Evaluation of Bacteria and Fungi DNA Abundance in Human Tissues

Whereas targeted and shotgun sequencing approaches are both powerful in allowing the study of tissue-associated microbiota, the human: microorganism abundance ratios in tissues of interest will ultimately determine the most suitable sequencing approach. In addition, it is possible that the knowledge of the relative abundance of bacteria and fungi during a treatment course or in pathological conditions can be relevant in many medical conditions. Here, we present a qPCR-targeted approach to determine the absolute and relative amounts of bacteria and fungi and demonstrate their relative DNA abundance in nine different human tissue types for a total of 87 samples. In these tissues, fungi genomes are more abundant in stool and skin samples but have much lower levels in other tissues. Bacteria genomes prevail in stool, skin, oral swabs, saliva, and gastric fluids. These findings were confirmed by shotgun sequencing for stool and gastric fluids. This approach may contribute to a more comprehensive view of the human microbiota in targeted studies for assessing the abundance levels of microorganisms during disease treatment/progression and to indicate the most informative methods for studying microbial composition (shotgun versus targeted sequencing) for various samples types

A computational approach for 3D modeling and integration of heterogeneous geo-data

This paper tackles the volumetric representation of geophysical and geotechnical data, gathered during exploration surveys of the subsoil; in particular, we focus on the modeling and analysis of underwater deposits. The creation of a 3D model as support to geological interpretation has to take into account the heterogeneity of the input data, coming from offshore acquisition campaigns. Some data are massive, but cover the domain unevenly, e.g., along dense differently spaced lines, while others are very sparse, e.g., borehole locations with soil sampling and CPTU (Piezocone Penetration Test) locations. A automatic process is presented to generate the subsurfaces and volume defining a sub-seabed deposit, starting from the identification of relevant morphological features in seismic data. In particular, simplification and refinement based on geostatistics have been applied to generate regular 2D meshes from strongly anisotropic data, in order to improve the quality of the final 3D tetrahedral mesh. Furthermore, we also use geostatistics to predict geotechnical parameters from local surveys and estimate their distribution on the whole domain: in this way the 3D model will include relevant geological features of the deposit and allow extrapolating different geotechnical information with associated uncertainty. The volume characterization and its 3D inspection will support geological analysis and planning of future engineering activities. The developed methodology has been tested on two real case studies

CLUB Working Papers in Linguistics

CLUB WORKING PAPERS IN LINGUISTICS (CLUB-WPL) è una collana editoriale a cura del CLUB – Circolo Linguistico dell'Università di Bologna. La collana ospita contributi relativi alle iniziative del CLUB e dei suoi membri. I volumi, sottoposti a una procedura di peer-review, sono pubblicati esclusivamente online – sulla piattaforma AMS Acta dell'Università di Bologna – e sono liberamente accessibili

Evaluation of Bacteria and Fungi DNA Abundance in Human Tissues

Whereas targeted and shotgun sequencing approaches are both powerful in allowing the study of tissue-associated microbiota, the human: microorganism abundance ratios in tissues of interest will ultimately determine the most suitable sequencing approach. In addition, it is possible that the knowledge of the relative abundance of bacteria and fungi during a treatment course or in pathological conditions can be relevant in many medical conditions. Here, we present a qPCR-targeted approach to determine the absolute and relative amounts of bacteria and fungi and demonstrate their relative DNA abundance in nine different human tissue types for a total of 87 samples. In these tissues, fungi genomes are more abundant in stool and skin samples but have much lower levels in other tissues. Bacteria genomes prevail in stool, skin, oral swabs, saliva, and gastric fluids. These findings were confirmed by shotgun sequencing for stool and gastric fluids. This approach may contribute to a more comprehensive view of the human microbiota in targeted studies for assessing the abundance levels of microorganisms during disease treatment/progression and to indicate the most informative methods for studying microbial composition (shotgun versus targeted sequencing) for various samples types