Biology subjects

Yan, K.

Publications and source records attributed to Yan, K..

At least 19 recordsLinked to original sources

bioRxiv2026

NeCS-Flow: Necrosis-Guided Contrast-Enhanced MRI Synthesis with Rectified-Flow Refinement

Background: Gadolinium-based contrast agents raise concerns about tissue deposition, adverse reactions, and increased costs. Purpose: To develop and validate a deep learning pipeline for gadolinium-free post-contrast T1w brain MRI synthesis incorporating necrotic scaling and Posterior-Mean Rectified Flow (PMRF) refinement, and to evaluate diagnostic utility through a blinded multi-reader study. Study Type: Retrospective. Population: 454 patients with adult-type gliomas (grade 2-4) from four publicly available datasets. Training used 374 patients; internal testing used 60 held-out patients; external validation used 20 patients. Field Strength/Sequence: 1.5-3.0 T; pre-contrast T1w, T2w, and FLAIR as inputs; post-contrast T1w as synthesis target. Assessment: A three-stage pipeline comprising nnU-Net Necrotic core segmentation, necrotic-scaling-guided U-Net Contrast Synthesis, and PMRF perceptual refinement (NeCS-Flow) was evaluated using whole-brain and tumor-region similarity metrics, enhancing tumor Dice scores, perceptual quality metrics, and a blinded three-reader study assessing diagnostic accuracy, enhancement detection, image quality, and real-versus-synthetic discriminability. Statistical Tests: Paired t-tests and two one-sided tests for model comparison; Fisher's exact test and two-sample t-tests for reader study comparisons, with p < 0.05 considered significant. Results: Necrotic scaling consistently improved real versus synthetic enhancing tumor Dice internally (HGG: 0.793 to 0.816) and externally (HGG: 0.465 to 0.612). NeCS-Flow outperformed two benchmark architectures on all quantitative metrics in internal and external testing, although absolute enhancing tumor accuracy declined for all models on the external cohort. PMRF refinement improved perceptual realism across both tumor types, reducing both FID and KID. Readers distinguished synthetic from real images only modestly above chance (overall accuracy 61.7%), and no significant differences between real and synthetic images were found for any clinical metric. Data Conclusion: NeCS-Flow synthesizes perceptually realistic and diagnostically equivalent post-contrast T1w brain MRI, with necrotic scaling improving enhancing tumor delineation and PMRF refinement improving perceptual realism across gliomas. Performance on an external cohort was preserved relative to benchmark methods, though reduced in absolute terms.

bioinformatics↗

bioRxiv2026

Genome-wide association study and genetic differentiation analysis reveal the genetic basis of Vibrio harveyi resistance in blackspotted croaker (Protonibea diacanthus)

Vibrio harveyi is a primary causative agent of vibriosis, leading to catastrophic economic losses in the blackspotted croaker (Protonibea diacanthus) aquaculture. However, the genetic architecture underlying its resistance remains poorly understood. In this study, we conducted the first integrated genome-wide association study (GWAS) and genetic differentiation analysis (F_ST) to investigate the genetic basis of V. harveyi resistance. A total of 450 juveniles were challenged, and 300 individuals (comprising 150 resistant and 150 susceptible) were selected for whole-genome resequencing. Genomic heritability (h^2) was estimated at 0.374+/-0.29 for survival time (ST) and 0.237+/-0.185 for survival status (SS), indicating moderate genetic control. Notably, an exceptionally high genetic correlation (r_g = 0.999) was observed between ST and SS, while resistance traits were genetically independent of growth performance (r_g < 0.03). Through the convergence of GWAS and selection sweep signals, a major-effect QTL was identified on chromosome 4. Candidate gene prioritization identified high-confidence targets involved in post-transcriptional regulation and mRNA stability, specifically elavl4 (harboring a top-tier exon variant), rorb, cbpc6, and epn4. Functional enrichment analysis further revealed that resistance is significantly associated with "rRNA processing", "mRNA surveillance pathway", and "nucleocytoplasmic transport", suggesting that efficient RNA metabolic control is a critical determinant of host survival. These findings provide novel insights into the non-canonical immune mechanisms of P. diacanthus and offer robust molecular markers for marker-assisted selection and genomic selection, facilitating the development of disease-resistant strains in the sciaenid industry.

genomics↗

bioRxiv2026

Unmasking genetic load: Genomic inbreeding drives growth depression in captive critically endangered Chinese Bahaba (Bahaba taipingensis)

Chinese bahaba (Bahaba taipingensis) is a critically endangered marine fish that has been commercially extinct in the wild. Conservation-oriented captive breeding has become an effective strategy for rescuing such endangered species, but concerns about inbreeding depression often remain. Here, after merely two generations of closed breeding from 18 wild founders, Chinese bahaba exhibited severe growth depression, with body length and weight diverging by more than three-fold. To further investigate the early genomic consequences of captive breeding, we analyzed whole-genome sequences from 348 F2 individuals together with 19 wild individuals from the same marine region. While genome-wide genetic diversity was overall preserved, closed breeding rapidly partitioned the F2 population into eight distinct genetic lineages. A significant elevation in genomic inbreeding was observed to facilitate the homozygous exposure of recessive deleterious mutations, which was strongly correlated with growth decline. An integrative framework combining GWAS, gene-level burden test, and ROH hotspots was applied to dissect the genetic architecture underlying growth decline, which converged predominantly on skeletal scaffolding and immune regulation. This was evidenced by candidate genes related to skeleton development and homeostasis (e.g. fam20b, c-fos, trpv5, and il23r), the GH/IGF axis (e.g. socs1a), and immune/inflammatory pathways (e.g. il23r, nlrp7, cd163, il12rb2), as well as calcium ion transport pathway. Together, our findings provide novel insights into the genomic consequences and genetic architecture of growth decline under captive conditions in Chinese bahaba, and offer critical guidance for genetic management in captive conservation programs of endangered species.

genetics↗

bioRxiv2026

Isolation, identification, and comparative genomic analysis of Vibrio harveyi as a causative agent for a skin ulcer disease of endangered fish Chinese bahaba (Bahaba taipingensis)

Chinese bahaba (Bahaba taipingensis) is a fish species endemic to China and listed as a Class I nationally protected wild animal. Although significant breakthroughs have been achieved in its artificial breeding, high mortality rates persist during cultivation. Beginning in August 2024, sustained mass mortalities occurred in artificially farmed Chinese bahaba at a farm in Guangdong Province. Diseased fish exhibited pronounced skin ulcers, ascites, gastroenteritis, and splenomegaly. Histopathological examination revealed severe necrotizing gastroenteritis, gill necrosis and edema, muscle congestion with inflammatory cell infiltration, hepatic congestion with marked vasculitis, renal interstitial necrosis with tubular atrophy, and abundant melanomacrophage centers in the spleen. Based on biochemical characterization and whole-genome phylogenomic analysis, the isolated strain HCY1 was identified as Vibrio harveyi. Artificial infection experiments with this strain resulted in 100% mortality and reproduced clinical signs similar to those in naturally infected fish. Antimicrobial susceptibility testing showed that HCY1 remained susceptible to florfenicol and trimethoprim-sulfamethoxazole, but was resistant to multiple antibiotics, including {beta}-lactams and tetracyclines. Comparative genomic analysis revealed that HCY1 carries various antimicrobial resistance genes primarily conferring resistance to {beta}-lactam and tetracycline antibiotics, consistent with the phenotypic resistance profile. The strain also harbored numerous virulence genes, including complete type III and type VI secretion systems (T3SS and T6SS), tlh, hap/vvp, and rtxB. Its plasmids encoded multiple virulence-enhancing genes, such as mcpA, pal, and esiB. To our knowledge, this is the first systematic investigation of a disease outbreak in cultured Chinese bahaba, and provides valuable insights for disease control and population conservation of this endangered species.

microbiology↗

bioRxiv2026

ApolipoproteinE drives inflammation resolution pathways essential for recovery from Japanese encephalitis

Effective control of viral encephalitis requires immune responses that clear infection without causing damaging neuroinflammation, yet the mechanisms governing resolution and recovery remain unclear. Using a Japanese encephalitis virus mouse model spanning asymptomatic, symptomatic, and lethal trajectories, together with single-cell spatial transcriptomics and RNA-seq, we identify apolipoprotein E (ApoE) as a driver of neuroinflammation resolution. Apoe was upregulated in microglia and infiltrating myeloid cells of symptomatic survivors, where Apoe-Trem2-Tyrobp signalling promoted a phagocytic, anti-inflammatory program. In contrast, immune cells in lethal disease failed to induce Apoe and remained pro-inflammatory. ApoE-deficient mice were unable to recover following encephalitis onset, demonstrating that ApoE signalling is essential for resolution and recovery. Analysis of cerebrospinal fluid from acute encephalitis patients linked APOE isoforms to neuroinflammation resolution, with APOE{varepsilon}2 carriers exhibiting reduced neutrophils and shorter hospitalisation. These findings identify ApoE as a critical driver of neuroinflammation resolution and a promising therapeutic target for viral encephalitis.

microbiology↗

bioRxiv2026

Hepatocellular Carcinoma Revisited from Single Cell Sequencing: Dynamic Evolution from Epithelial Dedifferentiation to Mesenchymal Remodeling

BackgroundSingle-cell RNA sequencing has provided new insights into hepatocellular carcinoma (HCC); however, a unified understanding of epithelial heterogeneity and immune evasion strategies in HCC remains lacking. MethodsWe re-analyzed publicly available single-cell datasets using conventional bioinformatics pipelines. Cell-type annotation of epithelial and T cell populations was further validated across multiple independent datasets to ensure robustness. ResultsWe systematically examined epithelial, immune, myeloid, and stromal lineages. In addition to recapitulating previously reported findings, we identified several novel observations. Notably, we uncovered a three-step dedifferentiation trajectory in epithelial cells and confirmed a bidirectional differentiation pattern within CD8{square} T cells. We also identified a subset of GZMK{square} CD4{square} T cells, whose transcriptional features resemble but are distinct from T follicular helper (Tfh) cells. Importantly, transcriptional drift within myeloid populations appeared to be closely associated with immune responsiveness. Furthermore, ligand-receptor analysis highlighted a potential cooperative role of LAMP3{square} dendritic cells and Tfh cells in promoting lymphoid follicle formation. ConclusionsIn the era of rapidly evolving single-cell sequencing technologies, we provide a framework for understanding cellular heterogeneity in HCC, which awaits further validation in future studies.

cancer biology↗

bioRxiv2026

Opposing regulatory logics converge on ABA receptors to govern the trade-off between growth and drought acclimation

Plants dynamically balance growth with stress responses through abscisic acid (ABA). How ABA signaling, but how ABA sensitivity is finely tuned is unclear. Here, we uncover a regulatory network of leucine-rich repeat receptor-like kinases (LRR-RLKs) that directly controls ABA receptors stability. We identify GASSHO1 (GSO1) as a core component that phosphorylates the PYL2 and PYL4 receptors, targeting them for degradation and thus serving as a brake on ABA signaling. Under drought stress, ABA accumulates and suppresses expression of GSO1-activating CIF peptides, releasing this brake to increase PYLs and sensitivity. This mechanism opposes our previously identified CEPR2 pathway, where drought-induced CEP peptides inhibit the kinase to stabilize PYLs. The integration of these two antagonistic modules within an LRR-RLK network enables precise, dynamic control of ABA perception. This work reveals a molecular framework explaining how plants calibrate the critical balance between growth and drought acclimation.

molecular biology↗

bioRxiv2026

Universal Baseline for in vitro Selection of Genetically Encoded Libraries

Genetically encoded (GE) libraries enable identification of high-affinity ligands for diverse molecular targets through iterative in vitro selection and DNA sequencing or next-generation sequencing (NGS). Despite their impact in therapeutic development, a systematic framework for evaluating reproducibility in GE-molecular discoveries remains limited. To aid such analysis, we introduce the concept of baseline response, which reproducibly partitions active and inactive members of in vitro selection. The baseline response is provided by spiking a random DNA-barcoded population. We calibrated the baseline concept using Bioconductor EdgeR differential enrichment (DE) analysis of NGS of phage-displayed selection on oligosaccharide chitin and hepatitis virus NS3a* protease as model targets. We further show that mixing discovery campaigns also offers an effective baseline: chitin-enriched peptides serve as a baseline for DE-analysis of NS3a* selection and NS3a*-enriched peptides serve as a baseline for chitin binders. We applied baseline-stratified DE-analysis to 66 parallel selections performed in 3-5 replicates across 22 extracellular targets, including HER1-3, EpCAM, CAIX, PD-L1, and eight integrin receptors. Automated DE-analysis across hundreds of NGS files produced hits validated in a secondary screen and yielded synthetic macrocyclic ligands with mid-nanomolar affinity confirmed in 2-3 biophysical assays. For PD-L1, we further demonstrated how baseline-calibrated NGS data provide decision-enabling information for optimization of peptide macrocycles to yield potent single-digit nanomolar ligands for the cell-surface receptor. We anticipate that baseline-based analyses of NGS data from in vitro selection procedures will offer a scalable framework for reproducible hit discovery and standardized analysis across diverse in vitro selection campaigns. Significance StatementGenetically encoded selection technologies such as phage, mRNA and ribosome display, have produced FDA-approved therapeutics and numerous clinical candidates. Yet reproducibility in such in vitro discovery systems is rarely evaluated against a defined experimental baseline. Here, we establish a universal baseline by spiking unrelated, DNA-barcoded peptide sequences into selection libraries and quantifying their binding alongside target-enriched populations. This composition-agnostic strategy enables rigorous normalization, confidence assessment, and cross-target comparison of molecular discovery outcomes. Our framework introduces practical standards for reproducibility and statistical benchmarking across genetically encoded display platforms.

biochemistry↗

bioRxiv2026

Pragmatic analysis with knowledge-guided for unraveling peptide-protein pairwise non-covalent mechanisms

Understanding peptide-protein interactions is vital for decoding cellular signaling and developing targeted therapies. However, the complexity of multi-molecular associations and diverse non-covalent interactions make accurate prediction and site-specific annotation challenging. Here, we propose KGIPA, a knowledge-guided pragmatic analysis framework that incorporates pragmatic concepts from natural language into life science, capturing the influence of biological environments on non-covalent interactions. KGIPA integrates intra- and extra-linguistic contextual information to combine multimodal single-molecule features and build residue-level interaction maps. It also uses biological prior knowledge to coordinate various non-covalent interaction types. Benchmark tests demonstrate KGIPA outperforms the state-of-the-art methods in evaluating molecular binding, including protein and peptide binding residues and residue-pair interactions. Furthermore, KGIPA demonstrates strong performance in peptide-protein binding affinity prediction and peptide virtual screening. Wet-lab experiments validate its reliability, revealing high consistency between predicted and experimentally measured binding behaviors. These results highlight KGIPAs potential to accelerate peptide drug discovery and establish pragmatic analysis as an effective paradigm for decoding the molecular language of interactions.

bioinformatics↗

bioRxiv2025

Organization of mouse prefrontal cortex subnetwork revealed by spatial single-cell multi-omic analysis of SPIDER-Seq

Deciphering the connectome, anatomy, transcriptome and spatial-omics integrated multi-modal brain atlas and the underlying organization principles remains a great challenge. We developed a Single-cell Projectome-transcriptome In situ Deciphering Sequencing (SPIDER-Seq) technique by combining viral barcoding tracing with single-cell sequencing and spatial-omics. This empowers us to delineate a integrated single-cell spatial molecular, cellular, anatomic and projectomic atlas of mouse prefrontal cortex (PFC). The projectomic and transcriptomic cell clusters display distinct modular organization principles, but are coordinately configured in the PFC. The projection neurons gradiently occupied different territories in the PFC aligning with their wiring patterns. Importantly, they show higher co-projection probability to the downstream nuclei with reciprocal circuit connections. Moreover, we integrated projectomic atlas with their distinct spectrum of neurotransmitter/neuropeptide and the receptors-related gene profiles and depicted PFC neural signal transmission network. By which, we uncovered potential mechanisms underlying the complexity and specificity of neural transmission. Finally, leveraging machine learning, we predicted neuron projections with high accuracy by combining gene profiles and spatial information. As a proof of concept, we used this model to predict projections of fear recall engram neurons. This study facilitates our understanding of brain multi-modal network and neural computation.

neuroscience↗

bioRxiv2025

Innovative Prevention Approach for Pan Allergens-Induced Allergy: Effective Regulation of Heat Shock Protein 70 and Profilin 3 by siRNA-Loaded Nanomaterial

Currently, the widely accepted approach to addressing pollen allergy primarily through altering the immune system of patients. However, the great potential of genetic engineering for downregulating allergenic proteins and reducing allergenicity is often overlooked in previous studies. Here, we report an effective solution to reducing plant allergenicity by utilizing RNA interference (RNAi) technology to calibrate levels of pan-allergenic proteins Heat Shock Protein 70 (HSP 70) and Profilin 3 (PFN 3) in transgenic Arabidopsis, Tobacco, and Osmanthus. This has been shown in research to effectively mitigate and prevent allergenic reactions in humans. 21-bp long siRNA sequences encased by Polyethyleneimine modified carbon dots (PEI-CDs) are synthesized to constitute a nanoparticle-mediated delivery system to efficiently deliver small-interfering RNA (siRNA) vectors into plants. Afterwards, RNA was extracted from Osmanthus fragrans and Gardenia jasminoides and underwent reverse transcription quantitative-polymerase chain reaction (RT-qPCR). The result indicated the expected suppression of mRNA corresponding to the targeted proteins, proving the functional aspect of RNAi in allergen suppression trunk injection and suggesting its applicability in real-life scenarios.

synthetic biology↗

bioRxiv2025

Study on Early pregnancy diagnosis in sows based on joint analysis of vaginal secretion metabolomics and machine learning

ObjectiveMetabolic transformations in female mammals throughout gestation manifest in the metabolite profiles of bodily fluids, potentially serving as biomarkers for the diagnosis of pregnancy. This investigation concentrated on sows 18 days post-mating, with the objective of identifying biomarkers pertinent to early pregnancy diagnosis through the analysis of variations in metabolic molecules within vaginal secretions. MethodsVaginal secretion samples were procured from both pregnant and non-pregnant sows 18 days post-mating, subsequently subjected to untargeted metabolomic analysis utilizing liquid chromatography-mass spectrometry (LC-MS). The samples were partitioned into training and testing datasets, and machine learning algorithms--specifically, Random Forest (RF) and support vector machine (SVM)--were integrated with metabolite weight ranking to identify key biological markers. ResultsA total of 3,249 metabolic molecules were identified, among which 534 exhibited significant differential expression in the vaginal secretions of pregnant versus non-pregnant sows. Notably, three hormones that correlate with the pregnant status of the sow were discerned: Progesterone, 3-Deoxyestradiol, and Prostaglandin E1. KEGG pathway analysis revealed that the differentially expressed metabolites were predominantly enriched in nucleotide metabolic pathways. The RF model demonstrated an impressive accuracy of 1.00 in the training dataset and 0.88 in the testing dataset, while the SVM model maintained an accuracy of 1.00 across both datasets. Utilizing model weights and differential expression data, three pivotal metabolites were identified: Indolepropionic acid, cis-Aconitate, and 4-p-Coumaroylquinic acid, which exhibited ROC curve AUC values of 0.90, 0.89, and 0.79, respectively. ConclusionThis study validates the viability of utilizing vaginal secretions for the early diagnosis of pregnancy in sows, thereby establishing a foundation for the advancement of non-invasive diagnostic methodologies.

zoology↗

bioRxiv2025

Autoantibodies targeting CRB2 and Nephrin correlate with extrafollicular B cells in idiopathic podocytopathies

Idiopathic podocytopathies lack mechanistic biomarkers and rely on empirical immunosuppression, yet the recent discovery of autoantibodies against slit diaphragm proteins implicates podocyte-directed autoimmunity as a driver of podocyte injury. However, the immune mechanisms underlying autoreactivity and phenotypic heterogeneity, particularly across age groups, remain unclear. Here, we identify expansion of CD21low T-bet+ atypical B cells (atBCs) in peripheral blood as a shared immunologic feature across idiopathic podocytopathies. In children, atBC accumulation was associated with heightened B cell activation, favoring extrafollicular responses and plasmablast differentiation. Serologic profiling revealed that autoantibodies against the slit diaphragm protein CRB2 are highly prevalent across disease phenotypes and frequently co-occur with anti-Nephrin antibodies, particularly in adults. Autoantibody abundance correlated with atBC expansion in affected children, implicating extrafollicular B cell responses as a key pathway for their generation, whereas adults showed additional involvement of follicular pathways. Complementary mouse modeling demonstrated intermolecular epitope spreading as a mechanism linking anti-CRB2 and anti-Nephrin autoreactivity. Together, these findings define a shared immune framework for idiopathic podocytopathies in which extrafollicular B cell responses drive autoreactivity to multiple slit diaphragm proteins, with implications for biomarker development and therapeutic stratification.

immunology↗

bioRxiv2025

Systematic Evaluation of Somatic Contamination in Germline Genomes

Large-scale genomic initiatives like the UK Biobank (UKB) have revolutionized our understanding of human disease. These studies typically assume that blood-derived DNA faithfully reflects an individuals germline genome. However, this assumption is challenged by somatic mutations arising from processes like clonal hematopoiesis. Although standard bioinformatics pipelines employ variant allele frequency (VAF)-based filtering to mitigate such contamination, the efficacy of these approaches requires systematic evaluation. By systematically analyzing whole-exome sequencing (WES) and whole-genome sequencing (WGS) data from large cohorts, including the UK Biobank, The Cancer Genome Atlas (TCGA), and the 1000 Genomes Project, we revealed critical limitations in current filtering methodologies. We found that the mutational spectrum of rare "germline" variants is highly similar to that of somatic mutations. Furthermore, we uncovered these variants show significant associations with phenotypes such as age, sex, and smoking status, established drivers of somatic mutagenesis. This persistent somatic contamination introduces substantial confounder effects, potentially generating spurious associations and reverse causality in genetic studies. Our work underscores the urgent reconsideration of two fundamental aspects of genomic research: (1) refinement of variant filtering strategies to better distinguish true germline variants from somatic contaminants, and (2) incorporation of somatic mutagenesis factors as essential covariates in study design. Our findings provide a basic framework for improving the accuracy and interpretability of large-scale genomic studies.

genomics↗

bioRxiv2025

Insect-specific Yada Yada virus chimeric vaccines protect against chikungunya and Ross River virus-induced arthritis

Arthritogenic alphaviruses such as chikungunya virus (CHIKV) and Ross River virus (RRV) are mosquito-borne viruses that can cause debilitating polyarthritis/polyarthralgia in humans. Although two CHIKV vaccines have been licensed, there are no licensed vaccines for RRV. Herein we generate a host-restricted, insect-specific alphavirus, Yada Yada virus (YYV), chimeric vaccine for CHIKV (YYV-CHIKVMauritius) and for RRV (YYV-RRVTT). YYV-CHIKVMauritius and YYV-RRVTT was able to replicate in C6/36 mosquito cells to similar titres as wild-type CHIKV and RRV. YYV-CHIKVMauritius was also neutralised by CHIKV monoclonal antibodies to the same titres as wild-type CHIKV, indicating its potential as a diagnostic antigen to detect neutralising CHIKV antibodies in human or animal sera. YYV-CHIKVMauritius further demonstrated protection against CHIKV infection and disease in a wild-type mouse model. Two doses of YYV-CHIKVMauritius showed anti-CHIKV ELISA and neutralising antibody responses, with protection against foot swelling, viraemia and viral feet tissue titres. Protection against CHIKV histopathology including myositis, tendonitis, arthritis, subcutaneous oedema and haemorrhage was also observed. YYV-RRVTT also demonstrated protection against RRV infection and disease in a wild-type mouse model, with two vaccine doses inducing anti-RRV ELISA and neutralising antibody responses. Protection against foot swelling, viraemia and viral feet tissue titres and RRV histopathology including myositis, tendonitis, arthritis and subcutaneous oedema was also observed. Cross-protection was also evaluated between YYV-CHIKVMauritius and RRV. Although cross-reactive total IgG were observed for YYV-CHIKVMauritius vaccinated mice, this offered no cross-neutralising antibodies and no protection against RRV infection and disease. Overall, our findings show that YYV-CHIKVMauritius and YYV-RRVTT are safe and efficacious vaccines against CHIKV and RRV, respectively, but do not offer cross-protection.

microbiology↗

bioRxiv2025

Characterisation and phylogenetic analysis of Murray Valley encephalitis virus (MVEV) from the Ralph Doherty collection.

Murray Valley encephalitis virus (MVEV) is a zoonotic flavivirus endemic to Australia and Papua New Guinea. A recent outbreak of MVEV has prompted renewed concerns regarding the potential for MVEV to generate disease outbreaks. Currently, nine full length sequences of MVEV are publicly available, divided into four genotypes (G1-G4). Herein, we sequenced MVEV isolates from the Ralph Doherty Virus Collection, a virus bank with Australian field isolates dating between the 1950s-1980s, and determined their phylogenetic relationship with existing isolates to provide insights into virus evolution and genetic diversity. Additionally, we characterised isolates from different genotypes both in vitro using human neuronal cells, and in vivo using C57BL/6J mice, to provide additional insight into MVEV pathogenicity and establish models of MVEV disease that recapitulate MVEV human disease. We found 15 new full length sequences of MVEV, which primarily clustered into the dominant genotype, G1. Additionally, we show MVEV can be lethal and neuroinvasive in C57BL/6J mice, recapitulating histological lesions identified in human infection. Overall, our study contributes significant genomic sequences to the current MVEV database and establishes mouse models of disease and infection which can be used for mechanistic studies and evaluation of new interventions.

microbiology↗

bioRxiv2025

Evaluation of Multiplexed Liquid Glycan Array (LiGA) for Serological Detection of Glycan-binding Antibodies

We test the performance of the multiplexed liquid glycan array (LiGA) technology in serological assays. Specifically, we use LiGA to detect ABO blood group antibodies in human serum. This LiGA, which we name ABO-LiGA, contains ABO blood group trisaccharide glycans with an ethylazido aglycone conjugated to groups of ten multi-barcoded M13 particles carrying dibenzocyclooctyne (DBCO) on p8 proteins. ELISA clonal binding assays to anti-A/B antibodies confirmed the functional performance of ABO-clones and aligned with next-generation sequencing (NGS) of the mixed clones. Multiple DNA-barcoded technical replicates in LiGA allow for quantification of reproducibility and robustness as determined by the Z-score using NGS. We then tested ABO-LiGA for specific detection of IgG and IgM anti-A and anti-B IgG and IgM antibodies in human serum samples. Comparison of antibody binding responses in sera from 31 healthy donors to ABO-LiGA with an ABO-Luminex-based method revealed consistent responses to LiGA-ABO but also minor deficiencies of ABO-LiGA such as low robustness of the current assay format and a limited ability to detect low intensity antibody responses. Some results point to undesired interactions of serum antibodies with small-footprint glycans conjugated to phage via the bulky DBCO moiety. This report illuminates the path for future development of LiGA-based serological assays and suggests the need to develop alternative methods for conjugating glycans to phage to avoid liabilities of the hydrophobic DBCO moiety.

biochemistry↗

bioRxiv2025

Spatially and non-spatially tuned hippocampal neurons are linear perceptual and nonlinear memory encoders

The hippocampus has long been regarded as a neural map of physical space, with its neurons categorized as spatially or non-spatially tuned according to their response selectivity. However, growing evidence suggests that this dichotomy oversimplifies the complex roles hippocampal neurons play in integrating spatial and non-spatial information. Through computational modeling and in-vivo electrophysiology in macaques, we show that neurons classified as spatially tuned primarily encode linear combinations of immediate behaviorally relevant factors, while those labeled as non-spatially tuned rely on nonlinear mechanisms to integrate temporally distant experiences. Furthermore, our findings reveal a temporal gradient in the primate CA3 region, where spatial selectivity diminishes as neurons encode increasingly distant past events. Finally, using artificial neural networks, we demonstrate that nonlinear recurrent connections are crucial for capturing the response dynamics of non-spatially tuned neurons, particularly those encoding memory-related information. These findings challenge the traditional dichotomy of spatial versus non-spatial representations and instead suggest a continuum of linear and nonlinear computations that underpin hippocampal function. This framework provides new insights into how the hippocampus bridges perception and memory, informing on its role in episodic memory, spatial navigation, and associative learning.

neuroscience↗