Tahas, S. A. | Search bioRxiv

bioRxiv2026

Spatial navigation through evolution: a single-cell atlas of the mammalian entorhinal cortex

Spatial navigation is a fundamental mammalian ability, supported by the entorhinal cortex (EC), a structurally conserved yet functionally diverse region across mammalian species. However, how molecular signaling underlies both shared and species-specific navigational strategies remains unclear. Here, we present a cross-species single-cell atlas of the EC from human, Hamadryas baboon, mouse, and Egyptian fruit bat - species spanning distinct evolutionary lineages and navigational demands, including true 3D navigation in bats. Using this resource, we identify conserved principal neuron populations as well as species-specific innovations, including mixed-layer or functional identities and fruit bat-specific subtypes. GABAergic interneurons neurons show strong conservation of somatostatin (SST) and parvalbumin (PV) families, while VIP GABAergic neurons exhibit pronounced species-specific divergence, with an expanded repertoire in primates. Integration with whole-brain diffusion tensor imaging reveals conserved and species-specific connectivity between the EC, hippocampus, and sensory cortices. Major species-specific cellular innovations were further validated using orthogonal histological approaches, confirming their anatomical and laminar organization. Overall, this atlas provides a comparative framework available for the research community to dissect the molecular, cellular, and circuit principles underlying conserved and specialized spatial navigation across mammals.

neuroscience↗

bioRxiv2025

New high accuracy diagnostics for avian Aspergillus fumigatus infection using Nanopore methylation sequencing of host cell-free DNA and machine learning prediction

Avian aspergillosis is a detrimental fungal infection affecting wild and domestic birds yet sensitive antemortem diagnostics for early clinical infections are lacking. Here we present new diagnostics for Aspergillus fumigatus (Af) infection developed from cell-free DNA (cfDNA) methylation markers. Broiler chickens were experimentally infected with either Af, a non-Af agent (Escherichia coli or Gallibacterium anatis) or assigned as controls. Oxford Nanopore (ONT) sequencing was performed on serum cfDNA (n = 124), and machine learning (ML) models were trained on infection-specific markers. Three tests were developed: A High Accuracy test for best performance (sensitivity: 100%, specificity: 89.2%) and robustness (ROC-AUC: 0.92) as well as Fast- and In situ tests for rapid turnaround and methylation PCR. Diagnostic accuracies were 92.3%, 82.7%, and 73.1%, respectively. In conclusion, new tests using on ML- and host cfDNA methylation markers demonstrated high diagnostic performance comparable to microbial cfDNA (mcfDNA) tests but without concern for environmental contamination. Key highlightsO_LIWe present three new high accuracy diagnostic tests for Aspergillus fumigatus infection in chickens that use methylation markers from serum cell-free DNA (cfDNA). C_LIO_LIDifferentially methylated cfDNA regions (DMRs) were detected by Oxford Nanopore sequencing (ONT) in experimentally infected chickens and used as markers to train machine learning (ML) models for development of three diagnostic tests. C_LIO_LIThe highest accuracy was found with 83 markers of 10 kilobases (KB) using the glmnet algorithm for the ML model, which classified 92.3% blinded samples correctly. C_LIO_LIA Fast test designed for cheap <1h sequencing using adaptive sampling could correctly classify 82.7% samples with 22 markers using a random forest (rf) model. C_LIO_LIAn In situ test with only four markers, envisioned for use in a simple methylation-specific PCR (MSP-PCR) assay, could correctly classify 73.1% blinded samples. C_LIO_LIReference values with associated probabilities of infection were calculated for each of the three tests and are presented for further evaluation. C_LI

microbiology↗