Biology subjects

Innocenti, G.

Publications and source records attributed to Innocenti, G..

3 recordsLinked to original sources

bioRxiv2023

Real-time identification of epistatic interactions in SARS-CoV-2 from large genome collections

The emergence and rapid spread of the SARS-CoV-2 virus has highlighted the importance of genomic epidemiology in understanding the evolution of pathogens and for guiding public health interventions. In particular, the Omicron variant underscored the role of epistasis in the evolution of lineages with both higher infectivity and immune escape, and therefore the necessity to update surveillance pipelines to detect them as soon as they emerge. In this study we applied a method based on mutual information (MI) between positions in a multiple sequence alignment (MSA), which is capable of scaling up to millions of samples. We showed how it could reliably predict known experimentally validated epistatic interactions, even when using as little as 10,000 sequences, which opens the possibility of making it a near real-time prediction system. We tested this possibility by modifying the method to account for sample collection date and applied it retrospectively to MSAs for each month between March 2020 and March 2023. We could detect a cornerstone epistatic interaction in the Spike protein between codons 498 and 501 as soon as 6 samples with a double mutation were present in the dataset, thus demonstrating the methods sensitivity. Lastly we provide examples of predicted interactions between genes, which are harder to test experimentally and therefore more likely to be overlooked. This method could become part of continuous surveillance systems tracking present and future pathogen outbreaks.

microbiology↗

bioRxiv2022

Assessing the influence of the Mediterranean diet on dental calculus microbiome composition: a pilot study

Human oral microbiome harbours hundreds of bacterial species, which, during evolution, assembled in different niches, such as the microbiome of saliva, tongue, hard palate, gingiva and dental plaque. Among these, saliva has been the most studied ecological niche of the oral microbiome. In this frame, scientific research has demonstrated that several factors concur to determine the saliva microbial composition, including diet, systemic diseases and drugs. However, the influence of such variables on other oral niches, such as the dental calculus, a calcified derivative of dental plaque, is still unexplored. During the last decade, dental calculus has become the primary target for evolutionary microbiome studies because of its ability to keep both bacterial DNA and dietary molecules (i.e., proteins and starch). As a consequence, dental calculus is now considered a powerful tool for obtaining information about oral microbiome composition, diet and individual health status in past populations, making it also appealing for clinical research. Here, we provide the first clinical study, to our knowledge, assessing the inter-variability of dental calculus microbiome in 40 patients. Samples were collected during routine dental inspection and analysed through 16S amplicon sequencing. In addition, we investigated the relationship between oral microbiome and host. Specifically, we tested the influence of Mediterranean diet style on the composition and functional pathways of oral bacteria, with the aim to test the dental calculus as a clinical bio-marker for diet impact and health status.

microbiology↗

bioRxiv2020

Tractography dissection variability: what happens when 42 groups dissect 14 white matter bundles on the same dataset?

White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same intended white matter pathways, which directly affects tractography results, quantification, and interpretation. In this study, we aim to evaluate and quantify the variability that arises from different protocols for bundle segmentation. Through an open call to users of fiber tractography, including anatomists, clinicians, and algorithm developers, 42 independent teams were given processed sets of human whole-brain streamlines and asked to segment 14 white matter fascicles on six subjects. In total, we received 57 different bundle segmentation protocols, which enabled detailed volume-based and streamline-based analyses of agreement and disagreement among protocols for each fiber pathway. Results show that even when given the exact same sets of underlying streamlines, the variability across protocols for bundle segmentation is greater than all other sources of variability in the virtual dissection process, including variability within protocols and variability across subjects. In order to foster the use of tractography bundle dissection in routine clinical settings, and as a fundamental analytical tool, future endeavors must aim to resolve and reduce this heterogeneity. Although external validation is needed to verify the anatomical accuracy of bundle dissections, reducing heterogeneity is a step towards reproducible research and may be achieved through the use of standard nomenclature and definitions of white matter bundles and well-chosen constraints and decisions in the dissection process.

neuroscience↗