Biology subjects

Legrand, J.

Publications and source records attributed to Legrand, J..

14 recordsLinked to original sources

bioRxiv2026

A mechanistic framework for photon-to-carbon efficiency: coupling photosynthetic energy supply and light respiration in microalgae

Photon-to-biomass conversion efficiency in oxygenic phototrophs can vary widely under controlled cultivation, yet its mechanistic origin remains difficult to resolve at the system level. Here, we combine a quantified description of light attenuation and primary photochemistry with a thermodynamically constrained metabolic framework to relate reactor-scale light forcing to intracellular energetics in Chlamydomonas reinhardtii chemostats. In a near-optimal regime, the specific growth rate scales linearly with an effective photochemical input, {phi}{gamma}, defined as the rate of photochemically productive photon absorption. This identifies a physiologically relevant forcing variable at the timescale of growth and an invariant biomass yield on productive photons. Imposing this experimentally grounded constraint reveals a compatible effective energetic coupling within photosynthetic electron transport and strongly restricts the admissible photosynthesis-respiration balance. A two-dimensional growth map in the space of photochemical forcing and respiratory activity reveals a respiration-limited region and a dissipative regime in which excessive respiration lowers photon-use efficiency. Analysis of feasible sub-optimal states identifies a small set of intracellular dissipative motifs. Among them, concomitant operation of the Calvin-Benson cycle and the oxidative pentose phosphate pathway emerges as a parsimonious reaction-level mechanism for dissipative carbon recycling. Overall, the results provide an experimentally anchored framework linking productive light absorption, energetic coupling, and light respiration to photon-yield losses in a controlled phototrophic system.

bioengineering↗

bioRxiv2025

How does selection for flowering in maize shapes defenses components against the European Corn Borer ?

Understanding how selection for flowering time affects maize susceptibility to the European corn borer (ECB, Ostrinia nubilalis) is essential in the context of climate change and increasing pest pressures. We investigated the consequences of divergent selection for flowering time on maize defense and susceptibility traits using two genetic backgrounds (MBS847 and F252). Three complementary approaches were combined: leaf palatability tests, ECB field incidence dynamics surveys, and biochemical analyses of maize stem walls. In the MBS847 background, early-flowering families exhibited lower content of defense compounds, higher leaf palatability, and higher field infestation compared to late-flowering families. In contrast, no significant differences were observed between early and late populations in the F252 background. Differences in susceptibility between families were associated with variation in stem biochemical composition, including fiber components which influence stem rigidity and resistance to ECB. Our results indicate that selection for flowering time can modify plant defense traits and susceptibility in a genetic-background-dependent manner. These findings highlight the interaction between plant phenology, biochemical defenses, and insect herbivory, with implications for breeding and adaptation under changing environmental conditions.

ecology↗

bioRxiv2024

Effects of maize development and phenology on the field infestation dynamics of the European Corn Borer

Phenological match/mismatch between cultivated plants and their pest could impact pest infestastion dynamics in the field. To explore how such match/mismatch of plant and pest phenologies may interact with plant defense dynamics, we studied the infestation dynamics of maize by one of its main pests in Europe, the European Corn Borer (Ostrinia nubilalis; Lepidoptera: Crambidae). A two-year field experiment was carried out on a collection of 23 maize inbred lines contrasted for their earliness. Each inbred line was sown at three different dates in order to expose different developmental stages of maize to natural European corn borer infestation. The effect of the sowing date depended on the inbred line, the pest generation and the year. In 2021, the final pest incidence ranged from 36% to 91% depending on inbred lines and sowing date. In 2022, it ranged from 2% to 77%. This variability in final pest incidence can be related to variations in plant development during plant exposure to pest infestation. However, this relationship was not straightforward. Indeed, the shape and intensity of the relationship depended on the timing of the onset of the pest infestation. When infestation occurred while plants were in a vegetative stage, a non-linear relationship between development and pest incidence was observed with the least and most developed plants being the most infested. When infestation occurred when all plants were in the mature phase, the most developed plants were the least infested. Our results highlight the effect of plant-pest phenological match/mismatch on pest infestation dynamics and underline the importance of taking plant-pest interactions into account to propose relevant control strategies.

ecology↗

bioRxiv2023

Large genetic variability of maize leaf palatability to european corn borer : metabolic insights

Maize is the most-produced cereal in the world, but its production faces constraints such as parasitic attacks from stemborers. We evaluated the resistance of a core-collection of 18 maize lines by measuring their palatability to European Corn Borer (ECB) larvae fed on maize leaf discs. Using an original consumption test device that takes into account the variability of larvae behaviour, we were able to phenotype the resistance of the 18 maize lines. We matched consumption data to existing enzymatic and metabolomic data that characterized the maize core-collection and identified some metabolites such as caffeoyl-lquinate, trocopherol, digalactosylglycerol and tyrosine that are positively or negatively correlated with the palatability to ECB larvae. Altogether, our results confirm the metabolic complexity involved in the establishment of plant defenses. Metabolic changes associated to leaf palatability mostly concern membrane and cell wall composition. Some of them, pointing-out to the phenylpropanoids pathway, were observed independently of plant developmental pace and plant earliness.

genetics↗

bioRxiv2021

Dominant Effect Of Host Genetics On Skin Microbiota Composition In Homeostasis And Wound Healing

Animal microbiota have complex interactions with hosts and environment that determines its composition. Yet the ability of hosts to determine their microbiota composition is less well studied. In this study, to investigate the role host genetics in determining skin microbiota, we used 30 different mouse strains from the recombinant inbred panel, the Collaborative Cross. Murine skin microbiota composition was strongly dependent on murine strain with > 50% of the variation explained by murine strain. In particular, a quantitative trait locus on chromosome 4 associates both with Staphylococcus abundance and principal-component multi-trait analyses. Additionally, excisional wound associated changes in microbiota composition were not uniform across mouse strains and were host-specific, the genetic background accounting for about 40% of the variation in microbiota. Genetic background also had the highest effect on the healing speed of wounds accounting for over 50% of the variation while mouse age and microbiota composition change accounted only for 20% and 5% of the healing speed despite reaching statistical significance. In conclusion, host genetics has a significant impact on the skin microbiota composition during both homeostasis and wound healing. These findings have long reaching implications in our understanding of associations between microbiota dysbiosis and disease.

systems biology↗

bioRxiv2021

A quantitative gibberellin signalling biosensor reveals a role for gibberellins in internode specification at the shoot apical meristem

Growth at the shoot apical meristem (SAM) is essential for shoot architecture construction. The phytohormones gibberellins (GA) play a pivotal role in coordinating plant growth, but their role in the SAM remains mostly unknown. Here, we developed a ratiometric GA signalling biosensor by engineering one of the DELLA proteins, to suppress its master regulatory function in GA transcriptional responses while preserving its degradation upon GA sensing. We demonstrate that this novel degradation-based biosensor accurately reports on cellular changes in GA levels and perception during development. We used this biosensor to map GA signalling activity in the SAM. We show that high GA signalling is found primarily in cells located between organ primordia that are the precursors of internodes. By gain- and loss-of-function approaches, we further demonstrate that GAs regulate cell division plane orientation to establish the typical cellular organisation of internodes, thus contributing to internode specification in the SAM.

plant biology↗

bioRxiv2020

A multiscale analysis of early flower development in Arabidopsis provides an integrated view of molecular regulation and growth control

The link between gene regulation and morphogenesis of multicellular organisms is a fundamental problem in biology. We address this question in the floral meristem of Arabidopsis, which generates new tissues and organs through complex changes in growth patterns. Starting from high-resolution time-lapse images, we generated a comprehensive 4-D atlas of early flower development including cell lineage, cellular growth rates and the expression patterns of 28 regulatory genes. This information was introduced in MorphoNet, a web-based open-access platform. The application of mechanistic computational models indicated that the molecular network based on the literature only explained a minority of the expression patterns. This was substantially improved by adding single regulatory hypotheses for individual genes. We next used the integrated information to correlate growth with the combinatorial expression of multiple genes. This led us to propose a set of hypotheses for the action of individual genes in morphogenesis, not visible by simply correlating gene expression and growth. This identified the central transcription factor LEAFY as a potential regulator of heterogeneous growth, which was supported by quantifying growth patterns in a leafy mutant. By providing an integrated, multiscale view of flower development, this atlas should represent a fundamental step towards mechanistic multiscale-scale models of flower development.

developmental biology↗

bioRxiv2020

A semi-automated design for high-throughput Lepidoptera larvae feeding bioassays

Lepidopteran pests cause considerable damage to all crops over the world. As larvae are directly responsible for these damages, many research efforts are devoted to find plant cultivars which are resistant or tolerant to pest attacks. However, such studies take time, efforts and are costly, especially when one wants to not only find resistance traits but also to evaluate their heritability. We present here a high throughput approach to screen plants for resistance or chemicals for their deterrence, using a leaf-disk consumption assay, which is both suitable for large scale tests and economically affordable. To monitor larvae feeding on leaf disks placed over a layer of agar, we designed 3D models of 50 cages plates. One webcam can sample simultaneously 3 of such plates at a rate of 1 image/min, and follow individual feeding activities on each leaf disk and the movements of 150 larvae. The resulting image stacks are first processed with a custom program running under an open-source image analysis package (Icy) to measure the surface of each leaf disk over time. We further developed statistical procedures running under the R software, to analyze the time course of the feeding activities of the larvae and to compare them between treatments. As a test case, we compared how European corn borer larvae respond to quinine, considered as a bitter alkaloid for many organisms, and to NeemAzal containing azadirachtin, which is a common antifeedant against pest insects. We found that increasing doses of azadirachtin reduce and delay feeding. However, contrary to our expectation, quinine was found poorly effective at the range of concentrations tested. The 3D printed model of the cage and the camera holder, the plugins running under Icy, and the R scripts are freely available, and can be modified according to the particular needs of the users.

animal behavior and cognition↗

bioRxiv2019

Artisanal and farmers bread making practices differently shape fungal species diversity in French sourdoughs

AO_SCPLOWBSTRACTC_SCPLOWPreserving microbial diversity in food systems is one of the many challenges to be met to achieve food security and quality. Although industrialization led to the selection and spread of specific fermenting microbial strains, there are still ongoing artisanal processes that may allow the conservation of a wider species diversity and genetic diversity. We examined whether the diversity of artisanal practices could lead to an increased level in fungal species diversity for bread making. We used an interdisciplinary participatory research approach including bakers, psycho-sociologists and microbiologists to analyze French bread making practices and describe fungal communities in naturally fermented sourdough of 27 bakers and 12 farmer bakers. Bread making practices were classified in two groups: the farmer-like practice group and the artisanal-like practice group. The well-known bakery yeast, Saccharomyces cerevisiae, was dominant (i.e. with a relative abundance over 50%) in only 24% of sourdoughs while other yeast species, belonging to the Kazachstania genus, were dominant in 54% of sourdoughs. Bread making practices were found to drive the distribution of fungal species across sourdoughs. The most striking bread making practice effect was the occurrence of Kazachstania humilis in sourdoughs made with artisanal-like practices and the occurrence of Kazachstania bulderi in sourdoughs made with farmer-like practices. Phenotypic divergences between sourdough and nonsourdough strains were found for K. humilis but not for K. bulderi. Overall, our results showed that preserving bread making practice diversity allows the preservation of a higher species and phenotypic diversity in microbial communities.

ecology↗

bioRxiv2019

PGxCorpus: a Manually Annotated Corpus for Pharmacogenomics

Pharmacogenomics (PGx) studies how individual gene variations impact drug response phenotypes, which makes knowledge related to PGx a key component towards precision medicine. A significant part of the state-of-the-art knowledge in PGx is accumulated in scientific publications, where it is hardly usable to humans or software. Natural language processing techniques have been developed and are indeed employed for guiding experts curating this amount of knowledge. But, existing works are limited by the absence of high quality annotated corpora focusing on the domain. This absence restricts in particular the use of supervised machine learning approaches. This article introduces PGxCorpus, a manually annotated corpus, designed for the automatic extraction of PGx relationships from text. It comprises 945 sentences from 911 PubMed abstracts, annotated with PGx entities of interest (mainly genes variations, gene, drugs and phenotypes), and relationships between those. We present in this article the method used to annotate consistently texts, and a baseline experiment that illustrates how this resource may be leveraged to synthesize and summarize PGx knowledge.

bioinformatics↗

bioRxiv2018

From spatio-temporal morphogenetic gradients to rhythmic patterning at the shoot apex

Rhythmic patterning is central to the development of eukaryotes, particularly in plant shoot post-embryonic development. The plant hormone auxin drives rhythmic patterning at the shoot apical meristem, but the spatio-temporal dynamics of the auxin gradients is unknown. We used quantitative imaging to demonstrate that auxin provides high-definition graded information not only in space but also in time. We provide evidence that developing organs are auxin-emitting centers that could self-organize spatio-temporal auxin gradients through a transport network converging on the meristem center. We further show that a memory of the exposition of cells to auxin allows to differentiate temporally sites of organ initiation, providing a remarkable example of how the dynamic redistribution of a morphogenetic regulator can be used to create rhythmicity.

plant biology↗

bioRxiv2018

PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison

BackgroundPharmacogenomics (PGx) studies how genomic variations impact variations in drug response phenotypes. Knowledge in pharmacogenomics is typically composed of units that have the form of ternary relationships gene variant - drug - adverse event. Such a relationship states that an adverse event may occur for patients having the speciifed gene variant and being exposed to the specified drug. State-of-the-art knowledge in PGx is mainly available in reference databases such as PharmGKB and reported in scientific biomedical literature. But, PGx knowledge can also be discovered from clinical data, such as Electronic Health Records (EHRs), and in this case, may either correspond to new knowledge or confirm state-of-the-art knowledge that lacks \"clinical counterpart\" or validation. For this reason, there is a need for automatic comparison of knowledge units from distinct sources.\n\nResultsIn this article, we propose an approach, based on Semantic Web technologies, to represent and compare PGx knowledge units. To this end, we developed PGxO, a simple ontology that represents PGx knowledge units and their components. Combined with PROV-O, an ontology developed by the W3C to represent provenance information, PGxO enables encoding and associating provenance information to PGx relationships. Additionally, we introduce a set of rules to reconcile PGx knowledge, i.e. to identify when two relationships, potentially expressed using different vocabularies and level of granularity, refer to the same, or to different knowledge units. We evaluated our ontology and rules by populating PGxO with knowledge units extracted from PharmGKB (2,701), the literature (65,720) and from discoveries reported from EHR analysis studies (only 10, manually extracted); and by testing their similarity. We called PGxLOD (PGx Linked Open Data) the resulting knowledge base that represents and reconciles knowledge units of those various origins.\n\nConclusionsThe proposed ontology and reconciliation rules constitute a first step toward a more complete framework for knowledge comparison in PGx. In this direction, the experimental instantiation of PGxO, named PGxLOD, illustrates the ability and difficulties of reconciling various existing knowledge sources.

bioinformatics↗

bioRxiv2018

The molecular signatures of compatible and incompatible pollination

Fertilization in flowering plants depends on the early contact and recognition of pollen grains by the receptive papilla cells of the stigma. To identify the associated molecular pathways, we developed a transcriptomic analysis based on single nucleotide polymorphisms (SNPs) present in two Arabidopsis thaliana accessions, one used as female and the other as male. We succeeded in distinguishing 80 % of transcripts according to their parental origins and drew up a catalog of genes whose expression is modified after pollen-stigma interaction. Global analysis of our data reveals that pattern-triggered immunity (PTI)-associated transcripts are upregulated after compatible pollination. From our analysis, we predicted the activation of the Mitogen-activated Protein Kinase 3 on the female side after compatible pollination, which we confirmed through expression and mutant analysis. Our work defines the molecular signatures of compatible and incompatible pollination, highlights the active status of incompatible stigmas, and unravels a new MPK3-dependent cell wall feature associated with stigma-pollen interaction.

plant biology↗

bioRxiv2018

Kinetic analysis of yeast-yeast interactions in oenological conditions

Fermentation by microorganisms is a key step in the production of traditional food products such as bread, cheese, beer and wine. In these fermentative ecosystems, microorganisms interact in various ways, namely competition, predation, commensalism and mutualism. Traditional wine fermentation is a complex microbial process performed by Saccharomyces and non-Saccharomyces (NS) yeast species. To better understand the different interactions occurring within wine fermentation, isolated yeast cultures were compared with mixed co-cultures of one reference strain of S. cerevisiae with one strain of four NS yeast species (Metschnikowia pulcherrima, M. fructicola, Hanseniaspora opuntiae and H. uvarum). In each case, we studied population dynamics, resource consumed and metabolites produced from central carbon metabolism. This phenotyping of competition kinetics allowed us to confirm the main mechanisms of interaction between strains of four NS species. S. cerevisiae competed with H. uvarum and H. opuntiae for resources although both Hanseniaspora species were characterized by a strong mortality either in isolated or mixed fermentations. M. pulcherrima and M. fructicola displayed a negative interaction with the S. cerevisiae strain tested, with a decrease in viability in co-culture, probably due to iron depletion via the production of pulcherriminic acid. Overall, this work highlights the importance of measuring specific cell populations in mixed cultures and their metabolite kinetics to understand yeast-yeast interactions. These results are a first step towards ecological engineering and the rational design of optimal multi-species starter consortia using modeling tools. In particular the originality of this paper is for the first times to highlight the joint-effect of different species population dynamics on glycerol production and also to discuss on the putative role of lipid uptake on the limitation of some non-conventional species growth although interaction processes.

microbiology↗