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Laurent, F.

Publications and source records attributed to Laurent, F..

At least 19 recordsLinked to original sources

A novel ciprofloxacin analogue enables daptomycin-mediated killing of resistant Staphylococcus aureus by increasing septum formation

Quinolone antibiotics such as ciprofloxacin inhibit DNA gyrase, leading to DNA double-strand breaks that result in rapid bacterial killing and induction of the mutagenic SOS DNA repair response. By contrast, the ciprofloxacin analogue IMP-1700 inhibits ciprofloxacin-induced SOS, suggesting a novel mechanism of action. Here, we provide evidence that IMP-1700 targets the quinolone binding domain of DNA gyrase but triggers a significantly higher frequency of division septa in S. aureus compared with other DNA gyrase targeting antibiotics, including ciprofloxacin. In keeping with this finding, the lipopeptide antibiotic daptomycin, which targets the division septum, bound more strongly to IMP-1700-treated cells relative to S. aureus exposed to other DNA gyrase inhibitors, leading to increased bacterial killing. This finding extended to a panel of paired daptomycin susceptible and resistant clinical isolates. We conclude that the ciprofloxacin analogue IMP-1700 has distinct effects on the cell envelope of S. aureus, despite appearing to share the same target as the parent drug, which result in the resensitisation of daptomycin resistant bacteria to the lipopeptide antibiotic.

microbiology↗

Exploring Phage-Staphylococcus aureus Host Dynamics Through Innovative In Vitro Experiment and Pharmacokinetic/pharmacodynamic Modeling

BackgroundPhage therapy is a promising approach against multidrug-resistant Staphylococcus aureus, but its clinical development is limited by gaps in pharmacokinetic/pharmacodynamic (PK/PD) understanding, especially concerning phage self-replication and resistance dynamics. MethodsWe combined in vitro time-kill assays with PK/PD modeling to study three anti-staphylococcal phages (V1SA019, V1SA020, V1SA022) against two S. aureus strains (SH1000 and USA300). A system of differential equations captured the co-dynamics of susceptible, resistant and infected bacteria and free phages. Nonlinear mixed-effect modeling quantified parameter variability. Resistance emergence was monitored through phenotyping and whole-genome sequencing of resistant clones. ResultsPhage-bacteria interactions followed a predator-prey pattern, with early bacterial growth, rapid phage amplification, and subsequent bacterial collapse. However, resistant subpopulations emerged, regrew over time, in a multiplicity of infection (MOI) dependent way. The model accurately described bacterial and phage dynamics and estimated kinetic parameters including adsorption and burst size. Proliferation and inundation thresholds varied by strain and phage. All resistant clones harbored mutations in genes involved in teichoic acid biosynthesis, with associated growth defects. Simulations demonstrated that only phage doses exceeding both susceptible and resistant bacterial inundation thresholds fully suppressed regrowth. ConclusionThis study provides a quantitative framework for understanding phage-S. aureus co-dynamics and resistance emergence. It emphasizes the importance of considering both proliferation and inundation thresholds when designing phage dosing regimens. These findings inform the rational development of phage therapy and support translation toward in vivo and clinical applications.

pharmacology and toxicology↗

Staphylococcal Internalization into Osteoblasts: A Partially Conserved Mechanism Across the Genus

Staphylococcus aureus, considered as a major human pathogen, is associated with severe infections such as bacteremia, endocarditis, skin and soft tissue infections, and bone and joint infections. Virulence mechanisms, such as biofilm formation and invasion/internalization of/into host cells, support the pathogenicity of S. aureus as they enable it to evade from the immune system and most antibiotic treatments. S. aureus can be internalized into non-professional phagocytic cells like fibroblasts, epithelial cells, endothelial cells and osteoblasts. The main pathway of internalization of S. aureus is FnBP-fibronectin-5{beta}1 integrin dependent. Interestingly, S. pseudintermedius, S. delphini and S. argenteus are able to invade osteoblasts, depending on the presence of FnBP-like proteins such as Staphylococcus pseudintermedius surface proteins D and L (SpsD/L) or Staphylococcus delphini surface protein Y (SdsY). However, the internalization capacity and mechanism have been poorly investigated in other staphylococci species. Here, we investigated the internalization capacity of staphylococci into osteoblasts at the genus level and attempted to correlate it with the presence of FnBP-like proteins by combining fibronectin adhesion assays, infection of osteoblasts and genome analysis. Over the 53 Staphylococcus species tested, half of them exhibited high internalization into osteoblasts. We highlighted that the "FnBP-fibronectin-5{beta}1 integrin" dependent internalization pathway of S. aureus, is well-conserved in 27 Staphylococcus species. In silico analysis identified multiple FnBP-like proteins correlating with the highly internalized species and showing diversity in their sequence organization, likely due to multiple acquisitions of such encoding genes throughout Staphylococcus evolution. AUTHOR SUMMARYStaphylococcus aureus is a pathogenic bacterium that causes severe infections including bone and joint infections. It invades bone cells, such as osteoblasts, using the bacterial surface protein FnBP, which binds to fibronectin, an extracellular compound, which subsequently binds to 5{beta}1 integrin on the surface of osteoblasts. This cross-linking enables active internalization of S. aureus by the cells and potential intracellular persistence, which are responsible for the ability to induce staphylococcal chronic infections. While four species have been studied for their internalization into osteoblasts, a comprehensive genus-level investigation remains unexplored. Therefore, we investigated the conservation of this internalization capacity among the genus Staphylococcus, including a significant number of species of animal origin. Approximately half of the genus is capable of invading osteoblasts at varying levels via 5{beta}1 integrin. Additionally, homologous proteins to FnBP were identified in most highly internalized species, suggesting a similar pathway of cell internalization to that of S. aureus. Genomic analysis reveals these proteins were acquired multiple times during evolution, suggesting they provide an advantage for host infection. In the context of One Health approach and the increasing number of animal pathogens causing human infections, understanding staphylococcal pathogenicity will help anticipate the emergence of new infectious diseases.

microbiology↗

Competition between glycine and GABAA receptors for gephyrin controls their equilibrium populations at inhibitory synapses

Glycine and GABA receptors are ligand-gated chloride channels that mediate inhibitory neurotransmission throughout the central nervous system. The receptors co-localise widely at inhibitory synapses in the spinal cord and in the brainstem due to their interaction with an overlapping binding site of the synaptic scaffold protein gephyrin, pointing to a direct competition between the different receptor types. We have put this hypothesis to the test using single molecule approaches to measure receptor-gephyrin interactions in cells and in vitro. We explored the effects of receptor competition at inhibitory synapses in living neurons by measuring the change in the accumulation and effective stabilisation energy of glycine receptors in the presence of interfering GABA receptor complexes through single molecule tracking and diffusion analysis. Secondly, using molecular tweezers, we quantified the thermodynamic properties of receptor-gephyrin binding, demonstrating direct and reversible competition through the addition of interacting peptides in solution. The relatively low affinity of GABA receptor subunits for gephyrin compared to the glycine receptor raises interesting questions about the role of this competition in synaptic plasticity. We hypothesize that GABA and glycine receptor competition constitutes a molecular system designed to reconcile synapse stability and plasticity at mixed inhibitory synapses.

neuroscience↗

Acquisition of daptomycin resistance in patients results in decreased virulence in Drosophila

Staphylococcus aureus can acquire antimicrobial resistance which in turn may affect its pathogenic potential. Using a panel of paired clinical isolates collected before and after daptomycin resistance acquisition, most frequently through single mprF mutation, we show a relationship between increasing daptomycin minimum inhibitory concentration and reduced virulence in a Drosophila systemic infection model. Analysing toxin production, in vitro bacterial growth characteristics, and cell surface properties, we failed to link daptomycin resistance-related attenuated virulence to either reduced virulence factor production, reduced fitness or to any of the cell surface characteristics investigated. Competition assays in Drosophila also did not support any altered ability in immune evasion. Instead, using a panel of mutant flies defective for various immune components, we show that this daptomycin resistance-related attenuated virulence is mostly explained by greater susceptibility to activity of Drosophila prophenoloxidase, a tyrosinase involved in melanization, but not to antimicrobial peptides or to Bomanin antimicrobial effectors. Further investigation could not link daptomycin resistance-related attenuation of virulence to a differential susceptibility to reactive oxygen species or to quinones prominently associated with phenoloxidase bacterial-killing activity. Taken together, it appears that daptomycin resistance attenuates Staphylococcus aureus virulence through an enhanced sensitivity to phenoloxidase based on a complex mechanism. Our study provides new insights in the understanding of the crosstalk between antimicrobial resistance, escape from immune killing, and virulence. Author summaryAcquiring antimicrobial resistance can increase or decrease bacterial virulence. However, the mechanisms causing these resistance-virulence linked effects are unclear. Here, we bring new insights on the crosstalk between antimicrobial resistance and virulence. We characterized a panel of Staphylococcus aureus strains isolated from patients before and after resistance acquisition to the antibiotic daptomycin. Relative to the parental strain, resistant isolates most often varied by one single mutation, in a gene involved in the composition of the bacterial membrane, and these strains were much less virulent when fruit-flies were infected. Our results indicate that the difference of virulence is unrelated to changes in bacterial toxin production, bacterial growth, immune evasion or cell surface properties. Instead, resistant strains were more vulnerable to a host proenzyme involved in the antibacterial melanization response, an important response deployed throughout the arthropods. We predict that daptomycin resistance forces staphylococci to alter the composition of their cell surface. This alteration causes the bacteria to become more vulnerable to killing by melanization. Our results contribute to our understanding of the link between antimicrobial resistance and pathogenicity.

microbiology↗

Exploring the impact of digestive physicochemical parameters of adults and infants on the pathophysiology of Cryptosporidium parvum using the dynamic TIM-1 gastrointestinal model

BackgroundHuman cryptosporidiosis is distributed worldwide, and it is recognised as a leading cause of acute diarrhoea and death in infants in low- and middle-income countries. Besides immune status, the higher incidence and severity of this gastrointestinal disease in young children could also be attributed to the digestive environment. For instance, human gastrointestinal physiology undergoes significant changes with age, however the role this variability plays in Cryptosporidium parvum pathogenesis is not known. In this study, we analysed for the first time the impact of digestive physicochemical parameters on C. parvum infection in a human and age-dependent context using a dynamic in vitro gastrointestinal model. ResultsOur results showed that the parasite excystation, releasing sporozoites from oocysts, occurs in the duodenum compartment after one hour of digestion in both child (from 6 months to 2 years) and adult experimental conditions. In the child small intestine, slightly less sporozoites were released from excystation compared to adult, however they exhibited a higher luciferase activity, suggesting a better physiological state. Sporozoites collected from the child jejunum compartment also showed a higher ability to invade human intestinal epithelial cells compared to the adult condition. Global analysis of the parasite transcriptome through RNA-sequencing demonstrated a more pronounced modulation in ileal effluents compared to gastric ones, albeit showing less susceptibility to age-related digestive condition. Further analysis of gene expression and enriched pathways showed that oocysts are highly active in protein synthesis in the stomach compartment, whereas sporozoites released in the ileum showed downregulation of glycolysis as well as strong modulation of genes potentially related to gliding motility and secreted effectors. ConclusionsDigestion in a sophisticated in vitro gastrointestinal model revealed that invasive sporozoite stages are released in the small intestine, and are highly abundant and active in the ileum compartment, supporting reported C. parvum tissue tropism. Our comparative analysis suggests that physicochemical parameters encountered in the child digestive environment can influence the amount, physiological state and possibly invasiveness of sporozoites released in the small intestine, thus potentially contributing to the higher susceptibility of young individuals to cryptosporidiosis.

microbiology↗

Statistical signature of subtle behavioural changes inlarge-scale behavioural assays

The central nervous system can generate various behaviours, including motor responses, which we can observe through video recordings. Recent advancements in genetics, automated behavioural acquisition at scale, and machine learning enable us to link behaviours to their underlying neural mechanisms causally. Moreover, in some animals, such as the Drosophila larva, this mapping is possible at unprecedented scales of millions of animals and single neurons, allowing us to identify the neural circuits generating particular behaviours. These high-throughput screening efforts are invaluable, linking the activation or suppression of specific neurons to behavioural patterns in millions of animals. This provides a rich dataset to explore how diverse nervous system responses can be to the same stimuli. However, challenges remain in identifying subtle behaviours from these large datasets, including immediate and delayed responses to neural activation or suppression, and understanding these behaviours on a large scale. We introduce several statistically robust methods for analyzing behavioural data in response to these challenges: 1) A generative physical model that regularizes the inference of larval shapes across the entire dataset. 2) An unsupervised kernel-based method for statistical testing in learned behavioural spaces aimed at detecting subtle deviations in behaviour. 3) A generative model for larval behavioural sequences, providing a benchmark for identifying complex behavioural changes. 4) A comprehensive analysis technique using suffix trees to categorize genetic lines into clusters based on common action sequences. We showcase these methodologies through a behavioural screen focused on responses to an air puff, analyzing data from 280,716 larvae across 568 genetic lines. Author SummaryThere is a significant gap in understanding between the architecture of neural circuits and the mechanisms of action selection and behaviour generation.Drosophila larvae have emerged as an ideal platform for simultaneously probing behaviour and the underlying neuronal computation [1]. Modern genetic tools allow efficient activation or silencing of individual and small groups of neurons. Combining these techniques with standardized stimuli over thousands of individuals makes it possible to relate neurons to behaviour causally. However, extracting these relationships from massive and noisy recordings requires the development of new statistically robust approaches. We introduce a suite of statistical methods that utilize individual behavioural data and the overarching structure of the behavioural screen to deduce subtle behavioural changes from raw data. Given our studys extensive number of larvae, addressing and preempting potential challenges in body shape recognition is critical for enhancing behaviour detection. To this end, we have adopted a physics-informed inference model. Our first group of techniques enables robust statistical analysis within a learned continuous behaviour latent space, facilitating the detection of subtle behavioural shifts relative to reference genetic lines. A second array of methods probes for subtle variations in action sequences by comparing them to a bespoke generative model. Together, these strategies have enabled us to construct representations of behavioural patterns specific to a lineage and identify a roster of "hit" neurons with the potential to influence behaviour subtly.

neuroscience↗

Inositol pyrophosphate catabolism by three families of phosphatases controls plant growth and development

Inositol pyrophosphates (PP-InsPs) are nutrient messengers whose cellular concentration must be tightly regulated. Diphosphoinositol pentakisphosphate kinases (PPIP5Ks) generate the active signaling molecule 1,5-InsP8. PPIP5Ks contain additional phosphatase domains involved in PP-InsP catabolism. Plant and Fungi Atypical Dual Specificity Phosphatases (PFA-DSPs) and NUDIX phosphatases (NUDTs) also hydrolyze PP-InsPs. Here we dissect the relative contributions of the three different phosphatase families to plant PP-InsP catabolism and nutrient signaling. We report the biochemical characterization of inositol pyrophosphate phosphatases from Arabidopsis and Marchantia polymorpha. Overexpression of different PFA-DSP and NUDT enzymes affects PP-InsP levels and leads to stunted growth phenotypes in Arabidopsis. nudt17/18/21 knock-out mutants have altered PP-InsP pools and gene expression patterns, but no apparent growth defects. In contrast, Marchantia polymorpha Mppfa-dsp1ge, Mpnudt1ge and Mpvip1ge mutants display severe growth and developmental phenotypes associated with changes in cellular PP-InsP levels. Analysis of Mppfa-dsp1geand Mpvip1ge supports a role for PP-InsPs in Marchantia phosphate signaling, and additional functions in nitrate homeostasis and cell wall biogenesis. Simultaneous removal of two phosphatase activities enhances the observed growth phenotypes. Taken together, PPIP5K, PFA-DSP and NUDT inositol pyrophosphate phosphatases play important roles in growth and development by collectively shaping plant PP-InsP pools. Author summaryOrganisms must maintain adequate levels of nutrients in their cells and tissues. One such nutrient is phosphorus, an essential building block of cell membranes, nucleic acids and energy metabolites. Plants take up phosphorus in the form of inorganic phosphate and require sufficient cellular phosphate levels to support their growth and development. It has been shown that plants and other eukaryotic organisms "measure" cellular phosphate levels using inositol pyrophosphate signaling molecules. The concentration of inositol pyrophosphates serves as a proxy for the cellular concentration of inorganic phosphate, and therefore inositol pyrophosphate synthesis and degradation must be tightly regulated. Here, we report that three different families of enzymes contribute to the degradation of inositol pyrophosphates in plants. The different phosphatases together shape cellular inositol pyrophosphate pools and thereby affect inorganic phosphate levels. Loss-of-function mutants of the different enzymes display additional defects in nitrate levels and cell wall architecture, suggesting that inositol pyrophosphates regulate cellular processes beyond inorganic phosphate homeostasis.

plant biology↗

LarvaTagger: Manual and automatic tagging of Drosophila larval behaviour

MotivationAs more behavioural assays are carried out in large-scale experiments on Drosophila larvae, the definitions of the archetypal actions of a larva are regularly refined. In addition, video recording and tracking technologies constantly evolve. Consequently, automatic tagging tools for Drosophila larval behaviour must be retrained to learn new representations from new data. However, existing tools cannot transfer knowledge from large amounts of previously accumulated data. We introduce LarvaTagger, a piece of software that combines a pre-trained deep neural network, providing a continuous latent representation of larva actions for stereotypical behaviour identification, with a graphical user interface to manually tag the behaviour and train new automatic taggers with the updated ground truth. ResultsWe reproduced results from an automatic tagger with high accuracy, and we demonstrated that pre-training on large databases accelerates the training of a new tagger, achieving similar prediction accuracy using less data. AvailabilityAll the code is free and open source. Docker images are also available. See git-lab.pasteur.fr/nyx/LarvaTagger.jl.

bioinformatics↗

Pervasive sublethal effects of agrochemicals as contributing factors to insect decline

Insect biomass is declining across the globe at an alarming rate. Climate change and the widespread use of pesticides have been hypothesized as two underlying drivers. However, the lack of systematic experimental studies across chemicals and species limits our causal understanding of this problem. Here, we employed a chemical library encompassing 1024 different molecules--including insecticides, herbicides, fungicides, and plant growth inhibitors --to investigate how insect populations are affected by varying concentrations of pesticides, focusing on sublethal doses. Using a controlled laboratory pipeline for Drosophila melanogaster, we found that 57% of these chemicals affect the behavior of larvae at sublethal concentrations, and an even higher proportion compromises long-term survivability after acute exposure. Consistent with these results, we observed that exposure to chemicals at doses orders of magnitude below lethality induced widespread phosphorylation changes across the larval proteome. The effects of agrochemicals were amplified when the ambient temperature was increased by four degrees. We also tested the synergistic effects of multiple chemicals at doses found widely in nature and observed fitness-reducing changes in larval developmental time, behavior, and reproduction. Finally, we expanded our investigation to additional fly species, mosquitos, and butterflies and detected similar behavioral alterations triggered by pesticides at sublethal concentrations. Our results provide experimental evidence that strongly suggests sublethal doses of agrochemicals coupled with changes in environmental temperatures are contributing to the global decline in insect populations. We anticipate that our assays can contribute to improving chemical safety assessment, better protect the environment, secure food supplies, and safeguard animal and human health, as well as understand our rapidly changing world.

ecology↗

Staphylococcus aureus can use an alternative pathway to be internalized by osteoblasts in absence of β1 integrins

Staphylococcus aureus main internalization mechanism in osteoblasts relies on a tripartite interaction between bacterial fibronectin-binding proteins, extracellular matrix soluble fibronectin, and osteoblasts {beta}1 integrins. Caveolins, and particularly caveolin-1, have shown to limit the plasma membrane microdomain mobility, and consequently reduce the uptake of S. aureus in keratinocytes. In this study, we aimed to deepen our understanding of the molecular mechanisms underlying S. aureus internalization in osteoblasts. Mechanistically, S. aureus internalization requires endosomal recycling {beta}1 integrins as well as downstream effectors such as Src, Rac1, and PAK1. Surprisingly, in {beta}1 integrin deficient osteoblasts, S. aureus internalization is restored when Caveolin-1 is absent and requires v{beta}3/v{beta}5 integrins as backup fibronectin receptors. Altogether, our data support that {beta}1 integrins regulate the level of detergent-resistant membrane at the plasma membrane in a an endosomal and Caveolin-1 dependent manner. SUMMARY STATEMENTStaphylococcus aureus can be internalized by osteoblasts via a different mechanism than the main 5{beta}1/fibronectin/fibronectin-binding protein that likely involves v{beta}3 or v{beta}5 integrin.

cell biology↗

Analysis of in-patient evolution of Escherichia coli reveals potential links to relapse of bone and joint infections

Bone and joint infections (BJIs) are difficult to treat and affect a growing number of patients, in which relapses are observed in 10-20% of the case. These relapses, which call for prolonged antibiotic treatment and increase the risk of emergence of resistance, may originate from ill understood adaptation of the pathogen to the host. Here, we studied three pairs of Escherichia coli strains corresponding to three cases of BJIs and their relapse to better understand in-patient adaptation. Whole genome comparison presented evidence for positive selection with prevalence of non-synonymous and loss of function mutations. Phenotypic characterization showed that biofilm formation capacity was not modified, contrary to what is usually described in such relapse cases. Although virulence was not modified, we identified the loss of two virulence factors (namely an AFA afimbrial adhesin and a YadA-like adhesin) contributing to immune system evasion in one of the studied relapse strain. Other selected strategies likely helped the relapse strains to outcompete competitors through global growth optimization and colicin production. This work highlights the variety of strategies allowing in-patient adaptation in BJIs.

microbiology↗

YAP promotes cell-autonomous immune responses to tackle intracellular Staphylococcus aureus in vitro

Transcriptional cofactors YAP/TAZ have recently been found to support autophagy and inflammation, which are part of cell autonomous immunity and are critical in antibacterial defense. Here, we studied the role of YAP against Staphylococcus aureus using CRISPR/Cas9-mutated HEK293 cells and a primary cell-based organoid model. We found that S. aureus infection increases YAP transcriptional activity, which is required to reduce intracellular S. aureus replication. A 770-gene targeted transcriptomic analysis revealed that YAP upregulates genes involved in autophagy/lysosome and inflammation pathways in both infected and uninfected conditions. The YAP/TEAD transcriptional activity promotes autophagic flux and lysosomal acidification, which are important for defense against intracellular S. aureus. Furthermore, the staphylococcal toxin C3 exoenzyme EDIN-B was found effective in preventing YAP-mediated cell-autonomous immune response. This study provides new insights on the anti-S. aureus activity of YAP, which could be conserved for defense against other intracellular bacteria. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/492111v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@6158f1org.highwire.dtl.DTLVardef@1164aedorg.highwire.dtl.DTLVardef@911558org.highwire.dtl.DTLVardef@11044b2_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

A maximum mean discrepancy approach reveals subtle changes in α-synuclein dynamics

Numerous models have been developed to account for the complex properties of the random walks of biomolecules. However, when analysing experimental data, conditions are rarely met to ensure model identification. The dynamics may simultaneously be influenced by spatial and temporal heterogeneities of the environment, out-of-equilibrium fluxes and conformal changes of the tracked molecules. Recorded trajectories are often too short to reliably discern such multi-scale dynamics, which precludes unambiguous assessment of the type of random walk and its parameters. Furthermore, the motion of biomolecules may not be well described by a single, canonical random walk model. Here, we develop a methodology for comparing biomolecule dynamics observed in different experimental conditions without beforehand identifying the model generating the recorded random walks. We introduce a two-step statistical testing scheme. We first use simulation-based inference to train a graph neural network to learn a fixed-length latent representation of recorded random walks. As a second step, we use a maximum mean discrepancy statistical test on the vectors of learnt features to compare biological conditions. This procedure allows us to characterise sets of random walks regardless of their generating models. We initially tested our approach on numerical trajectories. We then demonstrated its ability to detect changes in -synuclein dynamics at synapses in cultured cortical neurons in response to membrane depolarisation. Using our methodology, we identify the domains in the latent space where the variations between conditions are the most significant, which provides a way of interpreting the detected differences in terms of single trajectory characteristics. Our data show that changes in -synuclein dynamics between the chosen conditions are largely driven by increased protein mobility in the depolarised state. Author summaryThe continuous refinement of methods for single molecule tracking in live cells advance our understanding of how biomolecules move inside cells. Analysing the trajectories of single molecules is complicated by their highly erratic and noisy nature and thus requires the use of statistical models of their motion. However, it is often not possible to unambiguously determine a model from a set of short and noisy trajectories. Furthermore, the heterogeneous nature of the cellular environment means that the molecules motion is often not properly described by a single model. In this paper we develop a new statistical testing scheme to detect changes in biomolecule dynamics within organelles without needing to identify a model of their motion. We train a graph neural network on large-scale simulations of random walks to learn a latent representation that captures relevant physical properties of a trajectory. We use a kernel-based statistical test within that latent space to compare the properties of two sets of trajectories recorded under different biological conditions. We apply our approach to detect differences in the dynamics of -synuclein, a presynaptic protein, in axons and boutons during synaptic stimulation. This represents an important step towards automated single-molecule-based read-out of pharmacological action.

biophysics↗

SMAD4 target genes are part of a transcriptional network that integrates the response to BMP and SHH signaling during early limb bud patterning

SMAD4 regulates gene expression in response to BMP and TGF{beta} signal transduction and is required for diverse morphogenetic processes, but its target genes have remained largely elusive. Here, we use an epitope-tagged Smad4 allele for ChIP-seq analysis together with transcriptome analysis of wild-type and mouse forelimb buds lacking Smad4 in the mesenchyme. This analysis identifies the SMAD4 target genes during establishment of the feedback signaling system and establishes that SMAD4 predominantly mediates BMP signal-transduction during early limb bud development. Unexpectedly, the initial analysis reveals that the expression of cholesterol biosynthesis enzymes is precociously down-regulated and intracellular cholesterol levels reduced in Smad4-deficient limb bud mesenchymal progenitors. The SMAD4 target GRNs includes genes, whose expression in the anterior limb bud is up-regulated by interactions of SMAD4 complexes with enhancers active in the anterior mesenchyme. This reveals a predominant function of SMAD4 in up-regulating target gene expression in the anterior limb bud mesenchyme. Analysis of differentially expressed genes that are shared between Smad4- and Shh-deficient limb buds corroborates the positive role of SMAD4 in transcriptional regulation of anterior genes and reveals a repressive effect on posterior genes that are positively regulated by SHH signaling. This analysis uncovers the overall opposing effects of SMAD4-mediated BMP and SHH signalling on transcriptional regulation during early limb bud development. In summary, this analysis indicates that during early digit patterning and limb bud outgrowth, the anterior/proximal and proximo/distal expression dynamics of co-regulated genes are controlled by distinct and contrasting trans-regulatory inputs from SHH and SMAD4-mediated BMP signal transduction.

developmental biology↗

Potential role of Mercury pollutants in the success of Methicillin-Resistant Staphylococcus aureus USA300 in Latin America

Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) lineage known as USA300-North American (NA) has become highly prevalent in North America whilst a USA300 variant known as USA300-LV, harboring a mercury resistance element (COMER), has become dominant in South America. We investigated whether mercury pollution, which is common in South America notably because of artisanal gold mining, may explain the local dominance pattern of USA300-LV. Density-based estimation of epidemic success in 250 genomes of the ST8 lineage revealed that the acquisition of COMER in USA300 progenitors increased success in South American countries but decreased success elsewhere. The fitness of USA300-LV was impaired in vitro compared with USA300-NA, but the addition of sub-inhibitory concentration of mercury provided a strong fitness advantage to USA300-LV and triggered an overexpression of major virulence factors. The success of USA300-LV in South America may result from low-level mercury exposure selecting resistant and virulent strains.

microbiology↗

Metapopulation ecology links antibiotic resistance, consumption and patient transfers in a network of hospital wards

Antimicrobial resistance (AMR) is a global threat. A better understanding of how antibiotic use and between ward patient transfers (or connectivity) impact hospital AMR can help optimize antibiotic stewardship and infection control strategies. Here, we used metapopulation ecology to explain variations in infection incidences of 17 ESKAPE pathogen variants in a network of 357 hospital wards. Multivariate models identified the strongest influence of ward-level antibiotic use on more resistant variants, and of connectivity on nosocomial species and carbapenem-resistant variants. Pairwise associations between infection incidence and the consumption of specific antibiotics were significantly stronger when such associations represented a priori AMR selection, suggesting that AMR evolves within the network. Piperacillin-tazobactam consumption was the strongest predictor of the cumulative incidence of infections resistant to empirical sepsis therapy. Our data establish that both antibiotic use and connectivity measurably influence hospital AMR and provide a ranking of key antibiotics by their impact on AMR.

ecology↗

Novel Staphylococcal Cassette Chromosome composite island (SCC-CI) with a new subtype of SCCmecVI cassette found in ST5 MRSA in France

An emergent kanamycin-susceptible ST5-MRSA lineage has been identified in France. Whole genome sequencing revealed a 40 kb SCC composite island with a mosaic structure including 3 SCC elements: a {Psi}SCCcop/ars, a SCCLim88A with a ccrC recombinase, and a novel subtype of SCCmec type VI (VIb). This mosaic structure suggests a high recombination rate of SCC elements from distinct staphylococci species.

microbiology↗