Computational Modeling of Cardiac Excitation-Contraction Coupling in Physiological and Pathological Conditions

The cardiomyocyte is a complex biological system where many mechanisms interact non-linearly to regulate the coupling between electrical excitation and mechanical contraction. For this reason, the development of mathematical models is fundamental in the field of cardiac electrophysiology, where the use of computational tools has become complementary to the classical experimentation. My doctoral research has been focusing on the development of such models for investigating the regulation of ventricular excitation-contraction coupling at the single cell level. In particular, the following researches are presented in this thesis: 1) Study of the unexpected deleterious effect of a Na channel blocker on a long QT syndrome type 3 patient. Experimental results were used to tune a Na current model that recapitulates the effect of the mutation and the treatment, in order to investigate how these influence the human action potential. Our research suggested that the analysis of the clinical phenotype is not sufficient for recommending drugs to patients carrying mutations with undefined electrophysiological properties. 2) Development of a model of L-type Ca channel inactivation in rabbit myocytes to faithfully reproduce the relative roles of voltage- and Ca-dependent inactivation. The model was applied to the analysis of Ca current inactivation kinetics during normal and abnormal repolarization, and predicts arrhythmogenic activity when inhibiting Ca-dependent inactivation, which is the predominant mechanism in physiological conditions. 3) Analysis of the arrhythmogenic consequences of the crosstalk between β-adrenergic and Ca-calmodulin dependent protein kinase signaling pathways. The descriptions of the two regulatory mechanisms, both enhanced in heart failure, were integrated into a novel murine action potential model to investigate how they concur to the development of cardiac arrhythmias. These studies show how mathematical modeling is suitable to provide new insights into the mechanisms underlying cardiac excitation-contraction coupling and arrhythmogenesis.

Studio del comportamento meccanico di smalti porcellanati per substrati metallici

Composite porcelain enamels are inorganic coatings for metallic components based on a special ceramic-vitreous matrix in which specific additives are randomly dispersed. The ceramic-vitreous matrix is made by a mixture of various raw materials and elements and in particular it is based on boron-silicate glass added with metal oxides(1) of titanium, zinc, tin, zirconia, alumina, ecc. These additions are often used to improve and enhance some important performances such as corrosion(2) and wear resistance, mechanical strength, fracture toughness and also aesthetic functions. The coating process, called enamelling, depends on the nature of the surface, but also on the kind of the used porcelain enamel. For metal sheets coatings two industrial processes are actually used: one based on a wet porcelain enamel and another based on a dry-silicone porcelain enamel. During the firing process, that is performed at about 870°C in the case of a steel substrate, the enamel raw material melts and interacts with the metal substrate so enabling the formation of a continuous varying structure. The interface domain between the substrate and the external layer is made of a complex material system where the ceramic vitreous and the metal constituents are mixed. In particular four main regions can be identified, (i) the pure metal region, (ii) the region where the metal constituents are dominant compared with the ceramic vitreous components, (iii) the region where the ceramic vitreous constituents are dominant compared with the metal ones, and the fourth region (iv) composed by the pure ceramic vitreous material. It has also to be noticed the presence of metallic dendrites that hinder the substrate and the external layer passing through the interphase region. Each region of the final composite structure plays a specific role: the metal substrate has mainly the structural function, the interphase region and the embedded dendrites guarantee the adhesion of the external vitreous layer to the substrate and the external vitreous layer is characterized by an high tribological, corrosion and thermal shock resistance. Such material, due to its internal composition, functionalization and architecture can be considered as a functionally graded composite material. The knowledge of the mechanical, tribological and chemical behavior of such composites is not well established and the research is still in progress. In particular the mechanical performances data about the composite coating are not jet established. In the present work the Residual Stresses, the Young modulus and the First Crack Failure of the composite porcelain enamel coating are studied. Due to the differences of the porcelain composite enamel and steel thermal properties the enamelled steel sheets have residual stresses: compressive residual stress acts on the coating and tensile residual stress acts on the steel sheet. The residual stresses estimation has been performed by measuring the curvature of rectangular one-side coated specimens. The Young modulus and the First Crack Failure (FCF) of the coating have been estimated by four point bending tests (3-7) monitored by means of the Acoustic Emission (AE) technique(5,6). In particular the AE information has been used to identify, during the bending tests, the displacement domain over which no coating failure occurs (Free Failure Zone, FFZ). In the FFZ domain, the Young modulus has been estimated according to ASTM D6272-02. The FCF has been calculated as the ratio between the displacement at the first crack of the coating and the coating thickness on the cracked side. The mechanical performances of the tested coated specimens have also been related and discussed to respective microstructure and surface characteristics by double entry charts.

Reconstruction and analysis of the NF-kB pathway interactome: a systems biology approach

Background. One of the phenomena observed in human aging is the progressive increase of a systemic inflammatory state, a condition referred to as “inflammaging”, negatively correlated with longevity. A prominent mediator of inflammation is the transcription factor NF-kB, that acts as key transcriptional regulator of many genes coding for pro-inflammatory cytokines. Many different signaling pathways activated by very diverse stimuli converge on NF-kB, resulting in a regulatory network characterized by high complexity. NF-kB signaling has been proposed to be responsible of inflammaging. Scope of this analysis is to provide a wider, systemic picture of such intricate signaling and interaction network: the NF-kB pathway interactome. Methods. The study has been carried out following a workflow for gathering information from literature as well as from several pathway and protein interactions databases, and for integrating and analyzing existing data and the relative reconstructed representations by using the available computational tools. Strong manual intervention has been necessarily used to integrate data from multiple sources into mathematically analyzable networks. The reconstruction of the NF-kB interactome pursued with this approach provides a starting point for a general view of the architecture and for a deeper analysis and understanding of this complex regulatory system. Results. A “core” and a “wider” NF-kB pathway interactome, consisting of 140 and 3146 proteins respectively, were reconstructed and analyzed through a mathematical, graph-theoretical approach. Among other interesting features, the topological characterization of the interactomes shows that a relevant number of interacting proteins are in turn products of genes that are controlled and regulated in their expression exactly by NF-kB transcription factors. These “feedback loops”, not always well-known, deserve deeper investigation since they may have a role in tuning the response and the output consequent to NF-kB pathway initiation, in regulating the intensity of the response, or its homeostasis and balance in order to make the functioning of such critical system more robust and reliable. This integrated view allows to shed light on the functional structure and on some of the crucial nodes of thet NF-kB transcription factors interactome. Conclusion. Framing structure and dynamics of the NF-kB interactome into a wider, systemic picture would be a significant step toward a better understanding of how NF-kB globally regulates diverse gene programs and phenotypes. This study represents a step towards a more complete and integrated view of the NF-kB signaling system.

Una grande narrazione del capitalismo: potere e scienze sociali nel pensiero politico di Daniel Bell

Questa tesi punta a ricostruire il pensiero politico di Bell tra il secondo dopoguerra e la metà degli anni Settanta. In tale arco cronologico, la riflessione politica di Bell si profila, per usare una formula di Jean-François Lyotard, come una «grande narrazione» del capitalismo. Nel complesso, cioè, l’opera di Bell appare come una storia sociologica del capitalismo, che nella fine delle ideologie registra l’apogeo del fordismo e, in seguito, ne mette in luce le trasformazioni in senso post-industriale, indagando le ricadute che tali mutamenti implicano sul piano dei rapporti di potere e della legittimazione del sistema. Nell’ottica di Bell, pertanto, il capitalismo non costituisce soltanto un sistema economico, ma la forma specifica attraverso cui si dispiega la società nel suo complesso, attivando una serie di rapporti di potere mediante i quali gli individui vengono coordinati e subordinati. Una siffatta concezione del capitalismo agisce immediatamente la questione del potere e solleva un interrogativo a esso connesso: «che cosa tiene insieme una società?». Una domanda che attraversa la traiettoria intellettuale di Bell e, sia pure declinata mediante una terminologia sociologica, riflette in realtà l’ambizione delle scienze sociali di farsi teoria politica. Esse si presentano quindi come teoria politica della modernità, nella misura in cui distinguono il potere sociale dal potere politico e, al tempo stesso, instaurano tra i due poli una tensione dialettica produttiva. Mettendo a fuoco la concettualizzazione del potere nell’opera di Bell si analizzeranno le mutazioni nel rapporto tra Stato e società negli Stati Uniti durante la Golden Age del capitalismo. In particolare, si metterà in luce nella grande narrazione di Bell l’ascesa e il declino di un ordine istituzionale che, alla metà degli anni Settanta, appare percorso da molteplici tensioni politiche e sociali che preannunciano l’avvento dell’età globale e il bisogno di una nuova “scala” di governo.

Production of bioactive peptides through sequencial action of Yarrowia lipolytica proteases and chemical glycation

This PhD thesis is aimed at studying the suitability of proteases realised by Yarrowia lipolytica to hydrolyse proteins of different origins available as industrial food by-products. Several strains of Y. lipolytica have been screened for the production of extracellular proteases by zymography. On the basis of the results some strains released only a protease having a MW of 37 kDa, which corresponds to the already reported acidic protease, while other produced prevalently or only a protease with a MW higher than 200 kDa. The proteases have been screened for their "cold attitude" on gelatin, gluten and skim milk. This property can be relevant from a biotechnological point of view in order to save energy consumption during industrial processes. Most of the strains used were endowed with proteolytic activity at 6 °C on all the three proteins. The proteolytic breakdown profiles of the proteins, detected at 27 °C, were different related to the specific strains of Y. lipolytica. The time course of the hydrolysis, tested on gelatin, affected the final bioactivities of the peptide mixtures produced. In particular, an increase in both the antioxidant and antimicrobial activities was detected when the protease of the strain Y. lipolytica 1IIYL4A was used. The final part of this work was focused on the improvement of the peptides bioactivities through a novel process based on the production of glycopeptides. Firstly, the main reaction parameters were optimized in a model system, secondly a more complex system, based on gluten hydrolysates, was taken into consideration to produce glycopeptides. The presence of the sugar moiety reduced the hydrophobicity of the glycopeptides, thus affecting the final antimicrobial activity which was significantly improved. The use of this procedure could be highly effective to modify peptides and can be employed to create innovative functional peptides using a mild temperature process.

Monitoring Complex Processes to Verify System Conformance: A Declarative Rule-Based Framework

Over the last 60 years, computers and software have favoured incredible advancements in every field. Nowadays, however, these systems are so complicated that it is difficult – if not challenging – to understand whether they meet some requirement or are able to show some desired behaviour or property. This dissertation introduces a Just-In-Time (JIT) a posteriori approach to perform the conformance check to identify any deviation from the desired behaviour as soon as possible, and possibly apply some corrections. The declarative framework that implements our approach – entirely developed on the promising open source forward-chaining Production Rule System (PRS) named Drools – consists of three components: 1. a monitoring module based on a novel, efficient implementation of Event Calculus (EC), 2. a general purpose hybrid reasoning module (the first of its genre) merging temporal, semantic, fuzzy and rule-based reasoning, 3. a logic formalism based on the concept of expectations introducing Event-Condition-Expectation rules (ECE-rules) to assess the global conformance of a system. The framework is also accompanied by an optional module that provides Probabilistic Inductive Logic Programming (PILP). By shifting the conformance check from after execution to just in time, this approach combines the advantages of many a posteriori and a priori methods proposed in literature. Quite remarkably, if the corrective actions are explicitly given, the reactive nature of this methodology allows to reconcile any deviations from the desired behaviour as soon as it is detected. In conclusion, the proposed methodology brings some advancements to solve the problem of the conformance checking, helping to fill the gap between humans and the increasingly complex technology.