TSC2 cell-autonomously promotes the differentiation of astrocytes, which exhibit features of a disease-associated reactive state. TSC-/- astrocytes have pronounced changes in morphology and upregulation of proteins that are risk factors for neurodegenerative diseases, such as clusterin and APOE. Using multiplexed immunofluorescence in primary tubers from TSC patients, we show that tuber cells with hyperactive mTORC1 activity also express reactive astrocyte proteins, and we identify a unique population of cells with expression profiles that match the those observed in organoids. Together, this work reveals that reactive astrogliosis is a primary feature of TSC that arises early in cortical development. Dysfunctional glia are therefore poised to be drivers of pathophysiology, nominating a potential therapeutic target for treating TSC and related mTORopathies.

Motifs of brain cortical folding from birth to adulthood: structural asymmetry and folding-functional links
Cortical folding of brain is widely regarded as an interplay between genetic programming and biomechanical forces, closely linked to cytoarchitectonic regionalisation. Abnormal folding patterns are frequently observed in neurodevelopmental conditions and psychiatric disorders. However, significant inter-individual variability of secondary and tertiary folds obscures detection of shape biomarkers and confounds investigation of folding-functional relationships. Here we investigate cortical folding heterogeneity at fine scale, using novel hierarchical surface registration (MSM-HT) to parse cortical folding patterns into a representative family of distinct anatomical templates. By applying this technique both to young adults from the Human Connectome Project (HCP) and neonates in the Developing HCP and Brain Imaging in Babies (BIBS) cohorts, we identify and characterize common lobe-wise folding patterns: observing consistency across both age groups, with neonatal samples showing less variation. Crucially, we highlight significant hemispheric asymmetry within the temporal lobe for both adults and neonates, and show that improved correspondence of shape does not translate to improved areal correspondence, affirming previous studies that have pointed to dissociation of folding and functional organisation. This study provides a critical step towards understanding brain asymmetry and complex relationships between folding and function, offering a robust framework to generalise the uncovered cortical folding motifs across datasets and developmental stages.

Temporal variation in the acoustic dynamic range is a confounding factor in EEG-based tracking of absolute auditory attention to speech
Many studies have demonstrated that auditory attention to natural speech can be decoded from EEG data. However, most studies focus on selective auditory attention decoding (sAAD) with competing speakers, while the dynamics of absolute auditory attention decoding (aAAD) to a single target remains underexplored. The goal of aAAD is to measure the degree of attention to a single speaker, has applications for objective measurements of attention in psychological and educational contexts. To investigate this aAAD paradigm, we designed an experiment where subjects listened to a video lecture under varying attentive conditions. We trained neural decoders to reconstruct the speech envelope from EEG in the baseline attentive condition and use the correlation coefficient between the decoded and real speech envelope as a metric for attention to the speech. Our analysis shows that the envelope standard deviation (SD) of the speech envelope in the 1-4 Hz band strongly correlates with this metric across different segments of the speech stimulus. However, this correlation weakens in the 0.1-4 Hz band, where the degree of separation between the attentive and inattentive state becomes more pronounced. This highlights the unique contribution of the 0.1-1 Hz range, which enhances the distinction of attentional states and remains less affected by confounding factors such as the time-varying dynamic range of the speech envelope.

Formaldehyde induces and promotes Alzheimer's disease pathologies in a 3D human neural cell culture system
Alzheimers disease (AD) arises from complex multilevel interactions between genetic, epigenetic, and environmental factors. Recent studies suggest that exposure to the environmental and occupational toxicant formaldehyde (FA) may play a significant role in AD development. However, the effects of FA exposure on A{beta} and tau pathologies in human neural cell 3D culture systems remain unexplored. To investigate FAs role in AD initiation, we differentiated 3D-cultured immortalized human neural progenitor ReN cells (ReNcell VM) into neurons and glial cells, followed by FA treatment. FA exposure for 12 weeks resulted in a dose-dependent increase in A{beta}40, A{beta}42, and phosphorylated tau levels. To further examine FAs role in AD progression, we established a 3D human neural cell culture AD model by transfecting ReN cells with AD-related mutant genes, including mutant APP and PSEN1, which recapitulate key AD pathological events. Our findings demonstrate that FA exposure significantly elevated A{beta}40, A{beta}42, and phosphorylated tau levels in this 3D-cultured AD model. These results suggest that FA exposure contributes to the initiation and progression of AD pathology in 3D-cultured human neural cells.

Sleep Deprivation Alters Hippocampal Dendritic Spines in a Contextual Fear Memory Engram
Sleep is critically involved in strengthening memories. However, our understanding of the morphological changes underlying this process is still emerging. Recent studies suggest that specific subsets of dendritic spines are strengthened during sleep in specific neurons involved in recent learning. Contextual memories associated with traumatic experiences are involved in post-traumatic stress disorder (PTSD) and represent recent learning that may be strengthened during sleep. We tested the hypothesis that dendritic spines encoding contextual fear memories are selectively strengthened during sleep. Furthermore, we tested how sleep deprivation after initial fear learning impacts dendritic spines following re-exposure to fear conditioning. We used ArcCreERT2 mice to visualize neurons that encode contextual fear learning (Arc+ neurons), and concomitantly labeled neurons that did not encode contextual fear learning (Arc-neurons). Dendritic branches of Arc+ and Arc-neurons were sampled using confocal imaging to assess spine densities using three-dimensional image analysis from either sleep deprived (SD) or control mice allowed to sleep normally. Mushroom spines in Arc+ branches displayed decreased density in SD mice, indicating upscaling of mushroom spines during sleep following fear learning. In comparison, no changes were observed in dendritic spines from Arc-branches. When animals were re-exposed to contextual fear conditioning 4 weeks later, we observed lower density of mushroom spines in both Arc+ and Arc-branches, as well as lower density of thin spines in Arc-branches in mice that were SD following the initial fear conditioning trial. Our findings indicate that sleep strengthens dendritic spines in neurons that recently encoded fear memory, and sleep deprivation following initial fear learning impairs dendritic spine strengthening initially and following later re-exposure. SD following a traumatic experience thus may be a viable strategy in weakening the strength of contextual memories associated with trauma and PTSD.

A modular, adaptable, and accessible implant kit for chronic electrophysiological recordings in rats
Electrophysiological implants enable exploration of the relationship between neuronal activity and behavior. These technologies evolve rapidly, with multiple iterations of recording systems developed and utilized. Chronic implants must address a litany of complications, including retention of high signal-to-noise ratio in probes and the ability to withstand excess force over the experimental period. To overcome these issues, we designed a chronic implant for rats. Our comprehensive protocol optimizes the entire implant process, from assembling and testing the probes (Neuropixels) to implantation. In addition to addressing the complications previously mentioned, our implant can vertically adjust probes with micron precision and is constructed using modular components, allowing it to be easily modified for various research contexts, electrophysiological recording systems, headstages, and probe types.

Computational Methods for Optimal Coil Placement and Maximization of Lobule-Focused Cortical Activation in Cerebellar TMS
BackgroundCoil placement on the cerebellum lacks accuracy in targeting the intended lobules and limits the efficacy of cerebellar transcranial magnetic stimulation (TMS) in treating movement disorders.

ObjectiveDevelop a multiscale computational pipeline and method to rapidly predict the cellular response to cerebellar TMS and optimize the coil placement accordingly for lobule-specific activation.

MethodsThe pipeline integrates 3T T1/T2-weighted MRI scans of the human cerebellum, lobule parcellation, and finite element models of the TMS-induced electric (E-) fields for figure-of-eight coils (MagStim D70) and double-cone coils (Deymed 120BFV). A constrained optimization method is developed to estimate the fiber bundles from cerebellar cortices to deep nuclei and, for both coil types, find the coil placement and orientation that maximize the E-field intensity in a user-selected lobule. Multicompartmental Purkinje cell models with realistic axon geometries and Gaussian process regression are added to predict the recruitment in the Purkinje layer.

ResultsOur pipeline was tested in five individuals to target the left lobule VIII and resulted in normalized E-field intensities at the target 49.6{+/-}25.6% (D70) and 29.3{+/-}17.7% (120BFV) higher compared to standard coil positions (i.e., 3 cm left, 1 cm below the inion), mean{+/-}S.D. The minimum pulse intensity to recruit Purkinje cells on a 4 mm2-surface in the target decreased by 21.6% (range: 4.7-55.0%) and 10.7% (range: 7.9-18.2%), and the spillover to adjacent lobules decreased by 70.6{+/-}16.3% and 71.7{+/-}20.8% compared to standard positions (D70 and 120BFV, respectively).

ConclusionOur tools are effective at targeting specific lobules and pave the way toward patient-specific setups.

Ex vivo human brain volumetry: validation of magnetic resonance imaging measurements
BackgroundNeurodegenerative diseases are associated with brain atrophy. The volume of in vivo human brains is determined with various magnetic resonance imaging (MRI) measurement tools of which the validity has not been assessed against a gold standard. Here, we propose to validate the MRI brain volumes by scanning ex vivo-in situ specimens (i.e., anatomical heads), which allows the extraction of the brain after the scan to compare its volume with the gold standard water displacement method (WDM).

MethodsWe acquired 3T MRI T2-weighted, T1-weighted, and MP2RAGE images of seven anatomical heads fixed with an alcohol-formaldehyde solution routinely used in anatomy laboratories and segmented the gray and white matter of the brain using two methods: 1) a manual intensity-based threshold segmentation using Display (MINC-ToolKit, McConnell BIC), and 2) an automatic Deep-Learning-based segmentation tool (SynthSeg). The brains were then extracted, and their volumes were measured with the WDM after the removal of their meninges and a midsagittal cut (to allow water penetration into the ventricles). Volumes from all methods were compared to the ground truth (WDM volumes) using a repeated-measures ANOVA.

ResultsMean brain volumes, in cubic centimeters, were 1111.14{+/-}121.78 for WDM, 1020.29{+/-}70.01 for manual T2-weighted, 1056.29{+/-}90.54 for automatic T2-weighted, 1094.69{+/-}100.51 for automatic T1-weighted, 1066.56{+/-}96.52 for automatic MP2RAGE INV1, and 1156.18{+/-}121.87 for MP2RAGE INV2. All volumetry methods were significantly different (F=17.874; p<0.001) from the WDM volumes, except the automatic T1-weighted volumes.

ConclusionWe demonstrate that SynthSeg accurately determines the brain volume in ex vivo-in situ T1-weighted MRI scans. Our results also suggest that given the contrast similarity between our ex vivo and in vivo sequences, the brain volumes of clinical studies are most probably sufficiently accurate, with some degree of underestimation depending on the sequence used.