Biology subjects

Li, R.

Publications and source records attributed to Li, R..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

The Maine Coon Cat Harboring the MYBPC3-A31P Mutation: A Genotype-Stratified Phenotypic Characterization of Hypertrophic Cardiomyopathy

Abstract Background: Most animal models of HCM are mouse-based, but the thin interventricular septum in mice makes it difficult to clearly distinguish pathological hypertrophy, which introduces substantial errors and constrains basic HCM research. Cats develop HCM spontaneously, and the common MYBPC3-A31P variant in cats is homologous to human mutations in both genetics and pathology, with a larger body size that makes them suitable as large-animal models. This study examines how heterozygosity or homozygosity for the p.A31P mutation (c.91G>C) in the MYBPC3 gene affects the phenotype and severity of HCM in affected cats, with the aim of establishing an ideal large-animal model for clinical risk stratification and precision diagnosis and treatment of human HCM. Methods: Forty-nine Maine Coon cats were enrolled and stratified into homozygous mutant (HOM, n=8), heterozygous mutant (HET, n=26), and wild-type (WT, n=15) groups. All cats underwent echocardiography, blood pressure measurement, physiological assessment, hematological and biochemical analyses, and cross-species sequence conservation analysis. Results: No significant differences in baseline characteristics including age and body weight were observed among groups (P>0.05). HOM cats exhibited significantly higher left ventricular outflow tract pressure gradients and greater basal septal thickness compared to WT cats (P<0.05), with HET cats showing intermediate values. Analysis of hematological and serum biochemical parameters revealed no evidence of systemic inflammation or hepatic injury. Sequence conservation analysis confirmed that the A31 residue is highly conserved across mammalian species. Conclusions: This study provides a phenotypic characterization of Maine Coon cats carrying the MYBPC3-A31P mutation, revealing marked gene-dose effects on cardiac structure and function, with homozygous individuals exhibiting more severe phenotypic features. This model serves as a large-animal translational platform that not only clarifies genotype-phenotype correlations but also supports risk stratification and precision therapeutic strategies in human HCM. Its spontaneous nature and genetic homology to human disease make it particularly valuable for bridging preclinical findings to clinical application.

genetics↗

bioRxiv2026

Hypoxia and epithelial to mesenchymal transition pathways are enriched in bladder tumor epithelium adjacent to tertiary lymphoid structures

Formation of tertiary lymphoid structures (TLS) within the bladder microenvironment because of chronic mucosal inflammation has been associated with variable clinical outcomes. While the immune cell composition and functional states of TLS have been characterized in both non-invasive and muscle-invasive bladder tumors, the TLS-adjacent tumor epithelial compartments remain poorly characterized. Evaluation of a 16-gene TLS signature in treatment-naive tumor bulk RNA sequencing profiles from 283 non-muscle invasive bladder tumors, from patients treated with Bacillus Calmette-Guerin (BCG) immunotherapy, and 348 muscle-invasive bladder tumors from patients treated with immune checkpoint inhibitor therapy revealed overlapping enrichment of immune exhaustion pathways. High TLS gene expression scores correlated with upregulation of immune exhaustion, hypoxia, and epithelial-to-mesenchymal transition (EMT) pathways in tumors from both cohorts. Spatial whole transcriptomic analysis of tumor sections with high TLS density, revealed enrichment of genes associated with EMT, angiogenesis, extracellular matrix remodeling, and B cell receptor signaling pathways in tumor epithelial regions adjacent to TLS, whereas those distant from TLS exhibited enrichment of IFN-{gamma}, TNF-/NF-{kappa}B, p53, and metabolic pathways. Multiplex immunofluorescence further identified co-localization of exhausted immune cell populations within the core and periphery of peri-tumoral TLS. These findings indicate that a pro-tumorigenic microenvironment associated with disease progression in bladder cancer exists within peri-tumoral TLS and potentially a factor underlying contrasting therapeutic associations potentially driven by live microbial versus targeted immunomodulatory therapy in NMIBC and MIBC.

cancer biology↗

bioRxiv2026

LTBP isoforms differentially encode TGF-β spatial localization and activation

TGF-{beta} signals through a conserved pathway yet produces diverse outcomes, pointing to regulatory mechanisms upstream of receptor engagement. A family of four latent TGF-{beta} binding proteins (LTBPs) tether pro-TGF-{beta}s and control their localization and activation, but how distinct LTBPs contribute to this regulation is unclear. Here we combine cryo-electron microscopy with functional assays to dissect LTBP-pro-TGF-{beta} interactions. We resolve the LTBP-1/pro-TGF-{beta}1 and LTBP-3/pro-TGF-{beta}3 complex structures, revealing a conserved yet plastic hydrophobic binding interface, and systematically map key residues across all four LTBP and three pro-TGF-{beta} subtypes that determine binding specificity and affinity. Unexpectedly, LTBP-2, previously thought incapable of TGF-{beta} binding, engages pro-TGF-{beta}1 through a covalent linkage via its 16th EGF-like domain, providing a mechanistic link between LTBP-2 function and TGF-{beta} signaling. Beyond tethering, LTBP-3 shifts pro-TGF-{beta}3 from spontaneous activation toward integrin dependence, establishing LTPBs as dynamic modulators that dictate not only where but also how TGF-{beta} is unleashed. Collectively, these findings establish that LTBPs are not redundant ECM scaffolds but a family of functionally distinct regulators that differentially encode TGF-{beta} spatial localization and activation, with implications for isoform-selective therapeutic strategies.

biochemistry↗

bioRxiv2026

A Structural Antibody Benchmark of AlphaFold3 reveals Hallucinated Epitopes and a Bias for Orderness

AlphaFold3 has shown promise as a tool for predicting antibody-antigen binding, yet its performance across large datasets has not been fully characterized. In this study, 3401 experimentally validated antibody-antigen complexes were sourced from the Structural Antibody Database and screened alongside 23798 negative controls to benchmark AlphaFold3s binding prediction capabilities. Confidence metrics including Predicted Aligned Error and Interface Predicted Template Modeling score were used to achieving a maximum recall of 53% at 100 inference seeds. Several factors were found to influence prediction accuracy: a notable bias was observed toward antibodies derived from X-ray crystallography structures versus those from electron microscopy, and positive prediction rates were found to decrease with increasing target protein size and surface area. In contrast, neither the amino acid composition or lengths of the complementarity determining regions, nor training data leakage were found to introduce significant bias. An innate false positive rate of approximately 3% was identified, with AF3 shown to hallucinate plausible binding interfaces across the surface of decoy targets while avoiding disordered regions. Epitope mapping using DockQ, epitope shift, and antibody displacement revealed that approximately 34% of false negatives retained the correct epitope location despite poor structural alignment, suggesting that conformation refinement tools could recover additional true binding predictions. These findings provide a comprehensive characterization of AlphaFold3s strengths and limitations for antibody screening in computational drug discovery. Key MessagesO_LIAlphaFold3 has a recall of 50% and an innate false positive prediction rate of 3%. C_LIO_LIFalse negative predictions can still feature the correct epitope despite poor RMSD. C_LIO_LIFactors such as disorder and target size impact accuracy. C_LI

bioinformatics↗

bioRxiv2026

Single-cell profiling reveals MMP7-associated epithelial transition and immune-stromal remodeling in esophageal carcinogenesis

The progression from reflux esophagitis (RE) to Barretts esophagus (BE) and esophageal adenocarcinoma (EAC) is a major route of inflammation-associated esophageal tumorigenesis, but the cellular transitions involved remain incompletely understood. We performed single-cell transcriptomic profiling of RE, BE, and EAC tissues and integrated public EAC datasets, yielding 51,283 cells across the RE-BE-EAC continuum. The analysis identified stage-associated epithelial and microenvironmental differences. Pseudotime analysis placed Basal epithelial cells along two differentiation branches, one toward mature epithelial states and the other through proliferative and gastric-type metaplastic states toward copy number alteration-bearing malignant epithelial cells. MMP7 increased along this malignant branch, was enriched in cancer-associated epithelial cells. Its knockdown reduced the proliferation and migration of OE19 and OE33 cells, supporting an association with proliferative and migratory phenotypes. In parallel, the microenvironment shifted toward immune suppression and stromal remodeling, with increased T-cell exhaustion, macrophage polarization toward tumor-associated states, and enrichment of CAF-like myofibroblasts. Ligand-receptor analysis further suggested an epithelial-centered communication network involving MDK-SDC2/LRP1/NCL interactions between malignant epithelial cells and fibroblast, T-cell, and myeloid compartments. These results identify MMP7-associated epithelial states and candidate MDK-related communication pathways for further longitudinal and functional validation.

cancer biology↗

bioRxiv2026

VASP Promotes Aortic Valve Calcification by Interacting with FBLIM1 to Activate the Focal Adhesion Pathway

BackgroundCalcific aortic valve disease (CAVD) is the most prevalent valvular heart disease, yet there is no effective pharmacological therapy to halt or reverse its progression. Focal adhesions (FAs) are dynamic structures that connect cells to the extracellular matrix (ECM), serving not only as mechanical anchors but also as critical signalling hubs that regulate cell adhesion, spreading, migration, differentiation, and mechanotransduction. However, their specific role in CAVD pathogenesis remains largely unknown. MethodsTo identify upregulated hub genes, an integrated analysis of proteomics and RNA sequencing was performed on calcified aortic valves. To investigate functional roles in vitro, we utilized genetic knockdown and overexpression of VASP in valvular interstitial cells (VICs), followed by phenotypic evaluations of osteogenic differentiation, calcification, and elastin (ELN) secretion. Downstream mechanisms were explored using RNA-seq in VASP-overexpressing VICs, alongside pharmacological inhibition of the FA pathway. Finally, protein-protein interaction assays were conducted to map and analyze the physical binding between VASP and the structural domains of FBLIM1. ResultsIntegrated omics analysis identified VASP as a significantly upregulated gene in human calcified aortic valve tissues. Functionally, VASP knockdown inhibited, whereas its overexpression promoted, the osteogenic differentiation of VICs. RNA-seq revealed that VASP overexpression activated the FA pathway, and the pharmacological blockade of this pathway successfully suppressed calcification both in vitro and vivo. Mechanistically, we demonstrated a direct physical interaction between VASP and the third LIM zinc-binding domain of FBLIM1, and knockdown of FBLIM1 effectively reversed the pro-calcific effects of VASP. Finally, VASP overexpression was found to promote the secretion of ELN, which subsequently contributed to the calcification process. ConclusionOur study reveals that the interaction between VASP and FBLIM1 drives CAVD progression by activating the FA pathway, which subsequently leads to excessive ELN secretion. These findings reveal a novel mechanistic pathway and may provide a potential therapeutic target for CAVD intervention. What are the Clinical Implications?We have identified the VASP-FBLIM1-FA-ELN axis as a novel molecular pathway involved in CAVD pathogenesis, greatly enriching our understanding of the complex process of aortic valve calcification. This pathway intricately links cytoskeletal dynamics, cell adhesion signalling, and ECM remodelling, providing a new theoretical framework for pathophysiological research in CAVD. In clinical practice, VASP and its downstream pathway components, particularly FBLIM1 and the FA pathway, may serve as potential biomarkers and therapeutic targets for the early diagnosis and treatment of CAVD. For example, the FA pathway inhibitors PF-573228 and Y15 demonstrated significant anti-calcification effects both in vitro and in vivo, suggesting that targeting this pathway may offer a new nonsurgical intervention strategy for patients with CAVD.

cell biology↗

bioRxiv2026

Computational Design Strategies for Nanoscale 3D Auxetic Metastructures from DNA

Auxetic metamaterials exhibit negative Poissons ratio behaviors due to their architecture of periodically arranged unit cells. Although mechanical metamaterials are well established at the macroscale, programmable auxetic units remain scarce at the nanoscale. DNA origami offers a promising platform to bridge this gap, but design principles for dynamically deformable 3D auxetic nanostructures remain largely unexplored. Here, we develop design strategies for such 3D auxetic metastructures built from wireframe DNA origami. As a model system, we use a 3D re-entrant triangular unit composed of double-stranded DNA (dsDNA) bundle edges connected by single-stranded DNA (ssDNA) joints. Using coarse-grained molecular dynamics (MD) and umbrella-sampling free-energy simulations, we examine how edge design and joint-connection scheme govern auxetic responses and the energetics of the structural transformation. Our results show that auxetic performance and deformation energetics emerge from the coupled effects of DNA bundle rigidity and connector mechanics at the joints. This study provides mechanistic insights and design guidelines for programmable auxetic motion and energetics in 3D DNA origami metamaterials, advancing the development of stimuli-responsive nanomechanical devices.

biophysics↗

bioRxiv2026

HLiCA: An integrated cell atlas of the healthy human liver

The human liver is composed of a heterogeneous mix of cell types. How these distinct populations contribute individually and collectively to liver function remains poorly understood. Although single-cell technologies have advanced our understanding of liver biology, individual studies have often been limited by small donor cohorts and inconsistent cell type annotations. Integrating multiple datasets can overcome these challenges and better capture biological variability. We present the Human Liver Cell Atlas (HLiCA), an integrated reference of non-disease liver cells assembled from eight datasets across six research centers, encompassing more than 525,000 cells from 110 donors. Developed in collaboration with the Human Cell Atlas Liver Bionetwork, the HLiCA incorporates expert-curated cell annotations refined through community feedback and dedicated cell type annotation meetings. The HLiCA classifies cells into six lineages and expands the cell type resolution to include 47 distinct cell types. Starting from raw sequencing reads, we realigned all data and performed rigorous benchmarking to ensure robust integration across technical and biological variables. Genetic ancestry was inferred for all samples to evaluate the range of ancestral backgrounds represented in the atlas. The expanded cell type annotation enabled identification of previously unrecognized liver cell types, including NRXN1+ stromal cells. Their presence was validated using spatial transcriptomics, which localized NRXN1+ stromal cells to periportal regions. With the number of donors included in the HLiCA we were able to examine cell type specific associations with demographic covariates. In hepatocytes, drug metabolism genes showed differential expression between sexes, and in cholangiocytes, mucus-production genes varied with age. As the largest and most genetically diverse human liver cell atlas to date, the HLiCA provides a comprehensive, well-annotated reference for the field, annotated by expert consensus. This resource will enable deeper interrogation of liver cellular diversity, architecture, and function in the healthy human liver and serve as a reference to understand changes that occur with disease.

genomics↗

bioRxiv2026

Noise statistics drive background- and channel-specific interference in auditory midbrain representations of speech

Although humans and animals excel at interpreting target sounds in competing noise, sound recognition abilities can vary widely due to statistical characteristics of the interfering background. Yet, how the brain leverages statistical sound information to segregate sounds in noise remains unclear. Here, using many natural auditory textures as background stimuli, we test how the encoding of speech is altered by natural noises in the inferior colliculus (IC) of unanesthetized rabbits. We identify foreground- and background-driven neural response components to sound mixtures and find that the background statistics alter the neural representation of speech in a frequency- and modulation-specific manner. Neural encoding signal-to-noise ratios (SNRs) vary extensively across background categories, frequencies, and modulations, and these influence the encoding of speech independently of the acoustic SNR. This variability is driven by both the background spectrum and modulation statistics, which distort the speech representation and show distinct interference effects in the modulation ranges for rhythm and pitch. Thus, spectrum and modulation statistics critical to speech recognition in noise are reflected in IC neural population activity. These neural response statistics and resulting distortions likely determine the coding fidelity for speech in downstream cortical regions and provide a neural basis for differences in speech intelligibility in real-world noises.

neuroscience↗

bioRxiv2026

Mesothelial Plasticity Specifies a Pleural Immune Circuit that Orchestrates Lung Regeneration

Following injury, predisposition towards regenerative repair and away from degenerative remodeling is central to organismal health, yet the upstream determinants that instruct this fate choice remain poorly understood. Here, we identify mesothelial cell plasticity as a central determinant between regeneration and degeneration by comparing mouse models of pneumonectomy (PNX) versus chronic lung allograft dysfunction (CLAD). While mesothelial cells expand in both settings, following PNX, these cells undergo differentiation through multiple transitional states, culminating in an inflammatory population that orchestrates monocyte recruitment and subsequent tissue regeneration. In contrast, in CLAD, mesothelial cells enrich in an extracellular matrix-enriched state that lacks pro-regenerative signaling capacity. Using single cell epigenomic profiling and in vivo genetics, we define a mesothelium-specific TWIST1-CCL2 axis that governs mesothelium plasticity and signaling, monocyte recruitment and lung regrowth. Together, these findings demonstrate that context-dependent reprogramming of a pleural population, known to protect organs, can be leveraged to drive regeneration.

Developmental Biology↗

bioRxiv2026

EpiATLAS - a reference for human epigenomic research

The sequence of the human genome provides a foundation for understanding cellular processes in health and disease1. The organisation of this primary genetic information into cell-specific structure and function is critical to understanding the cell type-specific interpretation and execution of the genome. Epigenetic processes are essential for packaging and higher-level functional organisation of the genome, and changes therein are increasingly recognised as contributors to human disease. Building on primary data generated by multinational consortia, the International Human Epigenome Consortium2 (IHEC) has uniformly processed a collection of more than 2000 comprehensive human reference epigenomes, collectively referred to as EpiATLAS. This effort involved the development of standardised molecular and bioinformatics protocols, metadata models, and analytical tools to manage, integrate, display, and share vast amounts of epigenomic data. This includes the creation of a publicly available Epigenome Reference Registry, which provides a system for accessing protected human subject datasets and facilitates open searching of de-identified samples and experimental data. The integrated EpiATLAS ecosystem and its comprehensive human reference epigenome maps provide an unprecedented resource for the biosciences, expanding the annotated epigenomic landscape while uncovering previously unappreciated relationships among regulatory layers and revealing how epigenetic inputs underpin fundamental cellular functions and disease associations.

genomics↗

bioRxiv2026

Electrolytic-Microbubble Dynamics Delineate Safety Thresholds During Intracortical Microstimulation with Flexible Neural Interfaces

Intracortical microstimulation (ICMS) with ultraflexible neural electrodes enables low-threshold, chronically stable, and high-resolution modulation of neural circuits, providing a promising strategy for sensory restoration and closed-loop neuromodulation. However, the microscopic mechanisms delineating its safe and effective current range remain unclear. Here, we combine intravital two-photon (2P) imaging and electrophysiology in awake mice to examine the current-dependent neurovascular outcomes of charge-balanced stimulation via ultraflexible arrays. We observed gas bubbles formed along the electrode during ICMS, with bubble size increasing quadratically with current amplitude, consistent with a Faradaic bubble-growth model. Intravital 2P imaging reveals that at low-to-moderate currents (20-40 {micro}A), vascular leakage is small, spatially confined, and largely reversible, whereas higher currents ([≥]60 {micro}A) induce a sharp transition to extensive, field-dominated extravasation and secondary vessel disruption. This transition coincides with immediate, stimulus-locked motor responses and the onset of electrode degradation. Multiphysics simulations reproduce the observed nonlinear leakage-current relationship by incorporating gas bubble-induced electric field redistribution and voltage-dependent vessel wall permeability. The model indicates that gas bubbles act as local electric-field modulators, concentrating suprathreshold fields near the bubble boundary at lower currents while shielding more distant vessel segments; at higher currents, this confinement breaks down and the system enters a field-dominated damage regime. Collectively, these findings define a mechanistically informed safety window for ICMS with flexible neural interfaces and identify bubble-assisted vascular permeabilization as a key failure mode at high currents, crucial for the design of future bidirectional brain-computer interfaces and high-precision neuroprosthetic protocols.

neuroscience↗

bioRxiv2026

Field–Flow–Front mapping of breast cancer evolutionary dynamics in situ

Tumour progression reflects not only which clones arise but where, when and in what context they expand--dimensions genotype-centred reconstructions leave unresolved. Here we reconstruct breast cancer evolution in situ across 34 Visium HD, 16 Xenium, 32 MIBI-TOF and 10 CODEX samples, serial-section 3D reconstruction, single-cell and bulk transcriptomes, and genome-wide CRISPR dependency profiles. We partition tumours into 296 cancer microzones--stroma-bounded units within which expansion is reconstructed--and define in each a Cancer Progression Metric(CPM) coupling a transcriptomic clock to expansion geometry. Projected onto tissue, CPM yields a Field-Flow-Front model rendering progression as a continuous physical process and resolving subclonal architecture into spatially coherent domains rather than predefined branches. Unexpectedly, the most advanced fronts were not the most proliferative but low-dependency, slow-cycling populations with directional expansion, driven by an extracellular matrix programme whose evolutionary force exceeded inflammation by nearly an order of magnitude yet whose genes were the least cell-autonomous. Under chemotherapy it persisted while its clonal carriers reshuffled, marking a transferable, stroma-coupled front process--not a fixed clone--as the unit of advance. Distilled into an evolutionary advantage load, this front process predicted recurrence and survival across independent cohorts and improved on conventional staging, establishing a tissue-embedded paradigm for mapping tumour evolutionary dynamics, from local fronts to patient outcome.

Cancer Biology↗

bioRxiv2026

Deep learning reveals the individual-level effects of artificial light at night on a wild insect

Artificial light at night (ALAN) is a widespread anthropogenic phenomenon with varied physiological, behavioural, and ecosystem-level effects. Its impacts have been studied extensively at the population level, however less is known about the individual changes that underpin these larger trends. We use a networked video system combined with GryllAI--a deep learning-based system for continuous individual monitoring--to explore this in the field cricket, Gryllus campestris. Applying field-realistic artificial light (10-25lx) or a control treatment to burrows, we continuously track the activity of 144 nymphs across >38,000h of video footage, recording life history outcomes for each individual. Results indicate that ALAN exposure does not influence daily activity timing, total activity duration, predation risk, or nymphal development duration. However, changes in fine-scale behaviour were apparent, with ALAN causing crickets to enter and exit burrows less frequently, especially at night; and spent greater proportion of time outside burrows during daytime. These behavioural adjustments were not evident from broad scale activity trends that could be observed manually. Consequently, our findings suggest that aggregate measures of activity may fail to capture the full scope of ALAN-mediated impacts in nature, and that automated monitoring techniques offer a promising means of addressing this.

ecology↗

bioRxiv2026

GALE-dependent glycoproteome remodelling is a determinant of oncogenic RAS transformation

Oncogenic transformation is accompanied by extensive remodelling of the cellular glycosylation landscape, yet the mechanisms linking oncogenic signalling to glycoproteome reprogramming remain poorly defined. We used site-resolved intact glycoproteomics to systematically map oncogenic RAS-dependent changes across the N- and O-linked glycoproteome. Integrating multiomics profiling with functional approaches, we identify UDP-glucose 4-epimerase (GALE) as a transcriptional target of oncogenic RAS that is induced through MAPK signalling and MYC-dependent transcription. GALE depletion selectively disrupted RAS-dependent glycoproteome remodelling, preferentially impairing sialylation of N-linked glycans and O-linked GalNAc-type glycosylation. Functionally, these glycosylation defects were accompanied by suppressed anchorage-independent growth and reduced in vivo tumorigenicity of KRAS-mutant cells, establishing GALE-dependent nucleotide-sugar interconversion as a requirement for malignant growth. Clinically, GALE expression was elevated in pancreatic ductal adenocarcinoma, wherein KRAS mutations are highly prevalent, and across a broad spectrum of human cancers. Collectively, our findings define a regulatory axis that connects oncogenic signalling to nucleotide-sugar precursor availability and diversification of the cellular glycan repertoire, revealing GALE as a metabolic dependency in RAS-driven cancer.

Cancer Biology↗

bioRxiv2026

A missense mutation in FBXL3 links circadian regulation to out-of-season estrus in sheep

Seasonal breeding is a remarkable adaptive trait, but it constrains efficient production in the sheep industry. Recent studies have shown that seasonal breeding is associated with endogenous circannual rhythms, which are regulated in part by the circadian clock system. FBXL3, a pivotal component of the SCF (SKP1 - CUL1 - F-box) E3 ubiquitin ligase complex, is a known determinant of the mammalian circadian period. In this study, we identified a missense mutation, T183M, in FBXL3 through selective sweep analysis. The allele frequency of this mutation differed significantly between sheep breeds exhibiting year-round estrus and those showing seasonal breeding patterns. The association between the T183M mutation and seasonal breeding was further validated using an ovariectomized, estradiol-implanted sheep model. We then generated mice carrying the homologous T183M mutation and found that they exhibited significantly lengthened circadian periods, accompanied by reduced CRY1 expression and increased CLOCK expression. Co-immunoprecipitation assays confirmed that the mutation reduced the interaction between FBXL3 and CRY1. These findings demonstrate an evolutionarily conserved role of FBXL3 in the circadian clock system. We propose that the T183M mutation disrupts day-length recognition, thereby influencing seasonal estrus in sheep. Author summarySeasonal breeding limits sheep productivity and is regulated by circadian rhythms, yet the key genetic determinants remain poorly understood. Here, we identified an FBXL3 T183M missense mutation whose allele frequency differed markedly between year-round-estrous and seasonally breeding sheep, and validated its association with seasonal reproduction in a sheep population. Functional analyses in mutant mice showed that this variant lengthened the circadian period, disrupted the expression of core clock genes, and weakened the interaction between FBXL3 and CRY1. These findings suggest that the FBXL3 T183M variant impairs day-length perception, thereby modulating seasonal estrus in sheep. Our study reveals a conserved circadian mechanism underlying seasonal breeding and highlights FBXL3 T183M as a promising genetic target for improving reproductive performance in sheep.

genetics↗

bioRxiv2026

Stress-Related Transcriptional Regulators Dominate the Conserved Core GRN for Three Cyanobacteria: Network Topology Maps the Highest-Influence Nodes as Promising Engineering Targets

Cyanobacteria manage photosynthetic and environmental stresses through transcriptional programs controlled by regulators also affecting carbon flux, growth states, and metabolic output that bioproduction seeks to optimize. This regulatory architecture and its most influential nodes remain incompletely characterized. We hypothesized two influential regulator layers: a conserved core responding to common stresses, and species-specific regulators mediating strain-level niche adaptations. Mapping both layers underpins understanding genome[->]regulatory-network[->]phenotype flow, enabling global transcription machinery engineering for reliable bioproduction. To test our hypothesis, we constructed conserved-core and species-specific gene regulatory networks (GRNs) for three cyanobacteria, Synechococcus elongatus PCC 7942, Synechocystis sp. PCC 6803 and Picosynechococcus sp. PCC 7002, integrating a manually curated multi-pipeline regulator inventory with 1,098 harmonized transcriptome states for the 1,362-gene tri-homolog core genome. We quantified each regulator influence using local (degree, k-core), global (betweenness, closeness), and community-aware (eigenvector) centrality measures, and an Integrated Centrality score aggregating influence across complementary topological measures. High-influence regulators are predicted to exert broad metabolic effects when manipulated, making them priority candidates for single-target engineering interventions that modulate multiple genes and reprogram complex phenotypes. Across the three cyanobacteria, the two GRN layers proved topologically distinct: the conserved core concentrated influence in stress-related hubs (11 of its top 15 by Integrated Centrality were stress-related), while species-specific networks spread influence across functionally diverse regulators. Stress-coupled enrichment also held per individual centrality measure: regulators ranking top in both the core and species-specific GRNs by the same measure were mostly stress-related (15 of 19 instances), including the multi-stress regulators RpaB, Rre1, and BolA, the heat-shock HrcA, and the nitrogen NtcA. In species-specific GRNs, stress-related regulators remained the leading category alongside circadian, carbon-metabolism, morphology, and housekeeping regulators, including PlmA, Pex, TetR, and SrrB in PCC 7942; KaiC3, Sycrp1, Rre28, and Bhl in PCC 6803; and Zur, Sycrp1, and NarL in PCC 7002. High-influence putative regulators included the iron-stress AraC-family paralogs IutR1-IutR3, OmpR-family paralogs OmpR1-OmpR2, and chromosome- or plasmid-encoded Xre-family, AraC, and HypP. Stress regulation emerges as a recurring high-influence axis across these networks. The conserved core identifies universal regulatory programs, and species-specific layers reveal strain-level innovations for cross-strain transfer to support engineering of robust bioproduction. ImportanceCyanobacteria are studied as platforms for sustainable, carbon-recycling production of fuels and chemicals from sunlight, water, and atmospheric carbon dioxide. Their reliable deployment in industrial settings is limited by environmental stresses that depress photosynthetic efficiency and product yields. The same regulatory proteins that govern stress responses also control how cells partition carbon, switch growth states, and direct metabolic output, making them natural levers for engineering robust production strains. Yet systematic, cross-species maps of these regulators have been missing. We present the first comparative regulatory map spanning three biotechnologically important model cyanobacteria, Synechococcus elongatus PCC 7942, Synechocystis sp. PCC 6803, and Picosynechococcus sp. PCC 7002, and identify the conserved regulators most influential across all three. The resulting catalog prioritizes candidate targets for experimental validation, and the supporting datasets and analytical framework are released for reuse to support efforts to engineer cyanobacterial strains for reliable industrial bioproduction.

systems biology↗

bioRxiv2026

Identifying Ecological Restoration Priority Areas through a Function-Structure-Dynamic Framework: Integrating Ecological Security Patterns and Future Land-Use Simulation in the Anhui Section of the Yangtze River Basin

Rapid urbanization has intensified ecological degradation and threatened ecosystem sustainability in the Yangtze River Basin. This study proposes a Function-Structure-Dynamic (FSD) framework integrating ecological protection importance assessment, ecological security pattern (ESP) construction, and future land-use simulation to identify ecological restoration priorities in the Anhui section of the Yangtze River Basin. Ecologically important areas were identified by coupling ecosystem services and ecological vulnerability. MSPA, landscape connectivity analysis, resistance surface modeling, and circuit theory were applied to construct the ESP, while the PLUS model simulated land-use change and ecological risks in 2032. Results identified 37 ecological sources covering 6,901.39 km{superscript 2} and 84 ecological corridors with a total length of 916.80 km. Ecological pinch points, barrier areas, and 17 ecological warning areas were further delineated. Based on these findings, four ecological restoration zones were proposed with differentiated management strategies. The FSD framework effectively integrates ecological functions, spatial structure, and future dynamics, providing scientific support for ecological restoration and sustainable territorial spatial planning in rapidly urbanizing regions.

ecology↗