Urban development modifies lake food webs in the Pacific Northwest

Thesis (Master's)--University of Washington, 2015

River Sediment Sampling and Environment Quality Standards: A Case Study of the Ravensbourne River

Sediment is a major sink for heavy metals in river, and poses significant risks not only to river quality but also to aquatic and benthic organisms. At present in the UK, there are no mandatory sediment quality standards. This is partly due to insufficient toxicity data but also due to problems with identification of appropriate sediment monitoring and analytical techniques. The aim of this research was to examine the sampling different river sediment compartments in order to monitor compliance with any future UK sediment environmental quality standards (EQS). The significance of sediment physical and chemical characteristics on sampling and analysis was also determined. The Ravensbourne River, a tributary of the River Thames located in the highly urbanised South Eastern area of London was used for this study. Sediment was collected from the bed using the Van Veer grab, the bank using hand trowel, and from the water column (suspended sediment) using the time integrated suspended tube sampler between the period of July 2010 and December, 2011. The result for the total metal extraction carried out using aqua regia found that there were no significant differences in the metal concentrations retained in the different compartments by the <63μm sediment fraction but there were differences between the 63μm-2mm fractions of the bed and bank. The metal concentration in the bed, bank and suspended sediment exceeded the draft UK sediment quality guidelines. Sequential extraction was also carried out to determine metal speciation in each sediment compartment using the Maiz et al. (1997) and Tessier et al. (1979) methods. The Maiz et al. (1997) found over 80% of the metals in each sediment compartment were not bioavailable, while Tessier et al. (1979) method found most of the metals to be associated with the Fe/Mn and the residual phase. The bed sediment compartment and the <2mm (<63μm + 63μm-2mm) fraction appears to be the most suitable sediment sample for sediment monitoring from this study.

Environmental exposure to toxicants mixtures from a multi-purpose estuary: perspectives for a biomonitoring study in Portugal

This work was focused on a multi-purpose estuarine environment (river Sado estuary, SW Portugal) around which a number of activities (e.g., fishing, farming, heavy industry, tourism and recreational activities) coexist with urban centres with a total of about 200 000 inhabitants. Based on previous knowledge of the hazardous chemicals within the ecosystem and their potential toxicity to benthic species, this project intended to evaluate the impact of estuarine contaminants on the human and ecosystem health. An integrative methodology based on epidemiological, analytical and biological data and comprising several lines of evidence, namely, human contamination pathways, human health effects, consumption of local produce, estuarine sediments, wells and soils contamination, effects on commercial benthic organisms, and genotoxic potential of sediments, was used. The epidemiological survey confirmed the occurrence of direct and indirect (through food chain) exposure of the local population to estuarine contaminants. Furthermore, the complex mixture of contaminants (e.g., metals, pesticides, polycyclic aromatic hydrocarbons) trapped in the estuary sediments was toxic to human liver cells exposed in vitro, causing cell death, oxidative stress and genotoxic effects that might constitute a risk factor for the development of chronic-degenerative diseases, on the long term. Finally, the integration of data from several endpoints indicated that the estuary is moderately impacted by toxicants that affect also the aquatic biota. Nevertheless, the human health risk can only be correctly assessed through a biomonitoring study including the quantification of contaminants (or metabolites) in biological fluids as well as biomarkers of early biological effects (e.g., biochemical, genetic and omics-based endpoints) and genetic susceptibility in the target population. Data should be supported by a detailed survey to assess the impact of the contaminated seafood and local farm products consumption on human health and, particularly, on metabolic diseases or cancer development.

Immune responses in Bathymodiolus azoricus upon Vibrio challenges : approaches to characterize mussel survival strategies and physiological adaptations in deep sea extreme environments

Tese de Doutoramento, Ciências do Mar, especialidade de Biologia Marinha, 18 de Dezembro de 2015, Universidade dos Açores.

Avaliação ecotoxicológica de solos contaminados por ibuprofeno

Os produtos farmacêuticos são substâncias químicas muito utilizados em medicina, veterinária e ainda na agricultura. Nos anos 90, foi descoberta a presença de fármacos em meio aquático, verificando-se que a sua remoção nas Estações de Tratamento de Águas Residuais (ETAR) não era completa. Durante as duas últimas décadas foi identificada a presença de mais de oitenta compostos no meio ambiente e actualmente são considerados poluentes emergentes. Podem contaminar solos e águas, depois de serem usados e excretados (inalterados ou metabolizados) por humanos e animais, ou quando são indevidamente lançados directamente no meio ambiente. Os estudos ecotoxicológicos efectuados com estes poluentes têm sido direccionados, sobretudo, para as águas, existindo uma ausência de trabalhos sobre solos. O Ibuprofeno (IB) é um anti-inflamatório não esteróide, utilizado também como analgésico e antipirético, sendo um dos produtos farmacêuticos mais vendidos em todo o mundo, o que justifica a sua forte presença no meio ambiente. Por isso, e dada a ausência de trabalhos ecotoxicológicos de solos contaminados por fármacos, o IB foi o produto farmacêutico selecionado para a realização deste trabalho. A ecotoxicidade pode ser avaliada através de bioensaios. Estes têm a capacidade de avaliar a toxicidade de uma determinada substância de forma global, usando organismos vivos que funcionam como bio-indicadores. O presente trabalho tem como objectivos avaliar o impacte causado nos solos pelo IB, testar a toxicidade de dois processos de descontaminação para remover o referido fármaco dos solos assim como avaliar a toxicidade provocada por águas residuais, de três unidades hospitalares e de uma indústria farmacêutica. Esta avaliação foi efectuada através de ensaios de toxicidade aguda de germinação e de alongamento de raiz de sementes de alface, variedade bola de manteiga (Lactuca sativa), em solo arenoso. Os ensaios de ecotoxicidade aguda em solos contaminados por IB foram realizados para uma gama de concentrações entre 0,1 e 1000 μg/L. Verificou-se uma redução do número de sementes germinadas e do comprimento médio da planta no solo contaminado com 0,5 e 20 μg/L de IB. No solo contaminado com 1000 μg/L de IB observou-se uma redução da germinação, acompanhada por uma indução de crescimento da raiz da espécie Lactuca sativa. Os dois tratamentos de descontaminação de solos, reagente de Fenton e Nanopartículas de ferro zero valente, revelaram toxicidade, tendo-se obtido uma percentagem de germinação entre 32,2 ± 3,5 e 48,5 ± 6,2 e inibição do crescimento da raiz do organismo teste em cerca de 85,0 %. Em relação às águas residuais hospitalares verificou-se uma redução da percentagem de germinação entre 31,1 ± 5,0 e 72,3 ± 12,4 e uma inibição do crescimento da raiz situada entre 13,0 ± 6,4 e 20,2 ± 10,0 %. Para a água residual industrial ocorreu uma inibição da percentagem de germinação de 60,5 ± 13,1, contudo nas plantas germinadas observou-se uma indução do crescimento da raiz de 14,9 ± 7,7 %.

Multiple linear and principal component regressions for modelling ecotoxicity bioassay response

The ecotoxicological response of the living organisms in an aquatic system depends on the physical, chemical and bacteriological variables, as well as the interactions between them. An important challenge to scientists is to understand the interaction and behaviour of factors involved in a multidimensional process such as the ecotoxicological response.With this aim, multiple linear regression (MLR) and principal component regression were applied to the ecotoxicity bioassay response of Chlorella vulgaris and Vibrio fischeri in water collected at seven sites of Leça river during five monitoring campaigns (February, May, June, August and September of 2006). The river water characterization included the analysis of 22 physicochemical and 3 microbiological parameters. The model that best fitted the data was MLR, which shows: (i) a negative correlation with dissolved organic carbon, zinc and manganese, and a positive one with turbidity and arsenic, regarding C. vulgaris toxic response; (ii) a negative correlation with conductivity and turbidity and a positive one with phosphorus, hardness, iron, mercury, arsenic and faecal coliforms, concerning V. fischeri toxic response. This integrated assessment may allow the evaluation of the effect of future pollution abatement measures over the water quality of Leça River.

Development of paper-based color test-strip for drug detection in aquatic environment: Application to oxytetracycline

The wide use of antibiotics in aquaculture has led to the emergence of resistant microbial species. It should be avoided/minimized by controlling the amount of drug employed in fish farming. For this purpose, the present work proposes test-strip papers aiming at the detection/semi-quantitative determination of organic drugs by visual comparison of color changes, in a similar analytical procedure to that of pH monitoring by universal pH paper. This is done by establishing suitable chemical changes upon cellulose, attributing the paper the ability to react with the organic drug and to produce a color change. Quantitative data is also enabled by taking a picture and applying a suitable mathematical treatment to the color coordinates given by the HSL system used by windows. As proof of concept, this approach was applied to oxytetracycline (OXY), one of the antibiotics frequently used in aquaculture. A bottom-up modification of paper was established, starting by the reaction of the glucose moieties on the paper with 3-triethoxysilylpropylamine (APTES). The so-formed amine layer allowed binding to a metal ion by coordination chemistry, while the metal ion reacted after with the drug to produce a colored compound. The most suitable metals to carry out such modification were selected by bulk studies, and the several stages of the paper modification were optimized to produce an intense color change against the concentration of the drug. The paper strips were applied to the analysis of spiked environmental water, allowing a quantitative determination for OXY concentrations as low as 30 ng/mL. In general, this work provided a simple, method to screen and discriminate tetracycline drugs, in aquaculture, being a promising tool for local, quick and cheap monitoring of drugs.

Host factors and genetic susceptibility to infections due to intracellular bacteria and fastidious organisms.

While genetic polymorphisms play a paramount role in tuberculosis (TB), less is known about their contribution to the severity of diseases caused by other intracellular bacteria and fastidious microorganisms. We searched electronic databases for observational studies reporting on host factors and genetic predisposition to infections caused by intracellular fastidious bacteria published up to 30 May 2014. The contribution of genetic polymorphisms was documented for TB. This includes genetic defects in the mononuclear phagocyte/T helper cell type 1 (Th1) pathway contributing to disseminated TB disease in children and genome-wide linkage analysis (GWAS) in reactivated pulmonary TB in adults. Similarly, experimental studies supported the role of host genetic factors in the clinical presentation of illnesses resulting from other fastidious intracellular bacteria. These include IL-6 -174G/C or low mannose-binding (MBL) polymorphisms, which are incriminated in chronic pulmonary conditions triggered by C. pneumoniae, type 2-like cytokine secretion polymorphisms, which are correlated with various clinical patterns of M. pneumoniae infections, and genetic variation in the NOD2 gene, which is an indicator of tubal pathology resulting from Chamydia trachomatis infections. Monocyte/macrophage migration and T lymphocyte recruitment defects are corroborated to ineffective granuloma formation observed among patients with chronic Q fever. Similar genetic polymorphisms have also been suggested for infections caused by T. whipplei although not confirmed yet. In conclusion, this review supports the paramount role of genetic factors in clinical presentations and severity of infections caused by intracellular fastidious bacteria. Genetic predisposition should be further explored through such as exome sequencing.

NEW METHODS FOR DETECTION, SUSCEPTIBILITY TESTING AND BIOFILM ERADICATION OF DIFFICULT ORGANISMS

Aujourd'hui, les problèmes des maladies infectieuses concernent l'émergence d'infections difficiles à traiter, telles que les infections associées aux implants et les infections fongiques invasives chez les patients immunodéprimés. L'objectif de cette thèse était de développer des stratégies pour l'éradication des biofilms bactériens (partie 1), ainsi que d'étudier des méthodes innovantes pour la détection microbienne, pour l'établissement de nouveaux tests de sensibilité (partie 2). Le traitement des infections associées aux implants est difficile car les biofilms bactériens peuvent résister à des niveaux élevés d'antibiotiques. A ce jour, il n'y a pas de traitement optimal défini contre des infections causées par des bactéries de prévalence moindre telles que Enterococcus faecalis ou Propionibacterium acnés. Dans un premier temps, nous avons démontré une excellente activité in vitro de la gentamicine sur une souche de E. faecalis en phase stationnaire de croissance Nous avons ensuite confirmé l'activité de la gentamicine sur un biofilm précoce en modèle expérimental animal à corps étranger avec un taux de guérison de 50%. De plus, les courbes de bactéricidie ainsi que les résultats de calorimétrie ont prouvé que l'ajout de gentamicine améliorait l'activité in vitro de la daptomycine, ainsi que celle de la vancomycine. In vivo, le schéma thérapeutique le plus efficace était l'association daptomycine/gentamicine avec un taux de guérison de 55%. En établissant une nouvelle méthode pour l'évaluation de l'activité des antimicrobiens vis-à-vis de micro-organismes en biofilm, nous avons démontré que le meilleur antibiotique actif sur les biofilms à P. acnés était la rifampicine, suivi par la penicilline G, la daptomycine et la ceftriaxone. Les études conduites en modèle expérimental animal ont confirmé l'activité de la rifampicine seule avec un taux de guérison 36%. Le meilleur schéma thérapeutique était au final l'association rifampicine/daptomycine avec un taux de guérison 63%. Les associations de rifampicine avec la vancomycine ou la levofloxacine présentaient des taux de guérisons respectivement de 46% et 25%. Nous avons ensuite étudié l'émergence in vitro de la résistance à la rifampicine chez P. acnés. Nous avons observé un taux de mutations de 10"9. La caractérisation moléculaire de la résistance chez les mutant-résistants a mis en évidence l'implication de 5 mutations ponctuelles dans les domaines I et II du gène rpoB. Ce type de mutations a déjà été décrit au préalable chez d'autres espèces bactériennes, corroborant ainsi la validité de nos résultats. La deuxième partie de cette thèse décrit une nouvelle méthode d'évaluation de l'efficacité des antifongiques basée sur des mesures de microcalorimétrie isotherme. En utilisant un microcalorimètre, la chaleur produite par la croissance microbienne peut être-mesurée en temps réel, très précisément. Nous avons évalué l'activité de l'amphotéricine B, des triazolés et des échinocandines sur différentes souches de Aspergillus spp. par microcalorimétrie. La présence d'amphotéricine Β ou de triazole retardait la production de chaleur de manière concentration-dépendante. En revanche, pour les échinochandines, seule une diminution le pic de « flux de chaleur » a été observé. La concordance entre la concentration minimale inhibitrice de chaleur (CMIC) et la CMI ou CEM (définie par CLSI M38A), avec une marge de 2 dilutions, était de 90% pour l'amphotéricine B, 100% pour le voriconazole, 90% pour le pozoconazole et 70% pour la caspofongine. La méthode a été utilisée pour définir la sensibilité aux antifongiques pour d'autres types de champignons filamenteux. Par détermination microcalorimétrique, l'amphotéricine B s'est avéré être l'agent le plus actif contre les Mucorales et les Fusarium spp.. et le voriconazole le plus actif contre les Scedosporium spp. Finalement, nous avons évalué l'activité d'associations d'antifongiques vis-à-vis de Aspergillus spp. Une meilleure activité antifongique était retrouvée avec l'amphotéricine B ou le voriconazole lorsque ces derniers étaient associés aux échinocandines vis-à-vis de A. fumigatus. L'association échinocandine/amphotéricine B a démontré une activité antifongique synergique vis-à-vis de A. terreus, contrairement à l'association échinocandine/voriconazole qui ne démontrait aucune amélioration significative de l'activité antifongique. - The diagnosis and treatment of infectious diseases are today increasingly challenged by the emergence of difficult-to-manage situations, such as infections associated with medical devices and invasive fungal infections, especially in immunocompromised patients. The aim of this thesis was to address these challenges by developing new strategies for eradication of biofilms of difficult-to-treat microorganisms (treatment, part 1) and investigating innovative methods for microbial detection and antimicrobial susceptibility testing (diagnosis, part 2). The first part of the thesis investigates antimicrobial treatment strategies for infections caused by two less investigated microorganisms, Enterococcus faecalis and Propionibacterium acnes, which are important pathogens causing implant-associated infections. The treatment of implant-associated infections is difficult in general due to reduced susceptibility of bacteria when present in biofilms. We demonstrated an excellent in vitro activity of gentamicin against E. faecalis in stationary growth- phase and were able to confirm the activity against "young" biofilms (3 hours) in an experimental foreign-body infection model (cure rate 50%). The addition of gentamicin improved the activity of daptomycin and vancomycin in vitro, as determined by time-kill curves and microcalorimetry. In vivo, the most efficient combination regimen was daptomycin plus gentamicin (cure rate 55%). Despite a short duration of infection, the cure rates were low, highlighting that enterococcal biofilms remain difficult to treat despite administration of newer antibiotics, such as daptomycin. By establishing a novel in vitro assay for evaluation of anti-biofilm activity (microcalorimetry), we demonstrated that rifampin was the most active antimicrobial against P. acnes biofilms, followed by penicillin G, daptomycin and ceftriaxone. In animal studies we confirmed the anti-biofilm activity of rifampin (cure rate 36% when administered alone), as well as in combination with daptomycin (cure rate 63%), whereas in combination with vancomycin or levofloxacin it showed lower cure rates (46% and 25%, respectively). We further investigated the emergence of rifampin resistance in P. acnes in vitro. Rifampin resistance progressively emerged during exposure to rifampin, if the bacterial concentration was high (108 cfu/ml) with a mutation rate of 10"9. In resistant isolates, five point mutations of the rpoB gene were found in cluster I and II, as previously described for staphylococci and other bacterial species. The second part of the thesis describes a novel real-time method for evaluation of antifungals against molds, based on measurements of the growth-related heat production by isothermal microcalorimetry. Current methods for evaluation of antifungal agents against molds, have several limitations, especially when combinations of antifungals are investigated. We evaluated the activity of amphotericin B, triazoles (voriconazole, posaconazole) and echinocandins (caspofungin and anidulafungin) against Aspergillus spp. by microcalorimetry. The presence of amphotericin Β or a triazole delayed the heat production in a concentration-dependent manner and the minimal heat inhibition concentration (MHIC) was determined as the lowest concentration inhibiting 50% of the heat produced at 48 h. Due to the different mechanism of action echinocandins, the MHIC for this antifungal class was determined as the lowest concentration lowering the heat-flow peak with 50%. Agreement within two 2-fold dilutions between MHIC and MIC or MEC (determined by CLSI M38A) was 90% for amphotericin B, 100% for voriconazole, 90% for posaconazole and 70% for caspofungin. We further evaluated our assay for antifungal susceptibility testing of non-Aspergillus molds. As determined by microcalorimetry, amphotericin Β was the most active agent against Mucorales and Fusarium spp., whereas voriconazole was the most active agent against Scedosporium spp. Finally, we evaluated the activity of antifungal combinations against Aspergillus spp. Against A. jumigatus, an improved activity of amphotericin Β and voriconazole was observed when combined with an echinocandin. Against A. terreus, an echinocandin showed a synergistic activity with amphotericin B, whereas in combination with voriconazole, no considerable improved activity was observed.

Aquatic Centre Pillars

Work on the giant concrete pillars found in the Eleanor Misener Aquatic Centre.

Aquatic Centre Construction

Pouring the concrete in the construction of the Eleanor Misener Aquatic Centre.

Aquatic Centre Foundation

The steel, rock, and conrete foundation of the Aquatic Centre.

Aquatic Centre Walls

Construction of the concrete walls and pillars for the Aquatic Centre progress.

Trends in fish prey capture by common terns following zebra mussel invasion : do terns track fish species abundance? /

The Common Tern (Sterna hirundo) is a ground nesting colonial seabird. Terns rely primarily on small prey fishes which they obtain through plunge diving for their survival as well as the survival of their offspring during the breeding season. The zebra mussel (Dreissena polymorpha) is a small bivalve mollusk that invaded North American waters in the late 1980's. Through its suspension feeding, the zebra mussel has the ability to alter the entire aquatic ecosystem, ultimately leading to a reduction in pelagic organisms including small prey fish. The objective of the study was to determine what (if any) indirect effects the invasion of the zebra mussel has had on fish prey captured by terns. The study took place in two separate two-year periods, 1990-91 and 1995-96 on a concrete breakwall off the north shore of Lake Erie near Port Colborne, Ontario. Daily nest checks revealed clutch initiation dates, egg-laying chronology, hatching success and morphological egg characteristics (length and breadth). Behavioural observations included time each sex spent in attendance with its brood, the frequency of feeding chicks and the prey species composition and size fed to chicks as well as to females (courtship feeding). Egg sizes did not differ between study periods, nor did feeding rates to chicks, suggesting that food was not a limiting resource. Terns spent less time with their broods (more time foraging) in the 1995-96 period. However, they also had significantly larger broods and fledged more offspring. The time of each individual foraging trip decreased, suggesting that fish were easier to obtain in 1995 and 1996. Lastly, kleptoparasitism rates decreased, suggesting that the costs of foraging (time, energy) actually decreased as fewer birds adopted this strategy to compensate for what I assumed to be a lack of available food (fish). The only significant difference between the periods of 1990, 1991 and 1995, 1996 was a change in diet. Terns delivered significantly fewer rainbow smelt and more emerald shiner in 1995 and 1996. However, the average size of fish delivered did not change. Thus, there was little impact on prey captured by Common Terns in Lake Erie since the invasion of the zebra mussel.