Structural and functional analysis of centromeric chromatin

Animal neocentromeres are defined as ectopic centromeres that have formed in non-centromeric locations and avoid some of the features, like the DNA satellite sequence, that normally characterize canonical centromeres. Despite this, they are stable functional centromeres inherited through generations. The only existence of neocentromeres provide convincing evidence that centromere specification is determined by epigenetic rather than sequence-specific mechanisms. For all this reasons, we used them as simplified models to investigate the molecular mechanisms that underlay the formation and the maintenance of functional centromeres. We collected human cell lines carrying neocentromeres in different positions. To investigate the region involved in the process at the DNA sequence level we applied a recent technology that integrates Chromatin Immuno-Precipitation and DNA microarrays (ChIP-on-chip) using rabbit polyclonal antibodies directed against CENP-A or CENP-C human centromeric proteins. These DNA binding-proteins are required for kinetochore function and are exclusively targeted to functional centromeres. Thus, the immunoprecipitation of DNA bound by these proteins allows the isolation of centromeric sequences, including those of the neocentromeres. Neocentromeres arise even in protein-coding genes region. We further analyzed if the increased scaffold attachment sites and the corresponding tighter chromatin of the region involved in the neocentromerization process still were permissive or not to transcription of within encoded genes. Centromere repositioning is a phenomenon in which a neocentromere arisen without altering the gene order, followed by the inactivation of the canonical centromere, becomes fixed in population. It is a process of chromosome rearrangement fundamental in evolution, at the bases of speciation. The repeat-free region where the neocentromere initially forms, progressively acquires extended arrays of satellite tandem repeats that may contribute to its functional stability. In this view our attention focalized to the repositioned horse ECA11 centromere. ChIP-on-chip analysis was used to define the region involved and SNPs studies, mapping within the region involved into neocentromerization, were carried on. We have been able to describe the structural polymorphism of the chromosome 11 centromeric domain of Caballus population. That polymorphism was seen even between homologues chromosome of the same cells. That discovery was the first described ever. Genomic plasticity had a fundamental role in evolution. Centromeres are not static packaged region of genomes. The key question that fascinates biologists is to understand how that centromere plasticity could be combined to the stability and maintenance of centromeric function. Starting from the epigenetic point of view that underlies centromere formation, we decided to analyze the RNA content of centromeric chromatin. RNA, as well as secondary chemically modifications that involve both histones and DNA, represents a good candidate to guide somehow the centromere formation and maintenance. Many observations suggest that transcription of centromeric DNA or of other non-coding RNAs could affect centromere formation. To date has been no thorough investigation addressing the identity of the chromatin-associated RNAs (CARs) on a global scale. This prompted us to develop techniques to identify CARs in a genome-wide approach using high-throughput genomic platforms. The future goal of this study will be to focalize the attention on what strictly happens specifically inside centromere chromatin.

Model predictive control in thermal management of multiprocessor systems-on-chip

MultiProcessor Systems-on-Chip (MPSoC) are the core of nowadays and next generation computing platforms. Their relevance in the global market continuously increase, occupying an important role both in everydaylife products (e.g. smartphones, tablets, laptops, cars) and in strategical market sectors as aviation, defense, robotics, medicine. Despite of the incredible performance improvements in the recent years processors manufacturers have had to deal with issues, commonly called “Walls”, that have hindered the processors development. After the famous “Power Wall”, that limited the maximum frequency of a single core and marked the birth of the modern multiprocessors system-on-chip, the “Thermal Wall” and the “Utilization Wall” are the actual key limiter for performance improvements. The former concerns the damaging effects of the high temperature on the chip caused by the large power densities dissipation, whereas the second refers to the impossibility of fully exploiting the computing power of the processor due to the limitations on power and temperature budgets. In this thesis we faced these challenges by developing efficient and reliable solutions able to maximize performance while limiting the maximum temperature below a fixed critical threshold and saving energy. This has been possible by exploiting the Model Predictive Controller (MPC) paradigm that solves an optimization problem subject to constraints in order to find the optimal control decisions for the future interval. A fully-distributedMPC-based thermal controller with a far lower complexity respect to a centralized one has been developed. The control feasibility and interesting properties for the simplification of the control design has been proved by studying a partial differential equation thermal model. Finally, the controller has been efficiently included in more complex control schemes able to minimize energy consumption and deal with mixed-criticalities tasks

Partial Discharge Phenomena in Converter and Traction Transformers: Identification and Reliability

After the development of power electronics converters, the number of transformers subjected to non-sinusoidal stresses (including DC) has increased in applications such as HVDC links and traction (electric train power cars). The effects of non-sinusoidal voltages on transformer insulation have been investigated by many researchers, but still now, there are some issues that must be understood. Some of those issues are tackled in this Thesis, studying PD phenomena behavior in Kraft paper, pressboard and mineral oil at different voltage conditions like AC, DC, AC+DC, notched AC and square waveforms. From the point of view of converter transformers, it was found that the combined effect of AC and DC voltages produces higher stresses in the pressboard that those that are present under pure DC voltages. The electrical conductivity of the dielectric systems in DC and AC+DC conditions has demonstrated to be a critical parameter, so, its measurement and analysis was also taken into account during all the experiments. Regarding notched voltages, the RMS reduction caused by notches (depending on firing and overlap angles) seems to increase the PDIV. However, the experimental results show that once PD activity has incepted, the notches increase PD repetition rate and magnitude, producing a higher degradation rate of paper. On the other hand, the reduction of mineral oil stocks, their relatively low flash point as well as environmental issues, are factors that are pushing towards the use of esters as transformer insulating fluids. This PhD Thesis also covers the study of two different esters with the scope to validate their use in traction transformers. Mineral oil was used as benchmark. The complete set of dielectric tests performed in the three fluids, show that esters behave better than mineral oil in practically all the investigated conditions, so, their application in traction transformers is possible and encouraged.

Optimal Supervisory Control of Hybrid Vehicles

Hybrid vehicles (HV), comprising a conventional ICE-based powertrain and a secondary energy source, to be converted into mechanical power as well, represent a well-established alternative to substantially reduce both fuel consumption and tailpipe emissions of passenger cars. Several HV architectures are either being studied or already available on market, e.g. Mechanical, Electric, Hydraulic and Pneumatic Hybrid Vehicles. Among the others, Electric (HEV) and Mechanical (HSF-HV) parallel Hybrid configurations are examined throughout this Thesis. To fully exploit the HVs potential, an optimal choice of the hybrid components to be installed must be properly designed, while an effective Supervisory Control must be adopted to coordinate the way the different power sources are managed and how they interact. Real-time controllers can be derived starting from the obtained optimal benchmark results. However, the application of these powerful instruments require a simplified and yet reliable and accurate model of the hybrid vehicle system. This can be a complex task, especially when the complexity of the system grows, i.e. a HSF-HV system assessed in this Thesis. The first task of the following dissertation is to establish the optimal modeling approach for an innovative and promising mechanical hybrid vehicle architecture. It will be shown how the chosen modeling paradigm can affect the goodness and the amount of computational effort of the solution, using an optimization technique based on Dynamic Programming. The second goal concerns the control of pollutant emissions in a parallel Diesel-HEV. The emissions level obtained under real world driving conditions is substantially higher than the usual result obtained in a homologation cycle. For this reason, an on-line control strategy capable of guaranteeing the respect of the desired emissions level, while minimizing fuel consumption and avoiding excessive battery depletion is the target of the corresponding section of the Thesis.

Clinicopathologic findings in thoroughbred horses during a high speed – short term competition

The aim of this study was to examine whether a real high speed-short term competition influences clinicopathological data focusing on muscle enzymes, iron profile and Acute Phase Proteins. 30 Thoroughbred racing horses (15 geldings and 15 females) aged between 4-12 years (mean 7 years), were used for the study. All the animals performed a high speed-short term competition for a total distance of 154 m in about 12 seconds, repeated 8 times, within approximately one hour (Niballo Horse Race). Blood samples were obtained 24 hours before and within 30 minutes after the end of the races. On all samples were performed a complete blood count (CBC), biochemical and haemostatic profiles. The post-race concentrations for the single parameter were corrected using an estimation of the plasma volume contraction according to the individual Alb concentration. Data were analysed with descriptive statistics and the percentage of variation from the baseline values were recorded. Pre- and post-race results were compared with non-parametric statistics (Mann Whitney U test). A difference was considered significant at p<0.05. A significant plasma volume contraction after the race was detected (Hct, Alb; p<0.01). Other relevant findings were increased concentrations of muscular enzymes (CK, LDH; p<0.01), Crt (p<0.01), significant increased uric acid (p<0.01), a significant decrease of haptoglobin (p<0.01) associated to an increase of ferritin concentrations (p<0.01), significant decrease of fibrinogen (p<0.05) accompanied by a non-significant increase of D-Dimers concentrations (p=0.08). This competition produced relevant abnormalities on clinical pathology in galloping horses. This study confirms a significant muscular damage, oxidative stress, intravascular haemolysis and subclinical hemostatic alterations. Further studies are needed to better understand the pathogenesis, the medical relevance and the impact on performance of these alterations in equine sport medicine.

Dynamic analysis of the motorcycle chattering behaviour by means of symbolic multibody modelling

Aim of this research is the development and validation of a comprehensive multibody motorcycle model featuring rigid-ring tires, taking into account both slope and roughness of road surfaces. A novel parametrization for the general kinematics of the motorcycle is proposed, using a mixed reference-point and relative-coordinates approach. The resulting description, developed in terms of dependent coordinates, makes it possible to efficiently include rigid-ring kinematics as well as road elevation and slope. The equations of motion for the multibody system are derived symbolically and the constraint equations arising from the dependent-coordinate formulation are handled using a projection technique. Therefore the resulting system of equations can be integrated in time domain using a standard ODE algorithm. The model is validated with respect to maneuvers experimentally measured on the race track, showing consistent results and excellent computational efficiency. More in detail, it is also capable of reproducing the chatter vibration of racing motorcycles. The chatter phenomenon, appearing during high speed cornering maneuvers, consists of a self-excited vertical oscillation of both the front and rear unsprung masses in the range of frequency between 17 and 22 Hz. A critical maneuver is numerically simulated, and a self-excited vibration appears, consistent with the experimentally measured chatter vibration. Finally, the driving mechanism for the self-excitation is highlighted and a physical interpretation is proposed.

The biological basis of autism spectrum disorders: evaluation of oxidative stress and erytrocyte membrane alterations

This case-control study involved a total of 29 autistic children (Au) aged 6 to 12 years, and 28 gender and age-matched typically developing children (TD). We evaluated a high number of peripheral oxidative stress parameters, erythrocyte and lymphocyte membrane functional features and membrane lipid composition of erythrocyte. Erythrocyte TBARS, Peroxiredoxin II, Protein Carbonyl Groups and urinary HEL and isoprostane levels were elevated in AU (confirming an imbalance of the redox status of Au); other oxidative stress markers or associated parameters (urinary 8-oxo-dG, plasma Total antioxidant capacity and plasma carbonyl groups, erythrocyte SOD and catalase activities) were unchanged, whilst peroxiredoxin I showed a trend of elevated levels in red blood cells of Au children. A very significant reduction of both erythrocyte and lymphocyte Na+, K+-ATPase activity (NKA), a reduction of erythrocyte membrane fluidity, a reduction of phospatydyl serine exposition on erythrocyte membranes, an alteration in erythrocyte fatty acid membrane profile (increase in MUFA and in ω6/ω3 ratio due to decrease in EPA and DHA) and a reduction of cholesterol content of erythrocyte membrane were found in Au compared to TD, without change in erythrocyte membrane sialic acid content and in lymphocyte membrane fluidity. Some Au clinical features appear to be correlated with these findings; in particular, hyperactivity score appears to be related with some parameters of the lipidomic profile and membrane fluidity, and ADOS and CARS score are inversely related to peroxiredoxin II levels. Oxidative stress and erythrocyte structural and functional alterations may play a role in the pathogenesis of Autism Spectrum Disorders and could be potentially utilized as peripheral biomarkers.