A espectrometria de massas baseada na tecnologia MALDI-TOF (do inglês, matrix-assisted laser desorption ionization-time of flight) (MALDI-TOF MS) tem sido cada vez mais incorporada à rotina de identificações microbiológicas nos laboratórios farmacêuticos de controle de qualidade, principalmente para as atividades do Programa de Monitoramento Ambiental de Salas Limpas. Isso porque o longo tempo necessário para a obtenção dos resultados por meio de métodos convencionais tem incentivado a procura por técnicas que permitam métodos rápidos. O objetivo deste trabalho foi avaliar a adequação da técnica MALDI-TOF MS para a identificação de bactérias isoladas do ambiente de salas limpas utilizadas em algumas etapas da produção de uma vacina viral. Treze espécies bacterianas conhecidas, normalmente isoladas das salas limpas estudadas, e cinco cepas ATCC foram identificadas pela técnica MALDI-TOF MS e por uma técnica bioquímica (BBL Crystal®). O desempenho da técnica MALDI-TOF MS foi superior ao da técnica bioquímica na identificação correta das espécies bacterianas (88,89% e 38,89%, respectivamente) e produziu menos identificações não confiáveis (5,55% e 22,22%, respectivamente). Os resultados evidenciaram que a técnica MALDI-TOF MS pode ser implementada para identificação rotineira de bactérias em um laboratório de controle de qualidade farmacêutico. Entretanto, a dependência de bases de dados exige estudos adicionais de isolados não identificados e, se apropriado, a adição destes a uma base de dados interna. O aperfeiçoamento de métodos de identificação microbiana é muito relevante no contexto de salas limpas, pois permitem ações corretivas e proativas essenciais para garantir a segurança microbiológica do processamento asséptico. / Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been increasingly introduced in routine microbiological identifications of pharmaceutical quality control laboratories, mainly for the activities of the Environmental Monitoring Program of Clean Rooms. The long time needed to obtain the results through conventional methods has stimulated the search for techniques that allow rapid methods, as MALDI-TOF MS. Thus, the objective of this work was to evaluate the suitability of the MALDI-TOF MS technique for the identification of bacteria isolated from the environment of clean rooms used in some stages of the production of a viral vaccine. Thirteen bacterial species commonly isolated from clean rooms studied and five strains ATCC were identified by MALDI-TOF MS technique and by a biochemical technique (BBL Crystal® System). Performance of MALDI-TOF MS was better than biochemical technique for correct species identifications (88.89% and 38.89%, respectively) and produced fewer unreliable identifications (5.55% and 22.22%, respectively). MALDI-TOF MS can be implemented for routine identification of bacteria in a pharmaceutical quality control laboratory. However, as a database-dependent system, maybe some isolated not identified by this technique must be additionally studied and, if appropriate, added to an in-house database.

La réduction de la consommation énergétique dans le secteur de bâtiments présente aujourd’hui une priorité primordiale dans les politiques des pays industrialisés. En France, le secteur du bâtiment consomme environ 43 % de l’énergie finale et contribue pour près d’un quart aux émissions nationales de gaz à effet de serre [ADEME]. Il se positionne comme un acteur clé pour parvenir à résoudre les inquiétants défis environnementaux auxquels nous devons faire face. Face à ces véritables défis, l’augmentation des niveaux d’exigence des réglementations thermiques s’est poursuivie et intensifiée pendant les 40 dernières années, jusqu’à la naissance de la réglementation thermique 2012, qui a permis de construire des bâtiments basse consommation (BBC) qui équivaut à 50 kWh/m².an. Cette nouvelle réglementation plus exigeante constitue une incitation forte à l'innovation des matériaux, produits et systèmes d'enveloppe. Dans ces conditions, l’amélioration des performances hygrothermiques des matériaux de construction aura des retombées économiques et environnementales conséquentes. C’est dans ce contexte que ce travail a été mené. Il vise à étudier et à améliorer les performances des produits de l’entreprise Briqueteries du Nord (BdN). Il est réparti sur deux axes principaux : le premier consiste à l’étude de l’inertie thermique et du pouvoir hygroscopique des briques en terre crue. Le second axe vise à élaborer des solutions possibles concernant l’amélioration de la résistance thermique des briques en terre cuite. Ce travail de recherche a été réalisé au laboratoire de l’Ecole Centrale de Lille avec une étroite collaboration avec l’université d’Artois et l’entreprise (BdN) / Nowadays, the reduction of energy consumption in buildings industry represents a major issue in industrialized countries’ policies. In France, the building sector consumes about 43% of final energy and accounts for nearly a quarter of the national emissions of greenhouse gas emissions [ADEME]. It is considered as a key factor to overcome the environmental challenges we have to face.In front of these significant challenges, the thermal regulations requirements were seriously intensified during the last 40 years until the notification of the thermal regulation 2012. This latter enable the construction of low energy buildings (BBC) whose consumption is equivalent to 50 kWh/m² per year on average. This new regulation provides a strong incentive for innovation of materials, products and envelope systems. Under these conditions, improving hygrothermal performance of building materials will allow a substantial economic and environmental benefits. This work was conducted in this context. It aims to study and improve the performance of the company Briqueteries du Nord (BdN) products. It is divided in two main axis: the first consists on studying the thermal inertia and hygroscopic capacity of unfired clay bricks. However, the second axis aims to develop possible solutions for improving the thermal resistance of fired clay bricks. This research was conducted in the laboratory of the Ecole Centrale de Lille with close collaboration with the University of Artois and the BdN company

Cette thèse se consacre à la mise au point de techniques d’échantillonnage suivies d’analyses réalisées au laboratoire pour mettre en évidence les espèces majoritaires en air intérieur et caractériser leurs variations temporelles. Le développement analytique a été effectué pour 52 COVs et pour 16 HAPs associés à la phase particulaire de l’air. Les prélèvements des COVs ont été réalisés au moyen d’un préleveur automatique permettant d’échantillonner l’air sur des tubes extraits par désorption thermique et analysés par chromatographie gazeuse couplée à la détection FID. Pour la quantification des HAPs, le prélèvement des particules est effectué par un impacteur à cascade à trois étages permettant de fractionner l’aérosol en fonction de leur diamètre aérodynamique. Les HAPs sont quantifiés par chromatographie liquide haute performance couplée à la détection par fluorescence. Ces deux techniques ont été mises en application dans le cadre de la 1ère campagne intensive du projet MERMAID. / This work aims at developing rapid and simple air sampling techniques followed by laboratory analyses to highlight the occurrence of the main species in indoor air and to describe their temporal variations. The analytical development was focused on 52 VOCs belonging to a wide variety of chemical families to determine their concentrations. The sampling step was performed using an automatic sampler allowing the sampling of air on adsorbent tubes. These tubes were then thermally desorbed and analyzed by gas chromatography coupled to FID. Another analytical development was conducted to determine the particle bound PAHs concentrations. The sampling of particles was realized by the mean of a 3-stages cascade impactor allowing an aerosol fractionation depending on their aerodynamic diameter. Finally, quantification of PAHs was realized by liquid chromatography coupled to fluorescence detection. These two techniques were applied in a field campaign in the frame of the MERMAID program.

Les effluents industriels issus des activités de textile présentent souvent une importante charge polluante colorante difficilement biodégradable. Des travaux antérieurs ont montré le potentiel des argiles naturelles non traitées à dépolluer ces effluents teinturiers alors qu’ils sont généralement composés de colorants anioniques difficilement adsorbables sur ces supports. Or, les effluents contiennent également d’autres composés chimiques utilisés dans les différentes étapes du procédé de teinture, et qui sont de natures variées (sels, acides, bases, détergents, dérivés enzymatiques, etc…). Il semblerait que ces produits auxiliaires jouent un rôle dans l'adsorption de colorants anioniques sur l'argile non traitée. Cependant, aucune étude connue à ce jour, n'a porté sur l'effet des additifs de teinture dans le processus de décoloration par des absorbants en général, et par les argiles en particulier. Cette étude est la première à s’intéresser au système colorant-additif-argile. Des tests d’adsorption / désorption en batch ont été menés en considérant différents systèmes colorant-additif-argile. Les résultats des tests montrent que les additifs de type enzymatique favorisent l’adsorption de colorant anionique sur l’argile en neutralisant les charges négatives et en renforçant les liaisons argile-colorant. D’autres additifs ont un effet contraire mais n’annulent pas l’effet positif des additifs enzymatiques lorsqu’ils sont mélangés dans l’effluent. Des hypothèses d’interactions mises en jeu lors de l’adsorption de colorant ont été faites en s’aidant des résultats de la spectrométrie infra-rouge et de masse, de la zétamétrie et de la modélisation des isothermes d’adsorption. / Industrial effluents from textile activities often have a high pollution load readily biodegradable. Previous work has shown the potential of natural untreated clays to clean up these dyers effluents although anionic dyes are not easily absorbable on these media. The effluents also contain other chemical compounds used in the different stages of the dyeing process, and which are of various natures (salts, acids, bases, detergents, enzyme derivatives, etc ...). It appears that these auxiliary products play a role in the adsorption of anionic dyes on untreated clay. However, no currently known study has examined the effect of the additives from the dyeing process on the adsorption of dye onto clay. This is the first study to focus on the dye-clay-additive system. Adsorption / desorption batch tests were conducted considering different dye additive-clay systems. The tests’ results show that the enzyme like additives enhance the adsorption of anionic dye on the clay by neutralizing the negative charges and reinforcing clay-dye links. Other additives have the opposite effect, but do not offset the positive effect of enzyme like additives when mixed in the effluent. Assumptions of interactions involved in dye adsorption were made with the help of the results of infrared and mass spectrometry, zetametry and the modeling of adsorption isotherms.

Les travaux de cette thèse reposent sur l’étude des processus hétérogènes à la surface desparticules minérales en présence d’irradiation UV-A. Nous savons que les poussièresminérales contiennent des oxydes métalliques pouvant absorber la radiation solaire et ainsiactiver une chimie très différente de celle observée à l’obscurité. Un réacteur à écoulementd’aérosols a été utilisé pour étudier les interactions des gaz (SO2, NO2 et O3) avec devéritables poussières minérales, évitant ainsi les artéfacts de mesure liés à la naturemacroscopique des films comme dans les études précédentes.La mise en suspension des poussières minérales a permis d’observer une formation inattenduede nouvelles particules ultrafines en présence de SO2. Le mécanisme proposé pour expliquerce phénomène de nucléation suggère une désorption de radicaux OH photoproduits à lasurface des minéraux vers la phase gazeuse. Ce mécanisme a pu être corroboré par descampagnes de mesure en atmosphère réelle. Nous avons étudié la chimie des échantillons de réelles cendres volcaniques issus de la dernière éruption du volcan Eyjafjallajökull en Islande (2010). Ceci nous a permis d’élaborerdes cinétiques de capture du SO2 sur des films macroscopiques de cendres aboutissant à descoefficients de capture de l’ordre de 10-7. Ces cinétiques couplées à des analyses chimiquesont permis de proposer un mécanisme réactionnel expliquant la formation de sulfate de fer àla surface des cendres. Finalement, nous avons étudié les interactions photochimiques de O3 et NO2 sur les poussièresminérales dans le réacteur à écoulement mettant en évidence un bon accord avec des étudesantérieures sur des surfaces macroscopiques / The objective of this work is to study the heterogeneous processes of mineral dust surfacesunder UV-A radiation. It is know that mineral dust containing metal oxides which can absorbsolar radiation and therefore activate a different chemistry compared to that observed in thedark. In order to avoid measurement artifacts related to the nature of macroscopic films, anaerosol flow tube was developed during this work and applied to study the interactions ofSO2, NO2 and O3 with real mineral dust.An unexpected formation of new particles in the presence of SO2 was observed. In order toexplain this phenomenon, we suggest the desorption of OH radicals from the mineral dustsurface to the gas phase. This mechanism has also been supported by field campaigns.Using real samples of volcanic ash from the last eruption of Eyjafjallajökull in Iceland (2010)allowed us study capture of SO2 on macroscopic ashes films with uptake coefficient around10-7. Associated kinetic experiments combined with chemical analysis allowed us to propose areaction mechanism explaining the formation of iron sulfate on the surface of ashes.Finally, we investigated the photochemical interactions of O3 and NO2 with minerals dustaerosols in the flow tube reactor showing a good agreement with previous data obtained onmacroscopic surfaces.

L'objectif de cette thèse était trouver des solutions pour produire de hauts rendements d’ions négatifs (IN) H–/D– sur des surfaces dans des plasmas de H2/D2 sans Cs pour des applications en fusion thermonucléaire. La modélisation des fonctions de distribution en énergie des ions négatifs (FDEIN) a montré un accord remarquable avec l'expérience pour les matériaux carbonés. Une méthode de reconstruction mis au point dans le cadre de cette thèse a permis de déterminer les distributions en énergie et en angle des IN émis de la surface. La méthode de reconstruction peut être appliquée à tout type de surface et/ou d’IN. Une étude de la production des IN en surface a été réalisée sur une grande variété de matériaux (des différents types de graphite, couches de diamant et métaux). L'influence sur le rendement des IN de la température de surface, de la tension de polarisation et du temps d'exposition au plasma a été étudiée. Une méthode de polarisation pulsée a été développée pour permettre l'étude de production des IN sur les surfaces de matériaux isolants tels que le diamant microcristallin non dopé. L'utilisation de diagnostics de surface ex situ tels que la désorption programmée en température (DPT) et la spectroscopie Raman ont permis de caractériser l'état de surface des matériaux carbonés. L’ensemble des études a permis de montrer que pour optimiser le rendement des IN sur le diamant, il faut travailler avec une surface moins dégradée. Celle ci peut être obtenu en augmentant la température de surface jusqu’à 400°C – 500°C ce qui permet de restaurer les propriétés intrinsèques des diamants ou en appliquant une polarisation pulsée. / The objective of this thesis was to find solutions to produce high yields of H–/D– negative ions (NI) on surfaces in Cs-free H2/D2 plasmas for thermonuclear fusion applications. Modeling of the negative-ion energy distribution functions (NIEDF) has shown remarkable agreement with experiment for carbon materials. The reconstruction method developed in the course of this thesis has allowed to determine the distribution in energy and angle of NI emitted from the surface. The reconstruction method can be applied to any type of surface and/or NI. A study was performed on a large variety of materials: different types of graphite, diamond films and metals. The influence of surface temperature, bias and plasma exposure time on NI yield was investigated. The method of pulsed bias was developed to enable the study of NI production on surfaces of insulating materials such as microcrystalline non-doped diamond (MCD). The use of ex situ surface diagnostics such as temperature programmed desorption (TPD) and Raman spectroscopy has allowed to characterize the surface state of carbon materials. Basing on the performed studies, we demonstrated that to optimize the NI yield on diamond one has to work with a less degraded surface. This can be obtained rising the surface temperature to 400°C–500°C which allows restoring intrinsic properties of diamond. The less degraded surface state can also be obtained by applying the pulsed bias which gives the possibility to increase the H2/D2 surface coverage and diminish the defects induced by plasma exposure.

Dans les réacteurs nucléaires à eau pressurisée (REP) encore en service dans le parc nucléaire civil français, certaines pièces en contact avec le milieu du circuit primaire, comme les éléments constitutifs des tubes de générateurs de vapeur (en alliage base nickel A600) ou les internes de cuve (en acier inoxydable 316L), sont sujettes à des phénomènes de corrosion sous contrainte (CSC). La mise en évidence expérimentale de la fissuration par CSC de l'alliage A600, réputé résistant, a conduit à de nombreuses études consacrées à la description et à la compréhension de ce phénomène de CSC en milieu primaire des REP. Dans l'optique d'un allongement de la durée de vie des réacteurs en service, il est rapidement devenu critique et stratégique de pouvoir modéliser ces phénomènes de CSC, afin d'optimiser les matériaux, conditions de fonctionnement etc. et d'appréhender les paramètres critiques pour limiter la CSC des composants. Cette étude s'intéresse au rôle de l'hydrogène dans le phénomène de CSC et plus particulièrement aux interactions H-matériau. En effet, l'hydrogène, venant du milieu primaire (H dissous ou H de l'eau), peut être absorbé par l'alliage pendant le processus d'oxydation au cours du fonctionnement du réacteur. Une fois absorbé, H peut être transporté à travers le matériau, interagissant à la fois avec les sites interstitiels du réseau cristallin et des défauts locaux, comme les dislocations, les précipités, les lacunes, etc. La présence de ces sites peut ralentir le transport de l'hydrogène et provoquer une accumulation locale d'hydrogène dans l'alliage. Cette accumulation pouvant modifier les propriétés mécaniques locales du matériau et favoriser sa rupture prématurée, il est essentiel d'identifier la nature de ces interactions H-matériau, et plus particulièrement la vitesse de diffusion et les cinétiques de piégeage de l'hydrogène sur ces défauts. Concernant ces interactions H-piège, la littérature propose très peu de données cinétiques complètes ; il est donc nécessaire d'étudier et caractériser ces interactions finement. Ce travail est composée de deux parties interdépendantes : (i) le développement d'un code de calcul capable de gérer les interactions H-matériau et (ii) l'extraction les données cinétiques de piégeage et de dépiégeage à partir de résultats expérimentaux afin d'alimenter le code de calcul et créer une base de données fiable. Du fait de la complexité des matériaux industriels (A600 et 316L), des \enquote{matériaux modèles} ont été élaborés en utilisant une série de traitements thermomécaniques permettent d'étudier des systèmes simples et de décorréler les différentes contributions possibles entre hydrogène interstitiel et piégé. Ces échantillons ont été chargés en deutérium (traceur isotopique de l'hydrogène) par polarisation cathodique. Après chargement, les échantillons ont été soumis à un essai de spectroscopie de désorption thermique (TDS) où le flux de désorption de deutérium est enregistré pendant une rampe de température et/ou un isotherme. L'extraction des données de diffusion interstitielle et des constantes cinétiques de piégeage se fait par une démarche d'ajustement des spectres expérimentaux obtenus par TDS acquis sur les \enquote{matériaux modèles} en utilisant un code de calcul basé sur la résolution numérique des équations de McNabb et Foster. Grâce à cette étude, les coefficients de diffusion de l'hydrogène ont pu être déterminés dans deux alliages (A600 et 316L) sur une grande gamme de températures. Les constantes cinétiques relatives au piégeage et au dépiégeage sur deux types de pièges (défauts), les carbures de chrome et les dislocations, ont été déterminées. Ces constantes constituent une base de données qui sera intégrée dans un modèle numérique plus large visant à simuler les phénomènes de CSC dans les REP. / In France all of the nuclear power plant facilities in service today are pressurized water reactors (PWR). Some parts of the PWR in contact with the primary circuit medium, such as the steam generator tubes (fabricated in nickel base alloy A600) and some reactor core internal components (fabricated in stainless steel 316L), can fall victim to environmental degradation phenomena such as stress corrosion cracking (SCC). In the late 1950's, H. Coriou observed experimentally and predicted this type of cracking in alloys traditionally renowned for their SCC resistance (A600). Just some 20 to 30 years later his predictions became a reality. Since then, numerous studies have focused on the description and comprehension of the SCC phenomenon in primary water under reactor operating conditions. In view of reactor lifetime extension, it has become both critical and strategic to be capable of simulating SCC phenomenon in order to optimize construction materials, operating conditions, etc. and to understand the critical parameters in order to limit the damage done by SCC. This study focuses on the role hydrogen plays in SCC phenomenon and in particular H-material interactions. Hydrogen, from primary medium in the form of dissolved H gas or H from the water, can be absorbed by the alloy during the oxidation process taking place under reactor operating conditions. Once absorbed, hydrogen may be transported across the material, diffusing in the interstitial sites of the crystallographic structure and interacting with local defects, such as dislocations, precipitates, vacancies, etc. The presence of these [local defect] sites can slow the hydrogen transport and may provoke local H accumulation in the alloy. This accumulation could modify the local mechanical properties of the material and favor premature rupture. It is therefore essential to identify the nature of these H-material interactions, specifically the rate of H diffusion and hydrogen trapping kinetics at these defects. Concerning these H-trap site interactions, literature presents very few complete sets of kinetic data; it is therefore necessary to study and characterize these interactions in-depth. This work is composed of two interdependent parts: (i) the development of a calculation code capable to manage these H-material interactions and (ii) to extract the kinetic constants for trapping and detrapping from experimental results in order to fuel the simulation code and create a solid database. Due to the complexity of industrial materials (A600 and SS316L), \enquote{model materials} were elaborated using a series of thermomechanical treatments allowing for the study of simplified systems and the deconvolution of the different possible trapped and interstitial hydrogen contributions. These \enquote{model} specimens were charged with deuterium (an isotopic hydrogen tracer) by cathodic polarization. After charging, specimens were subjected to thermal desorption mass spectroscopy (TDS) analysis where the deuterium desorption flux is monitored during a temperature ramp or at an isotherm. Interstitial diffusion and kinetic trapping and detrapping constants were extracted from experimental TDS spectra using a numerical fitting routine based upon the numerical resolution of the McNabb and Foster equations. This study allowed for the determination of the hydrogen diffusion coefficient in two alloys, Ni base alloy 600 and stainless steel 316L, and the kinetic trapping and detrapping constants at two trap site types, chromium carbides and dislocations. These constants will be used to construct a kinetic database which will serve as input parameters for a numerical model for the prediction and simulation of SCC in PWRs

Orientadores: Laura Maria Mariscal Ottoboni, Tatiana Teixeira Torres / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-26T13:28:27Z (GMT). No. of bitstreams: 1 Stoppe_NancydeCastro_D.pdf: 4282286 bytes, checksum: f808229a92e702d707b4ebf6be210816 (MD5) Previous issue date: 2014 / Resumo: A contaminação fecal dos corpos hídricos é uma das principais causas de doenças entéricas veiculadas pela água no mundo, sendo importante efetuar a vigilância da água, a qual é feita utilizando-se micro-organismos indicadores de contaminação fecal. No entanto, os métodos tradicionais de detecção não são capazes de identificar a fonte de contaminação fecal. Este trabalho teve como objetivo a prospecção de marcadores moleculares nos hospedeiros e sua detecção em amostras de água de modo a permitir sua utilização na identificação de fontes de contaminação fecal em águas superficiais no Estado de São Paulo. Duas abordagens dependentes de biblioteca e cultivo, a classificação por meio de grupos filogenéticos e a técnica de MALDI-TOF/MS, foram utilizadas com linhagens de E. coli isoladas de diferentes hospedeiros e rios e reservatórios. O sequenciamento da região V3 do gene 16S ribossomal foi selecionado como o método independente de biblioteca e cultivo em DNA extraído de amostras de fezes humanas e bovinas e amostras de água. Os grupos filogenéticos foram utilizados na classificação dos hospedeiros utilizando análise de correspondência, onde foram observados agrupamentos por hábitos alimentares. A classificação das linhagens de E. coli isoladas de rios e reservatórios, sugere que a prevalência do subgrupo A1, seguido do subgrupo B23 está associada com contaminação de origem humana, enquanto o grupo B1 com contaminação de origem animal e os subgrupos D1 e D2 mais relacionados com ambientes prístinos. Na utilização de uma métrica de análise de rede social, w-clique, na distribuição dos grupos filogenéticos foi observado o agrupamento dos locais de amostragem associados ao grau de poluição, sugerindo seu uso como uma ferramenta complementar na avaliação da qualidade da água. Foram analisados os perfis proteicos de linhagens de E. coli de hospedeiros e amostras ambientais pela técnica de MALDI-TOF/MS. Foram identificados biomarcadores hospedeiro-específicos e sugerem sua utilização como potencial ferramenta na identificação da origem do hospedeiro. Os resultados da validação desses marcadores com perfis proteicos de linhagens de E. coli isoladas de rios e reservatórios mostraram que as amostras de água apresentaram marcadores de diferentes hospedeiros, sugerindo que esses rios possuam fontes de contaminação fecal mistas. No sequenciamento da região V3 do gene 16S ribossomal de amostras de fezes (humanas e bovinas) e águas foram identificadas 4.296 unidades taxonômicas operacionais (OTUs) . A maior diversidade foi observada nas amostras de fezes bovinas e a menor na amostra de água de ambiente prístino. Firmicutes foi o grupo predominante nas amostras de fezes humanas, enquanto que nas fezes bovinas foram os Firmicutes e Bacteroidetes. Nas amostras de água, o filo mais abundante foi Proteobacteria. A rede de interação entre as OTUs encontradas nas amostras também mostrou que as amostras de fezes apresentaram maior diversidade e entre as amostras de água, aquela com poluição de origem humana foi a que apresentou maior diversidade. Houve identificação de biomarcadores pelo método LEfSe para humanos (Actinobacteria, Betaproteobacteria e Firmicutes) e bovinos: (Bacteroidetes, Tenericutes e Spirochaetes). Marcadores hospedeiro-específicos foram identificados, mas esses não foram encontrados nas amostras de água sugerindo que as ferramentas utilizadas não apresentam a resolução para identificar os marcadores nas amostras ambientais ou que a contaminação nos corpos hídricos é mista. Adicionalmente, como os marcadores hospedeiro-específicos são oriundos de micro-organismos não autóctones, estes poderiam sofrer os efeitos adversos do ambiente, como fatores físico-químicos e competição com os organismos nativos / Abstract: The fecal contamination of water resources is the main cause of enteric waterborne diseases all over the world. Traditional indicator methods used in the water microbiological quality assessment are not able to identify fecal contamination source. This work intended to prospect molecular markers in hosts and track them in water samples to identify pollution sources in surface waters in the São Paulo State, Brazil. Two library-dependent methods with E. coli strains isolated from different hosts and water samples were used, a genotypic typing method (E. coli phylogenetic groups) and a phenotypic typing method (MALDI-TOF/MS). A library-independent method using 454 pyrosequencing of hypervariable16S rRNA gene V3 region was used in DNA from feces and water samples. Phylogenetic groups were used as a tool in host classification and correspondence analysis showed feeding habits clusters. The classification of environmental samples revealed higher frequencies of subgroups A1 and B23 in rivers impacted by human pollution sources, while subgroups D1 and D2 were associated with pristine sites, and subgroup B1 with domestic animal sources, indicating their use as a first screening for pollution source identification. A simple classification is proposed based on phylogenetic subgroup distribution using the w-clique metric, enabling differentiation of polluted and unpolluted sites. Protein profiles of E. coli strains isolated from host and water samples were analyzed by MALDI-TOF/MS. Specific host biomarkers were identified and their use was indicated as a potential tool for the source tracking. Validation with E. coli strains isolated from rivers and reservoirs showed that water samples presented markers from different hosts, suggesting these rivers have mixed sources of fecal contamination. Sequencing of the 16S rRNA V3 region in stool samples (human and bovine) and water showed 4296 operational taxonomic units (OTUs). The greatest diversity was observed in samples of cattle feces and the smallest one in the pristine water sample. Firmicutes was the predominant group in samples of human feces, while in the most common bovine feces are the Firmicutes and Bacteroidetes. The interaction network showed that the stool samples had the greatest diversity and, among them, the water sample with human pollution source showed the highest diversity. The LEfSe method was used to identify host biomarkers. As human biomarkers, Actinobacteria, Betaproteobacteria and Firmicutes were identified and for cattle the potential markers are Bacteroidetes, Tenericutes and Spirochaetes. Host-specific markers were identified, but they were not found in water samples suggesting that the used tools either do not have the resolution to identify markers in environmental samples or contamination in water bodies is mixed. Additionally, as the host-specific markers were isolated from non-autochthonous micro-organisms, they could be affected by the environmental adverse effects such as physical-chemical factors and competition with native organisms / Doutorado / Microbiologia / Doutora em Genética e Biologia Molecular

Orientador: Carlos Emílio Levy / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-27T01:21:38Z (GMT). No. of bitstreams: 1 CarvalhoFilho_ElioBarreto_M.pdf: 1484872 bytes, checksum: da445ed854a5a8f11143d06dd28aab5c (MD5) Previous issue date: 2015 / Resumo: Introdução: Bacilos gram-negativos não fermentadores (BGN-NFs) são microrganismos que se caracterizam pela incapacidade de utilizar a glicose como fonte de energia pela fermentação, degradando-a pela via oxidativa. A identificação dos BGN-NFs continua sendo um desafio para os laboratórios de rotina em microbiologia pela dificuldade de identificação, em virtude, da baixa ocorrência em amostras ambulatoriais, assim como, pela falta de recursos rápidos, eficientes e pela complexidade e alto custo dos testes de identificação. Estes microrganismos têm importância clínica para pacientes imunocomprometidos com infecções sistêmicas e pacientes com Fibrose Cística, com infecções oportunistas pulmonares. Nosso objetivo foi utilizar técnicas fenotípicas e de espectrometria de massas para identificar BGN-NFs pouco frequentes isolados em amostras clínicas de pacientes com FC e de pacientes internados no Hospital de Clínicas-Unicamp. Método: Foram analisados 71 isolados de amostras clínicas recuperadas do Banco de bactérias do Laboratório de Microbiologia do HC-Unicamp, envolvendo Chryseobacterium indologenes, Elizabethkingia meningoseptica, Cupriavidus pauculus, Ochrobactrum anthropi, Ralstonia pickettii, Ralstonia mannitolilytica, Ralstonia insidiosa, identificados por técnicas fenotípicas (provas bioquímicas manuais padronizadas pelo Laboratório de Microbiologia [método fenotípico manual] e automatizadas pelo Vitek®2, Phoenix¿) e por espectrometria de massa MALDI-TOF MS (BioMerieux®) e MALDI BD (Becton& Dickson®). Para 41 isolados de Ralstonia spp e Ochrobactrum anthropi estes métodos também foram comparados com PCR, pois não foram encontrados oligonucleotídeos específicos para os demais BGN-NFs estudados. Resultados: pelo método Fenotípico Manual foi possível identificar ao nível de espécie 54,9% dos isolados, apenas gênero 19,7% e 25,4% não puderam ser identificados. Houve uma baixa concordância entre as técnicas Fenotípica Manual e a Automatizada Vitek®2, sendo de 50,7%, quando considerada a concordância pelo menos ao nível de gênero. A maior concordância verificou-se entre os dois equipamentos de MALDI-TOF, de 87,3%, quando considerada a concordância pelo menos ao nível de gênero. Discussão: Quando comparamos todos os métodos utilizados para identificação dos 71 isolados encontramos uma concordância simultânea de 23,9% (17/71), quando considerado pelo menos ao nível de gênero e apenas 2 (2,8%) ao nível de espécie. Quando comparamos os métodos Fenotípico Manual, Vitek®2, Phoenix®, MALDI MS, MALDI BD e incluindo PCR para a identificação de 41 amostras de Ralstonia spp e Ochrobactrum anthropi, encontramos uma concordância simultânea de 19,5% (8/41) quando considerado pelo menos ao nível de gênero e 2 (2,8%) de espécie. Possíveis justificativas para a baixa concordância entre as metodologias seriam a diversidade de princípios, de acurácia e de bancos de dados dos métodos. Conclusão: É muito baixa a concordância entre as diferentes metodologias utilizadas, sendo que os equipamentos de MALDI-TOF possuem entre si uma correlação muito boa para identificação de BGN-NFs, porém mostram-se discordantes aos níveis de confiança dos resultados. Foi encontrada uma importante limitação na PCR apresentando reação cruzada com gêneros testados, sugerindo não ser confiável para este fim. Para os gêneros estudados e as metodologias empregadas, a discordância dos resultados sugerem cautela pela possibilidade de erro de identificação / Abstract: Introduction: Gram-negative non-fermenting (GN-NFB) are microorganisms that are characterized by the inability to use glucose by fermentation as an energy source, degrading it by the oxidative pathway. The identification of BGN-NFS remains a challenge for the routine of microbiology laboratories, due to the low occurrence in outpatient samples, the lack of fast and efficient resources and the complexity and high cost of the tests. These microorganisms are clinically important for immunocompromised patients with systemic infections and patients with Cystic Fibrosis, with opportunistic pulmonary infections. Our goal was to use phenotypic and mass spectrometry techniques to identify uncommon GN-NFB isolated in samples from CF patients and patients admitted to the Hospital de Clinicas Unicamp. Method: 71 isolates recovered from clinical specimens were selected from the from the Microbiology Laboratory bacteria collection, previously identified by fenotipic methods as Chryseobacterium indologenes, Elizabethkingia meningoseptica, Cupriavidus pauculus, Ochrobactrum anthropi, Ralstonia pickettii, Ralstonia mannitolilytica, Ralstonia insidiosa. The samples were identified by in house Phenotypic manual method, automated by Vitek®2, by Phoenix¿ and MALDI-TOF mass spectrometry MS (BioMerieux®) and MALDI BD (Becton Dickson®). These methods were also compared to PCR for only 41 isolates of Ralstonia spp and Ochrobactrum anthropi, because they were not found specific primers for the other GN-NFB analised. Results: the phenotypic Manual method identified to species level 54.9% of the isolates, 19.7% only to genera and 25.4% were not identified. There was a poor correlation between the techniques phenotypic Manual method and Automated Vitek®2, with 50.7% of agreement, when considering at least in terms of gender. The best agreement of 87.3% occurred between the results of the two MALDI-TOF equipment, when considering the correlation of at least at the level of genus. Discussion: When comparing all the methods used for the identification of 71 isolates were found simultaneous agreement of 23.9% (17/71) when considered at least to genus level and only 2 (2.8%) to species level. When analyzed the phenotypic Manual method, Vitek®2, Phoenix®, MALDI MS, MALDI BD and PCR applied to 41-GN-NFB samples, simultaneous agreement were found for 19.5% (8/41) when considered at least to genus level and 2 (2.8%) to species. Possible reasons for the low agreement between the methodologies could be the diversity of principles, accuracy and databases of the methods. Conclusion: The two methods of MALDI-TOF have a very good correlation for GN-NFB identification, however showed discordance for the confidence levels of results. With the primers tested one important limitation of the PCR is the cross-reaction among many genera, suggesting not to be safe for the discrimination of the analyzed genera. For the genera and methods analised the discrepancy of results suggests caution because of the possibility of wrong identification / Mestrado / Saude da Criança e do Adolescente / Mestre em Ciências

Lors de l’irradiation en réacteur, des gaz de fission tels que le xénon et le krypton sont produits. Ces gaz diffusent dans le combustible, mais peuvent également précipiter sous forme de bulles. En outre,les réactions de fission conduisent à la formation de défauts ponctuels (lacunes ou interstitiels) et sous forme d’amas (dislocations ou cavités). L’obtention de données expérimentales sur la migration des gaz de fission en présence de défauts est nécessaire afin d’améliorer la compréhension et la modélisation du comportement du combustible sous irradiation. La démarche mise en place dans ce travail a pour objectif d’étudier la diffusion thermique des gaz et de comprendre leur interaction avec les défauts d’irradiation. Elle repose sur la réalisation d’études à effets séparés couplant des irradiations/implantations aux ions à des techniques de caractérisation fines. La Spectroscopie d’Annihilation des Positons (SAP) complétée par la Microscopie Electronique en Transmission (MET)permet de caractériser les défauts (ponctuels et/ou sous forme d’amas) générés par l’irradiation et de suivre leur évolution en température. En parallèle, la modélisation des cinétiques de relâchement des gaz rares mesurées par désorption thermique couplée à la spectrométrie de masse, permet d’obtenir les coefficients de diffusion des gaz et de mettre en lumière les phénomènes de piégeage opérants. La synthèse de ces résultats expérimentaux nous amène à identifier les mécanismes de migration des gaz et à décrire leurs interactions avec les défauts d’irradiation. / During in-reactor irradiation, fission gases such as xenon or krypton are produced. In the fuel, those gases diffuse and precipitate to form bubbles. In addition, fission reactions induce small defects(vacancies and interstitials) and larger defects (cavities and dislocations) formation. Data acquire menton fission gases migration considering radiation-induced defects is thus necessary to better understand and improve models of in-pile fuel behavior. The experimental approach developed in this work aims to study thermal diffusion of rare gases and to understand their interaction with radiation-induced defects.To do this, separated effect studies were performed coupling ion implantations/irradiations to fine characterization techniques. Positron Annihilation Spectroscopy (PAS) coupled to Transmission Electron Microscopy (TEM) observations allows for defects characterizations (vacancies and/or cavities induced by ion implantation) and for their thermal behavior study. On the other hand, gas release measurements are performed by thermal desorption spectrometry. Simulation of gas kinetic release allows to determine diffusion coefficients and to lighten trapping mechanisms. The synthesis of those various experimental results brings us to identify gas migration mechanism and to describe their interaction with radiation-induced defects.