Biology subjects

Richard, E.

Publications and source records attributed to Richard, E..

14 recordsLinked to original sources

bioRxiv2026

Mucosal architecture, microbiota resilience and metabolic disruption reveal holobiont dynamics during bovine respiratory disease

The gut-airway axis is increasingly recognised as an important determinant of respiratory health in livestock. However, the interactions among respiratory infections, microbial communities, mucosal barrier function, and microbial metabolism that underpin this axis remain poorly understood. Here, we combined longitudinal immunological, mucosal, microbiological, and metabolic analyses to characterise host-microbiota interactions during antibiotic treatment and experimental bovine respiratory disease (BRD). We found that the bovine respiratory tract is organised as a hierarchically structured mucosal ecosystem, with compartment-specific mucin expression patterns associated with distinct microbial communities. Within this framework, increasing respiratory pathogen loads were associated with greater clinical severity, oxidative stress, acute inflammation, and targeted alterations in mucosal regulation and microbial composition, while serum amyloid A emerged as the host biomarker most closely reflecting infection intensity. Although infection altered host and microbial states, antimicrobial treatment represented the dominant ecological perturbation. Antibiotic exposure reshaped both respiratory and intestinal microbial communities, reducing diversity, increasing community drift, and driving coordinated ecological transitions across the gut-airway axis that exceeded the effects of infection alone. Importantly, these compositional changes were accompanied by profound reductions in acetate, propionate, butyrate, and valerate, identifying short-chain fatty acids as a major functional consequence of gut microbiota disruption. Integrative multi-omics analyses revealed that mucosal organisation, microbial diversity, microbial metabolism, and immune activity were embedded within a highly structured gut-airway network. Together, these findings support a holobiont view of BRD in which disease outcomes emerge not only from pathogen-host interactions but also from ecological disturbances that propagate across interconnected mucosal compartments. Notably, antimicrobial treatment affected ecosystem structure and function more than infection itself, highlighting potential trade-offs between pathogen control and microbiota stability. Preserving microbial resilience and its metabolic functions may therefore represent an important component of future strategies to improve respiratory health and disease resilience in cattle.

systems biology↗

bioRxiv2026

Nutritional Anthelmintics: Chicory Reconfigures the Equine Holobiont Across Microbial, Parasitic, and Host Scales

Anthelmintic resistance in cyathostomins is escalating worldwide, threatening equine health and highlighting the need for sustainable, ecology-based parasite control strategies. Chicory (Cichorium intybus, Puna II) has emerged as a promising antiparasitic forage, yet its broader effects on the equine holobiont, parasites, microbiota, and host physiology remain poorly understood. We conducted a 32-day longitudinal grazing trial in young horses to assess how chicory affects parasitological outcomes, gut microbial ecology, nemabiome composition, behaviour, and host physiological and immune responses. Twenty-six naturally infected Anglo-Arabian horses were monitored weekly, with 13 grazing a chicory-based sward and 13 grazing a permanent pasture. Clinical parameters, body weight, and serum biochemistry remained stable across treatments, indicating that chicory was well tolerated. Immune profiles showed limited variation, although IL-10 increased in chicory-fed horses, suggesting subtle immune modulation. Behavioural observations revealed no signs of discomfort and indicated slightly enhanced social interactions in the chicory group. Chicory grazing produced a marked reduction in cyathostomin egg excretion, accompanied by species-specific shifts in nemabiome composition. Several cyathostomin taxa, including Cylicocyclus ashworthi, C. leptostomus, and C. nassatus, declined in chicory-fed horses, whereas certain Cylicostephanus spp increased, indicating differential sensitivity rather than uniform suppression. Concomitantly, chicory induced profound ecological changes in the gut microbiota, including reduced alpha diversity, increased beta dispersion, and destabilised individual microbial trajectories. Several bacterial lineages, particularly Oscillospiraceae, Clostridiaceae, Lachnospiraceae, and Bacteroidales, were differentially enriched, reflecting a functional reorganisation of the intestinal ecosystem. Together, these findings demonstrate that chicory reduces parasite fitness, reshapes nemabiome composition, and alters gut microbial ecology while maintaining host physiological stability. Chicory thus emerges as a promising ecological tool for parasite control, capable of modulating the equine holobiont in ways that complement and potentially reduce reliance on conventional anthelmintic strategies. However, because its effects on gut microbial ecology remain uncertain, and may include shifts resembling dysbiosis, future studies are needed to monitor microbial dynamics more closely and clarify the long-term ecological consequences of chicory grazing. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/737212v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@7b7367org.highwire.dtl.DTLVardef@d5914aorg.highwire.dtl.DTLVardef@135ad65org.highwire.dtl.DTLVardef@10b0322_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2025

Temperate phages enhance host fitness via RNA-guided flagellar remodeling

Bacterial flagella drive motility and chemotaxis while also playing critical roles in host-pathogen interactions, as their oligomeric subunit, flagellin, is specifically recognized by the mammalian immune system and flagellotropic bacteriophages. We recently discovered a family of phage-encoded, RNA-guided transcription factors known as TldR that regulate flagellin expression. However, the biological significance for this regulation, particularly in the context of host fitness, remained unknown. By focusing on a human clinical Enterobacter isolate that encodes a Flagellin Remodeling prophage (FR{varphi}), here we show that FR{varphi} exploits the combined action of TldR and its flagellin isoform to dramatically alter the flagellar composition and phenotypic properties of its host. This transformation has striking biological consequences, enhancing bacterial motility and mammalian immune evasion, and structural studies by cryo-EM of host- and prophage-encoded filaments reveal distinct architectures underlying these physiological changes. Moreover, we find that FR{varphi} improves colonization in the murine gut, illustrating the beneficial effect of prophage-mediated flagellar remodeling in a host-associated environment. Remarkably, flagellin-regulating TldR homologs emerged multiple times independently, further highlighting the strong selective pressures that drove evolution of RNA-guided flagellin control. Collectively, our results reveal how RNA-guided transcription factors emerged in a parallel evolutionary path to CRISPR-Cas and were co-opted by phages to remodel the flagellar apparatus and enhance host fitness.

microbiology↗

bioRxiv2025

Methionine sulfoxide reductase B3 antioxidant activity is indispensable for mouse inner ear cuticular plate structure and hair bundle integrity

Methionine sulfoxide reductases (MSR) are enzymes responsible for catalyzing the reduction of methionine-sulfoxides. We previously demonstrated that variants in human MSRB3, a member of the MSR family, are associated with profound autosomal recessive prelingual non-syndromic hearing loss DFNB74. To better understand the role of MSRB3 in the auditory pathway, we generated a complete MsrB3 gene knock-out mouse model of human DFNB74 deafness. The MsrB3 deficient mouse showed profound hearing loss by postnatal day 16 (P16), which was accompanied by hair cell morphological abnormalities including altered stereocilia bundle shape and cuticular plate degeneration followed by hair cell apoptotic death. Although the absence of MSRB3 primarily affected the actin cytoskeleton, rootlets were present, and the expression and localization of major F-actin stereocilia-core proteins were unaltered. Biochemical assays demonstrated that wild-type MSRB3, but not MSRB3 harboring p.Cys89Gly, the same variant reported for human deafness DFNB74, can repolymerize oxidized actin. Consistent with these in vitro data, we observed a decreased ratio of reduced/total actin in the inner ears of Msrb3 knock-out mice. These data suggest a protective role of MSRB3 in the maintenance and maturation of stereocilia and hair cells, a conserved mechanism aimed at maintaining actin redox dynamics in these sensory cells.

genetics↗

bioRxiv2025

Cancer cells transfer invasive properties through microRNAs contained in collagen-tracks

Invasion is a prerequisite for metastasis formation. During tumor development, the extracellular matrix (ECM) is remodeled in part through overexpression of type I collagen, increasing tumor microenvironment stiffness, and facilitating cancer dissemination. During breast cancer cell migration, we observed membrane debris left behind, attached to the collagen fibrils, along the migration path. We named these structures collagen-tracks. These collagen-tracks can be deposited in 3D matrices in vitro and in vivo and their formation is stimulated by the interaction between the ECM and matrix receptors, such as the discoidin-domain receptor (DDR1). However, they are different from structures already known to be involved in cell-cell communication such as exosomes and migrasomes, due to their specific nucleic acid and protein contents. When deposited by highly invasive breast cancer cells, internalized collagen-tracks reprogram non-invasive cells into highly pro-metastatic ones by inducing a partial epithelial-mesenchymal transition (EMT). This cell reprogramming is dependent on specific miRNAs present in the collagen-tracks, that are necessary to promote ECM degradation, increase cell motility and invasiveness. Collagen-tracks thus represent a new form of cell-cell communication important for driving tumor invasion that could be targeted to prevent metastasis.

cell biology↗

bioRxiv2023

Emergence of RNA-guided transcription factors via domestication of transposon-encoded TnpB nucleases

Transposon-encoded tnpB genes encode RNA-guided DNA nucleases that promote their own selfish spread through targeted DNA cleavage and homologous recombination1-4. This widespread gene family was repeatedly domesticated over evolutionary timescales, leading to the emergence of diverse CRISPR-associated nucleases including Cas9 and Cas125,6. We set out to test the hypothesis that TnpB nucleases may have also been repurposed for novel, unexpected functions other than CRIS-PR-Cas. Here, using phylogenetics, structural predictions, comparative genomics, and functional assays, we uncover multiple instances of programmable transcription factors that we name TnpB-like nuclease-dead repressors (TldR). These proteins employ naturally occurring guide RNAs to specifically target conserved promoter regions of the genome, leading to potent gene repression in a mechanism akin to CRISPRi technologies invented by humans7. Focusing on a TldR clade found broadly in Enterobacteriaceae, we discover that bacteriophages exploit the combined action of TldR and an adjacently encoded phage gene to alter the expression and composition of the host flagellar assembly, a transformation with the potential to impact motility8, phage susceptibility9, and host immunity10. Col-lectively, this work showcases the diverse molecular innovations that were enabled through repeated exaptation of genes encoded by transposable elements, and reveals that RNA-guided transcription factors emerged long before the development of dCas9-based editors.

genetics↗

bioRxiv2023

Belt and braces: two escape ways to maintain the cassette reservoir of large chromosomal integrons

Integrons are adaptive devices that capture, stockpile, shuffle and express gene cassettes thereby sampling combinatorial phenotypic diversity. Some integrons called sedentary chromosomal integrons (SCIs) can be massive structures containing hundreds of cassettes. Since most of these cassettes are non-expressed, it is not clear how they remain stable over long evolutionary timescales. Recently, it was found that the experimental inversion of the SCI of Vibrio cholerae led to a dramatic increase of the cassette excision rate associated to a fitness defect. Here, we question the evolutionary sustainability of this apparently counter selected genetic context through experimental evolution. We find that the integrase is rapidly inactivated and that the inverted SCI can recover its original orientation by homologous recombination between two insertion sequences (ISs) present in the array. These two outcomes of SCI inversion restore the normal growth and prevent the loss of cassettes, enabling SCIs to retain their roles as reservoirs of functions. These results illustrate an interesting interplay between gene orientation, genome rearrangement, bacterial fitness and demonstrate how integrons can benefit from their embedded ISs.

genetics↗

bioRxiv2023

Regulating PCCA gene expression by modulation of pseudoexon splicing patterns to rescue enzyme activity in propionic acidemia

Pseudoexons are nonfunctional intronic sequences that can be activated by deep intronic sequence variation. Activation increases pseudoexon inclusion in mRNA and interferes with normal gene expression. The PCCA c.1285-1416A>G variation activates a pseudoexon and causes the severe metabolic disorder, propionic acidemia, by deficiency of the propionyl-CoA carboxylase enzyme encoded by PCCA and PCCB. We characterized this pathogenic pseudoexon activation event in detail and identified hnRNP A1 to be important for normal repression. The PCCA c.1285-1416A>G variation disrupts an hnRNP A1-binding splicing silencer and simultaneously creates a splicing enhancer. We demonstrate that blocking this region of regulation with splice-switching antisense oligonucleotides restores normal splicing and rescues enzyme activity in patient fibroblasts and in a cellular model created by CRISPR gene editing. The PCCA pseudoexon can be exploited as a gene-regulatory switch, as healthy tissues show relatively high levels of inclusion. By blocking inclusion of the non-activated wild type pseudoexon, we increase both PCCA and PCCB protein levels, which increases the activity of the heterododecameric enzyme. Surprisingly, we can increase enzyme activity from residual levels not only in patient fibroblasts harboring PCCA missense variants, but also those harboring PCCB missense variants. This could be a potential treatment strategy for propionic acidemia.

molecular biology↗

bioRxiv2022

A new route for integron cassette dissemination among bacterial genomes

Integrons are genetic elements involved in bacterial adaptation. They can capture, shuffle and express adaptive functions embedded in cassettes. These events are governed by the integron integrase through site-specific recombination between attC and attI integron sites. Here, we demonstrated that the integrase can efficiently catalyze insertion of cassettes in bacterial genomes, outside the att sites. We showed that, once inserted in genomes, cassettes can be expressed, if located near bacterial promoters, and can be excised at the insertion point and even outside, inducing chromosomal modifications in the latter case. Analysis of more than 5 x 105 independent insertion events revealed a very large genomic insertion landscape with recombination sites greatly different, in terms of sequence and structure, from classical att sites. We named these new sites attG. These results unveil a new efficient route for dissemination of adaptive functions and expand the role of integrons in bacterial evolution.

genetics↗

bioRxiv2022

Genetic drivers of chromosomal integron stability

Integrons are adaptive bacterial devices that rearrange promoter less gene cassettes into variable ordered arrays under stress conditions, to sample combinatorial phenotypic diversity. Chromosomal integrons often carry hundreds of silent gene cassettes, with integrase-mediated recombination leading to rampant DNA excision and integration, posing a potential threat to genome integrity. How this activity is regulated and controlled, particularly through selective pressures, to maintain such large cassette arrays is unknown. Here we show a key role of promoter-containing toxin-antitoxin (TA) cassettes as abortive systems that kill the cell when the overall cassette excision rate is too high. These results highlight the importance of TA cassettes regulating the cassette recombination dynamics and provide insight into the evolution and success of integrons in bacterial genomes. TeaserThe accumulation of cassette functions in integrons is ensured by toxin-antitoxin systems which kill the cell when the cassette excision rate is too high.

genetics↗

bioRxiv2020

Cassette recruitment in the chromosomal Integron of Vibrio cholerae

Integrons are genetic systems conferring to bacteria a rapid adaptation capability. The integron integrase is able to capture, stockpile and shuffle novel functions embedded in cassettes. This involves the recognition of both substrates, the attI site, and the cassette associated attC sites. Integrons can be sedentary and chromosomally located (SCI) or, carried by conjugative plasmids (Mobile Integron, MI), hence favoring their dissemination among bacteria. Here, for the first time, we investigate the cassette recruitment in the Vibrio cholerae SCI during conjugation and natural transformation. We demonstrated that horizontally transferred cassette can be recruited inside the chromosomal integron. The endogenous integrase expression is sufficiently triggered, after SOS response induction mediated by the entry of single-stranded cassettes during conjugation and natural transformation, to mediate significant cassette insertion. We demonstrate that the attIA insertion is preferential, despite the presence of 180 attC sites in the integron array. Thanks to the presence of a promoter in the attIA site vicinity, all these newly inserted cassettes are expressed and prone to adaptive selection. We also show that the RecA protein is critical for cassette recruitment in V. cholerae SCI but not in MIs. Moreover, a contrario to MIs, the V. cholerae SCI is not active in others bacterial hosts. MIs might have evolved from the SCIs by overcoming host factors, which would explain their large dissemination in bacteria and their role in the antibioresistance expansion.

molecular biology↗

bioRxiv2020

ATRX alteration contributes to tumor growth and immune escape in pleomorphic sarcomas

Whole genome and transcriptome sequencing of a cohort of 67 leiomyosarcomas revealed ATRX to be one of the most frequently mutated genes in leiomyosarcomas after TP53 and RB1. While its function is well described in the alternative lengthening of telomeres mechanism, we wondered whether its alteration could have complementary effects on sarcoma oncogenesis. ATRX alteration is associated with the down-expression of genes linked to differentiation in leiomyosarcomas, and to immunity in an additional cohort of 60 poorly differentiated sarcomas. In vitro and in vivo models showed that ATRX loss increases tumor growth rate and immune escape by decreasing the immunity load of active mast cells in sarcoma tumors. These data indicate that an alternative to unsuccessful targeting of the adaptive immune system in sarcoma could be to target the innate system. This might lead to a better outcome for sarcoma patients in terms of ATRX status.

cancer biology↗

bioRxiv2019

ExploreASL: an image processing pipeline for multi-center ASL perfusion MRI studies

Arterial spin labeling (ASL) has undergone significant development since its inception, with a focus on improving standardization and reproducibility of its acquisition and quantification. In a community-wide effort towards robust and reproducible clinical ASL image processing, we developed the software package ExploreASL, allowing standardized analyses across centers and scanners. The procedures used in ExploreASL capitalize on published image processing advancements and address the challenges of multi-center datasets with scanner-specific processing and artifact reduction to limit patient exclusion. ExploreASL is self-contained, written in MATLAB and based on Statistical Parameter Mapping (SPM) and runs on multiple operating systems. The toolbox adheres to previously defined international standards for data structure, provenance, and best analysis practice. ExploreASL was iteratively refined and tested in the analysis of >10,000 ASL scans using different pulse-sequences in a variety of clinical populations, resulting in four processing modules: Import, Structural, ASL, and Population that perform tasks, respectively, for data curation, structural and ASL image processing and quality control, and finally preparing the results for statistical analyses on both single-subject and group level. We illustrate ExploreASL processing results from three cohorts: perinatally HIV-infected children, healthy adults, and elderly at risk for neurodegenerative disease. We show the reproducibility for each cohort when processed at different centers with different operating systems and MATLAB versions, and its effects on the quantification of gray matter cerebral blood flow. ExploreASL facilitates the standardization of image processing and quality control, allowing the pooling of cohorts to increase statistical power and discover between-group perfusion differences. Ultimately, this workflow may advance ASL for wider adoption in clinical studies, trials, and practice.

neuroscience↗

bioRxiv2017

Development of an HPTLC method for determination of hypoglycin A in aqueous extracts of seedlings and samaras of Acer species

Hypoglycin A (HGA) is a toxin contained in seeds of the sycamore maple tree (Acer pseudoplatanus). Ingestion of this amino acid causes equine atypical myopathy (AM) in Europe. Another variety, A. negundo, is claimed to be present where AM cases were reported in the US. For unknown reasons, occurrence of this disease has increased. It is important to define environmental key factors that may influence toxicity of samaras from Acer species. In addition, the content of HGA in seedlings needs to be determined since AM outbreaks, during autumn period when the seeds fall but also during spring when seeds are germinating. The present study aims to validate a reliable method using high performance thin layer chromatography for determination and comparison of HGA in samaras and seedlings.\n\nThe working range of the method was between 20 g HGA to 408 g HGA per ml water, corresponding to 12 - 244 mg/kg fresh weight or 40 - 816 mg/kg dry weight, taking into account of an arbitrary average dry matter content of 30%. Instrumental limit of detection and limit of quantification were of 10 g HGA/ml and 20 g HGA/ml water, respectively. Instrumental precision was 4% (RSD on 20 repeated measurements) while instrumental accuracy ranged between 86% and 121% of expected value. The HGA recovery of the analytical method estimated from spiked samaras and seedlings samples ranged between 63 and 103%. The method was applied to 9 samples of samaras from Acer pseudoplatanus, A. platanoides and A. campestre and 5 seedlings samples from A. pseudoplatanus. The results confirm detection of HGA in samaras from A. pseudoplatanus and the absence of detection in samaras of other tested species. They also suggest that detected levels of HGA are highly variable. This confirmed the suitability of the method for HGA detection in samaras or seedling.

pharmacology and toxicology↗