Profilo genomico e di espressione dell'Osteosarcoma. Identificazione dei geni con alto grado di correlazione tra numero di copie ed espressione

To identify the regions of recurrent copy number abnormality in osteosarcoma and their effect on gene expression, we performed an integrated genome-wide high-resolution array CGH (aCGH) and gene expression profiling analysis on 40 human OS tissues and 12 OS cell lines. This analysis identified several recurrent chromosome regions that contain genes that show a gene dosage effect on gene expression. A further search, performed on those genes that were over-expressed and localized in the frequently amplified chromosomal regions, greatly reduced the number of candidate genes while their characterization using gene ontology (GO) analysis suggests the importance of the deregulation of the G1-to-S phase in the development of the disease. We also identified frequent deletions on 3q in the vicinity of LSAMP and performed a fine mapping analysis of the breakpoints. We precisely mapped the breakpoints in several instances and demonstrated that the majority do not involve the LSAMP gene itself, and that they appear to form by a process of non-homologous end joining. In addition, aCGH analysis revealed frequent gains of IGF1R that were highly correlated with its protein level. Blockade of IGF1R in OS cell lines with high copy number gain led to growth inhibition suggesting that IGF1R may be a viable drug target in OS, particularly in patients with copy number driven overexpression of this receptor.

Costrutti ed Applicazioni di Programmazione Generica in Linguaggi Object-Oriented

Generic programming is likely to become a new challenge for a critical mass of developers. Therefore, it is crucial to refine the support for generic programming in mainstream Object-Oriented languages — both at the design and at the implementation level — as well as to suggest novel ways to exploit the additional degree of expressiveness made available by genericity. This study is meant to provide a contribution towards bringing Java genericity to a more mature stage with respect to mainstream programming practice, by increasing the effectiveness of its implementation, and by revealing its full expressive power in real world scenario. With respect to the current research setting, the main contribution of the thesis is twofold. First, we propose a revised implementation for Java generics that greatly increases the expressiveness of the Java platform by adding reification support for generic types. Secondly, we show how Java genericity can be leveraged in a real world case-study in the context of the multi-paradigm language integration. Several approaches have been proposed in order to overcome the lack of reification of generic types in the Java programming language. Existing approaches tackle the problem of reification of generic types by defining new translation techniques which would allow for a runtime representation of generics and wildcards. Unfortunately most approaches suffer from several problems: heterogeneous translations are known to be problematic when considering reification of generic methods and wildcards. On the other hand, more sophisticated techniques requiring changes in the Java runtime, supports reified generics through a true language extension (where clauses) so that backward compatibility is compromised. In this thesis we develop a sophisticated type-passing technique for addressing the problem of reification of generic types in the Java programming language; this approach — first pioneered by the so called EGO translator — is here turned into a full-blown solution which reifies generic types inside the Java Virtual Machine (JVM) itself, thus overcoming both performance penalties and compatibility issues of the original EGO translator. Java-Prolog integration Integrating Object-Oriented and declarative programming has been the subject of several researches and corresponding technologies. Such proposals come in two flavours, either attempting at joining the two paradigms, or simply providing an interface library for accessing Prolog declarative features from a mainstream Object-Oriented languages such as Java. Both solutions have however drawbacks: in the case of hybrid languages featuring both Object-Oriented and logic traits, such resulting language is typically too complex, thus making mainstream application development an harder task; in the case of library-based integration approaches there is no true language integration, and some “boilerplate code” has to be implemented to fix the paradigm mismatch. In this thesis we develop a framework called PatJ which promotes seamless exploitation of Prolog programming in Java. A sophisticated usage of generics/wildcards allows to define a precise mapping between Object-Oriented and declarative features. PatJ defines a hierarchy of classes where the bidirectional semantics of Prolog terms is modelled directly at the level of the Java generic type-system.

Antropologia e Migrazioni: una storia di co-sviluppo tra l'Italia ed il Ghana

Nella tesi sono rielaborati i dati etnografici, prodotti in Italia ed in Ghana, con una ricerca sul campo di oltre un anno. Attraverso la ricostruzione di un progetto di co-sviluppo che mobilita i migranti in quanto attori di sviluppo, ed in questo caso l’associazione ghanese di Modena per avviare alcune iniziative di sviluppo economico, umano e sostenibile nel paese d’origine, si sono indagate le forme concrete di transnazionalismo attivate da questo gruppo sociale. Nell’analisi, prettamente antropologica, si rivela come, nel progetto di co-sviluppo osservato, le identità etniche, le relazioni asimmetriche di genere ed i processi di negoziazione politica sono celati ed agiti dai diversi attori sociali coinvolti. Si sono inoltre osservate le forme di partecipazione politica in Italia ed in Ghana rivelando come il collettivo ghanese abbia avviato un processo di depoliticizzazione dello sviluppo nel contesto d’origine e, nonostante ciò, sia divenuto nel paese d’immigrazione un nuovo attore politico. Particolare attenzione è stata posta alle produzioni discorsive dello sviluppo e della diaspora, evidenziando come i collettivi migranti se ne riapproprino e le riformulino nelle pratiche quotidiane.

Patologia ed epidemiologia molecolare delle infezioni associate all'impianto

Staphylococcus aureus and Staphylococcus epidermidis are leading pathogens of implant-related infections. This study aimed at investigating the diverse distribution of different bacterial pathogen factors in most prevalent S. aureus and S. epidermidis strain types causing orthopaedic implant infections. In this study the presence both of the ica genes, encoding for biofilm exopolysaccharide production, and the insertion sequence IS256, a mobile element frequently associated to transposons, was investigated in relationship with the prevalence of antibiotic resistance among Staphylococcus epidermidis strains. The investigation was conducted on 70 clinical isolates derived from orthopaedic implant infections. Among the clinical isolates investigated a dramatic high level of association was found between the presence of ica genes as well as of IS256 and multiple resistance to all the antibiotics tested. Noteworthy, a striking full association between the presence of IS256 and resistance to gentamicin was found, being none of the IS256-negative strain resistant to this antibiotic. This association is probably because of the link of the corresponding aminoglycoside-resistance genes, and IS256, often co-existing within the same staphylococcal transposon. Moreover we investigated the prevalence of aac(6’)-Ie-aph(2’’), aph (3’) IIIa, and ant(4’) genes, encoding for the three forms of aminoglycoside-modifying enzymes (AME), responsible for resistance to aminoglycoside antibiotics. All isolates were characterized by automated ribotyping, so that the presence of antibiotic resistance determinants was investigated in strains exhibiting different ribopatterns. Interestingly, combinations of coexisting AME genes appeared to be typical of specific ribopatterns. 200 S. aureus isolates, categorized into ribogroups by automated ribotyping, i.e. rDNA restriction fragment length polymorphism analysis, were screened for the presence of a panel of adhesins genes, accessory gene regulatory (agr) polymorphisms and toxins. For many ribogroups, characteristic tandem genes arrangements could be identified. Surprisingly, the isolates of the most prevalent cluster, enlisting 27 isolates, were susceptible to almost all antibiotics and never possessed the lukD/lukE gene, thus suggesting the role of factors other than antibiotic resistance and the here investigated toxins in driving the major epidemic clone to the larger success. Afterwards, .in the predominant S. aureus cluster, the bbp gene encoding bone sialoprotein-binding protein appeared a typical virulence trait, found in 93% of the isolates. Conversely, the bbp gene was identified in just 10% of the remaining isolates of the collection. In this cluster, co-presence of bbp with the cna gene encoding collagen adhesin was a pattern consistently observed. These findings indicate a crucial role of both these adhesins, able to bind the most abundant bone proteins, in the pathogenesis of orthopaedic implant infections, there where biomaterials interface bone tissues. Moreover a PCR screening for the ebpS gene, conducted on over two hundred S. aureus clinical isolates from implant related infections revealed the detection of six strains exhibiting an altered amplicon size, shorter than expected. In order to elucidate the sequence changes present in these gene variants, the trait comprised between the primers was analyzed in all six isolates bearing the modification and in four isolates exhibiting the regular amplicon size. From nucleotide translation, the corresponding encoded protein was found to lack an entire peptide segment of 60 amino acids. These variants, missing an entire hydrophobic region, could actually facilitate current structural studies, helping to assess whether the absent domain is strictly necessary for a functional adhesin conformation and its contribution to the topology of the protein. This study suggests that epidemic clones appear to pursue different survival strategies, where adhesins, when present, exhibit diverse importance as virulence factors. A practical message arising from the present study is that strategies for the prevention and treatment of implant orthopaedic infections should target adhesins conjointly present in epidemic clones. Furthermore, the choice of reference strains for testing the anti-infective properties of biomaterials should focus on a selection of the most prevalent clones as they exhibit distinct profiles of adhesins.

Studio genetico ed epidemiologico su Erysiphe necator agente eziologico dell'Oidio della vite

The objective was to analyse population structure and to determine genetic diversity of Erysiphe necator (syn. Uncinula necator) populations obtained from some vineyards located in the South-East Po valley (Italy). Powdery mildew is one of the most important fungal diseases of grapes (Vitis vinifera L.) throughout the world. The causal agent is the haploid, heterothallic ascomycete E. necator. It is an obligate biotrophic fungus and it can be found only on green organs of plants belonging to the family Vitaceae. For this pathogen, two sympatric populations (groups A and B) have been described in Europe and Australia. The two genetic groups differ at multiple genetic loci and previous studies reported a lack of interfertility among isolates of the two groups. There are now several well documented examples of plant pathogen species, such as Leptosphaeria maculans, Gaeumannomyces graminis var. tritici, Botrytis cinerea and Erysiphe syringae, which are indeed composed of genetically differentiated clades, that have led to the description of new groups or even new species. Several studies have suggested that genetic E. necator group A and B correlated with ecological features of the pathogen; some researchers proposed that group A isolates over-winter as resting mycelium within dormant buds, and in spring originate infected shoots, known as Flag shoots, while group B isolates would survive as ascospores in overwintering cleistothecia. However, the association between genetic groups and mode of over-wintering has been challenged by recent studies reporting that flag-shoot may be originated indifferently by group A or group B isolate. Previous studies observed a strong association between the levels of disease severity at the end of the growing season and the initial compositions of E. necator populations in commercial vineyards. The frequencies of E. necator genetic groups vary considerably among vineyards, and the two groups may coexist in the same vineyard. This finding suggests that we need more information on the genetics and epidemiology of E. necator for optimize the crop management In this study we monitored E. necator populations in different vineyards in Emilia – Romagna region (Italy), where the pathogen overwinters both as flagshoots and as cleistothecia. During the grape growing season, symptomatic leaves were sampled early in the growing season and both leaves and berries later during the epidemic growth of the disease. From each sample, single-conidial isolate was obtained. Each isolates was grown on V. vinifera leaf cv. Primitivo and after harvesting the mycelium, the DNA was purified and used as template for PCR amplification with SCAR primers (Sequences Characterised Amplified Region ), -tubulin, IGS sequences and Microsatellite markers (SSR). Amplified DNA from b-tubulin and IGS loci was digested with AciI and XhoI restriction enzymes, respectively, to show single-nucleotide polymorphisms specific for the two genetic groups. The results obtained indicated that SCAR primers are not useful to study the epidemiology. of E. necator conversely the b-tubulin IGS sequences and SSR. Summarize the results obtained with b-tubulin, IGS sequences, in treated vineyards we have found individuals of group B along all grape growing season, whereas in the untreated vineyard individuals of the two genetic groups A and B coexisted throughout the season, with no significant change of their frequency. DNA amplified from ascospores of single cleistothecia showed the presence of markers diagnostic for either groups A and B and were seldom observed also the coexistence of both groups within a claistothecium. These results indicate that individuals of the two groups mated in nature and were able to produced ascospores. With SSR we showed the possibility of recombination between A and B groups in field isolates. During winter, cleistothecia were collected repeatedly in the same vineyards sampling leaves fallen on ground, exfoliating bark from trunks, and from soil. From each substrate, was assess the percentage of cleistothecia containing viable ascospores. Our results confirmed that cleisthotecia contained viable ascospores, therefore they have the potential to be an additional and important source of primary inoculum in Emilia-Romagna vineyards.

Le funzioni metaboliche ed endocrinologiche nella narcolessia con cataplessia

Poco più di dieci anni fa, nel 1998, è stata scoperta l’ipocretina (ovvero orexina), un neuropeptide ipotalamico fondamentale nella regolazione del ciclo sonno-veglia, dell’appetito e della locomozione (de Lecea 1998; Sakurai, 1998; Willie, 2001). La dimostrazione, pochi mesi dopo, di bassi livelli di ipocretina circolanti nel liquido cefalo-rachidiano di pazienti affetti da narcolessia con cataplessia (Mignot 2002) ha definitivamente rilanciato lo studio di questa rara malattia del Sistema Nervoso Centrale, e le pubblicazioni a riguardo si sono moltiplicate. In realtà le prime descrizioni della narcolessia risalgono alla fine del XIX secolo (Westphal 1877; Gélineau 1880) e da allora la ricerca clinica è stata volta soprattutto a cercare di definire il più accuratamente possibile il fenotipo del paziente narcolettico. Accanto all’alterazione del meccanismo di sonno e di veglia, e dell’alternanza tra le fasi di sonno REM (Rapid Eye Movement) e di sonno non REM, sui quali l’ipocretina agisce come un interruttore che stimola la veglia e inibisce la fase REM, sono apparse evidenti anche alterazioni del peso e del metabolismo glucidico, dello sviluppo sessuale e del metabolismo energetico (Willie 2001). I pazienti narcolettici presentano infatti, in media, un indice di massa corporea aumentato (Dauvilliers 2007), la tendenza a sviluppare diabete mellito di tipo II (Honda 1986), un’aumentata prevalenza di pubertà precoce (Plazzi 2006) e alterazioni del metabolismo energetico, rispetto alla popolazione generale (Dauvilliers 2007). L’idea che, quindi, la narcolessia abbia delle caratteristiche fenotipiche intrinseche altre, rispetto a quelle più eclatanti che riguardano il sonno, si è fatta strada nel corso del tempo; la scoperta della ipocretina, e della fitta rete di proiezioni dei neuroni ipocretinergici, diffuse in tutto l’encefalo fino al ponte e al bulbo, ha offerto poi il substrato neuro-anatomico a questa idea. Tuttavia molta strada separa l’intuizione di un possibile legame dall’individuazione dei reali meccanismi patogenetici che rendano conto dell’ampio spettro di manifestazioni cliniche che si osserva associato alla narcolessia. Lo studio svolto in questi tre anni si colloca in questa scia, e si è proposto di esplorare il fenotipo narcolettico rispetto alle funzioni dell’asse ipotalamo-ipofisi-periferia, attraverso un protocollo pensato in stretta collaborazione fra il Dipartimento di Scienze Neurologiche di Bologna e l’Unità Operativa di Endocrinologia e di Malattie del Metabolismo dell’Ospedale Sant’Orsola-Malpighi di Bologna. L’ipotalamo è infatti una ghiandola complessa e l’approccio multidisciplinare è sembrato essere quello più adatto. I risultati ottenuti, e che qui vengono presentati, hanno confermato le aspettative di poter dare ulteriori contributi alla caratterizzazione della malattia; un altro aspetto non trascurabile, e che però verrà qui omesso, sono le ricadute cliniche in termini di inquadramento e di terapia precoce di quelle alterazioni, non strettamente ipnologiche, e però associate alla narcolessia.

Valutazione dell'efficacia delle procedure di Pushover convenzionali, modali ed adattive applicate a telai piani in c.a. regolari ed irregolari in elevazione.

The research performed during the PhD and presented in this thesis, allowed to make judgments on pushover analysis method about its application in evaluating the correct structural seismic response. In this sense, the extensive critical review of existing pushover procedures (illustrated in chapter 1) outlined their major issues related to assumptions and to hypothesis made in the application of the method. Therefore, with the purpose of evaluate the effectiveness of pushover procedures, a wide numerical investigation have been performed. In particular the attention has been focused on the structural irregularity on elevation, on the choice of the load vector and on its updating criteria. In the study eight pushover procedures have been considered, of which four are conventional type, one is multi-modal, and three are adaptive. The evaluation of their effectiveness in the identification of the correct dynamic structural response, has been done by performing several dynamic and static non-linear analysis on eight RC frames, characterized by different proprieties in terms of regularity in elevation. The comparisons of static and dynamic results have then permitted to evaluate the examined pushover procedures and to identify the expected margin of error by using each of them. Both on base shear-top displacement curves and on considered storey parameters, the best agreement with the dynamic response has been noticed on Multi-Modal Pushover procedure. Therefore the attention has been focused on Displacement-based Adative Pushover, coming to define for it an improvement strategy, and on modal combination rules, advancing an innovative method based on a quadratic combination of the modal shapes (QMC). This latter has been implemented in a conventional pushover procedure, whose results have been compared with those obtained by other multi-modal procedures. The development of research on pushover analysis is very important because the objective is to come to the definition of a simple, effective and reliable analysis method, indispensable tool in the seismic evaluation of new or existing structures.

Effetti termoregolatori ed ipnici indotti dalla stimolazione farmacologica del bulbo rostroventro mediale nel ratto

Recentemente è stato proposto che i premotoneuroni simpatici deputati al controllo della vasomozione cutanea siano localizzati nel bulbo rostoventromediale, una area che è delimitata rostralmente dal nucleo del nervo faciale (RVMM(io)) e causalmente dal polo rostrale del nucleo olivare inferiore (RVMM(io)). Per esplorare il ruolo che in neuroni contenuti nel RVMM(io) e nel (RVMM(fn) hanno nel controllare la vasomozione periferica, sono state effettuate in ciascuna delle due aree microiniezioni dell’agonista dei recettori GABAA muscimolo, dell’antagonista dei recettori GABAA bicucullina metiodide e di veicolo. La somministrazione di mucimolo induce una massiva vasodilatazione periferica sia se iniettato in RVMM(io) che in RVMM(fn). La disinibizione dei neuroni del RVMM(fn) produce invece una importate vasocostrizione periferica, antagonizzando la vasodilatazione indotta dall’esposizione ad alte temperature ambientali, mentre la disinibizione dei neuroni del RVMM(io) produce una vasodilatazione massimale, che è in grado di antagonizzare anche la vasocostrizione indotta da esposizione a bassa temperatura ambientale. L’inibizione sia dei neuroni del RVMM(io) che del RVMM(fn) induce inoltre modificazioni elettroencefalografiche e ipniche comparabili con quelle osservate durante il torpore. La somministrazione di muscimolo ha prodotto una rapida vasodilatazione periferica, seguita da una profonda ipotermia a da uno spostamento verso sinistra della banda Theta dell’EEG. Durante il periodo di ipotermia, la comparsa sia di sonno NREM che di sonno REM è risultata essere inibita. Questi dati mostrano che: a) a due popolazioni di premotoneuroni simpatici sono localizzati nella regione che va dal RVMM(io) al RVMM(fn), una termoregolatoria, tonicamente attiva e vasocostrittoria, l’altra non termoregolatoria, tonicamente inibita e vasodilatatoria; b) anche in una specie che non è va spontaneamente incontro a torpore, l’ipotermia centrale produce effetti elettroencefalografici simili a quelli osservati durante il torpore.