Biology subjects

Shrivastava, S.

Publications and source records attributed to Shrivastava, S..

12 recordsLinked to original sources

bioRxiv2026

SARS-CoV-2 maturation driven by a mechano-active nucleocapsid-RNA condensate

The nucleocapsid (N) protein, the core component of the SARS-CoV-2 virus, binds to the 30-kb viral genomic RNA (vgRNA) to form ribonucleoprotein assemblies that are packaged into ~100 nm membrane-enclosed virions. In addition to viral assembly, the N protein performs other functions, including roles in viral mRNA transcription, replication, and immune regulation, making it a key target for developing diagnostics and vaccines. Recent studies show that N protein and RNA undergo phase separation to form a biomolecular condensate that constitutes the viral core. However, how this condensate becomes selectively enveloped by a membrane remains unclear. Here, using a minimal reconstituted system, we demonstrate that N protein-vgRNA condensates are spontaneously enveloped by lipid bilayer membranes, whereas condensates formed by N protein alone or with genomic RNA fragments fail to undergo envelopment and instead adhere to or weakly deform membranes. We show that RNA length tunes the material properties of N protein condensates, with vgRNA imparting enhanced elasticity. We propose a physical model for SARS-CoV-2 maturation in which adhesion between the membrane and the N protein-vgRNA condensate drives membrane bending, while condensate elasticity preserves core geometry. These results identify RNA-dependent material properties as an underlying physical principle for selective SARS-CoV-2 maturation.

biophysics↗

bioRxiv2026

Millisecond nonlinear state changes during droplet coalescence identify therapeutic-antibody developability liabilities

Apoha's Liquid State Machine records ellipsometric waveforms from injections depositing sub-microgram quantities of antibody drop-by-drop onto a liquid reservoir. We previously showed that a behavioural feature extracted from the waveforms, VIBE1, identified antibodies carrying multiple biophysical liabilities in an industrial dataset of 71 monoclonal antibodies, and enriched for clinical failure across a larger dataset of 235 therapeutic antibodies. Here, we use an auxiliary coalescence-sensor channel to decode VIBE1 by separating the coalescence event from its propagation through the substrate. The per-titration drop-to-drop standard deviation of pinch-off time, {sigma}{tau}, explains most of VIBE1's variance across the dataset (R2 = 0.92, n = 1182). High-speed imaging at 10,000 frames per second reveals that all imaged drops initially thin at the same Newtonian capillary-inertial rate while the neck remains wide. In drops from certain antibodies, the thinning bridge then decelerates as internal strain builds in the narrowing neck. This elastocapillary stiffening response has a timescale {lambda} that decreases as pinch-off time {tau}i increases across the imaged set. {sigma}{tau} is therefore a readout of the antibody's propensity to undergo a transient gel-like stiffening response during coalescence, and that variability is what VIBE1 captures. The signal is concentration dependent, and absent in bovine serum albumin (BSA) tested at up to an order of magnitude higher concentration than the antibodies, despite BSA being a strongly surface-active globular protein. The instrument is configured so that complex behaviours of this kind appear in its recorded waveforms; the gel-like coalescence response we identify here is one such phenomenon.

biophysics↗

bioRxiv2025

Preclinical immunogenicity of the LP.8.1-adapted BNT162b2 COVID-19 vaccine

SARS-CoV-2 evolution toward antigenically distinct lineages drives escape from host immunity. JN.1 lineage derivatives have recently dominated the global epidemiologic landscape. In preclinical models, an LP.8.1-adapted BNT162b2 vaccine elicited higher serum neutralizing antibody responses against contemporary, circulating JN.1 sublineages, including the currently dominant XFG, as compared to JN.1-, KP.2- and XEC-adapted vaccines. These findings supported the selection of an LP.8.1-adapted vaccine for the composition of the 2025-26 COVID-19 vaccine formula.

immunology↗

bioRxiv2025

A High-Dimensional Interfacial Wave Assay for Early Biophysical Profiling of Therapeutic Antibodies

Therapeutic antibody performance depends not only on sequence and structure, but also on how the molecule responds to physico-chemical perturbations encountered in its environment. Whereas sequence and static structure can be inferred under controlled conditions, behaviour is a conditional, multidimensional response to environment, most directly characterised by applying defined perturbations and quantifying the resulting dynamics. Conventional early-stage developability methods capture isolated dimensions of this response under near-equilibrium conditions, deferring integrated behavioural assessment to late-stage characterisation, when the cost of correction is highest. We introduce Variations in Interfacial Behaviour under Excitation (VIBE), an interfacial wave method implemented via Liquid State Intelligence (LSI), a sensing architecture that transduces molecular perturbations at the air-liquid interface into high-dimensional wave patterns. A colloidal liquid substrate operated near a thermodynamic transition couples small molecular perturbations to large dynamical responses, integrating structural flexibility, charge distribution, and surface hydrophobicity into a single behavioural readout from microgram-scale samples. Applied to antibodies previously characterised by industrial benchmarks, the primary behavioural descriptor, VIBE1, functioned as a high-precision triage tool, flagging candidates carrying multiple biophysical liabilities. In a clinical-stage cohort, the proportion of high-VIBE1 antibodies declined progressively from early trials through approval, and high-VIBE1 candidates showed an elevated clinical failure rate. Concordance analysis against estab-lished methods confirmed that VIBE1 captures a composite signal spanning hydrophobicity, polyreactivity, self-interaction, and thermal stability rather than recapitulating any single conventional readout. These findings establish interfacial wave sensing as a low-material modality for early-stage developability assessment, repositioning molecular behaviour from late-stage validation to discovery-phase characterisation.

biophysics↗

bioRxiv2025

High and low exogenous nitrate concentrations produce distinct calcium signatures in Arabidopsis roots

Calcium (Ca2+) acts as a secondary messenger in plant responses to many stimuli, including nitrate (NO -) signaling in roots. Nitrate uptake in plants occurs through two distinct transporter systems that have different affinities for the anion, which result in divergent downstream regulatory responses. However, it is unknown if the concentration dependent NO - response is linked to differential Ca2+ response. In this study, we used an Arabidopsis transgenic line expressing CBL1-mRuby2-GCaMP6s to investigate if there are unique Ca2+ signatures in intact root tissue in response to high and low NO - concentrations. A significant Ca2+ response was observed in root hairs in response to both high (5 mM) and low (0.25 mM) NO - concentrations. A distinct Ca2+ wave was observed in the low NO - treated roots, and an asynchronous Ca2+ response was captured in individual root epidermal cells. Cell-specific analysis revealed a distinct Ca2+ profile, comprising waves and spikes in response to NO -, and prominent in root hairs but not in non-root hair bearing epidermal cells. The findings from this study demonstrate that there are distinct cell-specific and NO - condition-specific Ca2+ signatures in Arabidopsis roots.

plant biology↗

bioRxiv2024

Immunologic and Biophysical Features of the BNT162b2 JN.1- and KP.2-Adapted COVID-19 Vaccines

Vaccines remain a vital public health tool to reduce the burden of COVID-19. COVID-19 vaccines that are more closely matched to circulating SARS-CoV-2 lineages elicit more potent and relevant immune responses that translate to improved real-world vaccine effectiveness. The rise in prevalence of the Omicron JN.1 lineage, and subsequent derivative sublineages such as KP.2 and KP.3, coincided with reduced neutralizing activity and effectiveness of Omicron XBB.1.5-adapted vaccines. Here, we characterized the biophysical and immunologic attributes of BNT162b2 JN.1- and KP.2-adapted mRNA vaccine-encoded spike (S) protein immunogens. Biophysical interrogations of S revealed the structural consequences of hallmark amino acid substitutions and a potential molecular mechanism of immune escape employed by JN.1 and KP.2. The vaccine candidates were evaluated for their immunogenicity when administered as fourth or fifth doses in BNT162b2-experienced mice or as a primary series in naive mice. In both vaccine-experienced and naive settings, JN.1- and KP.2-adapted vaccines conferred improved neutralizing responses over the BNT162b2 XBB.1.5 vaccine against a broad panel of emerging JN.1 sublineages, including the predominant KP.3.1.1 and emerging XEC lineages. Antigenic mapping of neutralizing responses indicated greater antigenic overlap of JN.1- and KP.2-adapted vaccine responses with currently circulating sublineages compared to an XBB.1.5-adapted vaccine. CD4+ and CD8+ T cell responses were generally conserved across all three vaccines. Together, the data support the selection of JN.1- or KP.2-adapted vaccines for the 2024-25 COVID-19 vaccine formula. ONE-SENTENCE SUMMARYThe Omicron JN.1- and KP.2-adapted BNT162b2 mRNA vaccines encoding prefusion S proteins elicit similar preclinical neutralizing antibody responses against circulating JN.1 sublineage pseudoviruses that are more potent than those elicited by past iterations of BNT162b2 licensed vaccines, thus demonstrating the importance of annual strain changes to the COVID-19 vaccine.

immunology↗

bioRxiv2023

Monitoring and maturation of cardiomyocyte differentiated from human induced pluripotent stem cells using a multi-functional tissue engineering platform

BackgroundThe use of human induced pluripotent stem cells (hiPSCs) is attracting attention as a potential personalized therapy for damaged myocardium, as they are accessible and compatible with the human body. The hiPSCs can be effectively differentiated into cardiomyocytes (CMs), which are essential for myocardial regeneration. However, current approaches have been unable to fully replicate the electro-mechanical functions of natural CMs. MethodsAlthough several methods have been used to stimulate hiPSC-CMs for maturation, the ability to integrate multiple stimuli that influence myocardial cell function has been limited. To address this challenge, we have developed a multi-functional tissue engineering system for CMs that is based on a stretchable multielectrode array (SMEA). The SMEA is housed in a mini-incubator and is stretchable, durable and autoclavable. ResultsThe system can independently control co-stimulation parameters of electrical and mechanical stimuli simultaneously. Furthermore, the system can monitor the status of the cells throughout their proliferation and differentiation of hiPSCs, as well as the stimulation of hiPSC-CMs, through electrochemical cell impedance spectroscopy. By applying co-stimulation, we have observed the enhanced maturation of hiPSC-CMs. ConclusionsOur innovative system holds great potential as a tool for improving the culture and engineering of electrogenic cells with enhanced maturity.

bioengineering↗

bioRxiv2022

Inferring a cell's capabilities from omics data with ImmCellFie

ImmCellFie is a user-friendly, web-based platform for comprehensive analysis of metabolic functions inferred from transcriptomic or proteomic data. It enables researchers to leverage the powerful mechanistic insight provided by complex genome-scale metabolic models with little to no bioinformatics training required. The platform has been integrated with a series of useful tools and richly annotated scientific visualizations for interactive exploration by the user. ImmCellFie pushes beyond simple statistical enrichment and incorporates complex biological mechanisms to quantify cell activity. Graphical abstract

bioinformatics↗

bioRxiv2022

SARS-CoV-2 Variant Delta Potently Suppresses Innate Immune Response and Evades Interferon-Activated Antiviral Responses

Delta variant of SARS-CoV-2 has caused more severe infections than its previous variants. We studied the host innate immune response to Delta, Alpha and two earlier variants to map the evolution of the recent ones. Our biochemical and transcriptomic studies reveal that Alpha and Delta have progressively evolved over the ancestral variants by silencing innate immune response, thereby limiting cytokine and chemokine production. Though Alpha silenced RLR pathway just as Delta, it failed to persistently silence the innate immune response unlike Delta. Both Alpha and Delta have evolved to resist IFN treatment while they are still susceptible to RLR activation, further highlighting the importance of RLR-mediated, IFN-independent mechanisms in restricting SARS-CoV-2. Our studies reveal that SARS-CoV-2 Delta has integrated multiple mechanisms to silence host innate immune response and evade IFN response. Deltas silent replication and sustained suppression of host innate immune response, possibly resulting in delayed or reduced intervention by the adaptive immune response, could potentially contribute to the severe symptoms and poor recovery index associated with it.

immunology↗

bioRxiv2021

A spike-ferritin nanoparticle vaccine induces robust innate immune activity and drives polyfunctional SARS-CoV-2-specific T cells

Potent cellular responses to viral infections are pivotal for long -lived protection. Evidence is growing that these responses are critical in SARS -CoV-2 immunity. Assessment of a SARS -CoV-2 spike ferritin nanoparticle (SpFN) immunogen paired with two distinct adjuvants, Alhydrogel(R) (AH) or Army Liposome Formulation containing QS-21 (ALFQ) demonstrated unique vaccine evoked immune signatures. SpFN+ALFQ enhanced recruitment of highly activated classical and non -classical antigen presenting cells (APCs) to the vaccine-draining lymph nodes of mice. The multifaceted APC response of SpFN+ALFQ vaccinated mice was associated with an increased frequency of polyfunctional spike -specific T cells with a bias towards TH1 responses and more robust SARS-CoV-2 spike-specific recall response. In addition, SpFN+ALFQ induced Kb spike(539-546)-specific memory CD8+ T cells with effective cytolytic function and distribution to the lungs. This epitope is also present in SARS-CoV, thus suggesting that generation of cross-reactive T cells may provide protection against other coronavirus strains. Our study reveals that a nanoparticle vaccine, combined with a potent adjuvant, generates effective SARS-CoV-2 specific innate and adaptive immune T cell responses that are key components to inducing long-lived immunity. One Sentence SummarySpFN vaccine generates multifactorial cellular immune responses.

immunology↗

bioRxiv2020

Shock and Detonation Waves at an Interface and the Collision of Action Potentials

Action potentials in neurons are known to annihilate each other upon collision, while there are cases where they might penetrate each other. Compression waves that travel within the plasma membrane of a neuron have previously been proposed as a thermodynamic basis for the propagation of action potentials. In this context, it was recently shown that two-dimensional compressive shock waves in the model system of lipid monolayers can nearly annihilate each other upon head-on collision when excited close to a phase transition. However, weaker shock waves showed penetration. In general, once the approximation of small perturbation is not valid, compression waves do not interact linearly anymore. While experiments in lipid monolayers demonstrated this principle, a mechanism remained unclear. In this article, we summarise the fundamentals of shock physics as applied to an interface and how it previously explained the observation of threshold and saturation of shockwaves in the lipid monolayer (all - or - none). While the theory has the same fundamental premise as the soliton model, i.e. the conservation laws and thermodynamics, we elaborate on how the two approaches make different predictions with regards to collisions and the detailed structure of the wave-front. As a case study and a new result, we show that previously unexplained annihilation of shock waves in the lipid monolayer is a direct consequence of the nature of state changes, i.e. jump conditions, within these shockwaves, and elaborate on the consequence of these results for the general understanding of the excitation waves in a thermo-fluids framework.

biophysics↗

bioRxiv2020

A Thermodynamic Interpretation of the Stimulated Raman Spectroscopic Signature to Action Potential in Single Neurons

It has previously been suggested that the plasma membrane condenses and melts reversibly during an action potential in a neuron, analogous to an acoustic wave travelling in the compressive membrane region. If true it has fundamental consequences for our understanding of the regulation of biological functions during an action potential. It has long been known that the electrical dipoles in the neuronal membrane reorient during an action potential, observed through a variety of optical methods. However, this information has been insufficient to confirm if and how the collective thermodynamic state of the neuronal membrane changes during an action potential. Here, we show that hyperspectral stimulated Raman spectroscopy (SRS) can resolve the thermodynamic state of the neuronal membranes in a single neuron during an action potential. These measurements indicate that the system becomes ordered and compressed during the de-polarisation phase and disordered and expanded during hyper polarisation Therefore, the observation is consistent with the acoustic hypothesis and SRS provides a powerful tool to not only further validate the hypothesis in future, but also explore the role of membrane thermodynamics during an action potential.

biophysics↗