Biology subjects

Morin, X.

Publications and source records attributed to Morin, X..

15 recordsLinked to original sources

bioRxiv2026

Loss of competitive strength in European conifer species under climate change

Climate change is expected to alter species assemblages by affecting the outcome of competition between species. Investigating processes of competition remains challenging particularly in tree communities, as they unfold over extensive spatio-temporal scales. Here, we developed a deep-learning approach to leverage a novel database of 135 million simulated local-scale tree responses to climate across continental Europe to investigate changes in the competitiveness of nine major tree species under different scenarios of climate change. Specifically, we trained a Deep Neural Network on local process model projections to investigate climate change effects on indicators of competitive strength and species dominance. We found decreasing competitive strength for all investigated evergreen coniferous species across their distribution, while major deciduous broadleaved species such as Quercus robur and Fagus sylvatica increased in competitiveness. Changes in tree species competition with climate differed locally, but most investigated species lost competitive strength at their warm range edges. As a consequence of these changes, up to 19% of Europes forests could experience a change in the dominant tree species until the end of the 21st century. Our results suggest a profound climate-induced reassembly of Europes forests and identify areas that may require specific attention in forest policy and management.

ecology↗

bioRxiv2025

PhorEau: a new process-based model to predict forest functioning, from tree ecophysiology to forest dynamics and biogeography

Climate change impacts forest functioning and dynamics, yet significant uncertainties persist regarding the interactions between species composition, demographic processes, and environmental drivers. While the effects of climate change on individual plant ecophysiology are better understood, few robust tools integrate these processes dynamically, hindering accurate projections and recommendations for long-term sustainable forest management. Forest gap models strike a balance between complexity and generality and are widely used in predictive forest ecology. However, their lack of explicit representation of critical processes--such as plant phenology and water use--limits their ability to fully capture tree sensitivity to climate change, calling into question the robustness of their future predictions. Therefore, incorporating trait- and process-based representations of climate-sensitive processes within gap models is a crucial step toward generating realistic predictions of forest evolution under climate change. In this study, we coupled the ForCEEPS gap model, validated across a broad range of forest types and environmental conditions in Europe, with two process-based models: a plant phenology model (PHENOFIT) and a plant hydraulics model (SurEAU), each parameterized for the main European tree species. We then evaluated the performance of the resulting PHOREAU model across multiple processes, metrics, and time- and spatial-scales, thereby minimizing the risk of equifinality. PHOREAU demonstrated robust capabilities in predicting fine hydraulic processes at both the forest and stand scales for various species and forest types. This, combined with its enhanced ability to predict stand leaf areas from inventories, led to modest improvements in annual growth predictions compared to the original ForCEEPS model and a strong capacity to predict potential community compositions. By integrating recent advancements in plant hydraulics, phenology, and competition for light and water into a dynamic, individual-based framework, the PHOREAU model bridges the gap between trait diversity and long-term forest productivity and resilience. It offers insights into complex emergent properties and trade-offs linked to diversity effects under extreme climatic events, with significant implications for sustainable forest management strategies.

ecology↗

bioRxiv2024

Uneven mitochondrial segregation during embryonic neurogenesis

Asymmetric divisions of vertebrate neural progenitors are critical for generating neurons while preserving the stem cell pool, ensuring proper central nervous system development. It was previously shown that the post-mitotic remodeling of mitochondrial activity in daughter cells influences neural fates. In this study, we demonstrate that unequal distribution of mitochondria during asymmetric mitosis plays a decisive role in triggering this differentiation process. Using live imaging to monitor mitochondrial segregation in individual progenitors and track their progenys fate within embryonic neural tissue, we show that daughter cells inheriting fewer mitochondria consistently differentiate into neurons, whereas their sibling receiving more mitochondria retains the progenitor status. Furthermore, experimental displacement of mitochondria during mitosis to force their unequal inheritance was sufficient to drive premature neuronal differentiation. Our findings establish a direct causal relationship between unequal mitochondrial inheritance and the asymmetric fate of sister cells in vivo, uncovering a key mechanism in neural development.

developmental biology↗

bioRxiv2024

CRISPR/Cas9-based somatic knock-in of reporters in the avian embryo in ovo

Gene editing and protein tagging are at the heart of modern developmental and cell biology. The advent of CRISPR/Cas9 based methods offers the possibility to develop customized approaches for genomic manipulations in non-classical experimental models. Here, we show that highly efficient somatic knock-ins of long DNA fragments can be achieved in the developing chick neural tube in ovo. We compare different types of repair matrices and different methods for the delivery of the CRISPR/Cas9 machinery, and find that an all plasmid-based approach and short arms of homology provide an easy and efficient method to achieve high frequencies of knock-in insertions with virtually no background signal. We use this method to target fluorescent reporters and dynamically monitor the subcellular distribution of endogenously expressed tagged proteins, as well as to insert the Gal4-VP16 transcription factor or the Cre recombinase at specific loci to label neural sub-populations in the chick embryonic spinal cord. Finally, we show that the method can also be applied to target the epiblast and somitic mesoderm.

developmental biology↗

bioRxiv2024

A low CDKN1c/p57kip2 expression in spinal progenitors drives the transition from proliferative to neurogenic modes of division

During vertebrate neurogenesis, a progressive transition from symmetric proliferative to asymmetric neurogenic divisions is critical to balance growth and differentiation. Using single-cell RNA-seq data from chick embryonic neural tube, we identify the cell cycle regulator Cdkn1c as a key regulator of this transition. While Cdkn1 is classically associated with neuronal cell cycle exit, we show that its expression initiates at low levels in neurogenic progenitors. Functionally targeting the onset of this expression impacts the course of neurogenesis: Cdkn1c knockdown impairs neuron production by favoring proliferative symmetric divisions. Conversely, inducing a low-level CDKN1c misexpression in self-expanding progenitors forces them to prematurely undergo neurogenic divisions. CDKN1c exerts this effect primarily by inhibiting the cyclin D-CDK complex and lengthening G1 phase duration. We propose that Cdkn1c acts as a dual driver of the neurogenic transition whose low level of expression first controls the progressive entry of progenitors into neurogenic modes of division before a higher expression mediates cell cycle exit in daughter cells. This highlights that the precise control of neurogenesis regulators expression levels sequentially imparts distinct functions, and is essential for proper neural development.

developmental biology↗

bioRxiv2024

A tunable and versatile chemogenetic near infrared fluorescent reporter

Near-infrared (NIR) fluorescent reporters provide additional colors for highly multiplexed imaging of cells and organisms, and enable imaging with less toxic light and higher contrast and depth. Here, we present the engineering of nirFAST, a small tunable chemogenetic NIR fluorescent reporter that is brighter than top-performing NIR fluorescent proteins in cultured mammalian cells. nirFAST is a small genetically encoded protein of 14 kDa that binds and stabilizes the fluorescent state of synthetic, highly cell-permeant, fluorogenic chromophores (so-called fluorogens) that are otherwise dark when free. Engineered to emit NIR light, nirFAST can also emit far-red or red lights through change of chromophore. nirFAST allows the imaging of proteins in live cultured mammalian cells, chicken embryo tissues and zebrafish larvae. Its near infrared fluorescence provides an additional color for high spectral multiplexing. We showed that nirFAST is well-suited for stimulated emission depletion (STED) nanoscopy, allowing the efficient imaging of proteins with subdiffraction resolution in live cells. nirFAST enabled the design of a chemogenetic green-NIR fluorescent ubiquitination-based cell cycle indicator (FUCCI) for the monitoring of the different phases of the cell cycle. Finally, bisection of nirFAST allowed the design of a fluorogenic chemically induced dimerization technology with NIR fluorescence readout, enabling the control and visualization of protein proximity.

cell biology↗

bioRxiv2024

PDG-Arena: An ecophysiological model for characterizing tree-tree interactions in heterogeneous stands

In the context of the ongoing climate and biodiversity crises, mixed forest stands are increasingly considered as a sustainable management alternative to monocultures. We developed a new individual-based and process-based forest growth model, PDG-Arena, to simulate mixed forest functioning and test ecophysiological interactions among trees in mixed stands. The model builds upon the validated ecophysiological stand-scale model CASTANEA and integrates tree competition for light and water. We evaluated the performance of PDG-Arena by comparing the simulated growth with annual dendrochronological growth data from 37 common beech and silver fir monospecific and mixed plots in the French Alps. PDG-Arena showed a slightly better performance than CASTANEA when simulating even-age and monospecific forests (r2 of 32.1 versus 29.5%). When using structure-diverse and species-diverse inventories, PDG-Arena performed better than CASTANEA in pure beech (38.3 versus 22.9%) and mixed stands (40.5 versus 36.3%), but not in pure fir stands (39.8 versus 42.0%). The new model also showed a significant positive effect of species mixing on gross primary production (+5.5%), canopy absorbance (+11.1%) and transpiration (+15.8%). Our results thus show that tree-level process-based models such as PDG-Arena, formally simulating interspecific interactions, can serve as a valuable tool to understand and simulate the carbon, light and water dynamics of mixed stands.

ecology↗

bioRxiv2021

Annexin A1 is a polarity cue that directs planar mitotic spindle orientation during mammalian epithelial morphogenesis

Oriented cell divisions are critical for the formation and maintenance of structured epithelia. Proper mitotic spindle orientation relies on polarised anchoring of force generators to the cell cortex by the evolutionarily conserved Gi-LGN-NuMA complex. However, the polarity cues that control cortical patterning of this ternary complex remain largely unknown in mammalian epithelia. Here we identify the membrane-associated protein Annexin A1 (ANXA1) as a novel interactor of LGN in mammary epithelial cells. ANXA1 acts independently of Gi to instruct the accumulation of LGN and NuMA at the lateral cortex to ensure cortical anchoring of Dynein-Dynactin and astral microtubules and thereby planar alignment of the mitotic spindle. Loss of ANXA1 randomises mitotic spindle orientation, which in turn disrupts epithelial architecture and luminogenesis in three-dimensional cultures of primary mammary epithelial cells. Our findings establish ANXA1 as an upstream cortical cue that regulates LGN to direct planar cell divisions during mammalian epithelial morphogenesis.

cell biology↗

bioRxiv2021

Tree diversity effects on forest productivity: disentangling the effects of tree species addition vs. substitution

O_LIMixture effect on stand productivity is usually apprehended through a substitutive approach, whereby productivity in mixed stands is compared to productivity in monocultures, at equivalent stand density. This approach has proved that in many cases mixed stands perform better than monospecific forests, however, we do not yet have a solid theory about species behaviour in the mixture or even guidelines for combining species. The addition of a second tree species to an existing mono-specific stand has received much less consideration. Yet, this approach has the potential to separate the facilitation effect from the complementarity effect. C_LIO_LIWe compared the effect of tree species substitution vs. addition on the productivity of maritime pine and silver birch in a young tree diversity experiment implemented in 2008 in SW France. C_LIO_LISubstituting pines with birches to create two-species mixtures resulted in an increase of tree productivity at stand level beyond what was expected from monocultures (i.e., overyielding). In contrast, creating mixture through the addition of birches to pine stands had no effect on the maritime pine stand productivity (transgressive mixture effect not significant). This absence of effect is produced by two distinct density-dependence responses at an individual level. C_LIO_LIOur results allow clarifying the cases in which a mixed stand can be considered as an alternative to a monoculture of a productive species. In particular, the addition of a pioneer and soil low-demanding species during young developmental stages is a possibility to diversify the stand and potentially to increase ecosystem services without altering the productivity of the target species. C_LI

ecology↗

bioRxiv2021

An engineered multifunctional protein tag for advanced fluorescence imaging

Biocompatible fluorescent reporters with spectral properties spanning the entire visible spectrum are indispensable tools for imaging the biochemistry of living cells and organisms in real time. Here, we present the engineering of a fluorescent chemogenetic reporter with tunable optical and spectral properties. A collection of live-cell compatible fluorogenic chromophores with various electronic properties enables to generate bimolecular fluorescent assemblies that cover the visible spectrum from blue to red using a single protein tag engineered and optimized by directed evolution and rational design. We showed that the ability to tune the fluorescence color and properties through simple molecular modulation provides an unprecedent experimental versatility for imaging proteins in live cells, including delicate cultured hippocampal neurons, and in multicellular organisms. The ability to tune the spectral properties and fluorescence performance enables to match the spectral specifications and requirements of the most advanced imaging techniques, and allowed us to achieve efficient stimulated emission depletion (STED) nanoscopy of fusion proteins in live cells and live primary cultured neurons.

molecular biology↗

bioRxiv2020

Managing mixed stands can mitigate severe climate change impacts on ecosystem functioning

Climate change affects forest ecosystem processes and related services due to increasing temperature and increasing extreme drought event frequency. This effect can be direct through the alteration of the physiological responses of trees, but also indirect, by modifying interactions between trees and thus changing communities composition. Such changes might affect species richness with high impacts on ecosystem functioning, especially productivity. Regarding management issues, mixed stands are usually considered a good option to maintain forest cover and ecosystem services under climate change. However, the possibility to maintain these mixed stands with management actions with positive effects on forest functioning under climate change remains uncertain and deserves further investigations. Relying on a simulation-based study with a forest gap model, we thus addressed the following questions: (1) Are monospecific stands vulnerable to climate change? (2) Would mixed stands significantly mitigate climate change effects on forest productivity and wood production under climate change? (3) Would conversion to mixed stand management affect significantly forest productivity and wood production under climate change compare to monospecific management? With a 150 years simulation approach, we quantified potential climate change effect (using RCP 8.5) compared to present climate and managements effect in the French Alps, focusing on five tree species. The gap-model we used included a management module, which allowed testing six silvicultural scenarios on different stands, with various composition, structure or environmental conditions, under climate change. These simulations showed that monospecific stands currently growing in stressful conditions would be too vulnerable to climate change to be maintained. Managing mixed stands or conversion from pure to mixed stands would make it possible to maintain higher productivity in the long-term than monospecific stands, even under severe climate change. This pattern depends to species and sites considered. Our results will feed into discussion on forest management in the context of climate change.

ecology↗

bioRxiv2020

Beyond forest succession: a gap model to study ecosystem functioning and tree community composition under climate change

Climate change impacts forest functioning and dynamics, and large uncertainties remain regarding the interactions between species composition, demographic processes, and environmental drivers. There are few robust tools available to link these processes, which precludes accurate projections and recommendations for long-term forest management. Forest gap-models present a balance between complexity and generality and are widely used in predictive forest ecology. However, their relevance to tackle questions about the links between species composition, climate and forest functioning is unclear. In this regard, demonstrating the ability of gap-models to predict the growth of forest stands at the annual time scale - representing a sensitive and integrated signal of tree functioning and mortality risk - appears as a fundamental step. In this study, we aimed at assessing the ability of a gap-model to accurately predict forest growth in the short-term and potential community composition in the long-term, across a wide range of species and environmental conditions. To do so, we present the gap-model ForCEEPS, calibrated using an original parameterization procedure for the main tree species in France. ForCEEPS was shown to satisfactorily predict forest annual growth (averaged over a few years) at the plot level from mountain to Mediterranean climates, regardless the species. Such an accuracy was not gained at the cost of losing precision for long-term predictions, as the model showed a strong ability to predict potential community composition along a gradient of sites with contrasted conditions. The mechanistic relevance of ForCEEPS parameterization was explored by showing the congruence between the values of key model parameter and species functional traits. We further showed that accounting for the spatial configuration of crowns within forest stands, the effects of climatic constraints and the variability of shade tolerances in the species community are all crucial to better predict short-term productivity with gap-models. The dual ability of predicting short-term functioning and long-term community composition, as well as the balance between generality and realism (i.e., predicting accuracy) of the new generation of gap-models may open great perspectives for the exploration of the biodiversity-ecosystem functioning relationships, species coexistence mechanisms, and the impacts of climate change on forest ecosystems.

ecology↗

bioRxiv2020

A far-red fluorescent chemogenetic reporter for in vivo molecular imaging

Far-red emitting fluorescent labels are highly desirable for spectral multiplexing and deep tissue imaging. Here, we describe the generation of frFAST (far-red Fluorescence Activating and absorption Shifting Tag), a 14-kDa monomeric protein that forms a bright far-red fluorescent assembly with (4-hydroxy-3-methoxy-phenyl)allylidene rhodanine (HPAR-3OM). As HPAR-3OM is essentially non-fluorescent in solution and in cells, frFAST can be imaged with high contrast in presence of free HPAR-3OM, which allowed the rapid and efficient imaging of frFAST fusions in live cells, zebrafish embryo/larvae and chicken embryo. Beyond enabling genetic encoding of far-red fluorescence, frFAST allowed the design of a far-red chemogenetic reporter of protein-protein interactions, demonstrating its great potential for the design of innovative far-red emitting biosensors.

molecular biology↗

bioRxiv2020

Tree diversity and the temporal stability of mountain forest productivity: testing the effect of species composition, through asynchrony and overyielding

Climate change modifies ecosystem processes directly through its effect on environmental conditions, but also indirectly by changing community composition. Theoretical studies and grassland experiments suggest that diversity may increase and stabilize communities productivity over time. Few recent studies on forest ecosystems suggested the same pattern but with a larger variability between the results. In this paper, we aimed to test stabilizing diversity effect for two kinds of mixtures (Fagus sylvatica - Quercus pubescens and Fagus sylvatica - Abies alba), and to assess how climate may affect the patterns. We used tree ring data from forest plots distributed along a latitudinal gradient across French Alps. We found that diversity effect on stability in productivity varies with stand composition. Most beech-fir stands showed a greater stability in productivity over time than monocultures, while beech-oak stands showed a less stable productivity. Considering non-additive effects, no significant trends were found, regardless the type of mixed stands considered. We further highlighted that these patterns could be partially explained by asynchrony between species responses to annual climatic conditions (notably to variation in temperature or precipitation), overyielding, and climatic conditions. We also showed that the intensity of the diversity effect on stability varies along the ecological gradient, consistently with the stress gradient hypothesis for beech-oak forests, but not for beech-fir forests. This study showed the importance of the species identity on the relationships between diversity, climate and stability of forest productivity. Better depicting diversity and composition effects on forest ecosystem functioning appears to be crucial for forest managers to promote forest adaptation and maintain timber resource in the context of on-going climate change.

ecology↗

bioRxiv2019

Climate associated genetic variation in Fagus sylvatica and potential responses to climate change in the French Alps.

Local adaptation patterns have been found in many plants and animals, highlighting the genetic heterogeneity of species along their range of distribution. In the next decades, global warming must induce a change in the selective pressures that drive this adaptive variation, forcing a reshuffling of the underlying adaptive allele distributions. For species with low dispersion capacity and long generation time such as trees, the rapidity of the change could imped the migration of beneficial alleles and lower their capacity to track the changing environment. Identifying the main selective pressures driving the adaptive genetic variation is thus necessary when investigating species capacity to respond to global warming. In this study, we investigate the adaptive landscape of Fagus sylvatica along a gradient of populations in the French Alps. Using a ddRAD-seq approach, we identified 7,000 SNPs from 570 individuals across 36 different sites. An RDA-derived method allowed us to identify several SNPs that were strongly associated with climatic gradients; moreover, we defined the primary selective gradients along the natural populations of F. sylvatica in the Alps. Strong effects of elevation and humidity, which contrast north-western and south-eastern site, were found and were believed to be important drivers of genetic adaptation. Finally, simulations of future genetic landscapes that used these findings predicted a severe range contraction and a shift towards higher altitudes for F. sylvatica in the Alps and allowed to identify populations at risk, which could be helpful for future management plans.

evolutionary biology↗