Search bioRxiv⌕ Search

Biology subjects

Mittal, D.

Publications and source records attributed to Mittal, D..

7 recordsLinked to original sources

HCN channels enhance robustness of patterned activity propagation in heterogeneous conductance-based ring networks

Continuous attractor network (CAN) models lend a powerful framework that has provided deep insights about several aspects of brain physiology. However, most CAN models employ homogeneous, rate-based or artificially spiking neurons with precisely structured synaptic connectivity, precluding detailed analyses of the impact of specific neural-circuit components and associated heterogeneities on CAN dynamics. To address this caveat, we built populations of tunable and scalable conductance-based, physiologically constrained, ring network models consisting of distinct rings of excitatory and inhibitory neurons. We assessed the network for its ability to sustain robust propagation of patterned activity across the rings. First, in homogeneous ring networks, we found that robust activity propagation could be sustained through several different combinations of synaptic weights, demonstrating synaptic degeneracy in the emergence of robust activity propagation. We incorporated intrinsic heterogeneity through randomized perturbations to ion channel parameters of all neurons and synaptic heterogeneity by adding jitter to the Mexican-hat connectivity between inhibitory neurons. We found the number of networks exhibiting robust propagation of patterned activity to reduce with increase in the degree of synaptic or intrinsic heterogeneities. Motivated by the ability of intrinsic neuronal resonance to stabilize heterogeneous rate-based CAN models, we hypothesized that increasing HCN-channel (a resonating conductance) density would stabilize activity propagation in heterogeneous ring networks. Strikingly, we observed that increases in HCN-channel density resulted in a pronounced increase in the proportion of heterogeneous networks that exhibited robust activity propagation, across multiple trials and across three degrees of either form of heterogeneity. Together, heterogeneous networks made of neurons with disparate intrinsic properties and variable HCN channel densities yielded robust activity propagation, demonstrating intrinsic degeneracy in the emergence of robust activity propagation. Finally, as HCN channels also contribute to changes in excitability, we performed excitability-matched controls with fast HCN channels that do not introduce resonance. We found that fast HCN channels did not stabilize heterogeneous network dynamics over a wide range of conductance values, suggesting that the slow negative feedback loop introduced by HCN channels is a critical requirement for network stabilization. Together, our results unveil a cascade of degeneracy in ring-network physiology, spanning the molecular-cellular-network scales. These results also demonstrate a critical role for the widely expressed HCN channels in enhancing the robustness of heterogeneous neural circuits by implementing a slow negative feedback loop at the cellular scale.

neuroscience↗

Diverse transcriptomic response of cellular system following low-dose exposure of mesoporous nanoparticles

Mesoporous nanoparticles (NPs) are an interesting drug delivery system that has generated considerable attention in the biomedical sector. Despite recent attempts to conduct safety assessments using traditional methods based on phenotypic data, our understanding of the underlying molecular processes produced by mesoporous NPs is still in its infancy. In the present study, RNA sequencing was used to assess the biological perturbations and the pathways induced in response to early exposure of two different mesoporous NPs; mesoporous silica NPs (MSN) and mesoporous carbon NPs (MCN) in human liver hepatocellular carcinoma cells. In order to better understand the risks associated with NPs, it is required to consider the initial low-dose exposure effects that mimic the real exposure scenario. No overt toxicity was detected in the MTT assay when performed at 6 hours at low concentrations (MCN 25 g/ml and MSN 15 g/ml) of NPs; thus, we have selected this dose for RNA sequencing analysis. Our transcriptomics analysis showed significant differences in the expression of many genes after exposure to both NPs. Surprisingly, both NPs frequently deregulated 52.9 percent of upregulated and 42 percent of downregulated genes. Gene ontology categories, in particular, revealed comparable perturbations of biological reactions in the cellular system. HepG2 cells reacted to mesoporous NPs by allowing alterations in genes involved in cytoskeleton reorganisation (ATAT1, DMTN, PTK2 and PFN2). Exposure to mesoporous NPs increased transcripts expressing ubiquitin ligase (RNF187, ARIH2, VHL, and RAB40C), transferase (FBXO3 and WDSUB1), conjugating (UBE2J2), and also proteasomal subunits (PSMD2, PSMD13) enzymes, indicating that protein turnover rates are altered in response to environmental damage. In addition, DNA damage and DNA damage checkpoint genes were upregulated, indicating that NPs induced stress in the cells. These finding showed low dosage acute exposure have comparable responses between mesoporous NPs. These results may add further knowledge in conceptualization of Safer-by-Design strategy of NPs in biomedical field.

pharmacology and toxicology↗

ZnO nanoparticles and SWCNT induced general stress response pathway in HepG2 cells at non-cytotoxic doses revealed by RNA sequencing

Nanoparticles (NPs) are important in a variety of sectors, including disease diagnostics, medicine, nutrition, and many other industries. The risk of human exposure demands an early evaluation of both the basic dynamics of NPs interaction with biological systems and their potential consequences. Deciphering these occurrences will provide critical information regarding the health hazards and safety advantages associated with next-generation nanoformulations in clinical practice. We examined the HepG2 cell line in a systematic manner to determine the cellular response to single-walled carbon nanotubes (SWCNTs) and zinc oxide (ZnO) NPs. With the use of high-throughput transcriptomic methods, we found that both NPs induce comparable dysregulation of the endocytic and proteasomal complex genes in liver hepatocellular carcinoma cells, at levels (> 80 percent cell viability) that do not cause over-toxicity at early incubation period (6 h). SWCNT and ZnO NPs were shown to enter cells through clathrin-mediated pathways, affecting cytoskeleton gene expression, DNA damage and repair, protein ubiquitination, and cell transcriptional machinery. Our findings indicate that early response strategies activate stress-related mechanisms. Finally, this method for studying nanomaterial-cell interactions demonstrates how changes in the transcriptome profile may predict downstream consequences even at doses that do not cause acute toxicity.

pharmacology and toxicology↗

Stochastic resonance and bifurcations in a heterogeneous neuronal population explain intrinsic oscillatory patterns in entorhinal cortical stellate cells

Stellate cells in the medial entorhinal cortex manifest peri-threshold oscillatory patterns in their membrane voltage. Although different theoretical frameworks have been proposed to explain these activity patterns, these frameworks do not jointly account for heterogeneities in intrinsic properties of stellate cells and stochasticity in ion-channel and synaptic physiology. In this study, we first performed in vitro patch-clamp electrophysiological recordings from rat MEC stellate cells and found pronounced cell-to-cell variability in their characteristic physiological properties. We demonstrate that stochasticity introduced into either a simple nonlinear dynamical system (Hopf bifurcation) or into heterogeneous biophysical models yielded activity patterns that were qualitatively similar to peri-threshold oscillations in stellate cells. We developed five quantitative metrics for identification of valid oscillatory traces and confirmed that these metrics reliably captured the variable amplitude and non-rhythmic oscillatory patterns observed in our electrophysiological recordings. We analyzed traces from a stochastic Hopf bifurcation system for further confirmation on the reliability of these quantitative metrics in detecting oscillatory patterns. Apart from providing confirmation, these analyses provided a key insight about the manifestation of stochastic resonance in the stochastic bifurcation system, but not with theta-filtered noise. We then validated peri-threshold activity patterns obtained from a heterogeneous population of stellate cell models, with each model assessed with multiple trials of different levels and forms of noise (ion-channel, synaptic, and additive) at different membrane depolarizations. Strikingly, the validation process confirmed the manifestation of heterogeneous stochastic bifurcations across all models and revealed the detection of the highest number of valid oscillatory traces at an optimal level of each form of noise. The manifestation of stochastic resonance in this heterogeneous model population explained why intrinsic theta oscillations might not be observed under in vivo conditions where noise levels are typically high. Together, we provide several lines of evidence that demonstrate heterogeneous stochastic bifurcations as a unifying framework that fully explains peri-threshold oscillatory patterns in stellate cells and argue for state-dependence in the manifestation of these oscillations.

neuroscience↗

Resonating neurons stabilize heterogeneous grid-cell networks

A central theme that governs the functional design of biological networks is their ability to sustain stable function despite widespread parametric variability. Here, we investigated the impact of distinct forms of biological heterogeneities on the stability of a two-dimensional continuous attractor network (CAN) implicated in grid-patterned activity generation. We show that increasing degrees of biological heterogeneities progressively disrupted the emergence of grid- patterned activity and resulted in progressively large perturbations in low-frequency neural activity. We postulated that targeted suppression of low-frequency perturbations could ameliorate heterogeneity-induced disruptions of grid-patterned activity. To test this, we introduced intrinsic resonance, a physiological mechanism to suppress low-frequency activity, either by adding an additional high-pass filter (phenomenological) or by incorporating a slow negative feedback loop (mechanistic) into our model neurons. Strikingly, CAN models with resonating neurons were resilient to the incorporation of heterogeneities and exhibited stable grid-patterned firing. We found CAN networks with mechanistic resonators to be more effective in targeted suppression of low-frequency activity, with the slow kinetics of the negative feedback loop essential in stabilizing these networks. As low-frequency perturbations (1/f noise) are pervasive across biological systems, our analyses suggest a universal role for mechanisms that suppress low- frequency activity in stabilizing heterogeneous biological networks.

neuroscience↗

Determining the scale at which variation in WUE traits changes population yields

Functional variation is known to influence population yield, but the scale at which this happens is still unknown. Relevant signals might only reach immediate neighbors of a phenotypically diverse plant (neighbor-scale) or conversely may distribute across the population (population-scale). We use Nicotiana attenuata silenced in mitogen-activated protein kinase 4 (irMPK4), plants with low water-use efficiency (WUE), to study the scale at which water-use traits alter intraspecific population yields. In the field and glasshouse, populations with low percentages of irMPK4 plants planted among isogenic control plants produced maximum overall growth and yield. Through paired-plant and local-plant-configuration analyses, we determined that this occurred at the population scale. However, we find that this effect was not due to irMPK4s WUE phenotype. With micro-grafting, we additionally show that MPK4-deficiency may mediate the response at the population-scale: shoot-expressed MPK4 is required for N. attenuata to change yield in response to a neighbor.

ecology↗

Degeneracy in the robust expression of spectral selectivity, subthreshold oscillations and intrinsic excitability of entorhinal stellate cells

Biological heterogeneities are ubiquitous and play critical roles in the emergence of physiology at multiple scales. Although neurons in layer II (LII) of the medial entorhinal cortex (MEC) express heterogeneities in their channel properties, the impact of such heterogeneities on the robustness of cellular-scale physiology has not been assessed. Here, we performed a 55-parameter stochastic search spanning 9 voltage- or calcium-activated channels to assess the impact of channel heterogeneities on the concomitant emergence of 10 electrophysiological characteristics of LII stellate cells (SCs). We generated 50,000 models and found a heterogeneous subpopulation of 155 valid models to robustly match all electrophysiological signatures. We employed this heterogeneous population to demonstrate the emergence of cellular-scale degeneracy in LII SCs, whereby disparate parametric combinations expressing weak pairwise correlations resulted in similar models. We then assessed the impact of virtually knocking out each channel from all valid models and demonstrate that the mapping between channels and measurements was many-to-many, a critical requirement for the expression of degeneracy. Finally, we quantitatively predict that the spike-triggered average of LII SCs should be endowed with theta-frequency spectral selectivity and coincidence detection capabilities in the fast gamma-band. We postulate this fast gamma-band coincidence detection as an instance of cellular-scale efficient coding, whereby SC response characteristics match the dominant oscillatory signals in LII MEC. The heterogeneous population of valid SC models built here unveils the robust emergence of cellular-scale physiology despite significant channel heterogeneities, and forms an efficacious substrate for evaluating the impact of biological heterogeneities on entorhinal network function.\n\nKEY POINTSO_LIStellate cells (SC) in layer II (LII) of the medial entorhinal cortex express cellular-scale degeneracy in the concomitant manifestation of several of their unique physiological signatures.\nC_LIO_LISeveral disparate parametric combinations expressing weak pairwise correlations resulted in models with very similar physiological characteristics, including robust theta-frequency membrane potential oscillations spanning several levels of subthreshold depolarization.\nC_LIO_LIElectrophysiological measurements of LII SCs exhibited differential and variable dependencies on underlying channels, and the mapping between channels and measurements was many-to-many.\nC_LIO_LIQuantitative predictions point to theta-frequency spectral selectivity and fast gamma-range coincidence detection capabilities in class II/III spike-triggered average of LII SCs, with the postulate for this to be an instance of cellular-scale efficient coding.\nC_LIO_LIA heterogeneous cell population that accounts for both channel and intrinsic heterogeneities in LII SCs, which could be employed by network models of entorhinal function to probe the impact of several biological heterogeneities on spatial navigation circuits.\nC_LI

neuroscience↗