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Leon, A.

Publications and source records attributed to Leon, A..

17 recordsLinked to original sources
bioRxiv2026

Single cell sequencing during the entire life cycle reveals cell type diversity in Oikopleura dioica, and pools of genes expressed in the house-producing epithelium

In tunicates, larvaceans represent a fascinating case of evolution, where the chordate body plan has been maintained despite a rapidly evolving genome characterized by strong In contrast to other tunicates, larvaceans keep the chordate body plan during their entire life. They have acquired a highly specialized epithelium in charge of producing the "house", a complex extracellular apparatus used for filter feeding in the plankton. To what extent the house and this epithelium represent true molecular innovations withing chordates is a question for which thorough transcriptomics can bring novel insights. We conducted a developmental profiling of gene expression at the single-cell level in the larvacean Oikopleura dioica. We provide detailed descriptions of cellular transcriptomes associated with the house-synthesizing organ, which permits to define the molecular specifics of epithelial cell territories. We followed their emergence during development, and we identified genes that represent key candidate molecules for regulating the morphogenesis of the house-producing organ. Dynamic changes in gene expression and cell identities during major developmental transitions of the lifecycle illustrate that our dataset effectively allows access to the diversity of O. dioicas cell types in embryos and in adults. The resources presented here constitute critical assets to investigate larvacean biology and evolution for mechanistic and comparative goals.

evolutionary biology↗
bioRxiv2026

Analysis of the spatiotemporal dynamics of behavior in domestic dogs with free locomotion under appetitive Pavlovian contingencies

Spatiotemporal dynamics of behavior is key to understanding the organism-environment relationship. While often implicitly addressed, its relation to Pavlovian contingencies remains understudied in domestic dogs. This study quantitatively examined the spatial dimension of behavior of three freely moving dogs under pairing and extinction of a tone-food Pavlovian contingency. In pairing, a tone (CS) was paired with food delivery (US) on a fixed-time 60-second (FT 60 s) schedule; in extinction, only the tone was presented. Locomotion was recorded using two-dimensional tracking based on center of mass. During pairing, dogs moved closer to the dispenser, covered greater distances, displayed extended trajectories, and showed a conditional approach pattern to the dispenser during CS presentation. In extinction, they stayed closer to the owner or room periphery, traveled shorter distances, and exhibited more restricted trajectories. These findings show that spatial segments (dispenser area) are integrated into the CS-US relationship, demonstrate the usefulness of continuous recording of spatial behavior in the analysis of Pavlovian contingencies, and suggest potential application in contexts relevant to animal welfare. HighlightsO_LISpatial behavior remains largely unexplored in studies of Pavlovian contingencies C_LIO_LIDog locomotion was continuously tracked during pairing and extinction phases C_LIO_LIDistinct spatial patterns emerged across pairing and extinction phases C_LIO_LIIncorporating space into CS-US relations clarifies behavioral organization C_LIO_LITracking tools expand the experimental and applied scope of Pavlovian research C_LI

animal behavior and cognition↗
bioRxiv2025

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and re-patterning of snRNA m6A modification

In eukaryotes, the critical function of the spliceosome is to remove introns from newly transcribed pre-messenger RNA to produce functional mRNA. Spliced segments normally begin with a GT and end with an AG, and precise intron removal relies on the recognition of terminal dinucleotides by the spliceosomal RNA (snRNA) and by the U2AF heterodimer. Here, we reveal how the modification of these molecules was instrumental for shifting spliceosome specificity, enforcing splicing accuracy in genomes where 95% of introns escape the GT/AG rule. We show that the emergence of non-canonical introns in the Fritillaria borealis lineage is associated with the duplication of each U2AF subunit. Subunit paralogues can be combined to form multiple U2AF complexes that involve novel protein-protein interaction rules. Binding assays on RNA and transcriptome analysis of human cells expressing U2AF subunits show that divergent paralogues can contribute to the recognition of non-canonical splice signals at the 3 end of introns. In transfected cells, levels of N6-methyladenosine (m6A) modification on snRNA U2 and U6 are impacted by the presence of F. borealis U2AF2 and by AHCYL1, a specific partner of the divergent subunit U2AF2{beta}. In striking contrast with other species, F. borealis has lost m6A on the U6 snRNA while U1 snRNA has gained a stable, 5-terminal m6A. We used structure prediction to show how these snRNA modifications could play decisive roles during the recognition of non-GT/AG introns. In conclusion, we argue that spliceosome function can be profoundly impacted by gene neofunctionalization and post-transcriptional modifications, without implying major changes to conserved genetic components.

molecular biology↗
bioRxiv2025

Movement path as an ethological lens into interval timing

Interval timing behavior is traditionally investigated in operant chambers based on the very focal responses of the subjects (e.g., head entry to the magazine, lever press). These measures are blind to the movement trajectory of the animals and capture only a tiny segment and some-times an idiosyncratic component of the animals behavior. In other words, the state of the temporal expectancy is not observable at every time point in the trial. On the other hand, in nature, temporal expectancies guide actions in a much more complex fashion. For instance, an animal might approach a food patch at different degrees as a function of the expected time of food availability (e.g., nectar collection behavior). The current study aimed to investigate interval timing in a more naturalistic fashion by analyzing the movement trajectory of rats in fixed time (FT-30s) vs. variable time (VT-30s) schedules in modified open field equipment. We observed a temporally patterned movement in FT but not in a VT schedule. In the FT schedule, rats moved away from the reward grid after consuming the presented water and were farthest from it for around 15 seconds, after which they started to approach the reward grid again. There was no such temporal patterning of movement trajectory in the VT schedule. Temporal control in the FT schedule was stronger in the Wall compared to the Center condition. Our results show that movement trajectory may reflect instantaneous temporal expectancy.

animal behavior and cognition↗
bioRxiv2023

Pax37 gene function in Oikopleura dioica supports a neuroepithelial-like origin for its house-making Fol territory

Larvacean tunicates feature a spectacular innovation not seen in other animals - the trunk oikoplastic epithelium (OE). This epithelium produces a house, a large and complex extracellular structure used for filtering and concentrating food particles. Previously we have shown that several homeobox transcription factors may play a role in patterning the OE. Among these are two Pax3/7 duplicates that we named Pax37A and Pax37B. The vertebrate homologs, PAX3 and PAX7, are involved in developmental processes related to neural crest and muscles. In the ascidian tunicate Ciona robusta, Pax3/7 has been given a role in development of cells deriving from the neural plate border including trunk epidermal sensory neurons and tail nerve cord neurons as well as in neural tube closure. Here we have investigated the roles of Pax37A and Pax37B in the development of the OE using CRISPR-Cas9, analyzing scRNA-seq data from wild-type animals that were compared with scRNA-seq data from C. robusta. We revealed that Pax37B but not Pax37A is essential for the differentiation of cell fields that produce the food concentrating filter of the house: the anterior Fol, giant Fol and Nasse cells. Lineage analysis supports that expression of Pax37 is under influence of Wnt signaling and that Fol cells have a neuroepithelial-like transcriptional signature. We propose that the highly specialized secretory epithelial cells of the Fol region either maintained or evolved neuroepithelial features as do "glue" secreting collocytes of ascidians. Their development seems to be controlled by a GRN that also operates in some ascidian neurons.

developmental biology↗
bioRxiv2023

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

The mammalian brain is composed of millions to billions of cells that are organized into numerous cell types with specific spatial distribution patterns and structural and functional properties. An essential step towards understanding brain function is to obtain a parts list, i.e., a catalog of cell types, of the brain. Here, we report a comprehensive and high-resolution transcriptomic and spatial cell type atlas for the whole adult mouse brain. The cell type atlas was created based on the combination of two single-cell-level, whole-brain-scale datasets: a single- cell RNA-sequencing (scRNA-seq) dataset of [~]7 million cells profiled, and a spatially resolved transcriptomic dataset of [~]4.3 million cells using MERFISH. The atlas is hierarchically organized into five nested levels of classification: 7 divisions, 32 classes, 306 subclasses, 1,045 supertypes and 5,200 clusters. We systematically analyzed the neuronal, non-neuronal, and immature neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell type organization in different brain regions, in particular, a dichotomy between the dorsal and ventral parts of the brain: the dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. We also systematically characterized cell-type specific expression of neurotransmitters, neuropeptides, and transcription factors. The study uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types across the brain, suggesting they mediate a myriad of modes of intercellular communications. Finally, we found that transcription factors are major determinants of cell type classification in the adult mouse brain and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole-mouse-brain transcriptomic and spatial cell type atlas establishes a benchmark reference atlas and a foundational resource for deep and integrative investigations of cell type and circuit function, development, and evolution of the mammalian brain.

neuroscience↗
bioRxiv2022

Experimental infection of Mexican free-tailed bats (Tadarida brasiliensis) with SARS-CoV-2.

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus originated in wild bats from Asia, and as the resulting pandemic continues into its third year, concerns have been raised that the virus will expand its host range and infect North American wildlife species, including bats. Mexican free-tailed bats (Tadarida brasiliensis: TABR) live in large colonies in the southern United States, often in urban areas, and as such, could be exposed to the virus from infected humans. We experimentally challenged wild TABR with SARS-CoV-2 to determine the susceptibility, reservoir potential, and population impacts of infection in this species. Of nine bats oronasally inoculated with SARS-CoV-2, five became infected and orally excreted moderate amounts of virus for up to 18 days post inoculation. These five subjects all seroconverted and cleared the virus before the end of the study with no obvious clinical signs of disease. We additionally found no evidence of viral transmission to uninoculated subjects. These results indicate that while TABR are susceptible to SARS-CoV-2 infection, infection of wild populations of TABR would not likely cause mortality. However, the transmission of SARS-CoV-2 from TABR to or from humans, or to other animal species, is a distinct possibility requiring further investigation to better define.

pathology↗
bioRxiv2021

Effect of the Ecological Location of a Water Source on Entropy and other Spatio-temporal Behavioral Features: An extended and systematic replication

In behavior analysis, the modulation of the effect of time-based schedules by the spatial characteristics of the environment has been scarcely studied. Furthermore, the spatial organization of behavior, despite its ubiquity and ecological relevance, has not been widely addressed. The purpose of the present work was to analyze the effect of water delivery location (peripheral vs. central) on the spatial organization of water-feeding behavior under time-based schedules. One group of rats was exposed to a Fixed Time 30 s-water-delivery schedule and a second group to a Variable Time 30 s schedule. For both groups, in the first phase, the water dispenser was located in the perimetral zone. In the second condition, the water dispenser was located in the central zone. Each location was presented for 20 sessions. Rats trajectories, distance to the dispenser, accumulated time in regions, and entropy measures were analyzed. A differential effect of the location of water delivery in interaction with the time-based schedule was observed on all the analyzed spatial qualities of behavior. The findings are discussed in relation to the ecological proposal of Timberlakes behavioral systems.

animal behavior and cognition↗
bioRxiv2021

Beyond single discrete responses: An integrative and multidimensional analysis of behavioral dynamics assisted by Machine Learning

Behavioral systems, understanding it as an emergent system comprising the environment and organism subsystems, include spatial dynamics as a primary dimension in natural settings. Nevertheless, under the standard approaches, the experimental analysis of behavior is based on the single response paradigm and the temporal distribution of discrete responses. Thus, the continuous analysis of spatial behavioral dynamics has been a scarcely studied field. The technological advancements in computer vision have opened new methodological perspectives for the continuous sensing of spatial behavior. With the application of such advancements, recent studies suggest that there are multiple features embedded in the spatial dynamics of behavior, such as entropy, and that they are affected by programmed stimuli (e.g., schedules of reinforcement), at least, as much as features related to discrete responses. Despite the progress, the characterization of behavioral systems is still segmented, and integrated data analysis and representations between discrete responses and continuous spatial behavior are exiguous in the Experimental Analysis of Behavior. Machine Learning advancements, such as t-SNE, variable ranking, provide invaluable tools to crystallize an integrated approach for analyzing and representing multidimensional behavioral data. Under this rationale, the present work: 1) proposes a multidisciplinary approach for the integrative and multilevel analysis of behavioral systems, 2) provides sensitive behavioral measures based on spatial dynamics and helpful data representations to study behavioral systems, and 3) reveals behavioral aspects usually ignored under the standard approaches in the experimental analysis of behavior. To exemplify and evaluate our approach, the spatial dynamics embedded in phenomena relevant to behavioral science, namely water-seeking behavior, and motivational operations, are examined, showing aspects of behavioral systems hidden until now.

animal behavior and cognition↗
bioRxiv2019

A survey of spiking activity reveals a functional hierarchy of mouse corticothalamic visual areas

The mammalian visual system, from retina to neocortex, has been extensively studied at both anatomical and functional levels. Anatomy indicates the cortico-thalamic system is hierarchical, but characterization of cellular-level functional interactions across multiple levels of this hierarchy is lacking, partially due to the challenge of simultaneously recording activity across numerous regions. Here, we describe a large, open dataset (part of the Allen Brain Observatory) that surveys spiking from units in six cortical and two thalamic regions responding to a battery of visual stimuli. Using spike cross-correlation analysis, we find that inter-area functional connectivity mirrors the anatomical hierarchy from the Allen Mouse Brain Connectivity Atlas. Classical functional measures of hierarchy, including visual response latency, receptive field size, phase-locking to a drifting grating stimulus, and autocorrelation timescale are all correlated with the anatomical hierarchy. Moreover, recordings during a visual task support the behavioral relevance of hierarchical processing. Overall, this dataset and the hierarchy we describe provide a foundation for understanding coding and dynamics in the mouse cortico-thalamic visual system.

neuroscience↗
bioRxiv2019

Structural fuzziness of the RNA-organizing protein SERF1a determines a toxic gain-of-interaction

Members of the MOAG/SERF protein family have been attributed a neuropathologic significance because of their ability to enhance the proteotoxic polymerization of amyloidogenic proteins such as alpha-Synuclein (aSyn). However, the cellular function remains unknown. Here, we identify SERF1a as an RNA-organizing protein i) with no structural homology to canonical RNA-binding proteins, ii) with an RNA-chaperoning activity which favours the incorporation of RNA into nucleoli and liquid-like artificial RNA-organelles, and iii) with a high degree of conformational disorder in the RNA-bound state. We demonstrate that this type of structural fuzziness determines an undifferentiated interaction of SERF1a with aSyn and RNA. Both molecules bind to one identical, positively charged site of SERF1a by an analogous electrostatic binding mode, with similar binding affinities, and without any observable disorder-to-order transition. The absence of primary or secondary structure discriminants results in SERF1a being unable to distinguish between nucleic acid and amyloidogenic protein, leading the pro-amyloid aSyn:SERF1a interaction to prevail under conditions of cellular stress. We suggest that structural fuzziness of SERF1a accounts for an adverse gain-of-interaction which favours toxic binding to aSyn at the expense of non-toxic RNA binding, therefore promoting a functionally distorted and pathogenic process. Our results provide a direct link between structural disorder, amyloid aggregation and the malfunctioning of RNA-associated cellular processes, three hallmarks of neurodegenerative diseases.

biochemistry↗
bioRxiv2019

Experience shapes activity dynamics and stimulus coding of VIP inhibitory and excitatory cells

Cortical circuits are flexible and can change with experience and learning. However, the effects of experience on specific cell types, including distinct inhibitory types, are not well understood. Here we investigated how excitatory and VIP inhibitory cells in layer 2/3 of mouse visual cortex were impacted by visual experience in the context of a behavioral task. Mice learned to perform an image change detection task with a set of eight natural scene images, viewing these images thousands of times. Subsequently, during 2-photon imaging experiments, mice performed the task with these familiar images and three additional sets of novel images. Novel images evoked stronger overall activity in both excitatory and VIP populations, and familiar images were more sparsely coded by excitatory cells. The temporal dynamics of VIP activity differed markedly between novel and familiar images: VIP cells were stimulus-driven by novel images but displayed ramping activity during the inter-stimulus interval for familiar images. Moreover, when a familiar stimulus was omitted from an expected sequence, VIP cells showed extended ramping activity until the subsequent image presentation. This prominent shift in response dynamics suggests that VIP cells may adopt different modes of processing during familiar versus novel conditions.\n\nHIGHLIGHTSO_LIExperience with natural images in a change detection task reduces overall activity of cortical excitatory and VIP inhibitory cells\nC_LIO_LIEncoding of natural images is sharpened with experience in excitatory neurons\nC_LIO_LIVIP cells are stimulus-driven by novel images but show pre-stimulus ramping for familiar images\nC_LIO_LIVIP cells show strong ramping activity during the omission of an expected stimulus\nC_LI

neuroscience↗
bioRxiv2019

MgO nanoparticles coated with Polyethylene Glycol as carrier for 2-Methoxyestradiol anticancer drug.

Novel Magnesium Oxide (MgO) nanoparticles (NPs) modified with the polymer poliethylene glycol (PEG) were synthesized as carrier for the anticancer drug 2-Methoxyestradiol (2ME) to improve its clinical application. The functionalized NPs were characterized by Infrared spectroscopy with Fourier transform to elucidate the vibration modes of this conjugate, indicating the formation of the MgO-PEG-2ME nanocomposite. The studies of absorption and liberation determined that MgO-PEG-2ME NPs incorporated 98.51 % of 2ME while liberation of 2ME was constant during 7 days at pH 2, 5 and 7.35. Finally, the MgO-PEG-2ME NPs decreased the viability of the prostate cancer cell line LNCap suggesting that this nanocomposite is suitable as a drug delivery system for anticancer prostate therapy.

cancer biology↗
bioRxiv2018

Multi-plane Imaging of Neural Activity From the Mammalian Brain Using a Fast-switching Liquid Crystal Spatial Light Modulator

We report a novel two-photon fluorescence microscope based on a fast-switching liquid crystal spatial light modulator and a pair of galvo-resonant scanners for large-scale recording of neural activity from the mammalian brain. The utilized imaging technique is capable of monitoring large populations of neurons spread across different layers of the neocortex in awake and behaving mice. During each imaging session, all visual stimulus driven somatic activity could be recorded in the same behavior state. We observed heterogeneous response to different types of visual stimuli from ~ 3,300 excitatory neurons reaching from layer II/III to V of the striate cortex.

bioengineering↗
bioRxiv2018

Cbs overdosage is necessary and sufficient to induce cognitive phenotypes in mouse models of Down syndrome and interacts genetically with Dyrk1a

Identifying dosage sensitive genes is a key to understand the mechanisms underlying intellectual disability in Down syndrome (DS). The Dp(17Abcg1-Cbs)1Yah DS mouse model (Dp1Yah) show cognitive phenotype and needs to be investigated to identify the main genetic driver. Here, we report that, in the Dp1Yah mice, 3 copies of the Cystathionine-beta-synthase gene (Cbs) are necessary to observe a deficit in the novel object recognition (NOR) paradigm. Moreover, the overexpression of Cbs alone is sufficient to induce NOR deficit. Accordingly targeting the overexpression of human CBS, specifically in Camk2a-expressing neurons, leads to impaired objects discrimination. Altogether this shows that Cbs overdosage is involved in DS learning and memory phenotypes. In order to go further, we identified compounds that interfere with the phenotypical consequence of CBS overdosage in yeast. Pharmacological intervention in the Tg(CBS) with one selected compound restored memory in the novel object recognition. In addition, using a genetic approach, we demonstrated an epistatic interaction between Cbs and Dyrk1a, another human chromosome 21 gene encoding the dual-specificity tyrosine phosphorylation-regulated kinase 1a and an already known target for DS therapeutic intervention. Further analysis using proteomic approaches highlighted several pathways, including synaptic transmission, cell projection morphogenesis, and actin cytoskeleton, that are affected by DYRK1A and CBS overexpression. Overall we demonstrated that CBS overdosage underpins the DS-related recognition memory deficit and that both CBS and DYRK1A interact to control accurate memory processes in DS. In addition, our study establishes CBS as an intervention point for treating intellectual deficiencies linked to DS.\n\nSIGNIFICANT STATEMENTHere, we investigated a region homologous to Hsa21 and located on mouse chromosome 17. We demonstrated using three independent genetic approaches that the overdosage of the Cystathionine-beta-synthase gene (Cbs) gene, encoded in the segment, is necessary and sufficient to induce deficit in novel object recognition (NR).\n\nIn addition, we identified compounds that interfere with the phenotypical consequence of CBS overdosage in yeast and in mouse transgenic lines. Then we analyzed the relation between Cbs overdosage and the consequence of DYRK1a overexpression, a main driver of another region homologous to Hsa21 and we demonstrated that an epistatic interaction exist between Cbs and Dyrk1a affecting different pathways, including synaptic transmission, cell projection morphogenesis, and actin cytoskeleton.

genetics↗
bioRxiv2018

A large-scale, standardized physiological survey reveals higher order coding throughout the mouse visual cortex

To understand how the brain processes sensory information to guide behavior, we must know how stimulus representations are transformed throughout the visual cortex. Here we report an open, large-scale physiological survey of neural activity in the awake mouse visual cortex: the Allen Brain Observatory Visual Coding dataset. This publicly available dataset includes cortical activity from nearly 60,000 neurons collected from 6 visual areas, 4 layers, and 12 transgenic mouse lines from 221 adult mice, in response to a systematic set of visual stimuli. Using this dataset, we reveal functional differences across these dimensions and show that visual cortical responses are sparse but correlated. Surprisingly, responses to different stimuli are largely independent, e.g. whether a neuron responds to natural scenes provides no information about whether it responds to natural movies or to gratings. We show that these phenomena cannot be explained by standard local filter-based models, but are consistent with multi-layer hierarchical computation, as found in deeper layers of standard convolutional neural networks.

neuroscience↗