Biology subjects

Giraud, E.

Publications and source records attributed to Giraud, E..

14 recordsLinked to original sources

bioRxiv2026

The free-living wellspring of symbiotic nitrogen fixation in Bradyrhizobium

The evolutionary origin of nitrogen-fixing symbiosis has been a long-standing question. To address this, we focused on Bradyrhizobium, a globally abundant bacterial genus that includes classic symbiotic lineages, which rely on the common Nod factor signaling pathway to form nodules, and close relatives capable of fixing nitrogen in a free-living state. We isolated 88 strains carrying the key genes for nitrogen fixation (nif) from non-legume environments and analyzed them alongside 586 public Bradyrhizobium genomes harboring these genes to reconstruct a robust phylogeny of nif genes. Analysis reveals that the earliest-diverging nif lineages are members capable of free-living nitrogen fixation, establishing this as the ancestral state. The Nod factor-dependent symbiotic lineages are polyphyletic, demonstrating at least three independent origins via horizontal acquisition of symbiosis islands. This evolutionary history is reflected in a genomic dichotomy: lineages capable of free-living nitrogen fixation possess a conserved nif island architecture that consistently includes the oxygen-protective gene glbO, whereas the symbiotic nif-associated regions are highly variable and universally lack glbO. Using both loss-of-function and gain-of-function genetic approaches, we show that glbO contributes significantly to nitrogenase activity under free-living conditions, whereas it is dispensable within the protected nodule environment. This work establishes a new framework for the evolution of symbiosis, identifying free-living ancestors as the source from which nitrogen-fixing symbiosis repeatedly and independently evolved in Bradyrhizobium. SignificanceFor over a century, nitrogen-fixing bacteria called rhizobia have been celebrated for their symbiotic partnership with legumes like soybeans and peas. This study overturns the view that this symbiotic lifestyle was the original, advanced state. By discovering and analyzing diverse Bradyrhizobium bacteria from ordinary soils and non-legume plants, we show that the ancestor was capable of free-living nitrogen fixation. Root nodule nitrogen fixation evolved multiple independent times from free-living ancestors. We identify glbO, an oxygen-protective gene located immediately next to the nitrogen fixing genes, as critical for nitrogen fixation in variable soil conditions but dispensable and lost in Bradyrhizobium specialized inside nodules. This repositions free-living Bradyrhizobium as a major potential nitrogen source beyond legumes, with promise for sustainable agriculture.

microbiology↗

bioRxiv2026

Deep behavioral phenotyping of pathogen infected mosquitoes reveals species-specific behavior changes enhancing transmission

Mosquito-borne pathogens are often proposed to alter mosquito behavior to enhance transmission, yet the prevalence, magnitude, and consequences of such effects remain unclear. Using custom high- throughput behavioral assays and deep-learning analysis, we quantified the blood-feeding behavior of more than 5,000 mosquitoes, and long-term activity patterns of more than 1,000 mosquitoes across six clinically relevant mosquito-pathogen combinations. Infection effects were highly species-specific. Anopheles stephensi infected with an African Plasmodium falciparum strain showed elevated flight activity throughout infection, an increased tendency to blood-feed upon host contact, and prolonged feeding times. In contrast, infection with an Asian P. falciparum strain or P. vivax had little impact on An. stephensi behavior. We detected no behavioral changes associated with P. falciparum infection in Anopheles gambiae s.s. or Anopheles coluzzii. Interestingly, dengue virus infection in Aedes aegypti increased landing, probing, and engorgement rates. Together, these results demonstrate that infection-induced behavioral change is not a general phenomenon among mosquito-borne pathogens, yet differs markedly per mosquito and pathogen species. A transmission model parameterized with our data showed that even modest behavioral shifts can substantially increase transmission, underscoring the potential epidemiological importance of subtle phenotypic shifts.

animal behavior and cognition↗

bioRxiv2025

SpikeMAP: An unsupervised spike sorting pipeline for cortical excitatory and inhibitory neurons in high-density multielectrode arrays with ground-truth validation

Large-scale extracellular recording techniques represent a major advance in interrogating the structure and dynamics of neuronal circuits. However, methods that can resolve cell-type identity in a principled way, while simultaneously scaling to thousands of neurons, are currently lacking. Here, we introduce spikeMAP, a pipeline for the analysis of large-scale recordings of in vitro cortical activity that not only allows for the detection of spikes produced by single neurons (spike sorting), but also allows for the reliable distinction between genetically determined cell types by utilizing viral and optogenetic strategies as ground-truth validation. This approach tightly integrates the data analysis pipeline to an optogenetic, viral, and pharmacological protocol allowing for the dynamical probing of distinct cell-types while simultaneously recording from large populations. The novelty of spikeMAP is to combine a stream of well-established analysis techniques in an end-to-end fashion, creating a unified framework as follows. First, individual spike waveforms are fitted by spline interpolation to estimate their half-amplitude and peak-to-peak durations. These values are then entered in a principal component analysis with k-means clustering to identify uncorrelated signals from single channels on the array. Optimal separability of clusters is assessed by linear discriminant analysis. Finally, each channels source location is identified using spatiotemporal characteristics of spike waveforms across the array. We show that spikeMAP can resolve cell type identity in high-density arrays by analyzing activity monitored from mouse prefrontal cortex in vitro slices with an array of 4,096 closely-spaced channels. Using an optotagging functional strategy, we show an effective distinction of regular-spiking excitatory neurons from fast-spiking inhibitory interneurons using measures of action potential waveform, Fano factor, and spatially-dependent cross-correlations. In sum, the approach introduces a toolbox, validated by an experimental pipeline, that allows for a comprehensive characterization of neuronal activity obtained from different cell-types in high-density multielectrode recordings. This provides a scalable approach to investigate the interplay between distinct cell types in microcircuits of the brain. SummaryWe introduce spikeMAP, an automated cell-type specific spike sorting pipeline tailored to high-density, large-scale multielectrode array recordings. We integrate this analysis pipeline to an experimental protocol allowing for the dynamical probing of distinct cell-types while simultaneously recording from large populations of neurons. Using high-density multielectrode arrays containing 4,096 closely spaced electrodes, we monitor the spiking activity of PFC neurons in acute slice preparations. Our spike sorting technique combines spline interpolation and principal component analysis to distinguish regular-spiking excitatory neurons from fast-spiking inhibitory interneurons. We provide an experimental validation of our sorting algorithm using a targeted combination of pharmacological, viral and optogenetic strategies.

neuroscience↗

bioRxiv2024

Intranasal delivery of a broadly neutralizing single domain antibody targeting ACE2 protects against SARS-CoV-2 infection

SARS-CoV-2 accumulates mutations over time leading to the emergence of variants, which become largely resistant to existing vaccines and spike protein-targeted antiviral treatment. Therefore, there is a need for other therapies with broad efficiency. Here, we targeted the angiotensin-converting enzyme 2 (ACE2), the major entry receptor for SARS-CoV-2. We purified three single domain heavy chain antibodies (VHHs) after immunization of an alpaca with the ectodomain of ACE2. These VHHs bound ACE2 with nanomolar affinity and specifically detected membrane-anchored ACE2. Two of them (B07 and B09) neutralized by a competitive mechanism multiple SARS-CoV-2 isolates, including Omicron variants (XBB.1.16.1; EG.5.1.3; BA.2.86.1), without impacting the proteolytic activity of the enzyme. Fusion of B07 with conventional Fc domain markedly improved its binding and neutralizing efficacy. This dimeric Fc-conjugated B07 (B07-Fc) recognized specific residues of the N-terminal helix 1 of ACE2. When administrated prophylactically and intranasally, B07-Fc induced a strong dose-dependent protection of mice expressing human ACE2 (K18-hACE2) from SARS-CoV-2 Omicron. Hamsters were weakly protected due to low binding of B07-Fc to hamster ACE2. These single domain antibodies targeting hACE2 represent potential broad-spectrum therapeutic candidates against any emerging viruses using ACE2 as a receptor. These inhalable neutralizing single domain antibodies also represent a non-invasive approach against respiratory viral infection.

microbiology↗

bioRxiv2024

A Receptor Like Cytoplasmic Kinase evolved in Aeschynomene legumes to mediate Nod-independent rhizobial symbiosis

Many plants interact symbiotically with arbuscular mycorrhizal (AM) fungi to enhance inorganic phosphorus uptake, and legumes also develop a nodule symbiosis with rhizobia for nitrogen acquisition. Establishment and functioning of both symbioses rely on a common plant signaling pathway activated by structurally related Myc- and Nod-factors. Recently, a SPARK Receptor-like-Kinase (RLK)/Receptor-like Cytoplasmic Kinase (RLCK) complex was shown to be essential for AM in both monocot and dicot plants. Here, we show that in Aeschynomene legumes the RLCK component of this receptor complex has evolved following a gene duplication event and mediates a unique nodule symbiosis that is independent of rhizobial Nod factors. In Aeschynomene evenia, AeRLCK2 is crucial for nodule initiation but not for AM. Additionally, AeRLCK2 physically interacts with and is phosphorylated by the Cysteine-rich RLK, AeCRK, also required for nodulation. This work reveals a novel evolutionary origin of this Nod-independent symbiosis from AM.

plant biology↗

bioRxiv2024

Type 1 diabetes and parasite infection: an exploratory study in the NOD mouse

Microorganisms have long been suspected to influence the outcome of immune-related syndromes, particularly autoimmune diseases. Type 1 diabetes (T1D) results from the autoimmune destruction of the pancreatic islets insulin-producing beta cells, causing high glycemia levels. Genetics is part of its etiology, but environmental factors, particularly infectious microorganisms, also play a role. It was shown that bacteria, viruses, and parasites, influence the outcome of T1D in mice and humans. We have used the Non-Obese Diabetic (NOD) mouse that spontaneously develops T1D to address the influence of a parasitic infection, leishmaniasis. Leishmania amazonensis are intracellular eukaryotic parasites replicating predominantly in macrophages and are responsible for cutaneous leishmaniasis. The implication of Th1 immune responses in T1D and leishmaniasis led us to study this parasite in the NOD mouse model. We have previously constructed osteopontin knockout mice in an NOD genetic background and demonstrated that this protein plays a role in the T1D phenotype. In addition, osteopontin (OPN) has been found i) to play a role in the immune response to various infectious microorganisms and ii) to be implicated in other autoimmune conditions, such as multiple sclerosis in humans and experimental autoimmune encephalomyelitis (EAE) in mice. We present herein data demonstrating the implication of OPN in the response to Leishmania in the NOD mouse and the influence of this parasitic infection on T1D. This exploratory study aims to investigate the environmental infectious component of the autoimmune response, including through Th1 immunity, common to both T1D and leishmaniasis.

immunology↗

bioRxiv2023

High throughput screening identifies broad-spectrum Coronavirus entry inhibitors

The Covid-19 pandemic highlighted the pressing need for antiviral therapeutics capable of mitigating infection and spread of emerging coronaviruses (CoVs). A promising therapeutic strategy lies in inhibiting viral entry mediated by the Spike (S) glycoprotein. To identify small molecule inhibitors that block entry downstream of receptor binding, we established a high-throughput screening (HTS) platform based on pseudoviruses. We employed a three-step process to screen nearly 200,000 small molecules. First, we identified potential inhibitors by assessing their ability to inhibit pseudoviruses bearing the SARS-CoV-2 S glycoprotein. Subsequent counter-screening against pseudoviruses with the Vesicular Stomatitis Virus glycoprotein (VSV-G), yielding sixty-five SARS-CoV-2 S-specific inhibitors. These were further tested against pseudoviruses bearing the MERS-CoV S glycoprotein, which uses a different receptor. Out of these, five compounds including the known broad-spectrum inhibitor Nafamostat, were subjected to further validation and tested them against pseudoviruses bearing the S glycoprotein of the alpha, delta, and omicron variants as well as against bona fide SARS-CoV-2 in vitro. This rigorous approach revealed a novel inhibitor and its derivative as a potential broad-spectrum antiviral. These results validate the HTS platform and set the stage for lead optimization and future pre-clinical, in vivo studies.

microbiology↗

bioRxiv2023

Phylogenetic and population structure of the nod-free but nodulating Bradyrhizobium phylogroup

Bradyrhizobium is a main rhizobial lineage of which most members nodulate legume plants using Nod factors (NFs) synthetized by the nod genes. However, members of the Photosynthetic supergroup (phylogroup) within Bradyrhizobium (PB) are nod-free but still capable of establishing nitrogen-fixing nodules with some tropical legumes of the Aeschynomene genus. These unusual findings are based on the genomic sequences of only 13 PB strains, and almost all were isolated from Aeschynomene nodules. Here, we investigate the diversity of Bradyrhizobium in grassland, forest, and rice field by rpoB amplicon sequencing and report that PB is mainly associated with rice root and rhizosphere. Moreover, we sequenced 209 new PB members isolated mostly from the rice field. The extended PB supergroup comprises three major clades: a basal clade with significant expansion of its diversity, followed by an intermediate clade composed by two strains, and a new clade exclusively represented by our new strains. Although the PB strains universally lack the canonical nod genes, all 28 assayed strains covering the broad diversity of these clades induced nodules on Aeschynomene indica. Interestingly, the three clades displayed significant differences in the efficiency of symbiosis, aligning well with their phylogenetic branching order. Our strain collection expands the ecological, phylogenetic and functional diversity of nod-free but nodulating Bradyrhizobium. With this expanded diversity, we conclude that the NF-independent nodulation of Aeschynomene is a common trait of this supergroup, in contrast to the photosynthetic trait originally thought as its unifying feature.

genomics↗

bioRxiv2022

Enhanced neutralization escape to therapeutic monoclonal antibodies by SARS-CoV-2 Omicron sub-lineages

The landscape of SARS-CoV-2 variants dramatically diversified with the simultaneous appearance of multiple sub-variants originating from BA.2, BA.4 and BA.5 Omicron sub-lineages. They harbor a specific set of mutations in the spike that can make them more evasive to therapeutic monoclonal antibodies. In this study, we compared the neutralizing potential of monoclonal antibodies against the Omicron BA.2.75.2, BQ.1, BQ.1.1 and XBB variants, with a pre-Omicron Delta variant as a reference. Sotrovimab retains some activity against BA.2.75.2, BQ.1 and XBB as it did against BA.2/BA.5, but is less active against BQ.1.1. Within the Evusheld/AZD7442 cocktail, Cilgavimab lost all activity against all subvariants studied, resulting in loss of Evusheld activity. Finally, Bebtelovimab, while still active against BA.2.75, also lost all neutralizing activity against BQ.1, BQ.1.1 and XBB variants.

microbiology↗

bioRxiv2022

Potent Human Broadly SARS-CoV-2 Neutralizing IgA and IgG Antibodies Effective Against Omicron BA.1 and BA.2

Memory B-cell and antibody responses to the SARS-CoV-2 spike protein contribute to long-term immune protection against severe COVID-19, which can also be prevented by antibody-based interventions. Here, wide SARS-CoV-2 immunoprofiling in COVID-19 convalescents combining serological, cellular and monoclonal antibody explorations, revealed humoral immunity coordination. Detailed characterization of a hundred SARS-CoV-2 spike memory B-cell monoclonal antibodies uncovered diversity in their repertoire and antiviral functions. The latter were influenced by the targeted spike region with strong Fc-dependent effectors to the S2 subunit and potent neutralizers to the receptor binding domain. Amongst those, Cv2.1169 and Cv2.3194 antibodies cross-neutralized SARS-CoV-2 variants of concern including Omicron BA.1 and BA.2. Cv2.1169, isolated from a mucosa-derived IgA memory B cell, demonstrated potency boost as IgA dimers and therapeutic efficacy as IgG antibodies in animal models. Structural data provided mechanistic clues to Cv2.1169 potency and breadth. Thus, potent broadly neutralizing IgA antibodies elicited in mucosal tissues can stem SARS-CoV-2 infection, and Cv2.1169 and Cv2.3194 are prime candidates for COVID-19 prevention and treatment.

immunology↗

bioRxiv2021

Mosquito-bacteria interactions during larval development trigger metabolic changes with carry-over effects on adult fitness

In animals with distinct life stages such as holometabolous insects, adult phenotypic variation is often shaped by the environment of immature stages, including their interactions with microbes colonizing larval habitats. Such carry-over effects were previously observed for several adult traits of the mosquito Aedes aegypti after larval exposure to different bacteria, but the mechanistic underpinnings are unknown. Here, we investigated the molecular changes triggered by gnotobiotic larval exposure to different bacteria in Ae. aegypti. We initially screened a panel of 16 bacterial isolates from natural mosquito breeding sites to determine their ability to influence adult life-history traits. We subsequently focused on four bacterial isolates (belonging to Flavobacterium, Lysobacter, Paenibacillus, and Enterobacteriaceae) with significant carry-over effects on adult survival and found that they were associated with distinct transcriptomic profiles throughout mosquito development. Moreover, we detected carry-over effects at the level of gene expression for the Flavobacterium and Paenibacillus isolates. The most prominent transcriptomic changes in gnotobiotic larvae reflected a profound remodeling of lipid metabolism, which translated into phenotypic differences in lipid storage and starvation resistance at the adult stage. Together, our findings indicate that larval exposure to environmental bacteria trigger substantial physiological changes that impact adult fitness, uncovering a mechanism underlying carry-over effects of mosquito-bacteria interactions during larval development.

microbiology↗

bioRxiv2020

Genetics of nodulation in Aeschynomene evenia uncovers new mechanisms of the rhizobium-legume symbiosis

Among legumes (Fabaceae) capable of nitrogen-fixing nodulation, several Aeschynomene spp. use a unique symbiotic process that is independent of Nod factors and infection threads. They are also distinctive in developing root and stem nodules with photosynthetic bradyrhizobia. Despite the significance of these symbiotic features, their understanding remains limited. To overcome such limitations, we conducted genetic studies of nodulation in Aeschynomene evenia, supported by the development of a genome sequence for A. evenia and transcriptomic resources for 10 additional Aeschynomene spp. Comparative analysis of symbiotic genes substantiated singular mechanisms in the early and late nodulation steps. A forward genetic screen also showed that AeCRK, coding a novel receptor-like kinase, and the symbiotic signaling genes AePOLLUX, AeCCamK, AeCYCLOPS, AeNSP2 and AeNIN, are required to trigger both root and stem nodulation. This work demonstrates the utility of the A. evenia model and provides a cornerstone to unravel new mechanisms underlying the rhizobium-legume symbiosis.

plant biology↗

bioRxiv2018

A phylogenetic framework of the legume genus Aeschynomene for comparative genetic analysis of the Nod-dependent and Nod-independent symbioses

SUMMARYO_LISome Aeschynomene legume species have the property of being nodulated by photosynthetic Bradyrhizobium lacking the nodABC genes. Knowledge of this unique Nod (factor)-independent symbiosis has been gained from the model A. evenia but our understanding remains limited due to the lack of comparative genetics with related taxa using a Nod-dependent process.\nC_LIO_LITo fill this gap, this study significantly broadened previous taxon sampling, including in allied genera, to construct a comprehensive phylogeny. This backbone tree was matched with data on chromosome number, genome size, low-copy nuclear genes and strengthened by nodulation tests and a comparison of the diploid species.\nC_LIO_LIThe phylogeny delineated five main lineages that all contained diploid species while polyploid groups were clustered in a polytomy and were found to originate from a single paleo-allopolyploid event. In addition, new nodulation behaviours were revealed and Nod-dependent diploid species were shown to be tractable.\nC_LIO_LIThe extended knowledge of the genetics and biology of the different lineages in the legume genus Aeschynomene provides a solid research framework. Notably, it enabled the identification of A. americana and A. patula as the most suitable species to undertake a comparative genetic study of the Nod-independent and Nod-dependent symbioses.\nC_LI

plant biology↗

bioRxiv2018

Global biogeographical regions of freshwater fishes

AimTo define the major biogeographical regions and transition zones for freshwater fish species.\n\nTaxonStrictly freshwater species of actinopterygian fish (i.e., excluding marine and amphidromous fish families).\n\nMethodsWe based our bioregionalisation on a global database of freshwater fish species occurrences in drainage basins, which, after filtering, includes 11 295 species in 2 581 basins. On the basis of this dataset, we generated a bipartite (basin-species) network upon which we applied a hierarchical clustering algorithm (the Map Equation) to detect regions. We tested the robustness of regions with a sensitivity analysis. We identified transition zones between major regions with the participation coefficient, indicating the degree to which a basin has species from multiple regions.\n\nResultsOur bioregionalisation scheme showed two major supercontinental regions (Old World and New World, 50% species of the world and 99.96% endemics each). Nested within these two supercontinental regions lie six major regions (Nearctic, Neotropical, Palearctic, Ethiopian, Sino-Oriental and Australian) with extremely high degrees of endemism (above 96% except for the Palearctic). Transition zones between regions were of limited extent compared to other groups of organisms. We identified numerous subregions with high diversity and endemism in tropical areas (e.g. Neotropical), and a few large subregions with low diversity and endemism at high latitudes (e.g. Palearctic).\n\nMain conclusionsOur results suggest that regions of freshwater fish species were shaped by events of vicariance and geodispersal which were similar to other groups, but with freshwater-specific processes of isolation that led to extremely high degrees of endemism (far exceeding endemism rates of other continental vertebrates), specific boundary locations, and limited extents of transition zones. The identified bioregions and transition zones of freshwater fish species reflect the strong isolation of freshwater fish faunas for the past 10 to 20 million years. The extremely high endemism and diversity of freshwater fish fauna raises many questions about the biogeographical consequences of current introductions and extinctions.

ecology↗