Biology subjects

Apps, R.

Publications and source records attributed to Apps, R..

12 recordsLinked to original sources

bioRxiv2026

Cerebellar Gray Matter Volume Changes Across Development: Posterolateral and Vermal Transient Increases during Adolescence

The cerebellum undergoes substantial maturation with regionally distinct developmental trajectories. This study examined cerebellar gray matter volume (GMV) in healthy children, adolescents, and adults, using voxel-based morphometry, the ACAPULCO algorithm, and the SUIT toolbox for cerebellum-optimized analyses. A total of 104 typically developing children (n=31, 6-9 years), adolescents (n=35, 13-17 years), and adults (n=38, 30-40 years) were included. We hypothesized age group differences in cerebellar GMV, with adolescents showing the greatest volume, specifically in posterolateral regions. Results revealed significant group differences in GMV. We observed region-specific volumetric patterns, with some areas (e.g., Crus II, lobule X) increasing from childhood to adolescence followed by stabilization, whereas other areas (e.g., lobules I-IV and VI, Crus I, vermis VI and VIIb) exhibited peak GMV during adolescence, with lower volumes in both children and adults. These patterns were partly consistent with our hypothesis. Notably, no regions had greater GMV in adults than adolescents, suggesting that cerebellar growth peaks in adolescence before stabilizing. Our findings indicate differential developmental patterns both between and within lobules of the cerebellum, and highlight adolescence as a peak period of cerebellar growth, with potential implications for the development of cerebellar-supported cognitive and emotional functions that undergo significant changes during this period.

neuroscience↗

bioRxiv2025

Cerebellar involvement in self-timing

The cerebellum is well-established in sub-second motor timing, but its role in supra-second interval timing remains unclear. Here, we investigate how cerebellar output influences time estimation over longer timescales. Rats performed an interval timing task, estimating time based on an auditory cue, while chemogenetic inhibition of the lateral cerebellar nucleus assessed its role in both predictable (externally cued) and unpredictable (internally cued) timing conditions. Cerebellar inhibition produced bidirectional effects: delayed action initiation in predictable trials and premature responses in unpredictable trials. Despite slowed movement, overall task success rates remained unchanged, suggesting a specific impairment in temporal estimation rather than motor execution. These findings demonstrate that the cerebellum integrates motor and cognitive processes for supra-second timing, with differential effects on externally guided and self-generated timing. Our results provide evidence that the lateral cerebellum contributes to supra-second interval timing, supporting its role in adaptive behavior across extended timescales.

neuroscience↗

bioRxiv2024

Single-cell analyses reveal that monocyte gene expression profiles influence HIV-1 reservoir size in acutely treated cohorts

Elimination of latent HIV-1 is a major goal of AIDS research but the host factors determining the size of these reservoirs are poorly understood. Here, we investigated whether differences in host gene expression modulate the size of the HIV-1 reservoir during suppressive ART. Peripheral blood mononuclear cells (PBMC) from fourteen individuals initiating ART during acute infection who demonstrated effective viral suppression but varying magnitude of total HIV-1 DNA were characterized by single-cell RNA sequencing (scRNA-seq). Differentially expressed genes and enriched pathways demonstrated increased monocyte activity in participants with undetectable HIV-1 reservoirs. IL1B expression in CD14+ monocytes showed the greatest fold difference. The inverse association of IL1B with reservoir size was validated in an independent cohort comprised of 38 participants with different genetic backgrounds and HIV-1 subtype infections, and further confirmed with intact proviral DNA assay (IPDA(R)) measurements of intact HIV-1 proviruses in a subset of the samples. Modeling interactions with cell population frequencies showed that monocyte IL1B expression associated inversely with reservoir size in the context of higher frequencies of central memory CD4+ T cells, implicating an indirect effect of IL1B via the cell type well established to be a reservoir for persistent HIV-1. Signatures consisting of co-expressed genes including IL1B were highly enriched in the "TNF signaling via NF-{kappa}B" geneset. Functional analyses in cell culture revealed that IL1B activates NF-{kappa}B, thereby promoting productive HIV-1 infection while simultaneously suppressing viral spread, suggesting a natural latency reversing activity to deplete the reservoir in ART treated individuals. Altogether, unbiased high throughput scRNA-seq analyses revealed that monocyte IL1B variation could decrease HIV-1 proviral reservoirs in individuals initiating ART during acute infection.

immunology↗

bioRxiv2022

Multiparameter stimulation mapping of signaling states in single pediatric immune cells reveals heightened tonic activation during puberty

Cellular stimulation via factors such as cytokines followed by multiparameter single-cell measurements is a powerful approach to interrogate cellular functions. However, transforming such high-dimensional data into biological insights presents unique challenges, particularly given the extensive response heterogeneity among single cells, such as the presence of bimodal responding versus non-responding subpopulations upon stimulation. Here we present an unsupervised high-dimensional approach for analyzing stimulation responses at the single cell level (HDStIM) and apply it to evaluate how pediatric development may shape peripheral immune cell signaling states and responsiveness to stimulations in 42 subjects (age: 2 - 16). We show that in comparison to the conventional approach of assessing one marker at a time by averaging across single cells, HDStIM can effectively learn, in an unsupervised fashion, the multi-parameter signature of responding versus non-responding cells to accurately quantify responses within cell populations. HDStIM reveals that the extent of pre-stimulation/baseline activation of interferon-related and TCR signaling molecules in myeloid and T cells, respectively, increases during puberty. This suggests that puberty is marked by a heightened "tonic" activation state in these cells, perhaps to strengthen defense against pathogens during this period of human development.

immunology↗

bioRxiv2022

Cerebro-cerebellar networks facilitate learning through feedback decoupling

Behavioural feedback is critical for learning in the cerebral cortex. However, such feedback is often not readily available. How the cerebral cortex learns efficiently despite the sparse nature of feedback remains unclear. Inspired by recent deep learning algorithms, we introduce a systems-level computational model of cerebro-cerebellar interactions. In this model a cerebral recurrent network receives feedback predictions from a cerebellar network, thereby decoupling learning in cerebral networks from future feedback. When trained in a simple sensorimotor task the model shows faster learning and reduced dysmetria-like behaviours, in line with the widely observed functional impact of the cerebellum. Next, we demonstrate that these results generalise to more complex motor and cognitive tasks. Finally, the model makes several experimentally testable predictions regarding (1) cerebro-cerebellar task-specific representations over learning, (2) task-specific benefits of cerebellar predictions and (3) the differential impact of cerebellar and inferior olive lesions. Overall, our work offers a theoretical framework of cerebro-cerebellar networks as feedback decoupling machines.

neuroscience↗

bioRxiv2021

Cerebellum controls timing of periaqueductal grey encoding of fear memory and expression of fear conditioned behaviour

The pivotal role of the periaqueductal grey (PAG) in fear learning is reinforced by the identification of neurons in rat ventral PAG (vPAG) that encode fear memory through signalling the onset and offset of an auditory conditioned stimulus during presentation of the unreinforced conditioned tone during retrieval. Some units only display CS+ onset or offset responses and the two signals differ in extinction sensitivity, suggesting they are independent of each other. In addition, understanding cerebellar contributions to survival circuits is advanced by the discovery that: (i) reversible inactivation of the medial cerebellar nucleus (MCN) during fear consolidation leads in subsequent retrieval to: (a) disruption of the temporal precision of vPAG offset, but not onset responses to the unreinforced conditioned tone, and (b) an increase in duration of freezing behaviour. And (ii) chemogenetic manipulation of the MCN-vPAG projection during fear acquisition: (a) reduces the occurrence of fear- related ultrasonic vocalisations and (b) during subsequent retrieval, slows the extinction rate of fear- related freezing. These findings show that the cerebellum is part of the survival network that regulates fear memory processes at multiple timescales and in multiple ways; raising the possibility that dysfunctional interactions in the cerebellar-survival network may underlie fear-related disorders and comorbidities. Impact StatementCerebellar-periaqueductal grey interactions contribute to fear conditioned processes and, as such, provide a novel target for treating psychological conditions including post-traumatic stress disorder.

neuroscience↗

bioRxiv2020

Loss of cortical control over the descending pain modulatory system determines the development of the neuropathic pain state in rats

The loss of descending inhibitory control is thought critical to the development of chronic pain but what causes this loss in function is not well understood. We have investigated the dynamic contribution of prelimbic cortical neuronal projections to the periaqueductal grey (PrL-P) to the development of neuropathic pain in rats using combined opto- and chemo-genetic approaches. We found PrL-P neurons to exert a tonic inhibitory control on thermal withdrawal thresholds in uninjured animals. Following nerve injury, ongoing activity in PrL-P neurons masked latent hypersensitivity and improved affective state. However, this function is lost as the development of sensory hypersensitivity emerges. Despite this loss of tonic control, opto-activation of PrL-P neurons at late post-injury timepoints could restore the anti-allodynic effects by inhibition of spinal nociceptive processing. We suggest that the loss of cortical drive to the descending pain modulatory system underpins the expression of neuropathic sensitisation after nerve injury.

neuroscience↗

bioRxiv2020

A Purkinje cell model that simulates complex spikes

Purkinje cells are the principal neurons of the cerebellar cortex. One of their distinguishing features is that they fire two distinct types of action potential, called simple and complex spikes, which interact with one another. Simple spikes are stereotypical action potentials that are elicited at high, but variable, rates (0 - 100 Hz) and have a consistent waveform. Complex spikes are composed of an initial action potential followed by a burst of lower amplitude spikelets. Complex spikes occur at comparatively low rates (~ 1 Hz) and have a variable waveform. Although they are critical to cerebellar operation a simple model that describes the complex spike waveform is lacking. Here, a novel single-compartment model of Purkinje cell electrodynamics is presented. The simpler version of this model, with two active conductances and a leak channel, can simulate the features typical of complex spikes recorded in vitro. If calcium dynamics are also included, the model can capture the pause in simple spike activity that occurs after complex spike events. Together, these models provide an insight into the mechanisms behind complex spike spikelet generation, waveform variability and their interactions with simple spike activity.

neuroscience↗

bioRxiv2020

Sensory and motor electrophysiological mapping of the cerebellum in humans.

Damage to the cerebellum during posterior fossa surgery can lead to ataxia and in paediatric cases, the risk of cerebellar mutism syndrome. Animal electrophysiological and human imaging studies have shown compartmentalisation of sensorimotor and cognitive functions within the cerebellum. In the present study, electrophysiological monitoring of sensory and motor pathways was carried out to assess the location of limb sensorimotor representation within the human cerebellum, as a potential approach for real time assessment of neurophysiological integrity to reduce the incidence of cerebellar surgical morbidities. Thirteen adult and paediatric patients undergoing posterior fossa surgery were recruited. For sensory mapping (n=8), electrical stimulation was applied to the median nerves, the posterior tibial nerves, or proximal and distal limb muscles and evoked field potential responses were sought on the cerebellar surface. For motor mapping (n=5), electrical stimulation was applied to the surface of the cerebellum and evoked EMG responses were sought in facial and limb muscles. Evoked potentials on the cerebellar surface were found in two patients (25% of cases). In one patient, the evoked response was located on the surface of the right inferior posterior cerebellum in response to stimulation of the right leg. In the second patient, stimulation of the extensor digitorum muscle in the left forearm evoked a response on the surface of the left inferior posterior lobe. In the motor mapping cases no evoked EMG responses could be found. Intraoperative electrophysiological mapping, therefore, indicates it is possible to record evoked potentials on the surface of the human cerebellum in response to peripheral stimulation.

neuroscience↗

bioRxiv2020

Action-based organization and function of cerebellar cortical microcircuits

The cerebellum is the largest sensorimotor structure in the brain, but its mode of operation is not well understood. However, a fundamental organizational feature of the cerebellar cortex is division into elongated zones, defined by their inputs from specific parts of the inferior olive and Purkinje cell output to cerebellar and vestibular nuclei. Little is known about how the pattern of neuronal activity in zones, and their functional microcircuit subdivisions, microzones, is related to behaviour in awake animals. Here, we studied the organization of microzones within the C3 zone and their activity during a skilled forelimb reaching task in cats. Neurons in different parts of the C3 zone, functionally determined by receptive field characteristics, differed in their patterns of activity during movement. Our results suggest that the cerebellar C3 zone is organized and operates within an action-based frame of reference, with different microcircuits within the zone controlling specific muscle synergies.

neuroscience↗

bioRxiv2020

Pre-movement changes in sensorimotor beta oscillations predict motor adaptation drive.

Beta frequency oscillations in scalp electroencephalography (EEG) recordings over the primary motor cortex have been associated with the preparation and execution of voluntary movements. Here, we test whether changes in beta frequency are related to the preparation of adapted movements in human, and whether such effects generalise to other species (cat). Eleven healthy adult humans performed a joystick visuomotor adaptation task. Beta (15-25Hz) scalp EEG signals recorded over the motor cortex during a pre-movement preparatory phase were, on average, significantly reduced in amplitude during early adaptation trials compared to baseline or late adaptation trials (p=0.01). The changes in beta were not related to measurements of reaction time or duration of the reach. We also recorded LFP activity within the primary motor cortex of three cats during a prism visuomotor adaptation task. Analysis of these signals revealed similar reductions in motor cortical LFP beta frequencies during early adaptation. This effect was also present when controlling for any influence of the reaction time and reaching duration. Overall, the results are consistent with a reduction in pre-movement beta oscillations predicting an increase in adaptive drive in upcoming task performance when motor errors are largest in magnitude and the rate of adaptation is greatest.

neuroscience↗

bioRxiv2018

Susceptibility to Neutralization by Broadly Neutralizing Antibodies Correlates with Infected Cell Binding for a Panel of Clade B HIV Reactivated from Latent Reservoirs

Efforts to HIV cure are obstructed by reservoirs of latently infected CD4+ T-cells that can re-establish viremia. Broadly neutralizing HIV-specific antibodies (bNAbs), defined by unusually high neutralization breadths against globally diverse viruses, may contribute to the elimination of these reservoirs by binding to reactivated cells, targeting them for immune clearance. However, the relationship between neutralization of reservoir isolates and binding to corresponding infected primary CD4+ T-cells has not been determined. Thus, the extent to which neutralization breadths and potencies can be used to infer the corresponding parameters of infected-cell binding is currently unknown. We assessed the breadths and potencies of bNAbs against 36 viruses reactivated from peripheral blood CD4+ T-cells of ARV-treated HIV-infected individuals, using paired neutralization and infected-cell binding assays. Single antibody breadths ranged from 0-64% for neutralization (IC80[≤]10g/ml) and 0-89% for binding, with two-antibody combinations reaching 0-83% and 50-100%, respectively. Infected-cell binding correlated with virus neutralization for 10 out of 14 antibodies (e.g. 3BNC117, r=0.87, p<0.0001). Heterogeneity was observed, however, with a lack of significant correlations for 2G12, CAP256.VRC26.25, 2F5, and 4E10. Our results provide guidance on the selection of bNAbs for interventional cure studies; both by providing a direct assessment of intra-and inter-individual variability in neutralization and infected cell binding in a novel cohort, and by defining the relationships between these parameters for a panel of bNAbs.\n\nImportanceAlthough anti-retroviral therapies have improved the lives of people who are living with HIV, they do not cure infection. Efforts are being directed towards harnessing the immune system to eliminate the virus that persists, potentially resulting in virus-free remission without medication. HIV-specific antibodies hold promise for such therapies owing to their abilities to both prevent the infection of new cells (neutralization), and also to direct the killing of infected cells. We isolated 36 HIV strains from individuals whose virus was suppressed by medication, and tested 14 different antibodies for neutralization of these viruses and for binding to cells infected with the same viruses (critical for engaging natural killer cells). For both neutralization and infected-cell binding, we observed variation both between individuals, and amongst different viruses within an individual. For most antibodies, neutralization activity correlated with infected cell binding. These data provide guidance on the selection of antibodies for clinical trials.

immunology↗