Analisi del circuito di regolazione responsabile del controllo trascrizionale dei geni Heat-Shock in Helicobacter pylori

Helicobacter pylori, un patogeno umano in grado di colonizzare la nicchia gastrica, è associato a patologie del tratto gastrointestinale di varia gravità. Per sopravvivere nell’ambiente ostile dello stomaco dell’ospite, e mettere in atto un’infezione persistente, il batterio si serve di una serie di fattori di virulenza che includono anche le proteine Heat Shock (chaperone). I principali geni codificanti le proteine chaperone in H. pylori sono organizzati in tre operoni trascritti dall’RNA polimerasi contenente il fattore sigma vegetativo σ80. La trascrizione di due dei tre operoni è regolata negativamente da due regolatori trascrizionali, HspR e HrcA, mentre il terzo operone è represso solo da HspR. Fino ad ora, studi molecolari per la comprensione del ruolo di ciascuna proteina nel controllo trascrizionale dei geni heat shock sono stati ostacolati dalla citotossicità ed insolubilità di HrcA quando espressa in sistemi eterologhi. In questo lavoro, è stata analizzata la sequenza amminoacidica di HrcA ed è stata confermata sperimentalmente la predizione bioinformatica della sua associazione con la membrana interna. La citotossicità e l’insolubilità di HrcA in E. coli sono state alleviate inducendone l’espressione a 42°C. Saggi in vitro con le proteine ricombinanti purificate, HspR e HrcA, hanno consentito di definire i siti di legame dei due repressori sui promotori degli operoni heat shock. Ulteriori saggi in vitro hanno suggerito che l’affinità di HrcA per gli operatori è aumentata dalla chaperonina GroESL. Questi dati contribuiscono parzialmente alla comprensione del meccanismo di repressione della trascrizione espletato da HrcA e HspR e permettono di ipotizzare il coinvolgimento di altri regolatori trascrizionali. L’analisi di RNA estratti dal ceppo selvatico e dai mutanti hrcA, hspR e hrcA/hspR di H.pylori su DNAmacroarrays non ha evidenziato il coinvolgimento di altri regolatori trascrizionali, ma ha permesso l’identificazione di un gruppo di geni indotti da HrcA e/ HspR. Questi geni sono coinvolti nella biosintesi e regolazione dell’apparato flagellare, suggerendo un’interconnessione tra la risposta heat shock e la motilità e chemiotassi del batterio.

El Niño southern oscillation and its effect on fog oases along the Peruvian and Chilean coastal deserts

Fog oases, locally named Lomas, are distributed in a fragmented way along the western coast of Chile and Peru (South America) between ~6°S and 30°S following an altitudinal gradient determined by a fog layer. This fragmentation has been attributed to the hyper aridity of the desert. However, periodically climatic events influence the ‘normal seasonality’ of this ecosystem through a higher than average water input that triggers plant responses (e.g. primary productivity and phenology). The impact of the climatic oscillation may vary according to the season (wet/dry). This thesis evaluates the potential effect of climate oscillations, such as El Niño Southern Oscillation (ENSO), through the analysis of vegetation of this ecosystem following different approaches: Chapters two and three show the analysis of fog oasis along the Peruvian and Chilean deserts. The objectives are: 1) to explain the floristic connection of fog oases analysing their taxa composition differences and the phylogenetic affinities among them, 2) to explore the climate variables related to ENSO which likely affect fog production, and the responses of Lomas vegetation (composition, productivity, distribution) to climate patterns during ENSO events. Chapters four and five describe a fog-oasis in southern Peru during the 2008-2010 period. The objectives are: 3) to describe and create a new vegetation map of the Lomas vegetation using remote sensing analysis supported by field survey data, and 4) to identify the vegetation change during the dry season. The first part of our results show that: 1) there are three significantly different groups of Lomas (Northern Peru, Southern Peru, and Chile) with a significant phylogenetic divergence among them. The species composition reveals a latitudinal gradient of plant assemblages. The species origin, growth-forms typologies, and geographic position also reinforce the differences among groups. 2) Contradictory results have emerged from studies of low-cloud anomalies and the fog-collection during El Niño (EN). EN increases water availability in fog oases when fog should be less frequent due to the reduction of low-clouds amount and stratocumulus. Because a minor role of fog during EN is expected, it is likely that measurements of fog-water collection during EN are considering drizzle and fog at the same time. Although recent studies on fog oases have shown some relationship with the ENSO, responses of vegetation have been largely based on descriptive data, the absence of large temporal records limit the establishment of a direct relationship with climatic oscillations. The second part of the results show that: 3) five different classes of different spectral values correspond to the main land cover of Lomas using a Vegetation Index (VI). The study case is characterised by shrubs and trees with variable cover (dense, semi-dense and open). A secondary area is covered by small shrubs where the dominant tree species is not present. The cacti area and the old terraces with open vegetation were not identified with the VI. Agriculture is present in the area. Finally, 4) contrary to the dry season of 2008 and 2009 years, a higher VI was obtained during the dry season of 2010. The VI increased up to three times their average value, showing a clear spectral signal change, which coincided with the ENSO event of that period.

Investigation on laser shock peening capability by FE simulation

Laser shock peening is a technique similar to shot peening that imparts compressive residual stresses in materials for improving fatigue resistance. The ability to use a high energy laser pulse to generate shock waves, inducing a compressive residual stress field in metallic materials, has applications in multiple fields such as turbo-machinery, airframe structures, and medical appliances. The transient nature of the LSP phenomenon and the high rate of the laser's dynamic make real time in-situ measurement of laser/material interaction very challenging. For this reason and for the high cost of the experimental tests, reliable analytical methods for predicting detailed effects of LSP are needed to understand the potential of the process. Aim of this work has been the prediction of residual stress field after Laser Peening process by means of Finite Element Modeling. The work has been carried out in the Stress Methods department of Airbus Operations GmbH (Hamburg) and it includes investigation on compressive residual stresses induced by Laser Shock Peening, study on mesh sensitivity, optimization and tuning of the model by using physical and numerical parameters, validation of the model by comparing it with experimental results. The model has been realized with Abaqus/Explicit commercial software starting from considerations done on previous works. FE analyses are “Mesh Sensitive”: by increasing the number of elements and by decreasing their size, the software is able to probe even the details of the real phenomenon. However, these details, could be only an amplification of real phenomenon. For this reason it was necessary to optimize the mesh elements' size and number. A new model has been created with a more fine mesh in the trough thickness direction because it is the most involved in the process deformations. This increment of the global number of elements has been paid with an "in plane" size reduction of the elements far from the peened area in order to avoid too high computational costs. Efficiency and stability of the analyses has been improved by using bulk viscosity coefficients, a merely numerical parameter available in Abaqus/Explicit. A plastic rate sensitivity study has been also carried out and a new set of Johnson Cook's model coefficient has been chosen. These investigations led to a more controllable and reliable model, valid even for more complex geometries. Moreover the study about the material properties highlighted a gap of the model about the simulation of the surface conditions. Modeling of the ablative layer employed during the real process has been used to fill this gap. In the real process ablative layer is a super thin sheet of pure aluminum stuck on the masterpiece. In the simulation it has been simply reproduced as a 100µm layer made by a material with a yield point of 10MPa. All those new settings has been applied to a set of analyses made with different geometry models to verify the robustness of the model. The calibration of the model with the experimental results was based on stress and displacement measurements carried out on the surface and in depth as well. The good correlation between the simulation and experimental tests results proved this model to be reliable.

Measurement of the oscillation frequency of B s mesons in the hadronic decay mode B s pi D s (phi pi) X with the D0 detector at the Fermilab Tevatron collider

The standard model (SM) of particle physics is a theory, describing three out of four fundamental forces. In this model the Cabibbo-Kobayashi-Maskawa (CKM) matrix describes the transformation between the mass and weak eigenstates of quarks. The matrix properties can be visualized as triangles in the complex plane. A precise measurement of all triangle parameters can be used to verify the validity of the SM. The least precisely measured parameter of the triangle is related to the CKM element |Vtd|, accessible through the mixing frequency (oscillation) of neutral B mesons, where mixing is the transition of a neutral meson into its anti-particle and vice versa. It is possible to calculate the CKM element |Vtd| and a related element |Vts| by measuring the mass differences Dmd (Dms ) between neutral Bd and bar{Bd} (Bs and bar{Bs}) meson mass eigenstates. This measurement is accomplished by tagging the initial and final state of decaying B mesons and determining their lifetime. Currently the Fermilab Tevatron Collider (providing pbar{p} collisions at sqrt{s}=1.96 TeV) is the only place, where Bs oscillations can be studied. The first selection of the "golden", fully hadronic decay mode Bs->Ds pi(phi pi)X at DØ is presented in this thesis. All data, taken between April 2002 and August 2007 with the DØ detector, corresponding to an integrated luminosity of int{L}dt=2.8/fb is used. The oscillation frequency Dms and the ratio |Vtd|/|Vts| are determined as Dms = (16.6 +0.5-0.4(stat) +0.4-0.3(sys)) 1/ps, |Vtd|/|Vts| = 0.213 +0.004-0.003(exp)pm 0.008(theor). These results are consistent with the standard model expectations and no evidence for new physics is observable.

Optimierungen des Nachweises von Supernovae in IceCube

Kernkollaps-Supernovae werden von einem massiven Ausbruch niederenergetischer Neutrinos begleitet. Sie zählen zu den energiereichsten Erscheinungen im Universum und stellen die derzeit einzig bekannte Quelle extrasolarer Neutrinos dar.rnDie Detektion einer solchen Neutrinosignatur würde zu einem tieferen Verständnis des bislang unzureichend bekannten stellaren Explosionsmechanismus führen. rnDarüber hinaus würden neue Einblicke in den Bereich der Teilchenphysik und der Supernova-Modellierung ermöglicht. Das sich zur Zeit am geographischen Südpol im Aufbau befindliche Neutrinoteleskop IceCube wird 2011 fertig gestellt sein.rnIceCube besteht im endgültigen Ausbau aus 5160 Photovervielfachern, die sich in gitterförmiger Anordnung in Tiefen zwischen 1450m und 2450m unter der Eisoberfläche befinden. Durch den Nachweis von Tscherenkow-Photonenrnim antarktischen Gletscher ist es in der Lage, galaktische Supernovae über einen kollektiven Anstieg der Rauschraten in seinen Photonenvervielfachern nachzuweisen.rnIn dieser Arbeit werden verschiedene Studien zur Implementierung einer künstlichen Totzeit vorgestellt, welche korreliertes Rauschen unterdrücken und somit das Signal-Untergund-Verhältnis maximieren würden.rnEin weiterer Teil dieser Dissertation bestand in der Integration der Supernova-Datenakquise eine neue Experiment-Steuerungssoftware.rnFür den Analyseteil der Arbeit wurde ein Monte-Carlo für IceCube entwickelt und Neutinooszillations-Mechanismen und eine Reihe von Signalmodellen integriert. Ein Likelihoodhypothesen-Test wurde verwendet, um die Unterscheidbarkeit verschiedener Supernova- beziehungsweise Neutrinooszillations-Szenarien zu untersuchen. Desweiteren wurde analysiert inwieweit sich Schock-Anregungen und QCD-Phasenübergnag im Verlauf des Explosionsprozesses detektieren lassen.

Laser shock peening treatment to control and moderate fatigue crack growth in aircraft structure based on residual stress engineering approach

Laser Shock Peening (LSP) is a surface enhancement treatment which induces a significant layer of beneficial compressive residual stresses of up to several mm underneath the surface of metal components in order to improve the detrimental effects of the crack growth behavior rate in it. The aim of this thesis is to predict the crack growth behavior in metallic specimens with one or more stripes which define the compressive residual stress area induced by the Laser Shock Peening treatment. The process was applied as crack retardation stripes perpendicular to the crack propagation direction with the object of slowing down the crack when approaching the peened stripes. The finite element method has been applied to simulate the redistribution of stresses in a cracked model when it is subjected to a tension load and to a compressive residual stress field, and to evaluate the Stress Intensity Factor (SIF) in this condition. Finally, the Afgrow software is used to predict the crack growth behavior of the component following the Laser Shock Peening treatment and to detect the improvement in the fatigue life comparing it to the baseline specimen. An educational internship at the “Research & Technologies Germany – Hamburg” department of AIRBUS helped to achieve knowledge and experience to write this thesis. The main tasks of the thesis are the following: •To up to date Literature Survey related to “Laser Shock Peening in Metallic Structures” •To validate the FE model developed against experimental measurements at coupon level •To develop design of crack growth slowdown in Centered Cracked Tension specimens based on residual stress engineering approach using laser peened strip transversal to the crack path •To evaluate the Stress Intensity Factor values for Centered Cracked Tension specimens after the Laser Shock Peening treatment via Finite Element Analysis •To predict the crack growth behavior in Centered Cracked Tension specimens using as input the SIF values evaluated with the FE simulations •To validate the results by means of experimental tests

Effect of Laser Shock Peening on Fatigue Crack Propagation of Aeronautical Structures

Laser Shock Peening (LSP) is a surface enhancement treatment which induces a significant layer of beneficial compressive residual stresses up to several mm underneath the surface of metal components in order to improve the detrimental effects of crack growth behavior rate in it. The aim of this thesis is to predict the crack growth behavior of thin Aluminum specimens with one or more LSP stripes defining a compressive residual stress area. The LSP treatment has been applied as crack retardation stripes perpendicular to the crack growing direction, with the objective of slowing down the crack when approaching the LSP patterns. Different finite element approaches have been implemented to predict the residual stress field left by the laser treatment, mostly by means of the commercial software Abaqus/Explicit. The Afgrow software has been used to predict the crack growth behavior of the component following the laser peening treatment and to detect the improvement in fatigue life comparing to the specimen baseline. Furthermore, an analytical model has been implemented on the Matlab software to make more accurate predictions on fatigue life of the treated components. An educational internship at the Research and Technologies Germany- Hamburg department of Airbus helped to achieve knowledge and experience to write this thesis. The main tasks of the thesis are the following: -To up to date Literature Survey related to laser shock peening in metallic structures -To validate the FE models developed against experimental measurements at coupon level -To develop design of crack growth slow down in centered and edge cracked tension specimens based on residual stress engineering approach using laser peened patterns transversal to the crack path -To predict crack growth behavior of thin aluminum panels -To validate numerical and analytical results by means of experimental tests.

Daily modulation of the Heat shock proteins (Hsps) in three different species of scleractinian corals

Temperature and light intensity is the most important environmental parameters that influence circadian cycle of scleractinian corals. In this context, modulation of the biomarkers Hsp60 and Hsp70 in situ was investigated by three different healthy coral species (Acropora tenuis, Echinopora lamellosa and Porites lobata) not stress induced during time course of 24h. Significance species-specific modulation under natural conditions is displayed by all corals under study. A strong fluctuation in Hsps expression is shown by the most susceptible, branched coral A. tenuis, instead of fine and low modulation is shown by the massive coral P. lobata. From the results match between morphology difference and physiological difference response its suggest and similarity pattern between Hsps with different cellular compartments location is suggested too. Starting from this study health of coral reefs could be able to be investigated in the future with a set of biomarkers composed also by Hsps which will be set up.

The effect of high-energy extracorporeal shock waves on hyaline cartilage of adult rats in vivo

The aim of this study was to determine if extracorporeal shock wave therapy (ESWT) in vivo affects the structural integrity of articular cartilage. A single bout of ESWT (1500 shock waves of 0.5 mJ/mm(2)) was applied to femoral heads of 18 adult Sprague-Dawley rats. Two sham-treated animals served as controls. Cartilage of each femoral head was harvested at 1, 4, or 10 weeks after ESWT (n = 6 per treatment group) and scored on safranin-O-stained sections. Expression of tenascin-C and chitinase 3-like protein 1 (Chi3L1) was analyzed by immunohistochemistry. Quantitative real-time polymerase chain reaction (PCR) was used to examine collagen (II)alpha(1) (COL2A1) expression and chondrocyte morphology was investigated by transmission electron microscopy no changes in Mankin scores were observed after ESWT. Positive immunostaining for tenascin-C and Chi3L1 was found up to 10 weeks after ESWT in experimental but not in control cartilage. COL2A1 mRNA was increased in samples 1 and 4 weeks after ESWT. Alterations found on the ultrastructural level showed expansion of the rough-surfaced endoplasmatic reticulum, detachment of the cell membrane and necrotic chondrocytes. Extracorporeal shock waves caused alterations of hyaline cartilage on a molecular and ultrastructural level that were distinctly different from control. Similar changes were described before in the very early phase of osteoarthritis (OA). High-energy ESWT might therefore cause degenerative changes in hyaline cartilage as they are found in initial OA.

Plasma copeptin levels before and during exogenous arginine vasopressin infusion in patients with advanced vasodilatory shock

Plasma copeptin levels before and during exogenous arginine vasopressin infusion (AVP) were evaluated, and the value of copeptin levels before AVP therapy to predict complications during AVP therapy and outcome in vasodilatory shock patients was determined.

Current approach to the haemodynamic management of septic shock patients in European intensive care units: a cross-sectional, self-reported questionnaire-based survey

The aim of this survey was to investigate clinicians' current approach to the haemodynamic management and resuscitation endpoints in septic shock.

Role of selective V2-receptor-antagonism in septic shock: a randomized, controlled, experimental study

ABSTRACT : INTRODUCTION : V2-receptor (V2R) stimulation potentially aggravates sepsis-induced vasodilation, fluid accumulation and microvascular thrombosis. Therefore, the present study was performed to determine the effects of a first-line therapy with the selective V2R-antagonist (Propionyl1-D-Tyr(Et)2-Val4-Abu6-Arg8,9)-Vasopressin on cardiopulmonary hemodynamics and organ function vs. the mixed V1aR/V2R-agonist arginine vasopressin (AVP) or placebo in an established ovine model of septic shock. METHODS : After the onset of septic shock, chronically instrumented sheep were randomly assigned to receive first-line treatment with the selective V2R-antagonist (1 g/kg per hour), AVP (0.05 g/kg per hour), or normal saline (placebo, each n = 7). In all groups, open-label norepinephrine was additionally titrated up to 1 g/kg per minute to maintain mean arterial pressure at 70 ± 5 mmHg, if necessary. RESULTS : Compared to AVP- and placebo-treated animals, the selective V2R-antagonist stabilized cardiopulmonary hemodynamics (mean arterial and pulmonary artery pressure, cardiac index) as effectively and increased intravascular volume as suggested by higher cardiac filling pressures. Furthermore, left ventricular stroke work index was higher in the V2R-antagonist group than in the AVP group. Notably, metabolic (pH, base excess, lactate concentrations), liver (transaminases, bilirubin) and renal (creatinine and blood urea nitrogen plasma levels, urinary output, creatinine clearance) dysfunctions were attenuated by the V2R-antagonist when compared with AVP and placebo. The onset of septic shock was associated with an increase in AVP plasma levels as compared to baseline in all groups. Whereas AVP plasma levels remained constant in the placebo group, infusion of AVP increased AVP plasma levels up to 149 ± 21 pg/mL. Notably, treatment with the selective V2R-antagonist led to a significant decrease of AVP plasma levels as compared to shock time (P < 0.001) and to both other groups (P < 0.05 vs. placebo; P < 0.001 vs. AVP). Immunohistochemical analyses of lung tissue revealed higher hemeoxygenase-1 (vs. placebo) and lower 3-nitrotyrosine concentrations (vs. AVP) in the V2R-antagonist group. In addition, the selective V2R-antagonist slightly prolonged survival (14 ± 1 hour) when compared to AVP (11 ± 1 hour, P = 0.007) and placebo (11 ± 1 hour, P = 0.025). CONCLUSIONS : Selective V2R-antagonism may represent an innovative therapeutic approach to attenuate multiple organ dysfunction in early septic shock.

Early fish oil supplementation and organ failure in patients with septic shock from abdominal infections: a propensity-matched cohort study

Fish oil (FO) has immunomodulating effects and may improve organ function and outcome in critically ill patients. This retrospective, propensity-matched cohort study investigates the effects of early intravenous FO supplementation on organ failure in patients with septic shock from abdominal infection.

The association between body-mass index and patient outcome in septic shock: a retrospective cohort study

It is unknown whether body-mass index (BMI) and commonly defined BMI categories are associated with mortality in patients with septic shock.

The shock index and the simplified PESI for identification of low-risk patients with acute pulmonary embolism

We compared the test characteristics of the shock index (SI) and the simplified pulmonary embolism severity index (sPESI) for predicting 30-day outcomes in a cohort of 1,206 patients with objectively confirmed pulmonary embolism (PE). The primary outcome of the study was all-cause mortality. The secondary outcome was nonfatal symptomatic recurrent venous thromboembolism (VTE) or nonfatal major bleeding. Overall, 119 (9.9%) out of 1,206 patients died (95% CI 8.2-11.5%) during the first month of follow-up. The sPESI classified fewer patients as low-risk (369 (31%) out of 1,206 patients, 95% CI 28-33%) compared to the SI (1,024 (85%) out of 1,206 patients, 95% CI 83-87%) (p<0.001). Low-risk patients based on the sPESI had a lower 30-day mortality than those based on the SI (1.6% (95% CI 0.3-2.9%) versus 8.3% (95% CI 6.6-10.0%)), while the 30-day rate of nonfatal recurrent VTE or major bleeding was similar (2.2% (95%CI 0.7-3.6%) versus 3.3% (95%CI 2.2-4.4%)). The net reclassification improvement with the sPESI was 13.4% (p = 0.07). The integrated discrimination improvement was estimated as 1.8% (p<0.001). The sPESI quantified the prognosis of patients with PE better than the SI.