The photosynthetic bacterial reaction center in native and artificial envirnoments: effects on light-induced electron transfer

In this thesis we focussed on the characterization of the reaction center (RC) protein purified from the photosynthetic bacterium Rhodobacter sphaeroides. In particular, we discussed the effects of native and artificial environment on the light-induced electron transfer processes. The native environment consist of the inner antenna LH1 complex that copurifies with the RC forming the so called core complex, and the lipid phase tightly associated with it. In parallel, we analyzed the role of saccharidic glassy matrices on the interplay between electron transfer processes and internal protein dynamics. As a different artificial matrix, we incorporated the RC protein in a layer-by-layer structure with a twofold aim: to check the behaviour of the protein in such an unusual environment and to test the response of the system to herbicides. By examining the RC in its native environment, we found that the light-induced charge separated state P+QB - is markedly stabilized (by about 40 meV) in the core complex as compared to the RC-only system over a physiological pH range. We also verified that, as compared to the average composition of the membrane, the core complex copurifies with a tightly bound lipid complement of about 90 phospholipid molecules per RC, which is strongly enriched in cardiolipin. In parallel, a large ubiquinone pool was found in association with the core complex, giving rise to a quinone concentration about ten times larger than the average one in the membrane. Moreover, this quinone pool is fully functional, i.e. it is promptly available at the QB site during multiple turnover excitation of the RC. The latter two observations suggest important heterogeneities and anisotropies in the native membranes which can in principle account for the stabilization of the charge separated state in the core complex. The thermodynamic and kinetic parameters obtained in the RC-LH1 complex are very close to those measured in intact membranes, indicating that the electron transfer properties of the RC in vivo are essentially determined by its local environment. The studies performed by incorporating the RC into saccharidic matrices evidenced the relevance of solvent-protein interactions and dynamical coupling in determining the kinetics of electron transfer processes. The usual approach when studying the interplay between internal motions and protein function consists in freezing the degrees of freedom of the protein at cryogenic temperature. We proved that the “trehalose approach” offers distinct advantages with respect to this traditional methodology. We showed, in fact, that the RC conformational dynamics, coupled to specific electron transfer processes, can be modulated by varying the hydration level of the trehalose matrix at room temperature, thus allowing to disentangle solvent from temperature effects. The comparison between different saccharidic matrices has revealed that the structural and dynamical protein-matrix coupling depends strongly upon the sugar. The analyses performed in RCs embedded in polyelectrolyte multilayers (PEM) structures have shown that the electron transfer from QA - to QB, a conformationally gated process extremely sensitive to the RC environment, can be strongly modulated by the hydration level of the matrix, confirming analogous results obtained for this electron transfer reaction in sugar matrices. We found that PEM-RCs are a very stable system, particularly suitable to study the thermodynamics and kinetics of herbicide binding to the QB site. These features make PEM-RC structures quite promising in the development of herbicide biosensors. The studies discussed in the present thesis have shown that, although the effects on electron transfer induced by the native and artificial environments tested are markedly different, they can be described on the basis of a common kinetic model which takes into account the static conformational heterogeneity of the RC and the interconversion between conformational substates. Interestingly, the same distribution of rate constants (i.e. a Gamma distribution function) can describe charge recombination processes in solutions of purified RC, in RC-LH1 complexes, in wet and dry RC-PEM structures and in glassy saccharidic matrices over a wide range of hydration levels. In conclusion, the results obtained for RCs in different physico-chemical environments emphasize the relevance of the structure/dynamics solvent/protein coupling in determining the energetics and the kinetics of electron transfer processes in a membrane protein complex.

Analysis of ion channel stochastic signals for biosensing

In biological world, life of cells is guaranteed by their ability to sense and to respond to a large variety of internal and external stimuli. In particular, excitable cells, like muscle or nerve cells, produce quick depolarizations in response to electrical, mechanical or chemical stimuli: this means that they can change their internal potential through a quick exchange of ions between cytoplasm and the external environment. This can be done thanks to the presence of ion channels, proteins that span the lipid bilayer and act like switches, allowing ionic current to flow opening and shutting in a stochastic way. For a particular class of ion channels, ligand-gated ion channels, the gating processes is strongly influenced by binding between receptive sites located on the channel surface and specific target molecules. These channels, inserted in biomimetic membranes and in presence of a proper electronic system for acquiring and elaborating the electrical signal, could give us the possibility of detecting and quantifying concentrations of specific molecules in complex mixtures from ionic currents across the membrane; in this thesis work, this possibility is investigated. In particular, it reports a description of experiments focused on the creation and the characterization of artificial lipid membranes, the reconstitution of ion channels and the analysis of their electrical and statistical properties. Moreover, after a chapter about the basis of the modelling of the kinetic behaviour of ligand gated ion channels, a possible approach for the estimation of the target molecule concentration, based on a statistical analysis of the ion channel open probability, is proposed. The fifth chapter contains a description of the kinetic characterisation of a ligand gated ion channel: the homomeric α2 isoform of the glycine receptor. It involved both experimental acquisitions and signal analysis. The last chapter represents the conclusions of this thesis, with some remark on the effective performance that may be achieved using ligand gated ion channels as sensing elements.

Sistemi di sicurezza urbana

Il problema della sicurezza/insicurezza delle città, dalle grandi metropoli sino ai più piccoli centri urbani, ha sollecitato negli ultimi anni un’attenzione crescente da parte degli studiosi, degli analisti, degli organi di informazione, delle singole comunità. La delinquenza metropolitana viene oggi diffusamente considerata «un aspetto usuale della società moderna»: «un fatto – o meglio un insieme di fatti – che non richiede nessuna speciale motivazione o predisposizione, nessuna patologia o anormalità, e che è iscritto nella routine della vita economica e sociale». Svincolata dagli schemi positivistici, la dottrina criminologica ha maturato una nuova «cultura del controllo sociale» che ha messo in risalto, rispetto ad ogni visione enfatizzante del reo, l’esigenza di pianificare adeguate politiche e pratiche di prevenzione della devianza urbana attraverso «tutto l’insieme di istituzioni sociali, di strategie e di sanzioni, che mirano a ottenere la conformità di comportamento nella sfera normativa penalmente tutelata». Tale obiettivo viene generalmente perseguito dagli organismi istituzionali, locali e centrali, con diverse modalità annoverabili nel quadro degli interventi di: prevenzione sociale in cui si includono iniziative volte ad arginare la valenza dei fattori criminogeni, incidendo sulle circostanze sociali ed economiche che determinano l’insorgenza e la proliferazione delle condotte delittuose negli ambienti urbani; prevenzione giovanile con cui si tende a migliorare le capacità cognitive e relazionali del minore, in maniera tale da controllare un suo eventuale comportamento aggressivo, e ad insegnare a genitori e docenti come gestire, senza traumi ed ulteriori motivi di tensione, eventuali situazioni di crisi e di conflittualità interpersonale ed interfamiliare che coinvolgano adolescenti; prevenzione situazionale con cui si mira a disincentivare la propensione al delitto, aumentando le difficoltà pratiche ed il rischio di essere scoperti e sanzionati che – ovviamente – viene ponderato dal reo. Nella loro quotidianità, le “politiche di controllo sociale” si sono tuttavia espresse in diversi contesti – ed anche nel nostro Paese - in maniera a tratti assai discutibile e, comunque, con risultati non sempre apprezzabili quando non - addirittura – controproducenti. La violenta repressione dei soggetti ritenuti “devianti” (zero tolerance policy), l’ulteriore ghettizzazione di individui di per sé già emarginati dal contesto sociale, l’edificazione di interi quartieri fortificati, chiusi anche simbolicamente dal resto della comunità urbana, si sono rivelate, più che misure efficaci nel contrasto alla criminalità, come dei «cortocircuiti semplificatori in rapporto alla complessità dell’insieme dei problemi posti dall’insicurezza». L’apologia della paura è venuta così a riflettersi, anche fisicamente, nelle forme architettoniche delle nuove città fortificate ed ipersorvegliate; in quelle gated-communities in cui l’individuo non esita a sacrificare una componente essenziale della propria libertà, della propria privacy, delle proprie possibilità di contatto diretto con l’altro da sé, sull’altare di un sistema di controllo che malcela, a sua volta, implacabili contraddizioni. Nei pressanti interrogativi circa la percezione, la diffusione e la padronanza del rischio nella società contemporanea - glocale, postmoderna, tardomoderna, surmoderna o della “seconda modernità”, a seconda del punto di vista al quale si aderisce – va colto l’eco delle diverse concezioni della sicurezza urbana, intesa sia in senso oggettivo, quale «situazione che, in modo obiettivo e verificabile, non comporta l’esposizione a fattori di rischio», che in senso soggettivo, quale «risultante psicologica di un complesso insieme di fattori, tra cui anche indicatori oggettivi di sicurezza ma soprattutto modelli culturali, stili di vita, caratteristiche di personalità, pregiudizi, e così via». Le amministrazioni locali sono direttamente chiamate a garantire questo bisogno primario di sicurezza che promana dagli individui, assumendo un ruolo di primo piano nell’adozione di innovative politiche per la sicurezza urbana che siano fra loro complementari, funzionalmente differenziate, integrali (in quanto parte della politica di protezione integrale di tutti i diritti), integrate (perché rivolte a soggetti e responsabilità diverse), sussidiarie (perché non valgono a sostituire i meccanismi spontanei di prevenzione e controllo della devianza che si sviluppano nella società), partecipative e multidimensionali (perché attuate con il concorso di organismi comunali, regionali, provinciali, nazionali e sovranazionali). Questa nuova assunzione di responsabilità da parte delle Amministrazioni di prossimità contribuisce a sancire il passaggio epocale «da una tradizionale attività di governo a una di governance» che deriva «da un’azione integrata di una molteplicità di soggetti e si esercita tanto secondo procedure precostituite, quanto per una libera scelta di dar vita a una coalizione che vada a vantaggio di ciascuno degli attori e della società urbana nel suo complesso». All’analisi dei diversi sistemi di governance della sicurezza urbana che hanno trovato applicazione e sperimentazione in Italia, negli ultimi anni, e in particolare negli ambienti territoriali e comunitari di Roma e del Lazio che appaiono, per molti versi, esemplificativi della complessa realtà metropolitana del nostro tempo, è dedicata questa ricerca. Risulterà immediatamente chiaro come il paradigma teorico entro il quale si dipana il percorso di questo studio sia riconducibile agli orientamenti della psicologia topologica di Kurt Lewin, introdotti nella letteratura sociocriminologica dall’opera di Augusto Balloni. Il provvidenziale crollo di antichi steccati di divisione, l’avvento di internet e, quindi, la deflagrante estensione delle frontiere degli «ambienti psicologici» in cui è destinata a svilupparsi, nel bene ma anche nel male, la personalità umana non hanno scalfito, a nostro sommesso avviso, l’attualità e la validità della «teoria del campo» lewiniana per cui il comportamento degli individui (C) appare anche a noi, oggi, condizionato dalla stretta interrelazione che sussiste fra le proprie connotazioni soggettive (P) e il proprio ambiente di riferimento (A), all’interno di un particolare «spazio di vita». Su queste basi, il nostro itinerario concettuale prende avvio dall’analisi dell’ambiente urbano, quale componente essenziale del più ampio «ambiente psicologico» e quale cornice straordinariamente ricca di elementi di “con-formazione” dei comportamenti sociali, per poi soffermarsi sulla disamina delle pulsioni e dei sentimenti soggettivi che agitano le persone nei controversi spazi di vita del nostro tempo. Particolare attenzione viene inoltre riservata all’approfondimento, a tratti anche critico, della normativa vigente in materia di «sicurezza urbana», nella ferma convinzione che proprio nel diritto – ed in special modo nell’ordinamento penale – vada colto il riflesso e la misura del grado di civiltà ma anche delle tensioni e delle contraddizioni sociali che tormentano la nostra epoca. Notevoli spunti ed un contributo essenziale per l’elaborazione della parte di ricerca empirica sono derivati dall’intensa attività di analisi sociale espletata (in collaborazione con l’ANCI) nell’ambito dell’Osservatorio Tecnico Scientifico per la Sicurezza e la Legalità della Regione Lazio, un organismo di supporto della Presidenza della Giunta Regionale del Lazio al quale compete, ai sensi dell’art. 8 della legge regionale n. 15 del 2001, la funzione specifica di provvedere al monitoraggio costante dei fenomeni criminali nel Lazio.

Computational Methods in Biophysics and Medicinal Chemistry: Applications and Challenges

In this thesis I described the theory and application of several computational methods in solving medicinal chemistry and biophysical tasks. I pointed out to the valuable information which could be achieved by means of computer simulations and to the possibility to predict the outcome of traditional experiments. Nowadays, computer represents an invaluable tool for chemists. In particular, the main topics of my research consisted in the development of an automated docking protocol for the voltage-gated hERG potassium channel blockers, and the investigation of the catalytic mechanism of the human peptidyl-prolyl cis-trans isomerase Pin1.

Self-Assembled Monolayers (SAMs) in Organic Field-Effect Transistors

Organic printed electronics is attracting an ever-growing interest in the last decades because of its impressive breakthroughs concerning the chemical design of π-conjugated materials and their processing. This has an impact on novel applications, such as flexible-large-area displays, low- cost printable circuits, plastic solar cells and lab-on-a-chip devices. The organic field-effect transistor (OFET) relies on a thin film of organic semiconductor that bridges source and drain electrodes. Since its first discovery in the 80s, intensive research activities were deployed in order to control the chemico-physical properties of these electronic devices and consequently their charge. Self-assembled monolayers (SAMs) are a versatile tool for tuning the properties of metallic, semi-conducting, and insulating surfaces. Within this context, OFETs represent reliable instruments for measuring the electrical properties of the SAMs in a Metal/SAM/OS junction. Our experimental approach, named Charge Injection Organic-Gauge (CIOG), uses OTFT in a charge-injection controlled regime. The CIOG sensitivity has been extensively demonstrated on different homologous self-assembling molecules that differ in either chain length or in anchor/terminal group. One of the latest applications of organic electronics is the so-called “bio-electronics” that makes use of electronic devices to encompass interests of the medical science, such as biosensors, biotransducers etc… As a result, thee second part of this thesis deals with the realization of an electronic transducer based on an Organic Field-Effect Transistor operating in aqueous media. Here, the conventional bottom gate/bottom contact configuration is replaced by top gate architecture with the electrolyte that ensures electrical contact between the top gold electrode and the semiconductor layer. This configuration is named Electrolyte-Gated Field-Effect Transistor (EGOFET). The functionalization of the top electrode is the sensing core of the device allowing the detection of dopamine as well as of protein biomarkers with ultra-low sensitivity.

Studio elettrofisiologico di modificazioni a lungo termine della forza della trasmissione sinaptica nel sistema nervoso centrale

Il nucleo accumbens (NAc), il maggior componente del sistema mesocorticolimbico, è coinvolto nella mediazione delle proprietà di rinforzo e nella dipendenza da diverse sostanze d’abuso. Le sinapsi glutammatergiche del NAc possono esprimere plasticità, tra cui una forma di depressione a lungo termine (LTD) dipendente dagli endocannabinoidi (eCB). Recenti studi hanno dimostrato un’interazione tra le vie di segnalazione del sistema eCB e quelle di altri sistemi recettoriali, compreso quello serotoninergico (5-HT); la vasta colocalizzazione di recettori serotoninergici e CB1 nel NAc suggerisce la possibilità di un’interazione tra questi due sistemi. In questo studio abbiamo riscontrato che una stimolazione a 4 Hz per 20 minuti (LFS-4Hz) delle afferenze glutammatergiche in fettine cerebrali di ratto, induce una nuova forma di eCB-LTD nel core del NAc, che richiede l’attivazione dei recettori CB1 e 5-HT2 e l’apertura dei canali del Ca2+ voltaggio-dipendenti di tipo L. Inoltre abbiamo valutato che l’applicazione esogena di 5-HT (5 M, 20 min) induce una LTD analoga (5-HT-LTD) a livello delle stesse sinapsi, che richiede l’attivazione dei medesimi recettori e l’apertura degli stessi canali del Ca2+; LFS-4Hz-LTD e 5-HT-LTD sono reciprocamente saturanti. Questi risultati suggeriscono che la LFS-4Hz induce il rilascio di 5-HT, che si lega ai recettori 5-HT2 a livello postsinaptico incrementando l’influsso di Ca2+ attraverso i canali voltaggio-dipendenti di tipo L e la produzione e il rilascio di 2-arachidonoilglicerolo; l’eCB viaggia a ritroso e si lega al recettore CB1 a livello presinaptico, causando una diminuzione duratura del rilascio di glutammato, che risulta in una LTD. Queste osservazioni possono essere utili per comprendere i meccanismi neurofisiologici che sono alla base della dipendenza da sostanze d’abuso, della depressione maggiore e di altre malattie psichiatriche caratterizzate dalla disfunzione della neurotrasmissione di 5-HT nel NAc.

Design and characterization of Electrochemical Sensors for Organic Bioelectronics

This Ph.D. Thesis concerns the design and characterisation of functional electrochemical interfaces in organic electronic devices for bioelectronic applications. The Thesis is structured as follows: Chapter I – Technological context that has inspired the research, introduction to Organic Bioelectronics and literature review concerning Organic Electrochemical Transistors (OECTs) for sensing applications. Chapter II – Working principle of an all-polymeric OECT and operando microscopic characterization using scanning electrochemical techniques. Chapter III – Dopamine detection with all-polymeric OECT sensors. Development of a potentiodynamic approach to address selectivity issues in the presence of interfering species and design of a needle-type, sub-micrometric OECT sensor for spatially resolved detection of biological Dopamine concentrations. Chapter IV – Development of an OECT pH sensor. Characterization of the electrochemical transducer and functionalization of the OECT gate electrode with the sensing material. Potentiodynamic and potentiostatic operation modalities are explored and the sensing performances are assessed in both cases. The final device is realized on a flexible substrate and tested in Artificial Sweat. Chapter V – Study of two-terminal, electrochemically gated sensors inspired by the OECT configuration. Design and characterization of novel functional materials showing a potentiometric transduction of the chemical signal that can be exploited in the realization of electrochemical sensors with simplified geometry for wearable applications. Chapter VI – Conclusion.

Contribution of rare damaging variants in Autism Spectrum Disorder

Autism Spectrum Disorder (ASD) is a heterogeneous and highly heritable neurodevelopmental disorder with a complex genetic architecture, consisting of a combination of common low-risk and more penetrant rare variants. This PhD project aimed to explore the contribution of rare variants in ASD susceptibility through NGS approaches in a cohort of 106 ASD families including 125 ASD individuals. Firstly, I explored the contribution of inherited rare variants towards the ASD phenotype in a girl with a maternally inherited pathogenic NRXN1 deletion. Whole exome sequencing of the trio family identified an increased burden of deleterious variants in the proband that could modulate the CNV penetrance and determine the disease development. In the second part of the project, I investigated the role of rare variants emerging from whole genome sequencing in ASD aetiology. To properly manage and analyse sequencing data, a robust and efficient variant filtering and prioritization pipeline was developed, and by its application a stringent set of rare recessive-acting and ultra-rare variants was obtained. As a first follow-up, I performed a preliminary analysis on de novo variants, identifying the most likely deleterious variants and highlighting candidate genes for further analyses. In the third part of the project, considering the well-established involvement of calcium signalling in the molecular bases of ASD, I investigated the role of rare variants in voltage-gated calcium channels genes, that mainly regulate intracellular calcium concentration, and whose alterations have been correlated with enhanced ASD risk. Specifically, I functionally tested the effect of rare damaging variants identified in CACNA1H, showing that CACNA1H variation may be involved in ASD development by additively combining with other high risk variants. This project highlights the challenges in the analysis and interpretation of variants from NGS analysis in ASD, and underlines the importance of a comprehensive assessment of the genomic landscape of ASD individuals.

Cardiac functional and structural abnormalities in a mouse model of CDKL5 deficiency disorder

CDKL5 (cyclin-dependent kinase-like 5) deficiency disorder (CDD) is a rare and severe neurodevelopmental disease that mostly affects girls who are heterozygous for mutations in the X-linked CDKL5 gene. The lack of CDKL5 protein expression or function leads to the appearance of numerous clinical features, including early-onset seizures, marked hypotonia, autistic features, and severe neurodevelopmental impairment. Mouse models of CDD, Cdkl5 KO mice, exhibit several behavioral phenotypes that mimic CDD features, such as impaired learning and memory, social interaction, and motor coordination. CDD symptomatology, along with the high CDKL5 expression levels in the brain, underscores the critical role that CDKL5 plays in proper brain development and function. Nevertheless, the improvement of the clinical overview of CDD in the past few years has defined a more detailed phenotypic spectrum; this includes very common alterations in peripheral organ and tissue function, such as gastrointestinal problems, irregular breathing, hypotonia, and scoliosis, suggesting that CDKL5 deficiency compromises not only CNS function but also that of other organs/tissues. Here we report, for the first time, that a mouse model of CDD, the heterozygous Cdkl5 KO (Cdkl5 +/-) female mouse, exhibits cardiac functional and structural abnormalities. The mice also showed QTc prolongation and increased heart rate. These changes correlate with a marked decrease in parasympathetic activity to the heart and in the expression of the Scn5a and Hcn4 voltage-gated channels. Moreover, the Cdkl5 +/- heart shows typical signs of heart aging, including increased fibrosis, mitochondrial dysfunctions, and increased ROS production. Overall, our study not only contributes to the understanding of the role of CDKL5 in heart structure/function but also documents a novel preclinical phenotype for future therapeutic investigation.

Development of textile wearable chemical sensors

In this elaborate, a textile-based Organic Electrochemical Transistor (OECT) was first developed for the determination of uric acid in wound exudate based on the conductive polymer poly(3,4-ethylenedioxythiophene):polystyrene sulfonate (PEDOT:PSS), which was then coupled to an electrochemically gated textile transistor consisting of a composite of iridium oxide particles and PEDOT:PSS for pH monitoring in wound exudate. In that way a sensor for multiparameter monitoring of wound health status was assembled, including the ability to differentiate between a wet-dry status of the smart bandage by implementing impedance measurements exploiting the OECT architecture. Afterwards, for both wound management as well as generic health status tracking applications, a glass-based calcium sensor was developed employing polymeric ion-selective membranes on a novel architecture inspired by the Wrighton OECT configuration, which was later converted to a Proof-of-Concept textile prototype for wearable applications. Lastly, in collaboration with the King Abdullah University of Science and Technology (KAUST, Thuwal, Saudi Arabia) under the supervision of Prof. Sahika Inal, different types of ion-selective thiophene-based monomers were used to develop ion-selective conductive polymers to detect sodium ion by different methods, involving standard potentiometry and OECT-based approaches. The textile OECTs for uric acid detection performances were optimized by investigating the geometry effect on the instrumental response and the properties of the different textile materials involved in their production, with a special focus on the final application that implies the operativity in flow conditions to simulate the wound environment. The same testing route was followed for the multiparameter sensor and the calcium sensor prototype, with a particular care towards the ion-selective membrane composition and electrode conditioning protocol optimization. The sodium-selective polymer electrosynthesis was optimized in non-aqueous environments and was characterized by means of potentiostatic and potentiodynamic techniques coupled with Quartz Crystal Microbalance and spectrophotometric measurements.