Biology subjects

Fournier, C.

Publications and source records attributed to Fournier, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Disentangling shape and size variation to compare canopy architecture in maize

{middle dot} Comparing maize canopies is confounded by two problems: plants differ in the number of phytomers they produce, and phytomer size scales with that number. Position along the shoot is therefore an unreliable basis for comparison, confounding shape with size. {middle dot} We first position the floral transition (tassel initiation, T.I.) within shoot development, revealing it as the landmark that organizes a conserved canopy shape. This provides the foundation for aligning canopies that differ in phytomer number. {middle dot} Focusing on the leaf blade, we used functional data analysis on a maize panel across controlled and field environments to decompose variation in blade-length profiles, which was dominated (77%) by overall amplitude, identifying scaling as the major source of size variation. Because blades enlarge with each phytomer until the transition, later T.I. yields a larger maximum; this T.I.-linked component explains up to one-third of scaling variation, reinforced by a shared genetic association between T.I. and blade size with the flowering-time gene ZmCCT10. {middle dot} Regressing out this component leaves a residual that defines a new, heritable axis of intrinsic scaling, independent of flowering time. It distinguishes hyper- and hypo-scaling genotypes consistently across environments, offering a selection target decoupled from phenology.

plant biology↗

bioRxiv2026

Seasonal succession of nano- and picoplankton communities in Lake Constance: conserved dynamics despite compositional shifts under contrasting mixing and oxygen regimes

Lake Constance is a pre-Alpine, monomictic, oligotrophic lake situated at the southern end of Germany composed of two main water bodies: deep, oligotrophic Upper Lake Constance (ULC) and the shallow, more mesotrophic Lower Lake Constance (LLC). To date, no sequencing-based study exists of the seasonal succession of the microbial plankton in Lake Constance. Over one-year, microbial plankton communities were sampled biweekly from the top 20 m of the water column in both sites and separated into nanoplankton (NP) and picoplankton (PP). Communities were analysed using rDNA amplicon sequencing: NP samples were analysed by 18S rDNA, and PP samples by 18S and 16S rDNA sequencing. Temporal community diversity was compared between sites and the effect of two major environmental perturbations, winter vertical mixing in ULC and oxygen depletion of the bottom-water layer in LLC, on the community was examined. Despite strong environmental contrasts, microbial plankton communities exhibited conserved seasonal temporal dynamics across basins. In contrast, pronounced compositional shifts occurred during mixing and oxygen depletion events. Approximately 20% of detected taxa were positively associated with these events, with log fold changes reaching 9.82, reflecting rare or undetectable taxa outside these periods. Taxa favoured by these perturbations commonly exhibited high metabolic flexibility, including mixotrophy, fermentation, or anaerobic respiration, or possessed functional traits conferring tolerance to altered redox and mixing regimes. Our results suggest that the temporal dynamics of freshwater microbial plankton communities are driven by deterministic processes and highlight the profound impact of large, and less known, environmental changes on these communities.

ecology↗

bioRxiv2026

Systemic neoantigen-specific T cells reveal central determinants of PD-(L)1 blockade efficacy

The contribution of neoantigen-specific T cells to PD-(L)1 efficacy has largely been inferred from tumor mutational burden. We functionally profiled circulating T cell responses against 7,038 predicted HLA-I-restricted and 21,453 HLA-II-restricted neopeptides in 27 patients with advanced non-small cell lung cancer treated with anti-PD-(L)1. CD4 responses were frequent and correlated with neoantigen availability but not clinical benefit. In contrast, the magnitude and breadth of neoantigen-specific CD8 T cell responses were associated with clinical benefit, progression-free and overall survival, independently of tumor mutational burden. Patients mounting coordinated CD4 and CD8 responses experienced improved progression-free survival. Tumors from CD8 responders displayed immune signatures indicative of both T cell priming and effector functions. Circulating neoantigen-specific CD8 T cells recognized endogenously processed antigens, trafficked to tumors, and selectively expanded under therapy while retaining CD28, CD226, and CXCR3 expression. These findings identify coordinated, functionally engaged neoantigen-specific T cell responses as central determinants of PD-(L)1 efficacy.

cancer biology↗

bioRxiv2025

Nanostructured lipid carriers overcome the low immunogenicity of M2e peptide via surface click chemistry conjugation, improving the anti-M2e antibody response

Influenza vaccines are considered the most effective measure for preventing influenza. The key antigen of commercial vaccines is hemagglutinin (HA), the main protein on the surface of influenza viruses. This protein is genetically variable, necessitating the annual redefinition of the vaccine formulation. Furthermore, these vaccines do not offer protection against pandemic viral strains. The M2e peptide, a small surface protein conserved among influenza type A strains, could enable cross-immunity when used as an antigen. Nevertheless, its limited immunogenicity has restricted its application in universal influenza vaccines. To enhance the immune responses to M2e, we associated it with Nanostructured Lipid Carriers (NLCs). These NLCs are stable over time and their small diameter (<100 nm) enhances interactions with antigen-presenting cells and improve lymphatic drainage, facilitating their uptake by the immune system. The M2e specific antibody response in mice was enhanced by using "click" chemistry to conjugate the M2e peptide to the NLC surface. Also, the incorporation of PADRE-specific CD4+ T cells stimulating peptide between M2e peptide and its linking region greatly enhanced the specific antibody response to M2e and generated immune response levels that could be compatible with influenza protection. This promising M2e formulation vectorized by NLC represents a potential universal influenza vaccine candidate warranting further preclinical investigations and clinical evaluation.

immunology↗

bioRxiv2024

FROM FEAR TO FEAST: RATTLESNAKES NAVIGATE THE LANDSCAPE OF FEAR TO OPTIMIZE FORAGING

According to optimal foraging theory, mesopredators should forage in areas where their prey is abundant while avoiding high predation risk. Here, we investigate how environmental factors influence mesopredators abilities to minimize spatiotemporal overlap with predators while increasing spatiotemporal overlap with prey. We paired thirty western diamond-backed rattlesnake (Crotalus atrox) 3D-printed replicas with game cameras in West Texas for two years to quantify several spatiotemporal factors affecting prey availability and predation risk. Concurrently, 25 Crotalus atrox were radiotracked at the same site to gather activity and microhabitat selection data regarding free-ranging individuals. Random forest algorithms were trained using data obtained from the game camera and applied to predict the probability of predation and the probability of prey encounter for each radiotracking event. Time of day, month, vegetation structure, and concealment percentage, all had a significant association with the probability of predation and the probability of prey encounter. Our results suggest that rattlesnakes choose to be active when and where the probability of prey encounter was significantly higher than the probability of detection by predators, thus following optimal foraging theory. Our results demonstrate that mesopredators increase chances of prey capture while reducing predator detection in natural setting.

ecology↗

bioRxiv2024

Second generation of LNP based mRNA vaccine leads to a T-cell-inflamed tumor microenvironment favorable for improving PD-1/PD-L1 blocking therapy and long-term immunity in a cold tumor model

The delivery of mRNA-based cancer vaccines has demonstrated significant promise in triggering antitumor immune responses. With the aim of using them in combination with other immunotherapies already used in the clinical appropriately, the modifications of the intratumoral immune microenvironment needs to be deeply characterized. We have shown that the second generation of lipid nanoparticles (LNPs), nanostructured lipid carriers (so-called Lipidots(R)), are able to vector protein antigens and nucleic acids. Here, we test Lipidots(R) for the delivery of mRNA encoding OVA antigen and eliciting a specific antitumor immune response. We demonstrate in vitro that our LNPs deliver mRNA into dendritic cells (DCs), when complexed with mRNA, activate DCs through the TLR4/8 and ROS signaling pathways and induce specific CD4+ and CD8+ T cell activation. Our vaccinal strategy exhibits significant antitumor efficacy both in the context of tumor prevention and as a therapeutic vaccine in B16OVA and E.G7-OVA cold tumors. The LNP-Ova mRNA vaccine induces a profound intratumoral remodeling of the innate and adaptive immunity associated with an increase in the gene expression of chemokines (Cxcl10, Cxcl11, Cxcl9) involved in CD8+ T cell attraction. Additionally, the vaccine induces the establishment of an escape mechanism mediated by PD-1/PDL-1 axis, making it an adjuvant therapy for optimized responses to the blocking of this signaling pathway. Finally, the combination of vaccine and anti-PD-1 therapy achieves a much higher rate of complete responses and memory immune responses compared to monotherapies. Our work demonstrates the capability of Lipidots(R) as an effective platform for the development of preventive and therapeutic vaccines against cancer based on mRNA delivery and that combination with other immunotherapies such as immune checkpoint blockers could counter tumor resistance and promote long-term antitumor immunity.

immunology↗

bioRxiv2024

Induction of cytoplasmic dsDNA and cGAS-STING immune signaling after exposure of breast cancer cells to X-rays or high energetic carbon ions

Radiotherapy can trigger activation of the cGAS-STING axis via cytoplasmic dsDNA fragment induction. The activation of cGAS-STING initiates innate immune signaling mediated by interferon type-I that can contribute to eradicate the malignancy. The effect was shown to depend on the fractionation scheme employed. We hypothesized that the innate immune response can also depend on radiation quality because densely ionizing radiation, such as carbon ions, have different effects on DNA lesion quality. We show here that carbon ions induced a significantly higher yield of cytosolic dsDNA fragments per unit dose as compared to photons in an in vitro 4T1 breast cancer model. The higher efficiency also translated in expression and release of interferon-{beta} by the tumor cells. Cytoplasmic dsDNA fragments as well as interferon-{beta} release increased with doses up to 24 Gy and no differences for a fractionation scheme (3x8 Gy) were found as compared to the single high doses of photons. In conclusion, we found that the release of interferon-{beta} after radiation is increasing with the radiation dose up to 20 Gy and that carbon ions have the potential to elicit a strong innate immune signaling.

biophysics↗

bioRxiv2024

FLASH Bragg-peak irradiation with a therapeutic carbon ion beam: first in vivo results

Background and purposeIn recent years, ultra-high dose rate (UHDR) irradiation has emerged as a promising innovative approach to cancer treatment. Characteristic feature of this regimen, commonly referred to as FLASH effect, demonstrated primarily for electrons, photons or protons, is the improved normal tissue sparing, while the tumor control is similar to the one of the conventional dose-rate (CDR) treatments. The FLASH mechanism is, however, unknown. One major question is whether this effect is maintained when using densely ionizing (high-LET) heavy nuclei. Materials and MethodsHere we report the effects of 20 Gy UHDR heavy ion irradiation in clinically relevant conditions, i.e., at high-LET in the spread-out Bragg peak (SOBP) of a 12C beam using an osteosarcoma mouse model. ResultsWe show that UHDR irradiation was less toxic in the normal tissue compared to CDR while maintaining tumor control. The immune activation was also comparable in UHDR and CDR groups. We observed that the gut microbiome was altered in mice injected with the tumor compared to healthy animals, but both UHDR and CDR exposures steered the metagenome toward a balanced state. ConclusionsThe results show that the FLASH effect is safe and effective in heavy ion therapy and provide an important benchmark for the current mechanistic FLASH models. Highlights- FLASH irradiation with SOBP carbon ions spares normal tissue in mouse - Tumor control, immune response, and gut microbioma changes are induced at the same extent both at conventional and ultra-high dose rate - FLASH carbon ion irradiation is a safe and effective alternative to conventional radiotherapy.

cancer biology↗

bioRxiv2024

Genetic network analysis uncovers spatial variation in diversity and connectivity of a species presenting a continuous distribution

The conservation of genetic diversity and connectivity is essential for the long-term persistence and adaptive ability of a species. Recent calls have been made for the inclusion of genetic diversity and differentiation measures in the assessment, management, and conservation of species. However, the literature often lacks direction on how to do so for species with continuous distributions or no distinct breaks in genetic connectivity. There are many considerations to overcome when investigating genetic diversity and connectivity of such species. We combine multiple genetic network methodologies with more traditional population genetic analyses within a single framework to address the challenges of investigating population structure and quantifying variation in genetic diversity and connectivity of wide-ranging species with continuous distributions. We demonstrate the efficacy and applicability of our framework through a study on woodland caribou (Rangifer tarandus) occupying the boreal forest of Canada; a species of significant conservation concern. The dataset consisted of 4911 unique individuals genotyped at 9 microsatellite loci, which were subsequently partitioned into 103 spatial nodes to create a population-based genetic network. The Walktrap community detection algorithm was used to detect hierarchical population genetic structure within the study area and node-based network metrics such as mean inverse edge weight and clustering coefficient were used to quantify the variation in genetic connectivity across the range. Lastly, genetic diversity was assessed by calculating allelic richness and heterozygosity of the nodes making up the network. The community detection analysis identified two communities at the coarsest scale to nine communities at the optimal partition. A strong pattern of Isolation by Distance (IBD) was found across the range at multiple scales. Furthermore, signs of genetic erosion along the study areas southern boundaries were depicted by nodes presenting low genetic diversity and low centrality values. These results are important to the species status assessments in providing previously unavailable information on connectivity and diversity within and beyond the current local population units used in management. Our approach to quantify the patterns and extent of connectivity across the boreal range is comprehensive and could easily be adapted to other species. The results are robust and provide a solid foundation for the continued monitoring and recovery of the species.

ecology↗

bioRxiv2023

Inter-phylum circulation of a beta-lactamase - encoding gene: a rare but observable event

Beta-lactam degradation by beta-lactamases is the most common mechanism of beta-lactam resistance in Gram-negative bacteria. Beta-lactamase encoding genes can be transferred between closely-related bacteria, but spontaneous inter-phylum transfers (between distantly related bacteria) has never been reported. Here, we describe an extended-spectrum beta-lactamase (ESBL)-encoding gene (blaMUN-1) shared between the Peudomonadota and Bacteroidota phyla. An Escherichia coli strain was isolated from a patient in Munster (Germany). Its genome was sequenced (Illumina and Nanopore). The ESBL encoding gene was cloned and the corresponding enzyme was characterised. Distribution of the gene among bacteria was studied with BLASTN using RefSeq Genomes databases. Frequency of its closest homolog in the Global Microbial Gene Catalog (GMGC) was also analysed. The blaMUN-1 gene found in the E. coli strain, encoded for an Ambler subclass A2 beta-lactamase with 82.2% amino acid identity to TLA-1 and it was found to confer an ESBL phenotype. blaMUN-1 was found in four copies, two chromosomal copies and two located on a phage-plasmid p0111. Each copy was found on a 7.6kb genomic island associated with mobility. blaMUN-1 was found distributed among the Bacteroidales order and in Sutterella wardsworthensis (Pseudomonadota). Its closest homolog in the GMGC was found predominantly and frequently in the Human gut sub-catalog (found in 26.8% of the samples). This is the first reported case of inter-phylum transfer of an ESBL-encoding gene, between the Bacteroidota and Pseudomonadota phyla. While the gene was frequently found in the human gut, inter-phylum transfer was rare, suggesting that inter-phylum barriers are strong but not impassable.

microbiology↗

bioRxiv2023

A fast and reliable larval sampling method for improving the monitoring of fruit flies in soft and stone fruits

The spotted-wing drosophila, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae), threatens both the soft-skinned and stone fruit industry in Asia, Europe and America. Integrated pest management requires monitoring for infestation rates in real-time. Although baited traps are widely used for field monitoring, trap captures are weakly correlated to infestation rates. Thus, monitoring for larvae instead of adult flies represents the most reliable monitoring technique. Current methods for larval monitoring (e.g. dunk flotation) are both time-consuming and labor-intensive. In this study, we develop the sleeve method, a new method for monitoring larval infestation in strawberries through the inspection of fruits individually crushed within transparent plastic sleeves. Based on count data from both specialist and non-specialist observers, the estimation of larval infestation with the sleeve method is fast, precise and highly repeatable within and among all observers. Mean processing time is twice faster than previous methods and varies from 33 to 80 seconds per sample, depending on infestation levels. As the accuracy of the sleeve method decreases with infestation levels, we suggest ways to improve its accuracy by incubating fruits for 48h and calibrating data with exact counts. This new method is easier to use, faster and more cost-effective than previous monitoring methods. It could be used to monitor D. suzukii infestations in various fruit crops and is scalable to the farm-level for fruit growers or for academic research. Finally, the method represents a promising monitoring tool for effective management programs of D. suzukii and other insect pests of soft and stone fruits.

ecology↗

bioRxiv2023

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Coffea arabica, an allotetraploid hybrid of C. eugenioides and C. canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred [~]30.5 kya, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

genomics↗

bioRxiv2023

Ripening dynamics revisited: an automated method to track the development of asynchronous berries on time-lapse images

BackgroundGrapevine berries undergo asynchronous growth and ripening dynamics within the same bunch. Due to the lack of efficient methods to perform sequential non-destructive measurements on a representative number of individual berries, the genetic and environmental origins of this heterogeneity, as well as its impacts on both vine yield and wine quality, remain nearly unknown. To address these limitations, we propose to track the growth and coloration kinetics of individual berries on time-lapse images of grapevine bunches. ResultFirst, a deep-learning approach is used to detect berries with at least 50{+/-}10% of visible contours, and infer the shape they would have in the absence of occlusions. Second, a tracking algorithm was developed to assign a common label to shapes representing the same berry along the time-series. Training and validation of the methods were performed on challenging image datasets acquired in a robotised high-throughput phenotyping platform. Berries were detected on various genotypes with a F1-score of 91.8%, and segmented with a mean absolute error of 4.1% on their area. Tracking allowed to label and retrieve the temporal identity of more than half of the segmented berries, with an accuracy of 98.1%. This method was used to extract individual growth and colour kinetics of various berries from the same bunch, allowing us to propose the first statistically relevant analysis of berry ripening kinetics, with a time resolution lower than one day. ConclusionsWe successfully developed a fully-automated open-source method to detect, segment and track overlapping berries in time-series of grapevine bunch images. This makes it possible to quantify fine aspects of individual berry development, and to characterise the asynchrony within the bunch. The interest of such analysis was illustrated here for one genotype, but the method has the potential to be applied in a high throughput phenotyping context. This opens the way for revisiting the genetic and environmental variations of the ripening dynamics. Such variations could be considered both from the point of view of fruit development and the phenological structure of the population, which would constitute a paradigm shift.

plant biology↗

bioRxiv2022

PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time

BackgroundHigh-throughput phenotyping platforms allow the study of the form and function of a large number of genotypes subjected to different growing conditions (GxE). A number of image acquisition and processing pipelines have been developed to automate this process, for micro-plots in the field and for individual plants in controlled conditions. Capturing shoot development requires extracting from images both the evolution of the 3D plant architecture as a whole, and a temporal tracking of the growth of its organs. ResultsWe propose PhenoTrack3D, a new pipeline to extract a 3D+t reconstruction of maize at organ level from plant images. It allows the study of plant architecture and individual organ development over time during the entire growth cycle. PhenoTrack3D improves a former method limited to 3D reconstruction at a single time point [Artzet et al., 2019] by (i) a novel stem detection method based on deep-learning and (ii) a new and original multiple sequence alignment method to perform the temporal tracking of ligulated leaves. Our method exploits both the consistent geometry of ligulated leaves over time and the unambiguous topology of the stem axis. Growing leaves are tracked afterwards with a distance-based approach. This pipeline is validated on a challenging dataset of 60 maize hybrids imaged daily from emergence to maturity in the PhenoArch platform (ca. 250,000 images). Stem tip was precisely detected over time (RMSE < 2.1cm). 97.7% and 85.3% of ligulated and growing leaves respectively were assigned to the correct rank after tracking, on 30 plants x 43 dates. The pipeline allowed to extract various development and architecture traits at organ level, with good correlation to manual observations overall, on random subsets of 10 to 355 plants. ConclusionsWe developed a novel phenotyping method based on sequence alignment and deep-learning. It allows to characterise automatically and at a high-throughput the development of maize architecture at organ level. It has been validated for hundreds of plants during the entire development cycle, showing its applicability to the GxE analyses of large maize datasets.

plant biology↗

bioRxiv2021

Bacterial microcompartments for isethionate desulfonation in the taurine-degrading human-gut bacterium Bilophila wadsworthia

BackgroundBilophila wadsworthia, a strictly anaerobic, sulfite-reducing bacterium and common member of the human gut microbiota, has been associated with diseases such as appendicitis and colitis. It is specialized on organosulfonate respiration for energy conservation, i.e., utilization of dietary and host-derived organosulfonates, such as taurine (2-aminoethansulfonate), as sulfite donors for sulfite respiration, producing hydrogen sulfide (H2S), an important intestinal metabolite that may have beneficial as well as detrimental effects on the colonic environment. Its taurine desulfonation pathway involves a glycyl radical enzyme (GRE), isethionate sulfite-lyase (IslAB), which cleaves isethionate (2-hydroxyethane sulfonate) into acetaldehyde and sulfite. ResultsWe demonstrate that taurine metabolism in B. wadsworthia 3.1.6 involves bacterial microcompartments (BMCs). First, we confirmed taurine-inducible production of BMCs by proteomic, transcriptomic and ultra-thin sectioning and electron-microscopical analyses. Then, we isolated BMCs from taurine-grown cells by density-gradient ultracentrifugation and analyzed their composition by proteomics as well as by enzyme assays, which suggested that the GRE IslAB and acetaldehyde dehydrogenase are located inside of the BMCs. Finally, we are discussing the recycling of cofactors in the IslAB-BMCs and a potential shuttling of electrons across the BMC shell by a potential ironsulfur (FeS) cluster-containing shell protein identified by sequence analysis. ConclusionsWe characterized a novel subclass of BMCs and broadened the spectrum of reactions known to take place enclosed in BMCs, which is of biotechnological interest. We also provided more details on the energy metabolism of the opportunistic pathobiont B. wadsworthia and on microbial H2S production in the human gut.

microbiology↗

bioRxiv2021

Tuning the immunostimulation properties of cationic lipid nanocarriers for nucleic acid delivery

Nonviral systems, such as lipid nanoparticles, have emerged as reliable methods to enable nucleic acid intracellular delivery. The use of cationic lipids in various formulations of lipid nanoparticles enables the formation of complexes with nucleic acid cargo and facilitates their uptake by target cells. However, due to their small size and highly charged nature, these nanocarrier systems can interact in vivo with antigen-presenting cells (APCs), such as dendritic cells (DCs) and macrophages. As this might prove to be a safety concern for developing therapies based on lipid nanocarriers, we sought to understand how they could affect the physiology of APCs. In the present study, we investigate the cellular and metabolic response of primary macrophages or DCs exposed to the neutral or cationic variant of the same lipid nanoparticle formulation. We demonstrate that macrophages are the cells affected most significantly and that the cationic nanocarrier has a substantial impact on their physiology, depending on the positive surface charge. Our study provides a first model explaining the impact of charged lipid materials on immune cells and demonstrates that the primary adverse effects observed can be prevented by fine-tuning the load of nucleic acid cargo. Finally, we bring rationale to calibrate the nucleic acid load of cationic lipid nanocarriers depending on whether immunostimulation is desirable with the intended therapeutic application, for instance, gene delivery or messenger RNA vaccines.

immunology↗

bioRxiv2020

X-ray Irradiation activates immune response in human T-lymphocytes by eliciting a Ca2+ signaling cascade

Radiation therapy is efficiently employed for eliminating cancer cells and reducing tumor growth. To further improving its therapeutic application it is mandatory to unravel the molecular effects of ionizing irradiation and to understand whether they support or counteract tumor therapy. Here we examine the impact of X-ray irradiation on immune activation of human T cells with single doses typically employed in tumor therapy. We discover that exposing cells to radiation triggers in a population of leukemic Jurkat T cells and in peripheral blood mononuclear cells (PBMCs) a canonical Ca2+ signaling cascade, which elicits immune activation of these cells. An early step in the signaling cascade is the initiation of sustained oscillations of the cytosolic Ca2+ concentration, an event mediated by store operated Ca2+ entry (SOCE) via an X-ray induced clustering of the Calcium Release-Activated Calcium Modulator 1 with the stromal interaction molecule 1 (Oari1/STIM1). A functional consequence of the Ca2+ signaling cascade is the translocation of the transcription factor nuclear factor of activated T cells (NFAT) from the cytosol into the nucleus where it elicits the expression of genes required for immune activation. These data imply that a direct activation of blood immune cells by ionizing irradiation has an impact on toxicity and therapeutic effects of radiation therapy.

biophysics↗

bioRxiv2019

Phenomenal: An automatic open source library for 3D shoot architecture reconstruction and analysis for image-based plant phenotyping

In the era of high-throughput visual plant phenotyping, it is crucial to design fully automated and flexible workflows able to derive quantitative traits from plant images. Over the last years, several software supports the extraction of architectural features of shoot systems. Yet currently no end-to-end systems are able to extract both 3D shoot topology and geometry of plants automatically from images on large datasets and a large range of species. In particular, these software essentially deal with dicotyledons, whose architecture is comparatively easier to analyze than monocotyledons. To tackle these challenges, we designed the Phenomenal software featured with: (i) a completely automatic workflow system including data import, reconstruction of 3D plant architecture for a range of species and quantitative measurements on the reconstructed plants; (ii) an open source library for the development and comparison of new algorithms to perform 3D shoot reconstruction and (iii) an integration framework to couple workflow outputs with existing models towards model-assisted phenotyping. Phenomenal analyzes a large variety of data sets and species from images of high-throughput phenotyping platform experiments to published data obtained in different conditions and provided in a different format. Phenomenal has been validated both on manual measurements and synthetic data simulated by 3D models. It has been also tested on other published datasets to reproduce a published semi-automatic reconstruction workflow in an automatic way. Phenomenal is available as an open-source software on a public repository.

plant biology↗