The dissertation presented in this manuscript contributes to river science by providing a detailed overview on the state of the art on the interaction between riparian vegetation and hydrogeomorphological processes, by devising a novel model encompassing most of such processes and by proposing a field methodology aimed at providing means for improving the modelling of such interactions. The state of the art is summarized in an extensive review describing riparian vegetation and hydrogeomorphological processes mutual feedbacks. Such review did not simply seek to describe these feedbacks but, compiling from a large array of results from field, laboratory and modelling studies, provides a set of physical thresholds that trigger system changes. Therefore, processes are not only described terms but also explained with a quantitative approach. Processes description provided the conceptual foundation for the development of the novel simulation model while model parameterization was based on the quantitative information collected in the review. Such novel model, encompasses the main relationships entwining riparian woody vegetation and hydrogeomorphological processes and is able of replicating long term riparian landscape dynamics considering disturbance events, environmental stressor and riparian woody vegetation establishment from seeds and large wood. The manuscript presents the model structure and its conceptual validation by means of hydrological scenarios aimed at testing the coherence of the simulation results with expected system behaviour. Examples of such coherences are vegetation growth rate in response to hydrological regime, entrainment and establishment of large wood in an unconfined river system and vegetation effect on erosion and deposition patterns. Analysis of sedimentation patterns from the modelled results suggested that vegetation flow resistance should be modelled with greater detail. These conclusions pointed the dissertation research towards the testing of a novel class of vegetation flow resistance equations, proposed by different authors, able of describing woody vegetation flow resistance on a physical basis. These equations have the advantage of considering flow stage, plants foliation level and species-specific flexibility. However, the use of such equations is limited by the difficulty of measuring the vegetation properties required as equation-inputs. In order to test if these equations could effectively improve sediment dynamics predictions, a field method was formulated and tested. The field method allows to sample vegetation properties that can be used with these novel class of flow resistance equations. In the manuscript, such method is applied and the resulting vegetation properties used in several modelling scenarios. Such scenario proved that hydraulic variables modelled with these novel flow resistance approaches are more realistic and thus that the model developed during the dissertation could benefit from inclusion of such flow resistance equations in its source code.

Vitis vinifera L.(Vv), the European cultivated grapevine is one of the most worldwide important crops but is highly susceptible to the necrotrophic fungus Botrytis cinerea (Bc), the causal agent of bunch rot (BR) disease. In grapevine, as well as in other fruit species, it has been described a primary infection by Bc at full bloom, followed by a quiescence period during the berry development, and the fungal egression after veraison reaching the maximum at harvest. Today, this important disease is mainly controlled by massive use of fungicides, which are applied at different developmental stages that happen to be critical during the grapevine-Bc interaction. During the contact, the fungus must overcome several barriers from the host, which protect it from the pathogen attack and might be also modulated or activated due to the presence of the pathogen itself. The cuticle and the cell wall (CW) represent the first barriers from the plant encountered by the pathogen. To successfully colonize the plant tissue, Bc possesses several virulence factors, and CW modifying enzymes (CWMEs) are part of them. On the other hand, the regulated activity of the CWMEs, expressed both by the host and the pathogen, could alter the plant CW composition and porosity, therefore facilitating, or limiting the penetration of the fungus. Among the CWMEs, Pectin methylesterases (PMEs) regulate the degree of methyl esterification of the pectin homogalacturonan, also modifying the epitopes for the activity of other CWMEs such as polygalacturonases (PGs) and pectate lyases (PLs) by whose action, pectin becomes more susceptible to degradation and the CW more accessible by the pathogen. Previous works both in Arabidopsis thaliana and in crop species identified several PME genes with an altered expression in response to pathogens. A previous report characterizing Atpme17 mutant lines has highlighted a role of AtPME17 in the resistance response to Bc in contrast with the opposite role of AtPME3, suggesting that PME genes could have a completely different action during Bc response depending on the isoform involved. In this context, the main objective of the project was to identify new strategies for Bc BR-control, and specifically i) to identify candidate genes involved in the response to Bc, whose inactivation/overexpression would lead to Bc resistant plants and ii) to set up a molecular method to monitor the Bc load in the field and therefore implement a more sustainable control of the pathogen. To further understand the effects of the Bc primary infection in grapevine flowers at CW level, two contrasting genotypes (Souvignier gris (SG) and Teroldego (TE)) in their resistance to the fungus were considered. An artificial inoculation of different biological replicates, in vase maintained, was performed at full bloom, in controlled conditions, and samples were collected at 24 hours post-inoculation (hpi) with the fungus and post-treatment with the respective control, for the following RNA-seq analysis and biochemical characterization of PME activity and CW composition in the two genotypes before and upon infection. The Bc load was estimated in the flowers using qPCR and as expected, a higher biomass of Bc was found in TE, the susceptible cultivar, than in SG, the resistant one. The analysis of CW composition, PME activity and degree of pectin methyl-esterification, both in treated and control flowers, showed significant differences between the two genotypes, in particular SG showed a significant induction of PME activity with respect to the control, evidence not present in the susceptible genotype. The RNAseq analysis on the same samples showed a total of 4800 genes modulated, out of which 3064 are only modulated in TE, 739 only in SG and a common group of 997 genes. Regardless of the cultivar, upon infection there was a total 2919 genes upregulated vs 1909 genes downregulated. A gene set enrichment analysis (GSEA) indicated several over-represented categories upon infection, including response to pathogens and biosynthesis of secondary metabolites, with a general down-regulation of those genes related to CW organization and pectin modification (CWMEs), mostly in the resistant genotype. Within the down-regulated CWMEs, Pectin methylesterase (PME) genes were found highly represented. Unlike, a larger gene set, in many cases with a higher fold-change of induction, was identified in TE respect to SG. This is the case of genes involved in the defense response and its regulation, and in the modification/reinforcement of the cell wall, therefore attesting for an initial tentative by the susceptible genotype to counteract the pathogen, although at the end without success. This was also the case of the seven VviPME genes previously highlighted by the in-silico co-expression analysis and therefore of VviPME10, the gene with the highest homology to AtPME17. Among the regulators, one WRKY factor (VviWRKY3), known to be related to defense response in grapevine mediated by stilbene synthesis, was also further characterized as putative regulator of VviPME10, whose promoter hosts more than one several predicted binding sites for VviWRKY3. Indeed, luciferase assay results indicate a significant activation of VviPME10 promoter by VviWRKY3 factor. Parallelly, the genome-wide analysis of the last structural annotation of the grapevine genome assembly allowed us to identify 62 VviPME gene members, 15 more than a previous report, and manually curate the gene structure for 39 of them. Then, to corroborate the idea of the role of the CW, and in particular of PME activity, in the grapevine response to the fungus, an in silico co-expression analysis of the 62 VviPME members, considering the publicly available RNA-seq experiments related to grapevine-Bc interactions and the RNAseq experiment conducted in this project, was performed. The analysis highlighted a group of seven genes (VviPME1, VvPME9, VviPME10, VviPME11, VviPME12, VviPME13 and VviPME54) with significant induction upon Bc infection, five of them (VviPME8, VviPME9, VviPME10, VviPME11, and VviPME54) located in the same chromosome (chr06). VviPME10 showed the highest homology and was found to be phylogenetically close to the Arabidopsis thaliana PME17 gene, suggesting being considered as its putative orthologue. Afterward, Therefore, considering the increased VviPME10 expression upon infection, and the reported effect of AtPME17 in A. thaliana, VviPME10 was selected as a potential candidate to study its role in grapevine. In this regard, two strategies were adopted, i. VviPME10 knock-out (KO) with CRISPR/Cas9 and ii. VviPME10 overexpression (OE, under CaMV35S promoter) through embryogenic callus transformation of the grapevine cultivar ‘Sugraone’ mediated by Agrobacterium tumefaciens. More than 100 embryos developed, and around 20 plantlets per transformation were analyzed to check the presence of the transgenic construct. Then, the mutation profile, in the case of KO lines, and the expression analysis of the transgene, in the case of OE lines, were carried out to select the appropriate lines to acclimatize. OE lines were also tested for VviPME10 activity. A total protein extract was obtained from the leaves of the lines, showing a higher protein activity compared to the control, and indicating the functionality of the enzyme. Unfortunately, grapevine OE lines couldn’t be analyzed for their response to Bc, while KO lines showed a significantly larger lesion area when compared to the control at 5 days post fungal inoculation (dpi). However, the effect of VviPME10 overexpression upon Bc infection was evaluated also in Nicotiana benthamiana VviPME10-OE lines, generated in parallel. At 3 dpi a significant reduction was observed in the lesion area compared to the control. These results suggest that pectin modification, mediated by VviPME10, plays an important role in the grapevine response to Bc, in particular it seems to behave more like a resistance gene than a susceptibility one. For this reason, it could be considered as a valuable target to improve resistance to Bc in susceptible grapevine varieties. Finally, a molecular method for Bc detection, based on quantitative RT-PCR assays, was set up and applied to estimate the Bc load in field conditions. Although the method allowed the successful detection of the presence of the fungus in samples at different developmental stages, from two V. vinifera cultivars, in different vineyards, the lack of environmental conditions for the development of the disease might have impaired the correlation between detection and the development of the disease. Nonetheless, the method represents a good alternative for monitoring the Bc load in the field at the early season, to predict the BcBR severity at harvest and eventually apply the disease management protocols based on the real need.

Hydropower plants, in particular High-head Hydropower Plants (HPPs), are an important source of energy also for their role in covering the daily peaks of energy demand. However, HPPs, especially storage power plants, have several negative effects on the ecosystems of downstream watercourses inducing unnatural changes in flow regime (hydropeaking). One way to study ecological implications induced by hydropeaking is represented by the coupling of hydrodynamic models (CFD) with habitat suitability models, in which hydrodynamic parameters are typically used to describe the physical habitat of indicator species. The research activity wanted to investigate possible differences between the use of 2D and 3D CFD approaches to determine the watercourse hydraulic characteristics and their effects on habitat evaluations, performed with CASiMiR software, in complex morphology as usually presents in hydropeaked reaches. In particular the habitat suitability for the two case studies (Valsura River and Rio Selva dei Molini), is analysed comparing different approaches for the reconstruction of the velocity field (depth-averaged velocities from 2D modelling, bottom velocity field reconstruction with log-law approach from 2D modelling and bottom velocity field from 3D modelling). The results show that the habitat suitability index (HSI) using 2D or 3D hydrodynamic models can be significantly different. Considering the entire flow range of hydropeaking events, the habitat simulations with bottom flow velocities from 3D modelling provide suitable habitats over the entire flow range representing the availability of stable suitable habitats. The results from the hydraulics and habitat analyses are used to investigate the effects of a hydropeaking mitigation project on the Valsura River (realization of a compensation bypass tunnel to decrease the peak flow rate and to remodel the up and down flow ramping rates) and on Rio Selva dei Molini (morphological measures to reduce the hydropeaking effects).

La comprensione dei geni che controllano la crescita, lo sviluppo, e il metabolismo della ghiandola mammaria suina può rivelare potenziali vie metaboliche o di segnale per migliorare l'efficienza di sintesi del latte. Un microarray suino costituito da 13.263 oligonucleotidi (mer 70) è stato utilizzato per lo studio del profilo di trascrizione del tessuto mammario da 4.5 scrofe a -34, -14, -4, 0, 7, 14, 21, e 28 giorni rispetto alla data del parto. ANOVA (FDR ≤ 0.10) ha individuato 2664 geni differenzialmente espressi (DEG) in relazione allo stato fisiologico. L’analisi dei network e delle vie metaboliche ha identificato come funzioni molecolari più affette dallo stato fisiologico: crescita e proliferazione cellulare (548 geni) cellule di segnale(612 geni).La qPCR rimane il metodo migliore per la misurazione dell’ abbondanza mRNA ad alta precisione e per la validazione di dati array. Essenziale per assicurare l'affidabilità della qPCR è la normalizzazione dei dati con l’utilizzo di geni di controllo interno (ICG). Un analisi sulla stabilità dei geni ha identificato, tra i 19 potenziali ICG, API5, VABP, e MRPL39 come i più stabili ICG nel tessuto mammario suini e ha inoltre stabilito che l'uso di tali 3 geni è il più appropriato per il calcolo di un fattore di normalizzazione. I risultati sottolineano l'importanza di una corretta validazione dei controlli interni per qPCR ed evidenziano le limitazioni di utilizzo dell’assenza dell’effetto tempo come unico criterio per la selezione di CIG. / Elucidating genes controlling growth, development, and metabolism of swine mammary glands can reveal potential metabolic or signalling pathways that might help improve efficiency of milk synthesis. A swine microarray consisting of 13,263 oligonucleotides (70 mer) was used for transcript profiling of mammary tissue from 4-5 sows at -34, -14, -4, 0, 7, 14, 21, and 28 d relative to parturition. ANOVA (FDR ≤ 0.10) identified 2,664 differentially expressed genes (DEG) dueto physiological state. Gene network/pathway analysis revealed that cell growth and proliferation (548 genes) and cell signaling (612 genes) were among the most affected molecular functions due to physiological state in DEG. QPCR remains the chosen method for high-precision mRNA abundance analysis and for array data validation. Essential for reliability of qPCR data is normalization using appropriate internal control genes (ICG). Gene stability analysis identified , among 19 potential ICG, API5, VABP, and MRPL39 as the most stable ICG in porcine mammary tissue and indicated that the use of those 3 genes was most appropriate for calculating a normalization factor. Results underscore the importance of proper validation of internal controls for qPCR and highlight the limitations of using absence of time effects as the criteria for selection of appropriate ICG.

L’alimentazione proteica risulta di fondamentale importanza per l’ottimizzazione della produttività e per il benessere degli animali di interesse zootecnico. L’identificazione di fonti vegetali alternative e/o complementari a quelle attualmente utilizzate (soia in primis) nel razionamento degli animali si rende necessaria per motivi economici, ambientali e legislativi, cercando di evitare, tuttavia, penalizzazioni sull’appetibilità della razione e sulla risposta produttiva. La ricerca condotta ha riguardato lo studio della composizione nutrizionale di semi di cece (Cicer arietinum) e lupino azzurro (Lupinus angustifolius), con approfondimenti sul contenuto di composti nutrizionalmente attivi e/o antinutrizionali, la valutazione della fermentescibilità ruminale mediante tecniche in vitro, anche alla luce di possibili interazioni genetiche (varietà e linee genetiche) e colturali (epoca e densità di semina). I risultati ottenuti hanno permesso di comprendere eventuali limiti di utilizzo di tali leguminose per l’alimentazione degli animali, in particolar modo dei ruminanti, e di attribuire le fonti di variabilità per la massimizzazione produttiva e qualitativa. / Ruminants protein nutrition is an essential item for optimizing the productivity and welfare of animals. The identification of pulses sources as alternative or complementary to those currently used (primarily soya) in the ration of ruminants is necessary for economic, environmental and legislative reasons, trying to avoid, however, penalties on palatability and productive response. The research focused on the study of the nutritional composition of seeds of chickpea (Cicer arietinum) and blue lupine (Lupinus angustifolius), with insights on the content of nutritionally active compounds and / or antinutritionals, the evaluation of the ruminal fermentability using in vitro techniques, also considering possible genetic interactions (varieties and genetic lines) and farming practices (time and density of sowing). The results of the present study suggest that these pulses could be a potentially good feedstuff contributing at the same time to the energy and protein balance of animal diet. Moreover, the presence of active compounds like tannins at levels that should not be regarded as anti-nutritional, can be useful in ruminant feeding due to the moderating activities exerted by those compounds toward the ruminal degradation of proteins.

La presente tesi inizia con un’analisi dell’aspetto nutrizionale degli alimenti. In particolare, è stato discusso il concetto di dieta equilibrata, con riferimento ai principi della “dieta mediterranea”. Proprio da questo modello alimentare trae ispirazione la “ottimazione”, una tecnica sviluppata e utilizzata per programmare pasti conformi a specifici standard nutrizionali (15/30/55 tra proteine, lipidi e carboidrati sull’apporto energetico totale, proporzioni tipicamente mediterranee). Tali preparazioni alimentari sono state testate anche attraverso metodi di analisi sensoriale. Il passaggio successivo è stato l’estensione del concetto di “ottimizzazione nutrizionale” a quello di “ottimizzazione ambientale”, dovuto all’ipotizzato minor impatto ambientale della dieta mediterranea. Il LCA (Life Cycle Assessment) è la tecnica che è stata utilizzata per valutare l’impatto ambientale di alcuni prodotti alimentari, quali verdure surgelate, un salume e un formaggio. Un ulteriore passaggio è stata la creazione di uno strumento di comunicazione, una nuova etichetta ambientale, realizzata per essere utilizzata dalle aziende per comunicare le loro performance ambientali e quindi il loro impegno al miglioramento continuo, e dai consumatori per ottenere maggiori informazioni sull’impatto ambientale dei prodotti acquistati quotidianamente, al fine di accrescere il proprio senso critico ed effettuare acquisti consapevoli. / The thesis begins with an analysis of the nutritional aspects of foods. In particular, the concept of balanced diet has been discussed, by referring to the principles of "mediterranean diet". Just from this food model, the “optimation” draws inspiration, a technique developed and used to plan meals consistent with specific nutritional standards (15/30/55 between protein, fat and carbohydrate on the total energy intake, typically Mediterranean). These food preparations have been tested through sensory analysis methods. The next step is the extension of "nutritional optimization" concept to the "environmental optimization” one, owing to the presumed lower environmental impact of the Mediterranean diet. LCA (Life Cycle Assessment) is the technique used to assess the environmental impact of various food products, such as frozen vegetables, cured meats, dairy products. A further step is the creation of a communication tool, a new environmental label, designed to be used by companies to communicate their environmental performance and therefore their commitment to continuous improvement, and by consumers to obtain more information on the environmental impact of the foods daily consumed, in order to increase their critical sense and make purchases in a conscious way.

La tenerezza è la caratteristica più importante per definire l'accettabilità dei prodotti da parte dei consumatori, mentre le carni ottenute da bovini allevati con sistema estensivo solitamente sono dure. Dopo una dissertazione sulle reazioni biochimiche che avvengono durante il periodo di frollatura e che provoca l’intenerimento della carne, questo studio si è proposto di applicare diverse tecniche per migliorare la tenerezza della carne derivante da animali allevati in estensivo, cercando di modulare le reazioni biochimiche. In questo studio tre differenti tecniche, infusione di calcio (Ca), contrazione da freddo indotta (VFC) e la sospensione per le pelvi (PS), anziché per il tendine di Achille (AT), sono state testate in fase di pre-rigor sulla razza Maremmana e Frisona. L’infusione di Ca ha riportato uno sforzo di taglio più basso rispetto al gruppo di controllo (5,17 vs 10,48 kg) mentre il gruppo VFC ha occupato una posizione intermedia. L’attacco per le pelvi ha dimostrato una differenza significativa sullo sforzo di taglio e sulla lunghezza dei sarcomeri sui muscoli Longissimus thoracis e Biceps femoralis (4,26 vs 5,88 kg e 3,83 vs 4,78 kg e 1,97 e 1,64 µm e 2,10 vs 1,76 µm, rispettivamente per i muscoli per WBS e lunghezza dei sarcomeri in PS e AT). In conclusione, questi metodi possono influire sul processo di intenerimento della carne. / Tenderness is the most important characteristic to define products acceptability by consumers, while meat obtained from bull rearing in extensive system is usually tough. After a wide dissertation on biochemical reactions that occur during the ageing time that cause tenderization of meat, this study propose differences techniques to improve meat tenderness acting on this important pathway. In this study three different methods, Calcium infusion (Ca), Very Fast Chilling (VFC) and pelvic suspension hanging from aitch bone (PS) or the Achilles tendon (AT) are applied in pre-rigor phase on Maremmana and Holstein meat. Ca injection has reported the lowest shear force on cooked meat compared to control group (5.17 vs. 10.48 kg) instead VFC group has intermediate values. Pelvic hanging has shown significant differences on shear force and sarcomere length on Longissimus thoracis (LD) and Biceps femoralis (BF) muscles (4.26 vs. 5.88 kg and 3.83 vs. 4.78 kg and 1.97 and 1.64 µm and 2.10 vs. 1.76 µm respectively for LD and BF per WBS and sarcomere length in PS and AT). In conclusion these methods could influence tenderization processes even if the action of some processes are still unclear.

La presente tesi descrive i risultati del programma di controllo dei pesticidi in regione Lombardia da 1996 a 2008 ed analizza i dati per calcolarne, con metodi diversi, la valutazione dell’esposizione del consumatore. 9387 campioni sono stati analizzati con un numero di campioni irregolari pari all’1%. Il numero di campioni senza residuo era pari al 69% ed il numero di campioni con i residui al di sotto del valore limite stabilito per legge era del 30%. Successivamente per capire l'esposizione dei consumatori a residui di antiparassitari si è utilizzato un metodo deterministico sviluppato da EFSA (PRIMo). È stato trovato che fra i campioni irregolari analizzati, solo 31 potrebbero causare il danno alla salute del consumatore. Un’ ulteriore analisi è stata quella di effettuare una valutazione con metodo probabilistico (Creme) calcolando l'esposizione cumulativa di antiparassitari sulla salute dei consumatori. Coem primo passo, residui di uno stesso pesticida trovato su campioni di patate sono stati inseriti nel software. Inoltre, campioni contenenti residui di pesticidi organofosfati sono stati inseriti nel software accoppiati con i dati italiani di consumo. In entrambi i casi, la valutazione cumulativa probabilistica dimostrava un adeguato livello di sicurezza per adulti e bambini. / The presented thesis describes the results of the pesticide monitoring programme in Lombardy Region from 1996 to 2008 and analyses the data gathered to calculate consumer exposure assessment with different approaches. A total of 9387 samples were analysed and the number of irregular samples was equal to 1%. The number of samples without residues was 69% and the number of samples with residues within the MRL was 30%. A further step to understand the exposure of consumers to residue of pesticides was obtained with the use of a deterministic approach developed by EFSA (PRIMo Model). It was found that among the detected irregular samples, only 31 might cause harm to the health of the consumer. An additional step was constituted by the use of one probabilistic method (Creme Software) to calculate the cumulative exposure of pesticides for the consumers. As a first step, residues of Chlorprofam were plotted in the software on samples of potato. In addition, samples containing residues of Organophosphates were also plotted along with the Italian consumption data. In both the case studies, the probabilistic acute cumulative assessment indicated that the intake, for adults and toddlers was below the set toxicological endpoint.

L’amido è la maggiore fonte di energia per i ruminanti e la sua efficienza di utilizzazione nel tratto gastro-intestinale è importante per soddisfare i fabbisogni energetici dell’animale. La degradabilità dell’amido è misurata da diversi metodi (i.e., metodi in vivo, in situ, in vitro con inoculo ruminale e/o metodi enzimatici) e appare essere influenzata dal tipo di cereale, dai metodi di lavorazione e conservazione degli alimenti, dalla dimensione delle particelle, dal tipo di endosperma, etc.). La tesi è consistita di 4 esperimenti: Esperimento 1) la degradabilità dell’amido di diversi alimenti è stata valutata con un metodi condotto in situ ed il metodo in vitro proposto da Tilley&Terry: entrambi sono stati capaci di differenziare gli alimenti in base alla diversa degradabilità dell’amido. Esperimento 2) Un approccio enzimatico è stato studiato per determinare la quantità di amido degradato. Esperimento 3) Il metodo enzimatico ed il metodo Tilley&Terry sono stati comparati e sono risultati essere ben correlati, evidenziando la possibilità di utilizzare l’approccio enzimatico per studiare i fattori che influenzano la degradabilità dell’amido. Dato che pochi lavori scientifici hanno confrontato la degradabilità dell’amido di granelle e pastoni di mais, nell’Esperimento 4) sono stati raccolti campioni di mais conservati con diverse modalità (i.e., farina di mais, pastoni di granella e pastoni integrali di mais) per verificare quali le caratteristiche chimiche che influenzano la degradabilità dell’amido. I fattori che maggiormente condizionano la valutazione enzimatica della degradabilità dell’amido sono il contenuto in prolamine e l’umidità dei campioni. In conclusione, il metodo enzimatico può essere routinariamente utilizzato dai laboratori commerciali per la rapida valutazione della degradabilità dell’amido negli alimenti destinati all’uso animale. / Starch is the main energy source for ruminants and its efficient utilization in gastro-intestinal tract is important to meet animal energy requirements. The starch degradability is determined by several methods (i.e., in vivo, in situ, in vitro ruminal and/or enzymatic methods) and is affected by type of grain, processing and conservation methods, particle size, type of endosperm, etc.. Four experiments were conducted: Experiment 1) starch degradability of different feeds was evaluated with in-situ and in-vitro Tilley&Terry methods: both are able to differentiate starch degradability among feeds. Experiment 2) An in-vitro enzymatic approach was studied to determine the amount of starch degradation. Experiment 3) Enzymatic and Tilley-Terry methods were compared, resulting well correlated and highlighting the possible application of enzymatic method to investigate the factors affecting starch degradability. Because few works compared the starch degradability of dry-ground and high-moisture corns, in Experiment 4) a data set of different conserved corn samples (i.e., dry, high-moisture and high-moisture-ear corns) was produced and chemical factors affecting starch degradability were studied. The most important factors influencing the enzymatic starch degradability were prolamin and moisture. Concluding, the enzymatic method could be used by commercial laboratories as a routine method for rapid determination of feed starch degradability.

Enterococcus faecium è un componente fondamentale del microbiota di diversi alimenti fermentati quali formaggi e salumi e viene spesso isolato in alto numero in alimenti pronti al consumo. É inoltre largamente utilizzato come probiotico sia per l’uomo che per gli animali. Allo stesso tempo, però, questa specie batterica rappresenta una delle cause principali di infezioni nosocomiali quali endocarditi ed infezioni al tratto urinario. Studi recenti hanno dimostato che la specie E. faecium è costituita da due sub-popolazioni principali: la prima è denominate hospital associated (HA) clade “A” ed include la maggior parte dei ceppi responsabili di infezioni umane; la seconda è chiamata community associated (CA) clade “B”, e contiene principalmente ceppi commensali dell’uomo. Analisi più approfondite hanno rivelato un ulteriore suddivisione all’interno del clade A, nel sub-clade A1 (che raggruppa la maggioranza dei ceppi clinici) e nel sub-clade A2, associato agli animali e più sporadicamente ad infezioni umane. Nel 2012, EFSA ha redatto una linea guida per la valutazione della sicurezza di E. faecium usato come probiotico per gli animali, concludendo che i cepi appartenenti all’hospital-associated clade non devono essere utilizzati in nutrizione animale. Comunque, la distinzione tra le due sub-popolazioni è stata fatta utilizzando dati ottenuti prevalentemente da isolati umani e animali e solo un numero limitato di ceppi isolati dagli alimenti è stato considerato. Obiettivo di questa tesi di dottorato è stato quello di valutare la sicurezza di E. faecium negli alimenti fermentati, considerando ceppi isolati da formaggi artigianali e prodotti carnei e utilizzando sia tecniche di genomica che analisi fisiologiche. Nessuno dei ceppi alimentari studiati è risultato parte del clade A1, ma un ceppo isolato da un salame stagionato pronto al consumo ha rivelato diversi tratti tipici dei ceppi A1, tra cui particolari IS, transposase e geni di resistenza agli antibiotici. Questi risultati, così come altri dati, sottolineano la necessità di approfondire le conoscenze circa il ruolo dei ceppi di E. faecium isolati da alimenti come fattore di rischio per la salute umana. / Enterococcus faecium is commonly found in high numbers in ready to eat foods, being a member of the bacterial communities of a variety of fermented foods, including cheese and sausages, and is widely used as human and animal probiotic. However, this bacterial species is a leading cause of nosocomial infection, mainly endocarditis and urinary tract infections. Recent studies have demonstrated that E. faecium species consists of two very distinct clades: the hospital associated (HA) clade “A”, which includes most of the strains responsible for human infections, and the community associated (CA) clade “B”, that contains primarily human commensal isolates. Deeper analysis revealed a further split within clade A into sub-clade A1 (which groups the vast majority of clinical isolates), and sub-clade A2, associated with animals and sporadic human infections. In 2012, the European Food Safety Authority has issued a guideline for the safety assessment of E. faecium used as animal probiotics, concluding the strains belonging to the hospital-associated clade should not be used in animal nutrition. However, the differentiation of the two clades has been performed using data mainly deriving from human and animal isolates, and only a limited number of strains from the food chain were considered. Aim of this doctoral thesis was to assess the safety of E. faecium in fermented food, considering strains isolated from artisanal cheese and meat products, and using both whole genome-based techniques and physiological studies. None of the food isolates studied in this work belong to the epidemic clade A1, however a strain isolated from a ready to eat salami revealed several A1-specific traits, such as specific IS, transposases and antibiotic resistance genes. These results, as well as other data, underline the emergency of deeper understanding the role of E. faecium isolated from fermented foods as risk factor for human health.