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Piccinini, G.

Publications and source records attributed to Piccinini, G..

2 recordsLinked to original sources

Enhanced Intestinal Epithelial Co-Culture Model with Orbital Mechanical Stimulation: A Proof-of-Concept Application in Food Nanotoxicology

IntroductionCurrent in vitro intestinal models lack the mechanical forces present in the physiological environment, limiting their reliability for nanotoxicology studies. Here, we developed an enhanced Caco-2/HT29-MTX-E12 co-culture model incorporating orbital mechanical stimulation to better replicate intestinal conditions and investigate nanoparticle interactions. MethodsWe established co-cultures under static and dynamic conditions, validating their development through multiple approaches including barrier integrity measurements, gene expression analysis, and confocal microscopy. We introduced novel quantitative analysis of dome formation as a differentiation marker and demonstrated the model application by investigating cellular responses to titanium dioxide (TiO) nanoparticles in a digested food matrix. ResultsDynamic conditions accelerated epithelial differentiation, achieving functional barrier properties by day 14 rather than day 21, with enhanced mucin production and more organized three-dimensional structure. Mechanical stimulation selectively promoted goblet cell differentiation without affecting general epithelial markers. The optimized model successfully detected concentration-dependent oxidative stress responses to TiO exposure, revealing cellular dysfunction preceding membrane damage. DiscussionThis improved co-culture system provides a better physiological platform for nanotoxicology studies. By incorporating mechanical forces, each cell type exhibits more representative behavior, creating a more realistic experimental setup. The model bridges the gap between simple monocultures and complex 3D systems, offering a practical approach for investigating nanoparticle-epithelium interactions in a food-relevant context.

cell biology↗

BASE: a novel workflow to integrate non-ubiquitous genes in genomics analyses for selection.

Inferring the selective forces that different ortholog genes underwent across different lineages can make us understand the evolutionary processes which shaped their extant diversity. The more widespread metric to estimate coding sequences selection regimes across across their sites and species phylogeny is the ratio of nonsynonymous to synonymous substitutions (dN/dS, also known as{omega} ). Nowadays, modern sequencing technologies and the large amount of already available sequence data allow the retrieval of thousands of genes orthology groups across large numbers of species. Nonetheless, the tools available to explore selection regimes are not designed to automatically process all orthogroups and practical usage is often restricted to those consisting of single-copy genes which are ubiquitous across the species considered (i.e. the subset of genes which is shared by all the species considered). This approach limits the scale of the analysis to a fraction of single-copy genes, which can be as lower as an order of magnitude in respect to non-ubiquitous ones (i.e. those which are not present across all the species considered). Here we present a workflow named BASE that - leveraging the CodeML framework - ease the inference and interpretation of selection regimes in the context of comparative genomics. Although a number of bioinformatics tools have already been developed to facilitate this kind of analyses, BASE is the first to be specifically designed to ease the integration of non-ubiquitous genes orthogroups. The workflow - along with all the relevant documentation - is available at github.com/for-giobbe/BASE.

bioinformatics↗