Biology subjects

Legendre, P.

Publications and source records attributed to Legendre, P..

9 recordsLinked to original sources

bioRxiv2024

Birth order specified recruitment of motor circuits during spontaneous neural activity in zebrafish embryo

Modular organization of spinal neural circuits control dynamic regulation of locomotion. However, it is unknown when or how the distinct microcircuits emerge during development. We carried out high-resolution calcium imaging of neural activity driving the first motor behavior in one day old zebrafish embryo. During this period, at least two waves of neurogenesis occur to generate primary and secondary motoneurons. We found that embryos first display a single highly synchronized rhythmic neuronal circuit containing interneurons and motoneurons. Later, two distinct interneuron-motoneuron circuits emerge with one containing early-born motoneurons displaying low-frequency activity and the other containing later-born motoneurons with high-frequency activity. The results indicate a mode of birth order determined microcircuits where neurons that are born together are recruited together. Nicotine affected neuronal activity frequency, revealing a functional role for cholinergic signaling in the emergence of patterned spinal circuits. Indeed, we found aberrant arrhythmic synchronized activity in mutants for cholineacetyltransferase-a where acetylcholine is no longer synthesized. Overall, we reveal the sequential recruitment of birth order specified microcircuits during the emergence of the earliest motor behavior and highlight a conserved role for cholinergic signaling in regulating rhythmic neural activity in the embryonic spinal cord.

neuroscience↗

bioRxiv2023

Predicting genomic traits in ammonia-oxidizing archaea using phylogenetic signals

Phylogenetic conservatism of microbial traits has paved the way for phylogeny-based predictions, allowing us to move from descriptive to predictive functional microbial ecology. Here, we applied phylogenetic eigenvector mapping, an approach not previously used for microorganisms, to predict key traits of ammonia-oxidizing archaea (AOA), which are important players in nitrogen cycling. Using 168 nearly complete AOA genomes and metagenome assembled genomes from public databases, we predicted the distribution of 18 ecologically relevant genes across an updated amoA gene phylogeny, including a novel variant of an ammonia transporter found in this study. Of the selected genes, 94% displayed a significant phylogenetic signal and gene presence was predicted with >88% accuracy, >88% sensitivity, and >80% specificity. The phylogenetic eigenvector approach performed equally well as ancestral state reconstruction of traits. We implemented the predictive models on an amoA sequencing dataset of AOA soil communities and show key ecological predictions, e.g., that AOA communities in nitrogen rich soils have capacity for ureolytic metabolism while those adapted to low pH soils have the high affinity ammonia transporter (amt2). Predicting genomic traits can shed light on the potential functions that microbes perform across earth biomes, further contributing to a better mechanistic understanding of their community assembly.

ecology↗

bioRxiv2020

Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin

BackgroundThe SARS-CoV-2 pandemic is among the most dangerous infectious diseases that have emerged in recent history. Human CoV strains discovered during previous SARS outbreaks have been hypothesized to pass from bats to humans using intermediate hosts, e.g. civets for SARS-CoV and camels for MERS-CoV. The discovery of an intermediate host of SARS-CoV-2 and the identification of specific mechanism of its emergence in humans are topics of primary evolutionary importance. In this study we investigate the evolutionary patterns of 11 main genes of SARS-CoV-2. Previous studies suggested that the genome of SARS-CoV-2 is highly similar to the horseshoe bat coronavirus RaTG13 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the receptor binding (RB) domain of the spike protein. ResultsWe provide a detailed list of statistically significant horizontal gene transfer and recombination events (both intergenic and intragenic) inferred for each of 11 main genes of the SARS-Cov-2 genome. Our analysis reveals that two continuous regions of genes S and N of SARS-CoV-2 may result from intragenic recombination between RaTG13 and Guangdong (GD) Pangolin CoVs. Statistically significant gene transfer-recombination events between RaTG13 and GD Pangolin CoV have been identified in region [1215-1425] of gene S and region [534-727] of gene N. Moreover, some significant recombination events between the ancestors of SARS-CoV-2, RaTG13, GD Pangolin CoV and bat CoV ZC45-ZXC21 coronaviruses have been identified in genes ORF1ab, S, ORF3a, ORF7a, ORF8 and N. Furthermore, topology-based clustering of gene trees inferred for 25 CoV organisms revealed a three-way evolution of coronavirus genes, with gene phylogenies of ORF1ab, S and N forming the first cluster, gene phylogenies of ORF3a, E, M, ORF6, ORF7a, ORF7b and ORF8 forming the second cluster, and phylogeny of gene ORF10 forming the third cluster. ConclusionsThe results of our horizontal gene transfer and recombination analysis suggest that SARS-Cov-2 could not only be a chimera resulting from recombination of the bat RaTG13 and Guangdong pangolin coronaviruses but also a close relative of the bat CoV ZC45 and ZXC21 strains. They also indicate that a GD pangolin may be an intermediate host of SARS-CoV-2.

evolutionary biology↗

bioRxiv2020

Differential homeostatic regulation of glycinergic and GABAergic nanocolumns at mixed inhibitory synapses

Super-resolution imaging of synapses has revealed that key synaptic proteins are dynamically organized within sub-synaptic domains (SSDs). At mixed inhibitory synapses in spinal cord neurons, both GlyRs and GABAARs reside at the same post-synaptic density (PSD). To examine how the different inhibitory receptors are organized and regulated, we carried out dual-color direct stochastic optical reconstruction microscopy (dSTORM). We found that endogenous GlyRs and GABAARs as well as their common scaffold protein gephyrin form SSDs that align with pre-synaptic RIM1/2, thus forming trans-synaptic nanocolumns. Strikingly, GlyRs and GABAARs occupy different sub-synaptic spaces, exhibiting only a partial overlap at mixed inhibitory synapses. When network activity was increased by pharmacological treatment using the K+ channel blocker 4-aminopyridine (4-AP), the GABAAR copy numbers of as well as the number of GABAAR SSDs were reduced, while GlyRs remained largely unchanged. This differential regulation is likely the result of changes in gephyrin phosphorylation that preferentially occurred outside of the SSDs. The total gephyrin content was not altered by 4-AP application. The activity-dependent regulation of GABAARs versus GlyRs suggests that different signaling pathways control their respective sub-synaptic organization. Whereas gephyrin serves as a scaffold protein that upholds GlyR numbers at SSDs, it may act as a switch regulating GABAARs via its phosphorylation state. Taken together, our data reinforce the notion that the precise sub-synaptic organization of GlyRs, GABAARs and gephyrin has functional consequences for the homeostatic regulation of mixed inhibitory synapses. HighlightsAlignment of sub-synaptic domains (SSDs) in trans-synaptic nanocolumns at inhibitory synapses Differential spatial organization of SSDs formed by GlyRs and GABAARs at mixed inhibitory synapses Activity-dependent regulation of GABAARs but not GlyRs at mixed inhibitory synapses Gephyrin phosphorylation is compartmentalized in SSDs within the synaptic scaffold

neuroscience↗

bioRxiv2020

Early diversity in the firing pattern of embryonic Renshaw cells: just a synergy between two opposite voltage-dependent currents

Renshaw cells (V1R) are excitable as soon as they reach their final location next to the spinal motoneurons and are functionally heterogeneous. Using multiple experimental approaches, in combination with biophysical modeling and dynamical systems theory, we analyzed, for the first time, the mechanisms underlying the electrophysiological properties of V1R during early embryonic development of the spinal cord locomotor networks (E11.5-E16.5). We found that these interneurons are subdivided into several functional clusters from E11.5 and then display an unexpected transitory involution process during which they lose their ability to sustain tonic firing. We demonstrated that the essential factor controlling the diversity of the discharge pattern of embryonic V1R is the ratio of a persistent sodium conductance to a delayed rectifier potassium conductance. Taken together, our results reveal how a simple mechanism, based on the synergy of two voltage-dependent conductances that are ubiquitous in neurons, can produce functional diversity in V1R and control their early developmental trajectory.

neuroscience↗

bioRxiv2020

The floor-plate of His is a non-neuronal electrical conduction pathway

In the developing central nervous system, electrical signaling is thought to rely exclusively on differentiating neurons as they acquire the ability to generate action potentials. Accordingly, the neuroepithelial progenitors (NEPs) giving rise to all neurons and glial cells during development have been reported to remain electrically passive. Here, we investigated the physiological properties of NEPs in the mouse spinal cord at the onset of spontaneous neural activity (SNA) initiating motor behavior in embryos. Using patch-clamp recordings, we discovered that spinal NEPs exhibit spontaneous membrane depolarizations during episodes of SNA. These recurrent depolarizations exhibited a ventral-to-dorsal gradient with the highest amplitude located in the floor-plate - the ventral-most part of the neuroepithelium. Paired-recordings revealed that NEPs are extensively coupled via gap-junctions and form a single electrical syncytium. Although other NEPs were electrically passive, we discovered that floor-plate NEPs have the unique ability to generate large Na+/Ca++ action potentials. Unlike neurons, floor-plate action potentials relied primarily on the activation of voltage-gated T-type calcium channels (TTCCs). In situ hybridization showed that all 3 known subtypes of TTCCs are highly and predominantly expressed in the floor-plate. During SNA, we found that acetylcholine released by motoneurons recurrently trigger floor-plate action potentials by acting through nicotinic acetylcholine receptors. Finally, by expressing the genetically encoded calcium indicator GCaMP6f in the floor plate, we demonstrated that neuroepithelial action potentials are associated with calcium waves and propagate along the entire length of the spinal cord. By unraveling a novel physiological mechanism generating electrical signals which can propagate independently from neurons across a neural structure, our work significantly changes our understanding of the development, origin and extent of electrical signaling in the central nervous system. HIGHLIGHTSO_LISpinal neuroepithelial progenitors (NEP) are depolarized during spontaneous neural activity C_LIO_LINEPs form a single electrical syncytium connected by gap junctions C_LIO_LIFloor-plate NEPs generate large Na+/Ca++ action potentials in response to acetylcholine C_LIO_LINeuroepithelial action potentials propagate across the entire spinal cord C_LI

neuroscience↗

bioRxiv2019

Partitioning plant spectral diversity into alpha and beta components

Plant spectral diversity -- how plants differentially interact with solar radiation -- is an integrator of plant chemical, structural, and taxonomic diversity that can be remotely sensed. We propose to measure spectral diversity as spectral variance, which allows the partitioning of the spectral diversity of a region, called spectral gamma ({gamma}) diversity, into additive alpha (; within communities) and beta ({beta}; among communities) components. Our method calculates the contributions of individual bands or spectral features to spectral{gamma} -, {beta}-, and -diversity, as well as the contributions of individual plant communities to spectral diversity. We present two case studies illustrating how our approach can identify \"hotspots\" of spectral -diversity within a region, and discover spectrally unique areas that contribute strongly to {beta}-diversity. Partitioning spectral diversity and mapping its spatial components has many applications for conservation since high local diversity and distinctiveness in composition are two key criteria used to determine the ecological value of ecosystems.

ecology↗

bioRxiv2019

Diversity begets diversity in microbiomes

Microbes are embedded in complex communities where they engage in a wide array of intra- and inter-specific interactions. The extent to which these interactions drive or impede microbiome diversity is not well understood. Historically, two contrasting hypotheses have been suggested to explain how species interactions could influence diversity. Ecological Controls (EC) predicts a negative relationship, where the evolution or migration of novel types is constrained as niches become filled. In contrast, Diversity Begets Diversity (DBD) predicts a positive relationship, with existing diversity promoting the accumulation of further diversity via niche construction and other interactions. Using high-throughput amplicon sequencing data from the Earth Microbiome Project, we provide evidence that DBD is strongest in low-diversity biomes, but weaker in more diverse biomes, consistent with biotic interactions initially favoring the accumulation of diversity (as predicted by DBD). However, as niches become increasingly filled, diversity hits a plateau (as predicted by EC). Impact statementMicrobiome diversity favors further diversity in a positive feedback that is strongest in lower-diversity biomes (e.g. guts) but which plateaus as niches are increasingly filled in higher-diversity biomes (e.g. soils).

evolutionary biology↗

bioRxiv2018

The interaction of phylogeny and community structure: linking clades’ ecological structures and trait evolution

1AimCommunity phylogenetic studies use information about species evolutionary relationships to understand the processes of community ecological assembly. A central premise of the field is that species evolution maps onto ecological patterns, and phylogeny reveals something more than species traits alone. We argue, therefore, that there is a need to better understand and model the interaction of phylogeny with species traits and community composition.\n\nInnovationWe outline a new method that identifies clades with unusual ecological structures, based around partitioning the variation of species site occupancies ({beta}-diversity). Eco-phylogenetic theory would predict that these clades should also demonstrate distinct evolutionary trajectories. We suggest that modelling the evolution of independent trait data in these clades represents a strong test of whether there is an association between species ecological structure and evolutionary history.\n\nMain conclusionsUsing an empirical dataset of mammals from around the world, we identify two clades of rodents that tend not to co-occur (are phylogenetically overdispersed), and then find independent evidence of slower rates of body mass evolution in these clades. We suggest that our approach, which assumes nothing about the mode of species trait evolution but rather seeks to explain it using ecological information, presents a new way to examine eco-phylogenetic structure.

evolutionary biology↗