Mechanisms of cell senescence: p21 and DNA damage response in aging and longevity

Theory of aging postulates that aging is a remodeling process where the body of survivors progressively adapts to internal and external damaging agents they are exposed to during several decades. Thus , stress response and adaptation mechanisms play a fundamental role in the aging process where the capability of adaptating effects, certainly, also is related the lifespan of each individual. A key gene linking aging to stress response is indeed p21, an induction of cyclin-dependent kinase inhibitor which triggers cell growth arrest associated with senescence and damage response and notably is involved in the up-regulation of multiple genes that have been associated with senescence or implicated in age-related . This PhD thesis project that has been performed in collaboration with the Roninson Lab at Ordway Research Institute in Albany, NY had two main aims: -the testing the hypothesis that p21 polymorphisms are involved in longevity -Evaluating age-associated differences in gene expression and transcriptional response to p21 and DNA damage In the first project, trough PCR-sequencing and Sequenom strategies, we we found out that there are about 30 polymorphic variants in the p21 gene. In addition, we found an haplotpype located in -5kb region of the p21 promoter whose frequency is ~ 2 fold higher in centenarians than in the general population (Large-scale analysis of haplotype frequencies is currently in progress). Functional studies I carried out on the promoter highilighted that the ―centenarian‖ haplotype doesn’t affect the basal p21 promoter activity or its response to p53. However, there are many other possible physiological conditions in which the centenarian allele of the p21 promoter may potentially show a different response (IL6, IFN,progesterone, vitamin E, Vitamin D etc). In the second part, project #2, trough Microarrays we seeked to evaluate the differences in gene expression between centenarians, elderly, young in dermal fibroblast cultures and their response to p21 and DNA damage. Microarray analysis of gene expression in dermal fibroblast cultures of individuals of different ages yielded a tentative "centenarian signature". A subset of genes that were up- or downregulated in centenarians showed the same response to ectopic expression of p21, yielding a putative "p21-centenarian" signature. Trough RQ-PCR (as well Microarrays studies whose analysis is in progress) we tested the DNA damage response of the p21-centenarian signature genes showing a correlation stress/aging in additional sets of young and old samples treated with p21-inducing drug doxorubicin thus finding for a subset of of them , a response to stress age-related.

Effects of artificial defences and flooding on coastal habitats and assemblages

Since large stretches of European coasts are already retreating and projected scenarios are worsening, many artificial structures, such as breakwaters and seawalls, are built as tool against coastal erosion. However artificial structures produce widespread changes that alter the coastal zones and affect the biological communities. My doctoral thesis analyses the consequences of different options for coastal protection, namely hard engineering ‘artificial defences’ (i.e. impact of human-made structures) and ‘no-defence’ (i.e. impact of seawater inundation). I investigated two new aspects of the potential impact of coastal defences. The first was the effect of artificial hard substrates on the fish communities structure. In particular I was interested to test if the differences among breakwaters and natural rocky reef would change depending on the nature of the surrounding habitat of the artificial structure (prevalent sandy rather than rocky). The second was the effect on the native natural sandy habitats of the organic detritus derived from hard-bottom species (green algae and mussels) detached from breakwaters. Furthermore, I investigated the ecological implication of the “no-defend” option, which allow the inundation of coastal habitats. The focus of this study was the potential effect of seawater intrusion on the degradation process of marine, salt-marsh and terrestrial detritus, including changes on the breakdown rates and the associated macrofauna. The PhD research was conducted in three areas along European coasts: North Adriatic sea, Sicilian coast and South-West England where different habitats (coastal, estuarine), biological communities (soft-bottom macro-benthos; rocky-coastal fishes; estuarine macro-invertebrates) and processes (organic enrichment; assemblage structure; leaf-litter breakdown) were analyzed. The research was carried out through manipulative and descriptive field-experiments in which specific hypothesis were tested by univariate and multivariate analyses.

Data management and data analysis in the large European projects GEHA (GEnetics of Healthy Aging) and NU-AGE (NUtrition and AGEing): a bioinformatic approach

The aging process is characterized by the progressive fitness decline experienced at all the levels of physiological organization, from single molecules up to the whole organism. Studies confirmed inflammaging, a chronic low-level inflammation, as a deeply intertwined partner of the aging process, which may provide the “common soil” upon which age-related diseases develop and flourish. Thus, albeit inflammation per se represents a physiological process, it can rapidly become detrimental if it goes out of control causing an excess of local and systemic inflammatory response, a striking risk factor for the elderly population. Developing interventions to counteract the establishment of this state is thus a top priority. Diet, among other factors, represents a good candidate to regulate inflammation. Building on top of this consideration, the EU project NU-AGE is now trying to assess if a Mediterranean diet, fortified for the elderly population needs, may help in modulating inflammaging. To do so, NU-AGE enrolled a total of 1250 subjects, half of which followed a 1-year long diet, and characterized them by mean of the most advanced –omics and non –omics analyses. The aim of this thesis was the development of a solid data management pipeline able to efficiently cope with the results of these assays, which are now flowing inside a centralized database, ready to be used to test the most disparate scientific hypotheses. At the same time, the work hereby described encompasses the data analysis of the GEHA project, which was focused on identifying the genetic determinants of longevity, with a particular focus on developing and applying a method for detecting epistatic interactions in human mtDNA. Eventually, in an effort to propel the adoption of NGS technologies in everyday pipeline, we developed a NGS variant calling pipeline devoted to solve all the sequencing-related issues of the mtDNA.

The effect of cross-linker on endogenous enzymatic activity within radicular dentin and bond strength between intraradicular post and radicular dentin

The primary aim was to evaluate the effect of 1-ethyl-3-(3-dimethylamino-propyl) carbodiimide (EDC) on endogenous enzymatic activity within radicular dentin and push-out bond strength of adhesively luted fiber posts, at baseline and after artificial aging. Additionally, the effect of different cementation strategies on endogenous enzymatic activity and fiber post retention was evaluated. The experiment was carried out on extracted human teeth, following endodontic treatment and fiber post cementation. Three cementation strategies were performed: resin cement in combination with etch-and-rinse (EAR) adhesive system, with self-etch (SE) system and self-adhesive (SE) cement. Each of the mentioned strategies had a control and experimental (EDC) group in which root canal was irrigated with 0.3M EDC for 1 minute. The push-out bond strength test was performed 24h after cementation and after 40.000 thermocycles. In order to investigate the effect of EDC and different cementation strategies, in situ zymography analyses of the resin-dentin interfaces were conducted. Statistical analyses were conducted with the software Stata 12.0 (Stata Corp, College Station, Texas, USA) and the significance was set for p<0.05. The results of statistical analysis (ANOVA) showed that the variables “EDC”, “root region” and “artificial aging” significantly influenced fiber posts’ retention to root canal (p<0.05). The highest values were observed in coronal third. The mean values observed after artificial aging were lower when compared to baseline, however EDC was effective in preserving bond strength. The level of enzymatic activity varied between the groups and EDC had a beneficial effect on silencing the enzymatic activity. Within the limitations of the study, it was concluded that the choice of cementation strategy did not influence posts’ retention, while EDC contributed to the preservation of bond strength after artificial aging and reduced enzymatic activity within radicular dentin. In vivo trials are necessary to confirm the results of this in vitro study.

The Integrated European Project "GEHA - GEnetics of Healthy Aging": recruitment, health status assessment and survival of the Italian 90+ sibpairs

The present study is part of the EU Integrated Project “GEHA – Genetics of Healthy Aging” (Franceschi C et al., Ann N Y Acad Sci. 1100: 21-45, 2007), whose aim is to identify genes involved in healthy aging and longevity, which allow individuals to survive to advanced age in good cognitive and physical function and in the absence of major age-related diseases. Aims The major aims of this thesis were the following: 1. to outline the recruitment procedure of 90+ Italian siblings performed by the recruiting units of the University of Bologna (UNIBO) and Rome (ISS). The procedures related to the following items necessary to perform the study were described and commented: identification of the eligible area for recruitment, demographic aspects related to the need of getting census lists of 90+siblings, mail and phone contact with 90+ subjects and their families, bioethics aspects of the whole procedure, standardization of the recruitment methodology and set-up of a detailed flow chart to be followed by the European recruitment centres (obtainment of the informed consent form, anonimization of data by using a special code, how to perform the interview, how to collect the blood, how to enter data in the GEHA Phenotypic Data Base hosted at Odense). 2. to provide an overview of the phenotypic characteristics of 90+ Italian siblings recruited by the recruiting units of the University of Bologna (UNIBO) and Rome (ISS). The following items were addressed: socio-demographic characteristics, health status, cognitive assessment, physical conditions (handgrip strength test, chair-stand test, physical ability including ADL, vision and hearing ability, movement ability and doing light housework), life-style information (smoking and drinking habits) and subjective well-being (attitude towards life). Moreover, haematological parameters collected in the 90+ sibpairs as optional parameters by the Bologna and Rome recruiting units were used for a more comprehensive evaluation of the results obtained using the above mentioned phenotypic characteristics reported in the GEHA questionnaire. 3. to assess 90+ Italian siblings as far as their health/functional status is concerned on the basis of three classification methods proposed in previous studies on centenarians, which are based on: • actual functional capabilities (ADL, SMMSE, visual and hearing abilities) (Gondo et al., J Gerontol. 61A (3): 305-310, 2006); • actual functional capabilities and morbidity (ADL, ability to walk, SMMSE, presence of cancer, ictus, renal failure, anaemia, and liver diseases) (Franceschi et al., Aging Clin Exp Res, 12:77-84, 2000); • retrospectively collected data about past history of morbidity and age of disease onset (hypertension, heart disease, diabetes, stroke, cancer, osteopororis, neurological diseases, chronic obstructive pulmonary disease and ocular diseases) (Evert et al., J Gerontol A Biol Sci Med Sci. 58A (3): 232-237, 2003). Firstly these available models to define the health status of long-living subjects were applied to the sample and, since the classifications by Gondo and Franceschi are both based on the present functional status, they were compared in order to better recognize the healthy aging phenotype and to identify the best group of 90+ subjects out of the entire studied population. 4. to investigate the concordance of health and functional status among 90+ siblings in order to divide sibpairs in three categories: the best (both sibs are in good shape), the worst (both sibs are in bad shape) and an intermediate group (one sib is in good shape and the other is in bad shape). Moreover, the evaluation wanted to discover which variables are concordant among siblings; thus, concordant variables could be considered as familiar variables (determined by the environment or by genetics). 5. to perform a survival analysis by using mortality data at 1st January 2009 from the follow-up as the main outcome and selected functional and clinical parameters as explanatory variables. Methods A total of 765 90+ Italian subjects recruited by UNIBO (549 90+ siblings, belonging to 258 families) and ISS (216 90+ siblings, belonging to 106 families) recruiting units are included in the analysis. Each subject was interviewed according to a standardized questionnaire, comprising extensively utilized questions that have been validated in previous European studies on elderly subjects and covering demographic information, life style, living conditions, cognitive status (SMMSE), mood, health status and anthropometric measurements. Moreover, subjects were asked to perform some physical tests (Hand Grip Strength test and Chair Standing test) and a sample of about 24 mL of blood was collected and then processed according to a common protocol for the preparation and storage of DNA aliquots. Results From the analysis the main findings are the following: - a standardized protocol to assess cognitive status, physical performances and health status of European nonagenarian subjects was set up, in respect to ethical requirements, and it is available as a reference for other studies in this field; - GEHA families are enriched in long-living members and extreme survival, and represent an appropriate model for the identification of genes involved in healthy aging and longevity; - two simplified sets of criteria to classify 90+ sibling according to their health status were proposed, as operational tools for distinguishing healthy from non healthy subjects; - cognitive and functional parameters have a major role in categorizing 90+ siblings for the health status; - parameters such as education and good physical abilities (500 metres walking ability, going up and down the stairs ability, high scores at hand grip and chair stand tests) are associated with a good health status (defined as “cognitive unimpairment and absence of disability”); - male nonagenarians show a more homogeneous phenotype than females, and, though far fewer in number, tend to be healthier than females; - in males the good health status is not protective for survival, confirming the male-female health survival paradox; - survival after age 90 was dependent mainly on intact cognitive status and absence of functional disabilities; - haemoglobin and creatinine levels are both associated with longevity; - the most concordant items among 90+ siblings are related to the functional status, indicating that they contain a familiar component. It is still to be investigated at what level this familiar component is determined by genetics or by environment or by the interaction between genetics, environment and chance (and at what level). Conclusions In conclusion, we could state that this study, in accordance with the main objectives of the whole GEHA project, represents one of the first attempt to identify the biological and non biological determinants of successful/unsuccessful aging and longevity. Here, the analysis was performed on 90+ siblings recruited in Northern and Central Italy and it could be used as a reference for others studies in this field on Italian population. Moreover, it contributed to the definition of “successful” and “unsuccessful” aging and categorising a very large cohort of our most elderly subjects into “successful” and “unsuccessful” groups provided an unrivalled opportunity to detect some of the basic genetic/molecular mechanisms which underpin good health as opposed to chronic disability. Discoveries in the topic of the biological determinants of healthy aging represent a real possibility to identify new markers to be utilized for the identification of subgroups of old European citizens having a higher risk to develop age-related diseases and disabilities and to direct major preventive medicine strategies for the new epidemic of chronic disease in the 21st century.

Polymeric membranes for CO2 separation: effect of aging, humidity and facilitated transport

Polymeric membranes represent a promising technology for gas separation processes, thanks to low costs, reduced energy consumption and limited waste production. The present thesis aims at studying the transport properties of two membrane materials, suitable for CO2 purification applications. In the first part, a polyimide, Matrimid 5218, has been throughout investigated, with particular reference to the effect of thermal treatment, aging and the presence of water vapor in the gas transport process. Permeability measurements showed that thermal history affects relevantly the diffusion of gas molecules across the membrane, influencing also the stability of the separation performances. Subsequently, the effect of water on Matrimid transport properties has been characterized for a wide set of incondensable penetrants. A monotonous reduction of permeability took place at increasing the water concentration within the polymer matrix, affecting the investigated gaseous species to the same extent, despite the different thermodynamic and kinetic features. In this view, a novel empirical model, based on the Free Volume Theory, has been proposed to qualitatively describe the phenomenon. Moreover, according to the accurate representation of the experimental data, the suggested approach has been combined with a more rigorous thermodynamic tool (NELF Model), allowing an exhaustive description of water influence on the single parameters contributing to the gas permeation across the membrane. In the second part, the study has focused on the synthesis and characterization of facilitated transport membranes, able to achieving outstanding separation performances thanks to the chemical enhancement of CO2 permeability. In particular, the transport properties have been investigated for high pressure CO2 separation applications and specific solutions have been proposed to solve stability issues, frequently arising under such severe conditions. Finally, the effect of different process parameters have been investigated, aiming at the identification of the optimal conditions capable to maximize the separation performance.

Mitochondrial DNA rearrangements during human aging: a study on liver, muscle and adipose tissue

Aging is characterized by a chronic, low-grade inflammatory state called “inflammaging”. Mitochondria are the main source of reactive oxygen species (ROS), which trigger the production of pro-inflammatory molecules. We are interested in studying the age-related modifications of the mitochondrial DNA (mtDNA), which can be affected by the lifelong exposure to ROS and are responsible of mitochondrial dysfunction. Moreover, increasing evidences show that telomere shortening, naturally occurring with aging, is involved in mtDNA damage processes and thus in the pathogenesis of age-related disorders. Thus the primary aim of this thesis was the analysis of mtDNA copy number, deletion level and integrity in different-age human biopsies from liver, vastus lateralis skeletal muscle of healthy subjects and patients with limited mobility of lower limbs (LMLL), as well as adipose tissue. The telomere length and the expression of nuclear genes related to mitobiogenesis, fusion and fission, mitophagy, mitochondrial protein quality control system, hypoxia, production and protection from ROS were also evaluated. In liver the decrease in mtDNA integrity with age is accompanied with an increase in mtDNA copy number, suggesting the existence of a “compensatory mechanism” able to maintain the functionality of this organ. Different is the case of vastus lateralis muscle, where any “compensatory pathway” is activated and mtDNA integrity and copy number decrease with age, both in healthy subjects and in patients. Interestingly, mtDNA rearrangements do not incur in adipose tissue with advancing age. Finally, in all tissues a marked gender difference appears, suggesting that aging and also gender diversely affect mtDNA rearrangements and telomere length in the three human tissues considered, likely depending on their different metabolic needs and inflammatory status.

Structural changes and dynamic behaviour of vanadium oxide-based catalysts for gas-phase selective oxidations

Selective oxidation is one of the simplest functionalization methods and essentially all monomers used in manufacturing artificial fibers and plastics are obtained by catalytic oxidation processes. Formally, oxidation is considered as an increase in the oxidation number of the carbon atoms, then reactions such as dehydrogenation, ammoxidation, cyclization or chlorination are all oxidation reactions. In this field, most of processes for the synthesis of important chemicals used vanadium oxide-based catalysts. These catalytic systems are used either in the form of multicomponent mixed oxides and oxysalts, e.g., in the oxidation of n-butane (V/P/O) and of benzene (supported V/Mo/O) to maleic anhydride, or in the form of supported metal oxide, e.g., in the manufacture of phthalic anhydride by o-xylene oxidation, of sulphuric acid by oxidation of SO2, in the reduction of NOx with ammonia and in the ammoxidation of alkyl aromatics. In addition, supported vanadia catalysts have also been investigated for the oxidative dehydrogenation of alkanes to olefins , oxidation of pentane to maleic anhydride and the selective oxidation of methanol to formaldehyde or methyl formate [1]. During my PhD I focused my work on two gas phase selective oxidation reactions. The work was done at the Department of Industrial Chemistry and Materials (University of Bologna) in collaboration with Polynt SpA. Polynt is a leader company in the development, production and marketing of catalysts for gas-phase oxidation. In particular, I studied the catalytic system for n-butane oxidation to maleic anhydride (fluid bed technology) and for o-xylene oxidation to phthalic anhydride. Both reactions are catalyzed by systems based on vanadium, but catalysts are completely different. Part A is dedicated to the study of V/P/O catalyst for n-butane selective oxidation, while in the Part B the results of an investigation on TiO2-supported V2O5, catalyst for o-xylene oxidation are showed. In Part A, a general introduction about the importance of maleic anhydride, its uses, the industrial processes and the catalytic system are reported. The reaction is the only industrial direct oxidation of paraffins to a chemical intermediate. It is produced by n-butane oxidation either using fixed bed and fluid bed technology; in both cases the catalyst is the vanadyl pyrophosphate (VPP). Notwithstanding the good performances, the yield value didn’t exceed 60% and the system is continuously studied to improve activity and selectivity. The main open problem is the understanding of the real active phase working under reaction conditions. Several articles deal with the role of different crystalline and/or amorphous vanadium/phosphorous (VPO) compounds. In all cases, bulk VPP is assumed to constitute the core of the active phase, while two different hypotheses have been formulated concerning the catalytic surface. In one case the development of surface amorphous layers that play a direct role in the reaction is described, in the second case specific planes of crystalline VPP are assumed to contribute to the reaction pattern, and the redox process occurs reversibly between VPP and VOPO4. Both hypotheses are supported also by in-situ characterization techniques, but the experiments were performed with different catalysts and probably under slightly different working conditions. Due to complexity of the system, these differences could be the cause of the contradictions present in literature. Supposing that a key role could be played by P/V ratio, I prepared, characterized and tested two samples with different P/V ratio. Transformation occurring on catalytic surfaces under different conditions of temperature and gas-phase composition were studied by means of in-situ Raman spectroscopy, trying to investigate the changes that VPP undergoes during reaction. The goal is to understand which kind of compound constituting the catalyst surface is the most active and selective for butane oxidation reaction, and also which features the catalyst should possess to ensure the development of this surface (e.g. catalyst composition). On the basis of results from this study, it could be possible to project a new catalyst more active and selective with respect to the present ones. In fact, the second topic investigated is the possibility to reproduce the surface active layer of VPP onto a support. In general, supportation is a way to improve mechanical features of the catalysts and to overcome problems such as possible development of local hot spot temperatures, which could cause a decrease of selectivity at high conversion, and high costs of catalyst. In literature it is possible to find different works dealing with the development of supported catalysts, but in general intrinsic characteristics of VPP are worsened due to the chemical interaction between active phase and support. Moreover all these works deal with the supportation of VPP; on the contrary, my work is an attempt to build-up a V/P/O active layer on the surface of a zirconia support by thermal treatment of a precursor obtained by impregnation of a V5+ salt and of H3PO4. In-situ Raman analysis during the thermal treatment, as well as reactivity tests are used to investigate the parameters that may influence the generation of the active phase. Part B is devoted to the study of o-xylene oxidation of phthalic anhydride; industrially, the reaction is carried out in gas-phase using as catalysts a supported system formed by V2O5 on TiO2. The V/Ti/O system is quite complex; different vanadium species could be present on the titania surface, as a function of the vanadium content and of the titania surface area: (i) V species which is chemically bound to the support via oxo bridges (isolated V in octahedral or tetrahedral coordination, depending on the hydration degree), (ii) a polymeric species spread over titania, and (iii) bulk vanadium oxide, either amorphous or crystalline. The different species could have different catalytic properties therefore changing the relative amount of V species can be a way to optimize the catalytic performances of the system. For this reason, samples containing increasing amount of vanadium were prepared and tested in the oxidation of o-xylene, with the aim of find a correlations between V/Ti/O catalytic activity and the amount of the different vanadium species. The second part deals with the role of a gas-phase promoter. Catalytic surface can change under working conditions; the high temperatures and a different gas-phase composition could have an effect also on the formation of different V species. Furthermore, in the industrial practice, the vanadium oxide-based catalysts need the addition of gas-phase promoters in the feed stream, that although do not have a direct role in the reaction stoichiometry, when present leads to considerable improvement of catalytic performance. Starting point of my investigation is the possibility that steam, a component always present in oxidation reactions environment, could cause changes in the nature of catalytic surface under reaction conditions. For this reason, the dynamic phenomena occurring at the surface of a 7wt% V2O5 on TiO2 catalyst in the presence of steam is investigated by means of Raman spectroscopy. Moreover a correlation between the amount of the different vanadium species and catalytic performances have been searched. Finally, the role of dopants has been studied. The industrial V/Ti/O system contains several dopants; the nature and the relative amount of promoters may vary depending on catalyst supplier and on the technology employed for the process, either a single-bed or a multi-layer catalytic fixed-bed. Promoters have a quite remarkable effect on both activity and selectivity to phthalic anhydride. Their role is crucial, and the proper control of the relative amount of each component is fundamental for the process performance. Furthermore, it can not be excluded that the same promoter may play different role depending on reaction conditions (T, composition of gas phase..). The reaction network of phthalic anhydride formation is very complex and includes several parallel and consecutive reactions; for this reason a proper understanding of the role of each dopant cannot be separated from the analysis of the reaction scheme. One of the most important promoters at industrial level, which is always present in the catalytic formulations is Cs. It is known that Cs plays an important role on selectivity to phthalic anhydride, but the reasons of this phenomenon are not really clear. Therefore the effect of Cs on the reaction scheme has been investigated at two different temperature with the aim of evidencing in which step of the reaction network this promoter plays its role.

Biomolecular studies in Alzheimer’s Disease models: investigations in vitro and in vivo

The Alzheimer’s disease (AD), the most prevalent form of age-related dementia, is a multifactorial and heterogeneous neurodegenerative disease. The molecular mechanisms underlying the pathogenesis of AD are yet largely unknown. However, the etiopathogenesis of AD likely resides in the interaction between genetic and environmental risk factors. Among the different factors that contribute to the pathogenesis of AD, amyloid-beta peptides and the genetic risk factor apoE4 are prominent on the basis of genetic evidence and experimental data. ApoE4 transgenic mice have deficits in spatial learning and memory associated with inflammation and brain atrophy. Evidences suggest that apoE4 is implicated in amyloid-beta accumulation, imbalance of cellular antioxidant system and in apoptotic phenomena. The mechanisms by which apoE4 interacts with other AD risk factors leading to an increased susceptibility to the dementia are still unknown. The aim of this research was to provide new insights into molecular mechanisms of AD neurodegeneration, investigating the effect of amyloid-beta peptides and apoE4 genotype on the modulation of genes and proteins differently involved in cellular processes related to aging and oxidative balance such as PIN1, SIRT1, PSEN1, BDNF, TRX1 and GRX1. In particular, we used human neuroblastoma cells exposed to amyloid-beta or apoE3 and apoE4 proteins at different time-points, and selected brain regions of human apoE3 and apoE4 targeted replacement mice, as in vitro and in vivo models, respectively. All genes and proteins studied in the present investigation are modulated by amyloid-beta and apoE4 in different ways, suggesting their involvement in the neurodegenerative mechanisms underlying the AD. Finally, these proteins might represent novel potential diagnostic and therapeutic targets in AD.

Engineering Agent-Oriented Technologies and Programming Languages for Computer Programming and Software Development

Mainstream hardware is becoming parallel, heterogeneous, and distributed on every desk, every home and in every pocket. As a consequence, in the last years software is having an epochal turn toward concurrency, distribution, interaction which is pushed by the evolution of hardware architectures and the growing of network availability. This calls for introducing further abstraction layers on top of those provided by classical mainstream programming paradigms, to tackle more effectively the new complexities that developers have to face in everyday programming. A convergence it is recognizable in the mainstream toward the adoption of the actor paradigm as a mean to unite object-oriented programming and concurrency. Nevertheless, we argue that the actor paradigm can only be considered a good starting point to provide a more comprehensive response to such a fundamental and radical change in software development. Accordingly, the main objective of this thesis is to propose Agent-Oriented Programming (AOP) as a high-level general purpose programming paradigm, natural evolution of actors and objects, introducing a further level of human-inspired concepts for programming software systems, meant to simplify the design and programming of concurrent, distributed, reactive/interactive programs. To this end, in the dissertation first we construct the required background by studying the state-of-the-art of both actor-oriented and agent-oriented programming, and then we focus on the engineering of integrated programming technologies for developing agent-based systems in their classical application domains: artificial intelligence and distributed artificial intelligence. Then, we shift the perspective moving from the development of intelligent software systems, toward general purpose software development. Using the expertise maturated during the phase of background construction, we introduce a general-purpose programming language named simpAL, which founds its roots on general principles and practices of software development, and at the same time provides an agent-oriented level of abstraction for the engineering of general purpose software systems.

Analysis and development of ecologically based approaches to coastal defense

Climate-change related impacts, notably coastal erosion, inundation and flooding from sea level rise and storms, will increase in the coming decades enhancing the risks for coastal populations. Further recourse to coastal armoring and other engineered defenses to address risk reduction will exacerbate threats to coastal ecosystems. Alternatively, protection services provided by healthy ecosystems is emerging as a key element in climate adaptation and disaster risk management. I examined two distinct approaches to coastal defense on the base of their ecological and ecosystem conservation values. First, I analyzed the role of coastal ecosystems in providing services for hazard risk reduction. The value in wave attenuation of coral reefs was quantitatively demonstrated using a meta-analysis approach. Results indicate that coral reefs can provide wave attenuation comparable to hard engineering artificial defenses and at lower costs. Conservation and restoration of existing coral reefs are cost-effective management options for disaster risk reduction. Second, I evaluated the possibility to enhance the ecological value of artificial coastal defense structures (CDS) as habitats for marine communities. I documented the suitability of CDS to support native, ecologically relevant, habitat-forming canopy algae exploring the feasibility of enhancing CDS ecological value by promoting the growth of desired species. Juveniles of Cystoseira barbata can be successfully transplanted at both natural and artificial habitats and not affected by lack of surrounding adult algal individuals nor by substratum orientation. Transplantation success was limited by biotic disturbance from macrograzers on CDS compared to natural habitats. Future work should explore the reasons behind the different ecological functioning of artificial and natural habitats unraveling the factors and mechanisms that cause it. The comprehension of the functioning of systems associated with artificial habitats is the key to allow environmental managers to identify proper mitigation options and to forecast the impact of alternative coastal development plans.

Master Equation: Biological Applications and Thermodynamic Description

It is well known that many realistic mathematical models of biological systems, such as cell growth, cellular development and differentiation, gene expression, gene regulatory networks, enzyme cascades, synaptic plasticity, aging and population growth need to include stochasticity. These systems are not isolated, but rather subject to intrinsic and extrinsic fluctuations, which leads to a quasi equilibrium state (homeostasis). The natural framework is provided by Markov processes and the Master equation (ME) describes the temporal evolution of the probability of each state, specified by the number of units of each species. The ME is a relevant tool for modeling realistic biological systems and allow also to explore the behavior of open systems. These systems may exhibit not only the classical thermodynamic equilibrium states but also the nonequilibrium steady states (NESS). This thesis deals with biological problems that can be treat with the Master equation and also with its thermodynamic consequences. It is organized into six chapters with four new scientific works, which are grouped in two parts: (1) Biological applications of the Master equation: deals with the stochastic properties of a toggle switch, involving a protein compound and a miRNA cluster, known to control the eukaryotic cell cycle and possibly involved in oncogenesis and with the propose of a one parameter family of master equations for the evolution of a population having the logistic equation as mean field limit. (2) Nonequilibrium thermodynamics in terms of the Master equation: where we study the dynamical role of chemical fluxes that characterize the NESS of a chemical network and we propose a one parameter parametrization of BCM learning, that was originally proposed to describe plasticity processes, to study the differences between systems in DB and NESS.

Conservation genetics of European wildcat (Felis silvestris silvestris): a wide and integrating analysis protocol for admixture inferences and population structure

Introgression of domestic cat genes into European wildcat (Felis silvestris silvestris) populations and reduction of wildcats’ range in Europe, leaded by habitat loss and fragmentation, are considered two of the main conservation problems for this endangered feline. This thesis addressed the questions related with the artificial hybridization and populations’ fragmentation, using a conservation genetics perspective. We combined the use of highly polymorphic loci, Bayesian statistical inferences and landscape analyses tools to investigate the origin of the geographic-genetic substructure of European wildcats (Felis silvestris silvestris) in Italy and Europe. The genetic variability of microsatellites evidenced that European wildcat populations currently distributed in Italy differentiated in, and expanded from two distinct glacial refuges during the Last Glacial Maximum. The genetic and geographic substructure detected between the eastern and western sides of the Apennine ridge, resulted by adaptation to specific ecological conditions of the Mediterranean habitats. European wildcat populations in Europe are strongly structured into 5 geographic-genetic macro clusters corresponding to: the Italian peninsular & Sicily; Balkans & north-eastern Italy; Germany eastern; central Europe; and Iberian Peninsula. Central European population might have differentiated in the extra-Mediterranean Würm ice age refuge areas (Northern Alps, Carpathians, and the Bulgarian mountain systems), while the divergence among and within the southern European populations might have resulted by the Pleistocene bio geographical framework of Europe, with three southern refugia localized in the Balkans, Italian Peninsula and Iberia Peninsula. We further combined the use of most informative autosomal SNPs with uniparental markers (mtDNA and Y-linked) for accurately detecting parental genotypes and levels of introgressive hybridization between European wild and domestic cats. A total of 11 hybrids were identified. The presence of domestic mitochondrial haplotypes shared with some wild individuals led us to hypnotize the possibility that ancient introgressive events might have occurred and that further investigation should be recommended.

Epigenetics of nutrition in aging

There is a need to identify factors that are able to influence health in old age and to develop interventions that could slow down the process of aging and its associated pathologies. Lifestyle modifications, and especially nutrition, appear to be promising strategies to promote healthy aging. Their impact on aging biomarkers has been poorly investigated. In the first part of this work, we evaluated the impact of a one-year Mediterranean-like diet, delivered within the framework of the NU-AGE project in 120 elderly subjects, on epigenetic age acceleration measures assessed with Horvath’s clock. We observed a rejuvenation of participants after nutritional intervention. The effect was more marked in the group of Polish females and in subjects who were epigenetically older at baseline. In the second part of this work, we developed a new model of epigenetic biomarker, based on a gene-targeted approach with the EpiTYPER® system. We selected six regions of interest (associated with ELOVL2, NHLRC1, SIRT7/MAFG, AIM2, EDARADD and TFAP2E genes) and constructed our model through a ridge regression analysis. In controls, estimation of chronological age was accurate, with a correlation coefficient between predicted and chronological age of 0.92 and a mean absolute deviation of 4.70 years. Our model was able to capture phenomena of accelerated or decelerated aging, in Down syndrome subjects and centenarians and offspring respectively. Applying our model to samples of the NU-AGE project, we observed similar results to the ones obtained with the canonical epigenetic clock, with a rejuvenation of the individuals after one-year of nutritional intervention. Together, our findings indicate that nutrition can promote epigenetic rejuvenation and that epigenetic age acceleration measures could be suitable biomarkers to evaluate their impact. We demonstrated that the effect of the dietary intervention is country-, sex- and individual-specific, thus suggesting the need for a personalized approach to nutritional interventions.

Biomimetic surfaces for greener coastal infrastructures: an analysis of factors that contribute to make artificial structures more “natural”

The growing ecological awareness of Ocean Sprawl impacts is promoting the adoption of eco-engineering strategies to enhance the ecological performance of coastal infrastructures. Biomimicry, as an eco-engineering tool, aims to design infrastructure more suitable for wildlife by manipulating structural factors to mimic natural habitats. However, little is known about the extent to which natural and artificial substrates differ in their structure and to what extent such differences affect the biota. To fill these knowledge gaps and consequently design biomimetic surfaces, I initially explored how much physical structure diverges between various types of natural and artificial substrates and tested to what extent differences in physical structure and material composition affect the epibenthic communities. By mean of an in-field mensurative experiment and a systematic review coupled with a meta-analysis, I found that, although communities tended to differ between natural and artificial coastal habitats, both physical structure and material composition reported an overall mild effect on epibenthic communities. However, an informed choice of building material and an appropriate combination of multiple structural manipulations can promote ecological benefits at multiple levels, from increasing the ecological performance in situ to reducing the impacts during the production process. Thus, I combined my findings in a final experiment, still in progress, where I am testing the combined role of shape, brightness and inclination of biomimetic surfaces I have designed in producing benefits at multiple levels. Overall, I suggest that biomimicry has the potential to increase the ecological value of artificial habitats especially when a wide range of aspects is simultaneously considered. Indeed, none of the structural factors, individually, can fully mimic the “natural conditions” to effectively improve the ecological performance of the artificial substrates. This emphasizes the need to include in future works a multi-level perspective to fully achieve the great potential of biomimicry.