Biology subjects

Li, C.

Publications and source records attributed to Li, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Pulmonary colonization of Candida albicans drives breast cancer lung metastasis via candidalysin

The intratumoral mycobiome is emerging as a key modulator of cancer progression, with specific fungal taxa as potential biomarkers. However, whether and how mycobiomes colonizing distant organs contribute to tumor evolution remains largely unexplored. Here, we identify selective enrichment of Candida albicans in breast cancer lung metastases. Mechanistically, the fungal virulence factor candidalysin activates pulmonary mast cells, which release chemotactic mediators that expand immunosuppressive populations and suppress cytotoxic lymphocyte activity, remodeling the lung into a metastasis-permissive microenvironment. Analysis of clinical isolates and isogenic mutants further demonstrates that candidalysin secretion levels dictate metastasis-promoting potential. Informed by these findings, we developed a combination regimen that concurrently eliminates fungal colonization, stabilizes mast cells, and reverses the immunosuppressive microenvironment, thereby significantly curtailing metastatic progression. Collectively, our study establishes pulmonary C. albicans colonization as a driver of breast cancer lung metastasis and provides a mechanistic framework for targeting mycobiome-host interactions in metastatic disease.

cancer biology↗

bioRxiv2026

Ratio-preserving super-resolution FLIM for quantitative live-cell lifetime imaging

Super-resolution (SR) fluorescence lifetime imaging promises nanoscale maps of molecular environment and function, but photon-limited acquisition and computational reconstruction can distort lifetime estimates, particularly for ratio-derived frequency-domain measurements under SR conditions. Here we introduce structured-illumination frequency-domain FLIM (SIM-fdFLIM), an SR lifetime imaging platform that combines commercial dual-tap fdFLIM detection with ratio-preserving reconstruction. SIM-fdFLIM uses direct-current (DC)-stabilized lifetime estimation to improve reconstruction robustness under low signal-to-noise conditions, followed by ratio-domain integrated variational estimation (RIVE) to correct channel misregistration and suppress noise amplification after SR reconstruction. The method achieves ~100 nm spatial resolution in lifetime maps and enables live-cell imaging at 2.8 Hz over a 56 x 56 {micro}m2 field of view. Across representative fluorophore standards, RIVE reduces lifetime standard deviation by approximately threefold relative to non-RIVE SIM-fdFLIM while preserving mean lifetime agreement with calibrated widefield fdFLIM. In living cells, SIM-fdFLIM resolves mitochondrial cristae-scale lifetime heterogeneity, mitochondrion-to-mitochondrion functional dynamics, nanoscale lipid-environment variations and perturbation-sensitive organelle-contact signatures. These results establish SIM-fdFLIM as a ratio-preserving platform for quantitative SR lifetime imaging, extending live-cell FLIM into a regime that combines nanoscale spatial resolution, Hz-rate acquisition, and preserved lifetime fidelity.

bioengineering↗

bioRxiv2026

DNA methylation reveals molecular heterogeneity and urate excretion-associated subtypes of gout

Background: The molecular heterogeneity among gout patients remains largely unexplored, hindered the precise treatment for gout. Common indices for gout subtyping are cumbersome to measure, resulting in poor patient compliance. Methods: We elucidated the molecular heterogeneity of gout and developed a simple, reliable classification method for gout subtypes based on genome-wide DNA methylation, to facilitate individualized treatment. Genome-wide DNA methylation profiling was conducted in two independent cohorts, comprising a discovery cohort (n = 108) and a validation cohort (n = 100) representing four clinical gout subtypes. Results: We identified two gout subgroups associated with the fractional excretion of uric acid (FEUA) but not with 24-hour urinary uric acid levels (UUE) based on unsupervised clustering of whole-genome DNA methylation profiles, highlighting the contribution of epigenetic regulation to molecular heterogeneity in urate metabolism. Enrichment analysis links FEUA-associated subtypes to renal cell types, calcium related pathways and extended to the circulating immune compartment, with neutrophil- versus memory B cell-skewed leukocyte composition. A methylation-based classification model using 18 LASSO-selected CpGs with an XGBoost classifier effectively distinguished patients with high and low uric acid excretion, achieving excellent predictive performance (training cohort: AUC = 0.96, AP = 0.91; validation cohort: AUC = 0.86, AP = 0.85), outperforming the published model with clinical characteristics and SNPs. The signature site-associated genes NEK1 and TRPS1 display significant expression differences among urate-stratified patients and immune cells groups. TRPS1 may affect the AP-1/NF-{kappa}B inflammatory programme. Conclusions: These findings reveal distinct DNA methylation signatures underlying gout heterogeneity and demonstrate the feasibility of DNA methylation markers for gout subtype classification. The proposed methylation-based model provides a promising approach for personalized management of gout.

bioinformatics↗

bioRxiv2026

Ancient genomes chronicle the history of adaptive evolution in East Asia

The transition from hunting and gathering to farming brought about novel selection pressures related to metabolism and immunity, but for East Asian populations the evolutionary genetic dynamics of these adaptations and their relationships to agriculture remain unclear. Using one of the largest datasets of ancient East Asian genomes (N=2236), we performed a genome-wide scan to identify selected variants and reconstructed their allele frequency changes over time and space. We tested for genetic association with farming using an environmental variable to represent historical farming intensity based on a large database of archaeobotanical sites (N=1220). Our analyses indicate selection began prior to the Neolithic for several well-established adaptive loci such as FADS1, FUT2, and OCA2. For rs1229984 at ADH1B, the strongest selection signal in our genome-wide scan, we observed variation in timing and strength of selection in East Eurasia and found evidence for a southern origin. Furthermore, ADH1B*48His was positively associated with wheat farming. Given these results, we propose a novel hypothesis about the fitness advantage of this variant. Our work underscores the heterogeneity in the strength and timing of selection across East Eurasia and provides a quantitative framework for testing agriculture's role as a selection pressure.

evolutionary biology↗

bioRxiv2026

Decoding Cell-level Circadian Phase and Rhythm-state Remodeling in Single-cell Transcriptomes With scRhythmBayes

Current circadian omics analysis tools have been developed primarily for bulk time-series. However, heterogeneous single-cell datasets require analysis and interpretation of rhythmic programs across different cells, cell types, and biological conditions. In these datasets, cellular circadian phase is usually unobserved, and sample-level zeitgeber time provides temporal information but does not define the exact phase of every cell. Existing methods address only selected aspects of this problem and do not model how cell-level phase evidence informs gene-level rhythmic parameters and rhythm-state remodeling. Here we present scRhythmBayes, a new probabilistic algorithm for phase-resolved circadian analysis in heterogeneous single-cell transcriptomes. scRhythmBayes combines a seed-gene count likelihood with a stratum-aware circular prior to infer cell-level circadian phase, incorporates phase support into gene-level rhythmic modeling, and assigns posterior probabilities to interpretable rhythm-state categories, including rhythm gain, rhythm loss, amplitude remodeling and phase shifts. In heterogeneous simulations, scRhythmBayes achieved higher phase-recovery accuracy than existing phase-inference methods and maintained balanced performance across rhythmic gene detection, parameter recovery, and rhythm-state classification. Stress tests defined practical requirements for seed-gene support, zeitgeber anchoring, temporal sampling density, and cell number. In mouse liver, scRhythmBayes revealed distinct circadian phase occupancy and rhythm-state organization between periportal and pericentral hepatocytes, supporting a temporal dimension of liver zonation. It also identified cell-type-specific rhythmic markers that were largely distinct from conventional static markers, indicating that cellular identity includes temporal programs not captured by average expression. In human heart disease data, phase-coordination and phase-distribution analyses identified cell-type-selective temporal disorganization rather than uniform circadian disruption across the tissue. scRhythmBayes therefore provides a statistically grounded approach for resolving circadian organization across cells, genes, cell types and biological conditions.

bioinformatics↗

bioRxiv2026

Seipin and perilipin 3 promote distinct early steps of nascent lipid droplet biogenesis

Lipid droplets (LDs) are lipid storage organelles with critical roles in metabolism. Cells form LDs in response to various metabolic stresses (1). LD biogenesis occurs in the endoplasmic reticulum (ER) membrane and begins when triglyceride (TG) in the membrane phase separates (2-4). After nucleation, nascent LDs grow by absorbing TG from the membrane (5,6). How cells determine when TG in the ER membrane is added to existing LDs or is used to form new LDs or is not known. Here, we developed the first LD formation assay that allows the synthesis of TG in membranes, mimicking what occurs in cells. LDs arise stochastically after TG production begins. LD nucleation is affected by TG production rate and membrane phospholipid composition. Membrane-embedded LDs suppress nascent LD formation by sequestering TG and destabilizing nascent LDs by Ostwald ripening. We show that cells overcome this suppression in two ways. The ER membrane protein seipin accelerates LD nucleation where it localizes in a membrane, probably by increasing the kinetics of TG phase separation. The LD coat perilipin 3 inhibits nascent droplet dissipation by ripening. Together, our findings reveal a minimal LD formation machinery, and the mechanisms cells use to control whether TG in the ER drives new LD formation.

cell biology↗

bioRxiv2026

Molecular Engineering of Silk via Fatty Acid Esterification for Water-Stable, Anti-fouling, Biocompatible, Implantable Materials

Biopolymers offer attractive properties for implantable materials, but their limited aqueous and enzymatic stability constrains long-term performance in biological environments. Silk fibroin is mechanically tunable and thermoplastically processable, yet remains susceptible to swelling in aqueous environments, which can impact mechanical properties. Here, we establish fatty acid esterification as a strategy to transform silk into a hydrophobic, water-stable, yet still bioresorbable material (FAsilk). Fatty acid functionalization significantly increased resistance to aqueous swelling and enzymatic degradation while preserving structural and mechanical integrity and thermoplastic processability. The resulting FAsilk biomaterials also reduced microbial contamination, blood clot formation, and macrophage adhesion relative to native silk, due to the change in hydrophobicity, while maintaining cytocompatibility and hemocompatibility. Subcutaneous implantation in mice demonstrated favorable biological responses, including minimal impact on body weight and no significant pro-inflammatory responses, indicating no adverse effects on animal health. Thus, fatty acid functionalization enables silk to combine hydrophobicity and aqueous stability with processability and biodegradability, providing a mechanically robust materials platform for bioresorbable implants, including medical devices, tissue-engineered grafts and drug delivery systems.

bioengineering↗

bioRxiv2026

Stimulating microglial neuroinflammation with amyloid-beta oligomers compatible with solid-state NMR structural characterization

Soluble amyloid-{beta} (A{beta}) oligomers are considered the primary neurotoxic species in Alzheimer's disease, yet the relationship between oligomer structure and biological activity remains poorly understood. Oligomer sample preparations amenable to high-resolution structural characterization have not been tested in cell-based assays, mostly because detergents used to drive oligomer formation are toxic to cells. Here, we describe a detergent-free protocol in which size-exclusion chromatography-isolated A{beta}42 monomers spontaneously oligomerize at 37 {degrees}C in a concentration- and temperature-dependent manner. Biophysical characterization shows a {beta}-sheet structure by circular dichroism, a self-associating population above 100 kDa by silver-stained SDS-PAGE, and bead-like strings by negative-stain TEM resembling the previously characterized SDS-induced 150 kDa oligomer. Solid-state NMR spectroscopy of selectively 13C/15N-labeled 37 {degrees}C oligomers yields well-resolved spectra with {beta}-strand chemical shifts, and two-dimensional 13C-13C DARR and CHHC experiments provide initial inter-residue distance constraints that reveal both similarities to and differences from the 150 kDa oligomer. Treatment of mouse microglial cells (MMCs) with 50 nM 37 {degrees}C oligomers elicited a robust pro-inflammatory cytokine response that exceeded that of monomeric A{beta}42, as demonstrated by Luminex multiplex profiling and principal component analysis. hiPSC-derived microglia (iMGs) treated with 1 {micro}M oligomers also separated from vehicle, establishing activity in a human cellular model. Monomeric A{beta}42 was inactive in both systems, indicating that inflammatory activity depends on the assembly state of A{beta}42 rather than on the presence of peptide alone. These results establish a detergent-free A{beta}42 oligomer preparation that is simultaneously compatible with solid-state NMR structural characterization and biologically active in neuroinflammation assays, providing a platform for studying microglial immune responses to oligomers.

neuroscience↗

bioRxiv2026

Evolution-Guided Engineering of Non-conserved N-Glycosylation Sites Improves Heterologous Production of Sulfotransferases

Escherichia coli features low cost, mature fermentation technology and high recombinant protein output, but the expression of glycosylation-dependent eukaryotic proteins therein is severely limited. Many glycosylated proteins are key tool enzymes for the biosynthesis of various pharmaceutical molecules, such as glycosaminoglycan-related synthases, but there is a lack of universal protein engineering methods to enable the adaptive evolution of these enzymes in E. coli. We established an evolution-guided optimization strategy that targets non-conserved N-glycosylation sites (EGO-NGly). The core of this strategy lies in the phylogeny-guided selective reversion of evolutionarily acquired N-glycosylation sequons to naturally occurring non-glycosylated residues from early-divergent orthologs, thereby improving heterologous production and residual activity stability for selected sulfotransferases in E. coli. Using heparin 3-O-sulfotransferase 1 (3OST-1) as a model enzyme apparatus in eukaryotic organisms, EGO-NGly extended the residual activity half-life by 4.5-fold. Structural analysis and molecular dynamics simulations indicate that greater surface rigidity and remodeling of intramolecular interaction networks contribute to the improved conformational stability of M7 in an aglycosylated host. EGO-NGly was further applied to a panel of 3OST and 6OST homologs, demonstrating its applicability to a subset of the tested enzymes. Furthermore, EGO-NGly can be orthogonally integrated with other complementary protein engineering strategies, as exemplified by its combination with the machine learning-aided Protein Repair One-Stop Service, generating variants with 8-fold and 17-fold extensions in residual activity half-life. Collectively, these results establish EGO-NGly as a practical and potentially cost-effective engineering strategy for improving the prokaryotic expression and functional performance of selected glycosylation-dependent eukaryotic sulfotransferases.

biochemistry↗

bioRxiv2026

Establishing toxicologically relevant primary alveolar macrophage models to enable a realistic assessment of nanomaterials safety

Alveolar macrophages (AMs) are key sentinels of the distal lung, maintaining surfactant homeostasis and clearing inhaled particles through continuous surveillance and phagocytosis. Mechanistic studies of particle-cell interactions, important to assess the respiratory safety or toxicity of particles, however, are limited by the lack of suitable in vitro models that preserve the core features of resident AMs. Here, we benchmarked six murine AM models, including short-term cultured primary AMs (AMs 3 h, AMs 24 h), primary AMs maintained with GM-CSF, TGF-{beta}, and the PPAR-{gamma} agonist rosiglitazone (AMs GTR), bone marrow-derived AM-like cells (BM-AMs), the immortalized AM cell line MH-S, and the non-transformed fetal liver-derived AM-like cell line MPI, against in vivo AMs based on surface phenotype, transcriptomic identity, and their responses to three carbon-based nanomaterials (CBNs). Both cell lines showed limited AM identity, characterized by low CD11c and SiglecF but high CD11b surface expression. In contrast, AMs GTR and BM-AMs more closely preserved resident AM-like surface marker profiles. Transcriptomic features, although differing for alterations in metabolism-related pathways, particularly oxidative phosphorylation, revealed most in vivo-like for the primary AM models. Functional, toxicological assessment using soot-like carbon nanoparticles (CNP), double-walled carbon nanotubes (DWCNT) and multi-walled carbon nanotubes (MWCNT) demonstrated strong model-dependent responses. Consistent with MWCNT-induced reduction in AM numbers observed in vivo, AMs GTR and BM-AMs exhibited the strongest in vitro responses, including cytotoxicity and inflammatory cytokine release. MH-S cells in contrast stood out for their cytotoxic sensitivity supporting their use for high throughput cytotoxicity tests. Overall, these findings identify AMs GTR and BM-AMs as the closest models for studying AMs biology and AM-intrinsic responses to poorly soluble nanoparticles like CBNs, and with regard to availability of higher cell numbers, BM-AMs might provide a scalable platform for mechanistic and higher-throughput nanotoxicology studies.

pharmacology and toxicology↗

bioRxiv2026

HighFold-Lasso: Topology-Guided Prediction of Lasso Peptide Structures Using AlphaFold3

Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by a mechanically interlocked topology, in which the C-terminal tail is threaded through an N-terminal macrolactam ring formed by an isopeptide bond. This unique topology often confers high thermal stability and resistance to proteolytic degradation. However, the isopeptide linkage, threaded topology, and class-specific disulfide connectivity make lasso peptide structures difficult to reconstruct reliably using general-purpose structure prediction models. Here, we developed HighFold-Lasso, which combines custom covalent connectivity with lasso scaffold-guided adaptive low-noise initialization to enable conditional structure generation guided by lasso conformational priors. On a test set of 52 experimentally determined structures, HighFold-Lasso achieved a 100% lasso topology success rate, with a mean RMSD C-alpha of 1.942 Angstrom for the ring-loop region and 2.375 Angstrom for the full peptide. The framework supports modeling of the four classical lasso peptide classes (I-IV) and can represent noncanonical amino acids, providing computational support for structure-function studies and molecular engineering of lasso peptides.

bioinformatics↗

bioRxiv2026

Asymmetric flagellar filaments shape Borreliella burgdorferi morphology and motility

The Lyme disease spirochete Borreliella burgdorferi possesses bipolar periplasmic flagella that are essential for its distinctive flat-wave morphology, motility, and infectivity. However, how the molecular architecture of these flagella contributes to spirochetal morphology and motility remains poorly understood. Here, using in situ single-particle cryo-electron microscopy, we determine near-atomic structures of native periplasmic flagellar filaments and reveal two distinct architectures: half-sheathed and unsheathed. We show that the spirochete-specific protein FlaA forms an asymmetric sheath along the convex surface of the conserved FlaB filament core, with sheath assembly restricted to the proximal filament region near the flagellar motor. Atomic models reveal that FlaA anchors to the FlaB core through specific interactions with two surface-exposed loops, while genetic and motility analyses demonstrate distinct roles for these loops in maintaining cell morphology and motility. Structural comparisons reveal that the FlaB core possesses intrinsic curvature and supercoiling, which are substantially amplified by asymmetric FlaA assembly. These findings support a model in which localized FlaA sheath assembly reinforces the proximal filament and potentially modulates its mechanical properties. Together, our results uncover a previously unrecognized mechanism by which asymmetric sheath assembly enhances flagellar supercoiling, providing a molecular basis for understanding the distinctive morphology and motility of spirochetes.

microbiology↗

bioRxiv2026

SMARTFlexDB: a paired apo-holo RNA structure database and analysis platform for RNA conformational flexibility and small-molecule recognition

RNA structures can undergo substantial conformational changes upon small-molecule binding, yet existing structural resources provide only static RNA-ligand snapshots without connecting ligand-bound (holo) RNA structures to corresponding ligand-free (apo) conformations. SMARTFlexDB is a curated database and analysis platform that uses paired apo-holo RNA structures to characterize conformational differences and RNA-small-molecule recognition. Candidate pairs were identified from the Protein Data Bank by matching RNA chains with at least 90% sequence identity and coverage, and fully conserved binding pocket nucleotides. The current release contains 434 binding pockets from 266 holo structures, linked to 186 apo structures to yield 1,187 pocket-level apo-holo pairs organized into 734 database entries, spanning 150 small molecules and 23 RNA functional classes. Each entry integrates RNA sequence and secondary-structure annotations, apo and holo three-dimensional structures, RNA-ligand atomic interactions, and quantitative descriptors of global and local conformational changes. An interactive web interface enables users to explore sequence alignments and structural overlays, compare secondary structures and RNA motifs, and upload paired apo-holo structures for customized analysis. By linking ligand-bound and ligand-free RNA structures, SMARTFlexDB provides a robust foundation for investigating RNA structural flexibility and supporting RNA-targeted small-molecule drug discovery. The database and analysis platform are available at https://aidd.rc.ufl.edu/app/smartflexdb/.

bioinformatics↗

bioRxiv2026

DiffRhyShiny: A Benchmarking-Informed Platform for Differential Rhythmicity Analysis with Dependence-Aware Evidence Integration

Motivation: Differential rhythmicity analysis identifies condition-specific changes in biological oscillations, but diverse algorithmic assumptions complicate method selection. Furthermore, integrating complementary evidence across different tools while accounting for statistical dependence remains an unresolved challenge. Results: We benchmarked seven algorithms across diverse rhythmic scenarios, revealing that optimal selection depends heavily on specific biological variations and experimental designs. To overcome single-algorithm limitations, we introduced Kost's Method, a dependence-aware p-value integration approach. Building on this framework, we developed DiffRhyShiny, an interactive web platform that automates robust differential rhythmicity analysis, consensus evaluation, and visualization. Furthermore, we validated the platform's performance and statistical rigor using both extensive simulated scenarios and real-world transcriptomic datasets. Availability and implementation: DiffRhyShiny is freely available at https://omicsai.shinyapps.io/diffrhyshiny, with the latest source code at https://github.com/liuchuan111/diffrhyshiny. The code and data to reproduce all benchmarking results are archived on Figshare at https://doi.org/10.6084/m9.figshare.33070100.

bioinformatics↗

bioRxiv2026

The ammonia-senescence ratchet drives an adaptation-senescence-ammonioptosis transition in liver cancer

Senescence suppresses tumor proliferation while exposing survival dependencies, motivating separate, sequential steps of senescence induction and senescent-cell clearance. Whether senescence-sustaining metabolism can instead be overdriven to trigger cell-autonomous death remains unknown. Senescent cells generate ammonia through glutaminolysis to buffer intracellular acidification, yet extracellular ammonia can impair anti-tumor immunity, leaving unexplored whether ammonia can instead drive tumor-cell-intrinsic death. Here, we reverse this logic and identify a self-reinforcing ammonia-senescence ratchet in which ammonia accumulation promotes senescence, whereas senescence reciprocally enhances ammoniagenesis, progressively driving tumor cells from metabolic adaptation through senescence to ammonioptosis. Reducing intracellular ammonia suppressed senescence and cell death, whereas ammonia repletion restored lethality. We engineered acid-responsive H3B-120@CoGd-LDH (HBCG) to preferentially amplify tumor-cell ammonia by reinforcing senescence and ammoniagenesis, restricting ammonia disposal and weakening lysosomal buffering. HBCG limited extracellular ammonia accumulation and CD8+ T-cell exposure in co-cultures, induced ammonioptosis in patient-derived liver-cancer organoids and suppressed tumor growth in immunocompetent mice. This work reveals that adaptation, senescence and ammonioptosis can be connected through escalating intracellular ammonia stress, providing a mechanistic framework for understanding stress-driven tumor-cell fate transitions.

bioengineering↗

bioRxiv2026

Trigeminal Nerve Stimulation Attenuates Traumatic Brain Injury-Induced Neuronal Damage via CGRP-PINK1 Mitophagy Axis

Secondary damage after traumatic brain injury (TBI) is driven by progressive mitochondrial failure, yet clinically viable strategies to directly safeguard mitochondrial networks remain a major therapeutic gap. Here, we show that non-invasive trigeminal nerve stimulation (TNS), which engages the brain's endogenous oxygen-conserving diving reflex, preserves neuronal survival by directly regulating the mitochondrial PINK1/Parkin quality-control pathway. We demonstrate that TBI induces the pathological aggregation of the outer mitochondrial membrane receptor TOM20, in a CGRP-dependent manner, which affects binding of the damage-sensor PINK1 and renders downstream Parkin-mediated rescue ineffective. TNS-induced neuronal CGRP release prevents this TOM20 aggregation, restoring proper PINK1 function and downstream Parkin activation. This preservation of mitochondrial architecture reinforces the outer membrane's barrier function, limiting pro-apoptotic cytochrome c leakage and supporting NRF2 antioxidant defenses, ultimately reducing progressive infarct expansion and recovering sensorimotor functions. The significance of this work lies in bridging physical neuromodulation directly to the preservation of organelle-level architecture. By demonstrating that stimulation of trigeminal afferents to recruit an oxygen-conserving reflex can stabilize outer membrane signaling architecture and preserve mitochondrial survival machinery, this study outlines a non-pharmacological strategy to protect mitochondrial function and inhibit acute post-traumatic neurodegeneration.

neuroscience↗

bioRxiv2026

Cross-species analysis identifies APOBEC3-associated spliceosomal snRNA hypermutability

Spliceosomal small nuclear RNA (snRNA) genes show unusually high germline mutation rates, with R-loop formation previously implicated in this mutability. Our cross-species rare-variant and de novo mutation analyses show that hypermutability is concentrated in RNA polymerase II-transcribed spliceosomal snRNA genes, with strong enrichment in primates but a much weaker excess in rodents and chicken, consistent with lineage differences in APOBEC3 repertoires. Human Pol II-transcribed spliceosomal snRNA genes show mutational strand asymmetry, APOBEC3-associated mutational signatures and strong APOBEC3B binding signals. R-loops are also frequent at these loci, including in mouse genes with much weaker hypermutability, indicating that R-loop formation alone is insufficient to explain the phenotype. Together, cross-species comparisons support lineage-specific APOBEC3 activity, rather than R-loop formation alone, as a major contributor to spliceosomal snRNA gene hypermutability.

genomics↗

bioRxiv2026

Photostimulus intensity, rather than colour or polarization, is the key driver for stable fly visual attraction in laboratory bioassays

Foraging hematophagous flies such as the stable fly, Stomoxys calcitrans, are shown or expected to sense multiple characteristics of visual host cues. These include relative intensity, spectral composition, and the angle and degree of polarization. Here, we investigated the role of each of these visual cue characteristics on stable fly attraction. In laboratory two-choice bioassays, we offered groups of female or male stable flies a choice between paired photostimuli that differed in their visual characteristics, recording the flies' landing responses on stimuli as the response criterion. Bioassay flies preferentially selected lower-intensity visual stimuli even when paired stimuli markedly differed in spectral composition and polarization characteristics (a high degree of horizontal or vertical polarization). When paired stimuli had identical relative intensity, flies failed to discriminate between the stimulus that presented ultraviolet, blue, green, and red wavebands and a corresponding paired stimulus lacking one of these wavebands. Our results support the hypothesis that foraging stable flies may respond to colour and polarization characteristics of visual stimuli as modulations of perceived intensity. Acquired knowledge on the mechanisms that underlie stable fly visual attraction may inform the design of vision-based traps so that they become optimally attractive to stable flies and other biting flies.

animal behavior and cognition↗