Biology subjects

Jacques, M.-A.

Publications and source records attributed to Jacques, M.-A..

At least 19 recordsLinked to original sources

bioRxiv2026

Insights into the transmission of seedborne Pseudomonas syringae strains that cause zucchini diseases.

Vein clearing of zucchini (VCZ) and bacterial leaf spot (BLS) are caused by various strains of the Pseudomonas syringae species complex that infect zucchini (Cucurbita pepo) seeds. VCZ strains have a narrow host range of cucurbits and affect only seedlings, whereas BLS strains have a broader host range and cause symptoms on adult plants. A multiplex qPCR test showed that VCZ strains predominated in infected seed lots produced in different countries. We surveyed hybrid seed crops grown in parallel in two French regions to address inoculum sources. According to DNA-based approach, parental seed lots were positive to BLS strains, although no culturable bacteria were recovered. Hybrid seed lots produced in the Rhone Valley (southeastern France) showed higher infection rates than those produced in Limagne (central France), and VCZ strains were recovered only from the Rhone Valley. Two representative strains of VCZ and BLS colonized seeds through the vascular and floral pathways, whereas only the BLS strain was transmitted through the pericarp. These findings suggest that floral transmission, potentially mediated by pollinators, could explain the predominance of VCZ strains under favorable regional conditions, and that pericarp transmission in BLS strains could be linked to their capacity to cause disease on adult plants. Furthermore, some infections undetected in seeds became apparent after germination, indicating that testing germinated seeds rather than seeds could help seed industry to take in account only bacterial infections transmitted to the seedling. Together, these results provide valuable insights into the epidemiology of P. syringae transmission to zucchini seeds.

pathology↗

bioRxiv2026

An integrated single cell and spatial omics atlas of human prenatal development

Single cell genomics has enabled analysis of human prenatal development at unprecedented resolution. However, most studies have relied on dissociated tissues during restricted windows of development, limiting insights into how spatially distributed networks of cells, and multicellular niches emerge and adapt to distinct organ microenvironments in situ. Moreover, existing human developmental atlases have not yet been harmonised, and we thus lack a comprehensive catalogue of known cell types in the developing human body. Here, we introduce the Human Developmental Cell Atlas (HDCA), a unified structural, cellular and molecular resource for prenatal human development. The HDCA integrates published and unpublished single cell/nucleus RNAseq atlases across prenatal organs, and includes a newly generated, spatially resolved, multimodal cell atlas of intact human embryos. Spanning 4-22 post conceptional weeks, capturing embryonic and early to mid fetal stages, the HDCA contains [~]4.6 million cells/nuclei which resolve into [~]450 cell types, explorable with a bespoke web portal. For a global overview of the human embryos multicellular communities, we applied unsupervised deep learning to our intact human embryo spatial data, charting 114 tissue niches that are structural and signalling hubs for the cellular interactions of the embryo. Guided by these niches, we profiled cellular networks over space and time, not examinable using single-organ atlases. In so doing, we revealed tissue-specific fibroblast patterning from previously undescribed mesenchyme progenitors, early diversification of organ-specific blood capillaries and lymphatic vasculature, emergence of neural crest cell fates, the formation of placode-and neural crest-derived peripheral sensory neurons, and how tissue niches guide peripheral neuron maturation and axonal migration. The HDCA thus serves as a comprehensive step towards a comprehensive understanding of human prenatal development, and a template towards unravelling the biology of congenital disorders.

developmental biology↗

bioRxiv2026

Comparative Biology at Single-Cell Resolution: Rigorous Matching of Atlases for Cross-Species Analysis

Single-cell transcriptomics has revolutionised developmental biology by providing an unprecedented, fine-grained view of cellular lineages. However, our ability to compare species and distinguish universal from species-specific developmental principles remains limited by biological and technical variability. To address this, we introduce RIMA (RIgorous Matching of Atlases), a method for quantitatively comparing transcriptomic atlases across species at near-single-cell resolution. RIMA uses a novel computational approach to identify matching cell states across atlases and leverages this to enable quantitative comparative analyses. Applied to gastrulation in mouse, rabbit, and macaque, RIMA recapitulates a developmental hourglass pattern, identifying a molecular similarity bottleneck at the onset of organogenesis. It further uncovers conserved developmental programmes, including a core set of transcription factors driving epithelial-mesenchymal transition, and highlights transcriptional boosts of erythroid differentiation genes that are conserved across species but exhibit shifted onset timing. Furthermore, RIMA enables cross-species prediction of gene expression, augmenting sparse atlases and correcting differences between model and target organisms. Beyond cross-species comparisons, RIMAs framework extends naturally to any setting where large systematic differences exist across datasets, including in vitro to in vivo comparisons, opening new avenues for improving biological models and advancing translational research.

bioinformatics↗

bioRxiv2025

The hidden life of Xylella: Mining the NCBI Sequence Read Archive reveals potential new species, host plants and infected areas for this elusive bacterial plant pathogen

New crop disease outbreaks can occur when phytopathogenic bacterial pathogens acquire new traits, switch to a new host plant or are introduced into new geographic areas. Therefore, the rapid detection of a pathogen in a new environment and/or in a new host plant is essential to mitigate disease outbreaks. However, bacteria with a wide plant host range, many asymptomatic hosts and slow symptom development can sometimes remain unnoticed for years. This is the case for the vector-borne xylem-inhabiting bacteria Xylella fastidiosa known to infect hundreds of plant species worldwide and its sister species X. taiwanensis, currently thought to be restricted to Taiwan. To investigate whether the two Xylella species are already present in other parts of the world, potentially in unrecognised host species, we performed an in-depth data mining of raw sequence data available in the NCBI Sequence Read Archive. This led to the identification of 62 datasets from diverse plant and insect samples from around the world. Furthermore, nine draft and one circular Xylella genome could be assembled from these datasets. Our results reveal several potential new host plants and previously unrecognized infected areas in the Americas, Africa and southeast Asia. Moreover, the newly-assembled genomes represent several new strains of both X. fastidiosa and X. taiwanensis as well as an additional Xylella species infecting wild rice. Taken together, our work extends our knowledge on the genetic diversity, host range and global distribution of the genus Xylella and can orient surveillance programs towards new regions and host plants.

genomics↗

bioRxiv2024

Spatiotemporal map of the developing human reproductive tract at single-cell resolution

The human reproductive tract plays an essential role in species perpetuation. Its development involves complex processes of sex specification, tissue patterning and morphogenesis, which, if disrupted, can cause lifelong health issues, including infertility. Here, we generated an extensive single-cell and spatial multi-omic atlas of the human reproductive tract during prenatal development, which allowed us to answer questions that smaller-scale, organ-focused experiments could not address before. We identified potential regulators of sexual dimorphism in reproductive organs, pinpointing novel genes involved in urethral canalisation of the penis, with relevance to hypospadias. By combining histological features with gene expression data, we defined the transcription factors and cell signalling events required for the regionalisation of the Mullerian and Wolffian ducts. This led to a refinement of how the HOX code is established in the distinct reproductive organs, including increased expression of thoracic HOX genes in the rostral mesenchyme of the fallopian tube and epididymis. Our study further revealed that the epithelial regionalisation of the fallopian tube and epididymis required for sperm maturation in adulthood is established early in development. In contrast, later events in gestation or postnatally are necessary for the regionalisation of the uterocervical canal epithelium. By mapping sex-specific reproductive tract regionalisation and differentiation at the cellular level, our study offers valuable insights into the causes and potential treatments of reproductive disorders.

developmental biology↗

bioRxiv2024

Comparative transcriptomics reveal a highly polymorphic Xanthomonas HrpG virulence regulon

Bacteria of the genus Xanthomonas cause economically significant diseases in various crops. Their virulence is dependent on the translocation of type III effectors (T3Es) into plant cells by the type III secretion system (T3SS), a process regulated by the master response regulator HrpG. Although HrpG has been studied for over two decades, its regulon across diverse Xanthomonas species, particularly beyond type III secretion, remains understudied. In this study, we conducted transcriptome sequencing to explore the HrpG regulons of 17 Xanthomonas strains, encompassing six species and nine pathovars, each exhibiting distinct host and tissue specificities. We employed constitutive expression of plasmid-borne hrpG*, which encodes a constitutively active form of HrpG, to induce the regulon. Our findings reveal substantial inter- and intra-specific diversity in the HrpG* regulons across the strains. Besides 21 genes directly involved in the biosynthesis of the T3SS, the core HrpG* regulon is limited to only five additional genes encoding the transcriptional activator HrpX, the two T3E proteins XopR and XopL, a major facility superfamily (MFS) transporter, and the phosphatase PhoC. Interestingly, genes involved in chemotaxis and genes encoding enzymes with carbohydrate-active and proteolytic activities are variably regulated by HrpG*. The diversity in the HrpG* regulon suggests that HrpG-dependent virulence in Xanthomonas might be achieved through several distinct strain-specific strategies, potentially reflecting adaptation to diverse ecological niches. These findings enhance our understanding of the complex role of HrpG in regulating various virulence and adaptive pathways, extending beyond T3Es and the T3SS. IMPORTANCEIn the decades since its discovery, HrpG and its role in the regulation of the type III secretion system (T3SS) and its associated type III effectors (T3Es) in Xanthomonas has been the subject of extensive research. Despite notable progress in understanding its molecular regulatory mechanisms, the full spectrum of processes under control of HrpG, particularly beyond the T3SS and T3Es, and the degree of regulatory conservation across plant-pathogenic Xanthomonas species, remained unclear. To address this knowledge gap, we systematically compared the transcriptomes of 17 Xanthomonas strains, expressing a constitutively active form of HrpG, called HrpG*. We showed that HrpG* regulates different physiological processes other than the T3SS and T3Es and that this regulation shows substantial variation across the different strains. Taken together, our results provide new insights into Xanthomonas-plant interactions through the regulation of different metabolic and virulence pathways by the master response regulator HrpG.

microbiology↗

bioRxiv2024

Induction of common bean OVATE Family Protein 7 (PvOFP7) promotes resistance to common bacterial blight

Common bacterial blight of bean (CBB) is a devastating seed-transmitted disease caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans on common bean (Phaseolus vulgaris L.). The genes responsible for CBB resistance are largely unknown. moreover, the lack of reproducible and universal transformation protocol limits the study and improvement of genetic traits in common bean. We produced X. phaseoli pv. phaseoli strains expressing artificially-designed Transcription-Activator Like Effectors (dTALEs) to target 14 candidate genes and performed in planta assays in a susceptible common bean genotype to analyse if the transcriptional induction of these genes could confer resistance to CBB. Induction of PvOFP7, PvAP2-ERF71 and PvExpansinA17 resulted in CBB symptom reduction. In particular, PvOFP7 induction led to strong symptom reduction, linked to reduced bacterial growth in planta at early colonisation stages. RNA-Seq analysis revealed up-regulation of cell wall formation and primary metabolism, and major down-regulation of Heat Shock Proteins. Our results demonstrate that PvOFP7 is contributes to CBB resistance, and underline the usefulness of dTALEs for highlighting genes of quantitative activity.

plant biology↗

bioRxiv2023

Genetic and functional diversity help explain pathogenic, weakly pathogenic, and commensal lifestyles in the genus Xanthomonas

The genus Xanthomonas has been primarily studied for pathogenic interactions with plants. However, besides host and tissue specific pathogenic strains, this genus also comprises nonpathogenic strains isolated from a broad range of hosts, sometimes in association with pathogenic strains, and other environments, including rainwater. Based on their incapacity or limited capacity to cause symptoms on the host of isolation, nonpathogenic xanthomonads can be further characterized as commensal and weakly pathogenic. This study aimed to understand the diversity and evolution of nonpathogenic xanthomonads compared to their pathogenic counterparts based on their co-occurrence and phylogenetic relationship and to identify genomic traits that form the basis of a life-history framework that groups xanthomonads by ecological strategies. We sequenced genomes of 83 strains spanning the genus phylogeny and identified eight novel species, indicating unexplored diversity. While some nonpathogenic species have experienced a recent loss of a type III secretion system, specifically, the hrp2 cluster, we observed an apparent lack of association of the hrp2 cluster with lifestyles of diverse species. We gathered evidence for gene flow among co-occurring pathogenic and nonpathogenic strains, suggesting the potential of nonpathogenic strains to act as a reservoir of adaptive traits for pathogenic strains and vice versa. We further identified traits enriched in nonpathogens that suggest a strategy of stress tolerance, rather than avoidance, during their association with a broad range of host plants.

ecology↗

bioRxiv2023

Development of tools to detect and identify strains belonging to the Pseudomonas syringae species complex responsible for vein clearing of zucchini

Vein clearing of zucchini (VCZ) is a seed-borne bacterial disease that affects young plants of Cucurbita pepo subsp. pepo. VCZ agents are distributed into four phylogenetic clusters within the clades 2a and 2ba of the phylogroup 2 of Pseudomonas syringae species complex. Strains belonging to clades 2b and 2d are sometimes isolated from zucchini seeds but have not been associated with VCZ epidemics. Development of tools able to identify VCZ agents is important to better control the disease. Primers were designed to implement a seven-gene MLSA scheme on a collection of strains isolated from zucchini seeds. A clear predominance of strains with a host range on cucurbits limited to the genus Cucurbita (cluster 2ba-A) and the presence of VCZ strains in a fifth cluster (2ba-C) were evidenced. PCR tests were designed to characterize VCZ clusters and a multiplex qPCR test was proposed to distinguish strains having narrow cucurbit host range, associated to the presence of avrRpt2 and sylC, from broad host range strains associated to the presence of hopZ5 and sylC. Additional qPCR tests targeting clade 2b and 2d were also designed to gain insights on P. syringae strains that could be isolated from cucurbits. Specificity of these tools was evaluated in silico on the whole NCBI database and in vitro on a strain collection, showing a 100% inclusivity, except for the test dedicated to clade-2b strains, and an exclusivity ranging from to 96.7% to 100%. These different tools are intended to serve phylogenetic studies, epidemiological monitoring and seed testing.

pathology↗

bioRxiv2023

Influence of co-occurring weakly pathogenic bacterial species on bacterial spot disease dynamics on tomato

Mixed infections caused by multiple pathogenic and/ weakly pathogenic strains inhabiting the same host plants are common in nature and may modify pathogen dynamics. However, traditional plant pathogen studies have mostly focused on the binary interaction between a single host and a single pathogen. In this study, we have looked beyond this binary interaction and evaluated the impact of co-infection on disease dynamics on tomato using bacterial spot pathogen, Xanthomonas perforans (Xp) and two co-occurring weakly pathogenic strains of X. arboricola (Xa) and Pseudomonas capsici (Pc). Time-series greenhouse co-infection experiments monitoring disease severity and within-host population dynamics revealed higher disease severity in co-infection by three species compared to infection by Xp alone. However, co-infection by dual species, Xp and Pc or Xa resulted in lower disease severity compared to Xp alone. Thus, co-infection outcomes depend on interacting species. Weak pathogens could exploit Xp to colonize the host plant as indicated by their higher populations in co-infection. However, Xp population dynamics was dependent on co-infecting partner. While resource competition might be a possible explanation for lower Xp population in dual co-infection, interaction of Pc with the host was found to influence Xp population. Interestingly, Xp population was higher in presence of three-species interaction compared to Xp and Xa co-infection, suggesting potential modulation of co-operative interactions among Xp and Xa in three-species co-infection rather than competitive interactions. Humidity played a significant role in population dynamics of the three species. Overall, this study highlighted importance of co-infection dynamics in studying plant disease outbreaks.

ecology↗

bioRxiv2023

Analysis of the worldwide diversity of Xanthomonas hortorum pv. carotae, the agent of bacterial blight of carrot, reveals two distinct populations.

Xanthomonas hortorum pv. carotae is a pathogen responsible for the bacterial blight of carrot. While it infects carrot fields worldwide, its diversity remains unknown. Here, we validated by PCR the identification as X. hortorum pv. carotae of most of the strains isolated from carrot symptoms. We study their diversity by sequencing seven housekeeping genes. The analysis confirmed the identity of most of the strains previously identified as X. hortorum pv. carotae and highlighted the presence of two clusters inside the pathovar carotae. The 18 non-X. hortorum pv. carotae have been identified as Xanthomonas from other species. As the X. hortorum pv. carotae strains clustered only in two groups by this analysis, a new MLVA scheme was developed. It allowed to validate the subclusteration in two groups and observe diversity among them. At the same times based on this study and data from the literature, we proposed the strain CFBP 7900 as the neopathotype strain of the pathovar. The strain should replacement the holopathotype strain CFBP 4997, as it is no longer available in international collection.

pathology↗

bioRxiv2022

Systems-level transcriptional regulation of Caenorhabditis elegans metabolism

Metabolism is precisely controlled to ensure organismal development and homeostasis. Several mechanisms regulate metabolism, including allosteric control and transcriptional regulation of metabolic enzymes and transporters. So far, metabolism regulation has mostly been described for individual genes and pathways, and the extent of transcriptional regulation of the entire metabolic network remains largely unknown. Here, we find that more than three-quarters of all metabolic genes are transcriptionally regulated in the nematode Caenorhabditis elegans. We find that many annotated metabolic pathways are coexpressed, and we use gene expression data and the iCEL1314 metabolic network model to define coregulated sub-pathways in an unbiased manner. Using a large gene expression compendium, we determine the conditions where sub-pathways exhibit strong coexpression. Finally, we develop WormClust, a web application that enables a gene-by-gene query of genes to view their association with metabolic (sub)-pathways. Overall, this study sheds light on the ubiquity of transcriptional regulation of metabolism and provides a blueprint for similar studies in other organisms, including humans.

systems biology↗

bioRxiv2022

Automatic detection of spatio-temporal signalling patterns in cell collectives

An increasing experimental evidence points to physiological importance of space-time correlations in signalling of cell collectives. From wound healing to epithelial homeostasis to morphogenesis, coordinated activation of bio-molecules between cells allows the collectives to perform more complex tasks and better tackle environmental challenges. To understand this information exchange and to advance new theories of emergent phenomena, we created ARCOS, a computational method to detect and quantify collective signalling. We demonstrate ARCOS on cell and organism collectives with space-time correlations on different scales in 2D and 3D. We make a new observation that oncogenic mutations in the MAPK/ERK and PIK3CA/Akt pathways of MCF10A epithelial cells induce ERK activity waves with different size, duration, and frequency. The open-source implementations of ARCOS are available as R and Python packages, and as a plugin for napari image viewer to interactively quantify collective phenomena without prior programming experience.

cell biology↗

bioRxiv2022

Two bridgehead invasions of Xylella fastidiosa subsp. multiplex in France

Of American origin, a wide diversity of Xylella fastidiosa strains belonging to different subspecies have been reported in Europe since 2013 and its discovery in Italian olive groves. Strains from the subspecies multiplex (ST6 and ST7) were first identified in France in 2015 in urban and natural areas. To trace back the most probable scenario of introduction in France, the molecular evolution rate of this subspecies was estimated at 3.2165 x 10-7 substitutions per site per year, based on heterochronous genome sequences collected worldwide. This rate allowed the dating of the divergence between French and American strains in 1987 for ST6 and in 1971 for ST7. The development of a new VNTR-13 scheme allowed tracing the spread of the bacterium in France, hypothesizing an American origin. Our results suggest that both sequence types were initially introduced and spread in Provence-Alpes-Cote dAzur (PACA); then they were introduced in Corsica in two waves from the PACA bridgehead populations.

microbiology↗

bioRxiv2021

Optogenetic actuator/biosensor circuits for large-scale interrogation of ERK dynamics identify sources of MAPK signaling robustness.

Combining single-cell measurements of ERK activity dynamics with perturbations provides insights into the MAPK network topology. We built circuits consisting of an optogenetic actuator to activate MAPK signaling and an ERK biosensor to measure single-cell ERK dynamics. This allowed us to conduct RNAi screens to investigate the role of 50 MAPK proteins in ERK dynamics. We found that the MAPK network is robust against most node perturbations. We observed that the ERK-RAF and the ERK-RSK2-SOS negative feedbacks operate simultaneously to regulate ERK dynamics. Bypassing the RSK2-mediated feedback, either by direct optogenetic activation of RAS, or by RSK2 perturbation, sensitized ERK dynamics to further perturbations. Similarly, targeting this feedback in a human ErbB2-dependent oncogenic signaling model increased the efficiency of a MEK inhibitor. The RSK2-mediated feedback is thus important for the ability of the MAPK network to produce consistent ERK outputs and its perturbation can enhance the efficiency of MAPK inhibitors.

systems biology↗

bioRxiv2021

Metagenomic sequencing for rapid identification of Xylella fastidiosa from leaf samples

Xylella fastidiosa (Xf) is a globally distributed plant pathogenic bacterium. The primary control strategy for Xf diseases is eradicating infected plants; therefore, timely and accurate detection is necessary to prevent crop losses and further pathogen dispersal. Conventional Xf diagnostics primarily relies on quantitative PCR (qPCR) assays. However, these methods do not consider new or emerging variants due to pathogen genetic recombination and sensitivity limitations. We developed and tested a metagenomics pipeline using in-house short-read sequencing as a complementary approach for affordable, fast, and highly accurate Xf detection. We used metagenomics to identify Xf to strain level in single and mixed infected plant samples at concentrations as low as one picogram of bacterial DNA per gram of tissue. We also tested naturally infected samples from various plant species originating from Europe and the United States. We identified Xf subspecies in samples previously considered inconclusive with real-time PCR (Cq > 35). Overall, we showed the versatility of the pipeline by using different plant hosts and DNA extraction methods. Our pipeline provides taxonomic and functional information for Xf diagnostics without extensive knowledge of the disease. We hope this pipeline can be used for early detection of Xf and incorporated as a tool to inform disease management strategies. IMPORTANCEXylella fastidiosa (Xf) destructive outbreaks in Europe highlight this pathogens capacity to expand its host range and geographical distribution. The current disease diagnostic approaches are limited by a multiple-step process, biases to known sequences, and detection limits. We developed a low-cost, user-friendly metagenomic sequencing tool for Xf detection. In less than three days, we were able to identify Xf subspecies and strains in field-collected samples. Overall, our pipeline is a diagnostics tool that could be easily extended to other plant-pathogen interactions and implemented for emerging plant threat surveillance.

microbiology↗

bioRxiv2020

Spatio-temporal Control of ERK Pulse Frequency Coordinates Fate Decisions during Mammary Acinar Morphogenesis

The signaling events controlling proliferation, survival, and apoptosis during mammary epithelial acinar morphogenesis remain poorly characterized. By imaging single-cell ERK activity dynamics in MCF10A acini, we find that these fates depend on the average frequency of non-periodic ERK pulses. High pulse frequency is observed during initial acinus growth, correlating with rapid cell motility. Subsequent decrease in motility correlates with lower ERK pulse frequency and quiescence. Later, during lumen formation, coordinated ERK waves emerge across multiple cells of an acinus, correlating with high and low ERK pulse frequency in outer surviving and inner dying cells respectively. Optogenetic entrainment of ERK pulses causally connects high ERK pulse frequency with inner cell survival. Acini harboring the PIK3CA H1047R mutation, commonly observed in breast cancer, display increased ERK pulse frequency, inner cell survival and loss of lumen formation. Thus, fate decisions during acinar morphogenesis are fine-tuned by different spatio-temporal coordination modalities of ERK pulse frequency.

cell biology↗

bioRxiv2020

CODEX, a neural network approach to explore signaling dynamics landscapes

Fluorescent biosensors routinely yield thousands of single-cell, heterogeneous, multi-dimensional signaling trajectories that are difficult to mine for relevant information. We present CODEX, an approach based on artificial neural networks to guide exploration of time-series datasets and to identify motifs in dynamic signaling states.

cell biology↗