Theoretical investigation of geometric configurations and vibrational spectra in citric acid complexes

The performance of advanced electronic ceramics is directly related to the synthesis route employed. Sol-gel methods are widely used for this purpose. However, the physicochemical intermediate steps are still not well understood. Better understanding and control of these processes can improve the final quality of samples. In this work, we studied theoretically the formation of metal complexes between citric acid and lithium or barium metal cations with different citric acid/metal proportions, using Density Functional Theory electronic structure calculations. Infrared and Raman scattering spectra were simulated for the more stable geometric configurations. Using this methodology, we identified some features of complexes formed in the synthesis process. Our results show that the complexes can be distinguished by changes in the bands assigned to C=O, COH-, and COO- group vibrations. An estimate of the most stable complexes is made based on total energy.

Vibrational spectroscopy for probing molecular-level interactions in organic films mimicking biointerfaces

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

BENTHIC MACROFAUNA STRUCTURE IN THE NORTHEAST AREA OF TODOS OS SANTOS BAY, BAHIA STATE, BRAZIL: PATTERNS OF SPATIAL AND SEASONAL DISTRIBUTION

Structure of intertidal and subtidal benthic macrofauna in the northeastern region of Todos os Santos Bay (TSB), northeast Brazil, was investigated during a period of two years. Relationships with environmental parameters were studied through uni- and multivariate statistical analyses, and the main distributional patterns shown to be especially related to sediment type and content of organic fractions (Carbon, Nitrogen, Phosphorus), on both temporal and spatial scales. Polychaete annelids accounted for more than 70% of the total fauna and showed low densities, species richness and diversity, except for the area situated on the reef banks. These banks constitute a peculiar environment in relation to the rest of the region by having coarse sediments poor in organic matter and rich in biodetritic carbonates besides an abundant and diverse fauna. The intertidal region and the shallower area nearer to the oil refinery RLAM, with sediments composed mainly of fine sand, seem to constitute an unstable system with few highly dominant species, such as Armandia polyophthalma and Laeonereis acuta. In the other regions of TSB, where muddy bottoms predominated, densities and diversity were low, especially in the stations near the refinery. Here the lowest values of the biological indicators occurred together with the highest organic compound content. In addition, the nearest sites (stations 4 and 7) were sometimes azoic. The adjacent Caboto, considered as a control area at first, presented low density but intermediate values of species diversity, which indicates a less disturbed environment in relation to the pelitic infralittoral in front of the refinery. The results of the ordination analyses evidenced five homogeneous groups of stations (intertidal; reef banks; pelitic infralittoral; mixed sediments; Caboto) with different specific patterns, a fact which seems to be mainly related to granulometry and chemical sediment characteristics.

Unraveling the structure of squids' spermatophores: a combined approach based on Doryteuthis plei (Blainville, 1823) (Cephalopoda: Loliginidae)

Marian, J.E.A.R. and Domaneschi, O. 2012. Unraveling the structure of squids spermatophores: a combined approach based on Doryteuthis plei (Blainville, 1823) (Cephalopoda: Loliginidae). Acta Zoologica (Stockholm) 93: 281307. Male coleoid cephalopods produce elaborate spermatophores, which function autonomously outside the male body during copulation, undergoing a complicated process of evagination. In order to contribute to the understanding of this unique structure, this study investigated the morphology of the spermatophore of Doryteuthis plei applying several microscopy techniques. A hitherto unreported, much more complex structural arrangement was revealed for the loliginid spermatophore, the most striking findings being: (1) the complex, layered structure of the middle membrane, which bears an additional, chemically distinct segment surrounding part of the cement body; (2) the presence of a space between the inner tunic and middle membrane filled with a fine reticulated material; (3) the presence of stellate particles not only embedded in the spiral filament, but also closely applied to the inner membrane at the level of the cement body; (4) the presence of a pre-oral chamber in the cap region; and (5) the complex organization of the cement body, formed by two distinct layers encompassing contents of different chemical and textural properties. Careful literature reassessment suggests several of these features are common to loliginids, and to some extent to other squids. Their possible functional implications are discussed in light of our knowledge of the spermatophoric reaction mechanics.

A novel XML document structure comparison framework based-on sub-tree commonalities and label semantics

XML similarity evaluation has become a central issue in the database and information communities, its applications ranging over document clustering, version control, data integration and ranked retrieval. Various algorithms for comparing hierarchically structured data, XML documents in particular, have been proposed in the literature. Most of them make use of techniques for finding the edit distance between tree structures, XML documents being commonly modeled as Ordered Labeled Trees. Yet, a thorough investigation of current approaches led us to identify several similarity aspects, i.e., sub-tree related structural and semantic similarities, which are not sufficiently addressed while comparing XML documents. In this paper, we provide an integrated and fine-grained comparison framework to deal with both structural and semantic similarities in XML documents (detecting the occurrences and repetitions of structurally and semantically similar sub-trees), and to allow the end-user to adjust the comparison process according to her requirements. Our framework consists of four main modules for (i) discovering the structural commonalities between sub-trees, (ii) identifying sub-tree semantic resemblances, (iii) computing tree-based edit operations costs, and (iv) computing tree edit distance. Experimental results demonstrate higher comparison accuracy with respect to alternative methods, while timing experiments reflect the impact of semantic similarity on overall system performance.

Computational methods for the analysis of protein structure and function

The vast majority of known proteins have not yet been experimentally characterized and little is known about their function. The design and implementation of computational tools can provide insight into the function of proteins based on their sequence, their structure, their evolutionary history and their association with other proteins. Knowledge of the three-dimensional (3D) structure of a protein can lead to a deep understanding of its mode of action and interaction, but currently the structures of <1% of sequences have been experimentally solved. For this reason, it became urgent to develop new methods that are able to computationally extract relevant information from protein sequence and structure. The starting point of my work has been the study of the properties of contacts between protein residues, since they constrain protein folding and characterize different protein structures. Prediction of residue contacts in proteins is an interesting problem whose solution may be useful in protein folding recognition and de novo design. The prediction of these contacts requires the study of the protein inter-residue distances related to the specific type of amino acid pair that are encoded in the so-called contact map. An interesting new way of analyzing those structures came out when network studies were introduced, with pivotal papers demonstrating that protein contact networks also exhibit small-world behavior. In order to highlight constraints for the prediction of protein contact maps and for applications in the field of protein structure prediction and/or reconstruction from experimentally determined contact maps, I studied to which extent the characteristic path length and clustering coefficient of the protein contacts network are values that reveal characteristic features of protein contact maps. Provided that residue contacts are known for a protein sequence, the major features of its 3D structure could be deduced by combining this knowledge with correctly predicted motifs of secondary structure. In the second part of my work I focused on a particular protein structural motif, the coiled-coil, known to mediate a variety of fundamental biological interactions. Coiled-coils are found in a variety of structural forms and in a wide range of proteins including, for example, small units such as leucine zippers that drive the dimerization of many transcription factors or more complex structures such as the family of viral proteins responsible for virus-host membrane fusion. The coiled-coil structural motif is estimated to account for 5-10% of the protein sequences in the various genomes. Given their biological importance, in my work I introduced a Hidden Markov Model (HMM) that exploits the evolutionary information derived from multiple sequence alignments, to predict coiled-coil regions and to discriminate coiled-coil sequences. The results indicate that the new HMM outperforms all the existing programs and can be adopted for the coiled-coil prediction and for large-scale genome annotation. Genome annotation is a key issue in modern computational biology, being the starting point towards the understanding of the complex processes involved in biological networks. The rapid growth in the number of protein sequences and structures available poses new fundamental problems that still deserve an interpretation. Nevertheless, these data are at the basis of the design of new strategies for tackling problems such as the prediction of protein structure and function. Experimental determination of the functions of all these proteins would be a hugely time-consuming and costly task and, in most instances, has not been carried out. As an example, currently, approximately only 20% of annotated proteins in the Homo sapiens genome have been experimentally characterized. A commonly adopted procedure for annotating protein sequences relies on the "inheritance through homology" based on the notion that similar sequences share similar functions and structures. This procedure consists in the assignment of sequences to a specific group of functionally related sequences which had been grouped through clustering techniques. The clustering procedure is based on suitable similarity rules, since predicting protein structure and function from sequence largely depends on the value of sequence identity. However, additional levels of complexity are due to multi-domain proteins, to proteins that share common domains but that do not necessarily share the same function, to the finding that different combinations of shared domains can lead to different biological roles. In the last part of this study I developed and validate a system that contributes to sequence annotation by taking advantage of a validated transfer through inheritance procedure of the molecular functions and of the structural templates. After a cross-genome comparison with the BLAST program, clusters were built on the basis of two stringent constraints on sequence identity and coverage of the alignment. The adopted measure explicity answers to the problem of multi-domain proteins annotation and allows a fine grain division of the whole set of proteomes used, that ensures cluster homogeneity in terms of sequence length. A high level of coverage of structure templates on the length of protein sequences within clusters ensures that multi-domain proteins when present can be templates for sequences of similar length. This annotation procedure includes the possibility of reliably transferring statistically validated functions and structures to sequences considering information available in the present data bases of molecular functions and structures.

Derivati polimerici organometallici ancorati su matrice inorganica per applicazioni in chimica fine

Organotin compounds have found in the last few decades a wide variety of applications. Indeed, they are used successfully as antifouling paints, PVC stabilizers and ion carriers, as well as homogeneous catalysts. In this context, it has been proved that the Lewis acidity of the metal centre allows these compounds to promote the reaction between alcohol and ester. However their use is now limited by their well-known toxicity, moreover they are hardly removable from the reaction mixture. This problem can be overcome by grafting the organotin derivative onto a polymeric cross-linked support. In this way the obtained heterogeneous catalyst can be easily filtered off from the reaction mixture, thus creating the so-called "clean organotin reagents", avoiding the presence of toxic organotin residues in solution and the tin release in the environment. In the last few years several insoluble polystyrene resins containing triorganotin carboxylate moieties have been synthesized with the aim of improving their catalytic activity: in particular we have investigated and opportunely modified their chemical structure in order to optimize the accessibility to the metal centre and its Lewis acidity. Recently, we replaced the polymeric matrix with an inorganic one, in order to dispose of a relatively cheaper and easily available support. For this purpose an ordered mesoporous silica, characterized by 2D-hexagonal pores, named MCM-41, and an amorphous silica have been selected. In the present work two kinds of MCM-41 silica containing the triorganotin carboxylate moiety have been synthesized starting from a commercial Cab-O-Sil M5 silica. These catalysts have two different spacers between the core and the tin-carboxylate moiety, namely a polyaliphatic chain (compound FT29) or a poliethereal one (compound FT6), with the aim to improve the interaction between catalyst and reacting ester. Three catalysts supported onto an amorphous silica have been also synthesized: the structure is the same as silica FT29, i.e. a compound having a polialiphatic chain, and they have different percentage of organotin derivative grafted on the silica surface (10, 30, 50% respectively for silica MB9, SU27 and SU28). The performances of the above silica as heterogeneous catalysts in transesterification reactions have been tested in a model reaction between ethyl acetate and 1-octanol, a primary alcohol sensitive to the reaction conditions. The alcohol conversion was assessed by gas-chromatography, determining the relative amount of transesterified product and starting alcohol after established time intervals.

La nutrizione-idratazione artificiale è terapia? All'interfaccia tra scienza, diritto e bioetica, il fine vita in Italia, secondo una prospettiva di comunicazione della scienza post-accademica e Science&Technologies Studies (STS)

The question “artificial nutrition and hydration (ANH) is therapy or not?” is one of the key point of end-of-life issues in Italy, since it was (and it is also nowadays) a strategic and crucial point of the Italian Bioethics discussion about the last phases of human life: determining if ANH is therapy implies the possibility of being included in the list of treatments that could be mentioned for refusal within the living will document. But who is entitled to decide and judge if ANH is a therapy or not? Scientists? The Legislator? Judges? Patients? This issue at first sight seems just a matter of science, but at stake there is more than a scientific definition. According to several scholars, we are in the era of post-academic Science, in which Science broaden discussion, production, negotation and decision to other social groups that are not just the scientific communities. In this process, called co-production, on one hand scientific knowledge derives from the interaction between scientists and society at large. On the other hand, science is functional to co-production of social order. The continuous negotation on which science has to be used in social decisions is just the evidence of the mirroring negotation for different way to structure and interpret society. Thus, in the interaction between Science and Law, deciding what kind of Science could be suitable for a specific kind of Law, envisages a well defined idea of society behind this choice. I have analysed both the legislative path (still in progress) in the living will act production in Italy and Eluana Englaro’s judicial case (that somehow collapsed in the living will act negotiation), using official documents (hearings, texts of the official conference, committees comments and ruling texts) and interviewing key actors in the two processes from the science communication point of view (who talks in the name of science? Who defines what is a therapy? And how do they do?), finding support on the theoretical framework of the Science&Technologies Studies (S&TS).

Novel tools for conservation genetics in marine fish: population structure and evolution of the European hake (Merluccius merluccius) inferred by SNP variation and applications to traceability

The research presented in my PhD thesis is part of a wider European project, FishPopTrace, focused on traceability of fish populations and products. My work was aimed at developing and analyzing novel genetic tools for a widely distributed marine fish species, the European hake (Merluccius merluccius), in order to investigate population genetic structure and explore potential applications to traceability scenarios. A total of 395 SNPs (Single Nucleotide Polymorphisms) were discovered from a massive collection of Expressed Sequence Tags, obtained by high-throughput sequencing, and validated on 19 geographic samples from Atlantic and Mediterranean. Genome-scan approaches were applied to identify polymorphisms on genes potentially under divergent selection (outlier SNPs), showing higher genetic differentiation among populations respect to the average observed across loci. Comparative analysis on population structure were carried out on putative neutral and outlier loci at wide (Atlantic and Mediterranean samples) and regional (samples within each basin) spatial scales, to disentangle the effects of demographic and adaptive evolutionary forces on European hake populations genetic structure. Results demonstrated the potential of outlier loci to unveil fine scale genetic structure, possibly identifying locally adapted populations, despite the weak signal showed from putative neutral SNPs. The application of outlier SNPs within the framework of fishery resources management was also explored. A minimum panel of SNP markers showing maximum discriminatory power was selected and applied to a traceability scenario aiming at identifying the basin (and hence the stock) of origin, Atlantic or Mediterranean, of individual fish. This case study illustrates how molecular analytical technologies have operational potential in real-world contexts, and more specifically, potential to support fisheries control and enforcement and fish and fish product traceability.

Vibrational spectroscopic and electrochemical investigations of multi-centered heme proteins in biomimetic membrane architectures

Membrane proteins play a major role in every living cell. They are the key factors in the cell’s metabolism and in other functions, for example in cell-cell interaction, signal transduction, and transport of ions and nutrients. Cytochrome c oxidase (CcO), as one of the membrane proteins of the respiratory chain, plays a significant role in the energy transformation of higher organisms. CcO is a multi centered heme protein, utilizing redox energy to actively transport protons across the mitochondrial membrane. One aim of this dissertation is to investigate single steps in the mechanism of the ion transfer process coupled to electron transfer, which are not fully understood. The protein-tethered bilayer lipid membrane is a general approach to immobilize membrane proteins in an oriented fashion on a planar electrode embedded in a biomimetic membrane. This system enables the combination of electrochemical techniques with surface enhanced resonance Raman (SERRS), surface enhanced reflection absorption infrared (SEIRAS), and surface plasmon spectroscopy to study protein mediated electron and ion transport processes. The orientation of the enzymes within the surface confined architecture can be controlled by specific site-mutations, i.e. the insertion of a poly-histidine tag to different subunits of the enzyme. CcO can, thus, be oriented uniformly with its natural electron pathway entry pointing either towards or away from the electrode surface. The first orientation allows an ultra-fast direct electron transfer(ET) into the protein, not provided by conventional systems, which can be leveraged to study intrinsic charge transfer processes. The second orientation permits to study the interaction with its natural electron donor cytochrome c. Electrochemical and SERR measurements show conclusively that the redox site structure and the activity of the surface confined enzyme are preserved. Therefore, this biomimetic system offers a unique platform to study the kinetics of the ET processes in order to clarify mechanistic properties of the enzyme. Highly sensitive and ultra fast electrochemical techniques allow the separation of ET steps between all four redox centres including the determination of ET rates. Furthermore, proton transfer coupled to ET could be directly measured and discriminated from other ion transfer processes, revealing novel mechanistic information of the proton transfer mechanism of cytochrome c oxidase. In order to study the kinetics of the ET inside the protein, including the catalytic center, time resolved SEIRAS and SERRS measurements were performed to gain more insight into the structural and coordination changes of the heme environment. The electrical behaviour of tethered membrane systems and membrane intrinsic proteins as well as related charge transfer processes were simulated by solving the respective sets of differential equations, utilizing a software package called SPICE. This helps to understand charge transfer processes across membranes and to develop models that can help to elucidate mechanisms of complex enzymatic processes.

Nothing ever ends: il concetto di fine negli universi seriali

L'oggetto principale di questa tesi è il concetto di fine negli universi seriali. Spesso si intende il “The End” in un romanzo o in un film come un momento climatico, e che i finali sono collegati ad una teleologia che guida il testo nel suo insieme. Come risultato di questo modo di approcciare i finale, una delle opinioni più comuni è simile a quella di Henry James [1884] che diceva: “distribution at the last of prizes, pensions, husbands, wives, babies, millions, appended paragraph, and cheerful remarks”. Ma è molto difficile applicare la posizione di James a un romanzo modernista o a un film postmoderno e ancor ameno ai cosiddetti universi narrativi seriali, in cui la storia si sviluppa lungo decenni. Nel nostro contemporaneo panorama mediale, il testo non è più concepito come un'opera, ma deve essere costruito e concepito come un network, un ecosistema in cui nuove connessioni economiche e nuove relazioni bottom-up modellano una struttura inedita. Questa nuova struttura può riconfigurare il senso del finale e della fine, ma anche per le vast narratives spesso si dice che “Il finale non corrispondeva alla spirito della storia”, “il finale era deludente”. Potremmo sostenere che il concetto di finale sia ancora importante, nonostante sia stato superato dal punto di vista teorico. Per analizzare se il finale è costruito in un maniera non-lineare ma percepito come teleologico, la tesi è strutturata in due parti e di quattro capitoli. Prima parte “Storia” [1. Letteratura; 2. Cinema], seconda “Forme/strutture” [3. Transmedia; 4. Remix]

Tailoring, synthesis and structure-property relationships of 2,3-thienoimide based molecular materials

Organic molecular semiconductors are subject of intense research for their crucial role as key components of new generation low cost, flexible, and large area electronic devices such as displays, thin-film transistors, solar cells, sensors and logic circuits. In particular, small molecular thienoimide (TI) based materials are emerging as novel multifunctional materials combining a good processability together to ambipolar or n-type charge transport and electroluminescence at the solid state, thus enabling the fabrication of integrated devices like organic field effect transistors (OFETs) and light emitting transistor (OLETs). Given this peculiar combination of characteristics, they also constitute the ideal substrates for fundamental studies on the structure-property relationships in multifunctional molecular systems. In this scenario, this thesis work is focused on the synthesis of new thienoimide based materials with tunable optical, packing, morphology, charge transport and electroluminescence properties by following a fine molecular tailoring, thus optimizing their performances in device as well as investigating and enabling new applications. Investigation on their structure-property relationships has been carried out and in particular, the effect of different π-conjugated cores (heterocycles, length) and alkyl end chain (shape, length) changes have been studied, obtaining materials with enhanced electron transport capability end electroluminescence suitable for the realization of OFETs and single layer OLETs. Moreover, control on the polymorphic behaviour characterizing thienoimide materials has been reached by synthetic and post-synthetic methodologies, developing multifunctional materials from a single polymorphic compound. Finally, with the aim of synthesizing highly pure materials, simplifying the purification steps and avoiding organometallic residues, procedures based on direct arylation reactions replacing conventional cross-couplings have been investigated and applied to different classes of molecules, bearing thienoimidic core or ends, as well as thiophene and anthracene derivatives, validating this approach as a clean alternative for the synthesis of several molecular materials.

Recent advances into understanding some aspects of the structure and function of mammalian and avian lungs

Recent findings are reported about certain aspects of the structure and function of the mammalian and avian lungs that include (a) the architecture of the air capillaries (ACs) and the blood capillaries (BCs); (b) the pulmonary blood capillary circulatory dynamics; (c) the adaptive molecular, cellular, biochemical, compositional, and developmental characteristics of the surfactant system; (d) the mechanisms of the translocation of fine and ultrafine particles across the airway epithelial barrier; and (e) the particle-cell interactions in the pulmonary airways. In the lung of the Muscovy duck Cairina moschata, at least, the ACs are rotund structures that are interconnected by narrow cylindrical sections, while the BCs comprise segments that are almost as long as they are wide. In contrast to the mammalian pulmonary BCs, which are highly compliant, those of birds practically behave like rigid tubes. Diving pressure has been a very powerful directional selection force that has influenced phenotypic changes in surfactant composition and function in lungs of marine mammals. After nanosized particulates are deposited on the respiratory tract of healthy human subjects, some reach organs such as the brain with potentially serious health implications. Finally, in the mammalian lung, dendritic cells of the pulmonary airways are powerful agents in engulfing deposited particles, and in birds, macrophages and erythrocytes are ardent phagocytizing cellular agents. The morphology of the lung that allows it to perform different functions-including gas exchange, ventilation of the lung by being compliant, defense, and secretion of important pharmacological factors-is reflected in its "compromise design."

Conformational transitions of glycine induced by vibrational excitation of the O-H stretch

Vibrational energy flow and conformational transitions following excitation of the OH stretching mode of the most stable conformer of glycine are studied by classical trajectories. "On the fly" simulations with the PM3 semiempirical electronic structure method for the potential surface are used. Initial conditions are selected to correspond to the v = 1 excitation of the OH stretch. The main findings are: (1) An an equilibrium-like ratio is established between the populations of the 3 lowest-lying conformers after about 10 picoseconds. (2) There is a high probability throughout the 150 ps of the simulations for finding the molecule in geometries far from the equilibrium structures of the lowest-energy conformers. (3) Energy from the initial excited OH (v = 1) stretch flows preferentially to 5 other vibrational modes, including the bending motion of the H atom. (4) RRK theory yields conformational transition rates that deviate substantially from the classical trajectory results. Possible implication of these results for vibrational energy flow and conformational transitions in small biological molecules are discussed.

Structure and thermodynamics of H3O+(H2O)8 clusters: A combined molecular dynamics and quantum mechanics approach

We have studied the structure and stability of (H3O+)(H2O)8 clusters using a combination of molecular dynamics sampling and high-level ab initio calculations. 20 distinct oxygen frameworks are found within 2 kcal/mol of the electronic or standard Gibbs free energy minimum. The impact of quantum zero-point vibrational corrections on the relative stability of these isomers is quite significant. The box-like isomers are favored in terms of electronic energy, but with the inclusion of zero-point vibrational corrections and entropic effects tree-like isomers are favored at higher temperatures. Under conditions from 0 to 298.15 K, the global minimum is predicted to be a tree-like structure with one dangling singly coordinated water molecule. Above 298.15 K, higher entropy tree-like isomers with two or more singly coordinated water molecules are favored. These assignments are generally consistent with experimental IR spectra of (H3O+)(H2O)8 obtained at 150 K.