Biology subjects

Agarwal, K.

Publications and source records attributed to Agarwal, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Cancer Phenotypic Plasticity Quantification using Morphology-Migration Coupled Metric in Live Label-Free Optical Microscopy

Cancer phenotypic plasticity drives invasion, treatment resistance, and relapse. Quantifying how cells dynamically couple morphology and migration in real time, without molecular labels, remains unsolved. Static molecular markers report on protein expression state rather than functional migratory behavior. Existing image-based metrics treat shape and migration as independent features, missing the coordinated coupling that defines plastic migratory states. We introduce Directional Shape Coupling (DSC), a quantitative metric purpose-built for live label-free imaging. DSC integrates movement direction consistency, shape deformation, and directional-shape alignment into a single interpretable score. Component weights are derived from PCA, adapting automatically to any dataset without manual tuning. Applied to differential interference contrast imaging of pancreatic cancer cells on a tissue-mimicking substrate recapitulating desmoplastic tumor stroma, DSC exhibited a large phenotype-associated effect size,{varepsilon} 2 = 0.65, across five distinct migratory phenotypes within a genetically homogeneous population, demonstrating that behavioral heterogeneity is structured and non-genetic. DSC encodes information orthogonal to classical shape and motion descriptors. Critically, DSC reveals that dynamic shape adaptation to mechanical cues rather than directional commitment drives phenotypic identity in this system. DSC provides the label-free imaging community a transparent, generalizable framework for quantifying dynamic non-genetic plasticity directly from live imaging data.

biophysics↗

bioRxiv2026

PreS1-decorated recombinant adenovirus encoding HBV antigens generates neutralizing humoral and cellular immunity

Background & AimsAchieving functional cure for chronic hepatitis B (CHB) will likely require a combinatorial approach targeting multiple aspects of the complex hepatitis B virus (HBV) life cycle and host adaptive immune responses. Here, we developed a therapeutic vaccination strategy targeting the PreS1 region of L-HBsAg, required for cellular entry of both hepatitis B and D viruses. An established potent T-cell inducing platform, recombinant adenovirus (Ad), was used as a nanoparticle scaffold for PreS1 attachment, to generate antibodies that neutralize virus entry and to establish T-cell mediated immune control. Approach & ResultsScreening a cohort of 61 patients diagnosed with CHB revealed minimal evidence of natural anti-PreS1 responses. Thus, Ad particles encoding multiple HBV antigens were decorated with PreS1 peptide using DogTag/DogCatcher protein superglue. Mice vaccinated with PreS1-decorated Ad induced robust anti-PreS1 antibody responses that neutralized HBV and HDV infection. In contrast, an undecorated Ad encoding L-HBsAg failed to neutralize HBV, demonstrating that PreS1 decoration was required for potent HBV neutralization. Strong CD8+ and CD4+ T-cell responses were induced against HBV antigens encoded in the Ad genome. ConclusionsPreS1-decorated Ad combines immunological HBV and HDV entry inhibition with potent anti-HBV T-cell induction in a single platform, providing a promising addition to current therapeutic strategies against CHB, with particular utility in HBV/HDV co-infection.

bioengineering↗

bioRxiv2026

miRNA-mRNA Interaction Network Analysis in Alzheimer's Disease for Biomarker Discovery

--Alzheimers disease (AD) is a complex neurodegenerative disorder characterized by widespread dysregulation of gene expression and regulatory pathways. MicroRNAs (miRNAs) act as key post-transcriptional regulators by modulating messenger RNAs (mRNAs), and their disruption can influence synaptic function, neuroinflammation, and neuronal survival. In this study, we present an integrative transcriptome-driven framework to identify AD-associated miRNA-mRNA regulatory signatures and potential biomarkers. Transcriptomic and clinical data were obtained from the Alzheimers Disease Neuroimaging Initiative (ADNI) and the GEO dataset GSE48552. Differential expression analysis (Welchs t-test with FDR correction) identified 148 significantly dysregulated genes (35 up-regulated, 113 down-regulated) between AD and cognitively normal controls. Experimentally validated and predicted miRNA-target interactions were integrated using miRTarBase and additional target resources, yielding 1,669,089 miRNA-gene interactions involving 3,055 unique miRNAs, with strong enrichment toward down-regulated gene targeting. Functional enrichment analysis revealed convergence of miRNA-regulated genes on synaptic signaling, neuronal communication, intracellular transport, apoptosis, oxidative stress, and PI3K-Akt/MAPK-related pathways. A bipartite miRNA-mRNA regulatory network (2,343 nodes; 14,603 edges) was constructed and analyzed using centrality metrics, highlighting key hub regulators including PBX1 and SLC7A5. Finally, supervised machine learning models trained on selected molecular features achieved strong performance, with ensemble approaches (XGBoost/LightGBM) demonstrating robust discrimination of AD from controls.

bioinformatics↗

bioRxiv2026

Role of brown adipose tissue-specific sympathetic and sensory innervations in menthol-induced energy-expending phenotype

Menthol, a TRPM8 agonist and pharmacological cold mimic, activates brown adipose tissue (BAT) to increase adaptive thermogenesis and whole-body energy expenditure. BAT is highly innervated with sensory and sympathetic nerve fibers. There is existing literature that sympathetic nerves have a critical role in regulating menthols (or cold) effect on energy homeostasis, but there is minimal literature about the involvement of somatosensory innervations. Here, we ought to investigate whether short-term topical application (3 days) of menthol elicits sympathetic and sensory nerves. We used chemical denervation models of complete (100 mg/kg; 6-OHDA and 125 mg/kg; capsaicin, s.c.) and localized (in BAT, 20 {micro}L of 6-OHDA (20 mg/ml) and 20{micro}L of capsaicin (20{micro}g/{micro}L) in each BAT lobe) ablation of sympathetic (6-OHDA) and sensory (capsaicin) innervations to explore their roles in menthol induced BAT activation and energy expanding phenotype. In the present study we have shown that (i) short-term topical application of menthol (10 % menthol for 3 consecutive days) elicits sympathetic and sensory innervations, and induces thermogenesis, lipolysis and mitochondrial biogenesis in mice BAT; (ii) localized ablation of sympathetic innervation prevented menthol induced BAT activation and lipolysis (iii) localized ablation of sensory neurons augments sympathetic innervations induced BAT activation and modulated thermoregulation. Collectively, our results suggest that BAT activation following short-term topical application of menthol is dependent primarily but not exclusively on centrally mediated SNS activation. TRPV1-positive sensory neurons are partially necessary for thermoregulation and efficient BAT activation.

pharmacology and toxicology↗

bioRxiv2025

Uncovering Sleep's Hippocampal-Cortical Dialogue: The Role of Deltas' and Spindles' Cross-Area Synchronization and Ripple Subtypes

Hippocampal ripples, critical for sleep-related memory consolidation, are heterogeneous events with various sources and functions. Here we applied principal component analysis to identify ripple sub-types and relate them to hippocampal-cortical interactions as well as their role in consolidating simple and complex semantic-like memories in rats. Three main ripple types were discovered: baseline, large-input, and small-input ripples. Small-input ripples, were associated with increased prefrontal cortex to hippocampus connectivity, followed hippocampal delta waves, and were sufficient for simple learning. In contrast, large-input ripples exhibited increased hippocampus to prefrontal cortex connectivity, occurred during hippocampal spindles together as a doublet with a small-input ripple, and were critical for complex memory consolidation. Finally, learning induced heightened coupling between hippocampal delta and spindle oscillations and their cortical counterparts, consequently leading to an increased synchronization of ripples with cortical oscillations. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/644132v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@b94b1borg.highwire.dtl.DTLVardef@f1fff0org.highwire.dtl.DTLVardef@1da0c00org.highwire.dtl.DTLVardef@4a0008_HPS_FORMAT_FIGEXP M_FIG C_FIG Significance StatementThis pioneering, data-driven approach is the first to connect distinct ripple sub-types to precise cross- brain computational states, revealing their role in consolidating various types of memories.

neuroscience↗

bioRxiv2024

Potential Cancer Biomarkers: Mitotic Intra-S DNA Damage Checkpoint Genes

BACKGROUNDThe mitotic intra-S DNA damage checkpoint signaling gene set is potentially involved in cancers where the genes play an important role. 17 total genes are involved in this gene set: ATF2, CHEK2, EME1, EME2, FANCD2, HUS1, HUS1B, MDC1, MRE11, MSH2, MUS81, NEK11, RAD17, RAD9A, RAD9B, TIPIN, XPC. The aim of this study is to complete a pan-cancer profile of each gene in the mitotic intra-S DNA damage checkpoint signaling gene set in order to determine potential diagnostic and prognostic purposes, while also determining how they could be used in a clinical setting as therapeutic targets to help patients. METHODSMultiomic data was acquired for the 17 genes; over 9000 samples of 33 types of cancer were analyzed to create pan-cancer profiles of CNV, mRNA expression, and pathway analysis. RESULTSThe CNVs of some of these genes are associated with the survival of MESO, PCPG, BLCA, SKCM, LUAD, HNSC, LUSC, OV, and BRCA could be affected by the mRNA expression of the genes which can involve regulation of copy number. CONCLUSIONWith sufficient investigation, the genes involved in mitotic intra-S DNA damage checkpoint signaling may contribute to the development of cancer and may be used as biomarkers for cancer prognosis and diagnosis. To prove their clinical use for diagnosis and prognosis, however, and to create workable applications in clinical settings, further work is required. However, these pan-cancer profiles provide a more comprehensive knowledge of the mitotic intra-S DNA damage checkpoint signaling gene set in cancer as well as valuable information for future reference.

bioinformatics↗

bioRxiv2024

Randomly oriented microgrooved hydrogel guides cellular motility, modulates speed, and governs directionality of cellular spread

Cell migration is a fundamental biological process, yet the mechanisms underlying how cells sense and navigate complex environments remain poorly understood. In this study, we developed a system of randomly oriented microgrooves, designed at cellular length scales, to explore motility intelligence in response to varied topographies. These microgrooves allowed cells to freely choose their migratory paths, revealing key insights into how cells sense and adapt to topological cues. Using fibroblast cells migrating over these grooved substrates, we examined cellular processes such as actin cytoskeleton remodeling, cell adhesion dynamics, and the impact of groove alignment on migration speed and directionality. Our results demonstrate that cells align their cytoskeletal structures to groove geometries, forming actin-rich anchors that enhance migration in groove-aligned environments. Cells migrating in grooves aligned with their intrinsic polarity exhibited faster, more directed migration compared to those in misaligned or control conditions. This work advances our understanding of cell-topology interaction and provides new perspectives for tissue engineering applications in cancer therapy and wound healing.

bioengineering↗

bioRxiv2024

Label-free acoustic and optical microscopy of live tumor spheroids in hydrogel for high-throughput 3D In-vitro drug screening

3D cell cultures, including spheroids, have become essential tools in cancer research and drug discovery due to their ability to more accurately mimic in-vivo tissue environments compared to traditional 2D cultures. However, imaging these thick, complex structures remains a challenge, as conventional optical microscopy techniques are limited by shallow depth penetration. This study explores the complementary use of gradient light interference microscopy (GLIM) and scanning acoustic microscopy (SAM) for label-free imaging of 3D spheroid clusters embedded in hydrogels. GLIM offers high-resolution optical imaging but struggles with depth in dense samples, while SAM provides greater depth penetration and a larger field of view, albeit with lower resolution. By correlating SAM and GLIM imaging, this study demonstrates how the two techniques can be synergistically used to enhance the visualization of spheroids, capturing both large-scale structural features and fine cellular details. The benefits make such a platform suitable for screening high-number multi-well plates and evaluating necrotic and angiogenic features from the core of the thick sample. Such platforms have the potential of combining acoustic and optical imaging modalities for high-throughput screening and physical characterization in 3D cell culture research, advancing our understanding of drug efficacy in complex biological systems.

bioengineering↗

bioRxiv2024

Differential Contributions of CA3 and Entorhinal Cortex Inputs to Ripple Patterns in the Hippocampus Under Cannabidiol

Cannabidiol (CBD), increasingly recognized for its potential to treat insomnia, notably extends NonREM sleep phases and modifies sleep-associated ripple dynamics. Utilizing a threshold-based approach, our study differentiated distinct ripple types in rats, clarifying the contributions of intra-hippocampal (CA3) and cortical (mEC) regions to these events. The findings reveal that CBD primarily influences the CA3s input to the CA1, resulting in an increased occurrence of short ripples predominantly induced by cortical (mEC) activity and a corresponding decrease in long, intra-hippocampal sharp-wave-ripples. This study highlights the critical interplay between the CA3 and entorhinal cortex dynamics in shaping the characteristics of hippocampal ripples under the influence of CBD.

neuroscience↗

bioRxiv2024

Optimising crown-of-thorns starfish control effort on the Great Barrier Reef

Outbreaks of crown-of-thorns starfish Acanthaster planci (COTS), a disruptive coral-eating predator, are responsible for almost half of total coral cover loss on Australias Great Barrier Reef. As the pressures of climate change continue to intensify the frequency and severity of disturbance events such as cyclones and coral bleaching, efficiently managing COTS outbreaks is essential for reef protection. We aim to understand how the spatial distribution and intensity of crown-of-thorns starfish control - specifically manual culling of COTS by human divers - can impact coral cover on the GBR. We construct a metapopulation model based on a predator-prey model with larval dispersal and removal of crown-of-thorns starfish to simulate and compare spatial control strategies. When outbreaks begin on reefs between Cairns and Cooktown, we found the best strategy is to target those reefs at the source of the COTS outbreak. Increasing the spatial spread of control results in a larger spatial area protected across the GBR, but a lower total coral cover on the GBR. Our findings suggest that carefully targeting future control by considering larval connectivity patterns and spatial control strategies could lead to more efficient crown-of-thorns management. With the increasing pressures of climate change, any efficiency gains in reef management will prove beneficial for the Great Barrier Reef.

ecology↗

bioRxiv2023

Uncertainty Quantification in Acoustic Impedance ofAtlantic Salmon Fish Scale using Scanning AcousticMicroscopy

Scanning Acoustic Microscopy (SAM) emerges as a versatile label-free imaging technology with broad applications in biomedical imaging, non-destructive testing, and material research. This article presents a framework for the estimation of stochastic impedance through SAM, with a particular focus on its application to the salmon fish scale. The framework leverages uncertain reflectance, marking its pioneering application to uncertainty quantification in the acoustic impedance of fish scales through acoustic responses. The study uses maximal overlap discrete wavelet transform, to decompose acoustic responses effectively and is further processed to predict the acoustic impedance. To establish the effectiveness of the proposed framework, well-known materials like a pair of target medium (polyvinylidene fluoride) and reference medium (polyimide) are employed for impedance characterization. Results demonstrate over 90%accuracy in PVDF impedance estimation, validating the framework. A stochastic impedance map, using Kriging with a Gaussian variogram, offers insights into the complex biomechanics of a fishs scale.

biophysics↗

bioRxiv2023

Mechano-chemical Insights in Diabetic Kidney Disease through 3D Pathotypic Model of Mesangium

Diabetic kidney disease (DKD) is often diagnosed only after irreversible damage, limiting early treatment. The kidney mesangium, a structure highly sensitive to mechanical forces, plays a key role in early fibrosis development, yet its response to early disease cues like stiffness and biochemical changes is poorly understood. This is due to limitations in current in vitro models, poor in vivo accessibility, and static biopsy samples. To address this, we developed a 3D in vitro model of the mesangial microenvironment using stiffness-tunable gelatin methacrylate (GelMA) hydrogels that mimic healthy and fibrotic kidney tissue. Exposing mesangial cells to glucose and TGF-{beta}1 led to altered cell shape, increased dry mass, and elevated expression of fibrotic markers (-SMA and collagen IV), especially under stiffer conditions, indicating a synergistic effect of biochemical and mechanical stress. These responses were integrated using Gaussian process regression to create a 3D "severity cube" that maps DKD progression across mechanical and chemical inputs. This system quantifies early mesangial transitions and reveals key fibrosis-related mechanisms. By combining organotypic modeling with interpretable inference, our platform offers a predictive tool for early disease stratification and a basis for studying subclinical fibrosis progression in DKD.

biophysics↗

bioRxiv2023

LysoTracker Deep Red exhibits photoconversion in multi-color structured illumination microscopy

In new chemical environments or for untested combinations of illumination, unexpected changes to the fluorescent labels photophysical properties, such as photoconversion, can occur. This letter reports on photoblueing of a common cellular probe, LysoTracker Deep Red, in multi-color super-resolution structured illumination microscopy. The dye was found to exhibit a blue shift of its fluorescence spectrum as a step on the photobleaching pathway during such imaging. The observed photoblueing (emission spectrum shifted to lower wavelengths) of this probe is an important finding as many cellular assays rely on the spectral separation of this and such fluorescent cellular markers. No spectral shift of LysoTracker Deep Red was observed for longterm imaging using diffraction limited microscopy requiring significantly lower light dose. We expect that the knowledge of occurrence of photoconversion during super-resolved imaging using this popular dye will help researchers design better imaging experiments and avoid potentially erroneous interpretations in multi-color microscopy.

biophysics↗

bioRxiv2023

Spatial mapping of acoustic impedance of shrimp scale using multiple overlap discrete wavelet transform (moDWT)

There are lots of challenges associated with conventional optical observation of biological tissues, where specimens are typically sliced and stained for better contrast. In contrast, Scanning Acoustic Microscopy (SAM) is a versatile label-free imaging technology widely applied in various domains, including biomedical imaging, non-destructive testing, and material research. It excels in offering precise visualization of both surface and subsurface structures, providing valuable insights through visual inspection and quantitative analysis. Acknowledging the SAM, this paper presents acoustic impedance microscopy of the shrimp scale in a novel manner. The proposed technique aims to image the local distribution of cross-sectional acoustic impedance in biological tissue, which is a parameter closely related to sound speed and potentially valuable for tissue characterization. The study leverages advanced signal processing techniques, maximal overlap discrete wavelet transform (moDWT), to decompose acoustic responses effectively. The moDWT, with its ability to handle signals of various lengths without constraints, is highlighted as a promising approach. To determine shrimp scale impedance, we first establish the accuracy of the proposed algorithm using PVDF as the target and polyimide as reference material. The results indicate an algorithm accuracy exceeding 90%. An impedance map is generated through Gaussian process regression (GPR), which predicts the impedance over the complete domain, addressing spatial variations in biological specimens. The resulting acoustic impedance maps provide in-depth insights into the functional framework and advance our understanding of shrimp biomechanics.

biophysics↗

bioRxiv2023

Super-resolution histology of paraffin-embedded samples via photonic chip-based microscopy

Fluorescence-based super-resolution optical microscopy (SRM) techniques allow the visualization of biological structures beyond the diffraction limit of conventional microscopes. Despite its successful adoption in cell biology, the integration of SRM into the field of histology has been deferred due to several obstacles. These include limited imaging throughput, high cost, and the need for complex sample preparation. Additionally, the refractive index heterogeneity and high labeling density of commonly available formalin-fixed paraffin-embedded (FFPE) tissue samples pose major challenges to applying existing super-resolution microscopy methods. Here, we demonstrate that photonic chip-based microscopy alleviates several of these challenges and opens avenues for super-resolution imaging of FFPE tissue sections. By illuminating samples through a high refractive-index waveguide material, the photonic chip-based platform enables ultra-thin optical sectioning via evanescent field excitation, which reduces signal scattering and enhances both the signal-to-noise ratio and the contrast. Furthermore, the photonic chip provides decoupled illumination and collection light paths, allowing for total internal reflection fluorescence (TIRF) imaging over large and scalable fields of view. By exploiting the spatiotemporal signal emission via MUSICAL, a fluorescence fluctuation-based super-resolution microscopy (FF-SRM) algorithm, we demonstrate the versatility of this novel microscopy method in achieving superior contrast super-resolution images of diverse FFPE tissue sections derived from human colon, prostate, and placenta. The photonic chip is compatible with routine histological workflows and allows multimodal analysis such as correlative light-electron microscopy (CLEM), offering a promising tool for the adoption of super-resolution imaging of FFPE sections in both research and clinical settings.

pathology↗

bioRxiv2023

CBD lengthens sleep, shortens ripples and leads to intact simple but worse cumulative memory

Cannabidiol (CBD) is on the rise as over-the-counter medication to treat sleep disturbances, anxiety, pain and epilepsy due to its action on the excitatory/inhibitory balance in the brain. However, it remains unclear if CBD also leads to adverse effects via changes of sleep macro- and microarchitecture. To investigate the effect of CBD on sleep and sleep-related memory consolidation, we performed two experiments using the Object Space Task testing both simple and cumulative memory in rats. We show that oral CBD administration extended the sleep period but changed the properties of NonREM sleep oscillations (delta, spindle, ripples). Specifically, CBD also led to less long (>100ms) ripples and consequently worse cumulative memory consolidation. In contrast, simple memories were not affected. In sum, we can confirm the beneficial effect of CBD on sleep, however, this comes with changes in NonREM oscillations that negatively impact memory consolidation.

neuroscience↗

bioRxiv2022

The complexity of keratocyte migration in salmon explant cultures: initial results and future prospects

Intact skin is of uttermost importance for fish welfare. The fish skin provides an environmental barrier and protects against invading pathogens. However, both pathogens and physical insults cause skin wounds that are of major concern in modern fish farming. The behavior and interactions between keratocyte cells and sheets of cells are not well understood. The collective migration of keratocytes (skin epithelial cells) is of central importance for wound healing in fish. In this study, we aimed to elucidate the complex wound healing process in fish skin by studying in vitro cultures of these highly motile cells. Using explant cultures from farmed Atlantic salmon (Salmo salar) and differential interference contrast microscopy (DIC), we have captured the dynamics of sheets of cells from harvested fish scales and of individual cells interacting in the cell sheet vicinity. In addition to direct contact, the cells were observed to interact through long membrane tubes, turn, rotate, merge, and/or detach. Additionally, stationary cells and cells moving on top of the cell sheets were observed. Cell sheets approaching one another from different scales did not merge but dispersed.

cell biology↗

bioRxiv2022

Detailed investigation on the role of lipid metabolizing enzymes in the pathogenesis of retinopathy of prematurity among preterm infants.

PurposeExtremely preterm infants are at risk of developing retinopathy of prematurity (ROP), characterized by an initial insufficient vascular network development in the retina (due to hyperoxia) that progress to neovascularization and neuroinflammation (hypoxic phase) ultimately leading to partial or total vision loss. Lipid metabolism has been shown to be a significant pathway that is involved in the regulation of angiogenesis, inflammation, and apoptosis in oxygen induced retinopathy mouse model, however, it is not explored in human ROP patients. The present study aimed to explore the association of lipid metabolizing, angiogenic and apoptotic genes with altered lipid metabolites in the ROP patients with different severity. MethodsThe blood, vitreous humor (VH), and fibrovascular membrane (FVM) samples were collected from premature infants diagnosed with ROP and controls. Gene expression of lipid metabolizing enzymes, angiogenesis, and apoptotic genes were performed using semi-quantitative PCR in blood. Lipid metabolites were identified and quantified by LC-MS in VH and were correlated with gene expression. The expression of key lipid metabolizing enzymes in severe stages of ROP was assessed by measuring their expression in FVM by immunohistochemistry. ResultsGenes coding for the lipid metabolizing enzymes such as CYP1B1, CYP2C8, COX2, and ALOX15 were upregulated while EPHX2 responsible for the conversion of epoxide fatty acids into diol fatty acids was significantly downregulated in ROP cases. The increase in the metabolic intermediates generated from the lipid metabolism pathway further confirmed the role of these enzymes in ROP. except for EPHX2 which did not show any change in its activity. The glial cells in the FVM of ROP infants too showed a lack of EPHX2 expression. A significantly higher expression of genes involved in angiogenesis (VEGF165/189, NOTCH1, and APH1B) and apoptosis (CASP3/8) correlated with altered activity of lipid metabolizing enzymes (based on metabolites levels) among ROP cases. ConclusionsLipid metabolism may play a significant role in ROP development and progression. EPHX2 activity is a key step in the metabolic pathway of arachidonic acid that mediates and regulates inflammation and vascular pathology in preterm infants.

genomics↗