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Michel, F.

Publications and source records attributed to Michel, F..

9 recordsLinked to original sources

Implementing considered elements of standardisation for Time Kill Curve experiments across multiple sites: A European collaboration perspective

SynopsisO_ST_ABSBackgroundC_ST_ABSThe main advantages of Time Kill Curves (TKCs) in antimicrobial drug development are the ability to track bacterial kill and regrowth over time and with varying drug concentrations. Whilst there are guideline documents in place, such as M26-A in CLSI, there remains scope for individual laboratory differences in practice. Here we evaluated several factors which potentially influenced data generated in TKCs. MethodsFirstly, E. coli ATCC 25922 was used to determine optimum sampling volume, culture vessel volume, CFU enumeration variance factors and static versus agitated cultures in a single laboratory. Secondly, a ring test comprising of TKCs was performed by six laboratories focusing on: standardised inoculum, static culture and two culture vessel sizes 10 mL and 200 {micro}L. Data analysis was performed to determine consistency within centres and between them. ResultsConsistently accurate inocula could be achieved by use of: larger sampling volumes between 100 {micro}L > 20 mL; larger culture vessels volumes (10 mL > 100 {micro}L) and higher inocula (10 8 > 1.5x10 5 CFU). Culture agitation during the TKC experiment resulted in reduced killing compared to static cultures. Reproducibility of TKCs was best between centres when they were performed in 10 mL culture vessels. There was more variability per site when performing TKC in 96 well trays. ConclusionsTechnical factors such as preparation of inocula, agitation, vessel size and enumeration of cultures are important variables in performing TKCs that need to be standardised in drug development programmes involving multiple laboratory centres.

microbiology↗

Is there a need to implement standardisation into in vitro antimicrobial evaluation systems? A European collaboration perspective

SynopsisO_ST_ABSBackgroundC_ST_ABSTime kill curve (TKC) assessments are an essential step in the study of an antimicrobials pharmacodynamic characteristics. Surprisingly TKCs have not be formally standardised, therefore there remain concerns that different testing centres/methodologies may produce different results. Six centres participating in Gram-negative-Antibiotics NOW (GNA-NOW) consortium measured a series of TKCs with meropenem against E. coli to establish: Same-day (SD) vs different-day (DD) replication per centre (intra-site), and centre to centre (inter-site) correlations. MethodsMeropenem was tested against three strains of E. coli (ATCC 25922; ESBL producer C1.55; OXA-48 producer C1.62). An inoculum of 1.5x106 CFU was specified with meropenem concentrations of x0, x1 to x16 MIC; and sampling assessment of bacterial density was determined at 0-24h. Experiments were performed in triplicate, aerobically at 37{degrees}C. Centre-specific methodology was collected. Meropenem, media, bacterial strains, were shipped from one central laboratory to participating laboratories. ANOVA and Friedman tests were used to assess SD, DD and between centre replications. ResultsAssessment of the methodologies between centres revealed many differences, including bacterial inoculum, meropenem preparation, volume of TKC vessel, vessel materials, agitation vs static cultures and sampling volumes. Intra-centre SD and DD analysis for all strains were generally associated with P>0.05 suggesting consistency. Inter-centre SD and DD comparisons resulted in P<0.05, indicating variable total bacterial load measurement between centres. ConclusionsTKC methodologies varied between different centres, and while intra-centre comparison of SD and DD were generally consistent, inter-centre comparisons were not. Standardisation of TKC methodologies is required.

microbiology↗

Retracing the evolution of a modern periplasmic binding protein

Investigating the evolution of structural features in modern multidomain proteins helps to understand their immense diversity and functional versatility. The class of periplasmic binding proteins (PBPs) offers an opportunity to interrogate one of the main processes driving diversification: the duplication and fusion of protein sequences to generate new architectures. The symmetry of their two-lobed topology, their mechanism of binding, and the organization of their operon structure led to the hypothesis that PBPs arose through a duplication and fusion event of a single common ancestor. To investigate this claim, we set out to reverse the evolutionary process and recreate the structural equivalent of a single-lobed progenitor using ribose-binding protein (RBP) as our model. We found that this modern PBP can be deconstructed into its lobes, producing two proteins that represent possible progenitor halves. The isolated halves of RBP are well folded and monomeric proteins, albeit with a lower thermostability, and do not retain the original binding function. However, the two entities readily form a heterodimer in vitro and in-cell. The X-ray structure of the heterodimer closely resembles the parental protein. Moreover, the binding function is fully regained upon formation of the heterodimer with a ligand affinity similar to that observed in the modern RBP. This highlights how a duplication event could have given rise to a stable and functional PBP-like fold and provides insights into how more complex functional structures can evolve from simpler molecular components.

biochemistry↗

Reconstruction of the molecular evolution of Usutu virus in Germany: Insights into virus emersion and circulation

Usutu virus (USUV) is a mosquito-borne flavivirus that is widely distributed in southern and central Europe. The zoonotic virus circulates primarily between birds and mosquitoes, can, however, in rare cases infect other mammals including humans. In the past USUV has been associated with mass mortalities in birds, formerly blackbirds and owls. Birds commonly succumb either due to the peracute nature of the infection or due to severe encephalitis. In Germany, USUV has spread rapidly since its first detection in 2010 in mosquitoes under the presence of susceptible host and vector species. Nonetheless, there is to date limited access to whole genome sequences resulting in the absence of in-depth phylogenetic and phylodynamic analyses. In this study, 118 wild and captive birds were screened using a nanopore sequencing platform with prior target enrichment via amplicons. Due to the high abundancy of Europe 3 and Africa 3 in Germany an ample quantity of associated whole genome sequences was generated and the most recent common ancestor could be determined for each lineage. The corresponding clock phylogeny revealed an introduction of USUV Europe 3 and Africa 3 into Germany three years prior to their first isolation in the avifauna in 2011 and 2014, respectively. Based on the clustering and temporal history of the lineages, evidence exists for the genetic evolution of USUV within Germany as well as new introductions thereof into the country.

evolutionary biology↗

Human USP18 is regulated by miRNAs via the 3'UTR, a sequence duplicated in lincRNA genes residing in chr22q11.21

Ubiquitin-specific peptidase 18 (USP18) acts as gatekeeper of type I interferon (IFN) responses by binding to the IFN receptor subunit IFNAR2 and preventing activation of the downstream JAK/STAT pathway. In any given cell type, the level of USP18 is a key determinant of the output of interferon-stimulated transcripts. How the baseline level of USP18 is finely tuned in different cell types remains ill defined. Here we explored post-transcriptional regulation of USP18 by microRNAs (miRNAs) and identified four miRNAs (miR-24-3p, miR-191-5p, miR-423-5p and miR-532-3p) that efficiently target USP18 through binding to the 3UTR. Among these, three miRNAs are particularly enriched in circulating monocytes which exhibit low baseline USP18. Intriguingly, the USP18 3UTR sequence is duplicated in human and chimpanzee genomes. In human, we found several copies of the 3UTR that are embedded in long intergenic non-coding (linc) RNA genes residing in chr22q11.21 and exhibiting a tissue-specific expression pattern. Interestingly, one of these lincRNAs (here named linc-UR-B1) is uniquely and highly expressed in testis. RNA-seq data analyses from testicular cell subsets revealed a positive correlation between linc-UR-B1 and USP18 expression in spermatocytes and spermatids. Overall, our findings uncover a set of miRNAs and lincRNAs, which may be part of a network evolved to fine-tune baseline USP18, particularly in cell types where IFN responsiveness needs to be tightly controlled. SIGNIFICANT STATEMENTUSP18 is a non-redundant negative feedback regulator of type I IFN signaling and a key determinant of cell responsiveness to IFN. How baseline USP18 is set in different human cell types is ill defined. We identified three microRNAs that restrain USP18 level notably in primary monocytes through binding the 3UTR. We found several copies of the USP18 3UTR embedded in long intergenic non-coding (linc) RNAs which reside in a complex region of human chromosome 22. These lincRNAs are expressed in a tissue-specific manner. We describe one lincRNA expressed only in testis, and most notably in germ cells. Correlative analyses suggest that microRNAs and lincRNAs may form a network controlling baseline USP18 and IFN responsiveness.

immunology↗

Treating Influenza and SARS-CoV-2 via mRNA-encoded Cas13a

Here, Cas13a has been used to target and mitigate influenza virus A (IAV) and SARS-CoV-2 using a synthetic mRNA-based platform. CRISPR RNAs (crRNA) against PB1 and highly conserved regions of PB2 were screened in conjunction with mRNA-encoded Cas13a. Screens were designed such that only guides that decreased influenza RNA levels in a Cas13-mediated fashion, were valid. Cas13a mRNA and validated guides, delivered post-infection, simulating treatment, were tested in combination and across multiplicities of infection. Their function was also characterized over time. Similar screens were performed for guides against SARS-CoV-2, yielding multiple guides that significantly impacted cytopathic effect. Last, the approach was utilized in vivo, demonstrating the ability to degrade influenza RNA in a mouse model of infection, using polymer-formulated, nebulizer-based mRNA delivery. Our findings demonstrate the applicability of Cas13a in mitigating respiratory infections both in vitro and in a mouse model, paving the way for future therapeutic use.

bioengineering↗

Two common disease-associated TYK2 variants impact exon splicing and TYK2 dosage

TYK2 belongs to the JAK protein tyrosine kinase family and mediates signaling of numerous antiviral and immunoregulatory cytokines (type I and type III IFNs, IL-10, IL-12, IL-22, IL-23) in immune and non-immune cells. After many years of genetic association studies, TYK2 is recognized as a susceptibility gene for some inflammatory and autoimmune diseases (AID). Seven TYK2 variants have been associated with AIDs in Europeans, and establishing their causality remains challenging. Previous work showed that a protective variant (P1104A) is hypomorphic and also a risk allele for mycobacterial infection. Here, we have studied two AID-associated common TYK2 variants: rs12720270 located in intron 7 and rs2304256, a non-synonymous variant in exon 8 that causes a valine to phenylalanine substitution (c.1084 G > T, Val362Phe). We found that this amino acid substitution does not alter TYK2 expression, catalytic activity or ability to relay signaling in EBV-B cell lines or in reconstituted TYK2-null cells. Based on in silico predictions that these variants may impact splicing of exon 8, we: i) analyzed TYK2 transcripts in genotyped EBV-B cells and in CRISPR/Cas9-edited cells, ii) measured splicing using minigene assays, and iii) performed eQTL (expression quantitative trait locus) analysis of TYK2 transcripts in primary monocytes and whole blood cells. Our results reveal that the two variants promote the inclusion of exon 8, which, we demonstrate, is essential for TYK2 binding to cognate receptors. In addition and in line with GTEx (Genetic Tissue Expression) data, our eQTL results show that rs2304256 mildly enhances TYK2 expression in whole blood. In all, these findings suggest that these TYK2 variants are not neutral but instead have a potential impact in AID.

immunology↗

Mature dentate granule cells show different intrinsic properties depending on the behavioural context of their activation

The dentate gyrus (DG) plays a crucial role in learning, memory and spatial navigation. Only a small fraction of mature dentate granule cells (mDGCs) is active during behavior, while the large majority remains silent. To date, the properties of this active subset of neurons remain poorly investigated. Using fosGFP transgenic mice, we show ex vivo that activated mDGCs, from mice maintained in their home cage, exhibit a marked lower intrinsic excitability compared to the non-activated cells. Remarkably, activated mDGCs, from mice trained in a virtual environment, are more excitable than those from mice maintained in their home cage. Therefore, we show that activated mDGCs display different intrinsic properties and excitable states depending on the context of their activation. We propose that these properties could constitute a neural signature of cell assemblies recruited in different behavioral contexts.

neuroscience↗

Compound signaling activates endogenous retroviruses by inducing enhancer and gene-neighborhood transcription

SummaryMultiple sclerosis (MS) is a neuroinflammatory and autoimmune disease, in which various immune cell types and autoreactive T cells exert a pathogenic activity. This disease is also associated with increased transcription of several endogenous retroviruses (HERVs) normally kept in check by heterochromatin. Here, we have uncovered an organic pollutant dieldrin that activates several HERVs associated with MS and allowing us to examine the mechanism of their activation. Dieldrin singles out by its ability to simultaneously activate the MAP kinase and the PI3K pathways, while also triggering calcium dependent peptidylarginine deiminase activity. It was this association of pathways that caused HERV activation, a phenomenon that was only part of more generally increased transcription of heterochromatic regions. The HERV transcripts were generally not polyadenylated. Some arose as a consequence of activation of HERV-based enhancers, while others were the result of unusually strong activation at some mostly transcription factor genes causing transcription to leak out of the HERV-free region that surrounds them. Altogether, our data emphasized the hazard associated with simultaneous activation of multiples signaling pathways by xenobiotics, while also providing a very general toolbox for the interpretation of HERV transcription.

molecular biology↗