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.

Central autonomic control in spontaneously hypertensive rats: a study on phasic phenomena during rapid-eye-movement sleep

The cardiovascular regulation undergoes wide changes in the different states of sleepwake cycle. In particular, the relationship between spontaneous fluctuations in heart period and arterial pressure clearly shows differences between the two sleep states. In non rapid-eye-movement sleep, heart rhythm is under prevalent baroreflex control, whereas in rapid-eye-movement sleep central autonomic commands prevail (Zoccoli et al., 2001). Moreover, during rapid-eye-movement sleep the cardiovascular variables show wide fluctuations around their mean value. In particular, during rapid-eyemovement sleep, the arterial pressure shows phasic hypertensive events which are superimposed upon the tonic level of arterial pressure. These phasic increases in arterial pressure are accompanied by an increase in heart rate (Sei & Morita, 1996; Silvani et al., 2005). Thus, rapid-eye-movement sleep may represent an “autonomic stress test” for the cardiovascular system, able to unmask pathological patterns of cardiovascular regulation (Verrier et al. 2005), but this hypothesis has never been tested experimentally. The aim of this study was to investigate whether rapid-eye-movement sleep may reveal derangements in central autonomic cardiovascular control in an experimental model of essential hypertension. The study was performed in Spontaneously Hypertensive Rats, which represent the most widely used model of essential hypertension, and allow full control of genetic and environmental confounding factors. In particular, we analyzed the cardiovascular, electroencephalogram, and electromyogram changes associated with phasic hypertensive events during rapid-eyemovement sleep in Spontaneously Hypertensive Rats and in their genetic Wistar Kyoto control strain. Moreover, we studied also a group of Spontaneously Hypertensive Rats made phenotypically normotensive by means of a chronic treatment with an angiotensin converting enzyme inhibitor, the Enalapril maleate, from the age of four weeks to the end of the experiment. All rats were implanted with electrodes for electroencephalographic and electromyographic recordings and with an arterial catheter for arterial pressure measurement. After six days for postoperative recovery, the rats were studied for five days, at an age of ten weeks.The study indicated that the peak of mean arterial pressure increase during the phasic hypertensive events in rapid-eye-movement sleep did not differ significantly between Spontaneously Hypertensive Rats and Wistar Kyoto rats, while on the other hand Spontaneously Hypertensive Rats showed a reduced increase in the frequency of theta rhythm and a reduced tachicardia with respect to Wistar Kyoto rats. The same pattern of changes in mean arterial pressure, heart period, and theta frequency was observed between Spontaneously Hypertensive Rats and Spontaneously Hypertensive Rats treated with Enalapril maleate. Spontaneously Hypertensive Rats do not differ from Wistar Kyoto rats only in terms of arterial hypertension, but also due to multiple unknown genetic differences. Spontaneously Hypertensive Rats were developed by selective breeding of Wistar Kyoto rats based only on the level of arterial pressure. However, in this process, multiple genes possibly unrelated to hypertension may have been selected together with the genetic determinants of hypertension (Carley et al., 2000). This study indicated that Spontaneously Hypertensive Rats differ from Wistar Kyoto rats, but not from Spontaneously Hypertensive Rats treated with Enalapril maleate, in terms of arterial pH and theta frequency. This feature may be due to genetic determinants unrelated to hypertension. In sharp contrast, the persistence of differences in the peak of heart period decrease and the peak of theta frequency increase during phasic hypertensive events between Spontaneously Hypertensive Rats and Spontaneously Hypertensive Rats treated with Enalapril maleate demonstrates that the observed reduction in central autonomic control of the cardiovascular system in Spontaneously Hypertensive Rats is not an irreversible consequence of inherited genetic determinants. Rather, the comparison between Spontaneously Hypertensive Rats and Spontaneously Hypertensive Rats treated with Enalapril maleate indicates that the observed differences in central autonomic control are the result of the hypertension per se. This work supports the view that the study of cardiovascular regulation in sleep provides fundamental insight on the pathophysiology of hypertension, and may thus contribute to the understanding of this disease, which is a major health problem in European countries (Wolf-Maier et al., 2003) with its burden of cardiac, vascular, and renal complications.

Advances in methods to detect, isolate and quantify foodborne pathogens

Foodborne diseases impact human health and economies worldwide in terms of health care and productivity loss. Prevention is necessary and methods to detect, isolate and quantify foodborne pathogens play a fundamental role, changing continuously to face microorganisms and food production evolution. Official methods are mainly based on microorganisms growth in different media and their isolation on selective agars followed by confirmation of presumptive colonies through biochemical and serological test. A complete identification requires form 7 to 10 days. Over the last decades, new molecular techniques based on antibodies and nucleic acids allow a more accurate typing and a faster detection and quantification. The present thesis aims to apply molecular techniques to improve official methods performances regarding two pathogens: Shiga-like Toxin-producing Escherichia coli (STEC) and Listeria monocytogenes. In 2011, a new strain of STEC belonging to the serogroup O104 provoked a large outbreak. Therefore, the development of a method to detect and isolate STEC O104 is demanded. The first objective of this work is the detection, isolation and identification of STEC O104 in sprouts artificially contaminated. Multiplex PCR assays and antibodies anti-O104 incorporated in reagents for immunomagnetic separation and latex agglutination were employed. Contamination levels of less than 1 CFU/g were detected. Multiplex PCR assays permitted a rapid screening of enriched food samples and identification of isolated colonies. Immunomagnetic separation and latex agglutination allowed a high sensitivity and rapid identification of O104 antigen, respectively. The development of a rapid method to detect and quantify Listeria monocytogenes, a high-risk pathogen, is the second objective. Detection of 1 CFU/ml and quantification of 10–1,000 CFU/ml in raw milk were achieved by a sample pretreatment step and quantitative PCR in about 3h. L. monocytogenes growth in raw milk was also evaluated.

Sviluppo di un framework per l'automazione dei test al banco e la prototipazione di algoritmi di controllo di motori a combustione interna

Negli ultimi anni, i limiti sempre più stringenti sulle emissioni inquinanti dei gas di scarico, hanno portato ad un notevole aumento della complessità dei motori a combustione interna. Questa complicazione determina un aumento esponenziale del numero di test da effettuare nella sala prova. I metodi tipici di gestione dei test non possono più essere utilizzati, ma è essenziale creare un sistema che ottimizzi le prove. Per ridurre drasticamente il tempo di esecuzione, è necessario implementare un'architettura in grado di facilitare lo scambio di dati tra i sistemi presenti nella sala prova, e, in aggiunta, definire le strategie di automazione dei test. L'approccio a taluni metodi si presenta ancora complicato in molti gruppi di sviluppo di strategie di controllo motore, anche se, una volta sviluppati, portano e a grandi benefici durante la fase di test. Il lavoro illustra i metodi implementati per la gestione di queste strategie. Prima si descrive l'approccio utilizzato nella calibrazione di anticipo di accensione per mantenere livelli accettabili di detonazione durante il processo di calibrazione. Successivamente è mostrato il sistema di automazione dei test che consente il pieno controllo del punto di funzionamento del motore, la gestione dell'acquisizione e la verifica della stabilità delle condizioni ottenute. L'ultima parte mostra sistemi di prototipazione rapida per la gestione di componenti innovatici del motore.

Employment of Real-Time/FPGA Architectures for Test and Control of Automotive Engines

Nowadays the production of increasingly complex and electrified vehicles requires the implementation of new control and monitoring systems. This reason, together with the tendency of moving rapidly from the test bench to the vehicle, leads to a landscape that requires the development of embedded hardware and software to face the application effectively and efficiently. The development of application-based software on real-time/FPGA hardware could be a good answer for these challenges: FPGA grants parallel low-level and high-speed calculation/timing, while the Real-Time processor can handle high-level calculation layers, logging and communication functions with determinism. Thanks to the software flexibility and small dimensions, these architectures can find a perfect collocation as engine RCP (Rapid Control Prototyping) units and as smart data logger/analyser, both for test bench and on vehicle application. Efforts have been done for building a base architecture with common functionalities capable of easily hosting application-specific control code. Several case studies originating in this scenario will be shown; dedicated solutions for protype applications have been developed exploiting a real-time/FPGA architecture as ECU (Engine Control Unit) and custom RCP functionalities, such as water injection and testing hydraulic brake control.