RNA non-codificanti indotti da danno al DNA regolano il fattore di trascrizione HIF-1α

Recenti analisi sull’intero trascrittoma hanno rivelato una estensiva trascrizione di RNA non codificanti (ncRNA), le quali funzioni sono tuttavia in gran parte sconosciute. In questo lavoro è stato dimostrato che alte dosi di camptotecina (CPT), un farmaco antitumorale inibitore della Top1, aumentano la trascrizione di due ncRNA antisenso in 5’ e 3’ (5'aHIF-1α e 3'aHIF-1α rispettivamente) al locus genico di HIF-1α e diminuiscono i livelli dell’mRNA di HIF-1α stesso. Gli effetti del trattamento sono Top1-dipendenti, mentre non dipendono dal danno al DNA alla forca di replicazione o dai checkpoint attivati dal danno al DNA. I ncRNA vengono attivati in risposta a diversi tipi di stress, il 5'aHIF-1α è lungo circa 10 kb e possiede sia il CAP in 5’ sia poliadenilazione in 3’ (in letteratura è noto che il 3'aHIF-1α è un trascritto di 1,7 kb, senza 5’CAP né poliadenilazione). Analisi di localizzazione intracellulare hanno dimostrato che entrambi sono trascritti nucleari. In particolare 5'aHIF-1α co-localizza con proteine del complesso del poro nucleare, suggerendo un suo possibile ruolo come mediatore degli scambi della membrana nucleare. È stata dimostrata inoltre la trascrizione dei due ncRNA in tessuti di tumore umano del rene, evidenziandone possibili ruoli nello sviluppo del cancro. È anche noto in letteratura che basse dosi di CPT in condizioni di ipossia diminuiscono i livelli di proteina di HIF-1α. Dopo aver dimostrato su diverse linee cellulari che i due ncRNA sopracitati non potessero essere implicati in tale effetto, abbiamo studiato le variazioni dell’intero miRnoma alle nuove condizioni sperimentali. In tal modo abbiamo scoperto che il miR-X sembra essere il mediatore molecolare dell’abbattimento di HIF-1α dopo trattamento con basse dosi di CPT in ipossia. Complessivamente, questi risultati suggeriscono che il fattore di trascrizione HIF-1α venga finemente regolato da RNA non-codificanti indotti da danno al DNA.

Design and implementation of a novel multi-constellation FPGA-based dual frequency GNSS receiver for space applications

The PhD activity described in the document is part of the Microsatellite and Microsystem Laboratory of the II Faculty of Engineering, University of Bologna. The main objective is the design and development of a GNSS receiver for the orbit determination of microsatellites in low earth orbit. The development starts from the electronic design and goes up to the implementation of the navigation algorithms, covering all the aspects that are involved in this type of applications. The use of GPS receivers for orbit determination is a consolidated application used in many space missions, but the development of the new GNSS system within few years, such as the European Galileo, the Chinese COMPASS and the Russian modernized GLONASS, proposes new challenges and offers new opportunities to increase the orbit determination performances. The evaluation of improvements coming from the new systems together with the implementation of a receiver that is compatible with at least one of the new systems, are the main activities of the PhD. The activities can be divided in three section: receiver requirements definition and prototype implementation, design and analysis of the GNSS signal tracking algorithms, and design and analysis of the navigation algorithms. The receiver prototype is based on a Virtex FPGA by Xilinx, and includes a PowerPC processor. The architecture follows the software defined radio paradigm, so most of signal processing is performed in software while only what is strictly necessary is done in hardware. The tracking algorithms are implemented as a combination of Phase Locked Loop and Frequency Locked Loop for the carrier, and Delay Locked Loop with variable bandwidth for the code. The navigation algorithm is based on the extended Kalman filter and includes an accurate LEO orbit model.

Sviluppo di metodologie per la Stima in Tempo Reale delle Grandezze Indicate in Motori a Combustione Interna

Modern Internal Combustion Engines are becoming increasingly complex in terms of their control systems and strategies. The growth of the algorithms’ complexity results in a rise of the number of on-board quantities for control purposes. In order to improve combustion efficiency and, simultaneously, limit the amount of pollutant emissions, the on-board evaluation of two quantities in particular has become essential; namely indicated torque produced by the engine and the angular position where 50% of fuel mass injected over an engine cycle is burned (MFB50). The above mentioned quantities can be evaluated through the measurement of in-cylinder pressure. Nonetheless, at the time being, the installation of in-cylinder pressure sensors on vehicles is extremely uncommon mainly because of measurement reliability and costs. This work illustrates a methodological approach for the estimation of indicated torque and MFB50 that is based on the engine speed fluctuation measurement. This methodology is compatible with the typical on-board application restraints. Moreover, it requires no additional costs since speed can be measured using the system already mounted on the vehicle, which is made of a magnetic pick-up faced to a toothed wheel. The estimation algorithm consists of two main parts: first, the evaluation of indicated torque fluctuation based on speed measurement and secondly, the evaluation of the mean value of the indicated torque (over an engine cycle) and MFB50 by using the relationship with the indicated torque harmonic and other engine quantities. The procedure has been successfully applied to an L4 turbocharged Diesel engine mounted on-board a vehicle.

Individuazione e caratterizzazione dei prodotti di degradazione ossidativa dei secoiridoidi nell'olio vergine di oliva mediante tecniche analitiche innovative

Lo scopo di questo lavoro di tesi è la caratterizzazione dei prodotti di ossidazione di diversi fenoli idrofili contenuti nell’olio vergine d’oliva come idrossitirosolo, tirosolo e la forma dialdeidica dell’acido decarbossimetil elenolico legato all’idrossitirosolo, e la loro identificazione nel prodotto durante la conservazione. L’obiettivo della ricerca è trovare degli indici analitici che possono essere usati sia come marker di “freschezza” dell’olio vergine di oliva sia nella valutazione della “shelf life” del prodotto stesso. Due sistemi di ossidazione sono stati usati per ossidare le molecole sopracitate: ossidazione enzimatica e ossidazione di Fenton. I prodotti di ossidazione sono stati identificati come chinoni, dimeri e acidi.

Streptococcus agalactiae adapts to glucose stress conditions by modulating gene expression profile

Diabetes mellitus is considered a risk factor for Group B Streptococcus (GBS) infections. Typically, this pathology is associated to high glucose levels in the bloodstream. Although clinical evidences support this notion, the physiological mechanisms underlying GBS adaptation to such conditions are not yet defined. In the attempt to address this issue, we performed comparative global gene expression analysis of GBS grown under glucose-stress conditions and observed that a number of metabolic and virulence genes was differentially regulated. Of importance, we also demonstrated that by knocking-out the csrRS locus the transcription profile of GBS grown in high-glucose conditions was profoundly affected, with more than a third of glucose-dependent genes, including the virulence factor bibA, found to be controlled by this two-component system. Furthermore, in vitro molecular analysis showed that CsrR specifically binds to the bibA promoter and the phosphorilation increases the affinity of the regulator to this promoter region. Moreover, we demonstrated that CsrR acts as a repressor of bibA expression by binding to its promoter in vivo. In conclusion, this work by elucidating both the response of GBS to pathological glucose conditions and the underlined molecular mechanisms will set the basis for a better understanding of GBS pathogenesis.

Pratiche del possibile: i Participatory Guarantee Systems e le scelte d'acquisto del consumatore brasiliano

Negli ultimi anni, parallelamente all’espansione del settore biologico, si è assistito a un crescente interesse per i modelli alternativi di garanzia dell’integrità e della genuinità dei prodotti biologici. Gruppi di piccoli agricoltori di tutto il mondo hanno iniziato a sviluppare approcci alternativi per affrontare i problemi connessi alla certificazione di terza parte. Queste pratiche sono note come Sistemi di Garanzia Partecipativa (PGS). Tali modelli: (i) si basano sugli standard di certificazione biologica dell’IFOAM, (ii) riguardano il complesso dei produttori di una comunità rurale, (iii) comportano l’inclusione di una grande varietà di attori e (iv) hanno lo scopo di ridurre al minimo burocrazia e costi semplificando le procedure di verifica e incorporando un elemento di educazione ambientale e sociale sia per i produttori sia per i consumatori. Gli obiettivi di questo lavoro di ricerca: • descrivere il funzionamento dei sistemi di garanzia partecipativa; • indicare i vantaggi della loro adozione nei Paesi in via di sviluppo e non; • illustrare il caso della Rede Ecovida de Agroecologia (Brasile); • offrire uno spunto di riflessione che riguarda il consumatore e la relativa fiducia nel modello PGS. L’impianto teorico fa riferimento alla Teoria delle Convenzioni. Sulla base del quadro teorico è stato costruito un questionario per i consumatori con lo scopo di testare l’appropriatezza delle ipotesi teoriche. I risultati finali riguardano la stima del livello di conoscenza attuale, la fiducia e la volontà d’acquisto dei prodotti PGS da parte dei consumatori nelle aree considerate. Sulla base di questa ricerca sarà possibile adattare ed esportare il modello empirico in altri paesi che presentano economie diverse per cercare di comprendere il potenziale campo di applicazione dei sistemi di garanzia partecipativa.

Semantic Service Architectures for Smart Environments

Many industries and academic institutions share the vision that an appropriate use of information originated from the environment may add value to services in multiple domains and may help humans in dealing with the growing information overload which often seems to jeopardize our life. It is also clear that information sharing and mutual understanding between software agents may impact complex processes where many actors (humans and machines) are involved, leading to relevant socioeconomic benefits. Starting from these two input, architectural and technological solutions to enable “environment-related cooperative digital services” are here explored. The proposed analysis starts from the consideration that our environment is physical space and here diversity is a major value. On the other side diversity is detrimental to common technological solutions, and it is an obstacle to mutual understanding. An appropriate environment abstraction and a shared information model are needed to provide the required levels of interoperability in our heterogeneous habitat. This thesis reviews several approaches to support environment related applications and intends to demonstrate that smart-space-based, ontology-driven, information-sharing platforms may become a flexible and powerful solution to support interoperable services in virtually any domain and even in cross-domain scenarios. It also shows that semantic technologies can be fruitfully applied not only to represent application domain knowledge. For example semantic modeling of Human-Computer Interaction may support interaction interoperability and transformation of interaction primitives into actions, and the thesis shows how smart-space-based platforms driven by an interaction ontology may enable natural ad flexible ways of accessing resources and services, e.g, with gestures. An ontology for computational flow execution has also been built to represent abstract computation, with the goal of exploring new ways of scheduling computation flows with smart-space-based semantic platforms.

Trascriptome analysis and functional genomics of Neisseria meningitidis in human blood

Neisseria meningitidis (Nm) is the major cause of septicemia and meningococcal meningitis. During the course of infection, it must adapt to different host environments as a crucial factor for survival. Despite the severity of meningococcal sepsis, little is known about how Nm adapts to permit survival and growth in human blood. A previous time-course transcriptome analysis, using an ex vivo model of human whole blood infection, showed that Nm alters the expression of nearly 30% of ORFs of the genome: major dynamic changes were observed in the expression of transcriptional regulators, transport and binding proteins, energy metabolism, and surface-exposed virulence factors. Starting from these data, mutagenesis studies of a subset of up-regulated genes were performed and the mutants were tested for the ability to survive in human whole blood; Nm mutant strains lacking the genes encoding NMB1483, NalP, Mip, NspA, Fur, TbpB, and LctP were sensitive to killing by human blood. Then, the analysis was extended to the whole Nm transcriptome in human blood, using a customized 60-mer oligonucleotide tiling microarray. The application of specifically developed software combined with this new tiling array allowed the identification of different types of regulated transcripts: small intergenic RNAs, antisense RNAs, 5’ and 3’ untranslated regions and operons. The expression of these RNA molecules was confirmed by 5’-3’RACE protocol and specific RT-PCR. Here we describe the complete transcriptome of Nm during incubation in human blood; we were able to identify new proteins important for survival in human blood and also to identify additional roles of previously known virulence factors in aiding survival in blood. In addition the tiling array analysis demonstrated that Nm expresses a set of new transcripts, not previously identified, and suggests the presence of a circuit of regulatory RNA elements used by Nm to adapt to proliferate in human blood.

Innovative architecture of on-board and on-ground radio systems for space communication

The radio communication system is one of the most critical system of the overall satellite platform: it often represents the only way of communication, between a spacecraft and the Ground Segment or among a constellation of satellites. This thesis focuses on specific innovative architectures for on-board and on-ground radio systems. In particular, this work is an integral part of a space program started in 2004 at the University of Bologna, Forlì campus, which led to the completion of the microsatellite ALMASat-1, successfully launched on-board the VEGA maiden flight. The success of this program led to the development of a second microsatellite, named ALMASat-EO, a three-axis stabilized microsatellite able to capture images of the Earth surface. Therefore, the first objective of this study was focused on the investigation of an innovative, efficient and low cost architecture for on-board radio communication systems. The TT&C system and the high data rate transmitter for images downlink design and realization are thoroughly described in this work, together with the development of the embedded hardware and the adopted antenna systems. Moreover, considering the increasing interest in the development of constellations of microsatellite, in particular those flying in close formations, a careful analysis has been carried out for the development of innovative communication protocols for inter-satellite links. Furthermore, in order to investigate the system aspects of space communications, a study has been carried out at ESOC having as objective the design, implementation and test of two experimental devices for the enhancement of the ESA GS. Thus, a significant portion of this thesis is dedicated to the description of the results of a method for improving the phase stability of GS radio frequency equipments by means of real-time phase compensation and a new way to perform two antennas arraying tracking using already existing ESA tracking stations facilities.

Characterization of the structure and iron uptake mechanisms of the Staphylococcus aureus ferric hydroxamate-binding lipoprotein FhuD2

The Reverse Vaccinology (RV) approach allows using genomic information for the delineation of new protein-based vaccines starting from an in silico analysis. The first powerful example of the application of the RV approach is given by the development of a protein-based vaccine against serogroup B Meningococcus. A similar approach was also used to identify new Staphylococcus aureus vaccine candidates, including the ferric hydroxamate-binding lipoprotein FhuD2. S. aureus is a widespread human pathogen, which employs various different strategies for iron uptake, including: (i) siderophore-mediated iron acquisition using the endogenous siderophores staphyloferrin A and B, (ii) siderophore-mediated iron acquisition using xeno-siderophores (the pathway exploited by FhuD2) and (iii) heme-mediated iron acquisition. In this work the high resolution crystal structure of FhuD2 in the iron (III)-siderophore-bound form was determined. FhuD2 belongs to the Periplasmic Binding Protein family (PBP ) class III, and is principally formed by two globular domains, at the N- and C-termini of the protein, that make up a cleft where ferrichrome-iron (III) is bound. The N- and C-terminal domains, connected by a single long α-helix, present Rossmann-like folds, showing a β-stranded core and an α-helical periphery, which do not undergo extensive structural rearrangement when they interact with the ligand, typical of class III PBP members. The structure shows that ferrichrome-bound iron does not come directly into contact with the protein; rather, the metal ion is fully coordinated by six oxygen donors of the hydroxamate groups of three ornithine residues, which, with the three glycine residues, make up the peptide backbone of ferrichrome. Furthermore, it was found that iron-free ferrichrome is able to subtract iron from transferrin. This study shows for the first time the structure of FhuD2, which was found to bind to siderophores ,and that the protein plays an important role in S. aureus colonization and infection phases.

Sicurezza nelle reti di sensori wireless UWB: generazione di chiavi simmetriche da parametri fisici

Le reti di oggetti intelligenti costituiscono una realtà che si sta affermando nel mondo quotidiano. Dispositivi capaci di comunicare tra loro, oltre che svolgere la propria funzione primaria, possono comporre una nuvola che faccia riferimento al legittimo proprietario. Un aspetto fondamentale di questo scenario riguarda la sicurezza, in particolar modo per garantire una comunicazione protetta. Il soddisfacimento di questo requisito è fondamentale anche per altri punti come l'integrità dell'informazione condivisa e l'autenticazione. Lo strumento più antico e tutt'ora adatto alla riservatezza di una comunicazione è costituito dalla crittografia. Una tecnica crittografica è schematicamente composta da un algoritmo che, a seconda di una chiave e del messaggio in ingresso, restituisce in uscita un messaggio cifrato, il crittogramma. Questo viene poi inviato e al legittimo destinatario che, essendo in possesso della chiave e dell'algoritmo, lo converte nel messaggio originale. L'obiettivo è rendere impossibile ad un utente malevolo - non dotato di chiave - la ricostruzione del messaggio. L'assunzione che l'algoritmo possa essere noto anche a terze parti concentra l'attenzione sul tema della chiave. La chiave deve essere sufficientemente lunga e casuale, ma soprattutto deve essere nota ai due utenti che intendono instaurare la comunicazione. Quest'ultimo problema, noto come distribuzione della chiave, è stato risolto con il sistema RSA a chiave pubblica. Il costo computazionale di questa tecnica, specialmente in un contesto di dispositivi non caratterizzati da grandi potenze di calcolo, suggerisce però la ricerca di strade alternative e meno onerose. Una soluzione promettente ed attualmente oggetto di studio sembra essere costituita dalle proprietà del canale wireless. Un ponte radio è caratterizzato da una funzione di trasferimento che dipende dall'ambiente in cui ci si trova e, per il teorema di reciprocità, risulta essere lo stesso per i due utenti che l'hanno instaurato. Oggetto della tesi è lo studio ed il confronto di alcune delle tecniche possibili per estrarre una chiave segreta da un mezzo condiviso, come quello del canale wireless. Si presenterà il contesto in cui verrà sviluppato l'elaborato. Si affronteranno in particolare due casi di interesse, costituiti dalla attuale tecnologia di propagazione del segnale a banda stretta (impiegata per la maggior parte delle trasmissioni senza fili) per passare a quella relativamente più recente della banda Ultra-larga (UWB). Verranno poi illustrate delle tecniche per ottenere stringhe di bit dai segnali acquisiti, e saranno proposti dei metodi per la loro correzione da eventuali discordanze. Saranno infine riportate le conclusioni sul lavoro svolto e le possibili strade future.

Design And Implementation Of An End-To-End Simulator For The BepiColombo Rotation Experiment

Among the scientific objectives addressed by the Radio Science Experiment hosted on board the ESA mission BepiColombo is the retrieval of the rotational state of planet Mercury. In fact, the estimation of the obliquity and the librations amplitude were proven to be fundamental for constraining the interior composition of Mercury. This is accomplished by the Mercury Orbiter Radio science Experiment (MORE) via a strict interaction among different payloads thus making the experiment particularly challenging. The underlying idea consists in capturing images of the same landmark on the surface of the planet in different epochs in order to observe a displacement of the identified features with respect to a nominal rotation which allows to estimate the rotational parameters. Observations must be planned accurately in order to obtain image pairs carrying the highest information content for the following estimation process. This is not a trivial task especially in light of the several dynamical constraints involved. Another delicate issue is represented by the pattern matching process between image pairs for which the lowest correlation errors are desired. The research activity was conducted in the frame of the MORE rotation experiment and addressed the design and implementation of an end-to-end simulator of the experiment with the final objective of establishing an optimal science planning of the observations. In the thesis, the implementation of the singular modules forming the simulator is illustrated along with the simulations performed. The results obtained from the preliminary release of the optimization algorithm are finally presented although the software implemented is only at a preliminary release and will be improved and refined in the future also taking into account the developments of the mission.

Insights in the maturation of pathogenic bacteria vaccine candidates using mass spectrometry based approaches

The study of the maturation process that occurs to a protein is of pivotal importance for the understanding of its function. This is true also in the vaccine field but in this case is also important to evaluate if inappropriate protein conformation and maturation play roles in the impairment of the functional immunogenicity of protein vaccines. Mass spectrometry (MS) is the method of choice for the study of the maturation process since each modification that occurs during the maturation will lead to a change in the mass of the entire protein. Therefore the aim of my thesis is the development of mass spectrometry-based approaches to study the maturation of proteins and the application of these methods to proteic vaccine candidates. The thesis is divided in two main parts. In the first part, I focused my attention on the study of the maturation of different vaccine candidates using native mass spectrometry. The analyses in this case have been performed using recombinant proteins produced in E. coli. In the second part I applied different MS strategies for the identification of unknown PTMs on pathogenic bacteria surface proteins since modified surface proteins are now considered for vaccine candidate selection.

Investigation on the Navigation Anomaly of Pioneer 10 and 11 probes

The present work consists of the investigation of the navigation of Pioneer 10 and 11 probes becoming known as the “Pioneer Anomaly”: the trajectories followed by the spacecrafts did not match the ones retrieved with standard navigation software. Mismatching appeared as a linear drift in the Doppler data received by the spacecrafts, which has been ascribed to a constant sunward acceleration of about 8.5×10-10 m/s2. The study presented hereafter tries to find a convincing explanation to this discrepancy. The research is based on the analysis of Doppler tracking data through the ODP (Orbit Determination Program), developed by NASA/JPL. The method can be summarized as: seek for any kind of physics affecting the dynamics of the spacecraft or the propagation of radiometric data, which may have not been properly taken into account previously, and check whether or not these might rule out the anomaly. A major effort has been put to build a thermal model of the spacecrafts for predicting the force due to anisotropic thermal radiation, since this is a model not natively included in the ODP. Tracking data encompassing more than twenty years of Pioneer 10 interplanetary cruise, plus twelve years of Pioneer 11 have been analyzed in light of the results of the thermal model. Different strategies of orbit determination have been implemented, including single arc, multi arc and stochastic filters, and their performance compared. Orbital solutions have been obtained without the needing of any acceleration other than the thermal recoil one indicating it as the responsible for the observed linear drift in the Doppler residuals. As a further support to this we checked that inclusion of additional constant acceleration as does not improve the quality of orbital solutions. All the tests performed lead to the conclusion that no anomalous acceleration is acting on Pioneers spacecrafts.

Studio e sperimentazione di leghe ad elevata deformazione per applicazioni nel settore della prima lavorazione di materiali lapidei

Studio del componente di supporto del cavo utensile per taglio di materiali lapidei. Analisi delle applicazioni di leghe superelastiche e delle modalità di realizzazione del cavo utensile complessivo in relazione a specifiche esigenze poste a livello industriale.