Biology subjects

Mercier, C.

Publications and source records attributed to Mercier, C..

9 recordsLinked to original sources

bioRxiv2026

Environmental RNA improves detection and surveillance of schistosomiasis transmission

Environmental diagnosis of schistosomiasis, a tropical disease affecting more than 250 million people globally, is still challenging, which limits efficient eradication plans. There is a crucial need for resolutive and highly sensitive environmental tools to improve disease control. However, a major obstacle is the inability of current methods, including environmental DNA (eDNA), to distinguish infectious parasite life stages. Here, we develop and validate an environmental RNA (eRNA) approach that enables the detection and absolute quantification of Schistosoma mansoni miracidia and cercariae directly from water samples. After identifying life stage-specific transcripts, we design specific ddPCR assays which are strongly specific to S. mansoni and to each life stage. Comparing with eDNA assays, laboratory experiments demonstrate that stage-specific eRNA assays accurately reflect the relative abundance of each life stage, detect nucleic acids released from organisms, exhibit detection limits tenfold lower than eDNA assays. Also, under laboratory conditions, RNA persists in water longer than DNA. Field validation at six endemic sites in Brazil confirms that eRNA outperforms eDNA and conventional snail surveys in detecting active presence of S. mansoni cercariae, which indicates schistosomiasis transmission risk to humans locally. By enabling active-stage discrimination in environmental monitoring and improving sensitivity (compared to eDNA), our study advances both fundamental understanding and applied surveillance of schistosomiasis transmission, supporting elimination initiatives in affected regions.

ecology↗

bioRxiv2025

Mechanisms controlling the plasma membrane targeting and the nanodomain organization of the plant SPFH protein HIR2

HIR2 is a plant-specific protein belonging to the superfamily of SPFH domain-containing proteins that were proposed to play scaffolding functions in membranes. HIR2 organizes in plasma membrane (PM) nanodomains that correspond to nanometric scale structures enriched in specific lipids and proteins acting as signaling/regulation hubs. So far, how PM nanodomains are formed and maintained in plant cells remains largely unknown. Combining state of the art microscopy techniques, we investigated the mechanisms governing the trafficking and the organization into nanodomains of Arabidopsis HIR2 protein. We revealed that the mono S-acylation of HIR2 either on C6 or on C7 was required for HIR2 targeting to the PM of Arabidopsis cells, independently of the conventional secretory pathway. Investigating the mechanisms implicated in the arrangement of HIR2 into nanodomains, we provided evidences that the lipid composition in sterols and very long chain fatty acids of the PM influenced HIR2 organization. HIR2 forms oligomers and we demonstrated here that the C-terminal part of HIR2 is required for self-assembly, similarly to animal SPFH proteins. Interestingly, we highlighted that the oligomerization of HIR2 is essential for its organization in nanodomains and to ensure HIR2 lateral stability in the PM. Overall, we propose that HIR2 nanodomain organization is a complex mechanism relying on different parameters including PM lipid composition and oligomerization. HIR proteins are involved in plant immunity. Here, we revealed that HIR2 nanodomain organization is required to boost the apoplastic ROS burst induced by the bacterial peptide flg22. One sentence summaryS-acylation and oligomerization control the plasma membrane targeting and the organization into nanodomains of the Arabidopsis SPFH-domain containing protein HIR2, respectively.

plant biology↗

bioRxiv2024

genomesizeR: An R package for genome size prediction

The genome size of organisms present in an environment can provide many insights into evolutionary and ecological processes at play in that environment. The genomic revolution has enabled a rapid expansion of our knowledge of genomes in many living organisms, and most of that knowledge is classified and readily available in the databases of the National Center for Biotechnology Information (NCBI). The genomesizeR tool leverages the wealth of taxonomic and genomic information present in NCBI databases to infer the genome size of Archeae, Bacteria, or Eukaryote organisms identified at any taxonomic level. This R package uses statistical modelling on data from the most up-to-date NCBI databases and provides three statistical methods for genome size prediction of a given taxon, or group of taxa. A straightforward weighted mean method identifies the closest taxa with available genome size information in the taxonomic tree, and averages their genome sizes using weights based on taxonomic distance. A frequentist random effect model uses nested genus and family information to output genome size estimates. Finally a third option provides predictions from a distributional Bayesian multilevel model which uses taxonomic information from genus all the way to superkingdom, therefore providing estimates and uncertainty bounds even for under-represented taxa. All three methods use: O_LIA list of queries; a query being a taxon or a list of several taxa. The package was designed to make it easy to use with data coming from environmental DNA experiments, but works with any table of taxa. C_LIO_LIA reference database containing all the known genome sizes, built from the NCBI databases, with associated taxa, provided in an archive to download. C_LIO_LIA taxonomic tree structure as built by the NCBI, provided in the same archive. C_LI genomesizeR retrieves the taxonomic classification of input queries, estimates the genome size of each query, and provides 95% confidence intervals for each estimate.

bioinformatics↗

bioRxiv2024

Pollen Partners: The Symbiotic Microbes of Pinus radiata Pollen

Pollen, a crucial source of nutrients and energy for pollinators. It also provides a unique habitat for ecological microbiota. Previous research on the microbiome of pollen has largely focussed on angiosperm systems, with limited research into coniferous gymnosperms. This study characterises the pollen microbiome associated with one of the worlds most widely grown tree species, Pinus radiata. Trees were sampled from locations across Canterbury, New Zealand, with repeated collections in 2020 and 2021. Metabolomic analysis revealed the main compounds present on P. radiata pollen to be amino acids (principally proline), and carbohydrates (fructose, glucose, and sucrose). Although phenolic compounds such as {rho}-coumaric acid and catechin, and terpenoids such as dehydroabietic acid, were present at low concentrations, their strong bioactive natures mean they may be important in filtering of microbiome communities on pollen. Pinus radiata pollen was found to host a microbiome dominated by fungi; this directly contrasts with those for many angiosperm species. Geographic range and sampling years were evaluated as secondary drivers of microbiome assembly. Neither sampling location nor annual variation had a significant impact on the fungal component of the pine pollen microbiome, which was remarkably stable/conserved among samples. However, some bacterial taxa exhibited sensitivity to geographic distances and yearly variations, suggesting a secondary role for some. A core microbiome was identified in P. radiata pollen, characterized by a consistent presence of specific fungal and bacterial taxa across samples. While the dominant phyla, Proteobacteria and Ascomycota, align with findings from other pollen microbiome studies, unique core members were unidentified at genus level. This tree species-specific microbiome assembly emphasizes the crucial role of the host plant in shaping the pollen microbiome. These findings contribute to a deeper understanding of pollen microbiomes in gymnosperms, shedding light on the need to look further at their ecological and functional roles.

ecology↗

bioRxiv2024

Endothelial SHP-1 regulates diabetes-induced abnormal collateral vessel formation and endothelial cell senescence

ObjectiveIschemia due to narrowing of the femoral artery and distal vessels is a major cause of peripheral arterial disease and morbidity affecting patients with diabetes. Diabetes-induced premature senescence of endothelial cells (EC) has been proposed as a mechanism leading to impaired ischemia-driven angiogenesis. Importantly, our previous work has shown that hyperglycemia reduced vascular endothelial growth factor (VEGF) activity in ischemic muscle of diabetic mice, which was associated with increased expression of the protein tyrosine phosphatase Src homology region 2 domain-containing phosphatase-1 (SHP-1). Here, we evaluate the impact of SHP-1 deletion on EC function and senescence. Approach and ResultsLigation of the femoral artery was performed in nondiabetic (NDM) and 3 months diabetic (DM) mice with EC-specific deletion of SHP-1 and blood flow reperfusion was measured for 4 weeks. Blood flow reperfusion and limb function during voluntary wheel running were reduced by 43% and 82%, respectively in DM mice as compared to NDM mice. EC-specific deletion of SHP-1 in DM mice restored blood flow reperfusion by 60%, limb function by 86%, while capillary density was similar to NDM mice. Moreover, ablation of SHP-1 in EC prevented diabetes-induced expression of the senescence markers p53 and p21 and counteracted Nrf2 downregulation. In cultured EC, overexpression of dominant negative of SHP-1 prevented HG-induced inhibition of proliferation, migration, tubule formation and VEGFR2/Akt phosphorylation following VEGF stimulation. In addition, the expression of senescence markers and suppression of Nrf2 in EC exposed to HG levels were reversed by overexpression of dominant negative SHP-1. ConclusionSHP-1 in ECs is a central effector of diabetes-induced senescence that blocks VEGF action, and induces aberrant collateral vessel formation and blood flow reperfusion. Reduced SHP-1 expression counteracts these pathologic features suggesting the notion that it represents a promising therapeutic target. HIGHLIGHTSO_LIEndothelial specific deletion of SHP-1 (Scr homology 2-containing phosphatase-1) improves blood flow reperfusion, limb motricity and vessel density in the diabetic ischemic limb. C_LIO_LIDiabetes-induced SHP-1 protein expression inhibits VEGF proangiogenic actions and promotes endothelial senescence. C_LIO_LIEndothelial specific deletion of SHP-1 restores VEGF proangiogenic actions and prevents senescence in ischemic muscle and artery of diabetic mice and patients. C_LI

cell biology↗

bioRxiv2023

Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space

Marine environmental virus metagenomes, commonly referred to as viromes, are typically generated by physically separating virus-like particles (VLPs) from the microbial fraction based on their size and mass. However, most methods used to purify VLPs, enrich extracellular vesicles (EVs) and gene transfer agents (GTAs) simultaneously. Consequently, the sequence space traditionally referred to as a virome contains host-associated sequences, transported via EVs or GTAs. We therefore propose to call the genetic material isolated from size-fractionated (0.22 {micro}m) and DNase-treated samples protected environmental DNA (peDNA). This sequence space contains viral genomes, DNA transduced by viruses and DNA transported in EVs and GTAs. Since there is no genetic signature for peDNA transported in EVs, GTAs and virus particles, we rely on the successful removal of contaminating remaining cellular and free DNA when analyzing peDNA. Using marine samples collected from the North Sea, we generated a thoroughly purified peDNA dataset and developed a bioinformatic pipeline to determine the potential origin of the purified DNA. This pipeline was applied to our dataset as well as existing global marine viromes. Through this pipeline, we identified known GTA and EV producers, as well as organisms with actively transducing proviruses as the source of the peDNA, thus confirming the reliability of our approach. Additionally, we identified novel and widespread EV producers, and found quantitative evidence suggesting that EV-mediated gene transfer plays a significant role in driving horizontal gene transfer (HGT) in the worlds oceans.

microbiology↗

bioRxiv2022

Seeing our hand or a tool during visually-guided actions: different effects on the somatosensory and visual cortices

The processing of proprioceptive information in the context of a conflict between visual and somatosensory feedbacks deteriorates motor performance. Previous studies have shown that seeing ones hand increases the weighting assigned to arm somatosensory inputs. In this light, we hypothesized that the sensory conflict, when tracing the contour of a shape with mirror-reversed vision, will be greater for participants who trace with a stylus seen in their hand (Hand group, n=17) than for participants who trace with the tip of rod without seen their hand (Tool group, n=15). Based on this hypothesis, we predicted that the tracing performance with mirror vision will be more deteriorated for the Hand group than for the Tool group, and we predicted a greater gating of somatosensory information for the Hand group to reduce the sensory conflict. The participants of both groups followed the outline of a shape in two visual conditions. Direct vision: the participants saw the hand or portion of a light 40 cm rod directly. Mirror Vision: the hand or the rod was seen through a mirror. We measured tracing performance using a digitizing tablet and the cortical activity with electroencephalography. Behavioral analyses revealed that the tracing performance of both groups was similarly impaired by mirror vision. However, contrasting the spectral content of the cortical oscillatory activity between the Mirror and Direct conditions, we observed that tracing with mirror vision resulted in significantly larger alpha (8-12 Hz) and beta (15-25 Hz) powers in the somatosensory cortex for participants of the Hand group. The somatosensory alpha and beta powers did not significantly differ between Mirror and Direct vision conditions for the Tool group. For both groups, tracing with mirror vision altered the activity of the visual cortex: decreased alpha power for the Hand group, decreased alpha and beta power for the Tool group. Overall, these results suggest that seeing the hand enhanced the sensory conflict when tracing with mirror vision and that the increase of alpha and beta powers in the somatosensory cortex served to reduce the weight assigned to somatosensory information. The increased activity of the visual cortex observed for both groups in the mirror vision condition suggests greater visual processing with increased task difficulty. Finally, the fact that the participants of the Tool group did not show better tracing performance than those of the Hand group suggests that tracing deterioration resulted from a sensorimotor conflict (as opposed to a visuo-proprioceptive conflict).

neuroscience↗

bioRxiv2022

In depth characterization of an archaeal virus-host system reveals numerous virus exclusion mechanisms

Archaeal head-tailed viruses appear, at first sight, very closely related to head-tailed bacteriophages simply due to morphological similarities and similar life cycles. However, they encounter host cells that are very different from bacteria and share characteristics, that greatly influence virus life cycles, with eukaryotes. Here we present an in-depth characterization of the archaeal head-tailed virus, HRTV-Dl1, isolated from Deep Lake, Antarctica. The host Halorubrum lacusprofundi exhibits a large arsenal of virus exclusion mechanisms, indicating a long ongoing arms race with viruses. However, we uncover that the majority of this arsenal was lost spontaneously in a strain grown under non-challenging laboratory conditions. By challenging both the parental strain and the sensitive strain with HRTV-DL1, we discovered a number of putative virus exclusion mechanisms that are only activated in the sensitive strain upon the lack of defense systems present in the parental strain. We identify virus exclusion mechanisms that are also common in bacteria, mechanisms that are unique to archaea, and a potential mechanisms involving the archaeal homolog of the eukaryotic ORC1 and CDC6. We identify one of two S-layer proteins as primary receptor for HRTV-DL1, demonstrating that the presence of two different S-layer proteins in one strain provides a strong advantage in the arms race with viruses. Our results clearly reflect the differences between bacterial and archaeal head-tailed viruses. Finally, we observed that our intention to isolate a clean and stable model virus-host system led to the generation of a virus-host pair with reduced genomes. This model system is great to study in the laboratory, but barely reflects the entire spectrum of virus-host interactions as they would occur in the environment, emphasizing the importance of combining wet lab data with environmental data.

microbiology↗

bioRxiv2020

metabaR : an R package for the evaluation and improvement of DNA metabarcoding data quality

O_LIDNA metabarcoding is becoming the tool of choice for biodiversity studies across taxa and large-scale environmental gradients. Yet, the artefacts present in metabarcoding datasets often preclude a proper interpretation of ecological patterns. Bioinformatic pipelines removing experimental noise have been designed to address this issue. However, these often only partially target produced artefacts, or are marker specific. In addition, assessments of data curation quality and the appropriateness of filtering thresholds are seldom available in existing pipelines, partly due to the lack of appropriate visualisation tools. C_LIO_LIHere, we present metabaR, an R package that provides a comprehensive suite of tools to effectively curate DNA metabarcoding data after basic bioinformatic analyses. In particular, metabaR uses experimental negative or positive controls to identify different types of artefactual sequences, i.e. reagent contaminants and tag-jumps. It also flags potentially dysfunctional PCRs based on PCR replicate similarities when those are available. Finally, metabaR provides tools to visualise DNA metabarcoding data characteristics in their experimental context as well as their distribution, and facilitate assessment of the appropriateness of data curation filtering thresholds. C_LIO_LImetabaR is applicable to any DNA metabarcoding experimental design but is most powerful when the design includes experimental controls and replicates. More generally, the simplicity and flexibility of the package makes it applicable any DNA marker, and data generated with any sequencing platform, and pre-analysed with any bioinformatic pipeline. Its outputs are easily usable for downstream analyses with any ecological R package. C_LIO_LImetabaR complements existing bioinformatics pipelines by providing scientists with a variety of functions with customisable methods that will allow the user to effectively clean DNA metabarcoding data and avoid serious misinterpretations. It thus offers a promising platform for automatised data quality assessments of DNA metabarcoding data for environmental research and biomonitoring. C_LI

bioinformatics↗