bioRxiv Preprints

{
  "doi": "10.64898/2026.07.27.740543",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.27.740543v1",
  "title": "Leaf hydraulics is a core component of plant immunity",
  "source": "biorxiv",
  "authors": "Marty, S.; Bellenot, C.; vasselon, d.; Goussot, M.; Boulanger, A.; Audran, C.; Savourat, P.; Sarthou, A.-S.; Pouzet, C.; Routaboul, J.-M.; Laufs, P.; NOEL, L. D.",
  "version": "1",
  "abstract": "Hydathodes at leaf margins mediate guttation of xylem-derived fluids and serve as primary entry sites for adapted vascular bacterial pathogens such as Xanthomonas campestris. Infection of Arabidopsis mutants with fewer hydathodes resulted in spontaneous mesophyll water-soaking and revealed unexpectedly-large pathogen populations explained by direct infection of the mesophyll niche through stomata and subsequent proliferation. Physical blockage of hydathodes also induced mesophyll water-soaking and enhanced bacterial growth in both Arabidopsis and cauliflower leaves. These findings reveal a dual role for hydathodes as primary sites of infection while being essential to restrict pathogen proliferation in nonvascular tissues. More broadly, our study identifies leaf hydraulics and guttation as central components of water immunity in vascular plants.",
  "category": "plant biology",
  "published_at": "2026-07-28T00:00:00.000Z",
  "corresponding_author": "Laurent D NOEL",
  "journal_published_doi": null,
  "corresponding_institution": "LIPME"
}

{
  "doi": "10.64898/2026.07.27.740979",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.27.740979v1",
  "title": "Breakdown of sporophytic self-incompatibility: Diploids versus tetraploids",
  "source": "biorxiv",
  "authors": "Douet, D.; Billiard, S.; Vekemans, X.; Clo, J.",
  "version": "1",
  "abstract": "Many angiosperm species possess self-incompatibility (SI) systems that prevent self-fertilization. Because empirical studies often report higher selfing rates in tetraploids than in diploids, we investigate whether sporophytic self-incompatibility (SSI) is more likely to break down after the introduction of a self-compatible (SC) allele in tetraploid populations. To address this question, we use analytical models and individual-based simulations to compare diploid and tetraploid populations under two main scenarios: (1) all SI alleles are codominant, and (2) SI alleles are structured into dominance classes. Overall, our results indicate that SSI is more difficult to maintain in tetraploids than in diploids, with dominance relationships playing a key role in the invasion success of an SC allele. When SI alleles are organized into dominance classes, increasing the dominance of the SC allele generally favors SSI breakdown in tetraploids, while diploids show weaker sensitivity to dominance, with SSI maintained across all dominance scenarios for the SC allele under sufficiently high inbreeding depression. However, when the SC allele is dominant over all SI alleles, SSI is more readily m",
  "category": "plant biology",
  "published_at": "2026-07-28T00:00:00.000Z",
  "corresponding_author": "Diane Douet",
  "journal_published_doi": null,
  "corresponding_institution": "Université de Lille"
}

{
  "doi": "10.1101/2025.09.05.674523",
  "url": "https://www.biorxiv.org/content/10.1101/2025.09.05.674523v5",
  "title": "Semenogelin-1 Inhibition of Mouse Sperm Hyperactivation Reveals Two Functional Domains Modulating CatSper Channel",
  "source": "biorxiv",
  "authors": "Mariani, N. A. P.; Santos, N. C. M.; Andrade, J. J.; Andrade, A. D.; Rezende, B.; Steeman, T. J.; Novero, A. G.; de Lima-Junior, J. C.; Calderaro, G.; Themer, A. C. F.; Kushima, H.; Buffone, M. G.; Krapf, D.; Lishko, P. V.; Silva, E. J. R.",
  "version": "5",
  "abstract": "Seminal plasma is essential for sperm survival and function after ejaculation. Semenogelin-1 (SEMG1), the predominant seminal plasma protein, transiently suppresses sperm motility and hyperactivation after ejaculation through epididymal protease inhibitor (EPPIN) binding. However, the molecular mechanism underlying SEMG1-mediated inhibition of hyperactivation remains unclear. Here, we tested the hypothesis that SEMG1 inhibits CatSper, a sperm-specific calcium channel crucial for hyperactivation. Full-length recombinant mouse SEMG1 (mSEMG1; Q32-G375) inhibited both progressive motility and hyperactivation; the latter was not recovered with NH4Cl-induced alkalinization, indicating an effect downstream of capacitation-associated intracellular alkalinization. Electrophysiological recordings revealed that mSEMG1 reduced CatSper currents at physiologically relevant concentrations. Truncated mSEMG1 fragments mSEMG1Q32-V118 and mSEMG1R98-G375, but not mSEMG1Y221-G375, inhibited sperm hyperactivation and CatSper currents to a similar extent as full- length mSEMG1. Notably, only mSEMG1R98-G375 retained full EPPIN-binding capacity. Together, our findings identify two functional domains within",
  "category": "physiology",
  "published_at": "2026-07-28T00:00:00.000Z",
  "corresponding_author": "Erick J. R. Silva",
  "journal_published_doi": null,
  "corresponding_institution": "Universidade Estadual Paulista"
}

{
  "doi": "10.64898/2026.07.27.739831",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.27.739831v1",
  "title": "A p53-dependent FBXO44-RAD18 axis limits mutagenesis by terminating translesion DNA synthesis",
  "source": "biorxiv",
  "authors": "Butera, A.; Caporali, S.; Capradossi, F.; Smith, P.; Tabagari, N.; Nikoloska, N.; Mayans, O.; Janic, A.; Gruber, A. J.; D'Angiolella, V.; Amelio, I.",
  "version": "1",
  "abstract": "DNA lesions continually challenge genome replication and threaten genome integrity. DNA damage tolerance pathways, including translesion DNA synthesis (TLS), allow cells to bypass lesions and prevent stalled forks from collapsing into double-strand breaks. Because TLS polymerases are intrinsically error-prone, however, this pathway must be tightly restrained; persistent or deregulated TLS can increase mutagenesis, create therapeutic vulnerabilities, and promote aggressive cancer phenotypes. Through integrated transcriptional profiling, genome-wide CRISPR/Cas9 screening for replication-stress sensitivity, and complementary proteomic analyses, we identify F-box protein 44 (FBXO44) as a late p53-responsive regulator of the TLS mediator RAD18. FBXO44 promotes RAD18 ubiquitination during recovery from replication stress and facilitates shutdown of RAD18-dependent PCNA monoubiquitination. Consistently, FBXO44 loss delays resolution of replication stress and TLS signaling, increases mutation frequency, and is associated with elevated mutational burden and therapy resistance in experimental models and patient datasets. These findings define a p53-FBXO44-RAD18 regulatory axis that limits mu",
  "category": "cancer biology",
  "published_at": "2026-07-28T00:00:00.000Z",
  "corresponding_author": "Ivano Amelio",
  "journal_published_doi": null,
  "corresponding_institution": "University of Konstanz"
}

{
  "doi": "10.64898/2026.04.16.719043",
  "url": "https://www.biorxiv.org/content/10.64898/2026.04.16.719043v2",
  "title": "ProNA3D: Distance-Based Analysis of Nucleic Acid-Containing Interfaces",
  "source": "biorxiv",
  "authors": "Genz, L. R.; Topf, M.",
  "version": "2",
  "abstract": "1.Biomolecular interactions are central to many essential cellular processes, but RNA-containing complexes remain challenging to resolve structurally, even as experimental methods and AI-based prediction have expanded structural coverage. Tools for the integrated analysis of complex interfaces remain limited. We present ProNA3D, a tool that provides a unified platform for analyzing protein-nucleic acid and nucleic acid-only complexes, bridging the gap between structure prediction and functional interpretation. ProNA3D supports both experimental and computationally predicted structures, incorporating scoring metrics for AlphaFold3 predictions. It also offers interactive two-dimensional interface visualization and secondary-structure topology plots for RNA and DNA. An interface-based density zoning feature facilitates structure analysis in cryo-EM maps, allowing evaluation of dynamic complexes in the context of heterogeneous density. We demonstrate ProNA3D on diverse complexes solved by X-ray crystallography or cryo-EM, as well as on computational models. For example, in a trimeric complex of HIV-1 RNA and a human antibody, ProNA3D identified a high-connectivity nucleotide with poten",
  "category": "bioinformatics",
  "published_at": "2026-07-28T00:00:00.000Z",
  "corresponding_author": "Maya Topf",
  "journal_published_doi": null,
  "corresponding_institution": "Leibniz-Institut fuer Virologie (LIV) and Universitaetsklinikum Hamburg Eppendorf (UKE)"
}

{
  "doi": "10.64898/2026.07.27.740823",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.27.740823v1",
  "title": "Bio-CM{superscript 2}: Distributed computational optics for cortex-widecellular imaging",
  "source": "biorxiv",
  "authors": "Hu, G.; Deng, Q.; Qi, T.; Chen, Z.; Rauscher, B. C.; Chai, N.; Bogatova, D.; Weinberg, B.; Smith, J.; Davison, I. G.; Thunemann, M.; Devor, A.; Tian, L.",
  "version": "1",
  "abstract": "Understanding distributed biological systems, particularly neural circuits, requires simultaneous cellular-resolution imaging across millimeter-scale fields of view (FOV). Existing miniature microscopes remain fundamentally constrained by trade-offs among FOV, spatial resolution, and optical complexity, limiting their ability to bridge cellular microscopy with cortex-scale imaging. Here we introduce distributed computational optics, a framework that distributes image formation across coordinated optical modules and computationally integrates their measurements into a unified image. We realize this framework in Bio-CM2, a computational miniature mesoscope that partitions the imaging field across four optical modules while converging their measurements onto a common image sensor. This architecture overcomes the aberration-scaling limitations of conventional miniature optics while avoiding the hardware complexity of multi-camera systems and the contrast degradation associated with optical multiplexing. Bio-CM2 achieves a 7.5 x 10 mm2 FOV while enabling cellular-resolution in vivo imaging at video rates. We demonstrate its utility through two complementary imaging modalities in head-fi",
  "category": "bioengineering",
  "published_at": "2026-07-28T00:00:00.000Z",
  "corresponding_author": "Lei Tian",
  "journal_published_doi": null,
  "corresponding_institution": "Boston University"
}

{
  "doi": "10.64898/2026.07.27.740975",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.27.740975v1",
  "title": "Self-Actuating 4D Cell-Strand Bioprinting",
  "source": "biorxiv",
  "authors": "Ding, A.; Cunha, A. F.; Oliveira, M. B.; Mano, J. F.; Alsberg, E.",
  "version": "1",
  "abstract": "Engineering biomimetic tissues with dynamically evolving 3D architectures represents an important direction for next-generation tissue engineering, as it enables recapitulation of the continuous morphogenesis of native tissues during development and regeneration. Here, a self-actuating 4D cell-strand bioprinting platform is developed to engineer complex tissue architectures through autonomous cell contractile force (CCF)-driven morphing without requiring external stimuli. The platform integrates a mechanically compliant and self-softening base hydrogel with embedded high-density cell strands printed using a fast-degrading carrier bioink. During culture, the carrier bioink rapidly degrades while the encapsulated cells proliferate and establish connected cellular networks, generating localized contraction that drives programmable shape transformation. Through spatial patterning of embedded cell strands, constructs with diverse morphologies, including V-shaped, helical, folded, and tubular architectures, are generated via controllable self-actuated morphogenesis. The platform further enables engineering of cartilage-like and bone-like tissues with well-defined curvature configurations",
  "category": "bioengineering",
  "published_at": "2026-07-28T00:00:00.000Z",
  "corresponding_author": "Eben Alsberg",
  "journal_published_doi": null,
  "corresponding_institution": "University of Illinois Chicago"
}

{
  "doi": "10.64898/2026.07.26.740722",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.26.740722v1",
  "title": "DCGAN-Based Synthetic MRI Augmentation for Data-centric Brain Tumor Segmentation",
  "source": "biorxiv",
  "authors": "Das, P.; Rath, J.; Jaiswal, A.; Dash, B. B.",
  "version": "1",
  "abstract": "Accurate brain tumor segmentation from magnetic resonance imaging (MRI) remains a challenging task because supervised deep learning models require large quantities of annotated data, which are expensive and time-consuming to obtain. This study investigates whether synthetic MRI images generated using a Deep Convolutional Generative Adversarial Network (DCGAN) can improve U-Net-based brain tumor segmentation using synthetic data augmentation. Experiments were performed on the LGG-MRI dataset comprising 3,929 image-mask pairs. A baseline U-Net was first trained using the original training dataset. Synthetic MRI images were subsequently generated using a DCGAN, and threshold-derived pseudo-masks were assigned to the generated images to construct an augmented training dataset. The same U-Net architecture was then retrained using the augmented dataset and evaluated on an identical held-out test set. Compared with the baseline model, DCGAN-based augmentation increased the Dice coefficient from 0.2067 to 0.3037 and the Intersection over Union (IoU) from 0.1243 to 0.1918, while reducing the final test loss from 0.0474 to 0.0275. These results indicate that synthetic MRI augmentation was as",
  "category": "bioengineering",
  "published_at": "2026-07-28T00:00:00.000Z",
  "corresponding_author": "Bibhuti Bhusan Dash",
  "journal_published_doi": null,
  "corresponding_institution": "School of Computer Applications, KIIT Deemed to be University, Bhubaneswar, Odisha, India"
}

{
  "doi": "10.64898/2026.07.27.740463",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.27.740463v1",
  "title": "A Modular Bio-Hybrid Skin Model for Optical Testing Applications",
  "source": "biorxiv",
  "authors": "Bajrami, D.; Wei, K.; Spano, F.; Agah, N.; Bonmarin, M.; Rossi, R.",
  "version": "1",
  "abstract": "Synthetic optical skin models offer reproducible, tunable optical properties but lack biological responsiveness, while tissue engineered skin models provide cellular authenticity but suffer from optical variability and limited controllability. The growing demand for alternatives to animal models in the development and validation of optical biomedical technologies highlights the need for a new class of test system that combines the strengths of both approaches while addressing their respective limitations. Here, we introduce the concept of a modular biohybrid skin model, a new testing concept that integrates an optically defined artificial epidermal layer, incorporating polydopamine nanoparticles for changes in skin tone, with living human keratinocytes in two and three-dimensional configurations. In the Optical Protection Model, UV-B-induced apoptosis in primary keratinocytes is quantitatively modulated by model pigmentation level, demonstrating a relationship between optical attenuation and caspase 3/7 activity across three artificial skin tone conditions. In a Structured Dermal Model, keratinocytes seeded onto a hydrogel scaffold localize within follicle-like microcavities, as co",
  "category": "bioengineering",
  "published_at": "2026-07-28T00:00:00.000Z",
  "corresponding_author": "Dardan Bajrami",
  "journal_published_doi": null,
  "corresponding_institution": "Empa, Swiss Federal Laboratories for Materials Science and Technology"
}

{
  "doi": "10.64898/2026.07.27.740917",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.27.740917v1",
  "title": "An integrated biomaterials-centred approach of the ageing thymic microenvironment reveals design principles for regenerative biomaterials",
  "source": "biorxiv",
  "authors": "Di Bernarndo, A.; Zanirato, C.; Briatico, F.; Petrini, P.; Butnarasu, C. S.; Leo, F.; Ambrogio, C.; Patrucco, E.; Locatelli, A.; Oliva, F.; Passoni, A.; Medana, C.; Visentin, S.; Sardelli, L.",
  "version": "1",
  "abstract": "Thymic involution is commonly addressed as a loss of epithelial and lymphoid tissue, yet the accompanying remodelling of the microenvironment remains poorly defined. This work applied a biomaterials-centered approach to compare young and aged bovine thymus by integrating histology, oscillatory rheology, untargeted lipidomics, ICP-MS and AP-MALDI mass spectrometry imaging. This holistic approach connects the mechanical, compositional, and spatial features of the native thymus with the development of thymus-inspired biomaterials. Ageing increased both storage and loss moduli by more than one order of magnitude and reduced the linear viscoelastic region approximately fivefold, defining a markedly stiffer and more strain-sensitive material state. This mechanical transition was accompanied by lipid remodelling, with double realtive contribution of triacylglycerols to the lipid pool doubled and loss of membrane-associated phospholipids. The elemental profile also contracted, with total metal content decreasing by one-third and zinc showing a reduction of 70%. At the architectural level, the corticomedullary ratio was more than halved, while AP-MALDI imaging revealed an approximately 40% ",
  "category": "bioengineering",
  "published_at": "2026-07-28T00:00:00.000Z",
  "corresponding_author": "Lorenzo Sardelli",
  "journal_published_doi": null,
  "corresponding_institution": "Department of Molecular Biotechnology and Health Science, University of Torino, Torino, Italy"
}