Biology subjects

Ribeiro, L. F.

Publications and source records attributed to Ribeiro, L. F..

10 recordsLinked to original sources

bioRxiv2026

Extracellular neuroligin-ICAM5 coupling drives dendritic growth via actin remodeling

Neuroligins (NLGNs) organize neuronal connectivity by engaging a diverse set of interaction partners, yet how extracellular recognition couples to intracellular growth programs remains unclear. Using affinity proteomics, we identify intercellular adhesion molecule-5 (ICAM5), a cell-surface protein localized to dendritic filopodia, as a novel neuroligin interactor. Surface plasmon resonance and cell-based assays demonstrate direct binding between the ICAM5 and NLGN3 extracellular domains and reveal that ICAM5 engages all neuroligin isoforms. ICAM5 is required for NLGN-induced dendritic outgrowth, but the NLGN3-ICAM5 complex does not contribute to synaptogenesis. Mechanistically, ICAM5 sustains PAK-Cofilin signaling and F-actin organization in growth cones, positioning it as a downstream effector that links neuroligin engagement to actin remodeling. Together, these findings define a neuroligin-ICAM5 axis that couples extracellular recognition to intracellular actin remodeling to control neuronal structural development.

neuroscience↗

bioRxiv2024

Type I TARPs regulate Kv7.2 potassium channels andsusceptibility to seizures

The M-current is a low-threshold potassium current that modulates neuronal excitability and suppresses repetitive firing. However, the mechanisms regulating M-channel function remain unclear. We identified type I Transmembrane AMPA receptor Regulatory Proteins (TARPs) as M-channel Kv7.2 subunit interactors in cortical neurons, with their interaction increasing upon neuronal depolarization. Co-expression of TARPs with Kv7.2 increased channel surface expression and Kv7.2-mediated currents, while disrupting TARP-{gamma}2 expression in neurons perturbed dendritic Kv7.2 nano-clusters and decreased M-currents. Knock-in mice with an intellectual disability-associated TARP-{gamma}2 variant showed reduced hippocampal M-currents and increased seizure susceptibility, indicating that disrupting TARP-{gamma}2 regulation of Kv7.2-M-channels is epileptogenic. These findings show that TARP-{gamma}2, a synaptic protein crucial for excitatory transmission, also controls intrinsic excitability via M-channels. This discovery provides a link between synaptic transmission and neuronal excitability, with implications for disease, as the interplay between synaptic and intrinsic plasticity is pivotal to how the brain adapts to varying input signals. HighlightsO_LIType I TARPs bind to Kv7.2-M-channels and enhance Kv7.2-mediated currents. C_LIO_LITARP-{gamma}2 governs the neuronal nano-organization and function of Kv7.2 channels. C_LIO_LIIntellectual disability-associated TARP-{gamma}2 variant impairs M-currents and facilitates seizures. C_LIO_LIType I TARPs can serve as molecular integrators of synaptic and intrinsic excitability. C_LI

neuroscience↗

bioRxiv2024

Neuronal ARHGAP8 controls synapse structure and AMPA receptor-mediated synaptic transmission

The aberrant formation and function of neuronal synapses are recognized as major phenotypes in many cases of neurodevelopmental (NDDs) and -psychiatric disorders (NPDs). A growing body of research has identified an expanding number of susceptibility genes encoding proteins with synaptic function. Here, we present the first brain-focused characterization of a potential new susceptibility gene, ARHAGP8, which encodes a Rho GTPase activating protein (RhoGAP). Accumulating evidence suggests that ARHGAP8 plays a pivotal role in the pathogenesis of NPDs/NDDs. We provide the first evidence for ARHGAP8 as a novel player at excitatory synapses, with its synaptic localisation linked to the presence of the developmentally important NMDA receptor subunit GluN2B. By increasing ARHGAP8 levels in hippocampal neurons to mimic the copy number variant found in a subset of patients, we observed reductions in dendritic complexity and spine volume, accompanied by a significant decrease in synaptic AMPA receptor-mediated transmission. These results suggest that ARHGAP8 plays a role in shaping the morphology and function of excitatory synapses, and prompt further investigation of ARHGAP8 as a candidate gene in NDDs/NPDs.

neuroscience↗

bioRxiv2022

Microglial TNFα orchestrates brain phosphorylation during the sleep period and controls homeostatic sleep.

The time we spend asleep is adjusted to previous time spent awake, and therefore believed to be under tight homeostatic control. Here, we establish microglia as a new cellular component of the sleep homeostat circuit. By using quantitative phosphoproteomics we demonstrate that microglia-derived TNF controls thousands of phosphorylation sites during the sleep period. Substrates of microglial TNF comprise sleep-promoting kinases and numerous synaptic proteins, including a subset whose phosphorylation status codes sleep need and determines sleep duration. As a result, lack of microglial TNF attenuates the build-up of sleep need, as measured by slow wave activity, and prevents immediate compensation for loss of sleep. Together, we propose that microglia control sleep homeostasis by releasing TNF that acts at the neuronal circuitry through dynamic control of phosphorylation.

neuroscience↗

bioRxiv2020

Combining functional and structural genomics to track antibiotic resistance genes in mobile elements in clinical bacterial strains

The rise of multi-antibiotics resistant bacteria represents an emergent threat to human health. Here, we investigate antibiotic resistance mechanisms in bacteria of several species isolated from an intensive care unit in Brazil. We used whole-genome analysis to identify antibiotic resistance genes (ARGs) and plasmids in 35 strains of Gram-negative and Gram-positive bacteria, including the first genomic description of Morganella morganii and Ralstonia mannitolilytica clinical isolates from South America. We identify a high abundance of beta-lactamase genes in highly resistant organisms, including seven extended-spectrum {beta}-lactamases shared between organisms from different species. Additionally, we identify several ARGs-carrying plasmids indicating the potential for fast transmission of resistance mechanism between bacterial strains, comprising a novel IncFII plasmid recently introduced in Brazil from Asia. Through comparative genomic analysis, we demonstrate that some pathogens identified here are very distantly related to other bacteria isolated worldwide, demonstrating the potential existence of endemic bacterial pathogens in Brazil. Also, we uncovered at least two couples of (near)-identical plasmids exhibiting multi-drug resistance, suggesting that plasmids were transmitted between bacteria of the same or different species in the hospital studied. Finally, since many highly resistant strains carry several different ARGs, we used functional genomics to investigate which of them were indeed functional. In this sense, for three bacterial strains (Escherichia coli, Klebsiella pneumoniae, and M. morganii), we identify six beta-lactamase genes out of 15 predicted in silico as the main responsible for the resistance mechanisms observed, corroborating the existence of redundant resistance mechanisms in these organisms. ImportanceBig data and large-scale sequencing projects have revolutionized the field, achieving a greater understanding of ARGs identification and spreading at global level. However, given that microbiota and associated ARGs may fluctuate across geographic zones, hospital-associated infections within clinical units still remain underexplored in Brazil - the largest country in South America; 210 million inhabitants - and neighboring countries. This work highlighted the identification of several ARGs shared between species co-occurring simultaneously into a Brazilian hospital, some of them associated with large plasmids, mostly endowed with transposable elements. Also, genomic features of clinically underrepresented pathogens such M. morganii and B. cepacia were revealed. Taken together, our results demonstrate how structural and functional genomics can help to identify emerging mechanisms of shared antibiotic resistance in bacteria from clinical environments. Systematic studies as the one presented here should help to prevent outbreaks of novel multidrug resistance bacteria in healthcare facilities.

microbiology↗

bioRxiv2020

Constitutive ghrelin receptor activity modulates AMPA receptor traffic and supports memory formation

The ability of animals to store and retrieve food caches in the wild requires the integration of biological signals of hunger, satiety and memory. The role of ghrelin in regulating feeding and memory makes ghrelin receptors an important target to shape the required cellular and molecular responses. We investigated the effects of the high ligand-independent activity of the ghrelin receptor on the physiology of excitatory synapses. Blocking this type of activity produced a decrease in the synaptic content of AMPA receptors in hippocampal neurons and a reduction in GluA1 phosphorylation at Ser845. Impaired constitutive activity from the ghrelin receptor increased surface diffusion of AMPA receptors and impaired AMPA receptor synaptic delivery mediated by chemical long-term potentiation. These observations support a role for the constitutive activity of the ghrelin receptor in regulating AMPA receptor trafficking under basal conditions and synaptic plasticity. Accordingly, we found that blocking the ghrelin receptor constitutive activity impairs spatial and recognition memory. Impact statementThis work uncovers a role for the constitutive activity of the ghrelin receptor in memory, and in the regulation of the synaptic levels of AMPA receptors, their mobility and synaptic plasticity. Underscoring the importance of deciphering the physiological role of constitutive ghrelin receptor activity, ghrelin receptor inverse agonism is now being considered as a therapy to treat alcohol use disorder.

neuroscience↗

bioRxiv2019

Microbial communities profiling in intensive care units expose limitations in current sanitary standards

Hospital-associated infections (HAIs) are the leading cause of morbidity and mortality in intensive care units (ICUs) and neonatal intensive care units (NICUs). Organisms causing these infections are often present on surfaces around the patient. Given that microbiotas may vary across different ICUs, the HAI-related microbial signatures within these units remain underexplored. In this study, we use deep-sequencing analyses to explore and compare the structure of bacterial communities at inanimate surfaces of the ICU and NICU wards of The Medical School Clinics Hospital (Brazil). The data revealed that NICU presents higher biodiversity than ICU and surfaces closest to the patient showed a peculiar microbiota, distinguishing one unit from the other. Several facultative anaerobes or obligate anaerobes HAI-related genera were classified as biomarkers for the NICU, whereas Pseudomonas was the main biomarker for ICU. Correlation analyses revealed a distinct pattern of microbe-microbe interactions for each unit, including bacteria able to form multi-genera biofilms. Furthermore, we evaluated the effect of concurrent cleaning over the ICU bacterial community. The results showed that, although some bacterial populations decreased after cleaning, various HAI-related genera were quite stable to sanitization, suggesting being well-adapted to the ICU environment. Overall, these results enabled identification of discrete ICU and NICU reservoirs of potentially pathogenic bacteria and provided evidence for the presence of a set of biomarkers that distinguish these units. Moreover, the study exposed the inconsistencies of the routine cleaning to minimize HAI-related genera contamination.\n\nIMPORTANCEDue to the high impact of HAIs, there is an urgent need for the development of robust policies on microbial surveillance to help guide procedures, improving infection control. To the best of our knowledge, this is the first comprehensive study, using a high-throughput approach, focused on comparing the microbiota peculiarities of the ICU and NICU in one of the largest public hospitals in Brazil. The work highlighted bacteria associated with nosocomial infections, identifying the most potent reservoirs of contamination, and evaluated the microbiota changes related to the cleaning procedure. Therefore, this study contributes to increase the knowledge about (N)ICUs microbiomes and may help to reduce health-care-associated infections, especially in developing countries.

microbiology↗

bioRxiv2019

SorCS1-mediated Sorting of Neurexin in Dendrites Maintains Presynaptic Function

The pre- and postsynaptic membranes comprising the synaptic junction differ in protein composition. The mechanisms that maintain the polarized distribution of synaptic membrane proteins are poorly understood. The sorting receptor SorCS1 is a critical trafficking regulator of neuronal receptors, including neurexin (Nrxn), a presynaptic adhesion molecule essential for synaptic transmission. We find that SorCS1 controls a balance between axonal and dendritic Nrxn1 surface levels. Newly synthesized Nrxn1 traffics to the somatodendritic surface, followed by endocytosis. SorCS1 interacts with the Rab11 effector protein Rab11FIP5/Rip11 to facilitate the transition of internalized Nrxn1 from early to recycling endosomes and bias Nrxn1 surface polarization toward the axon. In the absence of SorCS1, Nrxn1 accumulates in early endosomes and mis-polarizes to the dendritic surface, impairing presynaptic function. The axonal/dendritic balance of Nrxn1 surface distribution is activity-dependent, indicating that SorCS1-mediated sorting in somatodendritic endosomes dynamically controls Nrxn1 axonal surface polarization required for proper presynaptic function.

neuroscience↗

bioRxiv2017

Phylogenomics of montane frogs of the Brazilian Atlantic Forest supports a scenario of isolation in sky islands followed by relative climatic stability

Despite encompassing a relatively small geographical area, montane regions harbor disproportionately high levels of species diversity and endemism. Yet, relatively little is known about the evolutionary mechanisms ultimately leading to montane diversity. In this study, we use target capture of ultraconserved elements to investigate the phylogenetic relationships and diversification patterns of Melanophryniscus (Bufonidae) and Brachycephalus (Brachycephalidae), two frog genera that occur in sky islands of the southern Atlantic Forest of Brazil. Specifically, we test whether diversification of montane species in these genera can be explained by a single climatic shift leading to isolation in sky islands, followed by relative climatic stability that maintained populations in allopatry. In both genera, the topologies inferred using concatenation and coalescent-based methods were concordant and had strong nodal support, except for a few recent splits. These recent splits tended to be supported by more informative loci (those with higher average bootstrap support), suggesting that, while individual trees may be well resolved, the relationships they recover are being obscured by non-informative data. Divergence dating of a combined dataset using both genera is consistent with concordant timing of their diversification. These results support the scenario of diversification-by-isolation in sky islands, and suggest that allopatry due to climatic gradients in montane regions are an important mechanism for generating species diversity and endemism in these regions.

evolutionary biology↗

bioRxiv2017

Phylogenomic Species Delimitation In Microendemic Frogs Of The Brazilian Atlantic Forest

The advent of next-generation sequencing allows researchers to use large-scale datasets for species delimitation analyses, yet one can envision an inflection point where the added accuracy of including more loci does not offset the increased computational burden. One alternative to including all loci could be to prioritize the analysis of loci for which there is an expectation of high informativeness, such as those with higher numbers of parsimony-informative sites. Here, we explore the issue of species delimitation and locus selection with species from two anuran genera: Melanophryniscus (Bufonidae) and Brachycephalus (Brachycephalidae). Montane species in these genera have been isolated in sky islands across the southern Brazilian Atlantic Forest, which led to the formation of a number of microendemic species. To delimit species, we obtained genetic data using target enrichment of ultraconserved elements from 32 populations (13 for Melanophryniscus and 19 for Brachycephalus), and we were able to create datasets that included over 800 loci with no missing data. We ranked loci according to their corresponding number of parsimony-informative sites, and we performed species delimitation analyses using BPP in each genus based on the top 10, 20, 40, 80, 160, 320, and 640 loci. We also conducted several additional analyses using 10 randomly sampled datasets containing the same numbers of loci to discriminate the relative contribution of increasing the number of loci from prioritizing those with higher informativeness. We identified three types of node: nodes with either consistently high or low support regardless of the number of loci or their informativeness, and nodes that were initially poorly supported, but their support became stronger with more data. Adding more loci had a stronger impact on model support than prioritizing loci for their informativeness, but this effect was less apparent in datasets with more than 160 loci. When viewed across all sensitivity analyses, our results suggest that the current species richness in both genera might have been underestimated. In addition, our results provide useful guidelines to the use of different sampling strategies to carry out species delimitation with phylogenomic datasets.

evolutionary biology↗