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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 37 records · Page 2Linked to original sources

bioRxiv2026

A mechanistic classification of GNAO1 mutations links Gβ γ sequestration to hyperkinetic disease and treatment response

Go is the most prevalent G protein subunit in the brain and is critical for signal transduction through G protein-coupled receptors. Mutations in the gene encoding Go (GNAO1) cause a rare neurodevelopmental disorder with involuntary movements (NEDIM) and, in some patients, developmental and epileptic encephalopathy (DEE). Here, we integrate human genetic analysis with cellular assays to define mechanistic classes of GNAO1 mutations and in vivo approaches to evaluate therapeutic strategies. We grouped variants into two functional categories: those predicted to sequester G{beta}{gamma} and those with reduced Go expression and therefore increased G{beta}{gamma} signaling. Analysis of patient data revealed that mutations predicted to impair G{beta}{gamma} release are significantly associated with NEDIM. Using the GNAO1R209H/+ mouse as a model of NEDIM, we evaluated two small molecules: caffeine, a nonselective adenosine receptor antagonist, and gallein, a selective modulator of G{beta}{gamma}-effector interactions. Both compounds significantly reduced hyperlocomotion in the open field test. Whole-cell patch-clamp electrophysiology revealed sex- and cell type-specific hyperexcitability in spiny projection neurons within the dorsolateral striatum of GNAO1R209H/+ mice. Together, these findings implicate dysfunction of dorsolateral striatal pathways in GNAO1-related disorder and suggest that mechanistic understanding of disease variants can guide targeted therapeutic strategies.

pharmacology and toxicology↗

bioRxiv2026

A Synthetic Consensus Chiroptera IFN-β Induces IFN-I Signaling Across Diverse Bat Taxa

Bat-associated viruses consistently spill over from bats into humans and other animals. Many bat-associated viruses, including Marburg virus and Nipah virus, cause severe disease in humans but their presentation is subclinical in bats. Advancements in tools and resources to study bat innate antiviral immune responses, including the type I IFN (IFN-I) pathway, are needed to evaluate the mechanisms that underlie differential infection outcomes between reservoir bats and spillover hosts. Commercially available IFN-Is are not bat-specific, and conspecific IFN-Is are impractical to produce for the over 1,500 described bat species. Here, we design and validate a bat order-level consensus IFN (Chiroptera IFN-{beta}) that is functional in bat cells from six diverse bat families, including representatives from both suborders. Using Jamaican fruit bat cells, we demonstrate that Chiroptera IFN-{beta} induces an IFN-stimulated gene repertoire comparable to conspecific IFN-{beta}. This valuable resource can accelerate the capacity of the field to study bat innate antiviral responses and illuminate differences between bats and humans.

immunology↗

bioRxiv2026

A Synthetic Virology Platform for Rapid Prototyping of Influenza A Virus mutants

Influenza A virus (IAV) remains a significant public health threat, with the need for effective vaccines and antiviral therapies remaining a high priority. In vitro testing is paramount in studying novel IAV viruses and their immunogenicity. To address this need, we developed a synthetic virology approach to rapidly prototype and test IAV mutants with altered antigenic sites. By strategically inserting restriction sites within an ambisense plasmid, we generated a tool where we can seamlessly replace either 1) the full hemagglutinin (HA), 2) the HA globular head domain to generate head/stalk chimeras or 3) the five canonical antigenic sites. The cloning inserts can be computationally designed and artificially synthesized, enabling rescue of synthetic Influenza A viruses. Using this platform we rescued IAV H1N1, H3N2 & H5N1, and went on to prototype their respective antigenic site mutants & chimeric IAVs using viral genome sequence alone. This platform could be useful for generating vaccine seed strains or to study anti-viral immunity.

synthetic biology↗

bioRxiv2026

Brain state locks silent memories in a trained fly connectome

Complete connectomes now exist for insect nervous systems, but whether a fixed wiring diagram can learn, and what its memories consist of, is unknown. Here, we trained a spiking model of the whole male Drosophila central nervous system, 167,106 neurons with fixed wiring, to plan moves and to remember a visual cue. Spikes write the cue into neuronal adaptation, which holds it silently until the next input reads it out. Cells that hold the trace are enriched for transcripts of a calcium-activated potassium channel in fly cell atlases. The learned readout recalls the trace only in the brain state of learning: the same trace evokes a different response at another delay, and a disease-like loss of potassium current rewrites the trace and changes how it is read. Learning in the new state is spared. Memory failure can arise from a change of state rather than a loss of storage.

neuroscience↗

bioRxiv2026

Phase Separation of Intracellular Proteins Influences Synaptic Bistability

Synaptic bistability at the post synaptic density has been proposed to be the result of the nucleation and evaporation of receptor clusters. The exact biophysical mechanism underlying these inter-receptor attractions that can trigger nucleation remains to be elucidated. Emerging evidence demonstrates that numerous postsynaptic density submembrane proteins, that interact with various membrane receptors, can undergo phase separation, necessitating a revised conceptual model. By employing Langevin dynamics simulations of coarse-grained scaffold proteins and interacting membrane receptors, we study how phase transitions of scaffold proteins alter receptor clustering at the membrane. In our model, scaffold macromolecules can undergo phase separation and interact with receptor molecules at the model membranes. We observed that the presence of scaffold polymers across the membrane creates an attractive interaction between otherwise purely repulsive receptors. By systematically varying the number of receptors at the membrane, we dissected the coupling between receptor clustering and the phase behavior of scaffold macromolecules. We show that the propensity for receptor clustering is enhanced by the condensation of scaffold proteins. We then used two different scaffolds and systematically varied the interaction between them, to change the spatial organization of two condensed phases w.r.t. one another. Interestingly, we observed that receptor clustering can be reduced by co-phase separation of scaffold macromolecules, indicating the role of competing interactions in receptor clustering. Our work advances understanding of receptor-mediated signaling and phase separation, providing insights into cellular compartmentalization and biochemical regulation at the synapse.

biophysics↗

bioRxiv2026

Spontaneous neural activity in the developing ant olfactory system

Spontaneous neural activity is a pillar of mammalian neurodevelopment. In mammals, developing olfactory sensory neurons (OSNs) show spontaneous activity patterns that depend on the olfactory receptor (OR) they express. This activity is necessary for proper sorting of OSN axons into olfactory bulb glomeruli. This contrasts with the simpler olfactory system of the fruit fly Drosophila melanogaster, where antennal lobe glomeruli form without functional ORs. Compared to Drosophila, ants have a vastly expanded olfactory system and, unlike Drosophila, require functional ORs for proper development. This raises the possibility that ants, like mammals, rely on spontaneous neural activity. To test whether developing ant OSNs are spontaneously active, we performed live calcium imaging in translucent pupae of the clonal raider ant Ooceraea biroi, using a transgenic line expressing the genetically encoded calcium indicator GCaMP6s in OSNs. Developing O. biroi OSNs exhibit spontaneous calcium transients from the earliest stages of glomerulus formation, and features of this activity change over the course of metamorphosis. During early stages, activity is faster, varies widely between cells, and is uncorrelated across the OSN population. By mid-metamorphosis, activity has slowed, with longer calcium events and fewer peaks per cell. As pupae approach eclosion, a new mode appears, with rhythmic, sawtooth-shaped calcium events that synchronously engage OSNs in both antennae. This stage-dependent spontaneous activity suggests that the expanded ant olfactory system may use a developmental logic more akin to mammals than to Drosophila.

neuroscience↗

bioRxiv2026

Adolescent Sugar-Induced Miswiring of Hippocampal Neurons Drives Adult Motivational Dysfunction in rats

Adolescence, a critical period for hippocampal maturation, involves the integration of newly generated neurons into circuits underlying adult behavior. While adolescent, but not adult, sugar overconsumption triggers lasting motivational deficits, the underlying mechanisms remain unclear. Here, we demonstrate that adolescent-born dentate gyrus granule neurons causally mediate adult reward-seeking behavior. Strikingly, sucrose overconsumption during adolescence abolishes this function, inducing selective remodeling of synaptic inputs and disrupting their functional integration.

neuroscience↗

bioRxiv2026

Validated backbone assignments for natural-abundance 1H,15N spectra of commercial hen egg white lysozyme and example applications thereof

Although backbone 1H and 15N assignments for hen egg white lysozyme (HEWL) have been reported in the literature and several related entries are available in the BMRB, these resources differ in sequence, experimental conditions, and the nuclei represented. In particular, there is no BMRB entry with an explicit set of 1H,15N backbone assignments applicable to spectra that can now be collected at natural 15N abundance on concentrated samples of commercial HEWL as shown by Bruker and reproduced here using a 800 MHz magnet with a cryoprobe. Therefore, here I make available the backbone 1H,15N chemical shifts of commercial (Sigma) HEWL at pH 3.8 and 308 K parsed from previous papers and checked against 1H,1H NOESY, 1H,1H TOCSY and 1H,15N correlation spectra of HSQC and SOFAST-HMQC types, acquired on a 3 mM sample at natural 15N abundance. I also provide backbone 1H,15N assignments transferred to pH 6 and 308 K via a pH titration, closer to physiological conditions as used by others. I discuss details about sample preparation and spectra acquisition, including the measurement times involved, and possible reasons for a few residues lacking assignments. The usefulness of these assignments and of detecting 1H,15N correlations at natural abundance are proven by (i) application to a titration with a small molecule, (ii) studies of hydration and dynamics via Het-SOFAST-HMQC experiments, and ultimately (iii) by their utilization in published papers even if without attribution. I deliver ready-to-use assignments as text-format Sparky files, and make selected spectra available on the PDB Manipulation Suite's WebNMR app for straightforward visualization online, useful also for swift educational demonstrations. Overall, I expect the data and methods presented here will be of use in protein biophysics and structural biology research and education, by enabling the interpretation of modern NMR-based studies on inexpensive samples of this widely studied protein.

molecular biology↗

bioRxiv2026

Retinal Phd2 ablation partially rescues Crb1Crb2-associated Leber congenital amaurosis and alters metabolic signaling

Leber congenital amaurosis (LCA) is a severe early-onset retinal dystrophy caused by pathogenic variants in several genes, including CRB1. CRB1-associated LCA is characterized by disrupted retinal polarity, lamination, and photoreceptor organization, with no restorative treatment. We investigated whether retinal deletion of Phd2 (Egln1), encoding prolyl hydroxylase domain protein 2 (PHD2), could provide mutation-independent neuroprotection in a severe developmental model of CRB1-associated LCA. Using conditional Crb1/Crb2-deficient mice, we additionally deleted Phd2 throughout the neural retina and assessed retinal function, structure, visually guided behavior, and glycolysis-associated gene and protein expression at one and two months. Compared with Crb1/Crb2-deficient mice, additional Phd2 deletion partially improved scotopic responses and significantly increased the optomotor spatial-frequency threshold, whereas b-wave and cone-mediated responses remained impaired. Phd2Crb1Crb2-deficient retinas displayed more organized photoreceptor rosettes containing rod- and cone-marker-positive cells, in contrast to the diffuse outer-retinal disorganization and nuclear-layer amalgamation observed in Crb1/Crb2-deficient retinas. Polarity- and synapse-associated proteins showed improved local compartmentalization within these structures. Metabolic responses were temporally selective: Glut1 and Vegfa transcript levels increased at one month, whereas GLUT1 and LDHA protein levels increased at two months; Pdk1 transcript levels decreased at 2M, whereas PDK1 protein abundance remained unchanged. Although Phd2 deletion did not correct the underlying Crumbs-complex defect or normalize retinal lamination, and elevated Vegfa coincided with persistent vascular abnormalities, these findings demonstrate that retinal Phd2 deletion partially modifies the structural and functional consequences of severe Crb1/Crb2 deficiency and supports further investigation of PHD2-associated metabolic signaling as a potential disease-modifying target for severe CRB1-associated retinal degeneration.

neuroscience↗

bioRxiv2026

Transcriptomic similarity guides source selection beyond tissue lineage

Perturbational and pharmacogenomic maps remain incomplete across cellular contexts, leaving a practical source-selection question before response prediction: which measured context should inform an unmeasured target? We tested whether baseline transcriptomic similarity ranks candidate sources for held-out targets, separating source ranking from aggregation and transfer-uncertainty decisions. Similarity tracked matched-response concordance in LINCS and GSE306429; selected-source utility exceeded random expectation in GSE306429 ({Delta}U = 0.034; P = 0.002) and in exact-time-matched MIX-Seq tasks ({Delta}U = 0.046). In the full GDSC2 analysis, the drug-balanced ranking effect was 0.359 (95% CI, 0.337-0.383). In a lineage-restricted analysis of the same eligible subset, within-tissue ranking remained positive at 0.130 (95% CI, 0.119-0.141), retaining 35.8% of the same-subset global effect (0.363; 95% CI, 0.342-0.386). Global transcriptomic top-1 selection exceeded tissue-matched random selection by 0.154 (95% CI, 0.143-0.164). Thus, baseline similarity adds source-ranking information after tissue matching in the evaluated setting, while ranking alone does not resolve whether to aggregate sources or how to quantify transfer uncertainty.

bioinformatics↗

bioRxiv2026

Interpreting Graph Neural Networks for Antibacterial Drug Repurposing against Acinetobacter baumannii

Antimicrobial resistance in Acinetobacter baumannii, whose carbapenem-resistant strains are classified by the World Health Organization as a critical priority, has motivated machine-learning screens for new antibacterials, but translating predictions into chemical hypotheses requires evaluating the molecular features on which a model relies. A graph neural network ensemble achieves competitive predictive performance against a descriptor-augmented reference model on the same antibacterial screen while using only atom features and connectivity, allowing interpretation to focus on the molecular graph without a separate input of handcrafted descriptors. The atom-level explanations identify features supporting the model's activity predictions under perturbation and restoration, while comparisons with equally sized perturbations within each molecule distinguish piperazine as the most consistently supported recurring contributor to predicted activity. Prospective screening of the Drug Repurposing Hub followed by developability and safety assessment yields a ranked shortlist for experimental follow-up and leads to testing of CE3F4, which reduced A. baumannii growth by 57% at 0.25 mM in a preliminary assay with a non-monotonic concentration--response profile.

bioinformatics↗

bioRxiv2026

Genomic Potential vs. Pathogenic Reality: Functional Virulence Variation in Pseudomonas aeruginosa

Despite the rapid expansion of bacterial genome sequencing, predicting pathogen virulence from genomic information remains a major challenge. To study this association, we integrate comparative genomics, functional phenotyping, host-pathogen interaction assays, and infection outcomes across a diverse collection of 28 Pseudomonas aeruginosa isolates, representing clinically relevant diversity in serotype, type IV pilus group, and flagellar type. While virulence-associated systems were broadly retained across the strain collection, isolates displayed substantial variation in phenotypic behavior and pathogenicity. Genotypic classifications based on pilus, flagellar, siderophore, or secretion system characteristics were poor predictors of virulence-associated phenotypes. Pathogenicity in a Galleria mellonella model varied markedly among strains and was most strongly associated with surface-associated motility, whereas other virulence traits and quorum-sensing genotypes showed limited predictive value. In a three-dimensional lung epithelial cell model, inflammatory responses were negatively correlated with activity of the type III secretion system effector ExoS, suggesting a role in modulation of host immune signaling. Together, these findings demonstrate that virulence emerges from functional deployment of conserved virulence repertoires, rather than their mere presence. By linking genomic diversity to phenotypic expression, pathogenicity, and host responses within a single strain collection, this study highlights fundamental limitations of gene-content-based virulence prediction and underscores the importance of integrating genomic and functional data to better understand P. aeruginosa virulence.

microbiology↗

bioRxiv2026

Oncostatin M-driven leak in human endothelial cells with preserved tight junctions

Blood vessels must preserve blood volume while permitting exchange of nutrients. Endothelial cells line the lumen of all blood vessels and form the intercellular junctions that govern vascular permeability. In acute critical illness the barrier fails, fluid escapes into tissues, and the resulting loss of volume and impaired nutrient exchange cause organ failure. Several inflammatory cytokines are known to disrupt junctions in cultured cells, yet therapies targeting these models have failed. How blood vessels respond to critical illness has remained largely elusive because endothelial cells are generally inaccessible. Here we profile endothelial cells recovered directly from critically ill children to show that oncostatin M drives a previously unrecognized mode of vascular leak. Oncostatin M increases permeability by forming narrow, nanoscale channels within the overlapping borders of adjacent cells, around intact tight junctions. These channels permit passage of small and intermediate sized solutes. Their formation depends on non-canonical signaling in which the kinase JAK1 activates two required parallel pathways (via ERK1 and AKT1) that converge on the transcription factor c-Fos. Inhibiting JAK1, either parallel pathway or depleting c-Fos, prevents oncostatin M-induced loss of barrier function. These results identify a permeability mechanism distinct from the junction disassembly driven by the cytokines that have dominated this field and implicate kinases already targeted by approved drugs as potential points of intervention. More broadly, vascular barriers are transiently loosened during immune-cell trafficking and metastasis, raising the possibility that diverse forms of vascular permeability arise through regulated nanoscale remodeling rather than junctional breakdown.

cell biology↗

bioRxiv2026

A single freshwater invasion gave rise to the world's dominant freshwater fish group

The ultraspeciose clade Otophysa - catfishes, carps, minnows, tetras, and their kin - accounts for most vertebrate diversity in modern freshwater ecosystems. However, a controversial assemblage of largely-fragmentary marine fossils has led some authors, most recently Liu et al., to advocate parallel freshwater invasions for this otherwise inland lineage. Here, we test this hypothesis under multiple sources of uncertainty. We provide the first phylogenetic analysis of the recently-named marine fossil genus Sooinichthys, resolving it as sister to all modern otophysans. We also find that Santanichthys, long treated as an early marine otophysan, lacks a Weberian apparatus and plausibly belongs outside Ostariophysi entirely. When increasing the taxon and marker sampling of Liu et al.'s genomic dataset, standardizing their ecological coding, accounting for alternative interpretations of important morphological characters, and applying a suite of biogeographic models, we find a marine origin in only 6 of 132 analyses, and only when enforcing fossil placements inconsistent with our own phylogenetic results. We contend that the parallel freshwater invasion hypothesis of otophysan diversification is an artifact of sparse taxon sampling, taphonomic biases, model selection errors, and fossil overinterpretation. The result is a cautionary case for inferences about the cradle of any ancient freshwater clade.

evolutionary biology↗

bioRxiv2026

Note on a Small Chlamyphoridae (Xenarthra, Cingulata) from the Amazon, Brazil

The Awa-Guaja are one of the last hunter-gatherer peoples in the world and live in Indigenous reserves in northwestern Maranhao, Brazil. The Guaja Ethnographic Collection consists of animal remains found during excavations of the community s refuse areas, conducted between 1987 and 1990. This study presents a taxonomic reassessment of a small Cingulata specimen from this collection. The specimen, previously identified as Euphractus sexcinctus, consists of a complete right femur whose taxonomic identity was reevaluated through comparative morphological and metric analyses using specimens from scientific collections and data from the specialized literature. The results revealed that the femur is smaller than those observed in individuals of E. sexcinctus and exhibits a combination of anatomical features resembling those found in the genera Chaetophractus, Cabassous, and Euphractus. Despite these similarities, the observed morphological differences do not allow a reliable identification at the genus level. Therefore, the specimen was provisionally assigned to the family Chlamyphoridae, and its identification was retained at the family level.

zoology↗

bioRxiv2026

New Zealand spider orchid (Corybas trilobus) exploits the reproductive behaviour of fungus gnats (Diptera: Mycetophila) for pollination.

Due to a reduce pollinator diversity, plant-pollinator interactions in remote habitats are commonly unspecialised. In New Zealand (NZ), many plants exhibit a generalist pollination syndrome where flowers are open-access and pollinated by a range of insects. Orchids in the genus Corybas seem to be the exception. It is believed they mimic mushrooms and their pollination occur by brood-site deception. This study aims to uncover whether this pollination strategy operates in a form of Corybas trilobus known by the tag-name Corybas Remutaka. We used hand-pollination experiments to determine the breeding system of this orchid. SEM observations and neutral red staining were used to study the floral micro-morphology and location of scent glands, respectively. Pollinators behaviour was observed, and filmed, in the field and ex situ. Olfactory signals were assessed using solid-phase micro-extraction and solvent extractions, and visual cues by photography with a UV sensor. Only hand self- and cross-pollinated flowers formed capsules, while natural fruit-set was low. Male and female individuals of the endemic fungus gnat Mycetophila phyllura (Diptera) were the only pollinators observed. Both sexes can remove and deposit pollinia. None of the typical fungal compounds, or other compounds linked to brood-site deception, were detected in the orchid but a prevalence of alkane, sesquiterpene and fatty aldehydes. Some of these compounds were also detected in a mushroom used by fungus gnats for mating and ovipositioning. Features in the labellum surface and base (e.g. exit holes) and UV reflectance may help directing movement of the gnats within the flower. Corybas Remutaka is a self-compatible, nectarless, pollinator-dependent orchid that relies on a mix of volatiles and micro-morphological features to attract a specific pollinator. The orchid exploits the reproductive instinct of male and female fungus gnats to secure its pollination. This deceptive pollination strategy combines features of rendezvous site pollination and brood-site deception.

plant biology↗

bioRxiv2026

Optimization of the NFκB-DNA ensemble leads to high affinity binding of partial consensus sites

Our ability to respond to a myriad of external stressors is dependent on the activity of specific transcription factors that precisely regulate gene expression. While some transcription factors have high specificity for their consensus DNA binding site, others such as NF{kappa}B (RelA/p50) readily bind to partial and nonconsensus sites. In fact, ChIP-Seq data shows that nearly half of the DNA-bound RelA occupies sequences that do not match the consensus. Here we explore how NF{kappa}B (RelA/p50) binds to alternative sequences that differ subtly from the consensus. The two subunits of the NF{kappa}B heterodimer, RelA and p50, form an extensive pocket where DNA binding is mediated by both base-specific contacts and nonspecific interactions with the DNA backbone. RelA and p50 each form sequence-specific contacts with DNA at different 4-nucleotide sequences separated by two nucleotides, together forming a 10-base pair consensus binding sequence. Partial consensus sequences, known as half-sites, match the consensus sequence at only one of these two 4-nucleotide interaction sites. Here, using hydrogen deuterium exchange mass spectrometry (HDX-MS) and molecular dynamics (MD) simulations to investigate protein structural dynamics, we observe that rearranging nucleotides at the RelA-interacting end of a consensus DNA sequence to form a half-site induces dynamic structural changes through both subunits of RelA/p50. MD simulations reveal a shift in the position of DNA within the RelA/p50 binding pocket that allows optimal interaction with the half-site sequence. Our results demonstrate how RelA/p50 fine-tunes its interactions to achieve high-affinity binding with multiple different target DNA sequences.

biochemistry↗

bioRxiv2026

Distributed brain-spinal cord dynamics during micturition revealed by functional ultrasound imaging

Micturition relies on coordinated activity across distributed neural circuits spanning the brain and spinal cord, yet the spatiotemporal dynamics of these processes remain poorly understood. Disruption of these pathways in conditions such as spinal cord injury, Parkinson's disease, multiple sclerosis, and aging can lead to neurogenic bladder dysfunction. Here, we used functional ultrasound imaging (fUSI), a modality with high spatiotemporal resolution and single-trial sensitivity, to investigate central nervous system activity during micturition. In anesthetized rats undergoing controlled bladder filling and volitional voiding, we recorded power Doppler signals from either the brain or the lumbosacral spinal cord. We observed distinct, region-specific hemodynamic responses associated with micturition across multiple brain regions, including the thalamus, hypothalamus, midbrain, and neocortex - particularly sensorimotor and retrosplenial areas - as well as dorsal and ventral spinal cord circuits. Furthermore, population-level activity in these regions enabled accurate decoding of bladder pressure dynamics. These results provide a systems-level characterization of central nervous system activity during micturition and establish fUSI as a platform for developing neural interfaces to restore bladder control.

bioengineering↗