Biology subjects

Valiadi, M.

Publications and source records attributed to Valiadi, M..

3 recordsLinked to original sources

bioRxiv2025

Universal rapid RNA-based quantification of toxigenic Alexandrium species (Dinophyceae) using quantitative recombinase polymerase amplification

Harmful algal blooms caused by toxigenic Alexandrium species pose recurrent risks to coastal ecosystems and public health, yet current monitoring approaches rely on microscopy and laboratory-based toxin analysis with limited capacity for rapid, functional early warning. Here, we present a universal quantitative reverse-transcriptase recombinase polymerase amplification (qRT-RPA) assay targeting the sxtA4 transcript, an essential gene in saxitoxin biosynthesis. The RPA chemistry is isothermal with a low running temperature, making it suitable for portable, on-site testing. The assay was designed against a conserved sxtA4 region and validated using isolated sxtA4 amplicons from multiple Alexandrium species, synthetic DNA and RNA templates, and total RNA of Alexandrium minutum as a widespread reference species. The assay achieved uniform amplification kinetics across species, a limit of detection below 103 synthetic RNA copies and 0.1 ng total RNA per reaction for A. minutum, and a runtime of less than 15 minutes. The assay selectively detected sxtA4 transcripts from toxigenic Alexandrium strains and showed no cross-reactivity with non-target phytoplankton. A limit of detection that is relevant to early warning for Alexandrium species (under 20 cells per reaction) was retained in complex RNA matrices. Mock samples prepared by spiking cultured cells into natural seawater also demonstrated detection at field-relevant concentrations. These results establish qRT-RPA as a rapid, RNA-based, functionally informative molecular tool that provides a foundation for portable, early-warning monitoring of potentially toxigenic Alexandrium blooms.

microbiology↗

bioRxiv2025

Insulated Outlier Chromosomes Drive Metabolic and Evolutionary Innovation in Minimal Eukaryotic Algae

Marine picoeukaryotes of the order Mamiellales, including Ostreococcus tauri, the smallest known free-living eukaryote, possess compact genomes yet maintain enigmatic "outlier chromosomes" characterised by lower GC content and hypervariability. To determine the structural and functional nature of these regions, we applied chromosome conformation capture to O. tauri and conducted comparative multi-omics analyses across the Mamiellales order, presenting the first analysis of three-dimensional genome organisation in marine picoeukaryotes. We reveal that outlier regions form structures resembling topologically associating domains, with sharp boundaries that spatially insulate them from the standard chromosomes. These compartments are defined by a distinctive chromatin state characterised by hypomethylation and transcriptional hyperactivity, and are frequently, though not universally, enriched in transposable elements. Crucially, species that lack transposable element enrichment in their outlier chromosomes nonetheless retain the transcriptional hyperactivity and distinct nucleotide composition of these regions, indicating that the functional identity of these compartments persists independently of transposon accumulation. The dynamic nature of these insulated domains is highlighted by the presence of structurally diverse giant polyketide synthase loci. We identify convergent genomic organisation in other chlorophytes, as well as phylogenetically distant stramenopiles. Our results suggest that such compartmentalisation of rapidly evolving, dynamic genomic regions represents a fundamental architectural principle of minimal eukaryotic genomes.

evolutionary biology↗

bioRxiv2023

Development of a quantitative colorimetric LAMP assay for fast and targeted molecular detection of the invasive lionfish Pterois miles from environmental DNA

The Mediterranean basin has seen an increased influx of invasive species since the Suez Canal expansion in 2015. The invasive lionfish species, Pterois miles, has rapidly established new populations in the Eastern Mediterranean Sea, impacting local fish biodiversity. Here, we have developed a new, fast (< 35 min) molecular approach to detect and quantify P. miles environmental DNA (eDNA) in combination with a portable device for field-based analysis. Using a species-specific real-time colorimetric loop-mediated isothermal amplification (qcLAMP) for the cytochrome oxidase subunit 1 (COI) gene, we demonstrate a high sensitivity with a limit of detection of 0.002 ng DNA per reaction, equivalent to only 50 copies of the COI gene. The assay is specific to the target in the presence of closely related and co-occurring species, and it is quantitative over five orders of magnitude. We validated the assay using aquarium water samples and further demonstrated its utility on natural eDNA samples collected from locations around the island of Crete where P. miles had been sighted. P. miles was indeed detected in three out of nine locations, two nature reserves and a closed bay. Lack of detection in the remaining locations suggest that populations are still at a low density. We also demonstrate the feasibility of P. miles eDNA qualitative detection directly from the filter used to collect eDNA-containing particles, completely omitting DNA extraction. Overall, we present a new approach for fast and targeted eDNA quantification. The developed LAMP assay together with the quantitative real-time colorimetric detection approach open new possibilities for monitoring invasive P. miles in the field.

ecology↗