Biology subjects

Sarkar, A.

Publications and source records attributed to Sarkar, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Inexpensive High-Throughput Multiplexed Cytokine Detection for Tuberculosis Diagnostics Using Amplified Enzymatic Metallization

Lack of accurate yet inexpensive diagnostics remains a critical bottleneck in the control and elimination of tuberculosis (TB). Interferon-gamma release assay (IGRA), which involve measurement of the release of the cytokine, interferon-gamma (IFN-{gamma}), in blood samples stimulated with Mycobacterium tuberculosis antigens, is used to detect latent TB infection (LTBI). Use of IGRA in resource-poor settings, in which TB is endemic, is however hindered by the need for specialized equipment for sensitive detection of low amounts of cytokine released. Additionally, recent research has shown the advantage of multiplexed detection of other non-IFN-{gamma} cytokines in improving diagnostic accuracy. However, this requires even more expensive instrumentation and there are no inexpensive or point-of-care compatible multiplexed cytokine detection tools available yet. Here we develop and demonstrate a low-cost, high-throughput, multiplexed cytokine detection platform based on amplified enzymatic silver metallization on a plastic substrate. The assay is performed in microwells formed on a commonly available plastic petri dish and the dry readout of the deposited silver is obtained using a cellphone camera, thus significantly reducing overall cost and complexity of multiplexed cytokine detection. We demonstrate the ability to measure clinically relevant sub-picomolar levels of multiple cytokines, including IFN-{gamma}, interleukin-2 (IL-2), and tumor necrosis factor alpha (TNF-) from a small volume (<5{micro}L) of the same blood sample used in an IGRA. Furthermore, we demonstrate the use of this assay to distinguish IGRA+ and IGRA-participant samples from a TB endemic setting.

bioengineering↗

bioRxiv2026

Pannexin 2 restrains ER stress-induced Ca2+ dysregulation and inflammatory cardiomyocyte death

BackgroundEndoplasmic reticulum (ER) stress and ER-mitochondria Ca2+ dysregulation contribute to cardiomyocyte injury, yet endogenous regulators at ER-mitochondria interfaces that restrain this cascade remain poorly defined. Pannexin 2 (Panx2), the most structurally divergent pannexin isoform, has been implicated in stress response, but its cardiac localization and function are unclear. MethodsPanx2 localization and function were assessed in human AC16 cardiomyocytes using high-resolution confocal imaging and complementary loss- and gain-of-function approaches during thapsigargin-induced ER stress, with validation in adult mouse ventricular cardiomyocytes. ResultsPanx2 localizes predominantly to the ER and mitochondria-associated membranes, rather than the plasma membrane. Panx2 knockdown reduced ER Ca2+ stores and increased basal cytosolic and mitochondrial Ca2+. During ER stress, Panx2 deficiency markedly amplified Ca2+ dysregulation, mitochondrial dysfunction, unfolded protein response activation, and cytotoxicity, with PERK-dominant signaling and increased IRE1a activation. Notably, PERK inhibition preferentially rescued the Panx2-deficient phenotype, providing the greatest improvement in viability and reduction in cytotoxicity. Panx2 deficiency also enhanced inflammasome/ pyroptotic signaling via the NLRP3-caspase-1-gasdermin D axis. Conversely, Panx2 overexpression suppressed PERK activation and attenuated ER stress-induced injury. Panx2 ablation similarly sensitizes adult ventricular cardiomyocytes to ER stress. ConclusionsPanx2 functions as an organelle-associated checkpoint at ER-mitochondria interfaces that stabilizes Ca2+ homeostasis and limits PERK-dominant ER stress signaling and inflammatory cell death programs in cardiomyocytes, providing a mechanistic framework for cardiomyocyte loss in cardiac disease. Research PerspectiveO_ST_ABS1. What New Question Does This Study Raise?C_ST_ABSDoes Panx2 serve as an endogenous "stress threshold" determinant in cardiomyocytes in vivo, governing when ER stress transitions from adaptive signaling to PERK-driven mitochondrial failure and inflammasome-associated inflammatory cell death during cardiac injury (e.g., ischemia-reperfusion, pressure overload, or cardiometabolic stress)? 2. What Question Should Be Addressed Next?In clinically relevant models of heart disease (ischemia-reperfusion), test whether cardiomyocyte-specific Panx2 loss or augmentation alters infarct size, arrhythmia burden, ventricular remodeling, and functional recovery, and determine whether targeting the Panx2-PERK axis (e.g., selective PERK modulation in the acute reperfusion window or Panx2-directed strategies) reduces cardiomyocyte loss without impairing adaptive stress signaling needed for repair.

cell biology↗

bioRxiv2025

Guiding treatment response by spatiotemporal control of α-particle deposition in solid tumors: the case for 'affinity cocktails' of antibody-radioconjugates

Antibody-radioconjugates are leading the investigational targeted alpha-particle (-particle) therapies for the treatment of solid tumors that do not respond to approved therapies. Yet, there is still treatment failure in the clinic largely attributed to the heterogenous patterns of tumor irradiation by -particles. Although -particles are essentially impervious to resistance, attributed to the complex double-strand DNA breaks they cause while traversing cells, cells not being directly hit by -particles will likely not be killed. The diffusion-limited poor tumor penetration of high-affinity (strongly-binding) antibody-radioconjugates combined with -particles short-range in tissue (only 40-80m), let tumor regions far from vasculature inadequately irradiated, therefore, possibly escaping treatment. METHODSTo improve penetration of delivered activity within tumors, we engineered separate actinium-225 antibody-radioconjugates of variable affinities ( affinity cocktails) targeting the same marker on cancer cells, that were chosen based on their preferential irradiation of complementary regions of the same tumors. The cocktails comprise: (a) high-affinity antibody-radioconjugates (as the ones on clinical trials), which mostly deliver their cargo in tumor cells close to the vasculature, where the low(er)-affinity antibody-radioconjugates fail to deliver effective doses, due to their fast clearance; and (b) low(er)-affinity antibody-radioconjugates, that penetrate the deeper parts of tumors farther from the vasculature, where the high-affinity antibodies fail to reach. The efficacy of affinity cocktails was assessed in spheroids, that were employed as surrogates of tumor avascular regions, and on mice with subcutaneous xenografts of different cancer origin, expression levels and/or type of the targeted receptor: HER2 highly-expressing BT-474 breast cancer cells, HER2 moderately-expressing HEPG2 hepatoma cells, and/or HER1 low-expressing BxPC-3 pancreatic cancer cells. RESULTSAlthough the high-affinity antibody-radioconjugates were most lethal against cancer cells in monolayers, affinity cocktails were most effective in inhibiting spheroid growth, due to better collective spreading of the antibody-conjugates within the spheroids volume. On all mouse models, and for the same total injected activity, affinity cocktails resulted in the best tumor growth inhibition, even at lower tumor absorbed doses, compared to the high-affinity antibody-radioconjugates alone. CONCLUSIONSThis proof-of-concept study in -particle antibody-delivery to solid tumors demonstrates that separating the two key processes of diffusion and reaction/binding improves treatment efficacy. This generalizable approach may augment antibody-radioconjugates already in clinical trials.

bioengineering↗

bioRxiv2025

OpEnHiMR: Optimization based Ensemble Model for Prediction of Histone Modification in Rice

Histone modifications are central to gene regulation, yet their systematic identification in plants remains limited due to the complexity of epigenomic landscapes. We present OpEnHiMR, an optimization-based ensemble learning framework for multiclass prediction of three key histone modifications, H3K4me3, H3K27me3, and H3K9ac, in rice. The framework integrates Support Vector Machines, Random Forest, and Gradient Boosting models, optimized via Ant Colony Optimization to maximize performance. Biologically meaningful features, including mononucleotide binary encoding, nucleotide chemical properties, GC content, and k-mer frequencies, were used for training after rigorous data curation and redundancy removal. OpEnHiMR achieved a classification accuracy of 77.54%, outperforming individual models and ensuring improved recall, specificity, and Matthews correlation coefficient. Model interpretability was enhanced using SHAP analysis, which highlighted critical sequence features influencing prediction outcomes. To promote community-wide adoption, a user-friendly webserver (https://dipro-sinha.shinyapps.io/OpEnHiMR/) and R package (https://cran.r-project.org/web/packages/OpEnHiMR/index.html) were developed. OpEnHiMR thus provides a scalable, accurate, and interpretable tool for histone modification prediction in plants, advancing epigenomics research and supporting data-driven crop improvement strategies.

bioinformatics↗

bioRxiv2025

Electrically Contrasting Periodic Polymer Interfaces Guide Neuronal Networks

The nervous system constitutes a highly ordered, integrated network of cells. Understanding this neuroanatomical architecture in vitro is fundamental to elucidating the cellular computations underlying functional network formation. Neuronal connectivity orchestrated through axonal pathfinding, is an interplay of biochemical signals and electromechanical properties of the growth substrate. This study focusses on how neuronal morphology and networking are affected by the periodic, micrometer-scale patterned stripes of two electrically contrasting polymers - poly(vinylidenefluoride-trifluoroethylene) (PVDF-TrFE) and poly(3,4-ethylenedioxythiophene) - poly(styrene sulfonate) (PEDOT:PSS). This periodic confinement provides a length-scale driven cue which unfolds as a self-organized, frequency-modulated spatial phenomenon. Primary cortical cultures on these patterned substrates reveal significant differences with more elaborate network formation on PVDF-TrFE stripe. The features observed at the stripe boundaries, along with the dependence on stripe width, suggest that the neurons exhibit a preference to remain confined within the PVDF-TrFE region, with growth cones deflecting away from the PEDOT:PSS regions. These observations show a promising route for development of a functional template capable of directing axonal growth, synapse formation and neural rewiring in early models of connectivity disorders in vivo.

neuroscience↗

bioRxiv2025

Microparticle-Enabled Single Cell Multiparameter Electronic Immunophenotyping for Selective Electroporation

Electroporation (EP) is one of the leading non-viral intracellular delivery methods used in various applications across research and cell therapy development and manufacturing. Currently widely used bulk EP methods, while they offer scalability, cost efficiency and simplicity, cannot be used for targeted or selective delivery to a defined subset of a input cell population. Here, we present a Microparticle-Enabled Selectively Permeabilizing Impedance Cytometer (ME-SPICy), a microfluidic single-cell EP platform that enables targeted EP of selected cell subpopulations based on their surface markers. Antibody conjugated microparticles (MPs) are used to label selected cell subpopulations within a larger heterogenous sample. Using multifrequency impedance detection, ME-SPICy discriminates, in real-time, non-labeled and labeled cells within the mixed sample as they flow through a 3D printed biconical micro-aperture. This allows for the system to analyze if a cell is a target cell and selectively apply a low voltage (<16 V) for targeted single-cell EP. Simulations and experimental validation demonstrate that MP binding substantially alters cell impedance and phase signature, enabling accurate label-based discrimination. We demonstrated selective EP first using Jurkat cells by targeting either the labeled or non-labeled populations. Then we demonstrated targeted delivery to primary human lymphocytes within peripheral blood mononuclear cells. ME-SPICy achieved high precision, with 98% purity and >5 fold enrichment of lymphocytes in the electroporated cell population. This approach expands the capabilities of EP, offering a promising solution to decrease manufacturing complexity in both research and clinical cell engineering workflows

bioengineering↗

bioRxiv2025

A dosage-sensitive ALLO-1 network coordinates mitochondrial quality control to enable functional recovery of structurally compromised muscle

Functional recovery of muscle can precede structural repair, yet the mechanisms enabling this dissociation remain elusive. In C. elegans, unc-45(m94) mutants recover motility after heat-induced paralysis despite persisting sarcomeric disorganisation, offering a model to dissect non-contractile drivers of early recovery. Quantitative proteomics identified ALLO-1, a selective autophagy adaptor previously characterised for mediating paternal mitochondrial elimination during embryogenesis, as strongly upregulated during the recovery phase. Proteomic and genetic analyses further revealed a network of ALLO-1-associated factors, including the kinase IKKE-1 (a known ALLO-1 activator), SIP-1 (a small heat shock protein), DIM-1 (a sarcomeric tether), and CAR-1 (an ER-associated RNA-binding protein). In adult muscle, ALLO-1 restrains mitophagy to preserve mitochondrial integrity. Its depletion triggers mitochondrial fragmentation and excessive turnover, especially in the sensitised unc-45(m94) background. Overexpression suppresses mitophagy but reduces oxidative capacity, revealing a dosage-sensitive checkpoint. While IKKE-1 and SIP-1 promote mitochondrial stability, DIM-1 and CAR-1 facilitate turnover when ALLO-1 levels fall below threshold. Together, this regulatory module integrates proteostatic, translational, and mechanical signals to safeguard mitochondrial homeostasis and enable recovery when contractile architecture is compromised.

cell biology↗

bioRxiv2025

Platelet factor 4 modulates endothelial cell antimicrobial activity to enhance bacterial clearance and improve sepsis outcomes

Sepsis is a life-threatening condition characterized by dysregulated host responses to infection. Here, we identify platelet factor 4 (PF4) as a key mediator of vascular antimicrobial defense. In vitro, PF4 enhanced endothelial cell internalization of Escherichia coli via interactions with the PF4 receptor CXCR3 and the endothelial glycocalyx, directing bacteria to clathrin-mediated endocytosis and lysosomal degradation. In vivo, PF4 administration improved survival and reduced sepsis severity, bacterial burden, inflammation, and thrombosis in wild-type (WT) and PF4 knockout (PF4-/-) mice challenged with systemic polymicrobial infection. Using intravital microscopy, we observed that infused bacteria were rapidly sequestered in the pulmonary microvasculature. However, PF4-/- mice exhibited impaired bacterial clearance and increased microvascular platelet adhesion and aggregation. In the liver, following Kupffer cell depletion, PF4-/- mice had increased sinusoidal platelet accumulation, larger bacterial aggregates, and elevated hepatic bacterial burden compared to WT controls. Collectively, these findings reveal that PF4 promotes bacterial clearance and restrains immunothrombosis during sepsis in part via endothelial cell uptake and destruction of microbes. By enhancing endothelial antimicrobial function, PF4 represents a significant yet previously underrecognized host defense mechanism that limits bacterial spread and alleviates vascular injury during infection. KEY POINTSO_LIIn vitro, PF4 accelerates bacterial clearance by enhancing endothelial uptake of bacteria and promoting their trafficking to the lysosome. C_LIO_LIIn murine sepsis, PF4 augments pathogen clearance to reduce infection severity, limit organ injury, and improve survival. C_LI

cell biology↗

bioRxiv2025

Actinium-225 dendrimer-radioconjugates combined with low-dose standard-of-care chemotherapy: site-independent treatment of triple negative breast cancer metastases

PURPOSEMetastatic triple negative breast cancer (mTNBC) is incurable largely due to the development of drug resistance, the lack of selective cell targeting, and/or limitations in tumor drug delivery that vary depending on the different (metastatic) tumor locations. METHODSThe potential of a single type of systemic, targeted alpha-particle therapy (TAT) was investigated for addressing the above challenges of TNBC tumors implanted at different anatomic sites in mice. Actinium-225 dendrimer-radioconjugates alone, and/or after pretreatment with low-dose standard-of-care cisplatin, were assessed in vitro and on immune-competent 4T1-Balb/c mouse models with tumors implanted intracranially, orthotopically or subcutaneously. RESULTSIn vitro, TATs efficacy was enhanced by cisplatin. In vivo, treatment was initiated well after tumors had grown (Vto = 39 {+/-} 14 mm3 in the intracranial model, and Vto=100mm3 in the orthotopic and subcutaneous models). Across all tumor implantation sites, a unified correlation was observed between animal mean survival and the dendrimer-delivered tumor absorbed doses, which were selectively increased by low-dose cisplatin pretreatment. Importantly, in all animal models, the mean survival following systemic treatment with both modalities was significantly longer vs. each modality alone and/or vs. no treatment, at injected doses that did not cause long-term (10-month) toxicities in tumor-free mice. CONCLUSIONSystemically-injected dendrimer-delivered TAT, combined with low-dose cisplatin pretreatment, can safely extend survival independent of mTNBC tumors anatomic site, potentially presenting a single type of therapy to simultaneously treat multi-site mTNBC.

bioengineering↗

bioRxiv2025

Glutamic Acid at position 168 is a constitutive activator of Tank Binding Kinase 1 catalytic function

TANK binding kinase 1 (TBK1) is serine/threonine protein kinase member of the inhibitor of nuclear factor-{kappa}B kinase family, with links to the etiology of familial as well as idiopathic Amyotrophic Lateral Sclerosis. It contributes to several regulatory cellular processes such as autophagy, inflammation and apoptosis. Reduction or loss of TBK1 kinase activity is associated with increased risk of ALS, and so understanding the molecular basis of this activity is an important research priority. In this current study, the role of the E168 residue, located adjacent to the active site of TBK1, has been assessed using a combination of artificial and naturally occurring variants found at this codon - evaluated using multiple readouts for TBK1 kinase activity. The results suggest that the negative charge resulting from the presence of a glutamic acid at this codon is a constitutive activator of TBK1 activity.

biochemistry↗

bioRxiv2025

Reprogrammed E. coli for secretion of thermophilic cellulase cocktail for seawater-compatible lignocellulosic bioprocessing

The development of efficient cellulase systems is crucial for sustainable lignocellulosic biorefining. In this study, we engineered Escherichia coli to co-express and secrete a thermophilic cellulase cocktail consisting of a Bacillus licheniformis processive endoglucanase (H1AD14), a Chaetomium thermophilum cellobiohydrolase (G0SAE6), and a glucose-tolerant engineered {beta}-glucosidase B8CYA8tm (V169C/E173L/I246A B8CYA8) from Halothermothrix orenii. Fusion with the AnsB secretion tag enabled extracellular yields of 0.2-0.4 g/L for each enzyme, bypassing costly purification while retaining activity. The secretion was confirmed via immunoblotting using anti-His antibody, and catalytic activity was validated through enzymatic assays. The absence of E. coli native periplasmic maltose-binding protein (detected with anti-MBP antibody) in the extracellular medium ruled out cell lysis, confirming protein secretion. Using the Golden Gate assembly, we constructed and systematically evaluated synergistic enzyme combinations for hydrolytic performance. By optimizing secretion conditions, including media, inducer concentration, and incubation temperature, the total yield of secreted enzyme cocktail increased from 0.31 g/L to 0.74 g/L. The secreted cocktail effectively hydrolysed diverse lignocellulosic substrates and exhibited 100 % activity in seawater, demonstrating potential for freshwater-independent biorefining. The work addresses key economic and environmental challenges in biomass conversion by integrating secretion engineering, thermostability, and seawater tolerance into a single scalable system.

bioengineering↗

bioRxiv2025

Label-Free Targeted High Efficiency Electroporation with Single-Cell Feedback Control Using Focused Microscale Electric Fields

Efficient, safe, and cell-selective intracellular delivery remains a bottleneck for scalable and cost-effective manufacturing of cell therapies. Here, we introduce Selective Permeabilization using Impedance Cytometry (SPICy) that couples multifrequency single-cell impedance cytometry with real-time, feedback-controlled, low-voltage single-cell electroporation. Electric field focusing in a 3-D printed biconical micro-aperture confines both sensing and electroporation to a microscale zone, enabling continuous-flow operation and the use of low voltages (<15 V) for electroporation. Impedance spectra are captured for each single cell and machine-learning based analysis enabled accurately distinguishing cells in a label-free manner. Selectively triggered low-voltage electroporation achieved simultaneous high delivery efficiency (>80 %) and high (>90 %) cell viability. Delivery of a range of different cargo sizes (4-500 kDa), GFP mRNA expression, CRISPR-Cas9 based knock-out and delivery to a variety of different cell lines, primary human T cells and peripheral blood mononuclear cells (PBMCs) was also demonstrated. Using heterogenous or mixed samples, selective delivery to both cell lines, and primary immune cell subpopulations, from PBMCs, was demonstrated. SPICy thus provides a label-free, continuous flow, targeted non-viral platform for precision cell engineering.

bioengineering↗

bioRxiv2025

Branching, crosslinking and decentralization of microtubules accelerates intracellular assembly

Before cell division, mitotic spindle is assembled from chromosomes and centrosomes. After the cell division, Golgi organelles assemble from multiple vesicles scattered across daughter cells. These are but two examples of intracellular assembly of vesicles, organelles and chromosomes made possible by dynamic microtubules. The most prominent microtubule networks are centrosome-focused asters that search for the vesicles and chromosomes, but there are also microtubules originating from the vesicles and chromosomes, raising the question whether a coordination between multiple microtubule networks optimizes the assembly process. This study uses a computational model to examine how microtubule dynamics influence the assembly of organelles from vesicles. The model includes two microtubule populations: microtubules anchored to the vesicles, which drive local clustering, and central microtubules anchored to the centrosome that aggregate the vesicles globally. Simulations show that a microtubule decentralization - balanced contribution from both microtubule populations -- accelerates the assembly of tens of vesicles, but that assigning all microtubules to hundreds of vesicles optimizes the assembly. Directionally biased microtubule growth, particularly when avoiding spontaneous catastrophe events, further accelerates the assembly. Additionally, microtubule branching, when occurring at optimal angles and spacings, enhances the assemblys efficiency. Lastly, rapid crosslinking of overlapping central and local microtubules can drastically accelerate the assembly. Applying this model to the spindle assembly in early mitosis reveals similar insights. The model suggests that the observed multiple microtubule networks optimize the intracellular assembly processes when molecular resources are limited. SIGNIFICANCEAssembly of intracellular structures is a time-sensitive process driven by multiple dynamic microtubule networks. For example, vesicles must be aggregated by microtubules to form Golgi apparatus after cell division, while mitotic spindle assembly requires bringing chromosomes closer together by microtubules growing from spindle poles and chromosomes. Delays in these processes can lead to genomic instability and disease. Using modeling, we show how microtubules originating from centrosomes, vesicles, or chromosomes can be optimally distributed to minimize the assembly time. The model reveals roles of microtubule decentralization, branching and crosslinking in accelerating assembly. The model suggests that the intracellular assembly can be optimized by diversifying microtubule networks and enhancing their interactions.

biophysics↗

bioRxiv2025

Tumor-Educated-Platelets interact with Breast Cancer-Stem-Cells via P-selectin- PSGL1 and ensure stemness and metastasis through WNT-β-Catenin-VEGF-VEGFR2 intra-cellular signaling: Therapeutic modulation by aspirin

BackgroundProtagonistic role of platelets promote capillary infiltration of tumors for distant metastasis along with immunosurveillance. Despite existing reports highlighting role of platelets in tumorigenesis, its impact on breast cancer stem cells (BCSCs) remain underexplored. Our first ever report on murine and human system, accentuate that, tumor educated platelets (TEPs) of luminal A and TNBC subtypes are distinct from healthy counterparts, collaborating with BCSCs to generate sub-variants that elevate tumor aggressiveness. MethodsImpact of TEPs on BCSCs was evaluated from primary breast tumor and blood samples of luminal A/TNBC patients along with EC/4T1 murine breast tumor models and MCF-7/MDA-MB-231 cell lines. For downstream assays, TEPs were co-cultured with breast tumor samples or cell lines, followed by magnetic sorting of lin-CD44+CD24- BCSCs. TEP induced alterations of BCSCs were evaluated from 3D tumorsphere, colony formation, transwell migration, scratch-wound healing, matrigel invasion, in-vitro tube formation assays. Fluorescence-confocal microscopy, RT-PCR, flow-cytometry, western-blotting was utilized to decipher the role of genes and protein involved in stemness, metastasis along with the transcription factors in the downstream signaling cascade, followed by verifications by RNAi. ResultsTEPs have elevated expression of P-selectin and interacts with BCSCs via P-selectin and PSGL1 on BCSCs surface. Treatment with aspirin had restorative impact on P-selectin level, converting TEPs from active to resting platelet (RP) state. Under TEPs influence, BCSCs were tumorigenic, clonogenic, multidrug resistant, invasive with numerous invadopodia and remained skewed towards mesenchymal phenotype. Administration of RP reduced TEP associated BCSC virulence both in-vivo and in-vitro. P-selectin-PSGL1 interaction results in binding of WNT to FRIZZLED followed by stabilization and nuclear translocation of {beta}-Catenin. Nuclear {beta}-Catenin promotes stemness-EMT (Epithelial to mesenchymal transition)- metastasis, along with stimulation of autocrine VEGF-VEGFR2 cascade. Inhibition of WNT and VEGFR2 by RNAi confirmed the critical role of this axis in regulating TEPs influence on BCSCs. ConclusionThese insights into TEPs-BCSC interplay, acknowledges TEPs, as-well-as unveils novel receptor-ligand signaling cascade between TEPs and BCSCs, that could be a beneficial therapeutic strategy to target cancer metastasis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/657784v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@11db5d0org.highwire.dtl.DTLVardef@18b7270org.highwire.dtl.DTLVardef@64c2borg.highwire.dtl.DTLVardef@172d68f_HPS_FORMAT_FIGEXP M_FIG C_FIG Cellular interaction between TEPs P-selectin and BCSCs PSGL1 to regulate stemness, EMT, metastasis and angiogenesis via WNT-{beta}-Catenin-VEGF-VEGFR2 cascade: Modulation by pharmacological inhibitor and RNAi.

cancer biology↗

bioRxiv2025

Sewing the future of cotton: a multi-omics study combining nanomechanics, transcriptomics, and phenotypic traits

Cellulose microfibrils that are essential for mechanical strength and overall quality of cotton fibers. This study quantifies and compares the nanoscale structural and mechanical properties of cellulose microfibrils such as microfibril dimensions, crossover count and angles, roughness, and Youngs modulus for two popular cotton species: Gossypium hirsutum (Gh) and Gossypium barbadense (Gb) fibers across four growth stages (8, 12, 18, and 22 days post-anthesis) using atomic force microscopy (AFM). Our results revealed for the first time that Gb fibers exhibit a better alignment, finer dimensions, and higher stiffness compared to Gh fibers at nanoscale, resulting in smoother fiber surfaces, and improved quality at macroscale. We are also the first to develop machine-learning models to predict macroscale phenotypic traits specifically boll length and cellulose content using nanoscale features alone and in combination with multi-omics modalities, substantially enhancing the predictive accuracy and highlighting opportunities for robust cross-species modeling of cotton fiber traits.

biophysics↗

bioRxiv2025

Understanding the impact of blast-induced traumatic brain injury on brain cellular differentiation and mechanics at nanoscale

Blast-induced traumatic brain injury (bTBI) causes significant disruptions in cellular and subcellular structures within the central nervous system (CNS) following the application of an extremely large force. The corresponding changes in biomechanical properties and cellular functionalities of neuronal and glial cells (i.e. astrocytes, oligodendrocytes) due to bTBI remain largely unexplored. In this work, controlled shockwave exposure was applied to adult hippocampal progenitor cells (AHPCs) and resultant alterations in nanomechanical, viscoelastic properties, cellular survival, proliferation, and differentiation were examined. bTBI was induced using a custom-designed compression-driven shock tube, and cellular responses to single (overpressure magnitude: 14.5 psi or 100 kPa) and double shockwave exposures (overpressure magnitude: 29.0 psi or 200 kPa) applied in two different directions (from top-to-bottom and bottom-to-top) were analyzed using atomic force microscopy (AFM) and immunocytochemistry (ICC). We observed noticeable changes in cellular mechanics, especially when exposed to a double shockwave from bottom-to-top direction. These variations were characterized by a significant reduction in Youngs modulus, surface roughness, and viscosity. Shockwave exposure from bottom to top direction caused pronounced actin cytoskeletal disruptions compared to top-to-bottom direction. However, ICC results showed that cell viability remained high for both cases of shockwave exposures despite mechanical changes; although the population of oligo-dendrocytes and immature neurons displayed significant decreases after double shockwave exposure. These findings emphasize the interplay between cellular behavior, resilience of neuronal and glial cells, and cellular nanomechanics in bTBI aftermath, leading to the development of novel therapeutic approaches against bTBI.

biophysics↗

bioRxiv2025

Development of Bioisosteric Iboga-alkaloids as Antinociceptive and Anxiolytic Agents with Neuroprotective Effects

The clinical importance of iboga alkaloids lies in their efficacy in reversing drug addiction and modulating drug tolerance. However, due to safety concerns, their use is restricted to appropriate medical supervision. These alkaloids often cause severe hallucinogenic effects due to differential binding to various brain receptors and cardiotoxicity by blocking the human ether-a-go-go-related gene (hERG) potassium channel. To create safer analogs, our group previously synthesized various benzofuran-containing iboga analogs with good opioid binding selectivity and excellent antinociceptive property. However, the present manuscript disclosed a step-economical and cost-effective synthesis of modified ibogaine/ibogamine analogs (C1, C2, C3 & C4) with bio-isosteric replacement of the indole scaffold with a benzofuran moiety, and comparing their antinociceptive/anxiolytic activity with their natural counterparts. Among the synthesized iboga analogs, the Endo-iboga analogs (C2 & C4, epimers of C1 and C3, respectively) not only exhibited superior anti-inflammatory and oxidative stress-relieving activity, but also effectively improved restricted locomotor activity in a formalin-induced acute pain model in mice. These Endo-iboga analogs significantly elevated the levels of inhibitory neurotransmitters (GABA and dopamine) and brain-derived neurotrophic factor (BDNF) compared to their Exo-counterparts or previously published benzofuran-containing iboga analogs lacking the tetrahydroazepine ring. Amongst, C2 and C4, the latter exhibited superior cardiac safety profile in C2C12 cells (IC50 = 235 {micro}M) and showed no adverse effects on rat hearts during in vivo ECG tests, indicated by no significant QTc prolongation. Overall, the development of bioisosteric iboga analogs, particularly C4, demonstrated significant potential for acute pain management without notable cardiotoxicity, representing a breakthrough in pain therapy innovation.

physiology↗

bioRxiv2025

PI(3)P signaling regulates endosomal flux underlying developmental synaptic remodeling via Rab4

Rab4 GTPase, essential for endosomal sorting and trafficking, is implicated in synaptic atrophy and dementia. To uncover the underlying mechanism, we studied the correlation between Rab4 vesicle transport in axons and episodic remodeling of synapses in the central nervous system (CNS) of Drosophila larvae. We found that synapse-bound traffic and presynaptic enrichment of Rab4 vesicles increase during the programmed, transient contraction of synapses in the ventral neuropil region at a specific larval stage. This coincides with the episodic activation of insulin and Vps34-mediated signaling, which elevates phosphatidylinositol-3-phosphate levels on Rab4 vesicles. The presence of this phospholipid on Rab4-associated vesicles recruit a PX-domain-containing motor protein, Klp98A, accelerating synapse-directed traffic. This, in turn, increases presynaptic enrichment of Rab4 during the developmentally programmed synapse contraction phase. Our findings elucidate the molecular mechanism that regulates developmental synaptic plasticity in the CNS via insulin signaling and directed axonal transport of endosomes. Author summaryHealthy brain function relies on the growth and remodeling of synaptic connections between nerve cells. This process involves carefully orchestrated movements of proteins and membranes inside the neurites. For instance, endosome movement in the nerve cell extensions helps guide neuronal growth, recycle parts of the synapse, and alter signal transmissions between neurons. Rab GTPases, a group of small G-proteins, are crucial for these processes. Here, we aimed to understand what triggers these processes and how the supply chain within nerve cell extensions is connected to changes at the synapse. In fruit fly larvae, we observed that the movement of Rab4 vesicles in the nerve cell extensions is inversely related to gross synapse content. A further examination revealed that onset of insulin signaling accelerates the Rab4 vesicles towards synapse through a lipid kinase called Vps34, which makes a signaling lipid called phospatidylinnositol-3-phosphate. Higher levels this lipid molecule on Rab4 vesicles attract a motor protein, Klp98A, speeding up their movement during the synaptic contraction phase. Our findings reveal a new mechanism that regulates Rab4 vesicle transport and its impact on synapse stability. The study further suggests potential targets for controlling age-related dementia likely to be caused by excessive insulin signaling in neurons.

neuroscience↗