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.

Medulloblastoma (MB) is a paediatric malignant brain tumour, sensitive to ionizing radiations (IR). However radiotherapy has detrimental effects on long-term survivors and the tumour is incurable in a third of patients, due to intrinsic radioresistance. Alterations of the Wnt pathway distinguish a molecular subgroup of MBs and nuclear beta-catenin, indicative of activated Wnt, is associated with good outcome in MB. Therefore there are increasing evidences about Wnt involvement in radio-response: IR induce activation of Wnt signalling with nuclear translocation of beta-catenin in MB cell lines. We studied effects of Wnt pathway activation in a MB cell line with p53 wild-type: UW228-1. Cells were stably transfected with a beta-catenin constitutively active and assessed for growth curves, mortality rate, invasiveness and differentiation. Firstly, activation of Wnt pathway by itself induced a slower cell growth and a higher mortality. After IR treatment, nuclear beta-catenin further inhibited cell growth, increasing mortality. Cell invasiveness was strongly inhibited by Wnt activation. Furthermore, Wnt cell population was characterized by club shaped cells with long cytoplasmic extensions containing neurofilaments, suggesting a neural differentiation of this cell line. These findings suggest that nuclear beta-catenin may leads to a less aggressive phenotype and increases radio-sensitivity in MB, accounting for its favourable prognostic value. In the future, Wnt/beta-catenin signalling will be considered as a molecular therapeutic target to develop new drugs for the treatment of MB.

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.

Stroke and traumatic brain injury are among the leading causes of death in the world. Until now, there are no effective treatments available. Current pharmaceutical treatments have limited benefits to repair the damaged tissue. Brain tissue engineering is a promising strategy to help brain regeneration after the damage induced by stroke or traumatic brain injury. In this thesis, our work focused on designing and evaluating appropriate silk fibroin-based hydrogels combined with stem cells therapy for brain tissue regeneration. The work initially started from looking for appropriate silk fibroin-based hydrogel substrates which can support the viability and neural differentiation of pluripotent cells. Mouse embryonic stem cells (mESC) were used as a model. Different processing procedures of silk fibroin-based hydrogel substrates were prepared by chemical genipin crosslinking and physical sonication crosslinking. The viability and neural differentiation of pluripotent cells on these hydrogel substrates were evaluated, using tissue culture plates (TCP) as control. Different crosslinking processes were found to modulate the neural differentiation of pluripotent cells. Chemical genipin crosslinked hydrogel substrates could inhibit the neural differentiation of mESC compared to control TCP, while the physical sonication crosslinked hydrogel substrates could support the neural differentiation as TCP. According to the results obtained in the first stage, the physically sonication-crosslinked 3D silk fibroin hydrogel was produced to encapsulate human neural stem cells (hNSC). In order to improve the hNSC attachment and neuronal differentiation, the isoleucine-lysine-valine-alanine-valine (IKVAV) peptide derived from laminin was covalently conjugated to the silk fibroin. The viability and neural differentiation of hNSC were evaluated in the unmodified and IKVAV peptide modified silk fibroin hydrogels. We found that the IKVAV peptide modified silk fibroin hydrogel could increase the viability, proliferation and neuronal differentiation of hNSC. Furthermore, the angiogenesis potential of sonication-induced 3D silk fibroin unmodified and modified with IKVAV and a scramble peptide VVIAK (as control) were evaluated in a human outgrowth endothelial cells (OEC) mono-culture system and a co-culture system in which OEC were cultured with human bone marrow mesenchymal stem cells (BM-MSC). Both the silk fibroin unmodified and modified with IKVAV peptide could not induce angiogenesis in the mono-culture system under the VEGF condition. However, in the co-culture system, we found that unmodified, IKVAV-modified and VVIAK-modified silk fibroin hydrogels all could support angiogenesis. Furthermore, there were no significant differences among unmodified, IKVAV modified and VVIAK modified silk fibroin hydrogels influencing on angiogenesis structure and gene expression related to angiogenesis. The thesis will introduce the detailed work in three different chapters (from chapter 3 to chapter 5) respectively.

Organ failure is one the biggest problems, doctors face every day. Many patients are not able to get a transplant, but even those who recieved it, may undergo painful process of organ rejection and be on the transplant waiting list again. Organ transplants shortage is severe problem in current medicine that has many ethical and medical issues. To solve this problem, the new direction in regenerative medicine was formed, organ prinitng. The main goal of organ printing is fabrication of organ replacements that would mimic the original ones in terms of complexity and functionality. By direct fabrication and maturation of organs in vitro, the problem of organ shortage can be solved, moreover, based on the advances in cell therapy, these organs can be printed with patients own cells, which will eliminte the problem of transplant rejection. Organ printing is multistep and complex process, composed of three main steps: tissue design, or theoretical modelling of replacement composition; tissue fabrication, or direct cell encapsulation and controlled assembly of building units; at last, tissue maturation to reach desirable functionality of the replacement. In the past decade, there was developed a variety of methods for the second step of organ printing, cell encapsulation, which is practicaly the main procedure for tissue fabrication. However, all these methods of cell encapsulation are complex and they might affect cells viability and functionality, which will result in changed tissue function. Thus, starting from the detailed analysis of the tissue fabrication process (encapsulation and assembly methods) the list of possible cell behavior affectors was composed. Based on this list, we designed a multistep protocol for coherent evaluation of cells behavior parameters, in terms of viability, functionality and activity during the tissue fabrication and its maturation steps. Three main materials were used for this study, two naturally (alginate and modified gelatin) and one synthetically (polyethilene glycol) derived polymers. The encapsulation step was performed with two different methods based on chemical or photo crosslinking of the material. Cell parameteres were evaluated on the molecular level for variety of parameters, including viability, activity, proliferation, stress markers expression, at last ability to adapt artificial environment to the cell functional niche with extracellular matrix markers expression, and proteoglycans. The innovation of the presented study consists in the developing a unique protocol for detailed cell functionality evaluation during the organ printing procedures. In fact, based on the conducted study, it was proved the safety of the encapsulation methods. Moreover, based on the cell parameters post-encapsulation, there was suggested the optimal time for tissue maturation for application of the fabricated structures in organ printing, but also in other fileds, like developmental and pathological biology, or drug screening. Eventully, a novel way of simple blocks assembly into 3D complex structures was developed and proved to be safe for cell parameters. At last, for the future research in organ printing, a detailed study over a cell behavior and functionality has to be performed for every fabrication method, what will improve the organ production process drastically.

In recent years, advancements in computational methodologies have shed light on the complex process that makes proteins fold into their three-dimensional shapes. These new tools have helped us understand the steps proteins take to achieve these structures, revealing the presence of metastable intermediates along the folding pathways. This newfound understanding has led to the development of a novel drug discovery strategy known as Pharmacological Protein Inactivation by Folding Intermediate Targeting (PPI-FIT). This approach specifically targets folding intermediates to modulate protein expression levels, thus opening new opportunities for pharmacological intervention. This approach could be particularly relevant for diseases linked to targets that were previously considered "undruggable." A promising outcome of the PPI-FIT strategy is the identification of SM875, a compound that has been shown to lower prion protein (PrP) levels, positioning it as a potential therapeutic candidate for prion diseases. This study describes the initial phase of optimization of the SM875 scaffold. It encompasses the chemical diversification of SM875, followed by systematic evaluations of its biological activity and toxicity, with the aim of establishing structure-activity relationships (SAR). This knowledge is instrumental in guiding the synthesis of analogs with enhanced properties, advancing them through the development pipeline toward clinical application. Furthermore, this work investigates the potential regulatory function of folding intermediates in physiological processes, hypothesizing that they may serve as substrates for post translational modifications (PTMs). This hypothesis proposes an expansion of the current paradigm, suggesting that folding intermediates could constitute an additional layer of regulation within the complex network of proteostasis.

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.