bioRxiv Subject Collection: Neuroscience's Journal

Comparative Analysis of Human-Chimpanzee Divergence in Brain Connectivity and its Genetic Underpinnings
Chimpanzees (Pan troglodytes) are humans' closest living evolutionary relatives, making them the most directly relevant comparison point for understanding human brain evolution. By zeroing in on the differences in brain connectivity between humans and chimpanzees, it can provide key insights into the specific evolutionary changes that occurred along the human lineage. However, conducting fair comparisons of brain connectivity between humans and chimpanzees remains challenging, as cross-species brain atlases established within the same framework are currently lacking. Without the availability of cross-species brain atlases, the region-wise connectivity patterns between humans and chimpanzees cannot be directly compared. To address this gap, we built the first Chimpanzee Brainnetome Atlas (ChimpBNA) by following the well-established connectivity-based parcellation framework. Leveraging this new resource, we found substantial divergence in connectivity patterns across most association cortices, notably in the lateral temporal and dorsolateral prefrontal cortex between the two species. Intriguingly, these patterns significantly deviate from the expected cortical expansion during brain evolution. Additionally, we identified regions displaying connectional asymmetries between species, likely resulting from evolutionary divergence. Genes associated with these divergent connectivities were found to be enriched in cell types crucial for cortical projection circuits and synapse formation. These genes exhibited more pronounced differences in expression patterns in regions with higher connectivity divergence, suggesting a potential foundation for brain connectivity evolution. Therefore, our study not only provides a fine-scale brain atlas of chimpanzees but also highlights the connectivity divergence between humans and chimpanzees in a more rigorous and comparative manner and suggests potential genetic underpinnings for the observed divergence in brain connectivity patterns between the two species. This can help us better understand the origins and development of uniquely human cognitive capabilities.

Neuronal activity inhibits axonal mitochondrial transport in a region-specific manner
Due to their large scale and uniquely branched architecture, neurons critically rely on active transport of mitochondria in order to match energy production and calcium buffering to local demand. Consequently, defective mitochondrial trafficking is implicated in various neurological and neurodegenerative diseases. A key signal regulating mitochondrial transport is intracellular calcium. Elevated Ca2+ levels have been demonstrated to inhibit mitochondrial transport in many cell types, including neurons. However, it is currently unclear to what extent calcium-signaling regulates axonal mitochondrial transport during realistic neuronal activity patterns. We created a robust pipeline to quantify with high spatial resolution, absolute Ca2+ concentrations. This allows us to monitor Ca2+ dynamics with pixel precision in the axon and other neuronal compartments. We found that axonal calcium levels scale with firing frequency in the range of 0.1-1M, whereas KCl-induced depolarization generated levels almost a magnitude higher. As expected, prolonged KCl-induced depolarization did inhibit axonal mitochondrial transport in primary hippocampal neurons. However, physiologically relevant neuronal activity patterns only inhibited mitochondrial transport in axonal segments which made connections to a target neuron. In non-connecting axonal segments, we were unable to trigger this inhibitory mechanism using realistic firing patterns. Thus, we confirm that neuronal activity can indeed regulate axonal mitochondrial transport, and reveal a spatial pattern to this regulation which went previously undetected. Together, these findings indicate a potent, but localized role for activity-related calcium fluctuations in the regulation of axonal mitochondrial transport.

The dominance of global phase dynamics in human cortex, from delta to gamma
The organization of the phase of electrical activity in the cortex is critical to inter-site communication, but the balance of this communication across macroscopic (>15cm), mesoscopic (1 to 15cm) and microscopic (<1cm) ranges is an open question. Traveling waves in the cortex are spatial phase gradients, such that phase values change smoothly through the cortical sheet over time. Macroscopic cortical traveling waves have been understudied compared to micro- or mesoscopic waves. The spatial frequencies (i.e., the characteristic scales) of cortical waves have been characterized in the grey-matter for micro- and mesoscopic scales of cortex and show decreasing spatial power with increasing spatial frequency. This research, however, has been limited by the size of the measurement array, thus excluding macroscopic traveling waves. Obversely, poor spatial resolution of extra-cranial measurements prevents incontrovertible macroscopic estimates of spatial power via electroencephalogram and magnetoencephalogram. We apply a novel method to estimate the spatial frequency spectrum of phase dynamics in order to quantify the uncertain macroscopic scale. Stereotactic electroencephalogram is utilized to leverage measurements of local-field potentials within the grey matter, while also taking advantage of the sometimes large extent of spatial coverage. Irregular sampling of the cortical sheet is offset by use of linear algebra techniques to empirically estimate the spatial frequency spectrum. We find the spatial power of the phase is highest at the lowest spatial frequencies (longest wavelengths), consistent with the power spectra ranges for micro- and meso-scale dynamics, but here shown up to the size of the measurement array (15-25cm), i.e., approaching the entire extent of cortex. Low spatial frequencies dominate the cortical phase dynamics. This has important functional implications as it means that the phase measured at a single contact in the grey-matter is more strongly a function of global phase organization than local. This result arises across a wide range of temporal frequencies, from the delta band (2Hz) through to the high gamma range (100Hz).

Phylogenetic divergence of GABAB receptor signalling in neocortical networks over adult life.
Cortical circuit activity is controlled by GABA-mediated inhibition in a spatiotemporally restricted manner. Much is known about fast GABA currents, GABAB receptor (GABABR) signalling exerts powerful slow inhibition that controls synaptic, dendritic and neuronal activity. However, little is known about how GABABRs contribute to circuit-level inhibition over the lifespan of rodents and humans. In this study, we quantitatively determine the functional contribution of GABABR signalling to pre- and postsynaptic domains in rat and human cortical principal cells (PC). We find that postsynaptic GABABR differentially control pyramidal cell activity within the cortical column as a function of age and species, and that these receptors contribute to co-ordination of local information processing in a layer- and species-dependent manner. These data directly increase our knowledge of translationally relevant local circuit dynamics, with direct impact on understanding the role of GABABRs in the treatment of seizure disorders.

The prelimbic prefrontal cortex mediates the development of lasting social phobia as a consequence of social threat conditioning.
Social phobia is highly detrimental for social behavior, mental health, and productivity. Despite much previous research, the behavioral and neurobiological mechanisms associated with the development of social phobia remain elusive. To investigate these issues, the present study implemented a mouse model of social threat conditioning in which mice received electric shock punishment upon interactions with unfamiliar conspecifics. This resulted in immediate reductions in social behavior and robust increases in defensive mechanisms such as avoidance, freezing, darting, and ambivalent stretched posture. Furthermore, social deficits lasted for prolonged periods and were independent of contextual settings, sex variables, or particular identity of the social stimuli. Shedding new light into the neurobiological factors contributing to this phenomenon, we found that optogenetic silencing of the prelimbic (PL), but not the infralimbic (IL), subregion of the medial prefrontal cortex (mPFC) during training led to subsequent forgetting and development of lasting social phobia. Similarly, pharmacological inhibition of NMDARs in PL also impaired the development of social phobia. These findings are consistent with the notion that social-related trauma is a prominent risk factor for the development of social phobia, and that this phenomenon engages learning-related mechanisms within the prelimbic prefrontal cortex to promote prolonged representations of social threat.

Arid1b haploinsufficiency in pyramidal neurons causes cellular and circuit changes in neocortex but is not sufficient to produce behavioral or seizure phenotypes
Arid1b is a high confidence risk gene for autism spectrum disorder that encodes a subunit of a chromatin remodeling complex expressed in neuronal progenitors. Haploinsufficiency causes a broad range of social, behavioral, and intellectual disability phenotypes, including Coffin-Siris syndrome. Recent work using transgenic mouse models suggests pathology is due to deficits in proliferation, survival, and synaptic development of cortical neurons. However, there is conflicting evidence regarding the relative roles of excitatory projection neurons and inhibitory interneurons in generating abnormal cognitive and behavioral phenotypes. Here, we conditionally knocked out either one or both copies of Arid1b from excitatory projection neuron progenitors and systematically investigated the effects on intrinsic membrane properties, synaptic physiology, social behavior, and seizure susceptibility. We found that disrupting Arid1b expression in excitatory neurons alters their membrane properties, including hyperpolarizing action potential threshold; however, these changes depend on neuronal subtype. Using paired whole-cell recordings, we found increased synaptic connectivity rate between projection neurons. Furthermore, we found reduced strength of excitatory synapses to parvalbumin (PV)-expression inhibitory interneurons. These data suggest an increase in the ratio of excitation to inhibition. However, the strength of inhibitory synapses from PV interneurons to excitatory neurons was enhanced, which may rebalance this ratio. Indeed, Arid1b haploinsufficiency in projection neurons was insufficient to cause social deficits and seizure phenotypes observed in a preclinical germline haploinsufficient mouse model. Our data suggest that while excitatory projection neurons likely contribute to autistic phenotypes, pathology in these cells is not the primary cause.

The node of Ranvier influences the in vivo axonal transport of mitochondria and signalling endosomes
Efficient long-range axonal transport is essential for maintaining neuronal function, and perturbations in this process underlie severe neurological diseases. We have previously demonstrated that signalling endosomes are transported in vivo at comparable speeds across motor neurons (MNs) innervating different hindlimb muscles, as well as between forelimb and hindlimb peripheral nerves. In contrast, axonal transport is faster in MNs compared to sensory neurons innervating the same muscle. Found periodically across the myelin sheath, Nodes of Ranvier (NoR) are short uncovered axonal domains that facilitate action potential propagation. Currently, it remains unresolved how the distinct molecular structures of the NoR impact axonal transport dynamics. Here, using intravital time-lapse microscopy of sciatic nerves in live, anaesthetised mice, we assessed diverse organelle dynamics at the NoR. We first observed that axonal morphologies were similar between fast and slow MNs, and found that signalling endosomes and mitochondria accumulate on the distal side of the NoR in both motor neuron subtypes. Assessment of axonal transport of signalling endosomes and mitochondria revealed a decrease in velocity and increase in pausing as the organelles transit through the NoR, followed by an increase in speed in the adjacent intranodal region. Collectively, this study has established axonal transport dynamics of two independent organelles at the NoR in vivo, and has relevance for several pathologies affecting peripheral nerves and the NoR, such as peripheral neuropathy, motor neuron diseases, and/or multiple sclerosis.

Individual differences in uncertainty evaluation explain opposing exploratory behaviors in anxiety and apathy
Navigating uncertain environments is a fundamental challenge for adaptive behavior, and affective states such as anxiety and apathy can profoundly influence an individual's response to uncertainty. Uncertainty encompasses both volatility and stochasticity, where volatility refers to how rapidly the environment changes and stochasticity describes outcomes resulting from random chance. This study investigates how anxiety and apathy modulate perceptions of environmental volatility and stochasticity and how these perceptions impact exploratory behavior. In a large online sample (N = 1001), participants completed a restless three-armed bandit task, and their choices were analyzed using latent state models to quantify the computational processes. We found that anxious individuals attributed uncertainty more to environmental volatility than stochasticity, leading to increased exploration, particularly after reward omission. Conversely, apathetic individuals perceived uncertainty as more stochastic than volatile, resulting in decreased exploration. The ratio of perceived volatility to stochasticity mediated the relationship between anxiety and exploratory behavior following adverse outcomes. These findings reveal distinct computational mechanisms underlying anxiety and apathy in uncertain environments. Our results provide a novel framework for understanding the cognitive and affective processes driving adaptive and potentially maladaptive behaviors under uncertainty, with implications for the characterization and treatment of neuropsychiatric disorders.

Trigeminal ganglion and tooth innervation modifications following genetic and pharmacological Nogo-A inhibition
Nogo-A is a major regulator of neural development and regeneration, but its role in tooth innervation remains largely unknown. Neurons from trigeminal ganglia support teeth homeostasis and regeneration, and disorders of their function could have significant pathophysiological consequences. In this study, we show that Nogo-A is expressed in the trigeminal ganglia and in the neurons innervating the teeth, and that its deletion affects both the number and patterning of neurons in teeth. In organotypic cultures, Nogo-A blocking antibodies affect the trigeminal ganglia-derived neuronal outgrowths and allow premature innervation of tooth germs. RNA sequencing analysis revealed that Nogo-A deletion induces alterations linked to functions at synapses and interference with neurotrophin signalling during the differentiation and maturation of trigeminal neurons. Taken together, these results reveal for the first time the importance of Nogo-A as a major regulator of tooth innervation and point to its potential as a clinical therapeutic target.

Sampling bias corrections for accurate neural measures of redundant, unique, and synergistic information
Shannon Information theory has long been a tool of choice to measure empirically how populations of neurons in the brain encode information about cognitive variables. Recently, Partial Information Decomposition (PID) has emerged as principled way to break down this information into components identifying not only the unique information carried by each neuron, but also whether relationships between neurons generate synergistic or redundant information. While it has been long recognized that Shannon information measures on neural activity suffer from a (mostly upward) limited sampling estimation bias, this issue has largely been ignored in the burgeoning field of PID analysis of neural activity. We used simulations to investigate the limited sampling bias of PID computed from discrete probabilities (suited to describe neural spiking activity). We found that PID suffers from a large bias that is uneven across components, with synergy by far the most biased. Using approximate analytical expansions, we found that the bias of synergy increases quadratically with the number of discrete responses of each neuron, whereas the bias of unique and redundant information increase only linearly or sub-linearly. Based on the understanding of the PID bias properties, we developed simple yet effective procedures that correct for the bias effectively, and that improve greatly the PID estimation with respect to current state-of-the-art procedures. We apply these PID bias correction procedures to datasets of 53117 pairs neurons in auditory cortex, posterior parietal cortex and hippocampus of mice performing cognitive tasks, deriving precise estimates and bounds of how synergy and redundancy vary across these brain regions.

OSBA: An open neonatal neuroimaging atlas and template for spina bifida aperta
We present the Open Spina Bifida Aperta (OSBA) atlas, an open atlas and set of neuroimaging templates for spina bifida aperta (SBA). Traditional brain atlases may not adequately capture anatomical variations present in pediatric or disease-specific cohorts. The OSBA atlas fills in this gap by representing the computationally averaged anatomy of the neonatal brain with SBA after fetal surgical repair. The OSBA atlas was constructed using structural T2-weighted and diffusion tensor MRI of 28 newborns with SBA who underwent prenatal surgical correction. The corrected gestational age at MRI was 38.1 {+/-} 1.1 weeks (mean {+/-} SD). The OSBA atlas consists of T2-weighted and fractional anisotropy templates, along with 9 tissue prior maps and region of interest (ROI) delineations. The OSBA atlas offers a standardized reference space for spatial normalization and anatomical ROI definition. Our image segmentation and cortical ribbon definition is based on a human-in-the-loop approach including manual segmentation. The precise alignment of the ROIs was achieved by a combination of manual image alignment and automated, non-linear image registration. By providing a dedicated neonatal atlas for SBA, we enable more accurate spatial standardization and support advanced analyses such as diffusion tractography and connectomic studies in newborns affected by this condition.

Binocular combination in the autonomic nervous system
The diameter of the pupil fluctuates in response to levels of ambient light and is regulated by the autonomic nervous system. Increasing light in one eye causes both pupils to constrict, implying the system must combine signals across the two eyes - a process of binocular integration occurring independently of visual cortex. Distinct classes of retinal photoreceptor are involved in controlling and maintaining pupil diameter, with cones and rods driving the initial constriction and intrinsically photosensitive retinal ganglion cells maintaining diameter over prolonged time periods. Here, we investigate binocular combination by targeting different photoreceptor pathways using the silent substitution method to modulate the input spectra. We find different patterns of binocular response in each pathway, and across the first and second harmonic frequencies. At the first harmonic, luminance and S-cone responses showed strong binocular facilitation, and weak interocular suppression. Melanopsin responses were invariant to the number of eyes stimulated. Notably, the L-M pathway involved binocular inhibition, whereby responses to binocular stimulation were weaker than for monocular stimulation. The second harmonic involved strong interocular suppression in all pathways, but with some evidence of binocular facilitation. Our results are consistent with a computational model of binocular signal combination (implemented in a Bayesian hierarchical framework), in which the weight of interocular suppression differs across pathways. We also find pathway differences in response phase, consistent with different lag times for phototransduction. This work demonstrates for the first time the algorithm governing binocular combination in the autonomic nervous system.

Bistable perception of symbolic numbers
Numerals, i.e., semantic expressions of numbers, enable us to have an exact representation of the amount of things. Visual processing of numerals plays an indispensable role in the recognition and interpretation of numbers. Here, we investigate how visual information from numerals is processed to achieve semantic understanding. We first found that partial occlusion of some digital numerals introduces bistable interpretations. Next, by using the visual adaptation method, we investigated the origin of this bistability in human participants. We showed that adaptation to digital and normal Arabic numerals, as well as homologous shapes, but not Chinese numerals, biases the interpretation of a partially occluded digital numeral. We suggest that this bistable interpretation is driven by intermediate shape processing stages of vision, i.e., by features more complex than local visual orientations but more basic than the abstract concepts of numerals.

Peptidergic neurons with extensive branching orchestrate the internal states and energy balance of male Drosophila melanogaster.
Neuropeptide SIFamide (SIFa) neurons in Drosophila melanogaster have been characterized by their exceptionally elaborate arborization patterns, which extend from the brain into the ventral nerve cord (VNC). SIFa neurons are equipped to receive signals that integrate both internal physiological cues and external environmental stimuli. These signals enable the neurons to regulate energy balance, sleep patterns, metabolic status, and circadian timing. These peptidergic neurons are instrumental in orchestrating the animal's internal states and refining its behavioral responses, yet the precise molecular underpinnings of this process remain elusive. Here we demonstrate that SIFa neurons coordinate a range of behavioral responses by selectively integrating inputs and outputs in a context-dependent manner. These neurons engage in a feedback loop with sNPF neurons in the ventral nerve cord, modifying behaviors such as long mating duration (LMD) and shorter mating duration (SMD). Furthermore, SIFa neurons receive essential inputs from neuropeptides Dsk, sNPF, and dilp2, which regulate interval timing behaviors. Activating SIFa neurons leads to reduced mating duration and increased food intake, while deactivating them reduces food intake. Overall, these findings demonstrate the importance of SIFa neurons in absorbing inputs and turning them into behavioral outputs, shedding light on animal's intricate behavioral orchestration.

Wound closure after brain injury relies on force generation by microglia in zebrafish
Wound closure after a brain injury is critical for tissue restoration but this process is still not well characterized at the tissue level. We use live observation of wound closure in larval zebrafish after inflicting a stab wound to the brain. We demonstrate that the wound closes in the first 24 hours after injury by global tissue contraction. Microglia accumulation at the point of tissue convergence precedes wound closure and computational modelling of this process indicates that physical traction by microglia could lead to wound closure. Indeed, genetically or pharmacologically depleting microglia leads to defective tissue repair. Live observations indicate centripetal deformation of astrocytic processes contacted by migrating microglia. Severing such contacts leads to retraction of cellular processes, indicating tension. Weakening tension by disrupting the F-Actin stabilising gene lcp1 in microglial cells, leads to failure of wound closure. Therefore, we propose a previously unidentified mechanism of brain repair in which microglia has an essential role in contracting spared tissue. Understanding the mechanical role of microglia will support advances in traumatic brain injury therapies

At the onset of active whisking, the input layer of barrel cortex exhibits a 24 h window of increased excitability that depends on prior experience.
The development of motor control over sensory organs is a critical milestone in sensory processing, enabling active exploration and shaping of the sensory environment. However, whether the onset of sensory organ motor control directly influences the development of corresponding sensory cortices remains unknown. Here, we exploit the late onset of whisking behavior in mice to address this question in the somatosensory system. Using ex vivo electrophysiology, we discovered a transient increase in the intrinsic excitability of excitatory neurons in layer IV of the barrel cortex, which processes whisker input, precisely coinciding with the onset of active whisking at postnatal day 14 (P14). This increase in neuronal gain was specific to layer IV, independent of changes in synaptic strength, and required prior sensory experience. Strikingly, the effect was not observed in layer II/III of the barrel cortex or in the visual cortex upon eye opening, suggesting a unique interaction between the development of active sensing and the thalamocortical input layer in the somatosensory system. Predictive modeling indicated that changes in active membrane conductances alone could reliably distinguish P14 neurons in control but not whisker-deprived hemispheres. Our findings demonstrate an experience-dependent, lamina-specific refinement of neuronal excitability tightly linked to the emergence of active whisking. This transient increase in the gain of the thalamic input layer coincides with a critical period for synaptic plasticity in downstream layers, suggesting a role in facilitating cortical maturation and sensory processing. Together, our results provide evidence for a direct interaction between the development of motor control and sensory cortex, offering new insights into the experience-dependent development and refinement of sensory systems. These findings have broad implications for understanding the interplay between motor and sensory development, and how the mechanisms of perception cooperate with behavior.

CHRFAM7A overexpression in human iPSC-derived Interneurons dysregulates α7-nAChR surface expression and alters response to oligomeric β-amyloid peptide
The alpha7 neuronal nicotinic receptor (alpha7-nAChR) gene, CHRNA7, is widely expressed within the brain and at the periphery. It plays various important roles in cognition and immune functions. Decreased expression of alpha7-nAChR has been associated with Alzheimer disease (AD) triggered by the accumulation of the 42-amino acid beta-amyloid peptide (ABeta1-42). The interactions of this peptide with alpha7-nAChR may represent a pivotal mechanism that is involved in pathogenesis of AD. The regulation of CHRNA7 is a complex process. Normal function of alpha7-nAChR in mammalian cells requires the co-expression of chaperone proteins such as RIC3 and NACHO which facilitate the formation of cell surface receptors. In humans, CHRNA7 regulation also involves the specific chimeric CHRFAM7A gene product dupalpha7, which may assemble with alpha7 subunits and lead to dominant negative regulation of alpha7-nAChR function. To further elucidate the complex interplay between CHRFAM7A gene product (dupalpha7), alpha7-nAChRs and ABeta1-42, we used human induced pluripotent stem cells (iPSC)-derived interneurons (INs). Four iPSC lines were analyzed for the presence of CHRFAM7A copies. Among them, a cell line with a null genotype was selected for the lentiviral overexpression of CHRFAM7A. Our data show that overexpression of CHRFAM7A led to a reduction in the surface detection of alpha7-nAChR ligand binding sites in iPSC-derived INs. INs expressing the alpha7-dupalpha7 subunit (alpha7-dupalpha7-INs) exhibited lower levels of RIC3 and NACHO. Upon agonist treatment by nicotine, an up-regulation of alpha7-nAChR ligand binding sites was observed in alpha7-dupalpha7-INs as compared to non-transduced INs (alpha7-INs). At low levels of ABeta treatment, alpha7-INs displayed a significant reduction in production of reactive oxygen species (ROS), while high levels resulted in a slight increase. In contrast, alpha7-dupalpha7-INs exhibited lower baseline levels of ROS that remained unaltered by A Beta treatment. ROS are known to exacerbate AD pathogenesis. We hypothesize that such effects may also be triggered by alpha7-dupalpha7-INs in the brain of patients. Further investigations are currently undertaken to confirm this hypothesis.