Pseudomonas aeruginosa diversification during infection development in cystic fibrosis lungs

Dissertação de mestrado integrado em Engenharia Biomédica (área de especialização em Engenharia Clínica)

Biogeochemical evolution of a marine shore tailings deposit during bioremediation

Summary : Mining activities produce enormous amounts of waste material known as tailings which are composed of fine to medium size particles. These tailings often contain sulfides, which oxidation can lead to acid and metal contamination of water; therefore they need to be remediated. In this work a tailings bioremediation approach was investigated by an interdisciplinary study including geochemistry, mineralogy and microbiology. The aim of the work was to study the effect of the implementation of wetland above oxidizing tailings on the hydrogeology and the biogeochemical element cycles, and to assess the system evolution over time. To reach these goals, biogeochemical processes occurring in a marine shore tailings deposit were investigated. The studied tailings deposit is located at the Bahìa de Ite, Pacific Ocean, southern Peru, where between 1940 and 1996 the tailings were discharged from the two porphyry copper mines Cuajone and Toquepala. After the end of deposition, a remediation approach was initiated in 1997 with a wetland implementation above the oxidizing tailings. Around 90% of the tailings deposits (total 16 km2) were thus remediated, except the central delta area and some areas close to the shoreline. The multi-stable isotope study showed that the tailings were saturated with fresh water in spite of the marine setting, due to the high hydraulic gradient resulting from the wetland implementation. Submarine groundwater discharge (SGD) was the major source of SO4 2-, C1-, Na+, Fe2+, and Mn2+ input into the tailings at the original shelf-seawater interface. The geochemical study (aquatic geochemistry and X-Ray diffraction (XRD) and sequential extractions from the solid fraction) showed that iron and sulfur oxidation were the main processes in the non-remediated tailings, which showed a top a low-pH oxidation zone with strong accumulation of efflorescent salts at the surface due to capillary upward transport of heavy metals (Fe, Cu, Zn, Mn, Cd, Co, and Ni) in the arid climate. The study showed also that the implementation of the wetland resulted in very low concentrations of heavy metals in solution (mainly under the detection limit) due to the near neutral pH and more reducing conditions (100-150 mV). The heavy metals, which were taken from solution, precipitated as hydroxides and sulfides or were bound to organic matter. The bacterial community composition analysis by Terminal Restriction Fragment Length Polymorphism (T-RFLP) and cloning and sequencing of 16S rRNA genes combined with a detailed statistical analysis revealed a high correlation between the bacterial distribution and the geochemical variables. Acidophilic autotrophic oxidizing bacteria were dominating the oxidizing tailings, whereas neutrophilic and heterotrophic reducing bacteria were driving the biogeochemical processes in the remediated tailings below the wetland. At the subsurface of the remediated tailings, an iron cycling was highlighted with oxidation and reduction processes due to micro-aerophilic niches provided by the plant rhizosphere in this overall reducing environment. The in situ bioremediation experiment showed that the main parameter to take into account for the effectiveness was the water table and chemistry which controls the system. The constructed remediation cells were more efficient and rapid in metal removal when saturation conditions were available. This study showed that the bioremediation by wetland implementation could be an effective and rapid treatment for some sulfidic mine tailings deposits. However, the water saturation of the tailings has to be managed on a long-term basis in order to guarantee stability. Résumé : L'activité minière produit d'énormes quantités de déchets géologiques connus sous le nom de « tailings » composées de particules de taille fine à moyenne. Ces déchets contiennent souvent des sulfures dont l'oxydation conduit à la formation d'effluents acides contaminés en métaux, d'où la nécessité d'effectuer une remédiation des sites de stockage concernés. Le but de ce travail est dans un premier temps d'étudier l'effet de la bio-remédiation d'un dépôt de tailings oxydés sur l'hydrogéologie du système et les cycles biogéochimiques des éléments et en second lieu, d'évaluer l'évolution du processus de remédiation dans le temps. Le site étudié dans ce travail est situé dans la Bahía de Ite, au sud du Pérou, au bord de l'Océan Pacifique. Les déchets miniers en question sont déposés dans un environnement marin. De 1940 à 1996, les déchets de deux mines de porphyre cuprifère - Cuajone et Toquepala - ont été acheminés sur le site via la rivière Locumba. En 1997, une première remédiation a été initiée avec la construction d'une zone humide sur les tailings. Depuis, environ 90% de la surface du dépôt (16 km2) a été traité, les parties restantes étant la zone centrale du delta du Locumba et certaines zones proches de la plage. Malgré la proximité de l'océan, les études isotopiques menées dans le cadre de ce travail ont montré que les tailings étaient saturés en eau douce. Cette saturation est due à la pression hydraulique résultant de la mise en place des zones humides. Un écoulement d'eau souterrain sous-marin a été à détecté à l'interface entre les résidus et l'ancien fond marin. En raison de la géologie locale, il constitue une source d'entrée de SO4 2-, Cl-, Na+, FeZ+, et Mn2+ dans le système. L'analyse de la géochimie aquatique, la Diffraction aux Rayons X (XRD) et l'extraction séquentielle ont montré que l'oxydation du fer et .des sulfures est le principal processus se produisant dans les déchets non remédiés. Ceci a entraîné le développement d'une zone d'oxydation à pH bas induisant une forte accumulation des sels efflorescents, conséquence de la migration capillaire des métaux lourds (Fe, Cu, Zn, Mn, Cd, Co et Ni) de la solution vers la surface dans ce climat aride. Cette étude a montré également que la construction de la zone humide a eu comme résultats une précipitation des métaux dans des phases minérales en raison du pH neutre et des conditions réductrices (100-150mV). Les métaux lourds ont précipité sous la forme d'hydroxydes et de sulfures ou sont adsorbés à la matière organique. L'analyse de la composition de la communauté bactérienne à l'aide la technique T-RFLP (Terminal Restriction Fragment Length Polymorphism) et par le clonage/séquençage des gènes de l'ARNr 16S a été combinée à une statistique détaillée. Cette dernière a révélé une forte corrélation entre la distribution de bactéries spécifiques et la géochimie : Les bactéries autotrophes acidophiles dominent dans les déchets oxydés non remédiés, tandis que des bactéries hétérotrophes neutrophiles ont mené les processus microbiens dans les déchets remédiés sous la zone humide. Sous la surface de la zone humide, nos analyses ont également mis en évidence un cycle du fer par des processus d'oxydoréduction rendus possibles par la présence de niches micro-aérées par la rhizosphère dans cet environnement réducteur. L'expérience de bio-remédiation in situ a montré que les paramètres clés qui contrôlent l'efficacité du traitement sont le niveau de la nappe aquifère et la chimie de l'eau. Les cellules de remédiation se sont montrées plus efficaces et plus rapides lorsque le système a pu être saturé en eau. Finalement, cette étude a montré que la bio-remédiation de déchets miniers par la construction de zones humides est un moyen de traitement efficace, rapide et peu coûteux. Cependant, la saturation en eau du système doit être gérée sur le long terme afin de garantir la stabilité de l'ensemble du système.

Petrology and chemistry of the Chalten Plutonic Complex and implications on the magmatic and tectonic evolution of the Southernmost Andes (Patagonia) during the Miocene

Résumé Scientific:Pétrologie et Géochimie du Complexe Plutonique de Chaltén et les conséquences pour l'évolution magmatique et tectonique du Andes du Sud (Patagonia) pendant le MiocèneLe sujet de cette thèse est le Complexe Plutonique de Chaltén (CHPC), situé à la frontière entre le Chili et l'Argentine, en Patagonie (49°15'S). Ce complexe s'est mis en place au début du Miocène, dans un contexte de changements tectoniques importants. La géométrie et la vitesse de migration des plaques en Patagonie a été modifiée suite l'ouverture de la plaque Farallon il y a 25Ma (Pardo-Casas and Molnar 1987) et la subduction de la ride active du Chili sous la plaque sud-américaine il y a 14Ma (Cande and Leslie 1986). Les effets de cette reconfiguration tectonique sur la morphologie et le magmatisme de la plaque supérieure sont encore sujets à discussion. Dans ce contexte, un groupe d'intrusions miocènes - telle que le CHPC - est particulièrement intriguant, car en position transitionnelle entre le batholithe patagonien et l'arc volcanique cénozoïque et récent à l'ouest, et les laves de plateau de Patagonie à l'est (Fig. 1). A cause de leur position tectonique transitoire, ces plutons isolés hors du batholithe représentent un endroit clé pour comprendre les interactions entre la tectonique à large échelle et le magmatisme en Patagonie. Ici, je présente de nouvelles données de terrain, petrologiques, géochimiques et géochronologiques dans le but de caractériser la nature du CHPC, qui était largement inconnu avant cette étude, dans le but de tester l'hypothèse de migration de l'arc et erosion par subduction.Les résultats de l'investigation géochimique (chapitre 2) montrent que le CHPC n'est qu'un exemple parmi les plutons isolés d'arrière arc ave une composition calco-alcaline caractéristique, c-à-d une signature d'arc. La plupart de ces plutons isolés ont une composition alcaline. Le CHPC, contrairement, a une signature calco-alcaline avec Κ intermédiaire, tel que le batholithe patagonien et la plupart des roches volcaniques quaternaires liées à l'arc le long des Andes.De nouvelles données géochronologiques U-Pb de haute précision sur des zircons, acquis par TIMS, sur le CHPC donnent des âges entre 17.0 et 16.4Ma. Les âges absolus sont en accord avec la séquence intrusive déduite des relations de terrain (chapitre 1). Ces données sont les premières contraintes d'âge U-Pb sur le CHPC. Elles montrent clairement que l'histoire magmatique du CHPC n'a pas de lien direct avec la subduction de la ride à cette latitude (Cande and Leslie 1986), car le complexe est au moins 6Ma plus ancien.Une comparaison en profondeur avec les autres intrusions d'âge Miocène en Patagonie révèlent - pour la première fois - une évolution temporelle intéressante. Il y a une tendance E-W distincte au magmatisme calco-alcalin entre 20-16Ma avec une diminution de l'âge vers l'est - le CHPC est l'expression la plus orientale de cette tendance. Je suggère que la relation espace-temps reflète une migration vers l'est (vers le continent) de l'arc magmatique. Je propose que le facteur principal contrôlant cette migration est la subduction rapide suite à la reconfiguration de la vitesse des plaques tectoniques après l'ouverture la plaque Farallon (à ~26Ma) qui résulterait en une déformation importante ainsi qu'à des taux élevés d'érosion dans la fosse de subduction.Les rapports d'isotopes radiogéniques (Pb, Sr, Nd) élevés, une signature 6018 basse et un rapport Th/La élevé sont des paramètres distinctifs pour les roches mafiques du CHPC. Le modèle isotopique présenté (chapitre 2) suggère que cette signature reflète une contamination de la source, dans le coin de manteau, plutôt qu'une contamination crustale. La signature des éléments en trace du CHPC indiquent que le coin de manteau a été contaminé par des composés terrigènes, le plus vraisemblablement par des sédiments paléozoïques.Les travaux de terrain, la pétrographie et la géothermobarométrie ont été utilisés dans le but de comprendre l'histoire interne du CHPC (chapitre 3). Ces données suggèrent deux niveaux distincts de cristallisation : l'un dans la croûte moyenne (6 à 4.5kbar) et l'autre à un niveau peu profond (3.5 à 2kbar). La modélisation isotopique AFC de la contamination crustale indique des taux variables d'assimilation, qui ne sont pas corrélés avec le degré de différenciation. Cela suggère que différents volumes de magma se sont différenciés en profondeur, de façon indépendante. Cela implique que le CHPC se serait formés en plusieurs puises de magmas provenant d'au moins trois sources différentes. Les textures des granodiorites et des granites indiquent des teneurs élevées en cristaux avant la mise en place et, par conséquent, des températures d'emplacement faibles. Les observations de terrain montrent que les roches mafiques sont déformées, alors que ce n'est pas le cas pour les granodiorites et granites (plus jeunes). La déformation des roches mafiques est encore sujet de recherche, afin de savoir si elle est liée à la déformation régionale en régime compressif ou à l'emplacement lui-même. Cependant, la mise en place de grand volume de magma felsique riche en cristaux suggère un régime d'extension.Scientific Abstract:Petrology and chemistry of the Chaltén Plutonic Complex and implications on the magmatic and tectonic evolution of the Southernmost Andes (Patagonia) during the MioceneThe subject of this thesis is the Chaltén Plutonic Complex (CHPC) located at the frontier between Chile and Argentina in Patagonia (at 49° 15 'Southern latitude). This complex intruded during early Miocene in a context of major tectonics changes. The plate geometry of Patagonia has been modified by changes in the plate motions after the break up of the Farallôn plate at 25Ma (Pardo-Casas and Molnar 1987) and by the subduction of the Chile spreading Ridge beneath South-America at 14 Ma (Cande and Leslie 1986). The effects of this tectonic setting on the morphology and the magmatism of the overriding plate are a matter of on-going discussion. Particularly intriguing in this context is a group of isolated Miocene intrusions - like the CHPC - which are located in a transitional position between the Patagonian Batholith and the Cenozoic and Recent volcanic arc in the West, and the Patagonian plateau lavas in the East (Fig. 1). Due to their transient tectonic position these isolated plutons outside the batholith represent a key to understanding the interaction between global-scale tectonics and magmatism in Patagonia. Here, I present new field, penological, geochemical and geochronological data to characterize the nature of the CHPC, which was largely unknown before this study, in order to test the hypothesis of time- transgressive magmatism.The results of the geochemical investigation (Chapter 2) show that the CHPC is only one among these isolated back-arc plutons with a characteristic calc-alkaline composition, i.e. arc signature. Most of these isolated intrusives have an alkaline character. The CHPC, in contrast, has a medium Κ calc-alkaline signature, like the Patagonian batholith and most of the Quaternary arc-related volcanic rocks along the Andes.New high precision TIMS U-Pb zircon dating of the CHPC yield ages between 17.0 to 16.4 Ma. The absolute ages support the sequence of intrusion relations established in the field (Chapter 1). These data are the first U-Pb age constraints on the CHPC, and clearly show that the magmatic history of CHPC has no direct link to the subduction of the ridge, since this complex is at least 6 Ma older than the time of collision of the Chile ridge at this latitude (Cande and Leslie 1986).An in-depth comparison with other intrusion of Miocene age in Patagonia reveals - for the first time - an interesting temporal pattern. There is a distinct E-W trend of calc-alkaline magmatism between 20-16 Ma with the younging of ages in the East - the CHPC is the easternmost expression of this trend. I suggest that this time-space relation reflects an eastward (landward) migration of the magmatic arc. I propose that main factor controlling this migration is the fast rates of subduction after the major reconfigurations of the plate tectonic motions after the break up of the Farallôn Plate (at -26 ) resulting in strong deformation and high rates of subduction erosion.High radiogenic isotope ratios (Pb, Sr, Nd) ratios, low 5018 signature and high Th/La ratios in mafic rocks are distinctive features of the CHPC. The presented isotopic models (Chapter 2) suggest that this signature reflects source contamination of the mantle wedge rather than crustal contamination. The trace element signature of the CHPC indicates that the mantle wedge was contaminated with a terrigenous component, most likely from Paleozoic sediments.Fieldwork, petrography and geothermobarometry were used to further unravel the internal history of the CHPC (Chapter 3). These data suggest two main levels of crystallization: one a mid crustal levels (6 to 4.5 kbar) and other a shallow level (3.5 to 2 kbar). Isotopic AFC modeling of crustal contamination indicate variable rates of assimilation, which are not correlated with the degree of differentiation. This suggests that different batches of magma differentiate independently at depths. This implies that the CHPC would have formed by several pulses of magmas from at least 3 different sources. Textures of granodiorites and granites indicate a high content of crystals previous to the emplacement and consequently low emplacement temperatures. Field observations show that the mafic rocks are deformed, whereas the (younger) granodiorites and granites are not. It is still subject of investigation whether the deformation of the mafic rocks is related to regional deformation during a compressional regime or to the emplacement it self. However, the emplacement of huge amount of crystal rich felsic magmas suggests an extensional regime.Résumé Grand PublicPétrologie et Géochimie du Complexe Plutonique de Chaltén et les conséquences pour l'évolution magmatique et tectonique du Andes du Sud (Patagonia) pendant le MiocèneLe Complexe Plutonique de Chaltén (CHPC) est un massif montagneux situé à 49°S à la frontière entre le Chili et l'Argentine, en Patagonie (région la plus au sud de l'Amérique du Sud). Il est composé de montagnes qui peuvent atteindre plus de 3000 mètres d'altitude, telles que le Cerro Fitz Roy (3400m) et le Cerro Torre (3100m). Ces montagnes sont composées de roches plutoniques, c.-à-d. des magmas qui se sont refroidis et ont cristallisés sous la surface terrestre.La composition chimique de ces roches montre que les magmas, qui ont formé ce complexe plutonique, font partie d'un volcanisme d'arc. Celui-ci se forme lorsqu'une plaque océanique plonge sous une plaque continentale. Les géologues appellent ce processus « subduction ». Dans un tel scénario, le manteau terrestre, qui se fait prendre entre ces deux plaques, fond pour former ainsi du magma. Ce magma remonte à travers la plaque continentale vers la surface. Si celui-ci atteint la surface, il forme les roches volcaniques, comme par exemple des laves. S'il n'atteint pas la surface, le magma se refroidit pour former finalement les roches plutoniques.Le long de la marge ouest d'Amérique du Sud, la plaque Nazca - qui se situe au sud-est de la plaque océanique pacifique - passe en dessous de la plaque d'Amérique du Sud. La bordure ouest du sud de la plaque sud-américaine a également été affectée par d'autres processus tectoniques, tels que des changements dramatiques dans les déplacements de plaques (il y a 25Ma) et la collision de la ride du Chili (depuis 15 Ma jusqu'à aujourd'hui). Ces caractéristiques tectoniques et magmatiques font de cette région un haut lieu pour les géologues. La plaque Nazca, s'est formée suite à l'ouverture d'une plaque océanique plus ancienne, il y a 25Ma. Cette ouverture est liée aux vitesses de subduction les plus rapides jamais connues. La ride du Chili est l'endroit où le sol de l'Océan Pacifique s'ouvre, formant deux plaques océaniques : les plaques Nazca et Antarctique. La ride du Chili subducte sous la plaque sud-américaine depuis 15Ma, en association avec la formation de grands volumes de magma ainsi que des changements morphologiques importants. La question de savoir lequel de ces changements tectoniques globaux affecte la géologie et la géographie de Patagonie a été, et est encore, discutée pendant de nombreuses années. De nombreux chercheurs suggèrent que la plupart des caractéristiques morphologiques et magmatiques en Patagonie sont liés à la subduction de la ride du Chili, mais cette suggestion est encore débattue comme le montre notre étude.Le batholithe de Patagonie du sud (SPB) est un énorme massif composé de roches plutoniques et il s'étend tout au long de la côte ouest de Patagonie (au sud de 47°S). Ces roches correspondent certainement aux racines d'un ancien arc volcanique, qui a été soulevé et érodé. Le CHPC, ainsi que d'autres petites intrusions dans la région, se situe dans une position exotique, à 100km à l'est du SPB. Certains chercheurs suggèrent que ces intrusions pourraient être liées à la subduction de la ride du Chili.Afin de débattre de cette problématique, nous avons utilisé différentes méthodes géochronologiques pour déterminer l'âge du CHPC et le comparer (a) à l'âge des roches intrusives similaires du SPB et (b) à l'âge de la collision de la ride du Chili. Dans ce travail, nous prouvons que le CHPC s'est formé au moins 7Ma avant la collision avec la ride du Chili. Sur la base des âges du CHPC et de la composition chimique de ses roches et minéraux, nous proposons que le CHPC fait partie d'un arc volcanique ancien. La migration de l'arc volcanique plus profondément dans le continent résulte de la grande vitesse de subduction entre 25 et lOMa. Des caractéristiques évidentes pour un tel processus - telles qu'une déformation importante et une vitesse d'érosion élevée - peuvent être rencontrées tout au long de la bordure ouest de l'Amérique du sud.

Bacterial contamination of platelet concentrates: pathogen detection and inactivation methods

Whereas the reduction of transfusion related viral transmission has been a priority during the last decade, bacterial infection transmitted by transfusion still remains associated to a high morbidity and mortality, and constitutes the most frequent infectious risk of transfusion. This problem especially concerns platelet concentrates because of their favorable bacterial growth conditions. This review gives an overview of platelet transfusion-related bacterial contamination as well as on the different strategies to reduce this problem by using either bacterial detection or inactivation methods.

Mineralogical, K-Ar, stable and Sr isotope systematics of K-white micas during very low-grade metamorphism of limestones (Helvetic nappes, Western Switzerland)

Mineralogical, K-Ar, Rb-Sr and stable isotope analyses have been carried out on K-white micas from Helvetic Malm limestones in order to examine their evolution during very low- to low-grade Alpine metamorphism, associated with intense ductile deformation. Metamorphic temperatures were estimated al approximately 300-degrees-C from stable isotopes (quartz-calcite thermometry), occurrence of chloritoid, and `'epizonal'' illite crystallinity index. K-white micas consist of variable mixtures of 2M, phengite and muscovite, as revealed by detailed X-ray diffraction analyses using peak decomposition of the (060, 331) spectra. K-Ar apparent ages display a strong grain-size dependence in which mainly fine-grained size fractions (< 2 mum) record Alpine ages (37-15 Ma). However, these ages provide a relative rather than an absolute chronology of the diachronous Alpine metamorphic evolution of the Helvetic nappes. The resetting of the K-Ar isotopic system of K-white micas to Alpine metamorphic conditions reflects an apparent combination of crystallization/recrystallization and radiogenic Ar-40 diffusion loss. The oxygen isotope compositions of micas (+ 15 to + 22 parts per thousand) are intermediate between detrital and O-18-enriched values expected for micas neoformed within an abundant marine carbonate matrix. No isotopic equilibrium has been reached between calcite and micas. The variable depletion of hydrogen isotope compositions (- 126 to - 82 parts per thousand) is influenced by the interaction with organic matter under closed-system conditions. Organic matter, if not removed, may also represent a serious source of error in K-Ar age determination, by introducing radiogenic Ar-40 contamination. Sr-87/Sr-86 isotope ratios of micas range from 0.70879 to 0.70902 with one outlier at 0.71794. The low values reflect Sr exchange with calcite occurring during crystallization/recrystallization of micas under closed-system conditions.

Assessment of airborne virus contamination in wastewater treatment plants

INTRODUCTION: Occupational exposure to bioaerosols in wastewater treatment plants (WWTP) and its consequence on workers׳ health are well documented. Most studies were devoted to enumerating and identifying cultivable bacteria and fungi, as well as measuring concentrations of airborne endotoxins, as these are the main health-related factors found in WWTP. Surprisingly, very few studies have investigated the presence and concentrations of airborne virus in WWTP. However, many enteric viruses are present in wastewater and, due to their small size, they should become aerosolized. Two in particular, the norovirus and the adenovirus, are extremely widespread and are the major causes of infectious gastrointestinal diseases reported around the world. The third one, hepatitis E virus, has an emerging status. GOAL AND METHODS: This study׳s objectives were to detect and quantify the presence and concentrations of 3 different viruses (adenovirus, norovirus and the hepatitis E virus) in air samples from 31 WWTPs by using quantitative polymerase chain reaction (qPCR) during two different seasons and two consecutive years. RESULTS: Adenovirus was present in 100% of summer WWTP samples and 97% of winter samples. The highest airborne concentration measured was 2.27×10(6) genome equivalent/m(3) and, on average, these were higher in summer than in winter. Norovirus was detected in only 3 of the 123 air samples, and the hepatitis E virus was not detected. CONCLUSIONS: Concentrations of potentially pathogenic viral particles in WWTP air are non-negligible and could partly explain the work-related gastrointestinal symptoms often reported in employees in this sector.

Accumulation of phosphorus fractions and contamination potential in vineyard soils in the southern region of the state of Santa Catarina, Brazil

In vineyards, if phosphate is applied both before planting and at intervals during growth without consideration of technical criteria, the soil P fractions may be increased and their proportions altered. This study was carried out to evaluate the accumulation of P fractions and the parameters of the adsorption isotherm in a sandy Typic Hapludalf soil in vineyards with a history of successive and excessive phosphate fertilization. In December 2010, two vineyards were selected, one 4 and the other 15 years old, in Urussanga, State of Santa Catarina (Brazil). Three trenches were dug in each area and soil was collected from the 0-5, 5-10 and 10-20 cm depth ranges. The soil samples were dried in a forced-air oven, sieved and subjected to chemical analyses, P chemical fractionation and P adsorption isotherms. Excessive phosphate fertilization, before and during cultivation, particularly in the older vineyard and, consequently, with a longer history of phosphate fertilization, increased the inorganic P concentrations to the depth of 20 cm, especially in labile fractions extracted by anion exchange resin and NaHCO3 in the non-labile fraction, as well as in the non-labile fraction extracted by 1.0 mol L-1 HCl. The application of phosphate fertilizers and the long cultivation period increased the P levels in the organic labile fraction extracted by 0.5 mol L-1 NaHCO3, and especially in the moderately labile fraction extracted by 0.1 and 0.5 mol L-1 NaOH. Phosphate fertilization of older vineyards, i.e., cultivated for 15 years, increased the amounts of P desorbed in water, indicating a risk of contamination of surface waters and groundwater. The phosphate fertilization before planting, without considering the results of soil analysis, and during cultivation, disregarding the results of soil analysis, leaf analysis and expected yield, led to a reduction in the maximum P adsorption capacity in the 0-5 cm layer of vineyard 2, indicating saturation of part of the reactive particle adsorption sites.

Study of post-deposition contamination in low-temperature deposited polysilicon films

The presence of hydrogen in polysilicon films obtained at low temperatures by hot-wire CVD and the post-deposition oxidation by air-exposure of the films are studied in this paper. The experimental results from several characterization techniques (infrared spectroscopy, X-ray photoelectron spectroscopy, secondary ion mass spectrometry and wavelength dispersive spectroscopy) showed that hydrogen and oxygen are homogeneously distributed at grain boundaries throughout the depth of the films. Hydrogen is introduced during the growth process and its concentration is higher in samples deposited at lower temperatures. Oxygen diffuses along the grain boundaries and binds to silicon atoms, mainly in Si 2O groups.

Capillary thermal desorption unit for near real-time analysis of VOCs at sub-trace levels. Application to the analysis of environmental air contamination and breath samples

A capillary microtrap thermal desorption module is developed for near real-time analysis of volatile organic compounds (VOCs) at sub-ppbv levels in air samples. The device allows the direct injection of the thermally desorbed VOCs into a chromatographic column. It does not use a second cryotrap to focalize the adsorbed compounds before entering the separation column so reducing the formation of artifacts. The connection of the microtrap to a GC–MS allows the quantitative determination of VOCs in less than 40 min with detection limits of between 5 and 10 pptv (25 °C and 760 mmHg), which correspond to 19–43 ng m−3, using sampling volumes of 775 cm3. The microtrap is applied to the analysis of environmental air contamination in different laboratories of our faculty. The results obtained indicate that most volatile compounds are easily diffused through the air and that they also may contaminate the surrounding areas when the habitual safety precautions (e.g., working under fume hoods) are used during the manipulation of solvents. The application of the microtrap to the analysis of VOCs in breath samples suggest that 2,5-dimethylfuran may be a strong indicator of a person's smoking status

Mycobiota evolution during storage of paddy, brown and milled rice in different genotypes

The rice grain is frequently infected by a series of pathogens (fungi) during its storage, producing damages to the economy and health of humans. The aim of this study was to identify the fungal genera present in different rice genotypes and to quantify their variation during storage. Paddy, brown and milled rice fractions of Nutriar, (N) H329-5(H329) and Don Ignacio genotypes were analyzed at 4, 8 and 12 months of storage. Fungi were identified based on their micromorphological characteristics and colonies. The observed genera according to their frequency were: Alternaria, Nigrospora, Epicoccum, Bipolaris, Curvularia, Cladosporium and Fusarium (field fungi) and Penicillium and Aspergillus (storage fungi). The mycobiota composition was different depending on the grain fraction and the period of storage: field fungi were located in the hulls and bran layers, while storage fungi were mainly in the endosperm. The different genotypes showed different susceptibility to contamination.

Identification of main contamination points by hygiene indicator microorganisms in beef processing plants

The microbiological quality of beef and meat products is strongly influenced by the conditions of hygiene prevailing during their production and handling. Without proper hygienic control, the environment in slaughterhouses and butcher shops can act as an important source of microbiological contamination. To identify the main points of microbiological contamination in the beef processing chain, 443 samples of equipment, installations and products were collected from 11 establishments (1 slaughterhouse and 10 butcher shops) located in the state of Paraná, Brazil. The microbiological quality of all the samples was evaluated using Petri dishes to obtain counts of mesophilic aerobes (AC), total coliforms, Escherichia coli (EC), yeasts and molds (YM). The main contamination points identified in butcher shops, in decreasing order, were stainless steel boxes, beef tenderizers, grinders, knives, mixers, sausage stuffers, plastic boxes, floors and drains. In the slaughterhouse, these points were sausage stuffers, platforms, floors and drains. The most severely contaminated products were fresh sausages and ground beef. This information about the main points of microbiological contamination in the beef processing chain is expected to aid professionals responsible for hygiene in similar establishments to set up proper hygienic procedures to prevent or reduce microbiological contamination of beef and meat products.

Influence of physical damage and freezing on histamine concentration and microbiological quality of yellowfin tuna during processing

Yellowfin tuna has a high level of free histidine in their muscle, which can lead to histamine formation by microorganisms if temperature abuse occurs during handling and further processing. The objective of this study was to measure levels of histamine in damaged and undamaged thawed muscle to determine the effect of physical damage on the microbial count and histamine formation during the initial steps of canning processing and to isolate and identify the main histamine-forming microorganisms present in the flesh of yellowfin tuna. Total mesophilic and psicrophilic microorganisms were determined using the standard plate method. The presence of histamine-forming microorganisms was determined in a modified Niven's agar. Strains were further identified using the API 20E kit for enterobacteriaceae and Gram-negative bacilli. Physically damaged tuna did not show higher microbiological contamination than that of undamaged muscle tuna. The most active histamine-forming microorganism present in tuna flesh was Morganella morganii. Other decarboxylating microorganisms present were Enterobacter agglomerans and Enterobacter cloacae. Physical damage of tune during catching and handling did not increase the level of histamine or the amount of microorganisms present in tuna meat during frozen transportation, but they showed a higher risk of histamine-forming microorganism growth during processing.

Green and brown propolis: efficient natural biocides for the control of bacterial contamination of alcoholic fermentation of distilled beverage

This study aimed to evaluate the efficiency of natural biocides, brown and green propolis, for the control of bacterial contamination in the production of sugarcane spirit. The treatments consisted of brown and green propolis extracts, ampicillin, and a control and were assessed at the beginning and end of harvest season in ten fermentation cycles. In the microbiological analyses, the lactic acid bacteria were quantified in the inoculum before and after the treatment with biocides, and the viability of yeast cells during fermentation was evaluated. The levels of acids, glycerol, total residual reducing sugars, and ethanol were analyzed for the wine resulting from each fermentation cycle. A reduction in the number of bacterial contaminants in the inoculum in the treatments with the natural biocides was observed, but it did not affect the viability of yeast cells. The control of the contaminants led to the production of higher levels of ethanol and reduced acidity in the wine produced. The results of the use of brown and green propolis to control the growth microorganisms in the fermentation of sugarcane spirit can be of great importance for using alternative strategies to synthetic antibacterials in fermentation processes including other distilled beverage or spirits.

Analyse de l'effet de la contamination du sol sur la croissance et la physiologie de 11 cultivars de Salix

Mon mémoire de maîtrise a été réalisé dans le cadre du projet Génorem (www.genorem.ca), un projet multidisciplinaire qui réunit différents chercheurs de l'Université de Montréal et de l'Université McGill dans le but d'améliorer les techniques utilisées en bioremédiation. Dans le cadre de l'étude, des saules à croissance rapide (Salix sp.) ont été utilisés comme plantes modèles dans l'étude. Ainsi, 11 cultivars de saule ont été suivis afin de déterminer leur potentiel à produire un bon rendement de biomasse, à tolérer des conditions de stress sévère causé par la présence de HAPs (hydrocarbures aromatiques polycycliques) , BPCs (biphényles polychlorés) et d'hydrocarbures pétroliers C10-C50. L'expérimentation consistait en une plantation de saule à forte densité qui a été mise en place en 2011 sur le site d'une ancienne industrie de pétrochimie à Varennes, dans le sud du Québec. Les boutures des génotypes sélectionnés ont été plantées sur une superficie d'environ 5000 m2. Les plantes ont été suivies pendant les deux saisons de croissance suivant le recépage et une série de paramètres de croissance et de mesures physiologiques ont été récoltés (surface foliaire, taux de chlorophylle, conductance stomatique et statut nutritionnel) dans le but d'évaluer et de comparer les performances de chaque génotype sur un sol pollué. Les analyses statistiques ont démontré que le cultivar S. miyabeana (SX61) était le meilleur producteur de biomasse sur le site contaminé, tandis que S. nigra (S05) et S. acutifolia (S54) présentaient la meilleure capacité photosynthétique. S. dasyclados (SV1), S. purpurea (‘Fish Creek’) et S. caprea (S365) ont semblé particulièrement affectés par la présence de contaminants. La capacité d'établissement et la croissance de S. nigra (S05), S. eriocephala (S25) and S. purpurea x S. miyabeana (‘Millbrook’) indiquent une tolérance globale supérieure à la pollution . Cette analyse comparative des différentes réponses physiologiques des saules cultivés sur un sol contaminé pourra guider le processus de sélection de plantes et les techniques de bioremédiation dans les futurs projets de phytoremédiation.

Potential public health significance of faecal contamination and multidrug-resistant Escherichia coli and Salmonella serotypes in a lake in India

To assess the prevalence of faecal coliform bacteria and multiple drug resistance among Escherichia coli and Salmonella serotypes from Vembanadu Lake. Study design: Systematic microbiological testing. Methods: Monthly collection of water samples were made from ten stations on the southern and northern parts of a salt water regulator constructed in Vembanadu Lake in order to prevent incursion of seawater during certain periods of the year. Density of faecal colifrom bacteria was estimated. E. coli and Salmonella were isolated and their different serotypes were identified. Antibiotic resistance analysis of E. coli and Salmonella serotypes was done and the MAR index of individual isolates was calculated. Results: Density of faecal coliform bacteria ranged from mean MPN value 2900 -7100/100ml. Results showed multiple drug resistance pattern among the bacterial isolates. E. coli showed more than 50% resistance to amickacin, oxytetracycline, streptomycin, tetracycline and kanamycin while Salmonella showed high resistance to oxytetracycline, streptomycin, tetracycline and ampicillin. The MAR indexing of the isolates showed that they have originated from high risk source such as humans, poultry and dairy cows. Conclusions: The high density of faecal coliform bacteria and prevalence of multi drug resistant E. coli and Salmonella serotypes in the lake may pose severe public health risk through related water borne and food borne outbreaks