Academic literature on the topic 'Pathogenic'

Glycosphingolipids in filamentous fungi are significant components of the plasma membrane and are vital for different cellular processes, such as growth, morphological transition or signal transduction. Fungal growth inhibitors targeting glycosylinositolphosphoceramide (GIPCs) biosynthesis or antifungal compounds binding to GIPCs present in membranes could present a safe way of preventing fungal growth on crops since GIPCs are not present in mammalian cells. Mass spectrometry-based shotgun lipidomics was used to analyze sphingolipids of 11 fungal strains isolated from plant material. Molecular species with inositol ceramides containing zero to five carbohydrates were identified. Differences in the amount of individual molecular species were influenced by the taxonomic affiliation. All tested strains exhibited a relatively high content (more than 40 mol.%) of GIPCs with three and more saccharides attached to the polar head. It could be assumed that the sphingolipid profiles of the tested plant pathogens would be an adaptation mechanism to antifungal plant defensins.

Avian Pathogenic Escherichia coli (APEC) is an important pathogen of the poultry industry, responsible for 43% of condemnations of broiler birds at slaughter and annual losses of between 1-8% of a laying flock. APEC is also a public health concern; consumption of poultry meat has been linked with urinary tract infections (UTI) in humans, and also as a reservoir of potential antimicrobial resistance genes. In this study of strain 3770, a reproductive tract associated isolate of APEC, the isolate was characterised for typical APEC virulence phenotypes, and also underwent full-genome sequencing in order to further advance our understanding of the pathogenomics of reproductive tract associated APEC infections. Additionally, a population study examined the virulence gene profiles within a population of reproductive tract associated E. coli, with a particular focus on virulence factors associated with infections in avian species and UTI in humans. It was found that 3770 exhibited characteristic extra-intestinal pathogenic E. coli (ExPEC) virulence phenotypes; serum resistant, adhesive, and able to persist in the short term within phagocytic cells. It was also able to induce reproductive tract infections via the aerosol route. The genome sequence was 5.02Mb in size with a high number of virulence genes. The most closely related E. coli was an adherent-invasive E. coli isolate associated with Crohn's Disease. The population study of reproductive tract infections revealed a high level of variance within the population, and a higher prevalence of ibeA and K1 capsule genes than seen in other populations. These results provide further evidence that there is no one single APEC pathotype. It is likely that virulence in APEC isolates is a complex relationship between the virulence profile of the bacterium and the health status of the host.

Naegleria fowleri, a free-living ameba, is the causative agent of Primary Amebic Meningoencephalitis. Highly-pathogenic mouse-passaged amebae (Mp) and weakly-pathogenic axenically-grown (Ax) N. fowleri were examined for peptidase activity. Zymography and azocasein peptidase activity assays demonstrated that Mp and Ax N. fowleri exhibited a similar peptidase pattern. Prominent for whole cell lysates, membranes and conditioned medium from Mp and Ax amebae were the presence of an activity band of approximately 58kDa and 100 kDa bands susceptible to the action of cysteine and metallopeptidase inhibitors, respectively. Further roles of the peptidases during the invasion process were examined by in vitro invasion assays in the presence of inhibitors and Cysteine and metallopeptidase inhibitors were found to greatly reduce invasion through the ECM. This study establishes a functional linkage of the expressed peptidases to the invasion process, and these peptidases may serve as a candidate target for therapeutic management of N. fowleri infection.

From 1994, Helicobacter pylori was classified by WHO (World Health Organization) as a class I carcinogen and its infection has been associated to gastroduodenal disease. It colonizes more than half of worldwide population, with a prevalent infection rate in developed countries. In spite of the majority of infected people are asymptomatic, around 20% develop severe pathologies like peptic ulcers and the 1% lymphoma of the mucosa-associated lymphoid tissue (MALT) and stomach cancer. This significant epidemiological study both of the unique characteristics of H. pylori inspired many scientists, as bacteriologist, gastroenterologists, cancer and pharmaceutical scientists to understand physio-pathological aspects of this bacterium, and also microbiologist, taxonomist, microbial ecologist and molecular biologist, for a more detailed molecular approach. H. pylori, a Gram negative, microaerophilic bacteria that colonize human gastric mucosa. It is not an acidophilus bacterium and even if the stomach lumen presents inhospitable condition for most microbes, it is able to survive for a short period, sufficient to enter in the highly viscous mucosa, reach gastric epithelium, and colonize the gastro-enteric tract. H. pylori colonization is mediated by a predominant virulence factor, the flagellar motility associated to chemotaxis. To avoid its discharge in the intestinal tract by peristalsis, the bacteria establish a persistent infection inside the viscous gastric mucus film that covers the gastric epithelium. A nickel containing enzyme, the urease, hydrolyzes the urea present in the stomach to ammonia and CO2, buffering the pH of the periplasm. The most severe clinical outcomes are always associated to cag+ strains. cag-PAI is defined as the “Cytotoxic Associated Genes Pathogenicity Island” and it consists of a characteristic chromosome, flanked by transposable elements. Another important virulent factor is the vacuolating cytotoxin A, known as VacA, which induces the formation of large cytoplasmic vacuoles in gastric cultured cell lines. Moreover the iron and nickel acquisition is essential grow factors and a large number of genes are responsible of this mechanism. While the development of an efficient vaccine against H. pylori is now the aim of many researchers, the search for new specific antibiotics as a new pharmaceutical target is required for the complete eradication of H. pylori. In this thesis has been investigate the structural and function role of different pathogenic proteins involved in the H. pylori colonization of human gastric mucosa. These potential drug targets have been cloned, 8 out of 11 were expressed in a heterologous expression system, after purification, 2 of them generate protein crystals and only one was possible to characterize the molecular structure. In particular it has been elucidated a possible physiological role of CeuE (HP1561), a Class III SPB (Substrate Binding Protein), crystalized with Ni(His)2 complex and it was determined its affinity to the complex by an in vitro approach. The H. pylori flagella play a key role during infection allowing the bacterium to move through the mucous layer. The H. pylori hook scaffolding protein FlgD were cloned, expressed, purified and crystalized. A study of other purified pathogenic H. pylori factors belonging to flagellar component apparatus and transcriptional factors involved in cellular stress response has been reported. To obtain these results, different experimental approaches has been used. Bioinformatics analysis of target proteins has been performed to predict the best candidates for a crystallographic study and for genetic construction design. Molecular cloning in plasmid vectors has been performed from PCR amplification. The expression conditions were optimized and performed in E. coli, a heterologous system. The solubility of recombinant proteins were checked and obtained also with protein refolding methods. Different purification techniques were used in order to obtain pure protein. Target characterization was performed due analytical gel filtration, UV spectroscopy, DLS (Dynamic Light Scattering) and CD (Circular Dichroism). The proteins were concentrated to crystallization trials. The protein crystals obtained were analyzed at ESRF synchrotron (Grenoble, France). Functional in vitro approaches were performed using fluorescence spectroscopy, SPR (Surface Plasmon Resonance) and Mass spectroscopy. In the second chapter is described the three dimensional structure of a H. pylori pathogenic protein crystalized in presence with its possible physiological substrate. HP1561 (CeuE) is a H. pylori protein predicted to be an ABC transporter component, periplasmic iron-bind transporter. Recently it was published that CeuE and fecDE genes of H. mustelae encode for a nickel and cobalt acquisition system. In Gram-negative bacteria, nickel uptake is guaranteed by multiple and complex systems that operate at the membrane and periplasmic level. H. pylori employs other yet uncharacterized systems to import the nickel required for the maturation of key enzymes, such as urease and hydrogenase. To understand this contradiction of the data about Ni2+ acquisition system in H. pylori CeuE was cloned, expressed, purified, crystallized and its structure determined. Identity between the sequences of the two Helicobacter is 44%. The two Histidine residues (H103 and H197), potentially involved in Siderophores/Ni2+ binding coordination in H. pylori CeuE, are partially conserved. The His corresponding to H. pylori position 103 is conserved, whilst His197 is replaced by a Leucine. In order to check, if this substitution influence the binding of siderophores/Ni2+, the mutant of H. pylori CeuE H197L was than produced and purified. The crystal structure of H. pylori CeuE has been determined at 1.65Å resolution using the SAD method, in Apo-form and in complex with Ni(His)2. It comprises two structurally similar globular domains, each consisting of a central five-stranded β-sheet surrounded by α-helices, an arrangement commonly classified as a Rossmann-like fold. Structurally, H. pylori CeuE belongs to the class III periplasmic substrate-binding protein. Crystallographic data, fluorescence binding assays and SPR analysis allow to exclude a role of the protein in the transport of VitB12, heme, enterobactin and isolated Ni2+ ions. On the contrary, the crystal structure of the protein/Ni(L-His)2 complex and dissociation constant obtained by SPR technique suggests that H. pylori CeuE binds and transport nickel in vivo thanks to the formation of a Ni2+/histidine complex or to some ligand that mimics it. In the third chapter is presented the study of FlgD, a flagellar component involved in the formation the extracellular complex, the flagellar hook. The motility of H. pylori is considered a colonization factor, due the fact that less motile strains are less able to colonize or survive in the host than full motile strains. In the flagellum machinery are involved more than 50 genomic genes for regulation and assembly. The three major components are the filament, the hook and the basal body. FlgD is not present when the flagellum is completed, but plays a key role during the assembly. Therefore, it has been classified as the hook-scaffolding protein, considering it also as the hook capping protein, interacting with FlgL and FlgK and the basal body rod – modification protein. In H. pylori G27 strain FlgD correspond to the gene hp0858 that was amplified from purified genomic DNA and cloned in an expression plasmid vector. The protein was produced in E. coli BL21 in reach medium ad it resulted to a soluble protein. DLS and analytical gel filtration confirm the oligomeric state of FlgD that resulted to be a tetramer in solution. The protein was concentrated to 30g/l and crystalized after a couple of month of incubation. The crystals had diffracted at 2.7Å of maximum resolution. For molecular replacement approach was used homology modeling. Different molecular models were built to fit experimental diffraction data. The secondary structure of the generated models was fitted with experimental CD spectra, where FlgD resulted to have around 12% of helices and 45% of β-sheets (190-260nm). Crystallographic statistics do not properly converged to a positive molecular refinement with the tested models. To solve FlgD structure are necessary crystals of recombinant Selenomethionine FlgD that was expressed, purified and crystalized. In the fourth chapter are reported H. pylori pathogenic proteins that had been characterized. These proteins could be divided in two groups, the first one of flagellar proteins and the second of cellular stress response factors, in collaboration with Professor V. Scarlato of the department of Biology of Bologna University. FliN is a cytosolic protein, localized in the C ring of the flagellar basal body. It interacts with the other two components FliM and FliG. Missense or mutation of fliN had been associated to non-motile strains. It has been reported that regulates the clockwise/counterclockwise switching of flagella. H. pylori FliN was cloned, expressed and purified from the inclusion body after refolding. Oligomerization after refolding was tested by DLS and analytical gel filtration. The protein resulted to be poly-disperse in solution and no protein crystals have been obtained. FliD is the filament capping protein and it was observed that interact with FliT that is not only a flagellar type III substrate specific export chaperone but also inhibits the expression of fliD thought its specific interaction with the master regulator FlhD4C2 complex. In order to analyze possible structure of the co-crystalized FliD-FliT, it was plan to co-express these proteins. Both were cloned with a different affinity purification system, but only FliT was possible to express and purify from inclusion bodies. The CD spectra presented a strong β-sheet component in the secondary structure. DLS and analytical gel filtration revealed that this protein is poly-disperse in solution and no protein crystals were be obtained. FlgN is a type III secretion chaperone and it has been reported to interact with the two hook junction protein FlgK and FlgL preventing the protein proteolysis when the flagellum is not assembled. These proteins have been cloned in different type of plasmid vectors for a co-expression experiment, but only FlgN was properly expressed in E. coli. Recombinant FlgN was purified by Ni-IMAC and resulted to be soluble in solution. The protein was characterized by analytical gel filtration, DLS and CD. The protein resulted to be a monomer in solution with a 30% of not defined secondary structure (190-260nm). FlgN was concentrated and different crystallization conditions were tested. In the latter group there are three proteins related to Heat shock response, produced when bacteria encounter stress such as the elevated temperatures, ethanol, H2O2 and acid. It was demonstrated that H. pylori Hsps play an important role during the host infection. HrcA and HspR are negative repressor of groESL and dnaK machinery. HrcA activity depends by the presence of HspR, because it is demonstrated that HrcA is not able to bind DNA in absence of HspR. These two proteins were expressed in E. coli and purified by Ni-IMAC affinity. During the concentration step, these proteins present a solubility limit influenced by the concentration. Mutagenesis of a Cys in HspR and detergent solubility screening with HrcA has been performed, but no suitable protein for crystallization trials has been obtained. Hp1026 is a gene present in the same operon of HspR (hp1025). The function of this gene has not been reported. From sequence homology was possible to identify a helicase domain and ATP-binding domain. This protein, ORF, has been expressed in E. coli and purified by Ni-IMAC affinity. Analytical gel filtration and CD has been performed to characterize this protein. The protein was a dimer in solution with a 35% of α-helices component. Crystallization trials have been performed at different protein concentrations and also in presence of its possible cofactor, ATPγS. No crystals have been obtained in tested condition. Appendix: Structural and functional study on a human protease S1P/ SKI1 The study of human S1P/SKI1 protease was performed in collaboration with Professor S. Kunz of the Institute of Microbiology, University Hospital Center and university of Lausanne, Switzerland. S1P/SKI-1 is a serine protease that belongs to the mammalian family of Proprotein Convertases (PC). The aim of this family member is to mediate the activation of different important substrates for cell live. Among these proteases, S1P has been shown to have unique substrate specificity, preferring cleavage after non-basic amino acids. Known S1P cellular targets are SREBP-2, involved in the biosynthesis and uptake of lipids and cholesterol, BDNF, ATF-6 and the surface glycoprotein of viruses belonging to the family of Arenaviridae. S1P is 118 kDa multi-domain protein; two regions of S1P have been investigated, the "Prodomain", involved in the regulation of S1P catalytic activity, and the so called "catalytic domain", which include the residues responsible for the cleavage reaction itself. Moreover it was analyzed an inactive mutant of cS1P: H249A. Also for ProD was chosen one constructs (ProD_AB and ProD_AC) involved in the affinity of the protease substrate. Hence, the sequences corresponding to the domains were synthesized as optimized genes for the expression in E. coli and sub-cloned in expression plasmids in order to obtain C-term His-tagged fusion proteins. These constructs have been expressed in E. coli, purified by Ni-IMAC and positive fractions have been collected and concentrated in order to perform crystallization trials. Unfortunately no protein crystals have been obtained in tested condition. To elucidate the role of a mutated variant of the cleavage site “C” of Pro Domain, it was performed a mass spectrometry analysis. Secreted S1P/SKI1 mutant C was purified from culture medium of HEK293 cell line was isolated by IMAC-Co. The sample, loaded in RP-HPLC, was denatured in 6 M Guanidine-HCl. The chromatographic fractions corresponding to the major HPLC peaks were dried out in a speed-vac concentrator and directly injected in the ESI source. Mass measurements were performed with a quadrupole-TOF spectrometer. Analysis of mass spectra, compared with wild-type form of S1P, allows generating a preliminary Pro Domain auto-processing profile.
Dal 1994 il batterio Helicobacter pylori è stato classificato come organismo cancerogeneno di prima classe e la sua infezione è associata a patologie gastroduodenali. Più di metà della popolazione mondiale ne è infettata con una maggiore prevalenza nei paesi sviluppati. Nonostante la maggior parte dei casi le infezioni sono asintomatiche, il 20% sviluppa gravi patologie come ulcere peptiche e nell’1% dei casi genera linfomi e gastro carcinomi. L’incidenza e le caratteristiche di questo batterio hanno ispirato batteriologi, gastroenterologi, oncologi e farmacologi per indagare gli aspetti fisiopatologici legati all’infezione, così come microbiologi, ecologi, biologi molecolari hanno cercato i fattori di virulenza coinvolti in nell’infezione. H. pylori è un batterio microaerofilico Gram negativo che colonizza la mucosa gastrica. Non è un batterio acidofilo, anche se è in grado di sopravvivere nel lume dello stomaco per un breve periodo necessario per raggiungere le cellule epiteliali spostandosi attraverso la mucosa gastrica. La colonizzazione è mediata da fattori di virulenza predominanti come la motilità flagellare associata alla chemiotassi. Per evitare che sia espulso dal tratto intestinale dalla peristalsi, il batterio H. pylori stabilisce un’infezione cronica. L’ureasi, che è un enzima nickel dipendente, che idrolizza l’urea presente in ammoniaca e CO2 tamponando il pH acido dello stomaco. I casi più gravi sono associati ai ceppi che esprimono l’isola di patogenicità cag-PAI, che consiste in un cromosoma delimitato da elementi trasponibili. Un altro importante fattore di virulenza è la tossina vacuolizzante VacA, che induce la formazione di vacuoli citoplasmatici. Anche il meccanismo di acquisizione di ferro e nickel è fondamentale per la colonizzazione batterica e dunque finemente regolata da un gran numero di geni. Lo sviluppo di un vaccino e nuovi antibiotici nutrono una costante ricerca di nuovi possibili bersagli farmacologici, necessari per completa ed efficiente eradicazione del batterio H. pylori. In questa tesi sono stati analizzati il ruolo e la struttura di alcune proteine patogenetiche del H. pylori. Questi potenziali target farmacologici sono stati clonati, otto su undici sono stati espressi in un sistema eterologo, due proteine di quelle purificate hanno generato cristalli e di una sola ne è stata definita la struttura molecolare. In particolare è stato definito un possibile ruolo della proteina CeuE (HP1561), appartenete alla famiglia delle proteine che legano un substrato, cristallizzata in presenza del complesso Ni(His)2 e definita l’affinità con lo stesso in vitro. Del flagello, che svolge un ruolo chiave durante l’infezione, ne è stata studiata la proteina coinvolta nella formazione dell’uncino FlgD che è stata clonata, espressa, purificata e cristallizzata. Inoltre è stato riportato anche uno studio di altri fattori del flagello e di alcune proteine coinvolte nella risposta allo stress cellulare. Per ottenere tali risultati sono stati utilizzati approcci differenti. Per individuare le migliori proteine candidate per uno studio cristallografico e progettare costrutti funzionali sono state effettuate predizioni bioinformatiche. Gli amplificati di PCR sono stati clonati in vettori plasmidici. Le condizioni di espressione sono state ottimizzate e fatte in E. coli, un sistema di espressione eterologo. La solubilità delle proteine ricombinanti è stata analizzata e ottenuta anche mediante refolding. Sono stati usati diversi sistemi di purificazione per ottenere un buon grado di purezza. Per la caratterizzazione proteica sono state usate come tecniche la gel filtrazione analitica, spettroscopia UV, DLS (Dynamic Light Scattering) e dicroismo circolare. Le proteine sono state concentrate e sottoposte a esperimenti di cristallizzazione. I cristalli sono stati analizzati al sincrotrone ESRF (Grenoble, France). Spettroscopia di fluorescenza, SPR (surface plasmon resonance) e spettroscopia di massa sono le tecniche utilizzate per la caratterizzazione In Vitro. Nel secondo capitolo viene decritta la struttura tridimensionale di una proteina patogenetica di H. pylori, cristallizzata in presenza del suo possibile substrato fisiologico. HP1561 (CeuE) è una proteina di H. pylori annotata come componente periplasmatico di un trasportatore ABC che lega e trasporta il ferro. Recentemente è stato pubblicato chele ceuE e fecDE di H. mustelae codificano per proteine coinvolte nel acquisizione del nickel e cobalto. Nei Gram negativi, l’acquisizione del nickel è garantita da sistemi di proteine che operano a livello di membrana e periplasmatico. Per l’acquisizione del nickel, l’ H. pylori integra diversi sistemi non ancora caratterizzati, necessari per la maturazione di enzimi chiave come l’ureasi e l’idrogenasi. Per chiarire tale contraddizione nel sistema di acquisizione del nickel nell’H. pylori, CeuE è stata clonata, espressa, purificata, cristallizzata e la sua struttura è stata risolta. L’identità di sequenza tra i due Helicobacter (pylori e mustelae) è del 44%. Le due Istidine (H103 e H197), potenzialmente coinvolte nel legame di coordinazione del sistema sideroforo/Ni2+ nel H. pylori CeuE, risultano essere parzialmente conservate. L’His corrispondente alla His103 di H. pylori è conservata, mentre His197 è sostituita da una Leucina. Al fine d’identificare se tale mutazione possa influenzare il legame sideroforo/Ni2+, è stato prodotto e purificato il mutante H. pylori CeuE H197L. La struttura molecolare di H. pylori CeuE è stata determinata con una risoluzione di 1.65 Å mediante metodo SAD, sia nella forma apo, che in complesso col Ni(His)2. Essa è costituita da due domini globulari simili, ognuno costituito da cinque foglietti-β circondati da α-eliche, comunemente classificato come Rossman fold. Strutturalmente H. pylori CeuE appartiene alla Classe III della famiglia di proteine che legano un substrato specifico (SBPs). Dati cristallografici, saggi di fluorescenza e analisi all’SPR ci permettono di escludere il coinvolgimento della proteina nel trasporto della VitB12, eme, entrobactina, e ioni Ni2+ isolati. Al contrario la struttura della proteina/complesso Ni(His)2 e le costanti di dissociazione ottenute mediante SPR suggeriscono che H. pylori CeuE lega e trasporta il nickel in vivo mediante il complesso Ni2+/His o altro ligando che lo mima. Nel terzo capitolo viene presentato lo studio su FlgD, una proteina flagellare fondamentale nella formazione di un complesso extracellulare, l’uncino del flagello. La motilità dell’H. pylori è considerata un fattore di colonizzazione, attraverso il quale ceppi meno motili hanno minori possibilità di colonizzare e sopravvivere nell’ospite di ceppi più motili. Per la formazione del flagello sono coinvolti più di 50 geni per la regolazione e l’assemblaggio delle varie componenti. Le tre componenti principali sono il filamento, l’uncino e il corpo basale. FlgD non è presente quando il flagello è maturo, ma ha un ruolo chiave durante l’assemblaggio. Perciò, è stato classificato come proteina necessaria per l’impalcatura dell’uncino (hook scaffolding protein), considerata anche proteina di testa dell’uncino (capping protein) in quanto interagisce con FlgL, FlgK e le proteine del corpo basale. Nel ceppo H. pylori G27, FlgD corrisponde al gene hp0858 che è stato amplificato dal DNA genomico purificato e clonato in un vettore plasmidico. La proteina è stata prodotta in E. coli BL21 e la proteina è risultata essere solubile. Gel filtrazione analitica e misure al DLS confermano il suo stato di oligomerizzazione, che risulta essere un tetramero in soluzione. La proteina è stata concentrata fino a 30 g/l e cristallizzata dopo un paio di mesi d’incubazione. I cristalli hanno diffratto a una risoluzione massima di 2.7 Å. Per la sostituzione molecolare è stata usata la tecnica del homology modelling. Sono stati costruiti diversi modelli molecolari per fittare i dati sperimentali. La struttura secondaria dei modelli generati è stata comparata con gli spettri di dicroismo circolare, dove FlgD è risultata essere composta da un 12% di eliche e complessivamente da un 45% di foglietti beta (190-260nm). Le statistiche cristallografiche non hanno dato convergenza positiva negli esperimenti di sostituzione molecolare con i modelli testati. Per risolvere la struttura di FlgD sono necessari cristalli di FlgD derivatizzata con Selenometionine, che è stata espressa, purificata e cristallizzata. Nel quarto capitolo sono riportate le proteine patogenetiche di H. pylori che sono state caratterizzate in questa tesi. Queste proteine possono essere divise in due gruppi, il primo delle proteine flagellarli ed il secondo delle proteine coinvolte nella risposta allo stress cellulare in collaborazione con il Prof. V. Scarlato del dipartimento di Biologia dell’università di Bologna. FliN è una proteina citosolica localizzata nell’anello C del corpo basale del flagello ed interagisce con altri due componenti FliM e FliG. Mutazioni missenso di fliN sono state associate a ceppi non-motili ed è stato riportato che regola la rotazione oraria/antioraria del flagello. H. pylori FliN è stata clonata, espresso e purificata dai corpi d’inclusione dopo refolding. Lo grado di oligomerizzazione è stato analizzato mediante DLS e gel filtrazione analitica. La proteina è risultata essere polidispersa i soluzione e non sono stati ottenuti cristalli di proteina. FliD è la proteina “capping” del filamento cellulare ed è stato osservato che interagisce con FliT, che non è solo un chaperon substrato specifico del sistema III di esporto flagellare, ma inibisce anche l’espressione di fliD attraverso l’interazione con il complesso FlhD4C2. Al fine di analizzare la struttura del complesso FliD-FliT, è stata pianificata la co-espressione di queste proteine. Entrambe sono state clonate con un sistema di purificazione differente, ma solo la purificazione di FliT è stata possibile dai corpi d’inclusione. Lo spettro di dicroismo circolare ha rivelato una forte componente di foglietti-β nella struttura secondaria. Secondo le misure di DLS e gel filtrazione analitica FliT è polidispersa in soluzione e perciò non stati ottenuti cristalli della stessa. FlgN è una proteina del sistema secrezione tipo III ed è stato osservato che interagisce in maniera specifica con le proteine di giunzione dell’uncino con il filamento FlgK ed FlgL, prevenendone la proteolizzazione prima della maturazione del flagello. Queste proteine sono state clonate in differenti tipi di vettori plasmidici, ma solo FlgN è stata efficacemente espressa in E. coli. FlgN ricombinante è stata purificata mediante Ni-IMAC è risultata essere solubile. La proteina è stata caratterizzata con gel filtrazione analitica, DLS e CD. La proteina è un monomero in soluzione con un 30% di struttura secondaria non definita (190-260 nm). FlgN è stata concentrata e sottoposta a test di cristallizzazione. Nell’ultimo gruppo ci sono tre proteine HSPs (Heat Shock Response), prodotte dal batterio quando incontra stress come elevate temperature, etanolo, H2O2 e acidi. E’ stato accurato che le HSPs di H. pylori svolgono un ruolo importante durante l’infezione dell’ospite. HrcA e HspR reprimono la trascrizione di groESL e dnaK. L’attività di HrcA è influenzata dalla presenza di HspR, in quanto è stato dimostrato che HrcA non è in grado di legare il DNA in assenza di HspR. Queste due proteine sono state espresse in E. coli e purificate con Ni-IMAC. Durante le fasi di concentrazione hanno mostrato un limite di solubilità. Mutagenesi mirata sul costrutto di HspR e screening di detergenti su HrcA sono hanno migliorato il sistema, senza però riuscire ad ottenere una condizione ottimale per la formazione di cristalli di proteina. HP1026 (ORF) è un gene presente nello stesso operone di HspR (hp1025), ma con funzione non nota. Dall’analisi della sequenza è stato identificato un dominio con attività elicasica ed un dominio legante l’ATP. La proteina è stata espressa in E. coli e purificata con Ni-IMAC. Per la caratterizzazione sono state effettuate gel filtrazione analitica e dicroismo circolare. La proteina risulta essere un dimero in soluzione con un 35% di α-elica. I test di cristallizzazione son stati effettuati scrinando diverse concentrazioni e anche in presenza del possibile cofattore, ATPγS in forma non idrolizzabile. Nessun cristallo è stato ottenuto dalle condizioni testate. Appendice: Studio strutturale e funzionale della proteasi umana S1P/SKI1 Lo studio di questa proteasi umana è stato effettuato in collaborazione con il Prof. S. Kunz dell’Istituto di Microbiologia, del Centro Universitario Ospedaliero e dall’ Univ. Di Lausanne, Svizzera. S1P/SKI1 è una serina proteasi della famiglia delle Proprotein Convertasi (PCs). Lo scopo di membri di questa famiglia è quello di mediare l’attivazione di diversi importanti substrati per la vita cellulare. Tra queste proteasi, S1P presenta una specificità di substrato, con un sito di taglio dopo un residuo non basico. Tra i target cellulari di S1P sono stati identificati SREBP-2, coinvolto nella biosintesi dei lipidi e del colesterolo, BDNF, ATF-6 e glicoproteine superficiali di virus appartenenti alla famiglia delle Arenaviridae. S1P pesa 118kDa ed è una proteina multidominio; quindi 2 regioni di S1P sono state studiate, il “Prodomain” (ProD) che regola l’attività catalitica, ed il “cathalytic domain” (cS1P) che include i residui responsabili per la reazione proteasica. Inoltre è stato analizzato un mutante inattivo (cS1P_H249A) e due costrutti per il dominio di regolazione (ProD_AB e ProD_AC). Le sequenze nucleotidiche dei corrispettivi costrutti sono state sintetizzate come geni ottimizzati per l’espressione in E. coli e subclonati in vettori plasmidici per l’espressione ottenendo proteine in fusione con una coda di 6-His. Questi costrutti sono stati espressi in E. coli, purificati con Ni-IMAC e le frazioni positive sono state raccolte e concentrate per test di cristallizzazione. Sfortunatamente non sono stati ottenuti cristalli di proteina nelle condizioni testate. Per chiarire il ruolo di una variante mutata nel sito di taglio “C” del dominio di regolazione è stata effettuata una analisi di spettrometria di massa. La proteina secreta S1P mut C (sS1P_MutC, 116kDa) è stata purificata dal medium di coltura di una linea di HEK293 trasfettate e isolata con Co-IMAC. Il campione è stato denaturato in Guanidinio 6M e caricato in HPLC. Le frazioni corrispondenti ai picchi predominanti sono stati essiccati ed iniettati in spettrometro di massa (ESI-TOF). L’analisi delle masse, confrontate con la forma nativa (sS1P_WT) ha permesso di generare un profilo preliminare del pattern di processamento del dominio di regolazione (ProD) with a quadrupole-TOF spectrometer. Analysis of mass spectra, compared with wild-type form of S1P, allows generating a Pro Domain auto-processing profile.

La investigació descrita en aquesta tesi es centra en la determinació de la influència de les pràctiques de maneig del cultiu, processament i les condicions d'emmagatzematge en la qualitat microbiològica de l'enciam mínimament processat i en l'estudi de les estratègies de mitigació per millorar la seva seguretat. S'ha estudiat l'efecte del sistema de producció, orgànica o convencional, de la qualitat microbiològica d'enciam fresc. Es va avaluar la transferència i la persistència de L. innocua i E. coli O157:H7 en els fulls d'enciam i en el sòl durant la tardor i la primavera utilitzant diferents mètodes de reg contaminats artificialment i el compost. La capacitat de L. monocytogenes, Salmonella i E. coli O157:H7 per créixer en enciam envasat en tres condicions d'atmosfera diferents creades per mitjà de la utilització de pel•lícules de diferents permeabilitats a dues temperatures d'emmagatzematge va ser evaluada. Es va examinar el potencial patogènic de dues soques de S. Typhimurium DT104, amb l'objectiu de mesurar la seva capacitat per sobreviure al tracte gastrointestinal simulat i d'adherir i envair cèl•lules diferenciades Caco-2, després d’una incubació seqüencial al sòl, l'enciam i enciam tallat emmagatzemat en condicions de MAP. En aquesta tesi l'efecte de millorar la microbiota d'enciam sotmesa a les diferents etapes de pre-condicionament en la supervivència de L. monocytogenes i E. coli O157:H7 com a mètode bioconservant també va ser avaluat. Finalment, s'ha estudiat l'ús de l'addició de bioconservants com a mètode per a controlar o reduir PTA en enciam mínimament processada.
La investigación descrita en esta tesis se enfoca en la determinación de la influencia de las prácticas de manejo del cultivo, procesamiento y condiciones de almacenamiento en la calidad microbiológica de la lechuga mínimamente procesada y en el estudio de las estrategias de mitigación para mejorar su seguridad. Se ha estudiado el efecto de los sistemas de producción, orgánico o convencional, en la calidad microbiológica de lechuga fresca. Se evaluó la transferencia y la persistencia de L. innocua y E. coli O157:H7 en las hojas de lechuga y en el suelo durante el otoño y la primavera, utilizando diferentes métodos de riego contaminado artificialmente y el compost. La capacidad de L. monocytogenes, Salmonella y E. coli O157:H7 para crecer en lechuga mínimamente procesada y envasada en tres diferentes condiciones de atmósfera, creada por la utilización de películas con diferentes permeabilidades a dos temperaturas de almacenamiento fue evaluada. Se examinó el potencial patogénico de dos cepas de S. Typhimurium DT104, con el objetivo de medir su capacidad para sobrevivir al tracto gastrointestinal simulado y de adherirse e invadir a las células diferenciadas Caco-2, después de la incubación secuencial en el suelo, lechuga y lechuga cortada almacenada en MAP. En esta tesis también se evaluó el efecto de aumentar la microbiota de lechuga sometida a las diferentes etapas de pre-acondicionamiento en la supervivencia de L. monocytogenes y E. coli O157:H7 como método bioconservante. Por último, se ha estudiado el uso de la adición de bioconservantes como método para controlar o reducir los PTA en lechuga mínimamente procesada.
The research described in this thesis is focused on the determination of the influence of field management practices, processing and storage conditions on the microbial quality of fresh-cut lettuce and on the study of mitigation strategies to enhance its safety. The effect of production system, organic or conventional, on the microbiological quality of fresh lettuce was studied. The transfer and persistence of L. innocua and E. coli O157:H7 on lettuce leaves and in soil during fall and spring using different artificially contaminated irrigation methods and compost was evaluated. The ability of L. monocytogenes, Salmonella and E. coli O157:H7 to grow on shredded lettuce packaged in three different atmosphere conditions created by means of using different permeability films at two storage temperatures was evaluated. The pathogenic potential of two S. Typhimurium DT104 strains was examined, with the aim to measure their capability to survive a simulated gastrointestinal tract system and to adhere to and invade differentiated Caco-2 cells, after sequential incubation into soil, lettuce and cut lettuce stored under MAP conditions. In this thesis the effect of enhancing native microbiota of lettuce submitted to different pre-conditioning steps on survival of L. monocytogenes and E. coli O157:H7 as a biopreservative method was also evaluated. Finally, the use of adding biopreservatives as a method to control or reduce FBP in fresh-cut lettuce was studied.

The Zur (zinc uptake regulator) regulon of a range of pathogenic and non-pathogenic E. coli strains was explored by combining in silico Zur binding site predictions with experimental approaches. Initially, novel Zur-binding sites were predicted in the genomes of K-12 MG1655, 0157:H7 str. Sakai, H10407 and CFT073 using patser. The effect of both zinc depletion and zur deletion was probed in each strain by transcriptomics analysis, in order to identify direct Zur targets. Known Zur targets, including zinT, an auxiliary component of the znuABC zinc uptake system, and ykgM, an alternative non-zinc-binding ribosomal protein were up-regulated in all strains under both zinc depletion and zur deletion conditions. In contrast, up-regulation of the high affinity zinc uptake system znuABC, was more modest and variable. Transcription of pUG (ycgK), encoding a periplasmic G-type lysozyme inhibitor, was up-regulated under zinc depletion conditions and upon zur deletion in all strains, and also possessed a high-scoring predicted Zur binding site within its promoter region, leading us to believe that it is a novel member of the conserved Zur regulon. Additionally, a novel Zurregulated operon, c1265-7 was predicted in the CFT073 genome, and validated by microarray data and the use of a promoter-lux fusion. C1265 appears to be a TonBdependent heme/hemoglobin receptor, whilst C1266 and C1267 showed significant homology to components of metal uptake systems. Deletion of c1265J 7, even in the presence of a znuABC deletion, showed no clear phenotypic outcome under a range of conditions tested. C1265-7 was found to be almost exclusively distributed in ExPEC strains suggesting it is of importance to extra-intestinal survival. Additionally, the severe growth defect of CFT073 D.zur, even in zinc-deplete media suggests the CFT073 zur regulon may include extra genes involved in zinc uptake. iii ... \ ...

Walnut plantations suffer from the impact caused by a number of pathogenic mycotic microorganisms. The most common pathogen fungus is Alternaria alternata and Fusarium poae. In the framework of the research, we aimed to determine the antagonistic activity of the strain Trichoderma harzianum CNMN - FD - 16 against the identified pathogens. Thus, on the 10th day the inhibition of the pathogen A. alternata by T. harzianum is 74%. On the same day, the inhibition of F. poae by T. harzianum is 73%. Trichoderma harzianum suppressed the colonies of A. alternata of 83% - this means 4 points, and the suppression of the colonies of F. poae was 69% - registering 3 points.

Chicken manure is one of the most wide spread waste worldwide. One of its hazardous properties is contamination with live pathogens or pathogens� spores. Being introduced into soil for fertilization, fresh, cured or treated manure can cause soil contamination with those pathogens. Further, transmission of the pathogens through soil and plant tissues to human or animal food is possible. The objective of the present work was to reveal the level of pathogenic contamination of wheat grains cultivated on soil that was previously treated with cured chicken manure. Two types of manures M1 and M2 sampled from the large poultry farms situated in Russia were used to fertilize soil and obtain wheat grains (samples G1 and G2, respectively). Grains obtained with mineral fertilizers were used as a control (G0). Among 10 pathogenic bacterial species investigated, 6 were detected in both M1 and M2 samples - Listeria monocytogenes, Mycobacterium paratuberculosis,, Enterococus spp,, Campylobacter jejuni,, Bacillus anthracis,, Streptococcus dysgalactiae, the gene copy numbers for those bacteria revealed using RT-PCR was found to range between 2.22*104 and 1.19*108 gene copies per g manure. 5 of those species, except of C. jejuni, were also detected in both types of grains, while the gene copies number were found to be lower, thus they ranged between 1.45*103 and 8.81*103 copies per g grain. No bacterial pathogens were detected in G0 sample. Viral particles of bursal disease virus and avian orthoreovirus were not found either in manures nor in grains. It can be concluded that the risk of pathogenic transmission from the manures to grains exists, and that higher attention should be paid on their treatment to avoid the secondary infection of livestock and human.

Plasmonic surface enhanced Raman scattering (SERS) probes were synthesized with different Raman reporter molecules and conjugated with pathogen specific antibodies to provide a rapid screening platform for the detection of pathogenic bacterium, S. aureus and S. Typhimurium.

Pathogenic fungi are the cause of various diseases of crops. Phytopathogens infect seeds as well as the host-plants in the course of the whole duration of their ontogenesis. Plants are infected when grown in greenhouses or in open fields by a single causal agent or several pathogenic fungi. In current study, a nested PCR protocol was applied for identification of tomatoes’ infection. An infestation with Alternaria spp. and Myrothecium roridum in the lowest leaves on the stem was stated using molecular diagnostics. The ‘Tomis’ and ‘Mary Gratefully’ tomato cultivars were used in current study. Alternaria spp. was iden-tified in each of the samples. The pathogen’s species was defined. Myrothecium roridum infested 10 sam-ples of the ‘Tomis’ genotype and 11 samples of the ‘Mary Gratefully’ genotype of the 12 samples.

Fungal plant pathogens are responsible for extensive annual crop and revenue losses throughout the world. To better understand why fungi cause diseases, we performed gene-disruption mutagenesis on several pathogenic Colletotrichum species and demonstrated that pathogenic isolates can be converted to symbionts expressing non-pathogenic lifestyles. One group of nonpathogenic mutants confer disease protection against pathogenic species of Col!etotrichum, Fusarium and Phytophthora; drought tolerance; and growth enhancement to host plants. These mutants have been defined as mutualists and disease resistance correlates to a decrease in the time required for hosts to activate defense systems when exposed to virulent fungi. A second group of non-pathogenic mutants did not confer disease resistance and were classified as commensals. In addition, we have demonstrated that wildtype pathogenic Colletotrichum species can express non-pathogenic lifestyles, including mutualism, on plants they colonize asymptomatically. We have been using wildtype and isogenic gene disruption mutants to characterize gene expression patterns in plants colonized with a pathogen, mutualist or commensal. The US group is contrasting genes expressed during colonization by mutuahstic and commensal mutants of C. magna and a pathogenic wildtype C. coccodes on tomato. The Israeli group is characterizing genes expressed during asymptomatic colonization of tomato by wildtype C. acutatum and a non-pathogenic mutant.To accomplish this we have been utilizing suppressive subtraction hybridization, microarray and sequencing strategies. The expected contribution of this research to agriculture in the US and Israel is: 1) understanding how pathogens colonize certain hosts asymptomatic ally will shed light on the ecology of plant pathogens which has been described as a fundamental deficiency in plant pathology; 2) identifying genes involved in symbiotically conferred disease resistance will help explain why and how pathogens cause disease, and may identify new candidate targets for developing genetically modified disease resistant crop plants.

Fungal plant pathogens are responsible for extensive annual crop and revenue losses throughout the world. To better understand why fungi cause diseases, we performed gene-disruption mutagenesis on several pathogenic Colletotrichum species and demonstrated that pathogenic isolates can be converted to symbionts (mutualism, commensalism, parasitism) expressing non-pathogenic lifestyles. The objectives of this proposal were to: 1- generate crop-specific mutants by gene disruption that express mutualistic lifestyles, 2- assess the ability of the mutualists to confer disease resistance, drought tolerance, and growth enhancement to host plants, 3- compare fslm1 sequences and their genomic locations in the different species, and 4- document the colonization process of each Colletotrichum species.It was demonstrated that wildtype pathogenic Colletotrichum isolates, can be converted by mutation from expressing a pathogenic lifestyle to symbionts expressing non-pathogenic lifestyles. In the US, mutants of Colletotrichum were isolated by homologous gene disruption using a vector containing a disrupted FSlm1 sequence while in Israel, C. acutatum mutants were selected by restriction enzyme mediated integration (REMI) transformation. One group (US) of non-pathogenic mutants conferred disease protection against pathogenic species of Colletotrichum, Fusarium, and Phytophthora; drought tolerance; and growth enhancement to host plants. These mutants were defined as mutualists and disease resistance correlated to a decrease in the time required for hosts to activate defense systems when exposed to virulent fungi. The second group (Israel) of non-pathogenic mutants did not confer disease resistance and were classified as commensals. In addition, we demonstrated that wildtype pathogenic Colletotrichum species can express non-pathogenic lifestyles, including mutualism, on plants they colonize asymptomatically. The expected long term contribution of this research to agriculture in the US and Israel is threefold. Host-specific mutualists will be utilized in the various crops to confer (1) disease resistance to reduce dependence on chemical fungicides; (2) drought tolerance to reduce water consumption for irrigation; (3) growth enhancement to increase yields.

The intent of this proposal was to study the interaction between nonpathogenic mutants of Colletotrichum magna and Fusarium oxysporum, and the cucurbit host defense system. We had shown previously that a nonpathogenic endophytic mutant path- 1 of C. magna, caused no visible disease symptoms but protected watermelon seedlings from disease caused by the wildtype isolate and F. o. niveum. Objectives were: 1) Determine the microscopic, biochemical and molecular genetic interaction between "protected" (path- 1 colonized) cucurbit hosts and wildtype isolates of C. magna; 2) Isolate non-pathogenic mutants of F.o. melonis and test feasibility for protecting plants against fungal diseases. We found that path-1 caused no visible disease symptoms in cucurbit seedlings but conferred disease resistance against pathogenic isolates of C. magna, C. orbiculare, and F. oxysporum. Disease resistance conferred by path-1 correlated to a decrease in the time of activation of host defense systems after exposure of path-1 colonized plants to virulent pathogens. This was determined by monitoring the biochemical activity of PAL and peroxidase, and the deposition of lignin. It appears that path-1-conferred disease resistance is a multigenic phenomenon which should be more difficult for pathogen to overcome than single gene conferred resistance. Based on the benefits conferred by path-1, we have defined this mutant as expressing a mutualistic lifestyle. REMI (restriction enzyme-mediated integration) nonpathogenic mutants were also isolated using pHA1.3 plasmid linearized with Hind III and transformed into wildtype C. magna. The integrated vector and flanking genomic DNA sequences in REMI mutant R1 was re-isolated and cloned resulting in a product of approximately 11 kb designated pGMR1. Transformations of wildtype C. magna with pGMR1 resulted in the same non-pathogenic phenotype. A nonpathogenic mutant of F.o. melonis (pathogenic to melon) was isolated that colonized melon plants but elicited no disease symptoms in seedlings and conferred 25 - 50% disease protection against the virulent wildtype isolate. Subsequently, nonpathogenic mutant isolates of F.o. niveum (pathogenic to watermelon) were also isolated. Their protection capacity against the respective wildtype parent is currently under investigation. This research has provided information toward a better understanding of host-parasite interactions; specifically, endophytes, pathogens and their hosts. It will also allow us to assess the potential for utilizing nonpathogenic mutants as biological control agents against fungal pathogens and isolating molecular genetic factors of pathogenicity in Fusarium.

Within the project "Pathogenic Streptococcus in Tilapia", gram positive cocci pathogens of fish in Israel and in the United States were characterized. We showed that Streptococcus shiloi, the name for an agent causing septicemic infection in fish, is a junior synonym of Streptococcus iniae and that Enterococcus seriolicida is a junior synonym of Lactococcus garvieae, a causative agent of septicemia and meningo-encephalitis in fish. Molecular epidemiology studies on these two pathogens, based on 16S rDNA sequences and ribotyping showed that although each country had specific clones, S. iniae originated probably from the U.S. and L. garvieae from Japan. PCR assays were developed for both pathogens and applied to clinical samples. S. agalactiael S. difficile was also recognized for the first time in the U.S. in tilapia. Our histopathological studies explained the noted paradox (abundant in vitro growth often accompanied by scant to small numbers of organisms within the meninges in histologic sections of brain) in diagnostic of fish streptococcus. The greatest concentration of cocci were consistently observed within macrophages infiltrating the extrameningeal fibroadipose tissue surrounding the brain within the calvarium. These results also suggests that the primary route of meningeal infection may be extension from the extrameningeal connective tissue rather than meningeal vascular emigration of cocci-containing macrophages. Our work has resulted in a cognizance of streptococcus as fish pathogen which goes beyond the pathology observed in tilapia and is already extended to many aquaculture fish species in Israel and in the United States. Finally, our data suggest that vaccines (bivalent or trivalent) could be developed to prevent most of the damages caused by streptococcus in aquaculture.