X-Ray studies of the physics of matter around super-massive black-holes in nearby Seyfert galaxies

Seyfert galaxies are the closest active galactic nuclei. As such, we can use them to test the physical properties of the entire class of objects. To investigate their general properties, I took advantage of different methods of data analysis. In particular I used three different samples of objects, that, despite frequent overlaps, have been chosen to best tackle different topics: the heterogeneous BeppoS AX sample was thought to be optimized to test the average hard X-ray (E above 10 keV) properties of nearby Seyfert galaxies; the X-CfA was thought the be optimized to compare the properties of low-luminosity sources to the ones of higher luminosity and, thus, it was also used to test the emission mechanism models; finally, the XMM–Newton sample was extracted from the X-CfA sample so as to ensure a truly unbiased and well defined sample of objects to define the average properties of Seyfert galaxies. Taking advantage of the broad-band coverage of the BeppoS AX MECS and PDS instruments (between ~2-100 keV), I infer the average X-ray spectral propertiesof nearby Seyfert galaxies and in particular the photon index (~1.8), the high-energy cut-off (~290 keV), and the relative amount of cold reflection (~1.0). Moreover the unified scheme for active galactic nuclei was positively tested. The distribution of isotropic indicators used here (photon index, relative amount of reflection, high-energy cut-off and narrow FeK energy centroid) are similar in type I and type II objects while the absorbing column and the iron line equivalent width significantly differ between the two classes of sources with type II objects displaying larger absorbing columns. Taking advantage of the XMM–Newton and X–CfA samples I also deduced from measurements that 30 to 50% of type II Seyfert galaxies are Compton thick. Confirming previous results, the narrow FeK line is consistent, in Seyfert 2 galaxies, with being produced in the same matter responsible for the observed obscuration. These results support the basic picture of the unified model. Moreover, the presence of a X-ray Baldwin effect in type I sources has been measured using for the first time the 20-100 keV luminosity (EW proportional to L(20-100)^(−0.22±0.05)). This finding suggests that the torus covering factor may be a function of source luminosity, thereby suggesting a refinement of the baseline version of the unifed model itself. Using the BeppoSAX sample, it has been also recorded a possible correlation between the photon index and the amount of cold reflection in both type I and II sources. At a first glance this confirms the thermal Comptonization as the most likely origin of the high energy emission for the active galactic nuclei. This relation, in fact, naturally emerges supposing that the accretion disk penetrates, depending to the accretion rate, the central corona at different depths (Merloni et al. 2006): the higher accreting systems hosting disks down to the last stable orbit while the lower accreting systems hosting truncated disks. On the contrary, the study of the well defined X–C f A sample of Seyfert galaxies has proved that the intrinsic X-ray luminosity of nearby Seyfert galaxies can span values between 10^(38−43) erg s^−1, i.e. covering a huge range of accretion rates. The less efficient systems have been supposed to host ADAF systems without accretion disk. However, the study of the X–CfA sample has also proved the existence of correlations between optical emission lines and X-ray luminosity in the entire range of L_(X) covered by the sample. These relations are similar to the ones obtained if high-L objects are considered. Thus the emission mechanism must be similar in luminous and weak systems. A possible scenario to reconcile these somehow opposite indications is assuming that the ADAF and the two phase mechanism co-exist with different relative importance moving from low-to-high accretion systems (as suggested by the Gamma vs. R relation). The present data require that no abrupt transition between the two regimes is present. As mentioned above, the possible presence of an accretion disk has been tested using samples of nearby Seyfert galaxies. Here, to deeply investigate the flow patterns close to super-massive black-holes, three case study objects for which enough counts statistics is available have been analysed using deep X-ray observations taken with XMM–Newton. The obtained results have shown that the accretion flow can significantly differ between the objects when it is analyzed with the appropriate detail. For instance the accretion disk is well established down to the last stable orbit in a Kerr system for IRAS 13197-1627 where strong light bending effect have been measured. The accretion disk seems to be formed spiraling in the inner ~10-30 gravitational radii in NGC 3783 where time dependent and recursive modulation have been measured both in the continuum emission and in the broad emission line component. Finally, the accretion disk seems to be only weakly detectable in rk 509, with its weak broad emission line component. Finally, blueshifted resonant absorption lines have been detected in all three objects. This seems to demonstrate that, around super-massive black-holes, there is matter which is not confined in the accretion disk and moves along the line of sight with velocities as large as v~0.01-0.4c (whre c is the speed of light). Wether this matter forms winds or blobs is still matter of debate together with the assessment of the real statistical significance of the measured absorption lines. Nonetheless, if confirmed, these phenomena are of outstanding interest because they offer new potential probes for the dynamics of the innermost regions of accretion flows, to tackle the formation of ejecta/jets and to place constraints on the rate of kinetic energy injected by AGNs into the ISM and IGM. Future high energy missions (such as the planned Simbol-X and IXO) will likely allow an exciting step forward in our understanding of the flow dynamics around black holes and the formation of the highest velocity outflows.

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.

La nutrizione-idratazione artificiale è terapia? All'interfaccia tra scienza, diritto e bioetica, il fine vita in Italia, secondo una prospettiva di comunicazione della scienza post-accademica e Science&Technologies Studies (STS)

The question “artificial nutrition and hydration (ANH) is therapy or not?” is one of the key point of end-of-life issues in Italy, since it was (and it is also nowadays) a strategic and crucial point of the Italian Bioethics discussion about the last phases of human life: determining if ANH is therapy implies the possibility of being included in the list of treatments that could be mentioned for refusal within the living will document. But who is entitled to decide and judge if ANH is a therapy or not? Scientists? The Legislator? Judges? Patients? This issue at first sight seems just a matter of science, but at stake there is more than a scientific definition. According to several scholars, we are in the era of post-academic Science, in which Science broaden discussion, production, negotation and decision to other social groups that are not just the scientific communities. In this process, called co-production, on one hand scientific knowledge derives from the interaction between scientists and society at large. On the other hand, science is functional to co-production of social order. The continuous negotation on which science has to be used in social decisions is just the evidence of the mirroring negotation for different way to structure and interpret society. Thus, in the interaction between Science and Law, deciding what kind of Science could be suitable for a specific kind of Law, envisages a well defined idea of society behind this choice. I have analysed both the legislative path (still in progress) in the living will act production in Italy and Eluana Englaro’s judicial case (that somehow collapsed in the living will act negotiation), using official documents (hearings, texts of the official conference, committees comments and ruling texts) and interviewing key actors in the two processes from the science communication point of view (who talks in the name of science? Who defines what is a therapy? And how do they do?), finding support on the theoretical framework of the Science&Technologies Studies (S&TS).

Atomic Force Microscopy Studies of the Amyloidogenic Processes of Intrinsically Unstructured Proteins related to Neurodegenerative Diseases

Protein aggregation and formation of insoluble aggregates in central nervous system is the main cause of neurodegenerative disease. Parkinson’s disease is associated with the appearance of spherical masses of aggregated proteins inside nerve cells called Lewy bodies. α-Synuclein is the main component of Lewy bodies. In addition to α-synuclein, there are more than a hundred of other proteins co-localized in Lewy bodies: 14-3-3η protein is one of them. In order to increase our understanding on the aggregation mechanism of α-synuclein and to study the effect of 14-3-3η on it, I addressed the following questions. (i) How α-synuclein monomers pack each other during aggregation? (ii) Which is the role of 14-3-3η on α-synuclein packing during its aggregation? (iii) Which is the role of 14-3-3η on an aggregation of α-synuclein “seeded” by fragments of its fibrils? In order to answer these questions, I used different biophysical techniques (e.g., Atomic force microscope (AFM), Nuclear magnetic resonance (NMR), Surface plasmon resonance (SPR) and Fluorescence spectroscopy (FS)).

The role of collective action in the provision of agri-environmental public goods: theoretical development through case studies in Italy

The thesis aims at analysing the role of collective action as a viable alternative to the traditional forms of intervention in agriculture in order to encourage the provision of agri-environmental public goods. Which are the main benefits of collective action, in terms of effectiveness and efficiency, compared to traditional market or public intervention policies? What are the drivers that encourage farmers to participate into collective action? To what extent it is possible to incorporate collective aspects into policies aimed at providing agri-environmental public goods? With the objective of addressing these research questions, the thesis is articulated in two levels: a theoretical analysis on the role of collective action in the provision of public goods and a specific investigation of two local initiative,s were an approach collective management of agro-environmental resources was successfully implemented. The first case study concerns a project named “Custodians of the Territory”, developed by the local agency in Tuscany “Comunità Montana Media Valle del Serchio”, which settled for an agreement with local farmers for a collective provision of environmental services related to the hydro-geological management of the district. The second case study is related to the territorial agri-environmental agreement experimented in Valdaso (Marche), where local farmers have adopted integrated pest management practices collectively with the aim of reducing the environmental impact of their farming practices. The analysis of these initiatives, carried out through participatory methods (Rapid Rural Appraisal), allowed developing a theoretical discussion on the role of innovative tools (such as co-production and co-management) in the provision of agri-environmental public goods. The case studies also provided some recommendations on the government intervention and policies needed to promote successful collective action for the provision of agri-environmental public goods.

Microglial involvement in brain physiopathology: in vitro studies using rat primary cultures

Microglial involvement in neurological disorders is well-established, being microglial activation not only associated with neurotoxic consequences, but also with neuroprotective effects. The studies presented here, based on microglia rat primary cell cultures and mainly on microglial conditioned medium (MCM), show insights into the mechanism of Superoxide dismutase 1 (SOD1) and Apolipoprotein E (ApoE) secretion by microglia as well as their neuroprotective effect towards primary cerebellar granule neurons (CGNs) exposed to the dopaminergic toxin 6-hydroxydopamine (6-OHDA). SOD1 and ApoE are released respectively through non-classical lysosomal or the classical ER/Golgi-mediated secretion pathway. Microglial conditioned medium, in which SOD1 and ApoE accumulated, protected CGNs from degeneration and these effects were replicated when exogenous SOD1 or ApoE was added to a non-conditioned medium. SOD1 neuroprotective action was mediated by increased cell calcium from an external source. ApoE release is negatively affected by microglia activation, both with lipopolysaccharide (LPS) and Benzoylbenzoyl-ATP (Bz-ATP) but is stimulated by neuronal-conditioned medium as well as in microglia-neurons co-culture conditions. This neuronal-stimulated microglial ApoE release is differently regulated by activation states (i.e. LPS vs ATP) and by 6-hydroxydopamine-induced neurodegeneration. In co-culture conditions, microglial ApoE release is essential for neuroprotection, since microglial ApoE silencing through siRNA abrogated protection of cerebellar granule neurons against 6-OHDA toxicity. Therefore, these molecules could represent a target for manipulation aimed at promoting neuroprotection in brain diseases. Considering a pathological context, and the microglial ability to adopt a neuroprotective or neurotoxic profile, we characterize the microglial M1/M2 phenotype in transgenic rats (McGill-R-Thy1-APP) which reproduce extensively the Alzheimer’s-like amyloid pathology. Here, for the first time, cortical, hippocampal and cerebellar microglia of wild type and transgenic adult rats were compared, at both early and advanced stages of the pathology. In view of possible therapeutic translations, these findings are relevant to test microglial neuroprotection, in animal models of neurodegenerative diseases.

Evaluation of 3D cell culture systems for host-pathogen interaction studies

Traditional cell culture models have limitations in extrapolating functional mechanisms that underlie strategies of microbial virulence. Indeed during the infection the pathogens adapt to different tissue-specific environmental factors. The development of in vitro models resembling human tissue physiology might allow the replacement of inaccurate or aberrant animal models. Three-dimensional (3D) cell culture systems are more reliable and more predictive models that can be used for the meaningful dissection of host–pathogen interactions. The lung and gut mucosae often represent the first site of exposure to pathogens and provide a physical barrier against their entry. Within this context, the tracheobronchial and small intestine tract were modelled by tissue engineering approach. The main work was focused on the development and the extensive characterization of a human organotypic airway model, based on a mechanically supported co-culture of normal primary cells. The regained morphological features, the retrieved environmental factors and the presence of specific epithelial subsets resembled the native tissue organization. In addition, the respiratory model enabled the modular insertion of interesting cell types, such as innate immune cells or multipotent stromal cells, showing a functional ability to release pertinent cytokines differentially. Furthermore this model responded imitating known events occurring during the infection by Non-typeable H. influenzae. Epithelial organoid models, mimicking the small intestine tract, were used for a different explorative analysis of tissue-toxicity. Further experiments led to detection of a cell population targeted by C. difficile Toxin A and suggested a role in the impairment of the epithelial homeostasis by the bacterial virulence machinery. The described cell-centered strategy can afford critical insights in the evaluation of the host defence and pathogenic mechanisms. The application of these two models may provide an informing step that more coherently defines relevant molecular interactions happening during the infection.