Widespread environmental contamination with Mycobacterium tuberculosis complex revealed by a molecular detection protocol

Environmental contamination with Mycobacterium tuberculosis complex (MTC) has been considered crucial for bovine tuberculosis persistence in multi-host-pathogen systems. However, MTC contamination has been difficult to detect due to methodological issues. In an attempt to overcome this limitation we developed an improved protocol for the detection of MTC DNA. MTC DNA concentration was estimated by the Most Probable Number (MPN) method. Making use of this protocol we showed that MTC contamination is widespread in different types of environmental samples from the Iberian Peninsula, which supports indirect transmission as a contributing mechanism for the maintenance of bovine tuberculosis in this multi-host-pathogen system. The proportion of MTC DNA positive samples was higher in the bovine tuberculosis-infected than in presumed negative area (0.32 and 0.18, respectively). Detection varied with the type of environmental sample and was more frequent in sediment from dams and less frequent in water also from dams (0.22 and 0.05, respectively). The proportion of MTC-positive samples was significantly higher in spring (p<0.001), but MTC DNA concentration per sample was higher in autumn and lower in summer. The average MTC DNA concentration in positive samples was 0.82 MPN/g (CI95 0.70-0.98 MPN/g). We were further able to amplify a DNA sequence specific of Mycobacterium bovis/caprae in 4 environmental samples from the bTB-infected area.

Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities

Dissertação de mestrado em Molecular Genetics

Phenanthroimidazole derivatives as fluorimetric chemosensors in aqueous medium

In recent years the research of sensors with good sensitivity and good selectivity in aqueous medium has been of great interest. Chemosensors soluble in aqueous media are very interesting, because of the importance in revealing a number of biological processes, disease states and environmental pollutions. 2,4,5-Triaryl-imidazoles are versatile compounds with application in medicine, due to their biological activity, and materials sciences, for their interesting optical properties. These properties can be tuned by careful selection of substituents at positions 2, 4 and 5: replacement of the aryl group by a heterocyclic group results in larger π-conjugated systems with improved optical properties for application in nonlinear optics, OLEDs, DNA intercalators, and chemosensors. In this communication, we report the synthesis of new phenanthroimidazoles, substituted at position 2 with (hetero)aryl groups of different electronic character, in order to evaluate their photophysical properties and chemosensory ability. The new derivatives were characterized by the usual techniques and a detailed photophysical study was undertaken. The evaluation of the compounds as fluorimetric chemosensors was carried out by performing titrations in acetonitrile and acetonitrile/water in the presence of relevant organic and inorganic anions, and of alkaline, alkaline-earth and transition metal cations.

Electromagnetic fields and environmental noise: human health impacts in Serzedelo, Guimarães (Portugal)

The present paper investigates the risks that arise from exposure to noise from powerpoles and powerlines in Serzedelo, in the municipality of Guimarães, in Portugal. This research focused on four guiding questions: Can powerlines cause noise? Do powerlines cause discomfort? Do powerlines cause discomfort due to noise? And can powerlines effect human health? Two groups were the basis of the study: people that were exposed to electromagnetic waves and people that were not. the research pointed to the harmful influence of the presence of powerlines and high-voltage masts in residential areas and the damage to the cells in the human body. This type of environmental noise, which has the spectral content of a low frequency, typically tonal noise and a very high speed of propagation, is a complex source to explain in terms of the health profiles of the human population living in Serzedelo, located in an area that is densely occupied by high voltage powerlines and powerpole.

Using stated preference methods to assess environmental impacts of forest biomass power plants in Portugal

As a renewable energy source, the use of forest biomass for electricity generation is advantageous in comparison with fossil fuels, however the activity of forest biomass power plants causes adverse impacts, affecting particularly neighbouring communities. The main objective of this study is to estimate the effects of the activity of forest biomass power plants on the welfare of two groups of stakeholders, namely local residents and the general population and we apply two stated preference methods: contingent valuation and discrete choice experiments, respectively. The former method was applied to estimate the minimum compensation residents of neighbouring communities of two forest biomass power plants in Portugal would be willing to accept. The latter method was applied among the general population to estimate their willingness to pay to avoid specific environmental impacts. The results show that the presence of the selected facilities affects individuals’ well-being. On the other hand, in the discrete choice experiments conducted among the general population all impacts considered were significant determinants of respondents’ welfare levels. The results of this study stress the importance of performing an equity analysis of the welfare effects on different groups of stakeholders from the installation of forest biomass power plants, as their effects on welfare are location and impact specific. Policy makers should take into account the views of all stakeholders either directly or indirectly involved when deciding crucial issues regarding the sitting of new forest biomass power plants, in order to achieve an efficient and equitable outcome.

Effect of environmental ageing on the numerical response of FRP-strengthened masonry walls

Recent durability studies have shown the susceptibility of bond in fiber-reinforced polymer (FRP) strengthened masonry components to hygrothermal exposures. However, it is not clear how this local material degradation affects the global behavior of FRP-strengthened masonry structures. This study addresses this issue by numerically investigating the nonlinear behavior of FRP-masonry walls after aging in two different environmental conditions. A numerical modeling strategy is adopted and validated with existing experimental tests on FRP-strengthened masonry panels. The model, once validated, is used for modeling of four hypothetical FRP-strengthened masonry walls with different boundary conditions, strengthening schemes, and reinforcement ratios. The nonlinear behavior of the walls is then simulated before and after aging in two different environmental conditions. The degradation data are taken from previous accelerated aging tests. The changes in the failure mode and nonlinear response of the walls after aging are presented and discussed.

Comparative environmental life-cycle analysis of concretes using biomass and coal fly ashes as partial cement replacement material

Nowadays, the concrete production sector is challenged by attempts to minimize the usage of raw materials and energy consumption, as well as by environmental concerns. Therefore, it is necessary to choose better options, e.g. new technologies or materials with improved life-cycle performance. One solution for using resources in an efficient manner is to close the materials' loop through the recycling of materials that result either from the end-of-life of products or from being the by-product of an industrial process. It is well known that the production of Portland cement, one of the materials most used in the construction sector, has a significant contribution to the environmental impacts, mainly related with carbon dioxide emission. Therefore, the study and utilization of by-products or wastes usable as cement replacement in concrete can supply more sustainable options, provided that these type of concrete produced has same durability and equivalent quality properties as standard concrete. This work studied the environmental benefits of incorporating different percentages of two types of fly ashes that can be used in concrete as cement replacement. These ashes are waste products of power and heat production sectors using coal or biomass as fuels. The results showed that both ashes provide a benefit for the concrete production both in terms of environmental impact minimization and a better environmental performance through an increase in cement replacement. It is possible to verify that the incorporation of fly ashes is a sustainable option for cement substitution and a possible path to improve the environmental performance of the concrete industry.

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

(Un)suitability of the use of pH buffers in biological, biochemical and environmental studies and their interaction with metal ions - a review

The use of buffers to maintain the pH within a desired range is a very common practice in chemical, biochemical and biological studies. Among them, zwitterionic N-substituted aminosulfonic acids, usually known as Good's buffers, although widely used, can complex metals and interact with biological systems. The present work reviews, discusses and updates the metal complexation characteristics of thirty one commercially available buffers. In addition, their impact on biological systems is also presented. The influences of these buffers on the results obtained in biological, biochemical and environmental studies, with special focus on their interaction with metal ions, are highlighted and critically reviewed. Using chemical speciation simulations, based on the current knowledge of the metal-buffer stability constants, a proposal of the most adequate buffer to employ for a given metal ion is presented.

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.

Spatio-temporal modelling of environmental data

Programa Doutoral em Matemática e Aplicações.

Extreme value Birnbaum-Saunders regression models applied to environmental data

Extreme value models are widely used in different areas. The Birnbaum–Saunders distribution is receiving considerable attention due to its physical arguments and its good properties. We propose a methodology based on extreme value Birnbaum–Saunders regression models, which includes model formulation, estimation, inference and checking. We further conduct a simulation study for evaluating its performance. A statistical analysis with real-world extreme value environmental data using the methodology is provided as illustration.

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.

Microscopy- or DNA-based analyses: Which methodology gives a truer picture of stream-dwelling decomposer fungal diversity?

We assessed aquatic hyphomycete diversity in autumn and spring on oak leaves decomposing in five streams along a gradient of eutrophication in the Northwest of Portugal. Diversity was assessed through microscopy-based (identification by spore morphology) and DNA-based techniques (Denaturing Gradient Gel Electrophoresis and 454 pyrosequencing). Pyrosequencing revealed five times greater diversity than DGGE. About 21% of all aquatic hyphomycete species were exclusively detected by pyrosequencing and 26% exclusively by spore identification. In some streams, more than half of the recorded species would have remained undetected if we had relied only on spore identification. Nevertheless, in spring aquatic hyphomycete diversity was higher based on spore identification, probably because many species occurring in this season are not yet connected to ITS barcodes in genetic databases. Pyrosequencing was a powerful tool for revealing aquatic hyphomycete diversity on decomposing plant litter in streams and we strongly encourage researchers to continue the effort in barcoding fungal species.

Polymer electrolyte based on DNA and N,N,N-trimethyl-N-(2-hydroxyethyl)ammonium bis(trifluoromethylsulfonyl)imide

Combining ionic liquids (ILs) with polymers offers the prospect of new applications, where they surpass the performance of conventional media, such as organic solvents, giving advantages in terms of improved safety and a higher operating temperature range. In this work we have investigated the morphology, thermal and electrochemical properties of polymer electrolytes prepared through the addition of con- trolled quantities of the cholinium based IL N,N,N-trimethyl-N-(2-hydroxyethyl)ammonium bis(trifluo- romethylsulfonyl)imide ([N1 1 1 2(OH)] [NTf2]) to a deoxyribonucleic acid (DNA) host network. These novel IL-based electrolytes have been analyzed aiming at applications in electrochemical devices. An optimized sample showed good thermal stability up to 155 °C and a wide electrochemical window of ~3.5 V. The highest conductivity was registered for the DNA[N1 1 1 2(OH)][NTf2] (1:1) (2.82 × 10-5 and 1.09 × 10-3 S cm-1 at 30 and 100 °C, respectively).