Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata)

Abstract Background Satellite DNAs (stDNAs) are highly repeated sequences that constitute large portions of any genome. The evolutionary dynamics of stDNA (e.g. copy number, nucleotide sequence, location) can, therefore, provide an insight into genome organization and evolution. We investigated the evolutionary origin of VSAREP stDNA in 17 monitor lizards (seven Asian, five Australian, and five African) at molecular and cytogenetic level. Results Results revealed that VSAREP is conserved in the genome of Asian and Australian varanids, but not in African varanids, suggesting that these sequences are either differentiated or lost in the African varanids. Phylogenetic and arrangement network analyses revealed the existence of at least four VSAREP subfamilies. The similarity of each sequence unit within the same VSAREP subfamily from different species was higher than those of other VSAREP subfamilies belonging to the same species. Additionally, all VSAREP subfamilies isolated from the three Australian species (Varanus rosenbergi, V. gouldii, and V. acanthurus) were co-localized near the centromeric or pericentromeric regions of the macrochromosomes, except for chromosomes 3 and 4 in each Australian varanid. However, their chromosomal arrangements were different among species. Conclusions The VSAREP stDNA family lack homogenized species-specific nucleotide positions in varanid lineage. Most VSAREP sequences were shared among varanids within the four VSAREP subfamilies. This suggests that nucleotide substitutions in each varanid species accumulated more slowly than homogenization rates in each VSAREP subfamily, resulting in non-species-specific evolution of stDNA profiles. Moreover, changes in location of VSAREP stDNA in each Australian varanid suggests a correlation with chromosomal rearrangements, leading to karyotypic differences among these species

Additional file 6: Table S4. of Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata)

T-test and F-test analyses using the average and standard deviation of nucleotide diversity of each VSAREP subfamily. (DOC 50 kb

Additional file 4: Table S2. of Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata)

Summary of repeat units and subfamilies in each species. (DOC 46 kb

Simulations and measurements of coupling impedance for modern particle accelerator devices

In this document it has been treated the study of the coupling impedance in modern devices, already installed or not, in different particle accelerators. In the specific case: • For a device in-phase of project, several simulations for impedance calculation have been done. • For a component already realized and used, measurements of coupling impedance value have been done. Simulations are used to determine the impact of the interconnect between to magnets, designed for the future particle accelerator FCC, on the overall impedance of the machine which is about 100 km long. In particular has been done a check between theory, simulations and measurements of components already built, allowing a better and deeper study of the component we have analysed. Controls that probably will be helpful to have a clear guideline in future works. The measurements instead concern in an existing component that was already used in LHC, the longest particle accelerator ever realised on the planet, 27 km long. The coupling impedance measurements, in that case, have been carried out to determine the real influence that the beam particle has on the material around it self. Material that may have changed some of its main properties after many hours of work. The study drove by Diego Ferrazza with the help of the entire research team BE-ABP-HSC and especially thanks to the constant presence of my two supervisors: Benoit Salvant and Nicolò Biancacci. Without forgetting the remote supervision of my thesis advisor: Prof. Andrea Mostacci