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Ferrarini, M. G.

Publications and source records attributed to Ferrarini, M. G..

4 recordsLinked to original sources

Transcriptional survey of ovarian bacteriomes in the cereal weevil, Sitophilus oryzae, shows down-regulation of immune effectors at the onset of sexual maturity

Insects often establish long-term relationships with intracellular symbiotic bacteria, i.e. endosymbionts, that provide them with essential nutrients such as amino acids and vitamins. Endosymbionts are typically confined within specialized host cells called bacteriocytes that may form an organ, the bacteriome. Compartmentalization within host cells is paramount for protecting the endosymbionts and also avoiding chronic activation of the host immune system. In the cereal weevil Sitophilus oryzae, bacteriomes are present as a single organ at the larval foregut-midgut junction, and in adults, at the apex of midgut mesenteric caeca and at the apex of the four ovarioles. While the adult midgut endosymbionts experience a drastic proliferation during early adulthood followed by complete elimination through apoptosis and autophagy, ovarian endosymbionts are maintained throughout the weevil lifetime by unknown mechanisms. Bacteria present in ovarian bacteriomes are thought to be involved in the maternal transmission of endosymbionts through infection of the female germline, but the exact mode of transmission is not fully understood. Here, we show that endosymbionts are able to colonize the germarium in one-week-old females, pinpointing a potential infection route of oocytes. To identify potential immune regulators of ovarian endosymbionts, we have analyzed the transcriptomes of the ovarian bacteriomes through young adult development, from one-day-old adults to sexually mature ones. In contrast with midgut bacteriomes, immune effectors are downregulated in ovarian bacteriomes at the onset of sexual maturation. We hypothesize that relaxation of endosymbiont control by antimicrobial peptides might allow bacterial migration and potential oocyte infection, ensuring endosymbiont transmission.

immunology↗

Transcriptomic-based selection of reference genes for quantitative real-time PCR in an insect endosymbiotic model

Reference genes are a fundamental tool for analyses of gene expression by real-time quantitative PCR (qRT-PCR), in that they ensure the correct comparison between conditions, stages, or treatments. Because of this, selection of appropriate genes to use as references is crucial for proper application of the technique. Nevertheless, efforts to find appropriate, stably expressed transcripts are still lacking, in particular in the field of insect science. Here, we took advantage of a massive transcriptomic high-throughput analysis of various developmental stages of the gut and associated-bacteriomes of the cereal weevil Sitophilus oryzae and identified a subset of stably expressed genes with the potential to be used as housekeeping genes from the larva to the adult stage. We employed several normalization techniques to select the most suitable genes among our subset. Our final selection includes three genes - TAO, YTH3 and PP12A - which can also be used to compare transcript abundance at various developmental stages in symbiotic insects, and in insects devoid of endosymbionts (aposymbiotic). Since they are well conserved, these genes have the potential to be useful for many other insect species. This work confirms the interest in using large-scale, unbiased methods for reference gene selection.

molecular biology↗

Investigating the human host - ssRNA virus interaction landscape using the SMEAGOL toolbox

Viruses are intracellular parasites that need their host cell to reproduce. Consequently, they have evolved numerous mechanisms to exploit the molecular machinery of their host cells, including the broad spectrum of host RNA-binding proteins (RBPs). However, the RBP interactome of viral genomes and the consequences of these interactions for infection are still to be mapped for most RNA viruses. To facilitate these efforts we have developed SMEAGOL, a fast and user-friendly toolbox to analyze the enrichment or depletion of RBP binding motifs across RNA sequences (https://github.com/gruber-sciencelab/SMEAGOL). To shed light on the interaction landscape of RNA viruses with human host cell RBPs at a large scale, we applied SMEAGOL to 197 single-stranded RNA (ssRNA) viral genome sequences. We find that the majority of ssRNA virus genomes are significantly enriched or depleted in binding motifs for human RBPs, suggesting selection pressure on these interactions. Our analysis provides an overview of potential virus - RBP interactions, covering the majority of ssRNA viral genomes fully sequenced to date, and represents a rich resource for studying host interactions vital to the virulence of ssRNA viruses. Our resource and the SMEAGOL toolbox will support future studies of virus / host interactions, ultimately feeding into better treatments.

bioinformatics↗

Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis

The novel betacoronavirus named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) caused a worldwide pandemic (COVID-19) after initially emerging in Wuhan, China. Here we applied a novel, comprehensive bioinformatic strategy to public RNA sequencing and viral genome sequencing data, to better understand how SARS-CoV-2 interacts with human cells. To our knowledge, this is the first meta-analysis to predict host factors that play a specific role in SARS-CoV-2 pathogenesis, distinct from other respiratory viruses. We identified differentially expressed genes, isoforms and transposable element families specifically altered in SARS-CoV-2 infected cells. Well-known immunoregulators including CSF2, IL-32, IL-6 and SERPINA3 were differentially expressed, while immunoregulatory transposable element families were overexpressed. We predicted conserved interactions between the SARS-CoV-2 genome and human RNA-binding proteins such as hnRNPA1, PABPC1 and eIF4b, which may play important roles in the viral life cycle. We also detected four viral sequence variants in the spike, polymerase, and nonstructural proteins that correlate with severity of COVID-19. The host factors we identified likely represent important mechanisms in the disease profile of this pathogen, and could be targeted by prophylactics and/or therapeutics against SARS-CoV-2. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/225581v3_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@15ca5a6org.highwire.dtl.DTLVardef@17f455forg.highwire.dtl.DTLVardef@a39f50org.highwire.dtl.DTLVardef@306ec1_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗