Characterization of mitochondrial genomes in bivalve species with doubly uniparental inheritance of mitochondria

Many bivalve species possess two distinct mtDNA lineages, called F and M, respectively inherited maternally and paternally: this system is called doubly uniparental inheritance (DUI). The main experimental project of my PhD was the quantification of the two mtDNAs during the development of the DUI species Ruditapes philippinarum, from early embryos to sub-adults, using Real-Time qPCR. I identified the time interval in which M mtDNA is lost from female individuals, while it is retained in males (which are heteroplasmic through all of their life cycle). The results also suggested absence of mtDNA replication during early embryogenesis, a process constituting a bottleneck that highly reduces the copy number of mtDNA molecules in cells of developing larvae. In males this bottleneck may produce cells homoplasmic for M mtDNA, and could be considered as a first step of the segregation of M in the male germ line. Another finding was the characterization, in young clams approaching the first reproductive season, of a significant boost in copy number of F mtDNA in females and of M in males. Given the age of animals in which this mtDNA-specific growth was observed, the finding could probably be the outcome of the first round of gonads and gametes production. Other lines of research included the characterization of the unassigned regions in mt genomes of DUI bivalves. These regions can harbor signals involved in the control of replication and/or transcription of the mtDNA molecule, as well as additional open reading frames (ORFs) not related to oxidative phosphorylation. These features in DUI species could be associated to the maintenance of separate inheritance routes for the two mtDNAs. Additional ORFs are also found in other animal mt genomes: I summarized the presence of gene duplications as a co-author in a review focusing on animal mt genomes with unusual gene content.

The rupture process of recent tsunamigenic earthquakes by geophysical data inversion

Subduction zones are the favorite places to generate tsunamigenic earthquakes, where friction between oceanic and continental plates causes the occurrence of a strong seismicity. The topics and the methodologies discussed in this thesis are focussed to the understanding of the rupture process of the seismic sources of great earthquakes that generate tsunamis. The tsunamigenesis is controlled by several kinematical characteristic of the parent earthquake, as the focal mechanism, the depth of the rupture, the slip distribution along the fault area and by the mechanical properties of the source zone. Each of these factors plays a fundamental role in the tsunami generation. Therefore, inferring the source parameters of tsunamigenic earthquakes is crucial to understand the generation of the consequent tsunami and so to mitigate the risk along the coasts. The typical way to proceed when we want to gather information regarding the source process is to have recourse to the inversion of geophysical data that are available. Tsunami data, moreover, are useful to constrain the portion of the fault area that extends offshore, generally close to the trench that, on the contrary, other kinds of data are not able to constrain. In this thesis I have discussed the rupture process of some recent tsunamigenic events, as inferred by means of an inverse method. I have presented the 2003 Tokachi-Oki (Japan) earthquake (Mw 8.1). In this study the slip distribution on the fault has been inferred by inverting tsunami waveform, GPS, and bottom-pressure data. The joint inversion of tsunami and geodetic data has revealed a much better constrain for the slip distribution on the fault rather than the separate inversions of single datasets. Then we have studied the earthquake occurred on 2007 in southern Sumatra (Mw 8.4). By inverting several tsunami waveforms, both in the near and in the far field, we have determined the slip distribution and the mean rupture velocity along the causative fault. Since the largest patch of slip was concentrated on the deepest part of the fault, this is the likely reason for the small tsunami waves that followed the earthquake, pointing out how much the depth of the rupture plays a crucial role in controlling the tsunamigenesis. Finally, we have presented a new rupture model for the great 2004 Sumatra earthquake (Mw 9.2). We have performed the joint inversion of tsunami waveform, GPS and satellite altimetry data, to infer the slip distribution, the slip direction, and the rupture velocity on the fault. Furthermore, in this work we have presented a novel method to estimate, in a self-consistent way, the average rigidity of the source zone. The estimation of the source zone rigidity is important since it may play a significant role in the tsunami generation and, particularly for slow earthquakes, a low rigidity value is sometimes necessary to explain how a relatively low seismic moment earthquake may generate significant tsunamis; this latter point may be relevant for explaining the mechanics of the tsunami earthquakes, one of the open issues in present day seismology. The investigation of these tsunamigenic earthquakes has underlined the importance to use a joint inversion of different geophysical data to determine the rupture characteristics. The results shown here have important implications for the implementation of new tsunami warning systems – particularly in the near-field – the improvement of the current ones, and furthermore for the planning of the inundation maps for tsunami-hazard assessment along the coastal area.

The role of mitochondria in the regulation of gamma rays induced mTOR-dependent senescence

The first aims of this study were to demonstrate if mitochondrial biogenesis and senescence can be induced simultaneously in cell lines upon exposure to a genotoxic stress, and if the presence of mtDNA mutations which impair the functionality of respiratory complexes can influence the ability of a cell to activate senescence. The data obtained on the oncocytic model XTC.UC1 demonstrated that the presence of mitochondrial dysfunction is involved in the maintenance of a senescent phenotype induced by γ-rays treatment. The involvement of mTORC1 in the regulation of senescence has been shown in this cell line. On the other hand, in cells which do not present mitochondrial dysfunction it has been verified that genotoxic stress determines the activation of both mitochondrial biogenesis and senescence. Further studies are necessary in order to verify if mitochondrial biogenesis sustains the activation of senescence. The second aim of this thesis was to determine the involvement of mTORC1 in the regulation of PGC-1α expression, in order to verify what is the cause of the development of oncocytoma in patients affected by two hereditary cancer syndromes; Cowden and Birt-hogg-Dubé . The study of oncocytic tumors developed by patients affected by these syndromes suggested that the double heterozigosity of the two causative genes, PTEN and FLCN respectively, induce the activation of mTORC1 and therefore the activation of PGC-1α expression. On XTC.UC1 cell line, the most suitable in vitro model, experiments of complementation of PTEN and FLCN were conducted. To date, these results demonstrated that mTORC1 is not involved in the regulation of PGC-1α expression, and PTEN and FLCN seem to have opposite effect on PGC-1α expression.

Unlocking the Potential of Women in the Rural Development Process of Republic of Srpska: The Role of Extension Service

In Bosnia Herzegovina the development of clear policy objectives and endorsement of a long-term, coherent and mutual agricultural and rural development policy have also been affected by structural problems: a lack of reliable information on population and other relevant issues, the absence of an adequate land registry system and cadastre. Moreover in BiH the agricultural and rural sectors are characterized by many factors that have typically affected transition countries such as land fragmentation, lack of agricultural mechanization and outdated production technologies, and rural aging, high unemployment and out-migration. In such a framework the condition and role of women in rural areas suffered for the lack of gender disaggregated data and a consequent poor information that lead to the exclusion of gender related questions in the agenda of public institutions and to the absence of targeted policy interventions. The aim of the research is to investigate the role and condition of women in the rural development process of Republic of Srpska and to analyze the capacity of extension services to stimulate their empowerment. Specific research questions include the status of women in the rural areas of Republic of Srpska, the role of government in fostering the empowerment of rural women, and the role of the extension service in supporting rural women. The methodology - inspired by the case study method developed by R. Yin - is designed along the three specific research questions that are used as building blocks. Each of the three research questions is investigated with a combination of methodological tools - including surveys, experts interviews and focus groups - aimed to overcome the lack of data and knowledge that characterize the research objectives.

At the intersection of Behavioural Economics, Nudging and Regulation: Rethinking the process of nudge design for regulation

Alongside the developments in behavioural economics, the concept of nudge was introduced as an intervention able to guide individual behaviour towards better choices without using coercion or incentives. While behavioural teams were created inside governmental units and regulatory authorities, nudging emerged in regulatory discourse, being increasingly regarded as a regulatory instrument that could overcome the disadvantages of other tools. This thesis analyses the viability of incorporating nudges into regulation. In particular, it investigates the implications for regulators of bringing iterative experimental testing – a widespread nudge design methodology outside regulation – into their own design practices. Nudges outside regulation are routinely designed using experiments of all kinds. This thesis intends to answer whether design premises rooted in iterative experimentation are still valid in the regulatory space, an arena that nudging entered into and that is distinct from the one where it originally emerged. The design and provision of nudges using the premises of iterative experimental testing is possible, but at a cost and burden for regulatory nudge designers. Therefore, the thesis evaluates how this burden can be reduced, in particular how nudges can be feasibly designed and provided through regulation or, put differently, how to more efficiently design and provide nudging as a regulatory tool.

Development of numerical methodologies to predict the liquid fuel sprays - wall interaction to optimize the mixing process of direct injection spark ignition engines

Nowadays the development of new Internal Combustion Engines is mainly driven by the need to reduce tailpipe emissions of pollutants, Green-House Gases and avoid the fossil fuels wasting. The design of dimension and shape of the combustion chamber together with the implementation of different injection strategies e.g., injection timing, spray targeting, higher injection pressure, play a key role in the accomplishment of the aforementioned targets. As far as the match between the fuel injection and evaporation and the combustion chamber shape is concerned, the assessment of the interaction between the liquid fuel spray and the engine walls in gasoline direct injection engines is crucial. The use of numerical simulations is an acknowledged technique to support the study of new technological solutions such as the design of new gasoline blends and of tailored injection strategies to pursue the target mixture formation. The current simulation framework lacks a well-defined best practice for the liquid fuel spray interaction simulation, which is a complex multi-physics problem. This thesis deals with the development of robust methodologies to approach the numerical simulation of the liquid fuel spray interaction with walls and lubricants. The accomplishment of this task was divided into three tasks: i) setup and validation of spray-wall impingement three-dimensional CFD spray simulations; ii) development of a one-dimensional model describing the liquid fuel – lubricant oil interaction; iii) development of a machine learning based algorithm aimed to define which mixture of known pure components mimics the physical behaviour of the real gasoline for the simulation of the liquid fuel spray interaction.

Development of quantitative methods for sustainability assessment in process industry

The increasing aversion to technological risks of the society requires the development of inherently safer and environmentally friendlier processes, besides assuring the economic competitiveness of the industrial activities. The different forms of impact (e.g. environmental, economic and societal) are frequently characterized by conflicting reduction strategies and must be holistically taken into account in order to identify the optimal solutions in process design. Though the literature reports an extensive discussion of strategies and specific principles, quantitative assessment tools are required to identify the marginal improvements in alternative design options, to allow the trade-off among contradictory aspects and to prevent the “risk shift”. In the present work a set of integrated quantitative tools for design assessment (i.e. design support system) was developed. The tools were specifically dedicated to the implementation of sustainability and inherent safety in process and plant design activities, with respect to chemical and industrial processes in which substances dangerous for humans and environment are used or stored. The tools were mainly devoted to the application in the stages of “conceptual” and “basic design”, when the project is still open to changes (due to the large number of degrees of freedom) which may comprise of strategies to improve sustainability and inherent safety. The set of developed tools includes different phases of the design activities, all through the lifecycle of a project (inventories, process flow diagrams, preliminary plant lay-out plans). The development of such tools gives a substantial contribution to fill the present gap in the availability of sound supports for implementing safety and sustainability in early phases of process design. The proposed decision support system was based on the development of a set of leading key performance indicators (KPIs), which ensure the assessment of economic, societal and environmental impacts of a process (i.e. sustainability profile). The KPIs were based on impact models (also complex), but are easy and swift in the practical application. Their full evaluation is possible also starting from the limited data available during early process design. Innovative reference criteria were developed to compare and aggregate the KPIs on the basis of the actual sitespecific impact burden and the sustainability policy. Particular attention was devoted to the development of reliable criteria and tools for the assessment of inherent safety in different stages of the project lifecycle. The assessment follows an innovative approach in the analysis of inherent safety, based on both the calculation of the expected consequences of potential accidents and the evaluation of the hazards related to equipment. The methodology overrides several problems present in the previous methods proposed for quantitative inherent safety assessment (use of arbitrary indexes, subjective judgement, build-in assumptions, etc.). A specific procedure was defined for the assessment of the hazards related to the formations of undesired substances in chemical systems undergoing “out of control” conditions. In the assessment of layout plans, “ad hoc” tools were developed to account for the hazard of domino escalations and the safety economics. The effectiveness and value of the tools were demonstrated by the application to a large number of case studies concerning different kinds of design activities (choice of materials, design of the process, of the plant, of the layout) and different types of processes/plants (chemical industry, storage facilities, waste disposal). An experimental survey (analysis of the thermal stability of isomers of nitrobenzaldehyde) provided the input data necessary to demonstrate the method for inherent safety assessment of materials.

Studies of OPA1 pathogenic mechanisms in Dominant Optic Atrophy and novel protein function in mitochondrial DNA stability

The mitochondrion is an essential cytoplasmic organelle that provides most of the energy necessary for eukaryotic cell physiology. Mitochondrial structure and functions are maintained by proteins of both mitochondrial and nuclear origin. These organelles are organized in an extended network that dynamically fuses and divides. Mitochondrial morphology results from the equilibrium between fusion and fission processes, controlled by a family of “mitochondria-shaping” proteins. It is becoming clear that defects in mitochondrial dynamics can impair mitochondrial respiration, morphology and motility, leading to apoptotic cell death in vitro and more or less severe neurodegenerative disorders in vivo in humans. Mutations in OPA1, a nuclear encoded mitochondrial protein, cause autosomal Dominant Optic Atrophy (DOA), a heterogeneous blinding disease characterized by retinal ganglion cell degeneration leading to optic neuropathy (Delettre et al., 2000; Alexander et al., 2000). OPA1 is a mitochondrial dynamin-related guanosine triphosphatase (GTPase) protein involved in mitochondrial network dynamics, cytochrome c storage and apoptosis. This protein is anchored or associated on the inner mitochondrial membrane facing the intermembrane space. Eight OPA1 isoforms resulting from alternative splicing combinations of exon 4, 4b and 5b have been described (Delettre et al., 2001). These variants greatly vary among diverse organs and the presence of specific isoforms has been associated with various mitochondrial functions. The different spliced exons encode domains included in the amino-terminal region and contribute to determine OPA1 functions (Olichon et al., 2006). It has been shown that exon 4, that is conserved throughout evolution, confers functions to OPA1 involved in maintenance of the mitochondrial membrane potential and in the fusion of the network. Conversely, exon 4b and exon 5b, which are vertebrate specific, are involved in regulation of cytochrome c release from mitochondria, and activation of apoptosis, a process restricted to vertebrates (Olichon et al., 2007). While Mgm1p has been identified thanks to its role in mtDNA maintenance, it is only recently that OPA1 has been linked to mtDNA stability. Missense mutations in OPA1 cause accumulation of multiple deletions in skeletal muscle. The syndrome associated to these mutations (DOA-1 plus) is complex, consisting of a combination of dominant optic atrophy, progressive external ophtalmoplegia, peripheral neuropathy, ataxia and deafness (Amati- Bonneau et al., 2008; Hudson et al., 2008). OPA1 is the fifth gene associated with mtDNA “breakage syndrome” together with ANT1, PolG1-2 and TYMP (Spinazzola et al., 2009). In this thesis we show for the first time that specific OPA1 isoforms associated to exon 4b are important for mtDNA stability, by anchoring the nucleoids to the inner mitochondrial membrane. Our results clearly demonstrate that OPA1 isoforms including exon 4b are intimately associated to the maintenance of the mitochondrial genome, as their silencing leads to mtDNA depletion. The mechanism leading to mtDNA loss is associated with replication inhibition in cells where exon 4b containing isoforms were down-regulated. Furthermore silencing of exon 4b associated isoforms is responsible for alteration in mtDNA-nucleoids distribution in the mitochondrial network. In this study it was evidenced that OPA1 exon 4b isoform is cleaved to provide a 10kd peptide embedded in the inner membrane by a second transmembrane domain, that seems to be crucial for mitochondrial genome maintenance and does correspond to the second transmembrane domain of the yeasts orthologue encoded by MGM1 or Msp1, which is also mandatory for this process (Diot et al., 2009; Herlan et al., 2003). Furthermore in this thesis we show that the NT-OPA1-exon 4b peptide co-immuno-precipitates with mtDNA and specifically interacts with two major components of the mitochondrial nucleoids: the polymerase gamma and Tfam. Thus, from these experiments the conclusion is that NT-OPA1- exon 4b peptide contributes to the nucleoid anchoring in the inner mitochondrial membrane, a process that is required for the initiation of mtDNA replication and for the distribution of nucleoids along the network. These data provide new crucial insights in understanding the mechanism involved in maintenance of mtDNA integrity, because they clearly demonstrate that, besides genes implicated in mtDNA replications (i.e. polymerase gamma, Tfam, twinkle and genes involved in the nucleotide pool metabolism), OPA1 and mitochondrial membrane dynamics play also an important role. Noticeably, the effect on mtDNA is different depending on the specific OPA1 isoforms down-regulated, suggesting the involvement of two different combined mechanisms. Over two hundred OPA1 mutations, spread throughout the coding region of the gene, have been described to date, including substitutions, deletions or insertions. Some mutations are predicted to generate a truncated protein inducing haploinsufficiency, whereas the missense nucleotide substitutions result in aminoacidic changes which affect conserved positions of the OPA1 protein. So far, the functional consequences of OPA1 mutations in cells from DOA patients are poorly understood. Phosphorus MR spectroscopy in patients with the c.2708delTTAG deletion revealed a defect in oxidative phosphorylation in muscles (Lodi et al., 2004). An energetic impairment has been also show in fibroblasts with the severe OPA1 R445H mutation (Amati-Bonneau et al., 2005). It has been previously reported by our group that OPA1 mutations leading to haploinsufficiency are associated in fibroblasts to an oxidative phosphorylation dysfunction, mainly involving the respiratory complex I (Zanna et al., 2008). In this study we have evaluated the energetic efficiency of a panel of skin fibroblasts derived from DOA patients, five fibroblast cell lines with OPA1 mutations causing haploinsufficiency (DOA-H) and two cell lines bearing mis-sense aminoacidic substitutions (DOA-AA), and compared with control fibroblasts. Although both types of DOA fibroblasts maintained a similar ATP content when incubated in a glucose-free medium, i.e. when forced to utilize the oxidative phosphorylation only to produce ATP, the mitochondrial ATP synthesis through complex I, measured in digitonin-permeabilized cells, was significantly reduced in cells with OPA1 haploinsufficiency only, whereas it was similar to controls in cells with the missense substitutions. Furthermore, evaluation of the mitochondrial membrane potential (DYm) in the two fibroblast lines DOA-AA and in two DOA-H fibroblasts, namely those bearing the c.2819-2A>C mutation and the c.2708delTTAG microdeletion, revealed an anomalous depolarizing response to oligomycin in DOA-H cell lines only. This finding clearly supports the hypothesis that these mutations cause a significant alteration in the respiratory chain function, which can be unmasked only when the operation of the ATP synthase is prevented. Noticeably, oligomycin-induced depolarization in these cells was almost completely prevented by preincubation with cyclosporin A, a well known inhibitor of the permeability transition pore (PTP). This results is very important because it suggests for the first time that the voltage threshold for PTP opening is altered in DOA-H fibroblasts. Although this issue has not yet been addressed in the present study, several are the mechanisms that have been proposed to lead to PTP deregulation, including in particular increased reactive oxygen species production and alteration of Ca2+ homeostasis, whose role in DOA fibroblasts PTP opening is currently under investigation. Identification of the mechanisms leading to altered threshold for PTP regulation will help our understanding of the pathophysiology of DOA, but also provide a strategy for therapeutic intervention.

Effect of hypoxia and hyperglycemia on cell bioenergetics

Mitochondria have a central role in energy supply in cells, ROS production and apoptosis and have been implicated in several human disease and mitochondrial dysfunctions in hypoxia have been related with disorders like Type II Diabetes, Alzheimer Disease, inflammation, cancer and ischemia/reperfusion in heart. When oxygen availability becomes limiting in cells, mitochondrial functions are modulated to allow biologic adaptation. Cells exposed to a reduced oxygen concentration readily respond by adaptive mechanisms to maintain the physiological ATP/ADP ratio, essential for their functions and survival. In the beginning, the AMP-activated protein kinase (AMPK) pathway is activated, but the responsiveness to prolonged hypoxia requires the stimulation of hypoxia-inducible factors (HIFs). In this work we report a study of the mitochondrial bioenergetics of primary cells exposed to a prolonged hypoxic period . To shine light on this issue we examined the bioenergetics of fibroblast mitochondria cultured in hypoxic atmospheres (1% O2) for 72 hours. Here we report on the mitochondrial organization in cells and on their contribution to the cellular energy state. Our results indicate that prolonged hypoxia cause a significant reduction of mitochondrial mass and of the quantity of the oxidative phosphorylation complexes. Hypoxia is also responsible to damage mitochondrial complexes as shown after normalization versus citrate synthase activity. HIF-1α plays a pivotal role in wound healing, and its expression in the multistage process of normal wound healing has been well characterized, it is necessary for cell motility, expression of angiogenic growth factor and recruitment of endothelial progenitor cells. We studied hypoxia in the pathological status of diabetes and complications of diabetes and we evaluated the combined effect of hyperglycemia and hypoxia on human dermal fibroblasts (HDFs) and human dermal micro-vascular endothelial cells (HDMECs) that were grown in high glucose, low glucose concentrations and mannitol as control for the osmotic challenge.

Neuroinflammation and the role of glia: relevance for neurodegenerative and neurosupportive roles

Inflammation is thought to contribute to the pathogenesis of neurodegenerative diseases. Among the resident population of cells in the brain, astroglia have been suggested to actively participate in the induction and regulation of neuroinflammation by controlling the secretion of local mediators. However, the initial cellular mechanisms by which astrocytes react to pro-inflammatory molecules are still unclear. Our study identified mitochondria as highly sensitive organelles that rapidly respond to inflammatory stimuli. Time-lapse video microscopy revealed that mitochondrial morphology, dynamics and motility are drastically altered upon inflammation, resulting in perinuclear clustering of mitochondria. These mitochondrial rearrangements are accompanied by an increased formation of reactive oxygen species and a recruitment of autophagic vacuoles. 24 to 48 hours after the acute inflammatory stimulus, however, the mitochondrial network is re-established. Strikingly, the recovery of a tubular mitochondrial network is abolished in astrocytes with a defective autophagic response, indicating that activation of autophagy is required to restore mitochondrial dynamics. By employing co-cultivation assays we observed that primary cortical neurons undergo degeneration in the presence of inflamed astrocytes. However, this effect was not observed when the primary neurons were grown in conditioned medium derived from inflamed astrocytes, suggesting that a direct contact between astrocytes and neurons mediates neuronal dysfunction upon inflammation. Our results suggest that astrocytes react to inflammatory stimuli by transiently rearranging their mitochondria, a process that involves the autophagic machinery.