Biology subjects

Bridoux, L.

Publications and source records attributed to Bridoux, L..

6 recordsLinked to original sources

bioRxiv2024

In vitro biofilms of Clostridioides difficile undomesticated strains: Morphology and properties according to strain diversity

Clostridioides difficile is a Gram-positive, spore-forming, obligate anaerobe and an entero-pathogen representing a One Health problem. C. difficile infections are difficult to treat and recurrences frequent. C. difficile biofilms may play a role in persistence. We studied the biofilms formed in vitro by a collection of C. difficile undomesticated strains (n=27, 20 toxigenic and 7 non-toxigenic) of 11 PCR-ribotypes (WRT) and isolated from equids. After growth in rich BHIS medium supplemented with glucose for 48h, the biomass of biofilms stained by crystal violet, i. e. adhesive to the surface, was measured, while intact biofilms were observed in situ, by confocal laser scanning microscopy, to determine their total biovolume and 3D morphology. All biofilms were relatively similar, even though adhesive, stained biofilms of non-toxigenic strains of ribotype 009 significantly displayed highest biomass. These results suggested that strains of ribotype 009 were able to form a highly cohesive and polystyrene-adhesive biofilm than any other strains. 8 common, representative ribotypes in equids, including 6 clinically important ribotypes in humans, were then selected and one strain chosen for each of them. Their biofilms and planktonic cultures grown under the same conditions were compared for sporulation, toxin production and susceptibility to vancomycin at a highly inhibitory concentration (8 MIC). In both the biofilm and planktonic culture of all selected strains, sporulation was low and toxin production undetectable. The addition of vancomycin at T0=24h followed by a 24 hours exposure barely reduced the viability of neither planktonic cultures nor biofilms of any strains. On the contrary, for all selected strains, addition of vancomycin at T0=6h followed by a 24 hours exposure significantly and more efficiently reduced the viability of planktonic cultures than that of biofilms, which was not decreased at all in the case of strains of ribotype WRT 005, 009 and 035. The biofilms of these selected strains of eight ribotypes, compared to their planktonic cultures, therefore showed a higher tolerance to vancomycin, suggesting that they could play a role in persistence.

microbiology↗

bioRxiv2024

Clostridioides difficile in Equidae necropsied in Normandie, France from 2019 to 2021: common carriage of toxigenic strains and virulence of emerging ribotype 017

Clostridioides difficile is an anaerobic, spore-forming enteropathogen, which is much more extensively studied in humans than animals, despite growing evidence supporting its importance in One Health. We evaluated C. difficile occurrence, diversity, circulation and virulence in French Equidae (n=100) after their necropsy in northwestern France (Normandy), from 2019 to 2021. We systematically recovered all cecal contents and any watery (possibly diarrheal) intestinal contents. We isolated C. difficile strains, determined their toxin gene profile by PCR and established their PCR-ribotype according to the WEBRIBO database. We also performed free toxin detection. Twenty-seven Equidae were positive for C. difficile and twenty had a toxigenic strain, including one animal also colonized by a non-toxigenic strain. Toxigenic isolates belonged to eight common ribotypes: i) 078 and 126 (tcdA+ tcdB+ cdt+ according to multiplex PCR, i.e. able to produce toxin A, toxin B and binary toxin), ii) 005, 012, 020, AI-53 and FR227 (tcdA+ tcdB+), and iii) 017 (tcdB+). Non-toxigenic isolates were of ribotypes 009, 035 and 439. Ribotypes 017 and 009 were predominant (n=5). In two cases, Equidae of the same premises shared the same ribotype, either 020 or 009. Free toxins were detected in four animals: they displayed signs of diarrhea and a C. difficile of ribotype 126 (n=1) or 017 (n=3) as the only detected enteropathogen, suggesting a C. difficile infection (CDI). Three of them had received antibiotics. Two had died from an entero-toxic infection, for which C. difficile ribotype 017 was the only identified cause. French Equidae were found to display common pathogenic C. difficile, and ribotype 017 was highly virulent. These findings are of concern from a One Health perspective. ImportanceC. difficile, a major enteropathogen widely disseminated in the environment, is a One Health issue. Animals are raising concern as human contamination sources. Equidae are in close contact with humans and also develop post-antibiotic and healthcare-associated CDIs. The systematic survey of Equidae necropsied from 2019 to 2021 in the leading region for horse breeding in France, revealed that 20% harbored pathogenic strains. These belonged to clinically important ribotypes, raising the possibility of cross-species, possibly zoonotic transmission. Free toxins, which are rarely tested in animals, were detected in four animals with signs of diarrhea and a toxigenic C. difficile as the only identified enteropathogen, suggesting CDI. In two of them, C. difficile ribotype 017 was the only identified cause of entero-toxic disease and death. French Equidae could play a role in the dissemination of pathogenic C. difficile and notably ribotype 017. They should be surveilled carefully from a One Health perspective.

microbiology↗

bioRxiv2024

The evolutionary ancient MEIS transcription factors actuate lineage-specific transcription to establish cardiac fate

Control of gene expression is commonly mediated by distinct combinations of transcription factors (TFs). This cooperative action allows multiple biological signals to be integrated at specific regulatory elements, resulting in highly specific gene expression patterns in space and time. It is unclear whether combinatorial binding is also necessary to bring together TFs with distinct biochemical functions, which collaborate to effectively recruit and activate RNA polymerase II. Using a cardiac differentiation model, we find that the largely ubiquitous, evolutionary ancient homeodomain proteins MEIS are essential for activating a cardiac-specific gene expression program. MEIS TFs act as actuators, fully activating transcriptional programs selected by lineage-restricted TFs to drive the dynamic progression of cardiac differentiation. Combinatorial binding of MEIS with lineage-enriched TFs, GATA and HOX, provides selectivity, guiding MEIS to function at cardiac-specific enhancers. In turn, MEIS TFs promote accumulation of the methyltransferase KMT2D to initiate lineage-specific enhancer commissioning. MEIS combinatorial binding dynamics, dictated by the changing dosage of its partners, drive cells into progressive stages of cardiac differentiation. Our results uncover tissue-specific transcriptional activation as the result of ubiquitous actuator TFs harnessing general transcriptional coactivators at tissue-specific enhancers, to which they are directed by binding with lineage- and domain-specific TFs.

developmental biology↗

bioRxiv2024

Waves of light at the bottom of the ocean: insights into the luminous systems of three Pennatuloidea (Anthozoa)

Bioluminescence is the production of visible light by living organisms. It occurs through the oxidation of a luciferin substrate catalysed by luciferase enzymes. Auxiliary proteins, such as fluorescent proteins and luciferin-binding proteins, can modify the light emitted wavelength or stabilize reactive luciferin molecules, respectively. Additionally, calcium ions are crucial for the luminescence across various species. Despite the large phylogenetic distribution of bioluminescent organisms, only a few systems have been comprehensively studied. Notably, cnidarian species of the Renilla genus utilize a coelenterazine-dependent luciferase, a calcium-dependent coelenterazine-binding protein and a green fluorescent protein. We investigated the bioluminescence of three sea pen species: Pennatula phosphorea, Anthoptilum murrayi and Funiculina quadrangularis (Pennatuloidea, Anthozoa). Their light-emission spectra reveal peaks at 510, 513 and 485 nm, respectively. A coelenterazine-based reaction was demonstrated in all three species. Using transcriptome analyses, we identified predicted transcripts coding for luciferases, green fluorescent proteins and coelenterazine-binding proteins for P. phosphorea and A. murrayi. Immunodetection confirmed the expression of luciferase in P. phosphorea and F. quadrangularis. We also expressed recombinant luciferase of A. murrayi, confirming its activity. We highlighted the role of calcium ions in bioluminescence, possibly associated with the mechanism of substrate release at the level of coelenterazine-binding proteins. The study proposes a model for anthozoan bioluminescence, offering new avenues for future ecological and functional research on these luminous organisms.

zoology↗

bioRxiv2019

HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation

Gene expression programs determine cell fate in embryonic development and their dysregulation results in disease. Transcription factors (TFs) control gene expression by binding to enhancers, but how TFs select and activate their target enhancers is still unclear. HOX TFs share conserved homeodomains with highly similar sequence recognition properties, yet they impart the identity of different animal body parts. To understand how HOX TFs control their specific transcriptional programs in vivo, we compared HOXA2 and HOXA3 binding profiles in the mouse embryo. HOXA2 and HOXA3 directly cooperate with TALE TFs and selectively target different subsets of a broad TALE chromatin platform. Binding of HOX and tissue-specific TFs convert low affinity TALE binding into high confidence, tissue-specific binding events, which bear the mark of active enhancers. We propose that HOX paralogs, alone and in combination with tissue-specific TFs, generate tissue-specific transcriptional outputs by modulating the activity of TALE TFs at selected enhancers.

developmental biology↗

bioRxiv2019

Uncovering tissue-specific binding features from differential deep learning

MotivationTranscription factors (TFs) can bind DNA in a cooperative manner, enabling a mutual increase in occupancy. Through this type of interaction, alternative binding sites can be preferentially bound in different tissues to regulate tissue-specific expression programmes. Recently, deep learning models have become state-of-the-art in various pattern analysis tasks, including applications in the field of genomics. We therefore investigate the application of convolutional neural network (CNN) models to the discovery of sequence features determining cooperative and differential TF binding across tissues. ResultsWe analyse ChIP-seq data from MEIS, TFs which are broadly expressed across mouse branchial arches, and HOXA2, which is expressed in the second and more posterior branchial arches. By developing models predictive of MEIS differential binding in all three tissues we are able to accurately predict HOXA2 co-binding sites. We evaluate transfer-like and multitask approaches to regularising the high-dimensional classification task with a larger regression dataset, allowing for creation of deeper and more accurate models. We test the performance of perturbation and gradient-based attribution methods in identifying the HOXA2 sites from differential MEIS data. Our results show that deep regularised models significantly outperform shallow CNNs as well as k-mer methods in the discovery of tissue-specific sites bound in vivo. AvailabilityFor implementation and models please visit https://doi.org/10.5281/zenodo.2635463.

bioinformatics↗