Geographical distribution and conservation of Cucurbita in Brazil.

The collection and conservation of the Cucurbita genus in Brazil happened in so dispersed institutions, an assessment of the storage conditions and the genetic diversity is needed, making it possible to identify new priorities for the genus. This work constitutes diagnosis of geographical distribution, storage conditions in situ and ex situ and on genetic diversity of the Cucurbita genus in Brazil. Research was done in herbariums, databases, literature and in situ (expeditions to rural areas and (markets) to map the areas of occurrence of the species. During these expeditions, questionnaires were applied to obtain information about the property and genus Cucurbita. Questionnaires were sent to 173 Brazilian institutions regarding the preservation conditions ex situ. A genetic variability of the Cucurbita genus was found in traditional Brazilian agriculture. Collections must be prioritized in the northern and southern regions (all states); the southeastern region, all states, except Minas Gerais; central-west, in Mato Grosso do Sul and Mato Grosso; the northeastern region, the states of Alagoas, Maranhão, Paraíba, Pernambuco, Piauí and Sergipe. Currently 5.545 entries are being conserved in the Germplasm banks, however, C. pepo, C. ficifolia, C. argyrosperma and wild species are poorly represented. The characterization level of conserved entries is low in the ex situcollections. Participative research projects must be financed as a way to stimulate the farmers to continue planting their local varieties. A coleta e conservação do gênero Cucurbita no Brasil aconteceu de forma dispersa pelas instituições, sendo necessário um diagnóstico sobre as condições de conservação e sobre a diversidade genética, tornando possível identificar novas prioridades para o gênero. Este trabalho realizou diagnóstico sobre distribuição geográfica, condições de conservação in situ e ex situ e sobre diversidade genética do gênro Cucurbita no Brasil. Para mapear as áreas de ocorrência das espécies, foram realizados levantamentos de informações em herbários, banco de dados, literatura e levantamentos in situ (expedições para áreas rurais, feiras livres e CEASAs). Nessas expedições foram aplicados questionários, buscando informações sobre a propriedade e o gênero Cucurbita. Em relação as condições de conservação ex situ, foram enviados questionários para 173 instituições brasileiras. Foi constatado que existe variabilidade genética do gênero Cucurbita na agricultura tradicional brasileira. Devem ser priorizadas coletas nas regiões Norte e Sul (todos os estados); região Sudeste, todos os estados, exceto Minas Gerais; região Centro-Oeste, no Mato Grosso do Sul e Mato Grosso; região Nordeste, os estados de Alagoas, Maranhão, Paraíba, Pernambuco, Piauí e Sergipe. Atualmente estão sendo conservados nos Bancos de Germoplasma 5.545 acessos, no entanto C. pepo, C ficifolia, C. argyrosperma e espécies silvestres estão pouco representadas. É baixa a taxa de caracterização dos acessos conservados nas coleções ex situ. Devem ser financiados projetos de pesquisa participativa como uma forma de estimular e dar condições aos agricultores de continuarem cultivado suas variedades locais.

Geographical distribution and conservation of Cucurbita in Brazil.

The collection and conservation of the Cucurbita genus in Brazil happened in so dispersed institutions, an assessment of the storage conditions and the genetic diversity is needed, making it possible to identify new priorities for the genus. This work constitutes diagnosis of geographical distribution, storage conditions in situ and ex situ and on genetic diversity of the Cucurbita genus in Brazil. Research was done in herbariums, databases, literature and in situ (expeditions to rural areas and (markets) to map the areas of occurrence of the species. During these expeditions, questionnaires were applied to obtain information about the property and genus Cucurbita. Questionnaires were sent to 173 Brazilian institutions regarding the preservation conditions ex situ. A genetic variability of the Cucurbita genus was found in traditional Brazilian agriculture. Collections must be prioritized in the northern and southern regions (all states); the southeastern region, all states, except Minas Gerais; central-west, in Mato Grosso do Sul and Mato Grosso; the northeastern region, the states of Alagoas, Maranhão, Paraíba, Pernambuco, Piauí and Sergipe. Currently 5.545 entries are being conserved in the Germplasm banks, however, C. pepo, C. ficifolia, C. argyrosperma and wild species are poorly represented. The characterization level of conserved entries is low in the ex situcollections. Participative research projects must be financed as a way to stimulate the farmers to continue planting their local varieties. A coleta e conservação do gênero Cucurbita no Brasil aconteceu de forma dispersa pelas instituições, sendo necessário um diagnóstico sobre as condições de conservação e sobre a diversidade genética, tornando possível identificar novas prioridades para o gênero. Este trabalho realizou diagnóstico sobre distribuição geográfica, condições de conservação in situ e ex situ e sobre diversidade genética do gênro Cucurbita no Brasil. Para mapear as áreas de ocorrência das espécies, foram realizados levantamentos de informações em herbários, banco de dados, literatura e levantamentos in situ (expedições para áreas rurais, feiras livres e CEASAs). Nessas expedições foram aplicados questionários, buscando informações sobre a propriedade e o gênero Cucurbita. Em relação as condições de conservação ex situ, foram enviados questionários para 173 instituições brasileiras. Foi constatado que existe variabilidade genética do gênero Cucurbita na agricultura tradicional brasileira. Devem ser priorizadas coletas nas regiões Norte e Sul (todos os estados); região Sudeste, todos os estados, exceto Minas Gerais; região Centro-Oeste, no Mato Grosso do Sul e Mato Grosso; região Nordeste, os estados de Alagoas, Maranhão, Paraíba, Pernambuco, Piauí e Sergipe. Atualmente estão sendo conservados nos Bancos de Germoplasma 5.545 acessos, no entanto C. pepo, C ficifolia, C. argyrosperma e espécies silvestres estão pouco representadas. É baixa a taxa de caracterização dos acessos conservados nas coleções ex situ. Devem ser financiados projetos de pesquisa participativa como uma forma de estimular e dar condições aos agricultores de continuarem cultivado suas variedades locais.

Novel catalytic systems and methidologies for organocatalysis and photocatalysis

The thesis is divided into two main parts. In the first one organocatalysis is briefly introduced. Then, new enantiopure trityl pyrrolidines modified with an ionic tag are described. All the catalysts are tested in the benchmark Michael addition reaction to prove their activity and stereoselectivity. In the second part, photocatalysis is first introduced. Then, four different research projects are described. At first, the construction of a hybrid metal-organo-photoredox catalyst is described. The hybrid photocatalysts obtained were employed in the benchmark photoredox alkylation of aldehydes. Then, the use of visible light and a photocatalytic system for the cyclization of iodoaryl vinyl derivatives to tetrahydroquinoline structures is described. In addition, the reaction can also be performed using flow-chemistry. Finally, a mechanistic proposal based on some mechanistic studies is described. Third, a new photoredox catalyzed transformation for the synthesis of 2,3-dihydrofurans is reported. Depending on the involved starting materials, different pathways have arisen. A mechanistic proposal based on reported literatures and experimental data is described. At last, a new photoredox catalyzed transformation for the synthesis of 2-aminofurans is described. Electrophilic radical addition on allenamides and subsequential intramolecular cyclization are exploited. The reaction proceeds under very mild conditions and in 2-aminofurans are obtained in good to high yield. It represents one of the few applications of allenamides in photoredox catalysis. A mechanistic proposal is described. Finally, preliminary investigations on the applicability of the developed transformation under flow chemistry conditions.

Computing the structural and vibrational properties of polymorphic organic molecular crystals through van der Waals corrected density functional theory and the electronic properties of organic thin films through microelectrostatic calculations.

The present Thesis reports on the various research projects to which I have contributed during my PhD period, working with several research groups, and whose results have been communicated in a number of scientific publications. The main focus of my research activity was to learn, test, exploit and extend the recently developed vdW-DFT (van der Waals corrected Density Functional Theory) methods for computing the structural, vibrational and electronic properties of ordered molecular crystals from first principles. A secondary, and more recent, research activity has been the analysis with microelectrostatic methods of Molecular Dynamics (MD) simulations of disordered molecular systems. While only very unreliable methods based on empirical models were practically usable until a few years ago, accurate calculations of the crystal energy are now possible, thanks to very fast modern computers and to the excellent performance of the best vdW-DFT methods. Accurate energies are particularly important for describing organic molecular solids, since they often exhibit several alternative crystal structures (polymorphs), with very different packing arrangements but very small energy differences. Standard DFT methods do not describe the long-range electron correlations which give rise to the vdW interactions. Although weak, these interactions are extremely sensitive to the packing arrangement, and neglecting them used to be a problem. The calculations of reliable crystal structures and vibrational frequencies has been made possible only recently, thanks to development of some good representations of the vdW contribution to the energy (known as “vdW corrections”).

Comparative Analysis of Genus Bifidobacterium: Insight into its Host Adaptation

Bifidobacteria is amongst one of the health promoting bacteria. The role of this important probiotic genera can be elucidated by understanding its genome. Comparative analysis of the whole genus of these bacteria can reveal their adaptation to a diverse host range. This study comprises of four research projects. In the first study, a reference library for genus Bifidobacterium was prepared. The core genes in each genus were selected based on a newly proposed statistical definition of core genome. Comparative analysis of Bifidobacterium with another probiotic genus Lactobacillus revealed the metabolic characteristics of genus Bifidobacterium. The second study investigated the immunomodulatory role of a B. bifidum strain TMC3115. The analysis of TMC3115 provided insights into its extracellular structures which might have their role in host interaction and immunomodulation. The study highlighted the variability among these genomes just not on species level but also on strain level in terms of host interaction. The last two studies aim to inspect the relationship between bifidobacteria and its host diet. Bifidobacteria, are both host- and niche-specific. Such adaptation of bifidobacterial species is considered relevant to the intestinal microecosystem and hosts’ oligosaccharides. Many species should have co-evolved with their hosts, but the phylogeny of Bifidobacterium is dissimilar to that of host animals. The discrepancy could be linked to the niche-specific evolution due to hosts’ dietary carbohydrates. The distribution of carbohydrate-active enzymes, in particular glycoside hydrolases (GHs) that metabolize unique oligosaccharides was examined. When bifidobacterial species were classified by their distribution of GH genes, five groups arose according to their hosts’ feeding behaviour. The distribution of GH genes was only weakly associated with the phylogeny of the host animals or with genomic features such as genome size. Thus, the hosts’ dietary pattern is the key determinant of the distribution and evolution of GH genes.

E-cadherin and Choline Kinase: two challenging drug discovery targets

The data presented in this thesis was generated using molecular biology, protein chemistry and X-ray crystallography techniques. However, while the methodologies employed are essentially the same, the research work presented here refers to two different proteins, which are part of different research projects in the laboratory. For this reason, the content of this thesis is divided in two independent parts, each provided with an introduction and a general overview of the research topic and state-ofthe- art, a materials and methods section discussing the techniques used and the protocols followed, and a section where the results are presented and discussed in detail. The first half of the thesis deals with the structural characterization of the complex between human E-cadherin and three different small molecule potential inhibitors identified via a fragment-based drug discovery (FBDD) screening campaign that was conducted using a library of commercially available small fluorinated chemical fragments. For this screening phase, we used 19F-NMR as readout. The NMR experiments were done by our collaborator Dr. Marina Veronesi at the D3 PharmaChemistry division of the Italian Institute of Technology (IIT) in Genova (Italy). Functional cell adhesion assays to validate the inhibitory effects of the fragments thus identified were carried out in collaboration with Prof. Frédéric André at the University of Marseille (France). The second half of the thesis describes the structural characterization of Plasmodium falciparum Choline Kinase (PfChoK), an important pharmaceutical target in the fight against malaria, as well as the biochemical characterization of a library of potential inhibitors of PfChoK. These inhibitors were synthetized in the group of Prof. Luisa Carlota López-Cara at the Department of Pharmaceutical and Organic Chemistry of the University of Granada (Spain) in the framework of an ongoing collaboration between the two groups.

Crystal engineering of co-crystals and host-guest systems for environmentally friendly applications: sunscreens stabilization, pollutant sequestering and herbicide reformulation.

Solid state engineered materials have proven to be useful and suitable tools in the quest of new materials. In this thesis different crystalline compounds were synthesized to provide more sustainable products for different applications, as in cosmetics or in agrochemistry, to propose pollutants removal strategy or to obtain materials for electrocatalysis. Therefore, the research projects presented here can be divided into three main topics: (i) sustainable preparation of solid materials of widely used active ingredients aimed at the reduction of their occurrence in the natural environment. The systems studied in this section are cyclodextrins host-guest compounds, obtained via mechanochemical and slurry synthesis. The first chemicals studied are sunscreens inclusion complexes, that proved to have enhanced photostability and desired photoprotection. The same synthetic methods were applied to obtain inclusion complexes of bentazon, a herbicide often found to leach in groundwaters. The resulting products showed to have desired water solubility properties. The same herbicide was also adsorbed on amorphous calcium phosphate nanoparticles, to obtain a biocompatible formulation of this agrochemical. This herbicide could benefit by the adsorption on nanoparticles for what concerns its kinetic release in different media as well as its photostability. (ii) Sustainable synthesis of co-crystals based on polycyclic aromatic hydrocarbons, for the proposal of a sequestering method with a resulting material with enhanced properties. The co-crystallization via mechanochemical means proved that these pollutants can be sequestered via simple solvent-free synthesis and the obtained materials present better photochemical properties when compared to the starting co-formers. (iii) Crystallization from mild solvents of nanosized materials useful for the application in electrocatalysis. The study of compounds based on nickel and cobalt metal ions resulted in the obtainment of 2D and 1D coordination polymers. Moreover, solid solutions were obtained. These crystals showed layered structures and, according to preliminary results, they can be exfoliated.

L'archeologia pubblica in Italia tra comunicazione online e offline: una proposta metodologica per la pianificazione e la misurazione

In Italia, l’archeologia pubblica ha subìto negli ultimi anni un accelerazione, grazie ad una maggiore consapevolezza da parte degli archeologi sulla necessità di un dialogo con il pubblico. Sempre più progetti di ricerca archeologica investono risorse nell’organizzazione di iniziative volte a coinvolgere la comunità, sia onsite che online. Ma per valutare effettivamente l’impatto di queste iniziative c’è bisogno di delineare una metodologia condivisa, assente attualmente in Italia: manca una progettualità, una pianificazione, una riflessione critica sull’argomento. Il mio lavoro, inserito all’interno del progetto di “Archeologia dei paesaggi di Ravenna” dell’Università di Bologna, ha l’obiettivo di individuare le strategie comunicative migliori per coinvolgere il pubblico verso tematiche storico-archeologiche, ricorrendo in particolare all’utilizzo dei social media, e di individuare una metodologia efficace per la realizzazione e valutazione delle iniziative di archeologia pubblica nell’ambito della ricerca universitaria. Essendoci la necessità di una pianificazione, ho deciso di considerare il mio progetto come se fosse un’azienda con un prodotto o servizio da portare sul mercato. In tal caso, l’azienda deve ricorrere alla stesura di un piano marketing, un documento che formalizza le analisi e le conseguenti decisioni di marketing per un determinato prodotto/mercato, in un determinato arco temporale/spaziale al fine di conseguire gli obiettivi prefissati.

Rhodium clusters: investigation of the reactivity towaeds phosphines and selected d- and p-metals

During my PhD we focused on different research projects concerning the synthesis and characterization of new rhodium carbonyl clusters. More specifically, we studied the reactivity between Rh4(CO)12 and different bidentate phosphines, obtaining seven different species: Rh4(CO)10(dppe), Rh4(CO)8(dppe)2, Rh4(CO)10(dppf), {Rh4(CO)10(dpp-hexane)}2, {Rh4(CO)10(t-dppe)}2, Rh2(CO)2(dppf)2 and Rh4(CO)9(μ2-dppe)(μ1-dppeO). The reactivity of [Rh7(CO)16]3- with [AuCl4]- and Au(Et2S)Cl led to the formation of seven bimetallic clusters, of which four new ones, namely [Rh16Au6(CO)36]6-, [Rh10Au(CO)26]3-, [Rh16Au6(CO)36]4-, [Rh16Au6(CO)36]5-, [Rh22Au3(CO)47]5-, [Rh19Au5(CO)40]4- and [Rh20Au7(CO)45]5-. The reactivity of [Rh16Au6(CO)36]6- and [Rh10Au(CO)26]3- was studied as well. The reactivity of [Rh7(CO)16]3- with AgBF4, AgNO3 and with Pt(Et2S)2Cl2 was investigated, yielding only to the already known [Rh6N(CO)15]-, [PtRh5(CO)15]- and [PtRh4(CO)14]2- compounds. [Rh7(CO)16]3- war reacted with SnCl2·2H2O in acetone obtaining [Rh7Sn4Cl10(CO)14]5-, and [Rh12Sn(CO)23Cl2]4- was reacted with H+ obtaining [Rh18Sn3Cl2(CO)44]4-. Reactivity of [Rh7(CO)16]3- with InCl3 resulted in the isolation of [Rh12In(CO)28]3- and [Rh11In3(CO)25Cl2]3-, already known in our research lab, and the new [HRh11In(CO)26]3-. Moreover, a more straightforward synthesis for [Rh6InCl3(CO)15]2- was found, and this also led to the isolation of the [Rh6InCl2(DMF)(CO)15]-. The recover or rhodium as valuable carbonyl compound was also studied, and starting from a mixture of by-products it was possible to obtain the starting material [Rh7(CO)16]3-.

Coaching agile methods in research and development projects

Agile coaching of a project team is one way to aid learning of the agile methods. The objective of this thesis is to present the agile coaching plan and to follow how complying the plan affects to the project teams. Furthermore, the agile methods are followed how they work in the projects. Two projects are used to help the research. From the thesis point of view, the task for the first project is to coach the project team and two new coaches. The task for the second project is also to coach the project team, but this time so that one of the new coaches acts as the coach. The agile methods Scrum process and Extreme programming are utilized by the projects. In the latter, the test driven development, continuous integration and pair programming are concentrated more precisely. The results of the work are based on the observations from the projects and the analysis derived from the observations. The results are divided to the effects of the coaching and to functionality of the agile methods in the projects. Because of the small sample set, the results are directional. The presented plan, to coach the agile methods, needs developing, but the results of the functionality of the agile methods are encouraging.

Informal communication networks and the diffusion of innovations in UK construction projects: A research design

The UK industry has been criticised for being slow to adopt construction process innovations. Research shows that the idiosyncrasies of participants, their roles in the system and the contextual differences between sections of the industry make this a highly complex problem. There is considerable evidence that informal social networks play a key role in diffusion of innovations. The aim is to identify informal communication networks of project participants and the role these play in the diffusion of construction innovations. The characteristics of this network will be analysed in order to understand how they can be used to accelerate innovation diffusion within and between projects. Social Network Analysis is used to determine informal communication routes. Control and experiment case study projects are used within two different organizations. This allows informal communication routes concerning innovations to be mapped, whilst testing if the informal routes can facilitate diffusion. Analysis will focus upon understanding the combination of informal strong and weak ties, and how these impede or facilitate the diffusion of the innovation. Initial work suggests the presence of an informal communication network. Actors within this informal network, and the organization's management are unaware of its' existence and their informal roles within it. Thus, the network remains an untapped medium regarding innovation diffusion. It is proposed that successful innovation diffusion is dependent upon understanding informal strong and weak ties, at project, organization and industry level.