Valorization of grape pomace through hot compressed water extraction/hydrolysis

The world energy consumption is expected to increase strongly in coming years, because of the emerging economies. Biomass is the only renewable carbon resource that is abundant enough to be used as a source of energy Grape pomace is one of the most abundant agro-industrial residues in the world, being a good biomass resource. The aim of this work is the valorization of grape pomace from white grapes (WWGP) and from red grapes (RWGP), through the extraction of phenolic compounds with antioxidant activity, as well as through the extraction/hydrolysis of carbohydrates, using subcritical water, or hot compressed water (HCW). The main focus of this work is the optimization of the process for WWGP, while for RWGP only one set of parameters were tested. The temperatures used were 170, 190 and 210 °C for WWGP, and 180 °C for RWGP. The water flow rates were 5 and 10 mL/min, and the pressure was always kept at 100 bar. Before performing HCW assays, both residues were characterized, revealing that WWGP is very rich in free sugars (around 40%) essentially glucose and fructose, while RWGP has higher contents of structural sugars, lignin, lipids and protein. For WWGP the best results were achieved at 210 °C and 10 mL/min: higher yield in water soluble compounds (69 wt.%), phenolics extraction (26.2 mg/g) and carbohydrates recovery (49.3 wt.% relative to the existing 57.8%). For RWGP the conditions were not optimized (180 °C and 5 mL/min), and the values of the yield in water soluble compounds (25 wt.%), phenolics extraction (19.5 mg/g) and carbohydrates recovery (11.4 wt.% relative to the existing 33.5%) were much lower. The antioxidant activity of the HCW extracts from each assay was determined, the best result being obtained for WWGP, namely for extracts obtained at 210 °C (EC50=20.8 μg/mL; EC50 = half maximum effective concentration; EC50 = 22.1 μg/mL for RWGP, at 180 ºC).

Semantic relations extraction from unstructured information for domain ontologies enrichment

Based in internet growth, through semantic web, together with communication speed improvement and fast development of storage device sizes, data and information volume rises considerably every day. Because of this, in the last few years there has been a growing interest in structures for formal representation with suitable characteristics, such as the possibility to organize data and information, as well as the reuse of its contents aimed for the generation of new knowledge. Controlled Vocabulary, specifically Ontologies, present themselves in the lead as one of such structures of representation with high potential. Not only allow for data representation, as well as the reuse of such data for knowledge extraction, coupled with its subsequent storage through not so complex formalisms. However, for the purpose of assuring that ontology knowledge is always up to date, they need maintenance. Ontology Learning is an area which studies the details of update and maintenance of ontologies. It is worth noting that relevant literature already presents first results on automatic maintenance of ontologies, but still in a very early stage. Human-based processes are still the current way to update and maintain an ontology, which turns this into a cumbersome task. The generation of new knowledge aimed for ontology growth can be done based in Data Mining techniques, which is an area that studies techniques for data processing, pattern discovery and knowledge extraction in IT systems. This work aims at proposing a novel semi-automatic method for knowledge extraction from unstructured data sources, using Data Mining techniques, namely through pattern discovery, focused in improving the precision of concept and its semantic relations present in an ontology. In order to verify the applicability of the proposed method, a proof of concept was developed, presenting its results, which were applied in building and construction sector.

An agent based architecture to support monitoring in plug and produce manufacturing systems using knowledge extraction

In recent years a set of production paradigms were proposed in order to capacitate manufacturers to meet the new market requirements, such as the shift in demand for highly customized products resulting in a shorter product life cycle, rather than the traditional mass production standardized consumables. These new paradigms advocate solutions capable of facing these requirements, empowering manufacturing systems with a high capacity to adapt along with elevated flexibility and robustness in order to deal with disturbances, like unexpected orders or malfunctions. Evolvable Production Systems propose a solution based on the usage of modularity and self-organization with a fine granularity level, supporting pluggability and in this way allowing companies to add and/or remove components during execution without any extra re-programming effort. However, current monitoring software was not designed to fully support these characteristics, being commonly based on centralized SCADA systems, incapable of re-adapting during execution to the unexpected plugging/unplugging of devices nor changes in the entire system’s topology. Considering these aspects, the work developed for this thesis encompasses a fully distributed agent-based architecture, capable of performing knowledge extraction at different levels of abstraction without sacrificing the capacity to add and/or remove monitoring entities, responsible for data extraction and analysis, during runtime.

Microsatellite instability in solitary and sporadic gastric cancer

Recently, the presence of microsatellite instability (MSI) has been reported in gastric cancer and associated with older age of presentation, distal tumor location, early disease staging, and better overall prognosis. Different characteristics in presentation and in tumor behavior may be explained by different genetic alterations during carcinogenesis of gastric cancer. Identification of specific genetic pathways in gastric cancer may have direct impact on prognosis and selection of treatment strategies. PATIENTS AND METHODS: All 24 patients were treated by radical surgery. Fragments of normal and tumor tissues were extracted from the specimen and stored at -80ºC before DNA purification and extraction. PCR amplification utilizing microsatellite markers was performed. Tumors presenting PCR products of abnormal sizes were considered positive for microsatellite instability (MSI+). RESULTS: Five patients (21%) had tumors that were MSI+ in at least 1 marker. In the group of patients with Lauren's intestinal-type gastric carcinoma, 3 had tumors that were MSI+ (23%), while in the group of diffuse-type gastric cancer, 2 patients had tumors that were MSI+ (19%). The mean age of presentation and the male:female ratio was similar in both groups. Tumors that were MSI+ were more frequently located in proximal portion of the stomach compared to microsatellite-stable (MSS) tumors (40% vs. 16%). Although there was a trend of patients with MSI+ tumors towards a proximal gastric tumor location, early staging, and negative lymph node metastasis, there was no statistical significance compared to those with MSS tumors (P >.1). Comparison of overall and disease-free survival between gastric tumors that were MSI+ and those that were MSS found no statistically significant differences (P >.1). CONCLUSIONS: Microsatellite instability is a frequent event in gastric carcinogenesis and shows a trend towards distinct clinical and pathological characteristics of gastric cancer.

Human identification and analysis of DNA in bones

The introduction of molecular biology techniques, especially of DNA analysis, for human identification is a recent advance in legal medicine. Substantial effort has continuously been made in an attempt to identify cadavers and human remains after wars, socio-political problems and mass disasters. In addition, because of the social dynamics of large cities, there are always cases of missing people, as well as unidentified cadavers and human remains that are found. In the last few years, there has also been an increase in requests for exhumation of human remains in order to determine genetic relationships in civil suits and court action. The authors provide an extensive review of the literature regarding the use of this new methodology for human identification of ancient or recent bones.

A descoberta da Dupla Hélice do DNA: contributo para possíveis narrativas

Até ao final dos anos 40, o DNA não era reconhecido como portador da informação genética. Era uma molécula demasiado simples, difícil de isolar e incompatível com os métodos de análise da química orgânica e da biologia. Quando alguns cientistas começam a acreditar na importância do DNA, percebem que são incapazes, tecnicamente, de determinar a sua estrutura. É nesse espírito que James Watson vai para a Europa e, na primavera de 1951, ao assistir à conferência de Maurice Wilkins, da King’s College, onde vê uma fotografia do padrão de difração de raios X, percebe que será esta a técnica chave para a determinação da estrutura do DNA e, subsequentemente, dos segredos da vida. É este o início de uma das possíveis narrativas sobre uma das principais descobertas científicas do séc. XX que muitas vezes se reduz a: “A dupla hélice do DNA foi descoberta em 1953 por Watson e Crick”. Esta dissertação propõe-se a demonstrar que, apesar de em termos estritos, se tratar de uma afirmação verdadeira, não é suficiente para garantir uma experiência pedagógica significativa, nem fazer jus ao que é o funcionamento da ciência, com todas as implicações humanas, contextuais, éticas, consequências e impacto.

Engineering of fatty acid production and secretion in Saccharomyces cerevisiae

Tese de Doutoramento em Ciências - Especialidade em Biologia

Hair coloration by gene regulation: fact or fiction?

The unravelling of hair pigmentation genetics and robust delivery systems to the hair follicle (HF) will allow the development of a new class of colouring products. The challenge will be changing hair colour from inside out by safely regulating the activity of target genes through the specific delivery of synthetic/natural compounds, proteins, genes, or small RNAs.

Development of computational tools for the integrated analysis of DNA microarray data with applications in cancer research

The MAP-i Doctoral Program of the Universities of Minho, Aveiro and Porto

The effects of solvent composition on the affinity of a peptide towards hair keratin: experimental and molecular dynamics data

The study of the interaction between hair filaments and formulations or peptides is of utmost importance in fields like cosmetic research. Keratin intermediate filaments structure is not fully described, limiting the molecular dynamics (MD) studies in this field although its high potential to improve the area. We developed a computational model of a truncated protofibril, simulated its behavior in alcoholic based formulations and with one peptide. The simulations showed a strong interaction between the benzyl alcohol molecules of the formulations and the model, leading to the disorganization of the keratin chains, which regress with the removal of the alcohol molecules. This behavior can explain the increase of peptide uptake in hair shafts evidenced in fluorescence microscopy pictures. The model developed is valid to computationally reproduce the interaction between hair and alcoholic formulations and provide a robust base for new MD studies about hair properties. It is shown that the MD simulations can improve hair cosmetic research, improving the uptake of a compound of interest.

Integrating data from heterogeneous DNA microarray platforms

DNA microarrays are one of the most used technologies for gene expression measurement. However, there are several distinct microarray platforms, from different manufacturers, each with its own measurement protocol, resulting in data that can hardly be compared or directly integrated. Data integration from multiple sources aims to improve the assertiveness of statistical tests, reducing the data dimensionality problem. The integration of heterogeneous DNA microarray platforms comprehends a set of tasks that range from the re-annotation of the features used on gene expression, to data normalization and batch effect elimination. In this work, a complete methodology for gene expression data integration and application is proposed, which comprehends a transcript-based re-annotation process and several methods for batch effect attenuation. The integrated data will be used to select the best feature set and learning algorithm for a brain tumor classification case study. The integration will consider data from heterogeneous Agilent and Affymetrix platforms, collected from public gene expression databases, such as The Cancer Genome Atlas and Gene Expression Omnibus.

High levels of Mercury and Lead detected by hair analysis in two Venezuelan environments

Mercury and Lead concentrations obtained by ICP-OAS analysis of human hair from riverside communities along the Orinoco river in the Amazon state (Venezuela) were compared with those from Caracas, Venezuela. Taking into account the characteristics of these two environments and the values of the average concentrations of Mercury and Lead, baselines were established suggesting that gold mining activity near the Orinoco river is responsible for the high levels of Mercury in hair from the Amazon state, whereas automobile activity is responsible for high levels of Lead in hair in Caracas.

Mercury and methylmercury concentration assessment in children's hair from Manaus, Amazonas state, Brazil

The present study evaluated Hg and MeHg content in hair samples of 201 children 2 to 7 years old, living in six neighborhoods of the city of Manaus, Amazonas State, Brazil. In general, the total Hg and MeHg median ranges in hair were similar (0.91 to 1.71 mg kg-1) except for the São Jose neighborhood, which was lower (0.16 mg kg-1). De spite the fact that the Manaus population consumes fish as part of the normal dietary intake, the Hg hair levels were below the level for an adult population not exposed to mercury (2.0 mg kg-1). These data were compared to demographic, socioeconomic information and eating habits of the families that took part in the study. The results were also compared to other published data from the Amazon region, other regions of Brazil and other countries. Future studies to set Hg and MeHg levels in hair of children in Brazil should take into account and assess the diversity of the country, mainly in terms of eating habits, socio-economic and cultural aspects.

Clinical characteristics of women diagnosed with carcinoma who tested positive for cervical and anal high-risk human papillomavirus DNA and E6 RNA

High-risk human papillomavirus (hrHPV) is an essential cause of cervical carcinoma and is also strongly related to anal cancer development. The hrHPV E6 oncoprotein plays a major role in carcinogenesis. We aimed to evaluate the frequency of hrHPV DNA and E6 oncoprotein in the anuses of women with cervical carcinoma. We analyzed 117 women with cervical cancer and 103 controls for hrHPV and the E6 oncogene. Positive test results for a cervical carcinoma included 66.7 % with hrHPV-16 and 7.7 % with hrHPV-18. One case tested positive for both HPV variants (0.9 %). The samples from the anal canal were positive for HPV-16 in 59.8 % of the cases. Simultaneous presence of HPV in the cervix and anal canal was found in 53.8 % of the cases. Regarding expression of E6 RNA, positivity for HPV-16 in the anal canal was found in 21.2 % of the cases, positivity for HPV-16 in the cervix was found in 75.0 %, and positivity for HPV-18 in the cervix was found in 1.9 %. E6 expression in both the cervix and anal canal was found in 19.2 % of the cases. In the controls, 1 % tested positive for HPV-16 and 0 % for HPV-18. Anal samples from the controls showed a hrHPV frequency of 4.9 % (only HPV16). The presence of hrHPV in the anal canal of women with cervical cancer was detected at a high frequency. We also detected E6 RNA expression in the anal canal of women with cervical cancer, suggesting that these women are at risk for anal hrHPV infection.

Enzymatic phosphorylation of hair keratin enhances fast adsorption of cationic moieties

The current study describes the in vitro phosphorylation of a human hair keratin, using protein kinase for the first time. Phosphorylation of keratin was demonstrated by 31P NMR (Nuclear Magnetic Resonance) and Diffuse Reflectance Infrared Fourier Transform (DRIFT) techniques. Phosphorylation induced a 2.5 fold increase of adsorption capacity in the first 10 minutes for cationic moiety like Methylene Blue (MB). Thorough description of MB adsorption process was performed by several isothermal models. Reconstructed fluorescent microscopy images depict distinct amounts of dye bound to the differently treated hair. The results of this work suggest that the enzymatic phosphorylation of keratins might have significant implications in hair shampooing and conditioning, where short application times of cationic components are of prime importance.