Biology subjects

He, Z.

Publications and source records attributed to He, Z..

At least 19 recordsLinked to original sources

bioRxiv2026

Two genomes in one mitochondrion: mitochondrial heteroplasmy and mitogenome dynamics in Chlamydomonas reinhardtii

The mitochondrial genome of the model green alga Chlamydomonas reinhardtii has long been described as a 15.8-kb linear molecule capped by inverted telomeres. By leveraging high-accuracy long-read sequencing to overcome limitations associated with conventional genome algorithm biases, we demonstrated that this classical paradigm was incomplete. Our analyses provided no evidence for canonical telomeric structures, instead revealed widespread structural heteroplasmy characterized by the coexistence of two distinct mitochondrial genome configurations. In addition to the historical 15.8-kb configuration (designated as config 2), we identified an expanded 19-kb configuration (config 1) containing 4,001-bp terminal inverted repeats that duplicate the cob and nad4 genes. Single-molecule long-read profiling captured these configurations as a dynamic network of multimeric mitochondrial DNA concatemers bridged with a conserved 17-bp homologous motif. Together, these structural features support a recombination-dependent replication (RDR) model that could enable mitochondrial DNA replication in the absence of conventional telomeric structures and reverse transcriptase-like (rtl) genes. We further identify widespread nuclear mitochondrial DNA segments (NUMTs), which complicate targeted amplification and quantification of these mitogenome configurations. Specifying NUMTs enabled configuration-specific digital PCR measurements across the CC-5325 lineage and additional field-isolated Chlamydomonas strains, revealing substantial variation in the relative abundance of the two mitogenome configurations. These findings revise a four-decade-old model of the C. reinhardtii mitogenome and provided a new framework for investigating mitochondrial genome architecture, structural heteroplasmy, and replication dynamics in photosynthetic eukaryotes.

plant biology↗

bioRxiv2026

Self-extending DNA recording with stochastic and programmed writing

Recording cellular histories requires new information to accumulate without erasing earlier records. Here we introduce Infinite Printer, a CRISPR recording architecture that couples self-extension to regeneration of a writable terminal context. A self-targeting prime-editing guide RNA (stpegRNA) directs repeat extension, while base editing generates diversity in situ without a separate insertion template for each character state. Earlier sequence remains upstream of the renewed terminus, linking substrate growth with record retention. Auxiliary pegRNAs specify payloads within a write-renew-write architecture. After three rounds of payload input, 4,436 distinct complete CCA-based records contained identities from all three pools. Longer AC/AT records retained shared upstream marks, and full-length sequence analysis resolved additional endpoint distinctions. Joint single-cell readout recovered 1,549 distinct records and 7,669 combinations across 12,302 transcriptome-linked cell labels from a single stpegRNA design. Spatial-transcriptomic readout recovered spacer records at 11,330 capture spots, linking record content to tissue coordinates and gene-expression profiles. Infinite Printer unites substrate renewal, sequence diversification and programmed writing with cell- and tissue-linked readout, providing a foundation for future lineage recording across large cell populations during mammalian development.

synthetic biology↗

bioRxiv2026

The Onset of Breathing at Birth Switches Off Regenerative Capacity

Many mammalian tissues, including the central nervous system (CNS), lose regenerative capacity in adulthood, but when and how this transition is initiated remains unclear. By monitoring mTOR activity, an evolutionarily conserved readout of cellular growth and intrinsic regenerative potential, we found that mTOR signaling declines within minutes after birth in murine CNS neurons and in other organs such as the heart and skeletal muscles. Focusing on retinal ganglion cells (RGCs), we show that this abrupt decline is driven primarily by CO2 exhalation following the onset of breathing after birth. Using real-time in vivo imaging of RGCs during the earliest postnatal period, we further discover that breathing-induced CO2 exhalation rapidly causes intracellular alkalinization, activates an AMPK-family kinase, SNF-related kinase (SNRK), which in turn suppresses mTOR signaling. Importantly, this process remains reversible in adulthood: CO2 inhalation or Snrk deletion restores mTOR activity in RGCs and enables robust regeneration of their axons after injury. Similar CO2 inhalation-induced mTOR reactivation occurs across multiple cell types and organs, suggesting a general mechanism by which breathing-associated CO2/pH signaling shapes the regenerative capacity across life and pointing to a potential CO2-based strategy for promoting tissue regeneration.

neuroscience↗

bioRxiv2026

SALL1 and neural microenvironmental contextspecify identity of stem cell derived humanmicroglia-like cells

Microglia, the immune cells of the brain parenchyma, play a pivotal role in neurodevelopment and neuroprotection. Human stem cell-derived microglia-like cells (MGL) offer a valuable, human-relevant system to study microglia in vitro. However, their cell states and intercellular interactions within complex 3-dimensional (3D) tissue contexts in vitro remain underexplored. Here, we analyze the gene expression profiles of MGL generated by two differentiation protocols in conventional 2D cultures. We show that co-culture with neural organoids promotes a more mature, in vivo-like MGL phenotype but this signature is lost during long-term co-culture. By varying media compositions, we modulate 2D MGL states toward more active or more homeostatic identities, which may enhance the similarity to primary microglia identities upon subsequent co-culture. Moreover, forced expression of the microglial lineage regulator SALL1 shifts MGL away from a general myeloid state toward a more defined pre-microglial fate. SALL1 overexpression within a 3D neural organoid environment further amplifies the shift toward a homeostatic developmental microglia population. Collectively, our transcriptomic analysis delineates human MGL states in 2D and 3D contexts, refines existing differentiation protocols toward more authentic MGL, and establishes a framework to investigate the intricate microglia-neural tissue interplay.

developmental biology↗

bioRxiv2026

The CREB-regulated co-activators 2/3, have a role, in vivo, in osteoblastic gene expression.

Many hormones and substances acting through G-protein coupled receptors and protein kinase A (PKA) activation inhibit the salt-inducible kinases (SIKs) by phosphorylation. SIKs tonically phosphorylate CREB-regulated transcriptional coactivators (CRTC1, 2 and 3), sequestering them in the cytoplasm and, thus, preventing their translocation into the nucleus. Once in the nucleus, CRTCs bind CREB family member transcription factors and enhance their activity. We and others have shown that parathyroid hormone (PTH) activation of PKA and resultant SIK2/3 inhibition allows CRTC2/3 nuclear translocation. One of the major actions of CRTC2/3 in the osteoblast lineage is the regulation of transcription of Rankl, as well as other PTH-controlled genes. However, little is known about the role of these co-activators in the osteoblast lineage in vivo. Here, we have investigated whether there are basal effects in vivo on bone examined at 2 different ages of conditional deletion of these two co-activators in the osteoblast lineage using Col2.3-Cre. We found significant increases in body weight, length, bone mineral density, bone volume/total volume, trabecular thickness and number with decreased trabecular separation in young (2 months old) male mice, all of which dissipated by 6 months of age. Female mice showed minimal changes in the bone phenotype at either age. Nevertheless, there were gene expression changes in bones of both sexes at both ages, and in particular decreases in Rankl, Runx2 and Sost, and accompanying changes in Wnt pathway genes. These effects may explain the changes in the bone phenotype in the young male mice, but it is notable that there is a sexual dimorphism in the action of CRTC2 and CRTC3. Overall, the work supports the data from research in vitro and forms a basis for investigation of the role of these co-activators in PTH action in vivo.

physiology↗

bioRxiv2026

Pectin is a critical contributor to the mechanical properties of Chara cell walls

Cellulose has long been viewed as the major load-bearing component in plant primary cell walls. Recent studies, however, suggest that pectin plays a significant role in cell wall mechanics despite a kPa-scaled modulus. Here we quantify the mechanical properties of centimeter-sized internodal cell walls of Chara corallina following treatments to remove calcium crosslinks or digest pectin. We also characterize the flow of water and gas through the cell wall as a function of pressure. We found that removal of calcium crosslinks did not affect wall strength and stress-relaxation behavior, yet it decreased the elastic modulus and increased permeability to water. In contrast, pectin removal had a dramatic impact on all measurements. Samples from which pectin had been removed exhibited lower strength and stiffness and had greater stress relaxation under constant strain. Pectin removal increased the permeability of the cell wall to water above that observed when calcium was removed and reduced the pressure at which gas "tunnels" through the cell wall ~ 2-fold. Our findings support the idea that pectin locally restricts the movement of cellulose microfibrils, with implications for understanding functional properties of primary cell walls in vascular plants and developing high-performance double-network materials.

biophysics↗

bioRxiv2026

Deconvolution of the mechanisms of T cell drug response in multiple myeloma induction therapy

Lenalidomide (Revlimid), bortezomib (Velcade), and dexamethasone, are used alone or in combination (RVd therapy) as first-line therapies for hematologic malignancies including the plasma cell dyscrasia, Multiple Myeloma (MM). The effects of RVd treatment on tumor cells have been documented, but little is known about their impacts on "healthy" immune cells. New therapeutics, including chimeric antigen receptor T cell (CAR-T) and bispecific T-cell engagers (BiTEs) depend on robust T cell function but these are often harvested for cellular therapies after or in tandem with RVd therapy. Understanding the molecular effects of these drugs on healthy T cells is therefore of particular importance. Since the molecular effects of each drug includes regulation of key transcription factors, we used a tri-modal, single-cell assay (TEA-seq), simultaneously profiling mRNA transcripts, cell surface proteins, and chromatin accessibility in primary human peripheral blood T cells treated for 4, 24, or 72 hours in vitro. Synergies and conflicts potentially arising from combinatorial therapy were identified and validated by flow cytometry. Doublet and triplet drug combinations were used to assess effects on cell-surface marker expression and on T cell activation. Our results suggest that T cell function can be optimized by the administration of these drugs individually and that sequential administration may offer an opportunity to enhance T cell function by affecting localization and altering T cell states. This work provides those interested in immunology, oncology, and cell therapies an opportunity to explore molecular pathways that could be manipulated by these commonly used drugs to modify T cell function.

immunology↗

bioRxiv2026

Unlocking Sensitive Data with SPHERE in the Age of AI

Sensitive human data underpin discoveries across medicine, biology and the social sciences, yet privacy regulation often prevents sharing them with collaborators or artificial intelligence (AI) systems. We introduce SPHERE, a model-free method that makes sensitive datasets directly usable by AI and shareable for open science as a synthetic twin, while the original records never leave the local environment. Across 33 datasets spanning five scientific domains, SPHERE protects individual privacy against adversarial re-identification attacks while preserving the data's statistical structure: means, variances and correlations are reproduced exactly, effect size and P value in linear statistical analysis is numerically identical, nonlinear machine-learning utility is retained, and each twin is generated in seconds on a laptop. Frontier AI agents running on the twin reach the same scientific conclusions as on the original records. Analyses of the twin reproduce genome- and proteome-wide results at UK Biobank scale and recover the findings of landmark studies across three independent cohorts and consortia. The approach also extends to deep-learning embeddings across language, vision and time-series, with minimal utility loss. We make the Stanford Alzheimer's Disease Research Center cohort openly available for the first time, as a SPHERE twin spanning nine modalities that any registered researcher can analyze without an approval process. We release SPHERE with certification of each twin's privacy and fidelity, and an AI agent that autonomously executes research tasks on sensitive data without ever accessing it. Sensitive datasets that are currently closed to research could thus become routine inputs to open science and AI to enable key discoveries.

bioinformatics↗

bioRxiv2026

LNP-CpG: deploy the self-adjuvant role of mRNA vaccines

With the rapid advancement of mRNA vaccines, lipid nanoparticles (LNPs) have emerged as pivotal carriers and adjuvants for non-mRNA vaccine modalities, driven by their superior nucleic acid delivery efficiency and intrinsic self-adjuvanting properties. In this study, we systematically evaluated various formulation strategies combining LNPs and the CpG adjuvant within a varicella-zoster virus glycoprotein E (VZV-gE) subunit vaccine framework. We demonstrated that uniform nanoparticles formed by LNP-encapsulated CpG (LNP-CpG), when simply admixed with the gE antigen, elicited superior immunogenicity compared to alternative encapsulation configurations. Intramuscular administration of a two-dose (LNP-CpG)+gE regimen significantly augmented both humoral and cellular immune responses in mice, markedly outperforming the commercial vaccine Shingrix (administered at a 1/10 human dose). Crucially, the identical regimen induced robust, comparable immune profiles to a full human dose of Shingrix in rhesus macaques. Furthermore, LNP-CpG displayed broad-spectrum utility across diverse vaccine platforms, demonstrating efficacy against both respiratory (RSV) and neurotropic (HSV) pathogens, compatibility with multiple modalities, including subunit (VZV-gE, RSV-Pre-F), live-attenuated (LA-HSV), and inactivated (i-HSV) vaccines; and versatile implementation in a combined VZV+RSV formulation. Collectively, our findings position LNP-CpG as a versatile, safe, highly efficacious adjuvant platform with substantial clinical translational potential, offering a compelling paradigm for next-generation vaccine development.

immunology↗

bioRxiv2026

Membrane Anisotropy Reshapes Scale-Free Correlations and Directional Mechanical Susceptibility in Transmembrane Proteins

Long-range correlated motions couple distant regions of a protein, providing a physical basis for allosteric communication, cooperative conformational change, and the balance between structural stability and sensitivity to perturbations. Yet membrane proteins operate within a strongly anisotropic lipid bilayer, and how this environment reshapes such system-spanning coordination remains unclear. Using an implicit-membrane anisotropic network model, we perform a proteome-wide analysis of more than 3,000 human transmembrane proteins. We find that long-range correlations remain scale free under membrane constraints but become strongly direction dependent. Across protein sizes and topologies, their correlation lengths continue to scale with the corresponding molecular dimensions, while increasing membrane anisotropy extends in-plane correlations and shortens those along the membrane normal. Because spontaneous correlations and perturbation responses arise from the same underlying mechanics, we further resolve residue-level responses into in-plane and normal components. The resulting directional mechanical susceptibility provides new predictions of mutation-sensitive sites in GPCRs beyond those captured by conventional scalar flexibility measures. Together, these results show how environmental symmetry breaking can organize protein mechanics across scales, linking collective dynamics to the functional sensitivity of individual residues and connecting a general physical mechanism to experimentally measurable protein function.

biophysics↗

bioRxiv2026

Patterns and environmental drivers of amphibian alpha and beta diversity in the Huangshan Mountains, southern Anhui, China

Understanding the spatial patterns of biodiversity and their environmental determinants is fundamental to ecology and conservation, particularly in mountainous transitional zones where species assemblages can shift rapidly. Amphibians, as highly sensitive organisms, are excellent indicators of environmental change, yet quantitative assessments of their diversity in the Huangshan Mountains-a biodiversity hotspot at the junction of the Palaearctic and Oriental realms in southern Anhui, China-remain limited. We conducted systematic line-transect surveys across 200 grids (5 km x 5 km) during the spring and autumn of 2023 and 2024, recording a total of 10,342 individuals belonging to 23 species, 20 genera, 9 families, and 2 orders. Three species (Fejervarya multistriata, Microhyla fissipes, and Bufo gargarizans) were identified as dominant, and two nationally protected species (Hoplobatrachus chinensis and Andrias davidianus) were detected. Inter-annual alpha diversity did not differ significantly, but pronounced seasonal variation was observed, with spring supporting higher Shannon-Wiener and Pielou evenness than autumn in both years. Using generalized additive models and model averaging, we found that annual precipitation and the normalized difference vegetation index (NDVI) were consistently the strongest positive predictors of Shannon-Wiener diversity, Simpson dominance, and species richness, while species richness also declined significantly with increasing human footprint. Total beta diversity (Soerensen dissimilarity) was very high (0.981) and overwhelmingly driven by species turnover (97.86%) rather than nestedness. Partial Mantel tests and distance-based redundancy analysis further revealed that environmental distances-particularly annual precipitation-significantly shaped overall beta diversity and its turnover component after accounting for geographic distance. These results highlight the predominant role of climatic and vegetation gradients in structuring amphibian assemblages in this subtropical mountainous region, providing baseline data to inform local conservation strategies.

ecology↗

bioRxiv2026

3D printing and deep learning enable holistic and dynamic analyses of tens of thousands of parasites infecting hundreds of genotypes

Host-parasite interactions are dynamic systems, where parasites usually outnumber hosts by one or more orders of magnitude. However, our understanding is often limited by the assessment of parts of the host, at arbitrary time points, and/or aggregate parasite responses. Here we combined custom-built 3D-printed hardware and deep-learning-based algorithms to enable holistic (i.e. all infecting individuals on the whole plant), spatio-temporal, and parasite-centric analyses of plant-parasitism by nematodes from timelapse videos of infection over months. In so doing, we tracked the dynamic growth and development of all individual parasites, at the organismal level, for thousands of hosts across hundreds of genotypes of Arabidopsis thaliana. Categorising traits into the static (i.e. in an acquired image at a given time point) and dynamic (i.e. phenotypic changes over time), we revealed a greater extent of host-genetic control of parasite traits, and new physiological limits of the species under these conditions. Using this capability, we identify Quantitative Trait Loci (QTL) in the host plant associated with 18 phenotypic traits in the parasite as a resource for the community. Finally, we leverage the large and diverse dataset to understand fundamental features of the parasite, independent of host genotype, revealing aspects of the life cycle which are pseudo-deterministic as well as local, deleterious interactions between co-infecting parasites. Given that plant-parasitic nematodes cause an estimated $100 billion in agricultural damages per year, these insights are contextualised in a global challenge driven by plant-parasitic nematodes.

pathology↗

bioRxiv2026

A Mechanical Theory for the Formation of Short Association Fibers in the Brain

The development of neural connections in the brain results from a complex interplay between biological processes and mechanical forces. A key question in neuroscience is how physical forces and the mechanical properties of brain tissue influence the formation of structural connections. Here, we demonstrate that mechanical forces play an essential role in shaping the emergence of short-range connections, particularly U-shaped fibers that link neighboring regions of the cortex. Using a computational model that incorporates our "stress-dependent axon reorientation" hypothesis, we simulate how growing axons respond to the mechanical stress field generated by cortical folding. Our results suggest that axonal growth and reorientation may be strongly influenced by local mechanical cues, helping establish the organization of these short-range pathways. Supported by in vivo diffusion tensor imaging and histological observations, our findings provide a physical explanation for why these fibers predominantly adopt U-shaped trajectories, and why connections between gyri (ridges) are more prevalent than those between sulci (valleys) or spanning gyri and sulci. These results suggest that understanding the mechanics of brain folding is critical for fully explaining the formation of brain connectivity and its variations in health and disorder. Teaser: Mechanical forces during cortical folding guide the formation of short association fibers in the brain.

bioengineering↗

bioRxiv2026

Beyond point estimates: quantifying predictive uncertainty reveals hidden dimensions of biological age acceleration and improves risk interpretation

Biological age estimates are increasingly used to study aging, disease risk, and mortality, yet their predictive uncertainty is rarely quantified. Consequently, conventional age-gap measures can treat deviations as equally informative even when the underlying biological age predictions differ substantially in reliability. We developed a framework for uncertainty-aware biological aging that generates calibrated prediction intervals and individualized probabilities of accelerated or decelerated aging alongside point estimates. We applied this framework to the UK Biobank Pharma Proteomics Project, evaluating three composite and eleven organ-specific biological age clocks. Predictive uncertainty varied substantially both within and across clocks, revealing that apparently extreme age gaps can differ markedly in the strength of evidence supporting accelerated or decelerated aging. In particular, low-accuracy clocks, including many organ-specific clocks, provided little evidence for confidently accelerated or decelerated aging. Beyond biological age gaps, prediction-interval width was independently associated with disease risk and mortality, particularly for composite, brain, and immune clocks, suggesting that predictive uncertainty captures an additional dimension of biological aging that may reflect increased molecular heterogeneity and dysregulation associated with aging and disease. We replicated these findings in Biobank Japan and an independent clinical cohort from Stanford. By incorporating individual-specific predictive uncertainty, our framework provides a more informative characterization of biological aging and enables improved individual-level risk stratification for disease prevention and longitudinal monitoring.

bioinformatics↗

bioRxiv2026

Multi-scale modeling of human tissues from spatial transcriptomics with TERRA

Spatial transcriptomics maps gene expression at cellular resolution, revealing how cells organize into multicellular niches. Yet computational analyses remain dataset-specific, without a transferable representation of tissue organization that generalizes across datasets, tasks and tissues or predicts how tissues behave under perturbation. We present TERRA, a foundation model pretrained on 112 million human cells profiled by spatial transcriptomics. From a single pretrained backbone, TERRA yields embeddings at the scale of cells, the genes they express and the neighborhoods in which they reside, and supports spatial in silico perturbation, all applied zero-shot to unseen tissues. At the cell level, in newly generated spatial data for developing pancreas, TERRA identified an islet-associated capillary state which we posit represents a developmental precursor of the mature islet microvasculature. At the gene level, in untreated kidney sections, in silico knockout of immune-checkpoint targets predicted a gene program of immune-checkpoint-blockade-associated nephrotoxicity, which we validated in treatment-exposed tissue and recovered in blood. At the neighborhood level, TERRA mapped macrophages across tissues to identify recurring cross-organ niches, which we term archetypes, including a tumor-boundary niche associated with poor prognosis in kidney cancer. Together, TERRA captures the spatial and multicellular logic of human tissue and predicts, in silico, its response to perturbation, providing a multi-scale framework for tissue biology, therapeutic development and clinical application.

genomics↗

bioRxiv2026

Language Dysfunction Associated with Pathological Brain Connectivity in Children with Epilepsy

Language impairment is common in childhood epilepsy and may arise in part from disruption of the distributed brain networks that support language. In self-limited epilepsy with centrotemporal spikes (SeLECTS)--the most common focal epilepsy of childhood--hyperconnectivity has been linked to poor language outcomes, but the specific network patterns associated with language dysfunction remain unclear, limiting the ability to target neurostimulation rationally. We recorded high-density EEG from 27 children with SeLECTS and 29 age-matched controls during verb generation and rest, and quantified functional connectivity across multiple frequency bands and bilateral frontal, temporal, occipital, and motor regions. Using multivariate pattern analysis, we identified connectivity patterns that predicted language ability, distinguished patterns shared across groups from those specific to SeLECTS and tested whether spatially specific connectivity provided information beyond whole-brain or hemispheric averages and conventional clinical variables. Frontal and occipitotemporal connectivity, particularly within the left hemisphere, predicted language ability across groups, whereas motor-network connectivity emerged as the dominant SeLECTS-specific predictor, linking the epileptogenic network to language dysfunction. Connectivity between specific regions outperformed averaged connectivity measures and predicted language beyond epilepsy diagnosis and antiseizure medication use. Task-based connectivity also outperformed resting-state connectivity. These findings show that language ability is associated with distributed yet spatially specific patterns of brain connectivity, while epilepsy introduces distinct alterations centered on the epileptogenic network. Identifying these disease-specific network patterns provides mechanistic insight into language dysfunction and a rational basis for spatially targeted neuromodulation.

neuroscience↗

bioRxiv2026

Anti-Z-NA antibodies can distinguish accessible Z-form states across DNA, RNA, and DNA-RNA substrates

Left-handed (Z-form) double-stranded nucleic acid conformers (Z-DNA and Z-RNA, collectively called Z-NA) are molecular patterns recognized by ADAR1 and ZBP1, which are sensor proteins involved in innate immunity. Monoclonal antibodies raised against Z-DNA, such as Z22 and Z-D11, are employed as probes for the study of Z-NAs, but their substrate specificity and functional equivalence remain unclear. Here, we used biochemical, biophysical, and structural approaches to compare the binding modes and target specificies of Z22 and Z-D11, using Z-prone CG-rich dsDNA, dsRNA, and DNA-RNA hybrids as substrates. Both antibodies failed to form stable complexes with short CG-rich dsRNA under conditions compatible with antibody stability, which suggests that they are unable to induce A-to-Z transitions in dsRNA. In contrast, both antibodies robustly complexed with dsDNA and DNA-RNA hybrid substrates. Cryo-EM structural analysis confirmed that both antibodies interact with Z-NA through a conserved interaction network, and demonstrated that complexes between the antibodies and DNA-RNA hybrids adopted distinct higher-order organizations. Z22 retained binding to both Z-DNA and Z-RNA segments, whereas Z-D11 displayed substrate-dependent organization and was restricted to Z-DNA segments Molecular modelling provided mechanistic explanation for the differences in Z-RNA binding ability between the two antibodies, which was confirmed in situ with ADAR1-depleted, IAV- infected and JTE607-treated cells. We also demonstrate that Z-D11, in contrast to previously described Z22, is unable to induce B-to-Z-transitions in short d(CG)6 oligos under physiological conditions. Together, these results show that anti Z-NA monoclonal antibodies are not functionally interchangeable: whereas Z22 recognizes pre-formed Z-RNA, Z-DNA- RNA hybrids, and Z-DNA, Z-D11 recognizes Z-DNA, and DNA segments in Z-DNA-RNA hybrids. These differences are dictated by substrate composition, local geometry, and conformational accessibility, which also likely impact their ability to induce NA structural transitions. These findings have important implications for interpreting antibody-based detection of left-handed nucleic acids in biological systems.

biophysics↗

bioRxiv2026

Latitudinal Patterns in Immunogenetic and Microbiome Diversity in two anuran species: Bufo bufo and Bufo spinosus

Evolutionary and demographic processes such as selection, drift and migration shape the genetic variation of populations. Genetic diversity is often lower in populations toward higher latitudes. This decrease potentially threatens their survival as several factors are putting more pressure on the populations, including the spread of infectious diseases. In this study, we combined whole-genome re-sequencing with MHC class II genotyping and skin microbiome profiling in Bufo bufo and B. spinosus, two closely related European toad species. We investigated the underlying immunogenetic and microbial variation resulting from different demographic histories and environmental conditions to identify their potential impact on infection outcomes in these two species. We found lower immunogenetic diversity in B. bufo compared to B. spinosus, with highly significant differences in genes related to adaptive and innate immunity. We found lower overall MHC class II diversity and skin microbiome diversity at the species level in B. bufo, compared with B. spinosus. In contrast, at the individual level, B. bufo showed higher MHC allelic diversity and greater diversity in the core skin microbiota than B. spinosus. Together, our findings suggest that divergence in immunogenetic background and host-associated microbial communities may underlie differences in susceptibility to emerging infectious diseases. This integrative framework provides new insight into how host genetics and microbial communities jointly influence disease outcomes across environmental gradients.

evolutionary biology↗