To date little effort has been expended on the construction of cellular mimics from a minimum number of component parts. Such systems are desirable, because the cellular mimics could serve as useful tools to more deeply delve into the systems level reactions that sustain life and as a platform from which new types of technologies could be generated. Herein the building of cellular mimics that can sense and respond to external stimuli is presented. The majority of our efforts in building cellular mimics are directed towards the sensory element. Initially, previously characterized natural and artificial RNA sensors, i.e. a riboswitches, are exploited. Subsequently, the cellular mimics are implemented as chemical translators for natural bacterial cells. To expand the capabilities of the engineered cellular mimics, we sought to develop a methodology for the selection of new RNA-based sensors capable of detecting new analytes. The tested methodologies were based on mRNA display and strand displacement reactions. The mRNA display selection did not lead to the identification of a sensor responsive to malachite green after eight cycles of selection. Conversely, via ligand induced triggering of a strand displacement reaction, new RNA sensors for thiamine pyrophosphate were selected from a small library. The sensors displayed translational control ability as is typical of certain classes of riboswitches. The strand displacement-based selection method represents a first step towards the in vitro evolution of sensing elements than can be exploited for new cellular mimics with programmable sensing capability.

In the last decades, the increase of industrial activities and of the request for the world food requirement, the intensification of natural resources exploitation, directly connected to pollution, have aroused an increasing interest of the public opinion towards initiatives linked to the regulation of food production, as well to the institution of a modern legislation for the consumer guardianship. This work was planned taking into account some important thematics related to marine environment, collecting and showing the data obtained from the studies made on different marine species of commercial interest (Chamelea gallina, Mytilus edulis, Ostrea edulis, Crassostrea gigas, Salmo salar, Gadus morhua). These studies have evaluated the effects of important physic and chemical parameters variations (temperature, xenobiotics like drugs, hydrocarbons and pesticides) on cells involved in the immune defence (haemocytes) and on some important enzymatic systems involved in xenobiotic biotransformation processes (cytochrome P450 complex) and in the related antioxidant defence processes (Superoxide dismutase, Catalase, Heat Shock Protein), from a biochemical and bimolecular point of view. Oxygen is essential in the biological answer of a living organism. Its consume in the normal cellular breathing physiological processes and foreign substances biotransformation, leads to reactive oxygen species (ROS) formation, potentially toxic and responsible of biological macromolecules damages with consequent pathologies worsening. Such processes can bring to a qualitative alteration of the derived products, but also to a general state of suffering that in the most serious cases can provoke the death of the organism, with important repercussions in economic field, in the output of the breedings, of fishing and of aquaculture. In this study it seemed interesting to apply also alternative methodologies currently in use in the medical field (cytofluorimetry) and in proteomic studies (bidimensional electrophoresis, mass spectrometry) with the aim of identify new biomarkers to place beside the traditional methods for the control of the animal origin food quality. From the results it’s possible to point out some relevant aspects from each experiment: 1. The cytofluorimetric techniques applied to O. edulis and C. gigas could bring to important developments in the search of alternative methods that quickly allows to identify with precision the origin of a specific sample, contributing to oppose possible alimentary frauds, in this case for example related to presence of a different species, also under a qualitative profile, but morpholgically similar. A concrete perspective for the application in the inspective field of this method has to be confirmed by further laboratory tests that take also in account in vivo experiments to evaluate the effect in the whole organism of the factors evaluated only on haemocytes in vitro. These elements suggest therefore the possibility to suit the cytofluorimetric methods for the study of animal organisms of food interest, still before these enter the phase of industrial working processes, giving useful information about the possible presence of contaminants sources that can induce an increase of the immune defence and an alteration of normal cellular parameter values. 2. C. gallina immune system has shown an interesting answer to benzo[a]pyrene (B[a]P) exposure, dose and time dependent, with a significant decrease of the expression and of the activity of one of the most important enzymes involved in the antioxidant defence in haemocytes and haemolymph. The data obtained are confirmed by several measurements of physiological parameters, that together with the decrease of the activity of 7-etossi-resourifine-O-deetilase (EROD linked to xenobiotic biotransformation processes) during exposure, underline the major effects of B[a]P action. The identification of basal levels of EROD supports the possible presence of CYP1A subfamily in the invertebrates, still today controversial, never identified previously in C. gallina and never isolated in the immune cells, as confirmed instead in this study with the identification of CYP1A-immunopositive protein (CYP1A-IPP). This protein could reveal a good biomarker at the base of a simple and quick method that could give clear information about specific pollutants presence, even at low concentrations in the environment where usually these organisms are fished before being commercialized. 3. In this experiment it has been evaluated the effect of the antibiotic chloramphenicol (CA) in an important species of commercial interest, Chamelea gallina. Chloramphenicol is a drug still used in some developing countries, also in veterinary field. Controls to evaluate its presence in the alimentary products of animal origin, can reveal ineffective whereas the concentration results to be below the limit of sensitivity of the instruments usually used in this type of analysis. Negative effects of CA towards the CYP1A- IPP proteins, underlined in this work, seem to be due to the attack of free radicals resultant from the action of the antibiotic. This brings to a meaningful alteration of the biotransformation mechanisms through the free radicals. It seems particularly interesting to pay attention to the narrow relationships in C. gallina, between SOD/CAT and CYP450 system, actively involved in detoxification mechanism, especially if compared with the few similar works today present about mollusc, a group that is composed by numerous species that enter in the food field and on which constant controls are necessary to evaluate in a rapid and effective way the presence of possible contaminations. 4. The investigations on fishes (Gadus morhua, and Salmo salar) and on a bivalve mollusc (Mytilus edulis) have allowed to evaluate different aspects related to the possibility to identify a biomarker for the evaluation of the health of organisms of food interest and consequently for the quality of the final product through 2DE methodologies. In the seafood field these techniques are currently used with a discreet success only for vertebrates (fishes), while in the study of the invertebrates (molluscs) there are a lot of difficulties. The results obtained in this work have underline several problems in the correct identification of the isolated proteins in animal organisms of which doesn’t currently exist a complete genomic sequence. This brings to attribute some identities on the base of the comparison with similar proteins in other animal groups, incurring in the possibility to obtain inaccurate data and above all discordant with those obtained on the same animals by other authors. Nevertheless the data obtained in this work after MALDI-ToF analysis, result however objective and the spectra collected could be again analyzed in the future after the update of genomic database related to the species studied. 4-A. The investigation about the presence of HSP70 isoforms directly induced by different phenomena of stress like B[a]P presence, has used bidimensional electrophoresis methods in C. gallina, that have allowed to isolate numerous protein on 2DE gels, allowing the collection of several spots currently in phase of analysis with MALDI-ToF-MS. The present preliminary work has allowed therefore to acquire and to improve important methodologies in the study of cellular parameters and in the proteomic field, that is not only revealed of great potentiality in the application in medical and veterinary field, but also in the field of the inspection of the foods with connections to the toxicology and the environmental pollution. Such study contributes therefore to the search of rapid and new methodologies, that can increase the inspective strategies, integrating themselves with those existing, but improving at the same time the general background of information related to the state of health of the considered animal organism, with the possibility, still hypothetical, to replace in particular cases the employment of the traditional techniques in the alimentary field.

MACPF/CDCs proteins are a huge family of pore-forming proteins present from the bacteria to the human genera. Cholesterol-dependent cytolysins (CDCs) are a family of toxins that participate in bacterial infection pathway at the membrane level. Great interest in this family is due to their similarity, in structure and in pore-forming mechanism, with some human immune system proteins (MACPF). We focused our attention particularly on two bacterial CDCs, Perfringolysin O and Listeriolysin O, and on the human protein Perforin, which is involved in the apoptotic pathway facilitating Granzyme release. In the literature, two possible configurations of CDCs and Perforin pores are proposed: ring and arc structures that could have different implications on the biological mechanism of action of these pore-forming proteins. By electrophysiological measurements and atomic force microscopy technique on different artificial membrane, we are able to enrich the ring and the arc fraction and demonstrate that both kinds of pore are active, i.e. conduct ions. Thus, my PhD work underlines two physiological structures which are involved in several ways, more than merely by disrupting membrane integrity, in pathogenic attack (bacterial CDCs proteins) as well as in immune response (human Perforin proteins).

Grape (Vitis vinifera L.) is among the most cultivated plants in the world. Its origin traces back to the Neolithic era, when the first human communities started to domesticate wild Vitis sylvestris L. grapes to produce wines. Domestication modified Vitis vinifera to assume characteristics imparted from the humans, selecting desired traits (e.g. specific aromas), and excluding the undesired ones. This process made this species very different from all the other wild grape species existing around the world, including its progenitor, Vitis sylvestris. Metabolomics is a field of the sciences that comparatively studies the whole metabolite set of two (or more) groups of samples, to point out the chemical diversity and infer on the variability in the metabolic pathways between the groups. Crude metabolomics observation can be often used for hypotheses generation, which need to be confirmed by further experiments. In my case, starting from the grape metabolome project (Mattivi et al. unpublished data), I had the opportunity to put hands on a huge dataset built on the berries of over 100 Vitis vinifera grape varieties, tens of grape interspecific hybrids and few wild grape species analyzed per four years; all included in a single experiment. Starting from this data handling, I designed specific experiments to confirm the hypotheses generated from the observation of the data, to improve compound identification, to give statistical meaning to the differences, to localize the metabolites in the berries and extrapolate further information on the variability existing among the grape genus. The hypotheses formulated were two: 1) several glyco-conjugated volatiles can be detected, identified and quantified in untargeted reverses-phase liquid chromatography-mass spectrometry; 2) The chemical difference between Vitis vinifera and wild grape berries is wider than reported in literature. Furthermore, handling a huge dataset of chemical standards injected under the same conditions of the sample set, I also formulated a third hypothesis: 3) metabolites with similar chemical structures are more likely to generate similar signals in LC-MS, therefore the combined use of the signals can predict the more likely chemical structure of unknown markers. In the first study (chapter 5), the signals putatively corresponding to glycoconjugated volatiles have been first enclosed in a specific portion of the temporal and spectrometric space of the LC-HRMS chromatograms, then they have been subjected to MS/MS analysis and lastly their putative identity have been confirmed through peak intensity correlation between the signals measured in LC-HRMS and GC-MS. In the second study (chapter 6), a multivariate regression model has been built between LC-HRMS signals and the substructures composing the molecular structure of the compounds and its accuracy and efficacy in substructure prediction have been demonstrated. In the third study (chapter 7), I comparatively studied some wild grapes versus some Vitis vinifera varieties separating the basic components of the grape berry (skin, flesh and seeds), with the aim to identify all the detected metabolites that differentiate the two groups, which determine a difference in quality between the wild versus domesticated grapes, especially regarding wine production.

Iron-sulfur clusters are indispensable to extant metabolism and are thought to have had an ancient role in mediating the chemical reactions that led to life. However, there has been no clear proposal for how these inorganic clusters came to occupy such an important position in biology. In this thesis I describe my efforts in delineating a plausible path from short, prebiotically plausible peptides to longer sequences with similar features to modern day iron-sulfur proteins. Small organic thiolates and short cysteine-containing peptides can give rise to [2Fe-2S] and [4Fe-4S] clusters in aqueous solution when irradiated with UV light in the presence of iron ions. Additionally, duplications of tripeptides coordinated iron-sulfur clusters give sequences which are better able to stabilize iron-sulfur clusters, resembling motifs with cysteinyl ligand spacing highly similar to contemporary ferredoxins. Moreover, the studied iron-sulfur clusters are redox active and are able to mimic extant metabolic pathways, such as the first step of the electron transport chain, within protocells favouring the formation of a proton gradient which could be exploited for central biosynthetic processes.

Cysteinyl peptides likely played an important role in the prebiotic synthesis of cofactors, such as iron-sulfur clusters. However, cysteinyl peptides must be reduced in order to coordinate iron-sulfur clusters. Mixtures of ferric ions and cysteinyl peptides leads to the reduction of ferric to ferrous ions and the concomitant formation of disulfide bridged, oxidized cysteinyl peptides that are incapable of coordinating an iron-sulfur cluster. Here, we develop a photochemically driven solution to this problem. Lipoic acid (( R )-5-(1,2-dithiolane-3-yl)pentanoic acid), a molecule structurally similar to fatty acids, can be photochemically reduced and can subsequently reduce the oxidized cysteinyl peptides needed for the coordination of an iron-sulfur cluster. Other dithilane ring containing molecules possess similar activity to lipoic acid. The synthesis of small peptides containing cysteines, such as glutathione and GCG (Gly-Cys-Gly) is easy by both solid phase and solution phase methodologies. However, as the length of the peptide increases, the yield begins to decrease, especially for peptides containing cysteines due to oxidation. One solution could be to exploit a previously uncovered mechanism for the joining of peptides into longer peptides. Such mechanisms, referred to as CPL for catalytic peptide ligation, rely on either thiols or metals as catalysts and peptide nitriles as substrates. Thus far, CPL has only been exploited with non-cysteinyl peptides. In this thesis, we extend CPL to cysteine containing peptides by taking advantage of the templating effects of Zn2+. Longer peptides with properly spaced cysteines are frequently better able to stabilize iron-sulfur clusters in aqueous solution than shorter peptides. Coordination can either be complete or an open coordination position, filled by solvent, can be used to bind substrate. Two well-known examples of such an arrangement are the radical SAM (S-adenosylmethionine) enzyme and aconitase being an enzyme of the citric acid cycle. We designed and synthesized peptide sequences that could coordinate a [4Fe-4S]2+ cluster with three cysteinyl ligands, leaving an open coordination position. The stability of the [4Fe-4S] cluster was affected by the intermediates of the citric acid cycle. The iron-sulfur can be reconstituted with the long peptidyl sequences from proteins such as SLC25A39 which contains four cysteine ligands to form [2Fe-2S] cluster, which is necessary for glutathione transport from cytosol to mitochondria.

Metabolism is a subset of chemistry that allows cells to defy thermodynamic equilibrium, a fundamental process that must have been in place from the very beginning of biology. Before evolution produced efficient catalysts in the form of complex protein machinery, short metal binding peptides might have preceded modern metalloproteins. Such prebiotic, metal-binding motifs have been hypothesized to have existed through analyses of extant protein sequences. However, it is unclear how metal-binding motifs might have evolved in the harsh prebiotic environment. Here, we show how certain environments, in particular seawater-like environments rich in divalent cations and especially Mg2+, support the survival of short peptides upon extreme temperatures as high as 150 °C. Moreover, while Mg2+ does not offer the same protection from UV light, peptides are protected from both heat and irradiation when bound to a metal ion. The results suggest that specific environments rich in metal ions may be better suited for the emergence of complex systems in the path toward life. Additionally, the conditional degradation of peptides depending on their ability of binding metals might have enabled a selection mechanism that would favor the survival of metal-binding motifs which resemble the motifs found in modern proteins. These short sequences could have acted as early, simple catalysts able to facilitate a restricted set of chemical reactions, which would shape the emergence and biology of the Last Universal Common Ancestor.

La contaminazione da micotossine può coinvolgere tutti i comparti della filiera agroalimentare e rappresenta a tutti gli effetti un potenziale di perdita economica. Il settore zootecnico è particolarmente esposto alle ricadute della contaminazione, in termini di costi sanitari per gli effetti cronici sulla salute animale conseguenti all’esposizione alle micotossine. La prevenzione in campo mediata da appropriate tecniche agronomiche rappresenta, per quanto ovvio, la più importante strategia per ridurre la contaminazione dei mangimi. Un approccio completamente differente è quello che si basa sulla possibilità di ridurre gli effetti delle tossine sull’animale, modificando la sua alimentazione attraverso l’integrazione nutrizionale di opportuni agenti chemiopreventivi. Numerose sono le specie chimiche, di origine naturale o sintetica, che hanno dimostrato una efficacia chemiopreventiva del danno ossidativo indotto da micotossine ed emergono per la loro efficacia il selenio e i suoi composti organici ed inorganici. L’azione antineoplastica del selenio è nota da molto tempo e ha trovato conferme in numerosi studi epidemiologici che indicano una relazione inversa tra assunzione di selenio con la dieta e rischio di sviluppo di una patologia neoplastica. Questa tesi di dottorato ha avuto come obiettivo la progettazione, la sintesi e lo studio di composti diamminoacidici contenenti un atomo di calcogeno (selenio o zolfo), mimici dalla glutatione perossidasi (GPx) e auspicabilmente attivi nel contrasto del danno ossidativo indotto dall’aflatossina B1 (AFB1). Le specie diamminoacidiche sintetizzate appartengono alla classe dei Sec-derivati, ovvero sono costitute da un residuo di L-selenocisteina (o L-cisteina) a cui è legato attraverso l’atomo di calcogeno un altro L-amminoacido. Alla porzione calcogenica, che rappresenta il sito redox, sono stati infatti ancorati rispettivamente un residuo di L-prolina modificata e un residuo di L-leucina. Al termine delle fasi di sintesi e caratterizzazione chimico-fisica dei calco-diamminoacidi è stata intrapresa una serie di indagini biochimiche in collaborazione con due distinti laboratori in Germania. I risultati ottenuti hanno permesso di dimostrare che alcuni Sec-derivati sono in grado di ridurre i perossidi attraverso un meccanismo catalitico che mima l’attività della GPx. Essi sembrano inoltre evidenziare che il “meccanismo antiossidante” sia mediato sostanzialmente dall’attività GPx mentre non sono particolarmente attivi meccanismi di radical scavenging né di puro trasferimento elettronico. Alcuni dei Sec-derivati sintetizzati sono stati oggetto di un’indagine cellulare preliminare volta a verificare una eventuale effettiva azione protettiva dei calco-diamminoacidi verso il danno cellulare indotto da AFB1. Le indagini sono state effettuate adoperando una linea cellulare HepG2. I dati ottenuti, nel loro insieme, hanno mostrato che i calco-diamminoacidi esaminati sono di per sé caratterizzati da una notevole attività biologica. In particolare, alla concentrazione più elevata utilizzata (100 µM), alcuni di essi hanno mostrato interessanti proprietà citoprotettive contro il danno indotto da AFB1. L’efficacia è paragonabile, e in qualche caso superiore, a quella riscontrabile per il composto di riferimento, la Se-metil-selenocisteina, principale forma di selenio organico che è naturalmente presente in specie vegetali quali Allium Sativum e Brassica juncea. / Mycotoxin contamination may involve all fields of the food agricultural chain and might potentially determine economic losses. In particular, the livestock sector is at risk of health costs, as a consequence of chronic diseases induced by mycotoxin exposure. It is obvious, although actual, that the mycotoxin contamination should be controlled on the field by a series of suitable agriculture practices in order to minimize the mycotoxin formation in feeds. Recently, dietary strategies (antioxidant compounds, medicinal herbs, plant extracts) to counteract the effects of mycotoxins have attracted considerable attention. Chemoprevention refers to the use of naturally occuring and/or synthetic chemicals to inhibit the development of mycotoxin induced chronic diseases. Selenium and its organic and inorganic compounds, have emerged as outstanding chemoprevention agents. Selenium antineoplastic properties have been well documented through the last decades, being supported by several epidemiological evidences on the association between selenium intake and the risk for some kinds of human/animal cancers. This PhD thesis was focussed on design, synthesis and study of a family of chalcogenic diamino acids (containing either selenium or sulfur), GPx mimics and potentially active to reduce the oxidative damage induced by aflatoxin B1 (AFB1). The diamino acids synthesized belong to the family of Sec-derivatives and consist of L-selenocysteine (or L-cysteine) linked through the calchogen atom to either a L-proline or a L-leucine moiety. The GPx-like catalytic activity of the various compounds was confirmed using both thiophenol and GPx assays. Their possible radical-scavenging activity, and electron-donor reducing character as well, could be ruled out by suitable assays. The cytoprotective capacity exhibited by several of the compounds synthesized was investigated in HepG2 cells by MTS assays. The results indicated that all the chalcogenic diamino acids tested had a strong biological activity. In particular, the pre-treatment of the test cells with two Sec-derivatives, employed at higher doses (100 µM), led to a protective effect on cell toxicity, lowering the AFB1-induced cell mortality, and this efficacy is comparable with that of the reference Se-metil-selenocysteine, main source of organic selenium in plants such as Allium Sativum and Brassica juncea.

Intracellular chloride and pH are fundamental regulators of neuronal excitability and they are often co-modulated during excitation-inhibition activity. The study of their homeostasis requires simultaneous measurements in vivo in multiple neurons. Combining random mutagenesis screening, protein engineering and two-photon-imaging this thesis work led to the discovery of new chloride-sensitive GFP mutants and to the establishment of ratiometric imaging procedures for the quantitative combined imaging of intraneuronal pH and chloride. These achievements have been demonstrated in vivo in the mouse cortex, in real-time monitoring the dynamic changes of ions concentrations during epileptic-like discharges, and in glioblastoma primary cells, measuring osmotic swelling responses to various drugs treatment.