Integrating omics in prion diseases as a model to explore the strain paradigm in neurodegenerative diseases

This project aims at deepening the understanding of the molecular basis of the phenotypic heterogeneity of prion diseases. Prion diseases represent the first and clearest example of “protein misfolding diseases”, that are all the neurodegenerative diseases caused by the accumulation of misfolded proteins in the central nervous system. In the field of protein misfolding diseases, the term “strain” describes the heterogeneity observed among the same disease in the clinical and pathologic progression, biochemical features of the aggregated protein, conformational memory and pattern of lesions. In this work, the two most common strains of Creutzfeldt-Jakob Disease (CJD), named MM1 and VV2, were analyzed. This thesis investigates the strain paradigm with the production of new multi omic data, and, on such data, appropriate computational analysis combining bioinformatics, data science and statistical approaches was performed. In this work, genomic and transcriptomic profiling allowed an improved characterization of the molecular features of the two most common strains of CJD, identifying multiple possible genetic contributors to the disease and finding several shared impaired pathways between the VV2 strain and Parkinson Disease. On the epigenomic level, the tridimensional chromatin folding in peripheral immune cells of CJD patients at onset and of healthy controls was investigated with Hi-C. While being the first application of this very advanced technology in prion diseases and one of the first in general in neurobiology, this work found a significant and diffuse loss of genomic interactions in immune cells of CJD patients at disease onset, particularly in the PRNP locus, suggesting a possible impairment of chromatin conformation in the disease. The results of this project represent a novelty in the state of the art in this field, both from a biomedical and technological point of view.

Development of a porcine lactation model for the evaluation of mammary transfer of exogenous molecules - A contribution from the conception project

Around 5 million women give birth each year in Europe and, while breastfeeding, the majority of them may need to take medications, either occasionally or continuously. Unfortunately, there is often scarce evidence of trustworthy information about how a specific molecule might affect the physiology of lactation. This is the reason that brought a European public-private partnership to fund the development of a reliable platform to provide women and health-care professionals a helpful instrument to reduce uncertainty about the effects of medication used during breastfeeding. On April 1st 2019, the ConcePTION project (Grant Agreement n°821520) started to develop such envisaged platform. The 3rd Work Package was in charge of the validation of in vitro, in vivo and in silico lactation models. Between the numerous species currently used in preclinical studies, pigs’ similarities with humans’ anatomy, physiology and genomics make them extremely useful as translational models, when proper veterinary expertise is applied. The ASA team from the University of Bologna, went first to characterize the translational lactation model using the swine species, chosen upon literature review. The aim of this work was to lay the foundations of a porcine lactation model that could be suitable for application within pharmaceutical tests, to study drug transfer through milk prior approval and commercialization. The obtained results highlighted both strengths and critical points of the study design, allowing a significant improvement in the knowledge of pharmacokinetic physiology in lactating mammals. Lastly, this project allowed the assessment of microbial changes in gut resident bacteria of newborns through an innovative in vitro colonic model. Indeed, even if there were no evident adverse effects determined by drug residues in milk, possible alterations in the delicate microbial ecology of newborns’ gastrointestinal tract was considered pivotal, giving its possible impact on the individual health and growth.

Computational tool for three-point hitch geometry optimization

The weight-transfer effect, consisting of the change in dynamic load distribution between the front and the rear tractor axles, is one of the most impairing phenomena for the performance, comfort, and safety of agricultural operations. Excessive weight transfer from the front to the rear tractor axle can occur during operation or maneuvering of implements connected to the tractor through the three-point hitch (TPH). In this respect, an optimal design of the TPH can ensure better dynamic load distribution and ultimately improve operational performance, comfort, and safety. In this study, a computational design tool (The Optimizer) for the determination of a TPH geometry that minimizes the weight-transfer effect is developed. The Optimizer is based on a constrained minimization algorithm. The objective function to be minimized is related to the tractor front-to-rear axle load transfer during a simulated reference maneuver performed with a reference implement on a reference soil. Simulations are based on a 3-degrees-of-freedom (DOF) dynamic model of the tractor-TPH-implement aggregate. The inertial, elastic, and viscous parameters of the dynamic model were successfully determined through a parameter identification algorithm. The geometry determined by the Optimizer complies with the ISO-730 Standard functional requirements and other design requirements. The interaction between the soil and the implement during the simulated reference maneuver was successfully validated against experimental data. Simulation results show that the adopted reference maneuver is effective in triggering the weight-transfer effect, with the front axle load exhibiting a peak-to-peak value of 27.1 kN during the maneuver. A benchmark test was conducted starting from four geometries of a commercially available TPH. As result, all the configurations were optimized by above 10%. The Optimizer, after 36 iterations, was able to find an optimized TPH geometry which allows to reduce the weight-transfer effect by 14.9%.

Study of charge, spin, and structural orderings in quantum materials using nuclei and muons as local probes

Quantum Materials are many body systems displaying emergent phenomena caused by quantum collective behaviour, such as superconductivity, charge density wave, fractional hall effect, and exotic magnetism. Among quantum materials, two families have recently attracted attention: kagome metals and Kitaev materials. Kagome metals have a unique crystal structure made up of triangular lattice layers that are used to form the kagome layer. Due to superconductivity, magnetism, and charge ordering states such as the Charge Density Wave (CDW), unexpected physical phenomena such as the massive Anomalous Hall Effect (AHE) and possible Majorana fermions develop in these materials. Kitaev materials are a type of quantum material with a unique spin model named after Alexei Kitaev. They include fractional fluctuations of Majorana fermions and non-topological abelian anyons, both of which might be used in quantum computing. Furthermore, they provide a realistic framework for the development of quantum spin liquid (QSL), in which quantum fluctuations produce long-range entanglements between electronic states despite the lack of classical magnetic ordering. In my research, I performed several nuclear magnetic resonance (NMR), nuclear quadrupole resonance (NQR), and muon spin spectroscopy (µSR) experiments to explain and unravel novel phases of matter within these unusual families of materials. NMR has been found to be an excellent tool for studying these materials’ local electronic structures and magnetic properties. I could use NMR to determine, for the first time, the structure of a novel kagome superconductor, RbV3Sb5, below the CDW transition, and to highlight the role of chemical doping in the CDW phase of AV3Sb5 superconductors. µSR has been used to investigate the effect of doping on kagome material samples in order to study the presence and behaviour of an anomalous phase developing at low temperatures and possibly related to time-reversal symmetry breaking.