Biology subjects

Amaral, D.

Publications and source records attributed to Amaral, D..

5 recordsLinked to original sources

bioRxiv2025

eDNA enables proof-of-origin of samples from reservoirs with rich and abundant biodiversity

Environmental DNA (eDNA) is increasingly used for biodiversity monitoring, but its application in verifying the geographic origin of samples remains limited. Here, we evaluated whether eDNA profiles from water samples can indicate sample provenance across three large Brazilian reservoirs. Using multi-marker metabarcoding (COI, 12S, 16S), we showed that biodiversity signatures enable spatial attribution. To ensure traceability, each report was encoded in a machine-readable format, hashed, and registered on the blockchain. This framework demonstrates a novel approach to independently verifying sample origin through molecular and cryptographic evidence.

ecology↗

bioRxiv2021

Charting Brain Growth and Aging at High Spatial Precision

Defining reference models for population variation, and the ability to study individual deviations is essential for understanding inter-individual variability and its relation to the onset and progression of medical conditions. In this work, we assembled a reference cohort of neuroimaging data from 82 sites (N=58,836; ages 2-100) and use normative modeling to characterize lifespan trajectories of cortical thickness and subcortical volume. Models are validated against a manually quality checked subset (N=24,354) and we provide an interface for transferring to new data sources. We showcase the clinical value by applying the models to a transdiagnostic psychiatric sample (N=1,985), showing they can be used to quantify variability underlying multiple disorders whilst also refining case-control inferences. These models will be augmented with additional samples and imaging modalities as they become available. This provides a common reference platform to bind results from different studies and ultimately paves the way for personalized clinical decision making.

neuroscience↗

bioRxiv2020

The genomes of invasive coral Tubastraea spp. (Dendrophylliidae) as tool for the development of biotechnological solutions

Corals have been attracting huge attention due to the impact of climate change and ocean acidification on reef formation and resilience. Nevertheless, some species like Tubastraea coccinea and T. tagusensis have been spreading very fast replacing the native ones which affect the local environment and decrease biodiversity of corals and other organisms associated with them. Despite some focal efforts to understand the biology of these organisms, they remain understudied at the molecular level. This knowledge gap hinders the development of cost-effective strategies for both conservation and management of invasive species. In this circumstance, it is expected that genome sequencing would provide powerful insights that could lead to better strategies for prevention, management, and control of this and other invasive species. Here, we present three genomes of Tubastraea spp. in one of the most comprehensive biological studies of corals, that includes flow cytometry, karyotyping, transcriptomics, genomics, and phylogeny. The genome of T. tagusensis is organized in 23 chromosomes pairs and has 1.1 Gb, the T. coccinea genome is organized in 22 chromosome pairs and has 806 Mb, and the Tubastraea sp. genome is organized in 21 chromosome pairs and has 795 Mb. The hybrid assembly of T. tagusensis using short and long-reads has a N50 of 227,978 bp, 7,996 contigs and high completeness estimated as 91.6% of BUSCO complete genes, of T. coccinea has a N50 of 66,396 bp, 17,214 contigs and 88.1% of completeness, and of Tubastraea sp. has a N50 of 82,672 bp, 12,922 contigs and also 88.1% of completeness. We inferred that almost half of the genome consists of repetitive elements, mostly interspersed repeats. We provide evidence for exclusive Scleractinia and Tubastraea gene content related to adhesion and immunity. The Tubastraea spp. genomes are a fundamental study which promises to provide insights not only about the genetic basis for the extreme invasiveness of this particular coral genus, but to understand the adaptation flaws of some reef corals in the face of anthropic-induced environmental disturbances. We expect the data generated in this study will foster the development of efficient technologies for the management of coral species, whether invasive or threatened.

evolutionary biology↗

bioRxiv2020

Alterations in retrotransposition, synaptic connectivity, and myelination implicated by transcriptomic changes following maternal immune activation in non-human primates

BackgroundMaternal immune activation (MIA) is a proposed risk factor for multiple neurodevelopmental and psychiatric disorders, including schizophrenia. However, the molecular and neurobiological mechanisms through which MIA imparts risk for these disorders remain poorly understood. A recently developed nonhuman primate model of exposure to the viral mimic poly:ICLC during pregnancy shows abnormal social and repetitive behaviors and elevated striatal dopamine, a molecular hallmark of human psychosis, providing an unprecedented opportunity for mechanistic dissection. MethodsWe performed RNA-sequencing across four psychiatrically-relevant brain regions (prefrontal cortex, anterior cingulate, hippocampus, and primary visual cortex) from 3.5-4-year old male MIA-exposed and control offspring--an age comparable to mid adolescence in humans. ResultsWe identify 266 unique genes differentially expressed (DE) in at least one brain region with the greatest number observed in hippocampus. Co-expression networks identified region-specific alterations in synaptic signaling and oligodendrocytes. Across regions, we observed temporal and regional differences, but transcriptomic changes were largely similar across 1st or 2nd trimester MIA exposures, including for the top DE genes--PIWIL2 and MGARP. In addition to PIWIL2, several other known regulators of retrotransposition, as well as endogenous transposable elements were dysregulated in MIA offspring. ConclusionsTogether, these results begin to elucidate the brain-level molecular mechanisms through which MIA may impart risk for psychiatric disease.

neuroscience↗

bioRxiv2018

First Draft Genome of a Brazilian Atlantic Rainforest Burseraceae reveals commercially-promising genes involved in terpenic oleoresins synthesis

BackgroundProtium species produce abundant aromatic oleoresins composed mainly of different types of terpenes, which are highly sought after by the flavor and fragrance industry.\n\nResultsHere we present (i) the first draft genome of an endemic tree of the Brazils Atlantic Rainforest (Mata Atlantica), Protium kleinii Cuatrec., (ii) a first characterization of its genes involved in the terpene pathways, and (iii) the composition of the resins volatile fraction. The de novo draft genome was assembled using Illumina paired-end-only data, totalizing 407 Mb in size present in 229,912 scaffolds. The N50 is 2.60 Kb and the longest scaffold is 52.26 Kb. Despite its fragmentation, we were able to infer 53,538 gene models of which 5,434 were complete. The draft genome of P. kleinii presents 76.67 % (62.01 % complete and 14.66 % partial) of plant-core BUSCO genes. InterProScan was able to assign at least one Gene Ontology annotation and one Pfam domain for 13,629 and 26,469 sequences, respectively. We were able to identify 116 enzymes involved in terpene biosynthesis, such as monoterpenes -terpineol, 1,8-cineole, geraniol, (+)-neomenthol and (+)-(R)-limonene. Through the phylogenetic analysis of the Terpene Synthases gene family, three candidates of limonene synthase were identified. Chemical analysis of the resins volatile fraction identified four monoterpenes: terpinolene, limonene, -pinene and -phellandrene.\n\nConclusionThese results provide resources for further studies to identify the molecular bases of the main aroma compounds and new biotechnological approaches to their production.

genomics↗