Biology subjects

Aime, S.

Publications and source records attributed to Aime, S..

7 recordsLinked to original sources

bioRxiv2026

Role of transposons in the specialization of Botrytis cinerea to grapevine: Insights into small RNAs and a new Starship

While transposable elements (TEs) are recognized as major drivers of fungal genome structure, evidence of their direct involvement in the interaction with host plants and the environment is only beginning to emerge. Retrotransposons can generate small RNA (sRNA) that act through cross-kingdom RNA interference, while giant DNA TEs called Starships carry dozens of cargo genes that enrich the accessory gene compartment of fungal genomes. In the polyphagous pathogen Botrytis cinerea, the Vv3 strain and other strains specialized on grapevine display a specific repertoire of TEs, including the retrotransposons BcCopia4, BcGypsy6, and BcGypsy7. This study first explored the putative role of sRNA generated from these retrotransposons in the interaction between the Vv3 strain and its host of origin, grapevine. Putative targets were identified among the host mRNAs, but predicted cleavage sites could not be experimentally validated. Moreover, Dicer mutants unable to produce retrotransposons-derived sRNA remained fully pathogenic on grapevine, indicating that these sRNAs do not act as virulence factors on this host. In parallel, this study provides an updated RNA-seq-based annotation of the accessory genes of the Vv3 strain, which revealed a new 93 kb-Starship harboring 43 cargo genes, some of which are related to arsenic resistance. A formal genetic approach confirmed that this locus confers resistance to this metalloid. This giant TE, named Ariane, was also detected in additional grapevine-specialized strains resistant to arsenic but not in strains isolated from other hosts such as tomato. In conclusion, this study highlights how a Starship giant transposon shaped the accessory genes compartment of the polyphagous fungus B. cinerea and may have contributed to its adaptation to vine cultivation by conferring resistance to arsenic, a compound widely used in vineyards during the last century. IMPACT STATEMENTFungal genomes contain many families of transposons whose functional role in adaptation to the environment and in biotic interactions remained hidden for a long time. In the grey mold fungus Botrytis cinerea, strains specialized on grapevine, such as Vv3, carry a specific repertoire of transposons which provides a valuable opportunity to investigate their role in niche adaptation. In this study, we first investigated retrotransposon-derived small RNA, previously described as effectors capable of manipulating the immunity of the model plant Arabidopsis thaliana. Although in silico analysis of the specific repertoire of small RNAs of the Vv3 strain suggested that some could target the expression of grapevine genes, a genetic approach demonstrated that they do not play a significant role in virulence on this host. In contrast, this study identified a new transposon, named Ariane, that carries 43 cargo genes and confers a selective advantage to the Vv3 strain. Ariane belongs to a family of giant transposons called Starships, recently discovered in fungi and considered to be responsible for horizontal genes transfers between unrelated species. Ariane was detected only in some B. cinerea strains isolated from grapevine, and a genetic cross showed that it provides these strains with the ability to grow in presence of arsenic. Arsenic was used in vineyards until the beginning of the 21st century to control fungal trunk diseases and insect pests. Therefore, Ariane appears to have played an important role in the adaptation of B. cinerea strains to cultivated grapevine. Overall, these results underline the importance of considering Starships when predicting emergence of resistance to antifungal compounds. DATA SUMMARYThe novel data described in this study, i.e., RNA-Seq data and the Starship element are accessible under NCBI GEO accession GSE327899 and at https://doi.org/10.57745/HYWRNM, respectively. All information related to Botrytis cinerea genomes used in this study are centralized and kept up to date at the Bioinfo Bioger genomic web portal: https://bioinfo.bioger.inrae.fr/portal/genome-portal/. Direct links to individual portals are respectively https://bioinfo.bioger.inrae.fr/portal/genome-portal/3/ for B. cinerea Vv3 genome, https://bioinfo.bioger.inrae.fr/portal/genome-portal/2/ for B. cinerea Sl3 genome, and https://bioinfo.bioger.inrae.fr/portal/genome-portal/4/ for B. cinerea populations isolated on tomato or grapevine. Each portal provides: (i) a centralized access to public genomic resources, including the genome, transposon, and RNA repositories; (ii) a data browser to download the genomic files; (iii) a genome browser that enables visualization of features within their genomic context, along with associated expression data. As a summary, the prior main public B. cinerea genomic accessions and resources used in this study are: GCA_039644125 for VV3 genome, GCA_022560135 for Sl3 genome, GCA_000143535 for B05.10 genome, PRJNA624742 for populations, https://doi.org/10.57745/HYWRNM for transposons, and GSE181592 for small RNAs. Furthermore, table S1 summarizes the list and characteristics of the 64 B. cinerea genomes publicly available to date. The genomic data for Vitis vinifera genome PN40024.v4 used in this study are available at: https://integrape.eu/resources/genes-genomes/genome-accessions/.

genomics↗

bioRxiv2025

High-throughput Mucus Microrheology for Phenotyping and Disease Modeling

Mucus mechanics regulate barrier, clearance, and transport functions across epithelial tissues, yet quantitative rheology remains difficult to scale because available assays require large volumes, specialized equipment, or extensive manual analysis. Here, a high-throughput microrheology workflow based on Differential Dynamic Microscopy is established for frequency-dependent measurements from 3-10 uL mucus samples and intact mucosal surfaces using standard epifluorescence microscopy. The workflow combines preloaded tracer chambers, controlled sample handling, short video acquisition, and automated analysis to reduce operator intervention while preserving sensitivity to mucus relaxation on 1--20 s time scales. Validation against shear rheometry and particle tracking in reconstituted mucin gels shows robust recovery of viscoelastic trends across mucus-like material states. Applications in human airway epithelial air--liquid interface cultures resolve culture-medium, age, donor, COPD, cigarette-smoke, cystic-fibrosis treatment, and IL-13-associated differences, including spatial heterogeneity in situ. Measurements of clinical cervical mucus further demonstrate parallel testing of scarce specimens and sensitivity to osmotic swelling. This platform provides a scalable route to quantitative mucus phenotyping for disease modeling, therapeutic testing, and future precision-medicine studies.

bioengineering↗

bioRxiv2023

UPR pathway is required for Arabidopsis thaliana resistance to necrophic fungal pathogens.

The Unfolded Protein Response (UPR) is a retrograde signalling pathway which is activated when endoplasmic reticulum (ER) proteostasis is disturbed. Here, we have investigated by reverse genetics the contribution of such pathway in Arabidopsis thaliana response to two necrotrophic fungi of agricultural importance, Botrytis cinere a which is responsible for the development of grey mold disease, and Alternaria brassicicola which triggers black spot disease. We found that the branch of UPR dependent on the INOSITOL-REQUIRING ENZYME 1 (IRE1) and the transcription factor (TF) bZIP60 is required to restrict foliar necrotic symptoms induced by both fungi. Accordingly, focussing on B. cinerea, we provided evidence for the production of the active bZIP60 form during infection. This activation was accompanied by an increased expression of UPR-responsive genes coding for ER-localized chaperones and co-chaperones that belong to the ER-Quality Control (ER-QC) system. Furthermore, mutants deficient for two ER-QC components were also more susceptible to infection. By contrast, investigating the involvement of CELL DIVISION CYCLE 48 (CDC48) AAA+-ATPAses that assist ER-Associated Degradation (ERAD) pathway for disposal of luminal unfolded proteins, we showed that a series of mutants and transgenics are more resistant to grey mold disease. Seeking for molecular insights into how the ER could shape Arabidopsis immune response to B. cinerea, we quantified the expression of defence gene and cell death markers in single bzip60 and double ire1 mutants. However, none of those genes were mis-regulated in mutant genetic backgrounds, indicating that IRE1-bZIP60 branch of UPR modulates the Arabidopsis response to B. cinerea by a yet-to-be-identified mechanism. Interestingly, we identified the NAC053/NTL4 TF as a potential actor of this unknown mechanism, linking the UPR and proteasome stress regulon. Author summaryNecrotrophic fungi are one of the most economically significant plant pathogens worldwide, inflicting massive pre- and post-harvest losses on a wide range of fruit and vegetable crops. They adopt a necrotrophic lifestyle, deriving their nutrients predominantly from dead plant tissues to complete their life cycle. Botrytis cinerea is the causal agent of grey mold and no plant shows complete resistance towards this pathogen. The use of genetic models such as the plant Arabidopsis thaliana has partially enabled the understanding of the immunity mechanisms involved in the plants response to B. cinerea. Our work provides new insights into the cellular mechanisms of how plants cope with this pathogen. In this context, by means of a reverse genetic approach, we explored the role of the Unfolded Protein Response (UPR), a cell signalling pathway regulating protein homeostasis within the endoplasmic reticulum (ER) and thus protecting cells from a harmful over-accumulation of aberrant or misfolded proteins.

plant biology↗

bioRxiv2022

Solid/liquid coexistence during aging of FUS condensates

A wide range of macromolecules undergo phase separation, forming biomolecular condensates in living cells. These membraneless organelles are typically highly dynamic, formed in a reversible manner, and carry out important functions in biological systems. Crucially, however, a further liquid-to-solid transition of the condensates can lead to irreversible pathological aggregation and cellular dysfunction associated with the onset and development of neurodegenerative diseases. Despite the importance of this liquid-to-solid transition of proteins, the mechanism by which it is initiated in normally functional condensates is unknown. Here we show, by measuring the changes in structure, dynamics and mechanics in time and space, that FUS condensates do not uniformly convert to a solid gel, but rather that liquid and gel phases co-exist simultaneously within the same condensate, resulting in highly inhomogeneous structures. We introduce two new optical techniques, dynamic spatial mapping and reflective confocal dynamic speckle microscopy, and use these to further show that the liquid-to-solid transition is initiated at the interface between the dense phase within condensates and the dilute phase. These results reveal the importance of the spatiotemporal dimension of the liquid-to-solid transition and highlight the interface of biomolecular condensates as a key element in driving pathological protein aggregation.

biophysics↗

bioRxiv2021

GlucoCEST MRI for the early evaluation response to chemotherapeutic and metabolic treatments in a murine triple negative breast cancer: a comparison with 18F-FDG-PET.

PurposeTriple-negative breast cancer (TNBC) patients have usually poor outcome after chemotherapy and early prediction of therapeutic response would be helpful. [18F]F-FDG-PET/CT acquisitions are often carried out to monitor variation in metabolic activity associated to response to the therapy, despite moderate accuracy and radiation exposure limit its application. The glucoCEST technique relies on the use of unlabelled D-glucose to assess glucose uptake with conventional MRI scanners and is currently under active investigations at clinical level. This work aims at validating the potential of MRI-glucoCEST in monitoring early therapeutic responses in a TNBC tumor murine model. ProceduresBreast tumor (4T1) bearing mice were treated with doxorubicin or dichloroacetate for one week. PET/CT with [18F]F-FDG and MRI-glucoCEST were performed at baseline and after 3 cycles of treatment. Metabolic changes measured with [18F]F-FDG-PET and glucoCEST were compared and evaluated with changes in tumor volumes. ResultsDoxorubicin treated mice showed a significant decrease in tumor growth when compared to the control group. GlucoCEST imaging provided early metabolic response after three cycles of treatment, conversely, no variations were detect by in [18F]F-FDG uptake. Dichloroacetate treated mice did not show any decrease either in tumor volume or in tumor metabolic activity as assessed by both glucoCEST and [18F]F-FDG-PET. ConclusionsEarly metabolic changes during doxorubicin treatment can be predicted by glucoCEST imaging that appears more sensitive than [18F]F-FDG-PET in reporting on early therapeutic response. These findings support the view that glucoCEST may be a sensitive technique for monitoring metabolic response, but future studies are needed to explore the accuracy of this approach in other tumor types and treatments.

biophysics↗

bioRxiv2021

In vitro and in vivo comparison of the MRI glucoCEST properties between native glucose and 3OMG in a murine tumor model

PurposeD-Glucose and 3-O-Methyl-D-glucose (3OMG) have been shown to provide contrast in MRI-CEST images. However, a systematic comparison between these two molecules has not yet been performed. This study dealt with the assessment of the effect of pH, saturation power level (B1) and magnetic field strength (B0) on the MRI-CEST contrast with the aim of comparing the in vivo CEST contrast detectability of these two agents in the glucoCEST procedure. MethodsPhosphate buffered solutions of D-Glucose or 3OMG (20 mM) were prepared at different pH values and Z-spectra acquired at several B1 levels and at 37{degrees}C. In vivo glucoCEST images were obtained at 3 T and 7 T over a period of 30 min after injection of D-Glucose or 3OMG (at the doses of 1.5 and 3 g/kg) in a murine melanoma tumour model. ResultsA markedly different pH dependence of CEST response was observed in vitro for D-Glucose and 3OMG. The glucoCEST contrast enhancement in the tumour region following the intravenous administration (at the dose 3 g/kg) resulted to be comparable for both the molecules: 1-2% at 3 T and 2-3% at 7 T. The ST% resulted almost constant for 3OMG over the 30 min period, whereas a significant increase in the case of D-Glucose was detected. ConclusionOur results show similar CEST contrast efficiency but different temporal kinetics for the metabolizable and the non-metabolizable glucose derivatives in tumour murine models when administered at the same doses.

biophysics↗

bioRxiv2019

Manganese-enhanced MRI (MEMRI) in breast and prostate cancers: exploring the potential role of calcium receptors.

ProceduresTo assess the relationship between Manganese Enhanced Magnetic Resonance Imaging (MEMRI) and the expression of calcium receptors in human prostate and breast cancer animal models.\n\nMethodsNOD/SCID mice were inoculated with MDA-MB-231 breast cancer cells and prostate PC3 cancer cells to develop orthotopic or pseudometastatic cancer animal models. Mice were studied on a clinical 3T scanner by using a prototype birdcage coil before and after intravenous injection of MnCl2. Assessment of receptors status was carried out after the MR images acquisition by immunohistochemistry on excised tumours.\n\nResultsManganese contrast enhancement in breast or prostate cancer animal models well correlated with CaSR expression (p<0.01), whereas TRPV6 expression levels appeared not relevant to the Mn uptake.\n\nConclusionMEMRI appears an efficient tool to characterize human breast and prostate cancer animal models in the presence of different expression level of CaSR.

cancer biology↗