Biology subjects

Khadra, A.

Publications and source records attributed to Khadra, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Intrinsic Ionic Mechanisms Underlying Burst Firing in Spontaneously Active Dorsal Horn Parvalbumin Interneurons

Parvalbumin-expressing interneurons (PVINs) in the spinal dorsal horn play a key role in preventing touch inputs from engaging nociceptive pathways through fast inhibitory control. Although most PVINs are typically quiescent and require external input to fire, a subset of these neurons exhibits spontaneous activity, including isolated spikes and bursts. The mechanisms underlying this behavior in spontaneously active PVINs (spPVINs) remain unclear. To address this, we developed a stochastic two-compartment Hodgkin-Huxley (HH) type model, consisting of a soma and an axon initial segment (AIS), to investigate the effects of synaptic noise and intrinsic electrical properties of spPVINs in driving their spontaneous firing. The model incorporates two subthreshold currents: the M-type K+ current (Im) and the hyperpolarization-activated current (Ih). The model revealed that, in the presence of Ornstein-Uhlenbeck noise, Ih promotes spontaneous firing by enhancing noise-driven depolarizations. Model simulations closely reproduced the firing patterns of spPVINs observed experimentally, including irregular spiking and bursting. Bifurcation analysis showed that varying the applied current can lead to transitions between quiescent, tonic, and elliptic bursting regimes, allowing stochastic fluctuations to switch between these states, which gives rise to irregular spontaneous activity. Reducing the conductance of Im and increasing the conductance of the fast Na+ current (INa) both enlarge the elliptic bursting regime, thereby enabling noise to promote bursting. Interestingly, when the model was incorporated into a circuit, the downstream inhibitory effects of spPVINs were enhanced by the expression of Ih. Taken together, these results demonstrate how intrinsic electrical properties of spPVINs shape their firing dynamics and circuit activity.

neuroscience↗

bioRxiv2026

Astrocytic FMRP regulates the function of spinal parvalbumin-expressing neurons in Fragile X Syndrome

Tactile hypersensitivity is a common symptom of Fragile X Syndrome (FXS) characterized by over-responsiveness to innocuous touch or textures. Yet, the neural circuitry underlying this altered sensory processing remains incompletely understood. Previous studies have focused on cortical and peripheral neuron dysfunction. However, the spinal dorsal horn circuits, which make up the first central site of somatosensory integration, also comprises elements that could contribute to the hypersensitivity to innocuous stimuli, yet its involvement in this pathology has remained incompletely understood. Here, we show that spinal parvalbumin (PV)-expressing interneurons (PVNs), an inhibitory population that gates touch sensory input from activating nociceptive pathways, are dysfunctional in FXS. Using a mouse model of FXS (global Fmr1 knockout; gKO), we showed that dorsal horn PVNs exhibit impaired function characterized by reduced PV expression and inability to sustain tonic firing. To determine whether these deficits arise through cell-intrinsic mechanisms, we selectively deleted Fmr1 in PVNs. This deletion failed to reproduce the molecular and electrophysiological changes observed in the gKO mice. In contrast, astrocyte-specific deletion of Fmr1 recapitulated key features of the gKO mice, including decreased PV expression and firing. To understand the biophysical basis of this firing deficit, we simulated spinal PVNs using conductance-based Hodgkin-Huxley type modelling. Surprisingly, modifying intrinsic membrane conductances alone was insufficient to account for the experimental data. In fact, PVN firing required incorporation of an additional calcium-dependent extrinsic synaptic component consistent with the experimental finding that astrocytic, but not PVN-specific, loss of FMRP reproduced the PVN phenotype in gKO mice. Together, these findings show that these deficits in spinal PVNs arise primarily from loss of FMRP in astrocytes rather than in PVNs themselves. It reveals astrocyte-dependent dysfunction of dorsal horn inhibitory circuits as a previously uncharacterized consequence of FXS.

neuroscience↗

bioRxiv2026

Gap junctional coupling of molecular layer interneurons enables transient NMDA driven synchronization

Molecular layer interneurons (MLIs) play a crucial role in modulating the output of the cerebellar cortex through their inhibition of Purkinje cells. MLIs also inhibit other MLIs synaptically and are coupled electrically through gap junctions. While synchronization of MLIs has been observed, comprehensive understanding of the role of gap junctional coupling in shaping MLI network activity is lacking. Dendro-dendritic gap junctional coupling in MLIs involves propagation of signals to and from the dendritic gap junction location which can lead to neural synchronization. However, how this is regulated by the intrinsic electrical properties of MLIs, including dendritic properties, is poorly understood. In this study, we apply conductance-based computational modelling to examine the effect of dendritic filtering on gap junctional coupling in pairs of ball-and-stick MLI models, demonstrating that gap junctional properties, rather than the active dendritic properties of MLIs, primarily dictate gap junction-driven synchronization. By systematically reducing the ball-and-stick model to a one-compartment MLI model, we additionally investigate the role of MLI gap junctional coupling in mediating MLI network synchrony. Our results reveal that transient AMPA input drives brief network-wide synchronization, whereas NMDA-mediated elevated firing enables gap junction-dependent oscillatory synchronization that is further enhanced by MLI-MLI inhibition in a positive feedback loop, producing pronounced peaks of network coactivity resembling sensory-evoked MLI activity observed in vivo. These findings provide important insights into network dynamics of MLIs and how gap junctions shape their activity, with broader implications for other neural networks that rely on gap junctional coupling.

neuroscience↗

bioRxiv2026

Deep learning-based decoding of axonal ultrastructure in gene-edited mice using electron microscopy imaging

Myelin forms an insulating sheath around axons enabling both rapid and energy-efficient conduction of action potentials and myelin abnormalities or loss can lead to severe motor, sensory, and cognitive impairment. While electron microscopy can resolve multiple axonal components that are affected myelin, their large-scale quantitative analysis is both difficult and time consuming. To overcome such limitations, we developed a machine learning framework that automatically recognizes and quantifies multiple features of axons and myelin including axonal mitochondrial density and periaxonal area. Applying that framework to fibers in the spinal cord of variably hypomyelinated mice, we show here that reduction in the thickness and length of myelin sheaths results in correlating changes in mitochondrial density and periaxonal area. The machine learning framework introduced here should contribute to future insight into the axon, myelin, and mitochondrial relationships that change during neurological plasticity and myelin disease progression.

neuroscience↗

bioRxiv2025

Dendritic Interaction of Timescales in Afterdepolarization Potentials and Nonmonotonic Spike--adding

Depolarizations that occur after action potentials, known as afterdepolarization potentials or ADPs, are important for neuronal excitability and stimulus evoked transient bursting. Slow inward and fast outward currents underlie the generation of such ADPs with modulation of ADP amplitudes occurring as a result of neuronal morphology. However, the relative contribution and role of these slow inward and fast outward currents in ADP generation is poorly understood in the context of somatic and dendritic localization as well as with varied dendritic properties. Using a two compartmental Hodgkin-Huxley type model, the role of somatic and dendritic compartmentalization of ADP associated currents is investigated, revealing that dendritic (rather than somatic) slow inward and fast outward currents are the main contributors to ADP and spike-adding during both brief step current and AMPA current input. Additionally, dendritic size and passive properties of the dendrites were found to be key modulators of ADP amplitude. However, increasing magnitudes of NMDA current conductance resulted in nonmonotonic spike-adding in a manner dependent on dendritic Ca2+ influx and Ca2+ activated K+ currents, which was found to be the result of tight regulation of stimulus evoked transient bursting through positive feedback on action potential generation by dendritic Ca2+ and subsequent negative feedback through Ca2+ activated K+ currents. This novel mechanism of ADP and spike-adding regulation highlights the role of currents with slow timescales in ADPs, stimulus evoked bursting and neuronal excitability with implications for Ca2+ dependent synaptic plasticity and neuromodulation.

neuroscience↗

bioRxiv2025

Calcium Signaling in Oligodendrocyte Precursor Cells Mediated by Spontaneous and Evoked Responses: A Modeling Investigation

Calcium (Ca2+) signaling has emerged as a central regulator of activity-dependent myelination in oligodendrocytes. These Ca2+ signals encompass both the stimulus-independent spontaneous Ca2+ local transients (SCaLTs) generated intrinsically in a voltage-independent manner or facilitated by the membrane voltage, as well as evoked responses triggered by ATP and glutamate release. To investigate the regulatory mechanisms underlying this combined spiking activity, we developed a stochastic spatiotemporal flux-balance model of Ca2+ transients in oligodendrocyte precursor cells (OPCs). The model incorporates all the relevant fluxes in these cells and integrates membrane voltage dynamics with a Ca2+-induced Ca2+-release (CICR) mechanism using parameters fitted to Ca2+ fluorescence recordings. The model reproduced the intrinsic and voltage-facilitated SCaLTs in OPCs in the absence of purinergic and glutamatergic receptors, and captured the three distinct patterns of evoked Ca2+ responses induced by ATP and glutamate identified using machine classifier. The model highlighted the role of ATP and glutamate concentrations in generating these clusters, and showed that the fast dynamics of CICR is key to producing these evoked responses. Further analysis of the model also revealed that voltage-gated L- and T-type Ca2+ channels slightly increase the frequency of SCaLTs, while stimulation with ATP and glutamate, using randomly distributed pulses mimicking in vivo conditions, leads to an increase in both the amplitudes of Ca2+ spikes (i.e., the combination of SCaLTs and evoked responses) and the prevalence of wide spikes, especially upon glutamate stimulation. Bifurcation analysis of the deterministic version of the model, in the absence of diffusion, demonstrated that ATP and glutamate stimulation can shift the system into an oscillatory regime, thereby increasing the deterministic component of SCaLT dynamics. This study thus offers a comprehensive representation of OPC Ca2+ transients linking recorded in vitro behaviors to in vivo dynamics. Author summaryOligodendrocytes are glial cells in the central nervous system that form myelin, the insulating sheath enabling rapid nerve signal transmission. Myelination is a dynamic process influenced by neuronal activity, with calcium (Ca2+) signaling emerging as a key regulator. These signals include spontaneous local Ca2+ transients (SCaLTs), generated intrinsically or facilitated by membrane voltage, as well as evoked responses triggered by neurotransmitters like ATP and glutamate. To understand how these signals arise and interact, we combined experimental recordings of Ca2+ activity in oligodendrocyte precursor cells (OPCs) with a data-driven biophysical model. The model incorporates stochastic Ca2+ fluxes, membrane voltage dynamics, and ca-induced Ca2+-release (CICR), allowing us to simulate diverse patterns of Ca2+ transients. Our simulations reproduced both intrinsic and voltage-facilitated SCaLTs and captured three distinct evoked response types induced by ATP and glutamate. We found that voltage-gated Ca2+ channels slightly enhance SCaLT frequency, while rapid CICR dynamics are critical for shaping the amplitude and timing of evoked signals. Furthermore, neurotransmitter stimulation can drive the system into an oscillatory regime, increasing the deterministic structure of Ca2+ transients. This work offers a mechanistic framework linking intracellular Ca2+ dynamics to the regulation of activity-dependent myelination in OPCs.

cell biology↗

bioRxiv2025

In vivo neural activity of electrosensory pyramidal cells: Biophysical characterization and phenomenological modeling

Burst firing is an important property of neuronal activity, thought to enhance sensory encoding. While previous studies show significant differences in burst firing between in vivo and in vitro conditions, how burst firing contributes to neural coding in vivo and how it is modulated by underlying biophysical mechanisms when neurons are under active synaptic bombardments remains poorly understood. Here, we combined intracellular recordings and computational modeling to investigate how cellular and synaptic mechanisms can explain the in vivo firing activity of electrosensory lateral line lobe (ELL) pyramidal cells in Apteronotus leptorhynchus. We developed a biophysically detailed compartmental model incorporating voltage-gated currents, NMDA receptor-mediated Ca2+ influx, Ca2+-activated SK channels, Ca2+ handling, and stochastic synaptic inputs to reproduce in vivo firing activities of ELL pyramidal cells. Specifically, using bifurcation analysis, we identified dynamical transitions between quiescent, tonic, and bursting regimes, governed by interactions among SK conductance, NMDA receptor activation, and applied current. Model parameters were optimized against in vivo data, accurately reproducing action potential waveforms and temporal dynamics, including characteristic bimodal interspike interval distributions reflecting intra- and inter-burst intervals. We further developed a modified Hindmarsh-Rose model incorporating dual adaptation variables and stochastic noise. This simplified phenomenological model successfully captured burst firings comparable to those observed in the biophysical model and recorded data, while replicating diverse firing patterns observed across the population. Finally, parameter sensitivity analysis revealed slow adaptation dynamics and noise intensity as key determinants of spiking variability within cells. Overall, our modeling results demonstrate that in vivo bursting arises from synergistic interactions between intrinsic conductances (e.g., NMDA-SK coupling), Ca2+ mobilization, and synaptic stochasticity, offering a potential reconciliation for discrepancies with in vitro firing activity. The models provide mechanistic insights into how background synaptic activity modulates burst firing and validate simplified frameworks for studying population-level dynamics.

neuroscience↗

bioRxiv2025

Within-host viral evolution varies with T cell receptor repertoire diversity independently of viral mutation rates

The specific T cell receptors (TCRs) present in an individual determine which antigens can be recognized, and hence a repertoire comprised of a vast number of unique TCRs ensures an effective T cell response can be mounted against a broad range of potential pathogens encountered. To evade the T cell response, pathogens, and viruses in particular, can accrue epitope escape mutations, establishing a host-pathogen tug-of-war between T cell-mediated control and viral evolution. Indeed, the evolutionary significance of TCR diversification in mammals is underscored by the sophisticated molecular machinery - spanning from somatic V(D)J recombination through non-templated nucleotide additions - that establish the TCR repertoire. Yet, whether greater oligoclonality among responding T cells, as is the case for elderly or immunocompromised individuals, might therefore accelerate pathogen immune escape remains unclear. Here, we constructed a computational model of T cell-mediated viral evolution to investigate how the number of unique virus-specific T cells clones impacts the balance between curtailing viral load through cross-reactivity to mutant strains on the one hand, versus promoting the generation of escape variants on the other. The model recapitulated prior experimental findings, such as T cell-dependent emergence of new viral mutants and the progressive decrease in the number of T cell clones present in the response over time. Our model simulations suggested that oligoclonality in the virus-specific T cell response can, if coupled with a resulting increase in viral replication, maximize viral immune escape despite constant mutation rates revealing a mechanism for how viruses with comparable mutation rates can nonetheless exhibit dramatically different adaption rates within hosts. Taken together, the model results suggest that variations in TCR repertoire diversity, and consequently in the number of pathogen-specific T cell clones within an individual, can have direct, non-linear impacts on viral immune escape.

immunology↗

bioRxiv2025

The geometry of pMHC-coated nanoparticles and T cell receptor clusters governs the sensitivity-specificity trade-off in T cell response.

T cells must reliably discriminate between foreign-derived antigens that require an adaptive immune response from non-specific self-antigens that do not. This discrimination is highly specific to the affinity of the bond between ligand and T cell receptors (TCRs), as well as highly sensitive to the concentration of ligand. In this study, we examined these features of T cell mediated immunity in the context of multivalent ligand-receptor interactions between clusters of TCRs with pMHC-coated nanoparticles (NPs). Using Monte Carlo simulations of NP-T cell surface interactions, we compared the effect of TCR clustering on the dose-response profiles of various NP designs. These simulations revealed a trade-off between sensitivity and specificity, mediated by the spatial clustering of TCRs and the geometry of the NP. In particular, large clusters of TCRs were more sensitive to both NP valence and ligand concentration at the expense of antigen specificity. Conversely, uniformly distributed TCR landscapes were better suited to affinity-based ligand discrimination, while sacrificing sensitivity to ligand concentration. These features of NP-mediated T cell activation depended significantly on NP size and valence rather than on the average ligand concentration. Furthermore, we demonstrated how kinetic proofreading mechanisms may help compensate for the limitations associated with TCR clustering. These findings thus highlight the importance of interacting geometries of NP design and TCR landscape in modulating the specificity and sensitivity of the T cell response. SignificanceT cells rely on surface T cell receptors (TCRs) to recognize foreign antigens presented as peptide-major histocompatibility complex (pMHC) molecules. TCR clustering is crucial for T cell activation, though its full role remains not entirely clear. Using Monte Carlo simulations, we demonstrate that TCR clustering profoundly influences both surface binding dynamics of multivalent pMHC-coated nanoparticles, used in autoimmune disease therapies, as well as downstream intracellular signals leading to T cell activation. Our findings thus provide important insights into the role of interaction geometries in shaping T cell response, with implications for optimizing nanoparticle design to enhance their therapeutic efficacy.

biophysics↗

bioRxiv2024

Serotonergic neurons in the dorsal raphe regulate visual attention

Visual attention enhances the neural representation of salient stimuli within the visual cortex. It is generally thought that this enhancement is driven by glutamatergic feedback from frontal cortical areas. Here we report the unexpected observation that dorsal raphe (DR) derived serotonin (5HT) controls visual attention. We developed a behavioral model that captured the way mice allocated attention to cued and uncued visual locations and features. Simultaneous photometry showed reduced DR activity when mice deployed attention to the cued locations and features, whereas high DR activity was observed when mice were less attentive. Optogenetic excitation of DR-5HT neurons impaired attention to the cue and degraded behavioral performance, while optogenetic suppression improved attention and performance. A genetically encoded sensor of 5HT release showed reduced 5HT levels in visual cortex when mice attend and detect stimuli. These results demonstrate that DR-5HT neurons are members of the brains attentional circuit and suggest that 5HT is a novel biological carrier of visual attention.

neuroscience↗

bioRxiv2024

Burst firing optimizes invariant coding of natural communication signals by electrosensory neural populations

Accurate perception of objects within the environment independent of context is essential for an organisms survival. While neurons that respond in an invariant manner to identity-preserving transformations of objects are thought to provide a neural correlate of context-independent perception, how these emerge in the brain remains poorly understood. Here we demonstrate that burst firing in neural populations can give rise to an invariant representation of highly heterogeneous natural communication stimuli. Multi-unit recordings from central sensory neural populations showed that considering burst spike trains led to invariant representations at the population but not the single neuron level. Computational modeling further revealed that optimal invariance is achieved for levels of burst firing seen experimentally. Taken together, our results demonstrate a novel function for burst firing towards establishing invariant representations of sensory input in neural populations.

neuroscience↗

bioRxiv2024

Spike frequency adaptation in primate lateral prefrontal cortex neurons results from interplay between intrinsic properties and circuit dynamics

Recordings of cortical neurons isolated from brain slices and dissociated from their networks, display intrinsic spike frequency adaptation (I-SFA) to a constant current input. Interestingly, extracellular recordings in behaving subjects also show extrinsic-SFA (E-SFA) in response to sustained visual stimulation. Because neurons are isolated from brain networks in slice recordings, it is challenging to infer how I-SFA contributes to E-SFA in interconnected brains during behavior. To investigate this, we recorded responses of macaque lateral prefrontal cortex neurons in vivo during a visually guided saccade task and in acute brain slices in vitro. Broad spiking (BS) putative pyramidal cells and narrow spiking (NS) putative inhibitory interneurons exhibited E-SFA in vivo. In acute brain slices, both cell types displayed I-SFA though their magnitudes differed. To investigate how in vitro I-SFA contributes to in vivo E-SFA, we developed a data-driven hybrid circuit model in which local NS neurons are driven by BS input. We observed that model NS cell responses show longer SFA than observed in vivo. Introducing inhibition of NS cells to the model circuit removed this discrepancy. Our results indicate that both I-SFA and inhibitory circuit dynamics contribute to E-SFA in LPFC neurons. They highlight the contribution of single neuron and network dependent computations to neural activity underlying behavior.

neuroscience↗

bioRxiv2024

Contributions of action potentials to scalp EEG: theory and biophysical simulations

Differences in the apparent 1/f component of neural power spectra require correction depending on the underlying neural mechanisms, which remain incompletely understood. Past studies suggest that neuronal spiking produces broadband signals and shapes the spectral trend of invasive macroscopic recordings, but it is unclear to what extent action potentials (APs) influence scalp EEG. Here, we combined biophysical simulations with statistical modelling to examine the amplitude and spectral content of scalp potentials generated by the electric fields from spiking activity. We found that under physiological conditions, synchronized aperiodic spiking can account for at most 1% of the spectral density observed in EEG recordings, suggesting that the EEG spectral trend reflects only external noise at high frequencies. Indeed, by analyzing previously published data from pharmacologically paralyzed subjects, we confirmed that the EEG spectral trend is entirely explained by synaptic timescales and electromyogram contamination. We also investigated rhythmic EEG generation, finding that APs can generate narrowband power between approximately 60 and 600 Hz, thus reaching frequencies much faster than the timescales of excitatory synaptic currents. Our results imply that different spectral detrending strategies are required for high frequency oscillations compared to slower synaptically generated EEG rhythms.

neuroscience↗

bioRxiv2023

The influence of circadian rhythms on CD8+ T cell proliferation upon vaccination: a mathematical modeling perspective

Circadian rhythms have been implicated in the modulation of many physiological processes, including those associated with the immune system. For example, these rhythms influence CD8+ T cell responses within the adaptive immune system. The mechanism underlying this immune-circadian interaction, however, remains unclear, particularly in the context of vaccination. Here, we devise a molecularly-explicit gene regulatory network model of early signaling in the nave CD8+ T cell activation pathway, comprised of three axes (or subsystems) labeled ZAP70, LAT and CD28, to elucidate the molecular details of this immune-circadian mechanism and its relation to vaccination. This is done by coupling the model to a periodic forcing function to identify the molecular players targeted by circadian rhythms, and analyzing how these rhythms subsequently affect CD8+ T cell activation under differing levels of T cell receptor (TCR) phosphorylation, which we designate as vaccine load. By performing both bifurcation and parameter sensitivity analyses on the model at the single cell and population levels, we find that applying periodic forcing on molecular targets within the ZAP70 axis is sufficient to create a day-night discrepancy in CD8+ T cell activation in a manner that is dependent on the bistable switch inherent in CD8+ T cell early signaling. We also demonstrate that the resulting CD8+ T cell activation is dependent on the strength of the periodic coupling as well as on the level of TCR phosphorylation. Our results show that this day-night discrepancy is not transmitted to certain downstream molecules within the LAT subsystem, such as mTORC1, suggesting a secondary, independent circadian regulation on that protein complex. We also corroborate experimental results by showing that the circadian regulation of CD8+ T cell primarily acts at a baseline, pre-vaccination state, playing a facilitating role in priming CD8+ T cells to vaccine inputs according to time of day. By applying a population level analysis using bifurcation theory and by including several hypothesized molecular targets of this circadian rhythm, we further demonstrate an increased variability between CD8+ T cells (due to heterogeneity) induced by its circadian regulation, which may allow a population of CD8+ T cells to activate at a lower vaccine load, improving its sensitivity. This modeling study thus provides insights into the immune targets of the circadian clock, and proposes an interaction between vaccine load and the influence of circadian rhythms on CD8+ T cell activation. HighlightsO_LIPotential targets of circadian rhythms within the ZAP70 signaling pathway were identified. C_LIO_LIThe level of vaccine load to a CD8+ T cell was shown to be crucial in dictating a circadian rhythms influence on its signaling response. C_LIO_LIThe priming effect of a circadian rhythm on CD8+ T cell activation upon vaccination was demonstrated. C_LIO_LImTORC1 and its immediate upstream signaling molecules were shown to be regulated by circadian rhythms through independent mechanisms. C_LIO_LIA heterogeneity in CD8+ T cells, induced by its circadian regulation, may influence their sensitivity to vaccination. C_LI

biophysics↗

bioRxiv2023

ElecFeX: A user-friendly toolkit for efficient feature extraction from single-cell electrophysiological recordings

MotivationProfiling neurons by their electrophysiological phenotype is essential for understanding their roles in information coding within and beyond the nervous systems. Technological development has unleashed our power to record neurons more than ever before, yet the booming size of the dataset poses new challenges for data analysis. Current software tools require users to have either significant programming knowledge or to devote great time and effort, which impedes their prevalence and adoption among experimentalists. To address this problem, here we present ElecFeX, a MATLAB-based graphical user interface designed for a more accessible and efficient analysis of single-cell electrophysiological recordings. ElecFeX has a simple and succinct graphical layout to enable effortless handling of large datasets. This tool includes a set of customizable methods for most common electrophysiological features, and these methods can process multiple files all at once in a reliable and reproducible manner. The output is assembled in a properly formatted file which is exportable for further analysis such as statistical comparison and clustering. By providing such a streamlined and user-friendly open-sourced interface, we hope ElecFeX can benefit broader users for their studies associated with neural activity. SummaryCharacterizing neurons by their electrophysiological phenotypes is essential for understanding the neural basis of behavioral and cognitive functions. Recent developments in electrode technologies have enabled the collection of hundreds of neural recordings; that necessitated the development of new toolkits capable of performing feature extraction efficiently. To address this urgent need for a powerful and accessible tool, we present ElecFeX, an open-source MATLAB-based toolbox that (1) has a succinct and intuitive graphical user interface, (2) provides generalized methods for wide-ranging electrophysiological features, (3) processes large-size dataset effortlessly, and (4) yields formatted output for further analysis such as neuronal characterization and classification. We implemented the toolbox on a diverse set of neural recordings and demonstrated its functionality, efficiency, and versatility in capturing features that can well-distinguish neuronal subgroups across brain regions and species. ElecFeX is thus presented as a powerful tool to significantly promote future studies on neuronal electrical activity.

neuroscience↗

bioRxiv2023

Calcium buffering tunes intrinsic excitability of spinal dorsal horn parvalbumin-expressing interneurons: A computational model

Parvalbumin-expressing interneurons (PVINs) play a crucial role within the dorsal horn of the spinal cord by preventing touch inputs from activating pain circuits. After nerve injury, their output is decreased via mechanisms that are not fully understood. In this study, we show that PVINs from nerve-injured mice change their firing pattern from tonic to adaptive. To examine the ionic mechanisms responsible for this decreased output, we employed a reparametrized Hodgkin-Huxley (HH) type model of PVINs, which predicted (1) the firing pattern transition is due to an increased contribution of small conductance calcium-activated potassium (SK) channels, enabled by (2) impairment in intracellular calcium buffering systems. Analyzing the dynamics of the HH-type model further demonstrated that a generalized Hopf bifurcation differentiates the two types of state transitions observed in the transient firing of PVINs. Importantly, this predicted mechanism holds true when we embed the PVINs model within the neuronal circuit model of the spinal dorsal horn. To experimentally validate this hypothesized mechanism, we used pharmacological modulators of SK channels and demonstrated that (1) tonic firing PVINs from naive mice become adaptive when exposed to an SK channel activator, and (2) adapting PVINs from nerve-injured mice return to tonic firing upon SK channel blockade. Our work provides important insights into the cellular mechanism underlying the decreased output of PVINs in the spinal dorsal horn after nerve injury and highlights potential pharmacological targets for new and effective treatment approaches to neuropathic pain. Significant StatementParvalbumin-expressing interneurons (PVINs) exert crucial inhibitory control over A {beta} fiber- mediated nociceptive pathways at the spinal dorsal horn. The loss of their inhibitory tone leads to neuropathic symptoms, like mechanical allodynia, via mechanisms that are not fully understood. This study identifies the reduced intrinsic excitability of PVINs as a potential cause for their decreased inhibitory output in nerve-injured condition. Combining computational and experimental approaches, we predict a calcium-dependent mechanism that modulates PVINs electrical activity following nerve injury: a depletion of cytosolic calcium buffer allows for the rapid accumulation of intracellular calcium through the active membranes, which in turn potentiates SK channels and impedes spike generation. Our results therefore pinpoint SK channels as interesting therapeutic targets for treating neuropathic symptoms.

neuroscience↗

bioRxiv2023

Decoding the relative contributions of extrinsic and intrinsic mechanisms in mediating heterogeneous spiking activities of sensory neurons in vivo using computational modeling

Neurons ubiquitously display heterogeneities in spiking activity even within a given cell type. To date, the relative contributions of extrinsic mechanisms (e.g., synaptic bombardment) and intrinsic mechanisms (e.g., conductances, cell morphology) towards determining spiking activity remain poorly understood. Here we address this important question using a novel approach that combines biophysical techniques, in which extracellular in vivo recordings of electrosensory pyramidal cells within weakly electric fish, are combined with computational modeling. Specifically, by varying parameters, a conductance-based computational model successfully reproduced the highly heterogeneous spiking activities seen experimentally. Model parameters that varied the most were then used to gauge the relative contributions of extrinsic vs. intrinsic mechanisms. Overall, extrinsic synaptic input was predicted to be the main factor accounting for spiking heterogeneities. We tested this prediction experimentally by performing two different manipulations: i) pharmacologically inactivating feedback; ii) applying the neuromodulator serotonin. Our model predicted that feedback inactivation should reduce while serotonin application should increase spiking heterogeneities. Experiments corroborated these predictions. Importantly, for serotonin application, increased heterogeneity occurred despite a strong reduction in intrinsic membrane conductance, further demonstrating that extrinsic synaptic input is the primary determinant of spiking heterogeneities in vivo. Taken together, our results demonstrate that devising a computational model to capture spiking heterogeneities in vivo and assessing which parameters are responsible can successfully determine the relative contributions of extrinsic vs. intrinsic inputs. We expect this approach to be generalizable to other systems and species.

neuroscience↗

bioRxiv2022

Polarity and mixed-mode oscillations may underlie different patterns of cellular migration

In mesenchymal cell motility, several migration patterns have been observed, including directional, exploratory and stationary. Two key members of the Rho-family of GTPases, Rac and Rho, along with an adaptor protein called paxillin, have been particularly implicated in the formation of such migration patterns and in regulating adhesion dynamics. Together, they form a key regulatory network that involves the mutual inhibition exerted by Rac and Rho on each other and the promotion of Rac activation by phosphorylated paxillin. Although this interaction is sufficient to generating wave-pinning that underscores cellular polarization comprised of cellular front (high active Rac) and back (high active Rho), it remains unclear how they interact collectively to induce other modes of migration detected in Chinese hamster Ovary (CHO-K1) cells. We previously developed a 6D reaction-diffusion model describing the interactions of these three proteins (in their active/phosphorylated and inactive/unphosphorylated forms) along with other auxiliary proteins, to decipher their role in generating wave-pinning. In this study, we explored, through computational modeling and image analysis, how differences in timescales within this molecular network can potentially produce the migration patterns in CHO-K1 cells and how switching between them could occur. To do so, the 6D model was reduced to an excitable 4D spatiotemporal model possessing three different timescales. The model produced not only wave-pinning in the presence of diffusion, but also mixed-mode oscillations (MMOs) and relaxation oscillations (ROs). Implementing the model using the Cellular Potts Model (CPM) produced outcomes in which protrusions in cell membrane changed Rac-Rho localization, resulting in membrane oscillations and fast directionality variations similar to those seen in CHO-K1 cells. The latter was assessed by comparing the migration patterns of CHOK1 cells with CPM cells using four metrics: instantaneous cell speed, exponent of mean square-displacement (called -value), directionality ratio and protrusion rate. Variations in migration patterns induced by mutating paxillins serine 273 residue was also captured by the model and detected by a machine classifier, revealing that this mutation alters the dynamics of the system from MMOs to ROs or nonoscillatory behaviour through variation in the concentration of an active form of an adhesion protein called p21-Activated Kinase 1 (PAK). These results thus suggest that MMOs and adhesion dynamics are the key ingredients underlying CHO-K1 cell motility.

cell biology↗