Assessing ecological impacts of shrimp and sewage effluent: Biological indicators with standard water quality analyses

Despite evidence linking shrimp farming to several cases of environmental degradation, there remains a lack of ecologically meaningful information about the impacts of effluent on receiving waters. The aim of this study was to determine the biological impact of shrimp farm effluent, and to compare and distinguish its impacts from treated sewage effluent. Analyses included standard water quality/sediment parameters, as well as biological indicators including tissue nitrogen (N) content, stable isotope ratio of nitrogen (delta N-15) and amino acid composition of inhabitant seagrasses, mangroves and macroalgae. The study area consisted of two tidal creeks, one receiving effluent from a sewage treatment plant and the other from an intensive shrimp farm. The creeks discharged into the western side of Moreton Bay, a sub-tropical coastal embayment on the east coast of Australia. Characterization of water quality revealed significant differences between the creeks, and with unimpacted eastern Moreton Bay. The sewage creek had higher concentrations of dissolved nutrients (predominantly NO3-/NO2- and PO43-, compared to NH4+ in the shrimp creek). In contrast, the shrimp creek was more turbid and had higher phytoplankton productivity. Beyond 750 m from the creek mouths, water quality parameters were indistinguishable from eastern Moreton Bay values. Biological indicators detected significant impacts up to 4 km beyond the creek mouths (reference site). Elevated plant delta N-15 values ranged from 10.4-19.6 parts per thousand at the site of sewage discharge to 2.9-4.5 parts per thousand at the reference site. The free amino acid concentration and composition of seagrass and macroalgae was used to distinguish between the uptake of sewage and shrimp derived N. Proline (seagrass) and serine (macroalgae) were high in sewage impacted plants and glutamine (seagrass) and alanine (macroalgae) were high in plants impacted by shrimp effluent. The delta N-15 isotopic signatures and free amino acid composition of inhabitant flora indicated that sewage N extended further from the creek mouths than shrimp N. The combination of physical/chemical and biological indicators used in this study was effective in distinguishing the composition and subsequent impacts of aquaculture and sewage effluent on the receiving waters. (C) 2001 Academic Press.

Postharvest quality of cocona (Solanum sessiliflorum Dunal) stored under ambient condition

Cocona (Solanum sessiliflorum Dunal) is an important genetic resource that has been traditionally used for a variety of purposes, including food, medical and cosmetics applications. The objective of this study was evaluated the quality and the period of postharvest shelf life of cocona 'Mosquet", through the physical, chemical and physiological characterization of fruits stored under the ambient conditions. Physiologically mature fruits were harvested from an orchard, washed with tap water and soaked in a solution of the fungicide Prochloraz (49.5 g/100 L of water) for 5 minutes. After air drying, the fruits were packed in plastic containers and stored at 24 ± 2 ºC and relative humidity 60 ± 5% for 15 days. The fruits developed a respiratory climacteric respiratory patern and remained fit for consumption up to day 6 of storage, that is, without visual symptoms of loss of water and firmness. At this stage, the fruits showed firmness of 117,42 kPa, soluble solids of 6.62º Brix and citric acid of 1.22 %.

RadiaLE: A framework for designing and assessing link quality estimators in wireless sensor networks

Stringent cost and energy constraints impose the use of low-cost and low-power radio transceivers in large-scale wireless sensor networks (WSNs). This fact, together with the harsh characteristics of the physical environment, requires a rigorous WSN design. Mechanisms for WSN deployment and topology control, MAC and routing, resource and mobility management, greatly depend on reliable link quality estimators (LQEs). This paper describes the RadiaLE framework, which enables the experimental assessment, design and optimization of LQEs. RadiaLE comprises (i) the hardware components of the WSN testbed and (ii) a software tool for setting-up and controlling the experiments, automating link measurements gathering through packets-statistics collection, and analyzing the collected data, allowing for LQEs evaluation. We also propose a methodology that allows (i) to properly set different types of links and different types of traffic, (ii) to collect rich link measurements, and (iii) to validate LQEs using a holistic and unified approach. To demonstrate the validity and usefulness of RadiaLE, we present two case studies: the characterization of low-power links and a comparison between six representative LQEs. We also extend the second study for evaluating the accuracy of the TOSSIM 2 channel model.

Optimization of River Water Quality Surveys by Multivariate Analysis of Physicochemical, Bacteriological and Ecotoxicological Data

This study aims to optimize the water quality monitoring of a polluted watercourse (Leça River, Portugal) through the principal component analysis (PCA) and cluster analysis (CA). These statistical methodologies were applied to physicochemical, bacteriological and ecotoxicological data (with the marine bacterium Vibrio fischeri and the green alga Chlorella vulgaris) obtained with the analysis of water samples monthly collected at seven monitoring sites and during five campaigns (February, May, June, August, and September 2006). The results of some variables were assigned to water quality classes according to national guidelines. Chemical and bacteriological quality data led to classify Leça River water quality as “bad” or “very bad”. PCA and CA identified monitoring sites with similar pollution pattern, giving to site 1 (located in the upstream stretch of the river) a distinct feature from all other sampling sites downstream. Ecotoxicity results corroborated this classification thus revealing differences in space and time. The present study includes not only physical, chemical and bacteriological but also ecotoxicological parameters, which broadens new perspectives in river water characterization. Moreover, the application of PCA and CA is very useful to optimize water quality monitoring networks, defining the minimum number of sites and their location. Thus, these tools can support appropriate management decisions.

Commercial squids: Characterization, assessment of potential health benefits/risks and discrimination based on mineral, lipid and vitamin E concentrations

The most consumed squid species worldwide were characterized regarding their concentrations of minerals, fatty acids, cholesterol and vitamin E. Interspecific comparisons were assessed among species and geographical origin. The health benefits derived from squid consumption were assessed based on daily minerals intake and on nutritional lipid quality indexes. Squids contribute significantly to daily intake of several macro (Na, K, Mg and P) and micronutrients (Cu, Zn and Ni). Despite their low fat concentration, they are rich in long-chain omega-3 fatty acids, particularly docosahexaenoic (DHA) and eicosapentanoic (EPA) acids, with highly favorable ω-3/ω-6 ratios (from 5.7 to 17.7), reducing the significance of their high cholesterol concentration (140–549 mg/100 g ww). Assessment of potential health risks based on minerals intake, non-carcinogenic and carcinogenic risks indicated that Loligo gahi (from Atlantic Ocean), Loligo opalescens (from Pacific Ocean) and Loligo duvaucelii (from Indic Ocean) should be eaten with moderation due to the high concentrations of Cu and/or Cd. Canonical discriminant analysis identified the major fatty acids (C14:0, C18:0, C18:1, C18:3ω-3, C20:4ω-6 and C22:5ω-6), P, K, Cu and vitamin E as chemical discriminators for the selected species. These elements and compounds exhibited the potential to prove authenticity of the commercially relevant squid species.

From the Bay of Biscay to the High Atlas: completing the anisotropic characterization of the upper mantle beneath the westernmost Mediterranean region

The knowledge of the anisotropic properties beneath the Iberian Peninsula and Northern Morocco has been dramatically improved since late 2007 with the analysis of the data provided by the dense TopoIberia broadband seismic network, the increasing number of permanent stations operating in Morocco, Portugal and Spain, and the contribution of smaller scale/higher resolution experiments. Results from the two first TopoIberia deployments have evidenced a spectacular rotation of the fast polarization direction (FPD) along the Gibraltar Arc, interpreted as an evidence of mantle flow deflected around the high velocity slab beneath the Alboran Sea, and a rather uniform N100 degrees E FPD beneath the central Iberian Variscan Massif, consistent with global mantle flow models taking into account contributions of surface plate motion, density variations and net lithosphere rotation. The results from the last Iberarray deployment presented here, covering the northern part of the Iberian Peninsula, also show a rather uniform FPD orientation close to N100 degrees E, thus confirming the previous interpretation globally relating the anisotropic parameters to the LPO of mantle minerals generated by mantle flow at asthenospheric depths. However, the degree of anisotropy varies significantly, from delay time values of around 0.5 s beneath NW Iberia to values reaching 2.0 sin its NE comer. The anisotropic parameters retrieved from single events providing high quality data also show significant differences for stations located in the Variscan units of NW Iberia, suggesting that the region includes multiple anisotropic layers or complex anisotropy systems. These results allow to complete the map of the anisotropic properties of the westernmost Mediterranean region, which can now be considered as one of best constrained regions worldwide, with more than 300 sites investigated over an area extending from the Bay of Biscay to the Sahara platform. (C) 2015 Elsevier B.V. All rights reserved.

Functional and structural characterization of the RNase II-family of enzymes

Dissertation presented to obtain a Doctoral Degree in Biology by Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

Reliable link quality estimation in low-power wireless networks and its impact on tree-routing

Radio link quality estimation is essential for protocols and mechanisms such as routing, mobility management and localization, particularly for low-power wireless networks such as wireless sensor networks. Commodity Link Quality Estimators (LQEs), e.g. PRR, RNP, ETX, four-bit and RSSI, can only provide a partial characterization of links as they ignore several link properties such as channel quality and stability. In this paper, we propose F-LQE (Fuzzy Link Quality Estimator, a holistic metric that estimates link quality on the basis of four link quality properties—packet delivery, asymmetry, stability, and channel quality—that are expressed and combined using Fuzzy Logic. We demonstrate through an extensive experimental analysis that F-LQE is more reliable than existing estimators (e.g., PRR, WMEWMA, ETX, RNP, and four-bit) as it provides a finer grain link classification. It is also more stable as it has lower coefficient of variation of link estimates. Importantly, we evaluate the impact of F-LQE on the performance of tree routing, specifically the CTP (Collection Tree Protocol). For this purpose, we adapted F-LQE to build a new routing metric for CTP, which we dubbed as F-LQE/RM. Extensive experimental results obtained with state-of-the-art widely used test-beds show that F-LQE/RM improves significantly CTP routing performance over four-bit (the default LQE of CTP) and ETX (another popular LQE). F-LQE/RM improves the end-to-end packet delivery by up to 16%, reduces the number of packet retransmissions by up to 32%, reduces the Hop count by up to 4%, and improves the topology stability by up to 47%.

Characterization of an antioxidant surfactant-free topical formulation containing Castanea sativa leaf extract

Context: Inclusion of antioxidants in topical formulations can contribute to minimize oxidative stress in the skin, which has been associated with photoaging, several dermatosis and cancer. Objective: A Castanea sativa leaf extract with established antioxidant activity was incorporated into a semisolid surfactant-free formulation. The objective of this study was to perform a comprehensive characterization of this formulation. Materials and methods: Physical, microbiological and functional stability were evaluated during 6 months storage at 20 °C and 40 °C. Microstructure elucidation (cryo-SEM), in vitro release and in vivo moisturizing effect (Corneometer® CM 825) were also assessed. Results and discussion: Minor changes were observed in the textural and rheological properties of the formulation when stored at 20 °C for 6 months and the antioxidant activity of the plant extract remained constant throughout the storage period. Microbiological quality was confirmed at the end of the study. Under accelerated conditions, higher modifications of the evaluated parameters were observed. Cryo-SEM analysis revealed the presence of oil droplets dispersed into a gelified external phase. The release rate of the antioxidant compounds (610 ± 70 µgh−0.5) followed Higuchi model. A significant in vivo moisturizing effect was demonstrated, that lasted at least 4 h after product’s application. Conclusion: The physical, functional and microbiological stability of the antioxidant formulation was established. Specific storage conditions should be recommended considering the influence of temperature on the stability. A skin hydration effect and good skin tolerance were also found which suggests that this preparation can be useful in the prevention or treatment of oxidative stress-mediated dysfunctions.

Ankylosing spondylitis: genomic and functional characterization of candidate genes and their repercussion in clinical practice

RESUMO: Introdução: A espondilite anquilosante (EA) é uma doença inflamatória crónica caracterizada pela inflamação das articulações sacroilíacas e da coluna. A anquilose progressiva motiva uma deterioração gradual da função física e da qualidade de vida. O diagnóstico e o tratamento precoces podem contribuir para um melhor prognóstico. Neste contexto, a identificação de biomarcadores, assume-se como sendo muito útil para a prática clínica e representa hoje um grande desafio para a comunidade científica. Objetivos: Este estudo teve como objetivos: 1 - caracterizar a EA em Portugal; 2 - investigar possíveis associações entre genes, MHC e não-MHC, com a suscetibilidade e as características fenotípicas da EA; 3 - identificar genes candidatos associados a EA através da tecnologia de microarray. Material e Métodos: Foram recrutados doentes com EA, de acordo com os critérios modificados de Nova Iorque, nas consultas de Reumatologia dos diferentes hospitais participantes. Colecionaram-se dados demográficos, clínicos e radiológicos e colhidas amostras de sangue periférico. Selecionaram-se de forma aleatória, doentes HLA-B27 positivos, os quais foram tipados em termos de HLA classe I e II por PCR-rSSOP. Os haplótipos HLA estendidos foram estimados pelo algoritmo Expectation Maximization com recurso ao software Arlequin v3.11. As variantes alélicas dos genes IL23R, ERAP1 e ANKH foram estudadas através de ensaios de discriminação alélica TaqMan. A análise de associação foi realizada utilizando testes da Cochrane-Armitage e de regressão linear, tal como implementado pelo PLINK, para variáveis qualitativas e quantitativas, respetivamente. O estudo de expressão génica foi realizado por Illumina HT-12 Whole-Genome Expression BeadChips. Os genes candidatos foram validados usando qPCR-based TaqMan Low Density Arrays (TLDAs). Resultados: Foram incluídos 369 doentes (62,3% do sexo masculino, com idade média de 45,4 ± 13,2 anos, duração média da doença de 11,4 ± 10,5 anos). No momento da avaliação, 49,9% tinham doença axial, 2,4% periférica, 40,9% mista e 7,1% entesopática. A uveíte anterior aguda (33,6%) foi a manifestação extra-articular mais comum. Foram positivos para o HLA-B27, 80,3% dos doentes. Os haplótipo A*02/B*27/Cw*02/DRB1*01/DQB1*05 parece conferir suscetibilidade para a EA, e o A*02/B*27/Cw*01/DRB1*08/DQB1*04 parece conferir proteção em termos de atividade, repercussão funcional e radiológica da doença. Três variantes (2 para IL23R e 1 para ERAP1) mostraram significativa associação com a doença, confirmando a associação destes genes com a EA na população Portuguesa. O mesmo não se verificou com as variantes estudadas do ANKH. Não se verificou associação entre as variantes génicas não-MHC e as manifestações clínicas da EA. Foi identificado um perfil de expressão génica para a EA, tendo sido validados catorze genes - alguns têm um papel bem documentado em termos de inflamação, outros no metabolismo da cartilagem e do osso. Conclusões: Foi estabelecido um perfil demográfico e clínico dos doentes com EA em Portugal. A identificação de variantes génicas e de um perfil de expressão contribuem para uma melhor compreensão da sua fisiopatologia e podem ser úteis para estabelecer modelos com relevância em termos de diagnóstico, prognóstico e orientação terapêutica dos doentes. -----------ABSTRACT: Background: Ankylosing Spondylitis (AS) is a chronic inflammatory disorder characterized by inflammation in the spine and sacroiliac joints leading to progressive joint ankylosis and in progressive deterioration of physical function and quality of life. An early diagnosis and early therapy may contribute to a better prognosis. The identification of biomarkers would be helpful and represents a great challenge for the scientific community. Objectives: The present study had the following aims: 1- to characterize the pattern of AS in Portuguese patients; 2- to investigate MHC and non-MHC gene associations with susceptibility and phenotypic features of AS and; 3- to identify candidate genes associated with AS by means of whole-genome microarray. Material and Methods: AS was defined in accordance to the modified New York criteria and AS cases were recruited from hospital outcares patient clinics. Demographic and clinical data were recorded and blood samples collected. A random group of HLA-B27 positive patients and controls were selected and typed for HLA class I and II by PCR-rSSOP. The extended HLA haplotypes were estimated by Expectation Maximization Algorithm using Arlequin v3.11 software. Genotyping of IL23R, ERAP1 and ANKH allelic variants was carried out with TaqMan allelic discrimination assays. Association analysis was performed using the Cochrane-Armitage and linear regression tests as implemented in PLINK, for dichotomous and quantitative variables, respectively. Gene expression profile was carried out using Illumina HT-12 Whole-Genome Expression BeadChips and candidate genes were validated using qPCR-based TaqMan Low Density Arrays (TLDAs). Results: A total of 369 patients (62.3% male; mean age 45.4±13.2 years; mean disease duration 11.4±10.5 years), were included. Regarding clinical disease pattern, at the time of assessment, 49.9% had axial disease, 2.4% peripheral disease, 40.9% mixed disease and 7.1% isolated enthesopathic disease. Acute anterior uveitis (33.6%) was the most common extra-articular manifestation. 80.3% of AS patients were HLA-B27 positive. The haplotype A*02/B*27/Cw*02/DRB1*01/DQB1*05 seems to confer susceptibility to AS, whereas A*02/B*27/Cw*01/DRB1*08/DQB1*04 seems to provide protection in terms of disease activity, functional and radiological repercussion. Three markers (two for IL23R and one for ERAP1) showed significant single-locus disease associations. Association of these genes with AS in the Portuguese population was confirmed, whereas ANKH markers studied did not show an association with AS. No association was seen between non-MHC genes and clinical manifestations of AS. A gene expression signature for AS was established; among the fourteen validated genes, a number of them have a well-documented inflammatory role or in modulation of cartilage and bone metabolism. Conclusions: A demographic and clinical profile of patients with AS in Portugal was established. Identification of genetic variants of target genes as well as gene expression signatures could provide a better understanding of AS pathophysiology and could be useful to establish models with relevance in terms of susceptibility, prognosis, and potential therapeutic guidance.

Quantification and characterization of the phenolic compounds of kenaf leaves

Dissertation for the Master Degree in Technology and Food Security

Development of an integrative approach for the characterization of ecological risk on marine transition ecosystems: the Sado Estuary as a case study

Estuaries and other transitional waters are complex ecosystems critically important as nursery and shelter areas for organisms. Also, humans depend on estuaries for multiple socio-economical activities such as urbanism, tourism, heavy industry, (taking advantage of shipping), fisheries and aquaculture, the development of which led to strong historical pressures, with emphasis on pollution. The degradation of estuarine environmental quality implies ecologic, economic and social prejudice, hence the importance of evaluating environmental quality through the identification of stressors and impacts. The Sado Estuary (SW Portugal) holds the characteristics of industrialized estuaries, which results in multiple adverse impacts. Still, it has recently been considered moderately contaminated. In fact, many studies were conducted in the past few years, albeit scattered due to the absence of true biomonitoring programmes. As such, there is a need to integrate the information, in order to obtain a holistic perspective of the area able to assist management and decision-making. As such, a geographical information system (GIS) was created based on sediment contamination and biomarker data collected from a decade-long time-series of publications. Four impacted and a reference areas were identified, characterized by distinct sediment contamination patterns related to different hot spots and diffuse sources of toxicants. The potential risk of sediment-bound toxicants was determined by contrasting the levels of pollutants with available sediment quality guidelines, followed by their integration through the Sediment Quality guideline Quotient (SQG-Q). The SQG-Q estimates per toxicant or class was then subjected to georreferencing and statistical analyses between the five distinct areas and seasons. Biomarker responses were integrated through the Biomarkers Consistency Indice and georreferenced as well through GIS. Overall, in spite of the multiple biological traits surveyed, the biomarker data (from several organisms) are accordant with sediment contamination. The most impacted areas were the shipyard area and adjacent industrial belt, followed by urban and agricultural grounds. It is evident that the estuary, although globally moderately impacted, is very heterogeneous and affected by a cocktail of contaminants, especially metals and polycyclic aromatic hydrocarbon. Although elements (like copper, zinc and even arsenic) may originate from the geology of the hydrographic basin of the Sado River, the majority of the remaining contaminants results from human activities. The present work revealed that the estuary should be divided into distinct biogeographic units, in order to implement effective measures to safeguard environmental quality.

Contributions towards smart cities : exploring block level census data for the characterization of change in Lisbon

The interest in using information to improve the quality of living in large urban areas and its governance efficiency has been around for decades. Nevertheless, the improvements in Information and Communications Technology has sparked a new dynamic in academic research, usually under the umbrella term of Smart Cities. This concept of Smart City can probably be translated, in a simplified version, into cities that are lived, managed and developed in an information-saturated environment. While it makes perfect sense and we can easily foresee the benefits of such a concept, presently there are still several significant challenges that need to be tackled before we can materialize this vision. In this work we aim at providing a small contribution in this direction, which maximizes the relevancy of the available information resources. One of the most detailed and geographically relevant information resource available, for the study of cities, is the census, more specifically the data available at block level (Subsecção Estatística). In this work, we use Self-Organizing Maps (SOM) and the variant Geo-SOM to explore the block level data from the Portuguese census of Lisbon city, for the years of 2001 and 2011. We focus on gauging change, proposing ways that allow the comparison of the two time periods, which have two different underlying geographical bases. We proceed with the analysis of the data using different SOM variants, aiming at producing a two-fold portrait: one, of the evolution of Lisbon during the first decade of the XXI century, another, of how the census dataset and SOM’s can be used to produce an informational framework for the study of cities.

Study of grapevine solute transporters involved in berry quality. A biochemical and molecular approach

Tese de Doutoramento em Biologia de Plantas

Structural and enzymatic characterization of ABgp46, a novel phage endolysin with broad anti-Gram-negative bacterial activity

The present study demonstrates the antibacterial potential of a phage endolysin against Gram-negative pathogens, particularly against multidrug resistant strains of Acinetobacter baumannii. We have cloned, heterologously expressed and characterized a novel endolysin (ABgp46) from Acinetobacter phage vb_AbaP_CEB1 and tested its antibacterial activity against several multidrug-resistant A. baumannii strains. LC-MS revealed that ABgp46 is an N-acetylmuramidase, that is also active over a broad pH range (4.0-10.0) and temperatures up to 50°C. Interestingly, ABgp46 has intrinsic and specific anti-A. baumannii activity, reducing multidrug resistant strains by up to 2 logs within 2 hours. By combining ABgp46 with several organic acids that act as outer membrane permeabilizing agents, it is possible to increase and broaden antibacterial activity to include other Gram-negative bacterial pathogens. In the presence of citric and malic acid, ABgp46 reduces A. baumannii below the detection limit (> 5 log) and more than 4 logs P. aeruginosa and Salmonella Typhimurium strains. Overall, this globular endolysin exhibits a broad and high activity against Gram-negative pathogens, that can be enhanced in presence of citric and malic acid, and be used in human and veterinary medicine.