Cette étude porte sur l'identification et la dispersion des bioaérosols générés sur les plates-formes de compostage et plus précisément lors du retournement des andains en cours de fermentation. L'analyse des bioaérosols émis sur cinq plates-formes par des inventaires moléculaires (ADNr 16S et ADNr 18S) a permis de montrer la dominance de deux phyla bactériens Firmicutes et Actinobacteria et du phylum fongique Ascomycota. En comparant la structure de la population microbienne des cinq bioaérosols, une signature a été identifiée. Dix phylotypes microbiens sont communs à au moins quatre bioaérosols. Deux sont présents dans les cinq bioaérosols : NA07 appartenant à l'espèce Saccharopolyspora rectivirgula et représentant 7% des séquences bactériennes totales et EQ07 affiliée à Thermomyces (49% des séquences fongiques). Un second phylotype bactérien, NC38, affilié à la famille des Thermoactinomycetaceae a été sélectionné du fait q u'il n'ait été identifié que dans le compost. Des systèmes de PCRq ont été développés pour quantifier ces trois indicateurs potentiels. Ces derniers ont été validés expérimentalement par des mesures sur sites industriels. La dispersion des bioaérosols a ensuite été caractérisée en utilisant plusieurs méthodologies, dont les trois indicateurs conçus et une technique d'empreinte moléculaire, la SSCP. Lors d'une activité de retournement, la concentration des indicateurs est supérieure à leur niveau basal dans l'air (bruit de fond). Les indicateurs présentent des profils de dispersion différents d'où l'intérêt de les coupler afin d'obtenir une meilleure vision de la dispersion des bioaérosols de compostage. / The aim of this work was to analyze the diversity and the dispersal of composting bioaerosol emitted during the turning of compost windrows in thermophilic phase on composting platforms. The study of the microbial diversity of aerosols emitted on five composting plants was realized by 16S and 18S rDNA molecular inventories. Two bacterial phyla Firmicutes and Actinobacteria and one fungal phylum Ascomycota dominated. A common microbial signature emerged from the five composting bioaerosols: ten microbial phylotypes (seven bacterial and three fungal) were common to at least four bioaerosols. Two have been identified in five bioaerosols: NA07 belonging to the species Saccharopolyspora rectivirgula, and representing 7% of total number of bacterial sequences, and EQ05,affiliated to Thermomyces (49% of total number of fungal sequences). A second bacterial phylotype, NC38, affiliated to the Thermoactinomycetaceae family, was selected because it was id entified only in the environmental source compost'. qPCR systems were then designed for each phylotype. Measurements performed on industrial composting sites validated the use of these microorganisms as indicators of composting bioaerosols. The dispersal of composting bioaerosols was then characterized using the three indicators developed and a fingerprint technique, the SSCP.

The main objective of this research was to exploit the interrelations between the rheological behavior and nano-microstructure of complex fluids in solving two state-of-the-art problems, one in the field of biomedical engineering: controlling the amount and characteristics of bioaerosol droplets generated during coughing, and the other in the bitumen-heavy oil industry: characterizing the nano-microstructure of asphaltene particles in bitumen and heavy oil from their rheological behavior. For the first problem, effect of viscoelastic and surface properties of artificial mucus simulant gels on the size distribution and amount of airborne bioaerosol droplets generated during simulated coughing were investigated. The results revealed that suppressing the generation of bioaerosol droplets and/or reducing the number of emitted droplets to a minimum during coughing are practically achievable through modulation of mucus viscoelastic properties. While variation of surface tension did not show any change in the droplet size distribution, an increase in particle size was observed as the samples changed from elastic solid type to viscoelastic type to viscous fluid type samples. This knowledge will help in the development of a new class of drugs being developed at the University of Alberta, aimed at controlling the transmission of airborne epidemic diseases by modifying the viscoelastic properties of mucus. For the second problem, studies of viscoelastic behavior of Athabasca bitumen (Alberta) and Maya crude (Mexico) oil samples, along with their Nano-filtered and chemically separated-plus-reconstituted samples were performed. The results revealed that the rheological behaviors of the bitumen-heavy oil samples are governed by their multiphase nature. The rheological behavior of all feeds, permeates and retentate samples followed a single master curve over the entire temperature interval, consistent with that of a slurry comprising a Newtonian liquid plus a dispersed solid comprising non-interacting hard spheres. The behavior of asphaltenes in the reconstituted samples, however, was found to be significantly different from that in nanofiltered samples. The information about the characteristics and behaviors of asphaltenes obtained in this study will help better understand the asphaltene structures, and support the effort to determine solutions for numerous asphaltene-related industrial problems. In the long run, this knowledge will help to create more efficient extraction and upgrading processes for bitumen and heavy oils. / Thermo Fluids

La détection d'agents biologiques dans l'air ambiant est devenue un enjeu majeur notamment en environnement hospitalier et dans la protection contre le bioterrorisme. Dans ce contexte, la miniaturisation des dispositifs d'analyse permet d'envisager leur utilisation directement sur la zone d'étude. Afin d'obtenir un échantillon concentré et représentatif, la filtration de l'air reste cependant un point délicat. Parmi les différents principes exploitables pour la collecte de particules aéroportées, l'emploi des forces électriques semble être prometteur pour améliorer les performances des dispositifs qui se trouvent généralement fondés sur des forces inertielles. Dans cette étude, une modélisation fine des collecteurs électrostatiques a été conduite pour une géométrie fil / cylindre. Elle décrit tout d'abord les champs hydrodynamiques d'un écoulement charriant des inclusions dans lequel est imposée une décharge couronne. Une injection éventuelle de vapeur dans la chambre de collecte a nécessité ensuite la détermination des champs de température et concentration de la vapeur. Une analyse dimensionnelle inspectionnelle a montré que ces champs possèdent deux termes de couplage fort dont on a justifié l'omission dans cette étude ; les phénomènes physiques mis en jeu ont alors pu être classés selon une cascade d'influences non réciproques et la résolution numérique du modèle s'en est trouvée facilitée. Quatre configurations d'écoulement différentes, caractérisées par des recirculations d'origine électro hydrodynamiques, ont été identifiées et leurs impacts sur les rendements de collecte quantifiés. De plus, une procédure de dimensionnement des filtres électrostatiques fondée sur un nombre de Deutsch représentatif des rendements a été mise en place. Son exploitation a montré l'intérêt de la mise en parallèle de petits collecteurs pour filtrer des débits d'air importants. Cette étude s'est achevée par l'analyse des effets engendrés par l'injection de vapeur dans la chambre de collecte. Elle a jeté les bases d'une explication pour l'augmentation des rendements de collecte résultant de cette injection. / Detection of airborne biological agents has become a major challenge especially in hospitals and the protection against bioterrorism. In this context, the miniaturization of analytical devices allows to consider their direct use in the field. To obtain a representative and concentrated sample, air filtration remains a delicate point. Among the various principles used to collect airborne particles, the use of electrical forces seems to be promising to improve performance beyond these of devices that are based on inertial forces.In this study, a detailed model of electrostatic collectors was developed in the wire/cylinder geometry. It first describes the hydrodynamic flow fields carring inclusions in which a corona discharge is imposed. Afterwards, the possible injection of steam into the collection chamber required the determination of the temperature and vapor concentration fields. An inspectionnal dimensional analysis justified the omission of two strong coupling terms. Therefore, in this study, the involved physical phenomena could be classified according to a non-reciprocal influences cascade and the numerical model is become simpler. Four different flow patterns, characterized by their electrohydrodynamic secondary flows, were identified and their impact on the collection efficiencies was quantified. In addition a design procedure of electrostatic filters, based on a representative efficiency Deutsch number, has been developed. This procedure shows the interest of parallelizing small collectors to filter important airflows. This study was completed by the analysis of the effects of steam into the collection chamber. It provides the basis for an explanation of the collection efficiencies increase related to this injection.

Les actinomycètes sont des bactéries ubiquitaires et certains sont reconnus comme potentiellement pathogènes pour l’Homme, dans l’air de certains lieux de travail. C’est notamment le cas dans l’air des plates-formes de compostage où les concentrations peuvent atteindre des valeurs relativement élevées. L’exposition des salariés à ce type de bioaérosols peut être la cause de pathologies diverses (notamment des pneumopathies d’hypersensibilité). Bien que le problème soit reconnu, la bibliographie démontre un manque de connaissances à propos de l’évaluation du risque : aucune méthode globale de prélèvement et d’analyse n’est, à l’heure actuelle, standardisée pour l’étude de ces bioaérosols, si bien qu’il n’existe aucune relation dose-effets pour la plupart de ces agents ni même de valeur limite d’exposition professionnelle. Les méthodes traditionnellement utilisées ne sont pas sans inconvénient (sous-estimation de la concentration réelle notamment) et le plus souvent non-spécificiques. C’est pourquoi l’objectif de la thèse, ici décrite, est le développement et l’évaluation de la technique de biologie moléculaire qu’est la PCR temps réel pour la quantification de bactéries dans ces bioaérosols. La méthode a tout d’abord été développée et optimisée notamment par le dessin d’oligonucléotides, par la comparaison de protocoles d’extraction d’ADN et par la réalisation de gammes étalons. Elle a ensuite été comparée aux techniques plus traditionnelles, encore largement utilisées, que sont le dénombrement du bacteries cultivable par mise en culture et l’épifluorescence, à la fois sur des cultures de cellules et sur des bioaérosols expérimentaux. Ce n’est qu’après l’avoir caractérisé qu’elle a été appliquée sur des bioaérosols prélevés en conditions réelles d’exposition, sur des plates-formes de compostage.La méthode développée, basée sur une extraction d’ADN et une PCR temps réel, permet la quantification de l’ADN de Thermoactinomyces vulgaris (basée sur l’amplification du gène GyrB), de Thermobifida fusca et T. alba (gène ecf) et des streptomycètes mésophiles (ARNr 23S). La PCR permet l’obtention de résultats fortement corrélés à ceux issus du dénombrement sur milieux gélosés mais offre de réels avantages par rapport à la culture. Comme ces quantifications prennent en compte n’importe quelle forme de la bactérie (cellules végétatives et spores), la PCR dépasse les inconvénients de sous-estimation liés aux méthodes traditionnelles. La technique a un réel avantage de spécificité, elle est répétable et sensible. Les campagnes de prélèvements effectuées sur 5 plates-formes de compostage en France ont permis de mesurer les concentrations en bactéries mésophiles et thermophiles par culture et d’établir celles en Thermoactinomyces vulgaris, Thermobifida sp. et Streptomyces sp. par PCR. L’étude confirme que les activités de compostage sont génératrices de bioaérosols avec parfois des valeurs relativement élevées selon les points échantillonnés. Elle met également en exergue des informations comme la distribution granulométrique du bioaérosol ou l’adéquation entre le type de prélèvement effectué et l’analyse par PCR. Les travaux menés, du développement de la méthode qPCR appliquée au groupe des actinomycètes à son application sur des échantillons environnementaux, apportent de nombreuses données pour la quantification des actinomycètes aéroportés. Ils ont permis d’acquérir des éléments de validation concernant la méthode mise en place et ont livré les seules mesures de concentrations disponibles à l’heure actuelle, pour T. vulgaris, Thermobifida sp., et les streptomycètes mésophiles dans l’air des plates-formes de compostage / Actinomycetes are ubiquitous bacteria and some can be potentially pathogen for Humans in the air of some working areas. It’s notably the case in composting plants where bacteria concentrations can reach high values. Workers exposure to these inhalable bioaerosols can be source of various diseases (hypersensitivity pneumonitis notably). Although this problem is admitted, bibliography reveals a lack of knowledge about risk assessment: currently, none global method for bioaerosols sampling and analysis is standardized. So much that neither dose-effects relationship for most of these bacteria, nor Threshold Limit Value exists. Traditional methods, that are used, have some drawbacks (concentrations underestimation notably) and most often, aren’t specific.It’s the reason why the aim of the thesis, here described, is the development and the evaluation of the biomolecular technique of real time PCR for the quantification of bacteria in these bioaerosols. First, this method was developed and improved by oligonucleotides design, by comparison of many DNA extraction protocols and by the construction of standard ranges. Then, the method was compared to traditional widely used methods such as cultivable bacteria counting by cultures and epifluorescence microscopy, both on cells culture samples and experimental bioaerosols. After this characterization, the analytic method was applied on environmental bioaerosols sampled on real exposure conditions (composting plants).The method that we have developed, based on DNA extraction and real-time PCR, allows the quantification of Thermoactinomyces vulgaris DNA (based on gyrB gene amplification), of Thermobifida fusca and T. alba (ecf gene) and of mesophilic streptomycetes (rDNA 23S). The results obtained by PCR are strongly correlated with those obtained by counting on agar but PCR method offers more advantages than cultures. As PCR quantifies any form of the bacteria (vegetative cells and spores), the method goes over the drawbacks of traditional methods, like underestimation. The method has a real advantage of specificity, it’s also repeatable and sensitive. Sampling campaigns realized on 5 composting plants implanted in France have permitted measuring mesophilic and thermophilic bacteria concentrations by culture and establishing Thermoactinomyces vulgaris, Thermobifida sp. and Streptomyces sp. ones by PCR. The study confirms that composting activities release bioaerosols. And according to the localization of the sampling, the values could be rather high. It also underlines some informations as particles size distribution of the bioaerosol or the adequacy between sampling apparatus and PCR analysis. The works carried out, from qPCR method development for actinomycetes group to its application on environmental samples, give a lot of datas concerning airborne actinomycetes quantification. It permit to validate the developed method and give the only currently available measures for T. vulgaris, Thermobifida sp., and mesophilic streptomycetes in the air of composting plants

Submitted by Angela Maria de Oliveira (amolivei@uepg.br) on 2018-03-02T13:04:32Z No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Carlos Rafael.pdf: 2751688 bytes, checksum: 31c547702ea9189c4ded0e1d56077de5 (MD5) / Made available in DSpace on 2018-03-02T13:04:32Z (GMT). No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Carlos Rafael.pdf: 2751688 bytes, checksum: 31c547702ea9189c4ded0e1d56077de5 (MD5) Previous issue date: 2017-08-14 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / O conhecimento da dinâmica espacial de doenças de plantas, aliado a quantificação de inóculo e monitoramento das condições meteorológicas é de grande importância para a adoção de estratégias de manejos adequados e com menor impacto ambiental. Sendo assim, os objetivos deste trabalho de pesquisa foram caracterizar a distribuição, variabilidade espacial e possíveis relações entre atributos referentes ao mofo branco e atributos de plantas de soja além de avaliar técnicas de identificação e quantificação de ascósporos de Sclerotinia sclerotiorum durante o florescimento da soja. Foram realizadas amostragens através de uma malha georreferenciada em uma área de 12 hectares (ha) no município de Mauá-da-Serra-PR nas safras 2013/14 e 2014/15 e uma área de quatro hectares no município de Ponta Grossa-PR na safra 2015/16. Foram utilizados quadrats com área útil de 7,2 m² para avaliação das seguintes variáveis: escleródios presentes no solo, estande da cultura, incidência, índice de doença, rendimento, escleródios produzidos na colheita, além da deposição do bioaerossol, partes de folha e flores da soja como uso de Meio Semi-seletivo a Sclerotinia sclerotiorum (MSS) e Reação em cadeia da polimerase quantitativa (qPCR), em 36 pontos de amostragem na área de Ponta Grossa-PR, em três datas durante o florescimento da soja. Os dados foram analisados com uso de estatística descritiva, ajuste de semivariogramas e matriz de correlação de Pearson. As condições meteorológicas observadas nos três experimentos foram adequadas para o desenvolvimento da cultura da soja e do mofo branco na soja. As variáveis referentes a cultura da soja apresentaram coeficientes de variação baixos ou moderados e as variáveis referentes ao mofo branco apresentaram coeficiente de variação muito elevados. Os ajustes dos semivariogramas apresentaram diferenças nos três experimentos, com efeito pepita puro, ajuste linear, esférico e exponencial. A variável escleródios do solo apresentou efeito pepita puro nos dois experimentos em Mauá-da-Serra. Foram encontradas correlações significativas positivas entre a incidência do mofo branco e a produção de escleródios na colheita, além de correlação negativa com o rendimento nos três experimentos. A identificação de inóculo de mofo branco com incubação em MSS mostrou-se a técnica com maior sensibilidade, mas demanda de até 15 dias para a confirmação de S. sclerotiorum, tanto para bioaerossol, como flores e partes de folhas de soja. Foi possível otimizar o protocolo de extração de DNA e ciclo de reação para qPCR, além de gerar uma curva padrão com DNA oriundo de ascósporos de S. sclerotiorum, com ajuste ao modelo linear (R²=0,99) e eficiência de 92,2%. O uso de qPCR mostrou-se promissor para partes de folhas, sendo possível resultados em um dia de trabalho. / The knowledge of the spatial dynamics of plant diseases, allied with the quantification of inoculum and monitoring of the meteorological conditions, is important for the adoption of adequate management strategies and with less environmental impact. The aim of this work was to characterize the distribution, spatial variability and possible relations between white mold attributes and soybean plants attributes, as well as to evaluate techniques for identification and quantification of ascospores of Sclerotinia sclerotiorum during soybean flowering. Samplings were carried out through a georeferenced grid on a field of 12 hectares (ha) in the municipality of Mauá-da-Serra-PR in the 2013/14 and 2014/15 crop seasons and, on a field of four hectares in the municipality of Ponta Grossa-PR in the 2015/16 crop season. Quadrats with a useful area of 7.2 m² were used to evaluate the following variables: sclerotia in the soil, crop stand, incidence, severity, yield, sclerotia produced at harvest, as well as bioaerosol deposition, soybean leaf parts and flowers on semi-selective medium to Sclerotinia sclerotiorum (MSS) and quantitative polymerase chain reaction (qPCR), at 36 sampling points in the Ponta Grossa- PR field, at three dates during soybean flowering. Data were analyzed using descriptive statistics, semivariogram adjustment and Pearson correlation matrix. The meteorological conditions observed in the three experiments were adequate for the development of soybean crop and white mold disease. The variables related to soybean plants, showed low or moderate coefficients of variation and the variables related to white mold showed a high coefficient of variation. The semivariograms adjustments showed differences in the three experiments, with pure nugget effect, linear, spherical and exponential adjustments. The variable sclerotia of soil showed pure nugget effect on the two experiments in Mauá-da-Serra. Significant positive correlations were found between the incidence of white mold and the production of sclerotia at harvest, in addition to negative correlation to yield in the three experiments. The identification of white mold inoculum with incubation on MSS was shown to be the most sensitive technique, but takes up to 15 days for the confirmation of S. sclerotiorum pathogen for bioaerossol, flowers and parts of soybean leaves. It was possible to optimize the protocol of DNA extraction and reaction cycle for qPCR, besides generating a standard curve with DNA from ascospores of S. sclerotiorum, adjusted to the linear model (R² =0, 99) and efficiency of 92.2%. The use of qPCR showed promise results for leaf parts, being possible achieve concluding results in one working day.

Denna rapport presenterar en utvärdering av en centrifugal luftrenare från företaget Airission som användes i en infektionsavdelning på Karolinska Universitetssjukhuset. Airissions luftrenare rensar bort partiklar och aerosoler, genom så kallad centrifugalteknologi, en relativt oprövad teknologi för luftrening. Målet var att undersöka och försöka verifiera luftrenarens funktion och prestanda samt jämföra den med en konventionell luftrenare som använder traditionella tvåstegsfilter för att rena luft.För att utföra studien användes ett bioaerosolmätinstrument som i realtid mäter partikelnivåerna i rummet. Testerna utfördes under olika driftförhållanden och tidsintervall med luftrenare påslagen respektive avstängd. Datainsamlingen och analysen inkluderade beräkningen av medelvärdet, jämförelse av partikelnivåerna mellan de olika testfallen och beräkning av standardavvikelsen.Resultaten visade att Airissions centrifugala luftrenare fungerar väl för rening av luft från partiklar och aerosoler. Reningseffektiviteten var jämförbar med en konventionell luftrenare. Den var mer effektiv än en konventionell luftrenare utan användning av högeffektiva luftfilter, mer allmänt känt som HEPA-filter. En signifikant minskning av antalet partiklar i luften observerades medan luftrenaren var i drift. Det uppstod dock en del komplikationer vid appliceringen av HEPA-filtret, vilka kunde ha haft en negativ påverkan på båda luftrenarna. Sammanfattningsvis visar analysen att den tillämpade centrifugalteknologin hos Airissions luftrenare fungerar väl. Jämförelsen av den konventionella luftrenaren visar vissa fördelar med en luftrenare som använder centrifugal teknologi - både gällande effektivitet och kvalitet.Denna rapport bidrar till kunskapen om luftreningslösningar för att förbättra luftkvaliteten och minska spridningen av luftburna sjukdomar, framför allt i sjukhusmiljöer. Resultaten kan vara till nytta för fortsatt forskning och utveckling av mer effektiva luftrenare som i sin tur ger ett bättre skydd för patienter och sjukhuspersonal som exponeras för luftburna smittämnen. / This report presents an evaluation of a centrifugal air purifier from the company Airission used in an infectious ward at Karolinska University Hospital. Airission's air purifier removes particles and aerosols using centrifugal technology, a relatively untested technology for air purification. The goal was to investigate and attempt to verify the functionality and performance of the air purifier and compare it to a conventional air purifier that uses traditional two-stage filters for air purification.To conduct the study, a bioaerosol measuring instrument was used to measure real-time particle levels in the room. The tests were performed under different operating conditions and time intervals with the air purifier turned on and off. Data collection and analysis included calculating the mean values, comparing the particle levels between different test cases, and calculating the standard deviation.The results showed that Airission's centrifugal air purifier effectively purifies air from particles and aerosols. The purification efficiency was comparable to a conventional air purifier. It was more effective than a conventional air purifier without the use of highefficiency air filters, commonly known as HEPA filters. A significant reduction in the number of particles in the air was observed while the air purifier was in operation. However, some complications arose during the application of the HEPA filter, which could have had a negative impact on both air purifiers.In summary, the analysis demonstrates that the applied centrifugal technology in Airission's air purifier works well. The comparison with the conventional air purifier shows certain advantages of an air purifier that uses centrifugal technology - in terms of both efficiency and quality.This report contributes to the knowledge of air purification solutions to improve air quality and reduce the spread of airborne diseases, especially in hospital environments. The results can be useful for further research and development of more effective air purifiers, which in turn provide better protection for patients and hospital staff exposed to airborne pathogens.