Molecular architecture of fur binding to iron-induced and - repressed genes in Helicobacter pylori

The ferric uptake regulator protein Fur regulates iron-dependent gene expression in bacteria. In the human pathogen Helicobacter pylori, Fur has been shown to regulate iron-induced and iron-repressed genes. Herein we investigate the molecular mechanisms that control this differential iron-responsive Fur regulation. Hydroxyl radical footprinting showed that Fur has different binding architectures, which characterize distinct operator typologies. On operators recognized with higher affinity by holo-Fur, the protein binds to a continuous AT-rich stretch of about 20 bp, displaying an extended protection pattern. This is indicative of protein wrapping around the DNA helix. DNA binding interference assays with the minor groove binding drug distamycin A, point out that the recognition of the holo-operators occurs through the minor groove of the DNA. By contrast, on the apo-operators, Fur binds primarily to thymine dimers within a newly identified TCATTn10TT consensus element, indicative of Fur binding to one side of the DNA, in the major groove of the double helix. Reconstitution of the TCATTn10TT motif within a holo-operator results in a feature binding swap from an holo-Fur- to an apo-Fur-recognized operator, affecting both affinity and binding architecture of Fur, and conferring apo-Fur repression features in vivo. Size exclusion chromatography indicated that Fur is a dimer in solution. However, in the presence of divalent metal ions the protein is able to multimerize. Accordingly, apo-Fur binds DNA as a dimer in gel shift assays, while in presence of iron, higher order complexes are formed. Stoichiometric Ferguson analysis indicates that these complexes correspond to one or two Fur tetramers, each bound to an operator element. Together these data suggest that the apo- and holo-Fur repression mechanisms apparently rely on two distinctive modes of operator-recognition, involving respectively the readout of a specific nucleotide consensus motif in the major groove for apo-operators, and the recognition of AT-rich stretches in the minor groove for holo-operators, whereas the iron-responsive binding affinity is controlled through metal-dependent shaping of the protein structure in order to match preferentially the major or the minor groove.

Transcriptional functions of DNA Topoisomerases at a genome-wide scale and a single gene levels

The DNA topology is an important modifier of DNA functions. Torsional stress is generated when right handed DNA is either over- or underwound, producing structural deformations which drive or are driven by processes such as replication, transcription, recombination and repair. DNA topoisomerases are molecular machines that regulate the topological state of the DNA in the cell. These enzymes accomplish this task by either passing one strand of the DNA through a break in the opposing strand or by passing a region of the duplex from the same or a different molecule through a double-stranded cut generated in the DNA. Because of their ability to cut one or two strands of DNA they are also target for some of the most successful anticancer drugs used in standard combination therapies of human cancers. An effective anticancer drug is Camptothecin (CPT) that specifically targets DNA topoisomerase 1 (TOP 1). The research project of the present thesis has been focused on the role of human TOP 1 during transcription and on the transcriptional consequences associated with TOP 1 inhibition by CPT in human cell lines. Previous findings demonstrate that TOP 1 inhibition by CPT perturbs RNA polymerase (RNAP II) density at promoters and along transcribed genes suggesting an involvement of TOP 1 in RNAP II promoter proximal pausing site. Within the transcription cycle, promoter pausing is a fundamental step the importance of which has been well established as a means of coupling elongation to RNA maturation. By measuring nascent RNA transcripts bound to chromatin, we demonstrated that TOP 1 inhibition by CPT can enhance RNAP II escape from promoter proximal pausing site of the human Hypoxia Inducible Factor 1 (HIF-1) and c-MYC genes in a dose dependent manner. This effect is dependent from Cdk7/Cdk9 activities since it can be reversed by the kinases inhibitor DRB. Since CPT affects RNAP II by promoting the hyperphosphorylation of its Rpb1 subunit the findings suggest that TOP 1inhibition by CPT may increase the activity of Cdks which in turn phosphorylate the Rpb1 subunit of RNAP II enhancing its escape from pausing. Interestingly, the transcriptional consequences of CPT induced topological stress are wider than expected. CPT increased co-transcriptional splicing of exon1 and 2 and markedly affected alternative splicing at exon 11. Surprisingly despite its well-established transcription inhibitory activity, CPT can trigger the production of a novel long RNA (5’aHIF-1) antisense to the human HIF-1 mRNA and a known antisense RNA at the 3’ end of the gene, while decreasing mRNA levels. The effects require TOP 1 and are independent from CPT induced DNA damage. Thus, when the supercoiling imbalance promoted by CPT occurs at promoter, it may trigger deregulation of the RNAP II pausing, increased chromatin accessibility and activation/derepression of antisense transcripts in a Cdks dependent manner. A changed balance of antisense transcripts and mRNAs may regulate the activity of HIF-1 and contribute to the control of tumor progression After focusing our TOP 1 investigations at a single gene level, we have extended the study to the whole genome by developing the “Topo-Seq” approach which generates a map of genome-wide distribution of sites of TOP 1 activity sites in human cells. The preliminary data revealed that TOP 1 preferentially localizes at intragenic regions and in particular at 5’ and 3’ ends of genes. Surprisingly upon TOP 1 downregulation, which impairs protein expression by 80%, TOP 1 molecules are mostly localized around 3’ ends of genes, thus suggesting that its activity is essential at these regions and can be compensate at 5’ ends. The developed procedure is a pioneer tool for the detection of TOP 1 cleavage sites across the genome and can open the way to further investigations of the enzyme roles in different nuclear processes.

Monooxygenases involved in the n-alkanes metabolism by Rhodococcus sp. BCP1: molecular characterization and expression of alkB gene

Bioremediation implies the use of living organisms, primarily microorganisms, to convert environmental contaminants into less toxic forms. The impact of the consequences of hydrocarbon release in the environment maintain a high research interest in the study of microbial metabolisms associated with the biodegradation of aromatic and aliphatic hydrocarbons but also in the analysis of microbial enzymes that can convert petroleum substrates to value-added products. The studies described in this Thesis fall within the research field that directs the efforts into identifying gene/proteins involved in the catabolism of n-alkanes and into studying the regulatory mechanisms leading to their oxidation. In particular the studies were aimed at investigating the molecular aspects of the ability of Rhodococcus sp. BCP1 to grow on aliphatic hydrocarbons as sole carbon and energy sources. We studied the ability of Rhodococcus sp. BCP1 to grow on gaseous (C2-C4), liquid (C5-C16) and solid (C17-C28) n-alkanes that resulted to be biochemically correlated with the activity of one or more monooxygenases. In order to identify the alkane monooxygenase that is involved in the n-alkanes degradation pathway in Rhodococcus sp. BCP1, PCR-based methodology was applied by using degenerate primers targeting AlkB monooxygenase family members. As result, a chromosomal region, including the alkB gene cluster, was cloned from Rhodococcus sp. BCP1 genome. We characterized the products of this alkB gene cluster and the products of the orfs included in the flanking regions by comparative analysis with the homologues in the database. alkB gene expression studies were carried out by RT-PCR and by the construction of a promoter probe vector containing the lacZ gene downstream of the alkB promoter. B-galactosidase assays revealed the alkB promoter activity induced by n-alkanes and by n-alkanes metabolic products. Furthermore, the transcriptional start of alkB gene was determined by primer extension procedure. A proteomic approach was subsequently applied to compare the protein patterns expressed by BCP1 growing on n-butane, n-hexane, n-hexadecane or n-eicosane with the protein pattern expressed by BCP1 growing on succinate. The accumulation of enzymes specifically induced on n-alkanes was determined. These enzymes were identified by tandem mass spectrometry (LC/MS/MS). Finally, a prm gene, homologue to the gene family coding for soluble di-iron monooxygenases (SDIMOs), has been isolated from Rhodococcus sp. BCP1 genome. This gene product could be involved in the degradation of gaseous n-alkanes in this Rhodococcus strain. The versatility in utilizing hydrocarbons and the discovery of new remarkable metabolic activities outline the potential applications of this microorganism in environmental and industrial biotechnologies.

Functional characterization of Streptococcus pyogenes pili

Group A Streptococcus is a Gram-positive human pathogen able to colonize both upper respiratory tract and skin. GAS is responsible for several acute diseases and autoimmune sequelae that account for half a million deaths worldwide every year (Cunningham et al., 2000). As other bacteria, GAS infections requires the capacity of the pathogen to adhere to host tissues and to form cell aggregates. The ability to persist in distinct host niches like the throat and the skin and to trigger infections is associated with the expression of different GAS virulence factors. GAS pili has been described as important virulence factors encoded by different FCT-operon regions. Based on this information, we decided to study the possible effect of environmental conditions that could regulate the pili expression. In this study we reported the influence of pH environment variations in biofilm formation for strains pertaining to a panel of different GAS FCT-types. The biofilm formation was promoted, excepted in the FCT-1 strains, by a changing in pH from physiological to acidic condition of growth in in vitro biofilm assay. By analyzing the possible association between biofilm formation and pH dependence, we have found that in FCT-2 and FCT-3 strains, the biofilm is promoted by pH reduction leading to an increase of pili expression. These data confirmed a direct link between pH dependent pilus expression and biofilm formation in GAS. As pili are a multi component structure we decided to investigate the functional role of one of its subunits, the AP-1 protein. AP-1 is highly conserved through the different FCT-types and suggests a possible essential role for the pili function. We focused our attention on the AP-1 protein encoded by the FCT-1 strains (M6). In particular this AP-1 protein contains the von Willebrand Factor A (VWFA) domain, which share an homology with the human VWFA domain that has been reported to be involved in adhesion process. We have demonstrated that the AP-1 protein binds to human epithelial cells by its VWFA domain, whereas the biofilm formation is mediated by the N-terminal region of AP-1 protein. Moreover, analyzing the importance of AP-1 in in vivo experiments we found a major capacity of tissue dissemination for the wild-type strain compared to the isogenic AP-1 deletion mutant. Pili have been also reported as potential vaccine candidates against Gram positive bacteria. For these reason we decided to investigate the relationship between cross reaction of sera raised against different GAS and GBS pilin subunits and the presence of a conserved Cna_B domain, in different pilin components. Our idea was to investigate if, using pilus conserved domains, a broad coverage vaccine against streptococcal infection could be possible.

Display Caotico. Mutazioni nell'arte del mostrare dagli anni Sessanta ad oggi

La mostra è diventata un nuovo paradigma della cultura contemporanea. Sostenuta da proprie regole e da una grammatica complessa produce storie e narrazioni. La presente ricerca di dottorato si struttura come un ragionamento critico sulle strategie del display contemporaneo, tentando di dimostrare, con strumenti investigativi eterogenei, assumendo fonti eclettiche e molteplici approcci disciplinari - dall'arte contemporanea, alla critica d'arte, la museologia, la sociologia, l'architettura e gli studi curatoriali - come il display sia un modello discorsivo di produzione culturale con cui il curatore si esprime. La storia delle esposizioni del XX secolo è piena di tentativi di cambiamento del rapporto tra lo sviluppo di pratiche artistiche e la sperimentazione di un nuovo concetto di mostra. Nei tardi anni Sessanta l’ingresso, nella scena dell’arte, dell’area del concettuale, demolisce, con un azzeramento radicale, tutte le convenzioni della rappresentazione artistica del dopoguerra, ‘teatralizzando’ il medium della mostra come strumento di potere e introducendo un nuovo “stile di presentazione” dei lavori, un display ‘dematerializzato” che rovescia le classiche relazioni tra opera, artista, spazio e istituzione, tra un curatore che sparisce (Siegelaub) e un curatore super-artista (Szeemann), nel superamento del concetto tradizionale di mostra stessa, in cui il lavoro del curatore, in quanto autore creativo, assumeva una propria autonomia strutturale all’interno del sistema dell’arte. Lo studio delle radici di questo cambiamento, ossia l’emergere di due tipi di autorialità: il curatore indipendente e l’artista che produce installazioni, tra il 1968 e il 1972 (le mostre di Siegelaub e Szeemann, la mimesi delle pratiche artistiche e curatoriali di Broodthaers e la tensione tra i due ruoli generata dalla Critica Istituzionale) permette di inquadrare teoricamente il fenomeno. Uno degli obbiettivi della ricerca è stato anche affrontare la letteratura critica attraverso una revisione/costruzione storiografica sul display e la storia delle teorie e pratiche curatoriali - formalizzata in modo non sistematico all'inizio degli anni Novanta, a partire da una rilettura retrospettiva della esperienze delle neoavanguardie – assumendo materiali e metodologie provenienti, come già dichiarato, da ambiti differenti, come richiedeva la composizione sfaccettata e non fissata dell’oggetto di studio, con un atteggiamento che si può definire comparato e post-disciplinare. Il primo capitolo affronta gli anni Sessanta, con la successione sistematica dei primi episodi sperimentali attraverso tre direzioni: l’emergere e l’affermarsi del curatore come autore, la proliferazione di mostre alternative che sovvertivano il formato tradizionale e le innovazioni prodotte dagli artisti organizzatori di mostre della Critica Istituzionale. Esponendo la smaterializzazione concettuale, Seth Siegelaub, gallerista, critico e impresario del concettuale, ha realizzato una serie di mostre innovative; Harald Szeemann crea la posizione indipendente di exhibition maker a partire When attitudes become forms fino al display anarchico di Documenta V; gli artisti organizzatori di mostre della Critica Istituzionale, soprattutto Marcel Broodhthears col suo Musée d’Art Moderne, Départment des Aigles, analizzano la struttura della logica espositiva come opera d’arte. Nel secondo capitolo l’indagine si sposta verso la scena attivista e alternativa americana degli anni Ottanta: Martha Rosler, le pratiche community-based di Group Material, Border Art Workshop/Taller de Arte Fronterizo, Guerrilla Girls, ACT UP, Art Workers' Coalition che, con proposte diverse elaborano un nuovo modello educativo e/o partecipativo di mostra, che diventa anche terreno del confronto sociale. La mostra era uno svincolo cruciale tra l’arte e le opere rese accessibili al pubblico, in particolare le narrazioni, le idee, le storie attivate, attraverso un originale ragionamento sulle implicazioni sociali del ruolo del curatore che suggeriva punti di vista alternativi usando un forum istituzionale. Ogni modalità di display stabiliva relazioni nuove tra artisti, istituzioni e audience generando abitudini e rituali diversi per guardare la mostra. Il potere assegnato all’esposizione, creava contesti e situazioni da agire, che rovesciavano i metodi e i formati culturali tradizionali. Per Group Material, così come nelle reading-room di Martha Rosler, la mostra temporanea era un medium con cui si ‘postulavano’ le strutture di rappresentazione e i modelli sociali attraverso cui, regole, situazioni e luoghi erano spesso sovvertiti. Si propongono come artisti che stanno ridefinendo il ruolo della curatela (significativamente scartano la parola ‘curatori’ e si propongono come ‘organizzatori’). La situazione cambia nel 1989 con la caduta del muro di Berlino. Oltre agli sconvolgimenti geopolitici, la fine della guerra fredda e dell’ideologia, l’apertura ai flussi e gli scambi conseguenti al crollo delle frontiere, i profondi e drammatici cambiamenti politici che coinvolgono l’Europa, corrispondono al parallelo mutamento degli scenari culturali e delle pratiche espositive. Nel terzo capitolo si parte dall’analisi del rapporto tra esposizioni e Late Capitalist Museum - secondo la definizione di Rosalind Krauss - con due mostre cruciali: Le Magiciens de la Terre, alle origini del dibattito postcoloniale e attraverso il soggetto ineffabile di un’esposizione: Les Immatériaux, entrambe al Pompidou. Proseguendo nell’analisi dell’ampio corpus di saggi, articoli, approfondimenti dedicati alle grandi manifestazioni internazionali, e allo studio dell’espansione globale delle Biennali, avviene un cambiamento cruciale a partire da Documenta X del 1997: l’inclusione di lavori di natura interdisciplinare e la persistente integrazione di elementi discorsivi (100 days/100 guests). Nella maggior parte degli interventi in materia di esposizioni su scala globale oggi, quello che viene implicitamente o esplicitamente messo in discussione è il limite del concetto e della forma tradizionale di mostra. La sfida delle pratiche contemporanee è non essere più conformi alle tre unità classiche della modernità: unità di tempo, di spazio e di narrazione. L’episodio più emblematico viene quindi indagato nel terzo capitolo: la Documenta X di Catherine David, il cui merito maggiore è stato quello di dichiarare la mostra come format ormai insufficiente a rappresentare le nuove istanze contemporanee. Le quali avrebbero richiesto - altrimenti - una pluralità di modelli, di spazi e di tempi eterogenei per poter divenire un dispositivo culturale all’altezza dei tempi. La David decostruisce lo spazio museale come luogo esclusivo dell’estetico: dalla mostra laboratorio alla mostra come archivio, l’evento si svolge nel museo ma anche nella città, con sottili interventi di dissimulazione urbana, nel catalogo e nella piattaforma dei 100 giorni di dibattito. Il quarto capitolo affronta l’ultima declinazione di questa sperimentazione espositiva: il fenomeno della proliferazione delle Biennali nei processi di globalizzazione culturale. Dalla prima mostra postcoloniale, la Documenta 11 di Okwui Enwezor e il modello delle Platforms trans-disciplinari, al dissolvimento dei ruoli in uno scenario post-szeemanniano con gli esperimenti curatoriali su larga scala di Sogni e conflitti, alla 50° Biennale di Venezia. Sono analizzati diversi modelli espositivi (la mostra-arcipelago di Edouard Glissant; il display in crescita di Zone of Urgency come estetizzazione del disordine metropolitano; il format relazionale e performativo di Utopia Station; il modello del bric à brac; la “Scuola” di Manifesta 6). Alcune Biennali sono state sorprendentemente autoriflessive e hanno consentito un coinvolgimento più analitico con questa particolare forma espressiva. Qual è l'impatto sulla storia e il dibattito dei sistemi espositivi? Conclusioni: Cos’è la mostra oggi? Uno spazio sotto controllo, uno spazio del conflitto e del dissenso, un modello educativo e/o partecipativo? Una piattaforma, un dispositivo, un archivio? Uno spazio di negoziazione col mercato o uno spazio di riflessione e trasformazione? L’arte del display: ipotesi critiche, prospettive e sviluppi recenti.

Sistemi embedded open source: Arduino come caso di studio

Il lavoro svolto in questa tesi è stato quello di introdurre alcuni concetti importanti dei sistemi embedded, in particolare ci si è soffermati su quelli open source. È stato trattato nello specifico Arduino come esempio di sistema embedded open source a basso costo.

Analisi numerica della combustione di gas a basso potere calorifico per applicazioni a microturbine a gas

Il presente lavoro si occupa dell’analisi numerica di combustione di gas a basso potere calorifico (gas di sintesi derivanti da pirolisi di biomasse). L’analisi è stata condotta su due principali geometrie di camera di combustione. La prima è un bruciatore sperimentale da laboratorio adatto allo studio delle proprietà di combustione del singas. Esso è introdotto in camera separatamente rispetto ad una corrente d’aria comburente al fine di realizzare una combustione non-premiscelata diffusiva in presenza di swirl. La seconda geometria presa in considerazione è la camera di combustione anulare installata sulla microturbina a gas Elliott TA 80 per la quale si dispone di un modello installato al banco al fine dell’esecuzione di prove sperimentali. I principali obbiettivi conseguiti nello studio sono stati la determinazione numerica del campo di moto a freddo su entrambe le geometrie per poi realizzare simulazioni in combustione mediante l’utilizzo di diversi modelli di combustione. In particolare è stato approfondito lo studio dei modelli steady laminar flamelet ed unsteady flamelet con cui sono state esaminate le distribuzioni di temperatura e delle grandezze tipiche di combustione in camera, confrontando i risultati numerici ottenuti con altri modelli di combustione (Eddy Dissipation ed ED-FR) e con i dati sperimentali a disposizione. Di importanza fondamentale è stata l’analisi delle emissioni inquinanti, realizzata per entrambe le geometrie, che mostra l’entità di tali emissioni e la loro tipologia. Relativamente a questo punto, il maggior interesse si sposta sui risultati ottenuti numericamente nel caso della microturbina, per la quale sono a disposizione misure di emissione ottenute sperimentalmente. Sempre per questa geometria è stato inoltre eseguito il confronto fra microturbina alimentata con singas a confronto con le prestazioni emissive ottenute con il gas naturale. Nel corso dei tre anni, l’esecuzione delle simulazioni e l’analisi critica dei risultati ha suggerito alcuni limiti e semplificazioni eseguite sulle griglie di calcolo realizzate per lo studio numerico. Al fine di eliminare o limitare le semplificazioni o le inesattezze, le geometrie dei combustori e le griglie di calcolo sono state migliorate ed ottimizzate. In merito alle simulazioni realizzate sulla geometria del combustore della microturbina Elliott TA 80 è stata condotta dapprima l’analisi numerica di combustione a pieno carico per poi analizzare le prestazioni ai carichi parziali. Il tutto appoggiandosi a tecniche di simulazione RANS ed ipotizzando alimentazioni a gas naturale e singas derivato da biomasse. Nell’ultimo anno di dottorato è stato dedicato tempo all’approfondimento e allo studio della tecnica Large Eddy Simulation per testarne una applicazione alla geometria del bruciatore sperimentale di laboratorio. In tale simulazione è stato implementato l’SGS model di Smagorinsky-Lilly completo di combustione con modelli flamelet. Dai risultati sono stati estrapolati i profili di temperatura a confronto con i risultati sperimentali e con i risultati RANS. Il tutto in diverse simulazioni a diverso valore del time-step imposto. L’analisi LES, per quanto migliorabile, ha fornito risultati sufficientemente precisi lasciando per il futuro la possibilità di approfondire nuovi modelli adatti all’applicazione diretta sulla MTG.

New insight on a Group A Streptococcus protective antigen contributing to bacterial cell division

Bioinformatic analysis of Group A Streptococcus (GAS) genomes aiming at the identification of new vaccine antigens, revealed the presence of a gene coding for a putative surface-associated protein, named GAS40, inducing protective antibodies in an animal model of sepsis. The aim of our study was to unravel the involvement of GAS40 in cell division processes and to identify the putative interactor. Firstly, bioinformatic analysis showed that gas40 shares homology with ezrA, a gene coding for a negative regulator of Z-ring formation during cell division process. Both scanning and transmission electron microscopy indicated morphological differences between wild-type and the GAS40 knock-out mutant strain, with the latter showing an impaired capacity to divide resulting in the formation of very long chains. Moreover, when the localization of the antigen on the bacterial surface was analyzed, we found that in bacteria grown at exponential phase GAS40 specifically localized at septum, indicating a possible role in cell division. Furthermore, by ELISA and co-sedimentation assays, we found that GAS40 is able to interact with FtsZ, a protein involved in Z-ring formation during cell division process. These data together with the co-localization of GAS40/FtsZ at bacterial septum demonstrated by by confocal microscopy, strongly support the hypothesis for a key role of GAS40 in bacterial cell division.

Identification and characterization of the sRNA network in Neisseria meningitidis

Bacterial small regulatory RNAs (sRNAs) are posttranscriptional regulators involved in stress responses. These short non-coding transcripts are synthesised in response to a signal, and control gene expression of their regulons by modulating the translation or stability of the target mRNAs, often in concert with the RNA chaperone Hfq. Characterization of a Hfq knock out mutant in Neisseria meningitidis revealed that it has a pleiotropic phenotype, suggesting a major role for Hfq in adaptation to stresses and virulence and the presence of Hfq-dependent sRNA activity. Global gene expression analysis of regulated transcripts in the Hfq mutant revealed the presence of a regulated sRNA, incorrectly annotated as an open reading frame, which we renamed AniS. The synthesis of this novel sRNA is anaerobically induced through activation of its promoter by the FNR global regulator and through global gene expression analyses we identified at least two predicted mRNA targets of AniS. We also performed a detailed molecular analysis of the action of the sRNA NrrF,. We demonstrated that NrrF regulates succinate dehydrogenase by forming a duplex with a region of complementarity within the sdhDA region of the succinate dehydrogenase transcript, and Hfq enhances the binding of this sRNA to the identified target in the sdhCDAB mRNA; this is likely to result in rapid turnover of the transcript in vivo. In addition, in order to globally investigate other possible sRNAs of N. meningitdis we Deep-sequenced the transcriptome of this bacterium under both standard in vitro and iron-depleted conditions. This analysis revealed genes that were actively transcribed under the two conditions. We focused our attention on the transcribed non-coding regions of the genome and, along with 5’ and 3’ untranslated regions, 19 novel candidate sRNAs were identified. Further studies will be focused on the identification of the regulatory networks of these sRNAs, and their targets.

Epidemiological and functional characterization of Streptococcus pneumoniae pili

Streptococcus pneumoniae is an important life threatening human pathogen causing agent of invasive diseases such as otitis media, pneumonia, sepsis and meningitis, but is also a common inhabitant of the respiratory tract of children and healthy adults. Likewise most streptococci, S. pneumoniae decorates its surface with adhesive pili, composed of covalently linked subunits and involved in the attachment to epithelial cells and virulence. The pneumococcal pili are encoded by two genomic regions, pilus islet 1 (PI-1), and pilus islet-2 (PI-2), which are present in about 30% and 16% of the pneumococcal strains, respectively. PI-1 exists in three clonally related variants, whereas PI-2 is highly conserved. The presence of the islets does not correlate with the serotype of the strains, but with the genotype (as determined by Multi Locus Sequence Typing). The prevalence of PI-1 and PI-2 positive strains is similar in isolates from invasive disease and carriage. To better dissect a possible association between PIs presence and disease we evaluated the distribution of the two PIs in a panel of 113 acute otitis media (AOM) clinical isolates from Israel. PI-1 was present in 30.1% (N=34) of the isolates tested, and PI-2 in 7% (N=8). We found that 50% of the PI-1 positive isolates belonged to the international clones Spain9V-3 (ST156) and Taiwan19F-14 (ST236), and that PI-2 was not present in the absence of Pl-1. In conclusion, there was no correlation between PIs presence and AOM, and, in general, the observed differences in PIs prevalence are strictly dependent upon regional differences in the distribution of the clones. Finally, in the AOM collection the prevalence of PI-1 was higher among antibiotic resistant isolates, confirming previous indications obtained by the in silico analysis of the MLST database collection. Since the pilus-1 subunits were shown to confer protection in mouse models of infection both in active and passive immunization studies, and were regarded as potential candidates for a new generation of protein-based vaccines, the functional characterization was mainly focused on S. pneumoniae pilus -1 components. The pneumococcal pilus-1 is composed of three subunits, RrgA, RrgB and RrgC, each stabilized by intra-molecular isopeptide bonds and covalently polymerized by means of inter-molecular isopeptide bonds to form an extended fibre. The pilus shaft is a multimeric structure mainly composed by the RrgB backbone subunit. The minor ancillary proteins are located at the tip and at the base of the pilus, where they have been proposed to act as the major adhesin (RrgA) and as the pilus anchor (RrgC), respectively. RrgA is protective in in vivo mouse models, and exists in two variants (clades I and II). Mapping of the sequence variability onto the RrgA structure predicted from X-ray data showed that the diversity was restricted to the “head” of the protein, which contains the putative binding domains, whereas the elongated “stalk” was mostly conserved. To investigate whether this variability could influence the adhesive capacity of RrgA and to map the regions important for binding, two full-length protein variants and three recombinant RrgA portions were tested for adhesion to lung epithelial cells and to purified extracellular matrix (ECM) components. The two RrgA variants displayed similar binding abilities, whereas none of the recombinant fragments adhered at levels comparable to those of the full-length protein, suggesting that proper folding and structural arrangement are crucial to retain protein functionality. Furthermore, the two RrgA variants were shown to be cross-reactive in vitro and cross-protective in vivo in a murine model of passive immunization. Taken together, these data indicate that the region implicated in adhesion and the functional epitopes responsible for the protective ability of RrgA may be conserved and that the considerable level of variation found within the “head” domain of RrgA may have been generated by immunologic pressure without impairing the functional integrity of the pilus.

Performance evaluation of low environmental impact asphalt concretes using the mechanistic empirical design method based on laboratory fatigue and permanent deformation models

The "sustainability" concept relates to the prolonging of human economic systems with as little detrimental impact on ecological systems as possible. Construction that exhibits good environmental stewardship and practices that conserve resources in a manner that allow growth and development to be sustained for the long-term without degrading the environment are indispensable in a developed society. Past, current and future advancements in asphalt as an environmentally sustainable paving material are especially important because the quantities of asphalt used annually in Europe as well as in the U.S. are large. The asphalt industry is still developing technological improvements that will reduce the environmental impact without affecting the final mechanical performance. Warm mix asphalt (WMA) is a type of asphalt mix requiring lower production temperatures compared to hot mix asphalt (HMA), while aiming to maintain the desired post construction properties of traditional HMA. Lowering the production temperature reduce the fuel usage and the production of emissions therefore and that improve conditions for workers and supports the sustainable development. Even the crumb-rubber modifier (CRM), with shredded automobile tires and used in the United States since the mid 1980s, has proven to be an environmentally friendly alternative to conventional asphalt pavement. Furthermore, the use of waste tires is not only relevant in an environmental aspect but also for the engineering properties of asphalt [Pennisi E., 1992]. This research project is aimed to demonstrate the dual value of these Asphalt Mixes in regards to the environmental and mechanical performance and to suggest a low environmental impact design procedure. In fact, the use of eco-friendly materials is the first phase towards an eco-compatible design but it cannot be the only step. The eco-compatible approach should be extended also to the design method and material characterization because only with these phases is it possible to exploit the maximum potential properties of the used materials. Appropriate asphalt concrete characterization is essential and vital for realistic performance prediction of asphalt concrete pavements. Volumetric (Mix design) and mechanical (Permanent deformation and Fatigue performance) properties are important factors to consider. Moreover, an advanced and efficient design method is necessary in order to correctly use the material. A design method such as a Mechanistic-Empirical approach, consisting of a structural model capable of predicting the state of stresses and strains within the pavement structure under the different traffic and environmental conditions, was the application of choice. In particular this study focus on the CalME and its Incremental-Recursive (I-R) procedure, based on damage models for fatigue and permanent shear strain related to the surface cracking and to the rutting respectively. It works in increments of time and, using the output from one increment, recursively, as input to the next increment, predicts the pavement conditions in terms of layer moduli, fatigue cracking, rutting and roughness. This software procedure was adopted in order to verify the mechanical properties of the study mixes and the reciprocal relationship between surface layer and pavement structure in terms of fatigue and permanent deformation with defined traffic and environmental conditions. The asphalt mixes studied were used in a pavement structure as surface layer of 60 mm thickness. The performance of the pavement was compared to the performance of the same pavement structure where different kinds of asphalt concrete were used as surface layer. In comparison to a conventional asphalt concrete, three eco-friendly materials, two warm mix asphalt and a rubberized asphalt concrete, were analyzed. The First Two Chapters summarize the necessary steps aimed to satisfy the sustainable pavement design procedure. In Chapter I the problem of asphalt pavement eco-compatible design was introduced. The low environmental impact materials such as the Warm Mix Asphalt and the Rubberized Asphalt Concrete were described in detail. In addition the value of a rational asphalt pavement design method was discussed. Chapter II underlines the importance of a deep laboratory characterization based on appropriate materials selection and performance evaluation. In Chapter III, CalME is introduced trough a specific explanation of the different equipped design approaches and specifically explaining the I-R procedure. In Chapter IV, the experimental program is presented with a explanation of test laboratory devices adopted. The Fatigue and Rutting performances of the study mixes are shown respectively in Chapter V and VI. Through these laboratory test data the CalME I-R models parameters for Master Curve, fatigue damage and permanent shear strain were evaluated. Lastly, in Chapter VII, the results of the asphalt pavement structures simulations with different surface layers were reported. For each pavement structure, the total surface cracking, the total rutting, the fatigue damage and the rutting depth in each bound layer were analyzed.

Structural and functional characterization of Group B Streptococcus class C sortases

In Group B Streptococcus (GBS) three structurally distinct types of pili have been discovered as potential virulence factors and vaccine candidates. The pilus-forming proteins are assembled into high-molecular weight polymers via a transpeptidation mechanism mediated by specific class C sortases. Using a multidisciplinary approach including bioinformatics, structural and biochemical studies and in vivo mutagenesis we performed a broad characterization of GBS sortase C. The high resolution X-ray structure of the enzymes revealed that the active site, located into the β-barrel core of the enzyme, is made of the catalytic triad His157-Cys219-Arg228 and covered by a loop, known as the “lid”. We show that the catalytic triad and the predicted N- and C-terminal trans-membrane regions are required for the enzyme activity. Interestingly, by in vivo complementation mutagenesis studies we found that the deletion of the entire lid loop or mutations in specific lid key residues had no effect on catalytic activity of the enzyme. In addition, kinetic characterizations of recombinant enzymes indicate that the lid mutants can still recognize and cleave the substrate-mimicking peptide at least as well as the wild type protein.

Use of E. coli OMVs as delivery system to elicit neutralizing antibodies against Chlamydia infectivity: the HtrA protein example

The obligate intracellular pathogen Chlamydia trachomatis is a gram negative bacterium which infects epithelial cells of the reproductive tract. C. trachomatis is the leading cause of bacterial sexually transmitted disease worldwide and a vaccine against this pathogen is highly needed. Many evidences suggest that both antigen specific-Th1 cells and antibodies may be important to provide protection against Chlamydia infection. In a previous study we have identified eight new Chlamydia antigens inducing CD4-Th1 and/or antibody responses that, when combined properly, can protect mice from Chlamydia infection. However, all selected recombinant antigens, upon immunization in mice, elicited antibodies not able to neutralize Chlamydia infectivity in vitro. With the aim to improve the quality of the immune response by inducing effective neutralizing antibodies, we used a novel delivery system based on the unique capacity of E. coli Outer Membrane Vesicles (OMV) to present membrane proteins in their natural composition and conformation. We have expressed Chlamydia antigens, previously identified as vaccine candidates, in the OMV system. Among all OMV preparations, the one expressing HtrA Chlamydia antigen (OMV-HtrA), showed to be the best in terms of yield and quantity of expressed protein, was used to produce mice immune sera to be tested in neutralization assay in vitro. We observed that OMV-HtrA elicited specific antibodies able to neutralize efficiently Chlamydia infection in vitro, indicating that the presentation of the antigens in their natural conformation is crucial to induce an effective immune response. This is one of the first examples in which antibodies directed against a new Chlamydia antigen, other than MOMP (the only so far known antigen inducing neutralizing antibodies), are able to block the Chlamydia infectivity in vitro. Finally, by performing an epitope mapping study, we investigated the specificity of the antibody response induced by the recombinant HtrA and by OMV-HtrA. In particular, we identified some linear epitopes exclusively recognized by antibodies raised with the OMV-HtrA system, detecting in this manner the antigen regions likely responsible of the neutralizing effect.

La valorizzazione della professionalità nella contrattazione collettiva: sistemi classificatori e percorsi di mobilità professionale

La tesi, che si articola in tre capitoli, analizza la rilevanza della professionalità del lavoratore nell’ambito del rapporto di lavoro subordinato con particolare riferimento all’interesse mostrato da parte della contrattazione collettiva nel settore privato e pubblico nella definizione dei sistemi classificatori e di inquadramento del personale. Nel primo capitolo, si dà conto dei fattori che hanno determinato l’emersione della professionalità quale bene giuridico meritevole di tutela da parte dell’ordinamento: si analizzano in particolare le trasformazioni organizzative e produttive, nonché le indicazioni provenienti dal testo costituzionale che si riverberano di poi nella legislazione ordinaria. Nel secondo si analizza quanto la professionalità, o le singole voci che la compongono, rilevi a fini classificatori: dunque in che termini le competenze, le conoscenze del lavoratore rilevino quali criteri classificatori. Nel terzo capitolo, viceversa, si pone maggiore attenzione rispetto all’ “importanza” della professionalità quale fattore che incide su meccanismi di progressione retributiva e in genere professionale (assumendosi tale espressione come una sorta di sinonimo del termine carriera, rispetto al quale si differenzia quanto al contesto organizzativo e produttivo in cui si svolge) del lavoratore. In un assetto simile, centrale è il rilievo della valutazione del lavoratore. I contratti collettivi analizzati sono per il settore privato quelli delle categorie chimici, terziario e tessile; per il settore pubblico, quelli del comparto sanità e regioni ed autonomie locali.

Development of bionanotechnological strategies for signal enhancement in nucleic acids biosensors

Nucleic acid biosensors represent a powerful tool for clinical and environmental pathogens detection. For applications such as point-of-care biosensing, it is fundamental to develop sensors that should be automatic, inexpensive, portable and require a professional skill of the user that should be as low as possible. With the goal of determining the presence of pathogens when present in very small amount, such as for the screening of pathogens in drinking water, an amplification step must be implemented. Often this type of determinations should be performed with simple, automatic and inexpensive hardware: the use of a chemical (or nanotechnological) isothermal solution would be desirable. My Ph.D. project focused on the study and on the testing of four isothermal reactions which can be used to amplify the nucleic acid analyte before the binding event on the surface sensor or to amplify the signal after that the hybridization event with the probe. Recombinase polymerase amplification (RPA) and ligation-mediated rolling circle amplification (L-RCA) were investigated as methods for DNA and RNA amplification. Hybridization chain reaction (HCR) and Terminal deoxynucleotidil transferase-mediated amplification were investigated as strategies to achieve the enhancement of the signal after the surface hybridization event between target and probe. In conclusion, it can be said that only a small subset of the biochemical strategies that are proved to work in solution towards the amplification of nucleic acids does truly work in the context of amplifying the signal of a detection system for pathogens. Amongst those tested during my Ph.D. activity, recombinase polymerase amplification seems the best candidate for a useful implementation in diagnostic or environmental applications.