Biology subjects

Robert, V.

Publications and source records attributed to Robert, V..

12 recordsLinked to original sources

bioRxiv2026

The StrainDiscoveryDatabase: an open framework for standardized microbial strain data

The vast amount of existing data on microbial strains holds immense potential to revolutionize bioindustry through the application of Artificial Intelligence (AI). However, the training of robust predictive AI models requires large-scale, unified, and non-redundant microbial datasets, which is currently severely hindered by the deep fragmentation of the data and the existence of synonymous strain identifiers in different culture collections. To overcome these infrastructural bottlenecks, we have established the StrainDiscoveryDatabase (SDD), a comprehensive, machine-readable dataset encompassing over 6.2 million harmonized data points for 256,889 microbial strains. The SDD does not rely on its own data repository, but rather on existing data that is retrieved on the fly from highly curated databases. Through an automated pipeline phenotypic, genotypic, and contextual data are systematically retrieved via the Application Programming Interfaces (APIs) of the Bacterial Diversity database (BacDive), the Microbial Resource Research Infrastructure Information System (MIRRI-IS) and the catalogue of the DSMZ. In order to reliably resolve synonymous strain identifiers, the StrainInfo database and its identification tools are employed, enabling the accurate deduplication and unification of records from disparate sources. The resulting aggregated, globally unique dataset is provided in a highly standardized JSON format in strict adherence to the FAIR data principles. By bridging isolated database silos and linking distributed knowledge to discrete biological entities, the SDD provides a high-quality, foundational resource designed to accelerate trait-based strain discovery, large-scale comparative analysis, and machine learning applications, thereby supporting the translation of the extensive existing knowledge on microbial traits to bioindustrial applications.

microbiology↗

bioRxiv2026

Morphological differences along the radial gradient of hippocampal area CA2 pyramidal neuron dendrites

Hippocampal area CA2 has recently emerged as a critical region for social recognition memory. Furthermore, this understudied region has been implicated in psychiatric diseases and neurodegenerative diseases. There has been accumulating evidence indicating that the pyramidal neurons (PNs) in area CA2 exhibit functional specializations that correlate with somatic position in stratum pyramidale (sp). In this study, we investigated the morphological differences in dendritic architecture of CA2 PNs with a focus on the radial gradient, i.e., along the deep-superficial axis of the sp. We conducted a comprehensive morphological analysis including Sholl intersection profiles, branching order distributions, root angle distributions, and dendritic cable lengths. We found that CA2 PNs have fewer oblique dendrites and a larger number of tuft-like dendrites as compared to CA1 PNs. Furthermore, within the CA2 population, we found that many of the dendritic structural features gradually changed along the radial axis from deep to superficial somatic location, indicating a continuum of dendritic morphology rather than two sharply defined subtypes of pyramidal neurons. This morphological characterization may serve as a starting point to better understand the corresponding functional organization of CA2. The gradual difference between deeper and superficial CA2 PNs suggests a continuum of their computational capabilities beyond two binary functional classes. In briefUsing several methods, we examine the dendritic morphology of over 130 CA2 and CA1 pyramidal neurons and find that many properties such as the cable length and terminal numbers of the dendritic arbors vary as a with the location of the soma in the pyramidal layer. HighlightsO_LIWe use scholl analysis, graph theory and machine learning techniques to quantify the different dendritic morphologies of CA2 pyramidal neurons. C_LIO_LIMany properties of CA2 pyramidal neuron apical dendrites vary as a function of somatic location in the pyramidal layer. C_LIO_LIMore superficial CA2 pyramidal neurons have longer oblique apical dendrites, and shorter tuft dendrites. C_LI

neuroscience↗

bioRxiv2026

Lateral entorhinal cortex supports behaviorally-induced hippocampal ensemble stability for reliable memory recall

Hippocampal pyramidal neurons function as place cells, showing location-specific activity during navigation, to form an internal spatial map of the environment. They are hypothesized to be the neural substrate of episodic memory. However, place cell receptive fields tend to drift or have poor tuning in low demand tasks, lacking operant goals such as random foraging, or in sensory context-deprived environments. Through chronic two-photon calcium imaging of hippocampal area CA1, we directly compare stability in a low versus a high demand task within the same animals over the course of learning and recall in the same environment. We find that compared to random foraging, an odor-context based navigational task stabilizes place cell representations and increases place cell quality and quantity. To investigate the circuit mechanism that may support this stability, we manipulated the activity of lateral entorhinal cortex (LEC) excitatory neurons, which provide both indirect and direct multisensory inputs about context, odor, and time to CA1. We chemogenetically suppressed activity of excitatory neurons in LEC during recall of the odor-context based navigation task and found that context discrimination is impaired at both the behavioral and neural level. With LEC silencing, mice had lower behavioral performance, less stable population activity, and greater similarity between opposing trial types. Our study finds that increasing task demand increases CA1 stability and that this stability is partially supported by LEC.

neuroscience↗

bioRxiv2026

Temporal Coding rather than Circuit Wiring allows Hippocampal CA3 Neurons to Dynamically Distinguish Different Cortical Inputs

Memory relies on associating and indexing multimodal information. How does this occur within single neurons? The hippocampus integrates multisensory information from medial (MEC) and lateral (LEC) entorhinal cortices to form environmental representations1-6, yet their synaptic dynamics, circuit organization, and integrative functions remain elusive. Contrary to canonical models emphasizing anatomical and functional segregation, our dual-color optogenetic7 circuit mapping revealed that both MEC and LEC inputs converge on virtually every CA3 pyramidal neuron and exhibit similar input-output functions and modulation via GABAergic microcircuitry. Divergence occurs in their frequency-dependent short-term plasticity. With increasing frequencies, facilitating LEC-evoked responses undergo synaptic depression, whereas MEC-evoked responses continue facilitating. In vivo, MEC-originating dentate spikes fire CA3 more than LEC, likely due to their distinct temporal relationship with oscillatory activity. Our findings support that hippocampal area CA3 processes region-specific information from MEC and LEC via temporal coding, rather than hard-wired circuit organization, at both single-neuron and network levels.

neuroscience↗

bioRxiv2025

The kisspeptin analog C6 reverses reproductive dysfunction in a mouse model of hyperprolactinaemia

Hyperprolactinaemia (HPRL), characterized by elevated prolactin levels, disrupts the hypothalamic-pituitary-gonadal axis, leading to reproductive dysfunctions such as menstrual irregularities, anovulation, and infertility. Current treatments rely on dopamine agonists but are limited by side effects and resistance. Kisspeptin (Kp), a key neuropeptide regulating the reproductive function, offers potential as an alternative therapy. However, Kps short half-life requires impractical administration regimens. To address this, we developed a synthetic Kp analog, C6, with enhanced pharmacokinetics. This study evaluated the effects of C6 compared to Kp in a mouse model of HPRL. Mice received subcutaneous PRL injections for 21 days to induce HPRL, followed by daily or alternate-day intraperitoneal administration of Kp10, C6, or vehicle. Estrous cyclicity, luteinizing hormone (LH) secretion, ovarian histology, and hypothalamic gene expression were analyzed. As expected, the HPRL treatment blocked estrous activity, which was restored by both Kp10, the shortest bioactive isoform of Kp and C6. Histological analysis revealed increased corpora lutea in Kp10- and C6-treated groups, indicating restored ovulation. C6 demonstrated equivalent efficacy to Kp10 in mitigating HPRL-induced reproductive dysfunctions, offering a promising alternative therapy. Future investigations should further explore the mechanistic advantages of C6, particularly its role in LH regulation, to optimize treatment strategies for HPRL-related reproductive disorders.

physiology↗

bioRxiv2023

Entorhinal cortex glutamatergic and GABAergic projections bidirectionally control discrimination and generalization of hippocampal representations

Discrimination and generalization are crucial brain-wide functions for memory and object recognition that utilize pattern separation and completion computations. Circuit mechanisms supporting these operations remain enigmatic. We show lateral entorhinal cortex glutamatergic (LECGLU) and GABAergic (LECGABA) projections are essential for object recognition memory. Silencing LECGLU during in vivo two-photon imaging increased the population of active CA3 pyramidal cells but decreased activity rates, suggesting a sparse coding function through local inhibition. Silencing LECGLU also decreased place cell remapping between different environments validating this circuit drives pattern separation and context discrimination. Optogenetic circuit mapping confirmed that LECGLU drives dominant feedforward inhibition to prevent CA3 somatic and dendritic spikes. However, conjunctively active LECGABA suppresses this local inhibition to disinhibit CA3 pyramidal neuron soma and selectively boost integrative output of LEC and CA3 recurrent network. LECGABA thus promotes pattern completion and context generalization. Indeed, without this disinhibitory input, CA3 place maps show decreased similarity between contexts. Our findings provide circuit mechanisms whereby long-range glutamatergic and GABAergic cortico-hippocampal inputs bidirectionally modulate pattern separation and completion, providing neuronal representations with a dynamic range for context discrimination and generalization.

neuroscience↗

bioRxiv2023

Tick-borne flavivirus NS5 antagonizes interferon signaling by inhibiting the catalytic activity of TYK2

The mechanisms utilized by different flaviviruses to evade antiviral functions of interferons are varied and incompletely understood. Using virological approaches, biochemical assays and mass spectrometry analysis, we report here that the NS5 protein of tick-borne encephalitis virus (TBEV) and Louping Ill virus (LIV), two related tick-borne flaviviruses, antagonize JAK-STAT signaling through interactions with tyrosine kinase 2 (TYK2). Co-immunoprecipitation (co-IP) experiments, yeast gap-repair assays, computational protein-protein docking and functional studies identified a stretch of 10 residues of the RNA dependent RNA polymerase domain of tick-borne flavivirus NS5, but not mosquito-borne NS5, that is critical for interaction with the TYK2 kinase domain. Additional co-IP assays performed with several TYK2 orthologs revealed that the interaction was conserved across mammal species. In vitro kinase assays showed that TBEV and LIV NS5 reduced the catalytic activity of TYK2. Our results thus illustrate a novel mechanism by which viruses suppress the interferon response. TeaserInhibition of the catalytic activity of a key kinase of the JAK/STAT pathway by a viral protein

microbiology↗

bioRxiv2022

Genetic and microbial diversity of the invasive mosquito vector species Culex tritaeniorhynchus across its extensive inter-continental geographic range

Culex (Cx.) tritaeniorhynchus is a mosquito species with an extensive and expanding inter-continental geographic distribution, currently reported in over 50 countries, across Asia, Africa, the Middle East, Europe and now Australia. It is an important vector of medical and veterinary concern, capable of transmitting multiple arboviruses which cause significant morbidity and mortality in human and animal populations. In regions endemic for Japanese encephalitis virus (JEV) in Asia, Cx. tritaeniorhynchus is considered the major vector and this species has also been shown to contribute to the transmission of several other significant zoonotic arboviruses, including Rift Valley fever virus and West Nile virus. Significant variation in vectorial capacity can occur between different vector populations. Obtaining knowledge of a species from across its geographic range is crucial to understanding its significance for pathogen transmission across diverse environments and localities. Vectorial capacity can be influenced by factors including the mosquito genetic background, composition of the microbiota associated with the mosquito and the co-infection of human or animal pathogens. In addition to enhancing information on vector surveillance and potential risks for pathogen transmission, determining the genetic and microbial diversity of distinct populations of a vector species is also critical for the development and application of effective control strategies. In this study, multiple geographically dispersed populations of Cx. tritaeniorhynchus from countries within Europe, Africa, Eurasia and Asia were sampled. Molecular analysis demonstrated a high level of genetic and microbial diversity within and between populations, including genetic divergence in the mosquito CO1 gene, as well as diverse microbiomes identified by 16S rRNA gene amplicon sequencing. Evidence for the detection of the endosymbiotic bacteria Wolbachia in some populations was confirmed using Wolbachia-specific PCR detection and sequencing of Wolbachia MLST genes; in addition to PCR-based detection of insect-specific viruses. Laboratory vector competence showed Cx. tritaeniorhynchus from a Greek population are likely to be competent vectors of JEV. This study expands understanding of the diversity of Cx. tritaeniorhynchus across its inter-continental range, highlights the need for a greater focus on this invasive vector species and helps to inform potential future directions for development of vector control strategies.

genetics↗

bioRxiv2020

Local circuit allowing hypothalamic control of hippocampal area CA2 activity and consequences for CA1

The hippocampus is critical for memory formation. The hypothalamic supramammillary nucleus (SuM) sends long-range projections to hippocampal area CA2. While the SuM-CA2 connection is critical for social memory, how this input acts on the local circuit is unknown. We found that SuM axon stimulation elicited mixed excitatory and inhibitory responses in area CA2 pyramidal neurons (PNs). We found that parvalbumin-expressing basket cells as responsible for the feedforward inhibitory drive of SuM over area CA2. Inhibition recruited by the SuM input onto CA2 PNs increased the precision of action potential firing both in conditions of low and high cholinergic tone. Furthermore, SuM stimulation in area CA2 modulates CA1 activity, indicating that synchronized CA2 output drives a pulsed inhibition in area CA1. Hence, the network revealed here lays basis for understanding how SuM activity directly acts on the local hippocampal circuit to allow social memory encoding.

neuroscience↗

bioRxiv2020

Cooperation between Caenorhabditis elegans COMPASS and condensin in germline chromatin organization

Deposition of histone H3 lysine 4 (H3K4) methylation at promoters by SET1/COMPASS is associated with context-dependent effects on gene expression and local changes in chromatin organization. Whether SET1/COMPASS also contributes to higher-order chromosome structure has not been investigated. Here, we address this question by quantitative FRET (Forster resonance energy transfer)-based fluorescence lifetime imaging microscopy (FLIM) on C. elegans germ cells expressing histones H2B-eGFP and H2B-mCherry. We find that SET1/COMPASS subunits strongly influence meiotic chromosome organization, with marked effects on the close proximity between nucleosomes. We further show that inactivation of SET-2, the C. elegans homologue of SET1, or CFP-1, the chromatin targeting subunit of COMPASS, strongly enhance chromosome organization defects and loss of fertility resulting from depletion of condensin-II. Defects in chromosome morphology resulting from conditional inactivation of topoisomerase II, another structural component of chromosomes, were also aggravated in the absence of SET-2. Combined, our in vivo findings suggest a model in which the SET1/COMPASS histone methyltransferase complex plays a role in shaping meiotic chromosome in cooperation with the non-histone proteins condensin-II and topoisomerase.

genetics↗

bioRxiv2019

Genome variation and population structure among 1,142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii

Mosquito control remains a central pillar of efforts to reduce malaria burden in sub-Saharan Africa. However, insecticide resistance is entrenched in malaria vector populations, and countries with high malaria burden face a daunting challenge to sustain malaria control with a limited set of surveillance and intervention tools. Here we report on the second phase of a project to build an open resource of high quality data on genome variation among natural populations of the major African malaria vector species Anopheles gambiae and Anopheles coluzzii. We analysed whole genomes of 1,142 individual mosquitoes sampled from the wild in 13 African countries, and a further 234 individuals comprising parents and progeny of 11 lab crosses. The data resource includes high confidence single nucleotide polymorphism (SNP) calls at 57 million variable sites, genome-wide copy number variation (CNV) calls, and haplotypes phased at biallelic SNPs. We used these data to analyse genetic population structure, and characterise genetic diversity within and between populations. We also illustrate the utility of these data by investigating species differences in isolation by distance, genetic variation within proposed gene drive target sequences, and patterns of resistance to pyrethroid insecticides. This data resource provides a foundation for developing new operational systems for molecular surveillance, and for accelerating research and development of new vector control tools.

genomics↗

bioRxiv2019

On the emergence of Candida auris: climate change, azoles, swamps and birds

The most enigmatic aspect of the rise of Candida auris as a human pathogen is that it emerged simultaneously in three continents with each clade being genetically distinct. Although new pathogenic fungal species are described regularly, these are mostly species associated with single cases in individuals who are immunosuppressed. In this study, we used phylogenetic analysis to compare C. auris with temperature susceptibility of close relatives and use these results to argue that it may be the first example of a new fungal disease emerging from climate change with the caveat that many other factors could have contributed.

microbiology↗