Biology subjects

Haddad, M.

Publications and source records attributed to Haddad, M..

8 recordsLinked to original sources

bioRxiv2026

Strain-level diversity shapes competitive outcomes in Fusarium: a multi-omic synthesis of fungal warfare

Fusarium head blight (FHB) is driven by co-occurring Fusarium species. Yet the molecular bases of their competitive interactions, particularly at the strain level, remain largely unknown. We performed an integrated multi-omic investigation of four Fusarium isolates cultivated in monoculture, self-confrontation (SC) and inter-specific confrontation (C) assays: two Fusarium graminearum strains FgrI349 and FgrPH-1, and two Fusarium avenaceum strains FaveI494 and FaLH03. Light microscopy and quantitative colorimetry revealed marked phenotypic heterogeneity. the F. graminearum strains formed expansive, red-pigmented colonies with rapid radial growth, whereas the F. avenaceum isolates grew more slowly and displayed distinct colony morphologies and pigmentation patterns. Untargeted LC-HRMS detected 1,008 metabolites in monocultures and 938 metabolites in confrontation zones. Species-level chemical signatures were confirmed, and strain-specific metabolite sets were identified, with FaLH03 producing more than 60 % of the metabolites being made exclusively by a single strain, highlighting its exceptionally unique metabolic profile. RNA-seq uncovered extensive transcriptional reprogramming during competition. In self-confrontations, strain-specific differences persisted but no major morphological or metabolic shifts were observed. Inter-specific confrontations elicited partner-dependent responses: FgrI349 up-regulated 1,492 genes against FaveI494 (including secondary-metabolite biosynthesis, oxidoreductase activity and transport) but only 407 genes against FaLH03, while down-regulating secondary-metabolite genes in the conspecific confrontation. Conversely, the F. avenaceum isolates showed opposite trends; FaLH03 strongly repressed ribosome-biogenesis and cell-wall genes while inducing oxidative-metabolism pathways, whereas FaveI494 displayed a modest transcriptional response dominated by down-regulation of cell-division and chromosome-segregation genes. Gene-ontology enrichment highlighted an opponent-specific reversal of the secondary-metabolite biosynthetic process category in F. graminearum: down-regulated in intra-specific confrontation but up-regulated in both inter-specific encounters. Collectively, our results demonstrate that competitive outcomes are shaped more by strain identity than by species identity, with each strain deploying a distinct molecular arsenal, ranging from metabolite-mediated antagonism to targeted transcriptional shutdown, when confronted with a specific opponent. These findings refine our understanding of Fusarium community dynamics and provide a framework for developing strain-targeted biocontrol strategies against FHB.

microbiology↗

bioRxiv2026

Serial Immunohistochemistry for High-Dimensional Single-Cell Spatial Analysis of Human Kidney Biopsies

BackgroundTraditional immunohistochemistry (IHC) with chromogen detection has limited multiplex capacity, detecting at most 4 protein markers per tissue section simultaneously, thereby restricting comprehensive spatial analysis of valuable human biopsies. We developed and validated a robust serial IHC (sIHC) staining method to detect multiple antigens on a single kidney biopsy slide, maximizing data yield for diagnosing and studying complex kidney diseases. MethodsFormalin-fixed, paraffin-embedded kidney biopsy sections were subjected to repeated IHC/imaging cycles with antibody removal using an optimized sodium dodecyl sulfate-glycerol buffer stripping protocol. Images were then co-registered, and analysis was performed using a variety of methodologies, including color deconvolution, cell segmentation, and spatial clustering. ResultsThis optimized sIHC method successfully detected up to 20 antigens on a single slide. Combining image analysis and artificial intelligence software, for example with HALO (Indica Labs), the assay assembles high-dimensional images and enables quantitative histology and single-cell spatial analysis. Using this advanced method, we were able to identify rare cell populations, such as double-negative T cells, that are challenging to detect conventionally. ConclusionWe have developed a validated, high-capacity sIHC protocol that uses standard IHC procedures with commercially available, clinically validated off-the-shelf antibodies. This method is a valuable, cost-effective tool for obtaining extensive, high-dimensional single-cell-resolved spatial data from limited pathology samples, such as a human kidney biopsy.

pathology↗

bioRxiv2025

Decoding ladybird's colours: structural mechanisms of colour production and pigment modulation.

This study investigates the mechanisms underlying colour production in the family Coccinellidae, focusing on two model species: A. bipunctata (L) and C. quatuordecimguttata (L). In this family, colours have traditionally been attributed primarily to pigments such as carotenoids and melanins. We propose an alternative perspective, considering the elytra as an integrated optical medium whose optical properties result from both its architectural design and the properties of its constituent materials, including matrix and pigments. In the present work, several methods were used, ranging from optical and electron microscopies, light-based techniques, to LC-HRMS analyses. Through local pigment analyses, microstructural examination of elytra, and modelling of interaction of elytra with light, we show that, while pigments are central to patterning and contribute to colour, overall colour also results from one or more physical mechanisms that may operate simultaneously. In the light of these results, we assume that the complex and diverse colouration in the Coccinellidae can only be elucidated by considering the interplay of pigments and the optical properties of the elytron cuticle.

evolutionary biology↗

bioRxiv2023

Gut microbiota promotes pain in fibromyalgia

Fibromyalgia is a chronic syndrome characterized by widespread pain in the absence of evident tissue injury or pathology, making it one of the most mysterious chronic pain conditions. Despite affecting 2-4% of the population, primarily women1, the cause and underlying mechanisms of fibromyalgia remain elusive, and effective targeted treatments are currently unavailable. The gut microbiota of women with fibromyalgia differs from healthy controls2,3. However, it is unknown whether changes in gut microbiota have a causal role in mediating pain and other symptoms of fibromyalgia. Here, we show that fecal microbiota transplantation (FMT) from individuals with fibromyalgia, but not from healthy controls, into germ-free mice induces persistent pain hypersensitivity. FMT from fibromyalgia patients led to a reduction in intraepidermal nerve fiber density and alterations in the peripheral immune profile, and induced activation of spinal microglia, which contributed to the development of pain in mice. Notably, the pain hypersensitivity in mice that were administered microbiota from fibromyalgia patients resolved after FMT from healthy controls. Consistent with these findings, an open-label pilot study showed that transplanting microbiota from healthy individuals to humans with fibromyalgia alleviated pain and reduced overall symptom severity. Thus, altered gut microbiota has a causal role in fibromyalgia pain, highlighting it as a promising target for therapeutic interventions.

neuroscience↗

bioRxiv2023

Murine classical monocyte subsets display distinct functions and fates

Monocytes are short-lived myeloid immune cells that arise from adult hematopoiesis and circulate for a short time in the blood. They comprise two main subsets, in mice defined as classical Ly6Chigh and non-classical Ly6Clow monocytes (CM, NCM). Recent fate mapping and transcriptomic analyses revealed that CM themselves are heterogeneous. Here, we report surface markers that allow segregation of murine GMP- and MDP-derived CM in the BM and blood. Functional characterization, including fate definition following adoptive cell transfer, established that GMP-Mo and MDP-Mo could equal rise to homeostatic CM progeny, such as NCM in blood and gut macrophages, but differentially seeded selected other tissues. Specifically, GMP-Mo and MDP-Mo gave rise to distinct interstitial lung macrophages, thus linking CM dichotomy to previously reported pulmonary macrophage heterogeneity. Collectively, we provide comprehensive evidence for the existence of two functionally distinct CM subsets in the mouse, which differentially contribute to peripheral tissue macrophage populations in homeostasis and following challenge. Our findings are indicative of impact of monocyte ontogeny on in situ differentiation.

immunology↗

bioRxiv2022

Metabotyping of Andean pseudocereals and characterization of emerging mycotoxins

Pseudocereals are best known for three crops derived from the Andes: quinoa (Chenopodium quinoa, Chenopods I), canihua (C. pallidicaule, Chenopods I), and kiwicha (Amaranthus caudatus). Their grains are recognized for their nutritional benefits; however, there is a higher level of polyphenism and the chemical foundation that would rely with such polyphenism has not been thoroughly investigated. Meanwhile, the chemical food safety of pseudocereals remains poorly documented. Here we applied untargeted and targeted metabolomics approach by LC-MS to achieve both: i) a comprehensive chemical mapping of pseudocereal samples collected in the Andes to classify them according to their chemotype; ii) a quantification of their contents in emerging mycotoxins. An inventory of the fungal community was also realized with the aims to better know the filamentous fungi present in these grains and try to parallel this information with the presence of the molecules produced, especially mycotoxins. Metabotyping permitted to add new insights into the chemotaxonomy of pseudocereals, confirming the previously established phylotranscriptomic clades: Chenopods I (clusters quinoa and canihua), and Amaranthaceae s.s. (cluster kiwicha). Moreover, we report for the first time the presence of mycotoxins in pseudocereals. Sixteen samples of Peru (out of 27) and one sample from France (out of one) were contaminated with Beauvericin, an emerging mycotoxin. There were several mycotoxigenic fungi detected, including Aspergillus sp., Penicillium sp., and Alternaria sp., but not Fusaria. Highlights{blacksquare} Twenty-seven grain samples of Andean pseudocereals were profiled by LC-HRMS. {blacksquare}Untargeted metabolomics was used to differentiate varieties from the whole metabolome dataset. {blacksquare}Five mycotoxins were quantify using targeted metabolomics. {blacksquare}Sixteen samples of Peru and one sample from France were contaminated with Beauvericin. {blacksquare}An inventory of the fungal community infesting the Andean pseudocereal samples was documented.

biochemistry↗

bioRxiv2021

Age-associated gut microbiota impairs hippocampus-dependent memory in a vagus dependent manner

Aging is known to be associated with hippocampus-dependent memory decline, but the underlying causes of the age-related memory impairment remain yet highly debated. Here we showed that fecal microbiota transplantation (FMT) from aged, but not young, animal donors in young mice is sufficient to trigger profound hippocampal alterations including astrogliosis, decreased adult neurogenesis, decreased novelty-induced neuronal activation and impairment in hippocampus-dependent memory. Furthermore, similar alterations were reported when mice were subjected to an FMT from aged human donors. To decipher the mechanisms involved in mediating these microbiota-induced effects on brain function, we mapped the vagus nerve (VN)-related neuronal activity patterns and report that aged-mice FM transplanted animals showed a reduction in neuronal activity in the ascending VN output brain structure, both in basal condition and following VN stimulation. Targeted pharmacogenetic manipulation of VN-ascending neurons demonstrated that the decrease in vagal activity is detrimental to hippocampal functions. In contrast, increasing vagal ascending activity alleviated the adverse effects of aged mice FMT on hippocampal functions, and had a pro-mnesic effect in aged mice. Thus, pharmacogenetic VN stimulation is a potential therapeutic strategy to lessen microbiota-dependent age-associated impairments in hippocampal functions. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=168 SRC="FIGDIR/small/428594v3_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@8e668borg.highwire.dtl.DTLVardef@ee5d18org.highwire.dtl.DTLVardef@1220a87org.highwire.dtl.DTLVardef@1e12fe7_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2020

Defective NETs Clearance contributes to sustained FXII Activation in COVID-19-associated Pulmonary Thrombo-Inflammation

BackgroundCoagulopathy and inflammation are hallmarks of Coronavirus disease 2019 (COVID-19) and are associated with increased mortality. Clinical and experimental data have revealed a role for neutrophil extracellular traps (NETs) in COVID-19 disease. The mechanisms that drive thrombo-inflammation in COVID-19 are poorly understood. MethodsWe performed proteomic analysis and immunostaining of postmortem lung tissues from COVID-19 patients and patients with other lung pathologies. We further compared coagulation factor XII (FXII) and DNase activities in plasma samples from COVID-19 patients and healthy control donors and determined NET-induced Factor XIII (FXII) activation using a chromogenic substrate assay. FindingsFXII expression and activity were increased in the lung parenchyma, within the pulmonary vasculature and in fibrin-rich alveolar spaces of postmortem lung tissues from COVID-19 patients. In agreement with this, plasma FXII activation (FXIIa) was increased in samples from COVID-19 patients. Furthermore, FXIIa colocalized with NETs in COVID-19 lung tissue indicating that NETs accumulation leads to FXII contact activation in COVID-19. We further showed that an accumulation of NETs is partially due to impaired NET clearance by extracellular DNases as DNase substitution improved NET dissolution and reduced FXII activation in vitro. InterpretationCollectively, our study supports that the NETs/FXII axis contributes to the pathogenic chain of procoagulant and proinflammatory responses in COVID-19. Targeting both, NETs and FXIIa, could provide a strategy to mitigate COVID-19-induced thrombo-inflammation. FundingThis study was supported by the European Union (840189), the Werner Otto Medical Foundation Hamburg (8/95) and the German Research Foundation (FR4239/1-1, A11/SFB877, B08/SFB841 and P06/KFO306).

molecular biology↗