bioRxiv Science⌕ Search

Biology subjects

Bernard, A.

Publications and source records attributed to Bernard, A..

At least 19 recordsLinked to original sources

A first description of the ichthyofauna of the Namibian Islands Marine Protected Area using baited remote underwater video systems

Data on the diversity, relative abundance and distribution of the ichthyofauna of Namibia's only marine protected area, the Namibian Islands Marine Protected Area (NIMPA), are limited and there is no active monitoring programme in place. Generating a baseline for these species is essential to inform management plans and policy. Baited remote underwater video system (BRUVs) surveys were conducted between 2022 and 2024 in the central eastern NIMPA. Data from 114 BRUVs samples, collected in water less than 45 m deep, were analysed in this study. Of the 17 fish species recorded, five were elasmobranchs, and three fish species - Galeorhinus galeus (CR), Notorynchus cepedianus (VU) and Argyrosomus inodorus (VU) - are classified as threatened on the IUCN Red List. The most frequently recorded elasmobranch, Haploblepharus pictus, was ubiquitous and typified all habitat types and depth categories. The most frequently recorded actinopterygian fish (Clinus spp.) was sighted at 37% of sites. Depth was an important predictor of fish species abundance and community composition, but habitat was not. Both ichthyofaunal relative abundance and diversity appeared lower than in similar surveys in neighbouring South Africa and other temperate waters. Future research should aim to identify the drivers of the observed patterns. The findings provide an important baseline for long-term monitoring of the NIMPA, necessary to better describe biodiversity and inform the development of management strategies.

zoology↗

Highly persistent antibody levels but limited population immunity in gannets after HPAI outbreak

The recent large-scale circulation of High Pathogenicity Avian Influenza (HP AI) viruses H5Nx of clade 2.3.4.4b has been responsible for massive die-offs in wild species, notably in long-lived seabirds, with unknown implications for the immunity of surviving individuals. In the North Atlantic, northern gannet colonies were heavily affected in 2022, with more than 40% mortality observed among breeding adults and some surviving individuals developing dark irises. Using samples collected in 2023 and 2024 on Rouzic colony (France), we report persistent individual anti-AI antibody levels and seroneutralisation titres, with most of the immune individuals showing dark irises. A modelling approach further stressed the importance of long-lasting immunity in such species by showing that the proportion of individuals which kept their immunity between years strongly limited decreases in population size in case of repeated outbreaks. Overall, our results highlight the existence and importance of long-lasting immunity in long-lived species for population persistence.

ecology↗

A Bayesian multidimensional approach to decipher the genetic basis of dynamic phenotypes in multiple species

Deciphering the genetic architecture of complex quantitative phenotypes remains challenging in quantitative genetics. These traits not only depend of multiple genetic factors but are also established over time and environments. Although quantitative genetics has investigated the genetic determinism of phenotypic plasticity in contrasted environmental conditions, the time related phenotypic plasticity has received less attention. Here we proposed a multivariate Bayesian framework, the Bayesian Varying Coefficient Model, designed for analysing the genetic architecture of the time related phenotypic plasticity by a multilocus approach. We applied the BVCM to time series phenotypes measured at various time scales (daily, monthly, yearly) across a diverse set of biological species. We included in this study: yeast (Saccharomyces cerevisiae), fungi (Fusarium graminearum), eucalyptus (Eucalyptus urophylla x E. grandis), and sweet cherry tree (Prunus avium). The BVCM results were compared with those obtained with a known genome-wide association method carried out time by time. For all species and traits, the BVCM was able to detect the major QTL identified by marker-trait association methods and revealed additional genetic regions of weak effect. It also increased the phenotypic variance explained for most of the phenotypes considered. It revealed dynamic QTLs with transitory, increasing or decreasing effects over time. By considering both the temporal and genetic multivariate structures in a single statistical model, we increased our understanding of the genetic architecture of complex traits notably by reducing the issue of missing heritability. More broadly, this work raises the foundation for extended applications in functional genomics, evolutionary ecology, and crop breeding programs, in which time-related phenotypic plasticity remains crucial for predicting and selecting key quantitative complex traits. Key messageBy capturing the genetic factors influencing the time related phenotypic plasticity, our approach contributes to a deeper understanding of the dynamic nature of genotype-phenotype relationships.

genetics↗

Diet- and metabolic state-dependent remodeling of the mouse brain lipidome

The hypothalamus and brainstem are key hubs of metabolic control that undergo dynamic molecular adaptations in response to changes in energy availability. This remodeling is associated with changes in the expression and activity of enzymes linked to energy homeostasis but also importantly, lipid metabolism. Given that lipids account for [~]50% of the brains dry weight, it is likely that lipid metabolism is a major determinant of brain function. Therefore, understanding how the hypothalamic and brainstem lipidome adapts to metabolic perturbation is key to understanding tissue function and metabolic health. Here we characterize the remodeling of [~]750 lipid species in mouse hypothalamus and brainstem, as well as the cerebrospinal fluid and plasma, in response to a metabolic challenge (an Ad Libitum-Fasting-Refeeding cycle). We show that around 45% and 36% of lipids in the hypothalamus and brainstem respectively, exhibit reversible, nutritional state-dependent remodeling during this metabolic challenge, and that this remodeling is substantially impacted by long-term high fat diet intervention. Of note, targeted analysis of specific lipids revealed that certain fatty acids were affected by this intervention in the hypothalamus and brainstem, most strikingly defined by the reversible fasting-induced increase in linoleic acid (18:2)-containing phosphatidylcholines in both the hypothalamus and brainstem, an effect that is abolished by high fat diet intervention. Such precise and intervention-specific regulation of linoleic acid (18:2)-containing phosphatidylcholines provides a previously unrecognized role for this lipid in the physiological response to fasting. Thus, these findings demonstrate that the brain lipidome undergoes robust, nutritional state-dependent remodeling, and provide a comprehensive resource for investigating its role in regulating metabolic adaptations.

physiology↗

Clathrin-coated vesicles are targeted for selective autophagy during osmotic stress.

Plants frequently encounter hyperosmotic stress due to drought and salinity, leading to rapid water loss, reduced turgor pressure, and decreased cell volume. This contraction drastically alters plasma membrane tension, a physical parameter that must be strictly maintained to support mechanosignaling and cell expansion. However, the mechanisms by which plants adjust their membrane surface area to match a shrinking cell volume remain poorly understood. Here, we identify selective autophagy dependent degradation of plasma membrane-derived clathrin-coated vesicles (CCVs) in response to hyperosmotic shock. This pathway involves the recruitment of the endocytic TPLATE complex (TPC) to autophagosomes in an osmotic-stress dependent manner. Through correlative light and electron microscopy (CLEM) and electron tomography (ET), we provide ultrastructural evidence of the physical association of CCVs with autophagosome membranes. These autophagosomes contain endocytic machinery, including TPC and clathrin, and are targeted to the vacuole. Mechanistically, we show that the conserved ATG8-interacting motifs (AIMs) in the AtEH1/Pan1 and AtEH2/Pan1 TPC subunits interact with ATG8, suggesting that they facilitate the recruitment of CCVs to autophagosomes. Using time-lapse imaging, we demonstrate that the acute induction of autophagy is precisely coupled to the reduction in cell volume under hyperosmolar conditions. Our results suggest that endocytic removal of excess plasma membrane to maintain membrane tension and cellular integrity is coupled to TPC-mediated CCV-phagy. These findings reveal a homeostatic mechanism that enables plants to adapt to the challenges of drought and salinity. Significance StatementAll living cells must maintain the physical integrity of their outer membrane. How cells can adapt their surface area to respond to rapid changes in cell volume, such as those caused by drought or salt stress, remains a fundamental question in biology. We identify a mechanism in plants involving autophagy - a cellular recycling pathway - where plasma membrane-derived vesicles are targeted for degradation following salt or osmotic stress. This pathway involves the TPLATE complex, an evolutionary ancient and essential endocytic complex in plants, which directly interacts with the autophagy protein ATG8. This discovery reveals how plants adapt to osmotic stress by modulating their membrane properties, supporting a framework for future improvement of crop resilience in response to salinity and drought.

plant biology↗

Unveiling the molecular identity of plant autophagic compartments: A proteo-lipidomic study in Arabidopsis thaliana

Autophagy is an intracellular degradation and recycling pathway essential for cell quality control and plant tolerance to stress. The formation and maturation of autophagosomes, the cargo-packing vesicles, rely on extensive membrane remodeling, yet little is known about the nature, dynamics and functions of lipids in these events. Here, we established a method combing cell fractionation and immuno-isolation in native conditions to purify autophagic membranes from Arabidopsis thaliana. By integrating proteomic and lipidomic analyses, we defined their molecular footprint which, coupled to colocalization analyses, revealed potent actors involved in lipid metabolism, membrane trafficking and membrane remodeling, supporting a close interplay between lipid homeostasis and autophagosome biology. Characterization of the phagophore lipid composition showed low sterol and sphingolipid content, a predominance of glycerophospholipids, including phosphoinositides, and a particular enrichment in phosphatidylcholine and phosphatidylglycerol. Comparisons with other plant endomembranes and autophagic compartments from other organisms revealed the singularity of this lipid signature and notably identified phosphatidylglycerol as a plant-specific component of autophagic membranes. Analyses of inducible phosphatidylglycerol-deficient plants showed defects in autophagy activity thereby supporting the functional relevance of the phagophore lipid composition, particularly that of phosphatidylglycerol homeostasis. Together, our findings place lipids as fundamental components of the autophagy molecular landscape and provide a framework to further investigate their contribution to autophagosome biology and functions in plant acclimation to environmental changes. Significance StatementAutophagy is catabolic pathway critical for eukaryotic life and essential for plant acclimation to stress. It hinges on the remarkable plasticity of a specialized membrane, the phagophore, to orchestrate and support intense membrane remodeling events towards the formation of the autophagic vesicle containing cargo. To resolve their elusive molecular bases, we need to integrate inputs from both components of biological membranes: proteins and lipids, yet information regarding lipids is still very limited. Here, we isolated plant phagophores, established their protein and lipid molecular footprint, revealed its singularity and showed its physiological and functional relevance for autophagy activity. Our work highlights lipids as key regulators of plant autophagy and opens new doors for investigating how membrane dynamics shape cellular stress responses.

plant biology↗

A dual component system instructs membrane hydrolysis during the final stages of plant autophagy

Autophagy is an intracellular catabolic process conserved across eukaryotes and critical for plant stress tolerance. Upon their delivery in the vacuole, how autophagic bodies containing cargo are hydrolyzed to warrant autophagy degradation remains poorly characterized. Here, we identify two Arabidopsis phospholipases as core components of the autophagy machinery. We find that LCAT3 and LCAT4 traffic to the vacuolar lumen and converge on autophagic bodies using differential pathways, placing them on the outer and inner side of the vesicle, respectively. Double knockouts lcat3,4 accumulate autophagic bodies and show reduced autophagy activity. In vivo reconstitution demonstrates that LCAT3 can hydrolyze the membrane of autophagic bodies, enabling the activity of LCAT4 to enhance this process. In sum, our work reveals that the concerted action of a multi-component system is required for the efficient and specific disruption of autophagic bodies as an obligatory step for the completion of the autophagy pathway.

plant biology↗

Island biogeography through the lens of multiscale metapopulation dynamics: insights into species-area relationships

While island biogeography focuses on species richness equilibrium driven by immigration and extinction, and metapopulation theory examines single-species dynamics across fragmented habitats, their interplay remains poorly understood. In particular, the species-area relationship remains a subject of ongoing debate, yet there are limited theoretical foundations to explain it. To address this, we developed a multiscale stochastic metapopulation model to investigate diversity patterns on islands, bridging the gap between island biogeography and metapopulation theory. Our model integrates regional colonization from a mainland with local colonization-extinction processes within islands at the single-species level, then extends this to multiple, independent species. By analyzing the stationary properties of this model, we generate novel predictions of Species Area Relationship (SAR) based on local extinction rates, within-island colonization rates, and mainland immigration rates. We demonstrate how the interplay of these parameters influences the relationship, predicting patterns that can resemble either the power-law of Arrhenius or the semi-logarithmic relationship of Gleason, depending on the relative importance of mainland immigration versus within-island dynamics, and on the nature of the species abundance distribution in the mainland. This unified framework offers new insights into the mechanisms driving species richness and distribution across spatial scales, providing a more holistic understanding of biodiversity patterns in fragmented landscapes.

ecology↗

A peptide-neurotensin conjugate that crosses the blood-brain barrier induces pharmacological hypothermia associated with anticonvulsant, neuroprotective and anti-inflammatory properties following status epilepticus in mice

Preclinical and clinical studies show that mild to moderate hypothermia is neuroprotective in sudden cardiac arrest, ischemic stroke, perinatal hypoxia/ischemia, traumatic brain injury and seizures. Induction of hypothermia largely involves physical cooling therapies, which induce several clinical complications, while some molecules have shown to be efficient in pharmacologically induced hypothermia (PIH). Neurotensin (NT), a 13 amino-acid neuropeptide that regulates body temperature, interacts with various receptors to mediate its peripheral and central effects. NT induces PIH when administered intracerebrally. However, these effects are not observed if NT is administered peripherally, due to its rapid degradation and poor passage of the blood brain barrier (BBB). We conjugated NT to peptides that bind the low-density lipoprotein receptor (LDLR) to generate "vectorized" forms of NT with enhanced BBB permeability. We evaluated their effects in epileptic conditions following peripheral administration. One of these conjugates, VH-N412, displayed improved stability, binding potential to both the LDLR and NTSR-1, rodent/human cross-reactivity and improved brain distribution. In a mouse model of kainate (KA)-induced status epilepticus (SE), VH-N412 elicited rapid hypothermia associated with anticonvulsant effects, potent neuroprotection and reduced hippocampal inflammation. VH-N412 also reduced sprouting of the dentate gyrus mossy fibers and preserved learning and memory skills in the treated mice. In cultured hippocampal neurons, VH-N412 displayed temperature-independent neuroprotective properties. To the best of our knowledge, this is the first report describing the successful treatment of SE with PIH. In all, our results show that vectorized NT may elicit different neuroprotection mechanisms mediated either by hypothermia and/or by intrinsic neuroprotective properties.

neuroscience↗

AtVPS13M1 is involved in lipid remodeling in low phosphate and is located at the mitochondria surface in plants

VPS13 are conserved lipid transporters with multiple subcellular localizations playing key roles in many fundamental cellular processes. While the localization and function of VPS13 have been extensively investigated in yeast and animals, little is known about their counterparts in plants, particularly regarding their role in stress response. In this study, we characterized AtVPS13M1, one of the four VPS13 paralogs of the flowering plant Arabidopsis thaliana. We show that AtVPS13M1 binds and transports glycerolipids with a low specificity in vitro. AtVPS13M1 interferes with phospholipids degradation in response to phosphate starvation, a nutrient stress that triggers a massive remodeling of membrane lipids. AtVPS13M1 is mainly expressed in young dividing and vascular tissues. Finally, we show that AtVPS13M1 is mainly located at the surface of mitochondria in leaves. Overall, our work highlights the conserved role in lipid transport of VPS13 in plants, reveals their importance in nutrient stress response and opens important perspectives for the understanding of lipid remodeling mechanisms and for the characterization of this protein family in plants.

cell biology↗

Chaperone-Mediated Autophagy in Fish: A Key Function Amid a Changing Environment

Chaperone-Mediated Autophagy (CMA) is a major pathway of lysosomal proteolysis critical for cellular homeostasis and metabolism. While extensively studied in mammals, CMAs existence in fish has only been confirmed recently, offering exciting insights into its role in species facing environmental stress. Here, we shed light on the existence of 2 genes encoding the CMA-limiting factor Lamp2A (lysosomal associated membrane protein 2A) in rainbow trout (RT, Oncorhynchus mykiss), revealing distinct expression patterns across various tissues. Notably, RT lacking the most expressed Lamp2A exhibit profound hepatic proteome disturbances during acute nutritional stress, underscoring its pivotal role as a guardian of hepatic proteostasis. Building upon these findings, we introduce and validate the CMA activation score as a reliable indicator of CMA status, providing a valuable tool for detecting cellular stress in fish under environmental threats. Overall, our study offers new perspectives into understanding CMA from evolutionary and environmental contexts. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=70 SRC="FIGDIR/small/585855v1_ufig1.gif" ALT="Figure 1"> View larger version (10K): org.highwire.dtl.DTLVardef@de3c56org.highwire.dtl.DTLVardef@4b711forg.highwire.dtl.DTLVardef@efb4a1org.highwire.dtl.DTLVardef@13be9cc_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

Strong breeding colony fidelity in northern gannets following High Pathogenicity Avian Influenza Virus (HPAIV) outbreak

High pathogenicity avian influenza virus (HPAIV) caused the worst seabird mass-mortalities on record in Europe across 2021-2022. The northern gannet (Morus bassanus) was one of the most affected species, with tens of thousands of casualties in the northeast Atlantic between April-September 2022. Disease outbreaks can drastically modify the movement ecology of animals and diminish spatial consistency, thereby increasing the potential for disease transmission. To detect potential changes in movement behaviour, we GPS-tracked breeding adults following the initial HPAIV outbreak, at three of the largest gannet breeding colonies where major mortality of adults and chicks occurred (Bass Rock, Scotland, UK; Grassholm, Wales, UK; Rouzic island, Brittany, France). Crucially, GPS-tracked birds remained faithful to their breeding sites and did not prospect other breeding colonies. They performed regular foraging trips at sea, similar to their behaviour before the outbreak. Gannet foraging effort was nonetheless lower than in 2019, thus surviving birds may have benefited from reduced intra- and interspecific food competition. Breeding colony fidelity of adult northern gannets following HPAIV mass-mortalities suggests limited long-term capacity to virus spread, which may contrast with the behaviour of adults during the disease outbreak, or with that of younger individuals.

ecology↗

The evolution of behavioral cues and signaling in displaced communication

Displaced communication, whereby individuals communicate regarding a subject that is not immediately present (spatially or temporally), is one of the key innovations of human language. It also occurs in a few animal species, most notably the honeybee, where the waggle dance is used to communicate the location and quality of a patch of flowers. However, it is difficult to study how it emerged given the paucity of species displaying this capacity and the fact that it often occurs via complex multimodal signals. To address this issue, we developed a novel paradigm in which we conducted experimental evolution with foraging agents endowed with neural networks that regulate their movement and the production of signals. Displaced communication readily evolved but, surprisingly, agents did not use signal amplitude to convey information on food location. Instead, they used signal onset-delay and duration-based mode of communication, which depends on the motion of the agent within a communication area. When agents were experimentally prevented from using these modes of communication, they evolved to use signal amplitude instead. Interestingly, this mode of communication was more efficient and led to higher performance. Subsequent controlled experiments suggested that this more efficient mode of communication failed to evolve because it took more generations to emerge than communication grounded on the onset-delay and length of signaling. These results reveal that displaced communication is likely to initially evolve from non-communicative behavioral cues providing incidental information with evolution later leading to more efficient communication systems through a ritualization process. Author SummaryThe evolution of displaced communication, the process through which individuals share information about a remote object (in space or time), is a key innovation in language. By conducting experimental evolution we found that displaced communication is more likely to leverage and evolve from behavioural cues, such as the agents movement, rather than from dedicated communication modes, such as the amplitude of emitted signals. This phenomenon is shown to happen because communication via signal amplitude -although more efficient-is slower to evolve. The simple behaviors and neural networks of the agents studied here, also suggest that communication may evolve more frequently than expected via ritualization, a process whereby an action or behavior pattern in an animal loses its original function but is retained for its role in display or other social interactions.

evolutionary biology↗

Bio-electric potentials in superior plants: electric collective behaviour

Electrical activity is used by plants in long term signalling and information transfer between the distant parts of the plant. Biopotential recordings from trees in a natural environment have been so far less discussed in scientific literature. Here we present our data about the open science experiment TRee-hUMAn iNterface (TRUMAN) located in Paneveggio forest (Valle di Fiemme, Trento, Italy), cultivated since one thousand years for the production of harmonic wood from Picea abies (red fir). We show that: i) biopotential features based on xylem can be correlated with the solar (and lunar) cycle ii) dead tree logs show an electrical activity that is correlated with that of neighbouring trees iii) statistical features of the spike-like peaks are evidenced, including amplitude, frequency, propagation speed, entropy iv) a quantum field theory is presented to highlight the collective behaviour of the forest, supported by preliminar correlation analyses between electrical signal Kolmogorov entropy and thermographies Shannon entropy.

biophysics↗

AtEH/Pan1 proteins drive phase separation of the TPLATE complex and clathrin polymerisation during plant endocytosis

Clathrin-mediated endocytosis (CME) is an essential cellular internalisation pathway involving the dynamic assembly of clathrin and accessory proteins to form membrane-bound vesicles. In plants, the evolutionarily ancient TSET/TPLATE complex (TPC) plays an essential, but not well-defined role in CME. Here, we show that two highly disordered TPC subunits, AtEH1 and AtEH2 function as scaffolds to drive biomolecular condensation of the complex. These condensates specifically nucleate on the plasma membrane through interactions with anionic phospholipids, and facilitate the dynamic recruitment and assembly of clathrin, early-, and late-stage endocytic accessory proteins. Importantly, clathrin forms ordered assemblies within the condensate environment. Biomolecular condensation therefore acts to promote dynamic protein assemblies throughout clathrin-mediated endocytosis. Furthermore, the disordered region sequence properties of AtEH1 regulate the material properties of the endocytic condensates in vivo and alteration of these material properties influences endocytosis dynamics, and consequently plant adaptive growth. HighlightsO_LIAtEH subunits are endocytic scaffolds which drive condensation of the TPC C_LIO_LIAtEH1 condensates nucleate on the plasma membrane via lipid interactions C_LIO_LICondensation of AtEH1/TPC facilitates clathrin re-arrangement and assembly C_LIO_LIAtEH1 IDR1 composition controls condensate properties to regulate endocytosis C_LI

cell biology↗

Cellular resolution anatomical and molecular atlases for prenatal human brains

Increasing interest in studies of prenatal human brain development, particularly using new single-cell genomics and anatomical technologies to create cell atlases, creates a strong need for accurate and detailed anatomical reference atlases. In this study, we present two cellular-resolution digital anatomical atlases for prenatal human brain at post-conceptional weeks (PCW) 15 and 21. Both atlases were annotated on sequential Nissl-stained sections covering brain-wide structures on the basis of combined analysis of cytoarchitecture, acetylcholinesterase staining and an extensive marker gene expression dataset. This high information content dataset allowed reliable and accurate demarcation of developing cortical and subcortical structures and their subdivisions. Furthermore, using the anatomical atlases as a guide, spatial expression of 37 and 5 genes from the brains respectively at PCW 15 and 21 was annotated, illustrating reliable marker genes for many developing brain structures. Finally, the present study uncovered several novel developmental features, such as the lack of an outer subventricular zone in the hippocampal formation and entorhinal cortex, and the apparent extension of both cortical (excitatory) and subcortical (inhibitory) progenitors into the prenatal olfactory bulb. These comprehensive atlases provide useful tools for visualization, targeting, imaging and interpretation of brain structures of prenatal human brain, and for guiding and interpreting the next generation of cell census and connectome studies.

neuroscience↗

Anatomical Structures, Cell Types, and Biomarkers Tables Plus 3D Reference Organs in Support of a Human Reference Atlas

1.This paper reviews efforts across 16 international consortia to construct human anatomical structures, cell types, and biomarkers (ASCT+B) tables and three-dimensional reference organs in support of a Human Reference Atlas. We detail the ontological descriptions and spatial three-dimensional anatomical representations together with user interfaces that support the registration and exploration of human tissue data. Four use cases are presented to demonstrate the utility of ASCT+B tables for advancing biomedical research and improving health.

cell biology↗

rasterdiv - an Information Theory tailored R package for measuring ecosystem heterogeneity from space: to the origin and back

O_LIEcosystem heterogeneity has been widely recognized as a key ecological feature, influencing several ecological functions, since it is strictly related to several ecological functions like diversity patterns and change, metapopulation dynamics, population connectivity, or gene flow. C_LIO_LIIn this paper, we present a new R package - rasterdiv - to calculate heterogeneity indices based on remotely sensed data. We also provide an ecological application at the landscape scale and demonstrate its power in revealing potentially hidden heterogeneity patterns. C_LIO_LIThe rasterdiv package allows calculating multiple indices, robustly rooted in Information Theory, and based on reproducible open source algorithms. C_LI

ecology↗