Identification and characterization of periplasmic proteins implicated in the adaptation of Helicobacter pylori to the human gastric niche

Helicobacter pylori è un batterio Gram-negativo in grado di colonizzare la mucosa gastrica umana e persistere per l'intero arco della vita dell'ospite. E' associato a patologie gastrointestinali, quali gastrite cronica, ulcere gastriche e duodenali, adenocarcinomi e linfomi gastrici. Si tratta di uno dei patogeni più diffusi, presente in circa metà della popolazione mondiale, e il solo che si è adattato a vivere nell'ambiente ostile dello stomaco umano. Molteplici sono i fattori di virulenza che permettono al batterio la colonizzazione della nicchia gastrica e contribuiscono, anche attraverso l' induzione di una risposta infiammatoria, a profonde modificazioni dell' omeostasi gastrica. Queste ultime si associano, ad esempio, all'iperproduzione di fattori proinfiammatori, ad alterazioni sia della regolazione della secrezione acida gastrica sia del ciclo cellulare e della morte cellulare programmata (apoptosi) delle cellule epiteliali gastriche, a disordini nel metabolismo del ferro e a carenze di elementi essenziali. Studi sulla diversità genetica di H. pylori osservata in ceppi isolati da varie regioni del mondo, dimostrano che tale batterio ha avuto una coevoluzione col genere umano attraverso la storia, ed è verosimile che H. pylori sia stato un costituente del microbiota gastrico per almeno 50.000 anni. Scopo della tesi è stato quello di identificare e caratterizzare proteine importanti per la colonizzazione e l'adattamento di H. pylori alla nicchia gastrica. In particolare gli sforzi si sono concentrati su due proteine periplasmatiche, la prima coinvolta nella difesa antiossidante (l'enzima catalasi-like, HP0485), e la seconda nel trasporto di nutrienti presenti nell'ambiente dello stomaco all'interno della cellula (la componente solubile di un ABC transporter, HP0298). La strategia utilizzata prevede un'analisi bioinformatica preliminare, l'ottenimento del gene per amplificazione, mediante PCR, dal genoma dell'organismo, la costruzione di un vettore per il clonaggio, l'espressione eterologa in E. coli e la successiva purificazione. La proteina così ottenuta viene caratterizzata mediante diverse tecniche, quali spettroscopia UV, dicroismo circolare, gel filtrazione analitica, spettrometria di massa. Il capitolo 1 contiene un'introduzione generale sul batterio, il capitolo 2 e il capitolo 3 descrivono gli studi relativi alle due proteine e sono entrambi suddivisi in un abstract iniziale, un'introduzione, la presentazione dei risultati, la discussione di questi ultimi, i materiali e i metodi utilizzati. La catalasi-like (HP0485) è una proteina periplasmatica con struttura monomerica, appartenente ad una famiglia di enzimi a funzione per la maggior parte sconosciuta, ma evolutivamente correlati alla ben nota catalasi, attore fondamentale nella difesa di H. pylori, grazie alla sua azione specifica di rimozione dell'acqua ossigenata. HP0485, pur conservando il fold catalasico e il legame al cofattore eme, non può compiere la reazione di dismutazione dell'acqua ossigenata; possiede invece un'attività perossidasica ad ampio spettro, essendo in grado di accoppiare la riduzione del perossido di idrogeno all'ossidazione di diversi substrati. Come la catalasi, lavora ad alte concentrazioni di aqua ossigenata e non arriva a saturazione a concentrazioni molto elevate di questo substrato (200 mM); la velocità di reazione catalizzata rimane lineare anche a questi valori, aspetto che la differenzia dalle perossidasi che vengono in genere inattivate da concentrazioni di perossido di idrogeno superiori a 10-50 mM. Queste caratteristiche di versatilità e robustezza suggeriscono che la catalasi-like abbia un ruolo di scavenger dell'acqua ossigenata e probabilmente anche un'altra funzione connessa al suo secondo substrato, ossia l'ossidazione di composti nello spazio periplasmatico cellulare. Oltre alla caratterizzazione dell'attività è descritta anche la presenza di un ponte disolfuro, conservato nelle catalasi-like periplasmatiche, con un ruolo nell'assemblaggio dell'eme per ottenere un enzima attivo e funzionale. La proteina periplasmatica HP0298, componente di un sistema di trasporto ABC, è classificata come trasportatore di dipeptidi e appartiene a una famiglia di proteine in grado di legare diversi substrati, tra cui di- e oligopeptidi, nichel, eme, glutatione. Benchè tutte associate a trasportatori di membrana batterici, queste proteine presentano un dominio di legame al substrato che risulta essere conservato nei domini extracellulari di recettori specifici di mammifero e uomo. Un esempio sono i recettori ionotropici e metabotropici del sistema nervoso. Per caratterizzare questa proteina è stato messo a punto un protocollo di ligand-fishing accoppiato alla spettrometria di massa. La proteina purificata, avente un tag di istidine, è stata incubata con un estratto cellulare di H. pylori per poter interagire con il suo substrato specifico all'interno dell'ambiente naturale in cui avviene il legame. Il complesso proteina-ligando è stato poi purificato per cromatografia di affinità e analizzato mediante HPLC-MS. L'identificazione dei picchi differenziali tra campioni con la proteina e 5 campioni di controllo ha portato alla caratterizzazione di pentapeptidi particolarmente ricchi in aminoacidi idrofobici e con almeno un residuo carico negativamente. Considerando che H. pylori necessita di alcuni aminoacidi essenziali, per la maggior parte idrofobici, e che lo stomaco umano è particolarmente ricco di peptidi prodotti dalla digestione delle proteine introdotte con il cibo, il ruolo fisiologico di HP0298 potrebbe essere l'internalizzazione di peptidi, con caratteristiche specifiche di lunghezza e composizione, che sono naturalmente presenti nella nicchia gastrica.

Chromospheric activity and rotation of FGK stars in the solar vicinity. An estimation of the radial velocity jitter

Context. Chromospheric activity produces both photometric and spectroscopic variations that can be mistaken as planets. Large spots crossing the stellar disc can produce planet-like periodic variations in the light curve of a star. These spots clearly affect the spectral line profiles, and their perturbations alter the line centroids creating a radial velocity jitter that might “contaminate” the variations induced by a planet. Precise chromospheric activity measurements are needed to estimate the activity-induced noise that should be expected for a given star. Aims. We obtain precise chromospheric activity measurements and projected rotational velocities for nearby (d ≤ 25 pc) cool (spectral types F to K) stars, to estimate their expected activity-related jitter. As a complementary objective, we attempt to obtain relationships between fluxes in different activity indicator lines, that permit a transformation of traditional activity indicators, i.e., Ca II H & K lines, to others that hold noteworthy advantages. Methods. We used high resolution (~50 000) echelle optical spectra. Standard data reduction was performed using the IRAF ECHELLE package. To determine the chromospheric emission of the stars in the sample, we used the spectral subtraction technique. We measured the equivalent widths of the chromospheric emission lines in the subtracted spectrum and transformed them into fluxes by applying empirical equivalent width and flux relationships. Rotational velocities were determined using the cross-correlation technique. To infer activity-related radial velocity (RV) jitter, we used empirical relationships between this jitter and the R’_HK index. Results. We measured chromospheric activity, as given by different indicators throughout the optical spectra, and projected rotational velocities for 371 nearby cool stars. We have built empirical relationships among the most important chromospheric emission lines. Finally, we used the measured chromospheric activity to estimate the expected RV jitter for the active stars in the sample.

Metal and precursor effect during 1-heptyne selective hydrogenation using an activated carbon as support

Palladium, platinum, and ruthenium supported on activated carbon were used as catalysts for the selective hydrogenation of 1-heptyne, a terminal alkyne. All catalysts were characterized by temperature programmed reduction, X-ray diffraction, transmission electron microscopy, and X-ray photoelectron spectroscopy. TPR and XPS suggest that the metal in all catalysts is reduced after the pretreatment with H2 at 673 K. The TPR trace of the PdNRX catalyst shows that the support surface groups are greatly modified as a consequence of the use of HNO3 during the catalyst preparation. During the hydrogenation of 1-heptyne, both palladium catalysts were more active and selective than the platinum and ruthenium catalysts. The activity order of the catalysts is as follows: PdClRX > PdNRX > PtClRX ≫ RuClRX. This superior performance of PdClRX was attributed in part to the total occupancy of the d electronic levels of the Pd metal that is supposed to promote the rupture of the H2 bond during the hydrogenation reaction. The activity differences between PdClRX and PdNRX catalysts could be attributed to a better accessibility of the substrate to the active sites, as a consequence of steric and electronic effects of the superficial support groups. The order for the selectivity to 1-heptene is as follows: PdClRX = PdNRX > RuClRX > PtClRX, and it can be mainly attributed to thermodynamic effects.

Modifying enzyme activity and selectivity by immobilization

Immobilization of enzymes may produce alterations in their observed activity, specificity or selectivity. Although in many cases an impoverishment of the enzyme properties is observed upon immobilization (caused by the distortion of the enzyme due to the interaction with the support) in some instances such properties may be enhanced by this immobilization. These alterations in enzyme properties are sometimes associated with changes in the enzyme structure. Occasionally, these variations will be positive. For example, they may be related to the stabilization of a hyperactivated form of the enzyme, like in the case of lipases immobilized on hydrophobic supports via interfacial activation. In some other instances, these improvements will be just a consequence of random modifications in the enzyme properties that in some reactions will be positive while in others may be negative. For this reason, the preparation of a library of biocatalysts as broad as possible may be a key turning point to find an immobilized biocatalyst with improved properties when compared to the free enzyme. Immobilized enzymes will be dispersed on the support surface and aggregation will no longer be possible, while the free enzyme may suffer aggregation, which greatly decreases enzyme activity. Moreover, enzyme rigidification may lead to preservation of the enzyme properties under drastic conditions in which the enzyme tends to become distorted thus decreasing its activity. Furthermore, immobilization of enzymes on a support, mainly on a porous support, may in many cases also have a positive impact on the observed enzyme behavior, not really related to structural changes. For example, the promotion of diffusional problems (e.g., pH gradients, substrate or product gradients), partition (towards or away from the enzyme environment, for substrate or products), or the blocking of some areas (e.g., reducing inhibitions) may greatly improve enzyme performance. Thus, in this tutorial review, we will try to list and explain some of the main reasons that may produce an improvement in enzyme activity, specificity or selectivity, either real or apparent, due to immobilization.

Organotitanias: a versatile approach for band gap reduction in titania based materials

The reduction of the band gap of titania is critically important to fully utilize its photocatalytic properties. Two main strategies, i.e. doping and partial reduction of Ti(IV), are the main alternatives available to date. Herein, we report a new synthesis strategy based on one-pot co-condensation of in situ prepared polymetallic titanium-alkoxide complexes with titanium tetrabutoxide. Using this direct reaction, it is possible to introduce organic compounds in the anatase phase, causing site distortions in the crystalline structure of the network. By using this strategy, a yellow and a black titania have been produced, with the latter showing a remarkable photocatalytic activity under visible-light.

Functionalization of carbon nanotubes using aminobenzene acids and electrochemical methods. Electroactivity for the oxygen reduction reaction

Functionalized carbon nanotubes (CNTs) using three aminobenzene acids with different functional groups (carboxylic, sulphonic, phosphonic) in para position have been synthesized through potentiodynamic treatment in acid media under oxidative conditions. A noticeable increase in the capacitance for the functionalized carbon nanotubes mainly due to redox processes points out the formation of an electroactive polymer thin film on the CNTs surface along with covalently bonded functionalities. The CNTs functionalized using aminobenzoic acid rendered the highest capacitance values and surface nitrogen content, while the presence of sulfur and/or phosphorus groups in the aminobenzene structure yielded a lower functionalization degree. The oxygen reduction reaction (ORR) activity of the functionalized samples was similar to that of the parent CNTs, independently of the functional group present in the aminobenzene acid. Interestingly, a heat treatment in N2 atmosphere with a very low O2 concentration (3125 ppm) at 800 °C of the CNTs functionalized with aminobenzoic acid produced a material with high amounts of surface oxygen and nitrogen groups (12 and 4% at., respectively), that seem to modulate the electron-donor properties of the resulting material. The onset potential and limiting current for ORR was enhanced for this material. These are promising results that validates the use of electrochemistry for the synthesis of novel N-doped electrocatalysts for ORR in combination with adequate heat treatments.

Characterisation of chlorate reduction in the haloarchaeon Haloferax mediterranei

Background: Haloferax mediterranei is a denitrifying haloarchaeon using nitrate as a respiratory electron acceptor under anaerobic conditions in a reaction catalysed by pNarGH. Other ions such as bromate, perchlorate and chlorate can also be reduced. Methods: Hfx. mediterranei cells were grown anaerobically with nitrate as electron acceptor and chlorate reductase activity measured in whole cells and purified nitrate reductase. Results: No genes encoding (per)chlorate reductases have been detected either in the Hfx. mediterranei genome or in other haloarchaea. However, a gene encoding a chlorite dismutase that is predicted to be exported across the cytoplasmic membrane has been identified in Hfx. mediterranei genome. Cells did not grow anaerobically in presence of chlorate as the unique electron acceptor. However, cells anaerobically grown with nitrate and then transferred to chlorate-containing growth medium can grow a few generations. Chlorate reduction by the whole cells, as well as by pure pNarGH, has been characterised. No clear chlorite dismutase activity could be detected. Conclusions: Hfx. mediterranei pNarGH has its active site on the outer-face of the cytoplasmic membrane and reacts with chlorate and perchlorate. Biochemical characterisation of this enzymatic activity suggests that Hfx. mediterranei or its pure pNarGH could be of great interest for waste water treatments or to better understand biological chlorate reduction in early Earth or Martian environments. General significance: Some archaea species reduce (per)chlorate. However, results here presented as well as those recently reported by Liebensteiner and co-workers [1] suggest that complete perchlorate reduction in archaea follows different rules in terms of biological reactions.

Carbon and nitrogen limitation increase chitosan antifungal activity in Neurospora crassa and fungal human pathogens

Chitosan permeabilizes plasma membrane and kills sensitive filamentous fungi and yeast. Membrane fluidity and cell energy determine chitosan sensitivity in fungi. A five-fold reduction of both glucose (main carbon (C) source) and nitrogen (N) increased 2-fold Neurospora crassa sensitivity to chitosan. We linked this increase with production of intracellular reactive oxygen species (ROS) and plasma membrane permeabilization. Releasing N. crassa from nutrient limitation reduced chitosan antifungal activity in spite of high ROS intracellular levels. With lactate instead of glucose, C and N limitation increased N. crassa sensitivity to chitosan further (4-fold) than what glucose did. Nutrient limitation also increased sensitivity of filamentous fungi and yeast human pathogens to chitosan. For Fusarium proliferatum, lowering 100-fold C and N content in the growth medium, increased 16-fold chitosan sensitivity. Similar results were found for Candida spp. (including fluconazole resistant strains) and Cryptococcus spp. Severe C and N limitation increased chitosan antifungal activity for all pathogens tested. Chitosan at 100 μg ml-1 was lethal for most fungal human pathogens tested but non-toxic to HEK293 and COS7 mammalian cell lines. Besides, chitosan increased 90% survival of Galleria mellonella larvae infected with C. albicans. These results are of paramount for developing chitosan as antifungal.

Role of the interfacial water structure on electrocatalysis: Oxygen reduction on Pt(1 1 1) in methanesulfonic acid

Most of electrocatalytic reactions occur in an aqueous environment. Understanding the influence of water structure on reaction dynamics is fundamental in electrocatalysis. In this work, the role of liquid water structure on the oxygen reduction at Pt(1 1 1) electrode is analyzed in methanesulfonic (MTSA) and perchloric acids. This is because these different anions can exert a different influence on liquid water structure. Results reveal a lower ORR electrode activity in MTSA than in HClO4 solutions and they are discussed in light of anion's influence on water structural ordering. From them, the existence of an outer-sphere, rate determining, step in the ORR mechanism is suggested.

Synthesis of palladium nanoparticles over graphite oxide and carbon nanotubes by reduction in ethylene glycol and their catalytic performance on the chemoselective hydrogenation of para-chloronitrobenzene

Pd nanoparticles have been synthesized over carbon nanotubes (CNT) and graphite oxide (GO) by reduction with ethylene glycol and by conventional impregnation method. The catalysts were tested on the chemoselective hydrogenation of p-chloronitrobenzene and the effect of the synthesis method and surface chemistry on their catalytic performance was evaluated. The catalysts were characterized by N2 adsorption/desorption isotherms at 77 K, TEM, powder X-ray diffraction, thermogravimetry, infrared and X-ray photoelectron spectroscopy and ICP-OES. It was observed that the synthesis of Pd nanoparticles employing ethylene glycol resulted in metallic palladium particles of smaller size compared to those prepared by the impregnation method and similar for both supports. The presence of oxygen groups on the support surface favored the activity and diminished the selectivity. It seems that ethylene glycol reacted with the surface groups of GO, this favoring the selectivity. The activity was higher over the CNT-based catalysts and both catalysts prepared by reduction in ethylene glycol were quite stable upon recycling.

Alteration of natural ³⁷Ar activity concentration in the subsurface by gas transport and water infiltration

High ³⁷Ar activity concentration in soil gas is proposed as a key evidence for the detection of underground nuclear explosion by the Comprehensive Nuclear Test-Ban Treaty. However, such a detection is challenged by the natural background of ³⁷Ar in the subsurface, mainly due to Ca activation by cosmic rays. A better understanding and improved capability to predict ³⁷Ar activity concentration in the subsurface and its spatial and temporal variability is thus required. A numerical model integrating ³⁷Ar production and transport in the subsurface is developed, including variable soil water content and water infiltration at the surface. A parameterized equation for ³⁷Ar production in the first 15 m below the surface is studied, taking into account the major production reactions and the moderation effect of soil water content. Using sensitivity analysis and uncertainty quantification, a realistic and comprehensive probability distribution of natural ³⁷Ar activity concentrations in soil gas is proposed, including the effects of water infiltration. Site location and soil composition are identified as the parameters allowing for a most effective reduction of the possible range of ³⁷Ar activity concentrations. The influence of soil water content on ³⁷Ar production is shown to be negligible to first order, while ³⁷Ar activity concentration in soil gas and its temporal variability appear to be strongly influenced by transient water infiltration events. These results will be used as a basis for practical CTBTO concepts of operation during an OSI.

Patrol activity - Utah ASAP. Analytic study number three. Final report.

National Highway Traffic Safety Administration, Washington, D.C.

An analysis of ASAP patrol activity. Analytical study #3. Final report.

National Highway Traffic Safety Administration, Washington, D.C.

Role of glutamic acid 216 in cytochrome P450 2D6 substrate binding and catalysis

Human cytochrome P450 (P450) 2D6 is an important enzyme involved in the metabolism of drugs, many of which are amines or contain other basic nitrogen atoms. Asp301 has generally been considered to be involved in electrostatic docking with the basic substrates, on the basis of previous modeling studies and site-directed mutagenesis. Substitution of Glu216 with a residue other than Asp strongly attenuated the binding of quinidine, bufuralol, and several other P450 2D6 ligands. Catalytic activity with the substrates bufuralol and 4-methoxyphenethylamine was strongly inhibited by neutral or basic mutations at Glu216 (>95%), to the same extent as the substitution of Asn at Asp301. Unlike the Asp301 mutants, the Gln216 mutant (E216Q) retained 40% enzyme efficiency with the substrate spirosulfonamide, devoid of basic nitrogen, suggesting that the substitutions at Glu216 affect binding of amine substrates more than other catalytic steps. Attempts to induce catalytic specificity toward new substrates by substitutions at Asp301 and Glu216 were unsuccessful. Collectively, the results provide evidence for electrostatic interaction of amine substrates with Glu216, and we propose that both of these acidic residues plus at least another residue(s) is (are) involved in binding the repertoire of P450 2D6 ligands.

Preparation and characterization of copper catalysts supported on mesoporous Al2O3 nanofibers for N2O reduction to N2

A series of mesoporous Al2O3 samples with different porous structures and phases were prepared and used as supports for Cu/Al2O3 catalysts. These catalysts were characterized by N-2 adsorption, NMR, TGA, XRD, and UV - vis spectroscopic techniques and tested for the catalytic reaction of N2O decomposition. The activity increased with the increasing calcination temperatures of supports from 450 to 900 degreesC; however, a further increase in calcination temperature up to 1200 degreesC resulted in a significant reduction in activity. Characterization revealed that the calcination temperatures of supports influenced the porous structures and phases of the supports, which in turn affected the dispersions, phases, and activities of the impregnated copper catalyst. The different roles of surface spinel, bulk CuAl2O4, and bulk CuO is clarified for N2O catalytic decomposition. Two mechanism schemes were thus proposed to account for the varying activities of different catalysts.