Biomolecular studies in Alzheimer’s Disease models: investigations in vitro and in vivo

The Alzheimer’s disease (AD), the most prevalent form of age-related dementia, is a multifactorial and heterogeneous neurodegenerative disease. The molecular mechanisms underlying the pathogenesis of AD are yet largely unknown. However, the etiopathogenesis of AD likely resides in the interaction between genetic and environmental risk factors. Among the different factors that contribute to the pathogenesis of AD, amyloid-beta peptides and the genetic risk factor apoE4 are prominent on the basis of genetic evidence and experimental data. ApoE4 transgenic mice have deficits in spatial learning and memory associated with inflammation and brain atrophy. Evidences suggest that apoE4 is implicated in amyloid-beta accumulation, imbalance of cellular antioxidant system and in apoptotic phenomena. The mechanisms by which apoE4 interacts with other AD risk factors leading to an increased susceptibility to the dementia are still unknown. The aim of this research was to provide new insights into molecular mechanisms of AD neurodegeneration, investigating the effect of amyloid-beta peptides and apoE4 genotype on the modulation of genes and proteins differently involved in cellular processes related to aging and oxidative balance such as PIN1, SIRT1, PSEN1, BDNF, TRX1 and GRX1. In particular, we used human neuroblastoma cells exposed to amyloid-beta or apoE3 and apoE4 proteins at different time-points, and selected brain regions of human apoE3 and apoE4 targeted replacement mice, as in vitro and in vivo models, respectively. All genes and proteins studied in the present investigation are modulated by amyloid-beta and apoE4 in different ways, suggesting their involvement in the neurodegenerative mechanisms underlying the AD. Finally, these proteins might represent novel potential diagnostic and therapeutic targets in AD.

Salinity Effect on Horticultural Crops: Morphological, Physiological, and Biomolecular Elements of Salinity Stress Response

Among abiotic stresses, high salinity stress is the most severe environmental stress. High salinity exerts its negative impact mainly by disrupting the ionic and osmotic equilibrium of the cell. In saline soils, high levels of sodium ions lead to plant growth inhibition and even death. Salt tolerance in plants is a multifarious phenomenon involving a variety of changes at molecular, organelle, cellular, tissue as well as whole plant level. In addition, salt tolerant plants show a range of adaptations not only in morphological or structural features but also in metabolic and physiological processes that enable them to survive under extreme saline environments. The main objectives of my dissertation were understanding the main physiological and biomolecular features of plant responses to salinity in different genotypes of horticultural crops that are belonging to different families Solanaceae (tomato) and Cucurbitaceae (melon) and Brassicaceae (cabbage and radish). Several aspects of crop responses to salinity have been addressed with the final aim of combining elements of functional stress response in plants by using several ways for the assessment of plant stress perception that ranging from destructive measurements (eg. leaf area, relative growth rate, leaf area index, and total plant fresh and dry weight), to physiological determinations (eg. stomatal conductance, leaf gas exchanges, water use efficiency, and leaf water relation), to the determination of metabolite accumulation in plant tissue (eg. Proline and protein) as well as evaluation the role of enzymatic antioxidant capacity assay in scavenging reactive oxygen species that have been generated under salinized condition, and finally assessing the gene induction and up-down regulation upon salinization (eg. SOS pathway).

Stem Cells as a therapy for myocardial infarction in animal models

Advances in stem cell biology have challenged the notion that infarcted myocardium is irreparable. The pluripotent ability of stem cells to differentiate into specialized cell lines began to garner intense interest within cardiology when it was shown in animal models that intramyocardial injection of bone marrow stem cells (MSCs), or the mobilization of bone marrow stem cells with spontaneous homing to myocardium, could improve cardiac function and survival after induced myocardial infarction (MI) [1, 2]. Furthermore, the existence of stem cells in myocardium has been identified in animal heart [3, 4], and intense research is under way in an attempt to clarify their potential clinical application for patients with myocardial infarction. To date, in order to identify the best one, different kinds of stem cells have been studied; these have been derived from embryo or adult tissues (i.e. bone marrow, heart, peripheral blood etc.). Currently, three different biologic therapies for cardiovascular diseases are under investigation: cell therapy, gene therapy and the more recent “tissue-engineering” therapy . During my Ph.D. course, first I focalised my study on the isolation and characterization of Cardiac Stem Cells (CSCs) in wild-type and transgenic mice and for this purpose I attended, for more than one year, the Cardiovascular Research Institute of the New York Medical College, in Valhalla (NY, USA) under the direction of Doctor Piero Anversa. During this period I learnt different Immunohistochemical and Biomolecular techniques, useful for investigating the regenerative potential of stem cells. Then, during the next two years, I studied the new approach of cardiac regenerative medicine based on “tissue-engineering” in order to investigate a new strategy to regenerate the infracted myocardium. Tissue-engineering is a promising approach that makes possible the creation of new functional tissue to replace lost or failing tissue. This new discipline combines isolated functioning cells and biodegradable 3-dimensional (3D) polymeric scaffolds. The scaffold temporarily provides the biomechanical support for the cells until they produce their own extracellular matrix. Because tissue-engineering constructs contain living cells, they may have the potential for growth and cellular self-repair and remodeling. In the present study, I examined whether the tissue-engineering strategy within hyaluron-based scaffolds would result in the formation of alternative cardiac tissue that could replace the scar and improve cardiac function after MI in syngeneic heterotopic rat hearts. Rat hearts were explanted, subjected to left coronary descending artery occlusion, and then grafted into the abdomen (aorta-aorta anastomosis) of receiving syngeneic rat. After 2 weeks, a pouch of 3 mm2 was made in the thickness of the ventricular wall at the level of the post-infarction scar. The hyaluronic scaffold, previously engineered for 3 weeks with rat MSCs, was introduced into the pouch and the myocardial edges sutured with few stitches. Two weeks later we evaluated the cardiac function by M-Mode echocardiography and the myocardial morphology by microscope analysis. We chose bone marrow-derived mensenchymal stem cells (MSCs) because they have shown great signaling and regenerative properties when delivered to heart tissue following a myocardial infarction (MI). However, while the object of cell transplantation is to improve ventricular function, cardiac cell transplantation has had limited success because of poor graft viability and low cell retention, that’s why we decided to combine MSCs with a biopolimeric scaffold. At the end of the experiments we observed that the hyaluronan fibres had not been substantially degraded 2 weeks after heart-transplantation. Most MSCs had migrated to the surrounding infarcted area where they were especially found close to small-sized vessels. Scar tissue was moderated in the engrafted region and the thickness of the corresponding ventricular wall was comparable to that of the non-infarcted remote area. Also, the left ventricular shortening fraction, evaluated by M-Mode echocardiography, was found a little bit increased when compared to that measured just before construct transplantation. Therefore, this study suggests that post-infarction myocardial remodelling can be favourably affected by the grafting of MSCs delivered through a hyaluron-based scaffold

Biomimetica per l'ingegneria tissutale dell'osso

Reconstruction of bone is needed for high bone loss due to congenital deformities, trauma or neoplastic diseases. Commonly, orthopaedic surgical treatments are autologus or allogenic bone implant or prosthetic implant. A choice to the traditional approaches could be represented by tissue engineering that use cells (and/or their products) and innovative biomaterials to perform bone substitutes biologically active as an alternative to artificial devices. In the last years, there was a wide improvement in biology on stem cells potential research and in biomedical engineering through development of new biomaterials designed to resemble the physiological tissues. Tissue engineering strategies and smart materials aim together to stimulate in vivo bone regeneration. This approaches drive at restore not only structure integrity and/or function of the original tissue, but also to induce new tissue deposition in situ. An intelligent bone substitute is now designed like not only a scaffold but also as carrier of regeneration biomolecular signals. Biomimetics has helped to project new tissue engineered devices to simulate the physiological substrates architecture, such extracellular matrix (ECM), and molecular signals that drive the integration at the interface between pre-existing tissue and scaffold. Biomimetic strategies want to increase the material surface biological activity with physical modifications (topography) o chemical ones (adhesive peptides), to improve cell adhesion to material surface and possibly scaffold colonization. This study evaluated the effects of biomimetic modifications of surgical materials surface, as poly-caprolattone (PCL) and titanium on bone stem cells behaviour in a marrow experimental model in vitro. Two biomimetic strategies were analyzed; ione beam irradiation, that changes the surface roughness at the nanoscale, and surface functionalization with specific adhesive peptides or Self Assembled Monolayers (SAMs). These new concept could be a mean to improve the early (cell adhesion, spreading..) and late phases (osteoblast differentiation) of cell/substrate interactions.

Modulation of epidermial growth factor receptor signaling in colon adenocarcinoma

The use of agents targeting EGFR represents a new frontier in colon cancer therapy. Among these, monoclonal antibodies (mAbs) and EGFR tyrosine kinase inhibitors (TKIs) seemed to be the most promising. However they have demonstrated low utility in therapy, the former being effective at toxic doses, the latter resulting inefficient in colon cancer. This thesis work presents studies on a new EGFR inhibitor, FR18, a molecule containing the same naphtoquinone core as shikonin, an agent with great anti-tumor potential. In HT-29, a human colon carcinoma cell line, flow cytometry, immunoprecipitation, and Western blot analysis, confocal spectral microscopy have demonstrated that FR18 is active at concentrations as low as 10 nM, inhibits EGF binding to EGFR while leaving unperturbed the receptor kinase activity. At concentration ranging from 30 nM to 5 μM, it activates apoptosis. FR18 seems therefore to have possible therapeutic applications in colon cancer. In addition, surface plasmon resonance (SPR) investigation of the direct EGF/EGFR complex interaction using different experimental approaches is presented. A commercially available purified EGFR was immobilised by amine coupling chemistry on SPR sensor chip and its interaction to EGF resulted to have a KD = 368 ± 0.65 nM. SPR technology allows the study of biomolecular interactions in real-time and label-free with a high degree of sensitivity and specificity and thus represents an important tool for drug discovery studies. On the other hand EGF/EGFR complex interaction represents a challenging but important system that can lead to significant general knowledge about receptor-ligand interactions, and the design of new drugs intended to interfere with EGFR binding activity.

Chlamydia psittaci nel colombo di città: aspetti anatomo-patologici, sierologici e biomolecolari

Scopo del lavoro della presente tesi è stato quello di valutare la prevalenza di Chlamydiaceae, ed in particolare Chlamydia psittaci, in una popolazione aviare con caratteristiche sinantropiche quale il colombo di città (Columba livia var. domestica) dell’areale veneziano. Per evidenziare il patogeno sono state utilizzate metodiche sierologiche, d’isolamento e biomolecolari tradizionali. Contestualmente, mediante tecnologie molecolari innovative, quali microarray ed MLVA (Multilocus VNTR Assay) sono stati valutati i genotipi di C. psittaci e le eventuali altre specie di Chlamydia presenti in tale popolazione. Inoltre, si è proceduto ad una classificazione delle lesioni anatomo-patologiche ed ad una loro correlazione con la presenza del patogeno. I risultati dimostrano che la prevalenza di C. psittaci nella popolazione oggetto dello studio è del 10%. Durante tale studio è stata dimostrata la presenza di un ceppo di C. psittaci atipico, in quanto non classificabile con le attuali tecniche a disposizione. La genotipizzazione dei ceppi di C. psittaci conferma la presenza nel colombo di città del genotipo B, E ed E/B, che solitamente risultano essere coinvolti con minore frequenza in episodi di infezione umana. Inoltre sono stati dimostrati alcuni ceppi classificati come Chlamydia spp., in quanto le metodologie applicate e le conoscenze attuali non permettono ulteriori distinzioni, prospettando la possibilità di un nuovo ceppo. Infine, attraverso l’analisi dei dati raccolti durante la prima fase di campionamenti e successivamente confermati durante la seconda fase, siamo riusciti a strutturare un sistema di selezione, basato su caratteristiche funzionali ed anatomopatologiche, che permette di selezionare in sede necroscopica i colombi molto probabilmente infetti, permettendo conseguentemente una migliore organizzazione e gestione dei campioni di interesse contenendo nel contempo i costi ma mantenendo elevati gli standards diagnostici.

Computational strategies to include protein flexibility in Ligand Docking and Virtual Screening

The dynamic character of proteins strongly influences biomolecular recognition mechanisms. With the development of the main models of ligand recognition (lock-and-key, induced fit, conformational selection theories), the role of protein plasticity has become increasingly relevant. In particular, major structural changes concerning large deviations of protein backbones, and slight movements such as side chain rotations are now carefully considered in drug discovery and development. It is of great interest to identify multiple protein conformations as preliminary step in a screening campaign. Protein flexibility has been widely investigated, in terms of both local and global motions, in two diverse biological systems. On one side, Replica Exchange Molecular Dynamics has been exploited as enhanced sampling method to collect multiple conformations of Lactate Dehydrogenase A (LDHA), an emerging anticancer target. The aim of this project was the development of an Ensemble-based Virtual Screening protocol, in order to find novel potent inhibitors. On the other side, a preliminary study concerning the local flexibility of Opioid Receptors has been carried out through ALiBERO approach, an iterative method based on Elastic Network-Normal Mode Analysis and Monte Carlo sampling. Comparison of the Virtual Screening performances by using single or multiple conformations confirmed that the inclusion of protein flexibility in screening protocols has a positive effect on the probability to early recognize novel or known active compounds.

Movimenti di genti in tempo di peste: studio antropologico e documentale dei deceduti nel Lazzaretto Vecchio di Venezia (xv-xvii secolo).

Fondato nel 1423 per decisione del Maggior Consiglio di Venezia, il Lazzaretto Vecchio, è la prima struttura permanente in Europa destinata al ricovero degli ammalati di peste e alla quarantena preventiva di coloro che erano entrati in contatto con infetti o che provenivano da zone epidemiche. Questo studio si pone come obiettivo quello di analizzare antropologicamente una parte dei resti umani rinvenuti e comparare i risultati ottenuti con le fonti edite riguardanti la composizione dei ricoverati all’interno della struttura. Sono stati selezionati 110 individui provenienti da 9 comuni appartenenti a due diversi archi cronologici, il 1575-1577 e il 1630-1631. Gli individui sono stati sottoposti a diverse analisi antropologiche tradizionali e indagini più dettagliate di stampo biomolecolare. Parallelamente, è stata vagliata la letteratura prodotta da studi popolazionistici editi. Le analisi antropologiche hanno rivelato un quadro popolazionistico con normale presenza di maschi e femmine, e attestazione di tutte le classi di età, dagli 0 agli oltre 50 anni. Le analisi chimico-fisiche hanno rivelato la presenza di sette individui non locali. Con riguardo all’alimentazione non vi sono particolari differenze in termini di periodi cronologici o di sesso degli individui, quanto invece si possono individuare schemi relativi alla qualità del cibo ingerito in relazione all’inserimento nel mondo del lavoro. Per quanto riguarda le indagini di carattere documentale, nonostante alcuni degli studi popolazionistici individuati non siano considerabili recenti, ci forniscono un quadro dell’andamento della popolazione a Venezia a partire dal 1500 fino al 1700, coprendo in questo modo le cronologie d’interesse del progetto, legate agli episodi di maggiore mortalità della peste. Si riscontra una sostanziale coerenza tra i dati riportati nei diversi resoconti e la sex ratio e le fasce di età alla morte riscontrate, anche se non mancano casi specifici di forte discostamento tra i dati.