Biology subjects

Weber, M.

Publications and source records attributed to Weber, M..

At least 19 recordsLinked to original sources

bioRxiv2026

The global distribution of human-visible flower color diversity

The spectacular diversity of flower colors is among the most widely appreciated features of the natural world. For over a century, biologists and naturalists have speculated about whether human-visible flower color diversity shifts predictably across ecological systems worldwide. Yet challenges in measuring color across the vast diversity of flowering plants have limited global tests of these patterns. Using a computer-vision enabled analysis of community science data across 64,000 species, we modeled the major global features of human-visible flower color. We find a robust latitudinal gradient in color diversity after standardizing the number of species sampled from each flora, with flower colors occurring in more even proportions toward the equator. Modeling flower color alongside climate and pollination strategy reveals associations with both biotic and abiotic factors. These findings provide a global basis for testing how ecological and evolutionary processes shape the relative representation of floral phenotypes, beyond differences in species richness.

evolutionary biology↗

bioRxiv2026

Intracellular accumulation of AAV6 genomes governs microglia reactivity and the inflammatory response in retinal gene therapy

Adeno-associated viral (AAV) vectors possess immense potential for gene therapy applications. However, microglia can mount an immune response against AAV vectors. Yet, microglia are therapeutic targets since they play a driving role in the progression of neurodegenerative diseases. Thus, it is critical to understand the cellular processes driving the microglia-mediated immune response against AAV vectors. To this end, we modelled AAV6 induced inflammation upon retinal gene therapy in minipigs. Upon AAV6 administration, the IBA1+ cells demonstrated a morphological transition to the amoeboid form, indicating microglial reactivity. We also observed the invasion of peripheral immune cells in the retina. To elucidate the underlying molecular mechanisms, we transduced human iPSC derived microglia-like cells (iMGLs) in vitro with AAV6 and AAV8 respectively. Only AAV6 transduced iMGLs exhibited morphological features and a transcriptomic signature of microglial reactivity. The magnitude of intracellular AAV6 viral genomes was significantly higher as compared to the AAV8 condition. The elevated levels of intracellular AAV6 genomes induced a DNA damage response in AAV6-transduced iMGLs, which is a key feature of neuroinflammation-linked microglial reactivity. Thus, our work highlights the impact of intracellular viral genome accumulation on microglial reactivity and its implications for retinal gene therapy associated inflammation.

neuroscience↗

bioRxiv2026

Glycosaminoglycan presentation-dependent regulation of glial responses by Orion during Drosophila neuronal pruning

Neuronal pruning refines neural circuits by eliminating unnecessary connections to ensure proper nervous system function. In Drosophila mushroom body gamma-neuron remodeling, the chemokine-like protein Orion is required for astrocyte infiltration and phagocytosis. This study investigated whether glial responses depend on how Orion is presented. We found that Orion interacts with glycosaminoglycans (GAG) associated to proteoglycans, which are essential for proper axon pruning. Tethering Orion to the gamma-neuron plasma membrane, mimicking glycosaminoglycan binding, was sufficient to induce astrocyte infiltration into axon bundles. However, membrane-bound Orion alone could not efficiently support phagocytosis, which additionally requires a soluble and mobile Orion pool. We also identified exosomes carrying GAG-bound Orion as potential mediators of neuronal remodeling. These findings provide the first evidence that glial infiltration can be uncoupled from phagocytosis, demonstrating that the mode of Orion presentation regulates distinct glial mechanisms during neuronal remodeling.

neuroscience↗

bioRxiv2026

Shedding light on fenestrations in carnivorous pitcher plants: a test for convergent function

A longstanding question in evolution is if similar morphologies shared by distantly related organisms facing similar environmental pressures belie similar functions. The carnivorous pitcher form has evolved in three distinct plant lineages and encompasses a suite of convergent morphological traits, providing a natural experiment to test hypothesized links between morphology and function. Multiple pitcher plant species possess fenestrations (i.e., small windows) that let light pass through the pitcher leaf. While research on one species, Nepenthes aristolochioides, demonstrates that fenestrations manipulate light to create false exits and increase prey capture, whether this convergent morphology serves this convergent function in other pitcher species remains unresolved. We explored the function of fenestrations in two additional species of pitcher plants, Nepenthes klossii and Cephalotus follicularis, where the morphology and function of fenestration were previously unexplored. We inspected micromorphology of pitcher structure, conducted an insect bioassay with live plants to test for links between morphology and function, and quantified traits associated with light manipulation from herbarium specimens. Both species exhibited fenestration and related pitcher morphology similar to N. aristolochioides. Yet our experiments did not reveal a significant effect of light passing through fenestrations on fly capture for these two species. Key differences between these species and the previously investigated species may be the presence of wax crystals and the absence of viscoelastic fluid. While future studies may uncover weak to moderate light manipulation function not detected in our study, our data do not support convergent function in these distantly related, morphologically similar species.

evolutionary biology↗

bioRxiv2026

FRET-guided integrative modeling resolves Mg2+-dependent RNA tertiary-contact formation

Tertiary contact interactions between GNRA tetraloops and their receptors are recurrent motifs that stabilize complex RNA folds and in the context of ribosome biogenesis contribute to ribosomal subunit maturation. High-resolution structure determination methods typically yield single structural snapshots, which may not fully describe the conformational collection populated by such contacts in solution. Here, we investigate a ribosomal RNA tertiary contact formed by a GAAA tetraloop and a kissing loop acting as its receptor using single-molecule FRET-guided integrative modeling. We used a minimal RNA model construct in which the tetraloop and its kissing loop receptor are connected by flexible poly(A)-linkers, assembled its bound state from the native ribosomal cryo-EM geometry, and combined restrained and unrestrained all-atom molecular dynamics simulations with in silico FRET and dynamic fluorescence anisotropy predictions to compare with the respective experiments under varying salt conditions. The modeled bound state matches the smFRET distribution only at non-physiologically high Mg2+ concentrations. At 10 mM Mg2+, however, the single-molecule FRET distribution remains heterogeneous and is reproduced by mixtures of bound and unbound conformations, indicating their coexistence under intermediate Mg2+ conditions. Thus, smFRET-guided integrative modeling resolves subpopulations invisible to static high-resolution structures and ensemble FRET, providing a route to validate and refine RNA structural models and conformational ensembles in solution.

biophysics↗

bioRxiv2026

A neuroimmune IL-13 axis is associated with human enteric nervous system development

The mechanisms governing maturation of the human enteric nervous system (ENS) during early postnatal life remain poorly defined. Here, we characterize the transcriptomic, cellular, and functional landscape of the neonatal human ileum and identify a neuro-immune axis associated with ENS expansion. Using human tissue transcriptomics, flow cytometry, iPSC-derived enteric neural lineages, and single-cell interactome analyses, we show that the neonatal ileum is enriched for pro-neurogenic transcriptional programs and harbors a greater abundance of enteric neurons and glia than the adult tissue. T cells emerge as a predominant source of interleukin-13 (IL-13) in the neonatal gut, and enteric neurons express its receptor IL13RA1, enabling direct immune-to-neuron signaling. Functional experiments demonstrate that IL-13 enhances expression of key enteric neuronal markers in a concentration-dependent manner. In parallel, single-cell analyses identify enteric neurons as a major predicted source of macrophage migration inhibitory factor (MIF), with signaling directed toward T and NK cell populations, suggesting that the ENS actively shapes the immune environment it depends upon. Together, these findings support a model in which bidirectional neuro-immune communication establishes a pro-neurogenic niche during a critical window of ENS development. This work positions the neonatal immune system as an active contributor to ENS maturation and offers a new perspective on how neuro-immune crosstalk shapes intestinal development in early life.

neuroscience↗

bioRxiv2026

Evolutionary exploration of drug-like chemical space utilizing generative AI and virtual screening

The identification of suitable lead molecules in the vast chemical space is a critical and challenging task in drug discovery campaigns. Recently, it has been demonstrated that large-scale virtual screening provides a powerful approach to accelerate the identification of novel drug candidates by screening ever increasing virtual ligand libraries, which have reached magnitudes of > 1020 compounds. However, this desirable increase in potentially bioactive molecules poses a new challenge as enumerating and virtually screening such huge compound libraries is computationally prohibitive. Consequently, advanced approaches to navigate ultra-large chemical spaces and to identify suitable candidate molecules therein are urgently needed. Here, we present an evolutionary algorithm framework using molecular generative AI, reaction-based substructure searching, and iterative model fine-tuning for a targeted and efficient exploration of chemical fragment spaces. Combining this approach with large-scale virtual screening we are able to identify target-specific candidate molecules within the commercially available Enamine REAL Space ([~]1015). We demonstrate the applicability of the approach by successfully identifying and biochemically validating pH-specific ligands of the {micro}-opioid receptor. Our results demonstrate that integrating generative AI with evolutionary algorithms provides a promising route to explore ultra-large chemical spaces for the discovery of novel, synthetically accessible lead molecules.

bioinformatics↗

bioRxiv2026

3D-MINSTED nanoscopy and protein tracking in densely labelled living cells

Investigating the movements and conformational changes of proteins in living cells is essential for understanding their function. The recently introduced fluorescence nanoscopy method called MINSTED has successfully tracked single fluorophore-labelled proteins, albeit in fixed cells and two dimensions only. Here we introduce a MINSTED setup for live-cell tracking of individual proteins in three dimensions (3D) with a localization precision {sigma} down to < 1 nm. Applied to the motor protein kinesin-1, our MINSTED nanoscope follows single proteins in 3D as they process along microtubules in 16 nm steps. Individual steps are resolved amid substantial intracellular background. The unique capability of the 3D stimulated emission depletion (STED) beam to carve out the signal of the protein label of interest enables efficient single-molecule investigations at hitherto unpractically high concentrations of labelled proteins and thus in crowded live-cell environments.

biophysics↗

bioRxiv2026

Convergent evolution of red pigmentation in extrafloral nectaries: global patterns and mechanisms

Convergent traits are a signature of adaptation, where shared selective pressures may lead to the replicated evolution of traits with similar function. Here, we present an integrative investigation of a widespread yet understudied feature of an iconic, convergent mutualistic plant trait - red pigmentation in extrafloral nectaries (EFNs). We surveyed 625 species to describe the distribution of red coloration in EFNs across plant morphology, biogeography, and phylogeny for the first time and propose several adaptive hypotheses for the drivers of their convergence across plants. We then test several of these hypotheses by integrating our global-scale biogeographic and phylogenetic analysis with phylogenetically paired common garden bioassays and a museum collections survey. We find that across the plant phylogeny, cold wet regions and deserts are hotspots of red EFN coloration, and multiple lines of evidence point to a fungal defense role of red pigments in EFNs. Ultimately, our findings highlight red EFNs as a highly convergent phenotype across plants and point to distinct selective pressures underlying the distribution of EFN coloration and EFNs themselves.

evolutionary biology↗

bioRxiv2026

Multiomic profiling of human and canine soft-tissue sarcomas reveals extensive molecular homology across species and identifies clinically relevant subgroups

Soft-tissue sarcoma (STS) are rare and heterogeneous mesenchymal tumours with over 100 recognized human subtypes. Despite advances in cytogenetic and molecular characterization, diagnostic precision and therapeutic options remain limited for most subtypes. Spontaneously occurring canine STS could represent valuable translational models, due to their higher incidence and clinical similarity to human counterparts. However, molecular cross-species comparisons of specific subtypes are largely missing. Here, we performed a tissue-resolved, cross-species analysis of tumour and matched adjacent normal tissue (NT) in human and canine fibrosarcoma (FSA) and myxofibrosarcoma (MFS) by laser-capture microdissection of FFPE specimens combined with RNAseq and LC-MS/MS. Multimodal profiling revealed FSA and MFS to represent a molecular continuum rather than distinct entities in both species, resulted in identification of clinically relevant subgroups based on immune activation, proliferative activity and copy number alterations, and identified a novel canine STS subtype associated with a gene fusion. Moreover, our analyses revealed cross-species conserved transcriptomic and proteomic alterations distinguishing tumour from NT, including pathways linked to extracellular matrix remodelling, immune modulation, and cell proliferation. These data establish the first comprehensive molecular comparison of canine and human FSA and MFS, highlight the translational relevance of canine models, and identify candidate biomarkers for diagnostic refinement and development of targeted therapeutic modalities.

cancer biology↗

bioRxiv2026

SATB1 is a targetable modulator of JAK-STAT signaling and cytokines in human Treg and Tconv cells

The chromatin organizer SATB1 is indispensable for thymic regulatory T cell (Treg cell) development and T helper cell induction. Several gene loci have been described to be SATB1-controlled, including the transcription factor GATA3 and the cytokine loci IL-4 and IL-17. However, the global effects of SATB1 on fully differentiated human CD4 conventional T cells (Tconv cells) and Treg cells, and thus SATB1s potential as a target for T cell engineering, are poorly understood. We describe SATB1-regulated gene signatures as largely subset-specific, with broader effects on Treg cells. Despite of the distinct gene-regulatory patterns, we observe overarching dysregulated cytokine and JAK-STAT signaling after SATB1 ablation. Functionally, SATB1 KO reduces human Treg cell suppressive capacities but boosts tumor clearance via CD4 CAR T cells in a preclinical, humanized mouse model. Together, Treg destabilization and simultaneous increased activation of CD4 CAR T cells by SATB1 modulation may be an interesting strategy to boost the efficiency of CAR T cell therapies.

immunology↗

bioRxiv2025

Uncovering Developmental Lineages from Single-cell Data with Contrastive Poincare Maps

Embeddings play a central role in single-cell RNA sequencing (scRNA-seq) data analysis by transforming complex gene expression profiles into interpretable, low-dimensional representations. While Euclidean embeddings distort hierarchical relationships in low dimensions, hyperbolic geometry can represent hierarchies accuractely in low dimensions. However, existing hyperbolic methods, such as Poincare Maps (PM), lose accuracy in deeper hierachies and require extensive feature engineering and memory. We present Contrastive Poincare Maps (CPM), a scalable approach that reliably preserves inherent hierarchical structures. On synthetic trees with up to five generations and 34,000 individuals, CPM reduces distortion by 99% (1.9 vs. 126.3) and requires 13-fold less memory than PM. We demonstrate CPMs utility across three case studies: scalable analysis of 116,312 mouse gastrulation cells, accurate reconstruction of hierarchical structure in mouse hematopoiesis, and faithful representation of multi-lineage hierarchies in chicken cardiogenesis. By integrating hyperbolic geometry with contrastive learning, CPM enables scalable, structure-preserving embeddings for developmental scRNA-seq data. Code: https://github.com/NithyaBhasker/ContrastivePoincareMaps

bioinformatics↗

bioRxiv2025

Systematic cross-study assessment of RNA-Seq experimental workflows for plasma cell-free transcriptome profiling

Plasma cell-free RNA (cfRNA) is a promising source of non-invasive biomarkers, but its clinical translation is hindered by technical challenges and a lack of protocol standardization, which compromises reproducibility and comparability across studies. There is a need for a systematic evaluation of existing cfRNA-Seq workflows to understand the drivers of technical variability. Here, we address this gap by performing a comprehensive cross-study analysis of 2,166 cfRNA-Seq samples from 15 published studies and an in-house generated dataset, applying a uniform bioinformatics pipeline to enable a controlled comparison of experimental workflows. Our analysis reveals that the donor phenotype typically explains a negligible fraction of the transcriptomic variation, whose main determinants are technical - principally protocol choice, genomic DNA contamination levels and library diversity. Remarkably, this technical noise is so profound that variation within plasma cfRNA samples exceeds that found across a wide range of human tissues. Finally, we demonstrate that critical pre-analytical factors are often confounded with patient phenotypes, jeopardizing the validity of biomarker discovery efforts. Our work serves as a comprehensive benchmark of current cfRNA-Seq methodologies and provides evidence-based guidelines to improve experimental design. By highlighting the dominance of controllable technical factors, we offer a path towards more robust and reproducible cfRNA research.

bioinformatics↗

bioRxiv2025

Complement C3aR deletion does not attenuate neurodegeneration in a tauopathy model or alter acute inflammation-induced gene expression changes in the brain

Aberrant activation of the classical complement pathway in the brain is implicated in contributing to synapse loss and neurodegeneration in various neurodegenerative conditions. Given that C3aR is a druggable target in the complement pathway, we evaluated the potential of C3aR KO to rescue neurodegeneration in a tauopathy model and neuroinflammatory responses in an acute endotoxemia model. We found that C3aR KO did not rescue tau pathology, microglia activation markers, neurodegeneration, or behavioral abnormalities in tauopathy model mice. While we found that endotoxemia resulted in numerous transcriptional changes including distinct alterations in subpopulations of microglia, astrocytes and oligodendrocytes, C3aR KO did not impact these alterations. Together, our results suggest that the beneficial effects of blocking the complement classical pathway in neurodegeneration models is likely independent of C3aR activation and raise questions about the rationale for therapeutically targeting C3aR for neurodegenerative disease.

neuroscience↗

bioRxiv2025

A Highly Potent Human Antibody Neutralizing All Serotypes of BK Polyomavirus

BK polyomavirus infection poses a significant risk to kidney transplant recipients. Reactivation of dormant virus in the transplanted kidney, triggered by immunosuppression, can lead to BK polyomavirus-associated nephropathy in up to 10% of transplants, often resulting in loss of graft function or even graft loss. Currently, there is no specific treatment that reliably prevents BK polyomavirus-associated nephropathy or halts its progression. Standard of care relies on reducing immunosuppression, allowing the immune system to gradually control the infection but at the risk of provoking rejection episodes and compromising kidney function. This study describes the discovery and characterization of an ultra-potent BK polyomavirus-neutralizing antibody, identified from a kidney transplant recipient who displayed rapid clearance of high-level BK viremia. Antibody mAb 319C07 (USAN potravitug) neutralizes all four BK polyomavirus serotypes and recognizes an epitope critical for viral cell attachment. mAb 319C07 is in clinical development for the treatment of BKPyV infection in renal transplant patients (NCT05769582).

immunology↗

bioRxiv2025

Identification of novel candidate regulators of human naive pluripotency by means of a genetic switch utilizing the chimeric receptor G-CSFR:GP130

This study investigated the molecular mechanisms underpinning the transition from primed to naive pluripotency in human pluripotent stem cells (hPSCs) by utilizing a dual genetic switch combining hormone-dependent STAT3-ERT2 and a chimeric GCSFR:gp130 receptor. Upon activation with tamoxifen and G-CSF, hPSCs demonstrated upregulation of naive markers, and sustained self-renewal independent of LIF. Transcriptomic analyses revealed distinct clusters of early response genes, with a subset of 26 genes significantly enriched in the human epiblast. Knockdown experiments further delineated essential regulators that modulate differentiation and proliferation during naive reprogramming including interferon gamma inducible protein (IFI)16 and interferon-induced transmembrane (IFITM) proteins. Moreover, functional assays using mutant chimeric GCSFR:gp130 receptor highlighted the critical role of JAK kinase recruitment in orchestrating epigenomic remodeling and early gene activation. This approach establishes a robust platform to dissect the signaling dynamics governing the accession of hPSCs to naive pluripotency.

cell biology↗

bioRxiv2025

Structural basis for human chondroitin sulfate chain polymerization

Chondroitin sulfates are complex polysaccharide chains that regulate various biological processes at the cell surface and within the extracellular matrix. Here, we identify four heterodimeric complexes responsible for chondroitin sulfate chain polymerization in humans: CHSY1-CHPF, CHSY1-CHPF2, CHSY3-CHPF and CHSY3-CHPF2. Using a novel in vitro glycosylation assay based on chemo-enzymatically synthesized fluorescent substrates, we demonstrate that all four complexes exhibit chain polymerization activity. The cryo-EM structure of the CHSY3-CHPF complex provides, for the first time, molecular insights into the chondroitin sulfate chain polymerization reaction. The architecture of the catalytic sites suggests that CHSY1 and CHSY3 are enzymatically active, while CHPF and CHPF2 primarily play a stabilizing role. Mutational analysis of purified enzyme complexes, combined with an in cellulo complementation assay, confirms that only CHSY1 and CHSY3 have bifunctional glycosyltransferase activities. Based on the spatial arrangement of the catalytic sites, we propose that chondroitin sulfates chain polymerization follows a non-processive, disruptive mechanism.

molecular biology↗

bioRxiv2025

Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map

Essentiality studies have traditionally focused on coding regions, often overlooking other small genetic regulatory elements. To address this, we obtained a high-resolution essentiality map at near-single-nucleotide precision of the genome-reduced bacterium Mycoplasma pneumoniae, combining transposon libraries containing promoter or terminator sequences. By integrating temporal transposon-sequencing data, we developed a novel method of essentiality assessment based on k-means unsupervised clustering, which provides dynamic and quantitative information on the fitness contribution of different genomic regions. We compared the insertion tolerance and persistence of the two engineered libraries, assessing the local impact of transcription and termination on cell fitness. Essentiality assessment at the local base-level revealed essential protein domains and small genomic regions that are either essential or inaccessible to transposon insertion. We also identified structural regions within essential genes that tolerate transposon disruptions, resulting in functionally split proteins. Overall, this study presents a nuanced view of gene essentiality, shifting from static and binary models to a more accurate perspective. Additionally, it provides valuable insights for genome engineering and enhances our understanding of the biology of genome-reduced cells.

systems biology↗