Mass spectrometry-based protein profiling strategies for biomarker discovery in liver and inflammatory bowel diseases

The study of protein expression profiles for biomarker discovery in serum and in mammalian cell populations needs the continuous improvement and combination of proteins/peptides separation techniques, mass spectrometry, statistical and bioinformatic approaches. In this thesis work two different mass spectrometry-based protein profiling strategies have been developed and applied to liver and inflammatory bowel diseases (IBDs) for the discovery of new biomarkers. The first of them, based on bulk solid-phase extraction combined with matrix-assisted laser desorption/ionization - Time of Flight mass spectrometry (MALDI-TOF MS) and chemometric analysis of serum samples, was applied to the study of serum protein expression profiles both in IBDs (Crohn’s disease and ulcerative colitis) and in liver diseases (cirrhosis, hepatocellular carcinoma, viral hepatitis). The approach allowed the enrichment of serum proteins/peptides due to the high interaction surface between analytes and solid phase and the high recovery due to the elution step performed directly on the MALDI-target plate. Furthermore the use of chemometric algorithm for the selection of the variables with higher discriminant power permitted to evaluate patterns of 20-30 proteins involved in the differentiation and classification of serum samples from healthy donors and diseased patients. These proteins profiles permit to discriminate among the pathologies with an optimum classification and prediction abilities. In particular in the study of inflammatory bowel diseases, after the analysis using C18 of 129 serum samples from healthy donors and Crohn’s disease, ulcerative colitis and inflammatory controls patients, a 90.7% of classification ability and a 72.9% prediction ability were obtained. In the study of liver diseases (hepatocellular carcinoma, viral hepatitis and cirrhosis) a 80.6% of prediction ability was achieved using IDA-Cu(II) as extraction procedure. The identification of the selected proteins by MALDITOF/ TOF MS analysis or by their selective enrichment followed by enzymatic digestion and MS/MS analysis may give useful information in order to identify new biomarkers involved in the diseases. The second mass spectrometry-based protein profiling strategy developed was based on a label-free liquid chromatography electrospray ionization quadrupole - time of flight differential analysis approach (LC ESI-QTOF MS), combined with targeted MS/MS analysis of only identified differences. The strategy was used for biomarker discovery in IBDs, and in particular of Crohn’s disease. The enriched serum peptidome and the subcellular fractions of intestinal epithelial cells (IECs) from healthy donors and Crohn’s disease patients were analysed. The combining of the low molecular weight serum proteins enrichment step and the LCMS approach allowed to evaluate a pattern of peptides derived from specific exoprotease activity in the coagulation and complement activation pathways. Among these peptides, particularly interesting was the discovery of clusters of peptides from fibrinopeptide A, Apolipoprotein E and A4, and complement C3 and C4. Further studies need to be performed to evaluate the specificity of these clusters and validate the results, in order to develop a rapid serum diagnostic test. The analysis by label-free LC ESI-QTOF MS differential analysis of the subcellular fractions of IECs from Crohn’s disease patients and healthy donors permitted to find many proteins that could be involved in the inflammation process. Among them heat shock protein 70, tryptase alpha-1 precursor and proteins whose upregulation can be explained by the increased activity of IECs in Crohn’s disease were identified. Follow-up studies for the validation of the results and the in-depth investigation of the inflammation pathways involved in the disease will be performed. Both the developed mass spectrometry-based protein profiling strategies have been proved to be useful tools for the discovery of disease biomarkers that need to be validated in further studies.

Sviluppo di metodologie di localizzazione nel contesto del Comprehensive Nuclear Test-Ban Treaty

Since the first underground nuclear explosion, carried out in 1958, the analysis of seismic signals generated by these sources has allowed seismologists to refine the travel times of seismic waves through the Earth and to verify the accuracy of the location algorithms (the ground truth for these sources was often known). Long international negotiates have been devoted to limit the proliferation and testing of nuclear weapons. In particular the Treaty for the comprehensive nuclear test ban (CTBT), was opened to signatures in 1996, though, even if it has been signed by 178 States, has not yet entered into force, The Treaty underlines the fundamental role of the seismological observations to verify its compliance, by detecting and locating seismic events, and identifying the nature of their sources. A precise definition of the hypocentral parameters represents the first step to discriminate whether a given seismic event is natural or not. In case that a specific event is retained suspicious by the majority of the State Parties, the Treaty contains provisions for conducting an on-site inspection (OSI) in the area surrounding the epicenter of the event, located through the International Monitoring System (IMS) of the CTBT Organization. An OSI is supposed to include the use of passive seismic techniques in the area of the suspected clandestine underground nuclear test. In fact, high quality seismological systems are thought to be capable to detect and locate very weak aftershocks triggered by underground nuclear explosions in the first days or weeks following the test. This PhD thesis deals with the development of two different seismic location techniques: the first one, known as the double difference joint hypocenter determination (DDJHD) technique, is aimed at locating closely spaced events at a global scale. The locations obtained by this method are characterized by a high relative accuracy, although the absolute location of the whole cluster remains uncertain. We eliminate this problem introducing a priori information: the known location of a selected event. The second technique concerns the reliable estimates of back azimuth and apparent velocity of seismic waves from local events of very low magnitude recorded by a trypartite array at a very local scale. For the two above-mentioned techniques, we have used the crosscorrelation technique among digital waveforms in order to minimize the errors linked with incorrect phase picking. The cross-correlation method relies on the similarity between waveforms of a pair of events at the same station, at the global scale, and on the similarity between waveforms of the same event at two different sensors of the try-partite array, at the local scale. After preliminary tests on the reliability of our location techniques based on simulations, we have applied both methodologies to real seismic events. The DDJHD technique has been applied to a seismic sequence occurred in the Turkey-Iran border region, using the data recorded by the IMS. At the beginning, the algorithm was applied to the differences among the original arrival times of the P phases, so the cross-correlation was not used. We have obtained that the relevant geometrical spreading, noticeable in the standard locations (namely the locations produced by the analysts of the International Data Center (IDC) of the CTBT Organization, assumed as our reference), has been considerably reduced by the application of our technique. This is what we expected, since the methodology has been applied to a sequence of events for which we can suppose a real closeness among the hypocenters, belonging to the same seismic structure. Our results point out the main advantage of this methodology: the systematic errors affecting the arrival times have been removed or at least reduced. The introduction of the cross-correlation has not brought evident improvements to our results: the two sets of locations (without and with the application of the cross-correlation technique) are very similar to each other. This can be commented saying that the use of the crosscorrelation has not substantially improved the precision of the manual pickings. Probably the pickings reported by the IDC are good enough to make the random picking error less important than the systematic error on travel times. As a further justification for the scarce quality of the results given by the cross-correlation, it should be remarked that the events included in our data set don’t have generally a good signal to noise ratio (SNR): the selected sequence is composed of weak events ( magnitude 4 or smaller) and the signals are strongly attenuated because of the large distance between the stations and the hypocentral area. In the local scale, in addition to the cross-correlation, we have performed a signal interpolation in order to improve the time resolution. The algorithm so developed has been applied to the data collected during an experiment carried out in Israel between 1998 and 1999. The results pointed out the following relevant conclusions: a) it is necessary to correlate waveform segments corresponding to the same seismic phases; b) it is not essential to select the exact first arrivals; and c) relevant information can be also obtained from the maximum amplitude wavelet of the waveforms (particularly in bad SNR conditions). Another remarkable point of our procedure is that its application doesn’t demand a long time to process the data, and therefore the user can immediately check the results. During a field survey, such feature will make possible a quasi real-time check allowing the immediate optimization of the array geometry, if so suggested by the results at an early stage.

Diagnostic techniques for EHD and MHD interaction

The impact of plasma technologies is growing both in the academic and in the industrial fields. Nowadays, a great interest is focused in plasma applications in aeronautics and astronautics domains. Plasma actuators based on the Magneto-Hydro-Dynamic (MHD) and Electro- Hydro-Dynamic (EHD) interactions are potentially able to suitably modify the fluid-dynamics characteristics around a flying body without utilizing moving parts. This could lead to the control of an aircraft with negligible response time, more reliability and improvements of the performance. In order to study the aforementioned interactions, a series of experiments and a wide number of diagnostic techniques have been utilized. The EHD interaction, realized by means of a Dielectric Barrier Discharge (DBD) actuator, and its impact on the boundary layer have been evaluated by means of two different experiments. In the first one a three phase multi-electrode flat panel actuator is used. Different external flow velocities (from 1 to 20m/s) and different values of the supplied voltage and frequency have been considered. Moreover a change of the phase sequence has been done to verify the influence of the electric field existing between successive phases. Measurements of the induced speed had shown the effect of the supply voltage and the frequency, and the phase order in the momentum transfer phenomenon. Gains in velocity, inside the boundary layer, of about 5m/s have been obtained. Spectroscopic measurements allowed to determine the rotational and the vibrational temperature of the plasma which lie in the range of 320 ÷ 440°K and of 3000 ÷ 3900°K respectively. A deviation from thermodynamic equilibrium had been found. The second EHD experiment is realized on a single electrode pair DBD actuator driven by nano-pulses superimposed to a DC or an AC bias. This new supply system separates the plasma formation mechanism from the acceleration action on the fluid, leading to an higher degree of the control of the process. Both the voltage and the frequency of the nano-pulses and the amplitude and the waveform of the bias have been varied during the experiment. Plasma jets and vortex behavior had been observed by means of fast Schlieren imaging. This allowed a deeper understanding of the EHD interaction process. A velocity increase in the boundary layer of about 2m/s had been measured. Thrust measurements have been performed by means of a scales and compared with experimental data reported in the literature. For similar voltage amplitudes thrust larger than those of the literature, had been observed. Surface charge measurements led to realize a modified DBD actuator able to obtain similar performances when compared with that of other experiments. However in this case a DC bias replacing the AC bias had been used. MHD interaction experiments had been carried out in a hypersonic wind tunnel in argon with a flow of Mach 6. Before the MHD experiments a thermal, fluid-dynamic and plasma characterization of the hypersonic argon plasma flow have been done. The electron temperature and the electron number density had been determined by means of emission spectroscopy and microwave absorption measurements. A deviation from thermodynamic equilibrium had been observed. The electron number density showed to be frozen at the stagnation region condition in the expansion through the nozzle. MHD experiments have been performed using two axial symmetric test bodies. Similar magnetic configurations were used. Permanent magnets inserted into the test body allowed to generate inside the plasma azimuthal currents around the conical shape of the body. These Faraday currents are responsible of the MHD body force which acts against the flow. The MHD interaction process has been observed by means of fast imaging, pressure and electrical measurements. Images showed bright rings due to the Faraday currents heating and exciting the plasma particles. Pressure measurements showed increases of the pressure in the regions where the MHD interaction is large. The pressure is 10 to 15% larger than when the MHD interaction process is silent. Finally by means of electrostatic probes mounted flush on the test body lateral surface Hall fields of about 500V/m had been measured. These results have been used for the validation of a numerical MHD code.

Human papillomavirus (HPV) and associated diseases: between applied diagnostic and basic research

Human Papillomavirus (HPV) is the cause of cervical cancers (among these, adenocarcinoma, AdCa) and is associated to a subgroup of oropharyngeal carcinomas (OPSCCs). Even if the risk for cancer development is linked to the infection by some viral genotypes, mainly HPV16 and 18, viral DNA alone seems not to be sufficient for diagnosis. Moreover, the role of the virus in OPSCCs has not been totally clarified yet. In the first part of the thesis, the performances concerning viral genotyping in clinical cervical samples of a new pyrosequencing-based test and a well-known hybridization-based assay have been compared. Similar results between the methods have been obtained. However, the former showed advantages in detecting intratype variants, higher specificity and a broader spectrum of detectable HPV types. The second part deals with the evaluation of virological markers (genotyping, viral oncoproteins expression, viral load, physical state and CpG methylation of HPV16 genome) in the diagnosis/prognosis of cervical AdCa and HPV-associated OPSCCs. HPV16 has been confirmed the most prevalent genotype in both the populations. Interestingly, the mean methylation frequency of viral DNA at the early promoter showed the tendency to be associated to invasion for cervical AdCa and to a worse prognosis for OPSCCs, suggesting a promising role as diagnostic/prognostic biomarker. The experiments of the third part were performed at the DKFZ in Heidelberg (Germany) and dealt with the analysis of the response to IFN-k transfection in HPV16-positive cervical cancer and head&neck carcinoma cell lines to evaluate its potential role as new treatment. After 24h, we observed increased IFN-b expression which lead to the up-regulation of genes involved in the antigens presentation pathway (MHC class I and immunoproteasome) and antiviral response as well, in particular in cervical cancer cell lines. This fact suggested also the presence of different HPV-mediated carcinogenic pathways between the two anatomical districts.

Valutazione dell’impiego dei test per la genotipizzazione di HPV e l’espressione degli oncogeni virali nel follow-up di donne conizzate per lesioni cervicali di alto grado nello screening del cervico-carcinoma della Regione Emilia-Romagna

Obiettivi: Valutare la prevalenza dei diversi genotipi di HPV in pazienti con diagnosi di CIN2/3 nella Regione Emilia-Romagna, la persistenza genotipo-specifica di HPV e l’espressione degli oncogeni virali E6/E7 nel follow-up post-trattamento come fattori di rischio di recidiva/persistenza o progressione di malattia; verificare l’applicabilità di nuovi test diagnostici biomolecolari nello screening del cervicocarcinoma. Metodi: Sono state incluse pazienti con citologia di screening anormale, sottoposte a trattamento escissionale (T0) per diagnosi di CIN2/3 su biopsia mirata. Al T0 e durante il follow-up a 6, 12, 18 e 24 mesi, oltre al Pap test e alla colposcopia, sono state effettuate la ricerca e la genotipizzazione dell'HPV DNA di 28 genotipi. In caso di positività al DNA dei 5 genotipi 16, 18, 31, 33 e/o 45, si è proceduto alla ricerca dell'HPV mRNA di E6/E7. Risultati preliminari: Il 95.8% delle 168 pazienti selezionate è risultato HPV DNA positivo al T0. Nel 60.9% dei casi le infezioni erano singole (prevalentemente da HPV 16 e 31), nel 39.1% erano multiple. L'HPV 16 è stato il genotipo maggiormente rilevato (57%). Il 94.3% (117/124) delle pazienti positive per i 5 genotipi di HPV DNA sono risultate mRNA positive. Abbiamo avuto un drop-out di 38/168 pazienti. A 18 mesi (95% delle pazienti) la persistenza dell'HPV DNA di qualsiasi genotipo era del 46%, quella dell'HPV DNA dei 5 genotipi era del 39%, con espressione di mRNA nel 21%. Abbiamo avuto recidiva di malattia (CIN2+) nel 10.8% (14/130) a 18 mesi. Il pap test era negativo in 4/14 casi, l'HPV DNA test era positivo in tutti i casi, l'mRNA test in 11/12 casi. Conclusioni: L'HR-HPV DNA test è più sensibile della citologia, l'mRNA test è più specifico nell'individuare una recidiva. I dati definitivi saranno disponibili al termine del follow-up programmato.

Ottimizzazione del consumo dei grassi durante esercizio fisico: studio di un test per il target mirato di allenamento individuale

Il primo studio ha verificato l'affidabilità del software Polimedicus e gli effetti indotti d'allenamento arobico all’intensità del FatMax. 16 soggetti sovrappeso, di circa 40-55anni, sono stati arruolati e sottoposti a un test incrementale fino a raggiungere un RER di 0,95, e da quel momento il carico è stato aumentato di 1 km/ h ogni minuto fino a esaurimento. Successivamente, è stato verificato se i valori estrapolati dal programma erano quelli che si possono verificare durante a un test a carico costante di 1ora. I soggetti dopo 8 settimane di allenamento hanno fatto un altro test incrementale. Il dati hanno mostrato che Polimedicus non è molto affidabile, soprattutto l'HR. Nel secondo studio è stato sviluppato un nuovo programma, Inca, ed i risultati sono stati confrontati con i dati ottenuti dal primo studio con Polimedicus. I risultati finali hanno mostrato che Inca è più affidabile. Nel terzo studio, abbiamo voluto verificare l'esattezza del calcolo del FatMax con Inca e il test FATmaxwork. 25 soggetti in sovrappeso, tra 40-55 anni, sono stati arruolati e sottoposti al FATmaxwork test. Successivamente, è stato verificato se i valori estrapolati da INCA erano quelli che possono verificarsi durante un carico di prova costante di un'ora. L'analisi ha mostrato una precisione del calcolo della FatMax durante il carico di lavoro. Conclusione: E’ emersa una certa difficoltà nel determinare questo parametro, sia per la variabilità inter-individuale che intra-individuale. In futuro bisognerà migliorare INCA per ottenere protocolli di allenamento ancora più validi.

Metodi di misurazione e implicazioni dell'albuminuria e della proteinuria nel cane

La proteinuria è un marker di danno renale nel cane. L’obiettivo dello studio è di valutare la capacità del dipstick urinario e dell’UPC di diagnosticare precocemente l’albuminuria nel cane. Sono stati raccolti 868 campioni di urina, con sedimento spento e assenza di ematuria, nell’Ospedale Didattico Veterinario della Facoltà di Medicina Veterinaria di Bologna. Per 550 campioni è stata effettuata l’analisi delle urine, la misurazione dell’UPC e dell’UAC, mentre UPC e UAC sono stati misurati in tutti gli 868 campioni. I campioni di urina sono stati analizzati con il metodo dipstick mediante lettura automatizzata. Utilizzando come valore di riferimento l’UAC è stata valutata l’accuratezza diagnostica del dipstick urinario e dell’UPC. L’intervallo di riferimento dell’UAC (0-0,024) è stato determinato utilizzando 60 cani sani. I dati raccolti sono stati classificati utilizzando differenti cut-off per il peso specifico urinario (1012 o 1030), per la proteinuria al dipstick (30 o 100 mg/dl), per l’UPC (0,2) e per l’UAC (0,024). Sono stati valutati l’agreement diagnostico e la correlazione di Spearman tra dipstick, UPC e UAC. E’ stata stimata l’accuratezza diagnostica misurando l’area al di sotto della curva di ROC nell’analisi dell’UAC. Il livello di significatività è stato definito per p < 0,05. Indipendentemente dal peso specifico urinario, l’agreement diagnostico tra dipstick, UPC e UAC è risultato forte (k=0,62 e k=0,61, rispettivamente; p<0,001) con valori di dipstick ≥30 mg/dl, debole (k=0,27 e k=0,26, rispettivamente; p<0,001) con valori di dipstick ≥100 mg/dl. L’accuratezza diagnostica del dipstick messa a confronto con UPC e con UAC è molto buona (AUC 0,84 e 0,84, rispettivamente; p<0,001) e i risultati negativi al dipstick presentano il 100% di sensitività. UPC e UAC sono fortemente correlate (r=0,90; p<0,001). Mettendo a confronto UPC e UAC, l’accuratezza diagnostica è risultata eccellente (AUC 0,94; p<0,001), con massima sensitività e specificità per UPC≥0.3.

Aging of nuclear power plant cables: in search of non-destructive diagnostic quantities

The safety systems of nuclear power plants rely on low-voltage power, instrumentation and control cables. Inside the containment area, cables operate in harsh environments, characterized by relatively high temperature and gamma-irradiation. As these cables are related to fundamental safety systems, they must be able to withstand unexpected accident conditions and, therefore, their condition assessment is of utmost importance as plants age and lifetime extensions are required. Nowadays, the integrity and functionality of these cables are monitored mainly through destructive test which requires specific laboratory. The investigation of electrical aging markers which can provide information about the state of the cable by non-destructive testing methods would improve significantly the present diagnostic techniques. This work has been made within the framework of the ADVANCE (Aging Diagnostic and Prognostics of Low-Voltage I\&C Cables) project, a FP7 European program. This Ph.D. thesis aims at studying the impact of aging on cable electrical parameters, in order to understand the evolution of the electrical properties associated with cable degradation. The identification of suitable aging markers requires the comparison of the electrical property variation with the physical/chemical degradation mechanisms of polymers for different insulating materials and compositions. The feasibility of non-destructive electrical condition monitoring techniques as potential substitutes for destructive methods will be finally discussed studying the correlation between electrical and mechanical properties. In this work, the electrical properties of cable insulators are monitored and characterized mainly by dielectric spectroscopy, polarization/depolarization current analysis and space charge distribution. Among these techniques, dielectric spectroscopy showed the most promising results; by means of dielectric spectroscopy it is possible to identify the frequency range where the properties are more sensitive to aging. In particular, the imaginary part of permittivity at high frequency, which is related to oxidation, has been identified as the most suitable aging marker based on electrical quantities.

A New Test Rig for In-Vitro Evaluation of the Knee Joint Behaviour

The evaluation of the knee joint behavior is fundamental in many applications, such as joint modeling, prosthesis and orthosis design. In-vitro tests are important in order to analyse knee behavior when simulating various loading conditions and studying physiology of the joint. A new test rig for in-vitro evaluation of the knee joint behavior is presented in this paper. It represents the evolution of a previously proposed rig, designed to overcome its principal limitations and to improve its performances. The design procedure and the adopted solution in order to satisfy the specifications are presented here. Thanks to its 6-6 Gough-Stewart parallel manipulator loading system, the rig replicates general loading conditions, like daily actions or clinical tests, on the specimen in a wide range of flexion angles. The restraining actions of knee muscles can be simulated when active actions are simulated. The joint motion in response to the applied loads, guided by passive articular structures and muscles, is permitted by the characteristics of the loading system which is force controlled. The new test rig guarantees visibility so that motion can be measured by an optoelectronic system. Furthermore, the control system of the new test rig allows the estimation of the contribution of the principal leg muscles in guaranteeing the equilibrium of the joint by the system for muscle simulation. Accuracy in positioning is guaranteed by the designed tibia and femur fixation systems,which allow unmounting and remounting the specimen in the same pose. The test rig presented in this paper permits the analysis of the behavior of the knee joint and comparative analysis on the same specimen before and after surgery, in a way to assess the goodness of prostheses or surgical treatments.