Biology subjects

Florio, A.

Publications and source records attributed to Florio, A..

3 recordsLinked to original sources

bioRxiv2026

Vegetation increases CH4 emissions and methanotroph diversity in marine sediments

Seagrass meadows are key blue carbon (C) ecosystems, storing large amounts of organic C over centuries. Their climate benefits may be reduced by methane (CH) emissions, whose microbial and environmental descriptors in Zostera noltei meadows, dominant seagrass in North-Western Europe, remain poorly understood. We studied CH fluxes, CH-producing and consuming microbial communities and sediment physico-chemical parameters in Z. noltei meadows and adjacent bare sediments across seven sites in Arcachon Bay, France. In situ CH fluxes were measured at low tide and microbial communities were characterised using targeted metagenomics of three functional genes (mcrA, mmoX, pmoA) and quantitative PCR. CH fluxes were higher in vegetated than bare sediments (24.4 {+/-} 2.6 vs. 9.4 {+/-} 0.7 {micro}mol m-{superscript 2} d-{superscript 1}). Mixed linear models and random forest analyses identified C accumulation rate and CO2 flux as the strongest positive descriptors of CH fluxes. Vegetated sediments hosted more diverse methanotrophs, while methanogens showed no habitat differences. Four genera (mcrA-Methanolobus, mmoX-Methylocella, pmoA-Methylococcus, Methyloglobulus) emerged as abundant, seagrass-associated, correlated with CH fluxes, and highlighted by models. Functional diversity, especially pmoA richness, was a stronger microbial descriptor of CH fluxes than gene abundance or a specific genus. Findings indicate Z. noltei meadows enhance C burial and CH emission, with methanotroph diversity potentially mitigating CH emissions. Our results provide the first integrated assessment of CH fluxes and their descriptors in Z. noltei meadows, highlighting the intertwined nature of C burial and CH emissions and the need to account for both in blue C climate assessments.

ecology↗

bioRxiv2024

Functional impact of the hyperduplication genomophenotype in high copy number endometrial cancer

High copy number endometrial cancers (HCNEC) are dominated by excessive duplications scattered across the genome, termed here as the HyperDuplication GenomoPhenotype (HDGP). Although correlated with cancer progression, its biological significance and implications for therapy have not yet been established. We identified locations and sizes of duplications in 171 endometrial cancer cases and designated 71 HCNEC cases as HDGP. We also investigated the response to the pan-ERBB inhibitor afatinib in a subset of HDGP-EC cases with ERBB2/ERBB3 duplications using a patient-derived three-dimensional culture model. Our analysis demonstrates that beyond tandem duplications there is a more general pattern involving coordinated duplication of multiple distant regions of the genome, demonstrating preferential selectivity to over-expressed potential oncogenes within a broad network. This suggests that HDGP increases tumor fitness and resistance to therapy by perturbing important gene networks in concert rather than only driver genes, suggesting a mechanistic basis for the ineffectiveness of targeted drugs in these patients and highlighting the need for combination therapies in these highly aggressive cases.

genomics↗

bioRxiv2023

R-loop landscapes in the developing human brain are linked to neural differentiation and cell-type specific transcription

Here, we construct genome-scale maps for R-loops, three-stranded nucleic acid structures comprised of a DNA/RNA hybrid and a displaced single strand of DNA, in the proliferative and differentiated zones of the human prenatal brain. We show that R-loops are abundant in the progenitor-rich germinal matrix, with preferential formation at promoters slated for upregulated expression at later stages of differentiation, including numerous neurodevelopmental risk genes. RNase H1-mediated contraction of the genomic R-loop space in neural progenitors shifted differentiation toward the neuronal lineage and was associated with transcriptomic alterations and defective functional and structural neuronal connectivity in vivo and in vitro. Therefore, R- loops are important for fine-tuning differentiation-sensitive gene expression programs of neural progenitor cells.

genomics↗