Biology subjects

Khadra, A.

Publications and source records attributed to Khadra, A..

26 records · Page 2Linked to original sources

bioRxiv2022

Excitable dynamics in a molecularly-explicit model of cell motility: Mixed-mode oscillations and beyond

Mesenchymal cell motility is mainly regulated by two members of the Rho-family of GTPases, called Rac and Rho. The mutual inhibition exerted by these two proteins on each others activation and the promotion of Rac activation by an adaptor protein called paxillin have been implicated in driving cellular polarization comprised of front (high active Rac) and back (high active Rho) during cell migration. Mathematical modeling of this regulatory network has previously shown that bistability is responsible for generating a spatiotemporal pattern underscoring cellular polarity called wave-pinning when diffusion is included. We previously developed a 6D reaction-diffusion model of this network to decipher the role of Rac, Rho and paxillin (along with other auxiliary proteins) in generating wave-pinning. In this study, we simplify this model through a series of steps into an excitable 3D ODE model comprised of one fast variable (the scaled concentration of active Rac), one slow variable (the maximum paxillin phosphorylation rate - turned into a variable) and a very slow variable (a recovery rate - also turned into a variable). We then explore, through slow-fast analysis, how excitability is manifested by showing that the model can exhibit relaxation oscillations (ROs) as well as mixed-mode oscillations (MMOs) whose underlying dynamics are consistent with a delayed Hopf bifurcation. By reintroducing diffusion and the scaled concentration of inactive Rac into the model, we obtain a 4D PDE model that generates several unique spatiotemporal patterns that are relevant to cell motility. These patterns are then characterized and their impact on cell motility are explored by employing the cellular potts model (CPM). Our results reveal that wave pinning produces purely very directed motion in CPM, while MMOs allow for meandering and non-motile behaviours to occur. This highlights the role of MMOs as a potential mechanism for mesenchymal cell motility.

cell biology↗

bioRxiv2022

Probing visual sensitivity and attention in mice using reverse correlation

Visual attention is a fundamental cognitive operation that allows the brain to evoke behaviors based on the most important stimulus features. Although mouse models offer immense potential to gain a circuit-level understanding of this phenomenon, links between visual attention and behavioral decisions in mice are not well understood. Here, we describe a new behavioral task for mice that addresses this limitation. We trained mice to detect weak vertical bars in a background of checkerboard noise while audiovisual cues manipulated their spatial attention. We then modified a reverse correlation method from human studies to link behavioral decisions to stimulus locations and features. We show that mice attended to stimulus locations just rostral of their optical axis, which was highly sensitive for vertically oriented stimulus energy whose spatial frequency matched those of the weak vertical bars. We found that the tuning of sensitivity to orientation and spatial frequency grew stronger during training, was multiplicatively scaled with attention, and approached that of an ideal observer. These results provide a new task to measure spatial- and feature-based attention in mice which can be leveraged with new recording methods to uncover attentional circuits.

neuroscience↗

bioRxiv2022

Chronic infection control relies on T cells with lower foreign antigen binding strength generated by N-nucleotide diversity

The pathogens to which T cells respond is determined by the T cell receptors (TCRs) present in an individuals repertoire. Although more than 90% of the TCR repertoire is generated by terminal deoxynucleotidyl transferase (TdT)-mediated N-nucleotide addition during V(D)J recombination, the benefit of TdT-modified TCRs remains unclear. Here, we computationally and experimentally investigated whether TdT systematically modifies the affinity distribution of a TCR repertoire in ways that impacts acute or chronic infection. Our computational model predicts a shift toward low-affinity T cells over time during chronic, but not acute, infections. Elimination of low-affinity T cells in silico substantially delayed chronic infection clearance. Corroborating an affinity-centric benefit for TCR diversity, we showed that infection of TdT-deficient mice delayed the clearance of a chronic viral pathogen, while acute viral control was unaffected. Our data thus suggest that TdT-mediated TCR diversity is of particular benefit in the control of prolonged pathogen replication.

immunology↗

bioRxiv2022

Characterizing the role of Ca2+ fluxes in defining fast and slow components of spontaneous Ca2+ local transients in OPCs using computational modeling

1Spontaneous Ca2+ local transients (SCaLTs) in isolated oligodendrocyte precursor cells (OPCs) are largely regulated by the following fluxes: store-operated Ca2+ entry (SOCE), Na+/Ca2+ exchange (NCX), Ca2+ pumping through Ca2+-ATPases, and Ca2+-induced Ca2+-release through Ryanodine receptors (RyR) and inositoltriphosphate receptors (IP3R). However, the relative contributions of these fluxes in mediating fast spiking and slow baseline oscillations seen in SCaLTs remain incompletely understood. Here, we developed a stochastic spatiotemporal computational model to simulate SCaLTs in a homogeneous medium with ion flow between the extracellular, cytoplasmic and endoplasmic-reticulum compartments. By simulating the model and plotting both the histograms of SCaLTs obtained experimentally and from the model as well as the standard deviation of interspike intervals (ISI) against ISI averages of multiple model and experimental realizations we revealed that: SCaLTs exhibit very similar characteristics between the two datasets, they are mostly random, they encode information in their frequency, and the slow baseline oscillations could be due to the stochastic slow clustering of IP3R (modeled as an Ornstein-Uhlenbeck noise process). Bifurcation analysis of a deterministic temporal version of the model shows that the contribution of fluxes to SCaLTs depends on the parameter regime and that the combination of excitability, stochasticity, and mixed-mode oscillations are responsible for irregular spiking and doublets in SCaLTs. Additionally, our results demonstrate that blocking each flux reduces SCaLTs frequency and that the reverse (forward) mode of NCX decreases (increases) SCaLTs. Taken together, these results provide a quantitative framework for SCaLT formation in OPCs.

neuroscience↗

bioRxiv2022

Theoretical Quantification of the Polyvalent Binding of Nanoparticles Coated with Peptide-MHC to TCR-Nanoclusters

Nanoparticles (NPs) coated with pMHCs can reprogram a specific type of CD4+ T cells into diseasesuppressing T regulatory type 1 cells by binding to their TCRs expressed as TCR-nanoclusters (TCRnc). NP size and number of pMHCs coated on them (called valence) can be adjusted to increase their efficacy. Here we explore how this polyvalent interaction is manifested and examine if it can facilitate T cell activation. This is done by developing a multiscale biophysical model that takes into account the complexity of this interaction. Using the model, we quantify pMHC insertion probabilities, dwell time of NP binding, TCRnc carrying capacity, the distribution of covered and bound TCRs by NPs, and cooperativity in the binding of pMHCs within the contact area. Model fitting and parameter sweeping further reveal that moderate jumps between IFN{gamma} dose-response curves at low valences can occur, suggesting that the geometry of NP binding can prime T cells for activation.

biophysics↗

bioRxiv2021

Aperiodic EEG activity masks the dynamics of neural oscillations during loss of consciousness from propofol

EEGs are known to provide biomarkers for consciousness. Although EEG correlates of loss of consciousness (LOC) are often ascribed to changes in neural synchrony, mounting evidence suggests that some changes result from asynchronous neural activity. By combining EEG recordings of humans undergoing propofol administration with biophysical modelling, we present here a principled decomposition of EEG changes during LOC into synchronous and asynchronous sources. Our results reveal that IPSP decay rate and mean spike rate shape aperiodic EEG features, and that propofols effects on these parameters largely explain the changes in EEG spectra following propofol infusion. We further show that traditional spectral EEG analysis likely conflates these effects with changes in rhythmic activity, thereby masking the true dynamics of neural synchrony. We conclude that the well-documented propofol-induced alpha rhythm in fact appears before LOC, and that the moment of LOC is uniquely correlated with the sudden appearance of a delta rhythm.

neuroscience↗

bioRxiv2021

High-affinity P2Y2 and low-affinity P2X7 receptor interaction modulates ATP-mediated calcium signaling in murine osteoblasts

1P2 purinergic receptor family implicated in many physiological processes, including neurotransmission, mechanical adaptation and inflammation, consist of ATP-gated non-specific cation channels P2XRs and G-protein coupled receptors P2YRs. Different cells, including bone forming osteoblasts, express multiple P2 receptors; however, how P2X and P2Y receptors interact in generating cellular responses to various doses of [ATP] remains poorly understood. Using primary bone marrow and compact bone derived osteoblasts and BMP2-expressing C2C12 osteoblastic cells, we demonstrated conserved features in the P2-mediated Ca2+ responses to ATP, including a transition of Ca2+ response signatures from transient at low [ATP] to oscillatory at moderate [ATP], and back to transient at high [ATP], and a non-monotonic changes in the response magnitudes which exhibited two troughs at 10-4 and 10-2 M [ATP]. We identified P2Y2 and P2X7 receptors as predominantly contributing to these responses, and constructed a mathematical model of P2Y2R-induced inositol trisphosphate (IP3) mediated Ca2+ release coupled to a Markov model of P2X7R dynamics to study this system. Model predictions were validated using parental and CRISPR/Cas9-generated P2Y2 and P2Y7 knockouts in osteoblastic C2C12-BMP cells. Activation of P2Y2 by progressively increasing [ATP] induced a transition from transient to oscillatory to transient Ca2+ responses due to the biphasic nature of IP3Rs and the interaction of SERCA pumps with IP3Rs. At high [ATP], activation of P2X7R modulated the response magnitudes through an interplay between the biphasic nature of IP3Rs and the desensitization kinetics of P2X7Rs. Moreover, we found that P2Y2 activity may alter the kinetics of P2X7 towards favouring naive state activation. Finally, we demonstrated the functional consequences of lacking P2Y2 or P2X7 in osteoblast mechanitransduction. This study thus provides important insights into the biophysical mechanisms underlying ATP-dependent Ca2+ response signatures, which are important in mediating bone mechanoadaptation. 2 Author SummaryATP-sensitive purinergic receptors comprise a network of cell-surface receptors that activate upon ATP binding, allowing them to transmit information in a tissue- and context-dependent manner. In bone, mechanically-stimulated osteoblasts release ATP that stimulates low- and high-affinity P2 receptors in neighboring cellular populations, inducing appropriate physiological responses. P2 receptor signaling is characterized by elevations in intracellular calcium levels. When simultaneously stimulated by their common ligand, ATP, the contribution of each P2 receptor subtype gives rise to a complex calcium response, exhibiting oscillatory characteristics and biphasic dose-dependent behaviours. Here we used experimental and computational modeling approaches to determine the underlying dynamics of ATP-mediated calcium signaling in osteoblasts. The latter was done by developing a mathematical model that was comprised of a subset of low-(P2X7) and high-(P2Y2) affinity P2 receptors, reflecting the conserved P2 expression observed across different osteoblast models. We demonstrated that this model recapitulates experimental recordings of ATP-induced calcium signaling in osteoblasts and describes the dynamic interplay between P2Y2 and P2X7 receptors in the P2 receptor network.

cell biology↗

bioRxiv2021

Intrinsic Gating Behavior of Voltage-Gated Sodium Channels Predetermines Regulation by Auxiliary β-subunits

Voltage-gated sodium (Nav) channels mediate rapid millisecond electrical signaling in excitable cells. Auxiliary subunits, {beta}1-{beta}4, are thought to regulate Nav channel function through covalent and/or polar interactions with the channel s voltage-sensing domains. How these interactions translate into the diverse and variable regulatory effects of {beta}-subunits remains unclear. Here, we find that the intrinsic movement order of the voltage-sensing domains during channel gating is unexpectedly variable across Nav channel isoforms. This movement order dictates the channel s propensity for closed-state inactivation, which in turn modulates the actions of {beta}1 and {beta}3. We show that the differential regulation of skeletal muscle, cardiac, and neuronal Nav channels is explained by their variable levels of closed-state inactivation. Together, this study provides a unified mechanism for the regulation of all Nav channel isoforms by {beta}1 and {beta}3, which explains how the fixed structural interactions of auxiliary subunits can paradoxically exert variable effects on channel function.

biophysics↗