Sias, Emanuela (2017) Dallo scavo al laboratorio: applicazione di tecniche di biologia molecolare in contesti archeologici. Doctoral Thesis.
This work joins different disciplines regarding the study of ancient DNA. In this thesis, it was applied and modified the protocol of sampling in situ and in the laboratory, based on the characteristics of the sample. During this work, several samples were collected from different sites of various dating and type, including 16 individuals, 40 samples from teeth and 237 samples from sediment. Ten samples from sediment and four from teeth were finally subjected to DNA extraction, library synthesis and next generation sequencing (NGS). Sequence data were processed via bioinformatics and results were analyzed considering the context. In the two samples from palazzo ducale, parasitological analysis were also performed, showing Ascaris, Trichiuris, Dyphillobotrium and Dricocelium genus. More accurate metagenomic analysis showed also Acanthamoeba castellani, confirmed Trichuris trichiura and identified the parasite Ascaris as A. suum. also, 18s rRNA sequencing showed Hartmanella sp. not confirmed by metagenomics. It is interesting the finding of Kribella sp. sequences with high similarity with the species K. catacombae (first described in a roman catacomb), in the sediments of the tombs. Future perspectives are a deeper sequencing of the metagenomes to reconstruct the genomes of the species already identified and other pathogens. This analysis will allow to evaluate the degradation of the DNA, a certain method to evaluate the antiquity of the species.
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