Innovative microbiome-based system for the improvement of productivity, safety and sustainability of mussels farming

Northwestern Adriatic Sea Mediterranean mussels are exposed to fluctuating environmental parameters and to natural and anthropogenic stressors. Today is well known that mussels can be defined as holobiont, even if remains a lot to elucidate about how an organism and its microbial component response to environmental stress. This PhD dissertation aims to investigate microbiome possible adaptive patters exploiting the organism physiology response to stress, using the NGS sequencing method. The experimental approach consisted of two phases to first determine (i) the microbiome at a tissue scale level, (ii) the microbiome and physiological response to natural and anthropogenic stress environment and the chemical assessment of the microecosystem the Northwestern Adriatic Sea Mediterranean Mussel lives in. Results revealed firstly a robust microbiome well differentiated from seawater microecosystem, with compositional variations at the organ level. Thanks to those findings, digestive gland, the organ in which digestive and detoxification processes allow animal to tolerate and accumulate xenobiotics of natural and anthropogenic origin, was the selected tissue for the second phase of the project. The second phase of the project evaluated the putative physiological variations and the compositional changes in microbiome of digestive gland. I then manage to assess microbiome region trends across the north Adriatic, with each sampling site well differentiated from the others. Finally, a chemical method able to a powerful tool for the analytical detection of the major pollutants in mussels were validated. These first results may provide baseline information for future studies approaches of seasonal and region trends of microbiota profiles and physiological responses in terms of metabolism.

Constraint handling rules. Compositional semantics and program transformation

This thesis intends to investigate two aspects of Constraint Handling Rules (CHR). It proposes a compositional semantics and a technique for program transformation. CHR is a concurrent committed-choice constraint logic programming language consisting of guarded rules, which transform multi-sets of atomic formulas (constraints) into simpler ones until exhaustion [Frü06] and it belongs to the declarative languages family. It was initially designed for writing constraint solvers but it has recently also proven to be a general purpose language, being as it is Turing equivalent [SSD05a]. Compositionality is the first CHR aspect to be considered. A trace based compositional semantics for CHR was previously defined in [DGM05]. The reference operational semantics for such a compositional model was the original operational semantics for CHR which, due to the propagation rule, admits trivial non-termination. In this thesis we extend the work of [DGM05] by introducing a more refined trace based compositional semantics which also includes the history. The use of history is a well-known technique in CHR which permits us to trace the application of propagation rules and consequently it permits trivial non-termination avoidance [Abd97, DSGdlBH04]. Naturally, the reference operational semantics, of our new compositional one, uses history to avoid trivial non-termination too. Program transformation is the second CHR aspect to be considered, with particular regard to the unfolding technique. Said technique is an appealing approach which allows us to optimize a given program and in more detail to improve run-time efficiency or spaceconsumption. Essentially it consists of a sequence of syntactic program manipulations which preserve a kind of semantic equivalence called qualified answer [Frü98], between the original program and the transformed ones. The unfolding technique is one of the basic operations which is used by most program transformation systems. It consists in the replacement of a procedure-call by its definition. In CHR every conjunction of constraints can be considered as a procedure-call, every CHR rule can be considered as a procedure and the body of said rule represents the definition of the call. While there is a large body of literature on transformation and unfolding of sequential programs, very few papers have addressed this issue for concurrent languages. We define an unfolding rule, show its correctness and discuss some conditions in which it can be used to delete an unfolded rule while preserving the meaning of the original program. Finally, confluence and termination maintenance between the original and transformed programs are shown. This thesis is organized in the following manner. Chapter 1 gives some general notion about CHR. Section 1.1 outlines the history of programming languages with particular attention to CHR and related languages. Then, Section 1.2 introduces CHR using examples. Section 1.3 gives some preliminaries which will be used during the thesis. Subsequentely, Section 1.4 introduces the syntax and the operational and declarative semantics for the first CHR language proposed. Finally, the methodologies to solve the problem of trivial non-termination related to propagation rules are discussed in Section 1.5. Chapter 2 introduces a compositional semantics for CHR where the propagation rules are considered. In particular, Section 2.1 contains the definition of the semantics. Hence, Section 2.2 presents the compositionality results. Afterwards Section 2.3 expounds upon the correctness results. Chapter 3 presents a particular program transformation known as unfolding. This transformation needs a particular syntax called annotated which is introduced in Section 3.1 and its related modified operational semantics !0t is presented in Section 3.2. Subsequently, Section 3.3 defines the unfolding rule and prove its correctness. Then, in Section 3.4 the problems related to the replacement of a rule by its unfolded version are discussed and this in turn gives a correctness condition which holds for a specific class of rules. Section 3.5 proves that confluence and termination are preserved by the program modifications introduced. Finally, Chapter 4 concludes by discussing related works and directions for future work.

Provenienza dei sedimenti arenitici nel bacino di Tracia (eo-oligocene, Turchia nord-occidentale e Grecia nord-orientale)

The Thrace Basin is the largest and thickest Tertiary sedimentary basin of the eastern Balkans region and constitutes an important hydrocarbon province. It is located between the Rhodope-Strandja Massif to the north and west, the Marmara Sea and Biga Peninsula to the south, and the Black Sea to the est. It consists of a complex system of depocenters and uplifts with very articulate paleotopography indicated by abrupt lateral facies variations. Its southeastern margin is widely deformed by the Ganos Fault, a segment of the North Anatolian strike-slip fault system . Most of the Thrace Basin fill ranges from the Eocene to the Late Oligocene. Maximum total thickness, including the Neogene-Quaternary succession, reaches 9.000 meters in a few narrow depocenters. This sedimentary succession consists mainly of basin plain turbiditic deposits with a significant volcaniclastic component which evolves upwards to shelf deposits and continental facies, with deltaic bodies prograding towards the basin center in the Oligocene. This work deals with the provenance of Eocene-Oligocene clastic sediments of the southern and western part of Thrace Basin in Turkey and Greece. Sandstone compositional data (78 gross composition analyses and 40 heavy minerals analyses) were used to understand the change in detrital modes which reflects the provenance and geodinamic evolution of the basin. Samples were collected at six localities, which are from west to est: Gökçeada, Gallipoli and South-Ganos (south of Ganos Fault), Alexandroupolis, Korudağ and North-Ganos (north of Ganos Fault). Petrologic (framework composition and heavy-mineral analyses) and stratigraphic-sedimentologic data, (analysis of sedimentologic facies associations along representative stratigraphic sections, paleocurrents) allowed discrimination of six petrofacies; for each petrofacies the sediment dispersal system was delineated. The Thrace Basin fill is made mainly of lithic arkoses and arkosic litharenites with variable amount of low-grade metamorphic lithics (also ophiolitic), neovolcanic lithics, and carbonate grains (mainly extrabasinal). Picotite is the most widespread heavy mineral in all petrofacies. Petrological data on analyzed successions show a complex sediment dispersal pattern and evolution of the basin, indicating one principal detrital input from a source area located to the south, along both the İzmir-Ankara and Intra-Pontide suture lines, and a possible secondary source area, represented by the Rhodope Massif to the west. A significant portion of the Thrace Basin sediments in the study area were derived from ophiolitic source rocks and from their oceanic cover, whereas epimetamorphic detrital components came from a low-grade crystalline basement. An important penecontemporaneous volcanic component is widespread in late Eocene-Oligocene times, indicating widespread post-collisional (collapse?) volcanism following the closure of the Vardar ocean. Large-scale sediment mass wasting from south to north along the southern margin of the Thrace Basin is indicated (i) in late Eocene time by large olistoliths of ophiolites and penecontemporaneous carbonates, and (ii) in the mid-Oligocene by large volcaniclastic olistoliths. The late Oligocene paleogeographic scenario was characterized by large deltaic bodies prograding northward (Osmancik Formation). This clearly indicates that the southern margin of the basin acted as a major sediment source area throughout its Eocene-Oligocene history. Another major sediment source area is represented by the Rhodope Massif, in particolar the Circum-Rhodopic belt, especially for plutonic and metamorphic rocks. Considering preexisting data on the petrologic composition of Thrace Basin, silicilastic sediments in Greece and Bulgaria (Caracciolo, 2009), a Rhodopian provenance could be considered mostly for areas of the Thrace Basin outside our study area, particularly in the northern-central portions of the basin. In summary, the most important source area for the sediment of Thrace Basin in the study area was represented by the exhumed subduction-accretion complex along the southern margin of the basin (Biga Peninsula and western-central Marmara Sea region). Most measured paleocurrent indicators show an eastward paleoflow but this is most likely the result of gravity flow deflection. This is possible considered a strong control due to the east-west-trending synsedimentary transcurrent faults which cuts the Thrace Basin, generating a series of depocenters and uplifts which deeply influenced sediment dispersal and the areal distribution of paleoenvironments. The Thrace Basin was long interpreted as a forearc basin between a magmatic arc to the north and a subduction-accretion complex to the south, developed in a context of northward subduction. This interpretation was challenged by more recent data emphasizing the lack of a coeval magmatic arc in the north and the interpretation of the chaotic deposit which outcrop south of Ganos Fault as olistoliths and large submarine slumps, derived from the erosion and sedimentary reworking of an older mélange unit located to the south (not as tectonic mélange formed in an accretionary prism). The present study corroborates instead the hypothesis of a post-collisional origin of the Thrace Basin, due to a phase of orogenic collapse, which generated a series of mid-Eocene depocenters all along the İzmir-Ankara suture (following closure of the Vardar-İzmir-Ankara ocean and the ensuing collision); then the slab roll-back of the remnant Pindos ocean played an important role in enhancing subsidence and creating additional accommodation space for sediment deposition.

Exercise associated factors affecting cardiovascular health and function: from myocyte signaling to genetic variations

The exact mechanisms of the exercise induced adaptations is not lucid, but recent studies have delineated two means of signaling by which the adaptations occur (1) substrate availability signaling (metabolic stress) (2) hormone-receptor signaling. We have decided to specifically investigate two metabolic signaling enzymes [AMP-activated kinase (AMPK) and Sirtuin 1(SIRT1)] and two hormones [Adiponectin and Adrenergic stimulation].Tis based on four papers with the following conclusions: (1)Increase in SIRT1 activity and expression in H9c2 cells treated with phenylephrine is an adaptive response to the hypertrophic stress, mediated by AMPK. (2)The lack of optimal nutritional conditions (energetic substrates) due to a prolonged activation of AMPK can contrast the establishment of hypertrophy, possibly also by means of the negative modulation of ODC activity. (3) Our findings offer a possibile hypothesis as to the fact the the G allele on site 45 could lead to the increasd risk of Type II diabetes through a decrease in lean body mass. (4) Our results suggest that there is an ADIPOQ gene effect in relation to bone parameters. Statistical analysis show that the presence of the T allele in position 45 favors an increase in lumbar spine bone mineral content (BMC) when compared to subjects with a G allele substitution, which can be do the the increase in lean body mass in this genotype group.

Sea Level Variations from Decades to Millennia: A few Case Studies

The main goals of this Ph.D. study are to investigate the regional and global geophysical components related to present polar ice melting and to provide independent cross validation checks of GIA models using both geophysical data detected by satellite mission, and geological observations from far field sites, in order to determine a lower and upper bound of uncertainty of GIA effect. The subject of this Thesis is the sea level change from decades to millennia scale. Within ice2sea collaboration, we developed a Fortran numerical code to analyze the local short-term sea level change and vertical deformation resulting from the loss of ice mass. This method is used to investigate polar regions: Greenland and Antarctica. We have used mass balance based on ICESat data for Greenland ice sheet and a plausible mass balance for Antarctic ice sheet. We have determined the regional and global fingerprint of sea level variations, vertical deformations of the solid surface of the Earth and variations of shape of the geoid for each ice source mentioned above. The coastal areas are affected by the long wavelength component of GIA process. Hence understanding the response of the Earth to loading is crucial in various contexts. Based on the hypothesis that Earth mantle materials obey to a linear rheology, and that the physical parameters of this rheology can be only characterized by their depth dependence, we investigate the Glacial Isostatic Effect upon the far field sites of Mediterranean area using an improved SELEN program. We presented new and revised observations for archaeological fish tanks located along the Tyrrhenian and Adriatic coast of Italy and new RSL for the SE Tunisia. Spatial and temporal variations of the Holocene sea levels studied in central Italy and Tunisia, provided important constraints on the melting history of the major ice sheets.

Studies on the dual in Mycenaean, in the Homeric poetry and in the Attic Theatre of the 5th century — morphological, dialectal and stylistical variations

The present dissertation focuses on the dual number in Ancient Greek in a diachronical lapse stretching from the Mycenaean age to the Attic Drama and Comedy of the 5th century BC. In the first chapter morphological issues are addressed, chiefly in a comparative perspective. The Indo European evidence on the dual is hence gathered in order to sketch patterns of grammaticalisation and paradigmatisation of specific grams, growing increasingly functional within the Greek domain. In the second chapter syntactical problems are tackled. After a survey of scholarly literature on the Greek dual, we engage in a functional and typological approach, in order to disentangle some biased assessments on the dual, namely its alleged lack of regularity and intermittent agreement. Some recent frameworks in General Linguistics provide useful grounds for casting new light on the subject. Internal Reconstruction, for instance, supports the facultativity of the dual in each and every stage of its development; Typology and the Animacy Hierarcy add precious cross linguistical insight on the behaviour of the dual toward agreement. Glaring differences also arise as to the adoption — or avoidance — of the dual by different authors. Idiolectal varieties prove in fact conditioned by stylistical and register necessity. By means of a comparison among Epics, Tragedy and Comedy it is possible to enhance differences in the evaluation of the dual, which led sometimes to forms of ‘censure’ — thus triggering the onset of competing strategies to express duality. The last two chapters delve into the tantalising variety of the Homeric evidence, first of all in an account of the notorious issue of the Embassy of Iliad IX, and last in a commentary of all significant Homeric duals — mostly represented by archaisms, formulae, and ad hoc coinages.

Diversity of the proximal femur in humans: morphological variations of the head-neck junction

The proximal femur is a high-diversity region of the human skeleton, especially at the anterior junction between head and neck, where various bony morphologies have been recognized since mid nineteenth century. Classical literature on this topic is chaotic and contradictory, making almost impossible the comparison of data from different researches. Starting from an extensive bibliographic review, the first standardized method to score these traits has been created. This method allows representing both the anatomical diversity of the region already described in literature and a part of variability not considered before, giving few and univocal definitions and allowing to collect comparable data. The method has been applied to three identified and five archaeological European skeletal collections, with the aim of investigating the distribution of these features by sex, age and side, in different places and time periods. It has also been applied to 3D digital reconstructions of femurs from CT scan files of coxo-femoral joints from fresh cadavers. In addition to the osseous traits described in the standardized method, the presence and frequency of some features known as herniation pits have been scored both on bones and on CT scans. The various osseous traits of the proximal femur are present at similar frequencies in skeletal samples from different countries and different historical periods, even if with clear local differentiation. Some of the features examined show significant trends related to their distribution by gender and age. Some hypotheses are proposed about the etiology of these morphologies and their possible implication with the acquisition of bipedalism in Humans. It is therefore highlighted the possible relation of some of these traits with the development of disorders of the hip joint. Moreover, it is not recommended the use of any of these features as a specific activity-related marker.

Global and regional sea level variations in the recent past and future: insight from observations and modeling

This work is focused on the analysis of sea–level change (last century), based mainly on instrumental observations. During this period, individual components of sea–level change are investigated, both at global and regional scales. Some of the geophysical processes responsible for current sea-level change such as glacial isostatic adjustments and current melting terrestrial ice sources, have been modeled and compared with observations. A new value of global mean sea level change based of tide gauges observations has been independently assessed in 1.5 mm/year, using corrections for glacial isostatic adjustment obtained with different models as a criterion for the tide gauge selection. The long wavelength spatial variability of the main components of sea–level change has been investigated by means of traditional and new spectral methods. Complex non–linear trends and abrupt sea–level variations shown by tide gauges records have been addressed applying different approaches to regional case studies. The Ensemble Empirical Mode Decomposition technique has been used to analyse tide gauges records from the Adriatic Sea to ascertain the existence of cyclic sea-level variations. An Early Warning approach have been adopted to detect tipping points in sea–level records of North East Pacific and their relationship with oceanic modes. Global sea–level projections to year 2100 have been obtained by a semi-empirical approach based on the artificial neural network method. In addition, a model-based approach has been applied to the case of the Mediterranean Sea, obtaining sea-level projection to year 2050.