Biology subjects

Chiappalone, M.

Publications and source records attributed to Chiappalone, M..

15 recordsLinked to original sources

bioRxiv2026

Distinct effects of different metabolic stress models on human-derived neuronal networks

Different in vitro models are widely used as experimental platforms to assess neuronal responses to metabolic stress and test potential treatments for patients with ischemic stroke. Results of those studies depend on the stress models used, and the link between cell viability-based readouts and electrophysiological activity remains poorly explored. We investigated the neuronal network activity of human-derived neuronal networks generated from human induced pluripotent stem cells (hiPSCs) under three commonly used metabolic stress models: hypoxia alone, oxygen and glucose deprivation (OGD), and hypoxia combined with different concentrations of glutamate. We aim to clarify the differences between three commonly used in vitro models, including the relation between microscopic and electrophysiological readouts. These conditions produced distinct effects on neuronal network activity. Hypoxia alone induced a progressive decline in activity over time. In contrast, OGD triggered a biphasic response, characterized by an early increase in activity followed by a decline. High concentration glutamate exposure under hypoxia also altered network dynamics, inducing a triphasic pattern consisting of a rapid activity decrease, a transient increase, and a subsequent decline. Across all these pathological conditions, neuronal activity progressively declined and converged toward network failure after prolonged hypoxia. Following reoxygenation, recovery was limited and condition-dependent: hypoxia alone, OGD, and high glutamate conditions showed limited recovery. On the other hand, low glutamate concentration was associated with good recovery. Microscopic assessment revealed that cellular viability was differentially affected across conditions. OGD was associated with the highest levels of cell death, whereas glutamate exposure, particularly at high concentrations, led to a marked reduction in synaptic puncta despite partial preservation of cell viability. These findings highlight that commonly used in vitro ischemia models induce distinct neuronal responses and highlight the importance of integrating electrophysiological and structural analyses to better characterize metabolic stress in human neuronal networks better.

bioengineering↗

bioRxiv2026

Functional human neurospheroids recapitulate key features of cortical complexity

BackgroundThree-dimensional in vitro neuronal cultures have emerged as promising platforms for modelling human brain function and disease under controlled conditions. However, their ability to recapitulate in vivo-like complexity and rich dynamics remains underexplored. In this study, we developed and characterized neurospheroids derived from human induced pluripotent stem cells (hiPSCs) to investigate how key features -- three-dimensionality, cellular heterogeneity, and modular organization -- contribute to replicating brain-like network dynamics. MethodsWe engineered neurospheroids with varying excitatory/inhibitory ratios and assembled them into modular constructs (assembloids), evaluating their electrophysiological activity using high-density micro-electrode arrays. We assessed spontaneous and evoked activity through established metrics of dynamical richness and perturbational complexity. ResultsOur findings show that three-dimensionality and modularity significantly enhance the richness and complexity of network activity, approaching levels observed in vivo, while cellular heterogeneity contribute to functional aspects of the network, such as nuanced activity patterns, dynamical variability, and modular coordination. ConclusionsOur work highlights the critical role of spatial organization in reproducing brain-like activity and provide a foundation for future studies using patient-derived neurospheroids to model disease-specific dynamics.

bioengineering↗

bioRxiv2025

Multi-scale disruption of sleep-related cortical activity following ischemic lesions

Sleep plays a critical role in neuroplasticity related processes of learning and memory consolidation. Moreover, its importance in recovery after stroke is known. Yet, how ischemic lesions affect the sleep-wake cycle (SWC) neural dynamics remains poorly explored, with most studies not addressing the multi-scale extent of this pathology effects in brain function. Here, we performed chronic wideband electrophysiological recordings in behaving rats to investigate ischemic stroke impact in the primary motor cortex on SWC organization in connected, non-lesioned, areas of the sensorimotor loop. We combined behavioral assessment with multi-scale analyses spanning global SWC architecture, network level events of privileged functional reshaping during sleep, and single-unit activity. Lesioned animals, exhibiting sharp motor impairments, displayed clear alterations of SWC macro-architecture, including reduced latency to slow-wave sleep and correlations between spectral features and motor asymmetry. At meso-scale, ischemia disrupted the physiological coordination between slow oscillations and spindles, and the latter showed shift in spectral power distribution during intermediate sleep. In contrast, units firing and coupling with spindles were largely preserved. These findings reveal that ischemia perturbs the fine coordination of sleep-related processes across scales stage-specifically. The study lays solid evidence to be possibly leveraged for innovative protocols of neurorehabilitation targeting privileged windows of neuroplasticity.

neuroscience↗

bioRxiv2025

'SpikeNburst' and 'Nicespike': Advanced Tools for Enhancing and Accelerating In Vitro High-Density Electrophysiology Analysis

High-density multi-electrode arrays (HD-MEAs) enable the recording of in vitro neuronal activity with exceptional spatial and temporal resolution. However, analysing these extensive datasets presents challenges, such as artefact removal, spike sorting, and accurate assessments of neuronal synchronization. Here, we introduce a structured protocol for conducting comprehensive HD-MEA analyses using two Python-based tools: spikeNburst and nicespike. This protocol provides a scalable and systematic approach to processing HD-MEA recordings, ensuring efficient data handling and robust analytical outcomes. The spikeNburst tool incorporates advanced methodologies for spike train filtering, burst and network burst detection, and synchronization analysis. Complementing this, we have implemented a full analysis pipeline in the nicespike tool, featuring GPU-accelerated spike sorting via template matching with Kilosort, enabling accurate identification of neuronal units across multiple electrodes. This protocol ensures more precise analyses by reducing redundancy and overestimation inherent in single-channel approaches. Moreover, both tools offer graphical user and command-line interfaces, ensuring accessibility for diverse user needs. We validated our protocol on in vitro neuronal culture recordings, demonstrating its suitability to identify somatic and dendritic features of neuronal units, characterize bursting behaviour, and quantify synchronization at both unit and network levels. By addressing critical limitations of existing methods, spikeNburst and nicespike provide a robust, scalable, and user-friendly framework for HD-MEA data analysis, enhancing the study of neural network dynamics and single-cell activity in detail.

neuroscience↗

bioRxiv2023

Enabling Model-based Design for closed-loop applications in neuroengineering

This study addresses the inherent difficulties in the creation of neuroengineering devices for closed-loop stimulation, a task typically characterized by intricate and technically demanding processes. Beneath the substantial hardware advancements in neurotechnology, there is often rather complex low-level code that poses challenges in terms of development, documentation, and long-term maintenance. To overcome these obstacles, we adopted an alternative strategy centered on Model-based Design (MBD) as a means to simplify the creation of closed-loop systems and reduce the entry barriers. MBD offers distinct advantages by streamlining the development workflow and facilitating the implementation of intricate systems. In this study, we applied MBD techniques to implement a spike detection algorithm on a Field-Programmable Gate Array (FPGA) using commercially available hardware that combines neural probe electronics with programmable FPGA-based hardware. The entire process of data handling and data processing was designed within the Simulink(R) environment, with subsequent generation of HDL code tailored to the FPGA hardware. The validation of our approach was conducted through in vivo experiments involving six animals. We have made all project code files open-source, thereby providing free access to fellow scientists interested in the development of closed-loop systems.

bioengineering↗

bioRxiv2023

Heterogeneous subpopulations of GABAAR-responding neurons coexist in physiological and pathological mature neuronal networks at increasing scales of complexity

GABA is the main inhibitory neurotransmitter in adults. Depolarizing/excitatory GABA responses have been well characterized at the level of neuronal-population average during typical neurodevelopment and partially in pathology. However, no investigation has specifically assessed whether a mosaicism of cells with either depolarizing/excitatory or hyperpolarizing/inhibitory GABAergic responses exists in adult animals in health/disease. Here, we showed that such mosaicism is present both in adult WT and Down syndrome (DS) mice, as assessed at increasing scales of neuronal-network complexity (cultures, brain- slices, behaving mice). Nevertheless, WT mice presented a lower percentage of cells with depolarizing GABA than DS mice. Restoring the mosaicism of hyperpolarizing and depolarizing GABA-responding neurons to WT levels rescued anxiety behaviour in DS mice. We also found heterogeneous GABAergic responses in mature control and trisomic human iPSC-derived neurons. Thus, a heterogeneous population of GABA-responding cells exists in physiological/pathological conditions in mature mouse and human neurons, possibly contributing to disease-associated behaviours.

neuroscience↗

bioRxiv2023

Biohybrid restoration of the hippocampal loop re-establishes the non-seizing state in an in vitro model of limbic seizures

ObjectiveThe compromise of the hippocampal loop is a hallmark of mesial temporal lobe epilepsy (MTLE), the most frequent epileptic syndrome in the adult population and the most often refractory to medical therapy. Hippocampal sclerosis is found in >50% of drug-refractory MTLE patients and primarily involves the CA1, consequently disrupting the hippocampal output to the entorhinal cortex (EC). Closed-loop deep brain stimulation (DBS) is the latest frontier to improve drug-refractory MTLE; however, current approaches do not restore the functional connectivity of the hippocampal loop, they are designed by trial-and-error and heavily rely on seizure detection or prediction algorithms. The objective of this study is to evaluate the anti-ictogenic efficacy and robustness of an artificial bridge restoring the dialog between hippocampus and EC. ApproachIn mouse hippocampus-EC slices treated with 4-aminopyridine and in which the Schaffer Collaterals are severed, we established an artificial bridge between hippocampus and EC wherein interictal discharges originating in the CA3 triggered stimulation of the subiculum so to entrain EC networks. Combining quantification of ictal activity with tools from information theory, we addressed the efficacy of the bridge in controlling ictogenesis and in restoring the functional connectivity of the hippocampal loop. Main resultsThe bridge significantly decreased or even prevented ictal activity and proved robust to failure; when operating at 100% of its efficiency (i.e., delivering a pulse upon each interictal event), it recovered the functional connectivity of the hippocampal loop to a degree similar to what measured in the intact circuitry. The efficacy and robustness of the bridge stem in mirroring the adaptive properties of the CA3, which acts as biological neuromodulator. Significance. This work is the first stepping stone toward a paradigm shift in the conceptual design of stimulation devices for epilepsy treatment, from function control to functional restoration of the salient brain circuits.

neuroscience↗

bioRxiv2023

The intrinsic clock of the hippocampal subfield CA3 rescues limbic seizures in a biohybrid graft-host interaction in vitro

Hippocampal dysfunction is the hallmark of mesial temporal lobe epilepsy (MTLE), the most common epileptic syndrome in adults and the most often refractory to medical therapy. Deep brain stimulation (DBS) may ameliorate drug-refractory MTLE, but it still cannot guarantee a seizure-free life. One major drawback is that the stimulation policy is informed by trial-and-error rather than by the operating mode of the brain. Thus, optimizing DBS parameters is still an unmet clinical need. Here, we propose the deployment of hippocampal interictal activity in a biohybrid approach to control limbic ictogenesis. Specifically, an electronic bridge establishes a graft-host interaction between the hippocampal subfield CA3 (graft) and the parahippocampal cortex (CTX - host) of distinct rodent brain slices, both treated with 4-aminopyridine; the electronic bridge relays the graft interictal events to the host via electrical pulses. We show that interictal activity generated by the graft CA3 controls limbic ictogenesis in the host CTX even in the absence of feedback from it, thus likely reflecting an intrinsic anti-ictogenic clock of this brain region. This work opens a translational perspective for MTLE treatment via biohybrid neuroprostheses relying on the intrinsic clock of incorporated hippocampal cells.

neuroscience↗

bioRxiv2020

Modulation of neural oscillations during working memory update, maintenance, and readout: an hdEEG study

Working memory (WM) performance is very often measured using the n-back task, in which the participant is presented with a sequence of stimuli, and required to indicate whether the current stimulus matches the one presented n steps earlier. In this study, we used high-density electroencephalography (hdEEG) coupled to source localization to obtain information on spatial distribution and temporal dynamics of neural oscillations associated with WM update, maintenance and readout. Specifically, we a priori selected regions from a large fronto-parietal network, including also the insula and the cerebellum, and we analyzed modulation of neural oscillations by event-related desynchronization and synchronization (ERD/ERS). During update and readout, we found larger {theta} ERS and smaller {beta} ERS respect to maintenance in all the selected areas. {gamma}LOW and {gamma}HIGH bands oscillations decreased in the frontal and insular cortices of the left hemisphere. In the maintenance phase we observed focally decreased {theta} oscillations and increased {beta} oscillations (ERS) in most of the selected posterior areas and focally increased oscillations in {gamma}LOW and {gamma}HIGH bands in the frontal and insular cortices of the left hemisphere. Finally, during WM readout, we also found a focal modulation of the {gamma}LOW band in the left fusiform cortex and cerebellum, depending on the response trial type (true positive vs. true negative). Overall, our study demonstrated specific spectral signatures associated with updating of memory information, WM maintenance and readout, with relatively high spatial resolution.

neuroscience↗

bioRxiv2020

Frequency-specific meso-scale structure of spontaneous oscillatory activity in the human brain

Recent studies provide novel insights into the meso-scale organization of the brain, highlighting the co-occurrence of different structures: classic assortative (modular), disassortative and core-periphery. However, the spectral properties of the brain meso-scale remain mostly unexplored. To fill this knowledge gap, we investigated how the meso-scale structure is organized across the frequency domain. We analyzed the resting state activity of healthy participants with source-localized high-density electroencephalography signals. Then, we inferred the community structure using weighted stochastic block-modelling to capture the landscape of meso-scale structures across the frequency domain. We found that meso-scale modalities were mixed over the frequency spectrum, with a core-periphery structure predominance. Nevertheless, we also highlighted a selective increase of disassortativity in the delta and theta bands, and of assortativity in the low gamma band (30-50 Hz). We further described other features of the meso-scale organization by identifying those brain regions which, at the same time, i) exhibited the highest degree of assortativity, disassortativity and core-peripheriness (i.e. participation), ii) were consistently assigned to the same community, irrespective from the granularity imposed by WSBM (i.e. granularity-invariance). We defined those brain areas as Participation and Granularity Invariant. In conclusion, we observed that the brain spontaneous activity shows frequency-specific meso-scale organization which may support spatially distributed and local information processing.

neuroscience↗

bioRxiv2020

Real-time detection of bursts in neuronal cultures using a Neuromorphic Auditory Sensor and Spiking Neural Networks

The correct identification of burst events is crucial in many scenarios, ranging from basic neuroscience to biomedical applications. However, none of the burst detection methods that can be found in the literature have been widely adopted for this task. As an alternative to conventional techniques, a novel neuromorphic approach for real-time burst detection is proposed and tested on acquisitions from in vitro cultures. The system consists of a Neuromorphic Auditory Sensor, which converts the input signal obtained from electrophysiological recordings into spikes and decomposes them into different frequency bands. The output of the sensor is sent to a trained spiking neural network implemented on a SpiNNaker board that discerns between bursting and non-bursting activity. This data-driven approach was compared with 8 different conventional spike-based methods, addressing some of their drawbacks, such as being able to detect both high and low frequency events and working in an online manner. Similar results in terms of number of detected events, mean burst duration and correlation as current state-of-the-art approaches were obtained with the proposed system, also benefiting from its lower power consumption and computational latency. Therefore, our neuromorphic-based burst detection paves the road to future implementations for neuroprosthetic applications.

neuroscience↗

bioRxiv2019

The paternally imprinted gene Snord116 regulates cortical neuronal activity

Prader-Willi syndrome (PWS) is a neurodevelopmental disorder that is characterized by rapid eye movement (REM) sleep abnormalities. The disease is caused by genomic imprinting defects that are inherited through the paternal line. Among the genes located in the PWS region on chromosome 15 (15q11-q13), small nucleolar RNA 116 (Snord116) has been previously associated with intrusions of REM sleep into wakefulness in both humans and mice.\n\nHere, we further explore the processes of sleep regulation by studying the PWScrm+/p- mouse line, which carries a paternal deletion of Snord116. We focused on microstructural electrophysiological components of sleep, such as REM sleep features and sleep spindles within NREM sleep. While the former are thought to contribute to neuronal network formation early in brain development, the latter are markers of thalamocortical processes. Both signals are often compromised in neurodevelopmental disorders and influence functional properties of cortical neurons. Thus, we isolated and characterized the intrinsic activity of cortical neurons using in vitro microelectrode array (MEA) studies.\n\nOur results indicate that the Snord116 gene in mice selectively influences REM sleep properties, such as theta rhythms and the organization of REM episodes throughout sleep-wake cycles. Moreover, sleep spindles present specific abnormalities in PWS model systems, indicating that these features of sleep may translate as potential biomarkers in human PWS. We observed abnormalities in the synchronization of cortical neuronal activity that are accounted for by high levels of norepinephrine.\n\nIn conclusion, our results provide support for an important role of Snord116 in regulating brain activity during sleep and, in particular, cortical neuronal properties, thereby opening new avenues for developing interventions in PWS.\n\nSignificance StatementWe found that the Snord116 gene, a major player in Prader-Willi syndrome (PWS), significantly impacts REM sleep and its regulation. Additionally, we found that sleep spindles, a subtle electroencephalography (EEG) marker that occurs during NREM sleep, are dysregulated in PWS mice that carry a paternal deletion of the Snord116 gene. Using a combination of in vivo and in vitro experiments, we identified sleep features at the network and molecular level that suggest that Snord116 is fundamental in the synchronization of neuronal networks. Our study also provides a new pre-clinical tool to investigate the pathophysiology of sleep in PWS.

neuroscience↗

bioRxiv2019

Differential effects of open- and closed-loop intracortical microstimulation on firing patterns of neurons in distant cortical areas

BackgroundIntracortical microstimulation can be used successfully to modulate neuronal activity. Activity-dependent stimulation (ADS), in which action potentials recorded extracellularly from a single neuron are used to trigger stimulation at another cortical location (closed-loop), is an effective treatment for behavioral recovery after brain lesion in rodents. Neurophysiological changes in cortical communication induced by ADS, and how these changes differ from those induced by open-loop random stimulation (RS) are still not clear. ObjectivesWe investigated the ability of ADS and RS to induce changes in firing patterns in distant populations of neurons in healthy anesthetized rats. MethodsFor this study we used 23 adult Long-Evan rats, recording from a total of 591 neuronal units. Stimulation was delivered to either forelimb or barrel field somatosensory cortex, using either randomly-timed stimulus pulses or ADS triggered from neuronal spikes recorded in the rostral forelimb area (RFA) of the motor cortex. ResultsBoth RS and ADS stimulation protocols rapidly altered spike firing within RFA compared with no stimulation. Changes consisted of increases in mean firing rates and patterns of spike firing as measured by the revised Local Variation metric. ADS was more effective than RS in increasing short-latency evoked spikes during the stimulation periods, by producing a reliable, progressive increase in stimulus-related activity over time. ConclusionsThese results are critical for understanding the efficacy of electrical microstimulation protocols in altering activity patterns in interconnected brain networks. These data further strengthen the idea that activity-dependent microstimulation, can be used to modulate cortical state and functional connectivity.

neuroscience↗

bioRxiv2019

A neuroprosthetic system to restore neuronal communication in modular networks

Recent advances in neurotechnology allow neurological impairments to be treated or reduced by brain machine interfaces and neuroprostheses. To develop energy-efficient and real-time capable devices, neuromorphic computing systems are envisaged as the core of next-generation neurobiohybrid systems for brain repair. We demonstrate here the first exploitation of a neuromorphic prosthesis to restore bidirectional interactions between two neuronal populations, even when one is damaged or completely missing. We used in vitro modular cell cultures to mimic the mutual interaction between neuronal assemblies and created a focal lesion to functionally disconnect the two populations. Then, we employed our neuromorphic prosthesis for two specific applications with future clinical implications: bidirectional bridging to artificially reconnect two disconnected neuronal modules and hybrid bidirectional bridging to replace the activity of one module with a neuromorphic spiking neural network. Our neuroprosthetic system opens up new avenues for the development of novel bioelectrical therapeutics for human applications.

bioengineering↗

bioRxiv2018

The emergence of dynamical instantaneous memory in the spontaneous activity of spatially confined neuronal assemblies in vitro

Understanding the dynamics between communicating cell assemblies is essential for deciphering the neural code and identifying the mechanism underlying memory formation. In this work, in order to unveil possible emergent intrinsic memory phenomena in the communication between cell assemblies, we study the spontaneous dynamics of in vitro spatially confined inter-connected neuronal circuits grown on multi-electrode arrays. The spontaneous dynamics of the global network was characterized by the coupling of the activity independently generated by each circuit. The asymptotic functional connectivity of the network reflected its modular organization. Instantaneous functional connectivity maps on ten seconds epochs, revealed more complex dynamical states with the simultaneous activation of distinct circuits. When looking at the similarity of the generated network events, we observed that spontaneous network events occurring at temporal distances below two dozens of seconds had an average higher similarity compared to randomly played network events. Such a memory phenomenon was not observed in networks where spontaneous events were less frequent and in networks topologically organized as open lines. These results support the hypothesis that dynamical instantaneous memory, characterized by drifting network dynamics with decaying degree of similarity, is an intrinsic property of neuronal networks.

neuroscience↗