bioRxiv Subject Collection: Neuroscience's Journal

Association of 10 VEGF Family Genes with Alzheimer's Disease Pathology at Single Cell Resolution
Background: The role of the vascular endothelial growth factors (VEGFs) in the pathogenesis of Alzheimer's disease (AD) has been recently described, including notable changes along the VEGFB/FLT1 signaling pathway. However, cell-type specific alterations are yet to be characterized in depth. In this study, we utilized a large single-nucleus RNA sequencing dataset (N = 424) to investigate the effect of 10 VEGF gene expression (VEGFA, VEGFB, VEGFC, VEGFD, PGF, FLT1, FLT4, KDR, NRP1, and NRP2) on cognitive performance and AD pathology, as well as on the associated VEGF signaling pathways in 8 cell types from postmortem human brains. Methods: The single-nucleus transcriptomes, derived from Dorsolateral Prefrontal Cortex (DLFPC) tissues of 424 unique donors from the Religious Orders Study and Memory and Aging Project (ROS/MAP; AD Knowledge Portal syn2580853), were collected by the Rush Alzheimer's Disease Center and processed at Columbia University Medical Center. Mean age of death of the cohort was 89 years, among which 68% were females, and 52% were clinical AD cases. Negative binomial mixed models implemented in Nebula R package were used for differential expression analysis between autopsy confirmed AD dementia and normal cognition groups, and for association analysis with amyloid burden, tangle burden, and both cross-sectional and longitudinal global cognitive function. Intercellular VEGF-associated communication pattern among cell types was also profiled using CellChat. Results: Higher microglia expressed FLT1, endothelial FLT4, astrocyte VEGFD, and oligodendrocyte precursor cell (opc) NRP1 expression associated with greater beta-amyloid burden. Higher oligodendrocyte VEGFB expression associated with greater beta-amyloid burden and worse cognitive trajectories, whereas higher VEGFB expression in inhibitory neurons was associated with lower beta-amyloid burden. Higher astrocyte NRP1 was associated with lower tangle burden. Higher expression of microglia and endothelial FLT1 associated with worse cognitive trajectories and lower cognition scores at the last clinic visit before death. As for association with diagnosis, prefrontal cortical FLT1 expression was upregulated in clinical AD patients compared to cognitively normal controls in both endothelial and microglial cells. For VEGF-associated intercellular communication, VEGFA-mediated signals contributed the most to the communication in both AD and normal cognition groups. Interestingly, although FLT1 expression was significantly elevated in AD endothelial cells, these cells still showed comparable VEGFA-FLT1 communication strength to the cognitively normal controls. Conclusions: Consistent with our previously reported results from bulk omics data, prefrontal cortical expression of FLT1 and FLT4 were associated with cross-sectional global cognitive function, longitudinal cognitive trajectories, and AD neuropathology, and our study showed these associations appear to be driven by endothelial and microglial cells. In contrast, VEGFB expression seems to have opposing effects on amyloid burden depending on the cell types, suggesting its more dynamic role in AD pathology.

Excitatory neurons of the anterior cingulate cortex encode chosen actions and their outcomes rather than cognitive state
The anterior cingulate cortex (ACC) causally influences cognitive control of goal-directed behaviour. However, it is unclear whether ACC directly encodes cognitive variables like attention or impulsivity, or implements goal-directed action selection mechanisms that are modulated by them. We recorded ACC activity with miniature endoscopic microscopes in mice performing the 5-choice serial reaction time task, and applied decoding and encoding analyses. ACC pyramidal cells represented specific actions before and during the behavioural response, whereas the response type (e.g. correct/incorrect/premature), indicating the state of attentional and impulse control, could only be decoded during and after the response with high reliability. Devaluation and extinction experiments further revealed that action encoding depended on reward expectation. Our findings support a role for ACC in goal-directed action selection and monitoring, that is modulated by cognitive state, rather than in tracking levels of attention or impulsivity directly in individual trials.

SleepInvestigatoR: A flexible R function for analyzing scored sleep in rodents
Analyzing scored sleep is a fundamental prerequisite to understanding how sleep changes between health and disease. Classically, this is accomplished by manually calculating various measures (e.g., percent of non-rapid eye movement sleep) from a collection of scored sleep files. This process can be tedious and error prone especially when studies include a large number of animals or involve long recording sessions. To address this issue, we present SleepInvestigatoR, a versatile tool that can quickly organize and analyze multiple scored sleep files into a single output. The function is written in the open-source statistical language R and has a total of 25 parameters that can be set to match a wide variety of experimenter needs. SleepInvestigatoR delivers a total of 22 unique measures of sleep, including all measures commonly reported in the rodent literature. A simple plotting function is also provided to quickly graph and visualize the scored data. All code is designed to be implemented with little formal coding knowledge and step-by-step instructions are provided on the corresponding GitHub page. Overall, SleepInvestigatoR provides the sleep researcher a critical tool to increase efficiency, interpretation, and reproducibility in analyzing scored rodent sleep.

Automatization and validation of the hippocampal-to-ventricle ratio in a clinical sample
Background: The hippocampal-to-ventricle ratio (HVR) is a biomarker of medial temporal atrophy, particularly useful in the assessment of neurodegeneration in diseases such as Alzheimer's disease (AD). To minimize subjectivity and inter-rater variability, an automated, accurate, precise, and reliable segmentation technique for the hippocampus (HC) and surrounding cerebro-spinal fluid (CSF) filled spaces - such as the temporal horns of the lateral ventricles - is essential. Methods: We trained and evaluated three automated methods for the segmentation of both HC and CSF (Multi-Atlas Label Fusion (MALF), Nonlinear Patch-Based Segmentation (NLPB), and a Convolutional Neural Network (CNN)). We then evaluated these methods, including the widely used FreeSurfer technique, using baseline T1w MRIs of 1,641 participants from the AD Neuroimaging Initiative study with various degree of atrophy associated with their cognitive status on the spectrum from cognitively healthy to clinically probable AD. Our gold standard consisted in manual segmentation of HC and CSF from 80 cognitively healthy individuals. We calculated HC volumes and HVR and compared all methods in terms of segmentation reliability, similarity across methods, sensitivity in detecting between-group differences and associations with age, scores of the learning subtest of the Rey Auditory Verbal Learning Test (RAVLT) and the Alzheimer's Disease Assessment Scale 13 (ADAS13) scores. Results: Cross validation demonstrated that the CNN method yielded more accurate HC and CSF segmentations when compared to MALF and NLPB, demonstrating higher volumetric overlap (Dice Kappa = 0.94) and correlation (rho = 0.99) with the manual labels. It was also the most reliable method in clinical data application, showing minimal failures. Our comparisons yielded high correlations between FreeSurfer, CNN and NLPB volumetric values. HVR yielded higher control:AD effect sizes than HC volumes among all segmentation methods, reinforcing the significance of HVR in clinical distinction. Associations: The positive association with age was significantly stronger for HVR compared to HC volumes on all methods except FreeSurfer. Memory associations with HC volumes or HVR were only significant for individuals with mild cognitive impairment. Finally, the HC volumes and HVR showed comparable negative associations with ADAS13, particularly in the mild cognitive impairment cohort. Conclusion: This study provides an evaluation of automated segmentation methods centered to estimate HVR, emphasizing the superior performance of a CNN-based algorithm. The findings underscore the pivotal role of accurate segmentation in HVR calculations for precise clinical applications, contributing valuable insights into medial temporal lobe atrophy in neurodegenerative disorders, especially AD.

Dynamics of sensorimotor reweighting: How light touch alters vestibular-evoked balance responses.
Integrated multisensory feedback plays a crucial role in balance control. Minimal fingertip contact with a surface (light-touch), reduces centre of pressure (CoP) by adding sensory information about postural orientation and balance state. Electrical vestibular stimulation (EVS) significantly increases sway by adding erroneous vestibular cues. This juxtaposition of conflicting sensory cues can be exploited to explore the dynamics of sensorimotor reweighting. We used continuous stochastic EVS (0-25Hz; {+/-} 4mA; 200-300s) to evoke balance responses in CoP (Exp-1, Exp-2) and segment accelerations (Exp-2). Systems analyses (coherence, gain) quantified coupling and size of balance responses to EVS. We had participants either touch (TOUCH; <2N) or not touch (NO-TOUCH) a load cell during EVS (Exp-1, Exp-2), or we intermittently removed the touch surface (Exp-2) to measure the effects of light touch on vestibular-evoked balance responses. We hypothesized that coherence and gain between EVS and CoP would decrease, consistent with the CNS down-weighting vestibular cues that conflict with light touch. Light touch reduced CoP displacement, but increased variation in the CoP signal explained by EVS input. Significant coherence between EVS and CoP was observed up to ~30Hz in both conditions but was significantly greater in the TOUCH condition from 12-28.5-Hz. Conversely, EVS-CoP gain was 63% lower in TOUCH, compared to NO-TOUCH. Our findings show that light touch can re-weight vestibular-evoked responses by reducing their size but also increasing high frequency vestibular contributions for sway. This suggests that the CNS can use novel sensory inputs to alter balance behavior but cannot completely ignore a salient balance cue.

Release the Krakencoder: A unified brain connectome translation and fusion tool
Brain connectivity can be estimated in many ways, depending on modality and processing strategy. Here we present the Krakencoder, a joint connectome mapping tool that simultaneously, bidirectionally translates between structural (SC) and functional connectivity (FC), and across different atlases and processing choices via a common latent representation. These mappings demonstrate unprecedented accuracy and individual-level identifiability; the mapping between SC and FC has identifiability 42-54% higher than existing models. The Krakencoder combines all connectome flavors via a shared low-dimensional latent space. This "fusion" representation i) better reflects familial relatedness, ii) preserves age- and sex- relevant information and iii) enhances cognition-relevant information. The Krakencoder can be applied without retraining to new, out-of-age-distribution data while still preserving inter-individual differences in the connectome predictions and familial relationships in the latent representations. The Krakencoder is a significant leap forward in capturing the relationship between multi-modal brain connectomes in an individualized, behaviorally- and demographically-relevant way.

Genetic screen to test microRNA function in peripheral glia morphology
Glial cells perform many functions in the nervous system, including maintaining the blood-brain/nerve barriers and structurally supporting axons. While their functions are well-characterized, the complex molecular mechanisms important for their development are less known. Here, we investigated whether microRNA-mediated post-transcriptional regulation is involved during glial development, ensheathment and blood-nerve-barrier formation in Drosophila. In this study, we systematically knocked down 120 different microRNAs by competitive inhibition using microRNA-sponges and analyzed peripheral glial morphology. Knockdown of miRNA-125 in the blood-nerve barrier-forming glia (subperineurial glia) resulted in the most penetrant morphological defects. Since microRNA-125 is co-transcribed with miRNAs-let7 and -100 in a genetic cluster, our further verification for subperineurial glia function included miRNA-125 plus all other members of this cluster. However, the loss of each individual gene and the entire cluster did not lead to any morphological defects in the subperineurial glia. To test the efficiency of the microRNA sponge approach in subperineurial glia, we expressed a sponge targeting a microRNA established to be vital for blood-brain barrier formation (microRNA-285) and found no defects in brain lobes and peripheral nerves. Given that a scrambled-sponge control also generated morphological defects, this suggests that using miRNA sponge lines may not be an effective approach to study miRNA function in Drosophila peripheral glia

Comparing the impact of contextual associations and statistical regularities in visual search and attention orienting
During visual search, we quickly learn to attend to an objects likely location. Research has shown that this process can be guided by learning target locations based on consistent spatial contextual associations or statistical regularities. Here, we tested how these different types of learning aid the utilisation of established memories for different purposes. Participants learned contextual associations or statistical regularities that predicted target locations within different scenes. The consequences of this learning for subsequent performance were then evaluated on attention-orienting and memory-recall tasks. Participants demonstrated facilitated attention-orienting and recall performance based on both contextual associations and statistical regularities. Contextual associations facilitated attention orienting with a different time course compared to statistical regularities. Benefits to memory-recall performance depended on the alignment between the learned association or regularity and the recall demands. The distinct patterns of behavioural facilitation by contextual associations and statistical regularities show how different forms of long-term memory may influence neural information processing through different modulatory mechanisms.

Measuring the dynamic balance of integration and segregation underlying consciousness, anesthesia, and sleep
Consciousness requires a dynamic balance of integration and segregation in functional brain networks. An optimal integration-segregation balance depends on two key aspects of functional connectivity: global efficiency (i.e., integration) and clustering (i.e., segregation). We developed a new fMRI-based measure, termed the integration-segregation difference (ISD), which captures both aspects. We used this metric to quantify changes in brain state from conscious wakefulness to loss of responsiveness induced by the anesthetic propofol. The observed changes in ISD suggest a profound shift to segregation in both whole brain and all brain subnetworks during anesthesia. Moreover, brain networks displayed similar sequences of disintegration and subsequent reintegration during, respectively, loss and return of responsiveness. Random forest machine learning models, trained with the integration and segregation of brain networks, identified the awake vs. unresponsive states and their transitions with accuracy up to 93%. We found that metastability (i.e., the dynamic recurrence of non-equilibrium transient states) is more effectively explained by integration, while complexity (i.e., diversity and intricacy of neural activity) is more closely linked with segregation. The analysis of a sleep dataset revealed similar findings. Our results demonstrate that the integration-segregation balance is a useful index that can differentiate among various conscious and unconscious states.

Spatial Coding Dysfunction and Network Instability in the Aging Medial Entorhinal Cortex
Across species, spatial memory declines with age, possibly reflecting altered hippocampal and medial entorhinal cortex (MEC) function. However, the integrity of cellular and network-level spatial coding in aged MEC is unknown. Here, we leveraged in vivo electrophysiology to assess MEC function in young, middle-aged, and aged mice navigating virtual environments. In aged grid cells, we observed impaired stabilization of context-specific spatial firing, correlated with spatial memory deficits. Additionally, aged grid networks shifted firing patterns often but with poor alignment to context changes. Aged spatial firing was also unstable in an unchanging environment. In these same mice, we identified 458 genes differentially expressed with age in MEC, 61 of which had expression correlated with spatial firing stability. These genes were enriched among interneurons and related to synaptic transmission. Together, these findings identify coordinated transcriptomic, cellular, and network changes in MEC implicated in impaired spatial memory in aging.

Hyperacetylation mimetics within the tau filament core inhibits prion-like propagation of misfolded tau
Acetylation of key Lysine residues characterizes aggregates of the microtubule-associated protein tau constituting the neuropathological hallmark of many neurodegenerative diseases, such as Alzheimers disease (AD) and Progressive Supranuclear Palsy (PSP). This has led to the idea that acetylation influences tau aggregation. Using a HEK293 cell-based aggregation assay, we tested whether acetylation-mimicking substitutions (K[->]Q) on five AD-associated acetyl-modified sites (AcK-311, 353, 369, 370, 375) influenced its propensity to aggregate when exposed to tau seeds derived from two clinically distinctive diseases - AD and PSP. In combination, the presence of 5K[->]Q sites ablated tau aggregation induced by seeds from both AD and PSP patients, indicating that acetylation within the filament core domain of tau could have an inhibitory effect on seed-mediated aggregation. We had previously identified that a phosphorylation-mimetic on Ser305 (S[->]E) abrogated tau aggregation by seeds from AD patients, without affecting seeding by PSP patients. Combining the S305[->]E to the 5K[->]Q acetyl-modified sites, we found that this tau could now be seeded only by PSP patients, but not by AD patients, confirming Ser305 as a critical determinant of strain-specific tau seeding. On the other hand, acetylation-nullifying substitutions (K[->]R or K[->]A) on these same Lys sites did not alter tau seeding abilities compared to the parental tau construct. Notably, the combined acetylation-nullifying Alanine substitutions on these 5 Lys sites resulted in spontaneous self-aggregation, with the filaments resembling amorphous deposits. All together, we demonstrate that cooperative acetyl-occupancy in the tau filament core influences seeded propagation of misfolded tau as well as drives self-aggregation.

Neuroprotective efficacy of the glucocorticoid receptor modulator PT150 in the rotenone mouse model of Parkinsons disease
Parkinsons disease (PD) is the most common neurodegenerative movement disorder worldwide. Current treatments for PD largely center around dopamine replacement therapies and fail to prevent the progression of pathology, underscoring the need for neuroprotective interventions. Approaches that target neuroinflammation, which occurs prior to dopaminergic neuron (DAn) loss in the substantia nigra (SN), represent a promising therapeutic strategy. The glucocorticoid receptor (GR) has been implicated in the neuropathology of PD and modulates numerous neuroinflammatory signaling pathways in the brain. Therefore, we investigated the neuroprotective effects of the novel GR modulator, PT150, in the rotenone mouse model of PD, postulating that inhibition of glial inflammation would protect DAn and reduce accumulation of neurotoxic misfolded -synuclein protein. C57Bl/6 mice were exposed to 2.5 mg/kg/day rotenone by intraperitoneal injection for 14 days, immediately followed by oral treatment with 30 mg/kg/day or 100 mg/kg/day PT150 in the 14-day post-lesioning incubation period, during which the majority of DAn loss and -synuclein (-syn) accumulation occurs. Our results indicate that treatment with PT150 reduced both loss of DAn and microgliosis in the nigrostriatal pathway. Although morphologic features of astrogliosis were not attenuated, PT150 treatment promoted potentially neuroprotective activity in these cells, including increased phagocytosis of hyperphosphorylated -syn. Ultimately, PT150 treatment reduced the loss of DAn cell bodies in the SN, but not the striatum, and prohibited intra-neuronal accumulation of -syn. Together, these data indicate that PT150 effectively reduced SN pathology in the rotenone mouse model of PD.

Robust self-supervised denoising of voltage imaging data using CellMincer
Voltage imaging enables high-throughput investigation of neuronal activity, yet its utility is often constrained by a low signal-to-noise ratio (SNR). Conventional denoising algorithms, such as those based on matrix factorization, impose limiting assumptions about the noise process and the spatiotemporal structure of the signal. While deep learning based denoising techniques offer greater adaptability, existing approaches fail to fully exploit the fast temporal dynamics and unique short- and long-range dependencies within voltage imaging datasets. Here, we introduce CellMincer, a novel self-supervised deep learning method designed specifically for denoising voltage imaging datasets. CellMincer operates on the principle of masking and predicting sparse sets of pixels across short temporal windows and conditions the denoiser on precomputed spatiotemporal auto-correlations to effectively model long-range dependencies without the need for large temporal denoising contexts. We develop and utilize a physics-based simulation framework to generate realistic datasets for rigorous hyperparameter optimization and ablation studies, highlighting the key role of conditioning the denoiser on precomputed spatiotemporal auto-correlations to achieve 3-fold further reduction in noise. Comprehensive benchmarking on both simulated and real voltage imaging datasets, including those with paired patch-clamp electrophysiology (EP) as ground truth, demonstrates CellMincer's state-of-the-art performance. It achieves substantial noise reduction across the entire frequency spectrum, enhanced detection of subthreshold events, and superior cross-correlation with ground-truth EP recordings. Finally, we demonstrate how CellMincer's addition to a typical voltage imaging data analysis workflow improves neuronal segmentation, peak detection, and ultimately leads to significantly enhanced separation of functional phenotypes.

A dual-receptor model of serotonergic psychedelics: therapeutic insights from simulated cortical dynamics
Serotonergic psychedelics have been identified as promising next-generation therapeutic agents in the treatment of mood and anxiety disorders. While their efficacy has been increasingly validated, the mechanism by which they exert a therapeutic effect is still debated. A popular theoretical account is that excessive 5-HT2a agonism disrupts cortical dynamics, relaxing the precision of maladaptive high-level beliefs, thus making them more malleable and open to revision. We extend this perspective by developing a theoretical framework and simulations based on predictive processing and an energy-based model of cortical dynamics. We consider the role of both 5-HT2a and 5-HT1a agonism, characterizing 5-HT2a agonism as inducing stochastic perturbations of the energy function underlying cortical dynamics and 5-HT1a agonism as inducing a global smoothing of that function. Within our simulations, we find that while both agonists are able to provide a significant therapeutic effect individually, mixed agonists provide both a more psychologically tolerable acute experience and better therapeutic efficacy than either pure 5-HT2a or 5-HT1a agonists alone. This finding provides a potential theoretical basis for the clinical success of LSD, psilocybin, and DMT, all of which are mixed serotonin agonists. Our results furthermore indicate that exploring the design space of biased 5-HT1a agonist psychedelics such as 5-MeO-DMT may prove fruitful in the development of even more effective and tolerable psychotherapeutic agents in the future.

Conservation of neuron-astrocyte coordinated activity among sensory processing centers of the developing brain
Afferent neurons in developing sensory organs exhibit a prolonged period of burst firing prior to the onset of sensory experience. This intrinsically generated activity propagates from the periphery through central processing centers to promote the survival and physiological maturation of neurons and refine their synaptic connectivity. Recent studies in the auditory system indicate that these bursts of action potentials also trigger metabotropic glutamate receptor-mediated calcium increases within astrocytes that are spatially and temporally correlated with neuronal events; however, it is not known if this phenomenon occurs in other sensory modalities. Here we show using in vivo simultaneous imaging of neuronal and astrocyte calcium activity in awake mouse pups that waves of retinal ganglion cell activity induce spatially and temporally correlated waves of astrocyte activity in the superior colliculus that depend on metabotropic glutamate receptors mGluR5 and mGluR3. Astrocyte calcium transients reliably occurred with each neuronal wave, but peaked more than one second after neuronal events. Despite differences in the temporal features of spontaneous activity in auditory and visual processing regions, individual astrocytes exhibited similar overall calcium activity patterns, providing a conserved mechanism to synchronize neuronal and astrocyte maturation within discrete sensory domains.

Ultrastructural Dynamics of Dopaminergic Presynaptic Release Sites revealed by Cryo-correlative Light and Electron Microscopy
Dopaminergic neurons are fundamental in governing motivation, movement, and many aspects of cognition. The targeted modulation of dopaminergic signaling serves as a cornerstone in developing therapeutic interventions for conditions such as Parkinson's disease, schizophrenia, and addiction. Despite the pivotal role of dopaminergic neurons, the ultrastructure and associated dynamics of dopaminergic synapses remain poorly understood. Here, we develop and utilize a cryo-correlative light and electron microscopy process chain to investigate the micro- to nanoscale architecture and organelle content of dopaminergic presynaptic release sites. Using cryo electron tomography, we identify several protein complexes crucial to dopaminergic function and we utilize subtomogram averaging to resolve in situ assemblies of the TRiC/CCT chaperone and vacuolar-type ATPase. Lastly, we find that pharmacological treatments using either dopamine or the dopamine D2 receptor antagonist, haloperidol, bidirectionally modulate vesicular content, mitochondrial size and calcium phosphate deposition. These findings contribute to our general understanding of the composition and ultrastructural dynamics of dopaminergic presynaptic release sites and provide a methodological platform for further studies of the structure and cell biology of dopaminergic neurons and their responses.

Slow kinesin-dependent microtubular transport facilitates ribbon synapse assembly in developing cochlear inner hair cells
Sensory synapses are characterized by electron-dense presynaptic specializations, so-called synaptic ribbons. In cochlear inner hair cells (IHCs), ribbons play an essential role as core active zone (AZ) organizers, where they tether synaptic vesicles, cluster calcium channels and facilitate the temporally-precise release of primed vesicles. While a multitude of studies aimed to elucidate the molecular composition and function of IHC ribbon synapses, the developmental formation of these signalling complexes remains largely elusive to date. To address this shortcoming, we performed long-term live-cell imaging of fluorescently-labelled ribbon precursors in young postnatal IHCs to track ribbon precursor motion. We show that ribbon precursors utilize the apico-basal microtubular (MT) cytoskeleton for targeted trafficking to the presynapse, in a process reminiscent of slow axonal transport in neurons. During translocation, precursor volume regulation is achieved by highly dynamic structural plasticity - characterized by regularly-occurring fusion and fission events. Pharmacological MT destabilization negatively impacted on precursor translocation and attenuated structural plasticity, whereas genetic disruption of the anterograde molecular motor Kif1a impaired ribbon volume accumulation during developmental maturation. Combined, our data thus indicate an essential role of the MT cytoskeleton and Kif1a in adequate ribbon synapse formation and structural maintenance.

Inhibitory control of locomotor statistics in walking Drosophila
In order to forage for food, many animals regulate not only specific limb movements but the statistics of locomotor behavior over time, for example switching between long-range dispersal behaviors and more localized search depending on the availability of resources. How pre-motor circuits regulate such locomotor statistics is not clear. Here we took advantage of the robust changes in locomotor statistics evoked by attractive odors in walking Drosophila to investigate their neural control. We began by analyzing the statistics of ground speed and angular velocity during three well-defined motor regimes: baseline walking, upwind running during odor, and search behavior following odor offset. We find that during search behavior, flies adopt higher angular velocities and slower ground speeds, and tend to turn for longer periods of time in one direction. We further find that flies spontaneously adopt periods of different mean ground speed, and that these changes in state influence the length of odor-evoked runs. We next developed a simple physiologically-inspired computational model of locomotor control that can recapitulate these statistical features of fly locomotion. Our model suggests that contralateral inhibition plays a key role both in regulating the difference between baseline and search behavior, and in modulating the response to odor with ground speed. As the fly connectome predicts decussating inhibitory neurons in the lateral accessory lobe (LAL), a pre-motor structure, we generated genetic tools to target these neurons and test their role in behavior. Consistent with our model, we found that activation of neurons labeled in one line increased curvature. In a second line labeling distinct neurons, activation and inactivation strongly and reciprocally regulated ground speed and altered the length of the odor-evoked run. Additional targeted light activation experiments argue that these effects arise from the brain rather than from neurons in the ventral nerve cord, while sparse activation experiments argue that speed control in the second line arises from both LAL neurons and a population of neurons in the dorsal superior medial protocerebrum (SMP). Together, our work develops a biologically plausible computational architecture that captures the statistical features of fly locomotion across behavioral states and identifies potential neural substrates of these computations.

The link between space and time along the human cortical hierarchy
In humans, very few studies have directly tested the link between the neural coding of time and space. Here we combined ultra-high field functional magnetic resonance imaging with neuronal-based modeling to investigate how and where the processing and the representation of a visual stimulus duration is linked to that of its spatial location. Results show a transition in the neural response to duration: from monotonic and spatially-dependent in early visual cortex, to unimodal and spatially-invariant in frontal cortex. This transition begins in extrastriate areas V3AB, and it fully displays in the intraparietal sulcus (IPS), where both unimodal and monotonic responses are present and where neuronal populations are selective to either space, time or both. In IPS, space and time topographies show a specific relationship, although along the cortical hierarchy duration maps compared to spatial ones are smaller in size, less clustered and more variable across participants. These results help to identify the mechanisms through which humans perceive the duration of a visual object with a specific spatial location and precisely characterize the functional link between time and space processing, highlighting the importance of space-time interactions in shaping brain responses.

A spatio-temporaral atlas of the growing brain for fMRI studies
Spatio-temporal atlases of the growing brain can help when building models of brain development, not only for anatomical structure, but also for the changing patterns of activation within the brain. In this paper, we build such an age-dependent atlas using registrations among a large number of anatomical datasets, acquired from neonatal subjects of different ages, and followed by kernel-based regression. fMRI activation data are then registered to this atlas to build a model of the development of brain networks, such as the default and motor networks, at this early age.

Scn2a deletion disrupts oligodendroglia function: Implication for myelination, neural circuitry, and auditory hypersensitivity in ASD
Autism spectrum disorder (ASD) is characterized by a complex etiology, with genetic determinants significantly influencing its manifestation. Among these, the Scn2a gene emerges as a pivotal player, crucially involved in both glial and neuronal functionality. This study elucidates the underexplored roles of Scn2a in oligodendrocytes, and its subsequent impact on myelination and auditory neural processes. The results reveal a nuanced interplay between oligodendrocytes and axons, where Scn2a deletion causes alterations in the intricate process of myelination. This disruption, in turn, instigates changes in axonal properties and neuronal activities at the single cell level. Furthermore, oligodendrocyte-specific Scn2a deletion compromises the integrity of neural circuitry within auditory pathways, leading to auditory hypersensitivity--a common sensory abnormality observed in ASD. Through transcriptional profiling, we identified alterations in the expression of myelin-associated genes, highlighting the cellular consequences engendered by Scn2a deletion. In summary, the findings provide unprecedented insights into the pathway from Scn2a deletion in oligodendrocytes to sensory abnormalities in ASD, underscoring the integral role of Scn2a-mediated myelination in auditory responses. This research thereby provides novel insights into the intricate tapestry of genetic and cellular interactions inherent in ASD.

Single-nuclei histone modification profiling of the adult human central nervous system unveils epigenetic memory of developmental programs
The adult human central nervous system (CNS) is remarkably complex, with neural cells displaying extensive transcriptional heterogeneity. However, how different layers of epigenetic regulation underpin this heterogeneity is poorly understood. Here, we profile the adult human CNS from distinct regions, for chromatin accessibility at the single-nuclei level. In addition, we simultaneously co-profiled the histone modifications H3K27me3 and H3K27ac at the single nuclei-level, providing their first map in all major human CNS cell types. We unveil primed chromatin signatures at HOX loci in spinal cord-derived human oligodendroglia (OLG) but not microglia. These signatures were reminiscent of developmental OLG but were decoupled from robust gene expression. Moreover, using high-resolution Micro-C, we show that induced pluripotent stem cell (iPS) derived human OLGs exhibit a HOX chromatin architecture compatible with the primed chromatin in adult OLGs, and bears a strong resemblance not only to OLG developmental architecture, but also high-grade pontine gliomas. Thus, adult OLG retain epigenetic memory from developmental states, which might enable them to promptly transcribe Hox genes, in contexts of regeneration, but also make them susceptible to gliomagenesis.

AUTS2, a causative gene for microcephaly, regulates division of intermediate progenitor cells and production of upper-layer neurons
AUTS2 mutations often exhibit neurodevelopmental disorders and microcephaly. However, how AUTS2 regulates neuron production and affects brain size remains unclear. Here, we show that AUTS2 cooperates with the Polycomb complex PRC2 to regulate gene expression and cortical neurogenesis. Auts2 mutant mice exhibit reduced division of intermediate progenitor cells (IPCs), leading to decreased neurons and thickness in the upper-layer cortex. Expression of Robo1 is increased in the mutants, which in turn suppresses IPC division. Transcriptome and chromatin profiling experiments show that, in IPCs, AUTS2 primarily represses transcription of genes, including Robo1. Promoter region of AUTS2 target genes is enriched with H3K27me3, a repressive histone modification, but its levels are reduced in Auts2 mutants. AUTS2 interacts with PRC2, and together, they promote IPC division. These suggest that AUTS2 collaborates with PRC2 to repress gene transcription through H3K27 trimethylation, promoting neuron production. This sheds light on AUTS2 pathophysiological mechanisms in neurogenesis and microcephaly.

Human adherent cortical organoids in a multiwell format
In the growing diversity of human iPSC-derived models of brain development, we present here a novel method that exhibits 3D cortical layer formation in a highly reproducible topography of minimal dimensions. The resulting adherent cortical organoids develop by self-organization after seeding frontal cortex patterned iPSC-derived neural progenitor cells in 384-well plates during eight weeks of differentiation. The organoids have stereotypical dimensions of 3 x 3 x 0.2 mm, contain multiple neuronal subtypes, astrocytes and oligodendrocyte lineage cells, and are amenable to extended culture for at least 10 months. Longitudinal imaging revealed morphologically mature dendritic spines, axonal myelination, and robust neuronal activity. Moreover, adherent cortical organoids compare favorably to existing brain organoid models on the basis of robust reproducibility in obtaining topographically-standardized singular radial cortical structures and circumvent the internal necrosis that is common in free-floating cortical organoids. The adherent human cortical organoid platform holds considerable potential for high-throughput drug discovery applications, neurotoxicological screening, and mechanistic pathophysiological studies of brain disorders.