Pathogenic mechanisms in mitochondrial optic neuropathies

Leber’s hereditary optic neuropathy (LHON) and Autosomal Dominant Optic Atrophy (ADOA) are the two most common inherited optic neuropathies and both are the result of mitochondrial dysfunctions. Despite the primary mutations causing these disorders are different, being an mtDNA mutation in subunits of complex I in LHON and defects in the nuclear gene encoding the mitochondrial protein OPA1 in ADOA, both pathologies share some peculiar features, such a variable penetrance and tissue-specificity of the pathological processes. Probably, one of the most interesting and unclear aspect of LHON is the variable penetrance. This phenomenon is common in LHON families, most of them being homoplasmic mutant. Inter-family variability of penetrance may be caused by nuclear or mitochondrial ‘secondary’ genetic determinants or other predisposing triggering factors. We identified a compensatory mechanism in LHON patients, able to distinguish affected individuals from unaffected mutation carriers. In fact, carrier individuals resulted more efficient than affected subjects in increasing the mitochondrial biogenesis to compensate for the energetic defect. Thus, the activation of the mitochondrial biogenesis may be a crucial factor in modulating penetrance, determining the fate of subjects harbouring LHON mutations. Furthermore, mtDNA content can be used as a molecular biomarker which, for the first time, clearly differentiates LHON affected from LHON carrier individuals, providing a valid mechanism that may be exploited for development of therapeutic strategies. Although the mitochondrial biogenesis gained a relevant role in LHON pathogenesis, we failed to identify a genetic modifying factor for the variable penetrance in a set of candidate genes involved in the regulation of this process. A more systematic high-throughput approach will be necessary to select the genetic variants responsible for the different efficiency in activating mitochondrial biogenesis. A genetic modifying factor was instead identified in the MnSOD gene. The SNP Ala16Val in this gene seems to modulate LHON penetrance, since the Ala allele in this position significantly predisposes to be affected. Thus, we propose that high MnSOD activity in mitochondria of LHON subjects may produce an overload of H2O2 for the antioxidant machinery, leading to release from mitochondria of this radical and promoting a severe cell damage and death ADOA is due to mutation in the OPA1 gene in the large majority of cases. The causative nuclear defects in the remaining families with DOA have not been identified yet, but a small number of families have been mapped to other chromosomal loci (OPA3, OPA4, OPA5, OPA7, OPA8). Recently, a form of DOA and premature cataract (ADOAC) has been associated to pathogenic mutations of the OPA3 gene, encoding a mitochondrial protein. In the last year OPA3 has been investigated by two different groups, but a clear function for this protein and the pathogenic mechanism leading to ADOAC are still unclear. Our study on OPA3 provides new information about the pattern of expression of the two isoforms OPA3V1 and OPA3V2, and, moreover, suggests that OPA3 may have a different function in mitochondria from OPA1, the major site for ADOA mutations. In fact, based on our results, we propose that OPA3 is not involved in the mitochondrial fusion process, but, on the contrary, it may regulate mitochondrial fission. Furthermore, at difference from OPA1, we excluded a role for OPA3 in mtDNA maintenance and we failed to identify a direct interaction between OPA3 and OPA1. Considering the results from overexpression and silencing of OPA3, we can conclude that the overexpression has more drastic consequences on the cells than silencing, suggesting that OPA3 may cause optic atrophy via a gain-of-function mechanism. These data provide a new starting point for future investigations aimed at identifying the exact function of OPA3 and the pathogenic mechanism causing ADOAC.

Sistemi adesivi con applicazioni in campo biomedicale

Polymeric adhesives have been used for many applications like suture and embolization, instead of classic surgical methods or as for dental uses. In this work both subjects have been investigated and the results separated in two parts. In the first, new dentinal adhesives with different polymerizable groups (methacrylic or vinyl-ethereal) were synthesized. A low sensitivity to hydrolysis and equal or enhanced properties, compared to existing commercial products, were considered essentials. Moreover, these monomers need to polymerize by radical photopolymerization and functional groups of different characteristics were tested. All these products were characterized by microtensile bond strength test to determine the bonding strength between the adhesive and tooth. Concerning embolization, cyanoacrylates are nowadays the most-used adhesives in surgery. Thus, they must respond to several requirements. For instance, polymerization time and adhesive strength need to be low, to avoid diffusion of the products in the body and adhesion to the catheter. In order to overcome these problems we developed new cyanoacrylates, which practically instantly polymerize upon contact with blood but do not demonstrate strong adhesion to the catheter, thank to the presence of fluorine atoms, linked to the ester chain. The synthesis of these products was carried out in several steps, such as the depolymerization of the corresponding oligomers at high temperature in acid conditions. Two types of adhesion strengths were determined. Bonding strength between human veins and a microcatheter was determined in vitro by using organic materials as the most realistic model. Another test, on two layers of skin, was conducted to verify the possible use of these new cyanoacrylates as a glue for sutures. As a conclusion, we were able to demonstrate that some of the prepared monomers posses adhesive strength and polymerization time lower than the commercial product Glubran2.

New catalytic processes for the synthesis of adipic acid

The aim of my Ph.D. research was to study the new synthetic ways for the production of adipic acid. Three different pathways were studied: i) oxidation of cyclohexanone with molecular oxygen using Keggin – heteropolycompounds as the catalyst, ii) Baeyer – Villiger oxidation of cyclohexanone with hydrogen peroxide in the presence of two different heterogeneous catalysts, titanium silicalite and silica grafted decatungstate, iii) two step synthesis of adipic acid starting from cyclohexene via 1,2-cyclohexanediol. The first step was catalyzed by H2WO4 in the presence of the phase transfer catalyst, the oxidant was hydrogen peroxide. The second step, oxidation of 1,2 – cyclohexanediol was performed in the presence of oxygen and the heterogeneous catalyst – ruthenium on alumina. The results of my research showed that: i) Oxidation of cyclohexanone with molecular oxygen using Keggin heteropolycompounds is possible, anyway the conversion of ketone is low and the selectivity to adipic acid is lowered by the consecutive reaction to from lower diacids. Moreover it was found out, that there are two mechanisms involved: redox type and radicalic chain-reaction autoxidation. The presence of the different mechanism is influenced by the reaction condition. ii) It is possible to perform thermally activated oxidation of cyclohexanone and obtain non negligible amount of the products (caprolactone and adipic acid). Performing the catalyzed reaction it was demonstrated that the choice of the reaction condition and of the catalyst plays a crucial role in the product selectivity, explaining the discrepancies between the literature and our research. iii) Interesting results can be obtained performing the two step oxidation of cyclohexene via 1,2-cyclohexanediol. In the presence of phase transfer catalyst it is possible to obtain high selectivity to alcohol with stoichiometric amount of oxidant. In the second step of the synthesis, the conversion of alcohol is rather low with modest selectivity to adipic acid

Development of bionanotechnological strategies for signal enhancement in nucleic acids biosensors

Nucleic acid biosensors represent a powerful tool for clinical and environmental pathogens detection. For applications such as point-of-care biosensing, it is fundamental to develop sensors that should be automatic, inexpensive, portable and require a professional skill of the user that should be as low as possible. With the goal of determining the presence of pathogens when present in very small amount, such as for the screening of pathogens in drinking water, an amplification step must be implemented. Often this type of determinations should be performed with simple, automatic and inexpensive hardware: the use of a chemical (or nanotechnological) isothermal solution would be desirable. My Ph.D. project focused on the study and on the testing of four isothermal reactions which can be used to amplify the nucleic acid analyte before the binding event on the surface sensor or to amplify the signal after that the hybridization event with the probe. Recombinase polymerase amplification (RPA) and ligation-mediated rolling circle amplification (L-RCA) were investigated as methods for DNA and RNA amplification. Hybridization chain reaction (HCR) and Terminal deoxynucleotidil transferase-mediated amplification were investigated as strategies to achieve the enhancement of the signal after the surface hybridization event between target and probe. In conclusion, it can be said that only a small subset of the biochemical strategies that are proved to work in solution towards the amplification of nucleic acids does truly work in the context of amplifying the signal of a detection system for pathogens. Amongst those tested during my Ph.D. activity, recombinase polymerase amplification seems the best candidate for a useful implementation in diagnostic or environmental applications.

Produzione e circolazione delle anfore greco italiche in area Adriatica

The present study, being part of a wide research program carried by the University of Bologna (Dipartimento di Scienze della Terra e Geo-Ambientali and Dipartimento di Archeologia) together with the Soprintendenze of Emilia-Romagna and Veneto, is aimed at examining the manufacturing and circulation of Greek Italic amphorae in the Adriatic area. This represents an essential step for the historical and archaeological reconstructions and in particular for: - the identification of local manufacturing though the archaeometric comparisons between ceramic samples and raw materials - the reconstruction of the ancient routes connecting different areas of the Roman world The examined archaeologic sites are representative of the main manufacturing areas in the Adriatic region both along the Italian and Albanian coasts: Adria, Cattolica, Rimini, Spina , Suasa and Phoinike. Notably, the Adriatic region not only represents the manufacturing area, but also coincides with the source area where the raw materials were collected. Archaeometric analyses of representative samples from the different areas of interests, were performed adapting the analytical tecniques used in mineralogy, petrography and geochemistry, to the study of ancient archaeological finds. These data were combined with the ones obtained from the analysis of clays, aimed at characterizing the nature of the raw materials. As a whole, an integration of these data with the available archaeologic observations led to significant advances in the scientific knowledge about of the main types of amphoric manufacturing and distribution in the Adriatic region. In particular, a local manufacturing is suggested for all the archaeological finds from Cattolica and for the main part of the archaeological finds from Suasa. Moreover, the occurrence of commercial routes between the sites of Rimini and Suasa and between Adria, Spina and Suasa is evidenced. On the contrary, for the amphorae from Phoinike a provenance from the examined sites is very unlikely.

Human bone: the tissue characteristics determining its mechanical behaviour

The present thesis illustrates the research carried out during the PhD studies in Bioengineering. The research was aimed to characterise the human bone tissue, with particular regard to the differences between cortical and trabecular bone. The bone tissue characteristics that affect its mechanical properties were verified or identified, using an experimental approach, to corroborate or refute hypotheses based on the state of the art in bone tissue biomechanics. The studies presented in the present PhD thesis were designed to investigate aspects of bone tissue biomechanics, which were in need of a more in-depth examination since the data found in the literature was contradictory or scarce. In particular, the work was focalised on the characterisation of the basic structure of the bone tissue (groups of lamellae), its composition, its spatial organisation (trabecular bone microarchitecture) and their influence on the mechanical properties. In conclusion, the present thesis integrates eight different studies on the characterisation of bone tissue. A more in-depth examination of some of the aspects of bone tissue biomechanics where the data found in the literature was contradictory or scarce was performed. Bone tissue was investigated at several scales, from its composition up to its spatial organization, to determine which parameters influence the mechanical behaviour of the tissue. It was found that although the composition and real density of bone tissue are similar, the differences in structure at different levels cause differences between the two types of bone tissue (cortical and trabecular) in mechanical properties. However, the apparent density can still be considered a good predictor of the mechanical properties of both cortical and trabecular bone. Finally, it was found that the bone tissue characteristics might change when a pathology is present, as demonstrated for OA.

Roles of Ecdysone signaling in cell survival and epithelium morphogenesis during Drosophila melanogaster development

In Drosophila the steroid hormone ecdysone regulates a wide range of developmental and physiological responses, including reproduction, embryogenesis, postembryonic development and metamorphosis. Drosophila provides an excellent system to address some fundamental questions linked to hormone actions. In fact, the apparent relative simplicity of its hormone signaling pathways taken together with well-established genetic and genomic tools developed to this purpose, defines this insect as an ideal model system for studying the molecular mechanisms through which steroid hormones act. During my PhD research program I’ve analyzed the role of ecdysone signaling to gain insight into the molecular mechanisms through which the hormone fulfills its pleiotropic functions in two different developmental stages: the oogenesis and the imaginal wing disc morphogenesis. To this purpose, I performed a reverse genetic analysis to silence the function of two different genes involved in ecdysone signaling pathway, EcR and ecd.

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.

Statistical analysis and simulation techniques in wall-bounded turbulence

The present work is devoted to the assessment of the energy fluxes physics in the space of scales and physical space of wall-turbulent flows. The generalized Kolmogorov equation will be applied to DNS data of a turbulent channel flow in order to describe the energy fluxes paths from production to dissipation in the augmented space of wall-turbulent flows. This multidimensional description will be shown to be crucial to understand the formation and sustainment of the turbulent fluctuations fed by the energy fluxes coming from the near-wall production region. An unexpected behavior of the energy fluxes comes out from this analysis consisting of spiral-like paths in the combined physical/scale space where the controversial reverse energy cascade plays a central role. The observed behavior conflicts with the classical notion of the Richardson/Kolmogorov energy cascade and may have strong repercussions on both theoretical and modeling approaches to wall-turbulence. To this aim a new relation stating the leading physical processes governing the energy transfer in wall-turbulence is suggested and shown able to capture most of the rich dynamics of the shear dominated region of the flow. Two dynamical processes are identified as driving mechanisms for the fluxes, one in the near wall region and a second one further away from the wall. The former, stronger one is related to the dynamics involved in the near-wall turbulence regeneration cycle. The second suggests an outer self-sustaining mechanism which is asymptotically expected to take place in the log-layer and could explain the debated mixed inner/outer scaling of the near-wall statistics. The same approach is applied for the first time to a filtered velocity field. A generalized Kolmogorov equation specialized for filtered velocity field is derived and discussed. The results will show what effects the subgrid scales have on the resolved motion in both physical and scale space, singling out the prominent role of the filter length compared to the cross-over scale between production dominated scales and inertial range, lc, and the reverse energy cascade region lb. The systematic characterization of the resolved and subgrid physics as function of the filter scale and of the wall-distance will be shown instrumental for a correct use of LES models in the simulation of wall turbulent flows. Taking inspiration from the new relation for the energy transfer in wall turbulence, a new class of LES models will be also proposed. Finally, the generalized Kolmogorov equation specialized for filtered velocity fields will be shown to be an helpful statistical tool for the assessment of LES models and for the development of new ones. As example, some classical purely dissipative eddy viscosity models are analyzed via an a priori procedure.

I materiali ceramici trasparenti: preparazione, caratterizzazione e correlazione microstruttura-proprietà

This thesis focuses on the ceramic process for the production of optical grade transparent materials to be used as laser hosts. In order to be transparent a ceramic material must exhibit a very low concentration of defects. Defects are mainly represented by secondary or grain boundary phases and by residual pores. The strict control of the stoichiometry is mandatory to avoid the formation of secondary phases, whereas residual pores need to be below 150 ppm. In order to fulfill these requirements specific experimental conditions must be combined together. In addition powders need to be nanometric or at least sub-micrometric and extremely pure. On the other hand, nanometric powders aggregate easily and this leads to a poor, not homogeneous packing during shaping by pressing and to the formation of residual pores during sintering. Very fine powders are also difficult to handle and tend to absorb water on the surface. Finally, the powder manipulation (weighting operations, solvent removal, spray drying, shaping, etc), easily introduces impurities. All these features must be fully controlled in order to avoid the formation of defects that work as scattering sources thus decreasing the transparency of the material. The important role played by the processing on the transparency of ceramic materials is often underestimated. In the literature a high level of transparency has been reported by many authors but the description of the experimental process, in particular of the powder treatment and shaping, is seldom extensively described and important information that are necessary to reproduce the described results are often missing. The main goal of the present study therefore is to give additional information on the way the experimental features affect the microstructural evolution of YAG-based ceramics and thus the final properties, in particular transparency. Commercial powders are used to prepare YAG materials doped with Nd or Yb by reactive sintering under high vacuum. These dopants have been selected as the more appropriate for high energy and high peak power lasers. As far as it concerns the powder treatment, the thesis focuses on the influence of the solvent removal technique (rotavapor versus spray drying of suspensions in ethanol), the ball milling duration and speed, suspension concentration, solvent ratio, type and amount of dispersant. The influence of the powder type and process on the powder packing as well as the pressure conditions during shaping by pressing are also described. Finally calcination, sintering under high vacuum and in clean atmosphere, and post sintering cycles are studied and related to the final microstructure analyzed by SEM-EDS and HR-TEM, and to the optical and laser properties.

Studio del processo CVI/CVD per lo sviluppo di compositi ceramici rinforzati a fibra lunga

The most relevant thermo-mechanical properties of SiC or C based CFCCs are high strength, high toughness, low weight, high reliability, thermal shock and fatigue resistance. Thanks to these special characteristics, the CFCCs are the best candidates to substitute metals and monolithic ceramics, traditionally employed to realize components in energy, aeronautic and nuclear fields. Among the commonly techniques for the CFCCs production, CVI still represents the most significant one. Its main advantages are the versatility, the high quality deposits and the fact that it is conducted under mild temperature conditions. On the other hand, this technique is quite complex, therefore the set up of all process parameters needs long development time. The main purpose of the present study was to analyze the parameters controlling the CVD and CVI processes. Specifically, deposition and infiltration of SiC and Py-C tests were conducted on non-porous and porous substrates. The experiments were performed with a pilot size Isothermal/Isobaric CVI plant, designed and developed by ENEA. To guarantee the control of the process parameters, a previously optimization of the plant was needed. Changing temperature, pressure, flow rates and methane/hydrogen ratio, the Py-C deposition rate value, for an optimal fibre/matrix interphase thickness, was determined. It was also underlined the hydrogen inhibiting effect over the Py-C deposition rate. Regarding SiC morphologies, a difference between the inner and outer substrate surfaces was observed, as a consequence of a flow rate non-uniformity. In the case of the Cf/C composites development, the key parameter of the CVI process was the gas residence time. In fact, the hydrogen inhibiting effect was evident only with high value of residence time. Furthermore, lower the residence time more homogeneous the Py-C deposition rate was obtained along the reaction chamber axis. Finally, a CVD and CVI theoretical modelling was performed.