Biology subjects

David, J.

Publications and source records attributed to David, J..

15 recordsLinked to original sources

bioRxiv2026

Nanoparticle mediated delivery of PD-L1 inhibitor enhances γδ T cell immunotherapy against metastatic ovarian cancer cells

IntroductionImmune checkpoint inhibitors (ICIs) have only shown limited efficacy for patients with ovarian cancer (OC), partly due to the immune suppressive tumour microenvironment (TME) and platelet cloaking of the cancer cells. We tested a nanomedicine strategy to enhance {gamma}{delta} T cell immunotherapy by conjugating the PD-L1 inhibitor (BMS202) to nanodiamonds (NDs). MethodsPatient-derived ascites cells were exposed to activated platelets to model platelet cloaking and the immunosuppressive phenotype in metastatic OC. ND/BMS202 nanocomplexes were then applied to platelet-conditioned OC cells and co-cultured with expanded {gamma}{delta} T cells. Cytotoxicity and immune activation were assessed by quantifying Granzyme B, CD107a, {gamma}-H2AX, cleaved caspase-3, and cleaved caspase-8. ResultsND-mediated delivery of BMS202 significantly enhanced {gamma}{delta} T cell-mediated killing of platelet cloaked OC cells in a dose-dependent manner, with greater efficacy than free BMS202 This enhanced cytotoxicity was supported by increased degranulation (CD107a), Granzyme B release, tumour cell apoptosis (caspase cleavage) and DNA damage ({gamma}-H2AX staining). ConclusionsND-based delivery of the PD-L1 inhibitor (BMS202) enhances {gamma}{delta} T cell-mediated killing of platelet-cloaked metastatic OC cells. While our data support enhanced {gamma}{delta} T cell cytotoxicity following BMS202 delivery, direct evidence of PD-L1 target engagement or PD-1/PD-L1 binding inhibition was not demonstrated in this study. These findings nonetheless justify further validation in patient-derived organoid models to optimize this {gamma}{delta} T cell-based combination immunotherapy and advance its development as a precision therapeutic strategy for metastatic OC.

immunology↗

bioRxiv2026

Multispecies Mixtures: An Individual-Centered Quantitative Genetic Framework for Complex Plant Neighborhoods

Mixing crop species or varieties in the same field can raise yield and stability, but performance varies widely among combinations that breeders cannot yet predict. What makes a good neighbor is partly heritable, and quantitative genetics models this as an indirect genetic effect describing a genotype's contribution to its neighbors' phenotypes. Here, we extend existing models with a complementary approach based on continuous neighborhoods, in which diverse genotypes of two species are mixed. In a continuous neighborhood design, several genotypes of each species are grown in a single trial, with every plant georeferenced. Each plant's phenotype is decomposed into direct genetic effects, indirect genetic effects from neighbors of both species, and environmental effects. Breeding values are then assembled for each genotype by combining its three genetic effects. We derived analytical expressions for the variances and covariance of these effects, validated the model, and evaluated its statistical properties through simulations spanning a wide range of parameter settings. For the same number of plants, the continuous neighborhood design estimated indirect effects far more accurately than a pairwise design and, in addition, allowed indirect environmental variance to be estimated. Applied to a wheat-alfalfa experiment comprising 3,840 plants, from 181 wheat pure lines and 106 alfalfa families, the model attributed 8.6% and 8.2% of the variance in wheat grain number and alfalfa biomass to direct genetic effects respectively, and 4.0% and 4.6% to indirect genetic effects from alfalfa. The framework therefore offers an individual-entered basis for analyzing multispecies neighborhoods and their breeding potential.

genetics↗

bioRxiv2026

Easy to use and low cost leaf disease quantification workflow using Ilastik

Accurate and reproducible assessment of foliar disease severity is essential for evaluating the performance of heterogeneous plant communities and understanding host-pathogen interactions. However, traditional visual scoring methods remain subjective, with limited precision, and difficult to scale in large phenotyping experiments. Here, we present a semi-automated image analysis workflow designed to quantify multiple foliar disease symptoms simultaneously on wheat flag leaves sampled from varietal mixtures. The workflow combines three methodological components: (i) a standardized protocol for leaf sampling and imaging, (ii) supervised machine learning segmentation using Random Forest implemented in Ilastik to classify multiple symptoms (powdery mildew and yellow rust), and (iii) a graphical user interface facilitating pipeline deployment by non-specialist operators. To evaluate the influence of image representation on classification performance, four color spaces (RGB, HSV, HLS, LAB) were systematically compared. The approach was validated using images of durum wheat flag leaves collected from a field experiment assessing eight-way varietal mixtures under natural fungal pressure. Cross-validation against manually annotated images demonstrated high segmentation accuracy across all symptom. Comparison among color spaces revealed only minor differences in performance. Overall, this workflow offers a cost-effective, annotation-efficient and reproducible alternative to deep learning approaches, leveraging open-source and actively maintained tools while requiring limited training data and enabling objective, reproducible and scalable disease phenotyping.

plant biology↗

bioRxiv2024

Complete telomere-to-telomere assemblies of two sorghum genomes to guide biological discovery

Sorghum is a C4 crop well-known for its high efficiency of biomass accumulation and adaptation to drought and hot environments. This study reports the assembly of complete genome sequence of two sorghum genomes using a combination of ultra-long reads from Oxford Nanopore Technology, high-fidelity long reads from Pacbio and Hi-C reads. The accuracy and completeness of the T2T assemblies were comprehensively validated using a range of parameters, including coverage depth assessment, BUSCO, LTR assembly index, ect. Our T2T assembly of BTx623 identified 36.25 Mb of new sequence, in addition to dozens of misoritation and mispositioning of large DNA segments in the BTx623-v3. Correcting these assembly errors in the reference genome is critical for exploiting genetic information in these complex regions in sorghum. Comparison of the two T2T genomes shed new insights on variation of centromeres in sorghum. The two high-quality T2T genomes represent an important resource for sorghum improvement and gene discovery. They would serve as the new reference genomes to unlock the full potential of global sequence variation of this valuable crop.

genomics↗

bioRxiv2023

Neutrophilia with damage to the blood-brain barrier and neurovascular unit following acute lung injury

BackgroundThe role of neutrophils in mediating neurovascular vulnerability has been increasingly implicated in various acute inflammatory models of neuroimmune crosstalk between the periphery and the brain. Whether neurovascular vulnerability is similarly modulated in the context of frequent, but not acute, inflammatory activation in the periphery is the aim of our study. Such a model of frequent inflammatory irritation is pertinent to understanding the neurologic risk of constant exposure to aerosolized environmental hazards leading to progressive pulmonary disease. MethodsTo model repeated pulmonary inflammation, we applied a three-dose regimen of intranasal (i.n.) lipopolysaccharide (LPS) in C57BL/6J mice and studied the impact on the inflammatory environment of the brain, with a specific focus on neutrophil dynamics at the neurovascular unit (NVU). Tissue and circulatory inflammatory profiles were screened via bronchoalveolar lavage (BAL) protein content and cellularity, transcript analysis of brain tissue, and flow cytometry of peripheral blood. Intravital two-photon microscopy (2PM) of the brain vasculature identified neutrophil dynamics at the NVU. Immunofluorescence validated neutrophil dynamics and identified neuroinflammatory hallmarks and peripheral immune factor interactions at the NVU. In vivo findings were corroborated and replicated in murine and human microphysiological systems (MPS) modeling the blood-brain barrier as a proxy demonstration of the translational relevance of our findings. Results2PM of tdTomato-Ly6G+ neutrophils demonstrated increased levels of circulating neutrophils and corresponding engagement with the brain vasculature after the three-dose repeated i.n. exposure regimen. Neutrophilia at the NVU was corroborated with increased transcript levels of Ly6G and other pro-inflammatory markers. This coordination between endothelial physiology and neutrophil phenotypes was recapitulated in murine and human MPS models. System-wide neutrophilia in the lung and circulation was found to be cotemporaneous to neutrophilia at the NVU based on the cellularity of BAL and peripheral blood samples collected at the same endpoints. Immunohistochemical analysis of brain tissue implicates temporal coordination between vascular surface adhesion molecules with changes in neutrophil dynamics from adhesion, crawling, stalling, and transmigration. Extravasation of neutrophils was complemented by sustained paravascular deposition of fibrinogen and microgliosis up to 72 hours after the final i.n. dosing. Microglia-associated effector functions for synaptic pruning and regulation of neutrophil activity demonstrated distinct temporal profiles. ConclusionsOur results identify systemic levels of neutrophilia accompanied by ingress and extravascular accumulation in brain parenchyma that correlated with sustained microglial activation. This neutrophil-centric lung-brain interaction is complemented by the observation of paravascular fibrinogen deposition that alters synaptic metabolism. Thus, we propose a mechanistic role for neutrophilia and associated inflammatory dysregulation as essential mediators along the lung-brain neuroimmune axis in a generalizable model of repeated respiratory exposure to inflammatory agents. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/562508v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@113d747org.highwire.dtl.DTLVardef@19a8a5corg.highwire.dtl.DTLVardef@f1a1eaorg.highwire.dtl.DTLVardef@1bd23c7_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

Nitrogen availability during domestication shaped the divergence of tetraploid wheat

The domestication of crops, with the development of the agroecosystems, is associated with major environmental changes and represent a model to test the role of phenotypic plasticity. Here we investigated 32 genotypes representing key stages of tetraploid wheat domestication. We developed a dedicated pipeline combining RNA-Seq data, estimates of evolvability and QST to characterize the plasticity of gene expression and identify signatures of selection under different nitrogen conditions. The analysis of gene expression diversity showed contrasting results between primary and secondary domestication in relation to nitrogen availability. Indeed, nitrogen triggered the expression of twice the number of genes in durum wheat compared to emmer and wild emmer. QST distributions and QST-FST comparisons revealed distinct selection signatures at each domestication stage. While primary domestication affected the expression of genes involved in biotic interactions, secondary domestication was associated with changes in expression of genes involved in metabolism of amino acids, particularly lysine. Selection signatures were found also in differentially expressed genes, specifically involved in nitrogen metabolism, such as glutamate dehydrogenase. Overall, our findings show that nitrogen availability had a pivotal role during the domestication and adaptive responses of a major food crop, with varying effects across different traits and growth conditions.

genetics↗

bioRxiv2023

Mating systems and recombination landscape strongly shape genetic diversity and selection in wheat relatives

How and why genetic diversity varies among species is a long-standing question in evolutionary biology. Life history traits have been shown to explain a large part of observed diversity. Among them, mating systems have one of the strongest impacts on genetic diversity, with selfing species usually exhibiting much lower diversity than outcrossing relatives. Theory predicts that a high rate of selfing amplifies selection at linked sites, reducing genetic diversity genome wide, but frequent bottlenecks and rapid population turn-over could also explain low genetic diversity in selfers. However, how linked selection varies with mating systems and whether it is sufficient to explain the observed difference between selfers and outcrossers has never been tested. Here, we used the Aegilops/Triticum grass species, a group characterized by contrasted mating systems (from obligate out-crossing to high selfing) and marked recombination rate variation across the genome, to quantify the effects of mating system and linked selection on patterns of neutral and selected polymorphism. By analyzing phenotypic and transcriptomic data of 13 species, we show that selfing strongly affects genetic diversity and the efficacy of selection by amplifying the intensity of linked selection genome wide. In particular, signatures of adaptation were only found in the highly recombining regions in outcrossing species. These results bear implications for the evolution of mating systems and more generally for our understanding of the fundamental drivers of genetic diversity.

evolutionary biology↗

bioRxiv2021

Using Oxford Nanopore Technology direct RNA sequencing to identify depurination events induced by ricin and other ribosome inactivating proteins

Depurination is a frequent modification to both DNA and RNA, in DNA causing point mutations through misincorporation, in RNA, disabling ribosomes and halting protein synthesis. Some modifications of nucleic acids can be determined by direct sequencing using Oxford Nanopore Technologies (ONT). However, the identification of modifications is often limited by noise and their variety and number. Ricin is a toxin which enters cells and depurinates an adenine base in the sarcin-ricin loop of the large ribosomal subunit. This leaves only a ribose backbone, thus inhibiting protein translation. In humans, biological threat agents and ribosome inactivating proteins, such as ricin and saporin, depurinate base 4605 on the 28S rRNA providing a single defined target to try and identify. We postulated that the depurination event could be detected using ONT direct RNA sequencing through a change in charge in the ricin loop. A software tool was developed, RIPpore, that quantified the adenine modification from direct RNA sequencing data of ribosomal RNA purified from respiratory epithelial cells exposed to ricin. This provided a novel method of directly identifying ricin exposure and a basis for ONTs utility in detecting lesions in nucleic acids caused by depurination events.

pharmacology and toxicology↗

bioRxiv2021

Comparative plastomics of Amaryllidaceae: Inverted repeat expansion and the degradation of the ndh genes in Strumaria truncata Jacq.

Amaryllidaceae is a widespread and distinctive plant family contributing both food and ornamental plants. Here we present an initial survey of plastomes across the family and report on both structural rearrangements and gene losses. Most plastomes in the family are of similar gene arrangement and content however some taxa have shown gains in plastome length while in several taxa there is evidence of gene loss. Strumaria truncata shows a substantial loss of ndh family genes while three other taxa show loss of cemA, which has been reported only rarely. Our sparse sampling of the family has detected sufficient variation to suggest further sampling across the family could be a rich source of new information on plastome variation and evolution.

plant biology↗

bioRxiv2020

The road to sorghum domestication: evidence from nucleotide diversity and gene expression patterns

Native African cereals (sorghum, millets) ensure food security to millions of low-income people from low fertility and drought-prone regions of Africa and Asia. In spite of their agronomic importance, the genetic bases of their phenotype and adaptations are still not well understood. Here we focus on Sorghum bicolor, which is the fifth cereal worldwide for grain production and constitutes the staple food for around 500 million people. We leverage transcriptomic resources to address the adaptive consequences of the domestication process. Gene expression and nucleotide variability were analyzed in 11 domesticated and 9 wild accessions. We documented a downregulation of expression and a reduction of diversity both in nucleotide polymorphism (30%) and gene expression levels (18%) in domesticated sorghum. These findings at the genome-wide level support the occurrence of a genetic bottleneck in the domestication history of sorghum, although several genes showed also patterns consistent with the action of selection. Nine hundred and forty-nine genes were significantly differentially expressed between wild and domesticated gene pools. Their functional annotation points to metabolic pathways most likely contributing to the sorghum domestication syndrome, such as photosynthesis and auxin metabolism. Coexpression network analyses revealed 21 clusters of genes sharing similar expression patterns. Four clusters (totalizing 2449 genes) were significantly enriched in differentially expressed genes between the wild and domesticated pools and two were also enriched in domestication and improvement genes previously identified in sorghum. These findings reinforce the evidence that domestication and improvement do not only affect the behaviors of a few genes but led to a large rewiring of the transcriptome during the domestication event and the improvement process. Overall, these analyses pave the way towards the identification of key domestication genes valuable for genetic resources characterization and breeding purposes.

evolutionary biology↗

bioRxiv2020

Genetic diversity of maize landraces from the South-West of France

From the 17th century until the arrival of hybrids in 1960s, maize landraces were cultivated in the South-West of France, a traditional region for maize cultivation. A set of landraces were collected in this region between the 1950s and 1980s and were then conserved ex situ in a germplam collection. Previous studies using molecular markers on approx. twenty landraces fo this region showed that they belonged to a Pyrenees-Galicia Flint genetic group and originated from hybridization between Caribbean and Northern Flint germplasms introduced in Europe. In this study, we assessed the structure and genetic diversity of 194 SWF maize landraces to elucidate their origin, using a 50K SNP array and a bulk DNA approach. We identified two weakly differentiated genetic groups, one in the Western part and the other in the Eastern part. We highlighted the existence of a longitudinal gradient along the SWF area that was probably maintained through the interplay between genetic drifts and restricted gene flows, rather than through differential climatic adaptation. The contact zone between the two groups observed near the Garonne valley may be the result of these evolutionnary forces. We found only few significant cases of hybridization between Caribbean and Northern Flint germplasms in the region. We also found gene flows from various maize genetic groups to SWF landraces. Thus, we assumed that SWF landraces had a multiple origin with a slightly higher influence of Tropical germplasm in the West and preponderance of Northern Flint germplasm in the East.

genetics↗

bioRxiv2020

Comparative analysis based on transcriptomics and metabolomics data reveal differences between emmer and durum wheat in response to nitrogen starvation

Mounting evidence indicates the key role of Nitrogen (N) on diverse processes in plant, including not only yield but also development and defense. Using a combined transcriptomics and metabolomics approach, we studied the response of seedlings to N starvation of two different tetraploid wheat genotypes from the two main domesticated subspecies, emmer (Triticum turgidum ssp. dicoccum) and durum wheat (Triticum turgidum ssp. durum). We found that durum wheat exhibits broader and stronger response in comparison to emmer as evidenced by the analysis of the differential expression pattern of both genes and metabolites and gene enrichment analysis. Emmer and durum wheat showed major differences in the responses to N starvation for transcription factor families. While emmer showed differential reduction in the levels of primary metabolites to N starvation, durum wheat exhibited increased levels of most metabolites, including GABA as an indicator of metabolic imbalance. The correlation-based networks including the differentially expressed genes and metabolites revealed tighter regulation of metabolism in durum wheat in comparison to emmer, as evidenced by the larger number of significant correlations. We also found that glutamate and GABA had highest values of centrality in the metabolic correlation network, suggesting their critical role in the genotype-specific response to N starvation of emmer and durum wheat, respectively. Moreover, this finding indicates that there might be contrasting strategies associated to GABA and Glutamate signaling modulating shoot vs root growth in the two different wheat subspecies.

plant biology↗

bioRxiv2018

Pervasive hybridizations in the history of wheat relatives

Bread wheat and durum wheat derive from an intricate evolutionary history of three genomes, namely A, B and D, present in both extent diploid and polyploid species. Despite its importance for wheat research, no consensus on the phylogeny of the wheat clade has emerged so far, possibly because of hybridizations and gene flows that make phylogeny reconstruction challenging. Recently, it has been proposed that the D genome originated from an ancient hybridization event between the A and B genomes1. However, the study only relied on four diploid wheat relatives when 13 species are accessible. Using transcriptome data from all diploid species and a new methodological approach, we provide the first comprehensive phylogenomic analysis of this group. Our analysis reveals that most species belong to the D-genome lineage and descend from the previously detected hybridization event, but with a more complex scenario and with a different parent than previously thought. If we confirmed that one parent was the A genome, we found that the second was not the B genome but the ancestor of Aegilops mutica (T genome), an overlooked wild species. We also unravel evidence of other massive gene flow events that could explain long-standing controversies in the classification of wheat relatives. We anticipate that these results will strongly affect future wheat research by providing a robust evolutionary framework and refocusing interest on understudied species. The new method we proposed should also be pivotal for further methodological developments to reconstruct species relationship with multiple hybridizations.

evolutionary biology↗

bioRxiv2017

Abundance and diversity of the fecal resistome in slaughter pigs and broilers in nine European countries

EFFORT groupHaitske Graveland, Alieda van Essen, Bruno Gonzalez-Zorn, Gabriel Moyano, Pascal Sanders, Claire Chauvin, Julie David, Antonio Battisti, Andrea Caprioli, Jeroen Dewulf, Thomas Blaha, Katharina Wadepohl, Maximiliane Brandt, Dariusz Wasyl, Magdalena Skarzynska, Magdalena Zajac, Hristo Daskalov, Helmut W Saatkamp, Katharina D.C. Stark.\n\nAbstractAntimicrobial resistance (AMR) in bacteria and associated human morbidity and mortality is increasing. Use of antimicrobials in livestock selects for AMR that can subsequently be transferred to humans. This flow of AMR between reservoirs demands surveillance in livestock as well as in humans. As part of the EFFORT project (www.effort-against-amr.eu), we have quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, generating more than 5,000 gigabases of DNA sequence, using shotgun metagenomics. We quantified acquired AMR using the ResFinder database and a database constructed for this study, consisting of AMR genes identified through screening environmental DNA. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than poultry. We found higher AMR loads in pigs, while poultry resistomes were more diverse. We detected several recently described, critical AMR genes, including mcr-1 and optrA, the abundance of which differed both between host species and countries. We found that the total acquired AMR level, was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns had similar resistomes. Novel, functionally-determined AMR genes were, however, not associated with total drug use.

microbiology↗

bioRxiv2016

Evolutionary forces affecting synonymous variations in plant genomes

Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear. Population genetics approaches allow to jointly estimating the intensity of selection, gBGC and mutational bias. We extended a recently developed method and applied it to a large population genomic datasets based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that base composition is far from mutation-drift equilibrium in most genomes and that gBGC is a widespread and stronger process than selection. gBGC could strongly contribute to base composition variation among plant species, implying that it should be taken into account in plant genome analyses, especially for GC-rich ones.

evolutionary biology↗