A molecular phylogeny of bivalve mollusks: ancient radiations and divergences as revealed by mitochondrial genes

The main scope of my PhD is the reconstruction of the large-scale bivalve phylogeny on the basis of four mitochondrial genes, with samples taken from all major groups of the class. To my knowledge, it is the first attempt of such a breadth in Bivalvia. I decided to focus on both ribosomal and protein coding DNA sequences (two ribosomal encoding genes -12s and 16s -, and two protein coding ones - cytochrome c oxidase I and cytochrome b), since either bibliography and my preliminary results confirmed the importance of combined gene signals in improving evolutionary pathways of the group. Moreover, I wanted to propose a methodological pipeline that proved to be useful to obtain robust results in bivalves phylogeny. Actually, best-performing taxon sampling and alignment strategies were tested, and several data partitioning and molecular evolution models were analyzed, thus demonstrating the importance of molding and implementing non-trivial evolutionary models. In the line of a more rigorous approach to data analysis, I also proposed a new method to assess taxon sampling, by developing Clarke and Warwick statistics: taxon sampling is a major concern in phylogenetic studies, and incomplete, biased, or improper taxon assemblies can lead to misleading results in reconstructing evolutionary trees. Theoretical methods are already available to optimize taxon choice in phylogenetic analyses, but most involve some knowledge about genetic relationships of the group of interest, or even a well-established phylogeny itself; these data are not always available in general phylogenetic applications. The method I proposed measures the "phylogenetic representativeness" of a given sample or set of samples and it is based entirely on the pre-existing available taxonomy of the ingroup, which is commonly known to investigators. Moreover, it also accounts for instability and discordance in taxonomies. A Python-based script suite, called PhyRe, has been developed to implement all analyses.

Produzione di virus sintetici per lo studio dei meccanismi di interazione coinvolti nell'induzione di resistenza

Beet soil-borne mosaic virus (BSBMV) and Beet necrotic yellow vein virus (BNYVV) are members of Benyvirus genus. BSBMV has been reported only in the United States while BNYVV has a worldwide distribution. Both viruses are vectored by Polymyxa betae, possess similar host ranges, particles number and morphology. Both viruses are not serologically related but have similar genomic organizations. Field isolates consist of four RNA species but some BNYVV isolates contain a fifth RNA. RNAs 1 and 2 are essential for infection and replication while RNAs 3 and 4 play important roles on plant and vector interactions, respectively. Nucleotide and amino acid analyses revealed BSBMV and BNYVV are different enough to be classified in two different species. Additionally in BNYVV/BSBMV mixed infections, a competition was previous described in sugar beet, where BNYVV infection reduces BSBMV accumulation in both susceptible and resistant cultivars. Considering all this observations we hypothesized that BNYVV and BSBMV crossed study, exploiting their similarities and divergences, can improve investigation of molecular interactions between sugar beets and Benyviruses. The main achievement of our research is the production of a cDNA biologically active clones collection of BNYVV and BSBMV RNAs, from which synthetic copies of both Benyviruses can be transcribed. Moreover, through recombination experiments we demonstrated, for the first time, the BNYVV RNA 1 and 2 capability to trans-replicate and encapsidate BSBMV RNA 3 and 4, either the BSBMV RNA 1 and 2 capability to replicate BNYVV RNA2 in planta. We also demonstrated that BSBMV RNA3 support long-distance movement of BNYVV RNA 1 and 2 in B. macrocarpa and that 85 foreign sequence as p29HA, GFP and RFP, are successfully expressed, in C. quinoa, by BSBMV RNA3 based replicon (RepIII) also produced by our research. These results confirm the close correlation among the two viruses. Interestingly, the symptoms induced by BSBMV RNA-3 on C. quinoa leaves are more similar to necrotic local lesions caused by BNYVV RNA-5 p26 than to strongly chlorotic local lesions or yellow spot induced by BNYVV RNA- 3 encoded p25. As previous reported BSBMV p29 share 23% of amino acid sequence identity with BNYVV p25 but identity increase to 43% when compared with sequence of BNYVV RNA-5 p26. Based on our results the essential sequence (Core region) for the longdistance movement of BSBMV and BNYVV in B. macrocarpa, is not only carried by RNA3s species but other regions, perhaps located on the RNA 1 and 2, could play a fundamental role in this matter. Finally a chimeric RNA, composed by the 5’ region of RNA4 and 3’ region of RNA3 of BSBMV, has been produced after 21 serial mechanically inoculation of wild type BSBMV on C. quinoa plants. Chimera seems unable to express any protein, but it is replicated and transcript in planta. It could represent an important tool to study the interactions between Benyvirus and plant host. In conclusion different tools, comprising a method to study synthetic viruses under natural conditions of inoculum through P. Betae, have been produced and new knowledge are been acquired that will allow to perform future investigation of the molecular interactions between sugar beets and Benyviruses.

Modellizzazione bioeconomica per la gestione dei piccoli pelagici nel Mar Adriatico

Stocks’ overexploitation and socio-economic sustainability are two major issues currently at stake in European fisheries. In this view the European Commission is considering the implementation of management plans as a means to move towards a longer-term perspective on fisheries management, to consider regional differences and to increase stakeholder involvement. Adriatic small pelagic species (anchovies and sardines) are some of the most studied species in the world from a biologic perspective; several economic analysis have also been realised on Italian pelagic fishery; despite that, no complete bioeconomic modelization has been carried out yet considering all biologic, technical and economic issues. Bioeconomic models cannot be considered foolproof tools but are important implements to help decision makers and can supply a fundamental scientific basis for management plans. This research gathers all available information (from biologic, technologic and economic perspectives) in order to carry out a bioeconomic model of the Adriatic pelagic fishery. Different approaches are analyzed and some of them developed to highlight potential divergences in results, characteristics and implications. Growth, production and demand functions are estimated. A formal analysis about interaction and competition between Italian and Croatian fleet is examined proposing different equilibriums for open access, duopoly and a form of cooperative solution. Anyway normative judgments are limited because of poor knowledge of population dynamics and data related to the Croatian fleet.

Reverse genetic studies of Benyvirus - Polymyxa betae molecular interaction: Role of the RNA4-encoded protein in virus transmission

Beet necrotic yellow vein virus (BNYVV), the leading infectious agent that affects sugar beet, is included within viruses transmitted through the soil from plasmodiophorid as Polymyxa betae. BNYVV is the causal agent of Rhizomania, which induces abnormal rootlet proliferation and is widespread in the sugar beet growing areas in Europe, Asia and America; for review see (Peltier et al., 2008). In this latter continent, Beet soil-borne mosaic virus (BSBMV) has been identified (Lee et al., 2001) and belongs to the benyvirus genus together with BNYVV, both vectored by P. betae. BSBMV is widely distributed only in the United States and it has not been reported yet in others countries. It was first identified in Texas as a sugar beet virus morphologically similar but serologically distinct to BNYVV. Subsequent sequence analysis of BSBMV RNAs evidenced similar genomic organization to that of BNYVV but sufficient molecular differences to distinct BSBMV and BNYVV in two different species (Rush et al., 2003). Benyviruses field isolates usually consist of four RNA species but some BNYVV isolates contain a fifth RNA. RNAs -1 contains a single long ORF encoding polypeptide that shares amino acid homology with known viral RNA-dependent RNA polymerases (RdRp) and helicases. RNAs -2 contains six ORFs: capsid protein (CP), one readthrough protein, triple gene block proteins (TGB) that are required for cell-to-cell virus movement and the sixth 14 kDa ORF is a post-translation gene silencing suppressor. RNAs -3 is involved on disease symptoms and is essential for virus systemic movement. BSBMV RNA-3 can be trans-replicated, trans-encapsidated by the BNYVV helper strain (RNA-1 and -2) (Ratti et al., 2009). BNYVV RNA-4 encoded one 31 kDa protein and is essential for vector interactions and virus transmission by P. betae (Rahim et al., 2007). BNYVV RNA-5 encoded 26 kDa protein that improve virus infections and accumulation in the hosts. We are interest on BSBMV effect on Rhizomania studies using powerful tools as full-length infectious cDNA clones. B-type full-length infectious cDNA clones are available (Quillet et al., 1989) as well as A/P-type RNA-3, -4 and -5 from BNYVV (unpublished). A-type BNYVV full-length clones are also available, but RNA-1 cDNA clone still need to be modified. During the PhD program, we start production of BSBMV full-length cDNA clones and we investigate molecular interactions between plant and Benyviruses exploiting biological, epidemiological and molecular similarities/divergences between BSBMV and BNYVV. During my PhD researchrs we obtained full length infectious cDNA clones of BSBMV RNA-1 and -2 and we demonstrate that they transcripts are replicated and packaged in planta and able to substitute BNYVV RNA-1 or RNA-2 in a chimeric viral progeny (BSBMV RNA-1 + BNYVV RNA-2 or BNYVV RNA-1 + BSBMV RNA-2). During BSBMV full-length cDNA clones production, unexpected 1,730 nts long form of BSBMV RNA-4 has been detected from sugar beet roots grown on BSBMV infected soil. Sequence analysis of the new BSBMV RNA-4 form revealed high identity (~100%) with published version of BSBMV RNA-4 sequence (NC_003508) between nucleotides 1-608 and 1,138-1,730, however the new form shows 528 additionally nucleotides between positions 608-1,138 (FJ424610). Two putative ORFs has been identified, the first one (nucleotides 383 to 1,234), encode a protein with predicted mass of 32 kDa (p32) and the second one (nucleotides 885 to 1,244) express an expected product of 13 kDa (p13). As for BSBMV RNA-3 (Ratti et al., 2009), full-length BSBMV RNA-4 cDNA clone permitted to obtain infectious transcripts that BNYVV viral machinery (Stras12) is able to replicate and to encapsidate in planta. Moreover, we demonstrated that BSBMV RNA-4 can substitute BNYVV RNA-4 for an efficient transmission through the vector P. betae in Beta vulgaris plants, demonstrating a very high correlation between BNYVV and BSBMV. At the same time, using BNYVV helper strain, we studied BSBMV RNA-4’s protein expression in planta. We associated a local necrotic lesions phenotype to the p32 protein expression onto mechanically inoculated C. quinoa. Flag or GFP-tagged sequences of p32 and p13 have been expressed in viral context, using Rep3 replicons, based on BNYVV RNA-3. Western blot analyses of local lesions contents, using FLAG-specific antibody, revealed a high molecular weight protein, which suggest either a strong interaction of BSBMV RNA4’s protein with host protein(s) or post translational modifications. GFP-fusion sequences permitted the subcellular localization of BSBMV RNA4’s proteins. Moreover we demonstrated the absence of self-activation domains on p32 by yeast two hybrid system approaches. We also confirmed that p32 protein is essential for virus transmission by P. betae using BNYVV helper strain and BNYVV RNA-3 and we investigated its role by the use of different deleted forms of p32 protein. Serial mechanical inoculation of wild-type BSBMV on C. quinoa plants were performed every 7 days. Deleted form of BSBMV RNA-4 (1298 bp) appeared after 14 passages and its sequence analysis shows deletion of 433 nucleotides between positions 611 and 1044 of RNA-4 new form. We demonstrated that this deleted form can’t support transmission by P. betae using BNYVV helper strain and BNYVV RNA-3, moreover we confirmed our hypothesis that BSBMV RNA-4 described by Lee et al. (2001) is a deleted form. Interesting after 21 passages we identifed one chimeric form of BSBMV RNA-4 and BSBMV RNA-3 (1146 bp). Two putative ORFs has been identified on its sequence, the first one (nucleotides 383 to 562), encode a protein with predicted mass of 7 kDa (p7), corresponding to the N-terminal of p32 protein encoded by BSBMV RNA-4; the second one (nucleotides 562 to 789) express an expected product of 9 kDa (p9) corresponding to the C-terminal of p29 encoded by BSBMV RNA-3. Results obtained by our research in this topic opened new research lines that our laboratories will develop in a closely future. In particular BSBMV p32 and its mutated forms will be used to identify factors, as host or vector protein(s), involved in the virus transmission through P. betae. The new results could allow selection or production of sugar beet plants able to prevent virus transmission then able to reduce viral inoculum in the soil.

1963-1968. Dall'avvento dell'amministrazione di Lyndon B. Johnson al Trattato di Non-Proliferazione. gli Stati Uniti, la Francia, la NATO e l'Europa agli esordi della distensione. Storia di una "non-crisi" transatlantica e della riorganizzazione dell'Alleanza.

The aim of this proposal is to explain the paradigm of the American foreign policy during the Johnson Administration, especially toward Europe, within the NATO framework, and toward URSS, in the context of the détente, just emerged during the decade of the sixties. During that period, after the passing of the J. F. Kennedy, President L. B. Johnson inherited a complex and very high-powered world politics, which wanted to get a new phase off the ground in the transatlantic relations and share the burden of the Cold war with a refractory Europe. Known as the grand design, it was a policy that needed the support of the allies and a clear purpose which appealed to the Europeans. At first, President Johnson detected in the problem of the nuclear sharing the good deal to make with the NATO allies. At the same time, he understood that the United States needed to reassert their leadeship within the new stage of relations with the Soviet Union. Soon, the “transatlantic bargain” became something not so easy to dealt with. The Federal Germany wanted to say a word in the nuclear affairs and, why not, put the finger on the trigger of the atlantic nuclear weapons. URSS, on the other hand, wanted to keep Germany down. The other allies did not want to share the onus of the defense of Europe, at most the responsability for the use of the weapons and, at least, to participate in the decision-making process. France, which wanted to detach herself from the policy of the United States and regained a world role, added difficulties to the manage of this course of action. Through the years of the Johnson’s office, the divergences of the policies placed by his advisers to gain the goal put the American foreign policy in deep water. The withdrawal of France from the organization but not from the Alliance, give Washington a chance to carry out his goal. The development of a clear-cut disarm policy leaded the Johnson’s administration to the core of the matter. The Non-proliferation Treaty signed in 1968, solved in a business-like fashion the problem with the allies. The question of nuclear sharing faded away with the acceptance of more deep consultative role in the nuclear affairs by the allies, the burden for the defense of Europe became more bearable through the offset agreement with the FRG and a new doctrine, the flexible response, put an end, at least formally, to the taboo of the nuclear age. The Johnson’s grand design proved to be different from the Kennedy’s one, but all things considered, it was more workable. The unpredictable result was a real détente with the Soviet Union, which, we can say, was a merit of President Johnson.

Comparing genetic and linguistic diversity in African populations with a focus on the Khoisan of southern Africa

The interaction between disciplines in the study of human population history is of primary importance, profiting from the biological and cultural characteristics of humankind. In fact, data from genetics, linguistics, archaeology and cultural anthropology can be combined to allow for a broader research perspective. This multidisciplinary approach is here applied to the study of the prehistory of sub-Saharan African populations: in this continent, where Homo sapiens originally started his evolution and diversification, the understanding of the patterns of human variation has a crucial relevance. For this dissertation, molecular data is interpreted and complemented with a major contribution from linguistics: linguistic data are compared to the genetic data and the research questions are contextualized within a linguistic perspective. In the four articles proposed, we analyze Y chromosome SNPs and STRs profiles and full mtDNA genomes on a representative number of samples to investigate key questions of African human variability. Some of these questions address i) the amount of genetic variation on a continental scale and the effects of the widespread migration of Bantu speakers, ii) the extent of ancient population structure, which has been lost in present day populations, iii) the colonization of the southern edge of the continent together with the degree of population contact/replacement, and iv) the prehistory of the diverse Khoisan ethnolinguistic groups, who were traditionally understudied despite representing one of the most ancient divergences of modern human phylogeny. Our results uncover a deep level of genetic structure within the continent and a multilayered pattern of contact between populations. These case studies represent a valuable contribution to the debate on our prehistory and open up further research threads.

Legal presumptions in national tax systems (Italy and Belgium) and in EU law

The thesis deals with the concept of presumptions, and in particular of legal presumptions, in the context of national tax systems (Italy and Belgium) and EU law. The purpose was to investigate the concept of legal presumption under a twofold comparative perspective. After having provided a general overview of the common core concept of presumption in the European context, an insight in the national approach to legal presumptions was given by examining two different national experiences, namely the Italian and Belgian tax systems. At this stage, the Constitutional framework and some of the most interesting and relevant at EU level presumptive measures were explored, with a view to underlining possible divergences and common grounds. The concept of (national) legal presumption was then investigated in the context of EU law, with the attempt to systematize under a uniform perspective a matter which has been traditionally dealt with either from the merely national point of view or, at EU level, through a fragmented form. In this instance, the EU law relevant framework and the most significant EUCJ case-law, in particular in the field of customs duties, VAT, on the issue of the repayment of taxes levied in breach of EU law and in the area of direct taxation, were examined so as to construe the overall EU approach to national legal presumptions. This was done with the finality of determining if and to what extent a common analytical framework may be identified, from which were extracted certain criteria governing the compatibility of national legal presumptions with EU law.

The market manipulation regime in the European Union

Market manipulation is an illegal practice that enables a person can profit from practices that artificially raise or lower the prices of an instrument in the financial markets. Its prohibition is based on the 2003 Market Abuse Directive in the EU. The current market manipulation regime was broadly considered as a big success except for enforcement and supervisory inconsistencies in the Member States at the initial. A review of the market manipulation regime began at the end of 2007, which became quickly incorporated into the wider EU crisis-era reform program. A number of weaknesses of current regime have been identified, which include regulatory gaps caused by the development of trading venues and financial products, regulatory gaps concerning cross-border and cross-markets manipulation (particular commodity markets), legal uncertainty as a result of various implementation, and inefficient supervision and enforcement. On 12 June 2014, a new regulatory package of market abuse, Market Abuse Regulation and Directive on criminal sanctions for market abuse, has been adopted. And several changes will be made concerning the EU market manipulation regime. A wider scope of the regime and a new prohibition of attempted market manipulation will ensure the prevention of market manipulation at large. The AMPs will be subject to strict scrutiny of ESMA to reduce divergences in implementation. In order to enhance efficiency of supervision and enforcement, powers of national competent authorities will be strengthened, ESMA is imposed more power to settle disagreement between national regulators, and the administrative and criminal sanctioning regimes are both further harmonized. In addition, the protection of fundamental rights is stressed by the new market manipulation regime, and some measures are provided to guarantee its realization. Further, the success EU market manipulation regime could be of significant reference to China, helping China to refine its immature regime.

Ricerche sulle Res cottidianae

Le Res cottidianae sive Aurea sono un’opera giuridica elementare di diritto privato romano. A differenza delle Institutiones di Gaio, di cui abbiamo conoscenza in larga misura grazie al palinsesto Codice Veronese, tutto ciò che sappiamo delle res cottidianae si arresta a ventisei frammenti che ci sono tramandati dal Digesto. Dibattuta è la loro paternità, dibattuta la genuinità del loro contenuto, dibattuti sono il titolo che recavano e di quanti libri fossero composte. La presente ricerca tenta di rispondere a queste vexatae quaestiones e offrire nuove prospettive alla risoluzione del c.d. «enigma gaiano». Punto di partenza sarà una indagine preliminare sul rapporto intercorrente tra le res cottidianae e le Institutiones di Gaio, volta a mostrare la struttura parallela delle due opere, le analogie testuali, i punti di contatto e divergenza. Ci si addentrerà, in seguito, nei ventisei frammenti delle res cottidianae, posto che qualsiasi riflessione scientifica sull’opera non può essere svincolata dall’analisi testuale. Si offrirà infine un bilancio complessivo delle res cottidianae, anche in relazione all’effettiva portata del lascito gaiano agli studi giuridici di diritto positivo.

La disciplina della contumacia del convenuto nei processi civili dell'Unione Europea. Standard comuni e possibilità di armonizzazioni

The fundamental right to a fair trial depends largely on the service of proceedings on the defendant; it is very important that this communication act informs the defendant of the existence of proceedings against him so that he has the possibility to defend himself in sufficient time. The casuistry shows that difficulties considerably increase when this first service of process has to be effected abroad. Indeed, the most problematic foreign judgments are those issued in absentia of the defendant. The European legislator has paid special attention to the service of the claim and to the default of appearance of the defendant; it has laid down both rules governing the ways in which the service of proceedings must be effected and the procedural treatment of involuntary default, including remedies available for

Forme (形 XING) e Visioni (象 XIANG): Nuove prospettive di ricerca per una storia comparata della Screendance in Europa e in Cina

La presente tesi si propone di trattare il soggetto della screendance, giovane disciplina in continua definizione nata combinando cinema e coreografia, da una prospettiva alternativa, coerente con le ultime trasformazioni sociali. La ricerca, suddivisa in quattro parti, inizia da una ricognizione critica sulla terminologia utilizzata per indicare la screendance nel suo sviluppo storico in Europa e in Cina durante il XX secolo. Adoperando una metodologia basata sugli strumenti della storiografia comparativa, vengono utilizzati come chiavi di lettura i due concetti taoisti di xiang o visione e xing o forma, l’uno riferito al contesto culturale, storico e artistico di una data società umana in un dato periodo storico, e l’altro alludente alle forme artistiche specifiche definite da quei principi. Nel focalizzarsi sul confronto tra i differenti sviluppi della screendance nel corso del XX secolo in Europa e in Cina, nella seconda parte, la tesi affronta una comparazione diacronica delle trasformazioni di xiang delle due aree geografiche, insieme a una comparazione sincronica delle xing, rendendo più evidenti analogie e divergenze di numerosi case studies occidentali e cinesi.  Uno sguardo sul panorama europeo, attento alle differenze nella disseminazione della screendance attraverso i festival in Gran Bretagna, Francia, Belgio e Italia, costituisce il focus della terza parte. Con la quarta ed ultima parte, la tesi riserva ampio spazio alla disamina della situazione contemporanea della screendance, seguendone la diffusione negli ultimi quattro decenni attraverso i festival e, più recentemente, i nuovi canali social di creazione e condivisione di contenuti video, e prospettando un futuro in cui la realtà della screendance europea e quella cinese potranno confrontare le proprie identità culturali. Il ricco apparato documentario include un elenco dei festival di screendance europei e cinesi, e una serie di interviste inedite ai maggiori operatori e professionisti del settore, italiani ed europei.

Procedimento applicativo delle misure di prevenzione personale e rito penale: un rapporto controverso

La tesi si prefigge di far luce sui rapporti intercorrenti tra il procedimento applicativo delle misure di prevenzione personale di competenza giudiziale e il processo penale. Nello specifico, l’obiettivo è quello di mettere in evidenza tanto le interferenze, quanto le somiglianze e le inaccettabili divergenze tra i due riti. Nonostante dall’art. 29 cod. ant. traspaia un’apparente indifferenza tra azione penale e azione di prevenzione, infatti, le due sfere di tutela sono così intrecciate da rendere estremamente difficile sostenere che l’una in qualche modo non sia almeno condizionata dall’andamento dell’altra. Il fatto poi che l’unica disposizione contenente la disciplina del procedimento preventivo rinvii, per quanto non espressamente previsto e sempreché vi sia compatibilità, a quella dell’incidente di esecuzione ex art. 666 c.p.p., rimarca la vicinanza con il rito penale; una vicinanza che obbliga dottrina e giurisprudenza a interrogarsi per comprendere se almeno le principali tra le regole e i principi dettati per il processo penale possano valere anche per quello di prevenzione. Il cuore del lavoro sarà dunque dedicato a questa controversa opera di ricostruzione, al fine di individuare le garanzie che devono (o almeno dovrebbero) essere riconosciute al proposto.