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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2026

Stop codon readthrough in Trichomonas is a mechanism for gene expression regulation and expanding protein function

Trichomonas vaginalis is the causative agent of trichomoniasis, a common sexually transmitted infection among women of reproductive and peri-menopausal age. The parasite has an unusually large genome, rich in complex repeats, including a vast repertoire of transposable elements and multi-copy gene families. Since very few T. vaginalis genes have introns, gene expression is usually straightforward, with ribosomal translational machinery proceeding from a start codon to the next in-frame stop codon of an unspliced poly(A)denylated mRNA. However, our previous studies raised the possibility of T. vaginalis gene expression involving stop codon readthrough (SCR), where transcription through in-frame stop codons produces longer-than-predicted mRNAs that translate to fully functional proteins. Here, we leverage long-read RNA-seq and new chromosome-scale assemblies of two T. vaginalis strains and two avian sister species to investigate and characterize ~1,400 long, mature mRNAs that contain more than one predicted protein-coding gene transcribed from what we call '' RT genes '', composites of adjacent predicted genes. We first identify RT genes in a second T. vaginalis strain and in close relatives T. vaginalis-like and T. stableri, indicating that this phenomenon is conserved among Trichomonas species and strains. Second, we find transcripts of RT genes to be more abundant by many orders of magnitude than monocistronic genes. Third, we found the distance between predicted genes within RT genes to be significantly shorter than between adjacent independent predicted genes. Fourth, functional annotation revealed that RT genes encode at least 50 distinct protein functions, suggesting that this unusual transcriptional mechanism has a role in an array of biological processes in Trichomonas. Our results from two Trichomonas species suggest that SCR is an important mechanism controlling gene expression and the diversity of protein function in this parasite.

molecular biology↗

bioRxiv2026

A geometric anthropomorphic phantom for quantitative susceptibility mapping: accuracy and repeatability

Quantitative Susceptibility Mapping (QSM) relies on a tissue's underlying macroscopic geometry to lead to measurable orientation-dependent field perturbations. To understand and assess QSM error in vivo, anthropomorphic phantoms provide a useful model that mimic the electromagnetic properties and morphology of underlying tissue. Herein, we designed and manufactured an MRI compatible anthropomorphic phantom with cylindrical and spheroid compartments containing realistic susceptibilities to mimic hemorrhages, calcifications, and blood vessels. We estimated accuracy ({epsilon}, bias, RMSE) and repeatability (RC) of MEDI-susceptibility measurements within ROIs. We evaluated voxel-based agreement to validate susceptibility mapping under different acquisition conditions (3T versus 7T) and reconstruction algorithms (COSMOS versus MEDI). Reliable MEDI-based susceptibility measurements were obtained from ellipsoids but not from straws. The ellipsoids (|{epsilon}| = 0.007 to 0.083 ppm at 3T; 0.050 to 0.118 ppm at 7T) were more accurate than the straws (|{epsilon}| = 0.084 to 0.190 ppm at 3T; 0.105 to 0.160 ppm at 7T). The repeatability coefficient across all 6 ROIs (RC = 0.652 ppm at 3T; 0.459 ppm at 7T) was substantially larger than across the 4 ellipsoid ROIs only (RC' = 0.168 ppm at 3T; 0.141 ppm at 7T). The accuracy at 3T (bias = -0.002 ppm, RMSE = 0.082 ppm) was better than the accuracy at 7T (bias = -0.056 ppm, RMSE = 0.092 ppm). Using voxels from the 4 ellipsoid ROIs, we observed excellent agreement between COSMOS and MEDI susceptibility maps at 3T, with linear regression of y=1.00x-0.01 (r=0.99). We observed some underestimation of MEDI susceptibility maps relative to COSMOS at 7T, with linear regression and y=0.93x-0.04 (r=0.99). The results imply that QSM reconstructions are reliable with 3T scanners but can be challenging with 7T scanners at high magnetic susceptibilities.

biophysics↗

bioRxiv2026

Behavioral signatures suggest distinct modes of suppressing irrelevant information during tactile temporal attention in human participants

To make adaptive perceptual judgments, the nervous system must selectively process behaviorally relevant sensory information while filtering out competing distractions. Although attentional control has been extensively studied in the visual domain, particularly in the context of spatial selection, considerably less is known about how attention operates in the tactile modality and across time rather than space. Here, we developed a paradigm to investigate temporal tactile attention in human participants, enabling the study of attentional behavior and underlying behavioral strategies in this sensory domain. Participants were instructed to categorize the intensity of a task-relevant tactile stimulus delivered to the fingertip while ignoring an irrelevant tactile stimulus. A visual cue indicated which of two sequentially presented stimuli was relevant on each trial. In addition, participants completed self-report questionnaires assessing autistic traits and aberrant salience (the tendency to assign significance to otherwise neutral stimuli or events). Across subjects, participants performed the task with high accuracy. However, clustering analyses based on behavioral features revealed distinct response profiles. One cluster did not exhibit biases induced by the irrelevant stimulus. In contrast, a third cluster displayed a repulsive effect of the irrelevant stimulus and showed lower overall performance. These behavioral phenotypes were also reflected, to some extent, in differences in learning trajectories across training sessions. We further explored participants' metacognitive awareness through a post-experiment questionnaire assessing subjective evaluations of task difficulty and performance. Although exploratory, the results suggest a relationship between metacognitive reports, behavioral strategies, and objective task performance. In contrast, neither autistic traits nor aberrant salience scores were associated with performance measures or behavioral phenotypes. Together, these findings support the view that attentional control is implemented through multiple, individualistic behavioral strategies rather than a single mechanism pertaining to all, suggesting that task structure interacts with individual predispositions to shape distinct modes of attentional control in human participants.

neuroscience↗

bioRxiv2026

Phylogeny and Species Delimitation in Isoxylosteum, a Lonicera Clade Endemic to the Himalayan-Tibetan-Hengduan Region

The Himalayan-Tibetan-Hengduan (HTH) region is the richest biodiversity hotspot for high-elevation plants. However, owing to its remote and physically challenging topography as well as the trans-national nature of the region, many taxonomic problems in the area remain unresolved, particularly in the Himalaya. This, in turn, has impeded our understanding of the assembly of its extraordinary high-elevation flora. Here, we resolve phylogenetic relationships and delimit species in a distinctive clade of honeysuckles that is endemic to the HTH, the Isoxylosteum clade of Lonicera, using restriction-site associated DNA sequencing (RADseq) and morphological data. Five species complexes of Isoxylosteum have standardly been recognized. Three of these complexes are highly variable and have been divided into several varieties or species each. Phylogenetic, population structure, and morphological analyses of leaf and floral traits from samples collected across the range of the clade support the recognition of five species, including a species that has most often been recognized as a variety of L. rupicola (L. rupicola var. minuta). Instead, we find that it is sister to L. spinosa. This is surprising because the geographic range of L. minuta is contiguous with the other varieties of L. rupicola in the northern Hengduan region but widely separated from L. spinosa whose range lies mainly to the west of the Tibetan plateau. On close examination we find that several morphological and ecological traits also support a closer relation of L. minuta to L. spinosa. None of the other eight previously recognized varieties and species were supported. Floral traits showed high discriminatory power, correctly classifying 89% of samples to species. By comparison, leaf dimensions classified species with 59% accuracy. Our results identify diagnostic morphological apomorphies for each recognized species and major clade and provide a revised taxonomic framework for Isoxylosteum.

evolutionary biology↗

bioRxiv2026

Plaque microbial community restructuring in rampant dental caries after exclusion of a confirmed Streptococcus mutans ASV: an analysis of public 16S rRNA sequencing data

Background: Dental caries is increasingly understood as an ecological biofilm disorder rather than the consequence of a single organism. Although Streptococcus mutans is strongly implicated in cariogenesis, it remains unclear whether caries-associated plaque-community differences persist beyond this organism. Methods: We reanalysed publicly available supragingival-plaque 16S rRNA sequencing data from 88 preschool children with rampant caries (n=44) or who were caries-free (n=44; BioProject PRJNA1141721). Single-end DADA2 processing yielded 25,669 amplicon sequence variants (ASVs), including one ASV confirmed as S. mutans by an eHOMD reference-window procedure. The pre-specified primary analysis compared Bray-Curtis community composition after exclusion of this ASV. Results: Non-S. mutans community composition differed between groups (PERMANOVA pseudo-R2=0.0462, pseudo-F=4.16, P<0.001), without evidence of unequal multivariate dispersion (P=0.796); rarefaction produced a nearly identical result. Shannon diversity did not differ (P=0.486). The confirmed S. mutans ASV was detected in 8/44 rampant-caries and 42/44 caries-free samples and was lower in abundance in rampant caries. Among 758 prevalence-filtered non-S. mutans ASVs, 239 showed conventional FDR-significant differential abundance, with more showing lower than higher bias-corrected abundance in rampant caries (176 versus 63); 239 additional ASVs were classified as structural zeros. Individual ASV findings were sensitive to prevalence filtering. Adjustment for S. mutans abundance attenuated the global caries-group association (marginal pseudo-R2=0.0149, P=0.085) in the presence of strong collinearity. Conclusions: Rampant caries was associated with modest but reproducible plaque-community restructuring after exclusion of a confirmed S. mutans ASV, without a corresponding Shannon-diversity difference. These findings support a community-level ecological interpretation but do not establish statistical independence from S. mutans or a causal role for individual taxa.

microbiology↗

bioRxiv2026

EcoEnamel: Development of a Gelatin-Pectin Film for S. mutans Inhibition and Enamel Preservation in an In Vitro Model

Rinsing-dependent dental hygiene presents a significant public health challenge in water-scarce environments. This study investigated combinations of xylitol (Xyl), chitosan (Chi), glycyrrhizin (Gly), epigallocatechin gallate (EGCG), dicalcium phosphate (DCP), and nano-hydroxyapatite (nHA) on the primary bacteria behind dental caries, S. mutans. These combinations were assessed for markers of dental caries by biofilm reduction, bacterial killing, and acid buffering against S. mutans when applied to an in vitro simulated enamel model using glass bead surfaces for biofilm formation, and gene expression was subsequently examined via RT-qPCR. Separately, mineral retention was also quantified. The EGCG-DCP-Xyl film demonstrated the highest overall efficacy, achieving a significant reduction in biofilm concentration compared to the untreated control and performing similarly in magnitude to the positive toothpaste control. Dead fluorescence staining confirmed that the EGCG-DCP-Xyl film induced the highest rate of non-viable cells, followed by the Chi-Gly film and the Gly-Xyl film. During 10-day pH cycling, the EGCG-DCP-Xyl and DCP-Xyl formulations buffered pH the most, consistently maintaining mean pH levels safely above the demineralization threshold of pH 5.5. The EGCG-DCP-Xyl also optimized mineral stability with the highest retained calcium concentration, significantly outperforming the Chi-Xyl film. At the transcript level, the EGCG-DCP-Xyl film induced substantial downregulation of key virulence genes, yielding decreases in expression for glucosyltransferase B (gtfB), associated with biofilm synthesis, collagen-binding protein (cnm), associated with tissue invasion, and lactate dehydrogenase (ldh), associated with lactic acid production, compared to the untreated control, with effects comparable in magnitude to the positive toothpaste control. This research suggests that targeting bacterial pathways and mineral loss through a portable film may have potential for preventing dental caries, especially in environments where water is limited. However, additional studies are necessary to evaluate real-world effectiveness.

microbiology↗

bioRxiv2026

Interactive downstream proteomics analysis with MiraProt using Mueller cell proteomes from equine recurrent uveitis

Mass spectrometry-based proteomics requires downstream analysis of processed protein abundance data, including data inspection, filtering, statistical testing, functional enrichment, protein set comparison, network analysis, and visualization. MiraProt was developed as a modular, metadata-aware R Shiny platform that integrates these steps in a single interactive workflow for processed protein-level proteomics data. Its metadata-aware design enables identifiers, sample information, experimental conditions, transformations, and derived data columns to be defined during data preparation and reused consistently across downstream analyses. To demonstrate its use, we reanalyzed a previously published label-free proteomic dataset of primary retinal Mueller cells from healthy horses and horses with equine recurrent uveitis (ERU). ERU is a naturally occurring autoimmune eye disease of horses characterized by recurrent intraocular inflammation triggered by autoreactive T-cells. Mueller cells are specialized retinal macroglia with various functions such as maintaining retinal ion homeostasis and supporting retinal neuron metabolism. Of 193 proteins with an adjusted p-value [≤] 0.05, 187 also showed at least a twofold abundance difference between ERU-derived and control Mueller cells. Functional enrichment highlighted nuclear RNA processing, chromatin-associated structures, DNA and RNA binding, interferon responses, and cell-cycle-associated programs. Gene set enrichment analysis identified positive enrichment of Interferon Alpha Response, Interferon Gamma Response, and MYC-, E2F-, and G2M-associated gene sets. Network analysis of shared proteins further linked this signature to DNA replication, mitotic checkpoint control, and RNA processing. ERU-derived Mueller cells also showed increased abundance of MHC class II-associated proteins. Together, these findings identified an interferon-responsive, cell-cycle-associated, and MHC class II-associated Mueller cell protein signature in ERU and generated experimentally testable hypotheses for further mechanistic studies. MiraProt provides an accessible, metadata-aware framework for reproducible downstream exploration of processed proteomic datasets and prioritization of candidate proteins and pathways for experimental follow-up.

bioinformatics↗

bioRxiv2026

Feeling the Music: Preceding Vibroacoustic Stimulation Modulates Oscillatory Brain Dynamics During Music Listening

Background: Although typically considered an auditory experience, music listening engages multiple sensory systems, including somatosensory and motor pathways, making it an inherently multisensory phenomenon. However, research has predominantly examined the influence of music on other sensory systems, while the reciprocal question - how the existing state of a sensory system modulates the music listening experience- has received considerably less attention. To address this gap, we examined neural activity during music listening in two somatosensory states: one preceded by vibroacoustic stimulation (VAS) and one preceded by rest alone. Methods: Forty participants completed two MEG sessions in a within-subject crossover design. In one session, they received 20 minutes of 40 Hz VAS before listening to 10 minutes of self-selected relaxing music (VAS_ML); in the other, they lay on the same mattress without stimulation (NoVAS_ML). Oscillatory and aperiodic activity were estimated using DICS beamforming and FOOOF decomposition for the whole music period and for early and late listening segments. Results: Across the full listening period, the VAS condition was associated with reduced alpha power in the posterior temporal lobe and increased low-gamma power in the medial somatosensory and motor cortices compared to the NoVAS condition, suggesting enhanced cortical excitability and stronger auditory-motor engagement. Over time, both music listening conditions showed increases in alpha and beta power, consistent with habituation to the musical stimulus, though the spatial distribution differed qualitatively: changes were widespread across temporal and occipital regions in the NoVAS condition but remained localized to temporal areas after VAS. Additionally, VAS uniquely increased temporal-lobe theta power over time, whereas the NoVAS condition showed a decrease in the aperiodic exponent. Subjectively, participants reported stronger emotional intensity during music listening after VAS. Conclusion: These findings suggest that preceding VAS induces a more engaged neural state and qualitatively alters the temporal dynamics of music processing.

neuroscience↗

bioRxiv2026

Early establishment acts as a selective filter shaping climate-associated genomic variation in European beech

Climate change is increasing drought and heat stress in European forests, raising concerns about the capacity of long-lived tree species to respond to rapidly changing environmental conditions. While local adaptation has been documented in many forest trees, it remains unclear whether newly established seedlings, which form the forests of the future, are able to persist and adapt to these new climatic conditions. Here, we investigated genomic differences between naturally regenerated seedlings and trees of European beech (Fagus sylvatica) across the three regions of the German Biodiversity Exploratories using low-coverage whole-genome sequencing (5x) of 1,032 individuals. Population structure was primarily driven by geographic region, whereas genetic diversity was similar across life stages. Despite this genome-wide similarity, we detected allele frequency shifts between trees and seedlings, concentrated in narrow genomic windows. These shifts were strongest in surviving seedlings, suggesting that environmental filtering during early establishment may contribute to shaping the genetic composition of regenerating populations. The strongest signals were observed within the Swabian Alb, where sampled seedlings were 2-years old and had experienced a longer period of potential filtering prior to sampling. Genotype - environment association analyses identified loci associated with climatic variables, and subsequent GO enrichment analyses of genes linked to these loci revealed significantly more enriched GO terms in seedlings than in trees, suggesting stronger environmental filtering by the current climate in seedlings. In particular, we found associations with maximum air temperature, relative humidity, soil moisture, and precipitation, affecting genes involved in stress responses, growth, metabolism, and developmental processes. Together, our results demonstrate that young cohorts of European beech differ genetically from trees and reveal genomic patterns consistent with life-stage-dependent environmental filtering. These findings suggest that the genetic composition of early life-stages is already altered by current environmental conditions, possibly contributing to adaptation to new climatic conditions.

ecology↗

bioRxiv2026

Bioengineering of Pea (Pisum sativum) for the Expression of Myoglobin, a Heme-containing Animal Protein

Myoglobin, an oxygen-binding animal protein, was engineered in Pisum sativum (pea) to explore its potential as a food ingredient and balance the amino acid profile. In this study, minimal expression cassettes and binary vectors were used to express bovine myoglobin using particle gun and Agrobacterium-mediated transformation, respectively. Successful integration and expression of the myoglobin gene was achieved in P. sativum, with both methods yielding similar transformation efficiencies (~1%). Expression analysis of T2 seeds revealed that Agrobacterium-mediated transformation-derived transgenic lines that expressed myoglobin under the regulation of a Soybean 7S seed-specific promoter and Tobacco Etch Virus (TEV) translation enhancer and a chimeric Rb7MAR Terminator (Ps-BpRG13 events) consistently yielded the highest level of expression (0.32-1.57% of TSP), while transgenic lines with myoglobin expression under the regulation of a Soybean Phaseolin promoter and Rb7MAR Terminator (Ps-BpRG14 events) resulted in moderate levels of heterologous protein expression (0.13-0.83% TSP). Transgenic events with constitutive 2xCaMV35S promoter, TEV translation enhancer and Rb7MAR terminator (Ps-BpRG15 events) exhibited the lowest level of myoglobin expression (0.09-0.14% TSP). Co-bombardment of two minimal expression cassettes - one with myoglobin under the regulation of the Phaseolin promoter and Rb7MAR Terminator and the other with the nptII selectable marker under the regulation of a 2X constitutive CaMV35S promoter, TEV translational enhancer and TNOS Terminator, yielded lines that exhibited variable expression (0.03-0.77% TSP), with some events comparable in expression to Agrobacterium-derived Ps-pRG14 events. To the best of our knowledge, this is the first report of producing a heme-containing animal protein, myoglobin, in peas, with potential implications for sustainable production of food ingredients and nutritionally fortified and value-added plant products using molecular farming.

plant biology↗

bioRxiv2026

RECON infers regions of interest from H&E images and reconstructs whole-slide molecular profiles at single-cell resolution

Spatial omics technologies resolve molecular expression and spatial architecture at single-cell resolution, but profiling whole slides remains costly. In practice, only a few regions of interest (ROIs) are profiled, leaving the rest of the tissue unmeasured. S2-omics was the first framework to unify ROI selection with out-of-ROI prediction, but it operates on superpixels rather than individual cells and predicts discrete cell types rather than continuous molecular profiles. Superpixel-based representations do not explicitly preserve cell boundaries, while categorical cell-type labels cannot quantify molecular expression within cells. Here we present RECON, a two-stage framework that performs ROI inference and whole-slide molecular reconstruction at single-cell resolution, predicting both continuous molecular profiles and discrete cell-type labels. In the first stage, RECON extracts morphological and microenvironmental features from individual cells to identify a representative ROI for spatially resolved single-cell molecular profiling. In the second stage, RECON trains deep learning models on molecular measurements acquired within the selected ROI and reconstructs transcriptomic or proteomic profiles for all remaining cells on the slide. Benchmarked against pathologist annotations, RECONs ROI selection outperforms the superpixel-based S2-omics approaches (IoU: 0.75 versus 0.64). For transcriptomics, refining the modeling unit from superpixels to single cells improves per-gene Pearson correlation by 22%. For proteomics, RECON surpasses the current state-of-the-art method, ROSIE, across all 16 markers, with a median per-cell Pearson correlation of 0.91 versus 0.84. Moreover, RECON delineates tumour boundaries and regions with distinct immune-cell densities, and highlights candidate tertiary lymphoid structures. Together, these results demonstrate that RECON enables informative ROI selection and whole-slide molecular reconstruction at single-cell resolution for both spatial transcriptomics and spatial proteomics.

bioinformatics↗

bioRxiv2026

Background proteome correction promotes confident identification of dynamic protein-protein interactions between different biological contexts

Affinity purification-mass spectrometry (AP-MS) enables the characterization of protein-protein interactions (PPIs), and the ease and sensitivity of such experiments has progressively increased. Beyond steady-state interactions of target proteins, a strong interest has emerged in monitoring how PPIs change upon significant biological perturbations, such as in disease contexts or small molecule modulation of the target protein. These perturbations likely not only induce PPI changes but can also lead to altered expression of proteins not of direct interest. Changes in protein abundance may alter which proteins adsorb to the affinity purification matrix, and due to the sensitivity of modern mass spectrometers, these differential ''background binders'' can masquerade as differential interactors. Contemporary approaches often do not account for differences in the background proteome, potentially inflating the number of false positives and negatives reported. Here, we provide technical considerations for the reliable annotation of dynamic PPIs, using the O-GlcNAc transferase (OGT) as a case study. We describe the installation of affinity epitope tags on endogenous OGT in mouse embryonic stem cells (mESCs), which we then apply for OGT interactor identification via AP-MS. We show that accurate representation of the bead background, which depends on the affinity matrix in use, is critical for elimination of false positive and false negative PPIs. This became even more pertinent as OGT PPI dynamics were measured under OGT catalytic inhibition via OSMI-4, which is known to perturb gene expression. The proteomes of OSMI-4-treated and control-treated mESCs differed, leading to distinct bead backgrounds in which the differential background proteins appeared as interaction gains or losses. These false positives were resolved by incorporating straightforward experimental controls through a practical statistical framework, allowing for a direct and confident comparison between treatment conditions. Incorporating these considerations into workflows investigating PPI dynamics will improve data fidelity and reproducibility.

biochemistry↗

bioRxiv2026

Complementary cytotoxicity of GD2-targeted photoimmunotherapy and 5-aminolevulinic acid photodynamic therapy in neuroblastoma and osteosarcoma

Phototherapy, a light-activated anticancer treatment, enables localized tumor-cell killing with distinct mechanisms of action. Photoimmunotherapy (PIT) produces immunogenic tumor cell death upon near-infrared light activation of a photoabsorber through antigen-specific targeting. Photodynamic therapy (PDT) produces reactive oxygen species through red-light activation of intracellular protoporphyrin IX generated from 5-aminolevulinic acid uptake and metabolism. PIT may have limited activity in antigen-low cells, whereas PDT has less precise tumor selectivity. We combined these modalities to define their interaction, broaden cytotoxicity, and determine whether dual treatment could reduce light-dose requirements. We conjugated dinutuximab, which targets the GD2 antigen, to IRDye 700DX and characterized plasma-membrane localization by confocal and widefield microscopy. PIT and PDT monotherapies were evaluated across agent and light doses in neuroblastoma (NB) and osteosarcoma (OS) cell lines. Combination matrices were tested using interaction, highest-single-agent, and Bliss analyses. Both monotherapies demonstrated significant light-dose-dependent effects in NB and OS. PIT produced no measurable cytotoxicity in antigen-blunted control cells, whereas PDT remained effective, confirming antigen-dependence of PIT and antigen-independence of PDT. The combination interaction was significant in SK-N-BE(2) but not LM7. At selected combinations, however, dual treatment produced greater killing than the more effective matched monotherapy in both SK-N-BE(2) and LM7 (Padj<0.022). Notably, lowest combination of PIT 10 J/cm2 plus PDT 10 J/cm2 achieved 90.3% killing in SK-N-BE(2), exceeding higher light-dose PIT or PDT monotherapy, suggesting a light-dose sparing effect. These findings establish potent and complementary PIT-PDT activity, supporting dual phototherapy to broaden cytotoxicity and reduce light-dose requirements in GD2-expressing tumor phototherapy.

cancer biology↗

bioRxiv2026

Quantifying sprint force-velocity elasticity: implications for individualized training decisions

This study aimed to (1) develop an elasticity framework for the sprint force-velocity (F-V) relationship and (2) examine how maximal force (F_{0}), maximal velocity (v_{0}), and sprint distance modulate the four derived elasticity metrics, and (3) explore these elasticity metrics' interrelation. After modelling the F-V relationship differential equation, four elasticity metrics were defined as force elasticity (F_{e}), the elasticity of sprint time to F_{0}; velocity elasticity (v_{e}), the elasticity of sprint time to v_{0}; the force-velocity elasticity norm {(\mathrm{F}-\mathrm{V}}_{\mathrm{EN}}=\sqrt{F_{e}^{2}+v_{e}^{2}}), capturing the combined sprint time sensitivity to proportional changes in F_{0} and v_{0}; and the force-velocity elasticity ratio {(\mathrm{F}-\mathrm{V}}_{\mathrm{ER}}=F_{e}{\div v}_{e}), indicating which variable dominates the sprint time response. Model simulations showed that F_{e} decreased with rising F_{0} and increased with rising v_{0}, while v_{e} showed the opposite pattern. With increasing sprint distance, F_{e} decreased and v_{e} increased. Given its negligible effect on sprint time, ignoring air resistance yields a conservation law (2F_{e}+v_{e}\equiv 1), indicating that a gain in one elasticity metric necessarily diminishes the other in a fixed proportion. This framework also identifies a valley distance (d_{valley}) at {\mathrm{F}-\mathrm{V}}_{\mathrm{ER}}=2, where {\mathrm{F}-\mathrm{V}}_{\mathrm{EN}} is minimized (\sqrt{0.2}) and sprint time is least responsive to changes in F-V relationship variables. Empirical data confirmed that the two theoretical laws still hold approximately when air resistance is considered. By linking changes in F_{0} and v_{0} to sprint time across different distances, the elasticity framework provides a quantitative basis for estimating the theoretical sprint time response to documented changes in F-V relationship variables.

biophysics↗

bioRxiv2026

Why are fishers retaining manta and devil ray bycatch?

Increasing fishing pressure, including from small-scale fisheries, has caused declines in more than one-third of all elasmobranch species. Tackling conservation issues in small-scale fisheries requires interdisciplinary approaches due to the coastal community's interdependence on marine resources. To support inclusive policy change and fisher engagement, an understanding of the motivations driving fishers' operational choices (i.e., the retention of elasmobranch bycatch) is needed. We assess the motivational drivers behind bycatch retention of one of the slowest-growing and most vulnerable elasmobranch groups, manta and devil rays (collectively, mobulids), through a case study in India, their largest fishery in the world. We conducted a best-worst scaling survey in the fishery-intensive states of Tamil Nadu and Andhra Pradesh, which make significant contributions to mobulid landings on India's east coast. Our results suggest that fishers exhibit varied motivations for retaining mobulid bycatch across states. Financial motivation to sell mobulids for additional revenue was the most important motivator for bycatch retention in both states. In Tamil Nadu, the top three motivators were all financially driven, whereas in Andhra Pradesh, the top three motivators included both financial and non-financial attributes, such as nutritional importance and storage optimisation. As the first socio-economic study of mobulid fisheries in India, we show that motivations underlying bycatch retention decisions vary geographically and may be influenced by cultural differences between states and the socio-economic characteristics of decision makers. Based on identified fisher motivations, we provide context-specific recommendations to align conservation strategies with the values fishers derive from the mobulid fishery and encourage participation in conservation. These include subsidies for net repair to encourage mobulid release; promotion of a minimum price measure for sustainably sourced alternative species; quality improvement of target species; and increased awareness of national and international regulatory obligations (e.g., CITES, CMS, IOTC).

ecology↗

bioRxiv2026

A novel target associated with senescence and inflammatory signaling in human intervertebral disc degeneration

Background Intervertebral disc degeneration (IDD) is a leading cause of chronic low back pain and disability worldwide, affecting most individuals over 50 years of age. Despite its prevalence, no disease-modifying therapies exist, and current interventions are limited to reducing pain. Cellular senescence and the associated secretory phenotype (SASP) have been increasingly recognized as major drivers of disc matrix degradation and inflammation. However, the upstream molecular mechanisms that lead to IDD degeneration are still unknown. Connexin 43 (Cx43), a gap junction protein implicated in progression of age-related diseases, has emerged as a key regulator of cellular senescence and inflammatory signalling in musculoskeletal tissues. Methods Human primary cells were isolated from intervertebral disc samples obtained from patients classified into clinically meaningful groups: healthy controls, chronic/mechanical degeneration (DDD, ADJ, ASD), and acute/inflammatory event (herniated nucleus pulposus, HNP). Cx43 expression was assessed by qPCR and Western blotting. Cellular senescence was evaluated through SA-{beta}-gal staining and analysis of p53/p21 expression. SASP factors and EMT-related markers were measured by qPCR. Protein expression was quantified by immunoblotting across different age groups and degeneration grades. Results In this current study Cx43, was identified as the most abundant connexin isoform in human intervertebral discs, showing a progressive increase in expression with age and disc degeneration. Also, high Cx43 expression correlated with increased expression of the senescent markers p53 and p21 and increased SA-{beta}-gal activity. Besides, increased expression of EMT-related and differentiation markers has been correlated with high Cx43 levels in human IDD samples, consistent with fibrotic remodeling processes. Conclusions These findings identify aberrant upregulation of Cx43 signaling as a potential mechanistic link between intervertebral disc cellular senescence and extracellular matrix degradation, with the ensuing inflammatory response, representing a novel potential therapeutic target to modulate senescence-driven pathogenesis and modulate IDD progression.

molecular biology↗

bioRxiv2026

INFORME: coupling information-theoretic experimental design with nonlinear mixed-effects modeling for efficient observation scheduling

Mathematical models of treatment response can inform individualized therapy, but their calibration often requires longitudinal measurements that are costly, burdensome, and collected on fixed schedules. Such schedules may be inefficient, over-sampling patients whose response is already well characterized while delaying informative measurements for those whose model parameters remain uncertain. We present INFORME (INFORmation-theoretic design with Mixed Effects), a framework that combines Bayesian information-theoretic experimental design with nonlinear mixed-effects modeling to adaptively select each patients next measurement time. Population and response-subgroup parameter distributions learned from an existing cohort provide informative priors, allowing candidate measurement times to be ranked by their expected reduction in patient-specific parameter uncertainty. As observations accumulate, priors can be updated to reflect the response subgroup most consistent with the patients data. We evaluate INFORME in two radiotherapy datasets: 150 synthetic tumor volume trajectories from a hybrid cellular automaton model of prostate cancer spheroids (HD1) and longitudinal tumor volumes from 39 patients with head-and-neck cancer (HD2). In HD1, population priors allowed omission of both pretreatment scans, while adaptive scheduling reduced the protocol from nine scans to three or four, with the response group identified from a single post-treatment scan on day 27. In HD2, the adaptive schedule used three scans instead of six and improved prediction by delaying the first on-treatment scan from week 1 to week 2, avoiding transient dynamics that produced false-positive and false-negative response projections. Across both datasets, the adaptive schedules used a mean of 2.7 scans in stead of seven and advanced completion of the patient-specific prediction by a mean of 15.5 days (95% CI, 6.7-24.3) relative to the equidistant protocol, while treatment duration remained unchanged. INFORME therefore reduces measurement burden and accelerates patient-specific prediction by concentrating observations at times that are most informative for model calibration.

systems biology↗

bioRxiv2026

Physiological and anatomical leaf acclimation of understory trees subjected to a through-fall precipitation exclusion in a temperate rain forest in southern South America.

Water input is a key component of the ecosystems. Water defines the functionality, composition, and structure of biomes; therefore, any change in its availability would have an impact on ecosystem features. Moreover, a change in the water balance of an ecosystem affects its persistence as well as biochemical cycles, such as the carbon and nitrogen. Forests are ecosystems structured using high amounts of water. Thus, trees, the oldest living plants, are the prime species in these ecosystems and are the main managers of this abiotic element. Trees uptake water from the soil, store it in their biomass, and exchange it with the environment through leaf stomata. They also intercepted rainfall and fog with their canopies. All of this water is also transmitted to the entire biological diversity that inhabits these ecosystems. Any change in water input affects the web described above. The ability of trees to modify their anatomy or processes, that is, to acclimate to novel climates, is of great advantage in maintaining the characteristics of ecosystems. In this study, we took advantage of a precipitation exclusion experiment to reveal the acclimation of shade-tolerant understory trees, which will be the main component of a cold temperate rainforest in the future. We evaluated different anatomical and physiological leaf traits involved in the use of water by these species. We hypothesized that, as observed in similar experiments, species would adopt more conservative water-use strategies by adjusting their functional traits accordingly. Contrary to our hypotheses, we found that understory tree species inhabiting this temperate ecosystem will not become more conservative when using water. In minimal, but significant differences, most of the studied species displayed traits, in the precipitation exclusion treatment, that were demonstrated to be water spender, rather than conservative. We attributed these contrasting changes to root metabolism alleviation due to the flooded soils of Chiloe inhabited by these forests.

ecology↗