Biology subjects

Ledoux, J.-B.

Publications and source records attributed to Ledoux, J.-B..

10 recordsLinked to original sources

bioRxiv2026

MRSIPrep: A Standardized Post-Quantification Framework for Preprocessing Whole-Brain Magnetic Resonance Spectroscopic Imaging

Magnetic resonance spectroscopic imaging (MRSI) enables non-invasive mapping of neu-rometabolites levels across the human brain. Although spectral fitting and metabolite quan-tification are increasingly supported by mature software tools, the downstream processing of quantified metabolite maps remains heterogeneous across laboratories. Here, we introduce MRSIPrep, an open-source, modular, and reproducible post-quantification framework for whole-brain MRSI. MRSIPrep standardizes quality control, tissue correction, spatial nor- malization, atlas projection, and derivative generation from quantified metabolite maps and associated quality metrics. The framework produces voxelwise, regional, and connectomics-ready outputs together with automated quality-control reports. We describe the architecture of MRSIPrep and demonstrate its utility for reproducible MRSI analysis across datasets,acquisition protocols, and downstream applications.

neuroscience↗

bioRxiv2026

Improved 3D Radial Phyllotaxis Trajectories for Uniform Density Distribution of Readout Directions and Sequential Binning

PurposeTo develop 3D radial spiral phyllotaxis trajectories that provide a uniform density distribution of readout directions and support retrospective sequential binning, thereby reducing ringing artifacts and improving image quality. MethodsUPhy trajectory redefines the polar angle to achieve uniform density distribution of readout directions. FlexiPhy further decouples the azimuthal and polar ordering of interleaves through a randomized permutation, improving robustness to sequential binning. The proposed trajectories were evaluated in vivo on 10 healthy volunteers using two gradient-echo sequences on a 3T MRI scanner. Sequential temporal reconstructions were compared with reference reconstructions using structural similarity and relative L2 error metrics. ResultsUPhy presents analytically demonstrated uniform density distribution of readout directions. Quantitative analysis shows significantly higher SSIM values and lower relative L2 errors for FlexiPhy compared with both the original phyllotaxis and UPhy trajectories after Bonferroni correction (pcorrected < 0.05). ConclusionFlexiPhy enables more reliable sequential binning reconstructions by reducing trajectory-induced ringing artifacts and temporal inconsistencies. Moreover, its randomized construction is not tied to a specific binning strategy, making it broadly compatible with retrospective binning approaches used in dynamic and motion-resolved MRI.

bioinformatics↗

bioRxiv2026

Sex differences in brain metabolism assessed with whole-brain magnetic resonance spectroscopic imaging

Sex differences in brain disorders span age at onset, symptom profiles, disease course and treatment response, and may partly reflect underlying differences in cellular metabolism. Indeed, in vivo evidence of sex-related neurometabolic variation remains sparse, with heterogenous and conflicting findings. Using fast high-resolution whole-brain three-dimensional magnetic resonance spectroscopic imaging, we mapped five brain metabolites in three independent cohorts of healthy participants (total n = 114). In a discovery sample of adolescents scanned at 3 Tesla (3T) (n = 61), males showed higher total N-acetylaspartate (tNAA) across widespread gray matter regions. Regional analyses further revealed opposing sex patterns with a complementary higher total creatine (tCr) observed in females, motivating examination of their ratio as an integrative metabolic index. The tNAA/tCr ratio was consistently higher in males in the discovery sample and this finding was replicated across two independent young-adult samples (3T, n = 26; 7T, n = 27), with a widespread gray and white matter distribution. This tNAA/tCr ratio may link neuronal mitochondrial metabolism with cellular energy buffering, positioning it as a potential index of bioenergetic balance relevant for conditions showing both sex differences and altered neurometabolism, notably multiple sclerosis, Alzheimer disease, and psychosis. Together, these findings reveal a reproducible, distributed metabolic sexual dimorphism in the human brain, and underscore the importance of accounting for sex-specific neurometabolic profiles in studies of brain health and disease.

neuroscience↗

bioRxiv2025

High-resolution whole-brain magnetic resonance spectroscopic imaging in youth at risk for psychosis

Advances in three-dimensional magnetic resonance spectroscopic imaging (3D-MRSI) allow for the high-resolution mapping of multiple neurometabolites throughout the entire brain in vivo and within clinically compatible time frames. Leveraging this capability, we created a voxel-based pipeline that corrects and spatially normalizes whole-brain maps of total N-acetylaspartate (tNAA), myo-inositol (Ins), choline compounds, glutamate + glutamine, and creatine + phosphocreatine. We examined 2 different 3D-MRSI dataset: first, a clinical sample of adolescents and young adults at risk for psychosis (n= 21) meeting DSM-5 criteria for Attenuated Psychosis Syndrome (APS) or Schizotypal Personality Disorder (SCZT), and age-/sex-matched healthy controls (n =13); and second, a non-clinical sample of adolescents (n = 61) scanned on a different site. The objective of the study was threefold: first, to assess the reproducibility of 3D-MRSI measures across datasets and scanning sites; second, to validate the feasibility of whole-brain, voxel-based analyses on 3D-MRSI data; and third, to test the sensitivity of this approach. Metabolite distributions showed reproducible regional variation in standard space between the two independent samples and scanning sites (r ranging from 0.82 to 0.99). Relative to controls, at-risk participants exhibited higher tNAA levels in frontal grey matter; the SCZT subgroup additionally displayed widespread cortical and subcortical elevations of Ins levels compared with both APS and controls. Voxel-based analyses of structural (i.e., gray and white matter volumes or densities) and diffusion (i.e., generalized fractional anisotropy) parameters yielded no significant differences between patients and controls. These preliminary findings suggest that high-resolution 3D-MRSI may be sensitive enough to detect subtle neurometabolic alterations at the group level in the early stages of psychotic disorders when structural or diffusion measures show no difference. High-resolution whole-brain metabolic mapping may have the potential to help with early identification of young people at risk for psychosis or other mental disorders.

neuroscience↗

bioRxiv2025

Monalisa: An Open Source, Documented, User-Friendly MATLAB Toolbox for Magnetic Resonance Imaging Reconstruction

PurposeAn open-source, user-friendly MATLAB framework for Magnetic Resonance Imaging (MRI) reconstruction was developed to simplify the reconstruction process, with a specific focus on non-Cartesian imaging and dynamic applications in the presence of motion. MethodsMonalisa is decomposing the reconstruction pipeline into clear modular steps, including raw data reading with flexible file-type abstraction, trajectory computation, density compensation, advanced coil sensitivity mapping, and tailored binning strategies through its "mitosius" preprocessing stage. The framework supports a suite of reconstruction methods, including iterative-SENSE (also named CG-SENSE), GeneRalized Autocalibrating Partial Parallel Acquisition (GRAPPA) reconstructions, and regularized reconstructions supporting both spatial and temporal regularization using l1 (Compressed Sensing (CS)) and l2 techniques, accommodating both Cartesian and non-Cartesian acquisitions. We performed benchmark experiments comparing Monalisa with the Berkeley Advanced Reconstruction Toolbox (BART) toolbox on simulated 2D radial acquisitions. ResultsResults of the comparison demonstrate competitive performance, yielding higher Structural Similarity Index (SSIM) and lower l2 error. Notably, Monalisa reconstructions exhibited fewer visible artifacts than BART. ConclusionBy providing comprehensive documentation, Monalisa serves not only as a powerful tool for research and clinical imaging but also as an educational platform to facilitate innovation in MRI reconstruction.

bioinformatics↗

bioRxiv2025

Does local adaptation influence thermal responses in red coral populations across depth gradients? Transcriptomic insights for effective conservation.

Marine heatwaves (MHWs) pose significant threats to marine biodiversity, including Mediterranean octocorals. Using a common garden experiment, we test whether differential transcriptomic responses to thermal stress between shallow and mesophotic populations of Corallium rubrum are shaped by their adaptation to the local environment, i.e. local adaptation. Six individuals from one shallow (15m) and one mesophotic (48m) population were exposed to control (18{degrees}C) and thermal stress (25{degrees}C) treatments, with samples collected at day 0 (T0), day 5 (T5), and day 10 (T10) for RNA sequencing (N=36). We revealed 1,957 differentially expressed genes (DEGs) in response to heat stress. Mild transcriptomic responses were observed in the shallow population (441 DEGs) characterized by heat shock proteins (HSPs) and developmental regulation. Conversely, a stronger and extensive response was observed in the mesophotic population with more than twice as many DEGs (1,081), predominantly associated with enhanced stress and wound healing mechanisms. Temporal transcriptional shifts were larger between T5 to T10 in the mesophotic population (1,497 vs 241), while more stable in the shallow (265 vs 271). Additionally, 172 DEGs, including HSPs, apoptosis and collagen, were found in the shallow population under control conditions, indicating transcriptional frontloading. The contrasting thermal stress responses between populations suggest distinct adaptative strategies potentially driven by local adaptation. These insights challenge the deep refugia hypothesis that considered mesophotic populations as potential sources for recolonization and active restoration of shallow populations threatened by MHWs. Our results support the need to integrate population-specific adaptive responses into conservation and restoration strategies for C. rubrum.

molecular biology↗

bioRxiv2024

Chromosome-level genome assembly and annotation of Corallium rubrum: a Mediterranean coral threatened by overharvesting and climate change.

Reference genomes are key resources in biodiversity conservation. Yet, sequencing efforts are not evenly distributed in the tree of life questioning our true ability to enlighten conservation with genomic data. Good quality reference genomes remain scarce in octocorals while these species are highly relevant target for conservation. Here, we present the first annotated reference genome in the red coral, Corallium rubrum (Linnaeus, 1758), a habitat-forming octocoral from the Mediterranean and neighboring Atlantic, impacted by overharvesting and anthropogenic warming-induced mass mortality events. Combining long reads from Oxford Nanopore Technologies (ONT), Illumina paired-end reads for improving the base accuracy of the ONT-based genome assembly and Arima Hi-C contact data to place the sequences into chromosomes, we assembled a genome of 475 Mb (21 chromosomes, 326 scaffolds) with contig and scaffold N50 of 1.6 Mb and 16.2 Mb, respectively. Fifty percent of the sequence (L50) was contained in eight superscaffolds. The consensus quality (QV) of the final assembly was 42 and the gene completeness reported by BUSCO was 74% (metazoa_odb10 database). We annotated 39,114 protein-coding genes and 32,678 non-coding transcripts. This annotated chromosome-level genome assembly, one of the first in octocorals, is currently used in a project based on whole genome re-sequencing dedicated to the conservation and management of C. rubrum. Significance StatementThe Mediterranean red coral, Corallium rubrum, is critically impacted by overharvesting and by mass mortality events linked to marine heat waves. Accordingly, C. rubrum is increasingly receiving conservation efforts. Previous population genetics studies based on microsatellites contributed to improving our knowledge of the species ecology. Yet, crucial questions regarding, admixture among lineages, demographic history, effective population sizes and local adaptation, are still open owing to a lack of genomic resources. Here, we present the first chromosome-level genome assembly for the species with high contiguity, good completeness and protein-coding genes and repeat sequence annotations. This genome, one of the first in octocorals, will pave the way for the integration of population genomics data into ongoing interdisciplinary conservation efforts dedicated to C. rubrum.

genomics↗

bioRxiv2024

Recurrent extreme climatic events are driving gorgonian populations to local extinction: low adaptive potential to marine heatwaves.

Extreme climatic events (ECEs), such as marine heatwaves (MHWs), are a major threat to biodiversity. Understanding the variability in ecological responses to recurrent ECEs within species and underlying drivers arise as a key issue owing to their implications for conservation and restoration. Yet, our knowledge on such ecological responses is limited since it has been mostly gathered following "single-event approaches" focused on one particular event. These approaches provide snapshots of ecological responses but fall short of capturing heterogeneity patterns that may occur among recurrent ECEs, questioning current predictions regarding biodiversity trends. Here, we adopt a "multi-event" perspective to characterize the effects of recurrent ECEs and the ecological responses in Paramuricea clavata, a Mediterranean temperate coral threatened by MHWs. Through a common-garden experiment repeated three consecutive years with the same individuals from three populations, we assessed the respective roles of environmental (year effect), genetic (population effect) and phenotypic (population-by-environment interactions effect) components in the ecological response to recurrent heat stress. The environmental component (year) was the main driver underlying the responses of P. clavata colonies across experiments. To build on this result, we showed that: i) the ecological responses were not related to population (genetic isolation) and individual (multilocus heterozygosity) genetic make-up, ii) while all the individuals were characterized by a high environmental sensitivity (genotype-by-environment interactions) likely driven by in-situ summer thermal regime. We confront our experimental results to in situ monitoring of the same individuals conducted in 2022 following two MHWs (2018, 2022). This confirms that the targeted populations harbor limited adaptive and plastic capacities to on-going recurrent ECEs and that P. clavata might face unavoidable population collapses in shallow Mediterranean waters. Overall, we suggest that biodiversity forecasts based on "single event" experiments may be overly optimistic and underscore the need to consider the recurrence of ECEs in assessing threats to biodiversity.

ecology↗

bioRxiv2022

Apicomplexans predict thermal stress mortality in the Mediterranean coral Paramuricea clavata

The octocoral Paramuricea clavata is an ecosystem architect of the Mediterranean temperate reefs that is currently threatened by episodic mass mortality events related to global warming. Local average thermal regimes nor recent thermal history have been shown to play a significant role in population thermotolerance in this species. The microbiome, however, may play an active role in the thermal stress susceptibility of corals, potentially holding the answer as to why corals show differential sensitivity to heat-stress. To investigate this, the prokaryotic and eukaryotic microbiome of P. clavata collected from around the Mediterranean was characterized before experimental heat-stress to determine if its microbial composition influences the thermal response of the holobiont. We found that the prokaryotic community was not informative in predicting the thermal susceptibility of P. clavata. On the other hand, members of P. clavatas microeukaryotic community were significantly correlated with thermal stress sensitivity. Syndiniales from the Dino-Group I Clade 1 were significantly enriched in thermally resistant corals, while the apicomplexan corallicolids were significantly enriched in thermally susceptible corals. Corallicolids are associated with 70% of coral genera around the world, yet the ecological role of this general anthozoan symbiont has yet to be determined. We hypothesize that P. clavata mortality following heat-stress may be caused by a shift from apparent commensalism to parasitism in the corallicolid-coral host relationship driven by the added stress. Our results show the potential importance of corallicolids and the rest of the microeukaryotic community of corals to understanding thermal stress response in corals and provides a useful tool to guide conservation efforts and future research into coral-associated microeukaryotes.

microbiology↗

bioRxiv2019

The genome sequence of the octocoral Paramuricea clavata - a key resource to study the impact of climate change in the Mediterranean

The octocoral, Paramuricea clavata, is a habitat-forming anthozoan with a key ecological role in rocky benthic and biodiversity-rich communities in the Mediterranean and Eastern Atlantic. Shallow populations of P. clavata in the North-Western Mediterranean are severely affected by warming-induced mass mortality events (MMEs). These MMEs have differentially impacted individuals and populations of P. clavata (i.e. varied levels of tissue necrosis and mortality rates) over thousands of kilometers of coastal areas. The eco-evolutionary processes and genetic factors contributing to these differential responses remain to be characterized. Here, we sequenced a P. clavata individual with short and long read technologies, producing 169.98 Gb of Illumina paired-end and 3.55 Gb of Oxford Nanopore Technologies (ONT) reads. We obtained a de novo hybrid assembly accounting for 712.4 Mb and 107,682 scaffolds. The contig and scaffold N50 are 15.85 Kb and 17.01 Kb, respectively. Despite of the low contiguity of the assembly, the gene completeness was relatively high, including 86% of the 978 metazoan genes contained in the metazoa_odb9 database. A total of 76,508 protein-coding genes and 85,763 transcripts have been annotated. This assembly is one of the few octocoral genomes currently available. This is undoubtedly a valuable resource for characterizing the genetic bases of the differential responses to thermal stress and for the identification of thermo-resistant individuals and populations. Overall, the genome of P. clavata will help to understand various aspects of its evolutionary ecology and to elaborate effective conservation plans such as active restoration actions to overcome the threats of global change.

genomics↗