Biology subjects

Oliveira, B.

Publications and source records attributed to Oliveira, B..

5 recordsLinked to original sources

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↗

bioRxiv2024

A secondary β-hydroxybutyrate metabolic pathway linked to energy balance

{beta}-hydroxybutyrate (BHB) is an abundant ketone body. To date, all known pathways of BHB metabolism involve interconversion of BHB and primary energy intermediates. Here we show that CNDP2 controls a previously undescribed secondary BHB metabolic pathway via enzymatic conjugation of BHB and free amino acids. This BHB-ylation reaction produces a family of endogenous ketone metabolites, the BHB-amino acids. Genetic ablation of CNDP2 in mice eliminates tissue amino acid BHB-ylation activity and reduces BHB-amino acid levels. Administration of BHB-Phe, the most abundant BHB-amino acid, to obese mice activates neural populations in the hypothalamus and brainstem and suppresses feeding and body weight. Conversely, CNDP2-KO mice exhibit increased food intake and body weight upon ketosis stimuli. CNDP2-dependent amino acid BHB-ylation and BHB-amino acid metabolites are also conserved in humans. Therefore, the metabolic pathways of BHB extend beyond primary metabolism and include secondary ketone metabolites linked to energy balance.

biochemistry↗

bioRxiv2024

Light-microscopy based dense connectomic reconstruction of mammalian brain tissue

The information-processing capability of the brains cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution with dense cellular labeling. Light microscopy is uniquely positioned to visualize specific molecules but dense, synapse-level circuit reconstruction by light microscopy has been out of reach due to limitations in resolution, contrast, and volumetric imaging capability. Here we developed light-microscopy based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning based segmentation and analysis of connectivity, thus directly incorporating molecular information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level brain tissue phenotyping in biological experiments in a readily adoptable manner. One-Sentence SummaryHydrogel expansion enables molecularly informed reconstruction of brain tissue at synaptic resolution with light microscopy.

neuroscience↗

bioRxiv2020

CHD8 haploinsufficiency alters the developmental trajectories of human excitatory and inhibitory neurons linking autism phenotypes with transient cellular defects

Chromodomain helicase DNA-binding 8 (CHD8) is one of the most frequently mutated genes causative of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses macrocephaly and hence implicates cortical abnormalities in this form of ASD, the neurodevelopmental impact of human CHD8 haploinsufficiency remains unexplored. Here we combined human cerebral organoids and single cell transcriptomics to define the effect of ASD-linked CHD8 mutations on human cortical development. We found that CHD8 haploinsufficiency causes a major disruption of neurodevelopmental trajectories with an accelerated generation of inhibitory neurons and a delayed production of excitatory neurons alongside the ensuing protraction of the proliferation phase. This imbalance leads to a significant enlargement of cerebral organoids aligned to the macrocephaly observed in patients with CHD8 mutations. By adopting an isogenic design of patient-specific mutations and mosaic cerebral organoids, we define genotype-phenotype relationships and uncover their cell-autonomous nature. Finally, our results assign different CHD8-dependent molecular defects to particular cell types, pointing to an abnormal and extended program of proliferation and alternative splicing specifically affected in, respectively, the radial glial and immature neuronal compartments. By identifying temporally restricted cell-type specific effects of human CHD8 mutations, our study uncovers developmental alterations as reproducible endophenotypes for neurodevelopmental disease modelling.

neuroscience↗

bioRxiv2020

A combined characterization of coelomic fluid cell types in the spiny starfish Marthasterias glacialis: inputs from flow cytometry and imaging

Coelomocytes is a generic name for a collection of cellular morphotypes, present in many coelomate animals, that has been reported as highly variable across echinoderm classes. The roles attributed to the major types of the free circulating cells present in the coelomic fluid of echinoderms include immune response, phagocytic digestion and clotting. The main aim of the present study is the thorough characterization of coelomocytes present in the coelomic fluid of Marthasterias glacialis (class Asteroidea) through the combined use of flow cytometry (FC) and fluorescence plus transmission electron microscopy. Two coelomocyte populations (here named P1 and P2) were identified by flow cytometry and subsequently studied in terms of abundance, morphology, ultrastructure, cell viability and cell cycle profiles. Ultrastructurally, P2 diploid cells showed two main morphotypes, similar to phagocytes and vertebrate thrombocytes, whereas the small P1 haploid cellular population was characterized by a low mitotic activity, relatively undifferentiated cytotype and a high nucleus/cytoplasm ratio. These last cells resemble stem-cell types present in other animals. P1 and P2 cells differ also in cell viability and cell cycle profiles. Additionally, two other morphotypes were only detected by fluorescence microscopy and a third one when using a combined microscopy/FC approach.

cell biology↗