Designing Hydrogels that Transform their Shape in Response to Molecular Cues

There has been considerable interest in developing shape-changing soft materials for potential applications in drug delivery, microfluidics and biosensing. These shape- changing materials are inspired by the morphological changes exhibited by plants in nature, such as the Venus flytrap. One specific class of shape-change is that from a flat sheet to a folded structure (e.g., a tube). Such “self-folding” materials are usually composed of polymer hydrogels, and these typically fold in response to external stimuli such as pH and temperature. In order to develop these hydrogels for the previously described applications, it is necessary to expand the range of triggers. The focus of this dissertation is the advancement of shape-changing polymer hydrogels that are sensitive to uncommon cues such as specific biomolecules (enzymes), the substrates for such enzymes, or specific multivalent cations. First, we describe a hybrid gel that responds to the presence of low concentrations of a class of enzymes known as matrix metalloproteinases (MMPs). The hybrid gel was created by utilizing photolithographic techniques to combine two or more gels with distinct chemical composition into the same material. Certain portions of the hybrid gel are composed of a biopolymer derivative with crosslinkable groups. The hybrid gel is flat in water; however, in the presence of MMPs, the regions containing the biopolymer are degraded and the flat sheet folds to form a 3D structure. We demonstrate that hydrogels with different patterns can transform into different 3D structures such as tubes, helices and pancakes. Furthermore, this shape change can be made to occur at physiological concentrations of enzymes. Next, we report a gel with two layers that undergoes a shape change in the presence of glucose. The enzyme glucose oxidase (GOx) is immobilized in one of the layers. GOx catalyzes the conversion of glucose to gluconic acid. The production of gluconic acid decreases the local pH. The decrease in local pH causes one of the layers to swell. As a result, the flat sheet folds to form a tube. The tube unfolds to form a flat sheet when it is transferred to a solution with no glucose present. Therefore, this biomolecule- triggered shape transformation is reversible, meaning the glucose sensing gel is reusable. Furthermore, this shape change only occurs in the presence of glucose and it does not occur in the presence of other small sugars such as fructose. In our final study, we report the shape change of a gel with two layers in the presence of multivalent ions such as Ca2+ and Sr2+. The gel consists of a passive layer and an active layer. The passive layer is composed of dimethylyacrylamide (DMAA), which does not interact with multivalent ions. The active layer consists of DMAA and the biopolymer alginate. In the presence of Ca2+ ions, the alginate chains crosslink and the active layer shrinks. As a result, the gel converts from a flat sheet to a folded tube. What is particularly unusual is the direction of folding. In most cases, when flat rectangular gels fold, they do so about their short-side. However, our gels typically fold about their long-side. We hypothesize that non-homogeneous swelling determines the folding axis.

mRNA-Seq and microarray development for the Grooved carpet shell clam, Ruditapes decussatus: a functional approach to unravel host -parasite interaction

Background The Grooved Carpet shell clam Ruditapes decussatus is the autochthonous European clam and the most appreciated from a gastronomic and economic point of view. The production is in decline due to several factors such as Perkinsiosis and habitat invasion and competition by the introduced exotic species, the manila clam Ruditapes philippinarum. After we sequenced R. decussatus transcriptome we have designed an oligo microarray capable of contributing to provide some clues on molecular response of the clam to Perkinsiosis. Results A database consisting of 41,119 unique transcripts was constructed, of which 12,479 (30.3%) were annotated by similarity. An oligo-DNA microarray platform was then designed and applied to profile gene expression in R. decussatus heavily infected by Perkinsus olseni. Functional annotation of differentially expressed genes between those two conditionswas performed by gene set enrichment analysis. As expected, microarrays unveil genes related with stress/infectious agents such as hydrolases, proteases and others. The extensive role of innate immune system was also analyzed and effect of parasitosis upon expression of important molecules such as lectins reviewed. Conclusions This study represents a first attempt to characterize Ruditapes decussatus transcriptome, an important marine resource for the European aquaculture. The trancriptome sequencing and consequent annotation will increase the available tools and resources for this specie, introducing the possibility of high throughput experiments such as microarrays analysis. In this specific case microarray approach was used to unveil some important aspects of host-parasite interaction between the Carpet shell clam and Perkinsus, two non-model species, highlighting some genes associated with this interaction. Ample information was obtained to identify biological processes significantly enriched among differentially expressed genes in Perkinsus infected versus non-infected gills. An overview on the genes related with the immune system on R. decussatus transcriptome is also reported.

Differential expression in “rogue” paramutation in peas (Pisum sativum L.)

Dissertação de Mestrado, Engenharia Biológica, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2014

Red wine sweetness preference according to consumer segmentation

The present work aims to evaluate the acceptance and preference for sweet taste in red wine, according to consumer segmentation in age, gender, personality type, tasting sensitivity and consumer experience in wine. A hundred and fourteen wine tasters were invited to the wine tasting, and the average age was 27 years. An addition of sugar was made with equal concentrations of glucose and fructose to the wine at 2g/L, 4g/L, 8g/L, 16g/L and 32g/L. Five pairs of glasses were presented for the subjects to taste containing each a control wine and a spiked sample. Pairs were presented in order of concentration, from 2g/L to 32g/l. The subjects were also asked to answer two online questionnaires at the end of the tasting, on the personality types and vinotype, which is related to mouth sensitivity. ISO-5495 paired comparison tests were used for sensorial analysis. The objective was to assess if any of the nine segmentation factors had influence on preference or rejection for spiked samples and to establish whether this preference was statistically significant. We concluded that it would be important to have subjects with an age average higher than 27 years and more experienced in wine drinking, mostly because the data relative to preferences in novices shows some dispersion and lack of attention. A panel of older and more experienced wine tasters is likely to be more attentive and focused and therefore yield differentiated results. It was also concluded that more research is required to extend this investigation to other wine styles because the differences in preferences can depend on other reasons, such as preferring a wine with more or less sugar according to the type of wine. Finally it was concluded also that some variables influence preference for sweet taste in red wine, such as gender, vinotype and category of experience

Materials design for ambipolar devices: tuning orbital energetics in oligothiophene-naphthalimides semiconductors

Ambipolar organic field-effect transistors (OFETs), which can efficiently transport both holes and electrons, using a single type of electrode, are currently of great interest due to their possible applications in complementary metal oxide semiconductor (CMOS)-like circuits, sensors, and in light-emitting transistors. Several theoretical and experimental studies have argued that most organic semiconductors should be able to transport both types of carrier, although typically unipolar behavior is observed. One factor that can compromise ambipolar transport in organic semiconductors is poor solid state overlap between the HOMO (p-type) or LUMO (n-type) orbitals of neighboring molecules in the semiconductor thin film. In the search of low-bandgap ambipolar materials, where the absence of skeletal distortions allows closer intermolecular π-π stacking and enhanced intramolecular π-conjugation, a new family of oligothiophene-naphthalimide assemblies have been synthesized and characterized, in which both donor and acceptor moieties are directly conjugated through rigid linkers. In previous works we found that oligothiophene-napthalimide assemblies connected through amidine linkers (NDI derivates) exhibit skeletal distortions (50-60º) arising from steric hindrance between the carbonyl group of the arylene core and the sulphur atom of the neighbored thiophene ring (see Figure 1). In the present work we report novel oligo- and polythiophene–naphthalimide analogues NAI-3T, NAI-5T and poly-NAI-8C-3T, in which the connections of the amidine linkage have been inverted in order to prevent steric interactions. Thus, the nitrogen atoms are directly connected to the naphthalene moiety in NAI derivatives while they were attached directly to the thiophene moiety in the previously investigated NDI-3T and NDI-5T. In Figure 1 is depicted the calculated molecular structure of NAI-3T together with that of NDI-3T showing how the steric interactions are not present in the novel NAI derivative. The planar skeletons in these new family induce higher degree of crystallinity and the carrier charge transport can be switched from n-type to ambipolar behaviour. The highest FET performance is achieved for vapor-deposited films of NAI-3T with mobilities of 1.95x10-4cm2V-1s-1 and 2.00x10-4cm2V-1s-1 for electrons and holes, respectively. Finally, these planar semiconductors are compared with their NDI derivates analogues, which exhibit only n-type mobility, in order to understand the origin of the ambipolarity in this new series of molecular semiconductors.

COMPOSITION OF FRESHLY HARVESTED BRAZILIAN ROYAL JELLY - IDENTIFICATION OF CARBOHYDRATES FROM THE SUGAR FRACTION

Samples of Brazilian royal jelly from Africanized Apis mellifera were analysed in order to determine the gross composition: crude moisture ranged from 67.80% to 69.40%, crude protein from 15.80% to 16.70%, crude lipid from 2.90% to 3.98% and-total sugars from 11.40% to 11.50%. The sugar fraction was investigated and revealed the presence of the following compounds identified by their retention time during HPLC analysis: ribose, fructose, glucose, sucrose, mannose, trehalose, erythritol, adonitol and mannitol.

Maltodextrin-incorporated-vacuum-dried honey powder: processing and stability

Honey is rich in sugar content and dominated by fructose and glucose that make honey prone to crystallize during storage. Due to honey composition, the anhydrous glass transition temperature of honey is very low that makes honey difficult to dry alone and drying aid or filler is needed to dry honey. Maltodextrin is a common drying aid material used in drying of sugar-rich food. The present study aims to study the processing of honey powder by vacuum drying method and the impact of drying process and formulation on the stability of honey powder. To achieve the objectives, the series of experiments were done: investigating of maltodextrin DE 10 properties, studying the effect of drying temperature, total solid concentration, DE value, maltodextrin concentration and anti-caking agent on honey powder processing and stability. Maltodextrin provide stable glass compared to lower molecular weight sugars. Dynamic Dew Point Isotherm (DDI) data could be used to determine amorphous content of a system. The area under the first derivative curve from DDI curve is equal to the amount of water needed by amorphous material to crystallize. The drying temperature affected the amorphous content of vacuum-dried honey powder. The higher temperature seemed to result in honey powder with more amorphous component. The ratio of maltodextrin affected more significantly the stability of honey powder compared to the treatments of total solids concentration, DE value and drying temperature. The critical water activity of honey powder was lower than water activity of the equilibrium water content corresponding to BET monolayer water content. Addition of anti-caking agent increased stability and flow-ability of honey powder. Addition of Calcium stearate could inhibit collapse of the honey powder during storage.

Guía de práctica clínica para la enfermedad hepática grasa no alcohólica

Objetivo: Brindar una guía de práctica clínica basada con la evidencia más reciente para el diagnóstico y tratamiento de la Enfermedad Hepática Grasa No alcohólica teniendo en cuenta la efectividad y seguridad de las intervenciones dirigidas a pacientes, personal asistencial, administrativo y entes gubernamentales de cualquier servicio de atención en Colombia. Materiales y métodos: Esta guía fue desarrollada por un equipo multidisciplinario con apoyo de la Asociación Colombiana de Gastroenterología, el Grupo Cochrane ITS y el Instituto de Investigaciones Clínicas de la Universidad Nacional de Colombia. Se desarrollaron preguntas clínicas relevantes y se realizó la búsqueda de guías nacionales e internacionales en bases de datos especializadas. Las guías existentes fueron evaluadas en términos de calidad y aplicabilidad. Una guía cumplió los criterios de adaptación, por lo que se decidió adaptar 3 preguntas clínicas. El Grupo Cochrane realizó la búsqueda sistemática de la literatura. Las tablas de evidencia y recomendaciones fueron realizadas con base a la metodología GRADE. Las recomendaciones de la guía fueron socializadas en una reunión de expertos con entes gubernamentales y pacientes. Resultados: Se desarrolló una guía de práctica clínica basada en la evidencia para el diagnóstico y tratamiento de la Enfermedad Hepática Grasa No alcohólica en Colombia Conclusiones: El diagnóstico y manejo oportuno de la Enfermedad Hepática Grasa No alcohólica contribuirá a disminuir la carga de la enfermedad en Colombia y las enfermedades asociadas

Prevalencia y factores asociados al consumo de bebidas azucaradas en escolares de 9 a 17 años de Bogotá, Colombia: Estudio FUPRECOL

Objetivo: Determinar la prevalencia y los factores asociados al consumo de bebidas azucaradas en una población escolar de Bogotá, Colombia, pertenecientes al estudio FUPRECOL. Métodos: Estudio descriptivo y transversal, realizado en 8136 niños y adolescentes en edad escolar entre 9 y 17 años de Bogotá, Colombia. El peso, la estatura, el índice de masa corporal (IMC), la circunferencia de cintura y el porcentaje de grasa, se recogieron como marcadores antropométricos y de composición corporal. El consumo de bebidas azucaradas (bebidas carbonatadas, jugos ultra-procesados y/o Té), y los factores asociados (sexo, edad, obesidad abdominal, clasificación del IMC, grado de estudios de la madre/padre, y nivel nutricional por cuestionario “Krece plus”), se recogieron por encuesta estructurada. Se establecieron asociaciones mediante la construcción de modelos de regresión logística simple. Resultados: De la población general, el 58,4% eran mujeres. En función al sexo, los varones acusaron la mayor ingesta de “bebidas carbonatadas” con una frecuencia semanal y diaria de 70,9% y 21,0%, respectivamente, seguido de “jugos ultra- procesados” (64,4% semanal vs. 11,3% diario). En ambos sexos, la prevalencia de obesidad abdominal fue mayor en los escolares que respondieron consumir diariamente “bebidas carbonatadas” (23,3%), “jugos ultra-procesados” (13,2%) y “bebidas Té” (9,7%). La edad, el grado de educación de los padres y el nivel nutricional, se asociaron como factores predisponentes al consumo diario de “bebidas carbonatadas”. Conclusión: El consumo de bebidas azucaradas cambia por los factores analizados. Se recomiendan intervenciones integrales en las que estén involucrados los componentes nutricional y educativo entre los niños y adolescentes de Bogotá, Colombia.

Diversity of new root nodule bacteria from Erythrina velutina Willd., a native legume from the Caatinga dry forest (Northeastern Brazil).

This study aims to evaluate the phenotypical characteristics of bacterial isolates from mulungu (Erythrina velutina Willd.) nodules and determinate their Box-PCR fingerprinting. All bacteria were evaluated by the following phenotypic characteristics: growth rate, pH change, colony color and mucus production. The bacterial isolates able to re-nodulate the original host were also evaluated regarding its tolerance to increased salinity and different incubation temperatures, ability to growth using different carbon sources, intrinsic antibiotic resistance and ?in vitro? auxin biosynthesis. The molecular fingerprints were set up using the Box-PCR technique and the isolates were clustered by their profiles. Among the 22 bacterial isolates obtained, eight were able to re-nodulate the original host. Among the nodule inducing isolates, some were tolerant to 1% of NaCl and 39° C and all of them metabolized the maltose, fructose, glucose, sucrose and arabinose, were resistant to rifampicin and produced auxin. The bacteria showed low genetic similarity among them and reference strains, which indicates the great genetic variability of the isolates. The results of this work are the first reports about the bacterial isolates able to nodulate this species. A more deep study of these bacteria may reveal the existence of isolates tolerant to environmental stresses and suitable as a future mulungu inoculant.

Open-cell Metallic Foams for the Electrochemical Conversion of Biomass-derived Compounds

The electrochemical conversion is a sustainable way for the production of added-value products, operating in mild conditions, using in-situ generated hydrogen/oxygen by water and avoiding the use of high H2/O2 pressures. The aim of this work is to investigate the electrocatalytic conversion of 5-hydroxymetilfurfural (HMF) and D-glucose, in alkaline media, using metallic open-cell foams based-catalysts. The electrochemical hydrogenation of HMF to 2,5-bis(hydroxymethyl)furan (BHMF) was performed using nanostructured Ag, deposited by galvanic displacement (GD) or electrodeposition (ED), on Cu foam, obtaining AgCu bimetallic nanoparticles (ED) or dendrites (GD) which enhanced electroactive surface area, charge and mass transfer, than bare foams. In diluted 0.02M HMF solutions, Ag/Cu samples selectively produce BHMF; the large surface area enhanced the productivity, compared to their 2D counterparts. Furthermore, at more concentrated solutions (0.05 – 0.10M) a gradually decrease of selectivity is observed. The performances of the electrodes is stable during the catalytic tests but a Cu-enrichment of particles occurred. The performances of Ni foam-based catalysts, obtained by calcination of Ni foam or by electrodeposition of Ni-hydroxide/Ni and Ni particle/Ni, were firstly investigated for the selective electrochemical oxidation of D-glucose toward gluconic acid (GO) and glucaric acid (GA). Then, the calcined catalyst was chosen to study the influence of the reaction conditions on the reaction mechanism. The GO and GA selectivities increase with the charge passed, while the formation of by-products from C-C cleavage/retro-aldol process is maximum at low charge. The fructose obtained from glucose isomerization favours the formation of by-products. The best glucose/NaOH ratio is between 0.5 and 0.1: higher values suppress the OER, while lower values favour the formation of low molecular weight products. The increases of the potential enhance the GO selectivity, nevertheless higher GA selectivity is observed at 0.6 – 0.7V vs SCE, confirmed by catalytic test performed in gluconate (30-35% GA selectivity).

Rilevamento e studio petrografico del Complesso di M. Calamita (Elba SE) nella zona di Spiaggia di Remaiolo

Lo scopo del lavoro di tesi consiste nello studio petrografico, dalla scala dell’affioramento a quella della sezione sottile, di rocce di basamento cristallino soggetto a metamorfismo e deformazione polifasiche. La zona di studio è la Spiaggia di Remaiolo, Elba SE. Questo settore da un punto di vista geologico fa parte del Complesso di M. Calamita, all’interno dell’Unità di Porto Azzurro. Gli affioramenti studiati mostrano diversi eventi metamorfici: il basamento metamorfico Ercinico e le sue coperture mesozoiche subiscono una sovraimpronta metamorfica Alpina di età Oligo-Miocenica correlabile alla strutturazione della catena dell’Appenino Settentrionale. Successivamente le rocce subiscono un’ulteriore sovraimpronta termometamorfica Mio-Pliocenica legata all’intrusione del plutone La Serra-Porto Azzurro. Il lavoro di campagna ha comportato un rilevamento di dettaglio per creare una Carta degli affioramenti (Allegato 1) e prelevare dei campioni rappresentativi delle litologie. Il lavoro di laboratorio si è svolto su 6 sezioni sottili, realizzate con i campioni prelevati in campagna, tramite l’ausilio del microscopio ottico a luce polarizzata.

Evaluation of the real nutritional value of processed food to improve their effect on health and increase their sustainability

Cured meats and dairy products are criticized for their salt content and synthetic additives. This has led to the development of strategies to reduce and replace these ingredients. Since the food matrix and technological processes can affect the bioaccessibility of nutrients, it is necessary to study their release during digestion to determine the real nutritional value of foods. In the first part of this PhD project, the impact on the nutritional quality of the reduction of sodium content and of the replacement of synthetic nitrates/nitrites with a combination of innovative formulations was evaluated in Parmigiano Reggiano Cheese and salami. For this purpose, an in vitro digestion model combined with different analytical techniques was used. The results showed that fatty acids and proteins release increased over time during digestion. At the end of digestion, the innovative formulation/processing did not negatively affect fatty acids release and protein hydrolysis, and led to the formation of bioactive peptides. The excessive intake of sugars is correlated with metabolic diseases. After the intestinal uptake, their release in the blood stream depends on their metabolic fate within the enterocyte. In the second part of this PhD project, the absorption and metabolism of glucose, fructose and sucrose was evaluated using intestinal cell line. A faster absorption of fructose than glucose was observed, and a different modulation of the synthesis/transport of other metabolites by monosaccharides was shown. Intestinal cells were also used to verify the stability and intestinal uptake of vitamins (A and D3) delivered to cells through two vehicles. It was shown that the presence of lipids protected the vitamin from external factors such as light, heat and oxygen, and improved their bioavailability Overall, the results obtained in this PhD project confirmed that considering only the chemical composition of foods is not sufficient to determine their nutritional value.

Development of processes for the valorization of lignocellulosic biomass based on renewable energies

The world grapples with climate change from fossil fuel reliance, prompting Europe to pivot to renewable energy. Among renewables, biomass is a bioenergy and bio-carbon source, used to create high-value biomolecules, replacing fossil-based products. Alkyl levulinates, derived from biomass, hold promise as bio-additives and biofuels, especially via acid solvolysis of hexose sugars, necessitating further exploration. Alkyl levulinate's potential extends to converting into γ-valerolactone (GVL), a bio-solvent produced via hydrogenation with molecular-hydrogen. Hydrogen, a key reagent and energy carrier, aids renewable energy integration. This thesis delves into a biorefinery system study, aligning with sustainability goals, integrating biomass valorization, energy production, and hydrogen generation. It investigates optimizing technologies for butyl levulinate production and subsequent GVL hydrogenation. Sustainability remains pivotal, reflecting the global shift towards renewable and carbon bio-resources. The research initially focuses on experimenting with the optimal technology for producing butyl levulinate from biomass-derived hexose fructose. It examines the solvolysis process, investigating optimal conditions, kinetic modeling, and the impact of solvents on fructose conversion. The subsequent part concentrates on the technological aspect of hydrogenating butyl levulinate into GVL. It includes conceptual design, simulation, and optimization of the fructose-to-GVL process scheme based on process intensification. In the final part, the study applies the process to a real case study in Normandy, France, adapting it to local biomass availability and wind energy. It defines a methodology for designing and integrating the energy-supply system, evaluating different scenarios. Sustainability assessment using economic, environmental, and social indicators culminates in an overall sustainability index, indicating scenarios integrating the GVL biorefinery system with wind power and hydrogen energy storage as promising due to high profitability and reduced environmental impact. Sensitivity analyses validate the methodology's reliability, potentially extending to other technological systems.

Tectonics of the wedge-top Epiligurian basins and implications for the syn-to-post orogenic evolution of the Northern Apennines fold-and-thrust belt (Italy)

This thesis has the aim to give an overview about the tectonic history of the Epiligurian units, which crop out in the axial portion of the Northern Apennines fold-and-thrust belt, from a structural and thermal point of view, through a multiscalar and multitecnique approach. I focused on a key example of Epiligurian wedge-top basin, (Marzabotto Basin) proceeding from macro-to-microscale approach. The study started from a remote sensing analysis of the lineaments and morphostructures which affected the study area to obtain the regional faulting pattern and an overview about the main tectonic structures, used as basis for the structural investigation at the mesoscale. On the basis of this, it was possible to reconstruct the succession of tectonic events that affected the Marzabotto Basin, consisting in: i) two sets of thrusts indicating a NE-SW and NW-SE shortening of the sedimentary succession; ii) NE-SW-left lateral transtensional faults related to a strike-slip tectonic phase; iii) three main sets of extensional structures which cut and displace the previous thrusts. Normal faults are related to the post-orogenic evolution and have been dated with U-Th method, getting an age of Middle-Late Pleistocene. From a thermal point of view, apatite fission-tracks and (U-Th)/He analyses of detrital minerals and thermal modelling on the middle-upper Eocene siliciclastic deposits allowed me to better constrain the local exhumation history and correlate it with the large-scale tectonic evolution of the Northern Apennines. In particular, the Marzabotto Basin experienced a complex burial-exhumation history, consisting in two cooling cooling phases related to the growth of the Northern Apennines belt (Oligo-Miocene in age) and a later cooling which tracks the accretion in the orogenic wedge concomitant with rollback-driven extension (late Miocene-Pliocene in age). In conclusion it is possible to affirm that the study shed new light on poorly constrained elements of fold-and-thrust belt.