Biology subjects

Carvalho, J. C.

Publications and source records attributed to Carvalho, J. C..

4 recordsLinked to original sources

bioRxiv2024

Optimizing Lipidomics Analysis Workflows for Biological Fluids and Extracellular Vesicles with Integrated Liquid Chromatography Tandem Mass Spectrometry Approaches

Lipidomics, a subfield of metabolomics, involves the comprehensive analysis of lipids within biological systems and has become a cornerstone of biomedical research, driven by recent technological advancements. Lipids are crucial biomolecules in cellular functions and have been increasingly recognized for their roles in physiological and pathological processes. This study focuses on innovative strategies for developing, validating, and applying comprehensive analytical methods for untargeted lipidomics using liquid chromatography-tandem mass spectrometry (LC-MS/MS) in human plasma and extracellular vesicles (EVs). We describe improvements based on analytical validation parameters, including inter-day repeatability, limit of quantification, precision, accuracy, recovery, and matrix effects. Plasma samples were used as a proof-of-concept study, and the method was ultimately applied to human macrophage-derived EVs. Samples preparations were achieved through four liquid-liquid extraction methods for lipids in order to achieve a broad coverage of lipid classes as well as high recovery and repeatability. Additionally, we demonstrated that a sonication-assisted homogenization step effectively facilitates lipid extraction from EVs. Through untargeted lipidomics, our study identifies and quantifies a diverse range of lipid species in human plasma (225 molecular lipids) and macrophage-derived EVs (124 molecular lipids) within different classes. Overall, we present an innovative methodology that combines pre-analytical lipid extraction techniques with high-resolution LC-MS/MS to enhance lipidomics research. This approach holds promise for personalized medicine and the discovery of novel lipid cargo associated with the various biological pathways involved with EVs biogenesis.

biochemistry↗

bioRxiv2022

Calculating functional diversity metrics using neighbor-joining trees

O_LIThe study of functional diversity (FD) provides ways to understand phenomena as complex as community assembly or the dynamics of biodiversity change under multiple pressures. Different frameworks are used to quantify FD, either based on dissimilarity matrices (e.g., Rao entropy, functional dendrograms) or multidimensional spaces (e.g. convex hulls, kernel-density hypervolumes). While the first does not enable the measurement of FD within a richness/divergence/regularity framework, or results in the distortion of the functional space, the latter does not allow for comparisons with phylogenetic diversity (PD) measures and can be extremely sensitive to outliers. C_LIO_LIWe propose the use of neighbor-joining trees (NJ) to represent and quantify functional diversity in a way that combines the strengths of current FD frameworks without many of their weaknesses. Our proposal is also uniquely suited for studies that compare FD with PD, as both share the use of trees (NJ or others) and the same mathematical principles. C_LIO_LIWe test the ability of this novel framework to represent the initial functional distances between species with minimal functional space distortion and sensitivity to outliers. The results using NJ are compared with conventional functional dendrograms, convex hulls, and kernel-density hypervolumes using both simulated and empirical datasets. C_LIO_LIUsing NJ we demonstrate that it is possible to combine much of the flexibility provided by multidimensional spaces with the simplicity of tree-based representations. Moreover, the method is directly comparable with PD measures, and enables quantification of the richness, divergence and regularity of the functional space. C_LI

ecology↗

bioRxiv2021

Distance decay 2.0 - a global synthesis of taxonomic and functional turnover in ecological communities.

Understanding the variation in community composition and species abundances, i.e., {beta}-diversity, is at the heart of community ecology. A common approach to examine {beta}-diversity is to evaluate directional turnover in community composition by measuring the decay in the similarity among pairs of communities along spatial or environmental distances. We provide the first global synthesis of taxonomic and functional distance decay along spatial and environmental distance by analysing 149 datasets comprising different types of organisms and environments. We modelled an exponential distance decay for each dataset using generalized linear models and extracted r2 and slope to analyse the strength and the rate of the decay. We studied whether taxonomic or functional similarity has stronger decay across the spatial and environmental distances. We also unveiled the factors driving the rate of decay across the datasets, including latitude, spatial extent, realm, and organismal features. Taxonomic distance decay was stronger along spatial and environmental distances compared with functional distance decay. The rate of taxonomic spatial distance decay was the fastest in the datasets from mid-latitudes while the rate of functional decay increased with latitude. Overall, datasets covering larger spatial extents showed a lower rate of decay along spatial distances but a higher rate of decay along environmental distances. Marine ecosystems had the slowest rate of decay. This synthesis is an important step towards a more holistic understanding of patterns and drivers of taxonomic and functional {beta}-diversity.

ecology↗

bioRxiv2018

Decomposing the causes for niche differentiation between species using hypervolumes

1. Hutchinsons n-dimensional hypervolume concept holds a central role across different fields of ecology and evolution. The question of the amount of hyper-volume overlap and differentiation between species is of great interest to understand the processes that drive niche dynamics, competitive interactions and, ultimately, community assembly.\n\n2. A novel framework is proposed to decompose overall differentiation among hypervolumes into two distinct components: niche shifts and niche contraction / expansion processes. Niche shift corresponds to the replacement of space between the hypervolumes occupied by two species, whereas niche contraction / expansion processes correspond to net differences between the amount of space enclosed by each hypervolume.\n\n3. Hypervolumes were constructed for two Darwin finches, Geospiza conirostris and Geospiza magnirostris, using intraspecific trait data from Genovesa Island, where they live in sympatry. Results showed that significant niche shifts, not niche contraction, occurred between these species. This means that Geospiza conirostris occupied a different niche space and not a reduced space on Genovesa.\n\n4. The proposed framework allows disentangling different processes and understand the drivers of niche partitioning between coexisting species. Niche displacement due to competition can this way be separated from niche contraction due to specialization or expansion due to lower pressure on newly occupied ecological settings.

ecology↗