Diversity of cwp loci in clinical isolates of Clostridium difficile

An increased incidence of Clostridium difficile infection (CDI) is associated with the emergence of epidemic strains characterised by high genetic diversity. Among the factors that may have a role in CDI there is a family of 29 paralogs, the cell wall proteins (CWPs), which compose the outer layer of the bacterial cell and are likely to be involved in colonisation. Previous studies have shown that 12 of the29 cwp genes are clustered in the same region, named after slpA (cwp1) the slpA locus, whereas the remaining 17 paralogs are distributed throughout the genome. The variability of 14 of these 17 cwp paralogs was determined in 40 C. difficile clinical isolates belonging to six of the currently prevailing PCR ribotypes. Based on sequence conservation, these cwp genes were divided into two groups, one comprising cwp loci having highly conserved sequences in all isolates, and the other 5 loci showing low genetic conservation between isolates of the same PCR ribotype as well as between different PCR ribotypes. Three conserved CWPs, Cwp16, Cwp18 and Cwp25, and two variable ones, Cwp26 and Cwp27, were characterised further by Western blot analysis of total cell extracts or S-layer preparations of the C. difficile clinical isolates. Expression of genetically invariable CWPs is well conserved in all isolates, while genetically variable CWPs are not always expressed at comparable levels even in strains containing identical sequences but belonging to different PCR ribotypes. In addition, we chose to analyse the immune response obtained in a protection experiment, carried out in hamsters, using a protein microarray approach to study the in vivo expression and the immunoreactivity of several surface proteins, including 18 Cwps.

High-Speed Laser Processing of Thin Single and Multi-Layer Films

Theoretical models are developed for the continuous-wave and pulsed laser incision and cut of thin single and multi-layer films. A one-dimensional steady-state model establishes the theoretical foundations of the problem by combining a power-balance integral with heat flow in the direction of laser motion. In this approach, classical modelling methods for laser processing are extended by introducing multi-layer optical absorption and thermal properties. The calculation domain is consequently divided in correspondence with the progressive removal of individual layers. A second, time-domain numerical model for the short-pulse laser ablation of metals accounts for changes in optical and thermal properties during a single laser pulse. With sufficient fluence, the target surface is heated towards its critical temperature and homogeneous boiling or "phase explosion" takes place. Improvements are seen over previous works with the more accurate calculation of optical absorption and shielding of the incident beam by the ablation products. A third, general time-domain numerical laser processing model combines ablation depth and energy absorption data from the short-pulse model with two-dimensional heat flow in an arbitrary multi-layer structure. Layer removal is the result of both progressive short-pulse ablation and classical vaporisation due to long-term heating of the sample. At low velocity, pulsed laser exposure of multi-layer films comprising aluminium-plastic and aluminium-paper are found to be characterised by short-pulse ablation of the metallic layer and vaporisation or degradation of the others due to thermal conduction from the former. At high velocity, all layers of the two films are ultimately removed by vaporisation or degradation as the average beam power is increased to achieve a complete cut. The transition velocity between the two characteristic removal types is shown to be a function of the pulse repetition rate. An experimental investigation validates the simulation results and provides new laser processing data for some typical packaging materials.

Monitoring Complex Processes to Verify System Conformance: A Declarative Rule-Based Framework

Over the last 60 years, computers and software have favoured incredible advancements in every field. Nowadays, however, these systems are so complicated that it is difficult – if not challenging – to understand whether they meet some requirement or are able to show some desired behaviour or property. This dissertation introduces a Just-In-Time (JIT) a posteriori approach to perform the conformance check to identify any deviation from the desired behaviour as soon as possible, and possibly apply some corrections. The declarative framework that implements our approach – entirely developed on the promising open source forward-chaining Production Rule System (PRS) named Drools – consists of three components: 1. a monitoring module based on a novel, efficient implementation of Event Calculus (EC), 2. a general purpose hybrid reasoning module (the first of its genre) merging temporal, semantic, fuzzy and rule-based reasoning, 3. a logic formalism based on the concept of expectations introducing Event-Condition-Expectation rules (ECE-rules) to assess the global conformance of a system. The framework is also accompanied by an optional module that provides Probabilistic Inductive Logic Programming (PILP). By shifting the conformance check from after execution to just in time, this approach combines the advantages of many a posteriori and a priori methods proposed in literature. Quite remarkably, if the corrective actions are explicitly given, the reactive nature of this methodology allows to reconcile any deviations from the desired behaviour as soon as it is detected. In conclusion, the proposed methodology brings some advancements to solve the problem of the conformance checking, helping to fill the gap between humans and the increasingly complex technology.

Conjugation of Toll Like Receptor 7 agonist through conjugation to immunogenic proteins. Synthesis, characterization, formulation and pre-clinical evaluation

The next generation of vaccine adjuvant are represented by a wide ranging set of molecules called Toll like agonists (TLR’s). Although many of these molecules are complex structures extracted from microorganisms, small molecule TLR agonists have also been identified. However, delivery systems have not been optimized to allow their effective delivery in conjunction with antigens. Here we describe a novel approach in which a small molecule TLR agonist has been conjugated directly to antigens to ensure effective co delivery. We describe the conjugation of a relevant protein, a recombinant protective antigen from S.pneumoniae (RrgB), which is linked to a TLR7 agonist. Following thorough characterization to ensure there was no aggregation, the conjugate was evaluated in a murine infection model. Results showed that the conjugate extended animals’ survival after lethal challenge with S.pneumoniae. Comparable results were obtained with a 10 fold lower dose than that of the native unconjugated antigen. Notably, the animals immunized with the same dose of unconjugated TLR7 agonist and antigen showed no adjuvant effect. The increased immunogenicity was likely a consequence of the co-localization of TLR7 agonist and antigen by chemical binding and is was more effective than simple co-administration. Likely, this approach can be adopted to reduce the dose of antigen required to induce protective immunity, and potentially increase the safety of a broad variety of vaccine candidates

The silent survival of Staphylococcus aureus phagocyted by HL-60 derived neutrophils

Staphylococcus aureus is a Gram positive pathogen that causes various human infections and represents one of the most common causes of bacteremia. S. aureus is able to invade a variety of non-professional phagocytes and that can survive engulfment by neutrophils, producing both secreted and surface components that compromise innate immune responses. In the contest of our study we evaluated the functional activity of vaccine specific antibodies by opsonophagocytosis killing assay (OPKA). Interestingly a low level of killing of the staphylococcal cells has been observed. In the meanwhile intracellular survival studies showed that S. aureus persisted inside phagocytes for several hours until a burst of growth after 5 hours in the supernatant. These data suggest that the strong ability of S. aureus to survive in the phagocytes could be the cause of the low killing measured by OPKA. Moreover parallel studies on HL-60 cells infected with S. aureus done by using transmission electron microscopy (TEM) interestingly showed that staphylococcal cells have an intracellular localization (endosomal vacuoles) and that they are able not only to maintain the integrity of their membrane but also to replicate inside vacuolar compartments. Finally in order to generate 3D volume of whole bacteria when present inside neutrophilic vacuoles, we collected a series of tomographic two-dimensional (2D) images by using a transmission electron microscope, generating 5 different tomograms. The three-dimensional reconstruction reveals the presence of intact bacteria within neutrophil vacuoles. The S. aureus membrane appears completely undamaged and integral in contrast with the physiological process of phagosytosis through vacuoles progression. S. aureus bacteria show a homogenous distribution of the density in all the three dimensions (X, Y, Z). All these evidences definitely explain the ability of the pathogen to survive inside the endosomal vacuoles and should be the cause of the low killing level.

Studio della reattività di etanolo in fase gas su catalizzatori a base di MgO e Mg/Si/O

A causa delle questioni economiche ed ambientali legate alla sostenibilità dei processi petrolchimici, recentemente l'industria chimica ha focalizzato il proprio interesse nello sviluppo di processi per la produzione di chemicals, che utilizzino materiali di partenza rinnovabili. L'etanolo, prodotto per via fermentativa, sembra essere uno dei bio-building block più promettenti e versatili e può essere utilizzato per numerose applicazioni. È noto da tempo che l’etanolo può reagire su catalizzatori costituiti da ossidi misti con caratteristiche acido-base a dare numerosi composti chimici tra cui acetaldeide, 1,3-butadiene, 1-butanolo e 2-butenale. Nonostante il lungo impiego dell’etanolo nell’industria chimica, il meccanismo di formazione di composti C4 a partire da etanolo è ancora però materia di dibattito. Il meccanismo generalmente accettato si basa sulle seguenti reazioni chiave: deidrogenazione di etanolo ad acetaldeide e condensazione aldolica di due molecole di acetaldeide. Tuttavia in letteratura sono riportate anche altre proposte alternative. In questo lavoro è stato studiato il processo di trasformazione di etanolo su catalizzatori a base di MgO e sistemi misti Mg/SiO, attraverso esperimenti di reattività condotti in un micro-impianto da laboratorio, al fine di fare chiarezza sul meccanismo di formazione di composti C4 a partire da etanolo. In particolare è stato condotto uno studio meccanicistico utilizzando MgO come catalizzatore modello, materiale che possiede esclusivamente proprietà basiche, ritenute essenziali per catalizzare la condensazione di molecole C2. Inoltre, è stata investigata l’influenza delle caratteristiche acido-base del catalizzatore sulla selettività del processo di conversione di etanolo, studiandone la reattività su materiali costituiti da ossidi misti Mg/Si/O, con diverso rapporto atomico tra i due cationi.

Crescita di nanoparticelle in flusso di gas inerte

Lo scopo della seguente tesi è quello di illustrare la disposizione dei campioni di sistemi binari Mg Pd e di deposizioni singole di Ti, nell’abito di due progetti di ricerca, l’SSHS, Solide State Hydrogen Storage nell’ambito dell’Azione COST, e la produzione di titania (TiO2) per la fotocatalisi, sintetizzati in differenti reggimi di flusso di gas d’He, realizzando la crescita con il metodo IGC. Sono state illustrate le nuove proprietà e i metodi di formazione dei materiali nanostrutturati, per poi passare alla descrizione dell’apparato dove sono stati prodotti i campioni, con la conseguente spiegazione della progettazione del controllore di flusso dei sistemi di alimentazione e interfacciamento di quest’ultimo. Dopo un’accurata analisi al microscopio elettronico, `e stata descritta la morfologia dei campioni a due diversi reggimi di flusso di gas He, per i campioni di Mg Pd non sono state apprezzate differenze al variare del flusso, per il Ti, invece, si può notare una variazione morfologica legata alle dimensioni.

Ruolo delle architetture ad eventi nello sviluppo delle applicazioni moderne

Attualmente il panorama informatico è dominato dai dispositivi mobile: smartphone e tablet pc dominano incontrastati la scena del mercato elettronico. Questo comporta un radicale ripensamento e cambiamento del software, le web app e le mobile application richiedono infatti una sempre maggiore reattività dell’interfaccia utente, la persistente connessione a Internet e l’interazione con una moltitudine di dispositivi esterni. Il progettista di software deve oggi far fronte a tutta una serie di problematiche, l’aumentata complessità dei sistemi e i sempre più ristretti tempi di sviluppo e consegna richiedono compromessi tra la semplicità delle tecniche di progettazione e l’efficienza del prodotto ottenuto. Le architetture ad eventi in primis, unitamente al paradigma di programmazione asincrona, si pongono come soluzione ottimale a queste esigenze. L’obbiettivo principale di questa tesi è quello di offrire una panoramica generale sullo stato dell’arte delle architetture ad eventi focalizzandosi sul ruolo che esse assumono nel contesto delle applicazioni moderne, intendendo principalmente con questo termine le web application e le mobile application. Partendo dal concetto di programmazione sincrona e parallela si giunge a descrivere un terzo modello, il modello asincrono, di fondamentale importanza per i sistemi event-driven. Utilizzando come principale linguaggio di riferimento JavaScript si affrontano le problematiche legate alla stesura del codice per la gestione degli eventi, l’asincronicità intrinseca degli eventi e l’utilizzo di funzioni di callback portano a produrre codice di difficile lettura e manutenzione. Si analizzano quindi in dettaglio i pattern fondamentali e le tecniche attualmente utilizzate per l’ottimizzazione della gestione del codice e delle problematiche esposte fornendo numerosi esempi esplicativi.

Jesolo - area pineta un parco per la cultura

Il paesaggio lagunare porta i segni di importanti interventi antropici che si sono susseguiti dall’epoca romana ad oggi, a partire dalle prima centuriazioni, per seguire con le grandi opere di bonifica e deviazione dei fiumi sino alla rapida trasformazione di Jesolo Lido, da colonia elioterapica degli anni ‘30 a località turistica internazionale. L’insediamento nella zona “Parco Pineta” si propone come costruzione di un paesaggio artificiale, funzionale all’uso particolare del tempo libero in un grande spazio aperto, strettamente connesso alla città e aderente a luoghi precisamente connotati quali sono la pineta, il borgo, il canale e le residenze turistiche progettate dall’architetto Gonçalo Byrne. Le scale di progetto sono due, quella territoriale e quella architettonica. Il progetto mira a connettere i centri di Jesolo e Cortellazzo con un sistema di percorsi ciclabili. Il fiume Piave consente di combinare il turismo sostenibile con la possibilità di ripercorrere i luoghi delle memorie storiche legate al primo conflitto bellico mondiale. L’intenzione è quella di rendere Cortellazzo parte integrante di un itinerario storico, artistico e naturalistico. Il Parco Pineta si configurerebbe così come il punto di partenza di un percorso che risalendo il fiume collega il piccolo borgo di Cortellazzo con San Donà e con il suo già noto Parco della Scultura in Architettura. Alla scala territoriale è l’architettura del paesaggio, il segno materiale, l’elemento dominante e caratterizzante il progetto. L’articolazione spaziale dell’intervento è costruita seguendo la geometria dettata dall’organizzazione fondiaria e la griglia della città di fondazione, con l’intento chiaro di costruire un “fatto territoriale” riconoscibile. L’unità generale è affidata al quadrato della Grande Pianta entro il quale vengono definite le altre unità spaziali. L’insieme propone uno schema organizzativo semplice che, scavalcando il Canale Cavetta, ricongiunge le parti avulse del territorio. Il grande quadrato consente di frazionare gli spazi definendo sistemi integrati diversamente utilizzabili cosicché ogni parte dell’area di progetto abbia una sua connotazione e un suo interesse d’uso. In questo modo i vincoli morfologici dell’area permettono di costruire ambienti specificamente indirizzati non solo funzionalmente ma soprattutto nelle loro fattezze architettoniche e paesistiche. Oggetto di approfondimento della tesi è stato il dispositivo della piattaforma legata all’interpretazione del sistema delle terre alte e terre basse centrale nel progetto di Byrne. Sulla sommità della piattaforma poggiano gli edifici dell’auditorium e della galleria espositiva.

Dispositivi di ultima generazione per l'immunorivelazione di marcatori proteici in fase solida

Oggetto della presente tesi di Laurea è lo studio delle nuove tecnologie disponibili per l’immunorivelazione di marcatori proteici in fase solida. Particolare attenzione è stata rivolta alle problematiche e alle esigenze tecniche nella quantificazione del complesso proteico in esame a seguito della rivelazione di un segnale, testimone proporzionale della grandezza biologica in esame. In altre parole l’identificazione e la quantificazione di proteine di interesse avviene a valle di un processo, chiamato “western blotting”, che genera un segnale (colore, luce, fluorescenza) al quale riferire la sostanza molecolare della misura. L’accuratezza della quantificazione, a seguito degli errori sperimentali dovuti alla tecnologia, rappresenta un problema complesso nella pratica biochimica e nello studio dei fenomeni di variazione dell’espressione genica, ovvero del fenotipo, in un organismo. Il primo capitolo si apre con la descrizione del processo di discriminazione delle proteine in base al loro rapporto carica/massa molecolare tramite elettroforesi su gel. Il capitolo prosegue con la disamina della tecnologia di ultima generazione per la visualizzazione delle proteine risolte e la loro eventuale quantificazione, paragonandone le prestazioni rispetto ai sistemi di visualizzazione e quantificazione classici. Argomenti del secondo capitolo sono lo studio delle prestazioni delle nuove tecnologie per l’esecuzione del “blotting” su supporto solido e per l’incubazione delle proteine con immunoglobuline. Seguono, rispettivamente nei capitoli terzo e quarto, l’analisi delle tecnologie analogiche e digitali per la rivelazione del segnale e la quantificazione tramite opportuni software.

Characterization of fold-related fractures in the carbonate rocks of the Cingoli anticline, northern Apennines, Italy

Thrust fault-related folds in carbonate rocks are characterized by deformation accommodated by different structures, such as joints, faults, pressure solution seams, and deformation bands. Defining the development of fracture systems related to the folding process is significant both for theoretical and practical purposes. Fracture systems are useful constrains in order to understand the kinematical evolution of the fold. Furthermore, understanding the relationships between folding and fracturing provides a noteworthy contribution for reconstructing the geodynamic and the structural evolution of the studied area. Moreover, as fold-related fractures influence fluid flow through rocks, fracture systems are relevant for energy production (geothermal studies, methane and CO2 , storage and hydrocarbon exploration), environmental and social issues (pollutant distribution, aquifer characterization). The PhD project shows results of a study carried out in a multilayer carbonate anticline characterized by different mechanical properties. The aim of this study is to understand the factors which influence the fracture formation and to define their temporal sequence during the folding process. The studied are is located in the Cingoli anticline (Northern Apennines), which is characterized by a pelagic multilayer characterized by sequences with different mechanical stratigraphies. A multi-scale analysis has been made in several outcrops located in different structural positions. This project shows that the conceptual sketches proposed in literature and the strain distribution models outline well the geometrical orientation of most of the set of fractures observed in the Cingoli anticline. On the other hand, the present work suggests the relevance of the mechanical stratigraphy in particular controlling the type of fractures formed (e.g. pressure solution seams, joints or shear fractures) and their subsequent evolution. Through a multi-scale analysis, and on the basis of the temporal relationship between fracture sets and their orientation respect layering, I also suggest a conceptual model for fracture systems formation.

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.

Pervasive Sensing in Future Networks

Pervasive Sensing is a recent research trend that aims at providing widespread computing and sensing capabilities to enable the creation of smart environments that can sense, process, and act by considering input coming from both people and devices. The capabilities necessary for Pervasive Sensing are nowadays available on a plethora of devices, from embedded devices to PCs and smartphones. The wide availability of new devices and the large amount of data they can access enable a wide range of novel services in different areas, spanning from simple data collection systems to socially-aware collaborative filtering. However, the strong heterogeneity and unreliability of devices and sensors poses significant challenges. So far, existing works on Pervasive Sensing have focused only on limited portions of the whole stack of available devices and data that they can use, to propose and develop mainly vertical solutions. The push from academia and industry for this kind of services shows that time is mature for a more general support framework for Pervasive Sensing solutions able to enhance frail architectures, promote a well balanced usage of resources on different devices, and enable the widest possible access to sensed data, while ensuring a minimal energy consumption on battery-operated devices. This thesis focuses on pervasive sensing systems to extract design guidelines as foundation of a comprehensive reference model for multi-tier Pervasive Sensing applications. The validity of the proposed model is tested in five different scenarios that present peculiar and different requirements, and different hardware and sensors. The ease of mapping from the proposed logical model to the real implementations and the positive performance result campaigns prove the quality of the proposed approach and offer a reliable reference model, together with a direction for the design and deployment of future Pervasive Sensing applications.

Identification and functional characterization of human cytomegalovirus Fc binding proteins

ABSTRACT Human cytomegalovirus (HCMV) employs many different mechanisms to escape and subvert the host immune system surveillance. Among these different mechanisms the role of human IgG Fc receptors (FcγR) in HCMV pathogenesis is still unclear. In mammalians, FcγRs are expressed on the surface of all haematopoietic cells and have a multifaceted role in regulating the activity of antibodies to generate a well-balanced immune response. Viral proteins with Fcγ binding ability are highly diffuse among herpesviruses. They interfere with the host receptors functions in order to counteract immune system recognition. So far, two human HCMV Fcγ binding proteins have been described: UL119 and RL11. This work was aimed to the identification and characterization of HCMV Fcγ binding proteins. The study is divided in two parts: first the characterization of UL119 and RL11; second the identification and characterization of novel HCMV Fcγ binding proteins. Regarding the first part, we demonstrated that both UL119 and RL11 internalize Fcγ fragments from transfected cells surface through a clathrin dependent pathway. In infected cells both proteins were found in the viral assembly complex and on virions surface as envelope associated glycoproteins. Moreover, internalized Fcγ in infected cells do not undergo lysosomal degradation but rather traffic in early endosomes up to the viral assembly complex. Regarding the second part, we were able to identify two novels Fcγ binding protein coded by CMV: RL12 and RL13. The latter was also further characterized as recombinant protein in terms of cellular localization, Fc binding site and IgG internalization ability. Finally binding specificity of both RL12 and RL13 seems to be confined to human IgG1 and IgG2. Taken together, these data show that HCMV codes for up to 4 FcγR and that they could have a double role both on virus and on infected cells.

Thermodynamic and mechanical properties of polymer-solvent systems

This work presents the results of theoretical and experimental characterization of thermodynamic, mechanical and transport properties in polymer solvent systems. The polymer solvent pairs considered ranged to those in which the polymer is rubbery, to those in which the initially glassy polymeric matrix is plasticized by the action of the low molecular weight species. Advanced Equation of State models have been adopted for thermodynamic modeling,along with a rigorous procedure that enables to extend their applicability to the non equilibrium, glassy region. Mass sorption kinetics had been modeled with phenomenological models and with advanced kinetic models.