Integration of sediment contamination with multi–biomarker responses in a novel bioindicator candidate (Sepia officinalis) for risk assessment in impacted estuaries

Dissertação para obtenção do Grau de Mestre em Engenharia do Ambiente

The WHO Collaborating Centre for Research and Control of Schistosomiasis at Niamey, Niger

The Centre de Recherche sur les Méningites et les Schistosomes (CERMES) is a research institute depending on the Organisation de Coordination et de Coopération pour la lutte contre les Grandes Endémies - a West African Organization for Public Health - devoted to the studies on schistosomiasis and meningitis. The staff includes 32 persons with 11 scientists and one financial officer. The activities of the CERMES involving schistosomiasis concern three research units: (a) ecology of human and animal schistosomiasis transmission; the CERMES defined the different patterns of schistosomiasis transmission in Niger (involving African dry savana); in this field, we have shown, (i) the existence of important variability in conditions of transmission of S. haematobium and, (ii) natural hybridization between parasitic species of the ruminants (S. bovis and S. curassoni) and genetic interaction between human and animal parasites; (b) definition of morbidity indicators usable for rapid assessment methods, for appraisal of the severity of the disease and for the evaluation of the efficiency of control methods; we have established the correlation between ultrasonographic data and some cheap and simple field indicators; (c) immune response and protective immunity induced by recombinant glutathion S-transferase (Sm28, Sb28 and Sh28) in homologous and heterologous animal models including goats, sheep and non human primates (Erythrocebus patas). In Niger, we participate in all control programs against schistosomiasis to define control strategies, to supervise operations and to participate in their evaluation with external experts. International collaborations constitute a frame including four laboratories in Africa and six laboratories in developed countries (Europe and USA)

A simple approach improving the performance of urine reagent strips for rapid diagnosis of urinary schistosomiasis in Nigerian schoolchildren

In Nigeria, schistosomiasis, caused predominantly by the species Schistosoma haematobium, is highly endemic in resource-poor communities. We performed a school-based survey in two rural communities in Osun State (Southwestern Nigeria) and assessed macrohaematuria, microhaematuria and proteinuria as indirect indicators for the presence of disease. Urine samples were inspected macroscopically for haematuria and screened for microhaematuria and proteinuria using urine reagent strips. The microscopic examination of schistosome eggs was used as the gold standard for diagnosis. In total, 447 schoolchildren were included in this study and had a 51% prevalence of urinary schistosomiasis. The sensitivity of microhaematuria (68%) and proteinuria (53%) for infection with S. haematobium was relatively low. In patients with a heavy infection (>500 eggs/10 mL), the sensitivity of microhaematuria was high (95%). When the presence of macrohaematuria and the concomitant presence of microhaematuria and proteinuria were combined, it revealed a sensitivity of 63%, a specificity of 93% and a positive predictive value of 91%. Macrohaematuria also showed high specificity (96%) and a positive predictive value of 92%, while sensitivity was < 50%. These data show that combining urine reagent strip tests (presence of proteinuria and microhaematuria) and information on macrohaematuria increased the accuracy of the rapid diagnosis of urinary schistosomiasis in an endemic rural West African setting. This simple approach can be used to increase the quality of monitoring of schistosomiasis in schoolchildren.

Biotransformation and endocrine disruptive effects of contaminants in ringed seals - implications for monitoring and risk assessment

Marine mammals are exposed to persistent organic pollutants (POPs), which may be biotransformed to metabolites some of which are highly toxic. Both POPs and their metabolites may lead to adverse health effects, which have been studied using various biomarkers. Changes in endocrine homeostasis have been suggested to be sensitive biomarkers for contaminant-related effects. The overall objective of this doctoral thesis was to investigate biotransformation capacity of POPs and their potential endocrine disruptive effects in two contrasting ringed seal populations from the low contaminated Svalbard area and from the highly contaminated Baltic Sea. Biotransformation capacity was studied by determining the relationships between congener-specific patterns and concentrations of polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs), polybrominated diphenyl ethers (PBDEs) and their hydroxyl (OH)- and/or methylsulfonyl (MeSO₂)-metabolites, and catalytic activities of hepatic xenobiotic-metabolizing phase I and II enzymes. The results suggest that the biotransformation of PCBs, PBDEs and toxaphenes in ringed seals depends on the congener-specific halogen-substitution pattern. Biotransformation products detected in the seals included OH-PCBs, MeSO₂-PCBs and –DDE, pentachlorophenol, 4-OHheptachlorostyrene, and to a minor extent OH-PBDEs. The effects of life history state (moulting and fasting) on contaminant status and potential biomarkers for endocrine disruption, including hormone and vitamin homeostasis, were investigated in the low contaminated ringed seal population from Svalbard. Moulting/fasting status strongly affected thyroid, vitamin A and calcitriol homeostasis, body condition and concentrations of POPs and their OH-metabolites. In contrast, moulting/fasting status was not associated with variations in vitamin E levels. Endocrine disruptive effects on multiple endpoints were investigated in the two contrasting ringed seal populations. The results suggest that thyroid, vitamin A and calcitriol homeostasis may be affected by the exposure of contaminants and/or their metabolites in the Baltic ringed seals. Complex and non-linear relationships were observed between the contaminant levels and the endocrine variables. Positive relationships between circulating free and total thyroid hormone concentration ratios and OH-PCBs suggest that OH-PCBs may mediate the disruption of thyroid hormone transport in plasma. Species differences in thyroid and bone-related effects of contaminants were studied in ringed and grey seals from low contaminated references areas and from the highly contaminated Baltic Sea. The results indicate that these two species living at the same environment approximately at the same trophic level respond in a very different way to contaminant exposure. The results of this thesis suggest that the health status of the Baltic ringed seals has still improved during the last decade. PCB and DDE levels have decreased in these seals and the contaminant-related effects are different today than a decade ago. The health of the Baltic ringed seals is still suggested to be affected by the contaminant exposure. At the present level of the contaminant exposure the Baltic ringed seals seem to be at a zone where their body is able to compensate for the contaminant-mediated endocrine disruption. Based on the results of this thesis, several recommendations that could be applied on monitoring and assessing risk for contaminant effects are provided. Circulating OH-metabolites should be included in monitoring and risk assessment programs due to their high toxic potential. It should be noted that endogenous variables may have complex and highly variable responses to contaminant exposure including non-linear responses. These relationships may be further confounded by life history status. Therefore, it is highly recommended that when using variables related to endocrine homeostasis to investigate/monitor or assess the risk of contaminant effects in seals, the life history status of the animal should be carefully taken into consideration. This applies especially when using thyroid, vitamin A or calcitriolrelated parameters during moulting/fasting period. Extrapolations between species for assessing risk for contaminant effects in phocid seals should be avoided.

Development of molecular-based techniques for the detection, identification and quantification of food-borne pathogens

La presencia de microorganismos patógenos en alimentos es uno de los problemas esenciales en salud pública, y las enfermedades producidas por los mismos es una de las causas más importantes de enfermedad. Por tanto, la aplicación de controles microbiológicos dentro de los programas de aseguramiento de la calidad es una premisa para minimizar el riesgo de infección de los consumidores. Los métodos microbiológicos clásicos requieren, en general, el uso de pre-enriquecimientos no-selectivos, enriquecimientos selectivos, aislamiento en medios selectivos y la confirmación posterior usando pruebas basadas en la morfología, bioquímica y serología propias de cada uno de los microorganismos objeto de estudio. Por lo tanto, estos métodos son laboriosos, requieren un largo proceso para obtener resultados definitivos y, además, no siempre pueden realizarse. Para solucionar estos inconvenientes se han desarrollado diversas metodologías alternativas para la detección identificación y cuantificación de microorganismos patógenos de origen alimentario, entre las que destacan los métodos inmunológicos y moleculares. En esta última categoría, la técnica basada en la reacción en cadena de la polimerasa (PCR) se ha convertido en la técnica diagnóstica más popular en microbiología, y recientemente, la introducción de una mejora de ésta, la PCR a tiempo real, ha producido una segunda revolución en la metodología diagnóstica molecular, como pude observarse por el número creciente de publicaciones científicas y la aparición continua de nuevos kits comerciales. La PCR a tiempo real es una técnica altamente sensible -detección de hasta una molécula- que permite la cuantificación exacta de secuencias de ADN específicas de microorganismos patógenos de origen alimentario. Además, otras ventajas que favorecen su implantación potencial en laboratorios de análisis de alimentos son su rapidez, sencillez y el formato en tubo cerrado que puede evitar contaminaciones post-PCR y favorece la automatización y un alto rendimiento. En este trabajo se han desarrollado técnicas moleculares (PCR y NASBA) sensibles y fiables para la detección, identificación y cuantificación de bacterias patogénicas de origen alimentario (Listeria spp., Mycobacterium avium subsp. paratuberculosis y Salmonella spp.). En concreto, se han diseñado y optimizado métodos basados en la técnica de PCR a tiempo real para cada uno de estos agentes: L. monocytogenes, L. innocua, Listeria spp. M. avium subsp. paratuberculosis, y también se ha optimizado y evaluado en diferentes centros un método previamente desarrollado para Salmonella spp. Además, se ha diseñado y optimizado un método basado en la técnica NASBA para la detección específica de M. avium subsp. paratuberculosis. También se evaluó la aplicación potencial de la técnica NASBA para la detección específica de formas viables de este microorganismo. Todos los métodos presentaron una especificidad del 100 % con una sensibilidad adecuada para su aplicación potencial a muestras reales de alimentos. Además, se han desarrollado y evaluado procedimientos de preparación de las muestras en productos cárnicos, productos pesqueros, leche y agua. De esta manera se han desarrollado métodos basados en la PCR a tiempo real totalmente específicos y altamente sensibles para la determinación cuantitativa de L. monocytogenes en productos cárnicos y en salmón y productos derivados como el salmón ahumado y de M. avium subsp. paratuberculosis en muestras de agua y leche. Además este último método ha sido también aplicado para evaluar la presencia de este microorganismo en el intestino de pacientes con la enfermedad de Crohn's, a partir de biopsias obtenidas de colonoscopia de voluntarios afectados. En conclusión, este estudio presenta ensayos moleculares selectivos y sensibles para la detección de patógenos en alimentos (Listeria spp., Mycobacterium avium subsp. paratuberculosis) y para una rápida e inambigua identificación de Salmonella spp. La exactitud relativa de los ensayos ha sido excelente, si se comparan con los métodos microbiológicos de referencia y pueden serusados para la cuantificación de tanto ADN genómico como de suspensiones celulares. Por otro lado, la combinación con tratamientos de preamplificación ha resultado ser de gran eficiencia para el análisis de las bacterias objeto de estudio. Por tanto, pueden constituir una estrategia útil para la detección rápida y sensible de patógenos en alimentos y deberían ser una herramienta adicional al rango de herramientas diagnósticas disponibles para el estudio de patógenos de origen alimentario.

Benchmarking consensus model quality assessment for protein fold recognition

Background: Selecting the highest quality 3D model of a protein structure from a number of alternatives remains an important challenge in the field of structural bioinformatics. Many Model Quality Assessment Programs (MQAPs) have been developed which adopt various strategies in order to tackle this problem, ranging from the so called "true" MQAPs capable of producing a single energy score based on a single model, to methods which rely on structural comparisons of multiple models or additional information from meta-servers. However, it is clear that no current method can separate the highest accuracy models from the lowest consistently. In this paper, a number of the top performing MQAP methods are benchmarked in the context of the potential value that they add to protein fold recognition. Two novel methods are also described: ModSSEA, which based on the alignment of predicted secondary structure elements and ModFOLD which combines several true MQAP methods using an artificial neural network. Results: The ModSSEA method is found to be an effective model quality assessment program for ranking multiple models from many servers, however further accuracy can be gained by using the consensus approach of ModFOLD. The ModFOLD method is shown to significantly outperform the true MQAPs tested and is competitive with methods which make use of clustering or additional information from multiple servers. Several of the true MQAPs are also shown to add value to most individual fold recognition servers by improving model selection, when applied as a post filter in order to re-rank models. Conclusion: MQAPs should be benchmarked appropriately for the practical context in which they are intended to be used. Clustering based methods are the top performing MQAPs where many models are available from many servers; however, they often do not add value to individual fold recognition servers when limited models are available. Conversely, the true MQAP methods tested can often be used as effective post filters for re-ranking few models from individual fold recognition servers and further improvements can be achieved using a consensus of these methods.

Assessment of projected changes in upland environments using simple climatic indices

Climate controls upland habitats, soils and their associated ecosystem services; therefore, understanding possible changes in upland climatic conditions can provide a rapid assessment of climatic vulnerability over the next century. We used 3 different climatic indices that were optimised to fit the upland area classified by the EU as a Severely Disadvantaged Area (SDA) 1961–1990. Upland areas within the SDA covered all altitudinal ranges, whereas the maximum altitude of lowland areas outside of the SDA was ca. 300 m. In general, the climatic index based on the ratio between annual accumulated temperature (as a measure of growing season length) and annual precipitation predicted 96% of the SDA mapped area, which was slightly better than those indices based on annual or seasonal water deficit. Overall, all climatic indices showed that upland environments were exposed to some degree of change by 2071–2100 under UKCIP02 climate projections for high and low emissions scenarios. The projected area declined by 13 to 51% across 3 indices for the low emissions scenario and by 24 to 84% for the high emissions scenario. Mean altitude of the upland area increased by +11 to +86 m for the low scenario and +21 to +178 m for the high scenario. Low altitude areas in eastern and southern Great Britain were most vulnerable to change. These projected climatic changes are likely to affect upland habitat composition, long-term soil carbon storage and wider ecosystem service provision, although it is not yet possible to determine the rate at which this might occur.

Improving sequence-based fold recognition by using 3D model quality assessment

Motivation: The ability of a simple method (MODCHECK) to determine the sequence–structure compatibility of a set of structural models generated by fold recognition is tested in a thorough benchmark analysis. Four Model Quality Assessment Programs (MQAPs) were tested on 188 targets from the latest LiveBench-9 automated structure evaluation experiment. We systematically test and evaluate whether the MQAP methods can successfully detect native-likemodels. Results: We show that compared with the other three methods tested MODCHECK is the most reliable method for consistently performing the best top model selection and for ranking the models. In addition, we show that the choice of model similarity score used to assess a model's similarity to the experimental structure can influence the overall performance of these tools. Although these MQAP methods fail to improve the model selection performance for methods that already incorporate protein three dimension (3D) structural information, an improvement is observed for methods that are purely sequence-based, including the best profile–profile methods. This suggests that even the best sequence-based fold recognition methods can still be improved by taking into account the 3D structural information.

Defining a fish bio-assessment tool to monitoring the biological condition of a cascade reservoirs system in tropical area

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Electric techniques for the assessment of quality parameters of foodstuffs

In food industry, quality assurance requires low cost methods for the rapid assessment of the parameters that affect product stability. Foodstuffs are complex in their structure, mainly composed by gaseous, liquid and solid phases which often coexist in the same product. Special attention is given to water, concerned as natural component of the major food product or as added ingredient of a production process. Particularly water is structurally present in the matrix and not completely available. In this way, water can be present in foodstuff in many different states: as water of crystallization, bound to protein or starch molecules, entrapped in biopolymer networks or adsorbed on solid surfaces of porous food particles. The traditional technique for the assessment of food quality give reliable information but are destructive, time consuming and unsuitable for on line application. The techniques proposed answer to the limited disposition of time and could be able to characterize the main compositional parameters. Dielectric interaction response is mainly related to water and could be useful not only to provide information on the total content but also on the degree of mobility of this ubiquitous molecule in different complex food matrix. In this way the proposal of this thesis is to answer at this need. Dielectric and electric tool can be used for the scope and led us to describe the complex food matrix and predict food characteristic. The thesis is structured in three main part, in the first one some theoretical tools are recalled to well assess the food parameter involved in the quality definition and the techniques able to reply at the problem emerged. The second part explains the research conducted and the experimental plans are illustrated in detail. Finally the last section is left for rapid method easily implementable in an industrial process.

Variability of anti-PF4/heparin antibody results obtained by the rapid testing system ID-H/PF4-PaGIA

BACKGROUND: Recent studies have shown that a low clinical pretest probability may be adequate for excluding heparin-induced thrombocytopenia. However, for patients with intermediate or high pretest probability, laboratory testing is essential for confirming or refuting the diagnosis. Rapid assessment of anti-PF4/heparin-antibodies may assist clinical decision-making. OBJECTIVES: To evaluate the performance of rapid ID-H/PF4-PaGIA. In particular, we verified reproducibility of results between plasma and serum specimens, between fresh and frozen samples, and between different ID-H/PF4-polymer lots (polystyrene beads coated with heparin/PF4-complexes). PATIENTS/METHODS: The samples studied were 1376 plasma and 914 corresponding serum samples from patients investigated for suspected heparin-induced thrombocytopenia between January 2000 and October 2008. Anti-PF4/heparin-antibodies were assessed by ID-H/PF4-PaGIA, commercially available ELISAs and heparin-induced platelet aggregation test. RESULTS: Among 914 paired plasma/serum samples we noted discordant results (negative vs. low-titre positive) in nine instances (1%; 95%CI, 0.4-1.6%). Overall, agreement between titres assessed in plasma vs. serum was highly significant (Spearman correlation coefficient, 0.975; P < 0.0001). Forty-seven samples tested both fresh and after freezing/thawing showed a good agreement, with one discordant positive/negative result (Spearman correlation coefficient, 0.970; P < 0.0001). Among 1376 plasma samples we noted a strikingly variable incidence of false negative results (none - 82%; 95%CI, 66-98%), depending on the employed ID-H/PF4-polymer lot. Faulty lots can be recognized by titrating commercial positive controls and stored samples of HIT-patients. CONCLUSION: Laboratories performing the assay should implement stringent internal quality controls in order to recognize potentially faulty ID-H/PF4-polymer lots, thus avoiding false negative results.

Equity-focused health impact assessment of Portuguese tobacco control legislation

The World Health Organization recommend the Equity-Focused Health Impact Assessment (HIA) as a means to assess the impact of social and economic policies on the health of populations, and acknowledges their contribution to health inequality. We describe the application of the Equity-focusedImpact Assessment methodology on the Portuguese law on Smoking Prevention and Tobacco Control (Law No. 37/2007). A rapid assessment was carried out to issue recommendations which could be incorporated into the law during a revision in 2014. Quantitative (consumption and health status indicators; equity analysis) and qualitative (Focus Group) approaches were taken to evaluate the impact of the law and formulate recommendations. Young people, men and women of low socioeconomic status, and pregnant women were identified as requiring specific and appropriate interventions to prevent smoking and support smoking cessation.

Cataract Remains an Important Cause of Blindness in Campinas, Brazil

Objective: To estimate the prevalence of blindness in the elderly population of Campinas, Brazil, and to describe the coverage and quality of cataract surgery services in the area. Methods: A brief assessment of cataract surgery services (using the RACSS (Rapid Assessment of Cataract Surgical Services Method) was conducted using random cluster sampling, with a sample composed of 60 clusters of 40 people aged 50 years or older. Visual acuity (VA) was measured and the lens status observed by direct visual ophthalmoscopy. From the selected sample of 2,400 subjects, 92.67% were examined. Results: Blindness (VA 3/60 with available correction) was found in 1.98 % (2.03 % among male subjects, and 1.94 % among female subjects). The prevalence of blindness varied with age, from 0.2%, in the group from 50 to 54 years, to 7.2% in those above 80. Cataract was the main cause of blindness (40.2%) followed by suspected posterior segment disorders (18.2%), diabetic retinopathy (15.9%), and glaucoma (11.4%). The cataract surgical coverage was of 93% (VA 3/60) and 82.18% when the criterion was VA 6/60 in the best eye. The main reasons the subjects did not receive surgical treatment were: fear of undergoing surgery, 11.1%; lack of awareness about the condition, 16.7%; waiting for maturity, 16.7%; and contraindication to surgery, 44.4%. Conclusion: Cataract is the major cause of blindness in Campinas. Education on eye diseases, their prevention and treatment must become part of the city`s public healthcare policies.

Electrochemical evaluation of total antioxidant capacity of beverages using a purine-biosensor

In this paper, it was evaluated the total antioxidant capacity (TAC) of beverages using an electrochemical biosensor. The biosensor consisted on the purine base (guanine or adenine) electro-immobilization on a glassy carbon electrode surface (GCE). Purine base damage was induced by the hydroxyl radical generated by Fenton-type reaction. Five antioxidants were applied to counteract the deleterious effects of the hydroxyl radical. The antioxidants used were ascorbic acid, gallic acid, caffeic acid, coumaric acid and resveratrol. These antioxidants have the ability to scavenger the hydroxyl radical and protect the guanine and adenine immobilized on the GCE surface. The interaction carried out between the purinebase immobilized and the free radical in the absence and presence of antioxidants was evaluated by means of changes in the guanine and adenine anodic peak obtained by square wave voltammetry (SWV). The results demonstrated that the purine-biosensors are suitable for rapid assessment of TAC in beverages.

Evaluation of the total antioxidant capacity of flavored water and electrochemical purine damage by sulfate radicals using a purine-based sensor

In this study, a method for the electrochemical quantification of the total antioxidant capacity (TAC) in beverages was developed. The method is based on the oxidative damage to the purine bases, adenine or guanine, that are immobilized on a glassy carbon electrode (GCE) surface. The oxidative lesions on the DNA bases were promoted by the sulfate radical generated by the persulfate/iron(II) system. The presence of antioxidants on the reactive system promoted the protection of the DNA bases immobilized on the GCE by scavenging the sulfate radical. Square-wave voltammetry (SWV) was the electrochemical technique used to perform this study. The efficiencies of five antioxidants (ascorbic acid, gallic acid, caffeic acid, coumaric acid and resveratrol) in scavenging the sulfate radical and, therefore, their ability to protect the purine bases immobilized on the GCE were investigated. These results demonstrated that the purine-based biosensor is suitable for the rapid assessment of the TAC in flavors and flavored water.