Biosynthesis of vitamins and cofactors in bacterium-harbouring trypanosomatids depends on the symbiotic association as revealed by genomic analyses

Some non-pathogenic trypanosomatids maintain a mutualistic relationship with a betaproteobacterium of the Alcaligenaceae family. Intensive nutritional exchanges have been reported between the two partners, indicating that these protozoa are excellent biological models to study metabolic co-evolution. We previously sequenced and herein investigate the entire genomes of five trypanosomatids which harbor a symbiotic bacterium (SHTs for Symbiont-Haboring Trypanosomatids) and the respective bacteria (TPEs for Trypanosomatid Proteobacterial Endosymbiont), as well as two trypanosomatids without symbionts (RTs for Regular Trypanosomatids), for the presence of genes of the classical pathways for vitamin biosynthesis. Our data show that genes for the biosynthetic pathways of thiamine, biotin, and nicotinic acid are absent from all trypanosomatid genomes. This is in agreement with the absolute growth requirement for these vitamins in all protozoa of the family. Also absent from the genomes of RTs are the genes for the synthesis of pantothenic acid, folic acid, riboflavin, and vitamin B6. This is also in agreement with the available data showing that RTs are auxotrophic for these essential vitamins. On the other hand, SHTs are autotrophic for such vitamins. Indeed, all the genes of the corresponding biosynthetic pathways were identified, most of them in the symbiont genomes, while a few genes, mostly of eukaryotic origin, were found in the host genomes. The only exceptions to the latter are: the gene coding for the enzyme ketopantoate reductase (EC:1.1.1.169) which is related instead to the Firmicutes bacteria; and two other genes, one involved in the salvage pathway of pantothenic acid and the other in the synthesis of ubiquinone, that are related to Gammaproteobacteria. Their presence in trypanosomatids may result from lateral gene transfer. Taken together, our results reinforce the idea that the low nutritional requirement of SHTs is associated with the presence of the symbiotic bacterium, which contains most genes for vitamin production.

Ontology for Data Representation in the Production of Cotton Fiber in Brazil

An important feature in computer systems developed for the agricultural sector is to satisfy the heterogeneity of data generated in different processes. Most problems related with this heterogeneity arise from the lack of standard for different computing solutions proposed. An efficient solution for that is to create a single standard for data exchange. The study on the actual process involved in cotton production was based on a research developed by the Brazilian Agricultural Research Corporation (EMBRAPA) that reports all phases as a result of the compilation of several theoretical and practical researches related to cotton crop. The proposition of a standard starts with the identification of the most important classes of data involved in the process, and includes an ontology that is the systematization of concepts related to the production of cotton fiber and results in a set of classes, relations, functions and instances. The results are used as a reference for the development of computational tools, transforming implicit knowledge into applications that support the knowledge described. This research is based on data from the Midwest of Brazil. The choice of the cotton process as a study case comes from the fact that Brazil is one of the major players and there are several improvements required for system integration in this segment.

Essays on the political economy of European integration

Recently, a rising interest in political and economic integration/disintegration issues has been developed in the political economy field. This growing strand of literature partly draws on traditional issues of fiscal federalism and optimum public good provision and focuses on a trade-off between the benefits of centralization, arising from economies of scale or externalities, and the costs of harmonizing policies as a consequence of the increased heterogeneity of individual preferences in an international union or in a country composed of at least two regions. This thesis stems from this strand of literature and aims to shed some light on two highly relevant aspects of the political economy of European integration. The first concerns the role of public opinion in the integration process; more precisely, how economic benefits and costs of integration shape citizens' support for European Union (EU) membership. The second is the allocation of policy competences among different levels of government: European, national and regional. Chapter 1 introduces the topics developed in this thesis by reviewing the main recent theoretical developments in the political economy analysis of integration processes. It is structured as follows. First, it briefly surveys a few relevant articles on economic theories of integration and disintegration processes (Alesina and Spolaore 1997, Bolton and Roland 1997, Alesina et al. 2000, Casella and Feinstein 2002) and discusses their relevance for the study of the impact of economic benefits and costs on public opinion attitude towards the EU. Subsequently, it explores the links existing between such political economy literature and theories of fiscal federalism, especially with regard to normative considerations concerning the optimal allocation of competences in a union. Chapter 2 firstly proposes a model of citizens’ support for membership of international unions, with explicit reference to the EU; subsequently it tests the model on a panel of EU countries. What are the factors that influence public opinion support for the European Union (EU)? In international relations theory, the idea that citizens' support for the EU depends on material benefits deriving from integration, i.e. whether European integration makes individuals economically better off (utilitarian support), has been common since the 1970s, but has never been the subject of a formal treatment (Hix 2005). A small number of studies in the 1990s have investigated econometrically the link between national economic performance and mass support for European integration (Eichenberg and Dalton 1993; Anderson and Kalthenthaler 1996), but only making informal assumptions. The main aim of Chapter 2 is thus to propose and test our model with a view to providing a more complete and theoretically grounded picture of public support for the EU. Following theories of utilitarian support, we assume that citizens are in favour of membership if they receive economic benefits from it. To develop this idea, we propose a simple political economic model drawing on the recent economic literature on integration and disintegration processes. The basic element is the existence of a trade-off between the benefits of centralisation and the costs of harmonising policies in presence of heterogeneous preferences among countries. The approach we follow is that of the recent literature on the political economy of international unions and the unification or break-up of nations (Bolton and Roland 1997, Alesina and Wacziarg 1999, Alesina et al. 2001, 2005a, to mention only the relevant). The general perspective is that unification provides returns to scale in the provision of public goods, but reduces each member state’s ability to determine its most favoured bundle of public goods. In the simple model presented in Chapter 2, support for membership of the union is increasing in the union’s average income and in the loss of efficiency stemming from being outside the union, and decreasing in a country’s average income, while increasing heterogeneity of preferences among countries points to a reduced scope of the union. Afterwards we empirically test the model with data on the EU; more precisely, we perform an econometric analysis employing a panel of member countries over time. The second part of Chapter 2 thus tries to answer the following question: does public opinion support for the EU really depend on economic factors? The findings are broadly consistent with our theoretical expectations: the conditions of the national economy, differences in income among member states and heterogeneity of preferences shape citizens’ attitude towards their country’s membership of the EU. Consequently, this analysis offers some interesting policy implications for the present debate about ratification of the European Constitution and, more generally, about how the EU could act in order to gain more support from the European public. Citizens in many member states are called to express their opinion in national referenda, which may well end up in rejection of the Constitution, as recently happened in France and the Netherlands, triggering a European-wide political crisis. These events show that nowadays understanding public attitude towards the EU is not only of academic interest, but has a strong relevance for policy-making too. Chapter 3 empirically investigates the link between European integration and regional autonomy in Italy. Over the last few decades, the double tendency towards supranationalism and regional autonomy, which has characterised some European States, has taken a very interesting form in this country, because Italy, besides being one of the founding members of the EU, also implemented a process of decentralisation during the 1970s, further strengthened by a constitutional reform in 2001. Moreover, the issue of the allocation of competences among the EU, the Member States and the regions is now especially topical. The process leading to the drafting of European Constitution (even if then it has not come into force) has attracted much attention from a constitutional political economy perspective both on a normative and positive point of view (Breuss and Eller 2004, Mueller 2005). The Italian parliament has recently passed a new thorough constitutional reform, still to be approved by citizens in a referendum, which includes, among other things, the so called “devolution”, i.e. granting the regions exclusive competence in public health care, education and local police. Following and extending the methodology proposed in a recent influential article by Alesina et al. (2005b), which only concentrated on the EU activity (treaties, legislation, and European Court of Justice’s rulings), we develop a set of quantitative indicators measuring the intensity of the legislative activity of the Italian State, the EU and the Italian regions from 1973 to 2005 in a large number of policy categories. By doing so, we seek to answer the following broad questions. Are European and regional legislations substitutes for state laws? To what extent are the competences attributed by the European treaties or the Italian Constitution actually exerted in the various policy areas? Is their exertion consistent with the normative recommendations from the economic literature about their optimum allocation among different levels of government? The main results show that, first, there seems to be a certain substitutability between EU and national legislations (even if not a very strong one), but not between regional and national ones. Second, the EU concentrates its legislative activity mainly in international trade and agriculture, whilst social policy is where the regions and the State (which is also the main actor in foreign policy) are more active. Third, at least two levels of government (in some cases all of them) are significantly involved in the legislative activity in many sectors, even where the rationale for that is, at best, very questionable, indicating that they actually share a larger number of policy tasks than that suggested by the economic theory. It appears therefore that an excessive number of competences are actually shared among different levels of government. From an economic perspective, it may well be recommended that some competences be shared, but only when the balance between scale or spillover effects and heterogeneity of preferences suggests so. When, on the contrary, too many levels of government are involved in a certain policy area, the distinction between their different responsibilities easily becomes unnecessarily blurred. This may not only leads to a slower and inefficient policy-making process, but also risks to make it too complicate to understand for citizens, who, on the contrary, should be able to know who is really responsible for a certain policy when they vote in national,local or European elections or in referenda on national or European constitutional issues.

Genomic and non genomic effects of elevated concentration of anabolic steroids in human neuronal cells

Nandrolone and other anabolic androgenic steroids (AAS) at elevated concentration can alter the expression and function of neurotransmitter systems and contribute to neuronal cell death. This effect can explain the behavioural changes, drug dependence and neuro degeneration observed in steroid abuser. Nandrolone treatment (10-8M–10-5M) caused a time- and concentration-dependent downregulation of mu opioid receptor (MOPr) transcripts in SH-SY5Y human neuroblastoma cells. This effect was prevented by the androgen receptor (AR) antagonist hydroxyflutamide. Receptor binding assays confirmed a decrease in MOPr of approximately 40% in nandrolonetreated cells. Treatment with actinomycin D (10-5M), a transcription inhibitor, revealed that nandrolone may regulate MOPr mRNA stability. In SH-SY5Y cells transfected with a human MOPr luciferase promoter/reporter construct, nandrolone did not alter the rate of gene transcription. These results suggest that nandrolone may regulate MOPr expression through post-transcriptional mechanisms requiring the AR. Cito-toxicity assays demonstrated a time- and concentration dependent decrease of cells viability in SH-SY5Y cells exposed to steroids (10-6M–10-4M). This toxic effects is independent of activation of AR and sigma-2 receptor. An increased of caspase-3 activity was observed in cells treated with Nandrolone 10-6M for 48h. Collectively, these data support the existence of two cellular mechanisms that might explain the neurological syndromes observed in steroids abuser.

Genomic characterization of the italian wolf (Canis lupus): the genes involved in black coat colour determination and application of microarray technique for snps detection.

This study provides a comprehensive genetic overview on the endangered Italian wolf population. In particular, it focuses on two research lines. On one hand, we focalised on melanism in wolf in order to isolate a mutation related with black coat colour in canids. With several reported black individuals (an exception at European level), the Italian wolf population constituted a challenging research field posing many unanswered questions. As found in North American wolf, we reported that melanism in the Italian population is caused by a different melanocortin pathway component, the K locus, in which a beta-defensin protein acts as an alternative ligand for the Mc1r. This research project was conducted in collaboration with Prof. Gregory Barsh, Department of Genetics and Paediatrics, Stanford University. On the other hand, we performed analysis on a high number of SNPs thanks to a customized Canine microarray useful to integrate or substitute the STR markers for genotyping individuals and detecting wolf-dog hybrids. Thanks to DNA microchip technology, we obtained an impressive amount of genetic data which provides a solid base for future functional genomic studies. This study was undertaken in collaboration with Prof. Robert K. Wayne, Department of Ecology and Evolutionary Biology, University of California, Los Angeles (UCLA).

Comparative genomic sequencing analysis of a region in human chromosome 11p15.3, mouse chromosome 7 and analysis of the novel STK33, Stk33 gene

The comparative genomic sequence analysis of a region in human chromosome 11p15.3 and its homologous segment in mouse chromosome 7 between ST5 and LMO1 genes has been performed. 158,201 bases were sequenced in the mouse and compared with the syntenic region in human, partially available in the public databases. The analysed region exhibits the typical eukaryotic genomic structure and compared with the close neighbouring regions, strikingly reflexes the mosaic pattern distribution of (G+C) and repeats content despites its relative short size. Within this region the novel gene STK33 was discovered (Stk33 in the mouse), that codes for a serine/threonine kinase. The finding of this gene constitutes an excellent example of the strength of the comparative sequencing approach. Poor gene-predictions in the mouse genomic sequence were corrected and improved by the comparison with the unordered data from the human genomic sequence publicly available. Phylogenetical analysis suggests that STK33 belongs to the calcium/calmodulin-dependent protein kinases group and seems to be a novelty in the chordate lineage. The gene, as a whole, seems to evolve under purifying selection whereas some regions appear to be under strong positive selection. Both human and mouse versions of serine/threonine kinase 33, consists of seventeen exons highly conserved in the coding regions, particularly in those coding for the core protein kinase domain. Also the exon/intron structure in the coding regions of the gene is conserved between human and mouse. The existence and functionality of the gene is supported by the presence of entries in the EST databases and was in vivo fully confirmed by isolating specific transcripts from human uterus total RNA and from several mouse tissues. Strong evidence for alternative splicing was found, which may result in tissue-specific starting points of transcription and in some extent, different protein N-termini. RT-PCR and hybridisation experiments suggest that STK33/Stk33 is differentially expressed in a few tissues and in relative low levels. STK33 has been shown to be reproducibly down-regulated in tumor tissues, particularly in ovarian tumors. RNA in-situ hybridisation experiments using mouse Stk33-specific probes showed expression in dividing cells from lung and germinal epithelium and possibly also in macrophages from kidney and lungs. Preliminary experimentation with antibodies designed in this work, performed in parallel to the preparation of this manuscript, seems to confirm this expression pattern. The fact that the chromosomal region 11p15 in which STK33 is located may be associated with several human diseases including tumor development, suggest further investigation is necessary to establish the role of STK33 in human health.

Kinematic description of the rupture from strong motion data: strategies for a robust inversion

We present a non linear technique to invert strong motion records with the aim of obtaining the final slip and rupture velocity distributions on the fault plane. In this thesis, the ground motion simulation is obtained evaluating the representation integral in the frequency. The Green’s tractions are computed using the discrete wave-number integration technique that provides the full wave-field in a 1D layered propagation medium. The representation integral is computed through a finite elements technique, based on a Delaunay’s triangulation on the fault plane. The rupture velocity is defined on a coarser regular grid and rupture times are computed by integration of the eikonal equation. For the inversion, the slip distribution is parameterized by 2D overlapping Gaussian functions, which can easily relate the spectrum of the possible solutions with the minimum resolvable wavelength, related to source-station distribution and data processing. The inverse problem is solved by a two-step procedure aimed at separating the computation of the rupture velocity from the evaluation of the slip distribution, the latter being a linear problem, when the rupture velocity is fixed. The non-linear step is solved by optimization of an L2 misfit function between synthetic and real seismograms, and solution is searched by the use of the Neighbourhood Algorithm. The conjugate gradient method is used to solve the linear step instead. The developed methodology has been applied to the M7.2, Iwate Nairiku Miyagi, Japan, earthquake. The estimated magnitude seismic moment is 2.6326 dyne∙cm that corresponds to a moment magnitude MW 6.9 while the mean the rupture velocity is 2.0 km/s. A large slip patch extends from the hypocenter to the southern shallow part of the fault plane. A second relatively large slip patch is found in the northern shallow part. Finally, we gave a quantitative estimation of errors associates with the parameters.

Bioinformatic methods in applied genomic research

Here I will focus on three main topics that best address and include the projects I have been working in during my three year PhD period that I have spent in different research laboratories addressing both computationally and practically important problems all related to modern molecular genomics. The first topic is the use of livestock species (pigs) as a model of obesity, a complex human dysfunction. My efforts here concern the detection and annotation of Single Nucleotide Polymorphisms. I developed a pipeline for mining human and porcine sequences. Starting from a set of human genes related with obesity the platform returns a list of annotated porcine SNPs extracted from a new set of potential obesity-genes. 565 of these SNPs were analyzed on an Illumina chip to test the involvement in obesity on a population composed by more than 500 pigs. Results will be discussed. All the computational analysis and experiments were done in collaboration with the Biocomputing group and Dr.Luca Fontanesi, respectively, under the direction of prof. Rita Casadio at the Bologna University, Italy. The second topic concerns developing a methodology, based on Factor Analysis, to simultaneously mine information from different levels of biological organization. With specific test cases we develop models of the complexity of the mRNA-miRNA molecular interaction in brain tumors measured indirectly by microarray and quantitative PCR. This work was done under the supervision of Prof. Christine Nardini, at the “CAS-MPG Partner Institute for Computational Biology” of Shangai, China (co-founded by the Max Planck Society and the Chinese Academy of Sciences jointly) The third topic concerns the development of a new method to overcome the variety of PCR technologies routinely adopted to characterize unknown flanking DNA regions of a viral integration locus of the human genome after clinical gene therapy. This new method is entirely based on next generation sequencing and it reduces the time required to detect insertion sites, decreasing the complexity of the procedure. This work was done in collaboration with the group of Dr. Manfred Schmidt at the Nationales Centrum für Tumorerkrankungen (Heidelberg, Germany) supervised by Dr. Annette Deichmann and Dr. Ali Nowrouzi. Furthermore I add as an Appendix the description of a R package for gene network reconstruction that I helped to develop for scientific usage (http://www.bioconductor.org/help/bioc-views/release/bioc/html/BUS.html).

Reliability and consistency affect the integration of visual depth cues

Abstract Originalsprache (englisch) Visual perception relies on a two-dimensional projection of the viewed scene on the retinas of both eyes. Thus, visual depth has to be reconstructed from a number of different cues that are subsequently integrated to obtain robust depth percepts. Existing models of sensory integration are mainly based on the reliabilities of individual cues and disregard potential cue interactions. In the current study, an extended Bayesian model is proposed that takes into account both cue reliability and consistency. Four experiments were carried out to test this model's predictions. Observers had to judge visual displays of hemi-cylinders with an elliptical cross section, which were constructed to allow for an orthogonal variation of several competing depth cues. In Experiment 1 and 2, observers estimated the cylinder's depth as defined by shading, texture, and motion gradients. The degree of consistency among these cues was systematically varied. It turned out that the extended Bayesian model provided a better fit to the empirical data compared to the traditional model which disregards covariations among cues. To circumvent the potentially problematic assessment of single-cue reliabilities, Experiment 3 used a multiple-observation task, which allowed for estimating perceptual weights from multiple-cue stimuli. Using the same multiple-observation task, the integration of stereoscopic disparity, shading, and texture gradients was examined in Experiment 4. It turned out that less reliable cues were downweighted in the combined percept. Moreover, a specific influence of cue consistency was revealed. Shading and disparity seemed to be processed interactively while other cue combinations could be well described by additive integration rules. These results suggest that cue combination in visual depth perception is highly flexible and depends on single-cue properties as well as on interrelations among cues. The extension of the traditional cue combination model is defended in terms of the necessity for robust perception in ecologically valid environments and the current findings are discussed in the light of emerging computational theories and neuroscientific approaches.

Integration of MFA and LCA methodologies: the anthropogenic aluminium cycle in Italy

MFA and LCA methodologies were applied to analyse the anthropogenic aluminium cycle in Italy with focus on historical evolution of stocks and flows of the metal, embodied GHG emissions, and potentials from recycling to provide key features to Italy for prioritizing industrial policy toward low-carbon technologies and materials. Historical trend series were collected from 1947 to 2009 and balanced with data from production, manufacturing and waste management of aluminium-containing products, using a ‘top-down’ approach to quantify the contemporary in-use stock of the metal, and helping to identify ‘applications where aluminium is not yet being recycled to its full potential and to identify present and future recycling flows’. The MFA results were used as a basis for the LCA aimed at evaluating the carbon footprint evolution, from primary and electrical energy, the smelting process and the transportation, embodied in the Italian aluminium. A discussion about how the main factors, according to the Kaya Identity equation, they did influence the Italian GHG emissions pattern over time, and which are the levers to mitigate it, it has been also reported. The contemporary anthropogenic reservoirs of aluminium was estimated at about 320 kg per capita, mainly embedded within the transportation and building and construction sectors. Cumulative in-use stock represents approximately 11 years of supply at current usage rates (about 20 Mt versus 1.7 Mt/year), and it would imply a potential of about 160 Mt of CO2eq emissions savings. A discussion of criticality related to aluminium waste recovery from the transportation and the containers and packaging sectors was also included in the study, providing an example for how MFA and LCA may support decision-making at sectorial or regional level. The research constitutes the first attempt of an integrated approach between MFA and LCA applied to the aluminium cycle in Italy.

Konfliktlinien und die Einstellungen zur Europäischen Integration in Norwegen : eine quantitativ-empirische Analyse basierend auf dem European Social Survey 2004/2005

In den konsultativen Referenden von 1972 und 1994 stimmte eine knappe Mehrheit der norwegischen Wählerschaft gegen einen Beitritt in die europäische Staatengemeinschaft. Regierung und Parlament zogen daraufhin ihr Aufnahmegesuch zurück. Ein erneuter Antrag auf Mitgliedschaft in der EU wird seither vermieden, da sich die Parteien des Konfliktpotenzials bewusst sind. Von der politischen Agenda ist diese Streitfrage jedoch nicht verschwunden. Die vorliegende Magisterarbeit greift den gängigen Erklärungsansatz der politikwissenschaftlichen Forschung auf: Das Scheitern der Referenden ist demnach auf die Aktualisierung traditioneller politischer Konfliktlinien zurückzuführen. Inwieweit diese Cleavages die Einstellungen norwegischer Staatsbürger zur Europäischen Integration bestimmen, wird anhand eines komplexen Konfliktlinienmodells und mittels aktueller Daten untersucht. Aufbauend auf dem klassischen Cleavage-Konzept von Seymour Lipset und Stein Rokkan (Zentrum/Peripherie, Staat/Kirche, Stadt/Land, Kapital/Arbeit), findet eine Konkretisierung von Stefano Bartolini und Peter Mair Anwendung, die jede der vier Konfliktlinien als dreidimensional (empirisch, normativ und organisatorisch) begreift. In einem historischen Überblick zeigt sich die Relevanz der tradierten Konfliktlinien für Norwegen, die sich sowohl im nationalen Parteiensystem als auch in den Standpunkten der Parteien zu einem EU-Beitritt widerspiegeln. Datengrundlage für die folgenden empirischen Analysen (Kreuztabellen, Mittelwert- und Korrelationsvergleiche, multiple lineare Regressionen) stellt die norwegische Teilstudie der zweiten Welle des European Social Survey von 2004/2005 dar. Europäische Integration wird von den meisten norwegischen Staatsbürgern, die sich empirisch, normativ und organisatorisch auf den Konfliktlinienpolen Peripherie, Kirche, Land oder Arbeit verorten lassen, negativ bewertet. Im Gegensatz dazu geht die recht häufig vertretene Kombination der empirischen Konfliktlinienpole Zentrum-Staat-Stadt-Kapital mit einer überdurchschnittlich positiven Einstellung einher. Insgesamt erweist sich der Zusammenhang mit der Zentrum/Peripherie-Konfliktlinie als am höchsten.

Functional and Genetic characterization of new genomic islands from an E. coli strain associated with neonatal meningitis.

Enterobacteriaceae genomes evolve through mutations, rearrangements and horizontal gene transfer (HGT). The latter evolutionary pathway works through the acquisition DNA (GEI) modules of foreign origin that enhances fitness of the host to a given environment. The genome of E. coli IHE3034, a strain isolated from a case of neonatal meningitis, has recently been sequenced and its subsequent sequence analysis has predicted 18 possible GEIs, of which: 8 have not been previously described, 5 fully meet the pathogenic island definition and at least 10 that seem to be of prophagic origin. In order to study the GEI distribution of our reference strain, we screened for the presence 18 GEIs a panel of 132 strains, representative of E. coli diversity. Also, using an inverse nested PCR approach we identified 9 GEI that can form an extrachromosomal circular intermediate (CI) and their respective attachment sites (att). Further, we set up a qPCR approach that allowed us to determine the excision rates of 5 genomic islands in different growth conditions. Four islands, specific for strains appertaining to the sequence type complex 95 (STC95), have been deleted in order to assess their function in a Dictyostelium discoideum grazing assays. Overall, the distribution data presented here indicate that 16 IHE3034 GEIs are more associated to the STC95 strains. Also the functional and genetic characterization has uncovered that GEI 13, 17 and 19 are involved in the resistance to phagocitation by Dictyostelium d thus suggesting a possible role in the adaptation of the pathogen during certain stages of infection.

Identification of stock units of Mullus barbatus (Linnaeus, 1758) in the Italian seas: development of genomic 2b-RAD markers and biological variation analysis.

This thesis is settled within the STOCKMAPPING project, which represents one of the studies that were developed in the framework of RITMARE Flagship project. The main goals of STOCKMAPPING were the creation of a genomic mapping for stocks of demersal target species and the assembling of a database of population genomic, in order to identify stocks and stocks boundaries. The thesis focuses on three main objectives representing the core for the initial assessment of the methodologies and structure that would be applied to the entire STOCKMAPPING project: individuation of an analytical design to identify and locate stocks and stocks boundaries of Mullus barbatus, application of a multidisciplinary approach to validate biological methods and an initial assessment and improvement for the genotyping by sequencing technique utilized (2b-RAD). The first step is the individuation of an analytical design that has to take in to account the biological characteristics of red mullet and being representative for STOCKMAPPING commitments. In this framework a reduction and selection steps was needed due to budget reduction. Sampling areas were ranked according the individuation of four priorities. To guarantee a multidisciplinary approach the biological data associated to the collected samples were used to investigate differences between sampling areas and GSAs. Genomic techniques were applied to red mullet for the first time so an initial assessment of molecular protocols for DNA extraction and 2b-RAD processing were needed. At the end 192 good quality DNAs have been extracted and eight samples have been processed with 2b-RAD. Utilizing the software Stacks for sequences analyses a great number of SNPs markers among the eight samples have been identified. Several tests have been performed changing the main parameter of the Stacks pipeline in order to identify the most explicative and functional sets of parameters.

Stock boundaries of Parapenaeus longirostris (Lucas, 1846) populations in the Italian seas: Development of genomic 2b-RAD markers and biological variation analysis.

This thesis is developed in the contest of Ritmare project WP1, which main objective is the development of a sustainable fishery through the identification of populations boundaries in commercially important species in Italian Seas. Three main objectives are discussed in order to help reach the main purpose of identification of stock boundaries in Parapenaeus longirostris: 1 -Development of a representative sampling design for Italian seas; 2 -Evaluation of 2b-RAD protocol; 3 -Investigation of populations through biological data analysis. First of all we defined and accomplished a sampling design which properly represents all Italian seas. Then we used information and data about nursery areas distribution, abundance of populations and importance of P. longirostris in local fishery, to develop an experimental design that prioritize the most important areas to maximize the results with actual project funds. We introduced for the first time the use of 2b-RAD on this species, a genotyping method based on sequencing the uniform fragments produced by type IIB restriction endonucleases. Thanks to this method we were able to move from genetics to the more complex genomics. In order to proceed with 2b-RAD we performed several tests to identify the best DNA extraction kit and protocol and finally we were able to extract 192 high quality DNA extracts ready to be processed. We tested 2b-RAD with five samples and after high-throughput sequencing of libraries we used the software “Stacks” to analyze the sequences. We obtained positive results identifying a great number of SNP markers among the five samples. To guarantee a multidisciplinary approach we used the biological data associated to the collected samples to investigate differences between geographical samples. Such approach assures continuity with other project, for instance STOCKMED, which utilize a combination of molecular and biological analysis as well.

Development of a microgrid with renewable energy sources and electrochemical storage system integration

Beside the traditional paradigm of "centralized" power generation, a new concept of "distributed" generation is emerging, in which the same user becomes pro-sumer. During this transition, the Energy Storage Systems (ESS) can provide multiple services and features, which are necessary for a higher quality of the electrical system and for the optimization of non-programmable Renewable Energy Source (RES) power plants. A ESS prototype was designed, developed and integrated into a renewable energy production system in order to create a smart microgrid and consequently manage in an efficient and intelligent way the energy flow as a function of the power demand. The produced energy can be introduced into the grid, supplied to the load directly or stored in batteries. The microgrid is composed by a 7 kW wind turbine (WT) and a 17 kW photovoltaic (PV) plant are part of. The load is given by electrical utilities of a cheese factory. The ESS is composed by the following two subsystems, a Battery Energy Storage System (BESS) and a Power Control System (PCS). With the aim of sizing the ESS, a Remote Grid Analyzer (RGA) was designed, realized and connected to the wind turbine, photovoltaic plant and the switchboard. Afterwards, different electrochemical storage technologies were studied, and taking into account the load requirements present in the cheese factory, the most suitable solution was identified in the high temperatures salt Na-NiCl2 battery technology. The data acquisition from all electrical utilities provided a detailed load analysis, indicating the optimal storage size equal to a 30 kW battery system. Moreover a container was designed and realized to locate the BESS and PCS, meeting all the requirements and safety conditions. Furthermore, a smart control system was implemented in order to handle the different applications of the ESS, such as peak shaving or load levelling.