Biology subjects

Ferreira, G. C.

Publications and source records attributed to Ferreira, G. C..

3 recordsLinked to original sources

bioRxiv2024

PI3Kγ pathway contributes to neuroinflammation and neuronal death induced by Zika virus infection

Zika virus (ZIKV) is an emerging arbovirus belonging to the Flaviviridae family and Orthoflavivirus genus, with a pronounced tropism for the central nervous system (CNS), where it induces neuroinflammation and neuronal death. ZIKV is known to exploit host cellular mechanisms, including the activation of survival pathways such as the PI3K/AKT signaling cascade, to evade apoptosis and enhance its replication. The phosphatidylinositol 3-kinase {gamma} (PI3K{gamma}) pathway regulates critical cellular processes, including differentiation, recruitment, and survival, and is abundantly expressed in both brain tissue and leukocytes. This study aimed to investigate the role of the PI3K{gamma} pathway during ZIKV infection. Primary neuronal cultures from PI3K{gamma}-deficient mice (PI3K{gamma}kd/kd) and human neuroblastoma SH-SY5Y cells treated with the PI3K{gamma} inhibitor AS605240 were infected with ZIKV to assess the impact of PI3K{gamma} signaling on viral replication and neuronal survival. Additionally, interferon /{beta} receptor knockout (A129) mice were treated with AS605240 either before or after ZIKV infection to evaluate the pathways role in neuroinflammation. In vitro, both genetic ablation and pharmacological inhibition of PI3K{gamma} suppressed ZIKV replication and prevented neuronal death. In vivo, mice treated with the PI3K{gamma} inhibitor exhibited enhanced protection against ZIKV infection, characterized by reduced viral load, and diminished brain and optic nerve damage. This neuroprotective effect correlated with altered astrocyte and microglia activation, marked by reduced TNF production in microglia. Furthermore, inhibition of PI3K{gamma} curtailed the recruitment and activation of CD8+ T cells and decreased the production of pro-inflammatory mediators, including IFN-{gamma} and IL-17, in the brains of ZIKV-infected mice. These findings suggest that PI3K{gamma} activation facilitates ZIKV infection and exacerbates neuroinflammation. Pharmacological inhibition of the PI3K{gamma} pathway may offer therapeutic benefits by limiting viral replication and alleviating neuroinflammatory responses during ZIKV infection.

immunology↗

bioRxiv2022

Developing best practices for genotyping-by-sequencing analysis using linkage maps as benchmarks

BackgroundGenotyping-by-Sequencing (GBS) provides affordable methods for genotyping hundreds of individuals using millions of markers. However, this challenges bioinformatic procedures that must overcome possible artifacts such as the bias generated by PCR duplicates and sequencing errors. Genotyping errors lead to data that deviate from what is expected from regular meiosis. This, in turn, leads to difficulties in grouping and ordering markers resulting in inflated and incorrect linkage maps. Therefore, genotyping errors can be easily detected by linkage map quality evaluations. ResultsWe developed and used the Reads2Map workflow to build linkage maps with simulated and empirical GBS data of diploid outcrossing populations. The workflows run GATK, Stacks, TASSEL, and Freebayes for SNP calling and updog, polyRAD, and SuperMASSA for genotype calling, and OneMap and GUSMap to build linkage maps. Using simulated data, we observed which genotype call software fails in identifying common errors in GBS sequencing data and proposed specific filters to better handle them. We tested whether it is possible to overcome errors in a linkage map using genotype probabilities from each software or global error rates to estimate genetic distances with an updated version of OneMap. We also evaluated the impact of segregation distortion, contaminant samples, and haplotype-based multiallelic markers in the final linkage maps. Through our evaluations, we observed that some of the approaches produce different results depending on the dataset (dataset-dependent) and others produce consistent advantageous results among them (dataset-independent). ConclusionsWe set as default in the Reads2Map workflows the approaches that showed to be dataset-independent for GBS datasets according to our results. This reduces the number required of tests to identify optimal pipelines and parameters for other empirical datasets. Using Reads2Map, users can select the pipeline and parameters that best fit their data context. The Reads2MapApp shiny app provides a graphical representation of the results to facilitate their interpretation.

bioinformatics↗

bioRxiv2020

Structural modeling and thermostability of a serine protease inhibitor belonging to the Kunitz family from the tick Rhipicephalus microplus

rBmTI-A is a recombinant serine protease inhibitor that belongs to the Kunitz-BPTI family and that was cloned from Rhipicephalus microplus tick. rBmTI-A has inhibitory activities on bovine trypsin, human plasma kallikrein, human neutrophil elastase and plasmin with dissociation constants in nM range. It is characterized by two inhibitory domains and each domain presents six cysteines that form three disulfide bonds, which contribute to the high stability of its structure. Previous studies suggest that serine protease inhibitor rBmTI-A has a protective potential against pulmonary emphysema in mice and anti-inflammatory potential, besides rBmTI-A presented a potent inhibitory activity against in vitro vessel formation. In this study, the tertiary structure of BmTI-A was modeled based on the structure of its Sabellastarte magnifica homologue. The structure stabilization was evaluated by molecular dynamics analysis. Circular dichroism data corroborated the secondary structure found by the homology modeling. Thermostability analysis confirmed the thermostability and the relation between the effects of the temperature in the inhibitor activity. The loss of activity observed was gradual, and, after 60 minutes of incubation at 90{degrees}C the inhibitor lost it completely.

biochemistry↗