Biology subjects

Salmon, M.

Publications and source records attributed to Salmon, M..

12 recordsLinked to original sources

bioRxiv2026

V-ATPase-Driven Lysosomal Activation Orchestrates MEK2-Induced Endothelial Reprogramming

Direct lineage reprogramming holds therapeutic promise but often depends on transcription factor overexpression, resulting in unstable phenotypes. Here, we describe a novel strategy to convert fibroblasts into endothelial-like cells by activating lysosomal activity. Constitutively active MEK2 induces an endothelial gene program via sustained MAPK/ERK signaling, leading to enhanced vacuolar ATPase (V-ATPase) activity, lysosomal acidification, extracellular matrix degradation, and angiogenic behavior. V-ATPase inhibition impairs these effects, whereas pharmacologic activation with EN6 recapitulates key features of reprogramming and promotes nuclear translocation of TFEB, a master lysosomal regulator. Consistently, TFEB overexpression-particularly a phospho-deficient mutant-boosts lysosomal function and endothelial gene expression. These findings define a MAPK-V-ATPase-TFEB axis that drives endothelial reprogramming and highlight the lysosome as a central hub for cell fate transitions, offering an organelle-centric framework for regenerative medicine. HighlightsO_LISustained MEK2 activation reprograms fibroblasts into endothelial-like cells C_LIO_LIMEK2 enhances lysosomal acidification by upregulating V-ATPase subunits C_LIO_LIV-ATPase drives acidification and ECM remodeling for endothelial reprogramming C_LIO_LIV-ATPase activation promotes TFEB nuclear entry and endothelial gene expression C_LI

cell biology↗

bioRxiv2026

Virus Induced Gene Silencing in Calendula officinalis (pot marigold)

Virus induced gene silencing (VIGS) is a method that exploits plant antiviral defence mechanisms to downregulate endogenous genes. The technique is versatile, rapid, and widely used for functional genomics studies. Here we report a method for VIGS in the medicinal plant, Calendula officinalis (pot marigold). This species produces anti-inflammatory triterpenoids and has also been bred and cultivated as an ornamental plant. We describe a method for the injection of Agrobacterium tumefaciens cultures into leaf midribs and compare visual marker genes for tracking VIGS utilising constructs that simultaneously target visual marker and target genes. We use these tools to demonstrate that silencing a gene encoding cycloartenol synthase results in changes to leaf phytosterols. This method could be used to further investigate the genetic basis of specialised metabolism in this species and could be adapted to other members of the Asteraceae family, many of which are of economical and chemical value.

plant biology↗

bioRxiv2026

Spatiotemporal dynamics of β-lactam-resistant E. coli in young diseased calves in Wallonia, Belgium

Calves are one of the most common carriers of antibiotic-resistant bacteria among farm animals. However, the impact of antibiotic usage on resistance mechanisms, transmission routes between farms, and the transmission of resistant bacteria to humans remain largely unknown. Here we analyzed the population of {beta}-lactam resistant E. coli isolated over five calving seasons on 444 farms scattered throughout Wallonia, Belgium. Restrictions on critical antibiotics usage led to a reduction of resistance to 3rd generation cephalosporins but has no impact on population structure and {beta}-lactamase genes indicating a resilient population. The correlation between short genetic distances and geographic proximity suggests indirect transmission between farms by fomites with differences between regions east and west of the river Meuse. Phylogenetic analysis of calf isolates with isolates from public databases indicates transitions from bovine to human adaptation. These findings provide new means to further model the spread of E. coli in livestock farming.

microbiology↗

bioRxiv2025

Unravelling the influence of light on inshore coral and sponge recruits and their substrate communities

Recruitment of progeny to coral reef populations involves complex ecological interactions, influenced by environmental factors such as altered underwater light conditions associated with poor water quality. Here, we exposed newly settled corals (Acropora millepora and Acropora cf. tenuis), the sponge (Phyllospongia foliascens), and their substrate communities to various light intensities and spectral profiles relevant to turbid inshore reefs. Coral and sponge recruit survivorship and growth generally exhibited an inverted U-shaped response to light intensity, suggesting environmental optima at lower light levels, while the influence of light spectra remained less clear within environmentally realistic treatment combinations. Crustose coralline algae cover similarly peaked at lower light levels, whereas turf algae increased with higher light conditions. Competitive interactions between the substrate communities and the recruits, along with photophysiological responses, were also assessed. Our results suggest that altered light characteristics associated with turbidity may not be as detrimental to coral and sponge recruits as other sediment-related stressors.

ecology↗

bioRxiv2025

Aging-Associated Nox4-Mediated Mitochondrial ROS and DNA Damage Promote Vascular Cell Reprogramming and Aortic Remodeling in Abdominal Aneurysms

AbstractO_ST_ABSBackgroundC_ST_ABSAging and male sex are major risk factors for abdominal aortic aneurysm (AAA), a disease characterized by vascular cell phenotypic switching and aortic wall remodeling. Mitochondrial oxidative stress (mtOS) has been implicated in these changes. We previously demonstrated that NOX4 expression and activity increase with age in cardiovascular cells, promoting mtOS and vascular dysfunction. This study investigates whether NOX4-driven mtOS and DNA damage promote AAA development through vascular cell reprogramming. MethodsWe used mitochondria-targeted Nox4-overexpressing (Nox4TG) mice with an Apoe-/- background to model Angiotensin II (Ang II)-induced AAA. AAA incidence, aortic morphology, reactive oxygen species (ROS) levels, DNA damage markers, and wall remodeling parameters were assessed in Apoe-/-, Apoe-/-/Nox4TG, and Apoe-/-/Nox4-/- mice. Vascular cell populations were analyzed by spectral flow cytometry and gene expression profiling. In vitro, Ang II-treated SMCs from wild-type, Nox4TG, and Nox4-/- mice were evaluated for mtROS, DNA damage, and activation of inflammatory pathways. ResultsApoe-/-/Nox4TG mice exhibited the highest AAA incidence, aortic dilation, ROS levels, DNA damage, and inflammation, while Apoe-/-/Nox4-/- mice were most protected. Macrophage-like SMCs increased, while contractile SMCs decreased in Nox4TG aortas. Ang II-treated Nox4TG SMCs showed elevated mtROS, DNA damage, and cGAS-STING activation. Flow cytometry analysis confirmed the presence of aneurysmal SMC with reduced ACTA2, MYH11, TAGLN and increased CD68, CD11b, LGALS3 expression. ConclusionsNOX4-dependent mitochondrial DNA damage and activation of DNA- sensing pathways promote SMC phenotypic switching, inflammation, and aortic wall remodeling in AAA. Targeting NOX4 and enhancing mitochondrial function may offer therapeutic strategies for AAA prevention. CLINICAL PERSPECTIVEO_ST_ABSWhat Is New?C_ST_ABSO_LIThis study identifies mitochondrial NOX4-derived ROS and oxidative mitochondrial DNA damage as early and causal events in AAA pathogenesis, promoting pro-inflammatory reprogramming of vascular smooth muscle cells toward a macrophage-like phenotype. C_LIO_LIActivation of cytosolic DNA sensing (cGAS-STING) and DNase II pathways in response to mitochondrial damage links redox imbalance to innate immune activation and progressive aortic wall remodeling in AAA. C_LI What Are the Clinical Implications?O_LITargeting mitochondrial-specific oxidative stress or downstream DNA-sensing pathways offers a novel therapeutic strategy to halt AAA progression in patients with small, asymptomatic aneurysms. C_LIO_LIThese findings provide a mechanistic basis for developing mitochondria-targeted antioxidants or NOX4 inhibitors as potential pharmacologic interventions to delay or prevent AAA rupture, which could reduce the need for surgical repairs. C_LI

physiology↗

bioRxiv2025

Biosynthesis and Bioactivity of Anti-Inflammatory Triterpenoids in Calendula officinalis (pot marigold)

Plants have been central to traditional medicine for millennia, yet the precise metabolites responsible for their therapeutic properties often remain unidentified. Moreover, the low natural abundance and structural complexity of bioactive molecules can hinder their accessibility and chemical synthesis. Here, we investigate the widely reported anti-inflammatory properties of Calendula officinalis (pot marigold), an ancient medicinal herb. We confirm C16-hydroxylated triterpenoids as key contributors to the anti-inflammatory activity of C. officinalis floral extracts and uncover a novel mechanism by which they act in modulating interleukin 6 release. Through biosynthetic pathway elucidation, we demonstrate that the oxidosqualene synthase catalysing the first committed step emerged early in Asteraceae evolution and identify residues governing product specificity. Further, we functionally characterise cytochrome P450s and acyltransferases responsible for downstream modifications. By reconstructing the complete biosynthetic pathway in the heterologous plant chassis Nicotiana benthamiana, we provide a platform for production of the anti-inflammatory components. Our work highlights how integrated studies of bioactivity and biosynthesis can unlock the therapeutic potential of medicinal plants.

plant biology↗

bioRxiv2024

Controlled 'out-of-season' spawning of reef-forming corals in aquaria using offset environmental profiles

The global climate crisis has heightened the urgency for developing interventions to enhance resilience and recovery of coral reef ecosystems. However, research programs are often bottlenecked by availability of coral early life stage material due to the seasonal (annual) nature of coral mass spawning events. Here, we present a proof-of-concept of "out-of-season" coral spawning, utilising advanced aquarium control technology to induce spawning in multiple key Great Barrier Reef (GBR) coral species held in long-term indoor aquaria. By developing a 6-month offset environmental profile encompassing seasonal temperature, photoperiod, and lunar profiles, we successfully induced synchronised mass coral spawning during austral autumn/winter (May - June) over consecutive years in 2022 and 2023. We also "phase-shifted" the hour of sunset by five hours on spawning nights, creating a more favourable time window (i.e., minimising late nights) for gamete fertilisation. The timing of gamete release in captive corals closely matched previous GBR field observations for both nights after full moon (NAFM) and time after sunset (TAS). Gamete fertilisation was successful for six GBR species: Acropora millepora, Acropora loripes, Acropora hyacinthus, Acropora elseyi, Acropora austera, and Montipora aequituberculata producing a total of 1.75 million larvae. We outline key physiological insights gained into environmental regulation of coral spawning synchronicity and discuss the potential for out-of-season spawning to accelerate various aspects of coral reproduction research and enhance the growing toolbox of active restoration strategies aimed at reversing global coral reef decline.

ecology↗

bioRxiv2024

Deficiency of mitophagy mediator Parkin in aortic smooth muscle cells exacerbates abdominal aortic aneurysm

Abdominal aortic aneurysms (AAAs) are a degenerative aortic disease and associated with hallmarks of aging, such as mitophagy. Despite this, the exact associations among mitophagy, aging, and AAA progression remain unknown. In our study, gene expression analysis of human AAA tissue revealed downregulation of mitophagy pathways, mitochondrial structure, and function-related proteins. Human proteomic analyses identified decreased levels of mitophagy mediators PINK1 and Parkin. Aged mice and, separately, a murine AAA model showed reduced mitophagy in aortic vascular smooth muscle cells (VSMCs) and PINK1 and Parkin expression. Parkin knockdown in VSMCs aggravated AAA dilation in murine models, with elevated mitochondrial ROS and impaired mitochondrial function. Importantly, inhibiting USP30, an antagonist of the PINK1/Parkin pathway, increased mitophagy in VSMCs, improved mitochondrial function, and reduced AAA incidence and growth. Our study elucidates a critical mechanism that proposes AAAs as an age-associated disease with altered mitophagy, introducing new potential therapeutic approaches.

molecular biology↗

bioRxiv2022

Development of nanobodies as theranostic agents against CMY-2-like class C β-lactamases

Soluble single-domain fragments derived from the unique variable region of camelid heavy-chain antibodies (VHHs) against enzymes may behave as potent inhibitors. The immunization of alpacas with the CMY-2 {beta}-lactamase led to the isolation of three VHHs that specifically recognized and inhibited CMY-2. The structure of the complex VHH cAbCMY-2(254)/CMY-2 was determined by X-ray crystallography. We showed that the epitope is close to the active site and that the CDR3 of the VHH protrudes in the catalytic site. The {beta}-lactamase inhibition was found to follow a mixed profile with a predominant non-competitive component. The three isolated VHHs recognized overlapping epitopes since they behaved as competitive binder. Our study identified a binding site that can be targeted by a new class of {beta}-lactamases inhibitors designed with the help of a peptidomimetic approach. Furthermore, the use of mono or bivalent VHH and rabbit polyclonal anti-CMY-2 antibodies enable the development of the first generation of ELISA test for the detection of CMY-2 produced by resistant bacteria. IMPORTANCEThe still increasing antimicrobial resistance in human clinic or veterinary medicine is a major threat for modern chemotherapy. Beside the major caution in the use of current antibiotics, it is important to develop new classes of antibiotics. This work was focused on {beta}-lactamases that are the enzymes involved in the hydrolysis of the major class of antibiotics, the {beta}-lactam compounds. We selected camelid antibodies that inhibit CMY-2, a class C {beta}-lactamase produced by bacteria isolated from the veterinary and human settings. We characterized the conformational epitope present in CMY-2 in order to create a new family of inhibitors based on the paratope of the antibody. Finally, we designed a primary version of a detection system based on an ELISA using VHH and polyclonal antibodies.

biochemistry↗

bioRxiv2020

The Transition from Acute to Chronic Pain: Dynamic Epigenetic Reprogramming of the Mouse Prefrontal Cortex up to One Year Following Nerve Injury

Chronic pain is associated with persistent structural and functional changes throughout the neuroaxis, including in the prefrontal cortex (PFC). The PFC is important in the integration of sensory, cognitive and emotional information and in conditioned pain modulation. We previously reported wide-spread epigenetic reprogramming in the PFC many months following nerve injury in rodents. Epigenetic modifications, including DNA methylation, can drive changes in gene expression without modifying DNA sequences. To date, little is known about epigenetic dysregulation at the onset of acute pain or how it progresses as pain transitions from acute to chronic. We hypothesize that acute pain following injury results in rapid and persistent epigenetic remodelling in the PFC that evolves as pain becomes chronic. We further propose that understanding epigenetic remodelling will provide insights into the mechanisms driving pain-related changes in the brain. Epigenome-wide analysis was performed in the mouse PFC 1 day, 2 weeks, 6 months, and 1 year following peripheral injury using the spared nerve injury (SNI) in mice. SNI resulted in rapid and persistent changes in DNA methylation, with robust differential methylation observed between SNI and sham-operated control mice at all time points. Hundreds of differentially methylated genes were identified, including many with known function in pain. Pathway analysis revealed enrichment in genes related to stimulus response at early time points, immune function at later time points and actin and cytoskeletal regulation throughout the time course. Increased attention to pain chronicity as a factor is recommended for both pain research and management.

neuroscience↗

bioRxiv2020

A Micro-Engineered Airway Lung-Chip Models Key Features of Viral-Induced Exacerbation of Asthma

RationaleViral-induced exacerbation of asthma remain a major cause of hospitalization and mortality. New human relevant models of the airways are urgently needed to understand how respiratory infections may trigger asthma attacks, and to advance treatment development. ObjectivesTo develop a new human relevant model of rhinovirus-induced asthma exacerbation that recapitulates viral infection of asthmatic airway epithelium, neutrophil transepithelial migration, and enables evaluation of immunomodulatory therapy. MethodsA micro-engineered model of fully differentiated human mucociliary airway epithelium was stimulated with IL-13 to induce a Th2-type asthmatic phenotype and infected with live human rhinovirus 16 (HRV16) to reproduce key features of viral-induced asthma exacerbation. Measurements and Main ResultsInfection with HRV16 replicated key hallmarks of the cytopathology and inflammatory responses observed in human airways. Generation of a Th2 microenvironment through exogenous IL-13 stimulation induced features of asthmatics airways, including goblet cell hyperplasia, reduction of cilia beating frequency, and endothelial activation, but did not alter rhinovirus infectivity or replication. High resolution kinetic analysis of secreted inflammatory markers revealed that IL-13 treatment altered the IL-6, IFN-{lambda}1, and CXCL10 secretion in response to HRV16. Neutrophil transepithelial migration was greatest when viral infection was combined with IL-13 treatment, while treatment with MK-7123, a CXCR2 antagonist, reduced neutrophil diapedesis in all conditions. ConclusionsThis micro-engineered Airway Lung-Chip provides a novel human-relevant platform for exploring the complex mechanisms underlying viral-induced asthma exacerbation. Our data suggest that IL-13 may impair the hosts ability to mount an appropriate and coordinated immune response to rhinovirus infection. We also show that the Airway Lung-Chip can be used to assess the efficacy of modulators of the immune response. NoteEmulate(R), Human Emulation System(R), S-1, ER-1, and ER-2 are trademarks of Emulate, Inc., and any other trademarks used herein remain with their respective holders. The technology disclosed in this document may be covered by one or more patents or patent applications, and no license to these is granted herein. You are solely responsible for determining whether you have all intellectual property rights that are necessary for your intended use of any of the disclosed materials, and whether you are required to obtain any additional intellectual property rights from a third party. Further information is available by contacting the authors. At a Glance CommentaryO_ST_ABSScientific Knowledge on the SubjectC_ST_ABSNew therapies for asthma exacerbations remain a significant unmet medical need. Development of human relevant preclinical models are needed to further elucidate the complex mechanisms underlying asthma exacerbation and investigate new therapeutic strategies. What This Study Adds to the FieldUsing a human Airway Lung-Chip model, we show here for the first time a live human rhinovirus (HRV) infection of the asthmatic epithelium that recapitulates complex features of viral-induced asthma exacerbation. The dynamic microenvironment of the chip enables the real-time study of virus infection, epithelial response, and immune cell recruitment under healthy and asthmatic conditions. The model reproduces key endpoints that have been observed in asthmatics and individuals infected with rhinovirus including the ciliated cell sloughing, altered cilia beating frequency, goblet cell hyperplasia, increased expression of adhesion molecules in microvascular endothelial cells, and inflammatory mediator release. High-resolution temporal analysis of secreted inflammatory markers enabled by dynamic sampling revealed alteration of IL-6, IFN-{lambda}1 and CXCL10 secretory phases after rhinovirus infection in an IL-13 high environment. Leveraging high-content imaging and analysis of circulating inflammatory cells, we demonstrated the efficacy of a CXCR2 antagonist to reduce adhesion, motility, and transmigration of perfused human neutrophils. Thus, this micro-engineered chip may offer a powerful addition to preclinical models for understanding mechanisms underlying asthma exacerbation pathology and developing new therapeutic strategies.

bioengineering↗

bioRxiv2019

Sparse epistatic patterns in the evolution of terpene synthases

We explore sequence determinants of enzyme activity and specificity in a major enzyme family of terpene synthases. Most enzymes in this family catalyze reactions that produce cyclic terpenes - complex hydrocarbons widely used by plants and insects in diverse biological processes such as defense, communication, and symbiosis. To analyze the molecular mechanisms of emergence of terpene cyclization, we have carried out in-depth examination of mutational space around (E)-{beta}-farnesene synthase, an Artemisia annua enzyme which catalyzes production of a linear hydrocarbon chain. Each mutant enzyme in our synthetic libraries was characterized biochemically, and the resulting reaction rate data was used as input to the Michaelis-Menten model of enzyme kinetics, in which free energies were represented as sums of one-amino-acid contributions and two-amino-acid couplings. Our model predicts measured reaction rates with high accuracy and yields free energy landscapes characterized by relatively few coupling terms. As a result, the Michaelis-Menten free energy landscapes have simple, interpretable structure and exhibit little epistasis. We have also developed biophysical fitness models based on the assumption that highly fit enzymes have evolved to maximize the output of correct products, such as cyclic products or a specific product of interest, while minimizing the output of byproducts. This approach results in a non-linear fitness landscape which is considerably more epistatic. Overall, our experimental and computational framework provides focused characterization of evolutionary emergence of novel enzymatic functions in the context of micro-evolutionary exploration of sequence space around naturally occurring enzymes.

evolutionary biology↗