Biology subjects

Silva, N. M.

Publications and source records attributed to Silva, N. M..

3 recordsLinked to original sources

bioRxiv2025

Dengue virus capsid protein interaction with nucleic acids

Dengue virus (DENV) transmission has greatly increased in the last decade, in part due to the geographical expansion of its vector, the Aedes spp. mosquitoes. These arthropods are now found even in temperate climates, including Europe, where outbreaks have already occurred. A better understanding of the virus life cycle is essential, as it may enable the development of specific treatments or therapies which are currently lacking. However, recent breakthroughs concerning the biologically relevant viral capsid (C) protein structure and function are encouraging. It is now clear the C protein binds both to host lipid droplets and to the viral genome, a set of interactions that is crucial for viral encapsidation and replication. Previously, we studied DENV C protein interaction with lipid droplets, at the molecular level. Here, we examine how the association of DENV C protein with the viral genome occurs. Using DENV C protein and single-stranded DNA (ssDNA) sequences analogous to previously identified important regions of the viral genome, we biophysically characterize their interactions. A decrease in fluorescence intensity and lifetime, an increase in both anisotropy and hydrodynamic diameter, as well as changes in the proteins secondary structure, were observed upon binding to ssDNA. These changes are consistent with molecular condensation and raise the possibility of liquid-liquid phase separation involvement in DENV C-nucleic acid complex formation. These findings may be useful for the development of future therapeutic strategies based on nucleic acids, not only for DENV but also for other related viruses.

biophysics↗

bioRxiv2021

Tetracycline exposure alters key gut microbiota in Africanized honey bees (Apis mellifera scutellata x spp.)

Honey bees play a critical role in ecosystem health, biodiversity maintenance, and crop yield. Antimicrobials, such as tetracyclines, are used widely used across agriculture, medicine, and in bee keeping, and bees can be directly or indirectly exposed to tetracycline residues in the environment. In European honey bees, tetracycline exposure has been linked with shifts in the gut microbiota that negatively impact bee health. However, the effects of antimicrobials on Africanized honey bee gut microbiota have not been examined. The aim of this study was to investigate the effects of tetracycline exposure on the gut microbial community of Africanized honey bees (Apis mellifera scutellata x spp), which are important pollinators in South, Central, and North America. Bees (n=1,000) were collected from hives in Areia-PB, Northeastern Brazil, placed into plastic chambers and kept under controlled temperature and humidity conditions. The control group (CON) was fed daily with syrup (10g) consisting of a 1:1 solution of demerara sugar and water, plus a solid protein diet (10g) composed of 60% soy extract and 40% sugar syrup. The tetracycline group (TET) was fed identically but with the addition of tetracycline hydrochloride (450 {micro}g/g) to the sugar syrup. Bees were sampled from each group before (day 0), and after tetracycline exposure (days 3, 6 and 9). Abdominal contents dissected out of each bee underwent DNA extraction and 16S rRNA sequencing (V3-V4) on an Illumina MiSeq. Sequences were filtered and processed through QIIME2 and DADA2. Microbial community composition and diversity and differentially abundant taxa were evaluated by treatment and time. Bee gut microbial composition (Jaccard) and diversity (Shannon) differed significantly and increasingly over time and between CON and TET groups. Tetracycline exposure was associated with decreased relative abundances of Bombella and Fructobacillus, along with decreases in key core microbiota such as Snodgrassella, Gilliamella, Rhizobiaceae, and Apibacter. These microbes are critical for nutrient metabolism and pathogen defense, and decreased abundances of these microbes could negatively affect bee health. Considering the global ecological and economic importance of honey bees as pollinators, it is critical to understand the effects of agrochemicals including antimicrobials on honey bees.

ecology↗

bioRxiv2017

The Population Genomics Of Archaeological Transition In West Iberia

We analyse new genomic data (0.05-2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200-3500 BC) to the Middle Bronze Age (1740-1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. While discontinuity is evident in the transition to agriculture across the region, sensitive haplotype-based analyses suggest a significant degree of local hunter-gatherer contribution to later Iberian Neolithic populations. A more subtle genetic influx is also apparent in the Bronze Age, detectable from analyses including haplotype sharing with both ancient and modern genomes, D-statistics and Y-chromosome lineages. However, the limited nature of this introgression contrasts with the major Steppe migration turnovers within third Millennium northern Europe and echoes the survival of non-Indo-European language in Iberia. Changes in genomic estimates of individual height across Europe are also associated with these major cultural transitions, and ancestral components continue to correlate with modern differences in stature.\n\nAuthor SummaryRecent ancient DNA work has demonstrated the significant genetic impact of mass migrations from the Steppe into Central and Northern Europe during the transition from the Neolithic to the Bronze Age. In Iberia, archaeological change at the level of material culture and funerary rituals has been reported during this period, however, the genetic impact associated with this cultural transformation has not yet been estimated. In order to investigate this, we sequence Neolithic and Bronze Age samples from Portugal, which we compare to other ancient and present-day individuals. Genome-wide imputation of a large dataset of ancient samples enabled sensitive methods for detecting population structure and selection in ancient samples. We revealed subtle genetic differentiation between the Portuguese Neolithic and Bronze Age samples suggesting a markedly reduced influx in Iberia compared to other European regions. Furthermore, we predict individual height in ancients, suggesting that stature was reduced in the Neolithic and affected by subsequent admixtures. Lastly, we examine signatures of strong selection in important traits and the timing of their origins.

genomics↗