Biology subjects

Simon, P.

Publications and source records attributed to Simon, P..

7 recordsLinked to original sources

bioRxiv2026

Selective inhibition of anaerobic ubiquinone biosynthesis in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a metabolically versatile opportunistic pathogen capable of adapting to diverse and challenging environments, including the oxygen- and nutrient-limited conditions encountered during chronic infections. Its ability to utilize a broad range of carbon sources and to switch from aerobic to anaerobic respiration contributes to its persistence within the host and its resilience to therapeutic interventions. In particular, denitrification enables P. aeruginosa to grow under oxygen-limited conditions by using nitrate and nitrite as alternative electron acceptors, a process particularly relevant in biofilms and chronic infections such as cystic fibrosis. Ubiquinone (UQ) is essential for respiratory metabolism in P. aeruginosa, which possesses two distinct UQ biosynthetic pathways that ensure UQ production across a broad range of oxygen concentrations. Recent studies have identified the O2-independent UQ biosynthetic pathway as a key determinant of chronic infection. Because this pathway is restricted to a limited group of bacteria, we hypothesized that its selective inhibition could represent a strategy to specifically target P. aeruginosa under anaerobic conditions. To test this hypothesis, we screened analogues of 4-hydroxybenzoic acid (4-HB), the earliest precursor of the UQ biosynthetic pathway, and identified 4-aminobenzoic acid, also known as para-aminobenzoic acid (pABA), as a potential inhibitor. pABA primarily affects the anaerobic metabolism of P. aeruginosa by acting as a competing substrate for UQ biosynthetic enzymes, thereby interfering with UQ biosynthesis. This inhibitory effect positions pABA as a valuable tool for investigating, and potentially targeting, anaerobic metabolism in P. aeruginosa.

microbiology↗

bioRxiv2025

Inference and validation of a dynamic gene regulatory network influencing cell fate during Duchenne muscular dystrophy initiation

The onset of gene regulatory disturbances leading to developmental disorders remains poorly understood, particularly when symptoms begin after birth. Using induced pluripotent stem cells, single-cell transcriptomics and computational modeling, we determined the gene expression waves guiding early myogenesis and how they are affected by a disease-causing mutation. We uncovered a dynamic gene regulatory network organized in two kernels that function as a toggle-switch controlling stochastic cell fate decisions. In cells derived from patients with Duchenne muscular dystrophy, these waves of regulation are less pronounced and the switch remains in the OFF state with a higher probability, resulting in convergence into a restricted cell fate. Experimental reactivation of the switch through RNA interference led to a rescued transcriptomic state and to a refined network topology. This work uncovers a dynamic regulatory mechanism underlying early cell fate divergence and provides a general framework to infer and validate dynamic gene regulatory networks involved in disease initiation.

bioinformatics↗

bioRxiv2024

Root exudation and rhizosphere microbial recruitment are influenced by novel plant trait diversity in carrot genotypes

Root exudate composition can influence rhizosphere microbial recruitment and is tightly controlled by plant genetics. However, little research has profiled root exudate in vegetable crops or determined their role in rhizosphere microbial community and metabolite composition. It is also not well understood how root exudates and resulting rhizosphere dynamics shift across plant trait diversity and with the development of novel crop genotypes. To address these knowledge gaps, this study paired metabolomics and microbiome analyses to evaluate associations between the composition of exudates, soil bacterial and fungal communities, and soil metabolites across four genotypes of organically produced carrot of differential breeding histories, including two experimental genotypes. Plant genotypes modified soil microbial diversity and composition, and differentially recruited bacterial taxa with demonstrated potential for plant-growth related functions including ammonia oxidation, nitrogen fixation, and phytohormone production. Bacterial rhizosphere recruitment from bulk soil was genotype and root exudate-mediated, while fungal recruitment was not. Moreover, root exudate composition was distinct in an heirloom genotype and a novel nematode resistant genotype, compared to other genotypes tested. Root exudate and rhizosphere metabolite composition was decoupled, and soil metabolites strongly associated with fungal, but not bacterial communities. Taken together, the results of this study suggest that novel crop trait diversity and breeding histories hold consequences for the functional potential of soils through the diversification of root exudate mediated plant-microbe interactions.

microbiology↗

bioRxiv2023

Assessment of technical and clinical utility of a bead-based flow cytometry platform for multiparametric phenotyping of CNS-derived extracellular vesicles

Extracellular vesicles (EVs) derived from the CNS are potential liquid-biopsy markers for early detection and monitoring of neurodegenerative diseases and brain tumors. This study assessed the performance of a bead-based flow cytometry assay (EV Neuro) for multiparametric detection of CNS-derived EVs and identification of disease-specific markers. Different sample materials and EV isolation methods were compared. Glioblastoma- and primary human astrocyte-derived EVs exhibited distinct EV profiles, with signal intensities increasing with higher EV input. Analysis of serum or plasma from glioblastoma, multiple sclerosis, Alzheimers Disease patients and healthy controls showed varying marker signal intensities. Notably, data normalization improved marker identification. Specific EV populations, such as CD36+EVs in glioblastoma and GALC+EVs in multiple sclerosis, were significantly elevated in disease compared to controls. Clustering analysis techniques effectively differentiated glioblastoma patients from controls. A potential correlation between CD107a+EVs and neurofilament levels in the blood was identified in multiple sclerosis patients. Together, the semi-quantitative EV Neuro assay demonstrated its utility for EV profiling in complex samples. However, reliable statistical results in biomarker studies require large sample cohorts and high effect sizes. Nonetheless, this exploratory trial confirmed the feasibility of discovering EV-associated biomarkers and monitoring circulating EV profiles in CNS diseases using the EV Neuro assay.

neuroscience↗

bioRxiv2021

Kinetics and topology of DNA associated with circulating extracellular vesicles released during exercise

Although it is widely accepted that cancer derived extracellular vesicles (EVs) carry DNA cargo, the association of cell-free circulating DNA (cfDNA) and EVs in plasma of healthy humans remains elusive. Using a physiological exercise model, where EVs and cfDNA are synchronously released, we aimed to characterize the kinetics and localization of DNA associated with EVs. EVs were separated from human plasma using size exclusion chromatography or immuno-affinity capture for CD9+, CD63+, and CD81+ EVs. DNA was quantified with an ultra-sensitive qPCR assay targeting repetitive LINE elements, with or without DNase digestion. This model shows that a minute part of circulating cell-free DNA is associated with EVs. During rest and following exercise, only 0.12 % of the total cfDNA occurs in association with CD9+/CD63+/CD81+EVs. DNase digestion experiments indicate that the largest part of EV associated DNA is sensitive to DNase digestion and only ~20 % are protected within the lumen of the separated EVs. A single bout of running or cycling exercise increases the levels of EVs, cfDNA, and EV associated DNA. While EV surface DNA is increasing, DNAse-resistant DNA remains at resting levels, indicating that EVs released during exercise (ExerVs) do not contain DNA. Consequently, DNA is largely associated with the outer surface of circulating EVs. ExerVs recruit cfDNA to their corona, but do not carry DNA in their lumen.

molecular biology↗

bioRxiv2019

MCC950/CRID3 potently targets the NACHT domain of wildtype NLRP3 but not disease-associated mutants for inflammasome inhibition

The NLRP3 inflammasome drives pathological inflammation in a suite of autoimmune, metabolic, malignant and neurodegenerative diseases. Additionally, NLRP3 gain-of-function point mutations cause systemic periodic fever syndromes that are collectively known as cryopyrin-associated periodic syndromes (CAPS). There is significant interest in the discovery and development of diarylsulfonylurea Cytokine Release Inhibitory Drugs (CRIDs) such as MCC950/CRID3, a potent and selective inhibitor of the NLRP3 inflammasome, for the treatment of CAPS and other diseases. However, drug discovery efforts have been constrained by the lack of insight in the molecular target and mechanism by which these CRIDs inhibit the NLRP3 inflammasome. Here, we show that the NACHT domain of NLRP3 is the molecular target of diarylsulfonylurea inhibitors. Interestingly, we find photoaffinity labelling of the NACHT domain requires an intact (d)ATP-binding pocket and is substantially reduced for most CAPS-associated NLRP3 mutants. In concordance, MCC950/CRID3 failed to inhibit NLRP3- driven inflammatory pathology in two mouse models of CAPS. Moreover, it abolished circulating levels of interleukin (IL)-1{beta} and IL-18 in LPS-challenged wildtype mice but not in Nlrp3L351P knock-in mice and ex vivo-stimulated mutant macrophages. These results identify wildtype NLRP3 as the molecular target of MCC950/CRID3, and show that CAPS-related NLRP3 mutants escape efficient MCC950/CRID3 inhibition. Collectively, this work suggests that MCC950/CRID3-based therapies may effectively treat inflammation driven by wildtype NLRP3, but not CAPS-associated mutants.

immunology↗

bioRxiv2017

Dissecting the genetic architecture of shoot growth in carrot (Daucus carota L.) using a diallel mating design

Crop establishment in carrot (Daucus carota L.) is limited by slow seedling growth and delayed canopy closure, resulting in high management costs for weed control. Varieties with improved growth habit (i.e. larger canopy and increased shoot biomass) may help mitigate weed control, but the underlying genetics of these traits in carrot is unknown. This project used a diallel mating design coupled with recent Bayesian analytical methods to determine the genetic basis of carrot shoot growth. Six diverse carrot inbred lines with variable shoot size were crossed in WI in 2014. F1 hybrids, reciprocal crosses, and parental selfs were grown in a randomized complete block design (RCBD) with two blocks in CA (2015, 2016) and in WI (2015). Measurements included canopy height, canopy width, shoot biomass, and root biomass. General and specific combining abilities were estimated using Griffings Model I. In parallel, additive, inbreeding, epistatic, and maternal effects were estimated from a Bayesian linear mixed model, which is more robust to dealing with missing data, outliers, and theoretical constraints than traditional biometric methods. Both additive and non-additive effects significantly influenced shoot traits, with non-additive effects playing a larger role early in the growing season, when weed control is most critical. Results suggest that early season canopy growth and root size express hybrid vigor and can be improved through reciprocal recurrent selection.\n\nArticle SummaryBreeding for improved competitive ability is a priority in carrot, which suffers yield losses under weed pressure. However, improvement and in-depth genetic studies for these traits relies on knowledge of the underlying genetic architecture. This study estimated heritable and non-heritable components of carrot shoot growth from a diallel mating design using a Bayesian mixed model. Results directly contribute to improvement efforts by providing estimates of combining ability, identifying a useful tester line, and characterizing the genetic and non-genetic influences on traits for improved competitive ability in carrot.

genetics↗