Biology subjects

Rousseau, C.

Publications and source records attributed to Rousseau, C..

8 recordsLinked to original sources

bioRxiv2025

The JEDI marker as a universal measure of planetary biodiversity

Despite its critical importance in the formation and maintenance of ecosystems and homeostasis on Earth, biodiversity remains a complex and non-unified concept. Consequently, standards for measuring global biodiversity are lacking, hindering our capacity to document Earths biota and track its change. Here, we propose the Joint, cellular life-Encompassing DIversity (JEDI) marker as a simple, effective and quantitative measure to assess and monitor biodiversity. The JEDI marker is a ribosomal RNA gene fragment that can be amplified from all domains of life using a single pair of PCR primers. We demonstrate the applicability and effectiveness of this approach for assessing biodiversity across ecological and biological scales, from holobionts to diverse ecosystems. In addition, we provide an automated bioinformatic workflow to support the standardised and reproducible analysis of the JEDI marker in future studies. While this approach is not free from trade-offs, we argue that its advantages outweigh its limitations by providing a unique, operational and scalable solution that builds on established infrastructure to integrate the microbial majority into biodiversity assessments and provide fundamental insights into organismal dynamics and associations across domains of life. Thus, the JEDI marker approach addresses the urgent need for a universal and standardised framework to effectively measure and monitor biodiversity at planetary scales in an era of profound global change.

ecology↗

bioRxiv2025

A duo of fungi and complex and dynamic bacterial community networks contribute to shape the Ascophyllum nodosum holobiont

The brown alga Ascophyllum nodosum and its microbiota form a dynamic functional entity named holobiont. Some microbial partners may play a role in seaweed health through bioactive compounds crucial for normal morphology, development, and physiological acclimation. However, the full spectrum of the microbial diversity and its variations according to algal life stage, season, and location have not been comprehensively studied. This study uses 208 short-read metabarcoding samples to characterize the bacterial, archaeal, and microeukaryotic communities of A. nodosum across three nearby sites, four thallus parts, and a monthly survey, aiming to explore the dynamics of ecological interactions within the holobiont. Our results revealed that A. nodosum harbors a predominantly bacterial microbiota, varying significantly across all covariables, while archaea were virtually absent. An innovative normalization using the co-amplified host reads provided an estimation of bacterial abundance, revealing a drastic decline in May, potentially linked to epidermal shedding. In contrast, fungal communities were stable, dominated by Mycophycias ascophylli and Moheitospora sp., which remained closely associated with the host year-round. We identified a core microbiome of 22 ASVs, consistently found in all samples, including Granulosicoccus, a genus consistently abundant in other brown algal microbiota. Sequence clustering revealed multiple species which vary according seasons, even in the overall stable Granulosicoccus genus. Co-occurrence network analysis revealed putative interactions between microbial groups in response to ecological niches. Overall, these findings highlight the dynamic of bacterial interactions and stable fungal associations within the A. nodosum holobiont, providing new insights into the ecology of its microbiota.

ecology↗

bioRxiv2024

Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data

Third-generation sequencing platforms, such as Oxford Nanopore Technology (ONT), have made it possible to characterise communities through the sequencing of long amplicons. Whilst this theoretically allows for an increased taxonomic resolution compared to short-read sequencing platforms such as Illumina, the high error rate remains problematic to accurately identify the community members present within a sample. Here we present and validate CONCOMPRA, a tool that allows the detection of closely related strains within a community by drafting and mapping to consensus sequences. We show that CONCOMPRA outperforms several other tools for profiling bacterial communities using full-length 16S rRNA gene sequencing. Since CONCOMPRA does not rely on a sequence database for profiling communities, it is applicable to systems and amplicons for which a reference framework is poorly developed. Our validation test shows that the amplification of long PCR products is likely to produce chimeric byproducts that inflate alpha diversity and skew community structure, stressing the importance of chimera detection. CONCOMPRA is available on GitHub (https://github.com/willem-stock/CONCOMPRA). Key points- We introduce a reference free tool for (long) amplicon Oxford Nanopore sequencing data - We show that it is capable of outperforming achieving a higher accuracy than preexisting tools - Chimera detection and removal is an essential step in the processing of long amplicon Oxford Nanopore sequencing data

bioinformatics↗

bioRxiv2023

Identification of new proviral and antiviral factors through the study of the Dicer-2 interactome in vivo during viral infection in Drosophila melanogaster

RNA interference, which has a major role in the control of viral infection in insects, is initialized by the sensing of double stranded RNA (dsRNA) by the RNAse III enzyme Dicer-2. Although many in vitro studies have helped understand how Dicer-2 is able to discriminate between different dsRNA substrate termini, much less is known about how this translates to the in vivo recognition of viral dsRNA. Indeed, although Dicer-2 associates with several dsRNA-binding proteins (dsRBPs) that can modify its specificity for a substrate, it remains unknown how Dicer-2 is able to recognize the protected termini of viral dsRNAs. In order to study how the ribonucleoprotein network of Dicer-2 impacts antiviral immunity, we used an IP-MS approach to identify in vivo interactants of different versions of GFP::Dicer-2 in transgenic lines. We provide a global overview of the partners of Dicer-2 in vivo, and reveal how this interactome is modulated by different factors such as the viral infection and/or different point mutations inactivating the helicase or RNase III domains of GFP::Dicer-2. Our analysis uncovers several previously unknown Dicer-2 interactants associated with RNA granules (i.e. Me31B, Rump, eIF4E1 & Syp). Functional characterization of the candidates reveals pro- and antiviral factors in the context of the infection by the picorna-like DCV virus. In particular, the protein Rasputin has been identified as a novel antiviral candidate. The resources provided by this work can be used to gain a better understanding of the molecular complexes assembled around Dicer-2 in the context of antiviral RNAi and beyond.

immunology↗

bioRxiv2020

Single cell RNA sequencing of blood antigen-presenting cells in severe Covid-19 reveals multi-process defects in antiviral immunity

COVID-19 can lead to life-threatening acute respiratory failure, characterized by simultaneous increase in inflammatory mediators and viral load. The underlying cellular and molecular mechanisms remain unclear. We performed single-cell RNA-sequencing to establish an exhaustive high-resolution map of blood antigen-presenting cells (APC) in 7 COVID-19 patients with moderate or severe pneumonia, at day-1 and day-4 post-admission, and two healthy donors. We generated a unique dataset of 31,513 high quality APC, including monocytes and rare dendritic cell (DC) subsets. We uncovered multiprocess and previously unrecognized defects in anti-viral immune defense in specific APC compartments from severe patients: i) increase of pro-apoptotic genes exclusively in pDC, which are key effectors of antiviral immunity, ii) sharp decrease of innate sensing receptors, TLR7 and DHX9, in pDC and cDC1, respectively, iii) down-regulation of antiviral effector molecules, including Interferon stimulated genes (ISG) in all monocyte subsets, and iv) decrease of MHC class II-related genes, and MHC class II transactivator (CIITA) activity in cDC2, suggesting a viral inhibition of antigen presentation. These novel mechanisms may explain patient aggravation and suggest strategies to restore defective immune defense.

immunology↗

bioRxiv2019

Altered hypothalamic diffusivity in Parkinsonian autonomic dysfunction

The pathophysiological basis of autonomic symptoms in Parkinsons disease remains incompletely understood. The hypothalamus plays a key regulatory role in autonomic function and has been shown to be affected in Parkinsons disease. Here, using diffusion magnetic resonance imaging, we investigated whether microstructural properties of the hypothalamus differ in Parkinsons disease patients with high compared to low autonomic symptom burden.\n\nParkinsons disease patients with low (n=25) and high (n=25) autonomic symptom burden were identified from a larger pool, based on scores from a questionnaire assessing autonomic symptoms in Parkinsons disease (SCOPA-AUT). In each patient, we first segmented the hypothalamus manually, based on anatomical landmarks. Diffusivity measures were then extracted from the hypothalamus. Diffusivity measures calculated in the brainstem and the putamen were used to assess the specificity of the results.\n\nRelative to patients with low autonomic symptom burden, patients with high burden showed increased mean, axial, and radial diffusivity in the hypothalamus. In contrast, we did not find significant group differences in any of these measures extracted from the brainstem or the putamen.\n\nThese results reveal consistent differences in the microstructural properties of the hypothalamus between patients with low and high autonomic symptom burden. Hypothalamic diffusivity properties can thus potentially be used as an imaging marker to assist in the identification of therapeutic targets for autonomic dysfunction in Parkinsons disease.

neuroscience↗

bioRxiv2019

Gravity highlights a dual role of the insula in internal models

Movements rely on a mixture of predictive and reactive mechanisms. With experience, the brain builds internal representations of actions in different contexts. Many factors are taken into account in this process among which the immutable presence of gravity. Any displacement of a massive body in the gravitational field generates forces and torques that must be predicted and compensated by appropriate motor commands. Studies have shown that the insular cortex is a key brain area for graviception. However, none attempted to address whether the same internal representation of gravity is shared between reactive and predictive mechanisms. Here, participants either mentally simulated (only predictive) or performed (predictive and reactive) vertical movements of the hand. We found that the posterior part of the insular cortex was engaged when feedback was processed. The anterior insula, however, was activated only in mental simulation of the action. A psychophysical experiment shows participants ability to integrate the effects of gravity. Our results demonstrate a dual internal representation of gravity within the insula and discuss how they can conceptually be linked.

neuroscience↗

bioRxiv2019

Excess significance bias in repetitive transcranial magnetic stimulation literature for neuropsychiatric disorders

IntroductionRepetitive transcranial magnetic stimulation (rTMS) has been widely tested and promoted for use in multiple neuropsychiatric conditions, but as for many other medical devices, some gaps may exist in the literature and the evidence base for rTMS clinical efficacy remains under debate. We aimed to empirically test for an excess number of statistically significant results in the literature on rTMS therapeutic efficacy across a wide range of meta-analyses and to characterize the power of studies included in these meta-analyses.\n\nMethodsBased on power calculations, we computed the expected number of \"positive\" datasets for a medium effect-size (standardized mean difference, SMD=0.30) and compared it with the number of observed \"positive\" datasets. Sensitivity analyses considered small (SMD=0.20), modest (SMD=0.50), and large (SMD=0.80) effect sizes.\n\nResults14 meta-analyses with 228 datasets (110 for neurological disorders and 118 for psychiatric disorders) were assessed. For SMD=0.3, the number of observed \"positive\" studies (n=94) was larger than expected (n=35). We found evidence for an excess of significant findings overall (p<0.0001) and in 8/14 meta-analyses. Evidence for an excess of significant findings was also observed for SMD=0.5 for neurological disorders. 0 (0 %), 0 (0 %), 3 (1 %), and 53 (23 %) of the 228 datasets had power >0.80, respectively for SMDs of 0.30, 0.20, 0.50, and 0.80.\n\nConclusionMost studies in the rTMS literature are underpowered. This results in fragmentation and waste of research efforts. The somewhat high frequency of \"positive\" results seems spurious and may reflect bias.\n\nTrial Registration: PROSPERO 2017 CRD42017056694

scientific communication and education↗