Biology subjects

Mane, A.

Publications and source records attributed to Mane, A..

3 recordsLinked to original sources

bioRxiv2026

Mesenchymal predominance in olfactory epithelium-derived cultures limits modeling of neurodevelopmental brain disorders

The human olfactory epithelium (OE) represents a lifelong source of neural progenitor cells and has been proposed as an accessible model to investigate molecular alterations associated with neurodevelopmental disorders in postnatal individuals. Globose basal cells are considered the immediate neuronal progenitors within the OE, and several studies have attempted to culture these cells from nasal exfoliates. However, the actual contribution of neurogenic lineages in these cultures remains largely unquantified. Here, we cultured human nasal explants using an established protocol and characterized the resulting cell populations by immunohistochemistry and single-cell RNA sequencing. Integration with primary in vivo OE datasets revealed that these cultures are predominantly composed of mesenchymal-like cells, with limited representation of globose basal cells and neurons, and low expression of canonical neuronal markers. Using curated gene sets associated with neurodevelopmental disorders and malformations of cortical development, we assessed the extent to which disease-relevant transcriptional programs are captured in OE-derived cultures. While disease-associated genes are enriched in neurogenic lineages in vivo, their representation in mesenchymal cells is reduced. Together, our results challenge the assumption that standard OE culture systems faithfully model neurogenic compartments and suggest that current approaches may need refinement to recover neurogenic lineages.

neuroscience↗

bioRxiv2026

A multi-flow approach for binning circular plasmids from short-reads assembly graphs

We address the problem of plasmid binning, that aims to group contigs - from a draft short-read assembly for a bacterial sample - into bins each expected to correspond to a plasmid present in the sequenced bacterial genome. We formulate the plasmid binning problem as a network multi-flow problem in the assembly graph and describe a Mixed-Integer Linear Program to solve it. We compare our new method, PlasBin-HMF, with state-of-the-art methods,MOB-recon, gplasCC, and PlasBin-flow, on a dataset of more than 500 bacterial samples, and show that PlasBin-HMF outperforms the other methods, by preserving the explainability.

genomics↗

bioRxiv2024

PlasEval: a framework for comparing and evaluating plasmid detection tools

Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active research area. Plasmid binning aims at detecting, in a draft genome assembly, groups (bins) of contigs likely to originate from the same plasmid. Several methods for plasmid binning have been developed recently, such as PlasBin-flow, HyAsP, gplas, MOB-suite, and plasmidSPAdes. This motivates the problem of evaluating the performances of plasmid binning methods, either against a given ground truth or between them. We describe PlasEval, a novel method aimed at comparing the results of plasmid binning tools. PlasEval computes a dissimilarity measure between two sets of plasmid bins, that can originate either from two plasmid binning tools, or from a plasmid binning tool and a ground truth set of plasmid bins. The PlasEval dissimilarity accounts for the contig content of plasmid bins, the length of contigs and is repeat-aware. Moreover, the dissimilarity score computed by PlasEval is broken down into several parts, that allows to understand qualitative differences between the compared sets of plasmid bins. We illustrate the use of PlasEval by benchmarking four recently developed plasmid binning tools - PlasBin-flow, HyAsP, gplas, and MOB-recon - on a data set of 54 E. coli bacterial genomes. PlasEval is freely available at https://github.com/acme92/PlasEval

bioinformatics↗