Biology subjects

Ferrari, G.

Publications and source records attributed to Ferrari, G..

At least 19 recordsLinked to original sources

bioRxiv2026

A genetic anemia disentangles the dual effect of chronically reduced thrombopoietin on hematopoietic stem cells and bone marrow niche

Many studies unraveled the reciprocal regulation between hematopoietic stem cells (HSC) and the bone marrow (BM) niche by using transgenic knock-out or reporter mice, often overlooking the pathophysiological relevance and the existence of compensatory mechanisms. Here, we exploit the th3 murine model of a genetic anemia, beta-thalassemia (BThal), to investigate the dual impact of chronically reduced thrombopoietin (TPO) production on HSC and megakaryocytic BM niche. Decreased systemic TPO downregulates stemness programs in HSC and impairs their commitment towards megakaryocytes (Mk). We uncover dysmegakaryopoiesis in the BM from BThal patients and mice with defective Mk maturation and reduced production of niche factors, altering the HSC-niche crosstalk. Notably, in vivo stimulation of the TPO signaling restores HSC quiescence, Mk maturation and niche support. These findings demonstrate that TPO regulates HSC through both direct and niche-mediated routes, underscoring the value of using a genetic disease model to disentangle general molecular mechanisms.

cell biology↗

bioRxiv2026

Paleogenomic time series reveal past population dynamics and their relevance for the conservation of the Alpine ibex

Endangered species often suffer from genetic threats such as inbreeding depression, the accumulation of mutation load and the general loss of genetic diversity, which may deprive them from future adaptation. Since the genetic make-up of a species is strongly affected by its evolutionary past, however, interspecific comparisons are difficult and absolute levels of genetic diversity may be a relatively poor predictor of extinction risk. To better interpret current levels of genetic diversity of actively managed species, the comparison of present-day genomic data to that of ancient material pre-dating recent anthropogenic population declines has been advocated, but remains rarely done at the evolutionary time scales necessary to understand past population dynamics. Here we demonstrate the usefulness of deep genomic time series through 40 high quality ancient genomes of the Alpine ibex, which faced near-extinction in the 19th century but has since been reintroduced across the Alps and recovered remarkably. The samples, which span the last 14,000 years, evidence strong and stable population structure at the continental scale, paired with frequent extinction and recolonization events at the local scale. These metapopulation dynamics resulted in small and largely isolated populations, with present-day, reintroduced populations only having 20% to 40% less neutral genetic diversity and 3% higher mutation load, likely due to efficient purging in the past. At the species level, however, the loss of genetic diversity was dramatic and reduced to the small fraction that segregated within the only surviving population in the Gran Paradiso area. Our analyses of ancient metapopulation dynamics in Alpine ibex underscore the importance of a healthy genetic pool for successful recolonization and long-term survival, as well as the real possibility of regional extinctions.

evolutionary biology↗

bioRxiv2026

A chromosome-level assembly of an aquatic passerine bird, the northern white-throated dipper, Cinclus cinclus cinclus (Linnaeus, 1758)

We present a chromosome-level genome assembly of a female Norwegian white-throated dipper (Cinclus cinclus cinclus) generated using Oxford Nanopore Technologies (ONT) long reads and Hi-C scaffolding. The assembly comprises two pseudo-haplotypes, hap1 (1186 Mb) and hap2 (1115 Mb), with 96.7% and 94.4% of sequences assigned to chromosome-scale scaffolds, respectively. Both pseudo-haplotypes contain 40 autosomes, with the Z and W sex chromosomes assigned to hap1. Compared with the PacBio HiFi-based C. c. gularis reference assembly bCinCin1.1.pri, which contains 38 autosomes, sequence represented as a single dot-chromosome (chr 36) is resolved into three distinct dot-chromosomes (chr 36, 39, and 40), a configuration supported by Hi-C contact patterns. BUSCO completeness was high for hap1 (99.2%) and hap2 (95.0%), with 19,003 and 17,746 predicted protein-coding genes, respectively. Compared with the HiFi-based C. c. gularis reference and HiFi-based assemblies generated from the same individual, the ONT-derived assemblies were substantially less fragmented and recovered more sequence from the smallest chromosomes. Synteny was otherwise largely conserved between subspecies. HiFi depletion increased strongly from macrochromosomes to micro- and dot-chromosomes, and HiFi-depleted regions were enriched for repeats and predicted non-B-DNA-associated features, particularly G-quadruplexes and direct repeats, whereas ONT coverage remained comparatively stable. These results show that conventional genome-wide assembly metrics can obscure substantial differences in the recovery of repeat-rich avian dot-chromosomes and highlight the value of chromosome-aware evaluation and ONT sequencing for recovering these regions.

genomics↗

bioRxiv2026

G4All: a database of experimentally confirmed G-quadruplex-forming sequences

G-quadruplexes (G4s) are non-canonical nucleic acid structures with critical roles in gene regulation, genomic stability, and disease, making them prime targets for therapeutic and biotechnological applications. However, the absence of a curated, centralized, experimentally validated repository of short (mostly synthetic) G4-forming sequences, paired with appropriate single-stranded or hairpin controls, has limited reproducibility and hindered progress in the field. Here, we introduce G4All, a comprehensive, curated database of G4-forming short DNA and RNA sequences, complemented by rigorously selected non-G4 controls, all studied under roughly similar experimental conditions (around 100 mM potassium ion at near neutral pH). G4All consolidates sequences validated by diverse experimental methods, including circular dichroism, NMR, UV spectroscopy, with standardized annotations for topology, thermal stability, and experimental conditions. By providing both positive and negative datasets, G4All enables rigorous comparative analyses, assay benchmarking, and the development of predictive models. The database supports a broad range of applications, from fundamental studies of G4 biophysics to the rational design of aptamers, as well as benchmarking prediction algorithms. Future developments will expand G4All to include user-submitted datasets and more RNA sequences. Freely accessible, G4All offers a searchable interface and downloadable datasets, establishing a community-driven hub to accelerate discovery and standardization in G4 research. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/743020v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@111d015org.highwire.dtl.DTLVardef@74447corg.highwire.dtl.DTLVardef@13c5642org.highwire.dtl.DTLVardef@432469_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Elicitation of stem-directed antibodies in rhesus macaques by a conventional hemagglutinin immunogen

Because they can bind many strains of influenza, antibodies targeting the hemagglutinin (HA) stem have been attractive targets for vaccine development. Many monoclonal antibodies (mAbs) directed at the HA stem have been isolated from humans, and these mAbs have mediated broad protection in animal models. We describe here HA stem-directed mAbs isolated from rhesus macaques immunized with an "ordinary" H1 HA trimer. All immunized rhesus macaques developed high serum titers with broad reactivity to diverse H1N1 and H5N1 viruses, and 7 isolated mAbs strongly blocked canonical stem antibody CR6261 binding to H1. MAb DH726.1 robustly protected mice from lethal challenge with H1N1 and H5N1 viruses, and cryo-EM showed the binding footprint overlapped that of some human mAbs. These findings suggest that vaccination with the standard, trimeric HA immunogens may be sufficient to elicit stem antibodies at titers adequate to protect against zoonotic H5N1 influenza. In BriefEfforts to achieve broad influenza protection have largely emphasized increasingly sophisticated immunogen designs to redirect antibody responses toward conserved epitopes. Here, we show that a single, conventional HA immunogen readily elicits antibodies targeting the conserved HA stem, suggesting that routine influenza vaccination may provide broader protection than previously appreciated. HighlightsO_LIMonovalent HA immunization induces strong, stem-directed immune responses in rhesus macaques C_LIO_LIEpitope on the HA stem confirmed by Cryo-EM C_LIO_LIFc-mediated activation of immune effector cell by rhesus-derived stem mAb C_LIO_LIHA stem-directed antibody protects mice against H1N1 and H5N1 viruses C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/738984v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1535b59org.highwire.dtl.DTLVardef@192422dorg.highwire.dtl.DTLVardef@136b3d5org.highwire.dtl.DTLVardef@586fd4_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2026

A chromosome-level reference genome of the largest cervid species - the European moose (Alces alces; Linnaeus, 1758)

We describe a chromosome-level, haplotype-resolved genome assembly from a male European moose (Alces alces alces). The assembly comprises two pseudo-haplotypes of 3,148 Mb and 3,112 Mb, with sex chromosomes in haplotype one, and 33 autosomes in each haplotype (68 in total). Assembly completeness is high (BUSCO 98.3% and 95.7%), with 21,496 and 20,498 annotated protein-coding genes for haplotypes one and two, respectively. This genome assembly is the most complete so far generated for European moose.

genomics↗

bioRxiv2026

A chromosome-level genome assembly of the Eurasian great grey owl, Strix nebulosa lapponica (Thunberg 1798)

We present a chromosome-level genome assembly of a female great grey owl (Strix nebulosa lapponica). The assembly comprises two pseudo-haplotypes of 1554 Mb and 1242 Mb, with 83.2% and 91.4% scaffolded into 40 autosomal chromosomes, in addition to the W and Z sex chromosomes both placed in hap1. Assembly completeness is high (BUSCO 99.2% and 94.8%), with 18,493 and 17,279 annotated protein-coding genes for hap1 and hap2, respectively. This genome establishes a reference for investigating genetic variation and chromosome evolution in great grey owls. Compared with the previous S. nebulosa assembly, this assembly includes both sex chromosomes, separates regions that were previously collapsed, and resolves 82 chromosomes total. While larger chromosomes show broadly conserved synteny across owl assemblies, the recovery of additional conserved microchromosome-associated genes suggests that ONT reads improved resolution of the smallest chromosomes relative to HiFi-based assemblies.

genomics↗

bioRxiv2026

A chromosome-level genome assembly of a "living fossil", the tadpole shrimp Lepidurus arcticus (Pallas, 1793)

We present the first chromosome-level reference genome for Lepidurus arcticus (Pallas, 1793), a freshwater crustacean with circumpolar distribution. L. arcticus belongs to the small order of freshwater Notostracan crustaceans that are representatives of the ancient group Branchiopoda. This group has a remarkable morphological stability and is frequently labelled "living fossils". Its ancient origin, streamlined genome (estimated to 0.11 Gb) and reproductive flexibility makes this a very interesting candidate for genomic studies. The haplotype-resolved assemblies are composed of two pseudo-haplotypes spanning 81.2 megabases (Mb) and 81.8 Mb, respectively, and each scaffolded into 6 chromosomes. Both haplotypes (hap) show high completeness and identical BUSCO scores of 98.3 for hap1 and hap2. The scaffold N50 length is 13.4 Mb for hap1 and 13.9 Mb for hap2, and k-mer completeness estimated from PacBio HiFi reads was 95.79% and 96.18%, respectively. The haplotypes display very low estimated genome-wide heterozygosity of 0.133%. The assembly contains 10901 (hap1) and 10910 (hap2) protein-coding genes. Repetitive elements comprised approximately 24-25% of each haplotype, with long terminal repeat retrotransposons representing the most abundant transposable element class at approximately 8-9%. Comparison with the near chromosome-level genome of Lepidurus packardi revealed substantial intrachromosomal rearrangements, despite similar chromosome numbers and chromosome sizes. Differences in transposable element content between L. arcticus and L. packardi were primarily driven by retrotransposons, particularly LTR and LINE elements. This reference genome provides a valuable resource for future population genomic studies and for investigating evolutionary stasis at the genome level.

genomics↗

bioRxiv2026

A haplotype-resolved bluethroat (Luscinia s. svecica) genome assembly uncovers the complex MHC region

We describe a chromosome-level, haplotype-resolved genome assembly from a female bluethroat (Luscinia s. svecica). The assembly comprises two pseudo-haplotypes of 1461 Mb and 1171 Mb, with 77.4% and 88.4% scaffolded into 40 autosomal chromosomes and the W and Z sex chromosomes (haplotype one). Assembly completeness is high (BUSCO 99.2% and 94.9%), with 22,462 and 18,769 annotated protein-coding genes for haplotypes one and two, respectively. The use of Oxford Nanopore Technologies sequencing enables resolution of genomic regions that are often fragmented in genome assemblies, including the hypervariable Major Histocompatibility Complex (MHC). We find that MHC loci include both the canonical organization of tandemly duplicated MHCII{beta} genes with a single MHCIIA, and a distinct arrangement in which MHCI and MHCII{beta} loci are interspersed in intermixed arrays, and that substantial structural differences between haplotypes are directly resolved in the assembly.

genomics↗

bioRxiv2026

Cross-Species Multi-Omics Profiling Identifies Conserved Activated Valvular Interstitial Cell Population Driving Myxomatous Mitral Valve Degeneration

BackgroundPrimary mitral regurgitation resulting from mitral valve prolapse can lead to life-threatening complications, including arrhythmias, heart failure, and sudden cardiac death. Mitral valve prolapse is classically associated with myxomatous mitral valve degeneration, characterized by leaflet thickening, extracellular matrix disorganization, and progressive structural remodeling. Valvular interstitial cells, the predominant stromal population within the valve, maintain extracellular matrix homeostasis; however, their molecular heterogeneity, and state-specific contributions to disease pathogenesis remain incompletely defined. MethodsUsing a fibrillin-1 deficient mouse model and human tissue specimens we integrated single-cell RNA sequencing with spatial transcriptomic profiling to construct a comprehensive atlas of cellular composition and extracellular matrix organization across normal mitral valves, sporadic mitral valve prolapse, and Marfan syndrome-associated mitral valve prolapse. ResultsAnalyses revealed spatially organized cellular niches and substantial heterogeneity within the valvular interstitial cell population. Across murine and human datasets, we identified a conserved activated valvular interstitial cell population enriched for profibrotic extracellular matrix remodeling programs and preferentially localized to mechanically vulnerable leaflet tip regions. This population exhibited coordinated upregulation of collagen- and matrix-associated genes, metabolic signatures consistent with enhanced mitochondrial activity, and transcriptional features suggesting fibro-inflammatory signaling. ConclusionsWe identified a transcriptionally and spatially distinct activated valvular interstitial cell state conserved across species and disease etiologies that is strongly implicated in fibrotic remodeling during myxomatous mitral valve degeneration and provides a candidate therapeutic target.

molecular biology↗

bioRxiv2026

SABER: A Multiparental Tomato Population Leveraging Wild Relative Diversity for High-Resolution QTL Mapping

The narrow genetic base of cultivated tomato (Solanum lycopersicum L.) represents a major constraint on crop improvement, necessitating the exploitation of wild relatives to broaden allelic diversity. Here we present SABER (Solanum lycopersicum Allele Biodiversity Enriched Resources), a novel eight-founder Multiparent Advanced Generation Intercross (MAGIC) population that, for the first time, incorporates the Galapagos wild relative Solanum cheesmaniae as a founder alongside seven elite S. lycopersicum lines. Following a structured crossing scheme and Single Seed Descent advancement, F6 recombinant inbred lines were genotyped at 5,850 high-confidence SNP markers using Single Primer Enrichment Technology (SPET). Population structure analyses confirmed low residual heterozygosity, limited substructure among offspring, and successful introgression of S. cheesmaniae alleles across all twelve chromosomes. Mapping performance was validated through three Mendelian traits with known genetic determinants, all of which resolved to genomic positions consistent with the literature. QTL mapping for quantitative agronomic traits identified known loci for fruit epicarp and flesh color, and two novel QTL for days to flowering, number of leaves before flowering, and soluble solids content. Together, these results demonstrate that SABER is a powerful and reliable platform for high-resolution QTL mapping and candidate gene discovery, and establish a replicable framework for integrating wild germplasm into multiparental tomato breeding resources

plant biology↗

bioRxiv2025

In vivo imaging of reactive oxygen species after myocardial ischemia-reperfusion injury: a large animal multimodal imaging and transcriptomic study

BackgroundReactive oxygen species (ROS) contribute to myocardial ischemia-reperfusion injury (IRI), but in-vivo data on the spatial myocardial distribution and systemic effects of ROS after IRI remain limited. This multimodal CMR and PET/CT study aimed to non-invasively image ROS activity in a clinically-relevant swine model of IRI using [18F]ROStrace, a fluorine-18-labeled analogue of dihydroethidium (DHE), and to investigate regional changes in ROS activity in the infarcted myocardium during the subacute post-IRI phase. MethodsIRI was induced by percutaneous occlusion of the left anterior descending artery for 90 minutes in swine (N=9). CMR and whole-body PET/CT imaging with [18F]ROStrace were performed before myocardial infarction (MI) and 3-5 days post-MI to assess ROS in non-infarct myocardium, lungs, bone marrow, spleen and skeletal muscle. Late gadolinium enhanced CMR was performed to structurally characterize infarct regions. Post-MI, in vivo [18F]ROStrace signal in infarcted myocardium was compared with remote, non-infarcted myocardium and validated via ex vivo DHE fluorescent imaging. Bulk RNA-sequencing (RNA-seq) and Gene Ontology pathway analysis were conducted on biopsies from infarct and remote myocardial tissue to identify differentially expressed genes and pathways connected to oxidative stress. ResultsDuring the subacute phase following MI, [18F]ROStrace fractional uptake rate (FUR; min-1) was significantly increased in skeletal muscle, compared to baseline (0.011{+/-}0.003 vs 0.016{+/-}0.005, p=0.04), with a trend toward increased FUR in bone marrow (0.046{+/-}0.009 vs 0.056{+/-}0.011, p=0.12) and the left ventricular free wall (0.067{+/-}0.007 vs 0.073{+/-}0.010, p=0.15). Within the myocardium, [18F]ROStrace FUR ((min-1)/(mL/min/g)) was significantly higher in infarcted compared to non-infarcted myocardium regions (0.110{+/-}0.034, vs 0.148{+/-}0.035, p=0.0005). DHE staining confirmed elevated ROS levels in the infarcted myocardium. RNA-seq identified 8,707 differentially expressed genes between infarct and remote myocardium, with downregulated pathways in the infarct associated with mitochondrial function, cellular respiration, and metabolic adaptation. ConclusionThis study demonstrated MI ROS imaging using [18F]ROStrace using a whole-body PET/CT scanner and structural assessment with CMR. Systemic and myocardial increases in ROS activity were observed post-MI, accompanied by substantial molecular alterations in infarcted tissue. These findings show potential imaging strategies to evaluate therapeutic targets that can mitigate oxidative stress after MI.

bioengineering↗

bioRxiv2025

Chromosomal fusions shaped the genome of the greater hornwrack bryozoan (Flustra foliacea) (Linnaeus, 1758)

The phylum Bryozoa is an understudied, yet commonly-occurring, globally distributed bilaterian metazoan organismal group. They have a colonial lifestyle and an evolutionary history that spans at least 480 million years but likely longer. Despite their contentious phylogenetic affinities among metazoans, disproportionately little genomic investigations have been performed thus far. Here, we describe the first chromosome-level genome assembly of an individual Flustra foliacea colony belonging to the order Cheilostomatida, collected in southern Norway. The haplotype-resolved assembly of F. foliacea contains two pseudo-haplotypes spanning 956 megabases and 880 megabases, respectively. Both assemblies are highly complete both in terms of scaffolding (>90% of sequences placed in 8 autosomal chromosomal pseudomolecules), and gene content (BUSCO completeness scores >90%). We also present gene and repeat annotations of the two assemblies. A comparison of our newly sequenced F. foliacea with five previously published bryozoan genomes supports the hypothesis that the group has undergone extensive genome rearrangements. This includes multiple chromosomal fusions in F. foliacea since their split with other cheilostome bryozoans. These fusions were enriched with long terminal repeat (LTR) retrotransposons, highlighting the complex interplay between genome organization and genomic repeats. Our study contributes to a deeper understanding of bryozoan genome evolution and the role of repeats in metazoan genome organization.

genomics↗

bioRxiv2025

3D Contractile and Remodeling Behaviors of Functionally Normal and Prolapsed Human Mitral Valve Interstitial Cells

Mitral valve prolapse (MVP) can lead to heart failure, arrhythmia, and death. The only treatments available for MVP are replacement or repair; alternative therapies remain elusive due to lack of knowledge of the underlying pathological processes. The goal of the present study was thus to explore how MVP affects human mitral valve interstitial cell (hMVICs) extracellular matrix (ECM) remodeling and basal contractility characteristics. Isolated MVP and physiologically normal hMVICs were embedded in poly(ethylene) glycolbased hydrogels containing fluorescent fiducial markers and 3D traction force microscopy via inverse modeling was employed to determine the local change in hMVIC hydrogels due to enzymatic degradation and collagen deposition. Results indicated pronounced hydrogel softening occurred generally further from the hMVICs, whereas stiffening occurred in close proximity to hMVICs due to collagen deposition as verified by collagen-staining. MVP hMVICs induced greater hydrogel stiffening and less degradation than normal hMVICs. Interestingly, even though MVP hMVICs had higher basal contractile displacements, their corresponding traction forces and hydrogel strain energy densities were significantly lower than those of normal hMVICs. These findings elucidate, for the first time, that MVP hMVICs have significantly altered biophysical contractile and ECM remodeling behaviors compared to normal hMVICs. Simple SummaryWhen a mitral heart valve gets thick, stiffened, and degraded, it can flip backwards (prolapse), causing blood to flow the wrong way. This can cause heart failure, arrhythmia, or even death. The only treatment for mitral valve prolapse (MVP) is surgery. To pave the way for a medication, this study aimed to understand how cells that maintain the mitral valve, mitral valve interstitial cells (MVICs), act on their surrounding tissue. The mechanical properties of the MVICs were tested, including how much they contract and how much they pull on their surroundings. Also, the mechanical properties that the MVICs place on their surroundings were tested, like how much they stiffen and degrade the tissue and how much energy is stored in the tissue as the MVICs contract. Compared to normal MVICs, we found that MVP MVICs stiffen their surroundings more and degrade their surroundings less. We also found that even though MVP MVICs contract more than normal MVICs, the energy that they place on their surroundings is less than that of normal MVICs, indicating that MVP MVICs are less mechanically effective. This is the first time that this ineffectiveness has been seen and may be key to targeting MVP with future medications.

cell biology↗

bioRxiv2025

Brownian DNA Computing

Conventional silicon computing is constrained by energy demands, limited parallelism, and poor compatibility with living systems, motivating the exploration of molecular alternatives. Here, we realize Brownian DNA computing, a hitherto theoretical framework, for energy efficient computation in which coupled molecular balances on a DNA origami scaffold form Brownian Logic Elements (BLEs) that harnesses thermal fluctuations for computation. By encoding multiple logic gates into a programmed energy landscape, these BLEs execute all fundamental Boolean logic gates, complex circuits such as half-adders, and multi-input operations, while also enabling non-Boolean logic with multi-valued outputs in a single compact gate. Computation arises through thermally driven exploration of a near-flat configurational energy landscape, without reliance on consumable fuel strands for cascading signal propagation, making the process fast, resettable, and compatible with operation near reversible thermodynamic limits. Transient-input protocols further allow the BLE energy landscape to be controlled quasistatically, providing a route toward reversible Brownian computation. In combination with single-molecule readout, Brownian DNA computing establishes a new foundation for molecular information processing with potential applications in biocomputing, soft robotics, and energy-efficient nanodevices.

biophysics↗

bioRxiv2025

Base editing of β0 thalassemia mutations as a therapeutic strategy for β-hemoglobinopathies: efficacy and genotoxicity studies

Gene therapy has emerged as a promising curative treatment for {beta}-hemoglobinopathies, the most common genetic disorders worldwide. However, current approved approaches still have some limitations in terms of safety and efficacy. Here, we used highly processive adenine base editors (ABE) variants to precisely correct some of the most prevalent and severe {beta}-thalassemia-causing mutations in the {beta}-globin gene. Efficient editing of hematopoietic stem/progenitor cells (HSPCs) led to potent {beta}-globin expression in their erythroid progeny and persistent correction of both {beta}-thalassemia and sickle cell-{beta}-thalassemia phenotypes. Safety of this strategy was confirmed in HSPCs in vitro and in vivo by the absence of gene dysregulation or any meaningful impact on the DNA mutational burden, the RNA deamination level, the {beta}-globin gene locus integrity and the clonality of the HSPC graft. Overall, base editing-mediated gene correction is a safe and effective strategy for treating {beta}-hemoglobinopathies. One sentence summaryPreclinical safety and efficacy studies of a new gene therapy approach for patients with severe {beta}-hemoglobinopathies.

genetics↗

bioRxiv2025

Localisation of Apicomplexa motor Myosin A with axial nanometric precision using graphene energy transfer

Migration in Apicomplexan parasites, a phylum that includes Plasmodium spp. responsible for malaria and the zoonotic Toxoplasma, is explained by the linear migration motor model. This model predicts that Myosin A is confined beneath the plasma membrane and above the inner membrane complex (IMC), a membranous barrier separating the cell membrane and the cytoplasm. Cumulative data, using mutant cell lines and biochemical data support this model. Paradoxically, a proof of the precise localization of Myosin A is still lacking due to limitations in resolving the motor with nanometric precision within the space comprising the membrane and the IMC. Here, we implement graphene energy transfer (GET), a novel axial nanometric ruler with a resolution of [~]1 nm, to determine the relative axial position of Myosin A and IMC1 (a reference protein defining IMC position). Using GET, we estimate the IMC dimensions with precision matching electron microscopy (EM) data and the added advantage of identifying specific bauplan proteins. We complement these measurements with 2D STED microscopy in MIRA confiners, uExMIC, and cryo-immunolabeling. Our data present the first direct localization of Myosin A populations with nanometric resolution in the third dimension, which is compatible with the linear motor model. One sentence summaryUsing the novel GET method, this study presents the first direct localization of Myosin A populations in Toxoplasma gondii with 1-4 nm axial precision, supporting the linear model.

biophysics↗

bioRxiv2025

A New Computational Inverse Modeling Approach for Cellular Traction Force Microscopy that Accounts for Hydrogel Compressibility

We have recently documented significant compressible behaviors in hydrogels implemented in 3D traction force microscopy (TFM). Therefore, here we have developed a new computational pipeline that accounts for this observation. Additionally, the new method accurately recovers large ranges and spatial heterogeneity of hydrogel moduli induced by cellular remodeling associated with enhanced extracellular matrix secretion and MMP-degradation. The algorithm sought best fit of the 3D displacement field with a multi-stage approach, wherein the Tikhonov regularization parameter in L-BFGS was progressively lowered. Forward simulations were performed in FEniCS, with gradients computed with FEniCS-adjoint and MOOLA to weight degrees of freedom according to hydrogel volume affected. Once developed, we conducted a series of synthetic test cases applying actual cell geometries, experimentally-matched compressibility, and realistic displacements with experimental noise levels. Employing an incompressible material model resulted in predicted moduli with over 415% mean relative error and predicted strain energies 5-fold greater than the prescribed values. Moreover, errors in predicted traction forces were amplified by a factor of 10. Thus, accounting for hydrogel compressibility was critical for accurate hydrogel moduli and strain energy recovery. To demonstrate the utility of our approach, we applied it to TFM data of human mitral valve interstitial cells embedded in PEG hydrogels with pre-altered moduli of 54 Pa. We determined that J [isin] [0.45, 1.66] and local hydrogel moduli exhibited large variations, 3.6 Pa to 2.4 MPa. This study underscores the need for correct handling of hydrogel compressibility for accurate estimation of local hydrogel moduli and traction forces.

bioengineering↗