Optimisation of an aptamer-biosensor to detect C-reactive protein

Dissertação de Mestrado, Engenharia Biológica, Faculdade de Engenharia de Recursos Naturais, Universidade do Algarve, 2009

Water framework directive implementation: intercalibration exercise for biological quality elements: a case study for the south coast of Portugal

This work summarises the Intercalibration Exercise (IE) required for the Common Implementation Strategy of the Water Framework Directive (WFD; 2000/60/EC) that was carried out in Portugal, and applied to a coastal region. The WFD aims to achieve good ec ological status for all waters in the European Community by 2015. The Ecological Status of a water body is determined us ing a range of Hydromorphological and Physico-Chemical Quality Elements as well Biological Quality Elements (BQE ). In coastal waters, the Biological Elements include Phytoplankton, Other Aquatic Flora and Benthic Inverteb rate Fauna. Good cooperation with the other Member States allowed the IE to proceed without a complete da ta set, and Portugal was ab le to intercalibrate and harmonise methods within the North Ea st Atlantic Geographica l Intercalibration Group for most of the BQE. The appropriate metrics and corre sponding methods were agreed under the framework of the RECITAL (Reference Conditions and Intercalibra tion) project, funded by the Port uguese Water Institu te, INAG. Some preliminary sampling was undertaken, but not su fficient to establish the Reference Conditions. The study area was a coastal lagoon in the southern part of Portugal. The focus was on the Phytoplankton Quality Element, but other BQE were also taken into account. Two sampli ng stations in Ria Formosa coastal lagoon were considered in this exercise: Ramalhete a nd Ponte. The metrics adopted by the Intercalibration Exercise groups were applied enabli ng the classification for the two sta tions of Good/High Status for the majority of the BQE parameters.

Study of transcripts and reactive oxygen species involved in the defence responses of Quercus suber against Phytophthora cinnamomi

The present work has the merit of exploring an insight into the activation of defence genes of Quercus suber during response to infection by Phytophthora cinnamomi. Thus, cDNA-AFLP methodology was used to identify gene fragments differentially present in the mRNA profiles of host cells of micropropagated Q. suber plantlets roots infected with zoospores of P. cinnamomi at different post challenge time points. Six candidate genes were selected based on their interesting cDNA-AFLP expression patterns and homology to genes known to play a role in defence. These six genes encode a cinnamyl alcohol dehydrogenase 2 (QsCAD2), a protein disulphide isomerase (QsPDI), a CC-NBS-LRR resistance protein (QsRPc), thaumatin-like protein (QsTLP), chitinase (QsCHI) and a 1,3-beta glucanase (QsGLU). The current work has been successful in evaluation of the expression of these genes by qRT-PCR. Data analysis revealed that transcript levels of QsRPc, QsCHI, QsCAD2 and QsPDI increased during the early hours of inoculation, while transcript profiles of thaumatin-like protein showed decreasing. No expression was detected for 1,3-beta-glucanase (QsGLU). Furthermore, the choice of suitable reference genes in any new experimental system is absolutely crucial in qRT-PCR; for this reason in this study and for the first time a set of potential reference genes were analyzed and validated for qRT-PCR normalization in the patho-system Phytophthora-Q. suber. Four candidate reference genes polimerase II (QsRPII), eukaryotic translation initiation factor 5A(QsEIF-5A), b-tubulin (QsTUB) and a medium subunit family protein of Clathrin adaptor complexes (QsCACs) were evaluated to determine the most stable internal references in Q. suber. Analysis of stability of genes was carried out using Genex software. Results indicated all these four potential reference genes assumed stable expression. Data analysis revealed that QsRPII and QsCACs were the two most stable genes, while genes QsTUB and QsEIF-5A were the third and the fourth most stable gene, respectively. In this study, a plasmid-based quantitative PCR method was developed to measure P. cinnamomi colonization during infection process of Q. suber. Plasmid-based detection of P. cinnamomi showed a gradual accumulation of the pathogen DNA in cork oak root tips up to 24 h post infection. The higher increase in P. cinnamomi/plasmid DNA ratio occurred between 18 and 24 h. One of the primary objectives of this research was to study the effect of cinnamomins (elicitins secreted by P. cinnamomin) on inducing defence mechanism against the pathogen, as recent histological and ultra-structural studies showed that P. cinnamomi was restricted to the outer cortex root fragments pre-treated with capsicien and cryptogein, suggesting that elicitins can stimulate plant defence reactions against P. cinnamomi. To complement these studies and to have a clear view of the nature of the interaction, the role of cinnamomins in the production of the oxidative burst [ROS and ROS scavenging enzymes such as superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD)] and in the defence responses was evaluated. Cork oak seedlings were pretreated with alpha-cinnamomin and then inoculated with P. cinnamomi mycelia. Results showed a significant higher production of reactive oxygen species (ROS) (H2O2 and O2•-) in elicitin and non-elicitin treated roots in interaction with P. cinnamomi in comparison to the corresponding control. The plant group inoculated with the pathogen after cinnamomin treatment showed an earlier increase in H2O2 production but this was lower as compared with that group inoculated with P. cinnamomi alone. Also, in elicitin pre-treated group generally, a lower level of O2•− production during infection was observed as compared with inoculated roots with P. cinnamomi alone without elicitin treatment. Furthermore, in this study, we evaluated activities of antioxidant enzymes upon challenge with P. cinnamomi, with and without pretreatment with alpha cinnamomin. Results indicated that the activities of defense enzymes POD, SOD and CAT increased after P. cinnamomi inoculation when compared with those in the control group. Also, in the group treated with alpha-cinnamomin followed by P. cinnamomi inoculation, a higher level of enzymatic activities was detected as compared with elicitin non-treated group, which suggest the protective effect of alpha-cinnamomin against the pathogen due to higher elevated levels of defense enzymes POD, SOD and CAT during the infection period. Furthermore, a sensitive qPCR method was applied to measure the pathogen biomass in elicited and non-elicited Q. suber roots challenged with P. cinnamomi to elucidate the effect of cinnamomins on the colonization of P. cinnamomi. Plasmid-based quantification of P. cinnamomi showed a significant decrease in accumulation of the pathogen DNA in cork oak roots after treatment with alpha and beta-cinnamomins which attest the role of cinnamomins in promoting defense responses in cork oak against P. cinnamomi invasion.

Joaquim Rodrigo:a contínua reinvenção da pintura

Tese de doutoramento, História (História da Arte), Universidade de Lisboa, Faculdade de Letras, 2014

Nuclear and mitochondrial control of the apoptosis machinery regulates neural stem cell fate

Tese de doutoramento, Farmácia (Bioquímica), Universidade de Lisboa, Faculdade de Farmácia, 2014

Caracterização da marcação imunohistoquímica da protein gene product 9.5 (PGP 9.5) em células astrocitárias

Tese de mestrado, Neurociências, Faculdade de Medicina, Universidade de Lisboa, 2015

Territories of scarcity and creativity: a critical view of informal settlements and emerging tactics under conditions of scarcity in Nairobi, Kenya and Quito, Ecuador

This thesis explores the processes through which scarcity is constructed in informal settlements and how conditions emerging within its limits gives way to particular socio-spatial phenomena and influence the emergence of self-organisation and creative strategies from a non-expert perspective. At the same time, this thesis deconstructs these emerging tactics (reactive and transformative) in a diagrammatic way to generate a critical study of their potential for socio-spatial change that goes beyond the everyday survival. Most people associate scarcity with “not having enough” of something, most usually of a material nature. In contrast, this paper is based on the premise that scarcity is a constructed condition, therefore exploring it beyond its immediate manifestation and illustrating its discursive, distributive and socio-material components. In this line, the research uses Assemblage Theory as both an approach and a tool for analysis. This approach allows the research to depart from everyday narratives of the residents, and gradually evolve into a multi-scalar, non-linear reading of scarcity, by following leads into different realms and unpacking a series of routine events to uncover their connections to wider processes and particular elements affecting the settlement and the city as a whole. For this purpose, the research is based on a qualitative, flexible and multi-sited methodology, using different case studies as testing grounds. Collected data stems from a 11-months ethnographic fieldwork in informal settlements in Ecuador and Kenya, analysing the socio-spatial practices and strategies deployed by the different actors producing the built environment and arising from everyday and latent experiences of scarcity. The thesis examines the multi-scalar nature of these strategies, including self-building and management tactics, the mobilisation of grassroots organisations, the innovative ways of collaborating deployed by different coalitions and the reformulation of urban development policies. As outcomes of the research, the thesis will show illustrative diagrams that allow a better understanding of, firstly, the construction of scarcity in the built environment beyond its immediate manifestation and secondly, the way that emerging tactics a) improve existing conditions of scarcity, b) reinforce the status quo or c) contribute to the worsening of the original condition. Therefore, this thesis aims to offer lessons with both practical and theoretical considerations, by firstly, giving an insight into the complexity and transcalar nature of the construction of scarcity in informal settlements; secondly, by illustrating how acute conditions related to scarcity gives birth to a plethora of particular phenomena shaping the territory, social relationships and processes; and thirdly, by identifying specific characteristics within the informal that might allow for new readings of the city and possibilities for socio-spatial change under conditions of scarcity.

Elements of a methodology to assess the alignment of core-values in collaborative networks

Collaborative networks are typically formed by heterogeneous and autonomous entities, and thus it is natural that each member has its own set of core-values. Since these values somehow drive the behaviour of the involved entities, the ability to quickly identify partners with compatible or common core-values represents an important element for the success of collaborative networks. However, tools to assess or measure the level of alignment of core-values are lacking. Since the concept of 'alignment' in this context is still ill-defined and shows a multifaceted nature, three perspectives are discussed. The first one uses a causal maps approach in order to capture, structure, and represent the influence relationships among core-values. This representation provides the basis to measure the alignment in terms of the structural similarity and influence among value systems. The second perspective considers the compatibility and incompatibility among core-values in order to define the alignment level. Under this perspective we propose a fuzzy inference system to estimate the alignment level, since this approach allows dealing with variables that are vaguely defined, and whose inter-relationships are difficult to define. Another advantage provided by this method is the possibility to incorporate expert human judgment in the definition of the alignment level. The last perspective uses a belief Bayesian network method, and was selected in order to assess the alignment level based on members' past behaviour. An example of application is presented where the details of each method are discussed.

Reactive power compensation by EPSO technique

This paper presents a methodology to address reactive power compensation using Evolutionary Particle Swarm Optimization (EPSO) technique programmed in the MATLAB environment. The main objective is to find the best operation point minimizing power losses with reactive power compensation, subjected to all operational constraints, namely full AC power flow equations, active and reactive power generation constraints. The methodology has been tested with the IEEE 14 bus test system demonstrating the ability and effectiveness of the proposed approach to handle the reactive power compensation problem.

Optimal dispatch with reactive power compensation by Genetic Algorithm

This paper presents a Unit Commitment model with reactive power compensation that has been solved by Genetic Algorithm (GA) optimization techniques. The GA has been developed a computational tools programmed/coded in MATLAB. The main objective is to find the best generations scheduling whose active power losses are minimal and the reactive power to be compensated, subjected to the power system technical constraints. Those are: full AC power flow equations, active and reactive power generation constraints. All constraints that have been represented in the objective function are weighted with a penalty factors. The IEEE 14-bus system has been used as test case to demonstrate the effectiveness of the proposed algorithm. Results and conclusions are dully drawn.

Fractional generalization of memristor and higher order elements

Fractional calculus generalizes integer order derivatives and integrals. Memristor systems generalize the notion of electrical elements. Both concepts were shown to model important classes of phenomena. This paper goes a step further by embedding both tools in a generalization considering complex-order objects. Two complex operators leading to real-valued results are proposed. The proposed class of models generate a broad universe of elements. Several combinations of values are tested and the corresponding dynamical behavior is analyzed.

Modeling of the lung impedance using a fractional order ladder network with constant phase elements

The self similar branching arrangement of the airways makes the respiratory system an ideal candidate for the application of fractional calculus theory. The fractal geometry is typically characterized by a recurrent structure. This study investigates the identification of a model for the respiratory tree by means of its electrical equivalent based on intrinsic morphology. Measurements were obtained from seven volunteers, in terms of their respiratory impedance by means of its complex representation for frequencies below 5 Hz. A parametric modeling is then applied to the complex valued data points. Since at low-frequency range the inertance is negligible, each airway branch is modeled by using gamma cell resistance and capacitance, the latter having a fractional-order constant phase element (CPE), which is identified from measurements. In addition, the complex impedance is also approximated by means of a model consisting of a lumped series resistance and a lumped fractional-order capacitance. The results reveal that both models characterize the data well, whereas the averaged CPE values are supraunitary and subunitary for the ladder network and the lumped model, respectively.

Serum trace elements in dysphagic gastrostomy candidates before endoscopic gastrostomy for long term enteral feeding

Background & aims - Patients who underwent endoscopic gastrostomy (PEG) present protein-energy malnutrition, but little is known about Trace Elements (TE), Zinc (Zn), Copper (Cu), Selenium (Se), Iron (Fe), Chromium (Cr). Our aim was the evaluation of serum TE in patients who underwent PEG and its relationship with serum proteins, BMI and nature of underlying disorder. Methods - A prospective observational study was performed collecting: patient's age, gender, underlying disorder, NRS-2002, BMI, serum albumin, transferrin and TE concentration. We used ferrozine colorimetric method for Fe; Inductively Coupled Plasma-Atomic Emission Spectroscopy for Zn/Cu; Furnace Atomic Absorption Spectroscopy for Se/Cr. The patients were divided into head and neck cancer (HNC) and neurological dysphagia (ND). Results - 146 patients (89 males), 21–95 years: HNC-56; ND-90. Low BMI in 78. Low values mostly for Zn (n = 122) and Fe (n = 69), but less for Se (n = 31), Cu (n = 16), Cr (n = 7); low albumin in 77, low transferrin in 94 and 66 with both proteins low. Significant differences between the groups of underlying disease only for Zn (t140.326 = −2,642, p < 0.01) and a correlation between proteins and TE respectively albumin and Zn (r = 0.197, p = 0.025), and albumin and Fe (r = 0.415, p = 0.000). Conclusions - When gastrostomy was performed, patients display low serum TE namely Zn, but also Fe, less striking regarding others TE. It was related with prolonged fasting, whatever the underlying disease. Low proteins were associated with low TE. Teams taking care of PEG-patients should use Zn supplementation and include other TE evaluation as part of the nutritional assessment of PEG candidates.

Nanoparticles based Permeable Reactive Barriers as an Eco-efficient Technology for nitrate remediation in soil and groundwater

The need to increase agricultural yield led, among others, to an increase in the consumption of nitrogen based fertilizers. As a consequence, there are excessive concentrations of nitrates, the most abundant of the reactive nitrogen (Nr) species, in several areas of the world. The demographic changes and projected population growth for the next decades, and the economic shifts which are already shaping the near future are powerful drivers for a further intensification in the use of fertilizers, with a predicted increase of the nitrogen loads in soils. Nitrate easily diffuses in the subsurface environments, portraying high mobility in soils. Moreover, the presence of high nitrate loads in water has the potential to cause an array of health dysfunctions, such as methemoglobinemia and several cancers. Permeable Reactive Barriers (PRB) placed strategically relatively to the nitrate source constitute an effective technology to tackle nitrate pollution. Ergo, PRB avoid various adverse impacts resulting from the displacement of reactive nitrogen downstream along water bodies. A four stages literature review was carried out in 34 databases. Initially, a set of pertinent key words were identified to perform the initial databases searches. Then, the synonyms of those initial key words were used to carry out a second set of databases searches. The third stage comprised the identification of other additional relevant terms from the research papers identified in the previous two stages. Again, databases searches were performed with this third set of key words. The final step consisted of the identification of relevant papers from the bibliography of the relevant papers identified in the previous three stages of the literature review process. The set of papers identified as relevant for in-depth analysis were assessed considering a set of relevant characterization variables.

Permeable Reactive Barriers using nanoparticles to remediate nitrate pollution

Nitrat e (NO3 - ) i s per vasi ve i n t he bi ospher e[ 1, 2]. Cont emporar y agri cult ural pr acti ces are a mong t he maj or ant hr opogeni c sources of r eacti ve nitrogen speci es, wher e nitrat ei s t he most abundant of t hese [ 2]. Excessi ve a mount s of r eacti ve nitrogen i n soil s and gr oundwat er ar e creati ng si gnifi cant t hr eat s t o hu man healt h and saf et y [ 3] as well as a host of undesirabl e environment al i mpact s [ 2]; it i s curr ently consi der ed t he second most r el evant environment al i ssue, aft er car bon di oxide e mi ssi ons. Nowadays, a mong t he most r el evant and pr omi si ng appr oaches t o r educe nitrat e concentrati on i n wat er, na mel y gr oundwat er, ar e denitrifi cati on- based pr ocesses [ 4]. Per meabl e r eacti ve barri ers ( PRB) have been pr oven eff ecti ve i n r educi ng vari ous cont ami nant s i n copi ous a mount s, parti cul arl y i n shall ow gr oundwat er [ 5]. However t he possi bl e added eff ecti veness of usi ng nanoparti cl es i n t hese structur es t o obt ai n nitrogen gas from nitrat es requires f urt her i nvesti gati on.