Biology subjects

Ribeiro, M. C.

Publications and source records attributed to Ribeiro, M. C..

8 recordsLinked to original sources

bioRxiv2025

A human engineered mini-heart platform for mimicking ventricular pump function

Engineered cardiac tissue models for in vitro physiological studies often fail to replicate the pump function of the heart. Despite promising advancements, the use of engineered cardiac chambers is often hindered by complex fabrication processes and invasive characterization techniques. Here, we engineered a human cardiac chamber, referred to as a mini-heart, by employing a novel sacrificial molding approach within a customized bioreactor. The mini-hearts pumping capability was confirmed through optical recording of fluid displacement at the engineered tissue inlet, enabling the non-invasive acquisition of hemodynamic parameters such as stroke volume, stroke work, ejection fraction, and developed pressure. Morphological analysis of the engineered tissues revealed organized sarcomeres and extracellular matrix self-determination, highlighting the advantage of our degradable mold technology. Additionally, we have measured calcium transients during both spontaneous and electrically-paced beating, and observed a positive inotropic response to the {beta}-adrenergic agonist drug isoproterenol. Altogether, our biomimicking engineered tissue platform provides a robust tool for exploring cardiac pressure-volume dynamics, thereby facilitating complex disease modelling and drug screening applications in vitro.

bioengineering↗

bioRxiv2025

The Freshwater Sounds Archive

Freshwater ecosystems are full of underwater sounds produced by amphibians, aquatic arthropods, reptiles, plants, fishes, and methane bubbles escaping from the sediment. Although much headway has been made in recent years investigating the overall soundscapes of various freshwater ecosystems around the world, there remains a significant knowledge gap in our collective inability to accurately and reliably link recorded sounds with the species that produced them. Here, we present The Freshwater Sounds Archive, a new global initiative, which seeks to address this knowledge gap by collating species-specific freshwater sound recordings into a publicly available database. By means of metadata collection, we also present a snapshot of the species studied, the recording equipment, and recording parameters used by freshwater ecoacousticians globally. In total, 61 entries were submitted to the archive between the 4th of March 2023 and the 30th of April 2025, representing 16 countries and 6 continents. The most numerous taxonomic group was arthropods (29 entries), followed by fishes (14 entries), amphibians (10 entries), macrophytes (7 entries), and a freshwater mollusk (1 entry). The majority of the submissions were from European countries (27 entries), of which the United Kingdom was the most represented with 14 entries. The next most represented region was North America (11 entries), followed by South America (8 entries), Oceania and Asia (5 entries each), Africa (3 entries), and the Middle East and Central America with 1 entry each. The global south, polar regions, and areas with an elevation >500 m (asl) were underrepresented. The field of freshwater ecoacoustics to date has largely focused on the analysis of sound types due to a current lack of knowledge of species-specific sounds. The Freshwater Sounds Archive presents an opportunity to move beyond the sound type approach, and towards an approach with higher taxonomic resolution, ultimately resulting in species-specific descriptions. Furthermore, The Freshwater Sounds Archive will provide freshwater ecoacousticians with one of the main tools required to start creating annotated training datasets for machine learning models from soundscape recordings by referring to known species sounds present in the archive. In the long-term, this will result in the automatic detection and classification of species-specific freshwater sounds from soundscape recordings, such as indicator, invasive, and endangered species.

ecology↗

bioRxiv2024

Relative fire-proneness of land cover types in the Brazilian Atlantic Forest

Fires are increasingly affecting tropical biomes, where landscape-fire interactions remain understudied. We investigate the fire-proneness--the likelihood of a land use or land cover (LULC) type burning more or less than expected based on availability--in the Brazilian Atlantic Forest (AF). This biodiversity hotspot is increasingly affected by fires due to human activities and climate change. Using a selection ratio-based approach, we analyzed fire-LULC interactions in 40,128 fires over a 35-year period (1987-2022) across various ecoregions in the AF. Our findings revealed that secondary forests, forest areas that have regrown after major disturbances, burned 61% more than expected by chance, whereas old-growth forests, native forests that have developed over very long periods, burned 57% less than expected, highlighting a nearly inverse relationship in their fire-proneness. Interestingly, our data indicate that pastures in the AF are less prone to fire than expected, despite being considered among the land uses that burn the most in Brazil. Other LULCs showed variable fire-proneness, with some differences between ecoregions. Over time, the fire-proneness of secondary forests decreased, likely due to forest aging and changes in land management practices. We emphasize the necessity for tailored fire management strategies that address the unique vulnerabilities of secondary forests, particularly in the context of ongoing restoration efforts aimed at increasing native forests. Effective measures, including the implementation of fire-smart management practices and enhancing the perceived value of secondary forests among local communities, are crucial for mitigating fire risks. Integrating these strategies with incentive-based approaches can bolster fire prevention, ensuring the long-term success of restoration programs. Our study provides a framework for understanding fire-landscape dynamics in tropical forests and offers actionable insights for practitioners working to safeguard these biomes from the escalating threat of wildfires. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=182 HEIGHT=200 SRC="FIGDIR/small/604452v2_ufig1.gif" ALT="Figure 1"> View larger version (70K): org.highwire.dtl.DTLVardef@612bc4org.highwire.dtl.DTLVardef@1806cc0org.highwire.dtl.DTLVardef@63c47corg.highwire.dtl.DTLVardef@1f8b252_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIEvaluation of land cover fire-proneness in a tropical biome using a selection ratio. C_LIO_LISecondary forests burned 61% more; old-growth forests 57% less than expected by chance. C_LIO_LIPastures in the Atlantic Forest seem less fire-prone than expected, despite frequent burns. C_LIO_LIFire-proneness of secondary forests has generally been decreasing over time. C_LIO_LITailored fire management is essential to protect secondary forests in restoration efforts. C_LI

ecology↗

bioRxiv2023

The Atlantic Forest of South America: spatiotemporal dynamic of remaining vegetation and implications for conservation

The Atlantic Forest in South America (AF) is one of the worlds most diverse and threatened biodiversity hotspots. We present a comprehensive spatiotemporal analysis of 34 years of AF landscape change between 1986-2020. We analyzed landscape metrics of forest vegetation only (FV), forest plus other natural vegetation (NV), and investigated the sensitivity of metrics to linear infrastructure. Currently, remnants comprise about 23% of FV and 36% of NV, and have decreased by 2.4% and 3.6% since 1986, respectively. Linear infrastructure negatively affected large fragments (>500,000 ha) by breaking them apart. Our findings suggest that AF protection legislation adopted in mid-2005 has taken effect: between 1986-2005, there was a loss of FV and NV (3% and 3.45%) and a decrease in the number of FV and NV fragments (8.6% and 8.3%). Between 2005-2020, there was a relative recovery of FV (1 Mha; 0.6%), slight loss of NV (0.25 Mha; 0.15%) and increase in the number of FV and NV fragments (12% and 9%). Still, 97% of the vegetation fragments are small (<50 ha), with an average fragment size between 16 and 26 ha. Furthermore, 50-60% of the vegetation is <90 m from its edges, and the isolation between fragments is high (250-830 m). Alarmingly, protected areas and indigenous territories cover only 10% of the AF and are very far from any fragments (>10 km). Our work highlights the importance of legislation and landscape dynamics analysis to help monitor and keep track of AF biodiversity conservation and restoration programs in the future. HighlightsO_LIThere is 23% forest and 36% natural vegetation cover remaining in the Atlantic Forest. C_LIO_LIBetween 1986-2020, native forest cover decreased by 2.4% and natural vegetation by 3.6%. C_LIO_LISince 2005, there has been a 1 Mha increase in forest area by small fragments (1 ha). C_LIO_LIRoads and railways reduced by 56%-89% fragment size, especially on large fragments. C_LIO_LIAlarmingly, 97% of fragments are small (<50 ha) and 60% are under edge effect (<90 m). C_LI

ecology↗

bioRxiv2021

Reconstruction and variability of tropical pollination networks in the Brazilian Atlantic Forest

O_LILoss of biodiversity comprehends not only the extinction of individual species, but also the loss of the ecological interactions among them. Survival of species, continuation of ecosystem functioning in nature, and ecosystem services to humans depend on the maintenance of well-functioning networks of species interactions (e.g. plant-pollinator networks and food webs). Analyses of ecological networks often rely on biased and incomplete survey data, especially in species-rich areas, such as the tropics. C_LIO_LIWe used a network inference method to reconstruct pollination data compiled from a large tropical rainforest habitat extent. To gain insight into the characteristics of plant-pollinator interactions across the region, we combined the reconstructed pollination network with species distribution modeling to obtain local pollination networks throughout the area. We explored how global network properties relate to natural forest cover and land cover heterogeneity. C_LIO_LIWe found that some network properties (the sum and evenness of link weights, connectance and nestedness) are positively correlated with forest cover, indicating that networks in sites with more natural habitat have greater diversity of interactions, stability and resilience. Modularity was not related to forest cover, but seemed to reflect habitat heterogeneity, due to the broad spatial scale of the study. C_LIO_LIWe believe that the methodology suggested here can facilitate the use of incomplete network data in a reliable way, and allow us to better understand and protect networks of species interactions in high biodiversity regions of the world. C_LI

ecology↗

bioRxiv2021

Vitamin D modulates cortical transcriptome and behavioral phenotypes in an Mecp2 heterozygous Rett syndrome mouse model

Rett syndrome (RTT) is an X-linked neurological disorder caused by mutations in the transcriptional regulator MECP2. Mecp2 loss-of-function leads to the disruption of many cellular pathways, including aberrant activation of the NF-{kappa}B pathway. Genetically attenuating the NF-{kappa}B pathway in Mecp2-null mice ameliorates hallmark phenotypes of RTT, including reduced dendritic complexity, raising the question of whether NF-{kappa}B pathway inhibitors could provide a therapeutic avenue for RTT. Vitamin D is a known inhibitor of NF-{kappa}B signaling; further, vitamin D deficiency is prevalent in RTT patients and male Mecp2-null mice. We previously demonstrated that vitamin D rescues the aberrant NF-{kappa}B activity and reduced neurite outgrowth of Mecp2-knockdown cortical neurons in vitro, and that dietary vitamin D supplementation rescues decreased dendritic complexity and soma size of neocortical projection neurons in both male hemizygous Mecp2-null and female heterozygous mice in vivo. Here, we have identified over 200 genes whose dysregulated expression in the Mecp2+/- cortex is modulated by dietary vitamin D. Genes normalized with vitamin D supplementation are involved in dendritic complexity, synapses, and neuronal projections, suggesting that the rescue of their expression could underpin the rescue of neuronal morphology. Further, motor and anxiety-like behavioral phenotypes in Mecp2+/- mice correlate with circulating vitamin D levels, and there is a disruption in the homeostasis of the vitamin D synthesis pathway in Mecp2+/- mice. Thus, our data indicate that vitamin D modulates RTT pathology and its supplementation could provide a simple and cost-effective partial therapeutic for RTT.

neuroscience↗

bioRxiv2019

Seed-dispersal networks lose complexity in tropical forest fragments

Seed dispersal interactions involve key ecological processes in tropical forests that help to maintain ecosystem functioning. Yet this functionality may be threatened by increasing habitat loss, defaunation and fragmentation. However, generalist species, and their interactions, can benefit from the habitat change caused by human disturbance while more specialized interactions mostly disappear. Therefore changes in the structure of the local, within fragment, networks can be expected. Here we investigated how the structure of seed-dispersal networks changes along a gradient of increasing habitat fragmentation. We analysed 16 bird seed-dispersal assemblages from forest fragments of a biodiversity-rich ecosystem. We found significant species-, interaction- and network-area relationships, yet the later was determined by the number of species remaining in each community. The number of frugivorous bird and plant species, their interactions, and the number of links per species decreases as area is lost in the fragmented landscape. In contrast, network nestedness has a negative relationship with fragment area, suggesting an increasing generalization of the network structure in the gradient of fragmentation. Network specialization was not significantly affected by area, indicating that some network properties may be invariant to disturbance. Still, the local extinction of partner species, paralleled by a loss of interactions and specialist-specialist bird-plant seed dispersal associations suggests the functional homogenization of the system as area is lost. Our study provides empirical evidence for network-area relationships driven by the presence/absence of remnant species and the interactions they perform.\n\nRESUMOInteracoes de dispersao de sementes formam um processo ecologico chave em florestas tropicais onde colaboram na manutencao do funcionamento do ecossistema. Porem, esta funcionalidade pode estar ameacada pelo aumento na perda e fragmentacao do habitat. Enquanto especies generalistas e suas interacoes podem se beneficiar da mudanca de habitat causada por disturbios antropicos, interacoes envolvendo especies mais especialistas sao, na maioria, eliminadas. Desta forma, mudancas nas redes locais, dentro de fragmentos florestais, sao esperadas. Neste trabalho nos investigamos como a estrutura de redes de dispersao de sementes mudam em um gradiente de fragmentacao do habitat. Nos analisamos 16 comunidades de dispersao de sementes espacialmente explicitas e distribuidas em fragmentos florestais de um ecossistema rico em biodiversidade. Nos encontramos relacoes significativas entre a area do fragmento e especies, interacoes e estrutura das redes, sendo que o ultimo foi determinado pelo numero de especies remanescentes em cada comunidade. O numero de especies de aves frugivoras e plantas e as interacoes entre eles, bem como o numero de links por especie diminuiram significativamente conforme a area dos fragmentos e perdida. Por outro lado, o aninhamento da rede mostrou uma relacao negativa com a area do fragmento, sugerindo um aumento da generalizacao da estrutura das redes com a fragmentacao do habitat. No entanto, o grau de especializacao das redes nao foi afetado pela area, indicando que algumas propriedades de rede podem ser resistentes a perturbacao. Sendo assim, a extincao local de especies parceiras, conjuntamente com a perda das interacoes e associacoes planta-dispersor mais especializadas, sugere uma homogeneizacao do sistema conforme a area do fragmento e perdida. Nosso estudo fornece evidencias empiricas para as relacoes rede-area, sendo estas direcionadas pela presenca e/ou ausencia das especies remanescentes bem como das interacoes que estas realizam.

ecology↗

bioRxiv2017

Versatile open software to quantify cardiomyocyte and cardiac muscle contraction in vitro and in vivo

Contraction of muscle reflects its physiological state. Methods to quantify contraction are often complex, expensive and tailored to specific models or recording conditions, or require specialist knowledge for data extraction. Here we describe an automated, open-source software tool (MUSCLEMOTION) adaptable for use with standard laboratory and clinical imaging equipment that enables quantitative analysis of normal cardiac contraction, disease phenotypes and pharmacological responses. MUSCLEMOTION allowed rapid and easy measurement of contractility in (i) single cardiomyocytes from primary adult heart and human pluripotent stem cells, (ii) multicellular 2D-cardiomyocyte cultures, 3D engineered heart tissues and cardiac organoids/microtissues in vitro and (iii) intact hearts of zebrafish and humans in vivo. Good correlation was found with conventional measures of contraction in each system. Thus, using a single method for processing video recordings, we obtained reliable pharmacological data and measures of cardiac disease phenotype in experimental cell- and animal models and human echocardiograms.

physiology↗