Biology subjects

Valero, M.

Publications and source records attributed to Valero, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Comparison of the performance of sporophytes derived from narrow and wide genetic crosses between strains of the cultivated kelp Saccharina latissima

Seaweed mariculture allows sustainable production of large quantities of biomass for multiple downstream applications but the genotypes cultivated by this industry need to be improved to increase efficiency and cost-effectiveness. It is important that the genetic improvement of cultivated strains does not lead to the introduction of foreign genetic material into wild seaweed populations, which are already under threat from global heating. To circumvent this problem, efforts are being made to develop breeding approaches based on the use of locally-resourced genetic material. The aim of this study was to evaluate the potential effectiveness of this 'local' breeding strategy compared to a classical breeding approach based on wide genetic crosses. Analyses of growth rates and cell wall composition of F1 hybrids derived from either intra- or inter-population crosses between Saccharina latissima strains from two localities, southern Brittany, France and the Faroe Islands, did not identify any clear advantage of inter- compared to intra-population crosses. Breeding based on locally-resourced strains would therefore appear to be a valid approach for current strain selection programs. The study also established a large collection of gametophyte strains from multiple sites for future breeding programs and showed that these strains retained the capacity to become fertile after more than ten years in culture.

genetics↗

bioRxiv2026

Life-cycle plasticity enables conditional asexual reproduction in a kelp

Many organisms alternate between distinct life stages and can reproduce either sexually or asexually, yet the mechanisms coordinating these developmental and reproductive transitions remain poorly understood. Here, we investigate the molecular basis of life stage identity and reproductive mode in the kelp Laminaria pallida, a multicellular organism with a complex life cycle. By combining gene expression analyses with developmental experiments and natural population-level approaches, we identify the genetic networks that govern developmental state transitions in both sexual and asexual contexts. We show that the capacity for asexual reproduction is broadly retained but rarely expressed in natural populations and is associated with reduced fitness. Moreover, we find that the presence of potential mating partners suppresses asexual development, revealing that reproductive mode is actively adjusted in response to reproductive opportunities. Together, these findings suggest that asexual reproduction functions as a conditional alternative to sex, promoting persistence when sexual reproduction is constrained while preserving the long-term benefits of sexual reproduction when mates are available. More broadly, our results reveal how organisms integrate developmental, environmental, and reproductive cues to balance alternative reproductive strategies across complex life cycles.

Developmental Biology↗

bioRxiv2026

Haplotype tagging sheds light on speciation between two divergent cryptic species of the brown algae Ectocarpus

Understanding how genome-wide divergence translates to barriers to gene flow is a central question in speciation research, particularly in marine environments where interconnected habitats frequently accommodate cryptic diversity. Using linked-read whole-genome data from the brown alga Ectocarpus, we investigated genome-wide reproductive isolation between two cryptic brown algal species E. siliculosus and E. crouaniorum across replicated hybrid zones in Europe and Chile. We first uncover deep genetic structure within E. crouaniorum, revealing a more intricate species complex than previously recognized. Despite this complexity, we found parallel patterns of asymmetric introgression that emerged independently in Europe and Chile, where we detected both, F1 and low-level introgressed individuals. However, the specific lineage pairs involved in hybridization depended on local demographic history. Demographic modeling further indicated that reproductive isolation strengthens gradually with divergence time and differs markedly between geographic regions, with ongoing asymmetric gene flow even between lineage pairs where hybrids were not detected in the field. In all cases, the genomic landscape of hybridization is consistent with a polygenic, genome-wide barrier to gene flow rather than a few large-effect regions. Our results show that cryptic speciation in brown algae is driven by repeatable, regionally parallel architectures of genome-wide reproductive isolation which is shaped by ecological and demographic context.

evolutionary biology↗

bioRxiv2025

Data-driven identification of functional networks in artificial and biological neural networks

Understanding how the brain represents information is a central challenge in neuroscience and a practical bottleneck for brain-computer interfaces. Existing analytical tools cannot identify neural representations directly from neural activity data. We introduce MultiPEC, a data-driven method that discovers neural representations by quantifying how sets of signals jointly reduce context prediction error. Applied to artificial neural networks, MultiPEC uncovered class-specific subnetworks whose targeted ablation disproportionately impaired performance, demonstrating their causal role in feature recognition. Applied to EEG recordings from 24 participants, MultiPEC revealed functional signatures of auditory and visual processing. Classification analyses showed that MultiPEC captured fine-grained stimulus submodalities (levels of stimulus meaningfulness) more effectively than broad stimulus domains, highlighting the context-sensitive nature of neural representations. Together, these results establish MultiPEC as a scalable approach for identifying data driven (natural) representations in both biological and artificial systems, with potential applications in adaptive neurotechnology, clinical diagnostics and cognitive neuroscience. HighlightsO_LIMultiPEC identifies neural representations by extracting information clusters from neural activity data. C_LIO_LIEEG analyses reveal individualized, condition-specific functional networks across auditory and visual modalities. C_LIO_LIIn convolutional neural networks, MultiPEC uncovers class-specific networks critical for model performance. C_LIO_LIProvides a data-driven, hypothesis-free framework for mapping neural representations in biological and artificial systems. C_LI

neuroscience↗

bioRxiv2025

Genetic structure of sugar kelp in the St. Lawrence Estuary and Gulf (Quebec, Canada)

The sugar kelp, Saccharina latissima is cultivated at low scale in Quebec, Canada and current practice involve seeding meiospores or gametophyte stocks onto spools carrying twine and transferring these to a seaweed farm site. As the stocks can originate from locations spanning several hundreds of kilometers from the farm sites, such practice could involve genetic contamination and disrupt local adaptations. Assessing genetic structure can inform of the potential risks associated with this practice. Here we characterized the genetic diversity and structure of S. latissima from locations in the St. Lawrence Estuary and Gulf at both microsatellite loci (308 sporophytes at 22 loci in 16 sites) and genomic markers (228 sporophytes at 6578 single nucleotide polymorphisms in 13 sites). Several populations had low heterozygosity values and significant FIS values at microsatellite loci. No genetic structure was found among populations with microsatellite loci but strong genetic structuring was found with the genomic data. Population structure followed a geographic pattern and was congruent with major currents. Individuals from the wild population in the vicinity of the farm site were genetically distinct from the sporophytes on the growing lines that belong to a genetically distinct group. There was no significant genetic differentiation between wild individuals living in proximity of the farm site and another wild population of the same area. Hence aquaculture practices have not resulted in changes in the genetic composition of the wild population at large scale. Our results are important to guide future conservation efforts and for the seaweed farming industry.

evolutionary biology↗

bioRxiv2025

Inhibitory and disinhibitory VIP IN-mediated circuits in neocortex

Cortical GABAergic interneurons (INs) expressing the neuropeptide vasoactive-intestinal peptide (VIP) predominantly function by inhibiting dendritic-targeting somatostatin (SST) expressing INs, thereby disinhibiting pyramidal cells (PCs) and facilitating cortical circuit plasticity. VIP INs are a molecularly heterogeneous group, but the physiological significance of this diversity is unclear at present. Here, we have characterized the functional diversity of VIP INs in the primary somatosensory cortex (vS1) using intersectional genetic approaches. We found that VIP INs are comprised of four primary populations that exhibit different laminar distributions, axonal and dendritic arbors, intrinsic electrophysiological properties, and efferent connectivity. Furthermore, we observe that these populations are differentially activated by long-range inputs, and display distinct responses to neuromodulation by endocannabinoids, acetylcholine and noradrenaline. Stimulation of VIP IN subpopulations in vivo results in differential effects on the cortical network, thus providing evidence for specialized modes of VIP IN-mediated regulation of PC activity during cortical information processing.

neuroscience↗

bioRxiv2025

Wild and farmed Saccharina latissima in Europe: genetic insights for sustainable cultivation, traceability and environmental challenges

Kelp cultivation is expanding rapidly worldwide, although the aquaculture of Saccharina latissima (sugar kelp) in Europe remains in its early stages. However, major concerns have emerged about the potential impact of selected cultivars of the species on native populations of S. latissima which are already vulnerable to stressors including climate change. To address these concerns and support sustainable cultivation, it is essential to characterise genetic diversity and structure of wild kelp populations to monitor potential farm-to-wild gene flow. In this study we used 21 microsatellite loci to characterise the genetic structure of 24 natural and 3 farmed populations of S. latissima along European coasts. Results confirmed strong genetic differentiation between the northern and southern coasts, refining the boundaries between these two clusters compared to previous studies. Within each cluster, a clear genetic substructure was detected, with population differentiation being far more pronounced in the southern cluster. Cultivated sporophytes exhibited pedigrees that were all traced back to the local parent populations. Bayesian model-based structure analysis, discriminant analysis of principal components and assignment tests revealed no significant genetic differentiation between the farms and their wild populations. This indicates that farmed populations and neighbouring populations share the same gene pool, reflecting current cultivation practices. These findings contribute to understanding risks of gene flow between wild and farmed populations and demonstrate that strain traceability is feasible. Additionally, the study highlights the challenge European seaweed farmers face in securing reliable seedling stock, especially in the context of global change.

genetics↗

bioRxiv2024

Structural and evolutionary features of red algal UV sex chromosomes

BackgroundSex chromosomes in red algae have remained relatively understudied, despite their fundamental role in understanding the evolution of sex determination across eukaryotes. In this study, we investigate the structure, gene composition, and evolutionary history of the U and V sex chromosomes in four Gracilaria species, which diverged approximately 100 million years ago (MYA). ResultsOur findings reveal that UV sex chromosomes, previously identified in green and brown algae as well as bryophytes, have also evolved in red algae, contributing to the diversity of sex determination systems across eukaryotes. The shared orthology of conserved sex-determining region (SDR) genes between Gracilaria and distantly related red algae suggests that this system may have originated approximately 390 MYA, making it one of the oldest known sex chromosome systems. The SDR in Gracilaria is relatively small but contains conserved gametologs and V-specific genes involved in transcriptional regulation and signaling, suggesting their essential role in sexual differentiation. Unlike the conserved V-specific genes, U-specific genes appear absent, pointing to a dominant role of the V chromosome in sex determination. The evolution of Gracilaria sex chromosomes involved recombination suppression, gene relocations, duplications, and potential gene loss. Despite their ancient origin, the sex chromosomes show low levels of degeneration, likely due to haploid purifying selection during the gametophytic phase of the life cycle. ConclusionThis study provides the first detailed characterization of the U and V sex chromosomes in red algae, preparing the ground for future studies on reproductive life cycles and speciation in this understudied group of eukaryotes.

evolutionary biology↗

bioRxiv2023

Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations

The long-term persistence of species in the face of climate change can be evaluated by examining the interplay between selection and genetic drift in the contemporary evolution of populations. In this study, we focused on spatial and temporal genetic variation in four populations of the cold-water kelp Laminaria digitata using thousands of SNPs (ddRAD-seq). These populations were sampled from the center to the south margin in the North Atlantic at two different time points, spanning at least two generations. By conducting genome scans for local adaptation from a single time point, we successfully identified candidate loci that exhibited clinal variation, closely aligned with the latitudinal changes in temperature. This finding suggests that temperature may drive the adaptive response of kelp populations, although other factors, such as the species demographic history should be considered. Furthermore, we provided compelling evidence of positive selection through the examination of allele frequency changes over time, offering additional insights into the impact of genetic drift. Specifically, we detected candidate loci exhibiting temporal differentiation that surpassed the levels typically attributed to genetic drift at the south margin, confirmed through simulations. This finding was in sharp contrast with the lack of detection of outlier loci based on temporal differentiation in a population from the North Sea, exhibiting low levels of genetic diversity, that further decreased over time. These contrasting evolutionary scenarios among populations can be primarily attributed to the differential prevalence of selection relative to genetic drift. In conclusion, our study highlights the potential of temporal genomics to gain deeper insights into the contemporary evolution of marine foundation species in response to rapid environmental changes.

evolutionary biology↗

bioRxiv2023

Influence of oceanography and geographic distance on genetic structure: how varying the sampled domain influences conclusions in Laminaria digitata

Understanding the environmental processes shaping connectivity can greatly improve management and conservation actions which are essential in the trailing edge of species distributions. In this study, we used a dataset built from 32 populations situated in the southern limit of the kelp species Laminaria digitata. By extracting data from 11 microsatellite markers, our aim was to (1) refine the analyses of population structure, (2) compare connectivity patterns and genetic diversity between island and mainland populations and (3) evaluate the influence of sampling year, hydrodynamic processes, habitat discontinuity, spatial distance and sea surface temperature on the genetic structure using a distance-based redundancy analysis (db-RDA). Analyses of population structure enabled to identify well connected populations associated to high genetic diversity, and others which appeared genetically isolated from neighboring populations and showing signs of genetic erosion verifying contrasting ecological (and demographic) status in Brittany and the English Channel. By performing db-RDA analyses on various sampling sizes, geographic distance appeared as the dominant factor influencing connectivity between populations separated by great distances, while hydrodynamic processes were the main factor at smaller scale. Finally, Lagrangian simulations enabled to study the directionality of gene flow which has implications on source-sink dynamics. Overall, our results have important significance in regard to the management of kelp populations facing pressures both from global warming and their exploitation for commercial use.

evolutionary biology↗

bioRxiv2023

THE RHODOEXPLORER PLATFORM FOR RED ALGAL GENOMICS AND WHOLE GENOME ASSEMBLIES FOR SEVERAL GRACILARIA SPECIES

Macroalgal (seaweed) genomic resources are generally lacking as compared to other eukaryotic taxa, and this is particularly true in the red algae (Rhodophyta). Understanding red algal genomes is critical to understanding eukaryotic evolution given that red algal genes are spread across eukaryotic lineages from secondary endosymbiosis and red algae diverged early in the Archaeplastids. The Gracilariales are highly diverse and widely distributed order whose species can serve as ecosystem engineers in intertidal habitats, including several notorious introduced species. The genus Gracilaria is cultivated worldwide, in part for its production of agar and other bioactive compounds with downstream pharmaceutical and industrial applications. This genus is also emerging as a model for algal evolutionary ecology. Here, we report new whole genome assemblies for two species (G. chilensis and G. gracilis), a draft genome assembly of G. caudata, and genome annotation of the previously published G. vermiculophylla genome. To facilitate accessibility and comparative analysis, we integrated these data in a newly created web-based portal dedicated to red algal genomics (https://rhodoexplorer.sb-roscoff.fr). These genomes will provide a resource for understanding algal biology and, more broadly, eukaryotic evolution.

genomics↗

bioRxiv2023

Intricate epileptiform discharges affect memory in an Alzheimer's Disease mouse model

Interictal epileptiform discharges (IEDs) are transient abnormal electrophysiological events commonly observed in epilepsy patients but are also present in other neurological disease, such as Alzheimers Disease (AD). Understanding the role IEDs have on the hippocampal circuit is important for our understanding of the cognitive deficits seen in epilepsy and AD. We characterize and compare the IEDs of human epilepsy patients from microwire hippocampal recording with those of AD transgenic mice with implanted multi-layer hippocampal silicon probes. Both the local field potential features and firing patterns of pyramidal cells and interneurons were similar in mouse and human. We found that as IEDs emerged from the CA3-1 circuits, they recruited pyramidal cells and silenced interneurons, followed by post-IED suppression. IEDs suppressed the incidence and altered the properties of physiological sharp-wave ripples (SPW-Rs), altered their physiological properties, and interfered with the replay of place field sequences in a maze. In addition, IEDs in AD mice inversely correlated with daily memory performance. Together, our work implicates that IEDs may present a common and epilepsy-independent phenomenon in neurodegenerative diseases that perturbs hippocampal-cortical communication and interferes with memory. Significant StatementPrevalence of neurodegenerative diseases and the number of people with dementia is increasing steadily. Therefore, novel treatment strategies for learning and memory disorders are urgently necessary. IEDs, apart from being a surrogate for epileptic brain regions, have also been linked to cognitive decline. Here we report that IEDs in human epilepsy patients and AD mouse models have similar local field potential characteristics and associated firing patterns of pyramidal cells and interneurons. Mice with more IEDs displayed fewer hippocampal SPW-Rs, poorer replay of spatial trajectories, and decreased memory performance. IED suppression is an unexplored target to treat cognitive dysfunction in neurodegenerative diseases.

neuroscience↗

bioRxiv2022

Id2 GABAergic interneurons comprise a neglected fourth major group of cortical inhibitory cells

Cortical GABAergic interneurons (INs) represent a diverse population of mainly locally projecting cells that provide specialized forms of inhibition to pyramidal neurons and other INs. Most recent work on INs has focused on subtypes distinguished by expression of Parvalbumin (PV), Somatostatin (SST), or Vasoactive Intestinal Peptide (VIP). However, a fourth group that includes neurogliaform cells (NGFCs) has remained enigmatic due to a lack of genetic tools. Here, we show that these INs can be accessed experimentally using intersectional genetics with the gene Id2. We find that outside of layer 1 (L1), the majority of Id2 INs are NGFCs that express high levels of neuropeptide Y (NPY) and exhibit a late-spiking firing pattern, with extensive local connectivity. While much sparser, non-NGFC Id2 INs had more variable properties, with most cells corresponding to a diverse group of INs that strongly expresses the neuropeptide CCK. In vivo, using silicon probe recordings, we observed several distinguishing aspects of NGFC activity, including a strong rebound in activity immediately following the cortical down state during NREM sleep. Our study provides insights into IN diversity and NGFC distribution and properties, and outlines an intersectional genetics approach for further study of this neglected group of INs.

neuroscience↗

bioRxiv2022

Brief synaptic inhibition persistently interrupts firing of fast-spiking interneurons

Neurons perform input-output operations that integrate synaptic inputs with intrinsic electrical properties, operations generally constrained by the brevity of synaptic events. Here we report that sustained firing of CA1 hippocampal fast-spiking parvalbumin-expressing interneurons (PV-INs) can be persistently interrupted for up to several hundred milliseconds following brief GABAAR-mediated inhibition in vitro and in vivo. A single presynaptic neuron could interrupt PV-INs firing, occasionally with a single action potential (AP), and reliably with AP bursts. Experiments and computational modeling revealed that the persistent interruption of firing maintains neurons in a depolarized, quiescent state through a cell-autonomous mechanism. Strikingly, interrupted PV-INs are highly responsive to Schaffer collateral inputs. The persistent interruption of firing provides a disinhibitory circuit mechanism favoring spike generation in CA1 pyramidal cells. Overall, our results demonstrate that neuronal silencing can far outlast brief synaptic inhibition owing to well-tuned interplay between neurotransmitter release and postsynaptic membrane dynamics, a phenomenon impacting microcircuit function.

neuroscience↗

bioRxiv2021

Sublayer- and cell-type-specific neurodegenerative transcriptional trajectories in hippocampal sclerosis

Hippocampal sclerosis, the major neuropathological hallmark of temporal lobe epilepsy, is characterized by different patterns of neuronal loss. The mechanisms of cell-type specific vulnerability, their progression and histopathological classification remain controversial. Here using single-cell electrophysiology in vivo and immediate early gene expression, we reveal that superficial CA1 pyramidal neurons are overactive in epileptic rats and mice in vivo. Bulk tissue and single-nucleus expression profiling disclosed sublayer-specific transcriptomic signatures and robust microglial pro-inflammatory responses. Transcripts regulating neuronal processes such as voltage-channels, synaptic signalling and cell adhesion molecules were deregulated by epilepsy differently across sublayers, while neurodegenerative signatures primarily involved superficial cells. Pseudotime analysis of gene expression in single-nuclei and in situ validation revealed separated trajectories from health to epilepsy across cell types, and identified a subset of superficial cells undergoing a later stage in neurodegeneration. Our findings indicate sublayer- and cell type-specific changes associated with selective CA1 neuronal damage contributing to progression of hippocampal sclerosis.

neuroscience↗

bioRxiv2020

Multimodal determinants of phase-locked dynamics across deep-superficial hippocampal sublayers during theta oscillations

Theta oscillations play a major role in temporarily defining the hippocampal rate code by translating behavioural sequences into neuronal representations. However, mechanisms constraining phase timing and cell-type specific phase preference are unknown. Here, we employ computational models tuned with evolutionary algorithms to evaluate phase preference of individual CA1 pyramidal cells recorded in mice and rats not engaged in any particular memory task. We applied unbiased and hypothesis-free approaches to identify effects of intrinsic and synaptic factors, as well as cell morphology, in determining phase preference. We found that perisomatic inhibition delivered by complementary populations of basket cells interacts with input pathways to shape phase-locked specificity of deep and superficial pyramidal cells. Somatodendritic integration of fluctuating glutamatergic inputs defined cycle-by-cycle by unsupervised methods demonstrated that firing selection is tuneable across sublayers. Our data identify different mechanisms of phase-locking selectivity that are instrumental for high-level flexible dynamical representations.

neuroscience↗

bioRxiv2019

Drug reformulation for a neglected disease. The NANOHAT project to develop a safer more effective sleeping sickness drug.

Human African trypanosomiasis (HAT or sleeping sickness) is caused by the parasite Trypanosoma brucei sspp. The disease has two stages, a haemolymphatic stage after the bite of an infected tsetse fly, followed by a central nervous system stage where the parasite penetrates the brain, causing death if untreated. Treatment is stage-specific, due to the blood-brain barrier, with less toxic drugs such as pentamidine used to treat stage 1. The objective of our research programme was to develop an intravenous formulation of pentamidine which increases CNS exposure by some 10-100 fold, leading to efficacy against a model of stage 2 HAT. This target candidate profile is in line with drugs for neglected diseases inititative recommendations. To do this, we evaluated the physicochemical and structural characteristics of formulations of pentamidine with Pluronic micelles (triblock-copolymers of polyethylene-oxide and polypropylene oxide), selected candidates for efficacy and toxicity evaluation in vitro, quantified pentamidine CNS delivery of a sub-set of formulations in vitro and in vivo, and progressed one pentamidine-Pluronic formulation for further evaluation using an in vivo single dose brain penetration study. Screening pentamidine against 40 CNS targets did not reveal any major neurotoxicity concerns, however, pentamidine had a high affinity for the imidazoline2 receptor. The reduction in insulin secretion in MIN6 {beta}-cells by pentamidine maybe secondary to pentamidine-mediated activation of {beta}-cell imidazoline receptors and impairment of cell viability. Pluronic F68 (0.01%w/v)-pentamidine formulation had a similar inhibitory effect on insulin secretion as pentamidine alone and an additive trypanocidal effect in vitro. However, all Pluronics tested (P85, P105 and F68) did not significantly enhance brain exposure of pentamidine. These results are relevant to further developing block-copolymers as nanocarriers, improving BBB drug penetration and understanding the side effects of pentamidine.

pharmacology and toxicology↗

bioRxiv2019

Evolution of life cycles and reproductive traits: insights from 1 the brown algae

Brown algae are characterized by a remarkable diversity of life cycles, sexual systems, and reproductive modes, and these traits seem to be very labile across the whole group. This diversity makes them ideal models to test existing theories on the evolution of alternation between generations, and to examine correlations between life cycle and reproductive life history traits. In this study, we investigate the dynamics of trait evolution for four life-history traits: life cycle, sexual system, level of gamete dimorphism and gamete parthenogenetic capacity. We assign states to up to 70 species in a multi-gene phylogeny of brown algae, and use maximum likelihood and Bayesian analyses of correlated evolution, taking phylogeny into account, to test for correlations between life history traits and sexual systems, and to investigate the sequence of trait acquisition. Our analyses are consistent with the prediction that diploid growth may evolve because it allows the complementation of deleterious mutations, and that haploid sex determination is ancestral in relation to diploid sex determination. However, the idea that increased zygotic and diploid growth is associated with increased sexual dimorphism is not supported by our analysis. Finally, it appears that in the brown algae isogamous species evolved from anisogamous ancestors.

evolutionary biology↗