Biology subjects

Faria, C.

Publications and source records attributed to Faria, C..

4 recordsLinked to original sources

bioRxiv2023

Ecological monitoring using Collembola metabarcoding with extremely low bycatch amplification.

Collembola are used widely to monitor soil health and functional parameters. Recent developments in high throughput sequencing (especially metabarcoding) have substantially increased their potential for these ends. Collembola are especially amenable to metabarcoding because of their small size, high abundance, and ubiquity in most habitat types. However, most Collembola sampling protocols collect a substantial and highly varied bycatch that can be a considerable impediment to metabarcoding, especially because of data lost to non-target species. We designed a primer set amplifying the D2 expansion segment of ribosomal DNA that is highly conserved across Collembola and successfully excludes from amplification nearly all other invertebrate taxa. We tested the diagnostic power of the primer set by clearly distinguishing Collembola communities between forest sites with differing habitat qualities in Sao Paulo State, Brazil. The oligos successfully amplified targets from all Collembola orders previously encountered in the sampling locations, with no non-target amplification, and also excluded the closely related Protura and Diplura. Alpha diversity (OTU count) and phylogenetic diversity was significantly higher in high quality habitats. Moreover, the beta diversity indices successfully differentiated high and low-quality habitats. This new addition to the biomonitoring toolbox greatly increases the accessibility of Collembola metabarcoding for various types of habitat assessments.

molecular biology↗

bioRxiv2023

Germination timing under climate change: warmer springs favor early germination of range-wide cork oak populations

Climate change is favoring the northward shift of Mediterranean species which are expanding their ranges at their leading edges, becoming natural candidates for increasing forest biodiversity in these regions. However, current knowledge on tree populations responses to climate change is mostly based on adult trees, even if tree early developmental stages are far more sensitive to climate and tightly linked to fitness. To fill this knowledge gap, we investigated the potential adaptation of cork oak range-wide populations to increasing spring temperature in germination and post-germination traits. We sowed 701 acorns from 11 populations at 15, 20 and 25{degrees}C, monitored germination daily and measured post-germination traits. We model germination timing through Coxs proportional-hazards models, assess populations adaptation to spring temperature transfer distances and quantify the effect of acorn mass and storage duration on all considered traits with fixed-effects models. We predict germination and post-germination climate niches under current and RCP 8.5 2080 scenarios. Large differences in germination timing are due to both the population origin and temperature treatment; germination and survival rates showed a sub-optimality towards warmer-than-origin temperatures and heavier acorns produced faster growing seedlings. The timing of germination is the early stage trait most affected by increasing spring temperatures, with germination in 2080 predicted to be 12 days earlier than to date in the northern part of the species range. Warmer spring temperatures will significantly accelerate the germination of other recalcitrant Mediterranean species, which could alter seedlings developmental environment and ultimately populations regeneration and species composition. As such, germination timing should receive more attention by scientists and stakeholders, and should be included in forest vulnerability assessments and assisted migration programs aiming at long-term forest regeneration to adapt forests to climate change.

ecology↗

bioRxiv2022

Exploring Xylella fastidiosa's metabolic traits using a GSM model of the phytopathogenic bacterium

Xylella fastidiosa is a gram-negative phytopathogenic bacterium that caused a significant economic impact around the world. In the last decade, genome-scale metabolic models have become important systems biology tools for studying the metabolic behaviour of different pathogens and driving the discovery of novel drug targets. This work is a second iteration of the iMS508 model for X. fastidiosa subsp. pauca De Donno. The model comprises 1138 reactions, 1234 metabolites, and 509 genes. in silico validation of the metabolic model was achieved through the comparison of simulations with available experimental data. Aerobic metabolism was simulated properly and fastidian gum production rates predicted accurately.

bioinformatics↗

bioRxiv2018

Drosophila IMP regulates Kuzbanian to control the timing of Notch signalling in the follicle cells

The timing of Drosophila egg chamber development is controlled by a germline Delta signal that activates Notch in the follicle cells to induce them to cease proliferation and differentiate. Here we report that follicle cells lacking the RNA-binding protein IMP go through one extra division due to a delay in the Delta-dependent S2 cleavage of Notch. The timing of Notch activation has previously been shown to be controlled by cis-inhibition by Delta in the follicle cells, which is relieved when the miRNA pathway represses Delta expression. imp mutants are epistatic to Delta mutants and give an additive phenotype with belle and dicer mutants, indicating that IMP functions independently of both cis-inhibition and the miRNA pathway. We find that the imp phenotype is rescued by over-expression of Kuzbanian, the metalloprotease that mediates the Notch S2 cleavage. Furthermore, Kuzbanian is not enriched at the apical membrane in imp mutants, accumulating instead in late endosomes. Thus, IMP regulates Notch signalling by controlling the localisation of Kuzbanian to the apical domain, where Notch cleavage occurs, revealing a novel regulatory step in the Notch pathway.\n\nSummaryIMP regulates Notch signalling in follicle cells by controlling Kuzbanian localisation to the apical domain, where Notch cleavage occurs, revealing a novel regulatory step in the Notch pathway.

developmental biology↗