Biology subjects

Ribeiro, S.

Publications and source records attributed to Ribeiro, S..

16 recordsLinked to original sources

bioRxiv2026

Integrated Resistome and Quantitative Proteomics Reveal Coordinated Resistance Architecture in MDR and XDR Gram-Negative ICU Pathogens

ObjectivesAntimicrobial resistance (AMR) in Gram-negative pathogens is driven by complex and coordinated molecular mechanisms that remain incompletely characterized. This study integrated phenotypic, genomic, and quantitative proteomic analyses to characterize multidrug-resistant (MDR) and extensively drug-resistant (XDR) Gram-negative bacteria circulating in an intensive care unit (ICU) in Northeastern Brazil. MethodsA total of 259 Gram-negative isolates collected between 2019 and 2021 underwent species identification, antimicrobial susceptibility testing, and targeted qPCR for resistance genes. Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa representing susceptible, MDR, and XDR phenotypes were selected for whole-genome sequencing and label-free quantitative proteomics. Differential protein abundance was assessed using Limma with |log2FC| > 1 and p < 0.05. ResultsK. pneumoniae (47%), A. baumannii (24%), and P. aeruginosa (21%) predominated. Carbapenem resistance reached 44%, 93%, and 61%, respectively, and MDR/XDR phenotypes occurred in >30% of isolates. Genomic analyses revealed dense resistomes with coexisting {beta}-lactamases (blaKPC, blaNDM, blaCTX-M, OXA) and widespread efflux systems. Proteomic profiling demonstrated phenotype-associated differences in outer membrane proteins, transport systems, regulatory proteins, and metabolic pathways. XDR isolates showed additional enrichment of envelope remodeling proteins, stress response mechanisms, and proteostasis-associated factors. ConclusionsMDR and XDR Gram-negative ICU pathogens exhibit coordinated resistance architecture characterized by accumulation of resistance genes and adaptive proteomic remodeling. Integrated multi-omics approaches provide mechanistic insight into antimicrobial resistance and support improved surveillance and therapeutic strategies. What is known?O_LIAntimicrobial resistance is a priority and a serious problem in global health, resulting in high rates of morbidity and mortality. C_LIO_LIKlebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa are on the World Health Organizations (WHO) priority list as major causes of morbidity and mortality worldwide. C_LIO_LIClassical characterization of susceptibility and resistance phenotypes does not capture the complexity of antimicrobial resistance and hampers effective control measures and actions to minimize the evolutionary dynamics of resistance in these bacteria. C_LI What is new?O_LIThe study characterizes the phenotypic pattern of antimicrobial susceptibility, the presence and sequencing of the resistome and virulome, and analyzes the label-free quantitative proteome of susceptible, MDR, and XDR phenotypes in strains of K. pneumoniae, A. baumannii, and P. aeruginosa circulating in hospital ICUs in Brazil. C_LIO_LIMDR and XDR gram-negative phenotypes are associated with a dense resistome, with widespread dissemination of beta-lactamase genes (bla_KPC, bla_NDM, bla_CTX-M, and OXA) and RND-type (MEXs) and acrAB-tolC efflux pumps, without changes in virulence genes. C_LIO_LIProteomic analysis demonstrated increased production of beta-lactamases, components of efflux pump systems, outer membrane protein synthesis, protection for oxidative stress mechanisms, proteins for iron acquisition, and systemic regulators. XDR strains additionally showed enhanced remodeling of the cell envelope, activation of proteostasis, and metabolic adaptation. C_LI

microbiology↗

bioRxiv2025

Does ecological restoration align prokaryotic community structure with natural references across European coastal wetlands?

AbstractCoastal wetlands are crucial for biodiversity and act as critical buffers for carbon sequestration and atmospheric greenhouse gases (GHG) concentrations, yet their degradation often turns them into GHG sources. Restoration is widely implemented to recover these services, but it remains unclear whether interventions successfully reestablish the microbial functional diversity underpinning biogeochemical cycles. We tested the hypothesis that restoration aligns prokaryotic community structure with natural references, analyzing, a European gradient of coastal wetlands, comparing well-preserved, altered, and restored sites in water and sediment. Using 16SrRNA-metabarcoding and IndVal-Analysis, we characterized community assembly identifying diagnostic functional consortia. Results revealed a marked difference in water and sediment recovery after restoration. Bacterioplankton communities rapidly converge to natural references, while sediment microbiome displayed significant "ecological memory". Restored wetlands show sediment communities structurally distinct from well-preserved, retaining alteration-associated guilds decades. Results support the initial hypothesis: restoration processes in coastal wetlands can re-establish communities and metabolisms resembling well-preserved conditions in the water in the short term, while sediments retain microbial communities and metabolisms inherited from altered conditions for a long time. Future strategies must integrate active sediment interventions using molecular bioindicators to validate not only the landscape appearance, but the effective reactivation of ecosystem processes and microbiota-related services.

ecology↗

bioRxiv2025

Dream content and slow waves benefit preys against predators in a video game confrontation

Every studied animal species exhibits some form of sleep, a state evolved under the sustained influence of prey and predator behaviors. Dreams have been proposed to have evolved as offline mental simulations able to warn against impending threats from the environment, such as predators. To assess how the roles of prey and predator interact with sleep and dreaming, we used a first-person shooter game as a proxy for predator-prey confrontations. Electroencephalographic (EEG) and electrocardiographic (ECG) signals were recorded from 30 human adults paired and simultaneously recorded while 1) playing a video game round against each other, in which one participant was armed with a gun and the other was not, 2) taking a nap, 3) reporting dreams and/or thoughts, and 4) playing another round with the same gun assignment. We found that the participants in the prey role were highly affected by sleep and dreaming. Their score gains were positively correlated with slow wave activity during the nap, with how much the dreams were related to the game, and with heart rate variability during the first round. In contrast, no significant correlations were found for participants in the predator role. The results suggest that slow wave activity and game-related dream content during sleep improve the post-sleep performance of individuals under stressful, prey-like situations.

neuroscience↗

bioRxiv2025

Microenvironmental TGF-β is an early driver of NF1-associated tumour formation

Neurofibromatosis Type 1 (NF1) is a common tumour predisposition syndrome characterised by neurofibromas - Nf1-/- Schwann cell (SC)-derived tumours of peripheral nerves. We and others have shown that Nf1 loss in SCs is insufficient for neurofibroma formation but cooperates with an injury microenvironment to form tumours, but the mechanisms remained unknown. Here, we identify macrophage-secreted TGF-{beta} as the microenvironmental injury signal that is essential for tumourigenesis. Analysis of the earliest stages of neurofibroma formation showed that tumours arise from a population of Nf1-/- SCs that escape the regenerating nerve shortly after injury. Here, they reside in a distinct microenvironment conducive for tumourigenesis, where TGF-{beta} disrupts SC/axonal interactions and SC re-differentiation. Pharmacological inhibition of TGF-{beta} for a short therapeutic window during this early stage inhibited tumour formation, highlighting the potential to normalise Nf1-/- SCs and identifying TGF-{beta} as a potential therapeutic target to both treat and prevent neurofibroma formation.

cell biology↗

bioRxiv2024

Electrophysiological correlates of lucid dreaming

Lucid dreaming (LD) is a state of conscious awareness of the current dream state, predominantly associated with REM sleep. Research progress in uncovering the neurobiological basis of LD has been hindered by low sample sizes, diverse EEG setups, and specific artifact issues like saccadic eye movements and signal non-stationarity. To address these matters, we developed a multi-stage preprocessing pipeline that integrates standardized early-stage preprocessing, artifact subspace reconstruction, and signal-space projection. This approach enhanced data quality by precisely removing saccadic potential effects even in setups with minimal channels. To robustly identify the electrophysiological correlates of LD, we applied this methodology to LD data collected across laboratories (pooled N = 44) and explored sensor-and source-level markers hypothesized to underlie LD. Compared to non-lucid REM sleep, we observed few robust differences on the EEG sensor level, which is in line with recent findings. In contrast, on the source level, gamma1 power (30-36 Hz) showed increases during LD in left-hemispheric temporal areas, which might reflect verbal insight processes. Gamma1 power also increased around the onset of LD eye signaling in right temporo-occipital regions including the right precuneus, in line with its involvement in self-referential thinking. Reductions in beta power (12-30 Hz) during LD in right central and parietal areas including the temporo-parietal junction are potentially associated with a conscious reassessment of the veridicality of the currently perceived reality. Notably, functional connectivity in alpha band (8-12 Hz) increased during LD, in contrast to the reductions typically seen in psychedelic states, highlighting enhanced self-awareness. Taken together, these findings illuminate the electrophysiological correlates of LD state, and may serve as a basis to uncover neural mechanisms at the time point of lucid dream insight.

neuroscience↗

bioRxiv2023

Mind the gap: exploring the usefulness of historical data to assess the impacts of land-use change on bird diversity in a farmland mosaic of Northeastern Portugal (1980-2000)

Agriculture intensification and land abandonment are the main threats to bird communities in farmlands. Although they represent the opposite endpoints of a gradient of land-use change, they are usually examined separately. In this study, we assessed the effects of the occurrence of both drivers in space and in time, on bird assemblages. The study was performed in a Mediterranean vineyard-dominated farmland mosaic located in North-Eastern Portugal, where land abandonment and (mechanized) intensification coexisted for twenty years. The aims of this study were (1) to describe the temporal patterns of land-use change; (2) to investigate whether these changes affected the local bird species composition and ecological guild structure; and (3) to assess which species/ecological traits were more responsive to land-use changes. We compared the occurrence of birds before (1979-84) and after (2002-03) the triggering of the land-use change proccess. Results showed the prevalence of three interacting gradients of land-use change: land intensification, and direct and indirect effects of land abandonment. While the composition and ecological structure of the bird communities remained stable during the period analyzed, trait and species-specific analysis showed significant correlations with the gradients of change. This suggest that the local bird communities were able to cope with the synergic dynamics of the land-use change, possibly due to a combination of a resilient pre-change bird assemblage and the buffering effect of the competing drivers. The pros and cons of the approach adopted and the utility of past datasets as baselines to assess and monitor the impacts of environmental change on farmland bird diversity are discussed.

ecology↗

bioRxiv2023

5-MeO-DMT induces sleep-like LFP spectral signatures in the hippocampus and prefrontal cortex of awake rats

5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT) is a potent classical psychedelic known to induce changes in locomotion, behaviour, and sleep in rodents. However, there is limited knowledge regarding its acute neurophysiological effects. Local field potentials (LFPs) are commonly used as a proxy for neural activity, but previous studies investigating psychedelics have been hindered by confounding effects of behavioural changes and anaesthesia, which alter these signals. To address this gap, we investigated acute LFP changes in the hippocampus (HP) and medial prefrontal cortex (mPFC) of freely behaving rats, following 5-MeO-DMT administration. 5-MeO-DMT led to an increase of delta power and a decrease of theta power in the HP LFPs, which could not be accounted for by changes in locomotion. Furthermore, we observed a dose-dependent reduction in slow (20-50 Hz) and mid (50-100Hz) gamma power, as well as in theta phase modulation, even after controlling for the effects of speed and theta power. State map analysis of the spectral profile of awake behaviour induced by 5-MeO-DMT revealed similarities to electrophysiological states observed during slow-wave sleep (SWS) and rapid-eye-movement (REM) sleep. Our findings suggest that the psychoactive effects of classical psychedelics are associated with the integration of waking behaviours with sleep-like spectral patterns in LFPs.

neuroscience↗

bioRxiv2023

From farm to fork: persistence of clinically-relevant multidrug-resistant and copper-tolerant Klebsiella pneumoniae long after colistin withdrawal in poultry production.

The concern of colistin-resistant bacteria in animal-food-environmental-human ecosystems prompted the poultry sector to implement colistin restrictions and explore alternative trace metals/copper feed supplementation. The impact of these strategies on the selection and persistence of colistin-resistant Klebsiella pneumoniae (Kp) in the whole poultry-production chain needs clarification. We assessed colistin-resistant and copper-tolerant Kp occurrence in chicken raised with inorganic and organic copper-formulas from one-day-old chicks to meat (7 farms/2019-2020), after long-term colistin withdrawal (>2-years). Clonal diversity and Kp adaptive features were characterized by cultural, molecular, and whole-genome-sequencing (WGS) approaches. Most chicken-flocks (75%) carried Kp at early+pre-slaughter stages, with a significant decrease (p<0.05) in meat batches (17%) and sporadic water/feed contamination. High rates (>50%) of colistin-resistant/mcr-negative Kp were observed among faecal samples, independently of feed. Most samples carried multidrug-resistant (90%) and copper-tolerant isolates (81%; pco+sil/MICCuSO4 [≥]16mM). WGS revealed accumulation of colistin resistance associated mutations and F-type multireplicon plasmids carrying antibiotic resistance and metal/copper-tolerance genes. The Kp population was polyclonal, with various lineages dispersed throughout poultry production. ST15-KL19, ST15-KL146 and ST392-KL27, and IncF plasmids were similar to those from global human clinical isolates, suggesting chicken-production as a reservoir/source of clinically-relevant Kp lineages and genes with potential risk to humans through food and/or environmental exposure. Despite long-term colistin ban limited mcr spread, it was ineffective in controlling colistin-resistant/mcr-negative Kp, regardless of feed. This study provides crucial insights into the persistence of clinically-relevant Kp in the poultry-production chain and highlights the need for continued surveillance and proactive food safety actions within a One-Health perspective. IMPORTANCEThe spread of bacteria resistant to last-resort antibiotics such as colistin throughout the food chain is a serious concern for public health. The poultry sector has responded by restricting colistin use and exploring alternative trace metals/copper feed supplements. However, it is unclear how and to which extent these changes impact the selection and persistence of clinically-relevant Klebsiella pneumoniae (Kp) throughout poultry chain. We found a high occurrence of copper-tolerant and colistin-resistant/mcr-negative Kp in chicken flocks, regardless of inorganic and organic copper-formulas and long-term colistin ban. Despite the high Kp diversity, the occurrence of identical lineages and plasmids across samples and/or clinical isolates suggests poultry as a potential source of human Kp exposure. This study highlights the need for continued surveillance and proactive farm-to-fork actions to mitigate the risks to public health, relevant for stakeholders involved in food industry and policymakers tasked with regulating food safety.

microbiology↗

bioRxiv2023

Cell Segmentation in Images Without Structural Fluorescent Labels

High-content screening (HCS) provides an excellent tool to understand the mechanism of action of drugs on disease-relevant model systems. Careful selection of fluorescent labels (FLs) is crucial for successful HCS assay development. HCS assays typically comprise (1) FLs containing biological information of interest, and (2) additional structural FLs enabling instance segmentation for downstream analysis. However, the limited number of available fluorescence microscopy imaging channels restricts the degree to which these FLs can be experimentally multiplexed. In this paper, we present a segmentation workflow that overcomes the dependency on structural FLs for image segmentation, typically freeing 2 fluorescence microscopy channels for biologically relevant FLs. It consists in extracting structural information encoded within readouts that are primarily biological, by fine-tuning pre-trained state-of-the-art generalist cell segmentation models for different combinations of individual FLs, and aggregating the respective segmentation results together. Using annotated datasets that we provide, we confirm our methodology offers improvements in performance and robustness across several segmentation aggregation strategies and image acquisition methods, over different cell lines and various FLs. It thus enables the biological information content of HCS assays to be maximized without compromising the robustness and accuracy of computational single-cell profiling. Impact StatementThis methodological paper describes a framework enabling cell segmentation for datasets without structural fluorescent labels to highlight cell organelles. Such capabilities favorably impact costs and possible discoveries in single-cell downstream analysis by improving our ability to incorporate more biological read-outs into a single assay. The perspective of computational and experimental biologist coauthors ensures a multidisciplinary viewpoint and accessibility for a wide readership.

bioinformatics↗

bioRxiv2022

Impact of Holocene environmental change on the evolutionary ecology of an Arctic top predator

The Arctic is among the most climatically sensitive environments on Earth, and the disappearance of multiyear sea-ice in the Arctic Ocean is predicted within decades. As apex predators, polar bears are sentinel species for addressing the impact of environmental variability on Arctic marine ecosystems. By integrating genomics, isotopic analysis, morphometrics, and ecological modelling, we investigate how Holocene environmental changes affected the evolutionary ecology of polar bears around Greenland. We show that throughout the last [~]11,000 years, Greenlandic polar bears have been heavily influenced by changes in sea-surface temperature (SST) and sea-ice cover. Most notable are major reductions in effective population size at the beginning of the Holocene and during the Holocene Thermal Maximum [~]6 kya, which coincide with increases in annual mean SST, reduction in sea-ice covers, declines in suitable habitat, and shifts in suitable habitat northwards. Furthermore, we show how individuals sampled from west and east Greenland are genetically, morphologically, and ecologically distinct. We find bears sampled in west Greenland to be larger, more genetically diverse and have diets dominated by ringed seals, whereas bears from east Greenland are smaller and less diverse with more varied diets, putatively driven by regional biotic differences. Taken together, we provide novel insights into the vulnerability of polar bears to environmental change, and how the Arctic marine ecosystem plays a vital role in shaping the evolutionary and ecological trajectories of its inhabitants. TeaserMultivariate investigations of the environments role in the evolutionary ecology of Greenlandic polar bears.

evolutionary biology↗

bioRxiv2020

Unilateral vocal nerve resection alters neurogenesis in the avian song system in a region-specific manner

New neurons undergo a critical period soon after migration during which the behavior of the animal may result in the survival or culling of these cells. In the songbird song system, new neurons may be maintained in the song motor pathway with respect to motor progression toward a target song--during juvenile song learning, seasonal song restructuring, and experimentally manipulated song variability. However, it is not known whether the quality of song per se, without progressive improvement, may also influence new neuron survival. To test this idea, we experimentally altered song acoustic structure by unilateral denervation of the syrinx. We found no effect of aberrant song on numbers of new neurons in the HVC of the song motor pathway, a loss of left-side dominance in new neurons in the auditory region caudomedial nidopallium (NCM), and a bilateral decrease in new neurons in the basal ganglia nucleus Area X. We propose new neuron survival may be determined in response to behavioral feedback in accordance with the function of new neurons within a given brain region. Studying the effects of singing behaviors on new neurons across multiple brain regions that subserve singing may give rise to general rules underlying the regulation of new neuron survival across taxa and brain regions more broadly.

neuroscience↗

bioRxiv2020

Structural differences between REM and non-REM dream reports assessed by graph analysis

Dream reports collected after rapid eye movement sleep (REM) awakenings are, on average, longer, more vivid, bizarre, emotional and story-like compared to those collected after non-REM. However, a comparison of the word-to-word structural organization of dream reports is lacking, and traditional measures that distinguish REM and non-REM dreaming may be confounded by report length. This problem is amenable to the analysis of dream reports as non-semantic directed word graphs, which provide a structural assessment of oral reports, while controlling for individual differences in verbosity. Against this background, the present study had two main aims: Firstly, to investigate differences in graph structure between REM and non-REM dream reports, and secondly, to evaluate how non-semantic directed word graph analysis compares to the widely used measure of report length in dream analysis. To do this, we analyzed a set of 125 dream reports obtained from 19 participants in controlled laboratory awakenings from REM and N2 sleep. We found that: (1) graphs from REM sleep possess a larger connectedness compared to those from N2; (2) measures of graph structure can predict ratings of dream complexity, where increases in connectedness and decreases in randomness are observed in relation to increasing dream report complexity; and (3) measures of the Largest Connected Component of a graph can improve a model containing report length in predicting sleep stage and dream complexity. These results indicate that dream reports sampled after REM awakening have on average a larger connectedness compared to those sampled after N2 (i.e. words recur with a longer range), a difference which appears to be related to underlying differences in dream complexity. Altogether, graph analysis represents a promising method for dream research, due to its automated nature and potential to complement report length in dream analysis.

animal behavior and cognition↗

bioRxiv2019

d-Lysergic acid diethylamide has major potential as a cognitive enhancer

Psychedelic agonists of serotonin receptors induce neural plasticity and synaptogenesis, but their potential to enhance learning remains uncharted. Here we show that a single dose of d-LSD, a potent serotonergic agonist, increased novel object preference in young and adult rats several days after treatment. d-LSD alone did not increase preference in old animals, but could rescue it to young levels when followed by a 6-day exposure to enriched environment (EE). Mass spectrometry-based proteomics in human brain organoids treated with d-LSD showed upregulation of proteins from the presynaptic active zone. A computational model of synaptic connectivity in the hippocampus and prefrontal cortex suggests that d-LSD enhances novelty preference by combining local synaptic changes in mnemonic and executive regions, with alterations of long-range synapses. Better pattern separation within EE explained its synergy with d-LSD in rescuing novelty preference in old animals. These results advance the use of d-LSD in cognitive enhancement.

neuroscience↗

bioRxiv2018

Criticality between cortical states

Since the first measurements of neuronal avalanches [1], the critical brain hypothesis has gained traction [2]. However, if the brain is critical, what is the phase transition? For several decades it has been known that the cerebral cortex operates in a diversity of regimes [3], ranging from highly synchronous states (e.g. slow wave sleep [4], with higher spiking variability) to desynchronized states (e.g. alert waking [5], with lower spiking variability). Here, using independent signatures of criticality, we show that a phase transition occurs in an intermediate value of spiking variability. The critical exponents point to a universality class different from mean-field directed percolation (MF-DP). Importantly, as the cortex hovers around this critical point [6], it follows a linear relation between the avalanche exponents that encompasses previous experimental results from different setups [7, 8] and is reproduced by a model.

neuroscience↗

bioRxiv2018

Computational fluid dynamic analysis reveals the underlying physical forces playing a role in 3D multiplex brain organoid cultures

Organoid cultivation in suspension culture requires agitation at low shear stress to allow for nutrient diffusion, which preserves tissue structure. Multiplex systems for organoid cultivation have been proposed, but whether they meet similar shear stress parameters as the regularly used spinner flask and its correlation with the successful generation of brain organoids, has not been determined. Herein, we used computational fluid dynamics (CFD) analysis to compare two multiplex culture conditions: steering plates on an orbital shaker and the use of a previously described bioreactor. The bioreactor had low speed and high shear stress regions that may affect cell aggregate growth, depending on volume, whereas the CFD parameters of the steering plates were closest to the parameters of the spinning flask. Our protocol improves the initial steps of the standard brain organoid formation, and organoids produced therefrom displayed regionalized brain structures, including retinal pigmented cells. Overall, we conclude that suspension culture on orbital steering plates is a cost-effective practical alternative to previously described platforms for the cultivation of brain organoids for research and multiplex testing.\n\nHighlightsO_LIImprovements to organoid preparation protocol\nC_LIO_LIMultiplex suspension culture protocol successfully generate brain organoids\nC_LIO_LIComputational fluid dynamics (CFD) reveals emerging properties of suspension cultures\nC_LIO_LICFD of steering plates is equivalent to that of spinner flask cultures\nC_LI

bioengineering↗

bioRxiv2017

Short term changes in the proteome of human cerebral organoids induced by 5-methoxy-N,N-dimethyltryptamine

Dimethyltryptamines are hallucinogenic serotonin-like molecules present in traditional Amerindian medicine (e.g. Ayahuasca, Virola) recently associated with cognitive gains, antidepressant effects and changes in brain areas related to attention, self-referential thought, and internal mentation. Historical and technical restrictions impaired understanding how such substances impact human brain metabolism. Here we used shotgun mass spectrometry to explore proteomic differences induced by dimethyltryptamine (5-methoxy-N, N-dimethyltryptamine, 5-MeO-DMT) on human cerebral organoids. Out of the 6,728 identified proteins, 934 were found differentially expressed in 5-MeO-DMT-treated cerebral organoids. In silico systems biology analyses support 5-MeO-DMTs anti-inflammatory effects and reveal a modulation of proteins associated with the formation of dendritic spines, including proteins involved in cellular protrusion formation, microtubule dynamics and cytoskeletal reorganization. Proteins involved in long-term potentiation were modulated in a complex manner, with significant increases in the levels of NMDAR, CaMKII and CREB, but a reduction of PKA and PKC levels. These results offer possible mechanistic insights into the neuropsychological changes caused by the ingestion of substances rich in dimethyltryptamines.

neuroscience↗