Biology subjects

Pradhan, S.

Publications and source records attributed to Pradhan, S..

At least 19 recordsLinked to original sources

bioRxiv2026

2C-RT Quantifies Genome-Wide DNA Replication Perturbationsand Redefines RIF1-CDC7 Regulation of Replication Timing

Replication timing (RT) coordinates DNA synthesis with genome organization and influences mutation rates, cancer evolution, and developmental plasticity. Current methods infer S-phase timing from DNA content, an assumption that obscures responses to replication perturbations and limits accurate comparisons of RT changes. Here, we develop 2C-RT, a multiplexed sequencing approach that uses DNA content-independent markers for robust RT profiling across S phase. Combining 2C-RT with imaging, we resolve distinct layers of human RT control and identify local and genome-wide responses to drugs and genetic perturbations. We find that RIF1 spatially restricts CDC7 activity and that its loss does not neutralize RT per se but advances replication across most RIF1-sensitive regions. A conserved MCM5 bob1 mutation lowers the origin-activation threshold and reveals a role for CDC7 in establishing local origin dominance. These findings support a revised model in which CDC7 primes early origins, CDK promotes permissive origin firing genome-wide, and RIF1 counteracts CDC7 in distinct chromatin states and peripheral nuclear domains.

cell biology↗

bioRxiv2026

Direct targeting of the WAVE-regulatory complex and the actin cytoskeleton by the Anaplasma phagocytophilum effector, AnkA

The obligate intracellular tick-borne pathogen Anaplasma phagocytophilum is unusual in its tropism for neutrophils, within which it survives and replicates. Central to the ability of this bacterium to colonize this hostile niche are secreted effector proteins. One such effector protein, AnkA, interacts with multiple host ligands in both the cytoplasm and the nucleus, yet how these interactions promote infection is largely unknown. We discovered that AnkA directly binds both the WAVE Regulatory Complex (WRC), a signal-integration hub that regulates the formation of branched actin networks underpinning diverse cell functions, and to monomeric and filamentous actin. We determined that AnkA uses two forms of molecular mimicry, first by binding to the Abi1 component of the WRC via a WRC-Recruiting Abi-binding Peptide (WRAP), and second by binding to actin via a WH2-like Actin Binding Motif (ABM). Via these interactions, AnkA can exert multi-factorial influence on the actin cytoskeleton and signaling pathways converging on this host structure. AnkA and the WRC co-localise during bacterial internalization and during the late stages of infection, suggesting a central role in both host-cell colonization and bacterial dissemination. Our work reveals AnkA as the first example of a bacterial effector that directly targets the WRC. The co-occurrence of WRAP- and ABM-like motifs in other bacterial effector proteins suggests that this mechanism of actin cytoskeleton subversion may represent a conserved strategy used by other obligate intracellular bacteria.

microbiology↗

bioRxiv2026

Target DNA-Mediated Plasmonic Coupling and Assembly Kinetics of Gold Nanorods for Label-Free Nucleic Acid Detection

DNA-programmed assembly of plasmonic nanostructures provides a powerful route to couple molecular recognition with optical signal generation. Here, we report the sequence-specific assembly of DNA-functionalized gold nanorods using a sesame allergen-derived DNA biomarker as a molecular bridge. Target-induced assembly produces concentration-dependent assembly growth, plasmon coupling, and distinct assembly kinetics that are readily monitored by absorption spectroscopy, enabling label-free detection of the target DNA in the nanomolar concentration range. The assembled nanorods further produce strong surface-enhanced Raman scattering (SERS) signals arising from plasmonic coupling within the assemblies, extending detection to the picomolar regime without the use of Raman reporters. Quantitative analysis reveals that both the extent and rate of assembly formation are governed by target DNA concentration. These results establish a direct relationship between molecular recognition, assembly growth, plasmonic coupling, and spectroscopic response, highlighting DNA-programmed gold nanorod assembly as a versatile platform for investigating hybridization-driven plasmonic self-assembly and nucleic acid detection. Table of Content O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/732610v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@e4fcb9org.highwire.dtl.DTLVardef@18c0d89org.highwire.dtl.DTLVardef@1ccb4bborg.highwire.dtl.DTLVardef@6d84ca_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2026

Modeling Reveals How Direct-Acting Antivirals Redirect HBV Capsid Assembly Pathways to Noninfectious Products

Hepatitis B virus (HBV) infections cause chronic liver disease, resulting in about one million deaths per year, and there is currently no cure. Recent work has shown that a class of small molecules called capsid assembly modulators (CAMs) is promising for treating HBV. CAMs bind to HBV capsid protein subunits and alter their assembly, leading to non-functional and malformed structures rather than functional, closed shells. However, the mechanisms by which CAMs alter capsid assembly pathways remain unclear. Here, we extend a recently-developed kinetic Monte Carlo (KMC) model for HBV capsid assembly to simulate how CAMs affect assembly. In the model, CAMs alter assembly by preferentially binding to interfaces between certain quasi-equivalent subunit conformations. Simulations of the model reproduce experimental assembly product distributions. By analyzing assembly trajectories, we clarify the roles of thermodynamics and kinetics in determining assembly products, identify assembly mechanisms, and predict the key intermediates that lead to either capsids or malformed structures. Our findings enhance our fundamental understanding of capsid assembly, help advance the development of CAMs as a treatment for HBV and, more broadly, inform efforts to direct self-assembly pathways toward specific products.

biophysics↗

bioRxiv2026

Mechanistic Insights into TMPyP4 Recognition of the HIV-1 LTR-III G-Quadruplex in Dilute and Protein Condensate Environments Reveal Hidden Dual Binding Modes

G-quadruplex (GQ) structures within the HIV-1 long terminal repeat (LTR) regulate viral transcription and represent promising antiviral targets; however, detailed mechanistic understanding of their ligand recognition at the molecular level remains limited and has largely been investigated under dilute conditions despite the crowded and compartmentalized nature of intracellular environment. Here, we investigate the interaction of the cationic porphyrin TMPyP4 with the HIV-1 LTR-III GQ under dilute conditions and inside protein-rich phase-separated condensates that mimic intracellular biocondensates. Steady-state and time-resolved fluorescence measurements reveal a dual binding behavior that is not discernible from absorption spectroscopy. A high-affinity guanine-rich binding mode leads to efficient fluorescence quenching through electron transfer from ground-state guanine to excited TMPyP4, whereas a weaker non-guanine binding mode gives rise to enhanced and long-lived emission. Nucleotide-specific control experiments validate the origin of these distinct binding environments. Molecular docking and molecular dynamics simulations further support preferential binding of TMPyP4 at the terminal G-quartet together with a secondary binding mode near the quadruplex-duplex junction. Importantly, both TMPyP4 and LTR-III GQ preferentially partition into the condensates, where the hybrid GQ structure, dual binding behavior, and associated excited-state signatures remain preserved despite the crowded and viscous environment. Although a slight reduction in binding affinity is observed inside the condensates, the overall binding mechanism remains largely preserved due to compensatory effects arising from the condensate microenvironment. Overall, this work demonstrates that ligand recognition of viral GQ remains preserved within protein condensates and establishes fluorescence spectroscopy as a sensitive approach for resolving hidden binding heterogeneity in GQ-ligand interactions.

biophysics↗

bioRxiv2026

Altered chromatin accessibility and nucleosome positioning landscape upon HDAC and LSD1 inhibition in cancer cell

Epigenetic enzymes, writers, readers and erasers regulate chromatin landscapes and participate in tumor heterogeneity. While therapeutic targeting of these enzymes has shown clinical promise, the comparative efficacy of mono-versus dual-inhibitor strategies remain unclear. Here, we introduce a multi-modal platform that uses NicE-viewSeq and integrates automated deep learning based spatially resolved chromatin accessibility profiling with high-throughput sequencing following epigenetic inhibitor application. Accessible chromatin landscapes were altered along with nucleosome positioning following inhibition of either LSD1 or HDACs alone, or both together. Coordinated modulation of histone marks and the CoREST complex on chromatin was observed across inhibitory conditions. Transcription factor binding analysis identified three predominant families, ETS, RUNT, and bZIP with enhanced chromatin association upon treatments. Mechanistically, a CoREST-RUNX regulatory axis was uncovered wherein JunB, a member of bZIP family displaces CoREST-RUNX at differentially accessible regions, triggering apoptotic pathways. Therefore, JunB-mediated mechanism reveals a convergent therapeutic vulnerability, offering new avenues for optimizing different combinatorial epigenetic therapy in cancer.

genetics↗

bioRxiv2026

Explainable protein-protein binding affinity prediction via fine-tuning protein language models

Protein-protein interactions underpin virtually every aspect of cellular life, and the precise quantification of their binding affinity is fundamental to understanding immune recognition, disease mechanisms, and the rational design of therapeutic antibodies. Yet predicting binding affinity at scale remains an unsolved challenge: reliable experimental assays are low-throughput and expensive, while computational methods that depend on three-dimensional complex struc-tures cannot be applied to the vast majority of clinically relevant targets where structural data are absent. Here we present BALM-PPI, a framework that predicts protein-protein binding affinity from amino acid sequence alone. Both proteins are encoded by a protein language model trained on evolutionary sequence data and projected into a shared representational space, where their distance directly reflects binding strength. Fine-tuning this protein language model requires updating fewer than 1% of its parameters, and we show that this targeted adaptation steers the model toward interface-relevant sequence signals rather than spurious background correlations. On a curated benchmark of over 12,000 protein complexes, BALM-PPI matches or exceeds the accuracy of structure-based methods and retains predictive power for proteins with less than 30% sequence identity to the training set. Using only a subset of project-specific assay data, BALM-PPI outperforms a recent method trained on three times the data, suggesting that the model has already encoded the underlying interaction signals and requires only minimal supervision to specialise to a new target. BALM-PPI further provides residue-level attribution maps that pinpoint the amino acid positions driving each affinity prediction, consistently re-covering experimentally validated interaction hotspots across enzyme-inhibitor, signalling, and antibody-antigen systems without any structural input during training. This allows predictions to be cross-validated against structural and mutagenesis evidence, providing a mechanistic basis for candidate shortlisting ahead of experimental follow-up. BALM-PPI is freely accessible via an interactive web server.

bioinformatics↗

bioRxiv2026

Proteomic Insights into the Mechanism of Action of Maduramicin, a Novel Ionophore with Potent Antimalarial Activity

Malaria is a common infectious disease in tropical countries and poses serious health burden due to limited treatment choices. In recent years, many of the state of the art anti-malarials such as Artemisinin, Chloroquine and Primaquine have been rendered ineffective due to emergence of resistant parasites. This underscores the urgent need to develop new anti-malarials and elucidate their mechanism of action. Recently, we have demonstrated the potent anti-malarial properties of a known anti-coccidial ionophore, Maduramicin. In this study, we investigated the mechanisms of action of Maduramicin in P. falciparum by assessing its stage-specific activity and time-dependent effect on parasite development. The drug exhibited maximum anti-malarial activity against the schizont stage and was characterised as a slow-acting drug. To gain mechanistic insights, we employed iTRAQ based quantitative proteomics approach to analyse global proteome alterations in P. falciparum following Maduramicin treatment. Analysis of the differentially regulated proteins were carried out by using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway database. The data reflected significant perturbations in protein synthesis, energy metabolism, and other key metabolic pathways in response to Maduramicin treatment. Collectively, our results of the proteomics study were validated by quantitative RT-PCR analysis of 9 representative genes. Our findings provide the basis for understanding the lethal activity of Maduramicin on P.falciparum.

biochemistry↗

bioRxiv2026

A PIWI protein-dependent DNA N6-adenine methylation pathway in Oxytricha protects genomic sequences from deletion

The ciliate Oxytricha undergoes massive genome rearrangements during development to produce a functional nucleus from an encrypted zygotic genome. PIWI-interacting small RNAs protect DNA regions against deletion, but how that protective mark is established has been a mystery. Recently our lab discovered MTA1, a methyltransferase that catalyzes DNA N6-adenine (6mA) methylation. Both MTA1 and the Oxytricha Piwi protein, Otiwi1, are required for development, and Otiwi1 mutation eliminates 6mA signal. To examine the role of 6mA, we analyzed its genome-wide distribution across development in wild-type and MTA1 mutant backcrossed cells. We find specific and abundant enrichment on retained sequences, suggesting a protective role for this epigenetic mark. Furthermore, programmed retention of a DNA region that is normally deleted leads to accumulation of new 6mA marks on the ectopically retained DNA sequence. Together, these results suggest that piRNA-guided 6mA DNA methylation leads to protection of DNA sequences against deletion during nuclear differentiation. HighlightsO_LIDNA N6-methyladenine accumulates on retained DNA regions during Oxytricha development. C_LIO_LImta1 mutant backcrosses have disrupted DNA methylation and a developmental delay. C_LIO_LIDNA N6-adenine methylation during genome rearrangement requires the presence of Otiwi1. C_LIO_LIProgrammed retention of a germline-limited region leads to developmental methylation. C_LI

molecular biology↗

bioRxiv2025

Regioisomer-controlled red-shifted DNA probes for imaging of living tissues

Fluorescence imaging of chromatin DNA with high resolution and specificity is key to understanding cellular processes and enabling molecular diagnostics. However, choosing the best DNA probe for in vivo imaging is often a challenging task, as systematic studies investigating the biocompatibility of these molecules are lacking. Red-shifted fluorescent probes are particularly advantageous for imaging thick tissues, as light scattering decreases at red and far-red wavelengths. We synthesized and characterized the 4', 5', and 6' carboxyrhodamine regioisomers of SiR-Hoechst and 610CP-Hoechst DNA probes and assessed their performance in mice following intravenous injection. All variants entered tissues and produced stable staining that persisted for several hours ex vivo. In particular, 5' regioisomers show the highest performance, yielding bright and specific nuclear labeling. Renal clearance of the probes was nearly complete within 24 h, as indicated by fluorescence analysis of urine samples. Owing to their low cytotoxicity, high specificity, and favourable photophysical properties, these probes enabled high-quality confocal, two-photon, and STED microscopy in liver, kidney, lung, and heart tissue. Our findings extend the application of rhodamine-based DNA probes to in vivo imaging highlight their potential for deep-tissue imaging in live animals.

biochemistry↗

bioRxiv2025

Regional adaptation to mosquito vectors shapes Plasmodium falciparum populations

Transmission of Plasmodium falciparum through mosquitoes represents the most severe population bottleneck in the parasites life cycle, yet the genetic basis of parasite-vector compatibility remains poorly understood. Here, we show that mosquito species-specific transmissibility depends on allelic variation in multiple P. falciparum genes expressed during midgut invasion, beyond the well-studied Pfs47. Using an allelic replacement strategy, we targeted highly geographically differentiated SNPs in P. falciparum that match regional variation in vector community composition. Transmissibility was compared across four mosquito species representing distinct geographic ranges (An. gambiae, An. stephensi, An. minimus, and An. albimanus). Two of five tested polymorphisms showed increased oocyst and sporozoite burdens in sympatric parasite-vector combinations compared to allopatric ones. Both substitutions occurred in ookinete micronemal proteins, CTRP and WARP, within von Willebrand factor A domains, suggesting that regional allelic variation modulates Plasmodium-vector compatibility by altering midgut adhesion interactions. These findings reveal that vector compatibility is a polygenic trait shaped by molecular interactions across several loci. Understanding this complexity refines models of parasite adaptation and can inform the design of transmission-blocking interventions effective across diverse vector-parasite combinations.

microbiology↗

bioRxiv2025

NPM1 mislocalization mediated by RNA Pol I inhibition alters chromatin landscape

RNA polymerase I inhibition affects rRNA synthesis from rDNA clusters residing in nucleolar organizer regions (NORs). Here we have demonstrated RNA Pol I inhibition disrupts nucleolar architecture, NPM1 localization, and alters the chromatin landscape using coordinated eraser and writer enzymes. siRNA mediated depletion or dissociation of NPM1 allows HDAC1 loading on the chromatin. HDAC1 mediated deacetylation of H3K9ac creates H3K9 that undegoes SUV39H1-mediated methylation. The stripping of active histone marks leads to enrichment of repressive H3K9me3 in the genome. These altered chromatin landscape corroborates with loss of genome-wide chromatin accessibility and DNA hypermethylation mediated by DNMT1. Chromatin architectural analysis revealed disrupted nucleolar associated domains (NADs) transforming to lamin associated domains (LADs) with specific histone signatures and repressive states. The 3D nuclear architecture was remodeled by A/B compartments reorganization and loss of Hi-C loops at the H3K9ac depleted sites.

molecular biology↗

bioRxiv2025

NAD+ precursor treatment prevents cardiomyopathybut disrupts erythroid maturation in mitochondrial progeria

Nicotinamide adenine dinucleotide (NAD+) plays a central role in energy metabolism, and its decline is linked to various degenerative diseases. While NAD+ restoration holds therapeutic promise, its long term, tissue-specific consequences remain poorly understood. We investigated effects of nicotinamide riboside (NR) supplementation for "mutator" mice manifesting mitochondrial progeria. Our results reveal strikingly divergent outcomes: in proliferative bone marrow, NR-treated mutators show reductive stress with accumulation of NADH/NADPH, altered amino acid, nucleotide, folate levels and impaired heme biosynthesis. In blood, erythrocyte maturation defects are aggravated, exacerbating anemia. Conversely, in postmitotic cardiac tissue, NR enhanced contractility, reduces stress response markers and normalized metabolic profile. These findings indicate that while being beneficial for heart, chronic NAD+ boosting can compromise erythrocyte maturation in the context of mitochondrial disease. The data emphasize importance of evaluating systemic effects of NAD+ boosting therapies beyond the primary affected tissues and development of tissue-specific metabolic interventions for degenerative diseases. HighlightsO_LIChronic nicotinamide riboside supplementation exacerbates anemia and disrupts erythroid maturation in progeric mice. C_LIO_LIIn proliferative bone marrow cells, NR induces redox imbalance and drives profound metabolic dysregulation. C_LIO_LINR suppresses heme biosynthesis and iron transport pathways in the bone marrow. C_LIO_LIIn the heart, NR restores NAD+ levels, enhances cardiac function, and reduces metabolic stress. C_LI

physiology↗

bioRxiv2025

Tretinoin, a Vitamin A derivative, exerts antiviral effects against Chikungunya virus infection through the nuclear retinoid receptor signaling pathways

Chikungunya virus (CHIKV) has reemerged as a global pathogen causing serious public health threat and socio-economic damage, particularly due to the absence of specific antivirals. Retinoids have been reported to exhibit antiviral potentials against multiple viral infections. In the present study, Tretinoin (TR) or all-trans retinoic acid (ATRA) was evaluated for its anti-CHIKV activity using in vitro, in vivo, and ex vivo models. TR was able to impede CHIKV infection efficiently in Vero and physiologically relevant muscle cells, C2C12, with drastic reduction in the viral RNA, proteins and progeny formation. The IC50 of TR against CHIKV was estimated to be 20.05 {micro}M and 19.71 {micro}M in Vero and C2C12 cells, respectively. In addition, the inhibition was effective during entry as well as in the early stages of post CHIKV-infection. Notably, TR showed remarkable virucidal activity. Next, global transcriptome profile demonstrated that the signaling by Retinoic acid pathway was highly upregulated after CHIKV infection and Retinoic acid receptors (RAR), specifically RAR-{beta} are the key mediators for the anti-CHIKV effect of TR. Further, the drug was also capable to modulate CHIKV-induced inflammatory responses by reducing the phosphorylated MAPKs, NF-{kappa}B and proinflammatory cytokines. Interestingly, TR protected C57BL/6 mice from CHIKV challenge by diminishing viral burden leading to reduced clinical scores and better survival. Similar observation was also noticed in the ex vivo model of CHIKV-infected hPBMC-derived monocyte-macrophage populations. In conclusion, this work demonstrated the repurposing potential of TR against CHIKV infection for the first time, encouraging its clinical validation towards future therapeutics. IMPORTANCECHIKV is an arbovirus causing Chikungunya Fever (CHIKF) leading to debilitating arthralgia and myalgia. The unavailability of licensed antivirals or potent vaccines against CHIKV encourages extensive research to find a therapeutic cure. Retinoids, the derivatives of vitamin A, have been repurposed as antiviral agents against a broad range of viruses; however, their efficacy against alphaviruses remains unexplored. Accordingly, Tretinoin (TR), also known as all-trans retinoic acid (ATRA), was validated for anti-CHIKV efficacy in this investigation. Significant perturbation of CHIKV titer through the modulation of Retinoic acid receptors (RAR) was observed upon drug-treatment. Further, TR reduced major inflammatory markers (MAPKs and proinflammatory cytokines) supporting its anti-inflammatory effect. Further, its anti-CHIKV potential was validated in the mouse model and hPBMC-derived monocyte-macrophage cells, indicating the pre-clinical efficacy. Finally, this is the first study to report the anti-CHIKV property of Tretinoin using in vitro, in vivo, and ex vivo approaches suggesting its repurposing potential.

microbiology↗

bioRxiv2025

Nutrient-dependent pathology in mitochondrial hypertrophic cardiomyopathy model

ObjectiveMitochondrial translation defects are a major cause of early childhood hypertrophic cardiomyopathy (CMP). While the genetic basis of these disorders is being increasingly uncovered, the downstream molecular mechanisms driving disease pathogenesis remain poorly understood. In this study, we investigated the consequences of defects in mitochondrial ribosomal large subunit protein 44 (MRPL44), associated with infantile-onset CMP in human cardiomyocytes, in nutrient environments relevant to cardiac development. MethodsInduced pluripotent stem cell line with MRPL44 patient mutation and controls were differentiated to cardiomyocytes and grown in glucose or lipid-enriched medium reflecting prenatal or postnatal fuel preferences, respectively. Mitochondrial, lipid metabolic and cellular characteristics were studied by immunofluorescence and cellular transcriptome by RNA-sequencing. ResultsIn glucose-rich medium, patient-derived cardiomyocytes exhibit increased mitochondrial DNA (mtDNA) content and elevated mitochondrial transcripts. In contrast the lipid-enriched medium triggered both mitochondrial and endoplasmic reticulum -related stress responses, disrupted lipid and cholesterol homeostasis, accompanied by remodeling of the central biosynthetic pathway of one carbon metabolism. The cells accumulated lipids while also inducing lipid uptake and synthesis genes, suggesting maladaptive metabolic rewiring. ConclusionOur findings indicate that glucose and lipids, the latter being the postnatally favored cardiac fuel, exert remarkably different consequences in MRPL44 deficient cardiomyocytes. The lipid enriched medium elicited robust activation of metabolic stress responses, with chronic upregulation of anabolic biosynthesis pathways and lipid accumulation indicative of conflicting metabolic homeostasis. These observations provide a mechanistic basis for postnatal disease manifestation and highlight nutrient metabolism as a key driver in development of infantile-onset mitochondrial hypertrophic cardiomyopathy. HighlightsO_LIMRPL44 deficiency impairs mitochondrial translation but induces mtDNA replication and transcription in iPSC-derived cardiomyocytes. C_LIO_LIIn glucose conditions, MRPL44 mutant cardiomyocytes upregulate mitochondrial replication and transcription program, but not translation. C_LIO_LILipid-enriched nutrient conditions exacerbate disease phenotype, inducing mitochondrial and ER stress responses in MRPL44 deficiency. C_LIO_LIMitochondrial ribosome defect disrupts lipid homeostasis in cardiomyocytes causing impaired fatty acid oxidation, lipid accumulation and altered cholesterol metabolism. C_LI

molecular biology↗

bioRxiv2025

Single-cell Genomic Copy Number Evolution Reveals Frequent Loss of the Y chromosome in Esophageal Adenocarcinoma

The incidence of esophageal adenocarcinoma (EAC), an aggressive cancer, is rising in Western countries, and incidence is higher in men. To better understand the roles of DNA copy number evolution, tumor heterogeneity, and tumor microenvironment in EAC and its origins, we evaluated EAC, Barretts Esophagus (BE), and normal adjacent tissue using our previously developed ultra-sensitive, single-nucleus DNA copy number analysis (12,186 nuclei, 20 specimens) and single-nucleus RNA-sequencing (snRNA-seq; 87,027 nuclei, 32 specimens). Loss of Y (LOY) chromosome was rare in BE but markedly enriched in EAC. In genome unstable cells, complete LOY chromosome often coincided with X-chromosome duplication. We did not detect X-chromosome inactivation via XIST expression in cells with LOY, suggesting increased expression of X-chromosome genes and potential effects on tumor immune evasion. When considering patients clinical features, we identified distinct differences in tumor microenvironment by sex, age, and obesity status, particularly massively reduced immune cell composition in obese patients. Finally, our cell line models recapitulate LOY, and we identify the first candidate anti-LOY agent. Our findings highlight how LOY affects tumor subpopulations and shapes the tumor microenvironment during EAC progression.

cancer biology↗

bioRxiv2025

Myosin II independent contraction of actin filaments in membrane nanotubes

The ability to generate active stresses within filamentous actin matrices is a fundamental and evolutionarily conserved process driving locomotion and morphogenetic changes in cells. The generation of pushing forces by actin polymerization is reasonably well understood, and is known to drive lamellipodia based motility and filopodial extension. Actin filaments decorated with myosin motors can also generate contractile stresses as in the cell cortex or in cytokinetic rings. In this article we use membrane nanotubes pulled out of axonal shaft to investigate actin dynamics and force generation. We report cyclic growth and retraction dynamics of actin within the tube and correlated contraction events giving rise to sustained load and fail cycles. The contraction mechanism operate independent of myosin II motor proteins. Furthermore, we analyzed the dynamics of actin within the tube, including under various biochemical or genetic perturbations. By combining these results with physical modeling, we argue that stresses generated in the actin filaments by the binding of actin depolymerizing factor (ADF/cofilin) proteins can explain the cyclic load-fail behavior.

biophysics↗

bioRxiv2025

Two mutations in the same MYC-bHLH transcription factor cause segregation of purple coloration of stolons and seed heads in Zoysia japonica x Zoysia matrella F2 and F1 populations

Anthocyanins play diverse roles in plants, including attracting pollinators and protecting cells from oxidative damage. In zoysiagrass, a warm season turfgrass, their accumulation in seed heads and stolons can decrease the aesthetic appeal. In this study, a high-density genetic map with [~]8000 single nucleotide polymorphism (SNP) markers organized into 20 linkage groups was generated in a Zoysia japonica acc. Meyer x Zoysia matrella acc. PI 231146 F2 population. Using this genetic map, a large-effect quantitative trait locus (QTL) for anthocyanin variation in stolons and seed heads was mapped to chromosome 12 (PP locus). Variant analysis of a candidate gene for PP, Zjn_sc00004.1.g07010.1.sm.mk, which encodes a MYC-bHLH transcription factor that regulates anthocyanin biosynthesis, revealed a SNP at an exon-intron boundary in Meyer that led to intron retention. Interestingly, an F1 population derived from the same parents segregated for seed head color but uniformly displayed purple stolons. Seed head color in the F1 population co-mapped with the PP locus which, combined with genotypic and yeast two-hybrid analyses, revealed that a SNP in PI 231146 leading to an Ala163Ser substitution in the MYB-interacting N-terminal domain of the same MYC-bHLH transcription factor was likely causal. The Ala163Ser substitution affected interaction of MYC-bHLH with MYB in a MYB-dependent manner. The identified mutations can be exploited to develop cultivars with green seed heads and stolons. The high-marker-density interspecific Z. japonica x Z. matrella F2 genetic map also provides a robust tool for identifying genomic regions and genes of agronomic interest that differentiate the two species.

genetics↗