Biology subjects

Goncalves, F.

Publications and source records attributed to Goncalves, F..

6 recordsLinked to original sources

bioRxiv2025

From smartphones to satellites: Uniting crowdsourced biodiversity monitoring and Earth observation to fill the gaps in global plant trait mapping

Plant functional traits are fundamental to ecosystem dynamics and Earth system processes, but their global characterization is limited by the availability of field surveys and trait measurements. Recent expansions in biodiversity data aggregation, including large collections of vegetation surveys, citizen science observations, and trait measurements, offer new opportunities to overcome these constraints. Here we demonstrate that combining these diverse data sources with high-resolution Earth observation data enables accurate modeling of key plant traits at up to 1 km resolution. Our approach achieves high predictive power, reaching correlations up to 0.63 (15 of 31 traits exceeding 0.50) and improved spatial transferability, effectively bridging gaps in under-sampled regions. By capturing a broad range of traits with high spatial coverage, these maps can enhance our understanding of plant community properties and ecosystem functioning globally, and can serve as useful tools in modeling global biogeochemical processes and informing worldwide conservation efforts. Ultimately, our framework highlights the power and necessity of crowdsourced biodiversity data in high-resolution plant trait modeling. We anticipate that advancements in biodiversity data collection and remote sensing capabilities will further refine global trait mapping, fostering a dynamic trait-based understanding of the biosphere.

ecology↗

bioRxiv2024

A computationally guided approach to improve expression of VHH binders

The variable heavy chain fragments derived from camelid antibodies, called VHHs or nanobodies, have recently shown promise as high-affinity reagents. They offer higher stability compared to conventional antibodies and fragments thereof. Furthermore, their smaller size ([~]15-20 kDa) allows better targeting of molecules localized inside the cell and in crowded environments, like tissues and protein aggregates. Despite these advantages, nanobody clones screened using phage display can suffer from poor soluble expression, which we hypothesized, is due to the presence of hydrophobic hotspots on their surface. In this work, we propose a novel computationally guided workflow for screening and production of nanobody binders for optimized expression. After an initial round of phage display screens against our target (K-Ras), we modeled the lead candidates to generate Spatial Aggregation Propensity (SAP) maps to highlight the hydrophobic hotspots with single amino acid resolution, which were subsequently used to guide mutagenesis of the binders for soluble expression. We followed two approaches to perform point hydrophilic mutations: i) performing point hydrophilic mutations in the hydrophobic hotspots; ii) combining point mutation resulting from a round of random mutagenesis that show favorable SAP scores. Both approaches led a remarkable increase in soluble expression which allowed production and characterization of their binding to their target (K-Ras) on soluble ELISA, and biolayer interferometry. We observed that the latter approach resulted in clones with stronger binding affinity compared to the former approach. Our results emphasize the need to perform a round of random mutagenesis to identify point mutations, which can then be used in an in-silico guided pipeline to identify the right combination of mutations for high soluble expression.

bioengineering↗

bioRxiv2024

Peptide Amphiphiles Hitchhike on Endogenous Biomolecules for Enhanced Cancer Imaging and Therapy

The interactions of nanomaterials with biomolecules in vivo determine their biological fate. Here, we show that self-assembled peptide amphiphile (PA) nanostructures can dynamically interact with endogenous biomolecules and take advantage of naturally occurring processes to target a broad range of solid tumors. In circulation, self-assembled PA nanostructures disassemble and reassemble mainly with lipoproteins, which prolongs blood circulation and dramatically improves tumor accumulation and retention. Mechanistic studies suggested that PAs internalize into cancer cells by assembling with their cell membranes and independently of specific receptors. By exploiting these interactions, a PA developed in this study (namely SA-E) demonstrated specific accumulation in various xenograft, syngeneic, patient-derived xenograft, or transgenic rodent models. In addition, SA-E enabled the effective delivery of highly potent chemotherapy to different syngeneic and xenografted tumors with reduced side effects. With its simple and modular design and universal tumor accumulation mechanism, SA-E represents a promising platform for broad applications in cancer imaging and therapy.

bioengineering↗

bioRxiv2023

Vessel normalization and maturation promotes nanoparticle delivery to solid tumors while minimizing metastases.

Nanoparticle delivery to solid tumors is known to be an inefficient process and various studies have tried to increase efficacy, but mechanistic and comparative studies remain scarce. Here, we use pharmacological agents to study the effect of vessel normalization or vessel disintegration on nanoparticle delivery to solid tumors. Using a multiparametric approach, we find that vessel disintegration fails to improve nanoparticle delivery and instead seems to have a limiting effect. Vessel normalization, however, improves delivery efficacy for nanoparticles ranging from 20 to 60 nm diameter. The normalization of the tumor blood vessels results in reduced hypoxia, reduced necrosis and an increase in Plvap+ CD276+ endothelial cells, which have been linked with nanoparticle delivery. Interestingly, where vessel disintegration stimulated cancer cell intravasation and associated metastases, vessel normalization impeded these processes. Together, these data reveal that, vessel normalization may be a safer and more suited approach for improving nanoparticle delivery to solid tumors, but its efficacy is limited by nanoparticle diameter and tumor parameters. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/538559v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@17e5e08org.highwire.dtl.DTLVardef@14f82dcorg.highwire.dtl.DTLVardef@118708eorg.highwire.dtl.DTLVardef@18593d0_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2021

Combined impacts of climate and land use change and the future of Neotropical bat biodiversity

Forecasting the effects of global change on biodiversity is necessary to anticipate the threats operating at different scales in space and time. Climate change may create unsuitable environmental conditions, forcing species to move to persist. However, land-use changes create barriers that limit the access of some species to future available habitats. Here, we project the impacts of climate and land-use change on 228 Neotropical bat species by forecasting changes in environmental suitability, while accounting for the effect of habitat type specialization and simulating dispersal across suitable patches. We also identify the most vulnerable ecoregions and those that may offer future stable refugia. We further investigate potential functional changes by analysing the response of different trophic guilds. We found that the range contraction of habitat specialists, especially frugivores, was more frequent and stronger under all simulated scenarios. Projected changes differ markedly across ecoregions. While the Amazon region is likely to undergo high turnover rates in bat composition, the Andean grassland, Cerrado and Chaco might experience the greatest losses. The expansion of habitat generalists, which forage in open areas and commonly establish large colonies in manmade structures, coupled with the range contraction of habitat specialists is projected to homogenize bat communities across the Neotropics. Overall, dispersal will likely be the key for the future of Neotropical bat diversity. Therefore, safeguarding the refugia highlighted here, by expanding and connecting the existing network of protected areas, for example, may allow species to move in response to global change.

ecology↗

bioRxiv2020

Prey choice of the common vampire bat on introduced species in an Atlantic forest land-bridge island

The proliferation of native, alien, invasive and domestic species provide novel and abundant food resources for the common vampire bat (Desmodus rotundus) that could alter its prey preference. Based on the analysis of carbon and nitrogen stable isotopes, we report the prey choice of D. rotundus on introduced mammals in an tropical land-bridge island where the domestic animals were removed and 100 individuals of 15 mammal species were intentionally introduced. Our analysis shows that, D. rotundus on Anchieta Island were more likely to prey upon species from open habitats (mean value of -14.8{per thousand}), i.e., animals with high {delta}13C values characterized by the consumption of C4 resources. As expected for a top predator species, {delta}15N values for D. rotundus were higher (mean value of 8.2{per thousand}) and overlapped the niche of the capybaras (Hydrochoerus hydrochaeris) from the Anchieta Island, while it was distant from coatis, and also from those potential prey from the preserved area in the mainland, including the capybaras, indicating that among all potential mammalian prey species, they fed exclusively on capybaras, the highest mammalian biomass on island. Based on previous information on human occupation, the domestic animals present on Anchieta island might be the main prey of D. rotundus and responsible for maintaining a viable population. As the capybaras were introduced only 36 years ago, this suggests a rapid prey shift due to anthropogenic disturbances, which has allowed common vampire bats to successfully exploit them. Literature records also show that common vampire bats were not captured in preserved areas of the mainland which are near Anchieta Island indicating that the percentage of capture of D. rotundus is usually low in natural forested habitats where potential prey are scattered. As three individuals of introduced capybaras were confirmed died from bat rabies viruses (RABV) in 2020, we suggest periodic monitoring of bat rabies viruses in common vampire bat populations on Anchieta Island and areas nearby, in order to quantify the magnitude of the outbreak area and develop strategies for controlling, especially considering that the island and areas nearby is frequently visited by tourists. We highlighted that this prey choice is context-dependent, and possibly influenced by the removal of domestic animals, the explosive population growth of introduced capybaras combined with their predictable foraging behavior.

ecology↗