Biology subjects

Carvalho, R.

Publications and source records attributed to Carvalho, R..

6 recordsLinked to original sources

bioRxiv2026

High-throughput functional genomics and transcriptomics reveal molecular mechanisms regulating the synergistic fungicidal activity of copper and zinc

Fungal diseases cause devastating crop infestations and millions of deaths annually. To improve disease treatment development, we must understand the biological processes these treatments target and the fungal cellular responses they elicit. Current methods to identify genetic responses of fungi to antifungal drugs and fungicides typically involve laborious molecular genetics experiments or transcriptomics. We utilized high-throughput screens in the basidiomycete yeast Rhodotorula (Rhodosporidium) toruloides to rapidly identify genes associated with the fungal response to a copper-zinc fungicide developed by VM Agritech and compared identified genes to those transcriptionally activated in response to the fungicide in R. toruloides and the filamentous ascomycete Neurospora crassa. These 'omics technologies combined with molecular genetics and biochemical analyses showed copper and zinc synergize to inhibit fungal growth due, at least in part, to an increase in cellular zinc concentrations when copper is present. Intriguingly, although we identified genes involved in the copper-zinc fungicide response using both high-throughput screens and transcriptomics, there was little overlap in genes identified through the two methods. Our findings demonstrate the power of combining functional genomics and transcriptomics approaches in identifying a more comprehensive map of the genetic mechanisms necessary for responding to fungicides.

microbiology↗

bioRxiv2025

FAVABEAN and FALAPhyl: Open-Source Pipelines for Scalable 16s rRNA Microbiome Data Processing and Visualization

Reproducible and scalable analysis of 16S rRNA amplicon sequencing data remains a persistent challenge in microbiome research due to the complexity of available tools, incompatibilities between platforms, and the need for extensive bioinformatics expertise. We developed two containerized workflows--FAVABEAN (Fast Amplicon Variant Annotation, Binning, Error-correction And ANalysis) and FALAPhyl (Forays into Automating Laborious Analyses of Phylogeny)--to address these challenges. FAVABEAN and FALAPhyl are Snakemake-based pipelines designed for flexible execution across local, cluster, and cloud environments. FAVABEAN automates preprocessing, ASV inference, and taxonomic assignment using DADA2 and FIGARO, including primer averaging when samples are sequenced with multiple primers. FALAPhyl supports downstream analysis including alpha/beta diversity, network analysis, and differential abundance testing, with integrated provenance tracking. We validated both pipelines using three case studies involving oral microbiome datasets. In Case Study 1, we compared oral microbiota across family members and niches, showing primer-dependent variability in ASV-based similarity and minimal reseeding from familial sources after prophylaxis. Case Study 2 analyzed dental aerosol samples, revealing no significant microbial differences between pre-, intra-, and post-procedure air. Case Study 3, a randomized trial of a nitrate mouthrinse, demonstrated no significant microbiome shifts, highlighting oral microbial stability. FALAPhyls integration of DAtest enabled empirical evaluation of multiple statistical tests, aiding robust differential abundance inference. FAVABEAN and FALAPhyl offer a reproducible, automated solution for 16S rRNA amplicon data analysis. Their modular design, containerization, and provenance tracking enhance accessibility and scientific rigor in microbiome research.

bioinformatics↗

bioRxiv2025

Hepatic Yap1 activates systemic catabolism and muscle loss during organ repair: evidence for a liver-derived common mechanism with cancer cachexia.

Recovery from critical injury concomitant with restoration of functional organ mass invokes a systemic catabolic response leading to muscle and fat loss, known as cachexia. We interrogated this process using mouse models of organ repair, including liver regeneration after hepatectomy, Yap1-mediated hepatomegaly, and pneumonectomy. Both hepatectomy and Yap1 induced systemic catabolism. Muscle and adipose wasting scaled with degree of liver growth, with 10-25% reduction of muscle mass and 50-80% of fat mass. In contrast, non-regenerative lung injury did not induce tissue wasting. Liver growth elevated resting energy expenditure. Tracer studies demonstrated redistribution of muscle-derived cholesterol and amino acids to regenerating liver. Gene expression changes in livers and muscles showed high concordance between the liver growth models and cancer cachexia models, including pancreatic adenocarcinoma cachexia. We propose that cachexia is a normal and essential reparative process in organ repair and regeneration and further, that cancer cachexia is a pathological exacerbation of an adaptive process mediated by activation of Yap1 in the liver.

physiology↗

bioRxiv2024

Deciphering the impact of cancer cells secretome and its derived-peptide VGF on breast cancer brain metastasis

Brain metastases (BM) are one of the most serious clinical problems in breast cancer (BC) progression, associated with lower survival rates and a lack of effective therapies. Thus, to dissect the early stages of the brain metastatic process, we have searched for a brain-tropic metastatic signature on BC cells secretome, as a promising source for the discovery of new biomarkers involved in brain metastatic progression. Therefore, six specifically deregulated peptides were found to be enriched in the secretome of brain organotropic BC cells. Importantly, these secretomes caused significant blood-brain barrier (BBB) disruption, as well as microglial activation, in vitro and in vivo. We identified the VGF nerve growth factor inducible as a brain-specific peptide, promoting BBB dysfunction similar to the secretome of brain organotropic BC cells. Concerning microglial activation, a slight increase was also observed upon VGF treatment. In a series of human breast tumors, VGF was found to be expressed in both cancer cells and in the adjacent stroma. VGF-positive tumors showed a significant worse prognosis and were associated with HER2 overexpression and triple-negative molecular signatures. Finally, in a cohort including primary breast tumors and their corresponding metastatic locations to the lung, bone, and brain, we found that VGF significantly correlates with the brain metastatic site. In conclusion, we found a specific BC brain metastatic signature, where VGF was identified as a key mediator in this process. Importantly, its expression was associated with poor prognosis for BC patients, probably due to its associated increased risk of developing BM.

cancer biology↗

bioRxiv2023

Muscle cell atrophy induced by miR-155-5p reveals molecular targets in skeletal muscle disorders

MicroRNAs are small regulatory molecules that control gene expression. An emerging property of muscle miRNAs is the cooperative regulation of transcriptional and epitranscriptional events controlling muscle phenotype. miR-155 has been related to muscular dystrophy and muscle cell atrophy. However, the function of miR-155 and its molecular targets in muscular dystrophies remain poorly understood. Through in silico and in vitro approaches we identify distinct transcriptional profile of muscle cell atrophy induced by miR-155-5p. The atrophic myotubes changed the expression of 359 genes (166 up-regulated and 193 down-regulated). We reanalyzed muscle transcriptomic data from dystrophin-deficient patients and detected overlap with gene expression patterns in miR-155-treated myotubes. Our analysis indicated that miR-155 regulates a set of transcripts, including Aldh1l, Nek2, Bub1b, Ramp3, Slc16a4, Plce1, Dync1i1, and Nr1h3. Enrichment analysis demonstrates 20 targets involved in metabolism, cell cycle regulation, muscle cell maintenance, and immune system. Moreover, digital cytometry confirmed a significant increase in M2 macrophages, indicating miR-155 effects on immune response in dystrophic muscles. We highlight a critical miR-155 associated with disease-related pathways in skeletal muscle disorders.

genomics↗

bioRxiv2020

Prediction of non-canonical routes for SARS-CoV-2 infection in human placenta cells

The SARS-CoV-2 is the causative agent of the COVID-19 pandemic. The data available about COVID-19 during pregnancy have demonstrated placental infection; however, the intrauterine transmission of SARS-CoV-2 is still debated. Intriguingly, while canonical SARS-CoV-2 cell entry mediators are expressed at low levels in placental cells, the receptors for viruses that cause congenital infections such as the cytomegalovirus and Zika virus are highly expressed in these cells. Here we analyzed the transcriptional profile (microarray and single-cell RNA-Seq) of proteins potentially interacting with coronaviruses to identify non-canonical mediators of SARS-CoV-2 infection and replication in the placenta. We show that, despite low levels of the canonical cell entry mediators ACE2 and TMPRSS2, cells of the syncytiotrophoblast, villous cytotrophoblast, and extravillous trophoblast co-express high levels of the potential non-canonical cell-entry mediators DPP4 and CTSL. We also found changes in the expression of DAAM1 and PAICS genes during pregnancy, which are translated into proteins also predicted to interact with coronaviruses proteins. These results provide new insight into the interaction between SARS-CoV-2 and host proteins that may act as non-canonical routes for SARS-CoV-2 infection and replication in the placenta cells.

developmental biology↗