Biology subjects

Davoudi, H.

Publications and source records attributed to Davoudi, H..

4 recordsLinked to original sources

bioRxiv2026

PIGSTI: a modular, reproducible pipeline for detecting species identity, pathogens, and microbes from animal palaeogenomic data

Ancient genomics has enabled discovery of diverse pathogens across various time periods, host species, and material types. However, existing palaeogenomic pipelines predominantly focus on screening data from human hosts, or do not incorporate microbial screening methodologies. We present PIGSTI (Pathogen anImal Genome Sequence ToolkIt), a bioinformatic pipeline specifically designed for both the initial screening and subsequent detection of pathogens in shotgun sequencing data from ancient animal remains. PIGSTI's integrated Snakemake workflow performs both host detection, genome mapping and pathogen identification, generating outputs suitable for population genetics and phylogenetic analyses. Testing on 952 newly sequenced and publicly available animal palaeogenomic datasets, we identified ~15 ancient zoonotic and animal pathogens with high confidence, including the first documented case of Rickettsia felis and Leptospira borgpetersenii in an ancient animal. Our results demonstrate PIGSTI's utility for screening pathogen diversity in ancient animal hosts and reconstructing historical host-pathogen relationships.

genomics↗

bioRxiv2025

Distinct brain regions map olfactory and visual spaces

The hippocampus contains a multisensory cognitive map that incorporates spatial cues from across the senses, such as vision and olfaction. However, how primary sensory information transforms along pathways to the hippocampus into this single, combined map is largely unknown. Specifically, does the hippocampus generate or inherit the multisensory map of space? Here, we used multisensory virtual reality and large-scale functional imaging to determine if and how the main input regions to hippocampus, the lateral and medial entorhinal cortices (LEC and MEC, respectively), map olfactory and visual sensory spaces in navigating mice. We discovered that, in contrast to multisensory mapping in the hippocampus, LEC preferentially maps olfactory space while MEC preferentially maps visual space, regardless of the behavioral relevance of the spaces. This establishes the existence of largely independent brain maps for different sensory spaces, suggesting that the hippocampus builds the cognitive map by combining modality-specific maps from pre-synaptic cortical regions.

neuroscience↗

bioRxiv2025

Hippocampal Representational Drift Persists in a Stable Multisensory Virtual Environment

Experiments tracking hippocampal place cells in mice navigating the same real environment have found significant changes in neural representations over days. However, there is currently a debate over whether such "representational drift" serves an intrinsic function, such as distinguishing similar experiences occurring at different times, or is instead observed due to subtle differences in the sensory environment or behavior. Here, we used the experimental control offered by a multisensory virtual reality (VR) system to determine that differences in sensory environment or behavior do not detectably change drift rate. We also found that the excitability of individual place cells was most predictive of their representational drift over subsequent days, with more excitable cells exhibiting less drift. These findings establish that representational drift occurs in mice even with highly reproducible environments and behavior and highlight neuronal excitability as a key factor of long-term representational stability.

neuroscience↗

bioRxiv2021

Exceptional ancient DNA preservation and fibre remains of a Sasanian saltmine sheep mummy in Chehrabad, Iran

Mummified remains have long attracted interest as a potential source of ancient DNA. However, mummification is a rare process that requires an anhydrous environment to rapidly dehydrate and preserve tissue before complete decomposition occurs. We present the whole genome sequences of a [~]1600 year old naturally mummified sheep recovered from Chehr[a]b[a]d, a salt mine in northwestern Iran. Comparative analyses of published ancient sequences revealed remarkable DNA integrity of this mummy. Hallmarks of postmortem damage, fragmentation and hydrolytic deamination, are substantially reduced, likely due to the high-salinity of this taphonomic environment. Metagenomic analyses reflect the profound influence of high salt content on decomposition; its microbial profile is predominated by halophilic archaea and bacteria, possibly contributing to the preservation of this sample. Applying population genomic analyses we find consistent clustering of this sheep with Southwest Asian modern breeds, suggesting ancestry continuity. Genotyping of a locus influencing the woolly phenotype showed the existence of an ancestral "hairy" allele in this sheep, consistent with hair fibre imaging, further elucidating Sasanian-period animal husbandry.

genomics↗