Development of synthetic molecular circuits for the control of cell systems

Synthetic biology is a young field of applicative research aiming to design and build up artificial biological devices, useful for human applications. How synthetic biology emerged in past years and how the development of the Registry of Standard Biological Parts aimed to introduce one practical starting solution to apply the basics of engineering to molecular biology is presented in chapter 1 in the thesis The same chapter recalls how biological parts can make up a genetic program, the molecular cloning tecnique useful for this purpose, and an overview of the mathematical modeling adopted to describe gene circuit behavior. Although the design of gene circuits has become feasible the increasing complexity of gene networks asks for a rational approach to design gene circuits. A bottom-up approach was proposed, suggesting that the behavior of a complicated system can be predicted from the features of its parts. The option to use modular parts in large-scale networks will be facilitated by a detailed and shared characterization of their functional properties. Such a prediction, requires well-characterized mathematical models of the parts and of how they behave when assembled together. In chapter 2, the feasibility of the bottom-up approach in the design of a synthetic program in Escherichia coli bacterial cells is described. The rational design of gene networks is however far from being established. The synthetic biology approach can used the mathematical formalism to identify biological information not assessable with experimental measurements. In this context, chapter 3 describes the design of a synthetic sensor for identifying molecules of interest inside eukaryotic cells. The Registry of Standard parts collects standard and modular biological parts. To spread the use of BioBricks the iGEM competition was started. The ICM Laboratory, where Francesca Ceroni completed her Ph.D, partecipated with teams of students and Chapter 4 summarizes the projects developed.

Trattamento della stenosi valvolare aortica: nuovi scenari dalla biologia molecolare alle nuove tecnologie

La stenosi valvolare aortica è la più frequente patologia valvolare cardiaca nei paesi sviluppati come diretta conseguenza dell’aumentata aspettativa di vita. In Europa si stima che il numero di soggetti sintomatici per stenosi valvolare aortica aumenterà da 1.3 milioni nel 2025 a 2.1 milioni in 2050. Di conseguenza la stenosi aortica ha e avrà un forte impatto sulla salute pubblica e sui costi che ne determina, poiché spesso associata a un declino funzionale dei pazienti ed aumentata incidenza di ospedalizzazione. D’altra parte è noto che la stenosi valvolare aortica severa non trattata si associa a prognosi infausta con una sopravvivenza del 50% a 2 anni dall’insorgenza dei sintomi e del 20% a 5 anni. Ad oggi non esiste una terapia medica efficace per la stenosi valvolare aortica in quanto andando a costituire un’ostruzione meccanica, resta di competenza del cardiochirurgo o del cardiologo interventista. La sostituzione valvolare aortica, sia essa chirurgica o percutanea, resta pertanto il solo trattamento definitivo per la stenosi valvolare aortica. Nel tempo il rischio operatorio è estremamente diminuito e i vantaggi in termini di miglioramento della qualità di vita sono evidenti. Questo progetto di ricerca prevede pertanto un’analisi delle più recenti tecnologie per il trattamento chirurgico della stenosi valvolare aortica a partire dalla tipologia di approccio chirurgico, se mini-invasivo o tradizionale, fino all’utilizzo delle più recenti protesi biologiche sutureless studiandone i vantaggi, svantaggi e risultati. Prima ancora, tuttavia, saranno analizzati i meccanismi di biologia molecolare alla base dell’eziologia della stenosi aortica al fine di poter identificare precocemente i pazienti, di prevedere l’andamento della patologia e forse, in futuro, anche di ipotizzare una terapia farmacologica mirata.

Insights on epidemiology and control of Marek’s disease through traditional and novel molecular tools

Marek's disease (MD) is a contagious, lymphoproliferative and neuropathic disease of poultry caused by a ubiquitous lymphotropic and oncogenic virus, Gallid alphaherpesvirus 2 (GaHV-2). MD has been reported in all poultry-rearing countries and is among the viral diseases with the highest economic impact in the poultry industry worldwide, including Italy. MD has been also recognized as one of the leading causes of mortality in backyard poultry. The present doctoral thesis aimed at exploring Marek's disease virus molecular epidemiology in Italian commercial and backyard chicken flocks and, for the first time, in commercial turkeys affected by clinical MD. Molecular biology techniques targeting the full-length meq gene, the major GaHV-2 oncogene, were used to detect and characterize the circulating GaHV-2 strains searching for genetic markers of virulence. A final study focused on the development of rapid, sensitive, and species-specific loop-mediated isothermal amplification assays coupled with a lateral flow device readout for the detection of conventional and recombinant HVT-based vaccines is included in the thesis. HVT vaccines, currently used to protect chickens from MD, are referred to as "leaky", as they do not impede the infection, replication, and shedding of field GaHV-2: vaccinal and field viruses can coexist in the vaccinated host and molecular tests able to discriminate between GaHV-2 and HVT are required. These new simple, fast, and accurate tests for the monitoring of MD vaccination success in the field could be greatly beneficial for field veterinarians, small laboratories, and more broadly for resource-limited settings.